EP1135144A1 - Compositions et methodes de regulation de la pathogenese bacterienne - Google Patents

Compositions et methodes de regulation de la pathogenese bacterienne

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Publication number
EP1135144A1
EP1135144A1 EP99963011A EP99963011A EP1135144A1 EP 1135144 A1 EP1135144 A1 EP 1135144A1 EP 99963011 A EP99963011 A EP 99963011A EP 99963011 A EP99963011 A EP 99963011A EP 1135144 A1 EP1135144 A1 EP 1135144A1
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EP
European Patent Office
Prior art keywords
autoinducer
harveyi
typhimurium
seq
alteration
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EP99963011A
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German (de)
English (en)
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EP1135144A4 (fr
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Bonnie Princeton University BASSLER
Michael G. Surette
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University Technologies International Inc
Princeton University
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Princeton University
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/12—Ketones
    • A61K31/121—Ketones acyclic
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/04—Antibacterial agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • This invention relates to the field of bacterial diseases of humans and other mammals.
  • the invention provides novel genes and signaling factors involved in inducing pathogenesis in certain bacteria, and methods for controlling such pathogenesis through manipulation of those factors and genes.
  • the autoinducer synthase is encoded by a gene homologous to luxl of V. fischeri , and response to the autoinducer is mediated by a transcriptional activator protein encoded by a gene homologous to luxR of V. fischeri (Bassler and Silverman, in Two component Signal
  • V. harveyi has two independent density sensing systems (called Signaling Systems 1 and 2), and each is composed of a sensor-autoinducer pair.
  • V. harveyi Signaling System 1 is composed of Sensor 1 and autoinducer 1 (AI-1) , and this autoinducer is N- (3-hydroxybutanoyl) -L-homoserine lactone (see Bassler et al . , Mol. Microbiol. 9: 773-786, 1993).
  • harveyi Signaling System 2 is composed of Sensor 2 and autoinducer 2 (AI-2) (Bassler et al . , Mol. Microbiol. 13 : 273-286, 1994) .
  • AI-2 autoinducer 2
  • Signaling System 1 is a highly specific system proposed to be used for intra-_ - - species communication and Signaling System 2 appears to be less species-selective, and is hypothesized to be for inter- species communication (Bassler et al . , J. Bacteriol . 179 : 4043-4045, 1997) .
  • V. harveyi reporter strains have been constructed that are capable of producing light exclusively in response to AI-1 or to AI-2 (Bassler et al . , 1993, supra ; Bassler et al . , 1994, supra) .
  • V. harveyi reporter strains have been used to demonstrate that a few species of bacteria produce stimulatory substances that mimic the action of AI-2 (Bassler et al . , 1997, supra) .
  • the signaling molecule is expected to stimulate a variety of pathogenesis related genes in the bacterial species that produce it.
  • a highly purified form of the signaling molecule is provided in the present invention.
  • the present invention provides an isolated bacterial extracellular signaling factor comprising at least one molecule that is polar and uncharged, and having an approximate molecular weight of less than 1,000 kDa, wherein said factor interacts with LuxQ protein thereby inducing expression of a Vibrio harveyi operon comprising luminescence genes luxCDABE.
  • the factor possesses a specific activity wherein about 0.1 to 1.0 mg of a preparation of the factor stimulates about a 1, 000-fold increase in — "" luminescense, as measured in a bioassay using a V. harveyi Sensor 2+ reporter strain.
  • the factor is purified in such a way that it possesses a specific activity wherein about 1 to 10 ⁇ g of a preparation of the factor stimulates about a 1, 000-fold increase in luminescence, as measured in a bioassay using a V. harveyi Sensor 2+ reporter strain.
  • the signaling factor of the invention is produced by a variety of bacteria, including but not limited to: Vi rio harveyi , Vibrio cholerae, Vibrio parahaemolyticus, Vibrio alginolyticus, Pseudomonas phosphoreum, Yersinia enterocoli tica, Escherichia coli , Salmonella typhimurium, Haemophilus influenzae, Helicobacter pylori , Bacillus subtilis, Borrelia burg f dor feri , Neisseria meningi tidis, Neisseria gonorrhoeae, Yersinia pestis, Campylobacter jejuni , Deinococcus radiodurans, Mycobacterium tuberculosis , Enterococcus faecalis, Streptococcus pneumoniae, Streptococcus pyogenes and Staphylococcus aureus
  • the invention provides an isolated bacterial signaling factor having the formula:
  • the invention provides a method for identifying a compound that regulates the activity of a signaling factor by contacting the signaling factor with the compound, measuring the activity of the signaling factor in the presence of the compound and comparing the activity of the signaling factor obtained in the presence of the compound to the activity of the signaling factor obtained in the absence of the compound and identifying a compound that regulates the activity of the signaling factor.
  • the invention provides a method for detecting an autoinducer molecule in a sample by contacting the sample with a bacterial cell, or extract thereof, comprising biosynthetic pathways that produce a detectable amount of light in response to an exogenous autoinducer, the bacterial cell having at least two distinct alterations in gene loci that participate in autoinducer pathways, wherein a first alteration in a gene locus comprises an alteration that inhibits detection of a first autoinducer and wherein a second alteration in a gene locus comprises an alteration that inhibits production of a second autoinducer and measuring light produced by the bacterial cell, or extract thereof.
  • the invention provides a bacterial cell having at least two distinct alterations in gene loci that participate in autoinducer pathways, wherein a first alteration in a gene locus comprises an altera -ioh " that inhibits detection of a first autoinducer and wherein a second alteration in a gene locus comprises an alteration that inhibits production of a second autoinducer and wherein the cell is bioluminescent when contacted with an autoinducer.
  • the invention provides a method for identifying an autoinducer analog that regulates the activity of an autoinducer by contacting a bacterial cell, or extract thereof, comprising biosynthetic pathways which will produce a detectable amount of light in response to an autoinducer with an autoinducer analog and comparing the amount of light produced by the bacterial cell, or extract thereof, in the presence of an autoinducer with the amount produced in the presence of the autoinducer analog, wherein a change in the production of light is indicative of an autoinducer analog that regulates the activity of an autoinducer.
  • the invention provides a method for producing autoinducer-2 by contacting S-adenosylhomo- cysteine (SAH) with a LuxS protein under conditions and for such time as to promote the conversion of S-adenosylhomo- cysteine to autoinducer-2.
  • SAH S-adenosylhomo- cysteine
  • the invention provides a method for producing autoinducer-2 by contacting S-ribosylhomo- cysteine (SRH) with a LuxS protein under conditions and for such time as to promote the conversion of S- ribosylhomocysteine to autoinducer-2.
  • S-ribosylhomo- cysteine S-ribosylhomo- cysteine
  • the invention provides A method for producing autoinducer-2 by contacting S-adenosylhomo- cysteine (SAH) with a 5 ' -methylthioadenosine/S-adenosylhomo- cysteine nucleosidase protein under conditions and for such time as to promote the conversion of S-adenosylhomocysteine to S-ribosylhomocysteine; contacting the above-described S- ribosylhomocysteine with a LuxS protein under conditions and for such time as to promote the conversion of S- ribosylhomocysteine to autoinducer-2.
  • SAH S-adenosylhomo- cysteine
  • a 5 ' -methylthioadenosine/S-adenosylhomo- cysteine nucleosidase protein under conditions and for such time as to promote the conversion of S-adenosylhomocystein
  • the invention provides a method for detecting an autoinducer-associated bacterial biomarker by contacting at least one bacterial cell with an autoinducer molecule under conditions and for such time as to promote induction of a bacterial biomarker and detecting the bacterial biomarker.
  • the invention provides a method for detecting a target compound that binds to a LuxP protein by contacting the LuxP protein with the target compound and detecting binding of the compound to LuxP.
  • the invention provides a method for regulating bacterial biofilm formation comprising contacting a bacterium capable of biofilm formation with a compound capable of regulating biofilm formation, wherein the compound regulates autoinducer-2 activity. — ⁇ "
  • a method is provided for purifying the aforementioned bacterial extracellular signaling factor.
  • the method comprises the steps of: (a) growing, in a culture medium, bacterial cells that produce the signaling molecule; (b) separating the bacterial cells from the culture medium; (c) incubating the bacterial cells in a solution having high osmolarity, under conditions that permit production and secretion of the signaling molecule from the bacterial cells; (d) separating the bacterial cells from the high osmolarity solution; and (e) purifying the factor from the high osmolarity solution.
  • the method may further comprise: (f) separating polar factors from non-polar factors in an evaporated sample of the high osmolarity solution; and (g) subjecting the polar factors to reverse-phase High Performance Liquid Chromatography.
  • the high osmolarity solution comprises at least 0.4 M monovalent salt, most preferably 0.4 - 0.5 M NaCl.
  • the method further comprises growing the bacterial cells in a culture medium containing a carbohydrate selected from the group consisting of glucose, fructose, mannose, glucitol, glucosamine, galactose and arabinose.
  • an isolated nucleic acid molecule which encodes a protein necessary for biosynthesis of a bacterial - ⁇ " extracellular signaling factor that induces expression of a Vibrio harveyi LuxQ luminescence gene.
  • the nucleic acid molecule may be isolated from a wide variety of bacteria, including but not limited to: Vibrio harveyi , Vibrio cholera, Salmonella typhimurium, Escherichia coli ,
  • the aforementioned nucleic acid molecule encodes a protein having between about 150 and 200 amino acid residues.
  • the encoded protein comprises an amino acid sequence substantially the same as a sequence selected from the group consisting of any of SEQ ID NOS: 10 - 17, or a consensus sequence derived from a comparison of two or more of SEQ ID NOS: 10-17.
  • the nucleic acid molecule preferably has a sequence substantially the same as a sequence selected from the group consisting of any of SEQ ID NOS : 1 - 9, or a consensus sequence derived from a comparison of two or more of SEQ ID NOS: 1-9.
  • FIG. 1 Signaling substance from E. coli AB1157 and S . typhimurium LT2 cell-free culture fluids that induces luminescence in V. harveyi .
  • the responses of V. harveyi reporter strains BB170 (Sensor 1 " , Sensor 2 + ) (Fig. 1A) , and BB886 (Sensor 1 + , Sensor 2 " ) (Fig. IB) to signaling substances present in cell-free culture fluids from E. coli , S . typhimurium and V. harveyi strains are shown.
  • a bright culture of each reporter strain was diluted 1:5000 into fresh medium, and the light production per cell was then measured during the growth of the diluted culture.
  • V. harveyi cell -free spent culture fluids were added at a final concentration of 10% (v/v) at the start of the experiment.
  • the data for the 5 hour time point are shown and are presented as the percent of the activity obtained when V. harveyi cell -free spent culture fluids are added.
  • Abbreviations used for the different strains are: V.h; Vijbrio harveyi , S.t; Salmonella typhimurium, and E.c; Escherichia coli .
  • Figure 2 Active secretion of the signaling molecule by viable E. coli and S. typhimurium . The response of the V.
  • V. harveyi reporter strain BB170 (Sensor 1 " , Sensor 2 + ) to a signaling substance produced and secreted by E. coli AB1157 and S . typhimurium LT2 but not E. coli DH5 is shown.
  • V. harveyi reporter strain BB170 was diluted 1:5000 in AB medium and light output per cell was monitored _duari ⁇ g growth.
  • 1 X 10 6 E. coli AB1157, S. typhimurium LT2 or E. coli DH5 washed and resuspended viable cells (left-hand, white bars) or UV- killed cells (right-hand, black bars) was added.
  • cell -free culture fluids were prepared and assayed for signaling activity in the luminescence stimulation assay (Bars) , and the concentration of glucose remaining (circles) .
  • the cell number was determined at each time by diluting and plating the S. typhimurium LT2 on LB medium and counting colonies the next day (squares) .
  • the signaling activity is presented as the percent of the activity obtained when V. harveyi cell-free spent culture fluids are added. These data correspond to the 5 h time point in the luminescence stimulation assay.
  • the glucose concentration is shown as % glucose remaining.
  • Cell number is cells/ml x 10 " .
  • the symbol ⁇ indicates that the time axis is not drawn to scale after 8 h. — Figure 4.
  • V. harveyi reporter strain BB170 (Sensor 1 " , Sensor 2 + ) was tested for its response to the addition of exogenous AI-2 made by V. harveyi strain BB152 (AI-1 " , AI-2 + ) and to that made by S. typhimurium LT2.
  • a bright culture of the reporter strain was diluted 1:5000 and either 10% (v/v) growth medium (closed circles) , cell-free culture fluid from V. harveyi BB152 grown overnight in AB (open circles) , or cell-free culture fluid from S. typhimurium LT2 grown for 6 h on LB +
  • RLU denotes relative light units and is defined as (counts min X 10 )/ (colony-forming units ml ) .
  • S . typhimurium LT2 was subjected to a variety of treatments after which cell-free culture fluids or osmotic shock fluids were prepared. These preparations were added to a diluted culture of the V. harveyi AI-2 reporter strain BB170 at 10% (v/v) and light output was measured thereafter. Fold activation is the level of light produced by the reporter following addition of the specified S . typhimurium preparation divided by the light output of the reporter when growth medium alone was added.
  • the bars in Fig. 5A represent cell -free fluids prepared from S .
  • typhimurium were pre-grown at 30°C for 6 h in LB containing 0.5% glucose, then pelleted and resuspended for 2 h under the following conditions: LB; in LB at 30°C, LB+Glc; in LB + 0.5% glucose at 30°C, LB pH 5; in LB at pH 5.0 at 30°C, 0.4M NaCl; in 0.4M NaCl at 30°C, 0.1M NaCl; in 0.1M NaCl at 30°C, and Heat Shock 43°; in LB + 0.5% glucose at 43°C. After these two hour treatments, cell -free fluids were prepared from each sample and assayed.
  • FIG. 6 S. typhimurium signaling activity in limiting and non-limiting concentrations of glucose.
  • S. typhimurium LT2 was grown in LB in the presence of limiting (0.1%) and non-limiting (1.0%) concentrations of glucose.
  • the activity present in the cell-free culture fluids black bars
  • the increase in signaling activity measured in the 0.4M NaCl osmotic shock fluids prepared from the same cells is shown as the white bars on top of the black bars. These data are also normalized for 1 X 10 9 cells.
  • the signaling activity for limiting glucose is shown in Figs. 6A, 6C, and 6E, and that for non-limiting glucose is shown in Figs.
  • Figs. 6A and 6B also show the percent glucose remaining (triangles)
  • Figs. 6C and 6D show the cell number (squares)
  • Panels E and F show the pH (circles) at each time point.
  • Figure 7. Effects of glucose and pH on signal production by S. typhimurium.
  • the quorum sensing signal released by S . typhimurium LT2 was measured when the cells were grown in LB medium containing 0.5% glucose at pH 7.2 (Fig. 7A, bars) , and when the cells were grown in LB at pH
  • FIG. 9A shows a restriction map of the V. harveyi luxS v h chromosomal region which was defined by Tn5 insertion. The sites of Tn5 insertions that disrupted the AI-2 production function and one control Tn5 insertion outside of the luxS v h , locus are shown (triangles).
  • Fig. 9B depicts the ygaG region in the E.
  • V. harveyi and S . typhimurium strains Cell-free culture fluids from V. harveyi and S . typhimurium strains were prepared and tested for AI-2 activity in the V. harveyi BB170 bioassay.
  • Fig. 10A AI-2 production phenotypes of the wild type V. harveyi strain MM28 which contains a Tn5 insertion outside of luxS Vt h _ (denoted WT) and the luxS v _ h - : :Tn5 mutant strain MM30 (denoted luxS ⁇ ) .
  • Fig. 10B AI-2 production phenotypes of wild type S.
  • typhimurium LT2 (denoted WT) and the ygaG: :MudJ insertion mutant strain CS132 (denoted ygaG ' ) .
  • Activity is reported as fold- induction of luminescence expression of the V. harveyi BB170 reporter strain over that when sterile medium was added.
  • FIG. 11A AI-2 activity in cell- free fluids from wild type V. harveyi BB120, E. coli
  • Fig. 11B Complementation of S . typhimurium CS132 ⁇ ygaG: :MudJ
  • Fig. 11C Complementation of E. coli DH5.
  • the in trans AI-2 production genes are the following: vector control (denoted: none), E. coli 0157:H7 ygaG; and V. harveyi BB120 luxS ⁇ ⁇ .
  • E. coli and V. harveyi are abbreviated E. c . and V. h . respectively.
  • FIG. 12 Alignment of LuxS and YgaG protein sequences.
  • the translated protein sequences for the AI-2 production family of proteins are shown.
  • the S. typhimurium LT2 ygaG (re-named herein luxS s , t , partial sequence came from the S . typhimurium database.
  • the site of the frame shift mutation in the E. coli DH5 DNA sequence is denoted by an "*".
  • the 20 altered amino acid residues that are translated following the frame shift are enclosed by the box.
  • FIG. 13 A diagram of the hybrid quorum sensing circuit of Vibrio harveyi is provided.
  • the AI-1 and AI-2 circuits are independently stimulated but integrate their signals for light expression. Each pathway, however, is also independently competent to generate light. This allows for reciprocal mutations in the LuxN or LuxQ sensors to be used to construct a reporter specific for AI-2 or AI-1, respectively.
  • Figure 14 Response phenotypes of V. harveyi wild- type and lux regulatory mutants.
  • cell-free culture fluids (10%) , or nothing (N.A) was added.
  • Relative light units are defined as cpm x 10 3 /CFU/ml.
  • FIG. 1 A diagram of the biosynthetic pathway of autoinducer-2 (AI-2) is shown.
  • FIG. 16 The structure of AI-2 and the biosynthetic precursors from which AI-2 is derived are shown . - DETAILED DESCRIPTION OF THE INVENTION
  • an extracellular signaling factor produced by several strains of pathogenic bacteria, including Salmonella typhimurium and Escherichia coli , which has a role in regulating the pathogenesis or virulence of these bacteria.
  • Salmonella typhimurium and Escherichia coli which has a role in regulating the pathogenesis or virulence of these bacteria.
  • the purification and/or cloning of this signaling molecule and the genes that encode proteins that catalyze its biosynthesis open a new avenue for drug design aimed at either inhibition of production of or response to this molecule by bacteria. Drugs designed to interfere with signaling by this molecule will constitute a new class of antibiotics.
  • the invention further provides methods for detecting an autoinducer and methods for the in vitro production of autoinducr-2.
  • isolated nucleic acid refers to a DNA molecule that is separated from sequences with which it is immediately contiguous (in the 5' and 3' directions) in the naturally occurring genome of the organism from which it was derived.
  • the "isolated nucleic acid” may comprise a DNA molecule inserted into a vector, such as a plasmid or virus vector, or integrated into the genomic DNA of a procaryote or eucaryote.
  • An “isolated nucleic acid molecule” may also comprise a cDNA molecule.
  • isolated nucleic acid primarily refers to an RNA molecule encoded by an isolated DNA molecule as defined above. Alternatively, the term may refer to an RNA molecule that has been sufficiently separated from RNA molecutes * with which it would be associated in its natural state (i.e., in cells or tissues) , such that it exists in a “substantially pure” form (the term “substantially pure” is defined below) .
  • isolated protein or “isolated and purified protein” is sometimes used herein. This term refers primarily to a protein produced by expression of an isolated nucleic acid molecule of the invention. Alternatively, this term may refer to a protein which has been sufficiently separated from other proteins with which it would naturally be associated, so as to exist in "substantially pure” form.
  • substantially pure refers to a preparation comprising at least 50-60% by weight the factor of interest (e.g., pathogenesis signaling factor, nucleic acid, oligonucleotide, protein, etc.). More preferably, the preparation comprises at least 75% by weight, and most preferably 90-99% by weight, the factor of interest. Purity is measured by methods appropriate for the factor of interest (e.g. chromatographic methods, agarose or polyacrylamide gel electrophoresis, HPLC analysis, and the like) .
  • the factor of interest e.g., pathogenesis signaling factor, nucleic acid, oligonucleotide, protein, etc.
  • the preparation comprises at least 75% by weight, and most preferably 90-99% by weight, the factor of interest. Purity is measured by methods appropriate for the factor of interest (e.g. chromatographic methods, agarose or polyacrylamide gel electrophoresis, HPLC analysis, and the like) .
  • the term "immunologically specific” refers to antibodies that bind to one or more epitopes of a protein of interest, but which do not substantially recognize and bind other molecules in a sample containing a mixed population of antigenic biological molecules.
  • the term “specifically hybridizing” refers to the association between two single-stranded nucleotide molecules of sufficiently complementary sequence to permit such hybridization under pre-determined conditions generally used in the art (sometimes termed “substantially complementary”).
  • the term refers to hybridization of an oligonucleotide with a substantially complementary sequence contained within a single-stranded DNA or RNA molecule of the invention, to the substantial exclusion of hybridization of the oligonucleotide with single-stranded nucleic acids of non-complementary sequence.
  • promoter region refers to the transcriptional regulatory regions of a gene, which may be found at the 5 ' or 3 ' side of the coding region, or within the coding region, or within introns .
  • selectable marker gene refers to a gene encoding a product that, when expressed, confers a selectable phenotype such as antibiotic resistance on a transformed cell .
  • reporter gene refers to a gene that encodes a product which is easily detectable by standard methods, either directly or indirectly.
  • operably linked means that the regulatory sequences necessary for expression of the coding sequence are placed in the DNA molecule in the appropriate positions relative to the coding sequence so as to enable expression of the coding sequence. This same definition is sometimes applied to the arrangement of transcription units and other regulatory elements (e.g., enhancers or translation regulatory sequences) in an expression vector.
  • the invention provides a heterologous bio-assay that has enabled the identification of an extracellular signaling factor produced by S . typhimurium and E. coli , among other pathogenic bacteria.
  • the factor is sometimes referred to herein as a "pathogenesis signaling" factor or molecule, though it acts as a signal for a variety of physiological changes in bacteria other than pathogenesis.
  • the factor mimics the action of AI-2 (autoinducer-2) of the quorum sensing bacterium Vibrio harveyi , and it acts specifically through the V. harveyi Signaling System 2 detector, LuxQ.
  • the signaling factor is a small, soluble, heat labile organic molecule that is involved in intercellular communication in all three bacteria.
  • Salmonella maximal secretion of the molecule occurs _in ⁇ mTd- exponential phase and the extracellular activity is degraded as glucose becomes depleted from the medium or by the onset of stationary phase. Destruction of the signaling molecule in stationary phase indicates that, in contrast to other quorum sensing systems, quorum sensing in bacteria that utilize the signaling molecule is critical for regulating behavior in the pre-stationary phase of growth. Protein synthesis is required for degradation of the activity, indicating that a complex regulatory circuitry controls quorum sensing in these enteric bacteria.
  • Increased signaling activity is observed if, after growing in the presence of glucose, the bacteria are transferred to a high osmolarity (e.g., 0.4M NaCl) or to a low pH (e.g., pH 5.0) environment. Moreover, degradation of the signal is induced by conditions of low osmolarity (e.g., 0.1M NaCl.
  • High osmolarity and low pH are two conditions encountered by pathogenic enteric bacteria, such as S . typhimurium and E. coli , when they undergo the transition to a pathogenic existence inside a host organism.
  • pathogenic enteric bacteria such as S . typhimurium and E. coli , when they undergo the transition to a pathogenic existence inside a host organism.
  • quorum sensing in these bacteria appears to play a role in regulating their virulence, by way of directing the bacteria to undergo the transition between a host-associated (i.e., pathogenic) and a free-living existence.
  • Example 2 Other factors that regulate the activity of the signaling molecule are described in greater detail in Example 2. Particularly exemplified is the regulation of the molecule in S . typhimurium.
  • the invention provides autoinducer-2 (AI-2) signaling factor and derivatives thereof.
  • AI-2 of the invention can be used to regulate bacterial growth in a variety of applications.
  • the present invention provides autoinducer-2 molecules having the structure :
  • Rl, R2 , R3 and R4 are independently selected from hydrido, halo, alkyl, haloalkyl, cycloalkyl, cycloalkenyl, heterocyclyl , methyl, cyano, alkoxycarbonyl , amino, carboxyl, hydroxyl, formyl , nitro, fluoro, chloro, bromo, methyl, aryl , heteroaryl, aralkyl, heteroarylalkyl , alkylsulfonyl, haloalkylsulfonyl , arylsulfonyl , heteroarylsulfonyl , hydroxyalkyl , mercaptoalkyl , alkoxyalkyl, aryloxyalkyl , heteroaryloxyalkyl , aralkyloxyalkyl , heteroarylalkyloxyalkyl , alkylthioalkyl , arylthio
  • hydrido denotes a single hydrogen atom (H) .
  • This hydrido radical may be attached, for example, to an oxygen atom to form a hydroxyl radical or two hydrido radicals may be attached to a carbon atom to form a methylene (-CH2-) radical.
  • alkyl radicals are "lower alkyl” radicals having one to about ten carbon atoms. Most preferred are lower alkyl radicals having one to about six carbon atoms.
  • radicals examples include methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, sec-butyl, tert-butyl, pentyl, iso-amyl, hexyl and the like.
  • halo means halogens such as fluorine, chlorine, bromine or iodine.
  • carboxy or “carboxyl” denotes -C02H.
  • the autoinducer-2 molecule of the invention is 4 , 5-Dihidroxy-2 , 3-pentanedione having the structure : -
  • an "autoinducer-2 (AI-2)" molecule of the invention includes a molecule that acts as a diffusable sensor for quorum sensing Signaling System 2.
  • AI-2 can regulate gene expression by increasing or decreasing expression of genes associated with pathogenesis of a microorganism.
  • autoinducer molecules are produced by microorganisms, such as bacteria, during metabolism.
  • the autoinducer-2 (AI-2) molecule of the invention can interact with LuxP which is the protein encoded by the homologue of the luxP gene of pathogenic bacteria such as V. cholerae, S. typhimurium and E. coli .
  • the AI-2 -LuxP complex can interact with LuxQ which is the protein product encoded by the luxQ gene.
  • the AI-2 -LuxP-LuxQ interaction can promote luminescence in bacteria such as Vibrio spp.
  • the AI-2 -LuxP-LuxQ interaction has been linked to the activation of biochemical pathways required for bacterial pathogenicity.
  • the invention provides a method for controlling bacterial gene expression and for regulating bacterial pathogenicity by modulating AI- 2-LuxP-LuxQ interactions.
  • the invention provides methods for using homocysteine as an autoinducer molecule.
  • the structure of homocysteine is as follows:
  • Homocysteine is produced by the activity of the LuxS protein on S-ribosylhomocysteine ( Figure 16).
  • the invention provides methods for using homoserine as an autoinducer.
  • the present invention also encompasses optically active isomers of an autoinducer-2 molecule.
  • an "isomer” is intended to include molecules having the same molecular formula as an autoinducer-2 molecule of the invention but possessing different chemical and physical properties due to a different arrangement of the atoms in the molecule. Isomers include both optical isomers and structural isomers.
  • optical active is intended to include molecules that have the ability to rotate a plane of polarized light.
  • An optically active isomer includes the L-isomer and the D- isomer of an autoinducer-2 molecule of the invention.
  • analogs of an autoinducer-2 molecule are included in the invention.
  • an AI-2 "analog" is intended to include molecules that are structurally similar but not identical to the claimed autoinducer molecule 4 , 5-Dihidroxy-2 , 3- pentanedione .
  • Analogs of AI-2 can include molecules that inhibit rather than stimulate the activity of the LuxP protein. For example, an analog of AI-2 that is capable of a nonproductive interaction with LuxP can be produced.
  • an AI-2 analog of the invention can act as an inhibitor of bacterial pathogenesis by competing with endogenous AI-2 for binding to LuxP.
  • an analog of AI-2 can be constructed such the analog AI-2 -LuxP complex is capable of nonproductively interacting with LuxQ.
  • the analog AI-2-LuxP-LuxQ complex is rendered nonfunctional for subsequent biochemical processes such as, for example, transcriptional activation of genes required for pathogenicity.
  • the invention also includes AI-2 analogs which act synergistically to enhance the ability of AI-2 to increase the activity of the LuxP protein.
  • the signaling factor of the present invention may be purified from its natural sources, i.e. the bacteria that produce it.
  • the bacteria that produce it With regard to purifying AI-2 from natural sources, altering the culture medium, e . g. , by adding glucose or another sugar, by increasing the osmolarity, and/or decreasing pH, can increase production of the signaling molecule in Salmonella and other enteric bacteria, has also enabled purification of the signaling molecule to near-homogeneity.
  • the molecule has now been highly purified from culture fluids of enteric bacteria (e.g., E. coli , S. typhimurium) using the following protocol:
  • Pellet the cells (10,000 rpm, 10 min, 4°C) . Collect the supernatant containing the secreted signaling molecule, filter the supernatant through a 0.2 M bacterial filter to remove any remaining cells.
  • the product from the C18 column contains the signaling molecule and a small number of other organic molecules.
  • This highly purified preparation of the signaling molecule has activity 50-100 times greater than that of the partially purified material described above (the preparation of which did not include the high osmoticum step or the final HPLC step), i.e., 1-10 ⁇ g material stimulates a 1, 000- fold increase in luminescence in the V. harveyi bioassay.
  • Subsequent strategies for purifying the AI-2 signaling molecule have led to the identification of a novel in vi tro system for producing AI-2.
  • a novel in vi tro system for producing AI-2 in addition to providing a cloned, overexpressed and purified S.
  • the present invention also provides a method for producing AI-2 in vi tro .
  • the present invention provides a mechanism for generating large — ⁇ ⁇ quantities of pure AI-2 useful for mass spectral and NMR analysis, and for screening compounds which regulate the activity of AI-2.
  • the present invention provides a method for determining the in vivo biosynthetic pathway for AI-2 synthesis.
  • the in vi tro method for AI-2 production is described below in Example 5 and Figure 15.
  • the method provides a novel means for efficiently producing autoinducer molecules for further study.
  • the method also provides a means for producing substantial quantities of AI-2 for use in commercial applications. Such applications include, but are not limited to, adding AI-2 of the invention to a growth media to increase bacterial growth.
  • Such a method is particularly useful in the in the production of antibiotics from cultured bacteria.
  • the addition of AI-2 can increase the antibiotic production of such organisms by promoting cell growth.
  • the signaling factor AI-2 is produced by the in vi tro method set forth in Example 5 of the disclosure.
  • the isolated and purified signaling molecules of the present invention are used as targets for the design of compounds that regulate the activity of AI-2.
  • “regulate” includes increasing or decreasing the activity of AI-2.
  • the "activity" of AI-2 encompasses any aspect of the molecules ability to act_ as " a signaling factor in bacterial quorum sensing.
  • a “compound” can be any agent or composition that effects the activity of AI-2.
  • a compound of the invention can be a nucleic acid, a protein or small molecule.
  • the invention provides a means for identifying a new class of antibiotics that inhibit the activity of the AI-2 molecule or otherwise block the signaling pathway in which the molecule participates.
  • Such inhibitors may be identified by large-scale screening of a variety of test compounds, using the V. harveyi bioassay in the presence of the purified signaling molecule. A reduction in signaling activity in the presence of a test compound would be indicative of the ability of that compound to inhibit the activity of the signaling molecule or to block some other part of the pathogenesis signaling pathway.
  • the invention provides a basis for the rational design of specific inhibitors or non-functional analogs of AI-2.
  • Such structure-specific inhibitors or analogs may be tested in the V. harveyi bioassay for their ability to inhibit the signaling molecule or to block the pathogenesis signaling pathway.
  • the invention also encompasses methods for identifying naturally produced compounds that inhibit the activity of a signaling molecule such as autoinducer-2.
  • a defensive strategy employed by eucaryotic organisms to avoid bacterial colonization is to specifieal ' ly target and inhibit quorum sensing controlled functions.
  • Such a mechanism has been identified in D. pulchra .
  • Recent studies indicate that halogenated furanones produced by D. pulchra inhibit quorum sensing by competing for the homoserine-lactone (HSL) autoinducer-binding site in LuxR.
  • HSL homoserine-lactone
  • the invention provides a method for selecting inhibitors or synergists of the autoinducer-2 molecule, 4 , 5-Dihidroxy-2 , 3-pentanedione .
  • an "inhibitor" of AI-2 is intended to include molecules- that interfere with the ability of the autoinducer molecule to act as a signal for luminescence or pathogenesis. Inhibitors include molecules that degrade or bind to AI-2.
  • the method comprises contacting the autoinducer molecule with a suspected inhibitor or synergist, measuring the ability of the treated autoinducer molecule to stimulate the activity of a selected gene then determining whether the suspected inhibitor or synergist represses or enhances the activity of the autoinducer molecule.
  • a suspected inhibitor can be mixed with 4,5- Dihidroxy-2 , 3-pentanedione and the mixture then combined with a reporter strain of V. harveyi disclosed herein.
  • the amount of luminescence in the presence of the suspected inhibitor can be compared with a control mixture which does not include the inhibitor.
  • a decrease in luminescence is indicative of AI-2 inhibition.
  • the invention also provides methods of selecting inhibitory and synergistic analogs of AI-2.
  • the method comprises mixing a known amount of the autoinducer molecule with a known amount of the suspected inhibitory or synergistic analog, measuring the ability of the treated autoinducer molecule to stimulate the activity of a selected gene then determining whether the suspected " " inhibitory or synergistic analog represses or enhances the activity of the autoinducer molecule. Actual inhibitory or synergistic analogs of the autoinducer molecule are then selected.
  • the autoinducer-2 molecule can be purified from the native source using conventional purification techniques, derived synthetically by chemical means, or preferably, produced by the in vi tro method of the invention described below. As used herein, "purified from a native source” is intended to include an autoinducer-2 molecule of the above formula that has been manufactured by an organism.
  • “Purified from the native source” includes isolating the autoinducer molecule from the culture media or cytoplasm of bacteria such as S . typhimurium using conventional purification techniques.
  • “synthesized by chemical means” is intended to include autoinducer molecules of the claimed formula that have been artificially produced outside of an organism.
  • the invention includes an autoinducer of the invention manufactured by a person skilled in the art from chemical precursors using standard chemical synthesis techniques.
  • the invention further provides methods of inhibiting the infectivity of a pathogenic organism as well as therapeutic compositions containing an AI-2 analog or AI- 2 inhibitor of the invention.
  • the methods comprise administering to a subject a therapeutically effective — "" amount of an pharmaceutical composition that is capable of inhibiting the activity of AI-2.
  • inhibiting infectivity includes methods of affecting the ability of a pathogenic organism to initially infect or further infect a subject that would benefit from such treatment.
  • a pharmaceutical composition of the invention can include, but is not restricted to, an agent that prevents the transcriptional activation of extracellular virulence factors such as exotoxin A and elastolytic proteases.
  • an “agent” includes molecules that inhibit the ability of the LuxP protein and LuxQ protein to activate transcription of extracellular virulence factors. Agents include inhibitors that interact directly with AI-2 such that AI-2 is prevented from acting as a sensor for quorum sensing Signaling System-2. Preferably, the agent interacts with 4 , 5-Dihidroxy-2 , 3-pentanedione . Agents further include analogs of AI-2 that can compete with 4 , 5-Dihidroxy-2 , 3- pentanedione for binding to LuxP or LuxQ.
  • the invention further provides pharmaceutical compositions for preventing or treating pathogen-associated diseases by targeting factors involved in the Signaling System type-2 pathway.
  • LuxP or LuxQ, or homologues thereof provide a common target for the development of a vaccine.
  • Antibodies raised to LuxP or LuxQ, or homologues thereof, can inhibit the activation of bacterial pathways associated with virulence.
  • _Lu-xF " and LuxQ provide common antigenic determinants which can be used to immunize a subject against multiple pathogen- associated disease states.
  • the autoinducer Signaling System type-2 is believed to exist in a broad range of bacterial species including bacterial pathogens.
  • the autoinducer-2 signaling factor is believed to be involved in inter-species as well as intra- species communication.
  • quorum sensing Signaling System type-2 In order for the quorum sensing Signaling System type-2 to be effective for inter-species communication, it is likely to be highly conserved among various bacterial species. Thus, challenging a subject with the LuxP or LuxQ polypeptide, or an antigenic fragment thereof, isolated from a particular organism may confer protective immunity to other disease states associated with a different organism. For example, a vaccine developed to the LuxP protein isolated from V. cholerae may be capable of cross-reacting with a LuxP homologue expressed by a different organism. Thus, it is envisioned that methods of the present invention can be used to treat pathogen- associated disease states.
  • treating is used herein to mean obtaining a desired pharmacologic and/or physiologic effect .
  • the effect may be prophylactic in terms of completely or partially preventing a spirochete infection or disease or sign or symptom thereof, and/or may be therapeutic in -terms of a partial "or complete cure for an infection or disease and/or adverse effect attributable to the infection or disease.
  • Treating covers any treatment of ( e . g. , complete or partial) , or prevention of, an infection or disease in a mammal, particularly a human, and includes:
  • the invention includes various pharmaceutical compositions useful for ameliorating symptoms attributable to a bacterial infection or, alternatively, for inducing a protective immune response to prevent such an infection.
  • a pharmaceutical composition according to the invention can be prepared to include an antibody against, for example, LuxP or LuxQ, a peptide or peptide derivative of LuxP or LuxQ, a LuxP or LuxQ mimetic, or a LuxP or LuxQ-binding agent according to the present invention into a form suitable for administration to a subject using carriers, excipients and additives or auxiliaries.
  • Frequently used carriers or auxiliaries include magnesium carbonate, titanium dioxide, lactose, mannitol and other sugars, talc, milk protein, gelatin,— starch, vitamins, cellulose and its derivatives, animal and vegetable oils, polyethylene glycols and solvents, such as sterile water, alcohols, glycerol and polyhydric alcohols.
  • Intravenous vehicles include fluid and nutrient replenishers .
  • Preservatives include antimicrobial, anti- oxidants, chelating agents and inert gases.
  • Other pharmaceutically acceptable carriers include aqueous solutions, non-toxic excipients, including salts, preservatives, buffers and the like, as described, for instance, in Remington ' s Pharmaceutical Sciences, 15th ed.
  • compositions according to the invention may be administered locally or systemically.
  • therapeutically effective dose is meant the quantity of a compound according to the invention necessary to prevent, to cure or at least partially arrest the symptoms of the disease and its complications. Amounts effective for this use will, of course, depend on the severity of the disease and the weight and general state of the patient.
  • dosages used in vi tro may provide useful guidance in the amounts useful for in situ administration of the pharmaceutical composition, and animal models may be used to determine effective dosages for treatment of particular disorders.
  • Various considerations are described, e . g. , in Langer, Science, 249: 1527, (1990); Gilman et al . (eds.) (1990), each of which is herein incorporated by reference.
  • administering a therapeutically effective amount is intended to include methods of giving or applying a pharmaceutical composition of the invention to a subject which allow the composition to perform its intended therapeutic function.
  • the therapeutically effective amounts will vary according to factors such as the degree of infection in a subject, the age, sex, and weight of the individual. Dosage procedures can be adjusted to provide the optimum therapeutic response. For example, several divided doses can be administered daily or the dose can be proportionally reduced as indicated by the exigencies of the therapeutic situation.
  • the pharmaceutical composition can be administered in a convenient manner such as by injection (subcutaneous, intravenous, etc.), oral administration, inhalation, transdermal application, or rectal administration.
  • the pharmaceutical composition can be coated with a material to protect the pharmaceutical composition from the action of enzymes, -acids and other natural conditions which may inactivate the pharmaceutical composition.
  • the pharmaceutical composition can also be administered parenterally or intraperitoneally .
  • Dispersions can also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations may contain a preservative to prevent the growth of microorganisms.
  • compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions.
  • the composition must be sterile and must be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi.
  • the carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyetheylene glycol, and the like), suitable mixtures thereof, and vegetable oils.
  • the proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
  • Prevention of the action of microorganisms can be- achieved " by various antibacterial and antifungal agents, for example, parabens, chlorobutanol , phenol, ascorbic acid, thimerosal , and the like.
  • isotonic agents for example, sugars, polyalcohols such as mannitol, sorbitol, sodium chloride in the composition.
  • Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.
  • Sterile injectable solutions can be prepared by incorporating the pharmaceutical composition in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization.
  • dispersions are prepared by incorporating the pharmaceutical composition into a sterile vehicle which contains a basic dispersion medium and the required other ingredients from those enumerated above.
  • the pharmaceutical composition can be orally administered, for example, with an inert diluent or an assimilable edible carrier.
  • the pharmaceutical composition and other ingredients can also be enclosed in a hard or soft shell gelatin capsule, compressed into tablets, or incorporated directly into the individual's diet.
  • the pharmaceutical composition can be incorporated with excipients and used in the form of ingestible tablets, buccal tablets, troches, capsules, - ⁇ " elixirs, suspensions, syrups, wafers, and the like.
  • Such compositions and preparations should contain at least 1% by weight of active compound.
  • the percentage of the compositions and preparations can, of course, be varied and can conveniently be between about 5 to about 80% of the weight of the unit.
  • the amount of pharmaceutical composition in such therapeutically useful compositions is such that a suitable dosage will be obtained.
  • the tablets, troches, pills, capsules and the like can also contain the following: a binder such as gum gragacanth, acacia, corn starch or gelatin; excipients such as dicalcium phosphate; a disintegrating agent such as corn starch, potato starch, alginic acid and the like; a lubricant such as magnesium stearate; and a sweetening agent such as sucrose, lactose or saccharin or a flavoring agent such as peppermint, oil of wintergreen, or cherry flavoring.
  • a binder such as gum gragacanth, acacia, corn starch or gelatin
  • excipients such as dicalcium phosphate
  • a disintegrating agent such as corn starch, potato starch, alginic acid and the like
  • a lubricant such as magnesium stearate
  • a sweetening agent such as sucrose, lactose or saccharin or a flavoring agent such as peppermint, oil of wintergreen, or
  • tablets, pills, or capsules can be coated with shellac, sugar or both.
  • a syrup or elixir can contain the agent, sucrose as a sweetening agent, methyl and propylparabens as preservatives, a dye and flavoring such as cherry or orange flavor.
  • any material used in preparing any dosage unit form should be pharmaceutically " " pure and substantially non-toxic in the amounts employed.
  • the pharmaceutical composition can be incorporated into sustained-release preparations and formulations.
  • a "pharmaceutically acceptable carrier” is intended to include solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like.
  • the use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the pharmaceutical composition, use thereof in the therapeutic compositions and methods of treatment is contemplated. Supplementary active compounds can also be incorporated into the compositions. It is especially advantageous to formulate parenteral compositions in dosage unit form for ease of administration and uniformity of dosage.
  • Dosage unit form as used herein refers to physically discrete units suited as unitary dosages for the individual to be treated; each unit containing a predetermined quantity of pharmaceutical composition is calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier.
  • the specification for the novel dosage unit forms of the invention are dictated by and directly dependent on (a) the unique characteristics of the pharmaceutical composition and the particular therapeutic effect to be achieve, and (b) the limitations inherent in the art of- " " compounding such an pharmaceutical composition for the treatment of a pathogenic infection in a subject.
  • compositions containing supplementary active ingredients are determined by reference to the usual dose and manner of administration of the said ingredients.
  • method of the invention can be used to induce cellular responses, particularly cytotoxic T- lymphocytes (CTLs) , to antigenic epitopes of, for example LuxP or LuxQ.
  • CTLs cytotoxic T- lymphocytes
  • CTL epitopes and helper epitopes have been identified in proteins from many infectious pathogens. Further, these epitopes can be produced concurrently such that multiple epitopes can be delivered in a form that can prime MHC class I restricted CTL responses.
  • An example of a system that can produce recombinant protein particles carrying one or more epitopes entails the use of the pi protein of the retrotransposon Tyl of Saccharomyces — cerevisiae (Adams, et al .
  • CTL epitopes can, for example, be fused to the C- terminus of pi and the resulting Ty virus-like particles (Ty-VLPs) may be able to generate a CTL response.
  • Ty-VLPs Ty virus-like particles
  • conserved regions of pathogenic antigens such as those that are involved in, or result from, the activation of Signaling System type-2, can be identified and incorporated together in a particle which enables the host immune system to mount an effective immune response against multiple spirochetal organisms.
  • the method of the invention can be used to generate particles with multiple epitopes to a single protein, such as LuxP, or multiple epitopes from various proteins .
  • the method of the invention also includes slow release antigen delivery systems such as microencapsulation of antigens into liposomes.
  • slow release antigen delivery systems such as microencapsulation of antigens into liposomes.
  • Such systems have been used as an approach to enhance the immunogenicity of proteins without the use of traditional adjuvants.
  • Liposomes in the blood stream are generally taken up by the liver and spleen, and are easily phagocytosed by macrophages . Liposomes also allow co-entrapment of immunomodulatory molecules along with the antigens, so that such molecules may be delivered to the site of antigen encounter, allowing modulation of the immune system towards protective responses.
  • the invention provides a method for identifying a compound which binds to a protein " of the invention, such as LuxP or LuxQ.
  • the method includes incubating components comprising the compound and LuxP or LuxQ under conditions sufficient to allow the components to interact and measuring the binding of the compound to LuxP or LuxQ.
  • Compounds that bind to LuxP or LuxQ include peptides, peptidomimetics, polypeptides, chemical compounds and biologic agents as described above.
  • Incubating includes conditions which allow contact between the test compound and LuxP or LuxQ. Contacting includes in solution and in solid phase.
  • the test ligand (s) /compound may optionally be a combinatorial library for screening a plurality of compounds.
  • Compounds identified in the method of the invention can be further evaluated, detected, cloned, sequenced, and the like, either in solution or after binding to a solid support, by any method usually applied to the detection of a specific DNA sequence such as PCR, oligomer restriction (Saiki, et al . , Bio/Technology, 3:1008-1012, 1985), allele-specific oligonucleotide (ASO) probe analysis (Conner, et al . , Proc . Natl .
  • the invention further provides a method for promoting the production of a bacterial product, such as, for example, an antibiotic, by contacting a culture of bacteria with an AI-2 of the invention at a concentration effective to stimulate or promote cellular metabolism, growth or recovery.
  • a bacterial product such as, for example, an antibiotic
  • AI-2 of the invention provides a method for increasing the amount of antibiotic produced by a culture.
  • “Culture medium”, as used herein, is intended to include a substance on which or in which cells grow.
  • the autoinducer molecule can be included in commercially available cell culture media including broths, agar, and gelatin.
  • the invention further provides a method for identifying factors that degrade or inhibit synthesis autoinducer-2.
  • autoinducer-1 concentration peaks in mid- to late log phase of a bacterial cell culture.
  • autoinducer-2 concentration increases earlier in log phase of bacterial cell -culture growth and is present in lower amounts in late log phase and stationary phase.
  • This data indicates that a mechanism exists for the degradation of autoinducer-2 at a specific point in bacterial growth.
  • the invention allows for the identification of the mechanism whereby autoinducer-2 levels are controlled. For example, partially purified bacterial extracts can be assayed against isolated autoinducer-2 to identify those fractions which degrade autoinducer-2. Fractions that degrade autoinducer-2 can be further fractionated by techniques known to those skilled in the art until those cellular components involved in autoinducer degradation are isolated.
  • the present invention also provides a method of regulating the expression of a gene.
  • the method comprises inserting a gene into bacteria chosen for enhancement of gene expression by an agent capable of stimulating the activity of the LuxQ protein and incubating the bacteria with an agent capable of stimulating the activity of the LuxP protein.
  • the signaling molecule of the invention can also be used in screens for other targets that are regulated by the molecule.
  • Cloned promoter- fusion libraries can be prepared from any species of bacteria and these libraries can be used to identify genes that are induced or repressed by the signaling factor, simply by screening for differences in reporter activity in petri or microtiter— plates containing the signaling molecule compared to plates that do not contain the molecule.
  • quorum sensing is a major regulator of biofilm control and quorum sensing blockers can therefore be used to prevent and/or inhibit biofilm formation.
  • quorum sensing blockers are effective in removing, or substantially decreasing the amount of, biofilms which have already formed on a surface.
  • quorum sensing blockers can reduce protease production by 50% in some strains of bacteria but the discovery that certain compounds can substantially eliminate protease production imparts clear significant clinical advantages. Furthermore, the unexpected finding that biofilm formation can be inhibited or prevented by quorum sensing blockers leads to the reasonable conclusion that other quorum sensing blockers which are known to exhibit quorum sensing blocking in other systems, such as protease production, will also be effective against biofilm formation.
  • the compounds of the invention are advantageously used to treat and/or prevent infections, such as those caused by V. angufflarum or Aeromonas spp .
  • infections such as those caused by V. angufflarum or Aeromonas spp .
  • Examples _of- t ⁇ is type of infection are vibriosis and furunculosis disease in fish.
  • Inhibition of biofilm formation by the bacteria optionally together with a reduction or elimination of extracellular protease production, renders the bacteria substantially non-pathogenic.
  • the compounds of the invention may be formulated by conventional methods for use in the treatment and/or prevention of bacterial infection.
  • the compounds may be used as solid or liquid preparations (such as tablets, suspensions or solutions for oral administration or sterile injectable compositions) , optionally together with pharmaceutically acceptable diluents, carriers or other additives.
  • the compounds or compositions containing them may be applied directly to the fish or they may be added to the fish's food or water.
  • the invention provides a method of removing a biofilm from a surface which comprises treating the surface with a compound of the invention.
  • the surface is preferably the inside of an aqueous liquid distribution system, such as a drinking water distribution system or a supply line connected to a dental air-water system.
  • the removal of biofilms from this type of surface can be particularly difficult to achieve.
  • the compound is preferably applied to the surface as a solution of the compound either alone or together with other materials such as conventional detergents or surfactants.
  • a further embodiment of the invention is an antibacterial composition
  • an antibacterial composition comprising a compound of the invention together with a bacteriocidal agent.
  • the compound of the invention helps to remove the biofilm whilst the bacteriocidal agent kills the bacteria.
  • the antibacterial composition is preferably in the form of a solution or suspension for spraying and/or wiping on a surface.
  • the invention provides an article coated and/or impregnated with a compound of the invention in order to inhibit and/or prevent biofilm formation thereon.
  • the article is preferably of plastics material with the compound of the invention distributed throughout the material .
  • luxS genes identified here bear no homology to other genes known to be involved in production of acyl-homoserine lactone autoinducers (luxl- like (Fuqua et al.,J. Bacteriol . r7_6, 269-275, 1994), luxLM- ainS-like (Bassler et al , 1993, supra ; Gilson et al , J. Bacteriol. 177, 6946-6951, 1995), further indicating that the signaling molecules of the present invention are novel.
  • harveyi are as follows: Haemophilus influenzae (88/72) , Helicobacter pylori (62/40) , Bacillus subtilis (58/38) , Borrelia burgfdorferi (52/32) , Neisseria meningi tidis (89/80) , Neisseria gonorrhoeae (89/80) , Yersinia pestis (85/77) , Ca pylobacter jejuni (85/74) ,
  • nucleotide sequences of the luxS genes from V. harveyi , E. coli and S. typhimurium are set forth at the end of the specification as SEQ ID NO:l, SEQ ID NO: 2 and SEQ ID NO:
  • SEQ ID NO: 10 SEQ ID NO: 11 and SEQ ID NO : 12 , respectively, it-is " believed that SEQ ID NOS : 1 and 2 constitute full-length clones, whereas SEQ ID NO : 3 and SEQ ID NO: 4 do not.
  • the LuxS genes from V. harveyi , E. coli and S . typhimurium are described in greater detail in Example 3. Although those particular LuxS genes and their encoded proteins are exemplified herein, this invention encompasses LuxS genes and their encoded enzymes from any bacterial species, having the sequence, structural and functional properties of the LuxS-encoded proteins described herein. As mentioned in Example 3, homologous nucleic acid sequences have been identified in a variety of bacterial species, but identity of those sequences as LuxS genes heretofore had not been appreciated.
  • LuxS nucleotide and deduced amino acid sequences from other bacterial species are set forth at the end of the specification as SEQ ID NOS: 5-9 and 13-17, respectively, and include sequences from the following species: Haemophilus influenzae, Helicobacter pylori , Bacillus subtilis, Borrelia burgdorferi and Vibrio cholerae .
  • SEQ ID NOS: 5-9 and 13-17 are set forth at the end of the specification as SEQ ID NOS: 5-9 and 13-17, respectively, and include sequences from the following species: Haemophilus influenzae, Helicobacter pylori , Bacillus subtilis, Borrelia burgdorferi and Vibrio cholerae .
  • variants and natural mutants of SEQ ID NOS: 1-9 are likely to exist within different species or strains of Vibrio, Escherichia and Salmonella (indeed, E.
  • this invention provides an isolated LuxS nucleic acid molecule and encoded protein having at least about 50-60% (preferably 60-80%, most preferably over 80%) sequence homology in the coding region with the nucleotide sequences set forth as SEQ ID NOS: 1-9, respectively (and, preferably, specifically comprising the coding regions of SEQ ID NOS: 1-9), and the amino acid sequence of SEQ ID NOS: 10-17.
  • the term “substantially the same” is intended to refer to the coding region and to conserved sequences . — ⁇ " governing expression, and refers primarily to degenerate codons encoding the same amino acid, or alternate codons encoding conservative substitute amino acids in the encoded polypeptide.
  • the term “substantially the same” refers generally to conservative substitutions and/or variations in regions of the polypeptide not involved in determination of structure or function.
  • the terms “percent identity” and “percent similarity” are also used herein in comparisons among amino acid sequences. These terms are intended to be defined as they are in the UWGCG sequence analysis program (Devereaux et al . , Nucl . Acids Res. 12: 387-397, 1984), available from the University of Wisconsin, and the parameters used by that program are the parameters intended to be used herein to compare sequence identity and similarity.
  • LuxS Nucleic acid molecules of the invention may be prepared by two general methods: (1) They may be synthesized from appropriate nucleotide triphosphates, or (2) they may be isolated from biological sources. Both methods utilize protocols well known in the art.
  • nucleotide sequence information such as the DNAs having SEQ ID NOS: 1-9, ena-bles preparation of an isolated nucleic acid molecule of the invention by oligonucleotide synthesis.
  • Synthetic oligonucleotides may be prepared by the phosphoramadite method employed in the Applied Biosystems 38A DNA Synthesizer or similar devices.
  • the resultant construct may be purified according to methods known in the art, such as high performance liquid chromatography (HPLC) .
  • HPLC high performance liquid chromatography
  • Such long double-stranded molecules may be synthesized as several smaller segments of appropriate complementarity.
  • Complementary segments thus produced may be annealed such that each segment possesses appropriate cohesive termini for attachment of an adjacent segment.
  • Adjacent segments may be ligated by annealing cohesive termini in the presence of DNA ligase to construct an entire 1.8 kb double-stranded molecule.
  • a synthetic DNA molecule so constructed may then be cloned and amplified in an appropriate vector.
  • a genomic clone is isolated from a cosmid expression library of an S . typhimurium or E. coli genome.
  • a genomic clone is isolated from a cosmid library of another bacterial genome " . "
  • nucleic acids having the appropriate level sequence homology with the protein coding region of any of SEQ ID NOS: 1-9 may be identified by using hybridization and washing conditions of appropriate stringency. For example, hybridizations may be performed, according to the method of Sambrook et al .
  • hybridization solution comprising: 5X SSC, 5X Denhardt ' s reagent, 1.0% SDS, 100 g/ml denatured, fragmented salmon sperm DNA, 0.05% sodium pyrophosphate and up to 50% formamide.
  • Hybridization is carried out at 37-42oc for at least six hours. Following hybridization, filters are washed as follows: (1) 5 minutes at room temperature in 2X SSC and 1% SDS; (2) 15 minutes at room temperature in 2X SSC and 0.1% SDS; (3) 30 minutes-1 hour at 37 ⁇ C in IX SSC and 1% SDS; (4) 2 hours at 42-65oin IX SSC and 1% SDS, changing the solution every 30 minutes.
  • T m 81.5C + 16.6Log [Na+] + 0.41(% G+C) - 0.63 (% formamide) - 600/#bp in duplex
  • the T m is 57C.
  • the T m _ . of a DNA duplex decreases by 1 - 1.5C with every 1% decrease in homology.
  • targets with greater than about 75% sequence identity would be observed using a hybridization temperature of 42C.
  • Another way to isolate the luxS nucleic acids is to search the publicly available databases for the luxS sequence in the bacterial genome of interest, design PCR primers from the sequence and amplify the gene directly from the chromosome. The PCR product can then be cloned.
  • nucleic acids of the present invention may be maintained as DNA in any convenient cloning vector.
  • clones are maintained in plasmid cloning/expression vector, such as pBluescript (Stratagene, La Jolla, CA) , which is propagated in a suitable ⁇ 7. coli host cell.
  • LuxS nucleic acid molecules of the invention include DNA, RNA, and fragments thereof which may be single- or double-stranded.
  • this invention provides oligonucleotides (sense or antisense strands of DNA or RNA) having sequences capable of hybridizing with at least one sequence of a nucleic acid molecule of - the present _;. — invention, such as selected segments of the DNA having SEQ ID NOS : 1 , 2 or 3.
  • Such oligonucleotides are useful as probes for detecting LuxS genes or transcripts.
  • a full-length LuxS gene product of the present invention may be prepared in a variety of ways, according to known methods.
  • the protein may be purified from appropriate sources, e.g., cultured bacteria such as S . typhimurium, E. coli or V. harveyi .
  • the enzyme may be produced by expression in a suitable expression system.
  • a DNA molecule such as the DNA having SEQ ID NO : 1 or 2
  • a plasmid vector adapted for expression in a bacterial cell, such as E. coli , or a eucaryotic cell, such as Saccharomyces cerevisiae or other yeast.
  • Such vectors comprise the regulatory elements necessary for expression of the DNA in the host cell, positioned in such a manner as to permit expression of the DNA in the host cell.
  • Such regulatory elements required for expression include promoter sequences, transcription initiation sequences and, optionally, enhancer sequences.
  • the protein produced by LuxS gene expression in a recombinant procaryotic or eucyarotic system may be purified according to methods known in the art .
  • a commercially available expression/secretion system can be used, whereby the recombinant protein is expressed and thereafter secreted from the host cell, to be easily purified from the surrounding medium.
  • an alternative approach involves purifying the recombinant protein by affinity separation, such as by immunological interaction with antibodies that bind specifically to the recombinant protein. Such methods are commonly used by skilled practitioners .
  • the protein encoded by the LuxS gene of the invention may be analyzed according to standard procedures .
  • the protein may be subjected to amino acid sequence analysis, according to known methods.
  • the stability and biological activity of the enzyme may be determined according to standard methods, such as by the ability of the protein to catalyze production of the signaling molecule under different conditions.
  • the present invention also provides antibodies capable of immunospecifically binding to the uxS-encoded protein of the invention.
  • Polyclonal antibodies may be prepared according to standard methods .
  • monoclonal antibodies are prepared, which react immunospecifically with various epitopes of the protein.
  • Monoclonal antibodies may be prepared according to general methods of K ⁇ hler and Milstein, following standard protocols.
  • Polyclonal or monoclonal antibodies that immunospecifically interact with the LuxS-encoded proteins can be utilized for identifying and purifying such proteins. For example, antibodies may be utilized for affinity separation of proteins with which they immunospecifically interact.
  • Antibodies may also be used to immunoprecipitate proteins from a sample containing a mixture of proteins and other biological molecules.
  • LuxS nucleic acids may be used for a variety of purposes in accordance with the present invention.
  • RNA, or fragments thereof may be used as probes to detect the presence of and/or expression of LuxS genes .
  • Methods in which LuxS nucleic acids may be utilized as probes for such assays include, but are not limited to: (1) in si tu hybridization; (2) Southern hybridization (3) northern hybridization; and (4) assorted amplification reactions such as polymerase chain reactions (PCR) .
  • the LuxS nucleic acids of the invention may also be utilized as probes to identify related genes from_ other bacteria.
  • hybridization stringencies may be adjusted to allow hybridization of nucleic acid probes with complementary sequences of varying degrees of homology.
  • LuxS nucleic acids are also used to advantage to produce large quantities of substantially pure encoded protein, or selected portions thereof.
  • the cloned genes inserted into expression vectors can be used to make large quantities of the signaling molecule itself, from any selected bacterial species, in a recombinant host such as E. coli DH5.
  • Specific luxS genes are cloned, a large quantity of the encoded protein produced, thereby producing a large quantity of the specific signaling molecule. This will be particularly useful determining differences in the structures of signaling molecules from different species, if such differences are found to exist.
  • a large quantity of signaling molecule from the species of interest could be made using the cloned gene in an expression vector, and thereafter used in library screens for potential targets in petri plate assays, as described above.
  • Purified LuxS gene products, or fragments thereof, may be used to produce polyclonal or monoclonal antibodies which also may serve as sensitive detection reagents for the presence and accumulation of those proteins in cultured cells. Recombinant techniques enable expression of fusion " proteins containing part or all of a selected LuxS-encoded protein.
  • the full length protein or fragments of the protein may be used to advantage to generate an array of monoclonal or polyclonal antibodies specific for various epitopes of the protein, thereby providing even greater sensitivity for detection of the protein in cells or tissue.
  • the LuxS proteins include overproduction to make a quantity of the LuxS proteins sufficient for crystallization. Solving the crystal structure of the LuxS proteins would enable the exact determination of the LuxS active site for catalysis of production of the signaling molecule.
  • the LuxS crystal structure can therefore be used for computer modeling that would greatly facilitate design of signaling molecule analogs, LuxS inhibitors, and rational drug design in general .
  • Polyclonal or monoclonal antibodies immunologically specific for a LuxS-encoded protein may be used in a variety of assays designed to detect and quantitate the protein. Such assays include, but are not limited to: (1) flow cytometric analysis; (2) immunochemical localization of a LuxS protein in cells or tissues; and (3) immunoblot analysis (e.g., dot blot, Western blot) of extracts from various cells and tissues. Additionally, as described above, antibodies can be used for purification of the proteins (e.g., affinity column purification, immunoprecipitation) .
  • the invention provides a novel strain of Vibrio Harveyi having a genotype that is luxN " , luxS " .
  • the Gram negative bacterium Vibrio harveyi contains two parallel quorum sensing circuits which synthesize and detect two different autoinducer molecules (Fig. 13) .
  • Circuit 1 synthesizes AI-1 a HSL autoinducer similar in structure to autoinducers synthesized by the Luxl/R pathway found in other gram negative bacteria.
  • Circuit 2 synthesizes AI-2, the structure of which has not been determined. Synthesis of AI-1 and AI-2 is dependent on LuxLM and LuxS respectively.
  • the AI-1 and AI-2 detectors, LuxN and LuxQ respectively, contain both a sensor kinase domain with a conserved histidine (HI) and an attached response regulator domain with a conserved aspartate (Dl) .
  • Signals from both sensors are channeled to the shared integrator protein LuxU, which is phosphorylated on a histidine residue (H2) .
  • the signal is transduced to a conserved aspartate residue (D2) on the response regulator protein LuxO.
  • LuxO- hosphate controls.
  • BB170 is a sensitive reporter for AI-2, however, the BB170 strain is not optimal for use as a reporter for inhibitors of the quorum pathway in a microtiter based assay.
  • the desired strain is defective in its ability to detect AI-1 (sensor 1 " ) and defective in its ability to synthesize AI-2.
  • the invention provides a strain of V. harveyi that is genotypically luxN " and luxS " .
  • the new strain, designated MM32 is useful for identifying inhibitors of the quorum sensing pathway. For example, since the new strain is sensor 1 " , its growth or ability to luminesce will not be affected by those organisms producing AI-1.
  • kit may comprise a carrier means being compartmentalized to receive in close confinement one or more container means such as vials, tubes, and the like, each of the container means comprising one of the separate elements to be used in the method.
  • the container means may comprise a strain of bacteria capable of detecting the presence of an autoinducer.
  • the bacterial strain will be capable of providing an easily detectable signal in the presence of autoinducer-2. More preferably, he desired strain is defective in its ability to detect AI-1 (sensor 1" ) and defective in its ability to synthesize AI-2.
  • the kit may provide a strain of V. harveyi that is genotypically luxN " and luxS " designated MM32. The bacterial strain is useful for identifying autoinducer-2 as well as inhibitors of autoinducer-2 and the quorum sensing pathway.
  • Pseudomonas aeruginosa is an opportunistic pathogen in humans with cystic fibrosis ⁇ — " " P. aeruginosa regulates various virulence determinants with Al .
  • Al producing bacteria include Erwinia carotovora, Pseudomonas aureofaciens, Yersinia enterocoli tica, Vibrio harveyi , and Agrobacterium tumefaciens .
  • Yersinia enterocoli tica is a bacterium which causes gastrointestinal disease in humans and has been reported to produce an autoinducer.
  • P. aureofaciens associates with the roots of plants and produces antibiotics that block fungus growth in the roots. The antibiotic synthesis is under autoinducer control.
  • the present invention provides novel autoinducer-2 and methods of using autoinducer-2. In contrast to autoinducer- 1, autoinducer-2 is believed to be an intra- species as well as inter-species signaling factor. Autoinducer-2 is further believed to regulate the expression of pathogenic and virulence factors not regulated by autoinducer- 1.
  • the present invention provides a method to identify and regulate the expression of bacterial biomarkers in, for example, pathogenic bacteria. Methods of the invention can be used to regulate the activity of bacterial pathogens that are present in both plants and animals .
  • the invention further provides a method for detecting an autoinducer-associated bacterial biomarker by " " contacting at least one bacterial cell with an autoinducer molecule under conditions and for such time as to promote induction of a bacterial biomarker.
  • an "autoinducer-associated bacterial biomarker” is any bacterial cell component which is regulated, modified, enhanced, inhibited or induced in response to an autoinducer.
  • a biomarker can be any bacterial cell component that is identifiable by known microscopial , histological or molecular biological techniques. Such biomarkers can be used, for example, to distinguish pathogenic from non-pathogenic bacteria.
  • a biomarker can be, for example, a molecule present on a cell surface, a protein, a nucleic acid, a phosphorylation event or any molecular or morphological characteristic of a bacterial cell that is modified as a result of the bacterium being contacted with an autoinducer.
  • the autoinducer is autoinducer-2.
  • the method of the invention is particularly useful for identifying a biomarker which is indicative of bacterial pathogenicity.
  • autoinducers are extracellular signalling factors used by a variety of bacteria to regulate cellular functions in response to various environmental stimuli, including high population density. It is believed that pathogenic bacteria express a biomarker, such as an antigenic determinant, as a result of increased autoinducer concentration in the surrounding environment.
  • the present invention _ — " provides a method for identifying a biomarker by contacting a bacterium with autoinducer-2 and assaying for the presence of the biomarker.
  • a probe can be a nucleic acid, protein, small molecule or antibody useful for detecting a bacterial biomarker present in a sample.
  • the probe can be used in a screening assay to identify a biomarker present in a sample after the sample has been contacted with, for example, an autoinducer.
  • a bacterial biomarker produced by a bacterium following contact with an autoinducer can be identified by contacting a sample containing the bacterium with a probe that binds to the biomarker.
  • Such assays can be used to detect, prognose, diagnose, or monitor various conditions, diseases, and disorders, or monitor the treatment thereof.
  • a probe can be detectably labeled such that the probe is detectable when bound to its target marker.
  • Such means for detectably labeling a probe include a biotin-binding protein, such as avidin or streptavidin, bound to a reporter molecule, such as an enzymatic, fluorescent, or radionuclide label.
  • reporter means and labels are well known in the art.
  • the method of the invention can be used to analyze differential gene expression in a bacterial cell following contact with an autoinducer.
  • the present invention provides a method for identifying a biomarker which can be a protein.
  • a bacterial protein expressed in response to an autoinducer molecule can be detected using the appropriate antibody.
  • the expressed protein can be, for example, an antigenic determinant indicative of a pathogenic bacterium.
  • Antibodies used in the method of the invention are suited for use, for example, in immunoassays for the detection of such a determinant.
  • antibody as used herein is meant to include intact molecules of polyclonal or monoclonal antibodies, as well as fragments thereof, such as Fab and F(ab') 2/ .
  • monoclonal antibodies are made from antigen containing fragments of a protein by methods well known to those skilled in the art (Kohler, et al . , Nature, 256:495, 1975).
  • radioisotopes may be bound to an immunoglobulin either directly or indirectly by using an intermediate — " " functional group.
  • Intermediate functional groups which often are used to bind radioisotopes which exist as metallic ions to immunoglobulins are the bifunctional chelating agents such as diethylenetriamine-pentacetic acid (DTPA) and ethylenediaminetetraacetic acid (EDTA) and similar molecules.
  • DTPA diethylenetriamine-pentacetic acid
  • EDTA ethylenediaminetetraacetic acid
  • metallic ions which can be bound to monoclonal antibodies are 11:L In, 97 Ru, 67 Ga, 68 Ga, 7 As, 89 Zr, and 201 T1.
  • a probe useful in the method of the invention can also be a nucleic acid probe.
  • nucleic acid hybridization techniques are well known in the art and can be used to identify an RNA or DNA biomarker present in a sample containing a bacterium contacted with an autoinducer. Screening procedures which rely on nucleic acid hybridization make it possible to identify a biomarker from any sample, provided the appropriate probe is available.
  • oligonucleotide probes which can correspond to a part of the sequence encoding a target protein, can be synthesized chemically. The DNA sequence encoding the protein can be deduced from the genetic code, however, the degeneracy of the code must be taken into account .
  • kits may comprise a carrier means being compartmentalized to receive in close confinement one or more container means such as vials, tubes, and the like, each of the container means comprising one of the separate elements to be used in the method.
  • a kit of the invention may contain a first container means comprising isolated autoinducer-2.
  • the isolated autoinducer-2 can be used to regulate the expression of a biomarker in a target bacterium.
  • autoinducer-2 can be used to induce expression of a particular biomarker which can then be identified by a probe.
  • the kit may contain a second container means comprising a probe that can be detectably labeled.
  • the kit may also have a third container comprising a reporter-means, such as a biotin-binding protein, such as avidin or streptavidin, bound to a reporter molecule, such as an enzymatic, fluorescent, or radionuclide label.
  • reporter-means such as a biotin-binding protein, such as avidin or streptavidin
  • reporter molecule such as an enzymatic, fluorescent, or radionuclide label.
  • Other reporter means and labels are well known in the art.
  • the kit of the invention may provide reagents necessary to perform nucleic acid hybridization analysis as described herein or reagents necessary to detect antibody binding to a target .
  • E. coli strains AB1157 and DH5 and S . typhimurium strain LT2 were grown at 30°C overnight with aeration in LB broth containing glucose at the concentrations specified in the text. The following morning fresh LB medium containing the same concentration of glucose used for the overnight growth was inoculated at a 1:100 dilution with the overnight grown cultures. The fresh cultures were grown for various times at 30°C with aeration. Cell-free culture fluids were prepared by removing the cells from the growth medium by centrifugation at 15,000 rpm for 5 min in a microcentrifuge .
  • V. harveyi Autoinducer-2 were prepared from V. harveyi strain BB152 (Autoinducer 1 ⁇ , Autoinducer 2 + ) .
  • V. harveyi BB120 Autoinducer 1 + , Autoinducer 2 +
  • the V. harveyi strains were grown overnight at 30°C with aeration in AB (Autoinducer Bioassay) (Bassler et al . , 1993, supra) medium.
  • Cell -free culture fluids from V. harveyi were prepared from the overnight culture exactly as described above for E. coli and S. typhimurium.
  • harveyi reporter strain BB170 or BB886 was grown for 16 h at 30°C with aeration in AB medium, diluted 1:5000 into fresh AB medium, and 90 1 of the diluted cells were added to the wells containing the E. coli and S. typhimurium cell- free culture fluids.
  • Positive control wells contained 10 1 of cell -free culture fluid from strain V. harveyi BB152 (Autoinducer-1 " , Autoinducer-2 + ) or V. harveyi BB120
  • Negative control wells contained 10 1 of sterile growth medium.
  • the microtiter dishes were shaken in a rotary shaker at 175 rpm at 30°C. Every hour, light production was measured using a Wallac Model 1450 Microbeta Plus liquid scintillation counter in the chemiluminescence mode.
  • the V. harveyi cell density was measured by diluting the same aliquots of cells used for measuring luminescence, spreading the dilutions onto solid LM medium (Bassler et al . , 1993, supra) , incubating the plates overnight at 30C, and counting the resulting colonies the following day.
  • E. coli AB1157, E. coli DH5 and S. typhimurium LT2 cultures were grown for 8 h in LB containing 0.5% glucose at 30°C with aeration. The cultures were subjected to centrifugation for 5 min_at- 15,000 rpm in a microcentrifuge and the growth medium was removed from the cell pellets by aspiration. The cell pellets were resuspended in AB medium and washed by vigorous mixing. The cells were again subjected to centrifugation for 5 min at 15,000 rpm.
  • the AB wash medium was removed and discarded and the cells were resuspended in fresh AB medium.
  • Each cell suspension was diluted to give 1 X 10 cells/10 1, and multiple 10 1 aliquots were added to wells of microtiter dishes. Half of the cell aliquots were treated with short wavelength ultraviolet light for 15 min at a distance of 10 cm. This treatment was sufficient to kill all of the cells as judged by plating and incubating the UV-treated cells, and ensuring that no growth occurred by the next day.
  • 90 1 of the diluted V. harveyi reporter strain BB170 was next added to the wells containing either the viable or dead E. coli and S. typhimurium cells, and the activity assay was carried out exactly as described in the previous section.
  • Glucose concentrations were determined in cell -free culture fluids prepared from S. typhimurium using a Trinder assay (Diagnostic Chemicals Ltd.) according to the recommendations of the manufacturer, except that the glucose standards were prepared in LB medium. The assay was sensitive to less than 0.002% glucose. No interfering. -- substances were present in LB medium or spent LB culture fluids .
  • V. harveyi reporter strain BB170 has the quorum sensing phenotype Sensor 1 " , Sensor 2 + . It induces lux expression in response to extracellular signals that act exclusively through the Signaling System 2 detector.
  • Addition of 10% cell-free spent culture fluid prepared from V. harveyi strain BB152 (which contains the System 2 autoinducer) stimulates the reporter strain roughly 1000 -fold over the endogenous level of luminescence expression.
  • the light production by V. harveyi BB170 induced by the addition of 10% cell-free spent culture fluids is normalized to 100% activity.
  • E. coli strain AB1157 and S. typhimurium strain LT2 were grown for 8 h in LB broth or LB broth containing 0.5% glucose. The E. coli and S. typhimurium cells were removed from the growth medium and the cell-free culture fluids were prepared and assayed for an activity that could induce luminescence expression in V. harveyi . Addition of 10% cell-free culture fluid from S. typhimurium LT2 or E. coli AB1157 grown in LB containing glucose maximally_ induced luminescence in the reporter strain BB170, similar to culture fluids from V. harveyi BB152 (Fig. 1A) . Specifically, E. coli AB1157 produced 106% and S.
  • V. harveyi BB170 can respond to some substance secreted by E. coli AB1157 and S. typhimurium LT2 when they are grown on LB containing glucose .
  • V. harveyi reporter strain BB886 (Sensor 1 + , Sensor 2 " ) .
  • V. harveyi BB886 is defective in its response to signaling molecules that act through the Signaling System 2 detector, but it is an otherwise wild type strain (Bassler et al . , Mol. Microbiol. 13: 273-286, 1994).
  • Fig. IB shows the normalized 100% activation of V. harveyi BB886 by cell-free spent culture fluids prepared from V. harveyi BB120.
  • harveyi BB120 produces the System 1 autoinducer N- (3 — hydroxybutanoyl) - -homoserine lactone (Bassler et al . , 1993, supra) .
  • Figure 1A and IB show that the signaling molecule produced by E. coli and S. typhimurium must act specifically through V. harveyi Signaling System 2 and not some other, unidentified pathway.
  • E. coli AB1157 and S. typhimurium LT2 are required for secretion of the signaling molecule.
  • E. coli AB1157 and S. typhimurium LT2 were grown for 8 h in LB containing 0.5% glucose; the conditions for maximal production of the signaling factor.
  • the cells were removed from the LB- glucose growth medium by centrifugation, and sterile V. harveyi luminescence assay medium was used to wash and resuspend the cell pellets.
  • 1 X10 6 E. coli AB1157 or S. typhimurium LT2 cells were added to the diluted V. harveyi BB170 culture at the start of the experiment.
  • the left-hand bar in each series shows that the presence of washed E. coli AB1157 or S. typhimurium LT2 cells is sufficient to fully induce luminescence in V. harveyi BB170.
  • E. coli AB1157 and S. typhimurium LT2 stimulated lux expression in V.
  • coli DH5 does not produce the signaling activity.
  • Clinical isolates of E. coli and Salmonella also produce the signaling compound.
  • Ten clinical isolates of Salmonella and five pathogenic isolates of E. coli 0157 were assayed and all produced the activity. It was conceivable that the signal was some normal byproduct of glucose metabolism that simply diffuses out of the cells. This is not the case however, because we show that E. coli DH5-, " " which is equally capable of utilizing glucose as E. coli AB1157 and S. typhimurium LT2 , does not produce the signaling activity.
  • Fig. 1A demonstrates that unlike E. coli AB1157 and S. typhimurium LT2 , the addition of 10% cell -free culture fluid prepared from E.
  • E. coli DH5 grown 8 h in LB containing 0.5% glucose does not stimulate light production in V. harveyi BB170.
  • inclusion of washed viable or killed E. coli DH5 cells in the luminescence assay does not stimulate V. harveyi BB170 to produce light ( Figure 2) .
  • the inability of E. coli DH5 to produce the activity indicates that this highly domesticated strain lacks the gene or genes necessary for either the production or the export of the signaling activity.
  • We assayed other laboratory strains of E. coli for the signaling activity (Table 1) . Only E. coli DH5 was completely defective in producing the extracellular signal.
  • V. harveyi reporter strain BB170 The induction of luminescence in V. harveyi reporter strain BB170 by cell-free culture fluids from V. harveyi , S . typhimurium and E. coli is shown.
  • Cell -free culture fluids were prepared from various strains of V. harveyi , S . typhimurium and E . coli as described and tested for production of a signaling substance that could stimulate light production in the reporter strain V. harveyi BB170.
  • the level of V. harveyi stimulation was normalized to 100%.
  • the data for the 5 h time point are shown.
  • Cell-free culture fluids from S. typhimurium LT2 and E. coli AB1157 cells grown in LB without added glucose did not stimulate the expression of luminescence in the reporter strain, indicating that metabolism of glucose is necessary -for " the production of the signal.
  • We tested other carbohydrates, and in general, growth in the presence of PTS sugars see Postma et al . , in Escherichia coli and Salmonella Cellular and Molecular Biology, (F.C. Niehardt, ed) , Am. Soc . Microbiol., Washington D.C., pp. 1149-1174, 1996) enabled E.
  • FIG. 3 shows results with S. typhimurium LT2 grown in LB containing limiting (0.1%) and non-limiting (0.5%) glucose concentrations.
  • Fig. 3A shows that when glucose is limiting, S. typhimurium LT2 produces the signal in mid- exponential phase (after 4 h growth) , but stops producing the signaling activity once glucose is depleted from the medium.
  • Fig. 3B shows that when glucose does not become limiting, S. typhimurium LT2 produces greater total activity and continues to produce the signaling activity throughout exponential phase, with maximal activity at 6 h growth.
  • the Figure also shows that the signaling activity synthesized by mid-exponential phase cells is degraded by the time the cells reach stationary phase r- " In conditions of limiting glucose, no activity remained at stationary phase, and when glucose was plentiful, only 24% of the activity remained. Increasing the concentration of glucose in the growth medium did not change these results, i . e . , the activity was secreted during mid-exponential growth and severely reduced activity remained in the spent culture fluids by stationary phase.
  • E. coli and S. typhimurium produce a signaling substance that stimulates one specific quorum sensing system in V. harveyi .
  • Many other bacteria have previously been assayed for such an activity, and only rarely were species identified that are positive for production of this factor (Bassler et al . , 1997, supra) .
  • the E. coli and S. typhimurium signal is potent, these bacteria make activity equal to that of V. harveyi .
  • the degradation of the E. coli and S. typhimurium signal prior to stationary phase indicates that quorum sensing in these bacteria is tuned to low cell densities, suggesting that quorum sensing in E.
  • quorum sensing in E. coli and S. typhimurium is modulated so that the response to the signal does not persist into stationary phase. Additionally, quorum sensing in E. coli and S. typhimurium is influenced by several environmental factors. The production and the degradation of the signal are sensitive not only to growth phase but also to the metabolic activity of the cells. These results indicate "that the quorum sensing signal in E. coli and S. typhimurium has two functions; it allows the cells to communicate to one another their growth phase and also the metabolic potential of the environment . Understanding the regulation of quorum sensing in
  • E. coli and S. typhimurium is important for understanding community structure and cell-cell interactions in pathogenesis. In the wild, pathogenic E. coli and S. typhimurium may never reach stationary phase because dispersion is critical . It is therefore appropriate that quorum sensing in E. coli and S. typhimurium should be functioning at low cell density. This situation is in contrast to that of V. fischeri , the luminescent marine symbiont, where the quorum sensing system is only operational at high cell densities; cell densities indicative of existence inside the specialized light organ of the host. The specific quorum sensing systems of V. fischeri and E. coli and S . typhimurium appear appropriately regulated for the niche in which each organism exists.
  • quorum sensing could be useful for communicating that the bacteria reside in the host, not free-living in the environment. Additional complexity exists in the E. coli and S. typhimurium systems because these bacteria channel both cell density information and metabolic cues into the quorum sensing circuit. Again, signals relaying information regarding the abundance of glucose or other metabolites" " could communicate to the bacteria that they should undergo the transition from a free-living mode to the mode of existence inside the host.
  • the signaling activity described in this example does not extract quantitatively into organic solvents and it does not bind to either a cation or anion exchange column.
  • Preliminary characterization indicates that the signal is a small (less than 1000 MW) polar but apparently uncharged organic compound.
  • the activity is acid stabile and base labile, it is heat resistant to 80 but not 100°C. Purification of the E. coli , S . typhimurium and V. harveyi signal is described in greater detail in the following examples .
  • S. typhimurium possess a protein called SdiA which is homologous to LuxR from V. fischeri (Wang et al . , EMBO J. 10: 3363-3372, 1991; Ah er et al . , J. Bacteriol. 180 : 1185-1193, 1998).
  • SdiA is proposed to respond to an extracellular factor (Sitnikov et al . ,
  • Luria broth contained 10 g Bacto Tryptone (Difco) , 5 g Yeast Extract (Difco) and 10 g NaCl per- liter (Sambrook et al . , 1989).
  • the recipe for Autoinducer Bioassay (AB) medium has been reported previously (Greenberg et al . , Arch. Microbiol. 120 : 87-91, 1979).
  • LM medium L-Marine contains 20 g NaCl, 10 g Bacto Tryptone, 5 g Bacto Yeast Extract and 15 g Agar per liter (Bassler et al . , 1994, supra) .
  • S. typhimurium LT2 was grown overnight in LB broth with shaking at 30°C. The next day, 30 1 of the overnight culture was used to inoculate 3 ml of fresh LB broth. In cultures containing additional carbon sources, at the time of inoculation, 20% sterile stock solutions were added to give the specified final concentrations. Following subculturing of the cells, the tubes were shaken at 200 rpm at 30C for the time periods indicated in the text. Cell-free culture fluids were prepared by removal of the cells from the culture medium by centrifugation for 5 min at 15,000 rpm in a microcentrifuge .
  • V. harveyi reporter strain BB170 (Sensor 1 " , Sensor 2 + ) (Bassler et al . , 1993, supra) was grown for 12 h at 30°C in AB medium, and diluted 1:5000 into fresh AB medium. Luminescence was measured as a function of cell density by quantitating light production at different times during growth with a Wallac Model 1409 liquid scintillation counter (Wallac Inc., Gaithersburg, MD) .
  • the cell density was measured by diluting the same aliquots of cells used for measuring luminescence, spreading the dilutions onto solid LM medium, incubating the plates overnight at 30°C, and counting the resulting colonies the following day. Relative Light Units are (counts min " ml X 10 ) / (colony forming units ml ) . Cell -free culture supernatants from V. harveyi or S. typhimurium strains were added to a final concentration of 10% (v/v) at the time of the first measurement. In control experiments, 10% (v/v) of AB medium, LB medium or LB medium containing 0.5% glucose was added instead of cell-free culture fluids. S.
  • the quorum sensing signaling activity released by S. typhimurium LT2 was assayed following growth under various conditions. 10 1 of cell-free culture fluids from S. typhimurium LT2 grown and harvested as described above were added to 96-well microtiter dishes. The V. harveyi reporter strain BB170 was grown overnight and diluted as described above. 90 1 of the diluted V. harveyi cells were added to the wells containing the S. typhimurium cell-free culture fluids. Positive control wells contained 10 1 of cell -free culture fluid from V.
  • harveyi BB152 Al-1 " , AI-2 + ) (Bassler et al . , 1993, supra) (Bassler et al . , 1993, supra) (Bassler et al . , 1993, supra) .
  • the microtiter dishes were shaken in a rotary shaker at 200 rpm at 30°C.
  • Light production was measured hourly using a Wallac Model 1450 Microbeta Plus liquid scintillation counter designed for microtiter dishes (Wallac Inc., Gaithersburg, MD) .
  • the cell density was not measured at each time point. Rather, to ensure that increased light production was due to a signaling activity and not a growth medium component, the luminescence production by V. harveyi in wells containing cell-free culture fluids was compared to that produced by V. harveyi in wells containing 10 1 of the identical growth medium alone. Data are reported as fold-stimulation over that obtained for growth medium alone.
  • S . typhimurium LT2 was grown for 6 h in LB containing 0.5% glucose as described above.
  • the mid- exponential phase culture was divided into several ⁇ identical aliquots.
  • One aliquot of cells was grown to stationary phase (24 h at 30°C with shaking) .
  • the cells were removed from the LB-glucose growth medium by centrifugation for 5 min at 15,000 rpm in a microcentrifuge.
  • the resulting cell pellets were resuspended at an OD 600 of 2.0 in either LB, LB + 0.5% glucose, LB at pH 5.0, or in 0.1M NaCl, or 0.4M NaCl (in water) .
  • the resuspended cells were shaken at 30°C or 43°C for 2 h.
  • Cell-free fluids were prepared from the stationary phase culture, and from the cells that had been resuspended and incubated in the various media or the osmotic shock solutions. The cell-free fluids were tested for signaling activity in the S. typhimurium activity assay as described above . Effects of growth phase, pH, glucose concentration and osmolarity on autoinducer production by S. typhimurium . S.
  • typhimurium LT2 was grown at 30°C for various times in LB containing limiting (0.1%) and non-limiting (1.0%) glucose concentrations. At the times specified in the text, the cell number was determined by plating dilutions of the S. typhimurium cultures onto LB medium and counting colonies the following day. The pH of the two cultures was measured, and the percent glucose remaining in each culture was determined using the Trinder assay as described in Example 1.
  • Cell-free culture fluids were prepared from the LB- glucose cultures as described above. The same cells from which the cell -free culture fluids were prepared were resuspended in 0.4M NaCl osmotic shock solution and shaken at 200 rpm, 30°C for 2 h.
  • S. typhimurium LT2 was pre-grown in LB containing 0.5% glucose at 30°C to an OD 600 of 2.5 (approximately 6-8 h) . The culture was divided into four identical aliquots. Two aliquots were treated with 100 g/ml Cm for 5 min at room temperature after which the cells were harvested by centrifugation at 15,000 rpm for 5 min. One Cm-treated cell pellet was resuspended in 0. IM NaCl containing 30 g/ml Cm, and the second pellet was resuspended in 0.4M NaCl containing 30 g/ml Cm.
  • a sequence that includes the ftsQlp and ftsQ2p promoters was amplified from E. coli MG1655 chromosomal DNA using the following primers: ftsQlp, 5'- CGGAGATCTGCGCTTTCAATGGATAAACTACG-3 ' ; ftsQ2p, 5'-
  • the amplified product contained both the ftsQ promoters and the first 14 codons of the ftsQ gene flanked by BamRI and Bglll sites.
  • the ftsQlp2p PCR product was cloned into the BamHI site of vector pMLB1034 (Silhavy et al . , Experiments with Gene
  • the plasmids pMS207 and pMS209 were transformed into E. coli strain MC4100 (Silhavy et al . , 1984, supra) , and the transformants were grown overnight in LB containing 100 mg/L ampicillin at 30°C with aeration.
  • S. typhimurium strains BA1105 (rck: :MudJ) and BA1305 (rck: :MudJ sdiA) were grown overnight in LB containing 100 mg/L kanamycin at 30°C with aeration. The overnight cultures were diluted 20- fold into fresh medium and grown for an additional 4.5 h.
  • each culture was divided into five identical aliquots and 10% (v/v) of one of the following was added to each aliquot: LB, 0.4M NaCl, 0.4M osmotic shock fluids from S. typhimurium LT2 , E. coli 0157 or E. coli strain DH5
  • the osmotic shock fluids were prepared as described above, following pre-growth of the S. typhimurium LT2 and E. coli in LB containing 0.5% glucose for 6h. The cell suspensions were incubated at 30°C for 2 h, after which standard -galactosidase reactions were performed on the samples (Miller, A Short Course in Bacterial Genetics, Cold Spring Harbor Laboratory Press, 1992) . RESULTS
  • S. typhimurium LT2 produces an autoinducer-like activity.
  • S. typhimurium and E. coli strains produce a signaling activity that stimulates lux expression in V. harveyi , and the signaling molecule acts exclusively through the V. harveyi quorum sensing System 2.
  • Figure 4 shows the induction of luminescence in the V. harveyi System 2 reporter strain BB170 (Sensor 1 " , Sensor 2 + ) .
  • the characteristic quorum sensing behavior of V. harveyi is shown in the control experiment (closed circles) .
  • the light emitted per cell by V. harveyi drops rapidly, over 1000-fold.
  • the luminescence per cell increases exponentially, approximately 3 orders of magnitude, to again reach the pre-dilution level.
  • Fig. 5A demonstrates three important aspects of the regulation of autoinducer production in S. typhimurium.
  • S. typhimurium LT2 was induced for signal production, by " pre- growth in LB containing 0.5% glucose for 6 h. We have shown that under these conditions, the glucose is not depleted (Surette and Bassler, 1998) . After the induction phase of growth, the culture fluid was removed and aliquots of the cells were resuspended and incubated for 2 h under a variety of conditions that are described in the description of Figure 2. Following each of these treatments cell-free fluids were prepared and tested for activity on BB170.
  • Fig. 5B shows that removal of the pre- growth culture fluid from these cells and resuspension of the cells in LB without glucose, in 0.1 M NaCl (hypotonic conditions) , or heat shock at 43°C for 2 h resulted in no or very low autoinducer production.
  • Example 1 The effect of glucose on signal production in S. typhimurium .
  • Example 1 we showed that the continued presence of glucose was required for S. typhimurium to produce the quorum sensing signaling factor.
  • sugar utilization both increases the growth rate while decreasing the pH of the culture
  • Figure 6 we measured signal production, growth rate, and pH in growing S. typhimurium LT2 cultures containing limiting (0.1%) and non-limiting (1.0%) concentrations of glucose.
  • Figure 6 shows that the pattern of production and disappearance of autoinducer observed in 0.4M NaCl osmotic shock fluids mimics that observed in cell-free culture fluids. However, at every time point that autoinducer is produced, much greater activity is detected in the osmotic shock £uids—than in ⁇ the _jcorresponding devisc_eJ, f ee_cjul_ture fluids. Under conditions of limiting (0.1%) glucose (Figs. 6A, 6C and 6E) , S. typhimurium produces the signaling activity between 2-4 h (Bars) . However, the glucose becomes completely depleted at 4 h, and at that time production of the factor ceases (Fig. 6A) .
  • S. typhimurium grows at roughly the same rate in both high and low glucose media during exponential phase.
  • the S. typhimurium culture grown in high glucose medium does not reach the cell density achieved by the S. typhimurium grown in the low glucose medium (Figs. 6C and 6D) .
  • Cell growth is probably inhibited in this culture by the dramatically reduced pH that occurs from increased glucose utilization.
  • Figs ._ . 6E_ and 6F show the pH of the low and high glucose cultures at each time point.
  • the pH of the culture initially decreases as the cells utilize the glucose. However, simultaneous to the complete depletion of the glucose, the pH begins to rise. In contrast, under conditions of high glucose, the pH of the medium decreases to below pH 5 (Fig. 6F) .
  • both_ j ucose catabolism and decreasing pH occur simultaneously suggesting that either or both of these factors could be responsible for signal production by S. typhimurium.
  • typhimurium that have degraded the factor (i.e., from cultures grown for 12 or 24 h in LB + glucose) does not result in degradation of the activity. This result indicates that the degradative activity is not released, but instead, is associated with the cells.
  • V. harveyi JAF305 was used as the reporter strain in the activity assay.
  • This V. harveyi strain contains a Cm r cassette in the luxN gene, and its phenotype is Sensor 1 " , Sensor 2 + , a phenotype identical to that of V. harveyi BB170.
  • a S. typhimurium was grown for 6 h in LB containing 0.5% glucose. The cells were pelleted and resuspended in either 0. IM or 0.4M NaCl for 2 h. Cell -free fluids were prepared and tested for activity.
  • the LuxR homolog SdiA is not involved in response to the AI-2 autoinducer.
  • a gene homologous to luxR of V. fischeri has been identified in E. coli and S. typhimurium and is called sdiA .
  • SdiA activity in S. typhimurium is proposed to be modulated by an extracellular factor.
  • S. typhimurium LT2 produces an amount of activity roughly equivalent to that produced by V. harveyi .
  • the timing of lux induction and the shape of the response curve of V. harveyi to the S. typhimurium signal are indistinguishable from those of V. harveyi responding to its own AI-2.
  • results presented in this example show that, in contrast to other quorum sensing systems, the S. typhimurium signal does not accumulate in stationary phase. At least two competing processes contribute to this regulation; autoinducer production and autoinducer degradation.
  • autoinducer production as an increase in the signaling activity present in cell-free fluids. We recognize that an increase in activity could result from release of newly biosynthesized autoinducer, release of stored autoinducer, repression of degradation of autoinducer, or some combination of these activities.
  • autoinducer degradation as the disappearance of signaling activity from the cell-free fluids. This disappearance could be due to destruction of the autoinducer, re-uptake of the autoinducer, or a combination of these activities.
  • S . typhimurium cells that are actively producing signal can be further stimulated to produce signal by specific environmental treatments, indicating that several independent regulatory pathways channel information into autoinducer synthesis.
  • One of these treatments is 0.4M NaCl osmotic shock.
  • autoinducer producing S. typhimurium cells are resuspended in 0.4M NaCl, the cells release significantly greater activity when they have the capability to synthesize protein than when protein synthesis is blocked. Furthermore, degradation of the signal also requires protein synthesis.
  • the Role for Quorum Sensing in Salmonella Pathogenesis The observations presented here on the regulation of signal production and degradation by S. typhimurium LT2 implicate a role for quorum sensing in pathogenesis of Salmonella .
  • the conditions favoring signal production are those likely to be encountered upon the first interaction of an enteric pathogen with its host.
  • Conditions favoring degradation of the signal are those most probably encountered as the pathogen exits the host.
  • the initial colonization of the host may be a concerted effort between a population of cells coordinated through this cell-cell signaling system. Other cues, that we have not yet tested, could also regulate quorum sensing in S.
  • Salmonella pathogenesis is a dynamic process of interaction between the host and metabolically active bacteria. Consistent with a role for quorum sensing in pathogenesis, our evidence suggests that this quorum sensing system is not functioning during stationary phase. We have shown that the signaling molecule is not produced during stationary phase, and furthermore, existing signal is degraded. Perhaps quorum sensing is critical for S. typhimurium to undergo the transition between a host- associated and a free-living existence.
  • the luxS genes do not bear homology to any other gene known to be involved in autoinducer production.
  • V. harveyi BB120 is the wild type strain (Bassler et al . , 1997, supra) .
  • S . typhimurium strain LT2 was obtained from Dr. K. Hughes (University of Washington), S. typhimurium 14028 is ATCC strain 14028 Organism: Salmonella choleraesuis .
  • E. coli 0157 :H7 is a clinical isolate supplied by Dr. Paddy Gibb (University of Calgary) .
  • Luria broth (LB) contained 10 g Bacto Tryptone (Difco) , 5 g Yeast Extract (Difco) and 10 g NaCl per liter.
  • V. harveyi BB120 genomic library was constructed in the cosmid pLAFR2 as described (Bassler et al . , 1993, supra) .
  • the method for Tn5 mutagenesis of cloned V. harveyi genes, and the allelic replacement technique for inserting Tn5 mutated genes into the V. harveyi chromosome have been reported (Bassler et al . , 1993, supra) . Bioluminescence Assay.
  • harveyi reporter strain BB170 (Sensor 1 ⁇ , Sensor " 2 + ) has been discussed in the previous examples.
  • Cell -free culture fluids from V. harveyi , E. coli , or S. typhimurium strains to be tested for AI-2 activity were prepared as described above, and assayed at 10% (v/v) .
  • AI-2 activity is reported as the fold-induction of the reporter strain over background, or as the percent of the activity obtained from V. harveyi BB120 (wild type) cell-free culture fluid.
  • MudJ insertion mutants of S. typhimurium LT2 were generated using a phage P22 delivery system as described (Maloy, S.R., Stewart, V.J., and Taylor, R.K. (1996) Genetic analysis of pathogenic bacteria : a laboratory manual . Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.) . Following growth to mid- exponential phase in LB containing 0.5% glucose, the S. typhimurium insertion mutants were tested for AI-2 production using the V. harveyi BB170 bioassay. The site of the MudJ insertion that inactivated the AI-2 production function in S.
  • typhimurium was identified by PCR amplification and sequencing of the chromosomal DNA at the insertion junction. A two-step amplification procedure was used (Caetano-Annoles, G. (1993) Meth . Appl . 3, 85-92). In the first PCR reaction, the arbitrary primer 5 ' - GGCCACGCGTCGACTAGTACNNNNNNNNACGCCC-3 ' , and the MudJ specific primer 5 ' -GCACTACAGGCTTGCAAGCCC-3 ' were used.
  • the library consisted of 2,500 clones each containing roughly 25 kb of V. harveyi genomic DNA. Five DH5 clones were identified that resulted in upwards of 300 -fold stimulation of the reporter strain in the bioassay. The recombinant cosmid DNA from the five AI-2 producing E. coli DH5 clones was analyzed by restriction analysis and Southern blotting. All five of the cosmids contained an overlapping subset of identical V. harveyi genomic restriction fragments, indicating that we had cloned the same locus several times. One cosmid, called pBB2929 was selected for further analysis.
  • Cosmid pBB2929 was digested with Hindlll and the 8 resulting fragments were subcloned in both orientations into pALTER (Promega) .
  • the pALTER subclones were transformed into E. coli DH5, and subsequently tested for AI-2 production.
  • the only strains capable of producing AI-2 contained the 2.6 kb Hindlll fragment identified in the Tn5 mutagenesis. This fragment was sequenced, and only one open reading frame (ORF) could be identified, and its location corresponded to the map positions of the four TnS insertions that eliminated AI-2 production.
  • ORF open reading frame
  • Fig. 10A we show the AI-2 production phenotypes of the wild type control Tn5 insertion strain
  • V. harveyi MM28 and MM30 were grown to high cell density, after which cell-free culture fluids were prepared. The culture fluids were assayed for AI-2 activity by the ability to induce luminescence in the AI-2 detector strain BB170.
  • Fig. 10A shows that addition of culture fluids from the control Tn5 insertion strain MM28 induced luminescence in the reporter 780-fold, while culture fluid from the luxS V h _ : : Tn5 insertion strain MM30 did not induce the expression of luminescence in the reporter. Therefore, a null mutation in luxS V- h - in V. harveyi eliminates AI-2 production.
  • S. typhimurium autoinducer production mutants In order to identify the gene responsible for AI-2 production in S. typhimurium, we randomly mutagenized S. typhimurium LT2 using the MudJ transposon (Maloy et al . , 1996, supra) . Ten-thousand S. typhimurium LT2 insertion mutants were assayed for AI-2 production in the V. harveyi BB170 bioassay. One S. typhimurium MudJ insertion mutant (strain CS132) was identified that lacked detectable AI-2 in culture fluids at mid-exponential phase.
  • Fig. 10B shows the AI-2 production phenotypes of S. typhimurium strain LT2 and the corresponding MudJ insertion strain CS132.
  • the strains were grown to mid- exponential phase in LB containing glucose, and cell -free culture fluids were prepared and assayed for AI-2.
  • _S i ⁇ typhimurium LT2 culture fluids induced the reporter strain 500-fold, while culture fluids from strain CS132 contained no AI-2 activity.
  • strain CS132 did not produce AI-2 under any of the growth conditions that we have previously reported induce AI-2 production in S. typhimurium (not shown) .
  • the site of the MudJ insertion in S. typhimurium CS132 was determined by PCR amplification followed by sequencing of the 110 bp of chromosomal DNA adjacent to the transposon. This sequence was used to search the database for DNA homologies. The sequence matched a site (89/105 bp identity) in the E. coli MG1655 genome that corresponded to an ORF of unknown function denoted ygaG (Blattner et al . , 1997, supra) . In the chromosome, the E. coli ygaG gene is flanked by the gshA and emrB genes (Fig. 9B) .
  • the ygaG gene is transcribed from its own promoter which is located immediately upstream of the gene, indicating that it is not in an operon with gshA .
  • the emrB gene is transcribed in the opposite direction.
  • E. coli 0157 :H7 produced 1.5 times and S. typhimurium LT2 produced 1.4 times more AI-2 activity than V. harveyi BB120 (i.e., 150% and 141% respectively).
  • Fig. 11B and 11C show the AI-2 complementation results for S. typhimurium CS132 and E. coli DH5.
  • Fig. 11B demonstrates that introduction of the E. coli 0157 :H7 ygaG gene into S. typhimurium CS132 restored AI-2 production beyond the level of production of wild type S. typhimurium ( i . e . , 209% activity) .
  • Comparison of the data in Fig. 11A and 11B shows that the E. coli ygaG gene in S. typhimurium resulted in AI-2 production exceeding that produced in vivo by E. coli 0157 :H7.
  • Fig. 11C shows that E. coli DH5 was also complemented to AI- 2 production by both the cloned E. coli 0157 :H7 and the V. harveyi BB120 AI-2 production genes.
  • introduction of E. coli 0157 :H7 ygaG and V. harveyi BB120 luxS v h - into E. coli DH5 resulted in only 31% and 43% of the V. harveyi BB120 AI-2 activity respectively.
  • AI-2 production genes from V. harveyi , E. coli and S . typhimurium We sequenced the AI-2 production gene luxS V- h , from V. harveyi BB120 and the ygaG loci from E. coli 0157 :H7, E. coli MG1655 and E. coli DH5.
  • the translated protein sequences encoded by the ygaG ORF ' s are shown in Figure 12, and they are aligned with the translated LuxS protein sequence from V. harveyi .
  • the non- bold, underlined amino acids indicate the residues in the E. coli proteins that differ from the V. harveyi LuxS protein.
  • the E. coli MG1655 and the E. coli 0157 :H7 YgaG proteins are 77% and 76% identical to LuxS from V. harveyi BB120.
  • the DNA sequence we determined for ygaG from E. coli 0157 :H7 differs at five sites from the reported (and our) sequence for the E. coli MG1655 ygaG gene. Four of the changes are silent, the fifth results in a conservative Ala to Val alteration at amino acid residue 103 in the E. coli 0157 :H7 protein.
  • E. coli DH5 possesses the ygaG gene because we could PCR amplify this region from the chromosome using the same primers we employed to -amplify it from E. coli MG1655 and E. coli 0157 :H7.
  • Examination of the E. coli DH5 ygaG promoter showed that it is identical to that of E. coli MG1655, indicating that the AI-2 defect in E. coli DH5 is not simply due to decreased transcription of ygaG.
  • coli DH5 ygaG coding region showed that a one G-C base pair deletion and a T to A transversion exist at bp 222 and 224 respectively.
  • the frameshift mutation resulting from the G/C deletion causes premature truncation of the E. coli DH5 protein.
  • Figure 12 shows that the truncated E. coli DH5 protein is 111 amino acids, while the E. coli MG1655 and E. coli 0157 :H7 proteins are 171 residues. Twenty altered amino acids are translated after the frame shift and prior to termination of the protein.
  • Our complementation results demonstrate that the AI-2 production defect in
  • E. coli DH5 is recessive to in trans expression of ygaG, which is consistent with the defect being due to a null mutation caused by the frame shift in the E. coli DH5 ygaG gene.
  • S. typhimurium database was searched using the sequence we obtained adjacent to the MudJ that inactivated the AI-2 production function in S. typhimurium CS132.
  • a perfect match (110/110 bp) was identified to fragment B_TR7095.85-T7 in the S. typhimurium LT2 genome sequencing database (Genome Sequencing Center, Washington University, St. Louis) .
  • the S. typhimurium LT2 database -ygaG sequence is incomplete ( Figure 12) .
  • the translated sequence matches the E. coli and V. harveyi sequences beginning at amino acid residue 8.
  • the translated sequence shows that the S. typhimurium protein is 75% identical to LuxS of V. harveyi .
  • In order to align the S. typhimurium sequence with the V. harveyi LuxS protein we corrected three apparent frame shift errors in the database sequence. Considering that only crude, unannotated sequence data is currently available for S. typhimurium, we predict that the S. typhimurium protein contains 7 more amino acids, and that the frame shift mutations are sequencing errors.
  • V. harveyi null mutants in each of the lux genes luxL, luxM, luxN, luxS and luxQ have been constructed.
  • V. harveyi luxS gene has been cloned into E. coli DH5 ⁇ on a broad host range mobilizable cosmid called pLAFR2. This construction restores AI-2 production to E. coli DH5 ⁇ .
  • a marked null mutation was engineered into the luxS gene by introducing a chloramphenicol resistance (Cm r ) cassette into an internal restriction site. Placement of the Cm r cassette at this site in luxS subsequently eliminated AI-2 production in E. coli DH5 ⁇ .
  • Cm r chloramphenicol resistance
  • the luxS: : Cm r null allele was transferred onto the chromosome of V. harveyi strain BB170.
  • Strain BB170 contains a Tn5Kan r in luxN and does not respond to AI-1.
  • triparental conjugations were carried out by mixing stationary phase cultures of E. coli DH5 ⁇ carrying the V. harveyi luxS: :CM r construction in pLAFR2 (pLAFR2 carries tetracycline resistance), E,. ⁇ coli DH5a carrying the tra donor plasmid pRK2013 and the V. harveyi recipient strain BB170.
  • V. harveyi strain MM30 (2uxS::Tn5 ) which is phenotypically AI-1 + , AI-2 "
  • V. harveyi strain BB152 luxM: :Tn5
  • AI-1 and AI-2 present in culture fluids of these strains was tested for stimulation of light production of the V.
  • harveyi luxN, luxS double mutant reporter strain In this assay, autoinducer preparations from MM30, BB152 or sterile medium controls were added to the wells of microtiter plates, followed by the addition of the V. harveyi reporter strain. The resulting light production was monitored using a liquid scintillation counter in the chemiluminescence mode.
  • the aformentioned screen will be optimized for use in 96-well microtiter assays.
  • the screen will be used in inhibitor assays for identifying inhibitors of AI-2.
  • Purified or synthetic AI-2 will be added to the microtiter wells containing the newly constructed reporter strain and inhibition will be measured by a decrease in light emission from the wells containing an inhibitor.
  • the assay will be optimized by determining the concentration of cells and AI-2 in the microtiter wells that will allow- for maximal sensitivity.
  • the optimal AI-2 concentration will be that which stimulates half-maximal light output for a given concentration of cells per unit time.
  • AI-2 acyl- homoserine lactone
  • HSL acyl- homoserine lactone
  • AI-1 from V. harveyi
  • the AI-2 activity does not extract quantitatively into organic solvents. Furthermore, it fails to bind to either a cation or anion exchange column.
  • the present characterization of AI-2 indicates that it has a molecular weight of less than 1000 kDa, and is a polar but apparently uncharged organic compound.
  • the AI-2 activity is acid stable and base labile and heat resistant to about 80 but not 100°C.
  • the present invention in addition to providing a cloned, overexpressed and purified S. typhimurium LuxS protein, the present invention also provides a method for producing AI-2 in vi tro .
  • the present invention provides a mechanism for generating large quantities of pure AI-2 useful for mass spectral and NMR analysis, and for screening compounds which modulate the activity of AI-2.
  • the present invention provides a method for determining the in vivo biosynthetic pathway for AI-2 synthesis.
  • the analysis of the genomic locations of the various luxS genes identified in the present invention indicates that the luxS genes do not consistently reside in any one location in the chromosome, nor are they typisally found in close proximity to any specific gene(s) .
  • the luxS gene is the third gene in a three-gene operon with two genes (metK and pfs) .
  • MetK and Pfs are involved in the conversion of S-adenosyl methionine (SAM) to homocysteine and 4 , 5-dihydroxy-2 , 3 pentanedione ( Figure 15).
  • MetK The function of MetK is to convert methionine to SAM which is an important cofactor in one-carbon metabolism.
  • SAM is used to methylate DNA, RNA and a variety of cell proteins, and several SAM dependent methyl transferases act at this step.
  • S-adenosyl homocysteine (SAH) is produced when the methyl group is transferred from SAM to its substrates.
  • SAH functions as a potent inhibitor of SAM dependent methyltransferases . Therefore, bacteria rapidly degrade SAH via the enzyme Pfs.
  • Pfs refers to an open reading frame in the E.coli genome that has recently been determined to encode the enzyme 5 ' -methylthioadenosine/S- adenosylhomocysteine nucleosidase, also known as MTA/SAH nucleosidase.
  • the enzyme cleaves the glycosidic bond in S-adenosylhomocycteine (SAH) .
  • SAH S-adenosylhomocycteine
  • the function of Pfs is to convert SAH to adenine and S-ribosyl homocysteine.
  • S-ribosyl homocysteine is converted to homocysteine and 4 , 5-dihydroxy-2 , 3- pentanedione .
  • Homocysteine can re-enter this pathway; it is methylated to generate methionine which can be converted to SAM by MetK.
  • the catabolism of SAH is considered a salvage pathway for recycling metabolic intermediates (adenine and homocysteine) .
  • some species of bacteria eliminate SAH by a different pathway.
  • adenosine is directly removed from SAH which generates homocysteine.
  • LuxS is involved in the pathway shown in Figure 15, and SAM and SAH are involved in AI-2 production.
  • the structure of AI-2 could be 4 , 5-dihydroxy-2 , 3 -pentanedione, in which case LuxS is the uncharacterized enzyme that acts on S-ribosyl homocysteine.
  • LuxS could act on one of the intermediates to make AI-2.
  • LuxS would represent a branch point off the known pathway.
  • the gene encoding the S. typhimurium LuxS protein was cloned, overexpressed and the S. typhimurium LuxS protein was purified. This protein was used in combination with dialyzed cell -free extracts prepared from a S.
  • SAM can react with an element in the cell extract before it can be used by LuxS to make AI-2.
  • SAM dependent methyl transferases present in the cell extract use SAM as a methyl donor and convert it to SAH in the process.
  • SAH was substituted for SAM in an in vi tro assay. Addition of SAH to the in vi tro assay resulted in much greater AI-2 production than when SAM was added. This result indicates that LuxS functions in the pathway subsequent to the conversion of SAM to SAH.
  • the proposed pathway shown in Figure 15 is not a salvage pathway for recycling secondary metabolites, but rather is the pathway for production of AI-2.
  • the present invention has narrowed the possibilities for point of LuxS activity in the biosynthesis of AI-2. The remaining possibilities are shown in Figure 15 (designated LuxS?) .
  • AI-2 is a deravitive of ribose. It is noteworthy that, in V. harveyi , LuxP, the primary sensor for AI-2, is a homologue of the E. coli and S. typhimurium ribose binding protein.
  • the invention further provides a method for an in vi tro procedure for large scale production of pure AI-2.
  • SAH is a precursor in the LuxS dependent biosynthesis " of AI-2.
  • LuxS does not act directly on SAH.
  • SAH Prior to the action of LuxS, SAH must first be acted on by some enzyme in dialyzed cell extracts. Presumably this step is the conversion of SAH to S-ribosyl homocysteine by Pfs. Therefore the substrate for LuxS is S-ribosyl homocysteine.
  • the Pfs enzyme can be purified and used to convert SAH to S-ribosyl homocysteine.
  • the pfs gene has been cloned from S. typhimurium 14028 placed into the overexpression vector pLM-1.
  • the Pfs enzyme will be overexpressed and SAH will be added to purified Pfs to produce S-ribosyl homocysteine.
  • the conversion of SAH to S- ribosyl homocysteine will be confirmed by reverse phase HPLC analysis (SAH is UV active while S-ribosyl homocysteine is not) .
  • the S-ribosyl homocysteine produced by Pfs will be added to purified LuxS. Following incubation, the mixture will be filtered over a 5000 MWCO centricon. The filtrate will be tested for AI-2 activity in the previously described V. harveyi bioassay. The identification of activity will confirm that 4 , 5-dihydroxy- 2 , 3 -pentanedione is AI-2.
  • AI-2 structure obtained from E. coli and V. harveyi AI-2 will be determined.
  • the E. coli and V. harveyi luxS genes have been cloned in to overexpression vectors.
  • the identity/biosynthesis of the S. typhimurium AI-2 provided by the present invention should greatly facilitate these analyses. In the event that the S. typhimurium, E. coli and V. harveyi AI-2's are identical these data will indicate that AI-2's are the same.

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Abstract

Cette invention concerne une molécule de signalisation, purifiée, extracellulaire, d'origine bactérienne, appelée autoinducteur 2 dont la production est régulée par des modifications environnementales accompagnant le passage d'une existence libre à une existence colonisatrice ou pathogène dans un organisme hôte. La molécule de signalisation stimule des gènes de luminescence LuxQ et, apparemment, divers gènes en rapport avec la pathogenèse dans l'espèce bactérienne qui produit ladite molécule. Cette invention concerne également une nouvelle classe de gènes bactériens intervenant dans la biosynthèse de la molécule de signalisation.
EP99963011A 1998-12-02 1999-12-02 Compositions et methodes de regulation de la pathogenese bacterienne Withdrawn EP1135144A4 (fr)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US11057098P 1998-12-02 1998-12-02
US110570P 1998-12-02
PCT/US1999/028751 WO2000032152A2 (fr) 1998-12-02 1999-12-02 Compositions et methodes de regulation de la pathogenese bacterienne

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EP1135144A1 true EP1135144A1 (fr) 2001-09-26
EP1135144A4 EP1135144A4 (fr) 2005-07-20

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EP (1) EP1135144A4 (fr)
JP (1) JP2003526327A (fr)
KR (1) KR20010093800A (fr)
AU (1) AU1933800A (fr)
CA (1) CA2351731A1 (fr)
WO (1) WO2000032152A2 (fr)

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JP2003532698A (ja) 2000-05-10 2003-11-05 プリンストン ユニバーシティ 細菌の増殖および病理発生を調節するための化合物ならびに方法
US6416785B1 (en) 2000-08-23 2002-07-09 Biolitec Ag Molecular probes for targeting of cell density-indicating compounds
WO2002088298A1 (fr) * 2001-04-27 2002-11-07 The Procter & Gamble Company Composes, compositions et procedes permettant de reguler des films biologiques
JP2005506953A (ja) * 2001-05-21 2005-03-10 クオレックス・ファーマシューティカルズ・インコーポレーテッド 細菌の調節方法
US7208612B2 (en) 2001-08-24 2007-04-24 Princeton University Crystals of LuxP and complexes thereof
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WO2005072274A2 (fr) * 2004-01-23 2005-08-11 The Trustees Of Princeton University Composes autoinducteurs-2 utilises comme agents immunomodulateurs
WO2005100544A2 (fr) 2004-04-12 2005-10-27 The Trustees Of Princeton University Petits arn et souches bacteriennes impliques dans la mesure de quorum
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WO2009051232A1 (fr) * 2007-10-17 2009-04-23 Kao Corporation Procédé de détermination de l'auto-inducteur 2
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Also Published As

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WO2000032152A3 (fr) 2002-12-12
EP1135144A4 (fr) 2005-07-20
AU1933800A (en) 2000-06-19
KR20010093800A (ko) 2001-10-29
CA2351731A1 (fr) 2000-06-08
JP2003526327A (ja) 2003-09-09
WO2000032152A2 (fr) 2000-06-08

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