Dynamics of Salmonella small RNA expression in non-growing bacteria located inside eukaryotic cells

Small non-coding regulatory RNAs (sRNAs) have been studied in many bacterial pathogens during infection. However, few studies have focused on how intracellular pathogens modulate sRNA expression inside eukaryotic cells. Here, we monitored expression of all known sRNAs of Salmonella enterica serovar Typhimurium (S. Typhimurium) in bacteria located inside fibroblasts, a host cell type in which this pathogen restrains growth. sRNA sequences known in S. Typhimurium and Escherichia coli were searched in the genome of S. Typhimurium virulent strain SL1344, the subject of this study. Expression of 84 distinct sRNAs was compared in extra- and intracellular bacteria. Non-proliferating intracellular bacteria upregulated six sRNAs, including IsrA, IsrG, IstR-2, RyhB-1, RyhB-2 and RseX while repressed the expression of the sRNAs DsrA, GlmZ, IsrH-1, IsrI, SraL, SroC, SsrS(6S) and RydC. Interestingly, IsrH-1 was previously reported as an sRNA induced by S. Typhimurium inside macrophages. Kinetic analyses unraveled changing expression patterns for some sRNAs along the infection. InvR and T44 expression dropped after an initial induction phase while IstR-2 was induced exclusively at late infection times (> 6 h). Studies focused on the Salmonella-specific sRNA RyhB-2 revealed that intracellular bacteria use this sRNA to regulate negatively YeaQ, a cis-encoded protein of unknown function. RyhB-2, together with RyhB-1, contributes to attenuate intracellular bacterial growth. To our knowledge, these data represent the first comprehensive study of S. Typhimurium sRNA expression in intracellular bacteria and provide the first insights into sRNAs that may direct pathogen adaptation to a non-proliferative state inside the host cell.     

Translational control and target recognition by Escherichia coli small RNAs in vivo

Small non-coding RNAs (sRNAs) are an emerging class of regulators of bacterial gene expression. Most of the regulatory Escherichia coli sRNAs known to date modulate translation of trans-encoded target mRNAs. We studied the specificity of sRNA target interactions using gene fusions to green fluorescent protein (GFP) as a novel reporter of translational control by bacterial sRNAs in vivo. Target sequences were selected from both monocistronic and polycistronic mRNAs. Upon expression of the cognate sRNA (DsrA, GcvB, MicA, MicC, MicF, RprA, RyhB, SgrS and Spot42), we observed highly specific translation repression/activation of target fusions under various growth conditions. Target regulation was also tested in mutants that lacked Hfq or RNase III, or which expressed a truncated RNase E (rne701). We found that translational regulation by these sRNAs was largely independent of full-length RNase E, e.g. despite the fact that ompA fusion mRNA decay could no longer be promoted by MicA. This is the first study in which multiple well-defined E.coli sRNA target pairs have been studied in a uniform manner in vivo. We expect our GFP fusion approach to be applicable to sRNA targets of other bacteria, and also demonstrate that Vibrio RyhB sRNA represses a Vibrio sodB fusion when co-expressed in E.coli.     

链球菌非编码小RNA研究进展

非编码小RNA(Small non-coding RNA,sRNA)是一种存在于原核和真核生物中的新型调控RNA,长度约为40～500个核苷酸。作为一类关键的调控因子,sRNA通过与靶mRNA或蛋白质结合来调控细胞内的基因表达。大部分细菌sRNA在大肠杆菌等革兰氏阴性菌中被发现并研究,但近十年来越来越多的sRNA在革兰氏阳性菌中被逐步发现。作为一类革兰氏阳性菌,链球菌属中sRNA目前研究主要集中在毒力调节,鲜有其他调控的报道。本文总结了链球菌中sRNA的最新进展,并介绍其主要功能和机理,以期为细菌sRNA研究提供借鉴。     

A Salmonella small non-coding RNA facilitates bacterial invasion and intracellular replication by modulating the expression of virulence factors

Small non-coding RNAs (sRNAs) that act as regulators of gene expression have been identified in all kingdoms of life, including microRNA (miRNA) and small interfering RNA (siRNA) in eukaryotic cells. Numerous sRNAs identified in Salmonella are encoded by genes located at Salmonella pathogenicity islands (SPIs) that are commonly found in pathogenic strains. Whether these sRNAs are important for Salmonella pathogenesis and virulence in animals has not been reported. In this study, we provide the first direct evidence that a pathogenicity island-encoded sRNA, IsrM, is important for Salmonella invasion of epithelial cells, intracellular replication inside macrophages, and virulence and colonization in mice. IsrM RNA is expressed in vitro under conditions resembling those during infection in the gastrointestinal tract. Furthermore, IsrM is found to be differentially expressed in vivo, with higher expression in the ileum than in the spleen. IsrM targets the mRNAs coding for SopA, a SPI-1 effector, and HilE, a global regulator of the expression of SPI-1 proteins, which are major virulence factors essential for bacterial invasion. Mutations in IsrM result in disregulation of expression of HilE and SopA, as well as other SPI-1 genes whose expression is regulated by HilE. Salmonella with deletion of isrM is defective in bacteria invasion of epithelial cells and intracellular replication/survival in macrophages. Moreover, Salmonella with mutations in isrM is attenuated in killing animals and defective in growth in the ileum and spleen in mice. Our study has shown that IsrM sRNA functions as a pathogenicity island-encoded sRNA directly involved in Salmonella pathogenesis in animals. Our results also suggest that sRNAs may represent a distinct class of virulence factors that are important for bacterial infection in vivo.     

A Peroxide-Responding sRNA Evolved from a Peroxidase mRNA

Small RNAs (sRNAs) are important gene regulators in bacteria, but it is unclear how new sRNAs originate and become part of regulatory networks that coordinate bacterial response to environmental stimuli. Using a covariance modeling-based approach, we analyzed the presence of hundreds of sRNAs in more than a thousand genomes across Enterobacterales, a bacterial order with a confluence of factors that allows robust genome-scale sRNA analyses: several well-studied organisms with fairly conserved genome structures, an established phylogeny, and substantial nucleotide diversity within a narrow evolutionary space. We discovered that a majority of sRNAs arose recently, and uncovered protein-coding genes as a potential source from which new sRNAs arise. A detailed investigation of the emergence of OxyS, a peroxide-responding sRNA, revealed that it evolved from a fragment of a peroxidase messenger RNA. Importantly, although it replaced the ancestral peroxidase, OxyS continues to be part of the ancestral peroxide-response regulon, indicating that an sRNA that arises from a protein-coding gene would inherently be part of the parental protein’s regulatory network. This new insight provides a fresh framework for understanding sRNA origin and regulatory integration in bacteria.     

革兰氏阳性菌非编码小RNA的研究进展

sRNA（非编码小RNA）通过碱基配对的方式与靶mRNA结合,抑制或激活转录过程、调节蛋白质的表达,以核酸的形式发挥其生物学功能。随着RNA深度测序（RNAseq）技术、生物信息学预测以及实验分析手段的日渐发展和完善,数以百计的sRNA被发现并得到验证。作为转录后调控因子,sRNA因在诸多生理过程中起到了关键的调节作用而得到了广泛的关注。以革兰氏阳性菌为切入点,总结了近年来sRNA的筛选、鉴定和功能研究等方面取得的进展,梳理分析了sRNA调控与毒力因子、群体感应、铁代谢和双组分系统等之间的内在联系,并展望了sRNA未来的研究方向。     

A survey of sRNA families in α-proteobacteria

We have performed a computational comparative analysis of six small non-coding RNA (sRNA) families in α-proteobacteria. Members of these families were first identified in the intergenic regions of the nitrogen-fixing endosymbiont S. meliloti by a combined bioinformatics screen followed by experimental verification. Consensus secondary structures inferred from covariance models for each sRNA family evidenced in some cases conserved motifs putatively relevant to the function of trans-encoded base-pairing sRNAs i.e., Hfq-binding signatures and exposed anti Shine-Dalgarno sequences. Two particular family models, namely αr15 and αr35, shared own sub-structural modules with the Rfam model suhB (RF00519) and the uncharacterized sRNA family αr35b, respectively. A third sRNA family, termed αr45, has homology to the cis-acting regulatory element speF (RF00518). However, new experimental data further confirmed that the S. meliloti αr45 representative is an Hfq-binding sRNA processed from or expressed independently of speF, thus refining the Rfam speF model annotation. All the six families have members in phylogenetically related plant-interacting bacteria and animal pathogens of the order of the Rhizobiales, some occurring with high levels of paralogy in individual genomes. In silico and experimental evidences predict differential regulation of paralogous sRNAs in S. meliloti 1021. The distribution patterns of these sRNA families suggest major contributions of vertical inheritance and extensive ancestral duplication events to the evolution of sRNAs in plant-interacting bacteria.     

细菌非编码小RNA功能及作用机制研究进展

生物体中除了编码蛋白质的mRNA外,还存在多种具有重要调控功能的非编码RNA。细菌中长度50~500 nt的非编码RNA通常定义为sRNA。sRNA在细菌的整个生命活动中发挥着极为广泛的作用,在感受环境压力、基因表达、细胞周期乃至个体发育等过程中均具有重要的调控作用。sRNA的功能学和调控机制的研究已成为当今细菌学研究的热点。本研究就细菌中的sRNA的特征,在细菌中的作用和作用机制进行文献综述。