EP1924711A2 - Puces liant les acides nucleiques, destinees a detecter des etats de carence en azote dans le cadre du controle de processus biologiques - Google Patents

Puces liant les acides nucleiques, destinees a detecter des etats de carence en azote dans le cadre du controle de processus biologiques

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Publication number
EP1924711A2
EP1924711A2 EP06791904A EP06791904A EP1924711A2 EP 1924711 A2 EP1924711 A2 EP 1924711A2 EP 06791904 A EP06791904 A EP 06791904A EP 06791904 A EP06791904 A EP 06791904A EP 1924711 A2 EP1924711 A2 EP 1924711A2
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EP
European Patent Office
Prior art keywords
putative
seq
homologue
protein
gene
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
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Application number
EP06791904A
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German (de)
English (en)
Inventor
Stefan Evers
Jörg FEESCHE
Karl-Heinz Maurer
Thomas Schweder
Michael Hecker
Birgit Voigt
Britta JÜRGEN
Le Thi Hoi
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Henkel AG and Co KGaA
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Henkel AG and Co KGaA
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Publication date
Application filed by Henkel AG and Co KGaA filed Critical Henkel AG and Co KGaA
Publication of EP1924711A2 publication Critical patent/EP1924711A2/fr
Withdrawn legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • the present invention relates to nucleic acid-binding chips for monitoring bioprocesses with a particular focus on the detection of nitrogen deficiency states and to the use of corresponding gene probes, in particular on such chips, or methods and applications based on such probes and chips
  • the monitoring of such processes is done on the one hand by observing the changing properties and requirements of the organisms under consideration during the process, which is reflected, for example, in the optical density and viscosity of the medium, in absorbed or emitted gases, in changes in the pH
  • This can also be used to measure enzymatic activities by means of suitable assays, for example the detection of activities of interest in the cultural supernatant
  • a recognition layer biological layer
  • a transducer for example an amperometric or potentiomet ⁇ sche electrode
  • an amplifier amplification / processing
  • the protein-specific chips can be disregarded.
  • MRNA-recognizing chips are usually doped with complementary DNA molecules or DNA analogs. Their preparation and use for very detailed questions, such as the differentiation of point mutations, for example, in the application WO 95/11995 A1.
  • DNA chip analyzes there are those with a PCR amplification of the target sequence and those without amplification. Furthermore, there are those with optical evaluation of the signals due to the recognition and those with electrical evaluation
  • fluorophores for example, fluorophores, Ac ⁇ diniumester or indirect detection of secondary binding processes, for example on biotin, avidin / streptavidin or digoxigenin described in the latter case, digoxigenin-specific antibodies are used for optical detection, the In this case, the enzyme activity is detected either kolo ⁇ metrisch or luminescence According to Westin et ai (2000), Nature Biotechnol, Volume 18, S 199-204, the hybridization with a PCR on the DNA chip be coupled so as to be able to carry out the entire detection reaction on a chip can ("Lab-on-a-Ch ⁇ p concept")
  • control genes can also be included to indicate when the process is developing in a direction that is not intended. In the course of this monitoring, for practical reasons, a not too high number of different genes should be observed
  • biotechnological processes with gram-positive bacteria are used especially for their ability to secretion for the industrial production of valuable materials.
  • nucleic acid-binding chips with individual of these genes are now disclosed in several publications, or at least the possibility of their production demonstrated
  • the two patent applications DE 10136987 A1 and DE 10108841 A1 each reveal a gene from Corynebacterium glutamicum, namely clpC or citB
  • Both genes are described as relevant for the amino acid metabolism, which is why a commercially interesting use of these genes should consist in inactivating or at least attenuating them in order to optimize the fermentative production of amino acids by this microorganism. Further application possibilities can then exist according to these applications. Submit probes for the relevant gene products on nucleic acid-binding chips
  • patent application WO 02/055655 A2 discloses more than 1,800 DNA sequences obtained by the complete sequencing of the Genome of the microorganism Methylococcus capsulatus have been identified
  • nucleic acid-binding chips that cover an almost complete genome or the associated transcptome (genomic DNA chips).
  • the application WO 2004/027092 A2 provides a representative cross-section with a manageable number of genes in order to identify various physiological states which an observed microorganism can undergo during cultivation.
  • these include starvation conditions for various nutrients or stress situations such as for example heat or cold shock, shear stress, oxidative stress or oxygen limitation
  • Nucleic acid-binding chips that are based on this selection of genes provide a certain, but overall rather rough overview of the respective metabolic situation. They usually are not able to particularly illuminate a single sub-problem, however, a single positive signal can be different Be situations out or even be false positive, which is why it often - and especially in such an unclear situation - makes sense to analyze a selected metabolic aspect separately
  • electrically readable nucleic acid-binding chips which have the advantage of a timely analysis, the Number of simultaneously assignable places limited, so that can not be easily applied additional gene probes to detect additional, specific metabolic situations
  • nucleic acid-binding chips for monitoring bioprocesses with a special focus on the detection of phosphate deficient states or glucose deficiency states respectively carry a limited number of probes to indicate these specific stress situations
  • a metabolic situation which can be critical for microorganisms and thus critical for a corresponding bioprocess, is that of nitrogen deficiency because nitrogen is an essential element for nucleic acids and amino acids and thus for proteins, which in turn represent the main function and building materials of biological organisms a lack of building material supply and can rapidly lead to the death of the cells or at least prevent the achievement of higher cell densities
  • a nitrogen deficiency also affects the product formation rate
  • a chip to carry out a based, timely analysis and to be able to intervene punctually and thus more purposefully in the ongoing bioprocess due to the result that can be obtained quickly
  • nucleic acid-containing chips with gene probes for single or several of these genes and thereby arrive at nucleic acid-binding chips that reliably indicate the signal "nitrogen deficiency" in the course of a monitored bioprocess (nitrogen deficiency sensors) was particularly suitable for those nucleic acid-binding chips whose number of assignable sites is comparatively low due to their design, in particular the electrically evaluable For these, on the other hand, have the advantages of rapid readability and thus enable an / A - // ne analysis This ensures if necessary early intervention in order to optimize the bioprocess concerned with regard to the supply of building materials
  • Such a DNA-binding chip should be usable for several comparable processes and be adapted to specific application possibilities with comparatively slight variations.
  • it should be based on bioprocesses on the basis of saccharomyces, in particular B subtilis, B amyloliquefaciens, B lentus, B globign, and be especially geared to ß licheniformis Bioprocesses focused on fermentations, in particular the technical production of products, especially overexpressed proteins
  • a nitrogen deficiency sensor should allow appropriate methods for measuring the physiological state of the cells under consideration, as well as appropriate uses for monitoring the biological processes under consideration
  • Table 1 shows all of the 210 genes of Bacillus lichemformis DSM13 identified in Example 1, the induction of which was observed under nitrogen deficiency, with a factor of at least three being considered significant. Of these, in table 2, all 49 genes are assembled whose induction by nitrogen deficiency is any of those measured Time points have been at least the factor 8 and where it could be concluded from parallel, not shown here studies that they were relatively specific for this signal. These are listed in Table 3 again in terms of strength of their observed maximum induction their DNA and amino acid sequences listed in the sequence listing for the present application, wherein the odd-numbered numbers for DNA and the subsequent even-numbered for the respective deduced amino acid sequences stand on these sequences also refer to the respective SEQ ID numbers in Tables 2 and 3 acts these are the following genes, in order of decreasing strength of the nitric-depleted induction (see Tables 2 and 3) - Gene coding for a hypothetical protein of unknown function (homolog to SEQ ID
  • - pckA phosphoenolpyruvate carboxykinase, SEQ ID NO 43, 44
  • - trpE anthranilate synthase, SEQ ID NO 67, 68
  • - nasB electro transfer subunit of assimilatory nitrate reductase, SEQ ID NO 33
  • -nasC catalytic subunit of the assimilatory nitrate reductase, SEQ ID NO 35, 36
  • -ycdH unknown function - similar to the binding protein of the ABC transporter, SEQ ID NO 35, 36
  • SEQ ID NO 85, 86 gene encoding a putative protein (putative serine protease) (homologue to SEQ ID NO 9,
  • trpF phospho-tosyl-anthranilate isomerase
  • glnR transcriptional repressor of the glutamine synthetase gene, SEQ ID NO 11, 12
  • nrgB nitrogen-regulated Pll-like protein, SEQ ID NO 3, 4
  • Example 5 Further investigations (see Example 5) showed that the following gene is also suitable according to the invention as an indicator
  • tnrA (a global transcriptional regulator involved in nitrogen metabolism regulation, SEQ ID NO 99, 100)
  • a solution of the problem is thus in a nucleic acid-binding chip, doped with probes for at least three of the following genes kdgR, citA, for a putative protein (putative ABC transporter / amino acid permease) coding gene (homolog to SEQ ID NO 91), MrA, ycnI, gene coding for a hypothetical protein of unknown function (homolog to SEQ ID NO 41), gene coding for a hypothetical protein of unknown function (homolog to SEQ ID NO 53), yppF, yqjN, ggt, as R, glnA, nrgA, yciC, yvtA, nrgB, gene encoding a conserved hypothetical protein of unknown function (homologue to SEQ ID NO 19), gene encoding a putative protein (ATP binding protein of a putative ABC transporter) (homologue
  • homologues it can be assumed that in species other than B. licheniformis the homologous genes are activated under nitrogen deficiency In a species of interest for one of these genes, there are several homologs capable of transcoding in vivo, the term "homologue to SEQ ID NO" refers to the closest of these various candidate genes
  • At least three of these genes are selected in order to obtain as reliable a statement as possible, that is, to exclude a single false-positive signal due to only one type of probe
  • a nucleic acid-comprising chip means all articles which are provided with nucleic acid-specific probes and in each case deliver an evaluable signal upon binding of one or more specifically recognized nucleic acids
  • RNA is isolated by methods known per se, for example cell disruption and use of a denaturing buffer. in particular mRNA isolated.
  • the strength of the hybridization signal over a certain range - optionally to be optimized in individual cases - is proportional to the number of specific mRNA present in the sample at the time of sampling in this way the strength of the signal provides a direct measure of the activity of the gene in question at the time of sampling
  • the time interval between sampling and measurement should be kept as short as possible, for example via a largely automated sampling, their processing and management via / through the sensor
  • probes are to be understood as meaning all molecules which are capable of reacting (binding) with nucleic acids.
  • binding binding
  • chip this interaction is exploited to provide a signal which can be assigned to a significant extent to obtain
  • a probe according to the invention is usually a compound capable of binding mRNA molecules or nucleic acids derived therefrom via hydrogen bonds, as for example also in the interaction of the two strands of a DNA or the DNA RNA
  • This may, for example, be a DNA which is more stable to hydrolysis than RNA
  • other molecules are known in the prior art, in particular chemically synthesized biomimetic allow the same interaction, but are more stable than DNA, for example, in that the phosphate ester bonds of the backbone have been exchanged for less hydrolysempfmdliche bonds
  • Such nucleic acid analog Preferred probes of the present application (see below)
  • the specific probes in question were to be synthesized according to the example of the sequence listing associated with this application. This is in contrast to the aspect that chips according to the invention should advantageously be usable several times, in particular during a single observed process, in the course of which constant monitoring is desirable
  • the degree of homology between the probe provided and the mRNA or the nucleic acid derived therefrom, which is to be recognized by hybridization, is ultimately limiting for the usefulness of a probe.
  • the degree of hybridization of the probe with the mRNA to be detected is decisive (see above).
  • sequences obtainable from ⁇ licheniformis are given in the Sequence Listing of the present application (SEQ ID NOs. 1 to 100), wherein the odd-numbered sequences are While the DNA sequences can be used directly for the production of probes (see above), the amino acid sequences serve, for example, via sequence data base sequences and DNA sequences which are each higher by a number higher sequences around the respectively derived amino acid sequences. Comparisons of gene function testing can also be used to generate similar nuclear acid-detecting probes through backward translation of the genetic code
  • Example 1 As shown in Example 1, numerous different gene transcripts, that is, mRNA molecules, in particular those of which participation in nitrogen metabolism was well known, were investigated. These mRNA molecules became a nitrogen deficient state at various times during the transition from B licheniformis DSM13 In Example 1 it is also described how the concentration increase of this mRNA in the cell interior of B licheniformis was determined experimentally. Alternative determination possibilities for this may be established in the prior art.
  • Table 1 (Example 2) is crucial to the understanding of the present invention shows the concentration changes associated with the transition for a total of 210 mRNAs. The following threshold values for the ratio of the amount of RNA of the respective gene to the control value were regarded as significant.
  • Example 3 there are 67 genes with at least ⁇ -fold induction at any of the observed time points under the conditions of the nitrogen deficiency described in Example 1. Of these, 18 may not be considered specific, so that, surprisingly, only those described in U.S. Pat These 49 genes are considered according to the invention as representative indicators of a nitrogen deficiency state Further information on these genes, for example on their function or deviating start codons are shown in Tables 2 and 3 and the sequence listing , the respective German-language names for the associated proteins have already been listed above, in the order of the statements in Table 3
  • the separately identified gene tnrA shows according to Example 5 30 min after the transition into the nitric acid-induced Staiffphase a more than 15-fold induction, so that this gene can be used to implement the teaching of the invention and is accordingly preferred
  • strain S licheniformis DSM 13 is available from the German Collection of Microorganisms and Cell Cultures GmbH, Mascheroder Weg 1b, 38124 Braunschweig, Germany (http://www.dsmz.de/) Generally available at the American Type Culture Collection, 10801 University Boulevard, Manassas, VA 20110-2209, USA (http://www.cc.org/), the accession number ATCC 14580
  • genes from other organisms corresponding to the abovementioned 50 genes are to a large extent likewise stored in generally accessible databases, for example for the well-characterized species B subtilis and E. coli, which are generally regarded as model organisms of gram-positive and / or gram-negative bacteria
  • B subtilis and E. coli which are generally regarded as model organisms of gram-positive and / or gram-negative bacteria
  • the databases of the Institut Pasteur, 25.28 rue du Do Budapest Roux, 75724 Paris CEDEX 15, France which are available on the Internet at http // genolist pasteur fr / Colib ⁇ / (for E.
  • nuclease acid-binding chip In the production of a nuclease acid-binding chip according to the invention for an organism not mentioned here, the associated homologous genes must therefore be identified for at least some of the genes mentioned for B lichemformis, for example by comparing the DNA sequences known for the organism concerned with those indicated here Sequences These or parts thereof (see below) can then serve as probes or as templates for the synthesis of corresponding probes, which are applied to a nucleic acid-binding chip by methods known per se
  • An essential feature of the present invention is then that the total number of different nitrogen metabolism-specific different probes does not exceed 80. This feature correlates with the stated task, according to which it should focus on such nucleic acid-binding chips, their number of assignable bursts due to their Type is comparatively low These are in particular the electrically analyzable chips
  • nitrogen-specific-change-specific probes may be, for example, those that are induced by a nitrogen excess, possibly also others that are apparently not directly related to the nitrogen metabolism, but due to this inducibility can be defined as such
  • a chip also gives a evaluable and useful in the process considered information when the lack of nitrogen, for example, has been overcome by taking appropriate countermeasures
  • nucleic acid-specific probes are usually only fragments of the complete genes (see below). In individual cases, for example in the case of regulation via splicing or large, multi-functional polypeptides, it may therefore be useful to use one and the same gene with two or more Thus, corresponding embodiments may be characterized by more than 50 probes which, however, respond to no more than these 50 genes
  • probes for further genes or gene products can also be contained on chips according to the invention (see below).
  • the core of the invention lies precisely in the specificity of the particular chip with which a specific metabolic situation should be detected.
  • the chips can be used with numerous different probes or with a representative cross section of various potentially relevant situations, such as they are provided with the application WO 2004/027092 A2, a rough overview about the state of the organism in question while a chip according to the invention is consulted for control when there is a concern that the cells in question may enter a nitrogen deficiency state
  • nucleic acid-binding chip according to the invention, which is increasingly preferably doped with the probes specified above in the order given there
  • TnrA lies between trpC and trpB according to example 5 and is accordingly preferred
  • it is a nucleic acid-binding chip according to the invention, wherein at least one, more preferably two or three of the probes are selected from the following 34 genes / are genes coding for a conserved hypothetical protein of unknown function (homologue to SEQ ID NO 19), for a putative protein (ATP B ⁇ ndungsprote ⁇ n a putative ABC transporter) encoding gene (homologue to SEQ ID NO 55), ycnJ, glnR, yvIA, yncE, yvlB, for a putative protein (putative hydrolase) encoding gene (homolog to SEQ ID NO 47), trpF, ydfS, trpD, gene coding for a putative protein (putative phage capsid protein) (homologue to SEQ ID NO 21), ycnK, trpB, trpC, for a putative protein (putative transcription protein).
  • a conserved hypothetical protein of unknown function
  • Regulator (homologue to SEQ ID NO 17), coding for a putative protein (putative sennprotease) encoding gene (homologue to SEQ ID NO 9), for a putative protein (putative glycosylhydrolase / lysozyme) of the gene (homolog to SEQ ID NO 85), for a putative protein (putative malate synthase, EC 4 1 3 2) coding gene (homolog to SEQ ID NO 45), for a putative protein (putative Na (+) - linked D- Alanine glycine permease) (homologue to SEQ ID NO 49), gene coding for a hypothetical protein of unknown function (homologue to SEQ ID NO 95), nasD, for a putative protein (putative ammonium Transporter) (homologue to SEQ ID NO 63), ycdH, nasC, for a hypothetical protein (close homolog to aldehyde dehydrogenase DhaS)
  • nucleic acid-binding chips wherein at least one, more preferably two or three of the probes are / are selected from the following 20 genes
  • UpC gene coding for a putative protein (putative transcriptional regulator) (homologue to SEQ ID NO 17), gene coding for a putative protein (homologous to SEQ ID NO 9), for a putative protein (putative glycosylhydrolase / Lysozyme) gene (homologue to SEQ ID NO 85), for a putative protein (putative malate synthase, EC 4 1 3 2) encoding gene (homologue to SEQ ID NO 45), for a putative protein (putative Na (+) - linked D-alanine glycine permease) (homologue to SEQ ID NO 49), gene encoding a hypothetical protein of unknown function (homologue to SEQ ID NO 95), nasD, gene coding for a putative protein (putative ammonium transporter) (homolog to SEQ ID NO 63), ycdH, nasC, gene encoding a hypothetical protein (close homolog to aldehyde dehydrogena
  • nucleic acid-binding chips wherein at least one, more preferably two or three of the probes are selected from the following 12 genes / nasD, gene coding for a putative protein (putative ammonium transporter) (homologue to SEQ ID NO 63), ycdH, nasC, gene encoding a hypothetical protein (close homolog to aldehyde dehydrogenase DhaS) (homologue to SEQ ID NO 15), nasB, trpE, pckA putative protein (putative nitrogen regulatory protein P-II) encoding gene (homologue to SEQ ID NO 93), nasF, yrkC, gene coding for a hypothetical protein of unknown function (homologue to SEQ ID NO 81)
  • nucleic acid-binding chips wherein at least one, increasingly preferably two or three of the probes are selected from the following 4 genes / are genes coding for a putative protein (putative nitrogen regulatory protein P-II) (homolog to SEQ ID NO 93), nasF, yrkC, gene coding for a hypothetical protein of unknown function (homologue to SEQ ID NO 81)
  • nucleic acid-binding chips according to the invention with at least 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 18, 20, 22, 24, 26 28, 30, 35, 40, 45 or 50 doped for the present invention, that is, in this sense called probes doped
  • the total number of all different probes is increasingly preferably not more than 80, 75, 70, 65, 60, 55, 50, 40, 30, 20 or 10
  • the probes referred to as being relevant to the invention are those which respond to the relevant or most highly homologous, in vivo transcribable genes from the organism selected for the bioprocess, preferably those from the relevant or most highly homologous , In vivo transc ⁇ bierbaren genes are derived just this organism
  • the genes closely related in the organism in question are used to derive corresponding probes
  • the genes closely related in the organism in question are used to derive corresponding probes
  • the organism selected for the bioprocess is a representative of unicellular eukaryotes, Gram-positive or Gram-negative bacteria
  • the unicellular eukaryotes are protozoa or fungi, including in particular yeast, very particularly Saccharomyces or Schizosaccharomyces
  • the object also includes chips according to the invention, which are directed to the monitoring of the course, in particular the growth of cell cultures of higher eukaryotes, such as rodents or humans They can be understood in some respects as at least largely single-celled eukaryotes, in particular in the Immunology have significant commercial importance, for example for the production of monoclonal antibodies
  • the gram-positive bacteria are Coryneform bacteria or those of the genera Staphylococcus, Corynebacteria or Bacillus, in particular the species Staphylococcus carnosus, Corynebacterium glutamicum, Bacillus subtilis, B licheniformis, B amyloliquefaciens, B agaradherens, B stearothermophilus, B globign or lentus, and especially B licheniformis
  • the gram-negative bacteria are those of the genera E. coli or Klebsiella, in particular derivatives of Escherichia coli K12, Escherichia coli B or Klebsiella planticola, and more particularly derivatives of the strains Escherichia coli BL21 (DE3), E. coli RV308, E. coli DH5 ⁇ , E. coli JM109, E. coli XL-1 or Klebsiella planticola (Rf)
  • nucleic acid-binding chips In preferred embodiments of nucleic acid-binding chips according to the invention, at least one, more preferably more, of the probes mentioned in connection with the invention described herein are / derived from the sequences which are listed in the Sequence Listing under the numbers SEQ ID NO 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97 and 99 are listed
  • nucleic acid-binding chips are those which are additionally doped with at least one probe for an additional gene, in particular one which is in a metabolic-related relationship to the process-related additionally-expired gene (s) , especially for one of them or this one
  • the processes under observation serve a technical interest, often associated with other specific genes.
  • the gene for that protein and, in the case of a low molecular weight compound
  • other cell-specific genes such as metabolic genes, which must be increasingly formed during the production of the product, for example a cell-derived oxidoreductase, if this is to be produced
  • Product should be obtained from a reactant or an intermediate via oxidation or reduction
  • the gene additionally expanded by the process is that for a commercially useful protein, in particular an amylase, cellulase, lipase, oxidoreductase, a hemicellulase or protease, or one which has a synthesis route for a low molecular weight chemical compound or at least partially regulated
  • bioprocesses especially fermentations, in which the said proteins are produced.
  • bioprocesses especially fermentations, in which the said proteins are produced.
  • These are commercially particularly important enzymes which are used, for example, in the food industry or the detergent industry. In the latter case, in particular for the removal of Soils caused by amylases, cellulases, lipases, hemicellulases and / or proteases are hydrolyzable, for the treatment of the materials in question, in particular by cellulases or to provide an oxidative based on an oxidative enzymatic bleaching system
  • nucleic acid-binding chips according to the invention, one, preferably several, of the probes mentioned in connection with the invention described here is / are provided in single-stranded form in the form of the codogenic strand
  • This embodiment has the aim to improve the hybridization between the probe and the sample to be detected. This is especially true in the case where the content of the relevant mRNA is actually determined from the sample because it is single-stranded and in its sequence with the coding strand the DNA matches, should an optimal hybridization with the complementary, that is the codogenic strand done
  • nucleic acid-binding chips according to the invention, one, preferably several, of the probes called relevant to the invention in the form of a DNA or of a nucleic acid analog, preferably of a nucleic acid analog, is / are made available
  • nucleic acid-binding chips according to the invention comprise / comprise one, preferably several, of the probes called relevant to the invention Gene regions which are transcribed into mRNA by the organism to be examined, in particular the gene regions which are close to the 5 'end of the mRNA
  • the aspect is taken into account that in many cases the regulatory DNA segments are also assigned to a specific gene.
  • the chip according to the invention should be used to detect the mRNA actually present in the observed cells, so that for the purpose considered here the first
  • the coding region is interrupted by sections that are not translated into mRNA Probes containing introns, therefore, were not allowed or
  • hybridization is often not necessary for the detection of an mRNA over the entire length of time. Therefore, the specific probes generally only need to comprise a smaller of the gene transcribed into mRNA. A selection of a region close to the 5 'end is advantageous for this purpose the mRNA is located, as it is first transcribed into mRNA and thus is the first to be detected after activation of the gene. This precludes timely detection
  • one or more of the probes called relevant to the invention are / are responsive to fragments of the relevant nucleic acids, in particular to those which have a low degree of secondary folding in the relevant mRNA, based on the respective total mRNA
  • one, preferably several, of the probes called relevant to the invention has a length of increasingly preferably less than 200, 150, 125 or 100 nucleotides, preferably from 20 to 60 nucleotides, particularly preferably from 45 to 55 nucleotides on
  • the probes used for the detection reaction need only to include parts of the mRNA to be detected, if the signal available on them is still specific enough This specificity, the distinctness of different mRNA sets the lower limit for the length of the respective probes and must be experimentally if necessary in preliminary experiments be determined
  • an electrical signal is triggered by the binding of the mRNA to the probe in question as being relevant to the invention
  • the time from sampling to measuring the signal for optically analyzable chips is approximately 24 hours.
  • the time required is currently less than 2 hours (see Figure 1).
  • the number of simultaneously analyzable samples is electrical evaluable chips currently in the double-digit range, but a rapid development suggests that this magnitude can be exceeded in Briefly limiting the electronic evaluation units for the various signals
  • a method for mRNA quantification established in the prior art is, for example, the RT-PCT.
  • This is described in the article "Quantification of Bacte ⁇ al mRNA by One-Step RT-PCR Using the LightCycler System "(2003) by S Tobisch, T Koburger, B Jürgen, S Leja, M Hecker and T Schweder in BIOCHEMICA, Volume 3, pages 5 to 8
  • the detection of electrical chips has another advantage, namely the higher reliability of the data, since these have significantly lower fluctuation ranges compared to RT-PCR
  • the mode of operation of electrically readable chips of a particularly preferred embodiment can be described as follows:
  • the gene-specific probes are covalently bound to magnetic carriers (beads) in known manner, which are located in chambers of the chips provided for this purpose.
  • the specific hybridization of the corresponding mRNA to the respective mRNA The beads are held in this chamber by a magnet.
  • a washing step is carried out to eliminate the non-beaded DNA probes. bound RNA, so that in the incubation only specific hybrids are still present, bound to the magnetic beads
  • a detection probe is introduced into the incubation chamber labeled with a biotin extravidin-linked alkaline phosphatase. This probe binds to a second free region of the hybridized mRNA. This hybrid is then washed again and with the alkaline phosphatase substrate para-aminophenol phosphate (pAPP) incubated The enzymatic reaction in the incubation chamber leads to the release of the redox-active product para-aminophenol (pAP) This is now passed over the Red / Ox electrode on the electrical chip and sent the signal to a potentiostat
  • System-specific software eg, MCDDE32
  • MCDDE32 reads the data obtained, and the results can be evaluated and displayed on another computer using another program (for example, Origin)
  • the detection reaction can also be carried out by another, but preferably a redox reaction because of the electrical measurement principle
  • a separate subject of the invention is thus the simultaneous use of nucleic acid or nucleic acid analog probes for at least three of the following genes kdgR, citA, for a putative protein (putative ABC transporter / amino acid permease) encoding gene (homolog to SEQ ID NO 91), htrA, ycnI, gene coding for a hypothetical protein of unknown function (homologue to SEQ ID NO 41), gene coding for a hypothetical protein of unknown function (homologue to SEQ ID NO 53), yppF, yqjN, ggt, as R, glnA, nrgA, y ⁇ C, yvtA, nrgB, gene encoding a conserved hypothetical protein of unknown function (homologue to SEQ ID NO 19), gene coding for a putative protein (ATP digestion protein of a putative ABC transporter) (homologue to SEQ ID NO 55), ycnJ, glnR, yvIA
  • these genes are selected so as to give an idea of the situation of the nitrogen metabolism of the organism under consideration, because they are as described in Examples 1 to 3 and 5 in the transition of the gram-positive bacterium to the nitrogen-deficient state be induced significantly and comparatively specifically Statements are to be expected also for other organisms, which have the homologous genes or proteins with essentially the same metabolically relevant properties
  • nucleic acid or nucleic acid analogue probes are increasingly preferred - use, wherein at least one, more preferably two or three, of the nucleic acid or nucleic acid analogue probes for genes from the following 34 genes is / are specific for a conserved hypothetical protein of unknown function gene (homologue to SEQ ID NO 19), for a putative protein (ATP B ⁇ ndungsprote ⁇ n a putative ABC T ranspor- ters) coding gene (homologue to SEQ ID NO 55), ycnJ, glnR, yvIA, yncE, yvlB, for a putative protein (putative hydrolase) encoding gene (homologue to SEQ ID NO 47), trpF, ydfS, trpD, for a putative protein (putative phage capsid protein) encoding gene ( Homolog to SEQ ID NO 21), ycnK, t
  • ycdH for a hypothetical protein (close homolog to aldehyde dehydrogenase DhaS) encoding gene (homologue to SEQ ID NO. 15), nasB, trpE, pckA, gene encoding a putative protein (putative nitrogen regulatory protein P-II) (homologue to SEQ ID NO: 93), nasF, yrkC, gene encoding a hypothetical protein of unknown function (homologue to SEQ ID NO. 81), tnrA;
  • genes from the following 20 genes trpC, for a putative protein (putative transcriptional regulator) encoding gene (homologue to SEQ ID NO. 17), for a putative protein (putative serine protease) coding gene (homolog to SEQ ID NO 9), a gene coding for a putative protein (putative glycosyl hydrolase / lysozyme) (homologue to SEQ ID NO: 85), gene coding for a putative protein (putative malate synthase, EC 4.1.3.2) (homologue to SEQ ID NO ) gene encoding a putative protein (putative Na (+) - linked D-alanine-glycine permease) (homologue to SEQ ID NO: 49), gene encoding a hypothetical protein of unknown function (homologue to SEQ ID NO: 95), nasD, gene encoding a putative protein (putative ammonium transporter) (homologue to SEQ
  • nasB for a putative protein n (putative nitrogen regulatory protein P-II) coding gene (homolog to SEQ ID NO. 93), nasF, yrkC, gene encoding a hypothetical protein of unknown function (homologue to SEQ ID NO: 81), tnrA;
  • genes from the following 12 genes nasD, for a putative protein (putative ammonium transporter) coding gene (homologue to SEQ ID NO. 63), ycdH, nasC, for a hypothetical protein (close homolog to aldehyde DhaSha gene encoding gene (homologue to SEQ ID NO: 15), nasB, trpE, pckA, gene coding for a putative protein (putative nitrogen regulatory protein P-II) (homologue to SEQ ID NO: 93), nasF, yrkC, gene encoding a hypothetical protein of unknown function (homologue to SEQ ID NO: 81);
  • genes from the following 4 genes gene encoding a putative protein (putative nitrogen regulatory protein P-II) (homologue to SEQ ID NO: 93), nasF, yrkC, gene coding for a hypothetical protein of unknown function (Homologue to SEQ ID NO. 81).
  • they are preferably uses according to the invention of simultaneously at least 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 35, 40 , 45 or 50 of said probes.
  • they are preferably uses according to the invention, wherein the total number of all different probes is increasingly preferably not more than 80, 75, 70, 65, 60, 55, 50, 40, 30, 20 or 10
  • probes are derived from the sequences which are listed in the sequence listing under the numbers SEQ ID NO 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97 and 99 are listed
  • a separate subject of the invention are methods of determining the physiological state of an organism passing through a biological process by using a nucleic acid-binding chip according to the invention
  • nucleic acid-binding chips apply correspondingly to the method of determining the physiological state of an organism passing through a biological process
  • a change in the nitrogen metabolism of the organism passing through the biological process is determined, preferably a nitrogen deficiency state
  • the organism selected for the bioprocess is a representative of unicellular eukaryotes, Gram-positive or Gram-negative bacteria
  • the unicellular eukaryotes are protozoa or fungi, including in particular yeast, especially Saccharomyces or Schizosaccharomyces
  • the gram-positive bacteria being Coryneform bacteria or those of the genera Staphylococcus, Corynebacteria or Bacillus, in particular the species Staphylococcus carnosus, Corynebacterium glutamicum, Bacillus subtilis, B lichemformis, B amyloliquefaciens , B agaradherens, B stearothermophilus, B globign or Lentus, and especially B lichenemis
  • the Gram-negative bacteria being those of the genera E. coli or Klebsiella, in particular derivatives of Escherichia coli K12, Escherichia coli B or Klebsiella planticola, and more particularly derivatives of strains Escherichia coli BL21 (DE3), E. coli RV308, E. coli DH5 ⁇ , E. coli JM109, E. coli XL-1 or Klebsiella planticola (Rf)
  • such methods according to the invention are preferred, using those of the named probes which are of the SEQ ID NO. 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21 given in the sequence listing.
  • such methods according to the invention are preferred, wherein the determination of the physiological state is carried out at different points in time of the same process, preferably using a plurality of identically constructed nucleic acid-binding chips, particularly preferably the same nucleic acid-binding chip
  • such processes according to the invention are furthermore preferred, the process being a fermentation, in particular the fermentative production of a commercially useful product, more preferably the production of a protein or a low-molecular chemical compound
  • the low-molecular chemical compound is a natural substance, a food supplement or a pharmaceutically relevant compound
  • the protein is an enzyme, in particular one of the group of ⁇ -amylases, proteases, cellulases, lipases, oxidoreductases, peroxidases, laccases, oxidases and hemicellulases
  • nucleic acid-binding chips according to the invention, as described in detail above, for determining the physiological state of an organism passing through a biological process
  • nucleic acid-binding chips apply correspondingly to the uses described herein for the determination of the physiological state of an organism passing through a biological process According to the above, such uses according to the invention are preferred, wherein a change in nitrogen metabolism of the organism passing through the biological process is determined, preferably a nitrogen deficiency state
  • the organism selected for the bioprocess is a representative of unicellular eukaryotes, Gram-positive or Gram-negative bacteria
  • the unicellular eukaryotes being protozoa or fungi, in particular yeast, especially Saccharomyces or Schizosaccharomyces
  • the Gram-positive bacteria being Coryneform bacteria or those of the genera Staphylococcus, Corynebacteria or Bacillus, in particular the species Staphylococcus carnosus, Corynebacterium glutamicum, Bacillus subtilis, B licheniformis, B amyloliquefaciens, B agaradherens, B stearothermophilus, B globign or B lentus, and especially B licheniformis
  • the Gram-positive bacteria being Coryneform bacteria or those of the genera Staphylococcus, Corynebacteria or Bacillus, in particular the species Staphylococcus carnosus, Corynebacterium glutamicum, Bacillus subtilis, B licheniformis, B amyloliquefaciens, B agaradherens, B stearothermophilus, B globign or B lentus, and especially B licheniformis
  • the Gram-negative bacteria being those of the genera E. coli or Klebsiella, in particular derivatives of Escherichia coli K12, Escherichia coli B or Klebsiella planticola, and more particularly derivatives strains Escherichia coli BL21 (DE3), E. coli RV308, E. coli DH5 ⁇ , E. coli JM109, E. coli XL-1 or Klebsiella planticola (Rf)
  • the process being a fermentation, in particular the fermentative production of a commercially useful product, more preferably the production of a protein or a low-molecular chemical compound
  • the low-molecular chemical compound is a natural substance, a food supplement or a pharmaceutically relevant compound
  • the protein is an enzyme, in particular one from the group of ⁇ -amylases, proteases, cellulases, lipases, oxidoreductases, peroxidases, laccases, oxidases and hemicellulases
  • the cell disruption was carried out with the "Hybaid RiboLyser TM Cell Disruptor” (Fa Thermo Electron Corporation, Dreieich, Germany) This method is based on the mechanical destruction of the cell wall and the cell membrane with the help of 0.1 mm small glass beads (Sartonus BBI, Melsungen , Germany)
  • the cells to be disrupted which had previously been resuspended in lysis buffer II (3 mM EDTA, 200 mM NaCl), together with the glass beads, were placed in a glass
  • acidic phenol was added to avoid degradation of the RNA by RNases. This tube was then clamped into the ribo-lyser, whereby under heavy debris, the glass beads collided with the cells, causing cell disruption
  • RNA-containing aqueous phase is separated by centrifugation from the protein and cell fragments, the chromosomal DNA and the glass beads, and from this the RNA is purified using the instrument KmgFisher ml_ (Thermo Electron Corporation, Dreieich, Germany) using the MagNA Pure LC RNA Isolation Kit I (Fa Roche Diagnostics, Penzberg, Germany) isolated This purification is based on the binding of RNA to magnetic glass particles in the presence of chaotropic salts, which also cause the inactivation of RNases.
  • the magnetic particles serve as transport of RNA between different reaction vessels filled with binding, washing and elution buffers
  • the used KmgFisher mL is a type of pipetting robot that uses magnets to transport the particles with the bound RNA between the vessels and also uses them for mixing the samples
  • the RNA is separated from the magnetic Particles dissolved and is purified
  • RNA 6000 Nano Kit from Agilent
  • ⁇ bosomal RNA (16 S and 23 S rRNA) is detected. These sites appear as clear bands It can be assumed that the RNA was not degraded in the course of processing and is therefore intact and can be introduced into the subsequent investigations. In addition, the exact concentration is also determined
  • the transcriptome analyzes were carried out using genomic slicheniformis DSM13 DNA microarrays, which had been prepared in a conventional manner (for example according to WO 95/11995 A1) and can be evaluated by an optical system. On these DNA microarrays, almost every gene was from B licheniformis in duplicate, so that two samples could be analyzed in parallel on the same chip and the values obtained could be averaged
  • the principle of the measurement carried out is that the respective mRNA molecules are transcribed from the sample removed in vitro via reverse transcription into DNA, wherein one of the added deoxynucleotides carries a color marker.
  • DUTP was chosen for this labeling, which was labeled with the fluorescent dye cyanine 3 or with cyanine 5.
  • the fluorescent dye cyanine 3 Fa Amersham Biosciences Europe GmbH, Freiburg, Germany
  • 25 ⁇ g total RNA of the respective stress test transient phase, 30, 60, 90 and 120 mm
  • the fluorescent dye cyanine 5 GE Healthcare, Freiburg, Germany
  • the DSMIS DNA microarray was performed for at least 16 hours at 42 ° C
  • the optical readout of the arrays was performed using the ScanArray® Express Laser Scanner (PerkinElmer Life and Analytical Sciences, Rodgau-Jugesheim, Germany). All hybridizations were repeated using the samples with the other dye The quantitative evaluation of the arrays was performed using the ScanArray® Express software (available from PerkinElmer Life and Analytical Sciences Rodgau-Jugesheim, Germany) according to the manufacturer's instructions and under standard parameters
  • the arrays were normalized and evaluated With the help of this "score card", which serves to control the efficiency and quality of the hybridization, were according to the manufacturer's information known control DNA and so-called spikes in the form of oligos were applied to the array and hybridized with complementary sequences in the hybridization Thus, one could control the success of hybridization and incorporation of the dyes after scanning
  • the controls should be present in both samples in the same amount and thus after appear yellow or have a ratio between both channels of 1, respectively.
  • the spikes are specific to the respective sample and are applied in different dilutions, ie they appear red or green after scanning for the respective sample
  • mean values from the two hybridizations and the respective standard deviations were calculated.
  • the following threshold values for the ratio of the amount of RNA of the respective gene to the control value are considered:
  • the genes whose RNA has a ratio of> 3 (ie at least one tripling) are considered as induced; clearly repressed are genes with an RNA ratio ⁇ 0.3 (that is, a lowering to less than 30%).
  • Table 1 below lists all the 210 genes of Bacillus licheniformis DSM13 determined in Example 1 whose induction (amounting to at least the factor 3) was observed under the conditions of the nitrogen deficiency described in Example 1.
  • the respective name of the derived protein or (if available) its abbreviation are given; the "BLi number” corresponds to the "locusjag" of entry AE017333 (bases 1 to 4,222,645) in the GenBank database (National Center for Biotechnology Information NCBI, National Institutes of Health, Bethesda, MD, USA; http: // /www.ncbi.nlm.nih.gov, as of December 2, 2004) of the entire genome of ß. licheniformis; This is followed by the factors observed at the times indicated above for increasing the concentration of the respectively associated mRNAs.
  • Example 1 The determined in Example 1 210 genes of Bacillus licheniformis DSM13, whose (at least the factor of 3 amounts) induction was observed under nitrogen deficiency (for explanations: see text).
  • Example 1 Under the conditions of the nitrogen deficiency described in Example 1 at any of the measured times, a total of 67 of the Bacillus licheniformis DSM 13 genes examined in Example 1 were induced by at least a factor of 8 have been induced to lack at least one other compound (data not shown) and therefore can not be considered as specific signals for nitrogen deficiency
  • Table 3 The 49 genes of Bacillus licheniformis DSM13 determined in Example 1 whose nitrogen-induced induction at any of the measured times was at least 8 times, in descending order of the maximum value measured in each case (last column).
  • Example 1 and Example 2 For this purpose, dilutions of known concentrations of / n-wfro transc ⁇ ten the mRNA determined in Example 1 and Example 2 were measured using the LightCycler and then using the device-specific software created the standard curve For this purpose, had to be selected in advance for each mRNA to be examined specific primer (with the help of the software "Array Designer", available from PREMIER Biosoft International, Paolo Alto, USA), which enable synthesis of / n-prtro transcripts and PCR amplification in the LightCycler.
  • Array Designer available from PREMIER Biosoft International, Paolo Alto, USA
  • the measurement started in the LightCycler.
  • two different dilutions were used for each sample to be analyzed.
  • the specific transcript was then amplified with the respective primers and the incorporation of the dye was measured.
  • TnrA is that shown in SEQ ID NO. 99 shown gene for a global, on the nitrogen metabolism regulation involved transcriptional regulator (indication in the sequence protocol: tnrA - transcriptional pleiotropic regulator involved in global nitrogen regulation - BLi 01490).
  • This 333 bp gene is from ß. licheniformis DSM 13 and recorded in the above database under number BLi 01490.
  • the deduced amino acid sequence is shown under SEQ ID NO. 100 indicated.
  • the gene-specific primers were derived using the Array Designer 2.0 program (PREMIER Biosoft International, Paolo Alto, USA) and purchased from Invitrogen (Karlsruhe, Germany).
  • Array Designer 2.0 program PREMIER Biosoft International, Paolo Alto, USA
  • Invitrogen Karlsruhe, Germany
  • an external standard curve was generated by means of an / n-weekly transcript.
  • the generation of the / nw ' fro transcript was carried out using a T7 polymerase, the gene-specific PCR product and the "DIG RNA Labeling" kit (Roche Diagnostics, Penzberg, Germany) / ⁇ -wfro transcripts were determined photometrically.
  • a dilution series (1 ng to 100 fg final concentration) of the / nw ' fro transcript was prepared and with MS2 RNA (final concentration 0.5 ⁇ g / ⁇ l; Roche Diagnostics) the forward and reverse primers and the LightCycler RNA master -SYBR Green 1 kit (Roche Diagnostics) as master mix, according to manufacturer's instructions, mixed.
  • the standard curve for the specific gene was generated using the manufacturer's protocol for the RNA master SYBRGreen I kit (Amplification, Segment 2, Temperature: 57 ° C; Amplification, segment 3, incubation time: 16 s).
  • the result of the LightCycler run was evaluated using the LightCycler software and the second-derivative-maximum method, and the quality of the RT-PCR products was checked by melting point determination.
  • RNA samples For the measurements of the RNA samples, dilution levels of 500 ng to 5 ng of the total RNA were prepared and with MS2-RNA (final concentration 0.5 ⁇ g / ⁇ l), the specific primer pairs and the LightCycler-RNA-Master-SYBR-Green I -Kit mixed. For the real-time RT-PCR run with the LightCycler device, the same conditions were used as those used to create the standard curve.
  • the negative control was RNase-free water with MS2 RNA at a final concentration of 0.5 ⁇ g / ⁇ l. A selected dilution of a sample from the standard curve was carried during each LightCycler run.
  • the evaluation of the LightCycler measurements was carried out with the LightCycler-specific software. Using the standard curve and the second-derivative-maximum method, it was possible to determine the molecular amounts of the specific RNA in the sample measured.
  • Table 4 Real-time RT-PCR quantification of the genes glnA, nrgB and tnrA with the entry of a nitrogen deficiency and the associated transition into the stationary phase
  • Figure 1 Schematic representation of / W - // ⁇ e monitoring a bioprocess with electrical DNA chips according to the invention
  • nucleic acids for example DNA
  • nucleic acid analogs for example, compounds which are difficult to hydrolyze, analogously constructed

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Abstract

L'invention concerne des puces liant les acides nucléiques, destinées à contrôler des processus biologiques, notamment à détecter des états de carence en azote. Lesdites puces portent des sondes destinées à au moins trois des 50 gènes suivants : kdgR, citA, htrA, ycnl, yppF, trpB, ggt, alsR, glnA, nrgA, yciC, yvtA, nrgB, ycnJ, glnR, yvIA, yncE, yvlB, trpF, ydfS, trpD, ycnK, trpB, trpC, nasD, ycdH, nasC, nasB, trpE, pckA, nasF, yrkC et tnrA ou des homologues de SEQ ID NO. 91, 41 , 53, 19, 55, 47, 21 , 17, 9, 85, 45, 49, 95, 63, 15, 93 ou 81, avec au maximum 80 sondes différentes, spécifiques au métabolisme d'azote. L'invention concerne également l'utilisation de sondes génétiques correspondantes, notamment sur de telles puces, ainsi que des procédés correspondants et des possibilités d'utilisation.
EP06791904A 2005-09-08 2006-09-07 Puces liant les acides nucleiques, destinees a detecter des etats de carence en azote dans le cadre du controle de processus biologiques Withdrawn EP1924711A2 (fr)

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DE102005042572A DE102005042572A1 (de) 2005-09-08 2005-09-08 Nukleinsäure-bindende Chips zur Detektion von Stickstoffmangelzuständen im Rahmen der Bioprozeßkontrolle
PCT/EP2006/008726 WO2007028608A2 (fr) 2005-09-08 2006-09-07 Puces liant les acides nucleiques, destinees a detecter des etats de carence en azote dans le cadre du controle de processus biologiques

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US7115364B1 (en) * 1993-10-26 2006-10-03 Affymetrix, Inc. Arrays of nucleic acid probes on biological chips
DE19916867A1 (de) * 1999-04-14 2000-10-19 Fraunhofer Ges Forschung Anordnung und Verfahren zur Herstellung planarer Arrays mit immobilisierten Molekülen
DE19916921A1 (de) * 1999-04-14 2000-10-19 Fraunhofer Ges Forschung Elektrisches Sensorarray
EP1313856B1 (fr) * 2000-08-31 2007-03-21 Degussa GmbH Gene citb issu d'une bacterie coryneforme et son utilisation dans la synthese d'acides l-amines
EP1315744A1 (fr) * 2000-09-09 2003-06-04 Degussa AG Sequences nucleotidiques codant le gene clpc
EP1355931A2 (fr) * 2000-10-06 2003-10-29 Novozymes Biotech, Inc. Methodes de surveillance de l'expression genetique multiple
DE10058394C1 (de) * 2000-11-24 2002-07-11 Siemens Ag Verfahren für die biochemische Analytik und zugehörige Anordnung
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DE102004061664A1 (de) * 2004-12-22 2006-07-06 Henkel Kgaa Nukleinsäure-bindende Chips zur Detektion von Phosphatmangelzuständen im Rahmen der Bioprozesskontrolle

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