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Meireles D, Pombinho R, Cabanes D. Signals behind Listeria monocytogenes virulence mechanisms. Gut Microbes 2024; 16:2369564. [PMID: 38979800 PMCID: PMC11236296 DOI: 10.1080/19490976.2024.2369564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/13/2024] [Indexed: 07/10/2024] Open
Abstract
The tight and coordinated regulation of virulence gene expression is crucial to ensure the survival and persistence of bacterial pathogens in different contexts within their hosts. Considering this, bacteria do not express virulence factors homogenously in time and space, either due to their associated fitness cost or to their detrimental effect at specific infection stages. To efficiently infect and persist into their hosts, bacteria have thus to monitor environmental cues or chemical cell-to-cell signaling mechanisms that allow their transition from the external environment to the host, and therefore adjust gene expression levels, intrinsic biological activities, and appropriate behaviors. Listeria monocytogenes (Lm), a major Gram-positive facultative intracellular pathogen, stands out for its adaptability and capacity to thrive in a wide range of environments. Because of that, Lm presents itself as a significant concern in food safety and public health, that can lead to potentially life-threatening infections in humans. A deeper understanding of the intricate bacterial virulence mechanisms and the signals that control them provide valuable insights into the dynamic interplay between Lm and the host. Therefore, this review addresses the role of some crucial signals behind Lm pathogenic virulence mechanisms and explores how the ability to assimilate and interpret these signals is fundamental for pathogenesis, identifying potential targets for innovative antimicrobial strategies.
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Affiliation(s)
- Diana Meireles
- Instituto de Investigação e Inovação em Saúde, Porto, Portugal
- Group of Molecular Microbiology, IBMC, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar – ICBAS, Porto, Portugal
| | - Rita Pombinho
- Instituto de Investigação e Inovação em Saúde, Porto, Portugal
- Group of Molecular Microbiology, IBMC, Porto, Portugal
| | - Didier Cabanes
- Instituto de Investigação e Inovação em Saúde, Porto, Portugal
- Group of Molecular Microbiology, IBMC, Porto, Portugal
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2
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Baur ST, Poehlein A, Renz NJ, Hollitzer SK, Montoya Solano JD, Schiel-Bengelsdorf B, Daniel R, Dürre P. Modulation of sol mRNA expression by the long non-coding RNA Assolrna in Clostridium saccharoperbutylacetonicum affects solvent formation. Front Genet 2022; 13:966643. [PMID: 36035128 PMCID: PMC9402939 DOI: 10.3389/fgene.2022.966643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 07/11/2022] [Indexed: 12/01/2022] Open
Abstract
Solvents such as butanol are important platform chemicals and are often produced from petrochemical sources. Production of butanol and other compounds from renewable and sustainable resources can be achieved by solventogenic bacteria, such as the hyper-butanol producer Clostridium saccharoperbutylacetonicum. Its sol operon consists of the genes encoding butyraldehyde dehydrogenase, CoA transferase, and acetoacetate decarboxylase (bld, ctfA, ctfB, adc) and the gene products are involved in butanol and acetone formation. It is important to understand its regulation to further optimize the solvent production. In this study, a new long non-coding antisense transcript complementary to the complete sol operon, now called Assolrna, was identified by transcriptomic analysis and the regulatory mechanism of Assolrna was investigated. For this purpose, the promoter-exchange strain C. saccharoperbutylacetonicum ΔPasr::Pasr** was constructed. Additionally, Assolrna was expressed plasmid-based under control of the native Pasr promoter and the lactose-inducible PbgaL promoter in both the wild type and the promoter-exchange strain. Solvent formation was strongly decreased for all strains based on C. saccharoperbutylacetonicum ΔPasr::Pasr** and growth could not be restored by plasmid-based complementation of the exchanged promoter. Interestingly, very little sol mRNA expression was detected in the strain C. saccharoperbutylacetonicum ΔPasr::Pasr** lacking Assolrna expression. Butanol titers were further increased for the overexpression strain C. saccharoperbutylacetonicum [pMTL83151_asr_PbgaL] compared to the wild type. These results suggest that Assolrna has a positive effect on sol operon expression. Therefore, a possible stabilization mechanism of the sol mRNA by Assolrna under physiological concentrations is proposed.
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Affiliation(s)
- Saskia Tabea Baur
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
- *Correspondence: Saskia Tabea Baur,
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Niklas Jan Renz
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | | | | | | | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
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3
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Micheel J, Safrastyan A, Wollny D. Advances in Non-Coding RNA Sequencing. Noncoding RNA 2021; 7:70. [PMID: 34842804 PMCID: PMC8628893 DOI: 10.3390/ncrna7040070] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 12/11/2022] Open
Abstract
Non-coding RNAs (ncRNAs) comprise a set of abundant and functionally diverse RNA molecules. Since the discovery of the first ncRNA in the 1960s, ncRNAs have been shown to be involved in nearly all steps of the central dogma of molecular biology. In recent years, the pace of discovery of novel ncRNAs and their cellular roles has been greatly accelerated by high-throughput sequencing. Advances in sequencing technology, library preparation protocols as well as computational biology helped to greatly expand our knowledge of which ncRNAs exist throughout the kingdoms of life. Moreover, RNA sequencing revealed crucial roles of many ncRNAs in human health and disease. In this review, we discuss the most recent methodological advancements in the rapidly evolving field of high-throughput sequencing and how it has greatly expanded our understanding of ncRNA biology across a large number of different organisms.
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Affiliation(s)
| | | | - Damian Wollny
- RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University, 07743 Jena, Germany; (J.M.); (A.S.)
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4
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Zhu LP, Song SZ, Yang S. Gene repression using synthetic small regulatory RNA in Methylorubrum extorquens. J Appl Microbiol 2021; 131:2861-2875. [PMID: 34021964 DOI: 10.1111/jam.15159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/07/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022]
Abstract
AIM Genetic tools are a prerequisite for engineering cell factories for synthetic biology and biotechnology. Methylorubrum extorquens is an important platform for a future one-carbon (C1) bioeconomy, but its application is currently limited by the availability of genetic tools. Small regulatory RNA (sRNA) is an important regulatory factor in bacteria and has been applied for gene repression in several strains. This study aimed to construct a synthetic sRNA system based on the MicC scaffold and the chaperone Hfq to control gene expression in M. extorquens. METHODS AND RESULTS Initially, the exogenous lacZ gene was transposed into the M. extorquens chromosome as a reporter, and corresponding β-galactosidase was measured to assess the knockdown efficiency of lacZ. A synthetic sRNA containing a 24-nt antisense RNA targeting lacZ and an Escherichia coli MicC scaffold were constructed, and different Hfqs from E. coli, M. extorquens AM1 and PA1 were further identified. The results showed that the expression of endogenous hfqs from the chromosome in M. extorquens strains was inadequate, and only when it was overexpressed via the plasmid did the colonies show a colour change and a corresponding decrease in β-galactosidase expression. More specifically, M. extorquens strains with overexpressing their own Hfq showed the best gene repression efficiency. Furthermore, this E. coli MicC scaffold and AM1 Hfq system were combined to knock down crtI gene expression in AM1, leading to an 86% decrease in carotenoid production (0·09 mg g-1 ) compared to that (0·65 mg g-1 ) in the wild-type strain. CONCLUSION A functional synthetic sRNA system combined with E. coli MicC and endogenous Hfq was constructed in M. extorquens strains, which was able to interfere with the target crtI gene and reduce carotenoid production. SIGNIFICANCE AND IMPACT OF THE STUDY The synthetic sRNA system reported in this study provides a genetic tool for the manipulation of M. extorquens. The present findings might be helpful for achieving high-throughput gene knockdown expression.
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Affiliation(s)
- L-P Zhu
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, and School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - S-Z Song
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, and School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - S Yang
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, and School of Life Sciences, Qingdao Agricultural University, Qingdao, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
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5
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Xu C, Luo S, Wei L, Wu H, Gu W, Zhou W, Sun B, Hu B, Zhou H, Liu Y, Chen H, Ye X, Yuan W. Integrated transcriptome and proteome analyses identify novel regulatory network of nucleus pulposus cells in intervertebral disc degeneration. BMC Med Genomics 2021; 14:40. [PMID: 33536009 PMCID: PMC7860219 DOI: 10.1186/s12920-021-00889-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 01/27/2021] [Indexed: 01/07/2023] Open
Abstract
Background Degeneration of intervertebral disc is a major cause of lower back pain and neck pain. Studies have tried to unveil the regulatory network using either transcriptomic or proteomic analysis. However, neither have fully elucidated the exact mechanism of degeneration process. Since post-transcriptional regulation may affect gene expression by modulating the translational process of mRNA to protein product, a combined transcriptomic and proteomic study may provide more insight into the key regulatory network of Intervertebral disc degeneration. Methods In order to obtain the proteomic and transcriptomic data, we performed label-free proteome analysis on freshly isolated nucleus pulposus cells and obtained transcriptome profiling data from the Gene Expression Omnibus repository. To identify the key regulatory network of intervertebral disc degeneration in nucleus pulposus cells, we performed bioinformatic analyses and established a protein-RNA interacting network. To validate the candidate genes, we performed in vitro experimentation and immunochemistry labeling to identify their potential function during nucleus pulposus degeneration. Results The label-free proteome analysis identified altogether 656 proteins, and 503 of which were differentially expressed between nucleus pulposus cells from degenerated or normal disc cells. Using the existing nucleus pulposus transcriptomic profiling data, we integrated the proteomic and transcriptomic data of nucleus pulposus cells, and established a protein-RNA interacting network to show the combined regulatory network of intervertebral disc degeneration. In the network, we found 9 genes showed significant changes, and 6 of which (CHI3L1, KRT19, COL6A2, DPT, TNFAIP6 and COL11A2) showed concordant changes in both protein and mRNA level. Further functional analysis showed these candidates can significantly affect the degeneration of the nucleus pulposus cell when altering their expression. Conclusions This study is the first to use combined analysis of proteomic and transcriptomic profiling data to identify novel regulatory network of nucleus pulposus cells in intervertebral disc degeneration. Our established protein-RNA interacting network demonstrated novel regulatory mechanisms and key genes that may play vital roles in the pathogenesis of intervertebral disc degeneration.
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Affiliation(s)
- Chen Xu
- Spine Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Shengchang Luo
- Spine Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China.,Microsurgery Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China.,Department of Orthopaedics, The First People's Hospital of Huzhou, Huzhou, 200003, China
| | - Leixin Wei
- Spine Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Huiqiao Wu
- Spine Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Wei Gu
- Spine Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Wenchao Zhou
- Spine Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Baifeng Sun
- Spine Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Bo Hu
- Spine Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Hongyu Zhou
- Spine Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Yang Liu
- Spine Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Huajiang Chen
- Spine Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China.
| | - Xiaojian Ye
- Microsurgery Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China. .,Department of Orthopaedics, Tongren Hospital, Shanghai Jiao Tong University, Shanghai, 200050, China.
| | - Wen Yuan
- Spine Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China.
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Chen L, Gu L, Geng X, Xu G, Huang X, Zhu X. A novel cis antisense RNA AsfD promotes Salmonella enterica serovar Typhi motility and biofilm formation. Microb Pathog 2020; 142:104044. [PMID: 32032766 DOI: 10.1016/j.micpath.2020.104044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/19/2020] [Accepted: 02/03/2020] [Indexed: 12/20/2022]
Abstract
Bacterial non-coding RNAs (ncRNAs) can participate in multiple biological processes, including motility, biofilm formation, and virulence. Using high-throughput sequencing and transcriptome analysis of Salmonella enterica serovar Typhi (S. Typhi), we identified a novel antisense RNA located at the opposite strand of the flhDC operon. In this study, a northern blot and qRT-PCR were used to confirm the expression of this newfound antisense RNA in S. Typhi. Moreover, 5' RACE and 3' RT-PCR were performed to reveal the molecular characteristics of the antisense RNA, which was 2079 nt - 2179 nt in length, covered the entire flhDC operon sequence, and termed AsfD. The level of AsfD expression was higher during the stationary phase of S. Typhi and activated by the regulators, OmpR and Fis. When AsfD was overexpressed, the level of flagellar gene flhDC transcription increased; moreover, the level of fliA and fljB expression, as well as the motility and biofilm formation of S. Typhi were also enhanced. The results of this study suggest that AsfD is likely to enhance the motility and biofilm formation of S. Typhi by up-regulating flhDC expression.
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Affiliation(s)
- Long Chen
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang, 215600, China
| | - Liping Gu
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang, 215600, China
| | - Xinfeng Geng
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang, 215600, China
| | - Guoxin Xu
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang, 215600, China
| | - Xinxiang Huang
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xiaojue Zhu
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang, 215600, China.
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7
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Xue XY, Mao XG, Zhou Y, Chen Z, Hu Y, Hou Z, Li MK, Meng JR, Luo XX. Advances in the delivery of antisense oligonucleotides for combating bacterial infectious diseases. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2018; 14:745-758. [PMID: 29341934 DOI: 10.1016/j.nano.2017.12.026] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/12/2017] [Accepted: 12/31/2017] [Indexed: 12/22/2022]
Abstract
Discovery and development of new antibacterial drugs against multidrug resistant bacterial strains have become more and more urgent. Antisense oligonucleotides (ASOs) show immense potential to control the spread of resistant microbes due to its high specificity of action, little risk to human gene expression, and easy design and synthesis to target any possible gene. However, efficient delivery of ASOs to their action sites with enough concentration remains a major obstacle, which greatly hampers their clinical application. In this study, we reviewed current progress on delivery strategies of ASOs into bacteria, focused on various non-virus gene vectors, including cell penetrating peptides, lipid nanoparticles, bolaamphiphile-based nanoparticles, DNA nanostructures and Vitamin B12. The current review provided comprehensive understanding and novel perspective for the future application of ASOs in combating bacterial infections.
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Affiliation(s)
- Xiao-Yan Xue
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi'an, China.
| | - Xing-Gang Mao
- Department of Neurosurgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Ying Zhou
- Department of Pharmacology, Xi'an Medical University, Xi'an, China
| | - Zhou Chen
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi'an, China
| | - Yue Hu
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi'an, China
| | - Zheng Hou
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi'an, China
| | - Ming-Kai Li
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi'an, China
| | - Jing-Ru Meng
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi'an, China
| | - Xiao-Xing Luo
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi'an, China.
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8
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Rath EC, Pitman S, Cho KH, Bai Y. Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data. BMC Bioinformatics 2017; 18:540. [PMID: 29297355 PMCID: PMC5751559 DOI: 10.1186/s12859-017-1897-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Small noncoding regulatory RNAs (sRNAs) are post-transcriptional regulators, regulating mRNAs, proteins, and DNA in bacteria. One class of sRNAs, trans-acting sRNAs, are the most abundant sRNAs transcribed from the intergenic regions (IGRs) of the bacterial genome. In Streptococcus pyogenes, a common and potentially deadly pathogen, many sRNAs have been identified, but only a few have been studied. The goal of this study is to identify trans-acting sRNAs that can be substrates of RNase III. The endoribonuclease RNase III cleaves double stranded RNAs, which can be formed during the interaction between an sRNA and target mRNAs. Results For this study, we created an RNase III null mutant of Streptococcus pyogenes and its RNA sequencing (RNA-Seq) data were analyzed and compared to that of the wild-type. First, we developed a custom script that can detect intergenic regions of the S. pyogenes genome. A differential expression analysis with Cufflinks and Stringtie was then performed to identify the intergenic regions whose expression was influenced by the RNase III gene deletion. Conclusion This analysis yielded 12 differentially expressed regions with >|2| fold change and p ≤ 0.05. Using Artemis and Bamview genome viewers, these regions were visually verified leaving 6 putative sRNAs. This study not only expanded our knowledge on novel sRNAs but would also give us new insight into sRNA degradation.
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Affiliation(s)
- Ethan C Rath
- Department of Biology, Indiana State University, Terre Haute, IN, 47809, USA
| | - Stephanie Pitman
- Department of Biology, Indiana State University, Terre Haute, IN, 47809, USA
| | - Kyu Hong Cho
- Department of Biology, Indiana State University, Terre Haute, IN, 47809, USA.
| | - Yongsheng Bai
- Department of Biology, Indiana State University, Terre Haute, IN, 47809, USA. .,The Center for Genomic Advocacy, Indiana State University, Terre Haute, IN, 47809, USA.
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Le Rhun A, Beer YY, Reimegård J, Chylinski K, Charpentier E. RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes. RNA Biol 2016; 13:177-95. [PMID: 26580233 PMCID: PMC4829319 DOI: 10.1080/15476286.2015.1110674] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Streptococcus pyogenes is a human pathogen responsible for a wide spectrum of diseases ranging from mild to life-threatening infections. During the infectious process, the temporal and spatial expression of pathogenicity factors is tightly controlled by a complex network of protein and RNA regulators acting in response to various environmental signals. Here, we focus on the class of small RNA regulators (sRNAs) and present the first complete analysis of sRNA sequencing data in S. pyogenes. In the SF370 clinical isolate (M1 serotype), we identified 197 and 428 putative regulatory RNAs by visual inspection and bioinformatics screening of the sequencing data, respectively. Only 35 from the 197 candidates identified by visual screening were assigned a predicted function (T-boxes, ribosomal protein leaders, characterized riboswitches or sRNAs), indicating how little is known about sRNA regulation in S. pyogenes. By comparing our list of predicted sRNAs with previous S. pyogenes sRNA screens using bioinformatics or microarrays, 92 novel sRNAs were revealed, including antisense RNAs that are for the first time shown to be expressed in this pathogen. We experimentally validated the expression of 30 novel sRNAs and antisense RNAs. We show that the expression profile of 9 sRNAs including 2 predicted regulatory elements is affected by the endoribonucleases RNase III and/or RNase Y, highlighting the critical role of these enzymes in sRNA regulation.
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Affiliation(s)
- Anaïs Le Rhun
- a The Laboratory for Molecular Infection Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology; Umeå University, S-90187 , Umeå , Sweden.,b Helmholtz Centre for Infection Research (HZI), Department of Regulation in Infection Biology, D-38124 , Braunschweig , Germany
| | - Yan Yan Beer
- b Helmholtz Centre for Infection Research (HZI), Department of Regulation in Infection Biology, D-38124 , Braunschweig , Germany
| | - Johan Reimegård
- c Science for Life Laboratory , Department of Cell and Molecular Biology, Uppsala University, S-75003 , Uppsala , Sweden
| | - Krzysztof Chylinski
- a The Laboratory for Molecular Infection Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology; Umeå University, S-90187 , Umeå , Sweden.,d Max F. Perutz Laboratories (MFPL), University of Vienna, A-1030 , Vienna , Austria
| | - Emmanuelle Charpentier
- a The Laboratory for Molecular Infection Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology; Umeå University, S-90187 , Umeå , Sweden.,b Helmholtz Centre for Infection Research (HZI), Department of Regulation in Infection Biology, D-38124 , Braunschweig , Germany.,e Hannover Medical School (MHH), D-30625 , Hannover , Germany.,f Max Planck Institute for Infection Biology , Department of Regulation in Infection Biology, D-10117 , Berlin , Germany
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Rossi CC, Bossé JT, Li Y, Witney AA, Gould KA, Langford PR, Bazzolli DMS. A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae. RNA (NEW YORK, N.Y.) 2016; 22:1373-85. [PMID: 27402897 PMCID: PMC4986893 DOI: 10.1261/rna.055129.115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 05/24/2016] [Indexed: 05/26/2023]
Abstract
Bacterial regulatory small RNAs (sRNAs) play important roles in gene regulation and are frequently connected to the expression of virulence factors in diverse bacteria. Only a few sRNAs have been described for Pasteurellaceae pathogens and no in-depth analysis of sRNAs has been described for Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, responsible for considerable losses in the swine industry. To search for sRNAs in A. pleuropneumoniae, we developed a strategy for the computational analysis of the bacterial genome by using four algorithms with different approaches, followed by experimental validation. The coding strand and expression of 17 out of 23 RNA candidates were confirmed by Northern blotting, RT-PCR, and RNA sequencing. Among them, two are likely riboswitches, three are housekeeping regulatory RNAs, two are the widely studied GcvB and 6S sRNAs, and 10 are putative novel trans-acting sRNAs, never before described for any bacteria. The latter group has several potential mRNA targets, many of which are involved with virulence, stress resistance, or metabolism, and connect the sRNAs in a complex gene regulatory network. The sRNAs identified are well conserved among the Pasteurellaceae that are evolutionarily closer to A. pleuropneumoniae and/or share the same host. Our results show that the combination of newly developed computational programs can be successfully utilized for the discovery of novel sRNAs and indicate an intricate system of gene regulation through sRNAs in A. pleuropneumoniae and in other Pasteurellaceae, thus providing clues for novel aspects of virulence that will be explored in further studies.
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Affiliation(s)
- Ciro C Rossi
- Laboratório de Genética Molecular de Micro-organismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária-BIOAGRO, Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil
| | - Janine T Bossé
- Section of Paediatrics, Imperial College London, St. Mary's Campus, London W2 1PG, United Kingdom
| | - Yanwen Li
- Section of Paediatrics, Imperial College London, St. Mary's Campus, London W2 1PG, United Kingdom
| | - Adam A Witney
- Institute for Infection and Immunity, St. George's, University of London, London SW17 0RE, United Kingdom
| | - Kate A Gould
- Institute for Infection and Immunity, St. George's, University of London, London SW17 0RE, United Kingdom
| | - Paul R Langford
- Section of Paediatrics, Imperial College London, St. Mary's Campus, London W2 1PG, United Kingdom
| | - Denise M S Bazzolli
- Laboratório de Genética Molecular de Micro-organismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária-BIOAGRO, Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil
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11
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Saberi F, Kamali M, Najafi A, Yazdanparast A, Moghaddam MM. Natural antisense RNAs as mRNA regulatory elements in bacteria: a review on function and applications. Cell Mol Biol Lett 2016; 21:6. [PMID: 28536609 PMCID: PMC5415839 DOI: 10.1186/s11658-016-0007-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 12/23/2015] [Indexed: 12/20/2022] Open
Abstract
Naturally occurring antisense RNAs are small, diffusible, untranslated transcripts that pair to target RNAs at specific regions of complementarity to control their biological function by regulating gene expression at the post-transcriptional level. This review focuses on known cases of antisense RNA control in prokaryotes and provides an overview of some natural RNA-based mechanisms that bacteria use to modulate gene expression, such as mRNA sensors, riboswitches and antisense RNAs. We also highlight recent advances in RNA-based technology. The review shows that studies on both natural and synthetic systems are reciprocally beneficial.
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Affiliation(s)
- Fatemeh Saberi
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mehdi Kamali
- Nanobiotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Alavieh Yazdanparast
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Zorgani MA, Quentin R, Lartigue MF. Regulatory RNAs in the Less Studied Streptococcal Species: From Nomenclature to Identification. Front Microbiol 2016; 7:1161. [PMID: 27507970 PMCID: PMC4960207 DOI: 10.3389/fmicb.2016.01161] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/12/2016] [Indexed: 12/23/2022] Open
Abstract
Streptococcal species are Gram-positive bacteria involved in severe and invasive diseases in humans and animals. Although, this group includes different pathogenic species involved in life-threatening infections for humans, it also includes beneficial species, such as Streptococcus thermophilus, which is used in yogurt production. In bacteria virulence factors are controlled by various regulatory networks including regulatory RNAs. For clearness and to develop logical thinking, we start this review with a revision of regulatory RNAs nomenclature. Previous reviews are mostly dealing with Streptococcus pyogenes and Streptococcus pneumoniae regulatory RNAs. We especially focused our analysis on regulatory RNAs in Streptococcus agalactiae, Streptococcus mutans, Streptococcus thermophilus and other less studied Streptococcus species. Although, S. agalactiae RNome remains largely unknown, sRNAs (small RNAs) are supposed to mediate regulation during environmental adaptation and host infection. In the case of S. mutans, sRNAs are suggested to be involved in competence regulation, carbohydrate metabolism, and Toxin–Antitoxin systems. A new category of miRNA-size small RNAs (msRNAs) was also identified for the first time in this species. The analysis of S. thermophilus sRNome shows that many sRNAs are associated to the bacterial immune system known as CRISPR-Cas system. Only few of the other different Streptococcus species have been the subject of studies pointed toward the characterization of regulatory RNAs. Finally, understanding bacterial sRNome can constitute one step forward to the elaboration of new strategies in therapy such as substitution of antibiotics in the management of S. agalactiae neonatal infections, prevention of S. mutans dental caries or use of S. thermophilus CRISPR-Cas system in genome editing applications.
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Affiliation(s)
- Mohamed A Zorgani
- ISP, INRA, Equipe 5 "Bactéries et Risque Materno-foetal", Faculté de Médecine, UMR 1282, Université François Rabelais de Tours, Tours France
| | - Roland Quentin
- ISP, INRA, Equipe 5 "Bactéries et Risque Materno-foetal", Faculté de Médecine, UMR 1282, Université François Rabelais de Tours, ToursFrance; Service de Bactériologie Virologie et Hygiène Hospitalière, Centre Hospitalier Régional Universitaire de Tours, ToursFrance
| | - Marie-Frédérique Lartigue
- ISP, INRA, Equipe 5 "Bactéries et Risque Materno-foetal", Faculté de Médecine, UMR 1282, Université François Rabelais de Tours, ToursFrance; Service de Bactériologie Virologie et Hygiène Hospitalière, Centre Hospitalier Régional Universitaire de Tours, ToursFrance
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The Mechanisms of Virulence Regulation by Small Noncoding RNAs in Low GC Gram-Positive Pathogens. Int J Mol Sci 2015; 16:29797-814. [PMID: 26694351 PMCID: PMC4691137 DOI: 10.3390/ijms161226194] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 12/01/2015] [Accepted: 12/04/2015] [Indexed: 11/30/2022] Open
Abstract
The discovery of small noncoding regulatory RNAs (sRNAs) in bacteria has grown tremendously recently, giving new insights into gene regulation. The implementation of computational analysis and RNA sequencing has provided new tools to discover and analyze potential sRNAs. Small regulatory RNAs that act by base-pairing to target mRNAs have been found to be ubiquitous and are the most abundant class of post-transcriptional regulators in bacteria. The majority of sRNA studies has been limited to E. coli and other gram-negative bacteria. However, examples of sRNAs in gram-positive bacteria are still plentiful although the detailed gene regulation mechanisms behind them are not as well understood. Strict virulence control is critical for a pathogen’s survival and many sRNAs have been found to be involved in that process. This review outlines the targets and currently known mechanisms of trans-acting sRNAs involved in virulence regulation in various gram-positive pathogens. In addition, their shared characteristics such as CU interaction motifs, the role of Hfq, and involvement in two-component regulators, riboswitches, quorum sensing, or toxin/antitoxin systems are described.
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