Control of a Salmonella virulence operon by proline-charged tRNA(Pro)

Determinants of bacterial survival and proliferation in blood

Bloodstream infection is a major public health concern associated with high mortality and high healthcare costs worldwide. Bacteremia can trigger fatal sepsis whose prevention, diagnosis, and management have been recognized as a global health priority by the World Health Organization. Additionally, infection control is increasingly threatened by antimicrobial resistance, which is the focus of global action plans in the framework of a One Health response. In-depth knowledge of the infection process is needed to develop efficient preventive and therapeutic measures. The pathogenesis of bloodstream infection is a dynamic process resulting from the invasion of the vascular system by bacteria, which finely regulate their metabolic pathways and virulence factors to overcome the blood immune defenses and proliferate. In this review, we highlight our current understanding of determinants of bacterial survival and proliferation in the bloodstream and discuss their interactions with the molecular and cellular components of blood.

Chaperone Hsp70 helps Salmonella survive infection-relevant stress by reducing protein synthesis

In all domains of life, Hsp70 chaperones preserve protein homeostasis by promoting protein folding and degradation and preventing protein aggregation. We now report that the Hsp70 from the bacterial pathogen Salmonella enterica serovar Typhimurium-termed DnaK-independently reduces protein synthesis in vitro and in S. Typhimurium facing cytoplasmic Mg2+ starvation, a condition encountered during infection. This reduction reflects a 3-fold increase in ribosome association with DnaK and a 30-fold decrease in ribosome association with trigger factor, the chaperone normally associated with translating ribosomes. Surprisingly, this reduction does not involve J-domain cochaperones, unlike previously known functions of DnaK. Removing the 74 C-terminal amino acids of the 638-residue long DnaK impeded DnaK association with ribosomes and reduction of protein synthesis, rendering S. Typhimurium defective in protein homeostasis during cytoplasmic Mg2+ starvation. DnaK-dependent reduction in protein synthesis is critical for survival against Mg2+ starvation because inhibiting protein synthesis in a dnaK-independent manner overcame the 10,000-fold loss in viability resulting from DnaK truncation. Our results indicate that DnaK protects bacteria from infection-relevant stresses by coordinating protein synthesis with protein folding capacity.

Fluoroquinolone and beta-lactam antimicrobials induce different transcriptome profiles in Salmonella enterica persister cells

Here, we investigate the transcriptome profiles of two S. Enteritidis and one S. Schwarzengrund isolates that present different persister levels when exposed to ciprofloxacin or ceftazidime. It was possible to note a distinct transcript profile among isolates, time of exposure, and treatment. We could not find a commonly expressed transcript profile that plays a role in persister formation after S. enterica exposure to beta-lactam or fluoroquinolone, as only three DEGs presented the same behavior under the conditions and isolates tested. It appears that the formation of persisters in S. enterica after exposure to ciprofloxacin is linked to the overexpression of genes involved in the SOS response (recA), cell division inhibitor (sulA), iron-sulfur metabolism (hscA and iscS), and type I TA system (tisB). On the other hand, most genes differentially expressed in S. enterica after exposure to ceftazidime appeared to be downregulated and were part of the flagellar assembly apparatus, citrate cycle (TCA cycle), glycolysis/gluconeogenesis, carbon metabolism, bacterial secretion system, quorum sensing, pyruvate metabolism pathway, and biosynthesis of secondary metabolites. The different transcriptome profiles found in S. enterica persisters induced by ciprofloxacin and ceftazidime suggest that these cells modulate their response differently according to each stress.

How Bacterial Pathogens Coordinate Appetite with Virulence

Cells adjust growth and metabolism to nutrient availability. Having access to a variety of carbon sources during infection of their animal hosts, facultative intracellular pathogens must efficiently prioritize carbon utilization. Here, we discuss how carbon source controls bacterial virulence, with an emphasis on Salmonella enterica serovar Typhimurium, which causes gastroenteritis in immunocompetent humans and a typhoid-like disease in mice, and propose that virulence factors can regulate carbon source prioritization by modifying cellular physiology. On the one hand, bacterial regulators of carbon metabolism control virulence programs, indicating that pathogenic traits appear in response to carbon source availability. On the other hand, signals controlling virulence regulators may impact carbon source utilization, suggesting that stimuli that bacterial pathogens experience within the host can directly impinge on carbon source prioritization. In addition, pathogen-triggered intestinal inflammation can disrupt the gut microbiota and thus the availability of carbon sources. By coordinating virulence factors with carbon utilization determinants, pathogens adopt metabolic pathways that may not be the most energy efficient because such pathways promote resistance to antimicrobial agents and also because host-imposed deprivation of specific nutrients may hinder the operation of certain pathways. We propose that metabolic prioritization by bacteria underlies the pathogenic outcome of an infection.

Nutrient stress is a target for new antibiotics

Novel approaches are required to address the looming threat of pan-resistant Gram-negative pathogens and forestall the rise of untreatable infections. Unconventional targets that are uniquely important during infection and tractable to high-throughput drug discovery methods hold high potential for innovation in antibiotic discovery programs. In this context, inhibitors of bacterial nutrient stress are particularly exciting candidates for future antibiotic development. Amino acid, nucleotide, and vitamin biosynthesis pathways are critical for bacterial growth in nutrient-limiting conditions in the laboratory and the host. Although historically dismissed as dispensable for pathogens, a wealth of transposon mutagenesis and single-mutant studies have emerged which demonstrate that several such pathways are critical for infection. Indeed, high-throughput screens of diverse synthetic compounds and natural products have uncovered inhibitors of nutrient biosynthesis. Herein, we review bacterial nutrient biosynthesis and its role during host infection. Further, we explore screening platforms developed to search for inhibitors of these targets and highlight successes among these. Finally, we feature important and sometimes surprising connections between bacterial nutrient biosynthesis, antibiotic activity, and antibiotic resistance.

Characterizing 5-oxoproline sensing pathways of Salmonella enterica serovar typhimurium

5-Oxoproline (5OP) is a poorly researched ubiquitous natural amino acid found in all life forms. We have previously shown that Salmonella enterica serovar Typhimurium (Salmonella) responds to 5OP exposure by reducing cyclic-di-GMP levels, and resultant cellulose dependent cellular aggregation in a YfeA and BcsA dependent manner. To understand if 5OP was specifically sensed by Salmonella we compared the interaction of Salmonella with 5OP to that of the chemically similar and biologically relevant molecule, l-proline. We show that l-proline but not 5OP can be utilized by Salmonella as a nutrient source. We also show that 5OP but not l-proline regulates cellulose dependent cellular aggregation. These results imply that 5OP is utilized by Salmonella as a specific signal. However, l-proline is a 5OP aggregation inhibitor implying that while it cannot activate the aggregation pathway by itself, it can inhibit 5OP dependent activation. We then show that in a l-proline transporter knockout mutant l-proline competition remain unaffected, implying sensing of 5OP is extracellular. Last, we identify a transcriptional effect of 5OP exposure, upregulation of the mgtCBR operon, known to be activated during host invasion. While mgtCBR is known to be regulated by both low pH and l-proline starvation, we show that 5OP regulation of mgtCBR is indirect through changes in pH and is not dependent on the 5OP chemical structure similarity to l-proline. We also show this response to be PhoPQ dependent. We further show that the aggregation response is independent of pH modulation, PhoPQ and MgtC and that the mgtCBR transcriptional response is independent of YfeA and BcsA. Thus, the two responses are mediated through two independent signaling pathways. To conclude, we show Salmonella responds to 5OP specifically to regulate aggregation and not specifically to regulate gene expression. When and where in the Salmonella life cycle does 5OP sensing takes place remains an open question. Furthermore, because 5OP inhibits c-di-GMP through the activation of an external sensor, and does not require an internalization step like many studied biofilm inhibitors, 5OP or derivatives might be developed into useful biofilm inhibitors.

Genetic Determinants in Salmonella enterica Serotype Typhimurium Required for Overcoming In Vitro Stressors in the Mimicking Host Environment

Salmonella enterica serotype Typhimurium, a nontyphoidal Salmonella (NTS), results in a range of enteric diseases, representing a major disease burden worldwide. There is still a significant portion of Salmonella genes whose mechanistic basis to overcome host innate defense mechanisms largely remains unknown. Here, we have applied transposon insertion sequencing (Tn-seq) method to unveil the genetic factors required for the growth or survival of S. Typhimurium under various host stressors simulated in vitro. A highly saturating Tn5 library of S. Typhimurium 14028s was subjected to selection during growth in the presence of short-chain fatty acid (100 mM propionate), osmotic stress (3% NaCl), or oxidative stress (1 mM H2O2) or survival in extreme acidic pH (30 min in pH 3) or starvation (12 days in 1× phosphate-buffered saline [PBS]). We have identified a total of 339 conditionally essential genes (CEGs) required to overcome at least one of these conditions mimicking host insults. Interestingly, all eight genes encoding FoF1-ATP synthase subunit proteins were required for fitness in all five stresses. Intriguingly, a total of 88 genes in Salmonella pathogenicity islands (SPI), including SPI-1, SPI-2, SPI-3, SPI-5, SPI-6, and SPI-11, are also required for fitness under the in vitro conditions. Additionally, by comparative analysis of the genes identified in this study and the genes previously shown to be required for in vivo fitness, we identified novel genes (marBCT, envF, barA, hscA, rfaQ, rfbI, and the genes encoding putative proteins STM14_1138, STM14_3334, STM14_4825, and STM_5184) that have compelling potential for the development of vaccines and antibacterial drugs to curb Salmonella infection. IMPORTANCE Salmonella enterica serotype Typhimurium is a major human bacterial pathogen that enters the food chain through meat animals asymptomatically carrying this pathogen. Despite the rich genome sequence data, a significant portion of Salmonella genes remain to be characterized for their potential contributions to virulence. In this study, we used transposon insertion sequencing (Tn-seq) to elucidate the genetic factors required for growth or survival under various host stressors, including short-chain fatty acids, osmotic stress, oxidative stress, extreme acid, and starvation. Among the total of 339 conditionally essential genes (CEGs) that are required under at least one of these five stress conditions were 221 previously known virulence genes required for in vivo fitness during infection in at least one of four animal species, including mice, chickens, pigs, and cattle. This comprehensive map of virulence phenotype-genotype in S. Typhimurium provides a roadmap for further interrogation of the biological functions encoded by the genome of this important human pathogen to survive in hostile host environments.

Cellular Adaptations to Cytoplasmic Mg2+ Limitation

Mg²⁺ is the most abundant divalent cation in living cells. It is essential for charge neutralization, macromolecule stabilization, and the assembly and activity of ribosomes and as a cofactor for enzymatic reactions. When experiencing low cytoplasmic Mg²⁺, bacteria adopt two main strategies: They increase the abundance and activity of Mg²⁺ importers and decrease the abundance of Mg²⁺-chelating ATP and rRNA. These changes reduce regulated proteolysis by ATP-dependent proteases and protein synthesis in a systemic fashion. In many bacterial species, the transcriptional regulator PhoP controls expression of proteins mediating these changes. The 5' leader region of some mRNAs responds to low cytoplasmic Mg²⁺ or to disruptions in translation of open reading frames in the leader regions by furthering expression of the associated coding regions, which specify proteins mediating survival when the cytoplasmic Mg²⁺ concentration is low. Microbial species often utilize similar adaptation strategies to cope with low cytoplasmic Mg²⁺ despite relying on different genes to do so.

How the PhoP/PhoQ System Controls Virulence and Mg2+ Homeostasis: Lessons in Signal Transduction, Pathogenesis, Physiology, and Evolution

The PhoP/PhoQ two-component system governs virulence, Mg2+ homeostasis, and resistance to a variety of antimicrobial agents, including acidic pH and cationic antimicrobial peptides, in several Gram-negative bacterial species. Best understood in Salmonella enterica serovar Typhimurium, the PhoP/PhoQ system consists o-regulated gene products alter PhoP-P amounts, even under constant inducing conditions. PhoP-P controls the abundance of hundreds of proteins both directly, by having transcriptional effects on the corresponding genes, and indirectly, by modifying the abundance, activity, or stability of other transcription factors, regulatory RNAs, protease regulators, and metabolites. The investigation of PhoP/PhoQ has uncovered novel forms of signal transduction and the physiological consequences of regulon evolution.

Low Cytoplasmic Magnesium Increases the Specificity of the Lon and ClpAP Proteases

Proteolysis is a fundamental property of all living cells. In the bacterium Salmonella enterica serovar Typhimurium, the HspQ protein controls the specificities of the Lon and ClpAP proteases. Upon acetylation, HspQ stops being a Lon substrate and no longer enhances proteolysis of the Lon substrate Hha. The accumulated HspQ protein binds to the protease adaptor ClpS, hindering proteolysis of ClpS-dependent substrates of ClpAP, such as Oat, a promoter of antibiotic persistence. HspQ is acetylated by the protein acetyltransferase Pat from acetyl coenzyme A (acetyl-CoA) bound to the acetyl-CoA binding protein Qad. We now report that low cytoplasmic Mg²⁺ promotes qad expression, which protects substrates of Lon and ClpSAP by increasing HspQ amounts. The qad promoter is activated by PhoP, a regulatory protein highly activated in low cytoplasmic Mg²⁺ that also represses clpS transcription. Both the qad gene and PhoP repression of the clpS promoter are necessary for antibiotic persistence. PhoP also promotes qad transcription in Escherichia coli, which shares a similar PhoP box in the qad promoter region with S. Typhimurium, Salmonella bongori, and Enterobacter cloacae. Our findings identify cytoplasmic Mg²⁺ and the PhoP protein as critical regulators of protease specificity in multiple enteric bacteria. IMPORTANCE The bacterium Salmonella enterica serovar Typhimurium narrows down the spectrum of substrates degraded by the proteases Lon and ClpAP in response to low cytoplasmic Mg²⁺, a condition that decreases protein synthesis. This control is exerted by PhoP, a transcriptional regulator activated in low cytoplasmic Mg²⁺ that governs proteostasis and is conserved in enteric bacteria. The uncovered mechanism enables bacteria to control the abundance of preexisting proteins.

A stress-induced block in dicarboxylate uptake and utilization in Salmonella

Bacteria have evolved to sense and respond to their environment by altering gene expression and metabolism to promote growth and survival. In this work we demonstrate that Salmonella displays an extensive (>30 hour) lag in growth when subcultured into media where dicarboxylates such as succinate are the sole carbon source. This growth lag is regulated in part by RpoS, the RssB anti-adaptor IraP, translation elongation factor P, and to a lesser degree the stringent response. We also show that small amounts of proline or citrate can trigger early growth in succinate media and that, at least for proline, this effect requires the multifunctional enzyme/regulator PutA. We demonstrate that activation of RpoS results in the repression of dctA, encoding the primary dicarboxylate importer, and that constitutive expression of dctA induced growth. This dicarboxylate growth lag phenotype is far more severe across multiple Salmonella isolates than in its close relative E. coli Replacing 200 nt of the Salmonella dctA promoter region with that of E. coli was sufficient to eliminate the observed lag in growth. We hypothesized that this cis-regulatory divergence might be an adaptation to Salmonella's virulent lifestyle where levels of phagocyte-produced succinate increase in response to bacterial LPS, however we found that impairing dctA repression had no effect on Salmonella's survival in acidified succinate or in macrophages.Importance Bacteria have evolved to sense and respond to their environment to maximize their chance of survival. By studying differences in the responses of pathogenic bacteria and closely related non-pathogens, we can gain insight into what environments they encounter inside of an infected host. Here we demonstrate that Salmonella diverges from its close relative E. coli in its response to dicarboxylates such as the metabolite succinate. We show that this is regulated by stress response proteins and ultimately can be attributed to Salmonella repressing its import of dicarboxylates. Understanding this phenomenon may reveal a novel aspect of the Salmonella virulence cycle, and our characterization of its regulation yields a number of mutant strains that can be used to further study it.

How Pathogens Feel and Overcome Magnesium Limitation When in Host Tissues

Host organisms utilize nutritional immunity to limit the availability of nutrients essential to an invading pathogen. Nutrients may include amino acids, nucleotide bases, and transition metals, the essentiality of which varies among pathogens. The mammalian macrophage protein Slc11a1 (previously Nramp1) mediates resistance to several intracellular pathogens. Slc11a1 is proposed to restrict growth of Salmonella enterica serovar Typhimurium in host tissues by causing magnesium deprivation. This is intriguing because magnesium is the most abundant divalent cation in all living cells. A pathogen's response to factors such as Slc11a1 that promote nutritional immunity may therefore reflect what the pathogen 'feels' in its cytoplasm, rather than the nutrient concentration in host cell compartments.

The mgtCBR mRNA Leader Secures Growth of Salmonella in Both Host and Non-host Environments

Upon intracellular cues, bacterial mRNA leaders often form secondary structures that determine expression of a downstream protein-coding region(s), thereby providing bacteria with a mechanism to control the amounts of necessary proteins in the right locales. Here we describe a polycistronic mRNA leader that secures bacterial growth by preventing dysregulated expression of the protein-coding regions. In Salmonella, the mgtCBR mRNA encodes the virulence protein MgtC and the Mg²⁺ transporter MgtB. A mutant designed to produce leaderless mgtCBR mRNA induced MgtC and MgtB in conditions that promote mgtC transcription. The dysregulated expression of MgtC and MgtB impaired bacterial growth under all such non-host environments. While MgtC, but not MgtB, normally reduces ATP levels in a process requiring the F₁F₀ ATP synthase, dysregulated MgtC and MgtB reduced ATP levels independently of the F₁F₀ ATP synthase, which correlated with the mutant’s growth defect. The mutant showed dysregulated MgtC expression and attenuated survival inside macrophages. While MgtB normally does not affect the phenotype, MgtB impaired intramacrophage survival of the mutant in the presence of MgtC. We provide an example showing that a polycistronic mRNA leader prevents the dysregulated function of protein-coding regions to allow bacteria to proliferate across complex niches.

NMR-based metabolomics reveals the metabolite profiles of Vibrio parahaemolyticus under blood agar stimulation

Vibrio parahemolyticus is a halophilic bacterium which causes widespread seafood poisoning pathogenicity. Although the incidence of disease caused by V. parahemolyticus was stepwise increased, the pathogenic mechanism remained unclear. Herein, the difference of V. parahemolyticus's metabonomic which on blood agar and seawater beef extract peptone medium was detected via nuclear magnetic resonance and 55 metabolites were identified. Among them, 40 kinds of metabolites were upregulated in blood agar group, and 12 kinds were downregulated. Nine pathways were verified by enrichment analysis which were predicted involved in amino acids and protein synthesis, energy metabolism, DNA and RNA synthesis and DNA damage repair. We supposed that the metabolic pathway obtained from this study is related to V. parahemolyticus pathogenicity and our findings will aid in the identification of alternative targets or strategies to treat V. parahemolyticus-caused disease.

The Salmonella virulence protein MgtC promotes phosphate uptake inside macrophages

The MgtC virulence protein from the intracellular pathogen Salmonella enterica is required for its intramacrophage survival and virulence in mice and this requirement of MgtC is conserved in several intracellular pathogens including Mycobacterium tuberculosis. Despite its critical role in survival within macrophages, only a few molecular targets of the MgtC protein have been identified. Here, we report that MgtC targets PhoR histidine kinase and activates phosphate transport independently of the available phosphate concentration. A single amino acid substitution in PhoR prevents its binding to MgtC, thus abrogating MgtC-mediated phosphate transport. Surprisingly, the removal of MgtC’s effect on the ability to transport phosphate renders Salmonella hypervirulent and decreases a non-replicating population inside macrophages, indicating that MgtC-mediated phosphate transport is required for normal Salmonella pathogenesis. This provides an example of a virulence protein directly activating a pathogen’s phosphate transport inside host.

The virulence factor MgtC is essential for intracellular macrophage survival of Salmonella enterica. Here, the authors show that MgtC targets the PhoB/PhoR regulatory system leading to phosphate uptake inside macrophages and that both phoR mutation and phoB deletion renders Salmonella hypervirulent in mice.

Regulation of Bacterial Gene Expression by Transcription Attenuation

A wide variety of mechanisms that control gene expression in bacteria are based on conditional transcription termination. Generally, in these mechanisms, a transcription terminator is located between a promoter and a downstream gene(s), and the efficiency of the terminator is controlled by a regulatory effector that can be a metabolite, protein, or RNA. The most common type of regulation involving conditional termination is transcription attenuation, in which the primary regulatory target is an essential element of a single terminator. The terminator can be either intrinsic or Rho dependent, with each presenting unique regulatory targets. Transcription attenuation mechanisms can be divided into five classes based primarily on the manner in which transcription termination is rendered conditional. This review summarizes each class of control mechanisms from a historical perspective, describes important examples in a physiological context and the current state of knowledge, highlights major advances, and discusses expectations of future discoveries.

Regulatory RNAs in Virulence and Host-Microbe Interactions

Bacterial regulatory RNAs are key players in adaptation to changing environmental conditions and response to diverse cellular stresses. However, while regulatory RNAs of bacterial pathogens have been intensely studied under defined conditions in vitro, characterization of their role during the infection of eukaryotic host organisms is lagging behind. This review summarizes our current understanding of the contribution of the different classes of regulatory RNAs and RNA-binding proteins to bacterial virulence and illustrates their role in infection by reviewing the mechanisms of some prominent representatives of each class. Emerging technologies are described that bear great potential for global, unbiased studies of virulence-related RNAs in bacterial model and nonmodel pathogens in the future. The review concludes by deducing common principles of RNA-mediated gene expression control of virulence programs in different pathogens, and by defining important open questions for upcoming research in the field.

The Major RNA-Binding Protein ProQ Impacts Virulence Gene Expression in Salmonella enterica Serovar Typhimurium

FinO domain proteins such as ProQ of the model pathogen Salmonella enterica have emerged as a new class of major RNA-binding proteins in bacteria. ProQ has been shown to target hundreds of transcripts, including mRNAs from many virulence regions, but its role, if any, in bacterial pathogenesis has not been studied. Here, using a Dual RNA-seq approach to profile ProQ-dependent gene expression changes as Salmonella infects human cells, we reveal dysregulation of bacterial motility, chemotaxis, and virulence genes which is accompanied by altered MAPK (mitogen-activated protein kinase) signaling in the host. Comparison with the other major RNA chaperone in Salmonella, Hfq, reinforces the notion that these two global RNA-binding proteins work in parallel to ensure full virulence. Of newly discovered infection-associated ProQ-bound small noncoding RNAs (sRNAs), we show that the 3'UTR-derived sRNA STnc540 is capable of repressing an infection-induced magnesium transporter mRNA in a ProQ-dependent manner. Together, this comprehensive study uncovers the relevance of ProQ for Salmonella pathogenesis and highlights the importance of RNA-binding proteins in regulating bacterial virulence programs.IMPORTANCE The protein ProQ has recently been discovered as the centerpiece of a previously overlooked "third domain" of small RNA-mediated control of gene expression in bacteria. As in vitro work continues to reveal molecular mechanisms, it is also important to understand how ProQ affects the life cycle of bacterial pathogens as these pathogens infect eukaryotic cells. Here, we have determined how ProQ shapes Salmonella virulence and how the activities of this RNA-binding protein compare with those of Hfq, another central protein in RNA-based gene regulation in this and other bacteria. To this end, we apply global transcriptomics of pathogen and host cells during infection. In doing so, we reveal ProQ-dependent transcript changes in key virulence and host immune pathways. Moreover, we differentiate the roles of ProQ from those of Hfq during infection, for both coding and noncoding transcripts, and provide an important resource for those interested in ProQ-dependent small RNAs in enteric bacteria.

High-level, constitutive expression of the mgtC gene confers increased thermotolerance on Salmonella enterica serovar Typhimurium

We found that mutations that increased the transcription of the mgtCBR (Mg²⁺ transport-related) operon conferred increased thermotolerance on this organism. The 5' leader of the mgtCBR mRNA contains two short open reading frames (ORFs), mgtM and mgtP, whose translation regulates the expression of the mgtCBR operon by a mechanism that is similar to attenuation in amino acid biosynthetic operons. We obtained two types of mutations that resulted in elevated transcription of the operon: defects in the mgtM ribosome-binding site, impairing the translation of this ORF and deletions encompassing the stop codon of mgtM that extend the translation of this ORF across a downstream Rho termination site. These mgtM mutations give further insights into the mechanism of the transcriptional control of the mgtCBR operon that we discuss in this work. We show that the increased thermotolerance requires elevated expression of the mgtC gene, but functional mgtB and mgtR, which respectively encode an Mg²⁺ transporter and a regulatory protein, are dispensable for this response. MgtC has been shown to have complex functions, including a requirement for virulence, flagella-independent motility and synthesis of cellulose and we now found that it has a role in the regulation of thermotolerance.

A rule governing the FtsH-mediated proteolysis of the MgtC virulence protein from Salmonella enterica serovar Typhimurium

A tightly controlled turnover of membrane proteins is required for lipid bilayer stability, cell metabolism, and cell viability. Among the energy-dependent AAA⁺ proteases in Salmonella, FtsH is the only membrane-bound protease that contributes to the quality control of membrane proteins. FtsH preferentially degrades the C-terminus or N-terminus of misfolded, misassembled, or damaged proteins to maintain physiological functions. We found that FtsH hydrolyzes the Salmonella MgtC virulence protein when we substitute the MgtC 226^th Trp, which is well conserved in other intracellular pathogens and normally protects MgtC from the FtsH-mediated proteolysis. Here we investigate a rule determining the FtsH-mediated proteolysis of the MgtC protein at Trp226 residue. Substitution of MgtC tryptophan 226^th residue to alanine, glycine, or tyrosine leads to MgtC proteolysis in a manner dependent on the FtsH protease whereas substitution to phenylalanine, methionine, isoleucine, leucine, or valine resists MgtC degradation by FtsH. These data indicate that a large and hydrophobic side chain at 226^th residue is required for protection from the FtsH-mediated MgtC proteolysis.

Characterisation of a putative glutamate 5-kinase from Leishmania donovani

Previous metabolic studies have demonstrated that leishmania parasites are able to synthesise proline from glutamic acid and threonine from aspartic acid. The first committed step in both biosynthetic pathways involves an amino acid kinase, either a glutamate 5‐kinase (G5K; http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/7/2/11.html) or an aspartokinase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/7/2/4.html). Bioinformatic analysis of multiple leishmania genomes identifies a single amino acid‐kinase gene (LdBPK 262740.1) variously annotated as either a putative glutamate or aspartate kinase. To establish the catalytic function of this Leishmania donovani gene product, we have determined the physical and kinetic properties of the recombinant enzyme purified from Escherichia coli. The findings indicate that the enzyme is a bona fide G5K with no activity as an aspartokinase. Tetrameric G5K displays kinetic behaviour similar to its bacterial orthologues and is allosterically regulated by proline, the end product of the pathway. The structure‐activity relationships of proline analogues as inhibitors are broadly similar to the bacterial enzyme. However, unlike G5K from E. coli, leishmania G5K lacks a C‐terminal PUA (pseudouridine synthase and archaeosine transglycosylase) domain and does not undergo higher oligomerisation in the presence of proline. Gene replacement studies are suggestive, but not conclusive that G5K is essential.

Enzymes

Glutamate 5‐kinase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/7/2/11.html); aspartokinase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/7/2/4.html).

Regulating Bacterial Virulence with RNA

Noncoding RNAs (ncRNAs) regulating virulence have been identified in most pathogens. This review discusses RNA-mediated mechanisms exploited by bacterial pathogens to successfully infect and colonize their hosts. It discusses the most representative RNA-mediated regulatory mechanisms employed by two intracellular [Listeria monocytogenes and Salmonella enterica serovar Typhimurium (S. Typhimurium)] and two extracellular (Vibrio cholerae and Staphylococcus aureus) bacterial pathogens. We review the RNA-mediated regulators (e.g., thermosensors, riboswitches, cis- and trans-encoded RNAs) used for adaptation to the specific niches colonized by these bacteria (intestine, blood, or the intracellular environment, for example) in the framework of the specific pathophysiological aspects of the diseases caused by these microorganisms. A critical discussion of the newest findings in the field of bacterial ncRNAs shows how examples in model pathogens could pave the way for the discovery of new mechanisms in other medically important bacterial pathogens.

Peptide transporter YjiY influences the expression of the virulence gene mgtC to regulate biofilm formation in Salmonella

Formation of a biofilm is one of the coping strategies of Salmonella against antimicrobial environmental stresses including nutrient starvation. However, the channeling of the starvation cue towards biofilm formation is not well understood. Our study shows that a carbon starvation gene, yjiY, coding for a peptide transporter, influences the expression of a virulence-associated gene mgtC in Salmonella to regulate biofilm formation. We demonstrate here that the mutant strain ΔyjiY is unable to form a biofilm due to the increased expression of mgtC. The upregulation of mgtC in the ΔyjiY strain correlates with the downregulation of the biofilm master regulator gene, csgD, and reduced levels of ATP. Our work further indicates that a yjiY-encoded peptide transporter may regulate the expression of mgtC by transporting proline peptides.

Osmosensing by the bacterial PhoQ/PhoP two-component system

The PhoQ/PhoP two-component system plays an essential role in the response of enterobacteria to the environment of their mammalian hosts. It is known to sense several stimuli that are potentially associated with the host, including extracellular magnesium limitation, low pH, and the presence of cationic antimicrobial peptides. Here, we show that the PhoQ/PhoP two-component systems of Escherichia coli and Salmonella can also perceive an osmotic upshift, another key stimulus to which bacteria become exposed within the host. In contrast to most previously established stimuli of PhoQ, the detection of osmotic upshift does not require its periplasmic sensor domain. Instead, we show that the activity of PhoQ is affected by the length of the transmembrane (TM) helix as well as by membrane lateral pressure. We therefore propose that osmosensing relies on a conformational change within the TM domain of PhoQ induced by a perturbation in cell membrane thickness and lateral pressure under hyperosmotic conditions. Furthermore, the response mediated by the PhoQ/PhoP two-component system was found to improve bacterial growth recovery under hyperosmotic stress, partly through stabilization of the sigma factor RpoS. Our findings directly link the PhoQ/PhoP two-component system to bacterial osmosensing, suggesting that this system can mediate a concerted response to most of the established host-related cues.

First gene-ontology enrichment analysis based on bacterial coregenome variants: insights into adaptations of Salmonella serovars to mammalian- and avian-hosts

Background

Many of the bacterial genomic studies exploring evolution processes of the host adaptation focus on the accessory genome describing how the gains and losses of genes can explain the colonization of new habitats. Consequently, we developed a new approach focusing on the coregenome in order to describe the host adaptation of Salmonella serovars.

Methods

In the present work, we propose bioinformatic tools allowing (i) robust phylogenetic inference based on SNPs and recombination events, (ii) identification of fixed SNPs and InDels distinguishing homoplastic and non-homoplastic coregenome variants, and (iii) gene-ontology enrichment analyses to describe metabolic processes involved in adaptation of Salmonella enterica subsp. enterica to mammalian- (S. Dublin), multi- (S. Enteritidis), and avian- (S. Pullorum and S. Gallinarum) hosts.

Results

The ‘VARCall’ workflow produced a robust phylogenetic inference confirming that the monophyletic clade S. Dublin diverged from the polyphyletic clade S. Enteritidis which includes the divergent clades S. Pullorum and S. Gallinarum (i). The scripts ‘phyloFixedVar’ and ‘FixedVar’ detected non-synonymous and non-homoplastic fixed variants supporting the phylogenetic reconstruction (ii). The scripts ‘GetGOxML’ and ‘EveryGO’ identified representative metabolic pathways related to host adaptation using the first gene-ontology enrichment analysis based on bacterial coregenome variants (iii).

Conclusions

We propose in the present manuscript a new coregenome approach coupling identification of fixed SNPs and InDels with regards to inferred phylogenetic clades, and gene-ontology enrichment analysis in order to describe the adaptation of Salmonella serovars Dublin (i.e. mammalian-hosts), Enteritidis (i.e. multi-hosts), Pullorum (i.e. avian-hosts) and Gallinarum (i.e. avian-hosts) at the coregenome scale. All these polyvalent Bioinformatic tools can be applied on other bacterial genus without additional developments.

Electronic supplementary material

The online version of this article (10.1186/s12866-017-1132-1) contains supplementary material, which is available to authorized users.

Sequestration from Protease Adaptor Confers Differential Stability to Protease Substrate

According to the N-end rule, the N-terminal residue of a protein determines its stability. In bacteria, the adaptor ClpS mediates proteolysis by delivering substrates bearing specific N-terminal residues to the protease ClpAP. We now report that the Salmonella adaptor ClpS binds to the N terminus of the regulatory protein PhoP, resulting in PhoP degradation by ClpAP. We establish that the PhoP-activated protein MgtC protects PhoP from degradation by outcompeting ClpS for binding to PhoP. MgtC appears to act exclusively on PhoP, as it did not alter the stability of a different ClpS-dependent ClpAP substrate. Removal of five N-terminal residues rendered PhoP stability independent of both the clpS and mgtC genes. By preserving PhoP protein levels, MgtC enables normal temporal transcription of PhoP-activated genes. The identified mechanism provides a simple means to spare specific substrates from an adaptor-dependent protease.

A trans-acting leader RNA from a Salmonella virulence gene

Bacteria use flagella to move toward nutrients, find its host, or retract from toxic substances. Because bacterial flagellum is one of the ligands that activate the host innate immune system, its synthesis should be tightly regulated during host infection, which is largely unknown. Here, we report that a bacterial leader mRNA from the mgtCBR virulence operon in the intracellular pathogen Salmonella enterica serovar Typhimurium binds to the fljB coding region of mRNAs in the fljBA operon encoding the FljB phase 2 flagellin, a main component of bacterial flagella and the FljA repressor for the FliC phase 1 flagellin, and degrades fljBA mRNAs in an RNase E-dependent fashion during infection. A nucleotide substitution of the fljB flagellin gene that prevents the mgtC leader RNA-mediated down-regulation increases the fljB-encoded flagellin synthesis, leading to a hypermotile phenotype inside macrophages. Moreover, the fljB nucleotide substitution renders Salmonella hypervirulent, indicating that FljB-based motility must be compromised in the phagosomal compartment where Salmonella resides. This suggests that this pathogen promotes pathogenicity by producing a virulence protein and limits locomotion by a trans-acting leader RNA from the same virulence gene during infection.

Intracellular Salmonella metabolism

Growth of Salmonella inside infected host cells is a key aspect of their ability to cause local enteritis or systemic disease. This growth depends on exploitation of host nutrients through a large Salmonella metabolism network with hundreds of metabolites and enzymes. Studies in cell culture infection models are unravelling more and more of the underlying molecular and cellular mechanisms but also show striking Salmonella metabolic plasticity depending on host cell line and experimental conditions. In vivo studies have revealed a qualitatively diverse, but quantitatively poor, host-Salmonella nutritional interface, which on one side makes Salmonella fitness largely resilient against metabolic perturbations, but on the other side severely limits Salmonella biomass generation and growth rates. This review discusses goals and techniques for studying Salmonella intracellular metabolism, summarises main results and implications, and proposes key issues that could be addressed in future studies.

TrmD: A Methyl Transferase for tRNA Methylation With m1G37

TrmD is an S-adenosyl methionine (AdoMet)-dependent methyl transferase that synthesizes the methylated m¹G37 in tRNA. TrmD is specific to and essential for bacterial growth, and it is fundamentally distinct from its eukaryotic and archaeal counterpart Trm5. TrmD is unusual by using a topological protein knot to bind AdoMet. Despite its restricted mobility, the TrmD knot has complex dynamics necessary to transmit the signal of AdoMet binding to promote tRNA binding and methyl transfer. Mutations in the TrmD knot block this intramolecular signaling and decrease the synthesis of m¹G37-tRNA, prompting ribosomes to +1-frameshifts and premature termination of protein synthesis. TrmD is unique among AdoMet-dependent methyl transferases in that it requires Mg²⁺ in the catalytic mechanism. This Mg²⁺ dependence is important for regulating Mg²⁺ transport to Salmonella for survival of the pathogen in the host cell. The strict conservation of TrmD among bacterial species suggests that a better characterization of its enzymology and biology will have a broad impact on our understanding of bacterial pathogenesis.

Elongation factor P restricts Salmonella's growth by controlling translation of a Mg2+ transporter gene during infection

When a ribosome translates mRNA sequences, the ribosome often stalls at certain codons because it is hard to translate. Consecutive proline codons are such examples that induce ribosome stalling and elongation factor P (EF-P) is required for the stalled ribosome to continue translation at those consecutive proline codons. We found that EF-P is required for translation of the mgtB gene encoding a Mg²⁺ transporter in the mgtCBR virulence operon from the intracellular pathogen Salmonella enterica serovar Typhimurium. Salmonella lacking EF-P decreases MgtB protein levels in a manner dependent on consecutive proline codons located in the mgtB coding region despite increasing transcription of the mgtCBR operon via the mgtP open reading frame in the leader RNA, resulting in an altered ratio between MgtC and MgtB proteins within the operon. Substitution of the consecutive proline codons to alanine codons eliminates EF-P-mediated control of the mgtB gene during infection and thus contributes to Salmonella's survival inside macrophages where Salmonella experiences low levels of EF-P. This suggests that this pathogen utilizes a strategy to coordinate expression of virulence genes by an evolutionarily conserved translation factor.

Bacterial peptide transporters: Messengers of nutrition to virulence

Bacteria possess numerous peptide transporters for importing peptides as nutrients. However, these peptide transporters are now consistently reported to play a role in the virulence of various bacterial pathogens. Their ability to transport peptides has implications in antibacterial therapy as well. Therefore, it would be instrumental to have complete knowledge about the role of peptide transporters in mediating this cross connection between metabolism and pathogenesis. Studies on various peptide transporters in bacterial pathogens have improved our understanding of this field. In this review, we have given an overview of the functioning of bacterial peptide transporters and their contribution in virulence of major bacterial pathogens.

tRNAPro -mediated downregulation of elongation factor P is required for mgtCBR expression during Salmonella infection

Bacterial ribosome requires elongation factor P to translate fragments harbouring consecutive proline codons. Given the abundance of ORFs with potential EF-P regulated sites, EF-P was assumed to be constitutively expressed. Here, we report that the intracellular pathogen Salmonella enterica serovar Typhimurium decreases efp mRNA levels during course of infection. We determined that the decrease in efp mRNA is triggered by low levels of charged tRNA^Pro , a condition that Salmonella experiences when inside a macrophage phagosome. Surprisingly, downregulation of EF-P selectively promotes expression of the virulence mgtC gene and contributes to Salmonella's ability to survive inside macrophages. The decrease in EF-P levels induces ribosome stalling at the consecutive proline codons of the mgtP open reading frame in the mgtCBR leader RNA, and thus allows formation of a stem-loop structure promoting transcription of the mgtC gene. The substitution of proline codons in the mgtP gene eliminates EF-P-mediated mgtC expression and thus Salmonella's survival inside macrophages. Our findings indicate that Salmonella benefits virulence genes by decreasing EF-P levels and inducing the stringent response inside host.

Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use

Genetic decoding is not ‘frozen’ as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational ‘correction’ of problem or ‘savior’ indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5′ or 3′ of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3′ from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression.

An RNA motif advances transcription by preventing Rho-dependent termination

The transcription termination factor Rho associates with most nascent bacterial RNAs as they emerge from RNA polymerase. However, pharmacological inhibition of Rho derepresses only a small fraction of these transcripts. What, then, determines the specificity of Rho-dependent transcription termination? We now report the identification of a Rho-antagonizing RNA element (RARE) that hinders Rho-dependent transcription termination. We establish that RARE traps Rho in an inactive complex but does not prevent Rho binding to its recruitment sites. Although translating ribosomes normally block Rho access to an mRNA, inefficient translation of an open reading frame in the leader region of the Salmonella mgtCBR operon actually enables transcription of its associated coding region by favoring an RNA conformation that sequesters RARE. The discovery of an RNA element that inactivates Rho signifies that the specificity of nucleic-acid binding proteins is defined not only by the sequences that recruit these proteins but also by sequences that antagonize their activity.

Analysis of Salmonella PhoP/PhoQ regulation by dimethyl-SRM-based quantitative proteomics

SRM (selected reaction monitoring), a tandem mass spectrometry-based method characterized by high repeatability and accuracy, is an effective tool for the quantification of predetermined proteins. In this study, we built a time-scheduled dimethyl-SRM method that can provide the precise relative quantification of 92 proteins in one run. By applying this method to the Salmonella PhoP/PhoQ two-component system, we found that the expression of selected PhoP/PhoQ-activated proteins in response to Mg(2+) concentrations could be divided into two distinct patterns. For the time-course SRM experiment, we found that the dynamics of the selected PhoP/PhoQ-activated proteins could be divided into three distinct patterns, providing a new clue regarding PhoP/PhoQ activation and regulation. Moreover, the results for iron homeostasis proteins in response to Mg(2+) concentrations revealed that the PhoP/PhoQ two-component system may serve as a repressor for iron uptake proteins. And ribosomal protein levels clearly showed a response to different Mg(2+) concentrations and to time.

Role of host cell-derived amino acids in nutrition of intracellular Salmonella enterica

The facultative intracellular pathogen Salmonella enterica resides in a specific membrane-bound compartment termed the Salmonella-containing vacuole (SCV). Despite being segregated from access to metabolites in the host cell cytosol, Salmonella is able to efficiently proliferate within the SCV. We set out to unravel the nutritional supply of Salmonella in the SCV with focus on amino acids. We studied the availability of amino acids by the generation of auxotrophic strains for alanine, asparagine, aspartate, glutamine, and proline in a macrophage cell line (RAW264.7) and an epithelial cell line (HeLa) and examined access to extracellular nutrients for nutrition. Auxotrophies for alanine, asparagine, or proline attenuated intracellular replication in HeLa cells, while aspartate, asparagine, or proline auxotrophies attenuated intracellular replication in RAW264.7 macrophages. The different patterns of intracellular attenuation of alanine- or aspartate-auxotrophic strains support distinct nutritional conditions in HeLa cells and RAW264.7 macrophages. Supplementation of medium with individual amino acids restored the intracellular replication of mutant strains auxotrophic for asparagine, proline, or glutamine. Similarly, a mutant strain deficient in succinate dehydrogenase was complemented by the extracellular addition of succinate. Complementation of the intracellular replication of auxotrophic Salmonella by external amino acids was possible if bacteria were proficient in the induction of Salmonella-induced filaments (SIFs) but failed in a SIF-deficient background. We propose that the ability of intracellular Salmonella to redirect host cell vesicular transport provides access of amino acids to auxotrophic strains and, more generally, is essential to continuously supply bacteria within the SCV with nutrients.

When Too Much ATP Is Bad for Protein Synthesis

Adenosine triphosphate (ATP) is the energy currency of living cells. Even though ATP powers virtually all energy-dependent activities, most cellular ATP is utilized in protein synthesis via tRNA aminoacylation and guanosine triphosphate regeneration. Magnesium (Mg(2+)), the most common divalent cation in living cells, plays crucial roles in protein synthesis by maintaining the structure of ribosomes, participating in the biochemistry of translation initiation and functioning as a counterion for ATP. A non-physiological increase in ATP levels hinders growth in cells experiencing Mg(2+) limitation because ATP is the most abundant nucleotide triphosphate in the cell, and Mg(2+) is also required for the stabilization of the cytoplasmic membrane and as a cofactor for essential enzymes. We propose that organisms cope with Mg(2+) limitation by decreasing ATP levels and ribosome production, thereby reallocating Mg(2+) to indispensable cellular processes.

Salmonella promotes virulence by repressing cellulose production

Cellulose is the most abundant organic polymer on Earth. In bacteria, cellulose confers protection against environmental insults and is a constituent of biofilms typically formed on abiotic surfaces. We report that, surprisingly, Salmonella enterica serovar Typhimurium makes cellulose when inside macrophages. We determine that preventing cellulose synthesis increases virulence, whereas stimulation of cellulose synthesis inside macrophages decreases virulence. An attenuated mutant lacking the mgtC gene exhibited increased cellulose levels due to increased expression of the cellulose synthase gene bcsA and of cyclic diguanylate, the allosteric activator of the BcsA protein. Inactivation of bcsA restored wild-type virulence to the Salmonella mgtC mutant, but not to other attenuated mutants displaying a wild-type phenotype regarding cellulose. Our findings indicate that a virulence determinant can promote pathogenicity by repressing a pathogen's antivirulence trait. Moreover, they suggest that controlling antivirulence traits increases long-term pathogen fitness by mediating a trade-off between acute virulence and transmission.