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Zhu H, Gong L, Wang R, Shao Z. The Effects and Toxicity of Different Pyrene Concentrations on Escherichia coli Using Transcriptomic Analysis. Microorganisms 2024; 12:326. [PMID: 38399729 PMCID: PMC10892627 DOI: 10.3390/microorganisms12020326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 01/28/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Pyrene is a pollutant in the environment and affects the health of living organisms. It is important to understand microbial-mediated pyrene resistance and the related molecular mechanisms due to its toxicity and biodegradability. Due to the unclear response mechanisms of bacteria to PAHs, this study detected the transcriptional changes in Escherichia coli under different pyrene concentrations using transcriptome sequencing technology. Global transcriptome analysis showed that the number of differentially expressed genes (DEGs) in multiple metabolic pathways increased with increasing concentrations of pyrene. In addition, the effects and toxicity of pyrene on Escherichia coli mainly included the up-regulation and inhibition of genes related to carbohydrate metabolism, membrane transport, sulfate reduction, various oxidoreductases, and multidrug efflux pumps. Moreover, we also constructed an association network between significantly differentially expressed sRNAs and key genes and determined the regulatory relationship and key genes of Escherichia coli under pyrene stress. Our study utilized pyrene as an exogenous stress substance to investigate the possible pathways of the bacterial stress response. In addition, this study provides a reference for other related research and serves as a foundation for future research.
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Affiliation(s)
- Han Zhu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
| | - Linfeng Gong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
| | - Ruicheng Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
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2
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Delcher HA, DeMeis JD, Ghobar N, Godang NL, Knight SL, Alqudah SY, Nguyen KN, Watters BC, Borchert GM. SARS-Cov-2 small viral RNA suppresses gene expression via complementary binding to mRNA 3' UTR. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.000790. [PMID: 38312351 PMCID: PMC10835431 DOI: 10.17912/micropub.biology.000790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 02/06/2024]
Abstract
SARS-CoV-2 (SC2) has been intensely studied since its emergence. However, the mechanisms of host immune dysregulation triggered by SC2 remain poorly understood. That said, it is well established that many prominent viral families encode microRNAs (miRNAs) or related small viral RNAs (svRNAs) capable of regulating human genes involved in immune function. Importantly, recent reports have shown that SC2 encodes its own svRNAs. In this study, we have identified 12 svRNAs expressed during SC2 infection and show that one of these svRNAs can regulate target gene expression via complementary binding to mRNA 3' untranslated regions (3'UTRs) much like human microRNAs.
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Affiliation(s)
- Haley A Delcher
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Jeffrey D DeMeis
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Nicole Ghobar
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Noel L Godang
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Sierra L Knight
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Shahem Y Alqudah
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Kevin N Nguyen
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Brianna C Watters
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Glen M Borchert
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
- Department of Biology, College of Arts and Sciences, University of South Alabama, Mobile, AL
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3
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Chen L, Wang C, Su J. Understanding the Effect of Different Glucose Concentrations in the Oligotrophic Bacterium Bacillus subtilis BS-G1 through Transcriptomics Analysis. Microorganisms 2023; 11:2401. [PMID: 37894061 PMCID: PMC10609351 DOI: 10.3390/microorganisms11102401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
Glucose is an important carbon source for microbial growth, and its content in infertile soils is essential for the growth of bacteria. Since the mechanism of oligotrophic bacterium adaptation in barren soils is unclear, this research employed RNA-seq technology to examine the impact of glucose concentration on the oligotrophic bacterium B. subtilis BS-G1 in soil affected by desertification. A global transcriptome analysis (RNA-Seq) revealed that the significantly differentially expressed genes (DEGs) histidine metabolism, glutamate synthesis, the HIF-1 signaling pathway, sporulation, and the TCA cycle pathway of B. subtilis BS-G1 were significantly enriched with a 0.015 g/L glucose concentration (L group), compared to a 10 g/L glucose concentration (H group). The DEGs amino acid system, two-component system, metal ion transport, and nitrogen metabolism system of B. subtilis BS-G1 were significantly enriched in the 5 g/L glucose concentration (M group), compared with the H group. In addition, the present study identified the regulation pattern and key genes under a low-glucose environment (7 mRNAs and 16 sRNAs). This study primarily investigates the variances in the regulatory pathways of the oligotrophic B. subtilis BS-G1, which holds substantial importance in comprehending the mechanism underlying the limited sugar tolerance of oligotrophic bacteria.
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Affiliation(s)
- Liping Chen
- Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources, School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Chenglong Wang
- Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources, School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Jianyu Su
- Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources, School of Life Sciences, Ningxia University, Yinchuan 750021, China
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4
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Naaz S, Sakib N, Houserova D, Badve R, Crucello A, Borchert GM. Characterization of a novel sRNA contributing to biofilm formation in Salmonella enterica serovar Typhimurium. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000796. [PMID: 37151214 PMCID: PMC10160853 DOI: 10.17912/micropub.biology.000796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/20/2023] [Accepted: 01/01/1970] [Indexed: 05/09/2023]
Abstract
Small RNAs (sRNAs) are short noncoding RNAs of ~50-200 nucleotides believed to primarily function in regulating crucial activities in bacteria during periods of cellular stress. This study examined the relevance of specific sRNAs on biofilm formation in nutrient starved Salmonella enterica serovar Typhimurium. Eight unique sRNAs were selected for deletion primarily based on their genomic location and/or putative targets. Quantitative and qualitative analyses confirm one of these, sRNA1186573, is required for efficient biofilm formation in S. enterica further highlighting the significance of sRNAs during Salmonella stress response.
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Affiliation(s)
- Sayema Naaz
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Najmuj Sakib
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Dominika Houserova
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Rani Badve
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Aline Crucello
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Glen M Borchert
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
- Correspondence to: Glen M Borchert (
)
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Imrat, Labala RK, Behara AK, Jeyaram K. Selective extracellular secretion of small double-stranded RNA by Tetragenococcus halophilus. Funct Integr Genomics 2022; 23:10. [PMID: 36542169 DOI: 10.1007/s10142-022-00934-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022]
Abstract
Small double-stranded RNAs (dsRNAs) abundantly produced by lactic acid bacteria demonstrate immunomodulatory activity and antiviral protective immunity. However, the extracellular secretion of dsRNA from lactic acid bacteria and their compositional and functional differences compared to the intracellular dsRNA is unknown. In this study, we compared the intracellular and secreted extracellular dsRNA of the lactic acid bacteria, Tetragenococcus halophilus, commonly present in fermented foods, by growing in RNA-free and RNase-free media. We used RNA deep sequencing and in-silico analysis to annotate potential regulatory functions for the comparison. A time series sampling of T. halophilus culture demonstrated growth phase-dependent dynamics in extracellular dsRNA secretion with no major change in the intracellular dsRNA profile. The RNA deep sequencing resulted in thousands of diverse dsRNA fragments with 14-21 nucleotides in size from T. halophilus culture. Over 70% of the secreted extracellular dsRNAs were unique in their sequences compared to the intracellular dsRNAs. Furthermore, the extracellular dsRNA abundantly contains sequences that are not T. halophilus genome encoded, not detected intracellularly and showed higher hits on human transcriptome during in-silico analysis, which suggests the presence of extrachromosomal mobile regulatory elements. Further analysis showed significant enrichment of dsRNA target genes of human transcriptome on cancer pathways and transcription process, indicating the extracellular dsRNA of T. halophilus is different not only at the sequence level but also in function. Studying the bacterial extracellular dsRNA is a promising area of future research, particularly for developing postbiotic fermented functional foods and understanding the impact of commensal gut bacteria on human health.
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Affiliation(s)
- Imrat
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal, 795001, Manipur, India.,Department of Biotechnology, Gauhati University, Guwahati, 781014, Assam, India
| | - Rajendra Kumar Labala
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal, 795001, Manipur, India
| | - Abhisek Kumar Behara
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal, 795001, Manipur, India
| | - Kumaraswamy Jeyaram
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal, 795001, Manipur, India.,IBSD Regional Centre, Tadong, Gangtok, 737102, Sikkim, India
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Houserova D, Dahmer DJ, Amin SV, King VM, Barnhill EC, Zambrano ME, Dean MA, Crucello A, Aria KM, Spector MP, Borchert GM. Characterization of 475 Novel, Putative Small RNAs (sRNAs) in Carbon-Starved Salmonella enterica Serovar Typhimurium. Antibiotics (Basel) 2021; 10:305. [PMID: 33809610 PMCID: PMC8000849 DOI: 10.3390/antibiotics10030305] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/05/2021] [Accepted: 03/11/2021] [Indexed: 11/25/2022] Open
Abstract
An increasingly apparent role of noncoding RNA (ncRNAs) is to coordinate gene expression during environmental stress. A mounting body of evidence implicates small RNAs (sRNAs) as key drivers of Salmonella stress survival. Generally thought to be 50-500 nucleotides in length and to occur in intergenic regions, sRNAs typically regulate protein expression through base pairing with mRNA targets. In this work, through employing a refined definition of sRNAs allowing for shorter sequences and sRNA loci to overlap with annotated protein-coding gene loci, we have identified 475 previously unannotated sRNAs that are significantly differentially expressed during carbon starvation (C-starvation). Northern blotting and quantitative RT-PCRs confirm the expressions and identities of several of these novel sRNAs, and our computational analyses find the majority to be highly conserved and structurally related to known sRNAs. Importantly, we show that deletion of one of the sRNAs dynamically expressed during C-starvation, sRNA4130247, significantly impairs the Salmonella C-starvation response (CSR), confirming its involvement in the Salmonella CSR. In conclusion, the work presented here provides the first-ever characterization of intragenic sRNAs in Salmonella, experimentally confirms that sRNAs dynamically expressed during the CSR are directly involved in stress survival, and more than doubles the Salmonella enterica sRNAs described to date.
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Affiliation(s)
- Dominika Houserova
- Department of Pharmacology, USA College of Medicine, Mobile, AL 36688-0002, USA; (D.H.); (D.J.D.); (S.V.A.); (K.M.A.)
| | - Donovan J. Dahmer
- Department of Pharmacology, USA College of Medicine, Mobile, AL 36688-0002, USA; (D.H.); (D.J.D.); (S.V.A.); (K.M.A.)
- Department of Biomedical Sciences, University of South Alabama, Mobile, AL 36688-0002, USA;
| | - Shivam V. Amin
- Department of Pharmacology, USA College of Medicine, Mobile, AL 36688-0002, USA; (D.H.); (D.J.D.); (S.V.A.); (K.M.A.)
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA; (V.M.K.); (E.C.B.); (M.E.Z.); (M.A.D.); (A.C.)
| | - Valeria M. King
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA; (V.M.K.); (E.C.B.); (M.E.Z.); (M.A.D.); (A.C.)
| | - Emmaline C. Barnhill
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA; (V.M.K.); (E.C.B.); (M.E.Z.); (M.A.D.); (A.C.)
| | - Mike E. Zambrano
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA; (V.M.K.); (E.C.B.); (M.E.Z.); (M.A.D.); (A.C.)
| | - Meghan A. Dean
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA; (V.M.K.); (E.C.B.); (M.E.Z.); (M.A.D.); (A.C.)
| | - Aline Crucello
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA; (V.M.K.); (E.C.B.); (M.E.Z.); (M.A.D.); (A.C.)
| | - Kevin M. Aria
- Department of Pharmacology, USA College of Medicine, Mobile, AL 36688-0002, USA; (D.H.); (D.J.D.); (S.V.A.); (K.M.A.)
| | - Michael P. Spector
- Department of Biomedical Sciences, University of South Alabama, Mobile, AL 36688-0002, USA;
| | - Glen M. Borchert
- Department of Pharmacology, USA College of Medicine, Mobile, AL 36688-0002, USA; (D.H.); (D.J.D.); (S.V.A.); (K.M.A.)
- Department of Biology, University of South Alabama, Mobile, AL 36688-0002, USA; (V.M.K.); (E.C.B.); (M.E.Z.); (M.A.D.); (A.C.)
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Balkir P, Kemahlioglu K, Yucel U. Foodomics: A new approach in food quality and safety. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2020.11.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Koul V, Srivastava D, Singh PP, Kochar M. Genome-wide identification of Azospirillum brasilense Sp245 small RNAs responsive to nitrogen starvation and likely involvement in plant-microbe interactions. BMC Genomics 2020; 21:821. [PMID: 33228533 PMCID: PMC7685610 DOI: 10.1186/s12864-020-07212-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 11/05/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Small RNAs (sRNAs) are non-coding RNAs known to regulate various biological functions such as stress adaptation, metabolism, virulence as well as pathogenicity across a wide range of bacteria, mainly by controlling mRNA stabilization or regulating translation. Identification and functional characterization of sRNAs has been carried out in various plant growth-promoting bacteria and they have been shown to help the cells cope up with environmental stress. No study has been carried out to uncover these regulatory molecules in the diazotrophic alpha-proteobacterium Azospirillum brasilense Sp245 to date. RESULTS Expression-based sRNA identification (RNA-seq) revealed the first list of ~ 468 sRNA candidate genes in A. brasilense Sp245 that were differentially expressed in nitrogen starvation versus non-starved conditions. In parallel, in silico tools also identified 2 of the above as candidate sRNAs. Altogether, putative candidates were stringently curated from RNA-seq data based on known sRNA parameters (size, location, secondary structure, and abundance). In total, ~ 59 significantly expressed sRNAs were identified in this study of which 53 are potentially novel sRNAs as they have no Rfam and BSRD homologs. Sixteen sRNAs were randomly selected and validated for differential expression, which largely was found to be in congruence with the RNA-seq data. CONCLUSIONS Differential expression of 468 A. brasilense sRNAs was indicated by RNA-seq data, a subset of which was confirmed by expression analysis. Four of the significantly expressed sRNAs were not observed in nitrogen starvation while 16 sRNAs were found to be exclusively expressed in nitrogen depletion. Putative candidate sRNAs identified have potential mRNA targets primarily involved in stress (abiotic and biotic) adaptability; regulation of bacterial cellular, biological and molecular pathways such as nitrogen fixation, polyhydroxybutyrate synthesis, chemotaxis, biofilm formation and transcriptional regulation. In addition to directly influencing bacteria, some of these sRNAs also have targets influencing plant-microbe interactions through adhesion of bacteria to plant roots directly, suppressing host response, inducing plant defence and signalling.
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Affiliation(s)
- Vatsala Koul
- The Energy and Resources Institute, Darbari Seth Block, India Habitat Centre, Lodhi Road, New Delhi, 110003, India
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, Gurugram-Faridabad Road, Gwal Pahari, Haryana, 122003, India
| | - Divya Srivastava
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, Gurugram-Faridabad Road, Gwal Pahari, Haryana, 122003, India
| | - Pushplata Prasad Singh
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, Gurugram-Faridabad Road, Gwal Pahari, Haryana, 122003, India.
| | - Mandira Kochar
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, Gurugram-Faridabad Road, Gwal Pahari, Haryana, 122003, India.
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McQuail J, Switzer A, Burchell L, Wigneshweraraj S. The RNA-binding protein Hfq assembles into foci-like structures in nitrogen starved Escherichia coli. J Biol Chem 2020; 295:12355-12367. [PMID: 32532816 PMCID: PMC7458820 DOI: 10.1074/jbc.ra120.014107] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/09/2020] [Indexed: 11/13/2022] Open
Abstract
The initial adaptive responses to nutrient depletion in bacteria often occur at the level of gene expression. Hfq is an RNA-binding protein present in diverse bacterial lineages that contributes to many different aspects of RNA metabolism during gene expression. Using photoactivated localization microscopy and single-molecule tracking, we demonstrate that Hfq forms a distinct and reversible focus-like structure in Escherichia coli specifically experiencing long-term nitrogen starvation. Using the ability of T7 phage to replicate in nitrogen-starved bacteria as a biological probe of E. coli cell function during nitrogen starvation, we demonstrate that Hfq foci have a role in the adaptive response of E. coli to long-term nitrogen starvation. We further show that Hfq foci formation does not depend on gene expression once nitrogen starvation has set in and occurs indepen-dently of the transcription factor N-regulatory protein C, which activates the initial adaptive response to N starvation in E. coli These results serve as a paradigm to demonstrate that bacterial adaptation to long-term nutrient starvation can be spatiotemporally coordinated and can occur independently of de novo gene expression during starvation.
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Affiliation(s)
- Josh McQuail
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Amy Switzer
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Lynn Burchell
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Sivaramesh Wigneshweraraj
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
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Phenotypes, transcriptome, and novel biofilm formation associated with the ydcI gene. Antonie Van Leeuwenhoek 2020; 113:1109-1122. [PMID: 32419108 DOI: 10.1007/s10482-020-01412-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/02/2020] [Indexed: 10/24/2022]
Abstract
The ydcI gene has previously been shown to encode a DNA-binding protein involved with acid stress resistance and induced biofilm formation in a strain of Salmonella enterica serovar Typhimurium. In addition, characterisation of the ydcI gene in Escherichia coli and other bacteria demonstrated strikingly different tolerance for induced ydcI expression across Gram negative species. In this report, we investigated the conservation of these phenotypes across multiple strains of S. Typhimurium and E. coli, and we used RNA Seq to identify the transcriptome of the ΔydcI mutant compared to WT in S. Typhimurium and E. coli (to establish the YdcI regulon in each species). We constructed deletion mutants in each species based on the RNA Seq results and tested these mutants for the relevant ydcI-related phenotypes. Though no evidence for a role in these phenotypes was found via the RNA Seq deletion mutants, we found that the ydcI-induced biofilm in S. Typhimurium is formed independently of the major biofilm genes csgA and bcsA indicating a potentially novel type of biofilm formation.
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Gao L, Chen X, Tian Y, Yan Y, Zhan Y, Zhou Z, Zhang W, Lin M, Chen M. The Novel ncRNA OsiR Positively Regulates Expression of katE2 and Is Required for Oxidative Stress Tolerance in Deinococcus radiodurans. Int J Mol Sci 2020; 21:ijms21093200. [PMID: 32366051 PMCID: PMC7247583 DOI: 10.3390/ijms21093200] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/17/2020] [Accepted: 04/28/2020] [Indexed: 02/07/2023] Open
Abstract
Deinococcus radiodurans is a polyextremophilic bacterium well known for its extreme resistance to irradiation, oxidative stress, and other damaging conditions. Many small noncoding RNAs (ncRNAs) in D. radiodurans have been identified by deep sequencing analysis and computational predictions. However, the precise roles of ncRNAs and their target genes in the oxidative stress response have not been investigated. Here, we report the identification and characterization of a novel ncRNA named OsiR (for oxidative stress-induced ncRNA). Oxidative stress tolerance analysis showed that deleting osiR significantly decreased viability, total antioxidant capacity, and catalase activity in D. radiodurans under oxidative stress conditions. Comparative phenotypic and qRT-PCR analyses of an osiR mutant identify a role of OsiR in regulating the expression of the catalase gene katE2. Microscale thermophoresis and genetic complementation showed that a 21-nt sequence in the stem–loop structure of OsiR (204–244 nt) directly base pairs with its counterpart in the coding region of katE2 mRNA (843–866 nt) via a 19 nt region. In addition, deletion of katE2 caused a significant reduction of catalase activity and oxidative stress tolerance similar to that observed in an osiR mutant. Our results show that OsiR positively regulates oxidative stress tolerance in D. radiodurans by increasing the mRNA stability and translation efficiency of katE2. This work provides a new regulatory pathway mediated by ncRNA for the oxidative stress response that most likely contributes to the extreme tolerances of D. radiodurans.
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Leonard S, Meyer S, Lacour S, Nasser W, Hommais F, Reverchon S. APERO: a genome-wide approach for identifying bacterial small RNAs from RNA-Seq data. Nucleic Acids Res 2019; 47:e88. [PMID: 31147705 PMCID: PMC6735904 DOI: 10.1093/nar/gkz485] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 05/06/2019] [Accepted: 05/20/2019] [Indexed: 12/02/2022] Open
Abstract
Small non-coding RNAs (sRNAs) regulate numerous cellular processes in all domains of life. Several approaches have been developed to identify them from RNA-seq data, which are efficient for eukaryotic sRNAs but remain inaccurate for the longer and highly structured bacterial sRNAs. We present APERO, a new algorithm to detect small transcripts from paired-end bacterial RNA-seq data. In contrast to previous approaches that start from the read coverage distribution, APERO analyzes boundaries of individual sequenced fragments to infer the 5′ and 3′ ends of all transcripts. Since sRNAs are about the same size as individual fragments (50–350 nucleotides), this algorithm provides a significantly higher accuracy and robustness, e.g., with respect to spontaneous internal breaking sites. To demonstrate this improvement, we develop a comparative assessment on datasets from Escherichia coli and Salmonella enterica, based on experimentally validated sRNAs. We also identify the small transcript repertoire of Dickeya dadantii including putative intergenic RNAs, 5′ UTR or 3′ UTR-derived RNA products and antisense RNAs. Comparisons to annotations as well as RACE-PCR experimental data confirm the precision of the detected transcripts. Altogether, APERO outperforms all existing methods in terms of sRNA detection and boundary precision, which is crucial for comprehensive genome annotations. It is freely available as an open source R package on https://github.com/Simon-Leonard/APERO
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Affiliation(s)
- Simon Leonard
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, 11 avenue Jean Capelle, F-69621 Villeurbanne, France
| | - Sam Meyer
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, 11 avenue Jean Capelle, F-69621 Villeurbanne, France
| | - Stephan Lacour
- Univ. Grenoble Alpes, CNRS, Inria, LiPhy (UMR5588), 38000 Grenoble, France
| | - William Nasser
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, 11 avenue Jean Capelle, F-69621 Villeurbanne, France
| | - Florence Hommais
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, 11 avenue Jean Capelle, F-69621 Villeurbanne, France
| | - Sylvie Reverchon
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, 11 avenue Jean Capelle, F-69621 Villeurbanne, France
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Barnhill EC, Crucello A, Houserova D, King VM, Amin SV, Roberts JT, Zambrano ME, DeMeis JD, Dahmer DJ, Ijaz Z, Barchie AA, Watters BC, Prusak JE, Dean MA, Holton NW, Ferreira-Filho JA, Sant'Ana AS, Spector MP, Borchert GM. Characterization of novel small RNAs (sRNAs) contributing to the desiccation response of Salmonella enterica serovar Typhimurium. RNA Biol 2019; 16:1643-1657. [PMID: 31390935 DOI: 10.1080/15476286.2019.1653680] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Noncoding RNA (ncRNA) modulation of gene expression has now been ubiquitously observed across all domains of life. An increasingly apparent role of ncRNAs is to coordinate changes in gene expressions in response to environmental stress. Salmonella enterica, a common food-born pathogen, is known for its striking ability to survive, adapt, and thrive in various unfavourable environments which makes it a particularly difficult pathogen to eliminate as well as an interesting model in which to study ncRNA contributions to cellular stress response. Mounting evidence now suggests that small RNAs (sRNAs) represent key regulators of Salmonella stress adaptation. Approximately 50-500 nucleotides in length, sRNAs regulate gene expression through complementary base pairing with molecular targets and have recently been suggested to outnumber protein-coding genes in bacteria. In this work, we employ small RNA transcriptome sequencing to characterize changes in the sRNA profiles of Salmonella in response to desiccation. In all, we identify 102 previously annotated sRNAs significantly differentially expressed during desiccation; and excitingly, 71 novel sRNAs likewise differentially expressed. Small transcript northern blotting and qRT-PCRs confirm the identities and expressions of several of our novel sRNAs, and computational analyses indicate the majority are highly conserved and structurally related to characterized sRNAs. Predicted sRNA targets include several proteins necessary for desiccation survival and this, in part, suggests a role for desiccation-regulated sRNAs in this stress response. Furthermore, we find individual knock-outs of two of the novel sRNAs identified herein, either sRNA1320429 or sRNA3981754, significantly impairs the ability of Salmonella to survive desiccation, confirming their involvements (and suggesting the potential involvements of other sRNAs we identify in this work) in the Salmonella response to desiccation.
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Affiliation(s)
| | - Aline Crucello
- Department of Biology, University of South Alabama , Mobile , AL , USA.,Department of Food Science, University of Campinas , Campinas , Brazil
| | | | - Valeria M King
- Department of Biology, University of South Alabama , Mobile , AL , USA.,Department of Molecular and Cell Biology, University of California Berkeley , Berkeley , CA , USA
| | - Shivam V Amin
- Department of Biology, University of South Alabama , Mobile , AL , USA.,Department of Pharmacology, USA College of Medicine , Mobile , AL , USA
| | - Justin T Roberts
- Department of Biology, University of South Alabama , Mobile , AL , USA.,Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine , Aurora , CO , USA
| | | | - Jeffrey D DeMeis
- Department of Biology, University of South Alabama , Mobile , AL , USA
| | - Donavon J Dahmer
- Department of Biomedical Sciences, University of South Alabama , Mobile , AL , USA
| | - Zara Ijaz
- Department of Biomedical Sciences, University of South Alabama , Mobile , AL , USA
| | - Addison A Barchie
- Department of Biology, University of South Alabama , Mobile , AL , USA
| | - Brianna C Watters
- Department of Biology, University of South Alabama , Mobile , AL , USA
| | - James E Prusak
- Department of Biology, University of South Alabama , Mobile , AL , USA
| | - Meghan A Dean
- Department of Biology, University of South Alabama , Mobile , AL , USA
| | | | - Jaire A Ferreira-Filho
- Center for Molecular Biology and Genetic Engineering, University of Campinas , Campinas , Brazil
| | | | - Michael P Spector
- Department of Biomedical Sciences, University of South Alabama , Mobile , AL , USA
| | - Glen M Borchert
- Department of Biology, University of South Alabama , Mobile , AL , USA.,Department of Pharmacology, USA College of Medicine , Mobile , AL , USA
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14
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Wang D, Li H, Ma X, Tang Y, Tang H, Hu X, Liu Z. Small RNA AvrA Regulates IscR to Increase the Stress Tolerances in SmpB Deficiency of Aeromonas veronii. Front Cell Infect Microbiol 2019; 9:142. [PMID: 31192158 PMCID: PMC6517841 DOI: 10.3389/fcimb.2019.00142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 04/17/2019] [Indexed: 12/13/2022] Open
Abstract
The superbacteria Aeromonas veronii displays not only a strong pathogenicity but also the resistance to nine kinds of antibiotics, resulting in the economic losses and health hazards. Small Protein B (SmpB) plays an important role in protein quality control, virulence, and stress reactions. Transcriptomic data revealed that expressions of the type IV pilus assembly and type VI secretion system (T6SS) proteins were downregulated in SmpB deficiency, indicating that the virulence of A. veronii might be attenuated. Although SmpB deletion decreased colonization in the mouse spleen and liver, LD50 of the smpB mutant was not altered as expected, compared with the wild type. Further, the transcriptomic and quantitative RT-PCR analyses showed that the combination of the downregulated AvrA and the upregulated iron-sulfur protein activator IscR, mediated the oxidative tolerance in smpB deletion. Next a reporter plasmid was constructed in which the promoter of iscR was applied to control the expression of the enhanced green fluorescent protein (eGFP) gene. When the reporter plasmid was co-expressed with the AvrA expression into E. coli, the relative fluorescence intensity was decreased significantly, suggesting that AvrA bound to iscR mRNA by base pairing, which in turn relieved the inhibition of iscR and intensified the downstream iron-sulfur proteins. Collectively, the smpB mutant exhibited an attenuated virulence in mice and enhanced tolerances to oxidative stress. This study demonstrates the complexity of gene regulation networks mediated by sRNA in systems biology, and also reflects the strong adaptability of superbacteria A. veronii in the process of evolution.
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Affiliation(s)
- Dan Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Hong Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Xiang Ma
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Yanqiong Tang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Hongqian Tang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Xinwen Hu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Zhu Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
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15
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Sharma A, Dubey V, Sharma R, Devnath K, Gupta VK, Akhter J, Bhando T, Verma A, Ambatipudi K, Sarkar M, Pathania R. The unusual glycine-rich C terminus of the Acinetobacter baumannii RNA chaperone Hfq plays an important role in bacterial physiology. J Biol Chem 2018; 293:13377-13388. [PMID: 30002121 DOI: 10.1074/jbc.ra118.002921] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/28/2018] [Indexed: 11/06/2022] Open
Abstract
Acinetobacter baumannii is a Gram-negative nosocomial pathogen that causes soft tissue infections in patients who spend a long time in intensive care units. This recalcitrant bacterium is very well known for developing rapid drug resistance, which is a combined outcome of its natural competence and mobile genetic elements. Successful efforts to treat these infections would be aided by additional information on the physiology of A. baumannii Toward that end, we recently reported on a small RNA (sRNA), AbsR25, in this bacterium that regulates the genes of several efflux pumps. Because sRNAs often require the RNA chaperone Hfq for assistance in binding to their cognate mRNA targets, we identified and characterized this protein in A. baumannii The homolog in A. baumannii is a large protein with an extended C terminus unlike Hfqs in other Gram-negative pathogens. The extension has a compositional bias toward glycine and, to a lower extent, phenylalanine and glutamine, suggestive of an intrinsically disordered region. We studied the importance of this glycine-rich tail using truncated versions of Hfq in biophysical assays and complementation of an hfq deletion mutant, finding that the tail was necessary for high-affinity RNA binding. Further tests implicate Hfq in important cellular processes of A. baumannii like metabolism, drug resistance, stress tolerance, and virulence. Our findings underline the importance of the glycine-rich C terminus in RNA binding, ribo-regulation, and auto-regulation of Hfq, demonstrating this hitherto overlooked protein motif to be an indispensable part of the A. baumannii Hfq.
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Affiliation(s)
- Atin Sharma
- From the Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India and
| | - Vineet Dubey
- From the Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India and
| | - Rajnikant Sharma
- From the Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India and
| | - Kuldip Devnath
- From the Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India and
| | - Vivek Kumar Gupta
- From the Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India and
| | - Jawed Akhter
- From the Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India and
| | - Timsy Bhando
- From the Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India and
| | - Aparna Verma
- From the Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India and
| | - Kiran Ambatipudi
- From the Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India and
| | - Mihir Sarkar
- the Division of Physiology and Climatology, ICAR-Indian Veterinary Research Institute, Izatnagar-Bareilly (UP) 243122, India
| | - Ranjana Pathania
- From the Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India and
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16
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Drecktrah D, Hall LS, Rescheneder P, Lybecker M, Samuels DS. The Stringent Response-Regulated sRNA Transcriptome of Borrelia burgdorferi. Front Cell Infect Microbiol 2018; 8:231. [PMID: 30027068 PMCID: PMC6041397 DOI: 10.3389/fcimb.2018.00231] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/19/2018] [Indexed: 12/12/2022] Open
Abstract
The Lyme disease spirochete Borrelia (Borreliella) burgdorferi must tolerate nutrient stress to persist in the tick phase of its enzootic life cycle. We previously found that the stringent response mediated by RelBbu globally regulates gene expression to facilitate persistence in the tick vector. Here, we show that RelBbu regulates the expression of a swath of small RNAs (sRNA), affecting 36% of previously identified sRNAs in B. burgdorferi. This is the first sRNA regulatory mechanism identified in any spirochete. Threefold more sRNAs were RelBbu-upregulated than downregulated during nutrient stress and included antisense, intergenic and 5′ untranslated region sRNAs. RelBbu-regulated sRNAs associated with genes known to be important for host infection (bosR and dhhp) as well as persistence in the tick (glpF and hk1) were identified, suggesting potential mechanisms for post-transcriptional regulation of gene expression.
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Affiliation(s)
- Dan Drecktrah
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Laura S Hall
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Philipp Rescheneder
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, Medical University of Vienna, Vienna, Austria
| | - Meghan Lybecker
- Department of Biology, University of Colorado, Colorado Springs, CO, United States
| | - D Scott Samuels
- Division of Biological Sciences, University of Montana, Missoula, MT, United States.,Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT, United States
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17
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Anderson CJ, Kendall MM. Salmonella enterica Serovar Typhimurium Strategies for Host Adaptation. Front Microbiol 2017; 8:1983. [PMID: 29075247 PMCID: PMC5643478 DOI: 10.3389/fmicb.2017.01983] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/26/2017] [Indexed: 12/21/2022] Open
Abstract
Bacterial pathogens must sense and respond to newly encountered host environments to regulate the expression of critical virulence factors that allow for niche adaptation and successful colonization. Among bacterial pathogens, non-typhoidal serovars of Salmonella enterica, such as serovar Typhimurium (S. Tm), are a primary cause of foodborne illnesses that lead to hospitalizations and deaths worldwide. S. Tm causes acute inflammatory diarrhea that can progress to invasive systemic disease in susceptible patients. The gastrointestinal tract and intramacrophage environments are two critically important niches during S. Tm infection, and each presents unique challenges to limit S. Tm growth. The intestinal tract is home to billions of commensal microbes, termed the microbiota, which limits the amount of available nutrients for invading pathogens such as S. Tm. Therefore, S. Tm encodes strategies to manipulate the commensal population and side-step this nutritional competition. During subsequent stages of disease, S. Tm resists host immune cell mechanisms of killing. Host cells use antimicrobial peptides, acidification of vacuoles, and nutrient limitation to kill phagocytosed microbes, and yet S. Tm is able to subvert these defense systems. In this review, we discuss recently described molecular mechanisms that S. Tm uses to outcompete the resident microbiota within the gastrointestinal tract. S. Tm directly eliminates close competitors via bacterial cell-to-cell contact as well as by stimulating a host immune response to eliminate specific members of the microbiota. Additionally, S. Tm tightly regulates the expression of key virulence factors that enable S. Tm to withstand host immune defenses within macrophages. Additionally, we highlight the chemical and physical signals that S. Tm senses as cues to adapt to each of these environments. These strategies ultimately allow S. Tm to successfully adapt to these two disparate host environments. It is critical to better understand bacterial adaptation strategies because disruption of these pathways and mechanisms, especially those shared by multiple pathogens, may provide novel therapeutic intervention strategies.
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Affiliation(s)
- Christopher J Anderson
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine,, Charlottesville, VA, United States
| | - Melissa M Kendall
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine,, Charlottesville, VA, United States
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18
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Jia K, Wang G, Liang L, Wang M, Wang H, Xu X. Preliminary Transcriptome Analysis of Mature Biofilm and Planktonic Cells of Salmonella Enteritidis Exposure to Acid Stress. Front Microbiol 2017; 8:1861. [PMID: 29018430 PMCID: PMC5622974 DOI: 10.3389/fmicb.2017.01861] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/12/2017] [Indexed: 11/13/2022] Open
Abstract
Salmonella has emerged as a well-recognized food-borne pathogen, with many strains able to form biofilms and thus cause cross-contamination in food processing environments where acid-based disinfectants are widely encountered. In the present study, RNA sequencing was employed to establish complete transcriptome profiles of Salmonella Enteritidis in the forms of planktonic and biofilm-associated cells cultured in Tryptic Soytone Broth (TSB) and acidic TSB (aTSB). The gene expression patterns of S. Enteritidis significantly differed between biofilm-associated and planktonic cells cultivated under the same conditions. The assembled transcriptome of S. Enteritidis in this study contained 5,442 assembled transcripts, including 3,877 differentially expressed genes (DEGs) identified in biofilm and planktonic cells. These DEGs were enriched in terms such as regulation of biological process, metabolic process, macromolecular complex, binding and transferase activity, which may play crucial roles in the biofilm formation of S. Enteritidis cultivated in aTSB. Three significant pathways were observed to be enriched under acidic conditions: bacterial chemotaxis, porphyrin-chlorophyll metabolism and sulfur metabolism. In addition, 15 differentially expressed novel non-coding small RNAs (sRNAs) were identified, and only one was found to be up-regulated in mature biofilms. This preliminary study of the S. Enteritidis transcriptome serves as a basis for future investigations examining the complex network systems that regulate Salmonella biofilm in acidic environments, which provide information on biofilm formation and acid stress interaction that may facilitate the development of novel disinfection procedures in the food processing industry.
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Affiliation(s)
- Kun Jia
- National Center of Meat Quality and Safety Control, Nanjing Agricultural University, Nanjing, China
| | - Guangyu Wang
- Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, Nanjing Agricultural University, Nanjing, China
| | - Lijiao Liang
- National Center of Meat Quality and Safety Control, Nanjing Agricultural University, Nanjing, China
| | - Meng Wang
- National Center of Meat Quality and Safety Control, Nanjing Agricultural University, Nanjing, China
| | - Huhu Wang
- National Center of Meat Quality and Safety Control, Nanjing Agricultural University, Nanjing, China
| | - Xinglian Xu
- Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, Nanjing Agricultural University, Nanjing, China
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19
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Small regulatory bacterial RNAs regulating the envelope stress response. Biochem Soc Trans 2017; 45:417-425. [PMID: 28408482 PMCID: PMC5736990 DOI: 10.1042/bst20160367] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 02/05/2017] [Accepted: 02/07/2017] [Indexed: 12/21/2022]
Abstract
Most bacteria encode a large repertoire of RNA-based regulatory mechanisms. Recent discoveries have revealed that the expression of many genes is controlled by a plethora of base-pairing noncoding small regulatory RNAs (sRNAs), regulatory RNA-binding proteins and RNA-degrading enzymes. Some of these RNA-based regulated processes respond to stress conditions and are involved in the maintenance of cellular homeostasis. They achieve it by either direct posttranscriptional repression of several mRNAs, including blocking access to ribosome and/or directing them to RNA degradation when the synthesis of their cognate proteins is unwanted, or by enhanced translation of some key stress-regulated transcriptional factors. Noncoding RNAs that regulate the gene expression by binding to regulatory proteins/transcriptional factors often act negatively by sequestration, preventing target recognition. Expression of many sRNAs is positively regulated by stress-responsive sigma factors like RpoE and RpoS, and two-component systems like PhoP/Q, Cpx and Rcs. Some of these regulatory RNAs act via a feedback mechanism on their own regulators, which is best reflected by recent discoveries, concerning the regulation of cell membrane composition by sRNAs in Escherichia coli and Salmonella, which are highlighted here.
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