Bacterial Cyclopropane Fatty Acid Synthase mRNA Is Targeted by Activating and Repressing Small RNAs

Defining the Functional Properties of Cyclopropane Fatty Acid Synthase from Pseudomonas aeruginosa PAO1

Cyclopropane fatty acid synthases (CFAS) catalyze the conversion of unsaturated fatty acids to cyclopropane fatty acids (CFAs) within bacterial membranes. This modification alters the biophysical properties of membranes and has been correlated with virulence in several human pathogens. Despite the central role played by CFAS enzymes in regulating bacterial stress responses, the mechanistic properties of the CFAS enzyme family and the consequences of CFA biosynthesis remain largely uncharacterized in most bacteria. We report the first characterization of the CFAS enzyme from Pseudomonas aeruginosa (PA) - an opportunistic human pathogen with complex membrane biology that is frequently associated with antimicrobial resistance and high tolerance to various external stressors. We demonstrate that CFAs are produced by a single enzyme in PA and that cfas gene expression is upregulated during the transition to stationary phase and in response to oxidative stress. Analysis of PA lipid extracts reveal a massive increase in CFA production as PA cells enter stationary phase and help define the optimal membrane composition for in vitro assays. The purified PA-CFAS enzyme forms a stable homodimer and preferentially modifies phosphatidylglycerol lipid substrates and membranes with a higher content of unsaturated acyl chains. Bioinformatic analysis across bacterial phyla shows highly divergent amino acid sequences within the lipid binding domain of CFAS enzymes, perhaps suggesting distinct membrane binding properties among different orthologues. This work lays an important foundation for further characterization of CFAS in Pseudomonas aeruginosa and for examining the functional differences between CFAS enzymes from different bacteria.

Transcriptional and post-transcriptional mechanisms modulate cyclopropane fatty acid synthase through small RNAs in Escherichia coli

The small RNA (sRNA) RydC strongly activates cfa, which encodes the cyclopropane fatty acid synthase. Previous work demonstrated that RydC activation of cfa increases the conversion of unsaturated fatty acids to cyclopropanated fatty acids in membrane lipids and changes the biophysical properties of membranes, making cells more resistant to acid stress. The regulators that control RydC synthesis had not previously been identified. In this study, we identify a GntR-family transcription factor, YieP, that represses rydC transcription. YieP positively autoregulates its own transcription and indirectly regulates cfa through RydC. We further identify additional sRNA regulatory inputs that contribute to the control of RydC and cfa. The translation of yieP is repressed by the Fnr-dependent sRNA, FnrS, making FnrS an indirect activator of rydC and cfa. Conversely, RydC activity on cfa is antagonized by the OmpR-dependent sRNA OmrB. Altogether, this work illuminates a complex regulatory network involving transcriptional and post-transcriptional inputs that link the control of membrane biophysical properties to multiple environmental signals.

IMPORTANCE

Bacteria experience many environmental stresses that challenge their membrane integrity. To withstand these challenges, bacteria sense what stress is occurring and mount a response that protects membranes. Previous work documented the important roles of small RNA (sRNA) regulators in membrane stress responses. One sRNA, RydC, helps cells cope with membrane-disrupting stresses by promoting changes in the types of lipids incorporated into membranes. In this study, we identified a regulator, YieP, that controls when RydC is produced and additional sRNA regulators that modulate YieP levels and RydC activity. These findings illuminate a complex regulatory network that helps bacteria sense and respond to membrane stress.

Multitier regulation of the E. coli extreme acid stress response by CsrA

CsrA is an RNA-binding protein that regulates processes critical for growth and survival, including central carbon metabolism, motility, biofilm formation, stress responses, and expression of virulence factors in pathogens. Transcriptomics studies in Escherichia coli suggested that CsrA repressed genes involved in surviving extremely acidic conditions. Here, we examine the effects of disrupting CsrA-dependent regulation on the expression of genes and circuitry for acid stress survival and demonstrate CsrA-mediated repression at multiple levels. We show that this repression is critical for managing the trade-off between growth and survival; overexpression of acid stress genes caused by csrA disruption enhances survival under extreme acidity but is detrimental for growth under mildly acidic conditions. In vitro studies confirmed that CsrA binds specifically to mRNAs of structural and regulatory genes for acid stress survival, causing translational repression. We also found that translation of the top-tier acid stress regulator, evgA, is coupled to that of a small leader peptide, evgL, which is repressed by CsrA. Unlike dedicated acid stress response genes, csrA and its sRNA antagonists, csrB and csrC, did not exhibit a substantial response to acid shock. Furthermore, disruption of CsrA regulation of acid stress genes impacted host-microbe interactions in Caenorhabditis elegans, alleviating GABA deficiencies. This study expands the known regulon of CsrA to genes of the extreme acid stress response of E. coli and highlights a new facet of the global role played by CsrA in balancing the opposing physiological demands of stress resistance with the capacity for growth and modulating host interactions.IMPORTANCETo colonize/infect the mammalian intestinal tract, bacteria must survive exposure to the extreme acidity of the stomach. E. coli does this by expressing proteins that neutralize cytoplasmic acidity and cope with molecular damage caused by low pH. Because of the metabolic cost of these processes, genes for surviving acid stress are tightly regulated. Here, we show that CsrA negatively regulates the cascade of expression responsible for the acid stress response. Increased expression of acid response genes due to csrA disruption improved survival at extremely low pH but inhibited growth under mildly acidic conditions. Our findings define a new layer of regulation in the acid stress response of E. coli and a novel physiological function for CsrA.

RpoS and the bacterial general stress response

SUMMARYThe general stress response (GSR) is a widespread strategy developed by bacteria to adapt and respond to their changing environments. The GSR is induced by one or multiple simultaneous stresses, as well as during entry into stationary phase and leads to a global response that protects cells against multiple stresses. The alternative sigma factor RpoS is the central GSR regulator in E. coli and conserved in most γ-proteobacteria. In E. coli, RpoS is induced under conditions of nutrient deprivation and other stresses, primarily via the activation of RpoS translation and inhibition of RpoS proteolysis. This review includes recent advances in our understanding of how stresses lead to RpoS induction and a summary of the recent studies attempting to define RpoS-dependent genes and pathways.

TrhA, a bacterial progestin and adiponectin receptor homolog, couples membrane energetics homeostasis and unsaturated fatty acid metabolism

Members of the widely conserved progestin and adipoQ receptor (PAQR) family function to maintain membrane homeostasis: membrane fluidity and fatty acid composition in eukaryotes and membrane energetics and fatty acid composition in bacteria. All PAQRs consist of a core seven transmembrane domain structure and five conserved amino acids (three histidines, one serine, and one aspartic acid) predicted to form a hydrolase-like catalytic site. PAQR homologs in Bacteria (called TrhA, for transmembrane homeostasis protein A) maintain homeostasis of membrane charge gradients, like the membrane potential and proton gradient that comprise the proton motive force, but their molecular mechanisms are not yet understood. Here, we show that TrhA in Escherichia coli has a periplasmic C-terminus, which places the five conserved residues shared by all PAQRs at the cytoplasmic interface of the membrane. Here, we characterize several conserved residues predicted to form an active site by site-directed mutagenesis. We also identify a specific role for TrhA in modulating unsaturated fatty acid biosynthesis with conserved residues required to either promote or reduce the abundance of unsaturated fatty acids. We also identify distinct roles for the conserved residues in supporting TrhA's role in maintaining membrane energetics homeostasis that suggest that both functions are intertwined and probably partly dependent on one another. An analysis of domain architecture of TrhA-like domains in Bacteria further supports a function of TrhA linking membrane energetics homeostasis with biosynthesis of unsaturated fatty acid in the membrane. IMPORTANCE Progestin and adipoQ receptor (PAQR) family proteins are evolutionary conserved regulators of membrane homeostasis and have been best characterized in eukaryotes. Bacterial PAQR homologs, named TrhA (transmembrane homeostasis protein A), regulate membrane energetics homeostasis through an unknown mechanism. Here, we present evidence linking TrhA to both membrane energetics homeostasis and unsaturated fatty acid biosynthesis. Analysis of domain architecture together with experimental evidence suggests a model where TrhA activity on unsaturated fatty acid biosynthesis is regulated by changes in membrane energetics to dynamically adjust membrane homeostasis.

Small RNAs, Large Networks: Posttranscriptional Regulons in Gram-Negative Bacteria

Small regulatory RNA (sRNAs) are key mediators of posttranscriptional gene control in bacteria. Assisted by RNA-binding proteins, a single sRNA often modulates the expression of dozens of genes, and thus sRNAs frequently adopt central roles in regulatory networks. Posttranscriptional regulation by sRNAs comes with several unique features that cannot be achieved by transcriptional regulators. However, for optimal network performance, transcriptional and posttranscriptional control mechanisms typically go hand-in-hand. This view is reflected by the ever-growing class of mixed network motifs involving sRNAs and transcription factors, which are ubiquitous in biology and whose regulatory properties we are beginning to understand. In addition, sRNA activity can be antagonized by base-pairing with sponge RNAs, adding yet another layer of complexity to these networks. In this article, we summarize the regulatory concepts underlying sRNA-mediated gene control in bacteria and discuss how sRNAs shape the output of a network, focusing on several key examples.

Coping with stress: How bacteria fine-tune protein synthesis and protein transport

Maintaining a functional proteome under different environmental conditions is challenging for every organism, in particular for unicellular organisms, such as bacteria. In order to cope with changing environments and stress conditions, bacteria depend on strictly coordinated proteostasis networks that control protein production, folding, trafficking, and degradation. Regulation of ribosome biogenesis and protein synthesis are cornerstones of this cellular adaptation in all domains of life, which is rationalized by the high energy demand of both processes and the increased resistance of translationally silent cells against internal or external poisons. Reduced protein synthesis ultimately also reduces the substrate load for protein transport systems, which are required for maintaining the periplasmic, inner, and outer membrane subproteomes. Consequences of impaired protein transport have been analyzed in several studies and generally induce a multifaceted response that includes the upregulation of chaperones and proteases and the simultaneous downregulation of protein synthesis. In contrast, generally less is known on how bacteria adjust the protein targeting and transport machineries to reduced protein synthesis, e.g., when cells encounter stress conditions or face nutrient deprivation. In the current review, which is mainly focused on studies using Escherichia coli as a model organism, we summarize basic concepts on how ribosome biogenesis and activity are regulated under stress conditions. In addition, we highlight some recent developments on how stress conditions directly impair protein targeting to the bacterial membrane. Finally, we describe mechanisms that allow bacteria to maintain the transport of stress-responsive proteins under conditions when the canonical protein targeting pathways are impaired.

Role of the 5' end phosphorylation state for small RNA stability and target RNA regulation in bacteria

In enteric bacteria, several small RNAs (sRNAs) including MicC employ endoribonuclease RNase E to stimulate target RNA decay. A current model proposes that interaction of the sRNA 5' monophosphate (5'P) with the N-terminal sensing pocket of RNase E allosterically activates cleavage of the base-paired target in the active site. In vivo evidence supporting this model is lacking. Here, we engineered a genetic tool allowing us to generate 5' monophosphorylated sRNAs of choice in a controllable manner in the cell. Four sRNAs were tested and none performed better in target destabilization when 5' monophosphorylated. MicC retains full activity even when RNase E is defective in 5'P sensing, whereas regulation is lost upon removal of its scaffolding domain. Interestingly, sRNAs MicC and RyhB that originate with a 5' triphosphate group are dramatically destabilized when 5' monophosphorylated, but stable when in 5' triphosphorylated form. In contrast, the processing-derived sRNAs CpxQ and SroC, which carry 5'P groups naturally, are highly stable. Thus, the 5' phosphorylation state determines stability of naturally triphosphorylated sRNAs, but plays no major role for target RNA destabilization in vivo. In contrast, the RNase E C-terminal half is crucial for MicC-mediated ompD decay, suggesting that interaction with Hfq is mandatory.

Identification and functional analysis of non-coding regulatory small RNA FenSr3 in Bacillus amyloliquefaciens LPB-18

Bacillus amyloliquefaciens is an interesting microbe in the food processing and manufacturing industries. Non-coding small RNAs (sRNAs) have been shown to play a crucial role in the physiology and metabolism of bacteria by post-transcriptionally regulating gene expression. This study investigated the function of novel sRNA FenSr3 by constructing fenSr3 deficient strain and complementary strains in B. amyloliquefaciens LPB-18 , which were named LPN-18N and LPB-18P, respectively. The result showed significant differences in fengycin yield between strain LPB -18N and LPB-18P. The production of fengycin was significantly enhanced in B. amyloliquefaciens LPB-18N, compared with that of the strain LPB-18 from 190.908 mg/L to 327.598 mg/L. Moreover, the production of fengycin decreased from 190.464 mg/L to 38.6 mg/L in B . amyloliquefaciens LPB-18P. A comparative transcriptome sequencing was carried out to better understand the complex regulatory mechanism. Transcription analysis revealed that 1037 genes were differentially expressed between B. amyloliquefaciens LPB-18 and B. amyloliquefaciens LPB-18N, including the key regulatory genes in fatty acid, amino acid biosynthesis, and central carbon metabolism, which could provide sufficient quantities of building precursors for fengycin biosynthesis. The biofilm formation and sporulation was also enhanced in the strain LPB-18N, which indicates that FenSr3 could play a vital role in stress resistance and promotes survival in B. amyloliquefaciens. Some sRNAs involved in stress response have been identified in the literature, but their regulatory roles in fengycin production remain unclear. The study will contribute a novel perspective to the regulation mechanism of biosynthesis and the optimization of key metabolites of B. amyloliquefaciens.

Small RNAs Activate Salmonella Pathogenicity Island 1 by Modulating mRNA Stability through the hilD mRNA 3' Untranslated Region

Salmonella enterica serovar Typhimurium is an enteric pathogen associated with foodborne disease. Salmonella invades the intestinal epithelium using a type three secretion system encoded on Salmonella pathogenicity island 1 (SPI-1). SPI-1 genes are tightly regulated by a complex feed-forward loop to ensure proper spatial and temporal expression. Most regulatory input is integrated at HilD, through control of hilD mRNA translation or HilD protein activity. The hilD mRNA possesses a 310-nucleotide 3' untranslated region (UTR) that influences HilD and SPI-1 expression, and this regulation is dependent on Hfq and RNase E, cofactors known to mediate small RNA (sRNA) activities. Thus, we hypothesized that the hilD mRNA 3' UTR is a target for sRNAs. Here, we show that two sRNAs, SdsR and Spot 42, regulate SPI-1 by targeting different regions of the hilD mRNA 3' UTR. Regulatory activities of these sRNAs depended on Hfq and RNase E, in agreement with previous roles found for both at the hilD 3' UTR. Salmonella mutants lacking SdsR and Spot 42 had decreased virulence in a mouse model of infection. Collectively, this work suggests that these sRNAs targeting the hilD mRNA 3' UTR increase hilD mRNA levels by interfering with RNase E-dependent mRNA degradation and that this regulatory effect is required for Salmonella invasiveness. Our work provides novel insights into mechanisms of sRNA regulation at bacterial mRNA 3' UTRs and adds to our knowledge of post-transcriptional regulation of the SPI-1 complex feed-forward loop. IMPORTANCE Salmonella enterica serovar Typhimurium is a prominent foodborne pathogen, infecting millions of people a year. To express virulence genes at the correct time and place in the host, Salmonella uses a complex regulatory network that senses environmental conditions. Known for their role in allowing quick responses to stress and virulence conditions, we investigated the role of small RNAs in facilitating precise expression of virulence genes. We found that the 3' untranslated region of the hilD mRNA, encoding a key virulence regulator, is a target for small RNAs and RNase E. The small RNAs stabilize hilD mRNA to allow proper expression of Salmonella virulence genes in the host.

Improving acid resistance of Escherichia coli base on the CfaS-mediated membrane engineering strategy derived from extreme acidophile

Industrial microorganisms used for the production of organic acids often face challenges such as inhibited cell growth and reduced production efficiency due to the accumulation of acidic metabolites. One promising way for improving the acid resistance of microbial cells is to reconstruct their membranes. Herein, the overexpression of cfa2 from extreme acidophile endowed E. coli with high-performance on resistance to the acid stress. The engineered strain M1-93-Accfa2, constructed by CRISPR/Cas9-mediated chromosome integration, also exhibited a significantly higher resistance to severe acid stress. The analysis of fatty acid profiles indicated that the proportion of Cy-19:0 in the cell membrane of M1-93-Accfa2 increased by 5.26 times compared with the control, while the proportion of C18:1w9c decreased by 5.81 times. Correspondingly, the permeability and fluidity of the membrane decreased significantly. HPLC analysis demonstrated that the contents of intracellular glutamic acid, arginine, methionine and aspartic acid of M1-93-Accfa2 were 2.59, 2.04, 22.07 and 2.65 times that of the control after environmental acidification, respectively. Meanwhile, transmission electron microscopy observation indicated that M1-93-Accfa2 could maintain a plumper cell morphology after acid stimulation. M1-93-Accfa2 also exhibited higher-performance on the resistance to organic acids, especially succinic acid stress. These results together demonstrated the great potential of M1-93-Accfa2 constructed here in the production of organic acids.

Microbial detoxification of lignocellulosic biomass hydrolysates: Biochemical and molecular aspects, challenges, exploits and future perspectives

Valorization of lignocellulosic biomass (LB) has the potential to secure sustainable energy production without impacting food insecurity, whist relieving over reliance on finite fossil fuels. Agro-derived lignocellulosic residues such as wheat straw, switchgrass, rice bran, and miscanthus have gained relevance as feedstocks for the production of biofuels and chemicals. However, the microorganisms employed in fermentative conversion of carbohydrates to fuels and chemicals are unable to efficiently utilize the sugars derived from LB due to co-production of lignocellulose-derived microbial inhibitory compounds (LDMICs) during LB pretreatment. LDMICs impact microbial growth by inhibition of specific enzymes, cause DNA and cell membrane damage, and elicit cellular redox imbalance. Over the past decade, success has been achieved with the removal of LDMICs prior to fermentation. However, LDMICs removal by chemical processes is often accompanied by sugar losses, which negatively impacts the overall production cost. Hence, in situ removal of LDMICs by fermentative organisms during the fermentation process has garnered considerable attention as the "go-to" approach for economical LDMICs detoxification and bio-chemicals production. In situ removal of LDMICs has been pursued by either engineering more robust biocatalysts or isolating novel microbial strains with the inherent capacity to mineralize or detoxify LDMICs to less toxic compounds. While some success has been made along this line, efficient detoxification and robust production of target bio-chemicals in lignocellulosic hydrolysates (LHs) under largely anaerobic fermentative conditions remains a lingering challenge. Consequently, LB remains an underutilized substrate for bio-chemicals production. In this review, the impact of microbial LH detoxification on overall target molecule production is discussed. Further, the biochemical pathways and mechanisms employed for in situ microbial detoxification of furanic LDMICs [e.g., furfural and 5-hydroxymethylfurfural (HMF)] and phenolic LDMICs (e.g., syringaldehyde, p-coumaric acid, 4-hydroxybenzaldehyde, vanillin, and ferulic acid) are discussed. More importantly, metabolic engineering strategies for the development of LDMIC-tolerant and bio-chemicals overproducing strains and processes are highlighted.

Unraveling Membrane Perturbations Caused by the Bacterial Riboregulator Hfq

Hfq is a pleiotropic regulator that mediates several aspects of bacterial RNA metabolism. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, usually via its interaction with small regulatory RNAs. Previously, we showed that the Hfq C-terminal region forms an amyloid-like structure and that these fibrils interact with membranes. The immediate consequence of this interaction is a disruption of the membrane, but the effect on Hfq structure was unknown. To investigate details of the mechanism of interaction, the present work uses different in vitro biophysical approaches. We show that the Hfq C-terminal region influences membrane integrity and, conversely, that the membrane specifically affects the amyloid assembly. The reported effect of this bacterial master regulator on membrane integrity is discussed in light of the possible consequence on small regulatory RNA-based regulation.

Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria

Chronic and recurrent bacterial infections are frequently associated with the formation of biofilms on biotic or abiotic materials that are composed of mono- or multi-species cultures of bacteria/fungi embedded in an extracellular matrix produced by the microorganisms. Biofilm formation is, among others, regulated by quorum sensing (QS) which is an interbacterial communication system usually composed of two-component systems (TCSs) of secreted autoinducer compounds that activate signal transduction pathways through interaction with their respective receptors. Embedded in the biofilms, the bacteria are protected from environmental stress stimuli, and they often show reduced responses to antibiotics, making it difficult to eradicate the bacterial infection. Besides reduced penetration of antibiotics through the intricate structure of the biofilms, the sessile biofilm-embedded bacteria show reduced metabolic activity making them intrinsically less sensitive to antibiotics. Moreover, they frequently express elevated levels of efflux pumps that extrude antibiotics, thereby reducing their intracellular levels. Some efflux pumps are involved in the secretion of QS compounds and biofilm-related materials, besides being important for removing toxic substances from the bacteria. Some efflux pump inhibitors (EPIs) have been shown to both prevent biofilm formation and sensitize the bacteria to antibiotics, suggesting a relationship between these processes. Additionally, QS inhibitors or quenchers may affect antibiotic susceptibility. Thus, targeting elements that regulate QS and biofilm formation might be a promising approach to combat antibiotic-resistant biofilm-related bacterial infections.

Advances in the Structural Biology, Mechanism, and Physiology of Cyclopropane Fatty Acid Modifications of Bacterial Membranes

Cyclopropane fatty acid (CFA) synthase catalyzes a remarkable reaction. The cis double bonds of unsaturated fatty acyl chains of phospholipid bilayers are converted to cyclopropane rings by transfer of a methylene moiety from S-adenosyl-L-methionine (SAM).

An overview of gene regulation in bacteria by small RNAs derived from mRNA 3' ends

Over the past two decades, small noncoding RNAs (sRNAs) that regulate mRNAs by short base pairing have gone from a curiosity to a major class of post-transcriptional regulators in bacteria. They are integral to many stress responses and regulatory circuits, affecting almost all aspects of bacterial life. Following pioneering sRNA searches in the early 2000s, the field quickly focused on conserved sRNA genes in the intergenic regions of bacterial chromosomes. Yet, it soon emerged that there might be another rich source of bacterial sRNAs—processed 3′ end fragments of mRNAs. Several such 3′ end-derived sRNAs have now been characterized, often revealing unexpected, conserved functions in diverse cellular processes. Here, we review our current knowledge of these 3′ end-derived sRNAs—their biogenesis through ribonucleases, their molecular mechanisms, their interactions with RNA-binding proteins such as Hfq or ProQ and their functional scope, which ranges from acting as specialized regulators of single metabolic genes to constituting entire noncoding arms in global stress responses. Recent global RNA interactome studies suggest that the importance of functional 3′ end-derived sRNAs has been vastly underestimated and that this type of cross-regulation between genes at the mRNA level is more pervasive in bacteria than currently appreciated.

Multiple in vivo roles for the C-terminal domain of the RNA chaperone Hfq

Hfq, a bacterial RNA chaperone, stabilizes small regulatory RNAs (sRNAs) and facilitates sRNA base-pairing with target mRNAs. Hfq has a conserved N-terminal domain and a poorly conserved disordered C-terminal domain (CTD). In a transcriptome-wide examination of the effects of a chromosomal CTD deletion (Hfq1-65), the Escherichia coli mutant was most defective for the accumulation of sRNAs that bind the proximal and distal faces of Hfq (Class II sRNAs), but other sRNAs also were affected. There were only modest effects on the levels of mRNAs, suggesting little disruption of sRNA-dependent regulation. However, cells expressing Hfq lacking the CTD in combination with a weak distal face mutation were defective for the function of the Class II sRNA ChiX and repression of mutS, both dependent upon distal face RNA binding. Loss of the region between amino acids 66-72 was critical for this defect. The CTD region beyond amino acid 72 was not necessary for distal face-dependent regulation, but was needed for functions associated with the Hfq rim, seen most clearly in combination with a rim mutant. Our results suggest that the C-terminus collaborates in various ways with different binding faces of Hfq, leading to distinct outcomes for individual sRNAs.

Mining RNA-seq data reveals the massive regulon of GcvB small RNA and its physiological significance in maintaining amino acid homeostasis in Escherichia coli

Bacterial small RNAs regulate the expression of multiple genes through imperfect base-pairing with target mRNAs mediated by RNA chaperone proteins such as Hfq. GcvB is the master sRNA regulator of amino acid metabolism and transport in a wide range of Gram-negative bacteria. Recently, independent RNA-seq approaches identified a plethora of transcripts interacting with GcvB in Escherichia coli. In this study, the compilation of RIL-seq, CLASH, and MAPS data sets allowed us to identify GcvB targets with high accuracy. We validated 21 new GcvB targets repressed at the posttranscriptional level, raising the number of direct targets to >50 genes in E. coli. Among its multiple seed sequences, GcvB utilizes either R1 or R3 to regulate most of these targets. Furthermore, we demonstrated that both R1 and R3 seed sequences are required to fully repress the expression of gdhA, cstA, and sucC genes. In contrast, the ilvLXGMEDA polycistronic mRNA is targeted by GcvB through at least four individual binding sites in the mRNA. Finally, we revealed that GcvB is involved in the susceptibility of peptidase-deficient E. coli strain (Δpeps) to Ala-Gln dipeptide by regulating both Dpp dipeptide importer and YdeE dipeptide exporter via R1 and R3 seed sequences, respectively.

Efflux Impacts Intracellular Accumulation Only in Actively Growing Bacterial Cells

For antibiotics with intracellular targets, effective treatment of bacterial infections requires the drug to accumulate to a high concentration inside cells. Bacteria produce a complex cell envelope and possess drug export efflux pumps to limit drug accumulation inside cells. Decreasing cell envelope permeability and increasing efflux pump activity can reduce intracellular accumulation of antibiotics and are commonly seen in antibiotic-resistant strains. Here, we show that the balance between influx and efflux differs depending on bacterial growth phase in Gram-negative bacteria. Accumulation of the fluorescent compound ethidium bromide (EtBr) was measured in Salmonella enterica serovar Typhimurium SL1344 (wild type) and efflux deficient (ΔacrB) strains during growth. In SL1344, EtBr accumulation remained low, regardless of growth phase, and did not correlate with acrAB transcription. EtBr accumulation in the ΔacrB strains was high in exponential phase but dropped sharply later in growth, with no significant difference from that in SL1344 in stationary phase. Low EtBr accumulation in stationary phase was not due to the upregulation of other efflux pumps but instead was due to decreased permeability of the envelope in stationary phase. Transcriptome sequencing (RNA-seq) identified changes in expression of several pathways that remodel the envelope in stationary phase, leading to lower permeability.

Subzero, saline incubations of Colwellia psychrerythraea reveal strategies and biomarkers for sustained life in extreme icy environments

Colwellia psychrerythraea is a marine psychrophilic bacterium known for its remarkable ability to maintain activity during long-term exposure to extreme subzero temperatures and correspondingly high salinities in sea ice. These microorganisms must have adaptations to both high salinity and low temperature to survive, be metabolically active, or grow in the ice. Here, we report on an experimental design that allowed us to monitor culturability, cell abundance, activity and proteomic signatures of C. psychrerythraea strain 34H (Cp34H) in subzero brines and supercooled sea water through long-term incubations under eight conditions with varying subzero temperatures, salinities and nutrient additions. Shotgun proteomics found novel metabolic strategies used to maintain culturability in response to each independent experimental variable, particularly in pathways regulating carbon, nitrogen and fatty acid metabolism. Statistical analysis of abundances of proteins uniquely identified in isolated conditions provide metabolism-specific protein biosignatures indicative of growth or survival in either increased salinity, decreased temperature, or nutrient limitation. Additionally, to aid in the search for extant life on other icy worlds, analysis of detected short peptides in -10°C incubations after 4 months identified over 500 potential biosignatures that could indicate the presence of terrestrial-like cold-active or halophilic metabolisms on other icy worlds.

A Novel sRNA in Shigella flexneri That Regulates Tolerance and Virulence Under Hyperosmotic Pressure

Regulation of the environmental stress response and virulence of Shigella flexneri may involve multiple signaling pathways; however, these mechanisms are not well-defined. In bacteria, small regulatory RNAs (sRNAs) regulate bacterial growth, metabolism, virulence, and environmental stress response. Therefore, identifying novel functional sRNAs in S. flexneri could help elucidate pathogenic adaptations to host micro-environmental stresses and associated virulence. The aim of this study was to confirm the presence of an sRNA, Ssr54, in S. flexneri and to determine its functions and possible mechanism of action. Ssr54 was found to regulate tolerance and virulence under hyperosmotic pressure. Its expression was verified by qRT-PCR and Northern blotting, and its genomic position was confirmed by 5'-rapid amplification of cDNA ends. Ssr54 expression was significantly decreased (~ 80%) under hyperosmotic conditions (680 mM NaCl), and the survival rate of the Ssr54 deletion strain increased by 20% under these conditions. This suggested that Ssr54 has been selected to promote host survival under hyperosmotic conditions. Additionally, virulence assessment, including guinea pig Sereny test and competitive invasion assays in mouse lungs, revealed that Ssr54 deletion significantly decreased S. flexneri virulence. Two-dimensional gel analyses suggest that Ssr54 may modulate the expression of tolC, ompA, and treF genes, which may affect the virulence and survival of S. flexneri under osmotic pressures. Furthermore, treF expression has been shown to improve the survival of S. flexneri under osmotic pressures. These results suggest that Ssr54 has a broad range of action in S. flexneri response to hyperosmotic environmental stresses and in controlling its virulence to adapt to environmental stresses encountered during host infection.

Regulation outside the box: New mechanisms for small RNAs

Regulation at the post‐transcriptional level is an important mode of gene expression control in bacteria. Small RNA regulators (sRNAs) that act via intramolecular base‐pairing with target mRNAs are key players in this process and most often sequester the target's ribosome binding site (RBS) to down‐regulate translation initiation. Over the past few years, several exceptions from this mechanism have been reported, revealing that sRNAs are able to influence translation initiation from a distance. In this issue of Molecular Microbiology, Azam and Vanderpool show that repression of the manY mRNA by the sRNA SgrS relies on an unconventional mechanism involving a translational enhancer element and ribosomal protein S1. Binding of S1 to an AU‐rich sequence within the 5ʹ untranslated region of the manY transcript promotes translation of the mRNA, and base‐pairing of SgrS to the same site can interfere with this process. Therefore, instead of blocking translation initiation by occluding the manY RBS, SgrS reduces ManY synthesis by inhibiting S1‐dependent translation activation. These findings increase the base‐pairing window for sRNA‐mediated gene expression control in bacteria and highlight the role of ribosomal protein S1 for translation initiation.

Small RNAs as Fundamental Players in the Transference of Information During Bacterial Infectious Diseases

Communication shapes life on Earth. Transference of information has played a paramount role on the evolution of all living or extinct organisms since the appearance of life. Success or failure in this process will determine the prevalence or disappearance of a certain set of genes, the basis of Darwinian paradigm. Among different molecules used for transmission or reception of information, RNA plays a key role. For instance, the early precursors of life were information molecules based in primitive RNA forms. A growing field of research has focused on the contribution of small non-coding RNA forms due to its role on infectious diseases. These are short RNA species that carry out regulatory tasks in cis or trans. Small RNAs have shown their relevance in fine tuning the expression and activity of important regulators of essential genes for bacteria. Regulation of targets occurs through a plethora of mechanisms, including mRNA stabilization/destabilization, driving target mRNAs to degradation, or direct binding to regulatory proteins. Different studies have been conducted during the interplay of pathogenic bacteria with several hosts, including humans, animals, or plants. The sRNAs help the invader to quickly adapt to the change in environmental conditions when it enters in the host, or passes to a free state. The adaptation is achieved by direct targeting of the pathogen genes, or subversion of the host immune system. Pathogens trigger also an immune response in the host, which has been shown as well to be regulated by a wide range of sRNAs. This review focuses on the most recent host-pathogen interaction studies during bacterial infectious diseases, providing the perspective of the pathogen.

Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation

By shaping gene expression profiles, small RNAs (sRNAs) enable bacteria to efficiently adapt to changes in their environment. To better understand how Escherichia coli acclimatizes to nutrient availability, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) to uncover Hfq-associated RNA-RNA interactions at specific growth stages. We demonstrate that Hfq CLASH robustly captures bona fide RNA-RNA interactions. We identified hundreds of novel sRNA base-pairing interactions, including many sRNA-sRNA interactions and involving 3’UTR-derived sRNAs. We rediscovered known and identified novel sRNA seed sequences. The sRNA-mRNA interactions identified by CLASH have strong base-pairing potential and are highly enriched for complementary sequence motifs, even those supported by only a few reads. Yet, steady state levels of most mRNA targets were not significantly affected upon over-expression of the sRNA regulator. Our results reinforce the idea that the reproducibility of the interaction, not base-pairing potential, is a stronger predictor for a regulatory outcome.