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Keywords:

  • Campylobacterales;
  • molecular responses to bile;
  • bile acids;
  • protein homology;
  • domain similarity

Abstract

  1. Top of page
  2. Abstract
  3. Introduction
  4. Background
  5. Materials and methods
  6. Results and discussion
  7. Conclusion
  8. Acknowledgement
  9. References
  10. Supporting Information

Campylobacter, Helicobacter and Wolinella are genera of the order Campylobacterales, belonging to the class Epsilonproteobacteria. Their habitats are various niches in the gastrointestinal tract of higher animals, where they may come into contact with bile. Microorganisms in these environments require mechanisms of resistance to the surface-active amphipathic molecules with potent antimicrobial activities present in bile. This review summarizes current knowledge on the molecular responses to bile by Campylobacterales and other bacterial species that inhabit the intestinal tract and belong to the phyla Proteobacteria, Bacteriodetes, Firmicutes and Actinobacteria. To date, 125 specific genes have been implicated in bile responses, of which 10 are found in Campylobacterales. Genome database searches, analyses of protein sequence and domain similarities, and gene ontology data integration were performed to compare the responses to bile of these bacteria. The results showed that 33 proteins of bacteria belonging to the four phyla had similarities equal to or greater than 50–46% proteins of Campylobacterales. Domain architecture analyses revealed that 151 Campylobacterales proteins had similar domain composition and organization to 60 proteins known to participate in the tolerance to bile in other bacteria. The proteins CmeB, CmeF and CbrR of Campylobacter jejuni involved in bile tolerance were homologous to 42 proteins identified in the Proteobacteria, Bacteriodetes and Firmicutes. On the other hand, the proteins CiaB, CmeA, CmeC, CmeD, CmeE and FlaAσ28 also involved in the response to bile of C. jejuni, did not have homologues in other bacteria. Among the bacteria inhabiting the gastrointestinal tract, the Campylobacterales seem to have evolved some mechanisms of bile resistance similar to those of other bacteria, as well as other mechanisms that appear to be characteristic of this order.


Introduction

  1. Top of page
  2. Abstract
  3. Introduction
  4. Background
  5. Materials and methods
  6. Results and discussion
  7. Conclusion
  8. Acknowledgement
  9. References
  10. Supporting Information

The genera Campylobacter, Helicobacter and Wolinella belong to the order Campylobacterales of the class Epsilonproteobacteria. A principal habitat of these organisms is the gastrointestinal tract of higher animals, where they may come into contact with bile. In this environment they need various levels of tolerance to bile according to their specific niches. Microorganisms require mechanisms of resistance to bile because bile contains surface-active amphipathic molecules with potent antimicrobial activities. Little is known about the molecular mechanisms by which Campylobacterales adapt to bile. This dearth of information may result from the relatively recent recognition of some of the members of the order as important human and animal pathogens, the paucity of molecular data for many bacteria of the gastrointestinal flora, and the lack of genetic and bioinformatic tools with which to conduct comparative studies (Golden et al., 2000).

Many bacteria of the phyla Proteobacteria, Bacteriodetes, Firmicutes and Actinobacteria inhabit the gastrointestinal tract, where bile is present. Molecular studies have shown that these bacteria adapt to the presence of bile using diverse mechanisms. The recent publication of the annotated genomes of Helicobacter hepaticus ATCC 51449 (Suerbaum et al., 2003) and Wolinella succinogenes DSMZ 1740 (Baar et al., 2003), together with those of Campylobacter jejuni strains 11168 and RM1221 (Parkhill et al., 2000; Fouts et al., 2005), and Helicobacter pylori strains 26695 and J99 (Tomb et al., 1997; Alm et al., 1999), makes possible an in silico comparative investigation of the responses to bile of these Campylobacterales and other bacteria. In this study, the known molecular mechanisms of tolerance to bile by Campylobacterales and other bacteria that inhabit the gastrointestinal tract were reviewed and compared employing genome database searches, analyses of protein sequence and domain architecture similarities, and gene ontology data integration. The data provided insights into the potential of these Campylobacterales to adapt to the unique environments in their hosts, and will help to formulate proteomic and transcriptomic studies aimed at understanding the interactions of these human and animal pathogens with endogenous host antimicrobial factors.

Background

  1. Top of page
  2. Abstract
  3. Introduction
  4. Background
  5. Materials and methods
  6. Results and discussion
  7. Conclusion
  8. Acknowledgement
  9. References
  10. Supporting Information

The Campylobacterales

The order Campylobacterales comprises three families: the Campylobacteraceae, which includes the genera Campylobacter, Arcobacter, and Sulfurospirillum; the Helicobacteraceae, which comprises the genera Helicobacter, Wolinella, Sulfuricurvum, Sulfurimonas and Thiovulum; and the Hydrogenimonaceae, which has only the genus Hydrogenimonas. The Campylobacterales known to inhabit the gastrointestinal tract of higher animals belong to the genera Arcobacter, Campylobacter, Helicobacter and Wolinella.

Campylobacter jejuni, H. hepaticus, H. pylori and W. succinogenes are some of the most studied species of their respective genera. They are microaerophilic slender Gram-negative rods, which can be straight, curved or helical, and are motile by polar flagella. Campylobacter jejuni cells are spiral-, comma-, or ‘S’-shaped. The bacterium has a wrinkled surface owing to the outer bipolar lipid layer, with the lipid moiety of a lipopolysaccharide layer embedded in it (Hoffman et al., 1979; Wassenaar & Newell, 2005). Morphologically, H. hepaticus cells are curved to spiral rods, with one to several spirals and one bipolar sheathed flagellum at each end, but they lack the periplasmic fibers that envelope the bacterial cells in other Helicobacter species (Schauer, 2001). Helicobacter pylori has a spiral shape, and in stationary phase it forms coccoid cells. This bacterium has up to seven polar sheathed flagella, and a unique composition of fatty acids in the cell wall giving it a smooth surface (O'Rourke & Bode, 2001). The cells of W. succinogenes are helical, curved or straight with rounded or tapered ends and a single polar nonsheathed flagellum (Simon et al., 2005).

Bacteria of these genera are associated with infections in humans and animals. Campylobacter jejuni is the most frequent cause of bacterial diarrhoea in humans in the developed world. It is transmitted to humans through contaminated food, primarily undercooked poultry or meat, and can also be transmitted in contaminated water. The diarrhoea probably results from the production of an enterotoxin and the destruction of intestinal epithelial cells by a cytotoxin or invasin. Helicobacter pylori colonizes the gastric mucus, where it causes inflammation, and is associated with gastritis, peptic ulcers, and some gastric cancers. More than 80% of peptic ulcer patients have H. pylori infections, and about 50% of all adults are chronically infected, with higher percentages in some developing countries (Madigan et al., 2000). Helicobacter hepaticus infects the liver of mice, inducing chronic hepatic inflammation, and subsequently liver cancer in a low percentage of certain breeds (Fox et al., 1994). In addition, the bacterium has been linked to inflammatory bowel disease in immuno-compromised mice (Cahill et al., 1997). Currently, W. succinogenes is not associated with any disease, but it is considered a potential pathogen of humans and animals. It has an extensive repertoire of genes homologous to known bacterial virulence factors (Baar et al., 2003). Organisms resembling W. succinogenes have been isolated from sewage (Yoshinari, 1980; Tanner et al., 1984), and DNA belonging to the genus Wolinella has been identified in 40% of South African patients suffering from oesophageal carcinoma (Bohr et al., 2003).

Bile

Bile is produced in the liver, concentrated and stored in the gall bladder, and eventually released into the intestine. It helps in the emulsification and hydrolysis of fats, contributing to their digestion and absorption. It participates also in the elimination of waste products from the body. Bile is composed of bile salts, lipids, proteins, ions such as Na+, K+, Ca2+, Cl, HCO3, cyclic alcohol derivatives, pigments such as bilirubin and biliverdin, and small metabolites such as creatinine, etc. The lipids include cholesterol, phospholipids, fatty acids and triglycerides. Immunoglobulins are the major protein components (Hofmann, 1998); alkaline phosphatase and other enzymes are also present. The synthesis of bile involves the conversion of cholesterol to bile acids, which enter the bile as glycine or taurine conjugates; for cholic acid, these are called glycocholates and taurocholates, respectively (Agellon & Torchia, 2000). Bile acids are surface-active amphipathic molecules, which exhibit the antimicrobial activities of detergents. Cholic and chenodeoxycholic acids are primary bile acids that can be converted by bacteria in the gut into secondary bile acids such as deoxycholic and lithocholic acids. Primary and secondary bile acids can be reabsorbed actively in the ileum and passively along the entire gut. Thus, in addition to de novo synthesis of bile acids, salvage of these compounds takes place by reabsorption in the distal small intestine and the gut (Gunn, 2000).

There are differences in the bile acid compositions of different vertebrate species. Under physiological conditions, the pool of bile acids in humans is made up of c. 40% cholic acid, 40% chenodeoxycholic acid and 20% deoxycholic acid, with traces of ursodeoxycholic acid and lithocholic acid (Carulli et al., 2000). The predominant bile acids in fowl, mice and cattle are chenodeoxycholic, muricholic and cholic acids, respectively (Washizu et al., 1991; van Nieuwerk et al., 1997). Generally, unconjugated bile acids are more toxic than conjugated bile acids. The bactericidal effect of different bile acids is associated with the number of hydroxyl groups linked to the nonpolar steroid nucleus: dihydroxy-acids are usually more toxic than trihydroxy-acids (Binder et al., 1975; Floch et al., 1971; Huhtanen, 1979). The bactericidal potency of bile acids is, in addition, modulated by other factors such as the positions of hydroxyl groups in the steroid nucleus. For example, chenodeoxycholic acid and deoxycholic acid have the same number of hydroxyl groups, but the latter is more toxic (Hanninen, 1991): in chenodeoxycholic acid the hydroxyl groups are at positions 3 and 7, and in deoxycholic acid they are at positions 3 and 12. Differences in toxicity depend also on the pKa value of the bile acid, which determines its ionization degree under physiological conditions: nonionized forms are more lipid-soluble and diffuse more easily across the bacterial membrane than ionized forms (Percy-Robb & Collee, 1972; Binder et al., 1975). The partition coefficient also plays a significant role in determining the toxicity of bile acids (Hofmann & Roda, 1984).

High concentrations of bile salts commonly used by organic biocides to achieve rapid antimicrobial action produce a generalized effect of disrupting the lipid bilayer of cell membranes. Bile salts can break up the bilayer into small disk-like fragments, or can be first incorporated into the membrane and then solubilize it by freeing mixed micelles made up of bile salts, membrane lipids and proteins. Tolerance to bile salts is essential in order for bacteria to be able to adapt and survive in the gastrointestinal tract. Consequently, normal and pathogenic intestinal microbial communities have evolved multiple mechanisms to resist the effects of bile.

Materials and methods

  1. Top of page
  2. Abstract
  3. Introduction
  4. Background
  5. Materials and methods
  6. Results and discussion
  7. Conclusion
  8. Acknowledgement
  9. References
  10. Supporting Information

A comprehensive review of the interactions of bacteria with bile was performed in order to identify specific genes known to be involved in responses to bile.

fasta formats of the protein sequences encoded by genes implicated in bacterial responses to bile were generated, and used to identify homologous proteins in the proteomes of the Campylobacterales employing the Basic Local Alignment Search Tool for proteins (blastp) of the National Centre for Biotechnology Information (NCBI). Conversely, the protein sequences encoded by genes known to participate in bile responses in the Campylobacterales were used to identify homologous proteins in the proteomes of other bacteria. Proteins with sequence similarity ≥50% were considered homologous. Domain architecture analyses were carried out employing the Simple Modular Architecture Research Tool (SMART) to identify Campylobacterales proteins that have common functional motifs with proteins involved in bile responses in other bacteria, and did not have sufficient sequence similarities.

Functional classifications of proteins were carried out using the Database for Annotation, Visualization and Integrated Discovery (DAVID 2.1) (http://david.abcc.ncifcrf.gov/). SWISS-PROT accession numbers of the proteins were generated, compiled into a file, uploaded and analysed at a medium classification stringency. The analysis parameters were: kappa similarity overlap of 4; 0.35 similarity threshold; initial and group membership classification of 4; and 0.5 group terms frequency. The program searched at random 14 functional annotation sources and classified highly related genes into functional groups. The functional groups generated were compared with the gene functions reported in the literature. Pathway analyses were performed employing the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database (http://www.genome.jp/kegg/pathway.html).

Results and discussion

  1. Top of page
  2. Abstract
  3. Introduction
  4. Background
  5. Materials and methods
  6. Results and discussion
  7. Conclusion
  8. Acknowledgement
  9. References
  10. Supporting Information

Bacteria identified in molecular responses to bile

Studies on the molecular mechanisms of bacterial responses to bile have been reported in 16 genera belonging to 11 orders of both Gram-negative and Gram-positive bacteria. The genera (order) are: Escherichia, Salmonella, Shigella, Yersinia (Enterobacteriales); Pseudomonas (Pseudomonadales); Vibrio (Vibrionales); Bacteroides (Bacteriodales); Campylobacter (Campylobacterales); Listeria (Bacillales); Clostridium (Clostridales); Eubacterium (Eubacteriales); Enterococcus, Lactobacillus, Streptococcus (Lactobacillales); Propionibacterium (Actinomycetales); and Bifidobacterium (Bifidobacteriales) (Supplementary Tables S1 and S2). These bacteria live in the gastrointestinal tract of higher vertebrates as either autochtonous or pathogenic flora, with the exception of Pseudomonas, which are found principally as free-living organisms in a diversity of natural environments and in association with plants and animals.

Bacterial genes associated with bile responses

A total of 125 distinct genes have been implicated in bacterial responses to bile (Tables S1 and S2). Ten of these genes were identified in Campylobacterales, 59 in Gammaproteobacteria, 1 in Bacteriodetes, 22 in Firmicutes, and 36 in Actinobacteria. The molecular responses to bile have been studied in greater detail in Bifidobacteria spp. (34 genes), Escherichia coli (27 genes) and Salmonella spp. (24 genes). Significantly less well studied are the responses to bile of Shigella spp. (three genes), Yersinia spp. (one gene), Vibrio spp. (nine genes), Pseudomonas spp. (three genes), Bacteroides spp. (one gene), Listeria spp. (10 genes), Clostridium spp. (seven genes), Eubacterium spp. (one gene), Enterococcus spp. (five genes), Lactobacillus spp. (three genes), Propionibacterium spp. (three genes), and Streptococcus spp. (three genes). Information exists on Pseudomonas aeruginosa that focus on its ability to utilize bile as a source of carbon. No genes have been identified as yet in the bile responses of bacteria found in the gastrointestinal tract belonging to the genera Klebsiella, Serratia, Proteus, Enterobacter and Citrobacter.

The gene ontology data integration tool DAVID was employed to classify the genes implicated in bacterial responses to bile into functional groups. The protein functional groups were chaperones, heat shock, membrane, regulation, secretion, and transport. The number of distinct categories identified indicates that bacteria utilize a variety of mechanisms in response to bile. These include the production of virulence factors, expressing efflux pumps, modulating the synthesis of lipopolysaccharide and of porins, and up-regulating the expression of specific enzymes such as bile salt hydrolase and superoxide dismutase (Sod).

The limited number of genes reported in the adaptation of bacteria to bile (Tables S1 and S2) reflects the relatively small number of studies conducted on the molecular mechanisms of these responses. Many physiological studies on the bile tolerance of bacteria that inhabit the gastrointestinal tract have been performed mainly for probiotic research, with analyses focused on the screening for bacteria strains capable of adapting effectively to the intestinal tract (Noh & Gilliland, 1993; Jacobsen et al., 1999; Kimoto et al., 1999, 2000, 2002; Hyronimus et al., 2000; Kim et al., 2002; Margolles et al., 2002).

Cholic acid and deoxycholic acid were the predominant bile acids used in the various studies on molecular responses by bacteria (Tables S1 and S2). Most studies on bile adaptation have employed ox-bile, with human and porcine bile used less extensively. The availability of ox-bile and its wide use in probiotic studies to assess in vitro tolerance of bile by bacteria may be important factors that determine its general use, and thus make it the reference bile; for example, strains of bacteria that survive 0.3% ox-bile concentration are considered tolerant. No studies have been reported on the molecular responses of bacteria to chicken or mouse bile, which Campylobacterales such as C. jejuni, H. hepaticus and H. bilis would come into contact with in their infection and colonization of these animals.

Few studies on the molecular mechanisms of responses to bile by bacteria have employed global techniques such as proteomics or transcriptiomics in their investigations. Notable exceptions are the studies by van Velkinburgh & Gunn (1999), Leverrier et al. (2003) and Flahaut et al. (1996) (Tables S1 and S2). Most studies have used gene mutation and inactivation, transcriptional regulation, and/or a transposon-directed approach targetting specific gene loci, such as those involved in the adaptation of bacteria to various other stresses. Thus, it is difficult to obtain systematic information on the effects of various types of bile on the same or different genes of a given bacterium. Nonetheless, studies by Flahaut et al. (1996) revealed that various proteins were differentially expressed in Salmonella typhimurium and Salmonella typhi in response to ox-bile or deoxycholate. In S. typhimurium, 3% ox-bile resulted in the up-regulation of 14 proteins and down-regulation of one protein; and 1% deoxycholate up-regulated seven proteins, and down-regulated another seven. In contrast, in S. typhi the presence of 3% ox-bile up-regulated one protein and down-regulated one; and the presence of 1% deoxycholate up-regulated two proteins and down-regulated four. These findings demonstrated that molecular bile responses in bacteria can be species-specific.

In spite of the importance of gastrointestinal Campylobacterales to human and animal health, very little is known about the molecular mechanisms of adaptation to antimicrobials such as bile salts present in the intestinal environment, and much of what is known refers to C. jejuni. Helicobacter pylori shows some bile tolerance, but exposure to several bile acids changes its morphology from bacillar helical rods to a spherical shape with blebs on the cell surface (Itoh et al., 1999). Helicobacter hepaticus is found in the hepatobiliary tree of several mammals, indicating that this bacterium tolerates bile. No studies have been performed on the effects of bile on W. succinogenes.

In silico analyses

Genomic analyses have indicated varying degrees of homology between Campylobacterales proteins and 114 proteins encoded by genes implicated in bile responses in the phyla Proteobacteria, Bacteriodetes, Firmicutes and Actinobacteria. Amongst these proteins, 32 showed greater than 50% similarity to 46 proteins of Campylobacterales, 29 of which were identified in C. jejuni, 26 in H. hepaticus, 23 in H. pylori and 30 in W. succinogenes (Supplementary Table S3). The number of proteins potentially involved in the responses to bile in the four Campylobacterales species studied reflects the different sizes of their genomes: the numbers of genes in the genomes of C. jejuni, H. hepaticus, H. pylori and W. succinogenes are 1875, 1598, 1491 and 2048, respectively. It should be noted, however, that the in silico analyses in this study were limited to genes known to be implicated in bile responses, and thus biased towards the better-studied E. coli, Salmonella spp., and Bifidobacterium spp., which together make up 74% of the total number of these genes (Tables S1 and S2). Thus, the homologues found in Campylobacterales to proteins involved in bile responses in other bacteria constitute only a subset of the putative array of proteins employed by the former in their responses to bile. Nonetheless, these findings suggested that Campylobacterales could employ multiple mechanisms to adapt to the presence of bile.

To determine if proteins similar to those employed by the Campylobacterales in bile responses were encoded by other bacteria, the sequences of C. jejuni CbrR, CiaB, CmeABCDEFR and FlaAσ28 were compared with the entire proteomes of species of Gammaproteobacteria, Bacteriodetes, Firmicutes and Actinobacteria known to tolerate bile. Forty-two homologues of CmeB, CmeF and CbrR with similarities between 55% and 59%, 50% and 53%, and 51% and 70% were found in the Gammaproteobacteria, Bacteriodetes and Firmicutes, respectively (Table 1). A 45% similarity was determined between the CmeA of C. jejuni and the AcrA of E. coli. These data suggest that there could be mechanisms of bile resistance common to the Campylobacterales and the other bacteria.

Table 1.   Proteins implicated in Campylobacterales responses to bile with homology to proteins of other bacteria
Camylobacterales proteinsGammaproteobacteria, Bacteriodetes and FirmicutesSimilarity (%)Protein definition
CmeBE. coli K1259Aminoglycoside/multidrug efflux pump (RND family)
Shigella flexneri 2a str 2457T59Multidrug resistance protein
E. coli 0157:H7 EDL93359Sensitivity to acriflavine, integral membrane protein, possible efflux pump
Sal. enterica serovar Typhi str CT1859Putative efflux pump
Sal. typhimurium LT259Aminoglycoside/multidrug efflux pump
Sal. typhimurium LT258Multidrug transport protein
Yersinia pestis CO9258Multidrug efflux protein; putative efflux pump
E. coli K1258Acridine efflux pump
E. coli CFT07358Acraflavine resistance protein B
Shigella flexneri 2a str2457T58Acraflavine resistance protein
E. coli 0157:H758Putative transport system permease protein
E. coli CFT07358Hypothetical protein YhiV
E. coli K1258Multidrug transport protein, RpoS-dependent (RND family); putative transport system permease protein
E. coli 0157:H7 EDL93358Putative transport system permease protein
Yersinia pseudotuberculosis IP 3295357RND family, acridine/multidrug efflux pump
Sal. typhimurium LT257Acridine efflux pump
Sal. enterica serovar typhi57Acriflavine resistance protein B
E. coli CFT07357Acriflavine resistance protein F
E. coli K1257Integral transmembrane protein; acridine resistance; multidrug transport protein, acriflavine resistance protein F (RND family)
Shigella flexneri 2a str 30157Acridine efflux pump
Sal. typhimurium LT257Putative action efflux system protein
Y. pseudotuberculosis IP 3295357HAEI family (RND superfamily) multidrug efflux protein
Y. pestis CO9256Putative integral membrane efflux protein
Y. pseudotuberculosis IP 3295356Multidrug efflux protein, RND family
Y. pestis CO9256Multidrug efflux protein
Y. pestis biovar Mediavalis str 9100156Multidrug efflux protein
Shigella flexneri 2a str 30155Hypothetical protein SF3598
E. coli 0157:H755Fragment of integral transmembrane protein involved with acridine resistance
CmeFClostridium beijerincki NCIMB 805253Outer membrane efflux protein
Bacteroides thetaiotaomicron VPI-548252Putatitive cation efflux transporter
Cl. beijerincki NCIMB 805250Putative acriflavine resistance protein D
Yersinia frederiksenii ATCC 3364150Cation/multidrug efflux pump
Clostridium difficile QCD-32g5851Cation/multidrug efflux pump
Bacteroides fragilis YCH4651Putative cation efflux transporter
B. fragilis NCTC 934351Putative transmembrane Acr-type transport protein
Vibrio cholerae N1696150Putative multidrug resistance protein
Vibrio parahaemolyticus RIMD 221063350Putative multidrug resistance protein
V. cholerae RC38550Cation/multidrug efflux pump
E. coli K1250Multidrug transport protein
CbrRStreptococcus thermophilus70Polar amino acid ABC uptake transporter substrate binding protein
Lactobacillus johnsonii61ABC transporter solute binding component
Lactobacillus acidophilus NCFM59Glutamine ABC transporter substrate-binding protein

Domain architecture analyses were carried out to identify Campylobacterales proteins that have common functional motifs with proteins involved in bile responses in other bacteria. A total of 59 bacterial proteins belonging to the functional categories of membrane/transport (20), secretion/regulation (23), heat shock (three), metabolism (10) and other general metabolism enzymes (three) exhibited sequence and domain similarities to 151 Campylobacterales proteins (Tables 2 and 3), suggesting that the latter may also take part in the resistance to bile of Campylobacterales. Functional classification revealed that out of the 151 homologues identified in the Campylobacterales 75 are membrane/transport proteins, 50 are secretion/regulation proteins, 18 are enzymes of central metabolism, five are enzymes of bile metabolism, and three are homologues of heat-shock proteins (Tables 2 and 3). The high number of Campylobacterales membrane/transport protein homologues identified suggest that a major mode of bile resistance in the Campylobacterales is by transport of bile out of the cytoplasm, and that these bacteria could employ multiple transport systems, which may interact to enhance bile resistance as observed in C. jejuni by Akiba et al. (2005). The results further indicate that the Campylobacterales could modify several membrane proteins in response to bile, a finding that reflects the fact that bile primarily exerts its effects on cell membranes (Albalak et al., 1996; Fujisawa & Mori, 1996; Pazzi et al., 1997; De Boever et al., 2000).

Table 2. Campylobacterales proteins with domain similarities and sequence homology to proteins implicated in the response to bile in other bacteria
Bacterial proteinDomain name/accession number/descriptionCampylobacterales speciesAccession numberProtein description
  • *

    Campylobacterales proteins that have both sequence and domain similarities to proteins implicated in the bile response in other bacteria.

  • Campylobacterales proteins that show domain but not sequence similarity to proteins implicated in the bile response in other bacteria.

AckAAcetate_kinase/PF00871/Acetokinase familyC. jejuniQ9PPL 8Acetate kinase*
 H. hepaticusQ7VGL3Acetate kinase *
 H. pyloriQ9ZKU5Acetate kinase*
AcrAHlyD/PF00529/HlyD family secretion proteinC. jejuniQ9PHR0Putative periplasmic protein
  Q9P ID5Putative membrane fusion component of efflux system
 H. hepaticusQ7VF21Hypothetical protein
  Q7VJR8Conserved hypothetical membrane protein
 H. pyloriP9485136 kDa antigen
 W. succinogenesQ7M8T9Periplasmic component of efflux system
  Q7M9I1Multidrug efflux membrane protein
  Q7M9Q0Acriflavin resistance protein A*
  Q7MA86Cation efflux system
AcrBACR_tran/PF00873/AcrB/AcrD/AcrF familyC. jejuniQ9PID6Transmembrane efflux protein*
  Q9PNQ8Putative integral membrane component of efflux system
 H. hepaticusQ7VII0Hypothetical protein
  Q7VJR9Conserved hypothetical membrane protein*
 H. pyloriO25328Acriflavine resistance protein
  O25622Cation efflux system protein
  Q9ZLM5Putative efflux transporter
 W. succinogenesQ7M912RND pump protein
  Q7M9I0Multidrug efflux transporter*
  Q7M9P9Multidrug resistance protein MexB*
  Q7MA85Acriflavin resistance protein D
  Q7MAL3Cation efflux, AcrB/AcrD/AcrF family
DnaKClp_N/PF02861/Clp amino terminal domain AAA/Sm00382/ATPases associated with a variety of cellular activitiesC. jejuniQ9PI02ATP-dependent Clp protease ATP-binding subunit*
 H. hepaticusQ7VJY3ATP-dependent Clp protease ClpA*
 H. pyloriP71 404ClpB protein
 W. succinogenesQ7M9X4Clp protease ATP-binding subunit*
ClpBClp_N/PF02861/Clp amino terminal domain AAA/Sm00382/ATPases associated with a variety of cellular activitiesC. jejuniQ9PI02ATP-dependent Clp protease ATP-binding subunit*
 H. hepaticusQ7VJY3ATP-dependent Clp protease ClpA*
 H. pyloriP71 404ClpB protein
 W. succinogenesQ7M9X4Clp protease ATP-binding subunit
EfpEFP/pf01132/Elongation factor P (Ef-P) OB domainC. jejuniQ9PHW3Translation elongation factor P*
 H. hepaticusQ7VJY4Translation elongation factor P*
 H. pyloriP56 004Translation elongation factor P*
 W. succinogenesQ7M904Translation elongation factor P*
FrrRRF/PF01765/Ribosome recycling factorC. jejuniQ9PIR0Ribosome recycling factor*
 H. hepaticusQ7VJ10Ribosome recycling factor*
 H. pyloriP56398Ribosome recycling factor*
 W. succinogenesQ7MAD8Ribosome recycling factor*
GapGp_dh_N/PF00044/Glyceraldehyd 3-phosphate dehydrogenase, NAD binding domain Gp_dh_C/PF02800/Glyceraldehyde 3-phosphate dehydrogenase C-binding domainC. jejuniQ9PMQ4Glyceraldehyde-3-phosphate dehydrogenase*
 H. hepaticusQ7VH10Glyceraldehyde-3-phosphate dehydrogenase*
 H. pyloriO25902Glyceraldehyde-3-phosphate dehydrogenase*
 W. succinogenesQ7M9C4Glyceraldehyde 3-phosphate dehydrogenase*
GatAAmidase/PF01425/AmidaseC. jejuniQ9PNN2Glutamyl-tRNA(Gln) amidotransferase subunit A*
 H. hepaticusQ7VIA7Glutamyl-tRNA(Gln) amidotransferase subunit A*
 H. pyloriP56114Glutamyl-tRNA(Gln) amidotransferase subunit A*
 W. succinogenesQ7M842Glutamyl-tRNA(Gln) amidotransferase subunit A*
  Q7M984Putative urea amidolyase
GltXtRNA-synt_1c/PF00749/tRNA synthetases class I (E and Q), catalytic domainC. jejuniO52914Glutamyl-tRNA synthetase 1 (Glutamate-tRNA ligase 1) (GluRS 1)*
 H. hepaticusQ7VHN8Glutamyl-tRNA synthetase (Glutamate-tRNA ligase) (GluRS)
 H. pyloriO25360GlutamylGlutaminyl-tRNA synthetase (GluGlnRS) (Glutamyl-tRNA synthetase 2) (Glutamate-tRNA ligase 2) (GluRS 2)*
 W. succinogenesQ7M7L9Glutamyl-tRNA synthetase (Glutamate – tRNA ligase) (GluRS)*
GroELCpn60_TCP1/PF00118/TCP-1/cpn60 chaperonin familyC. jejuniO6928960 kDa chaperonin (Protein Cpn60) (GroEL protein)*
 H. hepaticusQ7U31760 kDa chaperonin (Protein Cpn60) (GroEL protein)*
 H. pyloriP4238360 kDa chaperonin (Protein Cpn60) (GroEL protein)*
 W. succinogenesQ7MAE360 kDa chaperonin (Protein Cpn60) (GroEL protein)*
GroESCpn10/PF00166/Chaperonin 10 Kd subunitC. jejuniP5697010 kDa chaperonin (Protein Cpn10) (GroES protein)
 H. hepaticusQ7U318Chaperone protein HspA (GroES/HSP10 family)*
 H. pyloriP4822510 kDa chaperonin (Protein Cpn10) (GroES protein)
 W. succinogenesQ7MAE2Heat shock protein groES*
HtrMEpimerase/PF01370/NAD dependent epimerase/dehydratase familyC. jejuniQ9PMY0Putative nucleotide sugar dehydratase
  Q9PNE4ADP-l-glycero-d-manno-heptose-6-epimerase*
  Q9PNG3UDP-glucose 4-epimerase
 H. hepaticusQ7VFZ2ADP-l-glycero-d-manno-heptose-6-epimerase
  Q7VIF9Nucleotide sugar dehydratase
  Q7VJ63UDP-glucose 4-epimerase
  Q7VJZ3DTDP-d-glucose 4,6-dehydratase
 H. pyloriO25127UDP-glucose 4-epimerase
  O25530ADP-l-glycero-d-manoheptose-6-epimerase
 W. succinogenesQ7M9U2Glycero-mannoheptose6-epimerase
  Q7MAU1Putative UDP-glucuronic acid epimerase
Ldh2Ldh_1_N/PF00056/lactate/malate dehydrogenase, NAD binding domain Ldh_1_C/PF02866/lactate/malate dehydrogenase, alpha/beta C-terminal domain Pyr_redox/PF00070/Pyridine nucleotide-disulphide oxidoreductase NAD_Gly3P_dh_N/PF01210/NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus HCDH_N/PF02737/3-hydroxyacyl-CoA dehydrogenase, NAD binding domainC. jejuniYP179288l-lactate dehydrogenase*
  CAB75168Malate dehydrogenase*
 H. hepaticusNP861102Malate dehydrogenase*
 W. succinogenesNP907262Malate dehydrogenase*
LytBLYTB/PF02401/LytB proteinC. jejuniP 9 4 6 444-Hydroxy-3-methylbut-2-enyl diphosphate reductase
 H. hepaticusQ7VJV5Penicillin tolerance protein LytB*
 H. pyloriO251 604-Hydroxy-3-methylbut-2-enyl diphosphate reductase
 W. succinogenesQ7M8Y6Fusion penicillin tolerance LytB domain N-terminus and S1 ribosomal protein C-terminus*
 C. jejuniQ9PM25Methionine aminopeptidase*
 H. hepaticusQ7VGC4Methionine aminopeptidase*
  Q7VHM2Hypothetical protein
 H. pyloriO256 81Hypothetical protein HP1037
  P56102Methionine aminopeptidase*
  Q9ZM36Putative proline peptidase
 W. succinogenesQ7M8F2Methionine aminopeptidase*
  Q7M 8I2Proline aminopeptidase
MexAHlyD/PF00529/HlyD family secretionC. jejuniQ9PHR0Putative periplasmic protein
  Q9PID5Putative membrane fusion component of efflux system
 H. hepaticusQ7VF21Hypothetical protein
  Q7VJR8Conserved hypothetical membrane protein
 H. pyloriP9485136 kDa antigen
 W. succinogenesQ7M8T9Periplasmic component of efflux system
  Q7M9I1Membrane fusion protein MexC RND multidrug efflux membrane fusion protein MexC*
  Q7M9Q0Acriflavine resistance protein A*
  Q7MA86Cation efflux system
MexBSecD_SecF/PF02355/Protein export membrane protein CR_tran/PF00873/AcrB/AcrD/AcrF familyC. jejuniCAB73511Putative transmembrane efflux pump*
 H. hepaticusNP860995Conserved hypothetical protein*
 H. pyloriNP223272Putative efflux transporter*
 W. succinogenesNP907912Multidrug efflux transporter*
OprMOEP/PF02321/Outer membrane efflux proteinC. jejuniQ 9 PHQ8Putative outer membrane protein
  Q 9 P ID7Putative outer membrane channel protein
  Q 9 PNR0Putative outer membrane component of efflux system
 H. hepaticusQ 7 V F20Hypothetical protein
 H. pyloriO 2 6 0 22Lipase-like protein
  Q 9 Z JD0Putative
 W. succinogenesQ 7 M8U1Probable outer membrane protein
  Q 7 M9H9Outer membrane channel protein*
  Q 7 M SI3Hypothetical protein
PalOmpA/PF00691/OmpA familyC. jejuniQ 4 6 1 23Peptidoglycan associated lipoprotein precursor*
  Q 9PHR7Putative periplasmic protein
  Q9 P IG4Putative flagellar motor protein
  Q 9 PMI4Outer membrane fibronectin-binding protein
 H. hepaticusQ 7 V IV2Flagellar motor component MotB
  Q 9 X 691Hypothetical membrane-associated protein Map18*
 H. pyloriO 2 5 7 50Peptidoglycan associated lipoprotein precursor
  P 5 6 4 2 7Chemotaxis MotB protein (Motility protein B)
  Q 9 Z K87Putative outer membrane protein
 W. succinogenesQ 7 MAF3MotB protein
  Q 7 M SF2Lipoprotein
  Q 7 M SR2Outer membrane cation-ion binding protein
PhoPREC/SM00448/cheY-homologous receiver domain Trans_reg_C/PF00486/Transcriptional regulatory protein, C terminalC. jejuniO 6 8 7 9 5Response regulator protein (two-component regulator)*
  Q 9 P I E 6Two-component regulator*
  Q 9 P P 4 1Putative sensory transduction transcriptional regulator
 H. hepaticusQ 7 V FH9Hypothetical protein*
  Q 7 V FR7Two-component system response regulator
 H. pyloriO 2 4 9 7 3Response regulator OmpR*
  Q 9 Z MR6Putative transcriptional regulator*
 W. succinogenesP 7 4 9 6 8Response regulator of two-component regulatory system*
  Q 7 M 7M9Transcriptional regulator (PhoB-like)*
  Q 7 M 8 10Signal transduction regulatory protein-CheY like receiver domain
  Q 7 M 8 85Response regulator OmpR*
  Q 7 M 8N6Response regulator OmpR-CheY-like and winged-helix DNA-binding domain
  Q 7 M 9 F8Sensory transduction regulator
  Q7 M 9 v 5Transcriptional activator protein CopR*
PgkPGK/PF00162/Phosphoglycerate kinaseC. jejuniQ 9 P MQ5Phosphoglycerate kinase*
 H. hepaticusQ 7 V J B 6Phosphoglycerate kinase*
 H. pyloriP 5 6 1 5 4Phosphoglycerate kinase*
 W. succinogenesQ 7 M 9 C1Phosphoglycerate kinase*
PheSPhe_tRNA-synt_N/PF02912/ Aminoacyl tRNA synthetase class II, N-terminal domain tRNA-synt_2d/PF01409/tRNA synthetases class II core domain (F)C. jejuniQ 9 P P 3 4Phenylalanyl-tRNA synthetase alpha chain (Phenylalanine -tRNA ligase alpha chain) (PheS)*
 H. hepaticusQ 7 VK64Phenylalanyl-tRNA synthetase alpha chain (Phenylalanine-tRNA ligase alpha chain), PheS*
 H. pyloriP 5 6 1 46Phenylalanyl-tRNA synthetase alpha chain (Phenylalanine-tRNA ligase alpha chain), PheS*
 W. succinogenesQ 7 M8Y9Phenylalanyl-tRNA synthetase alpha chain (Phenylalanine-tRNA ligase alpha chain), PheS*
PmrASulfatase/PF00884/SulfataseC. jejuniQ 9 P I N9Putative integral membrane protein*
 H. hepaticusQ 7 V FK2Hypothetical protein*
 H. pyloriO 2 4 8 6 7Conserved hypothetical integral membrane protein
  O 2 5 3 0 1Hypothetical protein
 W. succinogenesQ 7MSA 0Hypothetical protein*
ProStRNA-synt_2b/PF00587/tRNA synthetase class II core domain (G, H, P, S and T) HGTP_anticodon/PF03129/ Anticodon binding domainC. jejuniQ 9 P HX1Prolyl-tRNA synthetase*
  Q 9 P I S 3Threonyl-tRNA synthetase
  Q 9 P P F4Histidyl-tRNA synthetase (Histidine-tRNA ligase), HisRS
 H. hepaticusQ 7 V F 68Histidyl-tRNA synthetase (Histidine-tRNA ligase) HisRS
  Q 7 V F F0Prolyl-tRNA synthetase*
  Q 7 V J 0 9Threonyl-tRNA synthetase
 H. pyloriP 5 6 0 7 1Threonyl-tRNA synthetase
  P 5 6 1 2 4Prolyl-tRNA synthetase*
  P 5 6 4 5 5Histidyl-tRNA synthetase (Histidine-tRNA ligase) HisRS*
 W. succinogenesQ 7M 8 L1Prolyl-tRNA synthetase*
  Q 7 M 8S6Histidyl-tRNA synthetase (Histidine-tRNA ligase) HisRS
  Q 7M9M0Threonyl-tRNA synthetase
PurHMGS/PF02142/MGS-like domain AICARFT_IMPCHas/PF01808 bienzymeC. jejuniQ 9 PNY2Bifunctional purine biosynthesis*
 H. hepaticusQ 7 V IX1AICAR transformylase PurH *
 W. succinogenesQ 7 M848Bifunctional purine biosynthesis *
PykPK/PF00224/Pyruvate kinase, barrel domain PK_C/PF02887/Pyruvate kinase, alpha/beta domainC. jejuniQ 9 PIB0Pyruvate kinase*
PyrGCTP_synth_N/PF06418/CTP synthase N-terminus GATase/PF00117Glutamine amidotransferase class-IC. jejuniQ 9 PJ84CTP synthase*
 H. hepaticusQ7VGH1CTP synthase*
 H. pyloriO 2 5116CTP synthase*
 W. succinogenesQ7MAI3CTP synthase*
RpsBRibosomal_S2/PF00318/Ribosomal protein S2C. jejuniQ9P NB330S Ribosomal protein S2*
 H. hepaticusQ7 VH9530S Ribosomal protein S2*
 H. pyloriP 5 6 0 0930S Ribosomal protein S2*
 W. succinogenesQ7MAK030S Ribosomal protein S2*
SodASod_Fe_N/PF00081/Iron/manganese superoxide dismutase, alpha-hairpin domain Sod_Fe_C/PF02777/Iron/manganese superoxide dismutase, C-terminal domainC. jejuniP 5 3 6 40Superoxide dismutase [Fe]*
 H. hepaticusQ 7 V F46Superoxide dismutase
 H. pyloriP 4 3 3 12Superoxide dismutase [Fe]*
 W. succinogenesQ 7 M864Superoxide dismutase*
TktTransketolase_N/PF00456/Transketolase, thiamine diphosphate binding domain Transket_pyr/PF02779/Transketolase, pyridine binding domain Transketolase_C/PF02780/Transketolase, C-terminal domainC. jejuniQ 9PM31Transketolase*
 H. pyloriO 2 5 720Transketolase A*
 W. succinogenesQ7M9Z7Transketolase A*
TufGTP_EFTU/PF00009/Elongation factor Tu GTP binding domain GTP_EFTU_D2/PF03144/Elongation factor Tu domain 2 GTP_EFTU_D3/PF03143/Elongation factor Tu C-terminal domainC. jejuniO 6 9303Translaion elongation factor EF-Tu*
 H. hepaticusQ 7VJ74Translation elongation factor EF-Tu *
 H. pyloriP5 6 003Translation elongation factor EF-Tu*
Table 3. Campylobacterales proteins with domain similarities but no sequence homology to proteins implicated in the response to bile in other bacteria
Bacterial proteinDomain name/accession number/descriptionCampylobacterales speciesAccession numberProtein description
EmrAHlyD/PF00529/HlyD family secretion proteinC. jejuniQ9 PHR0Putative periplasmic protein
  Q9 P ID5Putative membrane fusion component of efflux system
 H. hepaticusQ7 V F21Hypothetical protein
  Q7 V JR8Conserved hypothetical membrane protein
 H. pyloriP 4 8 5 136 kDa antigen
 W. succinogenesQ 7M8T9Periplasmic component of efflux system
  Q 7 M I 1Membrane fusion protein MexC RND
  Q7M9Q0Acriflavin resistance protein AcrA
  Q7MA86Cation efflux system
EmrBMFS_1/PF 07690/Major Facilitator SuperfamilyC. jejuniP4 5 4 90Hypothetical protein Cj0987c
  Q9 P I 23Putative sugar transporter
  Q9 P I 25Transmembrane transport protein
  Q9 PI 47Putative integral membrane protein
  Q9 P LZ1Putative efflux protein
  Q9 PM56Alpha-ketoglutarate permease
  Q9 PNZ5Putative 2-acylglycerophosphoethanolamine acyltransferase/acyl-acyl carrier protein synthetase
 H. hepaticusQ7V FR1Hypothetical protein
 H. pyloriO2 5 083Nitrite extrusion protein
  O2 5 723Alpha-ketoglutarate permease
  O2 5 780Putative tetracycline resistance protein
  O2 5 788Putative glucose/galactose transporter
  O2 5 793Multidrug-efflux transporter
  O2 5 797Probable sugar efflux transporter
  Q9 ZK35Putative transporter
  Q9 ZK41Putative glucose/galactose transporter
  Q9ZKR4Proline/betaine transporter
 W. succinogenesQ7 M811Transmembrane transport protein-permease
  Q7M8W2Putative transport protein
  Q7 M916Putative MFS transporter
  Q7M9C7Putative efflux protein
  Q7M9G5Putative integral membrane protein
  Q7MRK1Hypothetical protein
HtrBLip_A_acyltrans/PF03279/Bacterial lipid A biosynthesis acyltransferaseC. jejuniQ9 PNG0Putative lipid A biosynthesis lauroyl acyltransferase
 H. hepaticusQ7 V HI5Lauroyl/myristoyl acyltransferase involved in lipid A biosynthesis
 H. pyloriO 2 5 057Heat shock protein B
  Q9ZMF5Putative lipid A biosynthesis acyltransferase
 W. succinogenesQ7M834Lipid A biosynthesis acyltransferase
MdtAHlyD/PF00529/HlyD family secretion proteinC. jejuniQ9PHR0Putative periplasmic protein
  Q9PI D5Putative membrane fusion component of efflux system
 H. hepaticusQ7V F21Hypothetical protein
  Q7V JR8Conserved hypothetical membrane protein
 H. pyloriP 9 4 85136 kDa antigen
 W. succinogenesQ7M8T9Periplasmic component of efflux system
  Q 7M 9I1RND multidrug efflux membrane fusion protein MexC
  Q7M9Q0Acriflavin resistance protein AcrA
  Q7MA86Cation efflux system
MdtBACR_tran/PF00873/AcrB/AcrD/AcrF familyC. jejuniQ 9 PID6Transmembrane efflux protein
  Q9PNQ8Putative integral membrane component of efflux system
 H. hepaticusQ 7 V II0Hypothetical protein
  Q 7VJR9Conserved hypothetical membrane protein
 H. pyloriO 2 5328Acriflavine resistance protein AcrB
  O 2 5622Cation efflux system protein
  Q9ZLM5Putative efflux transporter
 W. succinogenesQ 7M912RND pump protein
  Q 7 M9I0Multidrug efflux transporter
  Q 7M9P9Multidrug resistance protein MexB
  Q7MA85Acriflavin resistance protein D
  Q7M AL3Cation efflux, AcrB/AcrD/AcrF family
MdtCACR_tran/PF00873/AcrB/AcrD/AcrF familyC. jejuniQ 9 P ID6Transmembrane efflux protein
  Q9P NQ8Putative integral membrane component of efflux system
 H. hepaticusQ 7 V I I0Hypothetical protein
  Q 7 VJR9Conserved hypothetical membrane protein
 H. pyloriO 2 5 328Acriflavine resistance protein AcrB
  O 2 5 622Cation efflux system protein
 W. succinogenesQ7M 912RND pump protein
  Q 7M9 I0Multidrug efflux transporter
  Q7M9 P9Multidrug resistance protein MexB
  Q7MA85Acriflavin resistance protein D
  Q7MAL3Cation efflux, AcrB/AcrD/AcrF family
RcsCHisKA/PF00512/His Kinase A (phosphoacceptor) domain HATPase_c/PF02518/Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase Response_reg/PF00072/Response regulator receiver domainW. succinogenes Hybrid histidine kinase
TolCOEP/PF02321/Outer membrane efflux proteinC. jejuniQ 9PHQ8Putative outer membrane protein
  Q 9PNR0Putative outer membrane component of efflux system
 H. hepaticusQ 7 VF20Hypothetical protein
 H. pyloriO 2 6 022Lipase-like protein
 W. succinogenesQ7M 8U1Probable outer membrane protein
  Q7 M9H9Outer membrane channel protein
  Q7MSM4Hypothetical protein
TolQMotA_ExbB/PF01618/MotA/TolQ/ExbB proton channel familyC. jejuniQ 9 P IG3Putative flagellar motor proton channel
  Q 9 P IV0Biopolymer transport protein
  Q 9 P J17ExbB/TolQ family transport protein
  Q 9PM 47Putative ExbB/TolQ family transport protein
 H. hepaticusQ 7V I V3Flagellar motor component MotA
  Q 7V J 19Biopolymer transport protein
 H. pyloriO 2 5 897Biopolymer transport ExbB protein
  P 5 6 4 26Chemotaxis MotA protein
 W. succinogenesQ7M7T8Flagellar motor component MotA
  Q7MA18ExbB/TolQ family transport protein
TolRExbD/PF02472/Biopolymer transport protein ExbD/TolRC. jejuniQ 9 PIU9Biopolymer transport protein
  Q 9 P J16ExbD/TolR family transport protein
  Q 9PM46Putative ExbD/TolR family transport protein
 H. hepaticusQ 7 V J18Biopolymer transport protein ExbD-like
 H. pyloriO 2 5 898Biopolymer transport ExbD protein
 W. succinogenesQ7M8T4Biopolymer transport ExbB protein
MarAHTH_AraC/PF00165/Bacterial regulatory helix-turn-helix proteins, AraC familyC. jejuniQ 9PNP9Putative transcriptional regulatory protein
 W. succinogenesQ7M9D7Transcriptional regulator, AraC/XYLS family
  Q 7M970Transcriptional regulator
  Q7M9P 2Transcriptional regulator
  Q7MR7 5Hypothetical protein
  Q7MSM8AraC-type DNA-binding proteins
MarRMarR/PF01047/MarR familyH. hepaticusQ7 VIM0Hypothetical protein
 W. succinogenesQ7 MS26Hypothetical protein
PhoQ PmrBHAMP/PF00672/HAMP domain. HisKA/PF00512/His Kinase A (phosphoacceptor) domain HATPase_c/PF02518/Histidine kinase-, DNA gyrase B-, and HSP90-like ATPaseC. jejuniQ9 PN36Two-component sensor histidine kinase
 H. hepaticusQ7 VFR8Two-component system histidine kinase
  Q7 M9F7Sensory transduction histidine kinase
HisKA/PF00512/His Kinase A (phosphoacceptor) domain. HAMP/PF00672/HAMP domain HATPase_c/PF02518/Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase MFS_1/PF00512/His Kinase A (phosphoacceptor) domainC. jejuniQ 9 PN71Putative two-component sensor
 H. pyloriQ9ZMR7Putative histidine kinase sensor protein
 W. succinogenesQ 7M884Histidine kinase sensor protein
  Q7 M9P2Transcriptional regulator
VirFHTH_AraC/PF00165/Bacterial regulatory helix-turn-helix proteins, AraC familyC. jejuniQ 9 PNP9Putative transcriptional regulatory protein
 W. succinogenesQ7 M9D7Transcriptional regulator, AraC/XYLS family
  Q7 M9 70Transcriptional regulator
  Q7 M9P2Transcriptional regulator
  Q 7MR75Hypothetical protein
  Q7MSM8AraC-type DNA-binding proteins
ToxRTrans_reg_C/PF00486/Transcriptional regulatory proteinC. jejuniO 6 8 7 95Response regulator
  Q 9 P P41Putative sensory transduction transcriptional regulator
 H. hepaticusQ 7VFH9Hypothetical protein
  Q 7VFR7Response regulator
 H. pyloriO 2 4 973Response regulator, OmpR
  Q9ZMR6Putative transcriptional regulator
 W. succinongenesP 7 4 9 68Response regulator
  Q7M7M9Transcriptional regulator, PhoB-like
  Q7M 810Signal transduction regulatory protein-CheY like receiver domain
  Q7M 9F8Sensory transduction regulator
  Q7 M9V5Transcriptional activator protein, CopR
ToxTHTH_AraC/PF00165/Bacterial regulatory helix-turn-helix proteins, AraC familyC. jejuniQ9 PN P9Putative transcriptional regulatory protein
 W. succinongenesQ7M 9D7Transcriptional regulator, AraC/XylS family
  Q7M 9 70Transcriptional regulator
  Q7M 9P2Transcriptional regulator
  Q7M R75Hypothetical protein
  Q7MSM8AraC-type DNA-binding proteins
YxiOMFS_1/PF00512/His Kinase A (phosphoacceptor) domain P 4 5 4 90Hypothetical protein Cj0987c
  Q 9 P I 23Putative sugar transporter
  Q 9 P I 25Transmembrane transport protein
  Q 9 P I 47Putative integral membrane protein
  Q 9 P LZ1Putative efflux protein
  Q 9 PM56Alpha-ketoglutarate permease
  Q 9 PNZ5Putative 2-acylglycerophosphoethanolamine acyltransferase/acyl-acyl carrier protein synthetase
ZurRFUR/PF01475/Ferric uptake regulator familyC. jejuniP 4 8 7 96Ferric uptake regulator
  Q 9 P IH7Peroxide stress regulator
 H. hepaticusQ7VHM4Transcriptional regulator
  Q 7 VHS0Ferric uptake regulator
 H. pyloriO 2 5 6 71Ferric uptake regulator
 W. succinogenesQ7M7W6Ferric uptake regulator
  Q 7MA07Peroxide stress regulator
  Q 7MRT9Hypothetical protein
OhrOsmC/PF02566/OsmC-like proteinW. succinogenesQ7MRM2Hypothetical protein
CbsTMFS_1/PF00512/His Kinase A (phosphoacceptor) domainC. jejuniQ 9 P IN2Zinc transporter, ZupT
 W. succinogenesQ 7M8C2Integral membrane protein
GusAGlyco_hydro_2_N/PF02837/Glycosyl_hydrolases family 2, sugar binding domain Glyco_hydro_2/PF00703/Glycosyl hydrolases family 2, immunoglobulin-like beta-sandwich domain Glyco_hydro_2_C/PF02836/Glycosyl hydrolases family 2, TIM barrel domainC. jejuniQ 9PMB1Putative transcriptional regulator
  Q 9 PN67Putative heat shock transcriptional regulator
 H. hepaticusQ 7VFN4Putative heat shock transcriptional regulator
  Q 7VH80Hypothetical protein
 H. pyloriO 2 5 669Putative heat shock protein, HspR
  Q9ZM24Putative transcriptional regulator
 W. succinogenesQ7M 920Putative transcriptional regulator
AdkADK/PF00406/Adenylate kinaseC. jejuniQ9PHM8Adenylate kinase
 H. hepaticusQ7VF A6Adenylate kinase
 H. pyloriP 5 6 104Adenylate kinase
 W. succinogenesQ7M8A5Adenylate kinase
HtrASerpin/PF00079/Serine protease inhibitorC. jejuniQ9PN 69Serine protease
 H. hepaticusQ 7 VIZ8Serine protease
 H. pyloriO 25663Serine protease
  Q9ZM18Serine protease
 W. succinogenesQ7M7L2Serine protease
NusANusA_N/PF08529/NusA N-terminal domainH. hepaticusQ7VGP8Transcription termination factor NusA
RplYRibosomal_L25p/PF01386/Ribosomal L25p familyC. jejuniQ 9 P II850S ribosomal protein
 H. hepaticusQ7V G30Ribosomal protein L25
 H. pyloriP 5 6 078Probable 50S ribosomal protein L25
 W. succinogenesQ7M7U7Putative 50S ribosomal protein L25
RpoARNA_pol_L/PF01193/RNA polymerase Rpb3/Rpb11 dimerisation domain RNA_pol_A_bac/PF01000/RNA polymerase Rpb3/RpoA insert domain RNA_pol_A_CTD/PF03118/Bacterial RNA polymerase, alpha chain C terminal domainC. jejuniQ9PM80DNA-directed RNA polymerase alpha chain
 H. hepaticusQ7VGB9DNA-directed RNA polymerase alpha chain
 H. pyloriP 5 6 001DNA-directed RNA polymerase alpha chain
 W. succinogenesQ7M8F7DNA-directed RNA polymerase alpha chain

Out of the 20 membrane/transport proteins with homologues in other bacteria, 18 were common to all four species of Campylobacterales studied. These data suggest that bile elicits responses in Campylobacterales that are similar to the responses elicited in other bacteria, by modulating proteins of the efflux systems that they have in common. Also common to the four Campylobacterales were 16 of the 23 homologues to secretion/regulation proteins, five of the 10 homologues to proteins involved in central metabolism, and the homologues of three heat-shock proteins and three enzymes of bile metabolism. This result shows that the various Campylobacterales share many biological features, including similarities in the response to environmental cues such as bile. Indeed, comparative genomic analyses of C. jejuni, H. pylori, H. hepaticus and W. succinogenes by Eppinger et al. (2004) found many orthologues with high degrees of identity in the predicted sequences of the four Campylobacterales species. For genes shared between W. succinogenes and C. jejuni, H. pylori or H. hepaticus the average identities were estimated at 48, 50 and 47%, respectively. For genes shared between C. jejuni and H. pylori or H. hepaticus the average identities were 46% and 47%, respectively. The average gene identity between the two H. pylori species was 51% (Eppinger et al., 2004). Hence, the significant number of proteins common to the four Campylobacterales with homologues in other bacteria may represent a common strategy of the former to respond to bile.

Thirty-two non-Campylobacterales proteins identified in the responses to bile exhibited both sequence and domain similarity to 99 distinct Campylobacterales proteins (Table 2), 14 of which were present in C. jejuni, H. hepaticus, H. pylori and W. succinogenes. Four of these 14 proteins are enzymes of intermediary metabolism, namely glyceraldehyde-3-phosphate dehydrogenase (Gap), phosphoglycerate kinase (Pgk), Glutamyl-tRNA(Gln) amidotransferase subunit A, and methionine aminopeptidase. Gap interconverts glyceraldehyde-3-phosphate and glyceraldehyde-1,3-bisphosphate, and is a major controlling point of carbon flux in the Campylobacterales. Both Gap and Pgk were up-regulated in Bifidobacterium longum in the presence of bile (Sanchez et al., 2005). Analysis of the glycolytic pathways revealed similarities in the pyruvate metabolism of B. longum, C. jejuni, H. pylori, H. hepaticus and W. succinogenes at the Gap and Pgk steps. A notable difference is that B. longum and H. hepaticus also encode an acylphosphatase, which as an alternative to Pgk interconverts glyceraldehyde-1,3-bisphosphate and 3-phosphoglycerate. Thus, it could be predicted that, similarly to the case for B. longum, in the four Campylobacterales species bile will activate the production of energy-rich intermediates and reducing equivalents. Glutamyl-tRNA(Gln) amidotransferase subunit A and methionine aminopeptidase are involved in the responses of Mycobacterium smegmatis to a number of stress conditions (Zheng & Dean, 1994).

Five of the 14 proteins common to both Campylobacterales and non-Campylobacterales were related to transcription and regulation, namely elongation factor P, ribosome recycling factor, response regulator proteins, prolyl-tRNA synthetase, and 30S ribosomal proteins. The remaining four common proteins were stress-response proteins, including the heat-shock proteins GroEL and GroES and Sod. GroEL and GroES function to maintain protein integrity under extreme conditions (Hendrick & Hartl, 1993). Sod is an oxidative stress-response protein, which protects bacteria against reactive singlet oxygen species; it has been reported to be induced in Propionibacterium freudenrichii in the presence of bile (Leverrier et al., 2003). These findings further suggest that the presence of molecular mechanisms to resist bile is common to the four Campylobacterales genera as well as to bacteria of the Proteobacteria, Bacteriodetes, Firmicutes and Actinobacteria phyla.

Twenty-eight non-Campylobacterales proteins from various bacterial genera exhibited only domain similarity to 78 Campylobacterales proteins (Table 3). In total, 177 Campylobacterales proteins showed either domain similarity or domain and sequence similarity to proteins employed by other bacteria in response to bile (Tables 2 and 3). Forty-seven of these were not common to all four Campylobacterales species, revealing that there are differences in their responses to bile. Among these 47 proteins, 24 were identified in W. succinogenes, 13 in C. jejuni, seven in H. hepaticus and three in H. pylori. In addition to the differences in their respective genome sizes mentioned earlier, host and habitat specificity may also contribute to the possible differences in the response to bile of the Campylobacterales. In the functional category of membrane/transport proteins, homologues to zinc transporters and integral membrane protein CbsT1,2 were identified in C. jejuni and W. succinogenes, but not in the two Helicobacter species (Table 3).

Similarly, seven homologues to secretion/regulation proteins were not common to the four Campylobacterales. MarRAB is a regulatory locus whose homologues were not present in the four Campylobacterales. MarRAB is involved in multiple antibiotic resistance to structurally unrelated antimicrobial agents; its activation in Salmonella induces a variety of phenotypes such as a decreased level of the OmpF porin to reduce influx and an increased level of AcrAB-TolC to boost efflux (Alekshun & Levy, 1999). MarR functions as a repressor of the MarRAB operon by binding to the promoter region, marO, to prevent transcription. Deoxycholate is able to interact with MarR and impairs its ability to bind the marO operator (Prouty et al., 2004). MarA is a global positive regulator and activates genes involved in antibiotic resistance phenotype such as sodA, zwf and micF. Homologues to this protein were identified only in C. jejuni and W. succinogenes. MarB is a small protein with unknown function that does not appear to play a significant role in antibiotic resistance (Martin et al., 1995). No homologue to MarB was identified in the Campylobacterales, but various transcriptional factors, DNA binding proteins and hypothetical proteins were identified as homologues to MarR in H. hepaticus and W. succinogenes (Table 3). Thus, the identification of homologues to MarRA suggest that bile might modulate antibiotic resistance in C. jejuni, H. hepaticus and W. succinogenes.

The HTH_ARAC-type DNA binding domain is a helix-turn-helix motif. Proteins exhibiting this motif seem to be positive transcriptional factors. This domain is found in MarA, VirF and ToxT. VirF and ToxT are plasmid-borne proteins, which in Y. enterocolitica and V. cholerae respectively mediate virulence. The three proteins are modulated in the presence of bile (Bhaduri et al., 1997; Gupta & Chowdhury, 1997; Prouty et al., 2004). Homologues to the HTH_ARAC-type DNA binding motif were identified in proteins of C. jejuni and W. succinogenes but not in H. hepaticus and H. pylori (Table 3). Thus, bile may also mediate virulence expression in C. jejuni and W. succinogenes.

Only W. succinogenes had orthologues of organic hydroperoxide resistance genes (ohr), and of the genes rcsC and phoQ encoding sensory kinases of two-component regulatory systems (Table 3). PhoP-PhoQ functions as a two-component regulatory system in which PhoQ is a membrane-bound kinase that, upon sensing specific environmental cues such as Mg2+ concentration, initiates a phosphorylation cascade to activate PhoP, a transcriptional regulator. In Salmonella, PhoP-PhoQ is necessary for virulence, and is involved in bile resistance (van Velkinburgh & Gunn, 1999), suggesting that in W. succinogenes bile may activate these two-component regulatory systems.

Homologues to three enzymes of carbohydrate metabolism involved in the bile response of other bacteria were not common to the four Campylobacterales species. Homologues to acetate kinase were found in C. jejuni, H. pylori and H. hepaticus but not in W. succinogenes; homologues to lactate dehydrogenase were found in C. jejuni, H. hepaticus and W. succinogenes but not in H. pylori; and pyruvate kinase homologues were identified only in C. jejuni. Thus, in pyruvate metabolism, the response to bile of the four Campylobacterales species would differ at the point of conversion of phosphoenol pyruvate to pyruvate by pyruvate kinase. This result suggests that in the four Campylobacterales species the presence of bile would modulate differently the activities of enzymes involved in the production of energy and metabolic intermediates such as lactate and acetate.

One hundred and thirty proteins common to the four Campylobacterales species showed either domain or domain and sequence similarity to proteins involved in the response to bile of other bacteria. Functions of these proteins included protein folding (chaperonins), ferric uptake, lipid biosynthesis, metabolism (serine protease, adenylate kinase, sugar epimerase), regulation of transcription, translation-elongation, transmembrane efflux, tRNA-synthesis, etc. (Tables 2 and 3). This diversity of functions suggests that bile has complex effects on the Campylobacterales, and that the four species will have some similarities in their response to bile.

Several of the Campylobacterales proteins implicated in the response to bile have homologues that do not as yet have identified functions in their respective species; nonetheless, analyses of the results in this study showed that there are responses to bile that are common, at least in part, to all bacteria. For example, membrane/transport, chaperone/heat-shock and secretion/regulation proteins are employed by many organisms in their responses to bile. On the other hand, bacteria from various genera appear to employ specific proteins as well; for example, as mentioned previously, 47 homologues to different proteins of other bacteria were not common in all four Campylobacterales species. In addition, bile salt hydrolase (Bsh) is used by Bacteroides, Listeria, Clostridium, Enterococcus and Bifidobacteria in response to bile, but this enzyme is not present in the other genera studied. The four Campylobacterales species studied have homologues of proteins involved in the bile responses in other bacteria, but at the same time there are significant differences between them; for example, no homologues of C. jejuni CiaB and FlaAσ28 were identified in the bacteria of the other phyla, indicating differences between their responses. Thus, the responses to bile involve various mechanisms common to all the bacteria studied, as well as others specific to the various genera.

Molecular mechanisms of responses to bile in Campylobacterales and other bacteria

Altering protein production

Some Salmonella species alter a large number of membrane proteins involved in metabolite transport upon interaction with bile (van Velkinburgh & Gunn, 1999), including the modulation of some regulatory proteins and inhibition of the expression of Salmonella invasion and type III secretion proteins (Gunn, 2000). On the other hand, expression of this secretion system is up-regulated in Shigella in the presence of bile (Pope et al., 1995). The mobility of V. cholerae increases in the presence of bile, but the production of cholera-toxin and toxin-regulated pilus by the bacterium is significantly down-regulated (Gupta & Chowdhury, 1997). Many bacteria alter the expression of heat-shock proteins in response to environmental stresses such as bile: the four heat-shock proteins frequently involved are DnaK, GroES and GroEL. Studies with a variety of bacterial genera have demonstrated elevated synthesis of GroEL following exposure to bile salts, low pH or ethanol (Salotra et al., 1995; Hartke et al., 1997; Kilstrup et al., 1997). In Enterococcus faecalis four proteins are differentially expressed in the presence of bile salts, including DnaK and GroEL (Flahaut et al., 1996). Escherichia coli also regulates DnaK and elevates the expression of transport systems such as the acridine transport system AcrAB, and the multidrug transport system MdtABC (Lomovskaya & Lewis, 1992). The results of the present analyses suggest that the expression of these proteins will also be modulated in Campylobacterales by the presence of bile (Table 2).

The molecular mechanisms by which bacteria ‘sense’ bile and alter protein production to increase bile resistance are not fully understood. Ligands that are specific to bile components may bind to regulatory proteins and alter their function to initiate promoter binding (Gunn, 2000). In Salmonella, of the two-component regulatory system PhoP-PhoQ, the sensor protein PhoP binds moieties of bile and initiates a phosphorylation cascade with the cognate response regulatory proteins (van Velkinburgh & Gunn, 1999). In other bacteria, bile sensory mechanisms may not be direct but involve a ‘sensing’ of the effects of bile on the cell, for example membrane damage. It has been suggested that the E. coli RcsCB two-component regulatory system responds to cell-surface perturbations by acting as a membrane damage sensor (Clavel et al., 1996). A molecular investigation of the responses of C. jejuni to bile showed stimulation of the synthesis of the CiaB Campylobacter invasion antigen (Rivera-Amill et al., 2001), and up-regulation of a sigma factor of the flagellum protein FlaA (Allen & Griffiths, 2001). Recently, a Campylobacter bile response regulator (CbrR) was identified (Raphael et al., 2005); its functions in C. jejuni have not yet been elucidated, but it was suggested that CbrR interacts with CmeR, a repressor of cmeABC. The CbrR-CmeR regulation would modulate the expression of the multidrug efflux system CmeABC involved in the extrusion of antimicrobials such as bile out of the C. jejuni cytoplasm. At present, no experimental information exists on changes in the expression of proteins in the presence of bile by H. hepaticus, H. pylori, and W. succinogenes, but the identification in this study of homologues to PhoP in all four Campylobacterales, and homologues to PhoQ only in C. jejuni and H. hepaticus suggest that PhoP may be involved in the general bile response in the Campylobacterales. The Campylobacterales lacking PhoQ homologues may employ other membrane-bound kinases to activate transcriptional regulation in bile response (Tables 2 and 3).

Efflux pumps

Bile salts can penetrate the protective outer membrane and enter the cell, but they can be removed by efflux pumps before significant damage occurs (Abate et al., 1994; Thanassi et al., 1997; Nikaido, 1998). The efflux of bile salts from the bacterial cytoplasm directly out of the cell is a well-known mechanism of bile salt resistance. The best characterized efflux pump is AcrAB (Ma et al., 1995; Lacroix et al., 1996; Thanassi et al., 1997; Zgurskaya & Nikaido, 1999). AcrB is a proton motive force-dependent drug efflux transporter, and AcrA aids in direct cytoplasm-to-environment efflux by bridging the inner and outer membranes in Gram-negative bacteria. This system is necessary for the intrinsic resistance of E. coli to solvents, detergents, dyes, lipophilic antibiotics (e.g. erythromycin), and bile salts. In Salmonella spp. and E. coli, when acrAB genes are overexpressed the bacteria become resistant to antibiotics such as tetracycline and chloramphenicol. As mentioned previously, overexpression is mediated by the marRAB operon, which is responsible for the regulation of more than 10 other genes (Seoane & Levy, 1995; Okusu et al., 1996; Alekshun & Levy, 1999; Prouty et al., 2004). Other Salmonella spp. and E. coli efflux systems such as EmrAB and MdtABC are also involved in bile excretion from the cell, but are less well characterized (Lomovskaya & Lewis, 1992; Lomovskaya et al., 1995). EmrA and MdtA are periplasmic membrane fusion proteins that bridge the inner and outer membranes; and EmrB and the heteromultimer MdtB/C are inner membrane efflux pumps. Strains of E. coli containing acrA and emrB double mutations are extremely sensitive to antibiotics and bile (Thanassi et al., 1997). The three systems AcrAB, EmrAB and MdtABC require the multifunctional outer membrane channel TolC for their function. Efflux systems similar to these three are present in other Gram-negative bacteria including P. aeruginosa (Li et al., 1994a, b; Li et al., 2000; Mine et al., 1999), Haemophilus influenza (Sanchez et al., 1997), Neisseria gonorrhoeae (Maier et al., 1975; Hagman et al., 1995; Shafer et al., 1998) and Vibrio cholerae (Colmer et al., 1998; Morita et al., 1998). For example, in P. aeruginosa, the efflux system MexAB-OprM, which is similar to AcrAB-TolC, plays a role in the export of toxic environmental lipids and hydrophobic substances such as bile salts.

In C. jejuni the CmeABC antibiotic resistance multidrug efflux pump is encoded by the three-gene operon cmeABC (Seoane & Levy, 1995; Pumbwe & Piddock, 2002; Luo et al., 2003). The CmeABC pump consists of the periplasmic protein CmeA, the inner membrane efflux transporter CmeB belonging to the resistance-nodulation-cell division superfamily, and the outer membrane protein CmeC. It has been shown that C. jejuni CmeABC is an important contributor to bile resistance (Lin et al., 2002) (Table S1). Recently, the efflux pump named CmeDEF was characterized in C. jejuni, and it is also involved in the extrusion of antimicrobials including bile and bile salts (Akiba et al., 2005) (Table S1). CmeDEF is expressed at a much lower level than CmeABC; the degree of resistance conferred by it is relatively moderate and is masked by that of CmeABC (Akiba et al., 2005). These data suggested that CmeABC is the dominant efflux pump in C. jejuni, whereas CmeDEF probably functions as a secondary efflux mechanism. The two efflux systems seem to function interactively, because inactivation of CmeF causes the elevation of the transcription of cmeABC and leads to higher resistance to bile in C. jejuni (Akiba et al., 2005). Other putative efflux pumps have been identified in the genome of C. jejuni (Lin et al., 2005), but have not yet been characterized. The high sequence and domain similarities found in this study between CmeABC and AcrAB-TolC, and between CmeR and AcrR suggest that C. jejuni CmeABC functions as an AcrAB-TolC-like system in the response of the bacterium to bile. In addition, significant sequence and structural homology was determined between proteins of Campylobacterales and the MexAB-OprM tripartite multidrug efflux pumps of P. aeruginosa (Tables 3 and 5). These results show similarities between the responses to bile of efflux mechanisms of Campylobacterales and bacteria of the Proteobacteria, Bacteriodetes, Firmicutes and Actinobacteria phyla.

In silico analyses in this study revealed homologues of CmeABC in the proteomes of C. coli and C. lari, with similarities between 74% and 99%. Orthologues of C. jejuni cmeA, cmeB and cmeC were present also in the genomes of the three Helicobacteriaceae: H. hepaticus, H. pylori and W. succinogenes (Table 2). Similarities between 47% and 57% were found for the homologues of CmeA encoded by hh0175, hp0606 and ws0769. The homologues of CmeB, encoded by hh0174, hp0607 and ws0770 showed 55−72% similarities, and putative homologues of CmeC encoded by hh0623, hp0971 and ws0771 had 33−53% similarities. For CmeDEF, homologues of CmeD with 99, 77 and 69% similarities were present in the proteomes of C. coli, C. lari and C. upsaliensis, respectively. No homologues of this protein were identified in the Helicobacteriaceae. Homologues of CmeE with high similarities of 71–98% were found in the proteomes of C. coli, C. lari, and C. upsaliensis; and homologues with lower similarities of 52–54% were found in H. hepaticus, H. pylori, and W. succinogenes. Finally, homologues of CmeF with similarities of 80–99% were found in the proteomes of C. coli, C. lari and C. upsaliensis; and homologues with 50–60% similarities were present in the H. hepaticus, H. pylori, and W. succinogenes proteomes. Thus, it would be reasonable to predict that CmeABC-like systems in the three Helicobacteriaceae species will contribute to the resistance to bile of these bacteria. Similarly, a CmeDEF-like system could be present in the Helicobacteriaceae, although a protein with the role of CmeD has yet to be found.

Outer membrane (OM) modifications

For Gram-negative bacteria, the OM is an excellent hydrophobic barrier to agents such as bile salts, and some information exists on the role of lipopolysaccharides, Tol proteins and outer-membrane pores in bile resistance.

Lipopolysaccharides

Lipopolysaccharides of Gram-negative bacteria are a major component of the external leaflet of the OM. The lipid A portion of lipopolysaccharide molecules anchors it in the membrane, and the O-antigen protruding from the surface of the membrane provides a major barrier to the entry of external compounds. In E. coli and S. typhimurium, the loss of O-antigens results in decreased resistance to bile (Picken & Beacham, 1977; Gunn, 2000). On the other hand, in S. typhimurium reduction of electrostatic interactions by covalent modification with ethanolamine of the phosphate groups of the lipopolysaccharide core and lipid A, and modification with aminoarabinose of the 4′-phosphate of lipid A do not affect bile resistance (Gunn & Miller, 1996). Thus, at least in S. typhimurium, electrostatic interactions between bile and lipopolysaccharides do not play a major role in resistance. There are numerous molecular studies on the lipopolysaccharides of C. jejuni and H. pylori, but there are no investigations into the relationship between lipopolysaccharides and the bile resistance of these bacteria.

Tol proteins

The Tol system comprises TolCQRAB and Pal proteins, which participate in the uptake of colicins, filamentous phage DNA, and many other solutes (Sun & Webster, 1987; Bourdineaud et al., 1989; Webster, 1991). The tolQRAB and pal genes are clustered in the genomes of most Gram-negative bacteria sequenced so far (Sturgis, 2001). TolQRA are cytoplasmic membrane proteins. TolQ is an integral inner-membrane protein containing three transmembrane domains with two cytoplasmic regions. TolR and TolA are anchored to the cytoplasmic membrane, and TolB is a periplasmic protein. TolC is a multifunctional OM protein. It is involved with the AcrAB efflux pump system, and its loss affects bile resistance in E. coli (Clavel et al., 1996). Mutations in the TolC and AcrAB loci result in cells with destabilized membranes, which allow greater access of bile salts to the cytoplasm of the cell and make E. coli more susceptible to their actions. Tol mutants are also more sensitive to a diverse group of antibiotics and detergents (Nagel de Zwaig & Luria, 1967; Whitney, 1971; Bernstein et al., 1972). Homologues of Tol proteins have been identified in a number of other Gram-negative bacteria. Domains corresponding to the TolC, TolQ and TolR of E. coli were identified in proteomes of C. jejuni, H. hepaticus, H. pylori and W. succinogenes (Table 3). No homologues of TolAB were found among Campylobacterales proteins.

OM pores

There is no molecular information on the specific contributions of lipopolysaccharides or Tol proteins to bile resistance in the Campylobacterales, but experimental evidence suggests that OM protein channels may be involved. The measurement of pore-forming activity in black lipid bilayer membranes indicated that a C. jejuni major OM porin (Omp) produced a channel with a mean single-channel conductance of 0.82 ns in 1 M KCl at 25°C, pH 6.0 and 20 mV voltage (Benz et al., 1985). By comparison, E. coli Omp form pores with a single-channel conductance of 1.8–2.2 ns (Benz et al., 1985). Thus, C. jejuni appears to have smaller OM pores compared with those of E. coli (Page et al., 1989), suggesting that the molecular weight limit for solutes to move through the C. jejuni pore will be considerably smaller than the c. 600 Da weight limit of E. coli pores. Page et al. (1989) showed that C. jejuni is usually less susceptible to antibiotics larger than 360 Da. The molecular weights of bile acids are greater than 360 Da; for example, chenodeoxycholic acid is 392.6 Da; cholic acid, 408.6 Da; deoxycholic acid, 392.6 Da; and taurocholic acid, 515.7 Da. Thus, based on pore size, C. jejuni could be expected to be less susceptible to bile acids than E. coli. However, the antimicrobial susceptibilities of bacteria are not related only to the permeability through OM pores, but to a combination of many factors including pore size, charge, concentration of antimicrobial agent, rate of extrusion of toxic compounds from the cells, etc. Hence, determination of the susceptibilities of C. jejuni to various bile acids could help to elucidate the role of Omp in the adaptation of the bacterium to bile.

Conclusion

  1. Top of page
  2. Abstract
  3. Introduction
  4. Background
  5. Materials and methods
  6. Results and discussion
  7. Conclusion
  8. Acknowledgement
  9. References
  10. Supporting Information

This study has found molecular evidence that, similar to the case in other bacteria, the responses to bile in the Campylobacterales involve complex physiological mechanisms that modulate the expression of proteins from a variety of functional categories, some of which were common to the four Campylobacterales species studied. Clear similarities as well as differences were found between the responses to bile of the Campylobacterales and those of other bacteria that inhabit the gastrointestinal tract. Detailed comparative molecular investigations of these mechanisms will provide new insights into the relationships between adaptation and host habitat specificity, as well as into mechanisms leading to inflammation, ulcers and cancers by infections of Campylobacterales. This knowledge should help in the development of antibacterial treatments, with direct implications for the prevention of serious enterogastric diseases.

Acknowledgement

  1. Top of page
  2. Abstract
  3. Introduction
  4. Background
  5. Materials and methods
  6. Results and discussion
  7. Conclusion
  8. Acknowledgement
  9. References
  10. Supporting Information

The support of an Endeavour International Postgraduate Research Scholarship to A.S.O. is gratefully acknowledged.

References

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  2. Abstract
  3. Introduction
  4. Background
  5. Materials and methods
  6. Results and discussion
  7. Conclusion
  8. Acknowledgement
  9. References
  10. Supporting Information
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Supporting Information

  1. Top of page
  2. Abstract
  3. Introduction
  4. Background
  5. Materials and methods
  6. Results and discussion
  7. Conclusion
  8. Acknowledgement
  9. References
  10. Supporting Information

Table S1. Genes implicated in response/adaptation to bile in Gram-negative bacteria Table S2. Genes implicated in response/adaptation to bile in Gram-positive bacteria Table S3. Proteins implicated in bacteria responses to bile with homology to Campylobacterales proteins

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