- Volume 154, Issue 4, 2008

Shewanella halifaxensis HAW-EB4 was previously isolated for its potential to mineralize hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) from a UXO (unexploded ordnance)-contaminated marine sediment site near Halifax Harbor. The present study was undertaken to determine the effect of terminal electron acceptors (TEA) on the growth of strain HAW-EB4 and on the enzymic processes involved in RDX metabolism. The results showed that aerobic conditions were optimal for bacterial growth, but that anaerobic conditions in the presence of trimethylamine N-oxide (TMAO) or in the absence of TEA favoured RDX metabolism. RDX as a substrate neither stimulated respiratory growth nor induced its own biotransformation. Strain HAW-EB4 used periplasmic proteins to transform RDX to both nitroso [hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine (MNX), hexahydro-1,3-dinitroso-5-nitro-1,3,5-triazine (DNX), and hexahydro-1,3,5-trinitroso-1,3,5-triazine (TNX)] and ring cleavage products (such as methylenedinitramine), with more nitroso formation in cells grown on TMAO or pre-incubated in the absence of TEA. Using spectroscopy, SDS-PAGE and haem-staining analysis, strain HAW-EB4 was found to produce different sets of c-type cytochromes when grown on various TEA, with several more cytochromes produced in cells grown on TMAO. Crude cytochromes from total periplasmic proteins of TMAO-grown cells metabolized RDX to products similar to those found in assays using total periplasmic proteins and whole cells. To prove the involvement of cytochrome in RDX metabolism, we monitored dithionite- or NADH-reduced cytochromes by their absorbance at the α (551 nm) or γ (418–420 nm) bands during anaerobic incubation with RDX. In both cases we found that RDX biotransformation was accompanied by oxidation of reduced cytochrome. Furthermore, O2, an oxidant of reduced cytochrome, inhibited RDX transformation. The present results demonstrate that S. halifaxensis HAW-EB4 metabolizes RDX optimally under TMAO-reducing conditions, and that c-type cytochromes are involved.

A novel pathway of molinate mineralization promoted by a defined mixed culture composed of five bacteria (named ON1 to ON5) was proposed previously. Evidence was obtained of a metabolic association between Gulosibacter molinativorax ON4T, capable of molinate breakdown, and the remaining bacteria. In the present study, the role of each isolate in that metabolic association was further explored and the possible synergistic effect of all the bacterial isolates for the stability of the mixed culture is discussed. The cleavage of the molinate thioester bond, whether occurring under aerobic or anaerobic conditions, releases ethanethiol (S-ethyl moiety) and an azepane moiety derivative, identified as azepane-1-carboxylic acid. This azepane moiety is degraded, in the presence of oxygen, by Pseudomonas strains ON1 and ON3 and G. molinativorax ON4T. Ethanethiol, which inhibits G. molinativorax ON4T, is consumed by Pseudomonas strain ON1 and Stenotrophomonas maltophilia ON2. Although a two-member mixed culture of G. molinativorax ON4T and Pseudomonas strain ON1 was able to promote the aerobic mineralization of molinate, after 20 successive transfers of the five-member mixed culture in mineral medium with molinate, none of these isolates were lost. The results obtained indicate that the whole mixed culture may have a higher fitness than the two-member culture, even when the basic degradative and cross-protection functions are assured.

Genome sequencing of Mycobacterium tuberculosis complex members has accelerated the search for new disease-control tools. Antigen mining is one area that has benefited enormously from access to genome data. As part of an ongoing antigen mining programme, we screened genes that were previously identified by transcriptome analysis as upregulated in response to an in vitro acid shock for their in vivo expression profile and antigenicity. We show that the genes encoding two methyltransferases, Mb1438c/Rv1403c and Mb1440c/Rv1404c, were highly upregulated in a mouse model of infection, and were antigenic in M. bovis-infected cattle. As the genes encoding these antigens were highly upregulated in vivo, we sought to define their genetic regulation. A mutant was constructed that was deleted for their putative regulator, Mb1439/Rv1404; loss of the regulator led to increased expression of the flanking methyltransferases and a defined set of distal genes. This work has therefore generated both applied and fundamental outputs, with the description of novel mycobacterial antigens that can now be moved into field trials, but also with the description of a regulatory network that is responsive to both in vivo and in vitro stimuli.

The Cg1547 protein of Corynebacterium glutamicum ATCC 13032 is a member of the LacI/GalR family of DNA-binding transcriptional regulators. A defined deletion in the cg1547 gene, now designated uriR (uridine utilization regulator), resulted in the mutant strain C. glutamicum KB1547. Comparison of gene expression levels in C. glutamicum KB1547 and the wild-type strain revealed enhanced expression of the uriR operon genes cg1546 (ribokinase), cg1545 (uridine transporter) and cg1543 (uridine-preferring nucleoside hydrolase). Gene expression of the uriR operon was stimulated by the presence of either uridine or ribose. Growth assays with C. glutamicum mutants showed that functional Cg1543 and Cg1545 proteins are essential for the utilization of uridine as the sole carbon source. Transcriptional regulation of the uriR operon is mediated by a 29 bp palindromic sequence composed of two catabolite-responsive element (cre)-like sequences and located in between the mapped −10 promoter region and the start codon of uriR. A similar cre sequence was detected in the upstream region of rbsK2 (cg2554), coding for a second ribokinase in C. glutamicum ATCC 13032. DNA band-shift assays with a streptavidin-tagged UriR protein and labelled oligonucleotides including the cre-like sequences of uriR and rbsK2 demonstrated the specific binding of the purified regulator in vitro. Whole-genome DNA microarray hybridizations comparing the gene expression in C. glutamicum KB1547 with that of the wild-type strain revealed that UriR is a pathway-specific repressor of genes involved in uridine utilization in C. glutamicum.

Escherichia coli O157:H7 tightly associates with host cells through the formation of a pedestal structure in which cell cytoskeleton rearrangement has been observed. These pathogenic properties have been attributed to an island, known as the locus of enterocyte effacement (LEE), located on the bacterial chromosome. Gene l0017 is one of the LEE genes that has been less well characterized. To understand further the function of the gene, an l0017-deleted mutant was created. The mutant lost type III protein secretion (TTS) capacity. In terms of intracellular components, there was a substantial decrease in the level of EspA, but no apparent effect on Tir and EspB was observed. Fractionation of the bacterial proteins indicated that L0017 was part of the inner-membrane fraction. This association with the membrane is consistent with the hypothesis that L0017 may act as one of the TTS components. In addition, L0017 was found to affect regulation of EspA at a post-transcriptional level. The presence of L0017 readily stabilized EspA and the interaction between L0017 and EspA was demonstrated by their co-purification as well as by a bacterial two-hybrid system. Therefore, L0017 is a chaperone, the second chaperone identified in this system after CesAB, and escorts EspA, a protein with a great tendency to polymerize.

Regulation of the length of the O-antigen (Oag) chain attached to LPS in Shigella flexneri is important for virulence and is dependent on the inner-membrane protein Wzz. A lack of high-resolution structural data for Wzz has hampered efforts so far to correlate mutations affecting function of Wzz with structure and describe a mechanism for chain length regulation. Here we have used secondary structure prediction to show that the periplasmic domain of the WzzpHS2 protein has three regions of significant coiled-coil (CC) potential, two of which lie within an extended helical region. We describe here the first site-directed mutagenesis study to investigate the role of individual predicted CC regions (CCRs) in Wzz function and oligomerization. We found that CCRs 2 and 3 are necessary for wild-type Oag chain length regulation by WzzpHS2. The in vivo cross-linking profile of mutants affected in the three CCRs was not altered, indicating that individually each CCR is not required for oligomerization. Interestingly, the CCR3 mutation resulted in a temperature-sensitive phenotype and an inhibitory effect on Oag polymerization. Analysis of WzzpHS2 and the mutant constructs in a S. flexneri degP mutant showed that DegP did not affect the function of wild-type WzzpHS2 but its presence influenced the phenotype of the WzzpHS2 CCR3 mutant. Additionally, the phenotype of the WzzpHS2 CCR3 mutant was suppressed by a cis mutation near the putative cytoplasmic C-terminus of WzzpHS2.

The human-pathogenic yersiniae represent an ideal species group to study the evolution of highly virulent bacteria, with Yersinia pestis having emerged from the enteropathogen Y. pseudotuberculosis an estimated 20 000 years ago. Sequence data reveal that the Y. pestis genome is in the early stages of decay and contains hundreds of non-functioning pseudogenes, some of which may be important in the enteric lifestyle of Y. pseudotuberculosis. Bioinformatic analysis of pseudogenes from seven Y. pestis genome sequences identified rcsD as a gene disrupted early in the evolution of this organism. This phosphotransfer protein is part the of the Rcs phosphorelay, a two-component system present in the Enterobacteriaceae which has been shown to regulate the expression of capsular polysaccharide and other virulence determinants in several species including Escherichia coli and Salmonella. Using microarray analysis, we determined that the Y. pseudotuberculosis Rcs phosphorelay regulates the expression of 136 coding sequences, of which 60 % are predicted to affect the cell envelope. Several putative virulence determinants were identified as being regulated by this phosphorelay, along with proteins involved in biofilm formation, motility, mammalian cell adhesion and stress survival. Phenotypic assays on defined mutants confirmed a role for the phosphorelay in these processes in both Y. pseudotuberculosis and Y. enterocolitica.

Streptococcus mutans, the primary causative agent of human dental caries, grows as a biofilm on the tooth surface, where it metabolizes dietary carbohydrates and generates acid byproducts that demineralize tooth enamel. A drop in plaque pH stimulates an adaptive acid-tolerance response (ATR) in this oral pathogen that allows it to survive acid challenge at pHs as low as 3.0. In the present study, we describe the growth of an S. mutans mutant, GMS901, that harbours an insertion–deletion mutation in gcrR, a gene that encodes a transcriptional regulatory protein. The mutant is acid-sensitive and significantly compromised in its ATR relative to the UA159 wild-type progenitor strain. Consistent with these findings are the results of real-time quantitative RT-PCR (qRT-PCR) experiments that support the GcrR-regulated expression of known ATR genes, including atpA/E and ffh. Although we observed gcrR transcription that was not responsive to acidic pH, we did note a significant increase in gcrR expression when S. mutans cells were grown in a manganese-restricted medium. Interestingly, the results of gel mobility shift assays indicate that the S. mutans SloR metalloregulatory protein is a potential regulator of gcrR by virtue of its manganese-dependent binding to the gcrR promoter region, and expression studies support the hypothesis that sloR transcription is responsive to manganese deprivation and acidic pH. Taking these results together, we propose that SloR–Mn modulates S. mutans gcrR expression as part of a general stress response, and that GcrR acts downstream of SloR to control the ATR.

Flavobacterium psychrophilum is a psychrotrophic fish-pathogenic bacterium that causes cold water disease (CWD) in salmonids. By means of Tn4351 mutagenesis a mutant named FP1033, deficient in growth on iron-depleted medium, was previously isolated. FP1033 recovered the parental phenotype in the presence of iron. The gene disrupted by the transposon in this mutant encoded a protein with similarity to ExbD proteins, which are members of the TonB complex system involved in iron uptake mediated by siderophores. Analysis of the DNA surrounding the transposon insertion showed the presence of a tonB cluster of genes composed of exbB, two exbD (exbD1 and exbD2) and tonB loci. RT-PCR analysis and complementation studies indicated that these genes are transcribed as an operon and that the exbD2 : : Tn4351 phenotype was caused by the lack of ExbD2. FP1033 showed decreased virulence and conferred a high level of protection in rainbow trout fry after vaccination. This is believed to be the first report of a F. psychrophilum attenuated strain that induces a protective immune response in rainbow trout against CWD. These results suggest that the exbD2 locus from this particular TonB system is a suitable target to generate a live attenuated vaccine.

To identify Haemophilus ducreyi transcripts that are expressed during human infection, we used selective capture of transcribed sequences (SCOTS) with RNA isolated from pustules obtained from three volunteers infected with H. ducreyi, and with RNA isolated from broth-grown bacteria used to infect volunteers. With SCOTS, competitive hybridization of tissue-derived and broth-derived sequences identifies genes that may be preferentially expressed in vivo. Among the three tissue specimens, we identified 531 genes expressed in vivo. Southern blot analysis of 60 genes from each tissue showed that 87 % of the identified genes hybridized better with cDNA derived from tissue specimens than with cDNA derived from broth-grown bacteria. RT-PCR on nine additional pustules confirmed in vivo expression of 10 of 11 selected genes in other volunteers. Of the 531 genes, 139 were identified in at least two volunteers. These 139 genes fell into several functional categories, including biosynthesis and metabolism, regulation, and cellular processes, such as transcription, translation, cell division, DNA replication and repair, and transport. Detection of genes involved in anaerobic and aerobic respiration indicated that H. ducreyi likely encounters both microenvironments within the pustule. Other genes detected suggest an increase in DNA damage and stress in vivo. Genes involved in virulence in other bacterial pathogens and 32 genes encoding hypothetical proteins were identified, and may represent novel virulence factors. We identified three genes, lspA1, lspA2 and tadA, known to be required for virulence in humans. This is the first study to broadly define transcripts expressed by H. ducreyi in humans.

HtrA is a heat-stress protein that functions both as a chaperone and as a serine protease. HtrA has been shown in several organisms to be involved in responses to stressful environmental conditions and involvement of HtrA in virulence has been reported in pathogenic species. A Porphyromonas gingivalis htrA mutant demonstrated no significant difference to the W83 parent strain when subjected to high temperature and pH values from 3 to 11. However, the htrA mutant showed increased sensitivity to H2O2. Cell invasion assays indicated that the total interaction (adherence) with KB cells, human coronary artery endothelial cells and gingival epithelial cells (GEC) was the same for both the wild-type and the htrA mutant. However, the htrA mutant showed increased invasion in KB cells and GEC. Microarray experiments indicated that a total of 253 genes were differentially regulated in the htrA mutant, including a group of stress-related genes, which might be responsible for the observed decreased resistance to H2O2. In animal experiments, a competition assay showed that the htrA mutant did not survive as well as the wild-type. In another in vivo assay, fewer mice infected with the htrA mutant died than mice infected with W83, suggesting that the htrA gene is virulence-related. These data indicate that the htrA gene in P. gingivalis does not relate to stress conditions such as high temperature and pH, but rather to H2O2 stress. The htrA gene also appears to be important for virulence and survival in in vivo animal models.

A comprehensive meningococcal vaccine is yet to be developed. In the absence of a vaccine that immunizes against the serogroup B capsular polysaccharide, this can only be achieved by targeting subcapsular antigens, and a number of outer-membrane proteins (OMPs) are under consideration as candidates. A major obstacle to the development of such a vaccine is the antigenic diversity of these OMPs, and obtaining population data that accurately identify and catalogue these variants is an important component of vaccine design. The recently proposed meningococcal molecular strain-typing scheme indexes the diversity of two OMPs, PorA and FetA, that are vaccine candidates, as well as the capsule and multilocus sequence type. This scheme was employed to survey 323 meningococci isolated from invasive disease in England and Wales from 1975 to 1995, before the introduction of meningococcal conjugated serogroup C polysaccharide vaccines in 1999. The eight-locus typing scheme provided high typeability (99.4 %) and discrimination (Simpson's diversity index 0.94–0.99). The data showed cycling of meningococcal genotypes and antigenic types in the absence of planned interventions. Notwithstanding high genetic and antigenic diversity, most of the isolates belonged to one of seven clonal complexes, with 11 predominant strain types. Combinations of PorA and FetA, chosen on the basis of their prevalence over time, generated vaccine recipes that included protein variants found in 80 % or more of the disease isolates for this time period. If adequate immune responses can be generated, these results suggest that control of meningococcal disease with relatively simple protein component vaccines may be possible.

Moraxella catarrhalis is generally associated with upper respiratory tract infections in children and lower respiratory tract infections in adults. However, little is known regarding the population biology of isolates infecting these two age groups. To address this, a population-screening strategy was employed to investigate 195 worldwide M. catarrhalis isolates cultured from children (<5 years of age) and adults (>20 years of age) presenting with respiratory disease in the years 2001–2002. Parameters compared included: genotype analysis; autoagglutination/biofilm-forming ability; serum resistance; uspA1, uspA2, uspA2H, hag and mcaP incidence; copB/LOS/ompCD/16S rRNA types; and UspA1/Hag expression. A significant difference in biofilm formation (P=0.002), but not in autoagglutination or serum resistance, was observed, as well as significant differences in the incidence of uspA2- and uspA2H-positive isolates, and the distribution of lipooligosaccharide (LOS) types (P<0.0001 and P=0.01, respectively). Further, a significant decrease in the incidence of Hag expression (for isolates possessing the hag gene) was observed in adult isolates (P=0.001). Both uspA2H and LOS type B were associated with 16S rRNA type 1 isolates only, and two surrogate markers (copB and ompCD PCR RFLP types) for the two major M. catarrhalis 16S rRNA genetic lineages were identified. In conclusion, there are significant differences in phenotype and gene incidence between M. catarrhalis isolates from children and adults presenting with respiratory disease, possibly as a result of immune evasion in the adult age group. Our results should also be useful in the choice of effective vaccine candidates against M. catarrhalis.

The protein Mpn474 encoded by the mpn474 gene of the human-pathogenic Mycoplasma pneumoniae contains 1033 amino acids and has an isoelectric point of 4.79, which is caused by the large excess of glutamic acid residues (11 %). Although the protein lacks recognizable export signals we showed by immuno-electron microscopy that Mpn474 is surface exposed, covering the cell completely. By combining cross-linking and careful treatment of the bacterial cells with Triton X-100, we found that this protein is weakly bound to the cell surface, while the true transmembrane protein Mpn141 (adhesin P1) is firmly attached under the same experimental conditions. A transposon mutant in the mpn474 gene, which has no obvious phenotype, served as negative control for the immunodetection.

The adhesion of Candida albicans to host tissues contributes to its virulence, and adhesion to tissues or medical devices is a necessary step in biofilm formation. EAP1 encodes a glycosylphosphatidylinositol (GPI)-anchored glucan-cross-linked cell wall protein that mediates adhesion of C. albicans to various materials and cells, and appears to be required for C. albicans biofilm formation in vitro and in vivo. In this study, we demonstrated that the Eap1p N-terminal signal peptide and C-terminal GPI-anchor sequences result in similar protein localization in Saccharomyces cerevisiae and C. albicans. To investigate the contribution of different Eap1p domains to adhesion, we expressed Eap1p domain deletion mutants in non-adherent S. cerevisiae strains. The N-terminal domain mediates yeast cell–cell adhesion and invasive growth. Two Ser/Thr-rich domains containing tandem repeats were required to project the N-terminal region into the extracellular environment and to mediate adhesion to polystyrene. The N-terminal tandem repeat domain mediated adhesion to mammalian epithelial cells and promoted S. cerevisiae pseudohyphal growth. These results suggest a modular structure of Eap1p in which each domain serves multiple, often distinct, functions.