WO2016066647A1 - Genetically encoded nitrogen monoxide sensors (genops) - Google Patents

Genetically encoded nitrogen monoxide sensors (genops) Download PDF

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Publication number
WO2016066647A1
WO2016066647A1 PCT/EP2015/074877 EP2015074877W WO2016066647A1 WO 2016066647 A1 WO2016066647 A1 WO 2016066647A1 EP 2015074877 W EP2015074877 W EP 2015074877W WO 2016066647 A1 WO2016066647 A1 WO 2016066647A1
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Prior art keywords
rons
seq
domain
amino acid
polypeptide
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PCT/EP2015/074877
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French (fr)
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Wolfgang Graier
Roland Malli
Emrah EROGLU
Markus WALDECK-WEIERMAIR
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Medizinische Universität Graz
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Publication of WO2016066647A1 publication Critical patent/WO2016066647A1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/24—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Enterobacteriaceae (F), e.g. Citrobacter, Serratia, Proteus, Providencia, Morganella, Yersinia
    • C07K14/245—Escherichia (G)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/60—Fusion polypeptide containing spectroscopic/fluorescent detection, e.g. green fluorescent protein [GFP]

Definitions

  • Reactive oxygen and nitrogen species As well as RONS-like molecules play important roles in biological processes as well as non-medical applications.
  • RONS and RONS-like molecules are integral chemical mediators of both acute and chronic inflammation and their generation occurs locally and within minutes in the inflammatory process, preceding the arrival of inflammatory cells.
  • NO nitric oxide
  • NO has been recognized as a key signaling molecule not only in inflammation but also in neurotransmission, the immune system and the cardiovascular system. Further, NO plays a central role in diverse pathological conditions, such as hypertension, diabetes, atherosclerosis, erectile dysfunctions, ischemic heart disease or stroke.
  • nitric oxide At least two important biological reaction mechanisms of nitric oxide are known, namely S-nitrosation of thiols and nitrosylation of transition metal ions.
  • S-nitrosation involves the (reversible) conversion of thiol groups, including cysteine residues in proteins, to form S-nitrosothiol.
  • S-Nitrosation is a mechanism for dynamic, post-translational regulation of most or all major classes of proteins.
  • the second mechanism involves the binding of NO to a transition metal ion like iron or copper.
  • NO is oftentimes referred to as a nitrosyl ligand.
  • Typical examples include the nitrosylation of heme, which is a prosthetic group containing ferrous iron in the center of a porphyrin ring. Proteins that comprise heme as a prosthetic group are also called hemoproteins which have diverse biological functions including the transportation of diatomic gases, chemical catalysis, diatomic gas detection, and electron transfer. Nitrosylation of hemoproteins such as cytochromes may negatively affect functions such as enzyme activity of the proteins.
  • nitrosylated ferrous iron such as in a nitrosylated heme group
  • Fe(II) ferrous iron
  • NO stimulates soluble guanylate cyclase, which is a heterodimeric enzyme containing heme as a prosthetic group which catalyzes the formation of cyclic-GMP (cGMP).
  • cGMP cyclic-GMP
  • Other proteins, such as Protein kinase G may be activated by cGMP, which may then for example cause the reuptake of Ca 2+ and the opening of calcium-activated potassium channels and thus may influence Ca 2+ second messenger signaling.
  • the detection of NO may also be useful for diagnostic purposes. For example, people suffering from asthma are able to monitor the intensity of their condition and to predict the likelihood of an asthmatic attack by monitoring the level of NO in their exhaled breath. Thus, the detection of NO may be an important tool in diagnostics of respiratory diseases.
  • NO has also been used in therapy. NO-generating agents have been shown to induce vasodilatation, and are beneficial in a variety of cardiovascular disorders including angina pectoris, hypertensive emergencies, and congestive heart failure (Elliott W. J. (2004) J. Clin. Hypertension 6:S87-S92; Vaughan C. J., and Delanty N. (2000) Lancet 356:411- 417; Teerlink J. R. (2005) Am. J. Cardiol. 96:59 G-67G; Stough W. G. et al. (2005) Amer. J. Cardiology 96:41 G-46G).
  • NO may be clinically relevant as a pre- and after- load reducing agent or as an anti-hypertensive drug (Lloyd-Jones D M et al. (1996) Annu. Rev. Med. 47:365-75).
  • its major drawback for clinical use is that it is an unstable gas, and, although inhaled NO may be used for pulmonary hypertension, administering it is technically challenging (Haj R M et al. (2006) Curr. Opin.
  • NO is, therefore, commonly provided as a NO-generating agent such as an organic nitrate, including nitroglycerin (glyceryl trinitrate), isosorbide dinitrate, or pentaerythritol tetranitrate.
  • a NO-generating agent such as an organic nitrate, including nitroglycerin (glyceryl trinitrate), isosorbide dinitrate, or pentaerythritol tetranitrate.
  • it is desirable to further investigate the pharmacological characteristics of existing and novel NO-generating agents e.g. by determining the NO-release rates of potential therapeutic candidate compounds, for instance by using in vitro cellular assays measuring the presence of NO in a sample.
  • NO is also relevant in non-medical applications.
  • the reduction of NO emissions for transportation systems running on diesel fuel requires that NO sensors discriminate between NO and other combustion gases.
  • the detection of NO may be used as a tool for the detection of nitro-based explosives such as trinitrotoluene (TNT), cyclotrimethylenetrinitramine (RDX), pentrite (PETN), ammonium nitrate/fuel oil.
  • TNT trinitrotoluene
  • RDX cyclotrimethylenetrinitramine
  • PETN pentrite
  • ammonium nitrate/fuel oil ammonium nitrate/fuel oil.
  • Direct detection of explosive target substances is often difficult and the detection of NO as a characteristic photofragment of nitro-based explosive materials is desirable (see also US2012145925 (Al)) .
  • nitric oxide measurements in biological samples Ziad H. Taha, Talanta 61 (2003) 3-10.
  • these detection methods do oftentimes not provide the desired sensitivity, use toxic dyes, suffer from artifacts by dye accumulation in the cell membrane and/or are irreversible and therefore may not be used for the detection of NO in biological samples such as single cells, cell culture or tissues samples.
  • NO detection based on molecular biological methods has been described.
  • This detection method relies on an indirect determination of NO by measuring the NO-induced production of cGMP by NO-activated guanylyl cylcases, thereby amplifying the detection signal (see for example Nausch et al., PNAS, January 8, 2008 Vol 105 NO 1, 365-370 and Sato et al., PNAS October 11, 2005, vol 102, NO 41, 14515- 1520).
  • polypeptide comprising: a) a first signaling domain
  • the RONS sensor domain is capable of binding RONS or RONS-like molecules and the first signaling domain, optionally together with the optional second signaling domain, is capable of generating a detectable signal upon binding of RONS or RONS- like molecules to the RONS sensor domain.
  • the RONS or RONS-like molecule is NO.
  • the present invention relates to a polynucleotide encoding for a polypeptide suitable for the detection of RONS or RONS-like molecules.
  • the present invention relates to methods for detecting a RONS or RONS-like molecule in a sample.
  • the present invention relates to the use of a polypeptide comprising SEQ ID NO: l, SEQ ID NO:2 or SEQ ID NO:3 or a sequence with at least 70 % identity to the sequence according to SEQ ID NO: l, SEQ ID NO:2 or SEQ ID NO:3 in the detection of a RONS or RONS-like molecule in a sample.
  • the present invention relates to a kit for detecting RONS or RONS-like molecules comprising a polypeptide or a polynucleotide.
  • the present invention relates to a cell comprising the polypeptide of the present invention or the polynucleotide or vector encoding the polypeptide.
  • FIGURES Figure 1: NOC-7 induced changes of the FRET ratio signal of Sensor 1 in HeLa cells. As indicated, 10 ⁇ NOC-7 was repetitively added.
  • Figure 2 FRET ratio signal of Sensor 1 in HeLa cells upon the repetitive addition of either 10 ⁇ NOC-7 or 10 ⁇ PROLI NONOate. As indicated, the NO donors were either added freshly by pipetting or a prepared buffer with a constant NO donor concentration was used.
  • Figure 3 Changes of the FRET signal in response to first the addition of 10 ⁇ and then of 20 ⁇ NOC-7 and the subsequent removal of NOC-7. The experiment was performed with transfected HeLa cells expressing Sensor 2.
  • Figure 4 NOC-7 induced changes of the mKok signal of Sensor 3 in Hela cells. The cells were either pre-incubated with 100 ⁇ iron (II) fumarate for 15 minutes at room temperature or kept in an iron-free buffer (control).
  • the RONS molecule NO may be detected by fusion proteins comprising an N-terminal cyan fluorescent protein domain, a RONS sensor domain of SEQ ID NO: 1 and a C-terminal yellow fluorescent protein domain, wherein the binding of NO to the RONS sensor domain may trigger a conformational change in said RONS sensor domain.
  • the conformational change may then be detected by an increase in FRET signaling.
  • the conformational change of a RONS sensor domain can of course also be detected in fusion proteins comprising other FRET pairs other than CFP/YFP or proximity -based signaling domains other than FRET pairs such as split- fluorescent protein domains or split enzyme domains that are affected by the conformational change of a RONS sensor domain in a fusion protein.
  • the conformational change of the RONS sensor domain may also be detectable in fusion proteins having only one signaling domain which is affected by the conformational change, such as by quenching of a fluorescence signal in a fluorescent protein (FP) domain which is induced by a conformational change of the RONS binding domain.
  • the sensitivity of the detection may be modified, e.g. by mutations in the RONS sensor domain that affect the binding of the RONS to the RONS binding domain or by mutations that affect the degree of conformational change in the RONS binding domain.
  • the sensitivity of the detection may also be modified by treating the
  • polypeptide according to the present invention with Fe(II) -containing compounds before the detection of RONS.
  • the present invention relates to a polypeptide for detecting reactive oxygen and nitrogen species (RONS) or RONS-like molecules, comprising:
  • the RONS sensor domain is capable of binding RONS or RONS-like molecules and the first signaling domain is capable of generating a detectable signal upon binding of RONS or RONS-like molecules to the RONS sensor domain.
  • the present invention also relates to a polypeptide for detecting reactive oxygen and nitrogen species (RONS) or RONS-like molecules, comprising:
  • the RONS sensor domain is capable of binding RONS or RONS-like molecules and the first signaling domain and the second signaling domain together are capable of generating a detectable signal upon binding of RONS or RONS-like molecules to the RONS sensor domain.
  • the RONS sensor domain is a domain derived from the anaerobic nitric oxide reductase transcription regulator (NorR) which is the only regulatory protein in enteric bacteria known to serve exclusively as an NO-responsive transcription factor.
  • the NorR protein comprises a regulatory domain, which is also called the GAF domain, which comprises a non-heme iron center.
  • NorR comprises an ATPase domain which is also called the AAA + domain and a helix-turn- helix (HTH) DNA-binding domain.
  • the GAF domain is covalently bound to Fe in the non-heme iron center.
  • other metal ions such as Cu 2+ and Co 2+ may also be bound in the non-heme center.
  • the RONS sensor domain does not comprise a heme-group.
  • the RONS sensor domain comprises an amino acid sequence corresponding to the GAF domain of NorR, preferably of SEQ ID NO: l. In one preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 50% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 55% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 60% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 65% identity to the sequence according to SEQ ID NO: 1.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 70% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 75% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 85% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 90% identity to the sequence according to SEQ ID NO: 1.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 95% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits 100% identity to the sequence according to SEQ ID NO: 1.
  • the RONS sensor domain comprises an amino acid sequence corresponding to the GAF domain and the AAA + domain of NorR, preferably of SEQ ID NO:2.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 50% identity to the sequence according to SEQ ID NO:2.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 55% identity to the sequence according to SEQ ID NO: 2.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 60% identity to the sequence according to SEQ ID NO: 2.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 65% identity to the sequence according to SEQ ID NO: 2.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 70% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 75% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 85% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 90% identity to the sequence according to SEQ ID NO: 2.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 95% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits 100% identity to the sequence according to SEQ ID NO: 2.
  • the RONS sensor domain comprises an amino acid sequence corresponding to the GAF domain, the AAA + domain and the HTH domain of NorR, preferably of SEQ ID NO:3.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 50% identity to the sequence according to SEQ ID NO:3.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 55% identity to the sequence according to SEQ ID NO: 3.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 60% identity to the sequence according to SEQ ID NO: 3.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 65% identity to the sequence according to SEQ ID NO: 3.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 70% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 75% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 85% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 90% identity to the sequence according to SEQ ID NO: 3.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 95% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits 100% identity to the sequence according to SEQ ID NO: 3. In a particularly preferred embodiment, the RONS sensor domain comprises an amino acid sequence of SEQ ID NO: l, SEQ ID NO:2 or SEQ ID NO: 3.
  • the RONS sensor domain comprises an amino acid sequence of SEQ ID NO: 1, SEQ ID NO:2 or SEQ ID NO: 3 with at least one amino acid substitution.
  • the amino acid sequence of SEQ ID NO: l, SEQ ID NO:2 or SEQ ID NO: 3 comprise from about 1 to about 10, more preferably from about 2 to about 8 and even more preferably from about 3 to about 7 amino acid substitutions.
  • at least one amino acid selected from the group consisting of R75, R81, D96 or D99 is substituted.
  • the first signaling domain is a fluorescent protein domain. It is also preferred that the first signaling domain is not a DNA-binding domain and more preferably not the HTH domain of NorR.
  • the first signaling domain and the second signaling domain are together selected as two domains that may together be capable of generating a detectable signal.
  • the detectable signal may be generated upon binding of the RONS or RONS-like molecule to the RONS sensor domain.
  • the binding of the RONS or RONS-like molecule to the RONS sensor domain may for example induce a
  • the first signaling domain and the second signaling domain are together selected from the group consisting of FRET-donor- acceptor pairs, split-enzyme pairs or split-fluorescent protein pairs, wherein the first signaling domain and the second signaling domain are the respective parts of a pair (for example, two halves of a split- enzyme or two halves of a split- fluorescent protein).
  • the binding of the RONS or RONS-like molecule to the RONS sensor domain may induce a conformational shift in the polypeptide and the first signaling domain and the second signaling domain may then be capable to generate the detectable signal, e.g. the FRET-donor- acceptor pair may generate a detectable FRET signal, the two halves of a split-enzyme may be functional and catalyze a reaction that may generate a detectable signal or the two halves of a split- fluorescent protein will be capable of emitting light with a specified wavelength as a detectable signal if excited with light with a wavelength within the appropriate range.
  • the first signaling domain and the second signaling domain may be a FRET-donor-acceptor pair.
  • the donor may be a CFP domain and the acceptor may be a YFP domain.
  • the first signaling domain may be the donor and the second signaling domain may be the acceptor.
  • the first signaling domain is the donor CFP domain and the second signaling domain is the acceptor YFP domain.
  • the CFP domain may comprise an amino acid sequence of SEQ ID NO:4 or an amino acid sequence of at least 70 %, 80%, 85%, 90%, 95 % or 100% identity to the sequence according to SEQ ID NO:4, wherein the excitation wavelength and the fluorescence emission wavelength are the same or substantially the same as for CFP domain according to SEQ ID NO:4, namely with an excitation peak at a wavelength of about 436 nm and an emission peak at a wavelength of about 477 nm.
  • the YFP domain may be the circularly permuted venus (CPV) protein which even more preferably comprises an amino acid sequence of SEQ ID NO:5 or an amino acid sequence of at least 70 %, 80%, 85%, 90%, 95 % or 100% identity to the sequence according to SEQ ID NO:5, wherein the excitation wavelength and the fluorescence emission wavelength are the same or substantially the same as for YFP domain according to SEQ ID NO:5, namely an excitation peak at a wavelength of about 514 nm and an emission peak at about 527 nm.
  • CPV circularly permuted venus
  • the first signaling domain and the second signaling domain comprise posttranslational modifications, such as a conjugated fluorescein molecule or other small molecule fluorophores or detectable moieties, which may contribute to generating the detectable signal of the first signaling domain together with the second signaling upon binding of the RONS or RONS-like molecule.
  • the RONS or RONS-like molecule may be selected from the group consisting of NO, OH and SH radicals.
  • the RONS or RONS-like molecule is NO.
  • the RONS sensor domain comprises an amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3 or an amino acid sequence which exhibits at least 70 % identity to the amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3;
  • the RONS- or RONS-like molecule is NO and the first signaling domain and the second signaling domain are a FRET-donor-acceptor pair, wherein preferably the first signaling domain is a CFP domain comprising an amino acid sequence of SEQ ID NO: 4 or an amino acid sequence of at least 70 % identity to the sequence according to SEQ ID NO: 4 and the second signaling domain is a YFP domain comprising an amino acid sequence of SEQ ID NO: 5 or an amino acid sequence of at least 70 % identity to the sequence according to SEQ ID NO: 5.
  • the polypeptide according to the present invention comprises an amino acid sequence which exhibits at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75 %, at least 80%, at least 85%, at least 90% or at least 95% identity to the sequence according to SEQ ID NO: 9.
  • the polypeptide according to the present invention comprises an amino acid sequence of SEQ ID NO: 9 (Sensor 1).
  • the polypeptide according to the present invention comprises an amino acid sequence which exhibits at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75 %, at least 80%, at least 85%, at least 90% or at least 95% identity to the sequence according to SEQ ID NO: 10.
  • the polypeptide according to the present invention comprises an amino acid sequence of SEQ ID NO: 10 (Sensor 2).
  • SEQ ID NO: 9 The sequences of SEQ ID NO: 9 and SEQ ID NO: 10 are shown below in Table 1A.
  • polypeptide of the present invention comprises from N-terminus to C-terminus: a) a first signaling domain; and
  • the first signaling domain comprises a fluorescent protein domain, such as CFP, YFP, mKok, EGFP, or GEM. More preferably, the RONS sensor domain comprises the NorR GAF domain.
  • polypeptide of the present invention comprises from N-terminus to C-terminus: a) a first signaling domain;
  • polypeptide comprises from N-terminus to C- terminus:
  • the polypeptide comprises from N-terminus to C-terminus: a) a first signaling domain,
  • the polypeptide comprises from N-terminus to C-terminus: a) a first signaling domain,
  • the present invention relates to a polynucleotide encoding the polypeptide according to the present invention.
  • the polynucleotide according to the invention has a length of less than 9000 nucleotides, less than 8000 nucleotides, less than 7000 nucleotides, less than 6000 nucleotides, less than 5000 nucleotides, less than 4000 nucleotides, less than 3000 nucleotides, less than 2000 nucleotides, less than 1000 nucleotides, less than 500 nucleotides or less than 300 nucleotides.
  • the isolated polynucleotide according to the invention has a length of between at least 24 and 9000 nucleotides, preferably between at least 24 and 8000 nucleotides, more preferably between at least 24 and 7000 nucleotides, more preferably between at least 24 and 6000 nucleotides, more preferably between at least 24 and 5000 nucleotides, and even more preferably between at least 24 and 4000
  • the polynucleotide according to the invention has a length of between at least 60 and 9000 nucleotides, preferably between at least 60 and 8000 nucleotides, more preferably between at least 60 and 7000 nucleotides, more preferably between at least 60 and 6000 nucleotides, more preferably between at least 60 and 5000 nucleotides, and even more preferably between at least 60 and 4000 nucleotides.
  • the polynucleotide according to the invention has a length of between at least 90 and 9000 nucleotides, preferably between at least 90 and 8000 nucleotides, more preferably between at least 90 and 7000 nucleotides, more preferably between at least 90 and 6000 nucleotides, more preferably between at least 90 and 5000 nucleotides, and even more preferably between at least 90 and 4000 nucleotides.
  • the polynucleotide according to the invention has a length of between at least 120 and 9000 nucleotides, preferably at least between 120 and 8000 nucleotides, more preferably between at least 120 and 7000 nucleotides, more preferably between at least 120 and 6000 nucleotides, more preferably between at least 120 and 5000 nucleotides, and even more preferably between at least 120 and 4000 nucleotides.
  • the isolated polynucleotide according to the invention has a length of between at least 300 and 9000 nucleotides, preferably between at least 300 and 8000 nucleotides, more preferably between at least 300 and 7000 nucleotides, more preferably between at least 300 and 6000 nucleotides, more preferably between at least 300 and 5000 nucleotides, and even more preferably between at least 300 and 4000 nucleotides.
  • an polynucleotide according to the invention has a length of at least 300 nucleotides, at least 1000 nucleotides, at least 1500 nucleotides, at least 2000 nucleotides or at least 2500 nucleotides.
  • the polynucleotide according to the invention comprises or consists of a sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO:6.
  • the polynucleotide according to the invention comprises or consists of a sequence which exhibits at least 85%, preferably at least 90%, more preferably at least 91%, even more preferably at least 92%, even more preferably at least 93%, even more preferably at least 94%, even more preferably at least 95%, even more preferably at least 96%, even more preferably at least 97%, even more preferably at least 98% or even more preferably at least 99% identity to the sequence according to SEQ ID NO:6.
  • the polynucleotide according to the invention comprises or consists of a sequence which exhibits at least 85%, preferably at least 90%, more preferably at least 95% or even more preferably at least 98% identity to the sequence according to SEQ ID NO:6.
  • polynucleotide according to the invention comprises or consists of a sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO:7.
  • polynucleotide according to the invention comprises or consists of a sequence which exhibits at least 85%, preferably at least 90%, more preferably at least 91%, even more preferably at least 92%, even more preferably at least 93%, even more preferably at least 94%, even more preferably at least 95%, even more preferably at least 96%, even more preferably at least 97%, even more preferably at least 98% or even more preferably at least 99% identity to the sequence according to SEQ ID NO:7.
  • the polynucleotide according to the invention comprises or consists of a sequence which exhibits at least 85%, preferably at least 90%, more preferably at least 95% or even more preferably at least 98% identity to the sequence according to SEQ ID NO:7.
  • polynucleotide according to the invention comprises or consists of a sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO: 8.
  • polynucleotide according to the invention comprises or consists of a sequence which exhibits at least 85%, preferably at least 90%, more preferably at least 91%, even more preferably at least 92%, even more preferably at least 93%, even more preferably at least 94%, even more preferably at least 95%, even more preferably at least 96%, even more preferably at least 97%, even more preferably at least 98% or even more preferably at least 99% identity to the sequence according to SEQ ID NO:8.
  • the polynucleotide according to the invention comprises or consists of a sequence which exhibits at least 85%, preferably at least 90%, more preferably at least 95% or even more preferably at least 98% identity to the sequence according to SEQ ID NO:8.
  • polynucleotide according to the invention comprises or consists of a sequence which exhibits 100% identity to the sequence according to SEQ ID NO:6.
  • isolated polynucleotide according to the invention comprises or consists of a sequence according to SEQ ID NO:6.
  • polynucleotide according to the invention comprises or consists of a sequence which exhibits 100% identity to the sequence according to SEQ ID NO:7.
  • isolated polynucleotide according to the invention comprises or consists of a sequence according to SEQ ID NO:7.
  • polynucleotide according to the invention comprises or consists of a sequence which exhibits 100% identity to the sequence according to SEQ ID NO: 8.
  • isolated polynucleotide according to the invention comprises or consists of a sequence according to SEQ ID NO: 8. Sequences of nucleotides with SEQ ID NO: 6 to 8 according to the present invention are shown below in Table 2. SEQ Nucleotide sequence
  • a polynucleotide according to the invention may be a single or double stranded RNA or DNA molecule.
  • the isolated polynucleotide according to the invention may be inserted into a vector such as an expression vector.
  • the expression vector may e.g. be a prokaryotic or eukaryotic expression vector such as e.g. an isolated plasmid, a minichromosome, a cosmid, a bacterial phage, a retroviral vector or any other vector known to the person skilled in the art.
  • the person skilled in the art will be familiar with how to select an appropriate vector according to the specific need.
  • the expression vector is an isolated plasmid.
  • the present invention thus also relates to an expression vector comprising a
  • the present invention relates to a cell comprising the polypeptide, the polynucleotide, expression vector and/or plasmid encoding the polypeptide of the present invention.
  • Said cell is not a human embryonic stem cell.
  • examples of cells include but are not limited to, in vitro cell culture cells or cell lysates of eukaryotic cells, such as mammalian cells, human cells or plant cells or prokaryotic cells each of which optionally may have been genetically modified by methods commonly known to the person skilled in the art such as transfecting or transforming of said cells.
  • the present invention relates to a method for detecting a RONS or RONS- like molecule in a sample, comprising the steps of a) providing a polypeptide according to the invention; b) contacting the polypeptide according to the invention with the sample; and c) measuring the signal generated by the first signaling domain.
  • the present invention relates to a method for detecting a RONS or RONS- like molecule in a sample, comprising the steps of a) providing a polypeptide according to the invention; b) contacting the polypeptide according to the invention with the sample; and c) optionally measuring the signal generated by the first signaling domain, and d) measuring the signal generated together by the first signaling domain and the second signaling domain.
  • the change in signal intensity after contact with the sample compared to the signal of the polypeptide in the absence of the sample indicates the presence of the RONS or RONS-like molecule in the sample.
  • the method according to the present invention is a (quantitative) in vivo imaging method.
  • the RONS or RONS-like molecule is selected from the group consisting of NO, OH and SH.
  • the RONS or RONS-like molecule is NO.
  • the measured signal is a fluorescence signal, a colorimetric signal or a FRET signal.
  • the signal may be generated upon binding of the RONS or RONS-like molecule to the RONS sensor domain of the polypeptide according to the present invention.
  • the signal may be generated by a FRET-donor-acceptor pair, split-enzyme pair or split- fluorescent protein pair. The detection may occur by methods commonly known to the person skilled in the art.
  • the measured signal is a fluorescence signal.
  • the fluorescence signal is quenched by binding of the RONS or RONS-like molecule to the RONS sensor domain.
  • the detectable signal is a FRET signal.
  • the FRET signal is generated by the first signaling domain and the second signaling domain. More preferably, the FRET signal is generated by a FRET-donor-acceptor pair, preferably YFP, such as CPV, and CFP.
  • YFP such as CPV
  • CFP CFP-donor-acceptor pair
  • the person skilled in the art is aware how to measure FRET signals.
  • the FRET between YFP and CFP is measured after excitation with light at a wavelength in the range of from about 430 nm to about 450 nm. More preferably, the measurement is performed after excitation with light at about 440 nm. It is also preferred that the emission of light is measured at a wavelength in the range from about 525 nm to about 545 nm and more preferably about 535 nm.
  • the FRET donor- acceptor pair is selected from the group consisting of Clover/mRubby and cpEGFP and mK02.
  • the step a) of the method for detecting a RONS or RONS-like molecule may comprise transfecting at least one cell outside the human or animal body or transforming a prokaryotic cell with a polynucleotide, a plasmid and/or an expression vector encoding the polypeptide according to the present invention.
  • the polypeptide according to the invention may then be provided by protein synthesis of said cell.
  • polypeptide according to the present invention may then either be isolated from the cell, secreted by the cell or remain inside the cell.
  • the polypeptide according to the present invention may be provided in step a) of the method according the present by providing a cell according to the present invention.
  • the method according to the present invention may be used to detect the presence of a RONS or RONS-like molecule in any concentration.
  • the method according to the present invention may detect the presence of a RONS or a RONS-like molecule in a concentration from about 0.1 nM to about 20 mM and preferably from about 0.1 nM to about 2 mM.
  • the method according to the present invention may detect the presence of a RONS or a RONS-like molecule in a concentration from about 0.1 nM to about 2 ⁇ and preferably from about 0.10 nM to about 1.00 ⁇ .
  • the method according to the present invention may detect the presence of a RONS or a RONS-like molecule in a concentration from about 500 nM to about 1 mM and preferably from about 1.0 ⁇ to about 100.0 ⁇ .
  • the method according to the present invention may detect the presence of a RONS or a RONS-like molecule in any kind of sample.
  • the sample is selected from the group consisting of biological samples, potential nitric oxide-bearing explosive samples, gaseous samples, or liquid samples such as liquid samples containing NO-generating agents.
  • the sample is a biological sample, a liquid sample or a combination thereof.
  • the sample is a cell culture, a cell pellet, a cell lysate, a tissue sample from a human or an animal, blood, breath, or a liquid containing NO-generating agents.
  • the sample may also comprise a biological sample, such as a cell culture, including the monolayer culture of cells or a 3-dimensional cell culture, a cell suspension, a cell pellet, a cell lysate, a tissue sample from a human or an animal and a liquid sample containing NO-generating agents.
  • a biological sample such as a cell culture, including the monolayer culture of cells or a 3-dimensional cell culture, a cell suspension, a cell pellet, a cell lysate, a tissue sample from a human or an animal and a liquid sample containing NO-generating agents.
  • the method according to the present invention may then be used to characterize the influence of the NO-generating agents on the biological sample by detecting the presence and/or distribution of NO and optionally in combination with determining other relevant parameters of the biological sample, such as cell apoptosis, cell signaling, cell gene expression or the like.
  • the polypeptide according to the present invention is treated with an Fe(II) containing compound in or before step a) and/or step b) of the method according to the present invention.
  • the Fe(II) containing compound may be any compound that comprises Fe(II). Examples of Fe(II) containing compounds include, but are not limited to, salts of
  • the polypeptide according to the present invention is treated with sodium nitroprusside, Fe(II) hexacyanoferrate or combinations thereof.
  • the polypeptide according to the present invention is treated with an Fe(II) containing compound in a concentration of from about 100 ⁇ to about 10 mM preferably from about 0.1 mM to about 10 mM.
  • the polypeptide according to the present invention may be treated with the Fe(II) containing compound for from about 5 min to about 30 min and preferably from about 5 min to about 15 min.
  • the treatment of the polypeptide according to the present invention with an Fe(II) containing compound may improve the sensitivity of the RONS detection.
  • the polypeptide according to the present invention comprises CPV or mKOk as a first signaling domain and is treated with an Fe(II) containing compound.
  • the method of the present invention may be used for the screening of NO-generating agents.
  • the present invention also relates to the use of a polypeptide comprising a RONS-sensor domain in the detection of a RONS- or RONS-like molecule in a sample.
  • the RONS sensor domain comprises an amino acid sequence corresponding to the GAF domain of NorR, preferably of SEQ ID NO: l. In one preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 50% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 55% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 60% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 65% identity to the sequence according to SEQ ID NO: 1.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 70% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 75% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 85% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 90% identity to the sequence according to SEQ ID NO: 1.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 95% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits 100% identity to the sequence according to SEQ ID NO: 1.
  • the RONS sensor domain comprises an amino acid sequence corresponding to the GAF domain and the AAA + domain of NorR, preferably of SEQ ID NO:2. In one preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 50% identity to the sequence according to SEQ ID NO:2. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 55% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 60% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 65% identity to the sequence according to SEQ ID NO: 2.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 70% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 75% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 85% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 90% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 95% identity to the sequence according to
  • the RONS sensor domain comprises an amino acid sequence which exhibits 100% identity to the sequence according to SEQ ID NO: 2.
  • the RONS sensor domain comprises an amino acid sequence corresponding to the GAF domain, the AAA + domain and the HTH domain of NorR, preferably of SEQ ID NO:3.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 50% identity to the sequence according to SEQ ID NO:3.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 55% identity to the sequence according to SEQ ID NO: 3.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 60% identity to the sequence according to SEQ ID NO: 3.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 65% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 70% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 75% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 85% identity to the sequence according to SEQ ID NO: 3.
  • the RONS sensor domain comprises an amino acid sequence which exhibits at least 90% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 95% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits 100% identity to the sequence according to SEQ ID NO: 3.
  • the RONS sensor domain comprises an amino acid sequence of SEQ ID NO: 1, SEQ ID NO:2 or SEQ ID NO: 3.
  • polypeptide according to the present invention comprises an amino acid sequence which exhibits at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75 %, at least 80%, at least 85%, at least 90% or at least 95% identity to the sequence according to SEQ ID NO: 9.
  • polypeptide according to the present invention comprises an amino acid sequence of SEQ ID NO: 9.
  • polypeptide according to the present invention comprises an amino acid sequence which exhibits at least 50%, at least 55%, at least
  • polypeptide according to the present invention comprises an amino acid sequence of SEQ ID NO: 10.
  • polypeptide of the present invention comprises from N-terminus to C-terminus: a) a first signaling domain; and
  • the first signaling domain comprises a fluorescent protein domain, such as CFP, YFP, mKok, EGFP, or GEM. More preferably, the RONS sensor domain comprises the NorR GAF domain.
  • polypeptide of the present invention comprises from N-terminus to C-terminus: a) a first signaling domain;
  • polypeptide comprises from N-terminus to C- terminus:
  • the polypeptide comprises from N-terminus to C-terminus: a) a first signaling domain,
  • the polypeptide comprises from N-terminus to C-terminus: a) a first signaling domain,
  • the present invention relates to the use of a polypeptide according to the present invention in the detection of a RONS or RONS-like molecule in a sample.
  • the present invention relates to the use of a polynucleotide according to the present invention in the detection of a RONS or RONS-like molecule in a sample.
  • the polynucleotide according to the present invention may be present in a vector for transfecting or transforming a cell.
  • the use of according to the present invention comprises the detection of RONS or RONS-like molecules selected from the group consisting of NO, OH and SH radicals.
  • the detected RONS is NO.
  • the use according to the present invention comprises detecting the presence of a RONS or a RONS-like molecule in any kind of sample.
  • the sample may be selected from the group consisting of biological samples, potential nitric oxide-bearing explosive samples, gaseous samples, liquid samples such as liquid samples containing NO-generating agents or a combination thereof. More preferably, the sample may be a biological sample, a liquid sample or a combination thereof.
  • the sample is a cell culture, a cell pellet, a cell lysate, a tissue sample from a human or an animal, blood, breath, or a liquid containing NO- generating agents.
  • the sample may also comprise a biological sample, such as a cell culture, including the monolayer culture of cells or a 3-dimensional cell culture, a cell suspension, a cell pellet, a cell lysate, a tissue sample from a human or an animal and a liquid sample containing NO-generating agents.
  • the use according to the present invention comprises the use in the characterization of the influence of the NO-generating agents on the biological sample by detecting the presence and/or distribution of NO or other relevant parameters of the biological sample, such as cell apoptosis, cell signaling, cell gene expression or the like.
  • the use according to the present invention comprises the use in the screening of NO-generating agents.
  • the use according to the present invention comprises the use of the polypeptide according to the present invention in (quantitative) in vivo imaging.
  • vivo imaging refers to the imaging in living cells outside the human body such as microscopy of isolated living cells that were cultured in vitro.
  • the use according to the present invention comprises the detection of NO in the analysis of exhaled breath.
  • the use according to the present invention comprises the use of the polypeptide of the present invention in an apparatus for analyzing nitric oxide concentration of exhaled breath, preferably in a sensor, wherein more preferably the polypeptide of the present invention may be encapsulated in a porous inert matrix.
  • the polypeptide according to the present invention has been treated with an Fe(II) containing compound as described above before the detection of a RONS or RONS-like molecule.
  • the present invention relates to a kit for detecting RONS or RONS-like molecules.
  • the kit comprises
  • the kit according to the present invention comprises at least one of a) to d) and suitable buffer for the polypeptide according to the present invention. In another embodiment, the kit according to the present invention comprises at least one of a) to d) and a suitable buffer for the cell according to the present invention.
  • domain refers to building blocks of polypeptides or fusion proteins.
  • the term domain thus comprises parts of a polypeptide that can fold, function and/or exist independently of the rest of the polypeptide chain or structure.
  • cyan fluorescent protein is considered as a domain when it is a part of a fusion protein.
  • domain also comprises each part of a split-enzyme or split fluorescent protein, wherein each part is considered as a domain even though the two domains of a split enzyme or split fluorescent protein may only fold and function together.
  • polypeptide and "protein” are used interchangeably herein to describe protein molecules that may comprise either partial or full-length proteins.
  • the term includes "fusion proteins", comprising proteins or polypeptides that have an amino acid sequence derived from two or more proteins.
  • the fusion protein may also include linking regions of amino acids between amino acid portions derived from separate proteins.
  • the term “suitreactive oxygen and nitrogen species (RONS)” refers to an oxygen-or nitrogen containing small molecule.
  • the molecule comprises less than 5 atoms.
  • Many, but not all, RONS are free radicals.
  • a radical is a group of atoms which behaves as a unit and has one or more unpaired electrons. Examples of RONS include, but are not limited to, 0 2 ⁇ (superoxide radical), OH (hydroxyl radical), ONOO " (peroxynitrite), 0 2 x (singlet oxygen), 0 3 (ozone), NO (nitric oxide, and N0 2 (nitrogen dioxide).
  • reactive oxygen and nitrogen species-like refers to a small molecule with RONS-like characteristics which does not contain oxygen or nitrogen. Examples include, but are not limited to, SH (sulfanyl radical).
  • RONS-sensor domain refers to a protein domain that is capable of binding a RONS or RONS-like molecule.
  • RONS-sensor domains include, but are not limited to, the NorR protein, a polypeptide of SEQ ID NO: l, SEQ ID NO:2 or SEQ ID NO:3 or polypeptide variants, homologs and orthologs thereof.
  • the RONS-sensor domain does not contain heme.
  • the RONS-sensor domain may be capable of binding a metal ion such as Fe, Cu, or CO.
  • the term "detectable signal” refers to an increase or decrease of signals commonly used in technical fields of biochemistry, chemistry, medical or diagnostic technology.
  • the detectable signal include, but is not limited to, an electrical (e.g., capacitance), mechanical, optical, acoustic or thermal signal.
  • the optical signal may be a fluorescence signal, a FRET signal, a colorimetric signal or an electrochemiluminescence signal.
  • the signal may be detectable, i.e. the signal and a respective change of the signal may be monitored using the appropriate technological equipment.
  • the detectable signal may be a signal generated or altered in a proximity-dependent manner, for example induced by a conformational change of a polypeptide.
  • fluorescent protein refers to any protein or protein domain in a fusion protein that is capable of emitting fluorescent light.
  • Fluorescent proteins are well known to the person skilled in the art. Example include, but are not limited to, GFP and variants thereof such as EGFP, cpGFP, CFP, YFP, EYFP, cpYFP, CPV, Citrine, Venus, and Ypet; blue fluorescent protein (BFP) such as EBFP, EBFP2, Azurite, mKalamal; cyan fluorescent protein (CFP) such as ECFP, Cerulean, CyPet; and other florescent proteins such as UnaG, dsRed, tdTomato eqFP611, Dronpa, TagRFPs, KFP, EosFP,
  • FRET fluorescence resonance energy transfer between or within molecules.
  • one fluorophore is able to act as an energy donor and one other is an energy acceptor. These are sometimes known as a reporter and a quencher, respectively.
  • the donor may be excited with a specific wavelength of light for which it will normally exhibit a fluorescence emission
  • the acceptor may also be excited at a wavelength such that it can accept the emission energy of the donor molecule by a variety of distance-dependent energy transfer mechanisms. Generally, the acceptor accepts the emission energy of the donor when they are in close proximity.
  • the donor and the acceptor may be different molecules or may be separate parts of the same molecule, such as two different domains of a polypeptide. FRET measuring techniques are well known in the art.
  • FRET-donor-acceptor pair refers to fluorophores representing the energy donor and the energy acceptor capable of FRET as described above.
  • fluorophore refers to a component of a molecule that causes a molecule to be fluorescent. It is a functional group in a molecule which will absorb light of a specific wavelength and re-emit light at a different (but equally specific) wavelength. The amount and wavelength of the emitted light depend on both the fluorophore and the chemical environment of the fluorophore.
  • Fluorophores include, but are not limited to, fluorescein isothiocyanate (FITC), a reactive derivative of fluorescein, rhodamine (TRrrC), coumarin, cyanin dyes (Cy) e.g.
  • Cyanine 3, Cyanine 5 or Cyanine 7, fluorescent proteins such as the green fluorescent protein (GFP) from Aequorea Victoria or Renilla reniformis or proteins variants thereof such as yellow fluorescent protein (YFP) including Citrine, Venus, and Ypet; blue fluorescent protein (BFP) such as EBFP, EBFP2, Azurite, mKalamal; cyan fluorescent protein (CFP) such as ECFP, Cerulean, CyPet; and other florescent proteins such as UnaG, dsRed, eqFP611, Dronpa, TagRFPs, KFP, EosFP, Dendra, IrisFP, Clover, mRubby, mKOk and mK02.
  • GFP green fluorescent protein
  • BFP blue fluorescent protein
  • CFP cyan fluorescent protein
  • CFP cyan fluorescent protein
  • other florescent proteins such as UnaG, dsRed, eqFP611, Dronpa, TagRFPs, KFP
  • Fluorescein isothiocyanate FITC
  • TRITC reactive derivative of fluorescein
  • Cy coumarin, cyanin
  • fluorophores that may be used as a FRET-donor- acceptor pair include, but are not limited to, CFP as donor and YFP as acceptor, EGFP as donor and Cy3 as acceptor, or EGFP as donor and YFP as acceptor, or Clover as Donor and mRubby as acceptor or cpEGFP as donor and mK02 as acceptor.
  • split enzyme refers to a biologically active enzyme that is split into at least two portions that have at least reduced or no biologically activity.
  • split enzyme pair refers to the at least two at least partially inactive enzyme portions. Upon close proximity, the enzyme portions interact to form the biologically active enzyme, which can be detected using conventional enzyme detection techniques. The split enzyme technology is also further described in WO 2005/094441 A2.
  • split enzymes include, but are not limited to, Renilla luciferase that can be reconstituted and monitored via bioluminescence; complementing split ⁇ -galactosidase wherein the activity can be monitored via colorometric, chemiluminescence, or fluorescence detection; split ⁇ -lactamase whose complementation may be assayed by the color change of nitrocefin upon hydrolysis or by fluorescence via CCF-2/AM; GTPases (change of charge), peroxidases (colorometric), nucleases (endo and exo cleavage), restriction endonucleases (sequence specific endo cleavage), proteases (protein cleavage), ligases (ligating nucleic acid oligos),and thiol-disulfide oxidoreductases (conformational change through disulfide bonds).
  • split fluorescent protein (SFP) pairs refers to at least two portions of a fluorescent protein. SFPs are composed of multiple peptide or polypeptide fragments that individually are not fluorescent, but, when complemented, form a functional fluorescent molecule.
  • Split-Green Fluorescent Protein Split- GFP
  • Some engineered Split-GFP molecules are self-assembling. (See, e.g., U.S. Pat. App. Pub. No. 2005/0221343 and PCT Pub. No. WO/2005/074436; Cabantous et al., Nat. Biotechnol., 23: 102-107, 2005; Cabantous and Waldo, Nat.
  • US2012282643 also describes Split- Yellow Fluorescent Protein variants and Split-Cyan Fluorescent Protein variants.
  • the determination of "percent identity" between two sequences as used herein is preferably accomplished using the mathematical algorithm of Karlin and Altschul (1993) Proc. Natl. Acad. Sci USA 90: 5873-5877. Such an algorithm is e.g. incorporated into the BLASTn and BLASTp programs of Altschul et al. (1990) J. Mol. Biol. 215: 403-410 available at NCBI (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi).
  • the determination of percent identity is preferably performed with the standard parameters of the BLASTn and BLASTp programs.
  • BLAST polynucleotide searches are preferably performed with the BLASTn program.
  • the "Max Target Sequences” box may be set to 100, the “Short queries” box may be ticked, the “Expect threshold” box may be set to 10 and the “Word Size” box may be set to 28.
  • the scoring parameters the "Match/mismatch Scores” may be set to 1,-2 and the "Gap Costs” box may be set to linear.
  • the "Low complexity regions” box may not be ticked, the "Low complexity regions” box may not be ticked, the
  • BLAST protein searches are preferably performed with the BLASTp program.
  • the "Max Target Sequences” box may be set to 100, the “Short queries” box may be ticked, the “Expect threshold” box may be set to 10 and the “Word Size” box may be set to "3”.
  • the scoring parameters the "Matrix” box may be set to "BLOSUM62”
  • the "Gap Costs” Box may be set to "Existence: 11 Extension: 1”
  • the “Compositional adjustments” box may be set to "Conditional compositional score matrix adjustment”.
  • the "Low complexity regions” box may not be ticked
  • the "Mask for lookup table only” box may not be ticked and the "Mask lower case letters” box may not be ticked.
  • the percent identity is determined over the entire length of the respective reference sequence, i.e. over the entire length of the sequence according to the SEQ ID NO or SEQ ID NOs recited in the respective context.
  • an amino acid sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO: 1 exhibits at least 80% identity to SEQ ID NO: 1 over the entire length of SEQ ID NO: 1.
  • a sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO:3 exhibits at least 80% identity to SEQ ID NO:3 over the entire length of SEQ ID NO:3.
  • isolated in the context of the present invention indicates that a polypeptide or polynucleotide has been removed from its natural environment and/or is presented in a form in which it is not found in nature.
  • An "isolated” polypeptide or an “isolated” polynucleotide may also be a polypeptide or polynucleotide that has been generated in vitro.
  • amino acid substitution refers to a substitution in an amino acid sequence according to a conservative or a non-conservative substitution, preferably a conservative substitution.
  • a substitution also includes the exchange of a naturally occurring amino acid with a non-natural amino acid.
  • conservative substitution comprises the substitution of an amino acid with another amino acid having a chemical property similar to the amino acid that is substituted.
  • the conservative substitution is a substitution selected from the group consisting of:
  • a basic amino acid is preferably selected from the group consisting of arginine, histidine, and lysine.
  • An acidic amino acid is preferably aspartate or glutamate.
  • An aromatic amino acid is preferably selected from the group consisting of
  • a non-polar, aliphatic amino acid is preferably selected from the group consisting of glycine, alanine, valine, leucine, methionine and isoleucine.
  • a polar, uncharged amino acid is preferably selected from the group consisting of serine, threonine, cysteine, proline, asparagine and glutamine.
  • a non-conservative amino acid substitution is the exchange of an amino acid with any amino acid that does not fall under the above- outlined conservative substitutions (i) through (v).
  • biological sample refers to a sample of tissue (e.g., tissue biopsy), organ, cell, cell lysate, or body fluid outside the body of a human or an animal. Further the term “biological sample” also includes in vitro cell cultured cells or cell lysates of eukaryotic cells, such as mammalian cells, human cells or plant cells or prokaryotic cells which optionally may have been genetically modified by methods commonly known to the person skilled in the art, including methods of transfecting and transforming.
  • gaseous sample refers to any kind of sample in gaseous form.
  • gaseous samples include, but are not limited to, human or animal breath, exhaust fumes and combustion gases.
  • binding refers to an attractive interaction between two molecules that results in a stable association in which the molecules are in close proximity to each other. The result of binding is sometimes the formation of a molecular complex in which the attractive forces holding the components together are generally non-covalent, and thus are normally energetically weaker than covalent bonds.
  • binding also includes the formation of a coordination complex, such as the coordination of a small molecule such as NO with a transition metal and/or amino acid residues in a protein domain such as the interaction of NO with the GAF domain of NorR.
  • the term “binding” does not include redox reactions, i.e. an electron transfer such as in the oxidation of glutathione with hydrogen peroxide (2 G-SH + H 2 0 2 ⁇ GS-SG + 2 H 2 0).
  • the present invention also relates to the following items:
  • the RONS sensor domain is capable of binding RONS or RONS-like molecules and the first signaling domain is capable of generating a detectable signal upon binding of RONS or RONS-like molecules to the RONS sensor domain.
  • the RONS sensor domain is capable of binding RONS or RONS-like molecules and the first signaling domain and the second signaling domain together are capable of generating a detectable signal upon binding of RONS or RONS-like molecules to the RONS sensor domain.
  • RONS sensor domain comprises an amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3 with at least one amino acid substitution of amino acid R75, R81, D96 or D99.
  • a cell comprising the polynucleotide of (13) or (14), the vector of (15) and/or the polypeptide according to (1) to (12).
  • a method for detecting a RONS or RONS-like molecule in a sample comprising the steps of
  • step a) The method of (17) to (21), wherein in step a) the providing of the polypeptide comprises (i) transfecting at least one eukaryotic cell outside the human or animal body or transforming a prokaryotic cell with a polynucleotide according to (13) to (14) or the vector of (15) or (ii) providing a cell according to (16).
  • sample is selected from the group consisting of biological samples, potential nitric oxide-bearing explosive samples, gaseous samples, liquid samples, liquid samples containing NO-generating agents or a combination thereof.
  • sample is selected from the group consisting of biological samples, potential nitric oxide-bearing explosive samples, gaseous samples, liquid samples, liquid samples containing NO-generating agents.
  • a kit for detecting RONS or RONS-like molecules comprising at least one of: a) a polypeptide according to (1) to (12);
  • DMEM Dulbecco's modified eagle's medium
  • 3-(2-Hydroxy-l-methyl-2- nitrosohydrazino)-N-methyl-l-propanamine was from Tocris (Tocris Cookson Ltd., Bristol, UK) and Disodium l-[2-(carboxylato)pyrrolidin-l-yl]diazen-l-ium-l,2- diolate (PROLI NONOate) was obtained from Santa Cruz (Santa Cruz Biotechnology, Inc., Heidelberg, Germany).
  • TransfastTM transfection reagent, restriction enzymes and Taq polymerase used for subcloning were purchased from Promega (Mannheim, Germany). All other chemicals were obtained from Roth (Karlsruhe, Germany).
  • HeLa cells were cultured in a humidified atmosphere at 37 °C and 5 % C0 2 using DMEM containing 10 % FCS, 100 U/ml penicillin, and 100 ⁇ g/ml streptomycin.
  • DMEM fetal calf serum
  • cells were grown on 30 mm glass cover slips and transfected at 50-80 % confluence with 1.5 ⁇ g of plasmid DNA (per 30 mm well) using 4 ⁇ g / well TransFastTM transfection reagent in 0.5 ml of serum and antibiotic-free transfection medium.
  • Cells were maintained in the incubator (37 °C, 5 % C0 2 , 95 % air) for 16-20 hours before changing the medium back to normal culture medium. Experiments were performed 24-48 hours after transfection.
  • GGCATCGATATGAGTTTTTCCGTTGATGTGC forward primer
  • GCCGAATTCATCCTTCAATCCCAGACGTTTC reverse primer
  • the primer pairs GGCATCGATATGAGTTTTTCCGTTGATGTGC (forward primer) and ATAGAATTCCGTGGCATCGCCTGGCAGCATA (reverse primer) was used to amplify the GAF domain for cloning Sensor 2, respectively.
  • the obtained fragments were inserted into the pcDNA3.1(-) vector (Invitrogene, Life Technologies, Vienna, Austria) containing the coding sequence of respective fluorescent proteins (eCFP and CPV) and the restriction sites Clal, which was inserted by PCR, and EcoRl.
  • the coding sequences of the fluorescent proteins including both restriction sites between the FPs were inserted into the pcDNA3.1 (-) vector's multi cloning site using common molecular biology methods known to the person skilled in the art.
  • Imaging system 1 was based on a Zeiss Axio Observer. A 1 (Zeiss, Gottingen, Germany) that was equipped with a polychromator illumination system (VisiChrome, Visitron Systems, Puchheim, Germany) and a thermoelectric-cooled CCD camera (Photometries CoolSNAP HQ, Visitron Systems).
  • Imaging system 2 consists of the fluorescence microscope Eclipse 300TE (Nikon, Vienna) with an epifluorescence system (150 W XBO; Optiquip, Highland Mills, NY, USA), a computer controlled z-stage (Ludl Electronic Products, Haawthrone, NY, USA) and a CCD camera (spot Persuit, Visitron Systems).
  • Imaging system 3 is a fully automated digital wide field system, Till iMIC (Till Photonics Graefelfing, Germany) that is equipped with an ultra fast switching monochromator, the Polychrome V (Till Photonics) and a CCD camera (AVT Stringray F145B, Allied Vision Technologies, Stadtroda, Germany).
  • Emission filters were either mounted on a a Ludl filterwheel (Imaging system 1), or the Dual View Micro-ImagerTM (480 and 535 nm; Optical Insights, Visitron Systems) was used (Imaging system 2), or a single beam splitter design (Imaging system 3; Dichrotome, Till Photonics) was installed.
  • Imaging system 1 the fluorescence microscopes VisiView Premier Acquisition software (Visitron Systems) was used for both imaging system 1 and 2, while the live acquisition software version 2.0.0.12 (Till Photonics) was used on imaging system 3.
  • Example 7 The following Examples 7 and 8 were performed using imaging system 1.
  • Example 5. Statistics Data shown represent the mean + s.e.m, and n indicates number of cells/independent experiments Statistical analyses were performed with unpaired Student's t-test and p ⁇ 0.05 was considered to be significant.
  • Example 6. Constructs
  • Sensor 1 and Sensor 2 were encoded by the respective nucleotide coding sequences of n_Sensor 1 (SEQ ID NO: 8) and n_Sensor 2 (SEQ ID NO: 6). The nucleotide sequences were cloned and transfected in HeLa cells as described above.
  • Example 9 Addition of Fe-containing compounds
  • the probe Sensor 3 (SEQ ID NO: 12) comprising from N-terminus to C-terminus a mKOk domain and a GAF-domain is encoded by the respective nucleotide coding sequences of n_Sensor 3 (SEQ ID NO: 11) (see Table 3). Table 3.
  • the transfected HeLa cells were then pre-incubated with either 1 mM to 10 mM sodium nitroprusside or 100 ⁇ to 200 ⁇ iron(II) fumarate in a medium containing (in mM): 138 NaCl, 5 KC1, 2 CaCl 2 , 1 MgCl 2 , 1 HEPES, 2.6 NaHC0 3 , 0.44 KH 2 P0 4 , 0.34 Na 2 HP0 4 , 10 D-glucose, 0.1 % vitamins, 0.2 % essential amino acids and 1%
  • Example 10 Determination of EC 50 values of NOC-7 on differently colored Sensors
  • HeLa cells expressing Sensor 3 were prepared as described above. The consecutive addition and removal of different concentrations of NOC-7 in range from 1 nM to 100 ⁇ revealed in fluorescence microscopy that the sensor responded in a
  • Table 4 EC 50 values of NOC-7 quenching by differently colored fluorescent sensor

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Abstract

The present invention relates to a polypeptide comprising a first signaling domain and a reactive oxygen and nitrogen species (RONS) sensor domain and optionally a second signaling domain, wherein the RONS sensor domain is capable of binding RONS or RONS-like molecules and the first signaling domain and optionally together with the second signaling domain is capable of generating a detectable signal upon binding of RONS or RONS-like molecules to the RONS sensor domain. Preferably, the RONS is NO. The invention also relates to a polynucleotide encoding said polypeptide and methods for detecting a RONS or RONS-like molecule in a sample.

Description

TITLE Genetically encoded nitrogen monoxide sensors (geNOps)
BACKGROUND OF THE INVENTION
Reactive oxygen and nitrogen species (RONS) as well as RONS-like molecules play important roles in biological processes as well as non-medical applications.
For example, RONS and RONS-like molecules are integral chemical mediators of both acute and chronic inflammation and their generation occurs locally and within minutes in the inflammatory process, preceding the arrival of inflammatory cells.
A particular relevant RONS is nitric oxide (NO). NO has been recognized as a key signaling molecule not only in inflammation but also in neurotransmission, the immune system and the cardiovascular system. Further, NO plays a central role in diverse pathological conditions, such as hypertension, diabetes, atherosclerosis, erectile dysfunctions, ischemic heart disease or stroke.
At least two important biological reaction mechanisms of nitric oxide are known, namely S-nitrosation of thiols and nitrosylation of transition metal ions.
The first mechanism, S-nitrosation, involves the (reversible) conversion of thiol groups, including cysteine residues in proteins, to form S-nitrosothiol. S-Nitrosation is a mechanism for dynamic, post-translational regulation of most or all major classes of proteins.
The second mechanism, nitrosylation, involves the binding of NO to a transition metal ion like iron or copper. In this function, NO is oftentimes referred to as a nitrosyl ligand. Typical examples include the nitrosylation of heme, which is a prosthetic group containing ferrous iron in the center of a porphyrin ring. Proteins that comprise heme as a prosthetic group are also called hemoproteins which have diverse biological functions including the transportation of diatomic gases, chemical catalysis, diatomic gas detection, and electron transfer. Nitrosylation of hemoproteins such as cytochromes may negatively affect functions such as enzyme activity of the proteins. It is commonly known that nitrosylated ferrous iron, such as in a nitrosylated heme group, is particularly stable, as the binding of the nitrosyl ligand to ferrous iron (Fe(II)) is very strong. For example, NO stimulates soluble guanylate cyclase, which is a heterodimeric enzyme containing heme as a prosthetic group which catalyzes the formation of cyclic-GMP (cGMP). Other proteins, such as Protein kinase G may be activated by cGMP, which may then for example cause the reuptake of Ca2+ and the opening of calcium-activated potassium channels and thus may influence Ca2+ second messenger signaling.
The detection of NO may also be useful for diagnostic purposes. For example, people suffering from asthma are able to monitor the intensity of their condition and to predict the likelihood of an asthmatic attack by monitoring the level of NO in their exhaled breath. Thus, the detection of NO may be an important tool in diagnostics of respiratory diseases.
NO has also been used in therapy. NO-generating agents have been shown to induce vasodilatation, and are beneficial in a variety of cardiovascular disorders including angina pectoris, hypertensive emergencies, and congestive heart failure (Elliott W. J. (2004) J. Clin. Hypertension 6:S87-S92; Vaughan C. J., and Delanty N. (2000) Lancet 356:411- 417; Teerlink J. R. (2005) Am. J. Cardiol. 96:59 G-67G; Stough W. G. et al. (2005) Amer. J. Cardiology 96:41 G-46G). NO may be clinically relevant as a pre- and after- load reducing agent or as an anti-hypertensive drug (Lloyd-Jones D M et al. (1996) Annu. Rev. Med. 47:365-75). However, its major drawback for clinical use is that it is an unstable gas, and, although inhaled NO may be used for pulmonary hypertension, administering it is technically challenging (Haj R M et al. (2006) Curr. Opin.
Anaesthesiol. 19:88-95). NO is, therefore, commonly provided as a NO-generating agent such as an organic nitrate, including nitroglycerin (glyceryl trinitrate), isosorbide dinitrate, or pentaerythritol tetranitrate. However, it is desirable to further investigate the pharmacological characteristics of existing and novel NO-generating agents, e.g. by determining the NO-release rates of potential therapeutic candidate compounds, for instance by using in vitro cellular assays measuring the presence of NO in a sample.
Moreover, the presence of NO is also relevant in non-medical applications. For example, the reduction of NO emissions for transportation systems running on diesel fuel requires that NO sensors discriminate between NO and other combustion gases. In addition, the detection of NO may be used as a tool for the detection of nitro-based explosives such as trinitrotoluene (TNT), cyclotrimethylenetrinitramine (RDX), pentrite (PETN), ammonium nitrate/fuel oil. Direct detection of explosive target substances is often difficult and the detection of NO as a characteristic photofragment of nitro-based explosive materials is desirable (see also US2012145925 (Al)) .
Several methods for the detection of NO have been developed. These methods include electron paramagnetic resonance spectrometry methods and methods of fluoremetry using NO-reactive small-molecule fluorescent probes (see for example "Bioimaging of Nitric Oxide", Tetsuo Nagano and Tetsuhiko Yoshimura, Chem Rev. 2002, 102 1235-1269;
"nitric oxide measurements in biological samples, Ziad H. Taha, Talanta 61 (2003) 3-10). However, it has been shown that these detection methods do oftentimes not provide the desired sensitivity, use toxic dyes, suffer from artifacts by dye accumulation in the cell membrane and/or are irreversible and therefore may not be used for the detection of NO in biological samples such as single cells, cell culture or tissues samples.
Further, NO detection based on molecular biological methods has been described. This detection method relies on an indirect determination of NO by measuring the NO-induced production of cGMP by NO-activated guanylyl cylcases, thereby amplifying the detection signal (see for example Nausch et al., PNAS, January 8, 2008 Vol 105 NO 1, 365-370 and Sato et al., PNAS October 11, 2005, vol 102, NO 41, 14515- 1520).
However, there is still a need for alternative detection methods of RONS and RONS-like molecules, e.g. using methods of molecular biology that do not involve an indirect measurement of a second messenger molecule such as cGMP. In this context, it is noted that the construction of proximity-based probes is challenging. So far, it cannot be reliably predicted whether the steric effects in a genetically encoded sensor due to ligand binding may induce a conformational change that can be detectable, e.g. by fluorescence quenching or FRET. The suitability of a genetically encoded sensor thus depends on a case-by-case basis on the individual binding domain, the extend and stability of its conformational change upon ligand binding, the linker sequence between the binding module and the detection domains.
Moreover, it is even more challenging to provide a genetically encoded sensor that may be used for performing quantitative in vivo imaging. Here, a higher dynamic range than for in vitro experiments is required due to factors such as background fluorescence.
Furthermore, the complexity in the cellular milieus could restrict motion of sensor proteins and hence influence the dynamic range. In addition, cellular and subcellular metabolite levels of second messengers such as NO are very difficult to capture due to a very high turnover rate. Thus, it is an object of the present invention to provide novel agents suitable for the detection of RONS and RONS-like molecules, particularly for the detection of NO.
Further, it is another object of the present invention to provide novel methods for detecting RONS or RONS-like molecules.
SUMMARY
The objects of the present invention are solved by a polypeptide comprising: a) a first signaling domain,
b) a RONS sensor domain, and
c) optionally a second signaling domain, wherein the RONS sensor domain is capable of binding RONS or RONS-like molecules and the first signaling domain, optionally together with the optional second signaling domain, is capable of generating a detectable signal upon binding of RONS or RONS- like molecules to the RONS sensor domain. Preferably, the RONS or RONS-like molecule is NO.
In one embodiment, the present invention relates to a polynucleotide encoding for a polypeptide suitable for the detection of RONS or RONS-like molecules.
Further, the present invention relates to methods for detecting a RONS or RONS-like molecule in a sample.
In one aspect, the present invention relates to the use of a polypeptide comprising SEQ ID NO: l, SEQ ID NO:2 or SEQ ID NO:3 or a sequence with at least 70 % identity to the sequence according to SEQ ID NO: l, SEQ ID NO:2 or SEQ ID NO:3 in the detection of a RONS or RONS-like molecule in a sample.
In addition, the present invention relates to a kit for detecting RONS or RONS-like molecules comprising a polypeptide or a polynucleotide. In one aspect, the present invention relates to a cell comprising the polypeptide of the present invention or the polynucleotide or vector encoding the polypeptide.
BRIEF DESCRIPTION OF FIGURES Figure 1: NOC-7 induced changes of the FRET ratio signal of Sensor 1 in HeLa cells. As indicated, 10 μΜ NOC-7 was repetitively added. Figure 2: FRET ratio signal of Sensor 1 in HeLa cells upon the repetitive addition of either 10 μΜ NOC-7 or 10 μΜ PROLI NONOate. As indicated, the NO donors were either added freshly by pipetting or a prepared buffer with a constant NO donor concentration was used.
Figure 3: Changes of the FRET signal in response to first the addition of 10 μΜ and then of 20 μΜ NOC-7 and the subsequent removal of NOC-7. The experiment was performed with transfected HeLa cells expressing Sensor 2. Figure 4: NOC-7 induced changes of the mKok signal of Sensor 3 in Hela cells. The cells were either pre-incubated with 100 μΜ iron (II) fumarate for 15 minutes at room temperature or kept in an iron-free buffer (control).
DETAILED DESCRIPTION
Before the present invention is described in detail below, it is to be understood that this invention is not limited to the particular methodology, protocols and reagents described herein as these may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention which will be limited only by the appended claims. Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art.
Although several documents are cited throughout the text of this specification, which are incorporated by reference in their entirety, nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.
It has surprisingly been found that the RONS molecule NO may be detected by fusion proteins comprising an N-terminal cyan fluorescent protein domain, a RONS sensor domain of SEQ ID NO: 1 and a C-terminal yellow fluorescent protein domain, wherein the binding of NO to the RONS sensor domain may trigger a conformational change in said RONS sensor domain. The conformational change may then be detected by an increase in FRET signaling.
The conformational change of a RONS sensor domain can of course also be detected in fusion proteins comprising other FRET pairs other than CFP/YFP or proximity -based signaling domains other than FRET pairs such as split- fluorescent protein domains or split enzyme domains that are affected by the conformational change of a RONS sensor domain in a fusion protein. The conformational change of the RONS sensor domain may also be detectable in fusion proteins having only one signaling domain which is affected by the conformational change, such as by quenching of a fluorescence signal in a fluorescent protein (FP) domain which is induced by a conformational change of the RONS binding domain. It is also possible that other structurally similar RONS sensor domains, such as other RONS sensor domains that do not comprise heme, are used accordingly or that the RONS sensor domain of SEQ ID NO: 1 is modified. This way, other RONS or RONS-like molecules may also be detected, respectively. Further, the sensitivity of the detection may be modified, e.g. by mutations in the RONS sensor domain that affect the binding of the RONS to the RONS binding domain or by mutations that affect the degree of conformational change in the RONS binding domain. For example, the sensitivity of the detection may also be modified by treating the
polypeptide according to the present invention with Fe(II) -containing compounds before the detection of RONS.
The present invention relates to a polypeptide for detecting reactive oxygen and nitrogen species (RONS) or RONS-like molecules, comprising:
a) a first signaling domain, and
b) a RONS sensor domain,
wherein preferably the RONS sensor domain is capable of binding RONS or RONS-like molecules and the first signaling domain is capable of generating a detectable signal upon binding of RONS or RONS-like molecules to the RONS sensor domain.
The present invention also relates to a polypeptide for detecting reactive oxygen and nitrogen species (RONS) or RONS-like molecules, comprising:
a) a first signaling domain,
b) a RONS sensor domain, and
c) a second signaling domain,
wherein preferably the RONS sensor domain is capable of binding RONS or RONS-like molecules and the first signaling domain and the second signaling domain together are capable of generating a detectable signal upon binding of RONS or RONS-like molecules to the RONS sensor domain.
In a preferred embodiment, the RONS sensor domain is a domain derived from the anaerobic nitric oxide reductase transcription regulator (NorR) which is the only regulatory protein in enteric bacteria known to serve exclusively as an NO-responsive transcription factor. The NorR protein comprises a regulatory domain, which is also called the GAF domain, which comprises a non-heme iron center. Further, NorR comprises an ATPase domain which is also called the AAA+ domain and a helix-turn- helix (HTH) DNA-binding domain. NO is known to bind to the non-heme iron center and to induce a steric rearrangement of NorR which may impact the GAF-AAA+ interaction and stimulate ATP hydrolysis and thereby enable the activation of transcription of proteins responsible for NO detoxification (see for example D'autreaux et al, 437, 769- 772, 29 September 2005). Preferably, the GAF domain is covalently bound to Fe in the non-heme iron center. However, other metal ions such as Cu2+ and Co2+ may also be bound in the non-heme center. In one preferred embodiment, the RONS sensor domain does not comprise a heme-group.
In a preferred embodiment, the RONS sensor domain comprises an amino acid sequence corresponding to the GAF domain of NorR, preferably of SEQ ID NO: l. In one preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 50% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 55% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 60% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 65% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 70% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 75% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 85% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 90% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 95% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits 100% identity to the sequence according to SEQ ID NO: 1.
In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence corresponding to the GAF domain and the AAA+ domain of NorR, preferably of SEQ ID NO:2. In one preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 50% identity to the sequence according to SEQ ID NO:2. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 55% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 60% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 65% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 70% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 75% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 85% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 90% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 95% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits 100% identity to the sequence according to SEQ ID NO: 2.
In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence corresponding to the GAF domain, the AAA+ domain and the HTH domain of NorR, preferably of SEQ ID NO:3. In one preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 50% identity to the sequence according to SEQ ID NO:3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 55% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 60% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 65% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 70% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 75% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 85% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 90% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 95% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits 100% identity to the sequence according to SEQ ID NO: 3. In a particularly preferred embodiment, the RONS sensor domain comprises an amino acid sequence of SEQ ID NO: l, SEQ ID NO:2 or SEQ ID NO: 3.
In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence of SEQ ID NO: 1, SEQ ID NO:2 or SEQ ID NO: 3 with at least one amino acid substitution. Preferably, the amino acid sequence of SEQ ID NO: l, SEQ ID NO:2 or SEQ ID NO: 3 comprise from about 1 to about 10, more preferably from about 2 to about 8 and even more preferably from about 3 to about 7 amino acid substitutions. In a preferred embodiment, at least one amino acid selected from the group consisting of R75, R81, D96 or D99 is substituted.
In another preferred embodiment, the first signaling domain is a fluorescent protein domain. It is also preferred that the first signaling domain is not a DNA-binding domain and more preferably not the HTH domain of NorR.
In another preferred embodiment, the first signaling domain and the second signaling domain are together selected as two domains that may together be capable of generating a detectable signal. Preferably, the detectable signal may be generated upon binding of the RONS or RONS-like molecule to the RONS sensor domain. The binding of the RONS or RONS-like molecule to the RONS sensor domain may for example induce a
conformational shift in the RONS sensor domain and then bring the first signaling domain and the second signaling domain in closer proximity or further away from each other, thereby at least contributing to generating the detectable signal. In a preferred embodiment, the first signaling domain and the second signaling domain are together selected from the group consisting of FRET-donor- acceptor pairs, split-enzyme pairs or split-fluorescent protein pairs, wherein the first signaling domain and the second signaling domain are the respective parts of a pair (for example, two halves of a split- enzyme or two halves of a split- fluorescent protein). Preferably, the binding of the RONS or RONS-like molecule to the RONS sensor domain may induce a conformational shift in the polypeptide and the first signaling domain and the second signaling domain may then be capable to generate the detectable signal, e.g. the FRET-donor- acceptor pair may generate a detectable FRET signal, the two halves of a split-enzyme may be functional and catalyze a reaction that may generate a detectable signal or the two halves of a split- fluorescent protein will be capable of emitting light with a specified wavelength as a detectable signal if excited with light with a wavelength within the appropriate range.
In a preferred embodiment, the first signaling domain and the second signaling domain may be a FRET-donor-acceptor pair. Preferably, the donor may be a CFP domain and the acceptor may be a YFP domain. More preferably, the first signaling domain may be the donor and the second signaling domain may be the acceptor. In an even more preferred embodiment, the first signaling domain is the donor CFP domain and the second signaling domain is the acceptor YFP domain. It is also preferred that the CFP domain may comprise an amino acid sequence of SEQ ID NO:4 or an amino acid sequence of at least 70 %, 80%, 85%, 90%, 95 % or 100% identity to the sequence according to SEQ ID NO:4, wherein the excitation wavelength and the fluorescence emission wavelength are the same or substantially the same as for CFP domain according to SEQ ID NO:4, namely with an excitation peak at a wavelength of about 436 nm and an emission peak at a wavelength of about 477 nm. Preferably, the YFP domain may be the circularly permuted venus (CPV) protein which even more preferably comprises an amino acid sequence of SEQ ID NO:5 or an amino acid sequence of at least 70 %, 80%, 85%, 90%, 95 % or 100% identity to the sequence according to SEQ ID NO:5, wherein the excitation wavelength and the fluorescence emission wavelength are the same or substantially the same as for YFP domain according to SEQ ID NO:5, namely an excitation peak at a wavelength of about 514 nm and an emission peak at about 527 nm.
In another preferred embodiment, the first signaling domain and the second signaling domain comprise posttranslational modifications, such as a conjugated fluorescein molecule or other small molecule fluorophores or detectable moieties, which may contribute to generating the detectable signal of the first signaling domain together with the second signaling upon binding of the RONS or RONS-like molecule. In another embodiment, the RONS or RONS-like molecule may be selected from the group consisting of NO, OH and SH radicals. In a more preferred embodiment, the RONS or RONS-like molecule is NO.
In a particular preferred embodiment, the RONS sensor domain comprises an amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3 or an amino acid sequence which exhibits at least 70 % identity to the amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3; the RONS- or RONS-like molecule is NO and the first signaling domain and the second signaling domain are a FRET-donor-acceptor pair, wherein preferably the first signaling domain is a CFP domain comprising an amino acid sequence of SEQ ID NO: 4 or an amino acid sequence of at least 70 % identity to the sequence according to SEQ ID NO: 4 and the second signaling domain is a YFP domain comprising an amino acid sequence of SEQ ID NO: 5 or an amino acid sequence of at least 70 % identity to the sequence according to SEQ ID NO: 5.
The amino acid sequences of SEQ ID NO: 1 to 5 are shown in Table 1 below. Table 1
SEQ Amino acid sequence
ID NO:
1 MSFSVDVLANIAIELQRGIGHQDRFQRLITTLRQVLECDASALLRYDS
RQFIPLAIDGLAKDVLGRRFALEGHPRLEAIARAGDVVRFPADSELPD
PYDGLIPGQESLKVHACVGLPLFAGQNLIGALTLDGMQPDQFDVFSD
EELRLIAALAAGALSNALLIEQLESQNMLPGDATPFEAVKQTQMIGL
SPG
2 MSFSVDVLANIAIELQRGIGHQDRFQRLITTLRQVLECDASALLRYDS
RQFIPLAIDGLAKDVLGRRFALEGHPRLEAIARAGDVVRFPADSELPD
PYDGLIPGQESLKVHACVGLPLFAGQNLIGALTLDGMQPDQFDVFSD
EELRLIAALAAGALSNALLIEQLESQNMLPGDATPFEAVKQTQMIGL
SPGMTQLKKEIEIVAASDLNVLISGETGTGKELVAKAIHEASPRAVNP
LVYLNCAALPESVAESELFGHVKGAFTGAISNRSGKFEMADNGTLFL
DEIGELSLALQAKLLRVLQYGDIQRVGDDRCLRVDVRVLAATNRDL
REEVLAGRFRADLFHRLSV
3 MSFSVDVLANIAIELQRGIGHQDRFQRLITTLRQVLECDASALLRYDS
RQFIPLAIDGLAKDVLGRRFALEGHPRLEAIARAGDVVRFPADSELPD
PYDGLIPGQESLKVHACVGLPLFAGQNLIGALTLDGMQPDQFDVFSD
EELRLIAALAAGALSNALLIEQLESQNMLPGDATPFEAVKQTQMIGL
SPGMTQLKKEIEIVAASDLNVLISGETGTGKELVAKAIHEASPRAVNP
LVYLNCAALPESVAESELFGHVKGAFTGAISNRSGKFEMADNGTLFL
DEIGELSLALQAKLLRVLQYGDIQRVGDDRCLRVDVRVLAATNRDL
REEVLAGRFRADLFHRLSVFPLSVPPLRERGDDVILLAGYFCEQCRLR
QGLSRVVLSAGARNLLQHYSFPGNVRELEHAIHRAVVLARATRSGD
EVILEAQHFAFPEVTLPTPEVAAVPVVKQNLREATEAFQRETIRQALA
QNHHNWAACARMLETDVANLHRLAKRLGLKD
4 MVSKGEELFTGVVPILVELDGDVNGHRFSVSGEGEGDATYGKLTLK
FICTTGKLPVPWPT
LVTTLTWGVQCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDDG NYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYISHNVYI TADKQKNGIKAHFKIRHNIEDGGVQLADHYQQNTPIGDGPVLLPDN H YLSTQS KLS KDPNEKRDHM VLLEF VT A A
5 MDGGVQLADHYQQNTPIGDGPVLLPDNHYLSYQSKLSKDPNEKRD
HMVLLEFVTAGITLGMDELYKGGSGGMVSKGEELFTGVVPILVELD
GDVNGHKFSVSGEGEGDATYGKLTLKLICTTGKLPVPWPTLVTTLG
YGLQCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAE
VKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYI
TADKQKNGIKANFKIRHNIE In another preferred embodiment, the polypeptide according to the present invention comprises an amino acid sequence which exhibits at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75 %, at least 80%, at least 85%, at least 90% or at least 95% identity to the sequence according to SEQ ID NO: 9. In another preferred embodiment, the polypeptide according to the present invention comprises an amino acid sequence of SEQ ID NO: 9 (Sensor 1).
In another preferred embodiment, the polypeptide according to the present invention comprises an amino acid sequence which exhibits at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75 %, at least 80%, at least 85%, at least 90% or at least 95% identity to the sequence according to SEQ ID NO: 10. In another preferred embodiment, the polypeptide according to the present invention comprises an amino acid sequence of SEQ ID NO: 10 (Sensor 2).
The sequences of SEQ ID NO: 9 and SEQ ID NO: 10 are shown below in Table 1A.
Table 1A
Protein SEQ comment Sequence
ID
NO:
Sensor 9 eCFP- MVSKGEELFTGVVPILVELDGDVNGHRFSVSGEGE 1 GAF- GDATYGKLTLKFICTTGKLPVPWPTLVTTLTWGVQ
AAA- CFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
HTH- GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILG cpV HKLEYNYISHNVYITADKQKNGIKAHFKIRHNIED
GGVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLS
KDPNEKRDHMVLLEFVTAAIDMSFSVDVLANIAIE
LQRGIGHQDRFQRLITTLRQVLECDASALLRYDSR
QFIPLAIDGLAKDVLGRRFALEGHPRLEAIARAGDV
VRFPADSELPDPYDGLIPGQESLKVHACVGLPLFA
GQNLIGALTLDGMQPDQFDVFSDEELRLIAALAAG
ALSNALLIEQLESQNMLPGDATPFEAVKQTQMIGL
SPGMTQLKKEIEIVAASDLNVLISGETGTGKELVAK
AIHEASPRAVNPLVYLNCAALPESVAESELFGHVK
GAFTGAISNRSGKFEMADNGTLFLDEIGELSLALQ
AKLLRVLQYGDIQRVGDDRCLRVDVRVLAATNRD
LREEVLAGRFRADLFHRLSVFPLSVPPLRERGDDVI
LLAGYFCEQCRLRQGLSRVVLSAGARNLLQHYSFP
GNVRELEHAIHRAVVLARATRSGDEVILEAQHFAF
PEVTLPTPEVAAVPVVKQNLREATEAFQRETIRQA
LAQNHHNWAACARMLETDVANLHRLAKRLGLKD
EFMDGGVQLADHYQQNTPIGDGPVLLPDNHYLSY
QSKLSKDPNEKRDHMVLLEFVTAGITLGMDELYK
GGSGGMVSKGEELFTGVVPILVELDGDVNGHKFS
VSGEGEGDATYGKLTLKLICTTGKLPVPWPTLVTT
LGYGLQCFARYPDHMKQHDFFKSAMPEGYVQERT IFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKED
GNILGHKLEYNYNSHNVYITADKQKNGIKANFKIR
HNIE
Sensor 10 eCFP- MVSKGEELFTGVVPILVELDGDVNGHRFSVSGEGE 2 GAF- GDATYGKLTLKFICTTGKLPVPWPTLVTTLTWGVQ
cpV CFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILG
HKLEYNYISHNVYITADKQKNGIKAHFKIRHNIED
GGVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLS
KDPNEKRDHMVLLEFVTAAIDMSFSVDVLANIAIE
LQRGIGHQDRFQRLITTLRQVLECDASALLRYDSR
QFIPLAIDGLAKDVLGRRFALEGHPRLEAIARAGDV
VRFPADSELPDPYDGLIPGQESLKVHACVGLPLFA
GQNLIGALTLDGMQPDQFDVFSDEELRLIAALAAG
ALSNALLIEQLESQNMLPGDATPFEAVKQTQMIGL
SPGEFMDGGVQLADHYQQNTPIGDGPVLLPDNHY
LS YQS KLS KDPNEKRDHM VLLEF VTAGITLGMDEL
YKGGSGGMVSKGEELFTGVVPILVELDGDVNGHK
FSVSGEGEGDATYGKLTLKLICTTGKLPVPWPTLV
TTLGYGLQCFARYPDHMKQHDFFKSAMPEGYVQE
RTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFK
EDGNILGHKLEYNYNSHNVYITADKQKNGIKANF
KIRHNIE
In another preferred embodiment, the polypeptide of the present invention comprises from N-terminus to C-terminus: a) a first signaling domain; and
b) a RONS sensor domain.
It is even more preferred in this embodiment that the first signaling domain comprises a fluorescent protein domain, such as CFP, YFP, mKok, EGFP, or GEM. More preferably, the RONS sensor domain comprises the NorR GAF domain.
In yet another preferred embodiment, the polypeptide of the present invention comprises from N-terminus to C-terminus: a) a first signaling domain;
b) a RONS sensor domain; and
c) a second signaling domain.
In another preferred embodiment, the polypeptide comprises from N-terminus to C- terminus:
a) a first signaling domain,
b) a second signaling domain, and c) a RONS sensor domain.
In yet another embodiment, the polypeptide comprises from N-terminus to C-terminus: a) a first signaling domain,
b) a second signaling domain,
c) a RONS sensor domain,
d) another second signaling domain, and
e) another first signaling domain. In yet another embodiment, the polypeptide comprises from N-terminus to C-terminus: a) a first signaling domain,
b) a second signaling domain,
c) a RONS sensor domain,
d) another RONS sensor domain,
e) another second signaling domain, and
f) another first signaling domain.
In another aspect the present invention relates to a polynucleotide encoding the polypeptide according to the present invention.
It will be apparent to the person skilled in the art that due to the degeneracy of the genetic code a given polypeptide according to the invention may be encoded by different nucleotide sequences. In a preferred embodiment, the polynucleotide according to the invention has a length of less than 9000 nucleotides, less than 8000 nucleotides, less than 7000 nucleotides, less than 6000 nucleotides, less than 5000 nucleotides, less than 4000 nucleotides, less than 3000 nucleotides, less than 2000 nucleotides, less than 1000 nucleotides, less than 500 nucleotides or less than 300 nucleotides.
In a further preferred embodiment the isolated polynucleotide according to the invention has a length of between at least 24 and 9000 nucleotides, preferably between at least 24 and 8000 nucleotides, more preferably between at least 24 and 7000 nucleotides, more preferably between at least 24 and 6000 nucleotides, more preferably between at least 24 and 5000 nucleotides, and even more preferably between at least 24 and 4000
nucleotides. In another preferred embodiment the polynucleotide according to the invention has a length of between at least 60 and 9000 nucleotides, preferably between at least 60 and 8000 nucleotides, more preferably between at least 60 and 7000 nucleotides, more preferably between at least 60 and 6000 nucleotides, more preferably between at least 60 and 5000 nucleotides, and even more preferably between at least 60 and 4000 nucleotides. In a further preferred embodiment the polynucleotide according to the invention has a length of between at least 90 and 9000 nucleotides, preferably between at least 90 and 8000 nucleotides, more preferably between at least 90 and 7000 nucleotides, more preferably between at least 90 and 6000 nucleotides, more preferably between at least 90 and 5000 nucleotides, and even more preferably between at least 90 and 4000 nucleotides. In yet another preferred embodiment the polynucleotide according to the invention has a length of between at least 120 and 9000 nucleotides, preferably at least between 120 and 8000 nucleotides, more preferably between at least 120 and 7000 nucleotides, more preferably between at least 120 and 6000 nucleotides, more preferably between at least 120 and 5000 nucleotides, and even more preferably between at least 120 and 4000 nucleotides. In yet another preferred embodiment the isolated polynucleotide according to the invention has a length of between at least 300 and 9000 nucleotides, preferably between at least 300 and 8000 nucleotides, more preferably between at least 300 and 7000 nucleotides, more preferably between at least 300 and 6000 nucleotides, more preferably between at least 300 and 5000 nucleotides, and even more preferably between at least 300 and 4000 nucleotides.
In another preferred embodiment an polynucleotide according to the invention has a length of at least 300 nucleotides, at least 1000 nucleotides, at least 1500 nucleotides, at least 2000 nucleotides or at least 2500 nucleotides. In a more preferred embodiment the polynucleotide according to the invention comprises or consists of a sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO:6. In a further preferred embodiment the polynucleotide according to the invention comprises or consists of a sequence which exhibits at least 85%, preferably at least 90%, more preferably at least 91%, even more preferably at least 92%, even more preferably at least 93%, even more preferably at least 94%, even more preferably at least 95%, even more preferably at least 96%, even more preferably at least 97%, even more preferably at least 98% or even more preferably at least 99% identity to the sequence according to SEQ ID NO:6. In a particularly preferred embodiment the polynucleotide according to the invention comprises or consists of a sequence which exhibits at least 85%, preferably at least 90%, more preferably at least 95% or even more preferably at least 98% identity to the sequence according to SEQ ID NO:6.
In another preferred embodiment the polynucleotide according to the invention comprises or consists of a sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO:7. In a further preferred embodiment the polynucleotide according to the invention comprises or consists of a sequence which exhibits at least 85%, preferably at least 90%, more preferably at least 91%, even more preferably at least 92%, even more preferably at least 93%, even more preferably at least 94%, even more preferably at least 95%, even more preferably at least 96%, even more preferably at least 97%, even more preferably at least 98% or even more preferably at least 99% identity to the sequence according to SEQ ID NO:7. In a particularly preferred embodiment the polynucleotide according to the invention comprises or consists of a sequence which exhibits at least 85%, preferably at least 90%, more preferably at least 95% or even more preferably at least 98% identity to the sequence according to SEQ ID NO:7.
In another preferred embodiment the polynucleotide according to the invention comprises or consists of a sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO: 8. In a further preferred embodiment the polynucleotide according to the invention comprises or consists of a sequence which exhibits at least 85%, preferably at least 90%, more preferably at least 91%, even more preferably at least 92%, even more preferably at least 93%, even more preferably at least 94%, even more preferably at least 95%, even more preferably at least 96%, even more preferably at least 97%, even more preferably at least 98% or even more preferably at least 99% identity to the sequence according to SEQ ID NO:8. In a particularly preferred embodiment the polynucleotide according to the invention comprises or consists of a sequence which exhibits at least 85%, preferably at least 90%, more preferably at least 95% or even more preferably at least 98% identity to the sequence according to SEQ ID NO:8.
In a particularly preferred embodiment the polynucleotide according to the invention comprises or consists of a sequence which exhibits 100% identity to the sequence according to SEQ ID NO:6. In another particularly preferred embodiment the isolated polynucleotide according to the invention comprises or consists of a sequence according to SEQ ID NO:6.
In a particularly preferred embodiment the polynucleotide according to the invention comprises or consists of a sequence which exhibits 100% identity to the sequence according to SEQ ID NO:7. In another particularly preferred embodiment the isolated polynucleotide according to the invention comprises or consists of a sequence according to SEQ ID NO:7.
In a particularly preferred embodiment the polynucleotide according to the invention comprises or consists of a sequence which exhibits 100% identity to the sequence according to SEQ ID NO: 8. In another particularly preferred embodiment the isolated polynucleotide according to the invention comprises or consists of a sequence according to SEQ ID NO: 8. Sequences of nucleotides with SEQ ID NO: 6 to 8 according to the present invention are shown below in Table 2. SEQ Nucleotide sequence
ID
NO:
6 ATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTC
GAGCTGGACGGCGACGTAAACGGCCACAGGTTCAGCGTGTCCGGCGAGGG
CGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCAC
CGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTGGGG
CGTGCAGTGCTTCGCCCGCTACCCCGACCACATGAAGCAGCACGACTTCTT
CAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGTACCATCTTCTTCAA
GGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACA
CCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGC
AACATCCTGGGGCACAAGCTGGAGTACAACTACATCAGCCACAACGTCTAT
ATCACCGCCGACAAGCAGAAGAACGGCATCAAGGCCCACTTCAAGATCCG
CCACAACATCGAGGACGGCGGCGTGCAGCTCGCCGACCACTACCAGCAGA
ACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGA
GCACCCAGTCCAAGCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATG
GTCCTGCTGGAGTTCGTGACCGCCGCCATCGATATGAGTTTTTCCGTTGATG
TGCTGGCGAATATCGCCATCGAATTGCAGCGTGGGATTGGTCACCAGGATC
GTTTTCAGCGCCTGATCACCACGCTACGTCAGGTGCTGGAGTGCGATGCGT
CTGCGTTGCTACGTTACGATTCGCGGCAG
TTTATTCCGCTTGCCATCGACGGTCTGGCAAAGGATGTACTCGGTAGACGC
TTTGCGCTGGAAGGGCATCCACGGCTGGAAGCGATTGCCCGCGCCGGGGAT
GTGGTGCGCTTTCCCGCAGACAGCGAATTGCCCGATCCCTATGACGGTTTG
ATTCCTGGGCAGGAGAGTCTGAAGGTTCACGCCTGCGTTGGTCTGCCATTG
TTTGCCGGGCAAAACCTGATCGGCGCACTGACGCTCGACGGGATGCAGCCC
GATCAGTTCGATGTTTTCAGCGACGAAGAGCTACGGCTGATTGCTGCGCTG
GCGGCGGGAGCGTTAAGCAATGCGTTGCTGATTGAACAACTGGAAAGCCA
GAATATGCTGCCAGGCGATGCCACGCCGTTTGAAGCGGTGAAACAGAC
GCAGATGATTGGCTTGTCCCCTGGCGAATTCATGGACGGCGGCGTGC
AGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCC
CGTGCTGCTGCCCGACAACCACTACCTGAGCTACCAGTCCAAGCTGA
GCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTT
CGTGACCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGGGT
GGCAGCGGTGGCATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGG
TGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAA
GTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAG
CTGACCCTGAAGCTGATCTGCACCACCGGCAAGCTGCCCGTGCCCTG
GCCCACCCTCGTGACCACCCTGGGCTACGGCCTGCAGTGCTTCGCCC
GCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATG
CCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACG
GCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCT
GGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGC
AACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACG
TCTATATCACCGCCGACAAGCAGAAGAACGGCATCAAGGCCAACTT
CAAGATCCGCCACAACATCGAGTAAGCTT
7 ATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTC
GAGCTGGACGGCGACGTAAACGGCCACAGGTTCAGCGTGTCCGGCGAGGG
CGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCAC
CGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTGGGG
CGTGCAGTGCTTCGCCCGCTACCCCGACCACATGAAGCAGCACGACTTCTT CAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGTACCATCTTCTTCAA
GGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACA
CCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGC
AACATCCTGGGGCACAAGCTGGAGTACAACTACATCAGCCACAACGTCTAT
ATCACCGCCGACAAGCAGAAGAACGGCATCAAGGCCCACTTCAAGATCCG
CCACAACATCGAGGACGGCGGCGTGCAGCTCGCCGACCACTACCAGCAGA
ACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGA
GCACCCAGTCCAAGCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATG
GTCCTGCTGGAGTTCGTGACCGCCGCCATCGATATGAGTTTTTCCGTTGATG
TGCTGGCGAATATCGCCATCGAATTGCAGCGTGGGATTGGTCACCAGGATC
GTTTTCAGCGCCTGATCACCACGCTACGTCAGGTGCTGGAGTGCGATGCGT
CTGCGTTGCTACGTTACGATTCGCGGCAG
TTTATTCCGCTTGCCATCGACGGTCTGGCAAAGGATGTACTCGGTAGACGC
TTTGCGCTGGAAGGGCATCCACGGCTGGAAGCGATTGCCCGCGCCGGGGAT
GTGGTGCGCTTTCCCGCAGACAGCGAATTGCCCGATCCCTATGACGGTTTG
ATTCCTGGGCAGGAGAGTCTGAAGGTTCACGCCTGCGTTGGTCTGCCATTG
TTTGCCGGGCAAAACCTGATCGGCGCACTGACGCTCGACGGGATGCAGCCC
GATCAGTTCGATGTTTTCAGCGACGAAGAGCTACGGCTGATTGCTGCGCTG
GCGGCGGGAGCGTTAAGCAATGCGTTGCTGATTGAACAACTGGAAAGCCA
GAATATGCTGCCAGGCGATGCCACGCCGTTTGAAGCGGTGAAACAGACGC
AGATGATTGGCTTGTCCCCTGGCATGACGCAACTGAAAAAAGAGATTGAG
ATTGTGGCGGCGTCCGATCTCAACGTCCTGATCAGCGGTGAGACTGGAACC
GGTAAGGAGCTGGTGGCGAAAGCGATTCATGAAGCCTCGCCACGGGCGGT
GAATCCGCTGGTCTATCTCAACTGTGCTGCACTGCCGGAAAGTGTGGCGGA
AAGTGAGTTGTTCGGGCATGTGAAAGGAGCGTTTACTGGCGCTATCAGTAA
TCGCAGCGGGAAGTTTGAAATGGCGGATAACGGCACGCTGTTTCTGGATGA
GATCGGCGAGTTGTCGTTGGCATTGCAGGCCAAGCTGCTGAGGGTGTTGCA
GTATGGCGATATTCAGCGCGTTGGCGATGACCGTTGTTTGCGGGTCGATGT
GCGCGTGCTGGCGGCGACTAACCGCGATTTACGCGAAGAGGTGCTGGCAG
GGCGATTCCGCGCCGATTTGTTTCATCGCCTGAGCGTGGAATTCATGGACG
GCGGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGAC
GGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCTACCAGTCCAAGCTG
AGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGT
GACCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGGGTGGCAGCG
GTGGCATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATC
CTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGG
CGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGCTGATCT
GCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGG
GCTACGGCCTGCAGTGCTTCGCCCGCTACCCCGACCACATGAAGCAGCACG
ACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCT
TCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAG
GGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGA
GGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACA
ACGTCTATATCACCGCCGACAAGCAGAAGAACGGCATCAAGGCCAACTTC
AAGATCCGCCACAACATCGAGTAAGCTT
ATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTC
GAGCTGGACGGCGACGTAAACGGCCACAGGTTCAGCGTGTCCGGCGAGGG
CGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCAC
CGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTGGGG
CGTGCAGTGCTTCGCCCGCTACCCCGACCACATGAAGCAGCACGACTTCTT
CAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGTACCATCTTCTTCAA
GGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACA
CCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGC AACATCCTGGGGCACAAGCTGGAGTACAACTACATCAGCCACAACGTCTAT
ATCACCGCCGACAAGCAGAAGAACGGCATCAAGGCCCACTTCAAGATCCG
CCACAACATCGAGGACGGCGGCGTGCAGCTCGCCGACCACTACCAGCAGA
ACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGA
GCACCCAGTCCAAGCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATG
GTCCTGCTGGAGTTCGTGACCGCCGCCATCGATATGAGTTTTTCCGTTGATG
TGCTGGCGAATATCGCCATCGAATTGCAGCGTGGGATTGGTCACCAGGATC
GTTTTCAGCGCCTGATCACCACGCTACGTCAGGTGCTGGAGTGCGATGCGT
CTGCGTTGCTACGTTACGATTCGCGGCAG
TTTATTCCGCTTGCCATCGACGGTCTGGCAAAGGATGTACTCGGTAGACGC
TTTGCGCTGGAAGGGCATCCACGGCTGGAAGCGATTGCCCGCGCCGGGGAT
GTGGTGCGCTTTCCCGCAGACAGCGAATTGCCCGATCCCTATGACGGTTTG
ATTCCTGGGCAGGAGAGTCTGAAGGTTCACGCCTGCGTTGGTCTGCCATTG
TTTGCCGGGCAAAACCTGATCGGCGCACTGACGCTCGACGGGATGCAGCCC
GATCAGTTCGATGTTTTCAGCGACGAAGAGCTACGGCTGATTGCTGCGCTG
GCGGCGGGAGCGTTAAGCAATGCGTTGCTGATTGAACAACTGGAAAGCCA
GAATATGCTGCCAGGCGATGCCACGCCGTTTGAAGCGGTGAAACAGACGC
AGATGATTGGCTTGTCCCCTGGCATGACGCAACTGAAAAAAGAGATTGAG
ATTGTGGCGGCGTCCGATCTCAACGTCCTGATCAGCGGTGAGACTGGAACC
GGTAAGGAGCTGGTGGCGAAAGCGATTCATGAAGCCTCGCCACGGGCGGT
GAATCCGCTGGTCTATCTCAACTGTGCTGCACTGCCGGAAAGTGTGGCGGA
AAGTGAGTTGTTCGGGCATGTGAAAGGAGCGTTTACTGGCGCTATCAGTAA
TCGCAGCGGGAAGTTTGAAATGGCGGATAACGGCACGCTGTTTCTGGATGA
GATCGGCGAGTTGTCGTTGGCATTGCAGGCCAAGCTGCTGAGGGTGTTGCA
GTATGGCGATATTCAGCGCGTTGGCGATGACCGTTGTTTGCGGGTCGATGT
GCGCGTGCTGGCGGCGACTAACCGCGATTTACGCGAAGAGGTGCTGGCAG
GGCGATTCCGCGCCGATTTGTTTCATCGCCTGAGCGTGTTTCCACTTTCGGT
GCCGCCGCTGCGTGAGCGGGGCGATGATGTCATTCTGCTGGCGGGGTATTT
CTGCGAGCAGTGTCGTTTGCGGCAGGGGCTCTCCCGCGTGGTATTAAGTGC
CGGAGCGCGAAATTTACTGCAACACTACAGTTTTCCGGGAAACGTGCGCGA
ACTGGAACATGCTATTCATCGGGCGGTAGTTCTGGCGAGAGCCACCCGCAG
CGGCGATGAAGTGATTCTTGAGGCGCAACATTTTGCTTTTCCTGAGGTGAC
GTTGCCGACGCCAGAAGTGGCGGCGGTGCCCGTTGTTAAGCAAAACCTGCG
TGAAGCGACAGAAGCGTTCCAGCGTGAAACTATTCGTCAGGCACTGGCAC
AAAATCATCACAACTGGGCTGCCTGCGCGCGGATGCTGGAAACCGACGTC
GCCAACCTGCATCGGCTGGCGAAACGTCTGGGATTGAAGGATGAATTCATG
GACGGCGGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGG
CGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCTACCAGTCCAA
GCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGT
TCGTGACCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGGGTGGCA
GCGGTGGCATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCC
ATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCC
GGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGCTGAT
CTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCT
GGGCTACGGCCTGCAGTGCTTCGCCCGCTACCCCGACCACATGAAGCAGCA
CGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCAT
CTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCG
AGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAG
GAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCA
CAACGTCTATATCACCGCCGACAAGCAGAAGAACGGCATCAAGGCCAACT
TCAAGATCCGCCACAACATCGAGTAAGCTT A polynucleotide according to the invention may be a single or double stranded RNA or DNA molecule.
In some embodiments the isolated polynucleotide according to the invention may be inserted into a vector such as an expression vector. The expression vector may e.g. be a prokaryotic or eukaryotic expression vector such as e.g. an isolated plasmid, a minichromosome, a cosmid, a bacterial phage, a retroviral vector or any other vector known to the person skilled in the art. The person skilled in the art will be familiar with how to select an appropriate vector according to the specific need. In a preferred embodiment, the expression vector is an isolated plasmid.
The present invention thus also relates to an expression vector comprising a
polynucleotide according to the invention. In one aspect, the present invention relates to a cell comprising the polypeptide, the polynucleotide, expression vector and/or plasmid encoding the polypeptide of the present invention. Said cell is not a human embryonic stem cell. Examples of cells include but are not limited to, in vitro cell culture cells or cell lysates of eukaryotic cells, such as mammalian cells, human cells or plant cells or prokaryotic cells each of which optionally may have been genetically modified by methods commonly known to the person skilled in the art such as transfecting or transforming of said cells.
In one aspect, the present invention relates to a method for detecting a RONS or RONS- like molecule in a sample, comprising the steps of a) providing a polypeptide according to the invention; b) contacting the polypeptide according to the invention with the sample; and c) measuring the signal generated by the first signaling domain.
In one aspect, the present invention relates to a method for detecting a RONS or RONS- like molecule in a sample, comprising the steps of a) providing a polypeptide according to the invention; b) contacting the polypeptide according to the invention with the sample; and c) optionally measuring the signal generated by the first signaling domain, and d) measuring the signal generated together by the first signaling domain and the second signaling domain. In one embodiment of said method, the change in signal intensity after contact with the sample compared to the signal of the polypeptide in the absence of the sample indicates the presence of the RONS or RONS-like molecule in the sample. In another preferred embodiment, the method according to the present invention is a (quantitative) in vivo imaging method.
In a preferred embodiment, the RONS or RONS-like molecule is selected from the group consisting of NO, OH and SH. Preferably, the RONS or RONS-like molecule is NO.
In a preferred embodiment, the measured signal is a fluorescence signal, a colorimetric signal or a FRET signal. Preferably, the signal may be generated upon binding of the RONS or RONS-like molecule to the RONS sensor domain of the polypeptide according to the present invention. In a preferred embodiment, the signal may be generated by a FRET-donor-acceptor pair, split-enzyme pair or split- fluorescent protein pair. The detection may occur by methods commonly known to the person skilled in the art.
In one embodiment, the measured signal is a fluorescence signal. In a preferred embodiment, the fluorescence signal is quenched by binding of the RONS or RONS-like molecule to the RONS sensor domain.
In a preferred embodiment, the detectable signal is a FRET signal. Preferably, the FRET signal is generated by the first signaling domain and the second signaling domain. More preferably, the FRET signal is generated by a FRET-donor-acceptor pair, preferably YFP, such as CPV, and CFP. The person skilled in the art is aware how to measure FRET signals. Preferably, the FRET between YFP and CFP is measured after excitation with light at a wavelength in the range of from about 430 nm to about 450 nm. More preferably, the measurement is performed after excitation with light at about 440 nm. It is also preferred that the emission of light is measured at a wavelength in the range from about 525 nm to about 545 nm and more preferably about 535 nm.
In another preferred embodiment, the FRET donor- acceptor pair is selected from the group consisting of Clover/mRubby and cpEGFP and mK02. In a preferred embodiment, the step a) of the method for detecting a RONS or RONS-like molecule, i.e. the providing a polypeptide according to the invention, may comprise transfecting at least one cell outside the human or animal body or transforming a prokaryotic cell with a polynucleotide, a plasmid and/or an expression vector encoding the polypeptide according to the present invention. The polypeptide according to the invention may then be provided by protein synthesis of said cell. The polypeptide according to the present invention may then either be isolated from the cell, secreted by the cell or remain inside the cell. In another preferred embodiment, the polypeptide according to the present invention may be provided in step a) of the method according the present by providing a cell according to the present invention.
In a preferred embodiment, the method according to the present invention may be used to detect the presence of a RONS or RONS-like molecule in any concentration. Preferably, the method according to the present invention may detect the presence of a RONS or a RONS-like molecule in a concentration from about 0.1 nM to about 20 mM and preferably from about 0.1 nM to about 2 mM. In one preferred embodiment, the method according to the present invention may detect the presence of a RONS or a RONS-like molecule in a concentration from about 0.1 nM to about 2 μΜ and preferably from about 0.10 nM to about 1.00 μΜ.
In one preferred embodiment, the method according to the present invention may detect the presence of a RONS or a RONS-like molecule in a concentration from about 500 nM to about 1 mM and preferably from about 1.0 μΜ to about 100.0 μΜ.
In a preferred embodiment, the method according to the present invention may detect the presence of a RONS or a RONS-like molecule in any kind of sample. More preferably, the sample is selected from the group consisting of biological samples, potential nitric oxide-bearing explosive samples, gaseous samples, or liquid samples such as liquid samples containing NO-generating agents. More preferably, the sample is a biological sample, a liquid sample or a combination thereof. Even more preferably, the sample is a cell culture, a cell pellet, a cell lysate, a tissue sample from a human or an animal, blood, breath, or a liquid containing NO-generating agents. In one embodiment, the sample may also comprise a biological sample, such as a cell culture, including the monolayer culture of cells or a 3-dimensional cell culture, a cell suspension, a cell pellet, a cell lysate, a tissue sample from a human or an animal and a liquid sample containing NO-generating agents. Preferably, the method according to the present invention may then be used to characterize the influence of the NO-generating agents on the biological sample by detecting the presence and/or distribution of NO and optionally in combination with determining other relevant parameters of the biological sample, such as cell apoptosis, cell signaling, cell gene expression or the like. In a preferred embodiment of the method according to the present invention, the polypeptide according to the present invention is treated with an Fe(II) containing compound in or before step a) and/or step b) of the method according to the present invention. The Fe(II) containing compound may be any compound that comprises Fe(II). Examples of Fe(II) containing compounds include, but are not limited to, salts of
[Fe(CN)sNO] " (nitroprusside), such as sodium nitroprusside or a solvate thereof such as Na2[Fe(CN)sNO] 2 H20; Fe(II) fumarate; salts of Fe(II) hexacyanoferrate or solvates thereof or combinations thereof. In a more preferred embodiment, the polypeptide according to the present invention is treated with sodium nitroprusside, Fe(II) hexacyanoferrate or combinations thereof. In another preferred embodiment, the polypeptide according to the present invention is treated with an Fe(II) containing compound in a concentration of from about 100 μΜ to about 10 mM preferably from about 0.1 mM to about 10 mM. The polypeptide according to the present invention may be treated with the Fe(II) containing compound for from about 5 min to about 30 min and preferably from about 5 min to about 15 min. The treatment of the polypeptide according to the present invention with an Fe(II) containing compound may improve the sensitivity of the RONS detection.
In a particularly preferred embodiment, the polypeptide according to the present invention comprises CPV or mKOk as a first signaling domain and is treated with an Fe(II) containing compound. In a particular preferred embodiment, the method of the present invention may be used for the screening of NO-generating agents.
In one aspect, the present invention also relates to the use of a polypeptide comprising a RONS-sensor domain in the detection of a RONS- or RONS-like molecule in a sample.
In a preferred embodiment, the RONS sensor domain comprises an amino acid sequence corresponding to the GAF domain of NorR, preferably of SEQ ID NO: l. In one preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 50% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 55% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 60% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 65% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 70% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 75% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 85% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 90% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 95% identity to the sequence according to SEQ ID NO: 1. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits 100% identity to the sequence according to SEQ ID NO: 1.
In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence corresponding to the GAF domain and the AAA+ domain of NorR, preferably of SEQ ID NO:2. In one preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 50% identity to the sequence according to SEQ ID NO:2. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 55% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 60% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 65% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 70% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 75% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 85% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 90% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 95% identity to the sequence according to
SEQ ID NO: 2. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits 100% identity to the sequence according to SEQ ID NO: 2. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence corresponding to the GAF domain, the AAA+ domain and the HTH domain of NorR, preferably of SEQ ID NO:3. In one preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 50% identity to the sequence according to SEQ ID NO:3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 55% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 60% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 65% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 70% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 75% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment the RONS sensor domain comprises an amino acid sequence which exhibits at least 85% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 90% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits at least 95% identity to the sequence according to SEQ ID NO: 3. In another preferred embodiment, the RONS sensor domain comprises an amino acid sequence which exhibits 100% identity to the sequence according to SEQ ID NO: 3.
In a particularly preferred embodiment, the RONS sensor domain comprises an amino acid sequence of SEQ ID NO: 1, SEQ ID NO:2 or SEQ ID NO: 3.
In another preferred embodiment, the polypeptide according to the present invention comprises an amino acid sequence which exhibits at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75 %, at least 80%, at least 85%, at least 90% or at least 95% identity to the sequence according to SEQ ID NO: 9. In another preferred embodiment, the polypeptide according to the present invention comprises an amino acid sequence of SEQ ID NO: 9.
In another preferred embodiment, the polypeptide according to the present invention comprises an amino acid sequence which exhibits at least 50%, at least 55%, at least
60%, at least 65%, at least 70%, at least 75 %, at least 80%, at least 85%, at least 90% or at least 95% identity to the sequence according to SEQ ID NO: 10. In another preferred embodiment, the polypeptide according to the present invention comprises an amino acid sequence of SEQ ID NO: 10.
In another preferred embodiment, the polypeptide of the present invention comprises from N-terminus to C-terminus: a) a first signaling domain; and
b) a RONS sensor domain.
It is even more preferred in this embodiment that the first signaling domain comprises a fluorescent protein domain, such as CFP, YFP, mKok, EGFP, or GEM. More preferably, the RONS sensor domain comprises the NorR GAF domain.
In yet another preferred embodiment, the polypeptide of the present invention comprises from N-terminus to C-terminus: a) a first signaling domain;
b) a RONS sensor domain; and
c) a second signaling domain.
In another preferred embodiment, the polypeptide comprises from N-terminus to C- terminus:
a) a first signaling domain,
b) a second signaling domain, and
c) a RONS sensor domain.
In yet another embodiment, the polypeptide comprises from N-terminus to C-terminus: a) a first signaling domain,
b) a second signaling domain,
c) a RONS sensor domain,
d) another second signaling domain;
e) another first signaling domain.
In yet another embodiment, the polypeptide comprises from N-terminus to C-terminus: a) a first signaling domain,
b) a second signaling domain,
c) a RONS sensor domain,
d) another RONS sensor domain,
e) another second signaling domain;
f) another first signaling domain.
In another embodiment, the present invention relates to the use of a polypeptide according to the present invention in the detection of a RONS or RONS-like molecule in a sample.
In another embodiment, the present invention relates to the use of a polynucleotide according to the present invention in the detection of a RONS or RONS-like molecule in a sample. For example, the polynucleotide according to the present invention may be present in a vector for transfecting or transforming a cell.
In a preferred embodiment, the use of according to the present invention comprises the detection of RONS or RONS-like molecules selected from the group consisting of NO, OH and SH radicals. Preferably, the detected RONS is NO. In a preferred embodiment, the use according to the present invention comprises detecting the presence of a RONS or a RONS-like molecule in any kind of sample. More preferably, the sample may be selected from the group consisting of biological samples, potential nitric oxide-bearing explosive samples, gaseous samples, liquid samples such as liquid samples containing NO-generating agents or a combination thereof. More preferably, the sample may be a biological sample, a liquid sample or a combination thereof. Even more preferably, the sample is a cell culture, a cell pellet, a cell lysate, a tissue sample from a human or an animal, blood, breath, or a liquid containing NO- generating agents. In one embodiment, the sample may also comprise a biological sample, such as a cell culture, including the monolayer culture of cells or a 3-dimensional cell culture, a cell suspension, a cell pellet, a cell lysate, a tissue sample from a human or an animal and a liquid sample containing NO-generating agents. Preferably the use according to the present invention comprises the use in the characterization of the influence of the NO-generating agents on the biological sample by detecting the presence and/or distribution of NO or other relevant parameters of the biological sample, such as cell apoptosis, cell signaling, cell gene expression or the like. In a particular preferred embodiment, the use according to the present invention comprises the use in the screening of NO-generating agents.
In a preferred embodiment, the use according to the present invention comprises the use of the polypeptide according to the present invention in (quantitative) in vivo imaging. The term in "vivo imaging" refers to the imaging in living cells outside the human body such as microscopy of isolated living cells that were cultured in vitro.
In another preferred embodiment, the use according to the present invention comprises the detection of NO in the analysis of exhaled breath. Preferably, the use according to the present invention comprises the use of the polypeptide of the present invention in an apparatus for analyzing nitric oxide concentration of exhaled breath, preferably in a sensor, wherein more preferably the polypeptide of the present invention may be encapsulated in a porous inert matrix. In another preferred embodiment of the use according to the present invention, the polypeptide according to the present invention has been treated with an Fe(II) containing compound as described above before the detection of a RONS or RONS-like molecule.
Further, the present invention relates to a kit for detecting RONS or RONS-like molecules. Preferably the kit comprises
a) a polypeptide according to the present invention;
b) a polynucleotide according to the present invention;
c) a cell according to the present invention; or
d) a combination thereof.
In one embodiment, the kit according to the present invention comprises at least one of a) to d) and suitable buffer for the polypeptide according to the present invention. In another embodiment, the kit according to the present invention comprises at least one of a) to d) and a suitable buffer for the cell according to the present invention. DEFINITIONS
The following definitions are introduced. As used in this specification and in the intended claims, the singular forms of "a" and "an" also include the respective plurals unless the context clearly dictates otherwise.
It is to be understood that the term "comprise", and variations such as "comprises" and "comprising" is not limiting. For the purpose of the present invention the term "consisting of is considered to be a preferred embodiment of the term "comprising". If hereinafter a group is defined to comprise at least a certain number of embodiments, this is meant to also encompass a group which preferably consists of these embodiments only.
The terms "about" and "approximately" or "substantially the same" in the context of the present invention denote an interval of accuracy that a person skilled in the art will understand to still ensure the technical effect of the feature in question. The term typically encompasses a deviation from the indicated numerical value of +10 % and preferably of +5 %. As used herein, the term "domain" refers to building blocks of polypeptides or fusion proteins. The term domain thus comprises parts of a polypeptide that can fold, function and/or exist independently of the rest of the polypeptide chain or structure. For example, cyan fluorescent protein is considered as a domain when it is a part of a fusion protein. Further, the term domain, as used herein, also comprises each part of a split-enzyme or split fluorescent protein, wherein each part is considered as a domain even though the two domains of a split enzyme or split fluorescent protein may only fold and function together.
As used herein, the term "polypeptide" and "protein" are used interchangeably herein to describe protein molecules that may comprise either partial or full-length proteins. The term includes "fusion proteins", comprising proteins or polypeptides that have an amino acid sequence derived from two or more proteins. The fusion protein may also include linking regions of amino acids between amino acid portions derived from separate proteins.
As used herein, the term„reactive oxygen and nitrogen species (RONS)" refers to an oxygen-or nitrogen containing small molecule. Preferably, the molecule comprises less than 5 atoms. Many, but not all, RONS are free radicals. A radical is a group of atoms which behaves as a unit and has one or more unpaired electrons. Examples of RONS include, but are not limited to, 02 ~ (superoxide radical), OH (hydroxyl radical), ONOO" (peroxynitrite), 02 x (singlet oxygen), 03 (ozone), NO (nitric oxide, and N02 (nitrogen dioxide).
As used herein, the term "reactive oxygen and nitrogen species-like (RONS-like)" refers to a small molecule with RONS-like characteristics which does not contain oxygen or nitrogen. Examples include, but are not limited to, SH (sulfanyl radical).
As used herein, the term "RONS-sensor domain" refers to a protein domain that is capable of binding a RONS or RONS-like molecule. Examples of RONS-sensor domains include, but are not limited to, the NorR protein, a polypeptide of SEQ ID NO: l, SEQ ID NO:2 or SEQ ID NO:3 or polypeptide variants, homologs and orthologs thereof.
Preferably, the RONS-sensor domain does not contain heme. Further, the RONS-sensor domain may be capable of binding a metal ion such as Fe, Cu, or CO.
As used herein, the term "detectable signal" refers to an increase or decrease of signals commonly used in technical fields of biochemistry, chemistry, medical or diagnostic technology. Examples of the detectable signal include, but is not limited to, an electrical (e.g., capacitance), mechanical, optical, acoustic or thermal signal. Preferably, the optical signal may be a fluorescence signal, a FRET signal, a colorimetric signal or an electrochemiluminescence signal. It is also preferred that the signal may be detectable, i.e. the signal and a respective change of the signal may be monitored using the appropriate technological equipment. Preferably, the detectable signal may be a signal generated or altered in a proximity-dependent manner, for example induced by a conformational change of a polypeptide.
As used herein, the term "fluorescent protein" refers to any protein or protein domain in a fusion protein that is capable of emitting fluorescent light. Fluorescent proteins are well known to the person skilled in the art. Example include, but are not limited to, GFP and variants thereof such as EGFP, cpGFP, CFP, YFP, EYFP, cpYFP, CPV, Citrine, Venus, and Ypet; blue fluorescent protein (BFP) such as EBFP, EBFP2, Azurite, mKalamal; cyan fluorescent protein (CFP) such as ECFP, Cerulean, CyPet; and other florescent proteins such as UnaG, dsRed, tdTomato eqFP611, Dronpa, TagRFPs, KFP, EosFP,
Dendra, IrisFP, Clover, Green-Emission fluorescent protein (GEM), mRuby, mKOk and mK02.
The term "FRET" as used herein refers to fluorescence resonance energy transfer between or within molecules. In FRET methods, one fluorophore is able to act as an energy donor and one other is an energy acceptor. These are sometimes known as a reporter and a quencher, respectively. The donor may be excited with a specific wavelength of light for which it will normally exhibit a fluorescence emission
wavelength. The acceptor may also be excited at a wavelength such that it can accept the emission energy of the donor molecule by a variety of distance-dependent energy transfer mechanisms. Generally, the acceptor accepts the emission energy of the donor when they are in close proximity. The donor and the acceptor may be different molecules or may be separate parts of the same molecule, such as two different domains of a polypeptide. FRET measuring techniques are well known in the art.
As used herein, the term "FRET-donor-acceptor pair" refers to fluorophores representing the energy donor and the energy acceptor capable of FRET as described above. In this context, the term "fluorophore" refers to a component of a molecule that causes a molecule to be fluorescent. It is a functional group in a molecule which will absorb light of a specific wavelength and re-emit light at a different (but equally specific) wavelength. The amount and wavelength of the emitted light depend on both the fluorophore and the chemical environment of the fluorophore. Fluorophores include, but are not limited to, fluorescein isothiocyanate (FITC), a reactive derivative of fluorescein, rhodamine (TRrrC), coumarin, cyanin dyes (Cy) e.g. Cyanine 3, Cyanine 5 or Cyanine 7, fluorescent proteins such as the green fluorescent protein (GFP) from Aequorea Victoria or Renilla reniformis or proteins variants thereof such as yellow fluorescent protein (YFP) including Citrine, Venus, and Ypet; blue fluorescent protein (BFP) such as EBFP, EBFP2, Azurite, mKalamal; cyan fluorescent protein (CFP) such as ECFP, Cerulean, CyPet; and other florescent proteins such as UnaG, dsRed, eqFP611, Dronpa, TagRFPs, KFP, EosFP, Dendra, IrisFP, Clover, mRubby, mKOk and mK02. Small molecule fluorophores such as fluorescein isothiocyanate (FITC), a reactive derivative of fluorescein, rhodamine (TRITC), coumarin, cyanin (Cy), may be conjugated to proteins and act as a fluorophore. Examples of fluorophores that may be used as a FRET-donor- acceptor pair include, but are not limited to, CFP as donor and YFP as acceptor, EGFP as donor and Cy3 as acceptor, or EGFP as donor and YFP as acceptor, or Clover as Donor and mRubby as acceptor or cpEGFP as donor and mK02 as acceptor.
As used herein, the term "split enzyme" refers to a biologically active enzyme that is split into at least two portions that have at least reduced or no biologically activity. In this context, the term "split enzyme pair" refers to the at least two at least partially inactive enzyme portions. Upon close proximity, the enzyme portions interact to form the biologically active enzyme, which can be detected using conventional enzyme detection techniques. The split enzyme technology is also further described in WO 2005/094441 A2. Examples of split enzymes include, but are not limited to, Renilla luciferase that can be reconstituted and monitored via bioluminescence; complementing split β-galactosidase wherein the activity can be monitored via colorometric, chemiluminescence, or fluorescence detection; split β-lactamase whose complementation may be assayed by the color change of nitrocefin upon hydrolysis or by fluorescence via CCF-2/AM; GTPases (change of charge), peroxidases (colorometric), nucleases (endo and exo cleavage), restriction endonucleases (sequence specific endo cleavage), proteases (protein cleavage), ligases (ligating nucleic acid oligos),and thiol-disulfide oxidoreductases (conformational change through disulfide bonds). As used herein, the term "split fluorescent protein (SFP) pairs" refers to at least two portions of a fluorescent protein. SFPs are composed of multiple peptide or polypeptide fragments that individually are not fluorescent, but, when complemented, form a functional fluorescent molecule. For example, Split-Green Fluorescent Protein (Split- GFP) is an SFP. Some engineered Split-GFP molecules are self-assembling. (See, e.g., U.S. Pat. App. Pub. No. 2005/0221343 and PCT Pub. No. WO/2005/074436; Cabantous et al., Nat. Biotechnol., 23: 102-107, 2005; Cabantous and Waldo, Nat. Methods, 3:845- 854, 2006.). US2012282643 also describes Split- Yellow Fluorescent Protein variants and Split-Cyan Fluorescent Protein variants. The determination of "percent identity" between two sequences as used herein is preferably accomplished using the mathematical algorithm of Karlin and Altschul (1993) Proc. Natl. Acad. Sci USA 90: 5873-5877. Such an algorithm is e.g. incorporated into the BLASTn and BLASTp programs of Altschul et al. (1990) J. Mol. Biol. 215: 403-410 available at NCBI (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi).
The determination of percent identity is preferably performed with the standard parameters of the BLASTn and BLASTp programs.
BLAST polynucleotide searches are preferably performed with the BLASTn program.
For the general parameters, the "Max Target Sequences" box may be set to 100, the "Short queries" box may be ticked, the "Expect threshold" box may be set to 10 and the "Word Size" box may be set to 28. For the scoring parameters the "Match/mismatch Scores" may be set to 1,-2 and the "Gap Costs" box may be set to linear. For the Filters and Masking parameters, the "Low complexity regions" box may not be ticked, the
"Species-specific repeats" box may not be ticked, the "Mask for lookup table only" box may be ticked, the "Mask lower case letters" box may not be ticked.
BLAST protein searches are preferably performed with the BLASTp program.
For the general parameters, the "Max Target Sequences" box may be set to 100, the "Short queries" box may be ticked, the "Expect threshold" box may be set to 10 and the "Word Size" box may be set to "3". For the scoring parameters the "Matrix" box may be set to "BLOSUM62", the "Gap Costs" Box may be set to "Existence: 11 Extension: 1", the "Compositional adjustments" box may be set to "Conditional compositional score matrix adjustment". For the Filters and Masking parameters the "Low complexity regions" box may not be ticked, the "Mask for lookup table only" box may not be ticked and the "Mask lower case letters" box may not be ticked.
The percent identity is determined over the entire length of the respective reference sequence, i.e. over the entire length of the sequence according to the SEQ ID NO or SEQ ID NOs recited in the respective context. For example, an amino acid sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO: 1 exhibits at least 80% identity to SEQ ID NO: 1 over the entire length of SEQ ID NO: 1. In another example, a sequence which exhibits at least 80% identity to the sequence according to SEQ ID NO:3 exhibits at least 80% identity to SEQ ID NO:3 over the entire length of SEQ ID NO:3.
The term "isolated" in the context of the present invention indicates that a polypeptide or polynucleotide has been removed from its natural environment and/or is presented in a form in which it is not found in nature. An "isolated" polypeptide or an "isolated" polynucleotide may also be a polypeptide or polynucleotide that has been generated in vitro.
As used herein, the term "amino acid substitution" refers to a substitution in an amino acid sequence according to a conservative or a non-conservative substitution, preferably a conservative substitution. In some embodiments, a substitution also includes the exchange of a naturally occurring amino acid with a non-natural amino acid. A
conservative substitution comprises the substitution of an amino acid with another amino acid having a chemical property similar to the amino acid that is substituted. Preferably, the conservative substitution is a substitution selected from the group consisting of:
(i) a substitution of a basic amino acid with another, different basic amino acid;
(ii) a substitution of an acidic amino acid with another, different acidic amino acid;
(iii) a substitution of an aromatic amino acid with another, different aromatic amino acid;
(iv) a substitution of a non-polar, aliphatic amino acid with another, different non-polar, aliphatic amino acid; and
(v) a substitution of a polar, uncharged amino acid with another, different polar, uncharged amino acid. A basic amino acid is preferably selected from the group consisting of arginine, histidine, and lysine. An acidic amino acid is preferably aspartate or glutamate.
An aromatic amino acid is preferably selected from the group consisting of
phenylalanine, tyrosine and tryptophane. A non-polar, aliphatic amino acid is preferably selected from the group consisting of glycine, alanine, valine, leucine, methionine and isoleucine. A polar, uncharged amino acid is preferably selected from the group consisting of serine, threonine, cysteine, proline, asparagine and glutamine. In contrast to a conservative amino acid substitution, a non-conservative amino acid substitution is the exchange of an amino acid with any amino acid that does not fall under the above- outlined conservative substitutions (i) through (v). As used herein, the term "biological sample" refers to a sample of tissue (e.g., tissue biopsy), organ, cell, cell lysate, or body fluid outside the body of a human or an animal. Further the term "biological sample" also includes in vitro cell cultured cells or cell lysates of eukaryotic cells, such as mammalian cells, human cells or plant cells or prokaryotic cells which optionally may have been genetically modified by methods commonly known to the person skilled in the art, including methods of transfecting and transforming.
As used herein, the term "gaseous sample" refers to any kind of sample in gaseous form. Examples of gaseous samples include, but are not limited to, human or animal breath, exhaust fumes and combustion gases.
As used herein, the term "binding" refers to an attractive interaction between two molecules that results in a stable association in which the molecules are in close proximity to each other. The result of binding is sometimes the formation of a molecular complex in which the attractive forces holding the components together are generally non-covalent, and thus are normally energetically weaker than covalent bonds. However, the term "binding" also includes the formation of a coordination complex, such as the coordination of a small molecule such as NO with a transition metal and/or amino acid residues in a protein domain such as the interaction of NO with the GAF domain of NorR. In a preferred embodiment, the term "binding" does not include redox reactions, i.e. an electron transfer such as in the oxidation of glutathione with hydrogen peroxide (2 G-SH + H202→ GS-SG + 2 H20).
The present invention also relates to the following items:
(1) A polypeptide comprising
a) a first signaling domain, and
b) a reactive oxygen and nitrogen species (RONS) sensor domain,
wherein the RONS sensor domain is capable of binding RONS or RONS-like molecules and the first signaling domain is capable of generating a detectable signal upon binding of RONS or RONS-like molecules to the RONS sensor domain.
(2) A polypeptide according to item (1) comprising:
a) a first signaling domain,
b) a reactive oxygen and nitrogen species (RONS) sensor domain, and c) a second signaling domain,
wherein the RONS sensor domain is capable of binding RONS or RONS-like molecules and the first signaling domain and the second signaling domain together are capable of generating a detectable signal upon binding of RONS or RONS-like molecules to the RONS sensor domain.
(3) The polypeptide of (1) or (2), wherein the RONS sensor domain comprises an amino acid sequence selected from the group consisting of
a) an amino acid sequence which exhibits at least 70 % identity to the sequence according to SEQ ID NO: 1 ;
b) an amino acid sequence which exhibits at least 70 % identity to the sequence according to SEQ ID NO: 2; and
c) an amino acid sequence which exhibits at least 70 % identity to the sequence according to SEQ ID NO: 3.
(4) The polypeptide of (1) to (3), wherein the RONS sensor domain comprises an amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3.
(5) The polypeptide of (1) to (3), wherein the RONS sensor domain comprises an amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3 with at least one amino acid substitution of amino acid R75, R81, D96 or D99.
(6) The polypeptide of (2) to (5), wherein the first signaling domain and the second signaling domain are together selected from the group consisting of a fluorescence resonance energy transfer (FRET) -donor- acceptor pairs, split-enzyme pairs or split- fluorescent protein pairs, wherein the first signaling domain and the second signaling domain are the respective parts of a pair.
(7) The polypeptide of (2) to (6), wherein the first signaling domain and the second signaling domain are a FRET-donor-acceptor pair.
(8) The polypeptide of (2) to (7), wherein the FRET-donor-acceptor pair is cyan fluorescent protein (CFP) domain and yellow fluorescent protein (YFP) domain such as the circularly permuted venus (CPV).
(9) The polypeptide of (8), wherein the CFP domain comprises an amino acid sequence of SEQ ID NO: 4 or an amino acid sequence of at least 70 % identity to the sequence according to SEQ ID NO: 4 and/or the YFP domain comprises an amino acid sequence of SEQ ID NO: 5 or an amino acid sequence of at least 70 % identity to the sequence according to SEQ ID NO: 5. (10) The polypeptide of (1) to (9), wherein the RONS or the RONS-like molecule is selected from the group consisting of NO, OH and SH radicals.
(11) The polypeptide of (10), wherein the RONS or RONS-like molecule is NO.
(12) The polypeptide of (l) to (l l), wherein the first signaling domain is a fluorescent protein domain and preferably a CFP domain.
(13) A polynucleotide encoding the polypeptide according to (1) to (12).
(14) The polynucleotide of (13), wherein said polynucleotide comprises a sequence which exhibits at least 80 % identity to the sequence according to SEQ ID NO: 6, SEQ ID NO: 7 or SEQ ID NO: 8.
(15) A vector encoding the polypeptide according to (1) to (12) suitable for eukaryotic or prokaryotic gene expression.
(16) A cell comprising the polynucleotide of (13) or (14), the vector of (15) and/or the polypeptide according to (1) to (12).
(17) A method for detecting a RONS or RONS-like molecule in a sample, comprising the steps of
a) providing a polypeptide according to (1) to (12);
b) contacting the polypeptide according to (1) to (12) with the sample;
c) optionally measuring the signal generated by the first signaling domain; and d) optionally measuring the signal generated together by the first signaling domain and the second signaling domain;
wherein a change in signal intensity after contact with the sample indicates the presence of the RONS or RONS-like molecule in the sample.
(18) The method of (17), wherein the RONS or RONS-like molecule is NO, OH or SH radicals.
(19) The method of (17) or (18), wherein the signal measured in step c) and/or d) is a fluorescence signal, a colorimetric signal or a FRET signal.
(20) The method of (17) to (19), wherein the measured signal is a FRET signal.
(21) The method of (20), wherein the FRET signal is measured after excitation with light at a wavelength in the range of from about 430 nm to about 450 nm and/or an emission of light in the range of from about 525 nm to about 545 nm.
(22) The method of (17) to (21), wherein in step a) the providing of the polypeptide comprises (i) transfecting at least one eukaryotic cell outside the human or animal body or transforming a prokaryotic cell with a polynucleotide according to (13) to (14) or the vector of (15) or (ii) providing a cell according to (16).
(23) The method of (17) to (22), wherein the RONS or RONS-like molecule may be detected in a concentration from about 0.1 nM to about 1.0 μΜ.
(24) The method of ( 17) to (22), wherein the RONS or RONS-like molecule may be detected in a concentration from about 1.0 μΜ to about 100.0 μΜ.
(25) The method of (17) to (24), wherein the sample is selected from the group consisting of biological samples, potential nitric oxide-bearing explosive samples, gaseous samples, liquid samples, liquid samples containing NO-generating agents or a combination thereof.
(26) The method of (17) to (25), wherein the polypeptide is treated with an Fe(II) containing compound in or before step a) or step b).
(27) Use of a polypeptide comprising a RONS sensor domain comprising
a) an amino acid sequence which exhibits at least 70 % identity to the sequence according to SEQ ID NO: 1 ;
b) an amino acid sequence which exhibits at least 70 % identity to the sequence according to SEQ ID NO: 2; or
c) an amino acid sequence which exhibits at least 70 % identity to the sequence according to SEQ ID NO: 3;
in the detection of a RONS or RONS-like molecule in a sample.
(28) Use of a polypeptide of (1) to (12) for detecting a RONS or RONS-like molecule in a sample.
(29) Use according to (27) to (28), wherein the RONS or RONS-like molecule is NO, OH or SH.
(30) Use according to (27) to (29), wherein the sample is selected from the group consisting of biological samples, potential nitric oxide-bearing explosive samples, gaseous samples, liquid samples, liquid samples containing NO-generating agents.
(31) Use according to (27) to (30), wherein the polypeptide has been treated with an Fe (II) -containing compound before the detection of a RONs-or RONs-like molecule. (32) A kit for detecting RONS or RONS-like molecules comprising at least one of: a) a polypeptide according to (1) to (12);
b) a polynucleotide according to (13) to (14) or a vector of (15); c) a cell of (16); or
d) a combination of a) to c).
EXAMPLES
Example 1. Chemicals and Buffer-Solutions
Cell culture media, fetal calf serum (FCS) and all plastic ware were purchased from PAA laboratories (Pasching, Austria). Dulbecco's modified eagle's medium (DMEM) was obtained from Sigma-Aldrich (Vienna, Austria). 3-(2-Hydroxy-l-methyl-2- nitrosohydrazino)-N-methyl-l-propanamine (NOC-7) was from Tocris (Tocris Cookson Ltd., Bristol, UK) and Disodium l-[2-(carboxylato)pyrrolidin-l-yl]diazen-l-ium-l,2- diolate (PROLI NONOate) was obtained from Santa Cruz (Santa Cruz Biotechnology, Inc., Heidelberg, Germany). Transfast™ transfection reagent, restriction enzymes and Taq polymerase used for subcloning were purchased from Promega (Mannheim, Germany). All other chemicals were obtained from Roth (Karlsruhe, Germany). Prior to imaging experiments cells were stored for 1 to 5 hours at room temperature in a HEPES buffered solution containing in mM: 135 NaCl, KCl, 2 CaCl2, 1 MgCl2, 1 HEPES, 2.6 NaHC03, 0.44 KH2P04, 0.34 Na2HP04, 10 D-glucose, 0.1 % vitamins, 0.2 % essential amino acids and 1 % penicillin/streptomycin pH 7.4. During the experiments cells were perfused with a physiological buffer solution containing in mM: 138 NaCl, 5 KCl, 2 CaCl2, 1 MgCl2, 10 D-glucose and 10 HEPES, pH adjusted to 7.4 with NaOH. Example 2. Cell Culture and Transfection
HeLa cells were cultured in a humidified atmosphere at 37 °C and 5 % C02 using DMEM containing 10 % FCS, 100 U/ml penicillin, and 100μg/ml streptomycin. For imaging experiments and transfection, cells were grown on 30 mm glass cover slips and transfected at 50-80 % confluence with 1.5 μg of plasmid DNA (per 30 mm well) using 4 μg / well TransFastTM transfection reagent in 0.5 ml of serum and antibiotic-free transfection medium. Cells were maintained in the incubator (37 °C, 5 % C02, 95 % air) for 16-20 hours before changing the medium back to normal culture medium. Experiments were performed 24-48 hours after transfection.
Example 3. Cloning
For the generation of Sensor 1, the whole genome from E. coli (DH5a) was extracted and the NorR gene was amplified by PCR using the following primers: GGCATCGATATGAGTTTTTCCGTTGATGTGC (forward primer) and GCCGAATTCATCCTTCAATCCCAGACGTTTC (reverse primer). The primer pairs GGCATCGATATGAGTTTTTCCGTTGATGTGC (forward primer) and ATAGAATTCCGTGGCATCGCCTGGCAGCATA (reverse primer), was used to amplify the GAF domain for cloning Sensor 2, respectively. The obtained fragments were inserted into the pcDNA3.1(-) vector (Invitrogene, Life Technologies, Vienna, Austria) containing the coding sequence of respective fluorescent proteins (eCFP and CPV) and the restriction sites Clal, which was inserted by PCR, and EcoRl. The coding sequences of the fluorescent proteins including both restriction sites between the FPs were inserted into the pcDNA3.1 (-) vector's multi cloning site using common molecular biology methods known to the person skilled in the art.
Example 4. Fluorescence microscopy
Experiments were performed on 3 different inverted fluorescence microscopes. Imaging system 1 was based on a Zeiss Axio Observer. A 1 (Zeiss, Gottingen, Germany) that was equipped with a polychromator illumination system (VisiChrome, Visitron Systems, Puchheim, Germany) and a thermoelectric-cooled CCD camera (Photometries CoolSNAP HQ, Visitron Systems). Imaging system 2 consists of the fluorescence microscope Eclipse 300TE (Nikon, Vienna) with an epifluorescence system (150 W XBO; Optiquip, Highland Mills, NY, USA), a computer controlled z-stage (Ludl Electronic Products, Haawthrone, NY, USA) and a CCD camera (spot Persuit, Visitron Systems). Imaging system 3 is a fully automated digital wide field system, Till iMIC (Till Photonics Graefelfing, Germany) that is equipped with an ultra fast switching monochromator, the Polychrome V (Till Photonics) and a CCD camera (AVT Stringray F145B, Allied Vision Technologies, Stadtroda, Germany). If not otherwise indicated cells expressing geNOps were illuminated at 440 + 10 nm (440AF21, Omega Optical, Brattleboro, VT, USA), and emission was recorded at 480 and 535 nm using emission filters (480AF30 and 535AF26, Omega Optical). Emission filters were either mounted on a a Ludl filterwheel (Imaging system 1), or the Dual View Micro-Imager™ (480 and 535 nm; Optical Insights, Visitron Systems) was used (Imaging system 2), or a single beam splitter design (Imaging system 3; Dichrotome, Till Photonics) was installed. For the data acquisition and the control of the fluorescence microscopes VisiView Premier Acquisition software (Visitron Systems) was used for both imaging system 1 and 2, while the live acquisition software version 2.0.0.12 (Till Photonics) was used on imaging system 3.
The following Examples 7 and 8 were performed using imaging system 1. Example 5. Statistics Data shown represent the mean + s.e.m, and n indicates number of cells/independent experiments Statistical analyses were performed with unpaired Student's t-test and p<0.05 was considered to be significant. Example 6. Constructs
The probes Sensor 1 (SEQ ID NO:9) and Sensor 2 (SEQ ID NO: 10) as shown in Table 1A were investigated.
Sensor 1 and Sensor 2 were encoded by the respective nucleotide coding sequences of n_Sensor 1 (SEQ ID NO: 8) and n_Sensor 2 (SEQ ID NO: 6). The nucleotide sequences were cloned and transfected in HeLa cells as described above.
Example 7. Addition of NO donors to cells expressing Sensor 1
First, the effect of NOC-7, a NO donor, on fluorescence signals of Sensor 1 was tested using HeLa cells expressing the respective constructs. The fluorescence signals were measured as described above. Repeated additions of NOC-7 induced immediate significant increases of the FRET ratio signal of Sensor 1, while upon removal of the NO donor the signals were instantly reduced as shown in Figure 1. In order to test if another NO donor also affects the FRET ratio signal of Sensor 1, similar experiments were performed using PROLI NONOate, a pyrrolidin derivate that liberates NO. Addition of PROLI NONOate also promptly increased the FRET ratio signal of Sensor 1 in a reversible manner as shown in Figure 2. Example 8. Addition of NO donors to cells expressing Sensor 2
Fluorescence microscopy experiments were performed with transfected HeLa cells expressing Sensor 2. The FRET signal in Sensor 2 was strongly reduced upon the addition of NOC-7 as shown in figure 3.
Example 9. Addition of Fe-containing compounds The probe Sensor 3 (SEQ ID NO: 12) comprising from N-terminus to C-terminus a mKOk domain and a GAF-domain is encoded by the respective nucleotide coding sequences of n_Sensor 3 (SEQ ID NO: 11) (see Table 3). Table 3.
SEQ ID NO: Nucleotide/Protein sequence
11 CTCGAGTATGGTGAGTGTGATTAAACCAGAGATGAAGAT
GAGGTACTACATGGACGGCTCCGTCAATGGGCATGAGTT
CACAATTGAAGGTGAAGGCACAGGCAGACCTTACGAGG
GACATCAAGAGATGACACTACGCGTCACAATGGCCAAG
GGCGGGCCAATGCCTTTCGCGTTTGACTTAGTGTCACAC
GTGTTCTGTTACGGCCACAGACCTTTTACTAAATATCCA
GAAGAGATACCAGACTATTTCAAACAAGCATTTCCTGAA
GGCCTGTCATGGGAAAGGTCGTTGGAGTTCGAAGATGGT
GGGTCCGCTTCAGTCAGTGCGCATATAAGCCTTAGAGGA
AACACCTTCTACCACAAATCCAAATTTACTGGGGTTAAC
TTTCCTGCCGATGGTCCTATCATGCAAAACCAAAGTGTT
GATTGGGAGCCATCAACCGAGAAAATTACTGCCAGCGA
CGGAGTTCTGAAGGGTGATGTTACGATGTACCTAAAACT
TGAAGGAGGCGGCAATCACAAATGCCAATTCAAGACTA
CTTACAAGGCGGCAAAAAAGATTCTTAAAATGCCAGGA
AGCCATTACATCAGCCATCGCCTCGTCAGGAAAACCGAA
GGCAACATTACTGAGCTGGTAGAAGATGCAGTAGCTCAT
TCCATCGATATGAGTTTTTCCGTTGATGTGCTGGCGAATA
TCGCCATCGAATTGCAGCGTGGGATTGGTCACCAGGATC
GTTTTCAGCGCCTGATCACCACGCTACGTCAGGTGCTGG
AGTGCGATGCGTCTGCGTTGCTACGTTACGATTCGCGGC
AGTTTATTCCGCTTGCCATCGACGGTCTGGCAAAGGATG
TACTCGGTAGACGCTTTGCGCTGGAAGGGCATCCACGGC
TGGAAGCGATTGCCCGCGCCGGGGATGTGGTGCGCTTTC
CCGCAGACAGCGAATTGCCCGATCCCTATGACGGTTTGA
TTCCTGGGCAGGAGAGTCTGAAGGTTCACGCCTGCGTTG
GTCTGCCATTGTTTGCCGGGCAAAACCTGATCGGCGCAC
TGACGCTCGACGGGATGCAGCCCGATCAGTTCGATGTTT
TCAGCGACGAAGAGCTACGGCTGATTGCTGCGCTGGCGG
CGGGAGCGTTAAGCAATGCGTTGCTGATTGAACAACTGG
AAAGCCAGAATATGCTGCCAGGCGATGCCACG
TAAGCTT
12 MVSVIKPEMKMRYYMDGSVNGHEFTIEGEGTGRPYEGHQ
EMTLRVTMAKGGPMPFAFDLVSHVFCYGHRPFTKYPEEIP
DYFKQAFPEGLSWERSLEFEDGGSASVSAHISLRGNTFYHK
SKFTGVNFPADGPIMQNQSVDWEPSTEKITASDGVLKGDV
TMYLKLEGGGNHKCQFKTTYKAAKKILKMPGSHYISHRLV
RKTEGNITELVEDAVAHSIDMSFSVDVLANIAIELQRGIGHQ
DRFQRLITTLRQVLECDASALLRYDSRQFIPLAIDGLAKDVL
GRRFALEGHPRLEAIARAGDVVRFPADSELPDPYDGLIPGQ
ESLKVHACVGLPLFAGQNLIGALTLDGMQPDQFDVFSDEE
LRLIA ALA AG ALS N ALLIEQLES QNMLPGD AT The nucleotide sequences were cloned using the respective restriction sites Xhol, Clal and Hindlll into the pcDNA3.1(-) vector and transfected in HeLa cells as described above. The transfected HeLa cells were then pre-incubated with either 1 mM to 10 mM sodium nitroprusside or 100 μΜ to 200 μΜ iron(II) fumarate in a medium containing (in mM): 138 NaCl, 5 KC1, 2 CaCl2, 1 MgCl2, 1 HEPES, 2.6 NaHC03, 0.44 KH2P04, 0.34 Na2HP04, 10 D-glucose, 0.1 % vitamins, 0.2 % essential amino acids and 1%
penicillin/streptomycin; pH adjusted to 7.4 with NaOH. After 5 - 30 minutes of incubation with the different iron compounds at room temperature cells were washed 3 times with PBS prior to imaging as described above, using the respective excitation and detection wavelengths of mKOk. Pre-incubation of HeLa cells with iron(II) fumarate strongly augmented the NOC-7 induced quenching of the fluorescence signal of mKOk in Sensor_3 (Figure 4). In a similar manner pre-incubation of cells with sodium
nitroprusside boosted NO-dependent signals of Sensor_3-
Example 10. Determination of EC50 values of NOC-7 on differently colored Sensors
HeLa cells expressing Sensor 3 were prepared as described above. The consecutive addition and removal of different concentrations of NOC-7 in range from 1 nM to 100 μΜ revealed in fluorescence microscopy that the sensor responded in a
concentration-dependent manner by fluorescence quenching. A half maximal effective concentration (EC 50) of 51.3 nM was obtained. The experiments were also performed accordingly using other sesnsor constructs, wherein the mKOK domain was replaced by a differently colored fluorescent domain, namely a CFP domain of SEQ ID NO: 4, a YFP domain of SEQ ID:5, enhanced green fluorescent protein (EGFP; GenBank: AFA52654.1) domain, and green emission fluorescent protein domain (GEM), respectively. The results are summarized below in Table 4.
Table 4: EC50 values of NOC-7 quenching by differently colored fluorescent sensor
Figure imgf000042_0001
Considering the short half-time of NOC-7 and NO, these results indicate that the sensors are suitable to record cellular NO concentrations in the low physiological nM range.

Claims

Claims
1. A polypeptide comprising
a) a first signaling domain, and
b) a reactive oxygen and nitrogen species (RONS) sensor domain,
wherein the RONS sensor domain is capable of binding RONS or RONS-like molecules and the first signaling domain is capable of generating a detectable signal upon binding of RONS or RONS-like molecules to the RONS sensor domain.
2. A polypeptide according to claim 1 comprising:
a) a first signaling domain,
b) a reactive oxygen and nitrogen species (RONS) sensor domain, and c) a second signaling domain,
wherein the RONS sensor domain is capable of binding RONS or RONS-like molecules and the first signaling domain and the second signaling domain together are capable of generating a detectable signal upon binding of RONS or RONS-like molecules to the RONS sensor domain.
3. The polypeptide of any one of claims 1 or 2 , wherein the RONS sensor domain comprises an amino acid sequence selected from the group consisting of
a) an amino acid sequence which exhibits at least 70 % identity to the sequence according to SEQ ID NO: 1;
b) an amino acid sequence which exhibits at least 70 % identity to the sequence according to SEQ ID NO: 2; and
c) an amino acid sequence which exhibits at least 70 % identity to the sequence according to SEQ ID NO: 3.
4. The polypeptide of any one of claims 1 to 3, wherein the RONS sensor domain comprises an amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3.
5. The polypeptide of any one of claims 1 to 3, wherein the RONS sensor domain comprises an amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3 with at least one amino acid substitution of amino acid R75, R81, D96 or D99.
6. The polypeptide of any one of claims 2 to 5, wherein the first signaling domain and the second signaling domain are together selected from the group consisting of a fluorescence resonance energy transfer (FRET) -donor- acceptor pairs, split-enzyme pairs or split-fluorescent protein pairs, wherein the first signaling domain and the second signaling domain are the respective parts of a pair and preferably wherein the first signaling domain and the second signaling domain are a FRET-donor-acceptor pair.
7. The polypeptide of any one of claims 2 to 6, wherein the FRET-donor- acceptor pair is cyan fluorescent protein (CFP) domain and yellow fluorescent protein (YFP) domain such as the circularly permuted venus (CPV).
8. The polypeptide of claim 7, wherein the CFP domain comprises an amino acid sequence of SEQ ID NO: 4 or an amino acid sequence of at least 70 % identity to the sequence according to SEQ ID NO: 4 and/or the YFP domain comprises an amino acid sequence of SEQ ID NO: 5 or an amino acid sequence of at least 70 % identity to the sequence according to SEQ ID NO: 5.
9. The polypeptide of any one of claims 1 to 8, wherein the RONS or the RONS-like molecule is selected from the group consisting of NO, OH and SH radicals and preferably is NO.
10. The polypeptide of claims 1 to 9, wherein the first signaling domain is a fluorescent protein domain, and preferably a CFP domain.
11. A polynucleotide encoding the polypeptide according to any one of claims 1 to 10.
12. The polynucleotide of claim 11, wherein said polynucleotide comprises a sequence which exhibits at least 80 % identity to the sequence according to SEQ ID NO: 6 , SEQ ID NO: 7 or SEQ ID NO: 8.
13. A vector encoding the polypeptide according to any one of claims 1 to 12 suitable for eukaryotic or prokaryotic gene expression.
14. A cell comprising the polynucleotide of claims 11 or 12, the vector of claim 13 and/or the polypeptide according to any one of claims 1 to 10.
15. A method for detecting a RONS or RONS-like molecule in a sample, comprising the steps of
a) providing a polypeptide according to any one of claims 1 to 10;
b) contacting the polypeptide according to any one of claims 1 to 9 with the sample;
c) optionally measuring the signal generated by the first signaling domain; and d) optionally measuring the signal generated together by the first signaling domain and the second signaling domain;
wherein a change in signal intensity after contact with the sample indicates the presence of the RONS or RONS-like molecule in the sample.
16. The method of claim 15, wherein the RONS or RONS-like molecule is an NO, OH or SH radical.
17. The method of any one of claims 15 or 16, wherein the signal measured in step c) and/or d) is a fluorescence signal, a colorimetric signal or a FRET signal.
18. The method of any one of claims 15 to 17, wherein the measured signal is a FRET signal.
19. The method of claim 18, wherein the FRET signal is measured after excitation with light at a wavelength in the range of from about 430 nm to about 450 nm and/or an emission of light in the range of from about 525 nm to about 545 nm.
20. The method of any one of claims 15 to 19, wherein in step a) the providing of the polypeptide comprises (i) transfecting at least one eukaryotic cell outside the human or animal body or transforming a prokaryotic cell with a polynucleotide according to any one of claims 11 or 12 or with a vector according to claim 13 or (ii) providing a cell according to claim 14.
21. The method of any one of claims 15 to 20, wherein the RONS or RONS-like molecule may be detected in a concentration from about 0.1 nM to about 1.0 μΜ.
22. The method of any one of claims 15 to 20, wherein the RONS or RONS-like molecule may be detected in a concentration from about 1.0 μΜ to about 100.0 μΜ.
23. The method of any one of claims 15 to 22, wherein the sample is selected from the group consisting of biological samples, potential nitric oxide -bearing explosive samples, gaseous samples, liquid samples, liquid samples containing NO-generating agents or a combination thereof.
24. The method of any one of claims 15 to 23, wherein the polypeptide is treated with an Fe(II) containing compound in or before step b).
25. Use of a polypeptide comprising a RONS sensor domain comprising
a) an amino acid sequence which exhibits at least 70 % identity to the sequence according to SEQ ID NO: 1;
b) an amino acid sequence which exhibits at least 70 % identity to the sequence according to SEQ ID NO: 2; or
c) an amino acid sequence which exhibits at least 70 % identity to the sequence according to SEQ ID NO: 3;
in the detection of a RONS or RONS-like molecule in a sample.
26. Use of a polypeptide of any one of claims 1 to 10 for detecting a RONS or RONS- like molecule in a sample.
27. Use according to claims 25 or 26, wherein the RONS or RONS-like molecule is NO, OH or SH.
28. Use according to any one of claims 25 to 27, wherein the sample is selected from the group consisting of biological samples, potential nitric oxide -bearing explosive samples, gaseous samples, liquid samples, liquid samples containing NO-generating agents.
29. Use according to any one of claims 25 to 28, wherein the polypeptide has been treated with an Fe(II)-containing compound before the detection of a RONS or RONS- like molecule.
30. A kit for detecting RONS or RONS-like molecules comprising at least one of: a) a polypeptide according to any one of claim 1 to 10;
b) a polynucleotide according to any one of claims 11 to 12 or the vector according to claim 13;
c) a cell of claim 14; or
d) a combination of a) to c).
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Publication number Priority date Publication date Assignee Title
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Publication number Priority date Publication date Assignee Title
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M. I. HUTCHINGS ET AL: "The NorR Protein of Escherichia coli Activates Expression of the Flavorubredoxin Gene norV in Response to Reactive Nitrogen Species", JOURNAL OF BACTERIOLOGY, vol. 184, no. 16, 15 August 2002 (2002-08-15), US, pages 4640 - 4643, XP055234376, ISSN: 0021-9193, DOI: 10.1128/JB.184.16.4640-4643.2002 *
N. P. TUCKER ET AL: "Analysis of the Nitric Oxide-sensing Non-heme Iron Center in the NorR Regulatory Protein", JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 283, no. 2, 11 January 2008 (2008-01-11), US, pages 908 - 918, XP055234576, ISSN: 0021-9258, DOI: 10.1074/jbc.M705850200 *
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