Pseudomonas plecoglossicida is a vital pathogen that poses a substantial risk to aquaculture. Small RNAs (sRNAs) are non-coding regulatory molecules capable of sensing environmental changes and ...modulating virulence-associated signaling pathways, such as the assembly of flagella. However, the relevant researches on P. plecoglossicida are an urgent need. Here, we report a novel sRNA, sRNA562, which has potential to regulate the post-transcriptional of fliP, a key component of the lateral flagellar type III secretion system. In this study, the effects of sRNA562 on the virulence of P. plecoglossicida and its role in regulating the pathogenic process were investigated through the use of a constructed sRNA562 deletion strain. The deletion of sRNA562 resulted in an up-regulation of fliP in P. plecoglossicida, and leading to increased swarming motility and enhanced the ability of biofilm formation, adhesion and chemotaxis. Subsequent artificial infection experiment demonstrated that the deletion of sRNA562 increased the virulence of P. plecoglossicida towards hybrid grouper, as evidenced by a reduction in survival rate, elevation of tissue bacterial load, and the exacerbation of histopathological damage. Further studies have found that the deletion of sRNA562 lead to an up-regulation of fliP expression during hybrid grouper infection, thereby enhancing bacterial swarming ability and ultimately heightening pathogenicity, leading to a dysregulated host response to infection, tissue damage and eventually death. Our work revealed a sRNA that exerts negative regulation on the expression of lateral flagella in P. plecoglossicida, thereby impacting its virulence. These findings provide a new perspective on the virulence regulation mechanism of P. plecoglossicida, contributing to a more comprehensive understanding in the field of pathogenicity research.
•SRNA 562 mediates virulence of P. plecoglossicida by regulating the expression of fliP.•Deletion of sRNA 562 increased virulence characteristics of P. plecoglossicida.•Deletion of the sRNA 562 significantly affected immune response of grouper to P. plecoglossicida infection.
Small regulatory RNAs (sRNAs) act as post-transcriptional regulators controlling bacterial adaptation to environmental changes. Our current understanding of the mechanisms underlying sRNA-mediated ...control is mainly based on studies in Escherichia coli and Salmonella. Ever since the discovery of sRNAs decades ago, these Gram-negative species have served as excellent model organisms in the field of sRNA biology. More recently, the role of sRNAs in gene regulation has become the center of attention in a broader range of species, including Gram-positive model organisms. Here, we highlight some of the most apparent similarities and differences between Gram-negative and Gram-positive bacteria with respect to the mechanisms underlying sRNA-mediated control. Although key aspects of sRNA regulation appear to be highly conserved, novel themes are arising from studies in Gram-positive species, such as a clear abundance of sRNAs acting through multiple C-rich motifs, and an apparent lack of RNA-binding proteins with chaperone activity.
•Bacterial sRNAs are post-transcriptional regulators of important cellular processes.•Key aspects of sRNA regulation appear to be conserved across bacterial species.•RNA chaperones often mediate sRNA-mRNA interactions in Gram-negative species.•The RNA chaperone Hfq is either absent or dispensable in Gram-positive species.•Many Gram-positive sRNAs rely on C- or CU-rich motifs for base pairing.
Streszczenie Małe, regulatorowe RNA (sRNA) wraz z dwuskładnikowymi systemami transdukcji sygnału (TCS) wchodzą w skład rozbudowanych sieci kontroli ekspresji genów bakteryjnych. Oddziałując ze sobą ...wzajemnie, zapewniają niezwykle szybką, jak również precyzyjną odpowiedź bakterii na zmieniające się warunki bytowania. Kontrolując wiele procesów wpływają na stan fizjologiczny komórki, skład proteomu osłon komórkowych czy zdolność do wzrostu w postaci biofilmu. Niezwykle często sRNA stanowią brakujące ogniwa, w odpowiedzi na złożone bodźce środowiskowe, pomiędzy dwuskładnikowymi systemami transdukcji sygnału, a genami docelowymi czy innymi systemami regulatorowymi. Współdziałanie TCS-sRNA wydaje się globalną cechą regulacyjną u wielu organizmów prokariotycznych. Zdobywanie wiedzy na temat tych mechanizmów kontroli toruje drogę do opracowania nowych strategii walki z drobnoustrojami patogennymi.
Non-coding RNAs (ncRNAs) make up to ~98% percent of the transcriptome of a given organism. In recent years one relatively new class of ncRNAs, long non-coding RNAs (lncRNAs), were shown to be more ...than mere by-products of gene expression and regulation. The unicellular eukaryote Paramecium tetraurelia is a member of the ciliate phylum, an extremely heterogeneous group of organisms found in most bodies of water across the globe. A hallmark of ciliate genetics is nuclear dimorphism and programmed elimination of transposons and transposon-derived DNA elements, the latter of which is essential for the maintenance of the somatic genome. Paramecium and ciliates in general harbour a plethora of different ncRNA species, some of which drive the process of large scale genome rearrangements, including DNA elimination, during sexual development. Here, we identify and validate the first known functional lncRNAs in ciliates to date. Using deep-sequencing and subsequent bioinformatic processing and experimental validation, we show that Paramecium expresses at least 15 lncRNAs. These candidates were predicted by a highly conservative pipeline and informatic analyses hint at differential expression during development. Depletion of two lncRNAs, lnc1 and lnc15, resulted in clear phenotypes, decreased survival, morphological impairment and a global effect on DNA elimination.
Computational comparative genomics and, later, high-throughput transcriptome profiling (RNAseq) have uncovered a plethora of small noncoding RNA species (sRNAs) with potential regulatory roles in ...bacteria. A large fraction of sRNAs are differentially regulated in response to different biotic and abiotic stimuli and have the ability to fine-tune posttranscriptional reprogramming of gene expression through protein-assisted antisense interactions with trans-encoded target mRNAs. However, this level of gene regulation is still understudied in most non-model bacteria. Here, we compile experimental methods to detect expression, determine 5'/3'-ends, assess transcriptional regulation, generate mutants, and validate candidate target mRNAs of trans-acting sRNAs (trans-sRNAs) identified in the nitrogen-fixing α-rhizobium Sinorhizobium meliloti. The workflow, molecular tools, and methods are suited to investigate the function of newly identified base-pairing trans-sRNAs in phylogenetically related α-rhizobia.
Spiroplasma eriocheiris is the major pathogen in the aquaculture shrimp and crab tremor disease; its infection causes heavy losses in aquaculture. Previous investigations concentrated on how the host ...responds to S. eriocheiris infection, with little known on the regulation of virulence and pathogenesis by the bacteria themselves. A body of increasing evidence shows that bacterial small noncoding RNAs (sRNAs) play a crucial part in regulating bacterial virulence and pathogenesis; however, whether there are some sRNAs in S. eriocheiris and how those sRNAs regulate virulence and pathogenesis are still unclear. This study analyzed multi-omics data integration to identify the potential sRNAs and their mediated regulatory network in S. eriocheiris. First, through an integration analysis of the public genomic and transcriptomic data, 54 potential sRNAs were identified in S. eriocheiris with a 50–250 nt length distribution and the base composition mainly AT. Next, sRNA profiling of the in vitro logarithmic and decline phase of S. eriocheiris, as well as the early and onset stage of infection in Eriocheir sinensis, was performed, showing that 4 sRNAs (SR01, SR05, SR08, and S04) were both down-regulated in the logarithmic and the onset stage of infection. Subsequently, integrated with sRNAs target gene prediction and target gene expression analysis, a regulatory network composed of four sRNAs and 96 target genes was constructed. Last, an RNA pull-down experiment was performed on the SR01, which exhibited the highest abundance and the highest number of target genes, resulting in 37 highly credible target genes with multiple genes related to bacterial virulence, such as GTPases and virulence factor coding genes. Collectively, this study identified the sRNAs in S. eriocheiris and revealed their mediated regulatory network for regulating virulence and pathogenesis, thus paving a new avenue for disease prevention and control in aquaculture.
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•Totally 54 sRNAs were identified in S. eriocheiris for the first time.•Four sRNAs which negatively regulate growth and pathogenicity were identified.•The sRNA-target network was constructed for S. eriocheiris.
Bacterial small regulatory RNAs (sRNAs) are key regulators of gene expression in many processes related to adaptive responses. A multitude of sRNAs have been identified in many bacterial species; ...however, their function has yet to be elucidated. A key step to understand sRNAs function is to identify the mRNAs these sRNAs bind to. There are several computational methods for sRNA target prediction, and the most accurate one is CopraRNA which is based on comparative-genomics. However, species-specific sRNAs are quite common and CopraRNA cannot be used for these sRNAs. The most commonly used transcriptome-wide sRNA target prediction method and second-most-accurate method is IntaRNA. However, IntaRNA can take hours to run on a bacterial transcriptome. Here we present sRNARFTarget, a machine-learning-based method for transcriptome-wide sRNA target prediction applicable to any sRNA. We comparatively assessed the performance of sRNARFTarget, CopraRNA and IntaRNA in three bacterial species. Our results show that sRNARFTarget outperforms IntaRNA in terms of accuracy, ranking of true interacting pairs, and running time. However, CopraRNA substantially outperforms the other two programsin terms of accuracy. Thus, we suggest using CopraRNA when homolog sequences of the sRNA are available, and sRNARFTarget for transcriptome-wide prediction or for species-specific sRNAs. sRNARFTarget is available at
https://github.com/BioinformaticsLabAtMUN/sRNARFTarget
.
Understanding the role of short-interfering RNA (siRNA) in diverse biological processes is of current interest and often approached through small RNA sequencing. However, analysis of these datasets ...is difficult due to the complexity of biological RNA processing pathways, which differ between species. Several properties like strand specificity, length distribution, and distribution of soft-clipped bases are few parameters known to guide researchers in understanding the role of siRNAs. We present RAPID, a generic eukaryotic siRNA analysis pipeline, which captures information inherent in the datasets and automatically produces numerous visualizations as user-friendly HTML reports, covering multiple categories required for siRNA analysis. RAPID also facilitates an automated comparison of multiple datasets, with one of the normalization techniques dedicated for siRNA knockdown analysis, and integrates differential expression analysis using DESeq2.
RAPID is available under MIT license at https://github.com/SchulzLab/RAPID. We recommend using it as a conda environment available from https://anaconda.org/bioconda/rapid.
Small regulatory RNAs (sRNAs) finely control gene expression in prokaryotes and synthetic sRNA has become a useful high-throughput approach to tackle current challenges in metabolic engineering ...because of its many advantages compared to conventional gene knockouts. In this review, we first focus on the modular structures of sRNAs and rational design strategies of synthetic sRNAs on the basis of their modular structures. The wide applications of synthetic sRNAs in bacterial metabolic engineering, with or without the aid of heterogeneously expressed Hfq protein, were also covered. In addition, we give attention to the improvements in implementing synthetic sRNAs, which make the synthetic sRNA strategy universally applicable in metabolic engineering and synthetic biology.
Key points
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Synthetic sRNAs can be rationally designed based on modular structures of natural sRNAs.
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Synthetic sRNAs were widely used for metabolic engineering in various microorganisms.
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Several technological improvements made the synthetic sRNA strategy more applicable.
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