Salmonella typhimurium loci involved in survival within macrophages

Intruders below the radar: molecular pathogenesis of Bartonella spp

Bartonella spp. are facultative intracellular pathogens that employ a unique stealth infection strategy comprising immune evasion and modulation, intimate interaction with nucleated cells, and intraerythrocytic persistence. Infections with Bartonella are ubiquitous among mammals, and many species can infect humans either as their natural host or incidentally as zoonotic pathogens. Upon inoculation into a naive host, the bartonellae first colonize a primary niche that is widely accepted to involve the manipulation of nucleated host cells, e.g., in the microvasculature. Consistently, in vitro research showed that Bartonella harbors an ample arsenal of virulence factors to modulate the response of such cells, gain entrance, and establish an intracellular niche. Subsequently, the bacteria are seeded into the bloodstream where they invade erythrocytes and give rise to a typically asymptomatic intraerythrocytic bacteremia. While this course of infection is characteristic for natural hosts, zoonotic infections or the infection of immunocompromised patients may alter the path of Bartonella and result in considerable morbidity. In this review we compile current knowledge on the molecular processes underlying both the infection strategy and pathogenesis of Bartonella and discuss their connection to the clinical presentation of human patients, which ranges from minor complaints to life-threatening disease.

The tmRNA ribosome-rescue system

The bacterial tmRNA quality control system monitors protein synthesis and recycles stalled translation complexes in a process termed "ribosome rescue." During rescue, tmRNA acts first as a transfer RNA to bind stalled ribosomes, then as a messenger RNA to add the ssrA peptide tag to the C-terminus of the nascent polypeptide chain. The ssrA peptide targets tagged peptides for proteolysis, ensuring rapid degradation of potentially deleterious truncated polypeptides. Ribosome rescue also facilitates turnover of the damaged messages responsible for translational arrest. Thus, tmRNA increases the fidelity of gene expression by promoting the synthesis of full-length proteins. In addition to serving as a global quality control system, tmRNA also plays important roles in bacterial development, pathogenesis, and environmental stress responses. This review focuses on the mechanism of tmRNA-mediated ribosome rescue and the role of tmRNA in bacterial physiology.

Pseudomonas aeruginosa enhances production of an antimicrobial in response to N-acetylglucosamine and peptidoglycan

Pseudomonas aeruginosa is an opportunistic pathogen often associated with chronic lung infections in individuals with the genetic disease cystic fibrosis (CF). Previous work from our laboratory revealed that five genes predicted to be important for catabolism of N-acetylglucosamine (GlcNAc) are induced during in vitro growth in CF lung secretions (sputum). Here, we demonstrate that these genes comprise an operon (referred to as the nag operon) and that NagE, a putative component of the GlcNAc phosphotransferase system, is required for growth on and uptake of GlcNAc. Using primer extension analysis, the promoter of the nag operon was mapped and shown to be inducible by GlcNAc and regulated by the transcriptional regulator NagR. Transcriptome analysis revealed that in addition to induction of the nag operon, several P. aeruginosa genes encoding factors critical for extracellular antimicrobial production are also induced by GlcNAc. Finally, we show that the GlcNAc-containing polymer peptidoglycan induces production of the antimicrobial pyocyanin. Based on this data, we propose a model in which P. aeruginosa senses surrounding bacteria by monitoring exogenous peptidoglycan and responds to this cue through enhanced production of an antimicrobial.

Importance of the tmRNA system for cell survival when transcription is blocked by DNA-protein cross-links

Anticancer drug 5-azacytidine (aza-C) induces DNA-protein cross-links (DPCs) between cytosine methyltransferase and DNA as the drug inhibits methylation. We found that mutants defective in the tmRNA translational quality control system are hypersensitive to aza-C. Hypersensitivity requires expression of active methyltransferase, indicating the importance of DPC formation. Furthermore, the tmRNA pathway is activated upon aza-C treatment in cells expressing methyltransferase, resulting in increased levels of SsrA tagged proteins. These results argue that the tmRNA pathway clears stalled ribosome-mRNA complexes generated after transcriptional blockage by aza-C-induced DPCs. In support, an ssrA mutant is also hypersensitive to streptolydigin, which blocks RNA polymerase elongation by a different mechanism. The tmRNA pathway is thought to act only on ribosomes containing a 3' RNA end near the A site, and the known pathway for releasing RNA 3' ends from a blocked polymerase involves Mfd helicase. However, an mfd knockout mutant is not hypersensitive to either aza-C-induced DPC formation or streptolydigin, indicating that Mfd is not involved. Transcription termination factor Rho is also likely not involved, because the Rho-specific inhibitor bicyclomycin failed to show synergism with either aza-C or streptolydigin. Based on these findings, we discuss models for how E. coli processes transcription/translation complexes blocked at DPCs.

PoxA, yjeK, and elongation factor P coordinately modulate virulence and drug resistance in Salmonella enterica

We report an interaction between poxA, encoding a paralog of lysyl tRNA-synthetase, and the closely linked yjeK gene, encoding a putative 2,3-beta-lysine aminomutase, that is critical for virulence and stress resistance in Salmonella enterica. Salmonella poxA and yjeK mutants share extensive phenotypic pleiotropy, including attenuated virulence in mice, an increased ability to respire under nutrient-limiting conditions, hypersusceptibility to a variety of diverse growth inhibitors, and altered expression of multiple proteins, including several encoded on the SPI-1 pathogenicity island. PoxA mediates posttranslational modification of bacterial elongation factor P (EF-P), analogous to the modification of the eukaryotic EF-P homolog, eIF5A, with hypusine. The modification of EF-P is a mechanism of regulation whereby PoxA acts as an aminoacyl-tRNA synthetase that attaches an amino acid to a protein resembling tRNA rather than to a tRNA.

A novel anti-virulence gene revealed by proteomic analysis in Shigella flexneri 2a

Background

Shigella flexneri is a gram-negative, facultative pathogen that causes the majority of communicable bacterial dysenteries in developing countries. The virulence factors of S. flexneri have been shown to be produced at 37 degrees C but not at 30 degrees C. To discover potential, novel virulence-related proteins of S. flexneri, we performed differential in-gel electrophoresis (DIGE) analysis to measure changes in the expression profile that are induced by a temperature increase.

Results

The ArgT protein was dramatically down-regulated at 37 degrees C. In contrast, the ArgT from the non-pathogenic E. coli did not show this differential expression as in S. flexneri, which suggested that argT might be a potential anti-virulence gene. Competitive invasion assays in HeLa cells and in BALB/c mice with argT mutants were performed, and the results indicated that the over-expression of ArgT_Y225D would attenuate the virulence of S. flexneri. A comparative proteomic analysis was subsequently performed to investigate the effects of ArgT in S. flexneri at the molecular level. We show that HtrA is differentially expressed among different derivative strains.

Conclusion

Gene argT is a novel anti-virulence gene that may interfere with the virulence of S. flexneri via the transport of specific amino acids or by affecting the expression of the virulence factor, HtrA.

The proteome of Shigella flexneri 2a 2457T grown at 30 and 37 degrees C

To upgrade the proteome reference map of Shigella flexneri 2a 2457T, the protein expression profiles of log phase and stationary phase cells grown at 30 and 37 degrees C were thoroughly analyzed using multiple overlapping narrow pH range (between pH 4.0 and 11.0) two-dimensional gel electrophoresis. A total of 723 spots representing 574 protein entries were identified by MALDI-TOF/TOF MS, including the majority of known key virulence factors. 64 hypothetical proteins and six misannotated proteins were also experimentally identified. A comparison between the four proteome maps showed that most of the virulence-related proteins were up-regulated at 37 degrees C, and the differences were more notable in stationary phase cells, suggesting that the expressions of these virulence factors were not only controlled by temperature but also controlled by the nutrients available in the environment. The expression patterns of some virulence-related genes under the four different conditions suggested that they might also be regulated at the post-transcriptional level. A further significant finding was that the expression of the protein ArgT was dramatically up-regulated at 30 degrees C. The results of semiquantitative RT-PCR analysis showed that expression of argT was not regulated at the transcriptional level. Therefore, we carried out a series of experiments to uncover the mechanism regulating ArgT levels and found that the differential expression of ArgT was due to its degradation by a periplasmic protease, HtrA, whose activity, but not its synthesis, was affected by temperature. The cleavage site in ArgT was between position 160 (Val) and position 161 (Ala). These results may provide useful insights for understanding the physiology and pathogenesis of S. flexneri.

The smpB-ssrA mutant of Yersinia pestis functions as a live attenuated vaccine to protect mice against pulmonary plague infection

The bacterial SmpB-SsrA system is a highly conserved translational quality control mechanism that helps maintain the translational machinery at full capacity. Here we present evidence to demonstrate that the smpB-ssrA genes are required for pathogenesis of Yersinia pestis, the causative agent of plague. We found that disruption of the smpB-ssrA genes leads to reduction in secretion of the type III secretion-related proteins YopB, YopD, and LcrV, which are essential for virulence. Consistent with these observations, the smpB-ssrA mutant of Y. pestis was severely attenuated in a mouse model of infection via both the intranasal and intravenous routes. Most significantly, intranasal vaccination of mice with the smpB-ssrA mutant strain of Y. pestis induced a strong antibody response. The vaccinated animals were well protected against subsequent lethal intranasal challenges with virulent Y. pestis. Taken together, our results indicate that the smpB-ssrA mutant of Y. pestis possesses the desired qualities for a live attenuated cell-based vaccine against pneumonic plague.

Pestilence, persistence and pathogenicity: infection strategies of Bartonella

It has been nearly two decades since the discovery of Bartonella as an agent of bacillary angiomatosis in AIDS patients and persistent bacteremia and 'nonculturable' endocarditis in homeless people. Since that time, the number of Bartonella species identified has increased from one to 24, and 10 of these bacteria are associated with human disease. Although Bartonella is the only genus that infects human erythrocytes and triggers pathological angiogenesis in the vascular bed, the group remains understudied compared with most other bacterial pathogens. Numerous questions regarding Bartonella's molecular pathogenesis and epidemiology remain unanswered. Virtually every mammal harbors one or more Bartonella species and their transmission typically involves a hematophagous arthropod vector. However, many details regarding epidemiology and the public health threat imposed by these animal reservoirs is unclear. A handful of studies have shown that bartonellae are highly-adapted pathogens whose parasitic strategy has evolved to cause persistent infections of the host. To this end, virulence attributes of Bartonella include the subversion of host cells with effector molecules delivered via a type IV secretion system, induction of pathological angiogenesis through various means, including inhibition of apoptosis and activation of hypoxia-inducing factor 1, use of afimbrial adhesins that are orthologs of Yersinia adhesin A, incorporation of lipopolysaccharides with low endotoxic potency in the outer membrane, and several other virulence factors that help Bartonella infect and persist in erythrocytes and endothelial cells of the host circulatory system.

Subcellular localization of a bacterial regulatory RNA

Eukaryotes and bacteria regulate the activity of some proteins by localizing them to discrete subcellular structures, and eukaryotes localize some RNAs for the same purpose. To explore whether bacteria also spatially regulate RNAs, the localization of tmRNA was determined using fluorescence in situ hybridization. tmRNA is a small regulatory RNA that is ubiquitous in bacteria and that interacts with translating ribosomes in a reaction known as trans-translation. In Caulobacter crescentus, tmRNA was localized in a cell-cycle-dependent manner. In G(1)-phase cells, tmRNA was found in regularly spaced foci indicative of a helix-like structure. After initiation of DNA replication, most of the tmRNA was degraded, and the remaining molecules were spread throughout the cytoplasm. Immunofluorescence assays showed that SmpB, a protein that binds tightly to tmRNA, was colocalized with tmRNA in the helix-like pattern. RNase R, the nuclease that degrades tmRNA, was localized in a helix-like pattern that was separate from the SmpB-tmRNA complex. These results suggest a model in which tmRNA-SmpB is localized to sequester tmRNA from RNase R, and localization might also regulate tmRNA-SmpB interactions with ribosomes.

Proteases in bacterial pathogenesis

Bacterial pathogens rely on proteolysis for protein quality control under adverse conditions experienced in the host, as well as for the timely degradation of central virulence regulators. We have focused on the contribution of the conserved Lon, Clp, HtrA and FtsH proteases to pathogenesis and have highlighted common biological processes for which their activities are important for virulence.

System-level analysis of Salmonella metabolism during infection

Infectious diseases represent a major threat to human health. To develop urgently needed new control strategies, a transition from research focusing on individual factors to a more integrated system-level analysis might be needed. Such an approach faces great challenges and might require development of new concepts in large-scale data analysis. Here, I discuss for the well-characterized model pathogen Salmonella, how extensively studied metabolism can be used as a training field for infection biology at the systems level. Extensive experimental data can be analyzed in context using metabolic network visualization tools and in silico modeling based on genome-scale metabolic reconstructions. Suitable approaches to obtain still missing comprehensive quantitative data on Salmonella nutrition in infected host tissues are described. Such an integrated investigation of Salmonella metabolism during infection will enable an unprecedented large-scale understanding of pathogen in vivo activities, help to evaluate concepts and strategies for system-level analysis of host/pathogen interactions in general, and provide a basis for rational development of novel antimicrobials and efficacious live vaccines.

Salmonella enterica Serovar Typhimurium HtrA: regulation of expression and role of the chaperone and protease activities during infection

HtrA is a bifunctional stress protein required by many bacterial pathogens to successfully cause infection. Salmonella enterica serovar Typhimurium (S. Typhimurium) htrA mutants are defective in intramacrophage survival and are highly attenuated in mice. Transcription of htrA in Escherichia coli is governed by a single promoter that is dependent on sigma(E) (RpoE). S. Typhimurium htrA also possesses a sigma(E)-dependent promoter; however, we found that the absence of sigma(E) had little effect on production of HtrA by S. Typhimurium. This suggests that additional promoters control expression of htrA in S. Typhimurium. We identified three S. Typhimurium htrA promoters. Only the most proximal promoter, htrAp3, was sigma(E) dependent. The other promoters, htrAp1 and htrAp2, are probably recognized by the principal sigma factor sigma(70). These two promoters were constitutively expressed but were also slightly induced by heat shock. Thus expression of htrA is different in S. Typhimurium and E. coli. The role of HtrA is to deal with misfolded/damaged proteins in the periplasm. It can do this either by degrading (protease activity) or folding/capturing (chaperone/sequestering, C/S, activity) the aberrant protein. We investigated which of these functions are important to S. Typhimurium in vitro and in vivo. Point or deletion mutants of htrA that encode variant HtrA molecules have been used in previous studies to investigate the role of different regions of HtrA in C/S and protease activity. These htrA variants were placed under the control of the S. Typhimurium htrAP123 promoters and expressed in a S. Typhimurium htrA mutant, GVB1343. Both wild-type HtrA and HtrA (HtrA S210A) lacking protease activity enabled GVB1343 to grow at high temperature (46 degrees C). Both molecules also significantly enhanced the growth/survival of GVB1343 in the liver and spleen of mice during infection. However, expression of wild-type HtrA enabled GVB1343 to grow to much higher levels than expression of HtrA S210A. Thus both the protease and C/S functions of HtrA operate in vivo during infection but the protease function is probably more important. Absence of either PDZ domain completely abolished the ability of HtrA to complement the growth defects of GVB1343 in vitro or in vivo.

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

BACKGROUND

Infections with Salmonella cause significant morbidity and mortality worldwide. Replication of Salmonella typhimurium inside its host cell is a model system for studying the pathogenesis of intracellular bacterial infections. Genome-scale modeling of bacterial metabolic networks provides a powerful tool to identify and analyze pathways required for successful intracellular replication during host-pathogen interaction.

RESULTS

We have developed and validated a genome-scale metabolic network of Salmonella typhimurium LT2 (iRR1083). This model accounts for 1,083 genes that encode proteins catalyzing 1,087 unique metabolic and transport reactions in the bacterium. We employed flux balance analysis and in silico gene essentiality analysis to investigate growth under a wide range of conditions that mimic in vitro and host cell environments. Gene expression profiling of S. typhimurium isolated from macrophage cell lines was used to constrain the model to predict metabolic pathways that are likely to be operational during infection.

CONCLUSION

Our analysis suggests that there is a robust minimal set of metabolic pathways that is required for successful replication of Salmonella inside the host cell. This model also serves as platform for the integration of high-throughput data. Its computational power allows identification of networked metabolic pathways and generation of hypotheses about metabolism during infection, which might be used for the rational design of novel antibiotics or vaccine strains.

Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications for virulence and global protein translation

Using sample-matched transcriptomics and proteomics measurements it is now possible to begin to understand the impact of post-transcriptional regulatory programs in Enterobacteria. In bacteria post-transcriptional regulation is mediated by relatively few identified RNA-binding protein factors including CsrA, Hfq and SmpB. A mutation in any one of these three genes, csrA, hfq, and smpB, in Salmonella is attenuated for mouse virulence and unable to survive in macrophages. CsrA has a clearly defined specificity based on binding to a specific mRNA sequence to inhibit translation. However, the proteins regulated by Hfq and SmpB are not as clearly defined. Previous work identified proteins regulated by hfq using purification of the RNA-protein complex with direct sequencing of the bound RNAs and found binding to a surprisingly large number of transcripts. In this report we have used global proteomics to directly identify proteins regulated by Hfq or SmpB by comparing protein abundance in the parent and isogenic hfq or smpB mutant. From these same samples we also prepared RNA for microarray analysis to determine if alteration of protein expression was mediated post-transcriptionally. Samples were analyzed from bacteria grown under four different conditions; two laboratory conditions and two that are thought to mimic the intracellular environment. We show that mutants of hfq and smpB directly or indirectly modulate at least 20% and 4% of all possible Salmonella proteins, respectively, with limited correlation between transcription and protein expression. These proteins represent a broad spectrum of Salmonella proteins required for many biological processes including host cell invasion, motility, central metabolism, LPS biosynthesis, two-component regulatory systems, and fatty acid metabolism. Our results represent one of the first global analyses of post-transcriptional regulons in any organism and suggest that regulation at the translational level is widespread and plays an important role in virulence regulation and environmental adaptation for Salmonella.

Coordinated regulation of virulence during systemic infection of Salmonella enterica serovar Typhimurium

To cause a systemic infection, Salmonella must respond to many environmental cues during mouse infection and express specific subsets of genes in a temporal and spatial manner, but the regulatory pathways are poorly established. To unravel how micro-environmental signals are processed and integrated into coordinated action, we constructed in-frame non-polar deletions of 83 regulators inferred to play a role in Salmonella enteriditis Typhimurium (STM) virulence and tested them in three virulence assays (intraperitoneal [i.p.], and intragastric [i.g.] infection in BALB/c mice, and persistence in 129X1/SvJ mice). Overall, 35 regulators were identified whose absence attenuated virulence in at least one assay, and of those, 14 regulators were required for systemic mouse infection, the most stringent virulence assay. As a first step towards understanding the interplay between a pathogen and its host from a systems biology standpoint, we focused on these 14 genes. Transcriptional profiles were obtained for deletions of each of these 14 regulators grown under four different environmental conditions. These results, as well as publicly available transcriptional profiles, were analyzed using both network inference and cluster analysis algorithms. The analysis predicts a regulatory network in which all 14 regulators control the same set of genes necessary for Salmonella to cause systemic infection. We tested the regulatory model by expressing a subset of the regulators in trans and monitoring transcription of 7 known virulence factors located within Salmonella pathogenicity island 2 (SPI-2). These experiments validated the regulatory model and showed that the response regulator SsrB and the MarR type regulator, SlyA, are the terminal regulators in a cascade that integrates multiple signals. Furthermore, experiments to demonstrate epistatic relationships showed that SsrB can replace SlyA and, in some cases, SlyA can replace SsrB for expression of SPI-2 encoded virulence factors.

Use of high-throughput mass spectrometry to elucidate host-pathogen interactions in Salmonella

Capabilities in mass spectrometry are evolving rapidly, with recent improvements in sensitivity, data analysis and, most important from the standpoint of this review, much higher throughput, allowing analysis of many samples in a single day. This short review describes how these improvements in mass spectrometry can be used to dissect host-pathogen interactions using Salmonella as a model system. This approach has enabled direct identification of the majority of annotated Salmonella proteins, quantitation of expression changes under various in vitro growth conditions and new insights into virulence and expression of Salmonella proteins within host cells. One of the most significant findings is that a relatively high percentage of all the annotated genes (>20%) in Salmonella are regulated post-transcriptionally. In addition, new and unexpected interactions have been identified for several Salmonella virulence regulators that involve protein-protein interactions, suggesting additional functions of these regulators in coordinating virulence expression. Overall high-throughput mass spectrometry provides a new view of host-pathogen interactions, emphasizing the protein products and defining how protein interactions determine the outcome of infection.

Biology of trans-translation

The trans-translation mechanism is a key component of multiple quality control pathways in bacteria that ensure proteins are synthesized with high fidelity in spite of challenges such as transcription errors, mRNA damage, and translational frameshifting. trans-Translation is performed by a ribonucleoprotein complex composed of tmRNA, a specialized RNA with properties of both a tRNA and an mRNA, and the small protein SmpB. tmRNA-SmpB interacts with translational complexes stalled at the 3' end of an mRNA to release the stalled ribosomes and target the nascent polypeptides and mRNAs for degradation. In addition to quality control pathways, some genetic regulatory circuits use trans-translation to control gene expression. Diverse bacteria require trans-translation when they execute large changes in their genetic programs, including responding to stress, pathogenesis, and differentiation.

Trans-translation in Helicobacter pylori: essentiality of ribosome rescue and requirement of protein tagging for stress resistance and competence

BACKGROUND

The ubiquitous bacterial trans-translation is one of the most studied quality control mechanisms. Trans-translation requires two specific factors, a small RNA SsrA (tmRNA) and a protein co-factor SmpB, to promote the release of ribosomes stalled on defective mRNAs and to add a specific tag sequence to aberrant polypeptides to direct them to degradation pathways. Helicobacter pylori is a pathogen persistently colonizing a hostile niche, the stomach of humans.

PRINCIPAL FINDINGS

We investigated the role of trans-translation in this bacterium well fitted to resist stressful conditions and found that both smpB and ssrA were essential genes. Five mutant versions of ssrA were generated in H. pylori in order to investigate the function of trans-translation in this organism. Mutation of the resume codon that allows the switch of template of the ribosome required for its release was essential in vivo, however a mutant in which this codon was followed by stop codons interrupting the tag sequence was viable. Therefore one round of translation is sufficient to promote the rescue of stalled ribosomes. A mutant expressing a truncated SsrA tag was viable in H. pylori, but affected in competence and tolerance to both oxidative and antibiotic stresses. This demonstrates that control of protein degradation through trans-translation is by itself central in the management of stress conditions and of competence and supports a regulatory role of trans-translation-dependent protein tagging. In addition, the expression of smpB and ssrA was found to be induced upon acid exposure of H. pylori.

CONCLUSIONS

We conclude to a central role of trans-translation in H. pylori both for ribosome rescue possibly due to more severe stalling and for protein degradation to recover from stress conditions frequently encountered in the gastric environment. Finally, the essential trans-translation machinery of H. pylori is an excellent specific target for the development of novel antibiotics.

Gene set analyses for interpreting microarray experiments on prokaryotic organisms

BACKGROUND

Despite the widespread usage of DNA microarrays, questions remain about how best to interpret the wealth of gene-by-gene transcriptional levels that they measure. Recently, methods have been proposed which use biologically defined sets of genes in interpretation, instead of examining results gene-by-gene. Despite a serious limitation, a method based on Fisher's exact test remains one of the few plausible options for gene set analysis when an experiment has few replicates, as is typically the case for prokaryotes.

RESULTS

We extend five methods of gene set analysis from use on experiments with multiple replicates, for use on experiments with few replicates. We then use simulated and real data to compare these methods with each other and with the Fisher's exact test (FET) method. As a result of the simulation we find that a method named MAXMEAN-NR, maintains the nominal rate of false positive findings (type I error rate) while offering good statistical power and robustness to a variety of gene set distributions for set sizes of at least 10. Other methods (ABSSUM-NR or SUM-NR) are shown to be powerful for set sizes less than 10. Analysis of three sets of experimental data shows similar results. Furthermore, the MAXMEAN-NR method is shown to be able to detect biologically relevant sets as significant, when other methods (including FET) cannot. We also find that the popular GSEA-NR method performs poorly when compared to MAXMEAN-NR.

CONCLUSION

MAXMEAN-NR is a method of gene set analysis for experiments with few replicates, as is common for prokaryotes. Results of simulation and real data analysis suggest that the MAXMEAN-NR method offers increased robustness and biological relevance of findings as compared to FET and other methods, while maintaining the nominal type I error rate.

Quality control of bacterial mRNA decoding and decay

Studies in eukaryotes and prokaryotes have revealed that gene expression is not only controlled through altering the rate of transcription but also through varying rates of translation and mRNA decay. Indeed, the expression level of a protein is strongly affected by the steady state level of its mRNA. RNA decay can, along with transcription, play an important role in regulating gene expression by fine-tuning the steady state level of a given transcript and affecting its subsequent decoding during translation. Alterations in mRNA stability can in turn have dramatic effects on cell physiology and as a consequence the fitness and survival of the organism. Recent evidence suggests that mRNA decay can be regulated in response to environmental cues in order to enable the organism to adapt to its changing surroundings. Bacteria have evolved unique post transcriptional control mechanisms to enact such adaptive responses through: 1) general mRNA decay, 2) differential mRNA degradation using small non-coding RNAs (sRNAs), and 3) selective mRNA degradation using the tmRNA quality control system. Here, we review our current understanding of these molecular mechanisms, gleaned primarily from studies of the model gram negative organism Escherichia coli, that regulate the stability and degradation of normal and defective transcripts.

RosE represses Std fimbrial expression in Salmonella enterica serotype Typhimurium

The Salmonella enterica serotype Typhimurium (S. typhimurium) genome contains a large repertoire of putative fimbrial operons that remain poorly characterized because they are not expressed in vitro. In this study, insertions that induced expression of the putative stdABCD fimbrial operon were identified from a random bank of transposon mutants by screening with immuno-magnetic particles for ligand expression (SIMPLE). Transposon insertions upstream of csgC and lrhA or within dam, setB and STM4463 (renamed rosE) resulted in expression of StdA and its assembly into fimbrial filaments on the cell surface. RosE is a novel negative regulator of Std fimbrial expression as indicated by its repression of a std::lacZ reporter construct and by binding of the purified protein to a DNA region upstream of the stdA start codon. Expression of Std fimbriae in the rosE mutant resulted in increased attachment of S. typhimurium to human colonic epithelial cell lines (T-84 and CaCo-2). A rosE mutant exhibited a reduced ability to compete with virulent S. typhimurium for colonization of murine organs, while no defect was observed when both competing strains carried a stdAB deletion. These data suggest that a tight control of Std fimbrial expression mediated by RosE is required during host pathogen interaction.

Studying tmRNA-mediated surveillance and nonstop mRNA decay

In bacteria, ribosomes stalled at the 3'-end of nonstop or defective mRNAs are rescued by the action of a specialized ribonucleoprotein complex composed of tmRNA and SmpB protein in a process known as trans-translation; for recent reviews see Dulebohn et al. [2007], Keiler [2007], and Moore and Sauer [2007]. tmRNA is a bifunctional RNA that acts as both a tRNA and an mRNA. SmpB-bound tmRNA is charged with alanine by alanyl-tRNA synthetase and recognized by EF-Tu (GTP). The quaternary complex of tmRNA-SmpB-EF-Tu and GTP recognizes stalled ribosomes and transfers the nascent polypeptide to the tRNA-like domain of tmRNA. A specialized reading frame within tmRNA is then engaged as a surrogate mRNA to append a 10 amino acid (ANDENYALAA) tag to the C-terminus of the nascent polypeptide. A stop codon at the end of the tmRNA reading frame then facilitates normal termination and recycling of the translation machinery. Through this surveillance mechanism, stalled ribosomes are rescued, and nascent polypeptides bearing the C-terminal tmRNA-tag are directed for proteolysis. Several proteases (ClpXP, ClpAP, Lon, FtsH, and Tsp) are known to be involved in the degradation of tmRNA-tagged proteins (Choy et al., 2007; Farrell et al., 2005; Gottesman et al., 1998; Herman et al., 1998, 2003; Keiler et al., 1996). In addition to its ribosome rescue and peptide tagging activities, trans-translation also facilitates the selective decay of nonstop mRNAs in a process that is dependent on the activities of SmpB protein, tmRNA, and the 3' to 5'-exonuclease, RNase R (Mehta et al., 2006; Richards et al., 2006; Yamamoto et al., 2003). Here, we describe methods and strategies for the purification of tmRNA, SmpB, Lon, and RNase R from Escherichia coli that are likely to be applicable to other bacterial species. Protocols for the purification of the Clp proteases, Tsp, and FtsH, as well as EF-Tu and other essential E. coli translation factors may be found elsewhere (Joshi et al., 2003; Kihara et al., 1996; Makino et al., 1999; Maurizi et al., 1990; Shotland et al., 2000). In addition, we present biochemical and genetic assays to study the various aspects of the trans-translation mechanism.

Reactive oxygen species are the major antibacterials against Salmonella Typhimurium purine auxotrophs in the phagosome of RAW 264.7 cells

Intramacrophage survival appears to be a pathogenic trait common to Salmonellae and definition of the metabolic requirements of Salmonella within macrophages might provide opportunities for novel therapeutic interventions. We show that loss of PurG function in Salmonella enterica serovar Typhimurium SL1344 leads to death of the bacterium in RAW264.7 cells, which was due to unavailability of purine nucleotides but not thiamine in the phagosome of RAW264.7 cells. Phagosomal escape of purG mutant restored growth, suggesting that the phagosomal environment, but not the cytosol, is toxic to Salmonella purine auxotrophs. NADPH oxidase inhibition restored the growth of purG mutant in RAW264.7 cells, implying that the Salmonella-containing vacuole acquires reactive oxygen species (ROS) that are lethal to purine auxotrophs. Under purine limiting conditions, purG mutant was unable to repair the damage caused by hydrogen peroxide or UV irradiation, suggesting that ROS-mediated DNA damage may have been responsible for the attenuated phenotype of purG mutant in RAW264.7 cells and in mice. These studies highlight the possibility of utilizing the Salmonella purine nucleotide biosynthetic pathway as a prospective therapeutic target and also underline the importance of metabolic pathways in assembling a comprehensive understanding of the host-pathogen interactions inside phagocytic cells.

Identification of novel genes in genomic islands that contribute to Salmonella typhimurium replication in macrophages

Salmonella enterica serovar Typhimurium (S. typhimurium) survives and proliferates within macrophage cells. A mutant library of strain ATCC 14028 based on gene disruption by homologous recombination was screened in order to identify genes that are required for wild-type-like intracellular replication. Randomly generated chromosomal fragments from the genome of S. typhimurium were cloned into a temperature-sensitive vector, and approximately 8000 individual mutant clones were obtained by insertional-duplication mutagenesis (IDM) upon selection at non-permissive temperature. Large-scale screening for replication defects in mouse macrophages, but not during growth in rich or minimal medium, revealed a set of attenuated mutants that were further characterized by PCR amplification and sequencing of the mutagenic fragments. Following analysis of a Salmonella genome map with the annotated positions of vector insertions, an accumulation of 33 attenuating insertions within genes of ten non-collinear regions was found. Insertions in virK, gipA and five SPI-2 genes as well as seven non-polar deletions validated the screen. No invasion deficiencies of the mutants were observed. The cob-cbi-pdu cluster containing the genes for cobalamin synthesis and 1,2-propanediol degradation was shown to be required for Salmonella replication within macrophages. These data gave rise to a model of eukaryotic glycoconjugates and phospholipids as alternative carbon, nitrogen and energy sources for intracellularly replicating bacteria. The contribution of as yet unknown components of SPI-6 and the Gifsy-1 and Gifsy-2 prophage islands to intracellular replication is reported, as well as the fivefold reduced intracellular growth rate of a mutant with a deletion of STM1677, which probably encodes a LysR-like transcriptional regulator. The intracellular replication rate of three double mutants, each lacking two gene products of the cob-cbi-pdu cluster or the Gifsy-1 prophage, was shown to be lower than that of the respective single mutants, suggesting that additive effects of subtle intracellular advantages contribute to Salmonella fitness in vivo.

Proteomic identification of tmRNA substrates

The tmRNA-SmpB system releases ribosomes stalled on truncated mRNAs and tags the nascent polypeptides to target them for proteolysis. In many species, mutations that disrupt tmRNA activity cause defects in growth or development. In Caulobacter crescentus cells lacking tmRNA activity there is a delay in the initiation of DNA replication, which disrupts the cell cycle. To understand the molecular basis for this phenotype, 73 C. crescentus proteins were identified that are tagged by tmRNA under normal growth conditions. Among these substrates, proteins involved in DNA replication, recombination, and repair were overrepresented, suggesting that misregulation of these factors in the absence of tmRNA activity might be responsible for the delay in initiation of DNA replication. Analysis of the tagging sites within these substrates revealed a conserved nucleotide motif 5' of the tagging site, which is required for wild-type tmRNA tagging.

The tmRNA system for translational surveillance and ribosome rescue

The tmRNA system performs translational surveillance and ribosome rescue in all eubacteria and some eukaryotic organelles. This system intervenes when ribosomes read to the 3' end of an mRNA or pause at internal codons with subsequent mRNA cleavage. A complex of alanyl-tmRNA (which functions as a tRNA and mRNA), SmpB protein, and EF-TucGTP binds stalled ribosomes, the nascent polypeptide is transferred to the alanine on tmRNA, and translation switches from the original message to a short tmRNA open reading frame (ORF) that encodes a degradation tag. Translation of the ORF and normal termination releases the tagged polypeptide for degradation and permits disassembly and recycling of ribosomal subunits for new rounds of protein synthesis. Structural and biochemical studies suggest mechanisms that keep tmRNA from interrupting normal translation and target ribosomes stalled with very short 3' mRNA extensions. Additional biological roles of tmRNA include stress management and the regulation of transcriptional circuits.

Susceptibility of germ-free pigs to challenge with protease mutants of Salmonella enterica serovar Typhimurium

Salmonella protease mutants, clpP and especially htrA, are candidate live oral vaccines in humans. A functional and mature immune system is, however, required to cope with them in mice. Here, we test the cytokine response of highly susceptible germ-free pigs to infection with Salmonella Typhimurium clpP and htrA mutants. Cytokine levels (IL-4, IL-10, IL-18 and IFN-gamma) were measured by ELISA in plasma and washes from the terminal small bowel 24h after oral challenge. Unlike the infection with the wild type strain, no IFN-gamma response and low IL-18 intestinal levels were found in pigs infected with the protease mutants. Despite this and regardless of partially reduced ability of htrA and clpP mutants to invade and multiply in a 3D4 porcine macrophage-like cell line, both the mutants were as virulent as was the wild type LT2 strain and caused fatal septicaemia in germ-free pigs. IFN-gamma and IL-18 response therefore did not correlate with the virulence of Salmonella Typhimurium. Our results indicate that htrA and clpP attenuations should be used with caution in populations in which an increased number of immunocompromised individuals can be expected.

Qualitative and comparative proteomic analysis ofXanthomonas campestris pv.campestris 17

The bacterium Xanthomonas campestris pathovar campestris (XCC) 17 is a local isolate that causes crucifer black rot disease in Taiwan. In this study, its proteome was separated using 2-DE and the well-resolved proteins were excised, trypsin digested, and analyzed by MS. Over 400 protein spots were analyzed and 281 proteins were identified by searching the MS or MS/MS spectra against the proteome database of the closely related XCC ATCC 33913. Functional categorization of the identified proteins matched 141 (50%) proteins to 81 metabolic pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. In addition, we performed a comparative proteome analysis of the pathogenic strain 17 and an avirulent strain 11A to reveal the virulence-related proteins. We detected 22 up-regulated proteins in strain 17 including the degrading enzymes EngXCA, HtrA, and PepA, which had been shown to have a role in pathogenesis in other bacteria, and an anti-host defense protein, Ohr. Thus, further functional studies of these up-regulated proteins with respect to their roles in XCC pathogenicity are suggested.

SIMPLE approach for isolating mutants expressing fimbriae

Genomes of members of the family Enterobacteriaceae contain large repertoires of putative fimbrial operons. Since many of these operons are poorly expressed in vitro, a convenient method for inducing elaboration of the encoded fimbriae would greatly facilitate their functional characterization. Here we describe a new technique for identifying fimbriated bacteria from a library of transposon mutants by screening with immunomagnetic particles for ligand expression (SIMPLE). The SIMPLE method was applied to identify the T-POP mutants of Salmonella enterica serotype Typhimurium carrying on their surfaces filaments composed of PefA, the major subunit product of a fimbrial operon (pef) that is not expressed during growth in Luria-Bertani broth. Four such mutants were identified from a library of 24,000 mutants, each of which carried a T-POP insertion within the hns gene, which encodes a global silencer of horizontally acquired genes. Our data suggest that the SIMPLE method is an effective approach for isolating fimbriated bacteria, which can be readily applied to fimbrial operons identified by whole-genome sequencing.

Physiology of tmRNA: what gets tagged and why?

Transfer-messenger RNA (tmRNA) enters stalled translational complexes and, with small protein B (SmpB), mediates peptide tagging of the nascent protein and release of the stalled ribosome. Recent studies clarify how the tmRNA system is targeted to ribosomes and suggest that tmRNA-tagging is used for both quality control and specific regulation of cellular physiology.

The SsrA-SmpB ribosome rescue system is important for growth of Bacillus subtilis at low and high temperatures

Bacillus subtilis has multiple stress response systems whose integrated action promotes growth and survival under unfavorable conditions. Here we address the function and transcriptional organization of a five-gene cluster containing ssrA, previously known to be important for growth at high temperature because of the role of its tmRNA product in rescuing stalled ribosomes. Reverse transcription-PCR experiments detected a single message for the secG-yvaK-rnr-smpB-ssrA cluster, suggesting that it constitutes an operon. However, rapid amplification of cDNA ends-PCR and lacZ fusion experiments indicated that operon transcription is complex, with at least five promoters controlling different segments of the cluster. One sigma(A)-like promoter preceded secG (P(1)), and internal sigma(A)-like promoters were found in both the rnr-smpB (P(2)) and smpB-ssrA intervals (P(3) and P(HS)). Another internal promoter lay in the secG-yvaK intercistronic region, and this activity (P(B)) was dependent on the general stress factor sigma(B). Null mutations in the four genes downstream from P(B) were tested for their effects on growth. Loss of yvaK (carboxylesterase E) or rnr (RNase R) caused no obvious phenotype. By contrast, smpB was required for growth at high temperature (52 degrees C), as anticipated if its product (a small ribosomal binding protein) is essential for tmRNA (ssrA) function. Notably, smpB and ssrA were also required for growth at low temperature (16 degrees C), a phenotype not previously associated with tmRNA activity. These results extend the known high-temperature role of ssrA and indicate that the ribosome rescue system is important at both extremes of the B. subtilis temperature range.

Characterization and expression patterns of Sinorhizobium meliloti tmRNA (ssrA)

tmRNA (ssrA) in Sinorhizobium meliloti is a small RNA annotated by homology with the Bradyrhizobium japonicum sra molecule. Here, this molecule is described in Sinorhizobium meliloti as a model for such molecules in Alphaproteobacteria subgroup-2. Northern blot analysis and mapping of both 5' and 3' ends of this tmRNA allow the identification of two pieces: a 214 nt mRNA-like domain and an 82 nt tRNA-like domain, both highly stable, whereas the premature form is unstable. Transcriptional studies reveal that Sinorhizobium meliloti tmRNA is mainly expressed during growth resumption, replication initiation and various stress responses.

Mutation and virulence assessment of chromosomal genes of Rhodococcus equi 103

Rhodococcus equi can cause severe or fatal pneumonia in foals as well as in immunocompromised animals and humans. Its ability to persist in macrophages is fundamental to how it causes disease, but the basis of this is poorly understood. To examine further the general application of a recently developed system of targeted gene mutation and to assess the importance of different genes in resistance to innate immune defenses, we disrupted the genes encoding high-temperature requirement A (htrA), nitrate reductase (narG), peptidase D (pepD), phosphoribosylaminoimidazole-succinocarboxamide synthase (purC), and superoxide dismutase (sodC) in strain 103 of R. equi using a double-crossover homologous recombination approach. Virulence testing by clearance after intravenous injection in mice showed that the htrA and narG mutants were fully attenuated, the purC and sodC mutants were unchanged, and the pepD mutant was slightly attenuated. Complementation with the pREM shuttle plasmid restored the virulence of the htrA and pepD mutants but not that of the narG mutant. A single-crossover mutation approach was simpler and faster than the double-crossover homologous recombination technique and was used to obtain mutations in 6 other genes potentially involved in virulence (clpB, fadD8, fbpB, glnA1, regX3, and sigF). These mutants were not attenuated in the mouse clearance assay. We were not able to obtain mutants for genesfurA, galE, and sigE using the single-crossover mutation approach. In summary, the targeted-mutation system had general applicability but was not always completely successful, perhaps because some genes are essential under the growth conditions used or because the success of mutation depends on the target genes.

A positive feedback loop promotes transcription surge that jump-starts Salmonella virulence circuit

The PhoP/PhoQ two-component system is a master regulator of Salmonella pathogenicity. Here we report that induction of the PhoP/PhoQ system results in an initial surge of PhoP phosphorylation; the occupancy of target promoters by the PhoP protein; and the transcription of PhoP-activated genes, which then subsides to reach new steady-state levels. This surge in PhoP activity is due to PhoP positively activating its own transcription, because a strain constitutively expressing the PhoP protein attained steady-state levels of activation asymptotically, without the surge. The strain constitutively expressing the PhoP protein was attenuated for virulence in mice, demonstrating that the surge conferred by PhoP's positive feedback loop is necessary to jump-start Salmonella's virulence program.

Proteolytic adaptor for transfer-messenger RNA-tagged proteins from alpha-proteobacteria

We have identified an analog of SspB, the proteolytic adaptor for transfer-messenger RNA (tmRNA)-tagged proteins, in Caulobacter crescentus. C. crescentus SspB shares limited sequence similarity with Escherichia coli SspB but binds the tmRNA tag in vitro and is required for optimal proteolysis of tagged proteins in vivo.

Role of the universal stress protein UspA of Salmonella in growth arrest, stress and virulence

Pathogenic bacteria employ a variety of mechanisms to resist a barrage of stresses they encounter during active growth in or outside the host as well as during growth stasis. An in silico screen of the Salmonella genome sequence revealed that Salmonella typhimurium LT2 possesses a homologue belonging to the universal stress protein A (UspA) family. We assessed the transcriptional profile of uspA in S. typhimurium C5 by constructing a lacZ fusion revealing that uspA is induced by metabolic, oxidative, and temperature stresses. The highest transcriptional levels occurred in cells entering stationary phase, an observation consistent with expression patterns in Escherichia coli. The protein was purified as a fusion with GST (UspA(F)) and antibodies raised against UspA(F) revealed elevated protein levels in stressed and growth-arrested cells. Inactivation of uspA in S. typhimurium C5, lead to increased susceptibility to stress conditions. Furthermore, UspA makes an important contribution to the in vivo virulence of Salmonella in mice thus highlighting the importance of stress resistance regulation in pathogenicity and survival within the host.

Single, double and triple mutants of Salmonella enterica serovar Typhimurium degP (htrA), degQ (hhoA) and degS (hhoB) have diverse phenotypes on exposure to elevated temperature and their growth in vivo is attenuated to different extents

DegP (HtrA) is a well-studied protease involved in survival of bacteria under stress conditions in vitro and in vivo. There are two paralogues of DegP in the Salmonella enterica serovar Typhimurium genome, DegQ and DegS. In order to understand more about the biological significance of this gene family, a series of deg-deletion mutants was generated in S. Typhimurium strain SL3261 by allelic replacement. At elevated temperature in vitro, the viability of degP and degS mutants was reduced when compared with the parent strain whereas the viability of a degQ mutant was not significantly affected. The viability of a double degP-degS mutant at elevated temperature was severely decreased when compared with the respective single mutants or, interestingly, with a triple degP-degQ-degS mutant. All the deg deletions were transduced into the mouse-virulent strain SL1344 and the resultant mutants were injected intravenously into BALB/c mice to test virulence. degP and degS single mutants and all combinations of double and triple mutants were attenuated to different degrees, whereas the single degQ mutant was as virulent as the wild-type strain. Thus, within this gene family, degP and degS appear important for survival at elevated temperature and are necessary for full virulence, whereas a single degQ deletion appears to have no clear role in survival and growth at elevated temperature or in mice.

Distribution of prophages and SGI-1 antibiotic-resistance genes among different Salmonella enterica serovar Typhimurium isolates

Recently, the authors identified Salmonella enterica serovar Typhimurium (S. Typhimurium) definitive type (DT)104-specific sequences of mainly prophage origin by genomic subtractive hybridization. In the present study, the distribution of the prophages identified, ST104 and ST64B, and the novel prophage remnant designated prophage ST104B, was tested among 23 non-DT104 S. Typhimurium isolates of different phage types and 19 isolates of the DT104 subtypes DT104A, DT104B low and DT104L, and the DT104-related type U302. The four S. Typhimurium prophages Gifsy-1, Gifsy-2, Fels-1 and Fels-2 were also included. Analysis of prophage distribution in different S. Typhimurium isolates may supply additional information to enable development of a molecular method as an alternative to phage typing. Furthermore, the presence of the common DT104 antibiotic resistance genes for the penta-resistance type ACSSuT, aadA2, floR, pse-1, sul1 and tet(G), was also studied because of the authors' focus on this emerging type. Based on differences in prophage presence within their genome, it was possible to divide S. Typhimurium isolates into 12 groups. Although no clear relationship was found between different phage type and prophage presence, discrimination could be made between the different DT104 subtypes based on diversity in the presence of prophages ST104, ST104B and ST64B. The novel prophage remnant ST104B, which harbours a homologue of the Escherichia coli O157 : H7 HldD LPS assembly-related protein, was identified only in the 14 DT104L isolates and in the DT104-related U302 isolate. In conclusion, the presence of the genes for penta-resistance type ACSSuT, the HldD homologue containing ST104 prophage remnant and phage type DT104L are most likely common features of the emerging subtype of S. Typhimurium DT104.

Pushing the envelope: extracytoplasmic stress responses in bacterial pathogens

Despite being nutrient rich, the tissues and fluids of vertebrates are hostile to microorganisms, and most bacteria that attempt to take advantage of this environment are rapidly eliminated by host defences. Pathogens have evolved various means to promote their survival in host tissues, including stress responses that enable bacteria to sense and adapt to adverse conditions. Many different stress responses have been described, some of which are responsive to one or a small number of cues, whereas others are activated by a broad range of insults. The surface layers of pathogenic bacteria directly interface with the host and can bear the brunt of the attack by the host armoury. Several stress systems that respond to perturbations in the microbial cell outside of the cytoplasm have been described and are known collectively as extracytoplasmic or envelope stress responses (ESRs). Here, we review the role of the ESRs in the pathogenesis of Gram-negative bacterial pathogens.

Antimicrobials: targeting virulence genes necessary for intracellular multiplication

Intracellular bacteria constitute a major class of pathogens for humans and animals. Their pathogenicity is linked to their ability to multiply inside a host cell. A set of virulence genes (virulome) is required for this intracellular lifestyle. Recent studies have shown that blocking the enzymes encoded by these virulence genes impairs intracellular multiplication of the pathogen. These specific factors could constitute a new set of possible targets for antimicrobial drugs. The potential advantages, pitfalls and challenges of a strategy that targets these virulence factors are discussed.

Robust Salmonella metabolism limits possibilities for new antimicrobials

New antibiotics are urgently needed to control infectious diseases. Metabolic enzymes could represent attractive targets for such antibiotics, but in vivo target validation is largely lacking. Here we have obtained in vivo information about over 700 Salmonella enterica enzymes from network analysis of mutant phenotypes, genome comparisons and Salmonella proteomes from infected mice. Over 400 of these enzymes are non-essential for Salmonella virulence, reflecting extensive metabolic redundancies and access to surprisingly diverse host nutrients. The essential enzymes identified were almost exclusively associated with a small subgroup of pathways, enabling us to perform a nearly exhaustive screen. Sixty-four enzymes identified as essential in Salmonella are conserved in other important human pathogens, but almost all belong to metabolic pathways that are inhibited by current antibiotics or that have previously been considered for antimicrobial development. Our comprehensive in vivo analysis thus suggests a shortage of new metabolic targets for broad-spectrum antibiotics, and draws attention to some previously known but unexploited targets.

A Role for the SmpB-SsrA system in Yersinia pseudotuberculosis pathogenesis

Yersinia utilizes a sophisticated type III secretion system to enhance its chances of survival and to overcome the host immune system. SmpB (small protein B) and SsrA (small stable RNA A) are components of a unique bacterial translational control system that help maintain the bacterial translational machinery in a fully operational state. We have found that loss of the SmpB-SsrA function causes acute defects in the ability of Yersinia pseudotuberculosis to survive in hostile environments. Most significantly, we show that mutations in smpB-ssrA genes render the bacterium avirulent and unable to cause mortality in mice. Consistent with these observations, we show that the mutant strain is unable to proliferate in macrophages and exhibits delayed Yop-mediated host cell cytotoxicity. Correspondingly, we demonstrate that the smpB-ssrA mutant suffers severe deficiencies in expression and secretion of Yersinia virulence effector proteins, and that this defect is at the level of transcription. Of further interest is the finding that the SmpB-SsrA system might play a similar role in the related type III secretion system that governs flagella assembly and bacterial motility. These findings highlight the significance of the SmpB-SsrA system in bacterial pathogenesis, survival under adverse environmental conditions, and motility.

Bacteria have evolved sophisticated mechanisms to monitor, adapt, and respond to environmental and host-mediated assaults. Many Gram-negative pathogenic bacteria utilize a needle-like type III secretion system (TTSS) to inject a cocktail of effector proteins into host cells, disabling the host defenses against the pathogen. There is evolutionary, structural, and sequence similarity between this TTSS and the bacterial motility apparatus, the flagellum. Experiments described in this study examine the role played by the SmpB-SsrA system in Yersinia virulence, motility, and adaptation to adverse environments. The authors present evidence to demonstrate that an smpB-ssrA mutant of Yersinia pseudotuberculosis is more sensitive to adverse environmental conditions, lacks motility, exhibits severe defects in Yop secretion, and is avirulent in a mouse infection model. On the basis of these findings, they postulate that the SmpB-SsrA system, through its ribosome rescue, and protein tagging for directed degradation functions, affects the expression of the Ysc-Yop TTSS, and likely the flagellar TTSS, at the level of transcription. Their findings are consistent with a proposed regulatory role for the SmpB-SsrA system in regulation of bacterial gene expression.

Alternative sigma factors and their roles in bacterial virulence

Sigma factors provide promoter recognition specificity to RNA polymerase holoenzyme, contribute to DNA strand separation, and then dissociate from the core enzyme following transcription initiation. As the regulon of a single sigma factor can be composed of hundreds of genes, sigma factors can provide effective mechanisms for simultaneously regulating expression of large numbers of prokaryotic genes. One newly emerging field is identification of the specific roles of alternative sigma factors in regulating expression of virulence genes and virulence-associated genes in bacterial pathogens. Virulence genes encode proteins whose functions are essential for the bacterium to effectively establish an infection in a host organism. In contrast, virulence-associated genes can contribute to bacterial survival in the environment and therefore may enhance the capacity of the bacterium to spread to new individuals or to survive passage through a host organism. As alternative sigma factors have been shown to regulate expression of both virulence and virulence-associated genes, these proteins can contribute both directly and indirectly to bacterial virulence. Sigma factors are classified into two structurally unrelated families, the sigma70 and the sigma54 families. The sigma70 family includes primary sigma factors (e.g., Bacillus subtilis sigma(A)) as well as related alternative sigma factors; sigma54 forms a distinct subfamily of sigma factors referred to as sigma(N) in almost all species for which these proteins have been characterized to date. We present several examples of alternative sigma factors that have been shown to contribute to virulence in at least one organism. For each sigma factor, when applicable, examples are drawn from multiple species.

Alternative sigma factors and their roles in bacterial virulence

Sigma factors provide promoter recognition specificity to RNA polymerase holoenzyme, contribute to DNA strand separation, and then dissociate from the core enzyme following transcription initiation. As the regulon of a single sigma factor can be composed of hundreds of genes, sigma factors can provide effective mechanisms for simultaneously regulating expression of large numbers of prokaryotic genes. One newly emerging field is identification of the specific roles of alternative sigma factors in regulating expression of virulence genes and virulence-associated genes in bacterial pathogens. Virulence genes encode proteins whose functions are essential for the bacterium to effectively establish an infection in a host organism. In contrast, virulence-associated genes can contribute to bacterial survival in the environment and therefore may enhance the capacity of the bacterium to spread to new individuals or to survive passage through a host organism. As alternative sigma factors have been shown to regulate expression of both virulence and virulence-associated genes, these proteins can contribute both directly and indirectly to bacterial virulence. Sigma factors are classified into two structurally unrelated families, the sigma70 and the sigma54 families. The sigma70 family includes primary sigma factors (e.g., Bacillus subtilis sigma(A)) as well as related alternative sigma factors; sigma54 forms a distinct subfamily of sigma factors referred to as sigma(N) in almost all species for which these proteins have been characterized to date. We present several examples of alternative sigma factors that have been shown to contribute to virulence in at least one organism. For each sigma factor, when applicable, examples are drawn from multiple species.

Salmonella typhimurium grown in iron-rich media, inactivated with ferric chloride and adjuvanted with homologous bacterial DNA is potent and efficacious vaccine in mice

The present study describes our attempt to construct a novel vaccine formulation that affords full protection against murine typhoid under experimental conditions. Ferric chloride, 100mM, as inactivating agent, bacterial growth under iron-rich conditions and homologous bacterial DNA as adjuvant were used for construction of the experimental Salmonella typhimurium vaccine. The vaccine inoculated twice at 2 weeks interval in Swiss albino mice elicited statistically significant IgG levels when compared with non-adjuvanted and other control groups. All the mice inoculated with the novel vaccine withstood challenge with 50 LD(50) dose of S. typhimurium strain St 585. No significant safety problems were found in mice.

Identification of novel Salmonella enterica serovar Typhimurium DT104-specific prophage and nonprophage chromosomal sequences among serovar Typhimurium isolates by genomic subtractive hybridization

Genomic subtractive hybridization was performed between Salmonella enterica serovar Typhimurium LT2 and DT104 to search for novel Salmonella serovar Typhimurium DT104-specific sequences. The subtraction resulted mainly in the isolation of DNA fragments with sequence similarity to phages. Two fragments identified were associated with possible virulence factors. One fragment was identical to irsA of Salmonella serovar Typhimurium ATCC 14028, which is suggested to be involved in macrophage survival. The other fragment was homologous to HldD, an Escherichia coli O157:H7 lipopolysaccharide assembly-related protein. Five selected DNA fragments-irsA, the HldD homologue, and three fragments with sequence similarity to prophages-were tested for their presence in 17 Salmonella serovar Typhimurium DT104 isolates and 27 non-DT104 isolates by PCR. All five selected DNA fragments were Salmonella serovar Typhimurium DT104 specific among the serovar Typhimurium isolates tested. These DNA fragments can be useful for better detection and typing of Salmonella serovar Typhimurium DT104.

Identification of a protein subset of the anthrax spore immunome in humans immunized with the anthrax vaccine adsorbed preparation

We identified spore targets of Anthrax Vaccine Adsorbed (AVA)-induced immunity in humans by screening recombinant clones of a previously generated, limited genomic Bacillus anthracis Sterne (pXO1(+), pXO2(-)) expression library of putative spore surface (spore-associated [SA]) proteins with pooled sera from human adults immunized with AVA (immune sera), the anthrax vaccine currently approved for use by humans in the United States. We identified 69 clones that reacted specifically with pooled immune sera but not with pooled sera obtained from the same individuals prior to immunization. Positive clones expressed proteins previously identified as localized on the anthrax spore surface, proteins highly expressed during spore germination, orthologs of proteins of diverse pathogens under investigation as drug targets, and orthologs of proteins contributing to the virulence of both gram-positive and gram-negative pathogens. Among the reactive clones identified by this immunological screen was one expressing a 15.2-kDa hypothetical protein encoded by a gene with no significant homology to sequences contained in databases. Further studies are required to define the subset of SA proteins identified in this study that contribute to the virulence of this pathogen. We hypothesize that optimal delivery of a subset of SA proteins identified by such studies to the immune system in combination with protective antigen (PA), the principal immunogen in AVA, might facilitate the development of defined, nonreactogenic, more-efficacious PA-based anthrax vaccines. Future studies might also facilitate the identification of SA proteins with potential to serve as targets for drug design, spore inactivation, or spore detection strategies.

Envelope stress responses and Gram-negative bacterial pathogenesis

The sigma(E), Cpx and Bae envelope stress responses of Escherichia coli are involved in the maintenance, adaptation and protection of the bacterial envelope in response to a variety of stressors. Recent studies indicate that the Cpx and sigma(E) stress responses exist in many Gram-negative bacterial pathogens. The envelope is of particular importance to these organisms because most virulence determinants reside in, or must transit through, this cellular compartment. The Cpx system has been implicated in expression of pili, type IV secretion systems and key virulence regulators, while the sigma(E) pathway has been shown to be critical for protection from oxidative stress and intracellular survival. Homologues of the sigma(E)- and Cpx-regulated protease DegP are essential for full virulence in numerous pathogens, and, like sigma(E), DegP appears to confer resistance to oxidative stress and intracellular survival capacity. Some pathogens contain multiple homologues of the Cpx-regulated, disulphide bond catalyst DsbA protein, which has been demonstrated to play roles in the expression of secreted virulence determinants, type III secretion systems and pili. This review highlights recent studies that indicate roles for the sigma(E), Cpx and Bae envelope stress responses in Gram-negative bacterial pathogenesis.