On the facultative requirement of the bacterial RNA chaperone, Hfq

Non-coding RNA and its potential role in Mycobacterium tuberculosis pathogenesis

It is estimated that one third of the human population is infected with Mycobacterium tuberculosis. Efforts to understand the molecular basis of its gene regulation have been focused on identification of protein encoding genes and regulons implicated in pathogenesis. Recently, a number of studies have described the identification of several non-coding RNAs that are likely to contribute significantly to the regulatory networks responsible for adaptation and virulence in M. tuberculosis. We have reviewed emerging information on the presence and abundance of different types of non-coding RNA in M. tuberculosis and consider their potential contribution to the adaptive responses that underlie disease pathogenesis.

Current knowledge on regulatory RNAs and their machineries in Staphylococcus aureus

Staphylococcus aureus is one of the major human pathogens, which causes numerous community-associated and hospital-acquired infections. The regulation of the expression of numerous virulence factors is coordinated by complex interplays between two component systems, transcriptional regulatory proteins, and regulatory RNAs. Recent studies have identified numerous novel RNAs comprising cis-acting regulatory RNAs, antisense RNAs, small non coding RNAs and small mRNAs encoding peptides. We present here several examples of RNAs regulating S. aureus pathogenicity and describe various aspects of antisense regulation.

Global discovery of small RNAs in Yersinia pseudotuberculosis identifies Yersinia-specific small, noncoding RNAs required for virulence

A major class of bacterial small, noncoding RNAs (sRNAs) acts by base-pairing with mRNAs to alter the translation from and/or stability of the transcript. Our laboratory has shown that Hfq, the chaperone that mediates the interaction of many sRNAs with their targets, is required for the virulence of the enteropathogen Yersinia pseudotuberculosis. This finding suggests that sRNAs play a critical role in the regulation of virulence in this pathogen, but these sRNAs are not known. Using a deep sequencing approach, we identified the global set of sRNAs expressed in vitro by Y. pseudotuberculosis. Sequencing of RNA libraries from bacteria grown at 26 °C and 37 °C resulted in the identification of 150 unannotated sRNAs. The majority of these sRNAs are Yersinia specific, without orthologs in either Escherichia coli or Salmonella typhimurium. Six sRNAs are Y. pseudotuberculosis specific and are absent from the genome of the closely related species Yersinia pestis. We found that the expression of many sRNAs conserved between Y. pseudotuberculosis and Y. pestis differs in both timing and dependence on Hfq, suggesting evolutionary changes in posttranscriptional regulation between these species. Deletion of multiple sRNAs in Y. pseudotuberculosis leads to attenuation of the pathogen in a mouse model of yersiniosis, as does the inactivation in Y. pestis of a conserved, Yersinia-specific sRNA in a mouse model of pneumonic plague. Finally, we determined the regulon controlled by one of these sRNAs, revealing potential virulence determinants in Y. pseudotuberculosis that are regulated in a posttranscriptional manner.

Small Regulatory RNA and Legionella pneumophila

Legionella pneumophila is a gram-negative bacterial species that is ubiquitous in almost any aqueous environment. It is the agent of Legionnaires’ disease, an acute and often under-reported form of pneumonia. In mammals, L. pneumophila replicates inside macrophages within a modified vacuole. Many protein regulators have been identified that control virulence-related properties, including RpoS, LetA/LetS, and PmrA/PmrB. In the past few years, the importance of regulation of virulence factors by small regulatory RNA (sRNAs) has been increasingly appreciated. This is also the case in L. pneumophila where three sRNAs (RsmY, RsmZ, and 6S RNA) were recently shown to be important determinants of virulence regulation and 79 actively transcribed sRNAs were identified. In this review we describe current knowledge about sRNAs and their regulatory properties and how this relates to the known regulatory systems of L. pneumophila. We also provide a model for sRNA-mediated control of gene expression that serves as a framework for understanding the regulation of virulence-related properties of L. pneumophila.

Microbial linguistics: perspectives and applications of microbial cell-to-cell communication

Inter-cellular communication via diffusible small molecules is a defining character not only of multicellular forms of life but also of single-celled organisms. A large number of bacterial genes are regulated by the change of chemical milieu mediated by the local population density of its own species or others. The cell density-dependent "autoinducer" molecules regulate the expression of those genes involved in genetic competence, biofilm formation and persistence, virulence, sporulation, bioluminescence, antibiotic production, and many others. Recent innovations in recombinant DNA technology and micro-/nano-fluidics systems render the genetic circuitry responsible for cell-to-cell communication feasible to and malleable via synthetic biological approaches. Here we review the current understanding of the molecular biology of bacterial intercellular communication and the novel experimental protocols and platforms used to investigate this phenomenon. A particular emphasis is given to the genetic regulatory circuits that provide the standard building blocks which constitute the syntax of the biochemical communication network. Thus, this review gives focus to the engineering principles necessary for rewiring bacterial chemo-communication for various applications, ranging from population-level gene expression control to the study of host-pathogen interactions.

Small RNA biology is systems biology

During the last decade small regulatory RNA (srRNA) emerged as central players in the regulation of gene expression in all kingdoms of life. Multiple pathways for srRNA biogenesis and diverse mechanisms of gene regulation may indicate that srRNA regulation evolved independently multiple times. However, small RNA pathways share numerous properties, including the ability of a single srRNA to regulate multiple targets. Some of the mechanisms of gene regulation by srRNAs have significant effect on the abundance of free srRNAs that are ready to interact with new targets. This results in indirect interactions among seemingly unrelated genes, as well as in a crosstalk between different srRNA pathways. Here we briefly review and compare the major srRNA pathways, and argue that the impact of srRNA is always at the system level. We demonstrate how a simple mathematical model can ease the discussion of governing principles. To demonstrate these points we review a few examples from bacteria and animals.

The Vibrio cholerae quorum sensing response is mediated by Hfq-dependent sRNA/mRNA base pairing interactions

Vibrio cholerae quorum sensing controls expression of four redundant sRNAs, Qrr1-4. The Qrr sRNAs are predicted to alter the translation of several mRNAs, including, hapR, which encodes a transcription factor that controls genes for virulence factors, biofilm formation, protease production and DNA uptake. Each Qrr contains a 21 nucleotide region absolutely conserved among pathogenic Vibrios, and predicted to base pair with mRNA targets, like hapR, aided by the RNA chaperone Hfq. This molecular mechanism was not experimentally tested previously, and we provide here both in vivo and in vitro evidence to validate this model. In Escherichia coli, Qrr expression repressed a HapR-GFP translational fusion, and a specific nucleotide substitution in the 21 nucleotide region eliminated HapR control, while a compensatory mutation in hapR restored it. In V. cholerae, the identical mutations also deregulated HapR-dependent gene expression and corresponding QS phenotypes by altering HapR protein levels. We calculated in vitro binding affinities of a Qrr/hapR complex and show that Hfq stabilizes complex formation. Finally, the Qrr mutation with in vivo defects also prevented Qrr/hapR binding, while the compensatory hapR mutation restored binding. These results demonstrate that the V. cholerae QS response is mediated by base pairing interactions between Qrr sRNAs and hapR mRNA.

Evidences of autoregulation of hfq expression in Sinorhizobium meliloti strain 2011

Riboregulation comprises gene expression regulatory mechanisms that rely upon the activity of small non-coding RNAs (sRNAs) and in most cases RNA binding proteins. In γ-proteobacteria, the Sm-like protein Hfq is a key player in riboregulatory processes, because it promotes sRNA-mRNA interactions and influences mRNA polyadenylation or translation. In the α-proteobacterium Sinorhizobium meliloti, the large number of detected small RNA transcripts and the pleiotropic effects of hfq mutations lead to the hypothesis that riboregulatory mechanisms are important in this soil microorganism to adjust gene expression both in free-living conditions and as a nitrogen-fixing endosymbiont within legume root nodules. In this study, homology modeling of S. meliloti Hfq protein and cross-complementation experiments of S. meliloti and Escherichia coli mutants indicates that hfq ( Sm ) encodes an RNA chaperone that can be functionally exchanged by its homolog from E. coli. A transcriptional and translational analysis of S. meliloti hfq expression by means of lacZ reporter fusions strongly suggests that the S. meliloti Hfq protein autocontrols its expression at the translational level, a phenomenon that was evident in the natural host S. meliloti as well as in the heterologous host E. coli.

The Staphylococcus aureus RNome and its commitment to virulence

Staphylococcus aureus is a major human pathogen causing a wide spectrum of nosocomial and community-associated infections with high morbidity and mortality. S. aureus generates a large number of virulence factors whose timing and expression levels are precisely tuned by regulatory proteins and RNAs. The aptitude of bacteria to use RNAs to rapidly modify gene expression, including virulence factors in response to stress or environmental changes, and to survive in a host is an evolving concept. Here, we focus on the recently inventoried S. aureus regulatory RNAs, with emphasis on those with identified functions, two of which are directly involved in pathogenicity.

The roles of pathogen small RNAs

Regulatory small RNAs (sRNAs), also known as non-coding RNA, are not translated into proteins and widespread in prokaryotes and eukaryotes. sRNAs involve in multiple fundamental cellular events. They are emerging regulatory elements that are gaining momentum. Knowledge of sRNA largely originates from eukaryotes. Prokaryotic sRNAs, particularly those of pathogen are only recently explored. The main types, function, and methodology to predict pathogen sRNAs are summarized in this review. Special focus is sRNAs regulating pathogen gene expression, particularly that of Mycobacterium tuberculosis, which is hitherto the most successful pathogen afflicting mankind.

Honing the message: post-transcriptional and post-translational control in attaching and effacing pathogens

Bacteria evolve their capacity to cause disease by acquiring virulence genes that are usually clustered in discrete genetic modules termed pathogenicity islands (PAI). Stable integration of PAIs into pre-existing transcriptional networks coordinates expression from PAIs with ancestral genes in response to diverse environmental cues. Such transcriptional controls are evident in the regulation of the locus of enterocyte effacement (LEE), a PAI of enteropathogenic and enterohemorrhagic Escherichia coli. However, recent reports indicate that global post-transcriptional and post-translational regulators, including CsrA, Hfq and ClpXP, fine-tune the transcriptional output from the LEE. In this opinion article, we highlight recent advances in the understanding of post-transcriptional and post-translational regulation in attaching and effacing pathogens.

Structural insights into the dynamics and function of the C-terminus of the E. coli RNA chaperone Hfq

The hexameric Escherichia coli RNA chaperone Hfq (Hfq(Ec)) is involved in riboregulation of target mRNAs by small trans-encoded RNAs. Hfq proteins of different bacteria comprise an evolutionarily conserved core, whereas the C-terminus is variable in length. Although the structure of the conserved core has been elucidated for several Hfq proteins, no structural information has yet been obtained for the C-terminus. Using bioinformatics, nuclear magnetic resonance spectroscopy, synchrotron radiation circular dichroism (SRCD) spectroscopy and small angle X-ray scattering we provide for the first time insights into the conformation and dynamic properties of the C-terminal extension of Hfq(Ec). These studies indicate that the C-termini are flexible and extend laterally away from the hexameric core, displaying in this way features typical of intrinsically disordered proteins that facilitate intermolecular interactions. We identified a minimal, intrinsically disordered region of the C-terminus supporting the interactions with longer RNA fragments. This minimal region together with rest of the C-terminal extension provides a flexible moiety capable of tethering long and structurally diverse RNA molecules. Furthermore, SRCD spectroscopy supported the hypothesis that RNA fragments exceeding a certain length interact with the C-termini of Hfq(Ec).

Artificial trans-encoded small non-coding RNAs specifically silence the selected gene expression in bacteria

Recently, many small non-coding RNAs (sRNAs) with important regulatory roles have been identified in bacteria. As their eukaryotic counterparts, a major class of bacterial trans-encoded sRNAs acts by basepairing with target mRNAs, resulting in changes in translation and stability of the mRNA. RNA interference (RNAi) has become a powerful gene silencing tool in eukaryotes. However, such an effective RNA silencing tool remains to be developed for prokaryotes. In this study, we described first the use of artificial trans-encoded sRNAs (atsRNAs) for specific gene silencing in bacteria. Based on the common structural characteristics of natural sRNAs in Gram-negative bacteria, we developed the designing principle of atsRNA. Most of the atsRNAs effectively suppressed the expression of exogenous EGFP gene and endogenous uidA gene in Escherichia coli. Further studies demonstrated that the mRNA base pairing region and AU rich Hfq binding site were crucial for the activity of atsRNA. The atsRNA-mediated gene silencing was Hfq dependent. The atsRNAs led to gene silencing and RNase E dependent degradation of target mRNA. We also designed a series of atsRNAs which targeted the toxic genes in Staphyloccocus aureus, but found no significant interfering effect. We established an effective method for specific gene silencing in Gram-negative bacteria.

Accessibility and evolutionary conservation mark bacterial small-rna target-binding regions

Bacterial small noncoding RNAs have attracted much interest in recent years as posttranscriptional regulators of genes involved in diverse pathways. Small RNAs (sRNAs) are 50 to 400 nucleotides long and exert their regulatory function by directly base pairing with mRNA targets to alter their stability and/or affect their translation. This base pairing is achieved through a region of about 10 to 25 nucleotides, which may be located at various positions along different sRNAs. By compiling a data set of experimentally determined target-binding regions of sRNAs and systematically analyzing their properties, we reveal that they are both more evolutionarily conserved and more accessible than random regions. We demonstrate the use of these properties for computational identification of sRNA target-binding regions with high specificity and sensitivity. Our results show that these predicted regions are likely to base pair with known targets of an sRNA, suggesting that pointing out these regions in a specific sRNA can help in searching for its targets.

Unique Evolution of Symbiobacterium thermophilum Suggested from Gene Content and Orthologous Protein Sequence Comparisons

Comparisons of gene content and orthologous protein sequence constitute a major strategy in whole-genome comparison studies. It is expected that horizontal gene transfer between phylogenetically distant organisms and lineage-specific gene loss have greater influence on gene content-based phylogenetic analysis than orthologous protein sequence-based phylogenetic analysis. To determine the evolution of the syntrophic bacterium Symbiobacterium thermophilum, we analyzed phylogenetic relationships among Clostridia on the basis of gene content and orthologous protein sequence comparisons. These comparisons revealed that these 2 phylogenetic relationships are topologically different. Our results suggest that each Clostridia has a species-specific gene content because frequent genetic exchanges or gene losses have occurred during evolution. Specifically, the phylogenetic positions of syntrophic Clostridia were different between these 2 phylogenetic analyses, suggesting that large diversity in the living environments may cause the observed species-specific gene content. S. thermophilum occupied the most distant position from the other syntrophic Clostridia in the gene content-based phylogenetic tree. We identified 32 genes (14 under relaxed selection and 18 under functional constraint) evolving under Symbiobacterium-specific selection on the basis of synonymous-to-nonsynonymous substitution ratios. Five of the 14 genes under relaxed selection are related to transcription. In contrast, none of the 18 genes under functional constraint is related to transcription.

Identification of genes for small non-coding RNAs that belong to the regulon of the two-component regulatory system CiaRH in Streptococcus

BACKGROUND

Post-transcriptional regulation by small RNAs (sRNAs) in bacteria is now recognized as a wide-spread regulatory mechanism modulating a variety of physiological responses including virulence. In Streptococcus pneumoniae, an important human pathogen, the first sRNAs to be described were found in the regulon of the CiaRH two-component regulatory system. Five of these sRNAs were detected and designated csRNAs for cia-dependent small RNAs. CiaRH pleiotropically affects β-lactam resistance, autolysis, virulence, and competence development by yet to be defined molecular mechanisms. Since CiaRH is highly conserved among streptococci, it is of interest to determine if csRNAs are also included in the CiaRH regulon in this group of organisms consisting of commensal as well as pathogenic species. Knowledge on the participation of csRNAs in CiaRH-dependent regulatory events will be the key to define the physiological role of this important control system.

RESULTS

Genes for csRNAs were predicted in streptococcal genomes and data base entries other than S. pneumoniae by searching for CiaR-activated promoters located in intergenic regions that are followed by a transcriptional terminator. 61 different candidate genes were obtained specifying csRNAs ranging in size from 51 to 202 nt. Comparing these genes among each other revealed 40 different csRNA types. All streptococcal genomes harbored csRNA genes, their numbers varying between two and six. To validate these predictions, S. mitis, S. oralis, and S. sanguinis were subjected to csRNA-specific northern blot analysis. In addition, a csRNA gene from S. thermophilus plasmid pST0 introduced into S. pneumoniae was also tested. Each of the csRNAs was detected on these blots and showed the anticipated sizes. Thus, the method applied here is able to predict csRNAs with high precision.

CONCLUSIONS

The results of this study strongly suggest that genes for small non-coding RNAs, csRNAs, are part of the regulon of the two-component regulatory system CiaRH in all streptococci.

Identification of regulatory RNAs in Bacillus subtilis

Post-transcriptional regulatory mechanisms are widespread in bacteria. Interestingly, current published data hint that some of these mechanisms may be non-random with respect to their phylogenetic distribution. Although small, trans-acting regulatory RNAs commonly occur in bacterial genomes, they have been better characterized in Gram-negative bacteria, leaving the impression that they may be less important for Firmicutes. It has been presumed that Gram-positive bacteria, in particular the Firmicutes, are likely to utilize cis-acting regulatory RNAs located within the 5' mRNA leader region more often than trans-acting regulatory RNAs. In this analysis we catalog, by a deep sequencing-based approach, both classes of regulatory RNA candidates for Bacillus subtilis, the model microorganism for Firmicutes. We successfully recover most of the known small RNA regulators while also identifying a greater number of new candidate RNAs. We anticipate these data to be a broadly useful resource for analysis of post-transcriptional regulatory strategies in B. subtilis and other Firmicutes.

Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA

The alternative sigma factor RpoS responds to multiple stresses and activates a large number of genes that allow bacteria to adapt to changing environments. The accumulation of RpoS is regulated at multiple levels, including the regulation of its translation by small regulatory RNAs (sRNAs). A library of plasmids expressing each of 26 Escherichia coli sRNAs that bind Hfq was created to globally and rapidly analyse regulation of an rpoS-lacZ translational fusion. The approach can be easily applied to any gene of interest. When overexpressed, four sRNAs, including OxyS, previously shown to repress rpoS, were observed to repress the expression of the rpoS-lacZ fusion. Along with DsrA and RprA, two previously defined activators of rpoS translation, a third new sRNA activator, ArcZ, was identified. The expression of arcZ is repressed by the aerobic/anaerobic-sensing ArcA-ArcB two-component system under anaerobic conditions and adds translational regulation to the ArcA-ArcB regulon. ArcZ directly represses, and is repressed by, arcB transcription, providing a negative feedback loop that may affect functioning of the ArcA-ArcB regulon.

E. coli DNA associated with isolated Hfq interacts with Hfq's distal surface and C-terminal domain

The RNA-binding protein Hfq has been studied extensively for its function as a modulator of gene expression at the post-transcriptional level. While most Hfq studies have focused on the protein's interaction with sRNAs and mRNAs, Hfq binding to DNA has been observed but is less explored. During the isolation of Hfq from Escherichiacoli, we found genomic DNA fragments associated with the protein after multiple steps of purification. Sequences of 41 amplified segments from the DNA fragments associated with Hfq were determined. A large fraction of the DNA segments were predicted to have significant helical axis curvature and were from genes associated with membrane proteins, characteristics unexpected for non-specific binding. Analysis by analytical ultracentrifugation indicated that rA(18) binding to Hfq disrupts Hfq-DNA interactions. The latter observation suggests Hfq binding to DNA involves its distal surface. This was supported by a gel mobility shift assay that showed single amino acid mutations on the distal surface of Hfq inhibited Hfq binding to duplex DNA, while six of seven mutations on the proximal surface and outer circumference of the hexamer did not prevent Hfq binding. Two mutated Hfq which have portions of their C-terminal domain removed also failed to bind to DNA. The apparent K(d) for binding wild type Hfq to several duplex DNA was estimated from a gel mobility shift assay to be ~400nM.

A Staphylococcus aureus small RNA is required for bacterial virulence and regulates the expression of an immune-evasion molecule

Staphylococcus aureus, a pathogen responsible for hospital and community-acquired infections, expresses many virulence factors under the control of numerous regulatory systems. Here we show that one of the small pathogenicity island RNAs, named SprD, contributes significantly to causing disease in an animal model of infection. We have identified one of the targets of SprD and our in vivo data demonstrate that SprD negatively regulates the expression of the Sbi immune-evasion molecule, impairing both the adaptive and innate host immune responses. SprD interacts with the 5′ part of the sbi mRNA and structural mapping of SprD, its mRNA target, and the ‘SprD-mRNA’ duplex, in combination with mutational analysis, reveals the molecular details of the regulation. It demonstrates that the accessible SprD central region interacts with the sbi mRNA translational start site. We show by toeprint experiments that SprD prevents translation initiation of sbi mRNA by an antisense mechanism. SprD is a small regulatory RNA required for S. aureus pathogenicity with an identified function, although the mechanism of virulence control by the RNA is yet to be elucidated.

Bacteria possess numerous and diverse means of gene regulation using RNA molecules, including small RNAs (sRNAs). Here we show that one sRNA is essential for a major human bacterial pathogen, Staphylococcus aureus, to cause a disease in an animal model of infection. Our study provides evidence that this RNA regulates the expression of an immune evasion molecule secreted by the bacterium to impair the host immune responses, and we have solved the mechanism of the RNA-based regulation at molecular level. So far, the mechanism of bacterial virulence controlled by SprD is unrevealed, but that small RNA has a huge impact in the course of a bacterial infection. It implies possible new strategies in fighting against that major human and animal bacterial pathogen in preventing the expression of this regulatory RNA.

RNA-mediated regulation in bacteria: from natural to artificial systems

Bacteria use various means of RNA-mediated gene regulation. Regulatory RNAs include mRNA leaders that affect expression in cis or in trans, non-coding RNAs that trap regulatory proteins or interact with one or multiple target mRNAs, and RNAs that protect the bacteria against foreign and invasive DNA. The aim of this review is to outline the basic principles of bacterial RNA-mediated regulation, with a special focus on both cis-acting regulatory regions of mRNAs and antisense RNAs (asRNAs), and to give a brief overview of selected examples of RNA-based technology that have paved the way for biotechnological applications.

Defining a role for Hfq in Gram-positive bacteria: evidence for Hfq-dependent antisense regulation in Listeria monocytogenes

Small trans-encoded RNAs (sRNAs) modulate the translation and decay of mRNAs in bacteria. In Gram-negative species, antisense regulation by trans-encoded sRNAs relies on the Sm-like protein Hfq. In contrast to this, Hfq is dispensable for sRNA-mediated riboregulation in the Gram-positive species studied thus far. Here, we provide evidence for Hfq-dependent translational repression in the Gram-positive human pathogen Listeria monocytogenes, which is known to encode at least 50 sRNAs. We show that the Hfq-binding sRNA LhrA controls the translation and degradation of its target mRNA by an antisense mechanism, and that Hfq facilitates the binding of LhrA to its target. The work presented here provides the first experimental evidence for Hfq-dependent riboregulation in a Gram-positive bacterium. Our findings indicate that modulation of translation by trans-encoded sRNAs may occur by both Hfq-dependent and -independent mechanisms, thus adding another layer of complexity to sRNA-mediated riboregulation in Gram-positive species.