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Goh KJ, Altuvia Y, Argaman L, Raz Y, Bar A, Lithgow T, Margalit H, Gan YH. RIL-seq reveals extensive involvement of small RNAs in virulence and capsule regulation in hypervirulent Klebsiella pneumoniae. Nucleic Acids Res 2024:gkae440. [PMID: 38804271 DOI: 10.1093/nar/gkae440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 04/29/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
Hypervirulent Klebsiella pneumoniae (hvKp) can infect healthy individuals, in contrast to classical strains that commonly cause nosocomial infections. The recent convergence of hypervirulence with carbapenem-resistance in K. pneumoniae can potentially create 'superbugs' that are challenging to treat. Understanding virulence regulation of hvKp is thus critical. Accumulating evidence suggest that posttranscriptional regulation by small RNAs (sRNAs) plays a role in bacterial virulence, but it has hardly been studied in K. pneumoniae. We applied RIL-seq to a prototypical clinical isolate of hvKp to unravel the Hfq-dependent RNA-RNA interaction (RRI) network. The RRI network is dominated by sRNAs, including predicted novel sRNAs, three of which we validated experimentally. We constructed a stringent subnetwork composed of RRIs that involve at least one hvKp virulence-associated gene and identified the capsule gene loci as a hub target where multiple sRNAs interact. We found that the sRNA OmrB suppressed both capsule production and hypermucoviscosity when overexpressed. Furthermore, OmrB base-pairs within kvrA coding region and partially suppresses translation of the capsule regulator KvrA. This agrees with current understanding of capsule as a major virulence and fitness factor. It emphasizes the intricate regulatory control of bacterial phenotypes by sRNAs, particularly of genes critical to bacterial physiology and virulence.
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Affiliation(s)
- Kwok Jian Goh
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Yael Altuvia
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Liron Argaman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yair Raz
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Amir Bar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yunn-Hwen Gan
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
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Ning C, Li N, Wang L, Guo Y, Ji C, Li Z, Shang Y, Zhang X, Sun Y, Huang X, Leng Q, Cai X, Meng Q, Qiao J. STnc1280, a trans-coding sRNA is involved in virulence modulation via targeting gldA mRNA in Salmonella Typhimurium. J Med Microbiol 2024; 73. [PMID: 38353511 DOI: 10.1099/jmm.0.001804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Introduction. Salmonella Typhimurium (STM) is a food-borne Gram-negative bacterium, which can infect humans and a wide range of livestock and poultry, causing a variety of diseases such as septicaemia, enteritis and abortion.Hypothesis/Gap Statement. We will decipher the impacts of sRNA STnc1280 on STM virulence and provide a theoretical basis to reveal the regulatory role and molecular mechanism of STnc1280.Aim. The main objective of this study was to clarify whether sRNA STnc1280 exerts regulatory roles on STM pathogenicity.Methodology. The STnc1280 gene was amplified and its molecular characteristics were analysed in this study. Then, STnc1280 gene deletion strain (STM-ΔSTnc1280) and the complementary strain (ΔSTnc1280/STnc1280) were constructed by λ-Red homologous recombination method, respectively, to analyse of adhesion and invasive ability and pathogenicity of different strains. Subsequently, the potential target gene regulated by STnc1280 was predicted using target RNA2 software, followed by the verification of the interaction between STnc1280 and target mRNA using the dual plasmid reporter system (DPRS). Furthermore, the mRNA and protein level of target gene was determined using qRT-PCR and Western blot, respectively.Results. The results revealed that the cell adhesion and invasive ability and pathogenicity of STM-ΔSTnc1280 were significantly reduced compared to STM-SL1344 strain, indicating that the deficiency of STnc1280 gene significantly influenced STM pathogenicity. The DPRS results showed that STnc1280 can interact with the mRNA of target gene gldA, thus suppressing the expression of lacZ gene. Furthermore, the level of gldA mRNA was not influenced in STM-ΔSTnc1280, but the expression of GldA protein decreased significantly.Conclusion. Combining the bioinformatic analysis, these findings suggested that STnc1280 may bind to the SD sequence of gldA mRNA, hindering the binding of ribosomes to gldA mRNA, thereby inhibiting the expression of GldA protein to modulate the virulence of STM.
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Affiliation(s)
- Chengcheng Ning
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, PR China
- College of Animal Science and Technology, Xinjiang Agricultural Vocational and Technical College, Changji, Xinjiang, 831100, PR China
| | - Na Li
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Lixia Wang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Yun Guo
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Chunhui Ji
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Zhiyuan Li
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Yunxia Shang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Xingxing Zhang
- Institute of Animal Science and Veterinary Research, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, Xinjiang, 832000, PR China
| | - Yaoqiang Sun
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Xiaoxing Huang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Qingwen Leng
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Xuepeng Cai
- State Key Lab of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, PR China
| | - Qingling Meng
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Jun Qiao
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, PR China
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A Small RNA, SaaS, Promotes Salmonella Pathogenicity by Regulating Invasion, Intracellular Growth, and Virulence Factors. Microbiol Spectr 2023; 11:e0293822. [PMID: 36688642 PMCID: PMC9927236 DOI: 10.1128/spectrum.02938-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Salmonella enterica serovar Enteritidis is a common foodborne pathogen that infects both humans and animals. The S. Enteritidis virulence regulation network remains largely incomplete, and knowledge regarding the specific virulence phenotype of small RNAs (sRNAs) is limited. Here, we investigated the role of a previously identified sRNA, Salmonella adhesive-associated sRNA (SaaS), in the virulence phenotype of S. Enteritidis by constructing mutant (ΔsaaS) and complemented (ΔsaaS/psaaS) strains. SaaS did not affect S. Enteritidis; it was activated in the simulated intestinal environment (SIE), regulating the expression of virulence target genes. We discovered that it directly binds ssaV mRNA. Caco-2 and RAW 264.7 cell assays revealed that SaaS promoted S. Enteritidis invasion and damage to epithelial cells while suppressing macrophage overgrowth and destruction. Furthermore, a BALB/c mouse model demonstrated that the deletion of SaaS significantly reduced mortality and attenuated the deterioration of pathophysiology, bacterial dissemination into systemic circulation, and systemic inflammation. Our findings indicate that SaaS is required for S. Enteritidis virulence and further highlight its biological role in bacterial pathogenesis. IMPORTANCE Salmonella is a zoonotic pathogen with high virulence worldwide, and sRNAs have recently been discovered to play important roles. We explored the biological characteristics of the sRNA SaaS and developed two cell infection models and a mouse infection model. SaaS is an SIE-responsive sRNA that regulates the expression of virulence-targeted genes. Additionally, it differentially mediates invasion and intracellular growth for survival and infection of the epithelium and macrophages. We further found that SaaS enhanced bacterial virulence by promoting lethality, colonization, and inflammatory response. These findings provide a better understanding of the critical role of sRNA in bacterial virulence.
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Small RNAs Activate Salmonella Pathogenicity Island 1 by Modulating mRNA Stability through the hilD mRNA 3' Untranslated Region. J Bacteriol 2023; 205:e0033322. [PMID: 36472436 PMCID: PMC9879128 DOI: 10.1128/jb.00333-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Salmonella enterica serovar Typhimurium is an enteric pathogen associated with foodborne disease. Salmonella invades the intestinal epithelium using a type three secretion system encoded on Salmonella pathogenicity island 1 (SPI-1). SPI-1 genes are tightly regulated by a complex feed-forward loop to ensure proper spatial and temporal expression. Most regulatory input is integrated at HilD, through control of hilD mRNA translation or HilD protein activity. The hilD mRNA possesses a 310-nucleotide 3' untranslated region (UTR) that influences HilD and SPI-1 expression, and this regulation is dependent on Hfq and RNase E, cofactors known to mediate small RNA (sRNA) activities. Thus, we hypothesized that the hilD mRNA 3' UTR is a target for sRNAs. Here, we show that two sRNAs, SdsR and Spot 42, regulate SPI-1 by targeting different regions of the hilD mRNA 3' UTR. Regulatory activities of these sRNAs depended on Hfq and RNase E, in agreement with previous roles found for both at the hilD 3' UTR. Salmonella mutants lacking SdsR and Spot 42 had decreased virulence in a mouse model of infection. Collectively, this work suggests that these sRNAs targeting the hilD mRNA 3' UTR increase hilD mRNA levels by interfering with RNase E-dependent mRNA degradation and that this regulatory effect is required for Salmonella invasiveness. Our work provides novel insights into mechanisms of sRNA regulation at bacterial mRNA 3' UTRs and adds to our knowledge of post-transcriptional regulation of the SPI-1 complex feed-forward loop. IMPORTANCE Salmonella enterica serovar Typhimurium is a prominent foodborne pathogen, infecting millions of people a year. To express virulence genes at the correct time and place in the host, Salmonella uses a complex regulatory network that senses environmental conditions. Known for their role in allowing quick responses to stress and virulence conditions, we investigated the role of small RNAs in facilitating precise expression of virulence genes. We found that the 3' untranslated region of the hilD mRNA, encoding a key virulence regulator, is a target for small RNAs and RNase E. The small RNAs stabilize hilD mRNA to allow proper expression of Salmonella virulence genes in the host.
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Gene Regulatory Network of the Noncoding RNA Qrr5 Involved in the Cytotoxicity of Vibrio parahaemolyticus during Infection. Microorganisms 2022; 10:microorganisms10102084. [PMID: 36296357 PMCID: PMC9610228 DOI: 10.3390/microorganisms10102084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/09/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022] Open
Abstract
Small non-coding RNAs (sRNAs) in bacteria are important regulatory molecules for controlling virulence. In Vibrio spp., Qrr sRNAs are critical for quorum-sensing pathways and regulating the release of some virulence factors. However, the detailed role of Qrr sRNAs in the virulence of Vibrio parahaemolyticus remains poorly understood. In this study, we identified a Vibrio sRNA Qrr5 that positively regulates cytotoxicity and adherence in Caco-2 cells by primarily regulating the T3SS1 gene cluster. A number of 185, 586, 355, and 74 differentially expressed genes (DEGs) detected at 0, 2, 4, and 6 h post-infection, respectively, were mainly associated with ABC transporters and two-component system pathways. The DEGs exhibited a dynamic change in expression at various time points post-infection owing to the deletion of Qrr5. Accordingly, 17 related genes were identified in the co-expression network, and their interaction with Qrr5 was determined based on weighted co-expression network analysis during infection. Taken together, our results provide a comprehensive transcriptome profile of V. parahaemolyticus during infection in Caco-2 cells.
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Cui Z, Zhang Y, Kakar KU, Kong X, Li R, Loh B, Leptihn S, Li B. Involvement of non-coding RNAs during infection of rice by Acidovorax oryzae. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:540-554. [PMID: 34121356 DOI: 10.1111/1758-2229.12982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 06/12/2023]
Abstract
The expression of non-coding RNAs (ncRNAs) has been observed in a variety of bacteria. However, the function of ncRNAs and their regulatory targets are largely unknown, and few ncRNAs are found to be associated with bacterial virulence. The bacterial brown stripe pathogen Acidovorax oryzae (Ao) RS-1 shows a high level of condition-dependent differential expression of ncRNA, which we identified in a genome wide screen. We experimentally validated 66 differentially expressed ncRNAs using an integrative analysis of conservative genome sequences and transcriptomic data during in vivo interaction of the bacterial pathogen with the rice plant. To test the relevance of the differentially expressed ncRNAs, we chose four with different positions within the genome, and with different secondary structures and promoter activities. The results show that the overexpression of the four ncRNAs caused a significant change in virulence-related phenotypes, resistance to various environmental stresses, expression of secretion systems and effector proteins, while changing the expression of ncRNA putative target genes. We conclude that these ncRNAs are examples for the inherent regulatory roles for many of the observed ncRNAs in response to changing conditions such as host interaction or environmental adaption.
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Affiliation(s)
- Zhouqi Cui
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, 06511, USA
| | - Yang Zhang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, China
| | - Kaleem U Kakar
- Department of Microbiology, University of Balochistan, Quetta, Pakistan
| | - Xiangdong Kong
- Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Ruihui Li
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Belinda Loh
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Hangzhou, 314400, China
| | - Sebastian Leptihn
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Hangzhou, 314400, China
| | - Bin Li
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
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Peñaloza D, Acuña LG, Barros MJ, Núñez P, Montt F, Gil F, Fuentes JA, Calderón IL. The Small RNA RyhB Homologs from Salmonella Typhimurium Restrain the Intracellular Growth and Modulate the SPI-1 Gene Expression within RAW264.7 Macrophages. Microorganisms 2021; 9:microorganisms9030635. [PMID: 33803635 PMCID: PMC8002944 DOI: 10.3390/microorganisms9030635] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/21/2022] Open
Abstract
Growing evidence indicates that small noncoding RNAs (sRNAs) play important regulatory roles during bacterial infection. In Salmonella Typhimurium, several sRNAs are strongly up-regulated within macrophages, but little is known about their role during the infection process. Among these sRNAs, the well-characterized paralogs RyhB-1 and RyhB-2 are two regulators of gene expression mainly related with the response to iron availability. To investigate the role of the sRNAs RyhB-1 and RyhB-2 from S. Typhimurium in the infection of RAW264.7 macrophages, we analyzed several phenotypic traits from intracellular mutant strains lacking one and both sRNAs. Deletion of RyhB-1 and/or RyhB-2 resulted in increased intracellular survival and faster replication within macrophages. The bacterial metabolic status inside macrophages was also analyzed, revealing that all the mutant strains exhibited higher intracellular levels of ATP and lower NAD+/NADH ratios than the wild type. Expression analyses from bacteria infecting macrophages showed that RyhB-1 and RyhB-2 affect the intra-macrophage expression of bacterial genes associated with the Salmonella pathogenicity island 1 (SPI-1) and the type III secretion system (T3SS). With a two-plasmid system and compensatory mutations, we confirmed that RyhB-1 and RyhB-2 directly interact with the mRNAs of the invasion chaperone SicA and the regulatory protein RtsB. Altogether, these results indicate that the RyhB homologs contribute to the S. Typhimurium virulence modulation inside macrophages by reducing the intracellular growth and down-regulating the SPI-1 gene expression.
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Affiliation(s)
- Diego Peñaloza
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, 8370186 Santiago, Chile; (D.P.); (L.G.A.); (M.J.B.); (P.N.); (F.M.)
| | - Lillian G. Acuña
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, 8370186 Santiago, Chile; (D.P.); (L.G.A.); (M.J.B.); (P.N.); (F.M.)
| | - M. José Barros
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, 8370186 Santiago, Chile; (D.P.); (L.G.A.); (M.J.B.); (P.N.); (F.M.)
| | - Paula Núñez
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, 8370186 Santiago, Chile; (D.P.); (L.G.A.); (M.J.B.); (P.N.); (F.M.)
| | - Fernanda Montt
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, 8370186 Santiago, Chile; (D.P.); (L.G.A.); (M.J.B.); (P.N.); (F.M.)
| | - Fernando Gil
- Microbiota-Host Interactions and Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, 8370186 Santiago, Chile
- ANID-Millennium Science Initiative Program-Millennium Nucleus in the Biology of the Intestinal Microbiota, 8370186 Santiago, Chile
- Correspondence: (F.G.); (J.A.F.); (I.L.C.); Tel.: +56-2-2770-3065 (F.G.); +56-2-2661-8373 (J.A.F.); +56-2-2770-3422 (I.L.C.)
| | - Juan A. Fuentes
- Laboratorio de Genética y Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, 8370186 Santiago, Chile
- Correspondence: (F.G.); (J.A.F.); (I.L.C.); Tel.: +56-2-2770-3065 (F.G.); +56-2-2661-8373 (J.A.F.); +56-2-2770-3422 (I.L.C.)
| | - Iván L. Calderón
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, 8370186 Santiago, Chile; (D.P.); (L.G.A.); (M.J.B.); (P.N.); (F.M.)
- Correspondence: (F.G.); (J.A.F.); (I.L.C.); Tel.: +56-2-2770-3065 (F.G.); +56-2-2661-8373 (J.A.F.); +56-2-2770-3422 (I.L.C.)
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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: 3] [Impact Index Per Article: 1.0] [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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9
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Kim S, Lee YH. Impact of small RNA RaoN on nitrosative-oxidative stress resistance and virulence of Salmonella enterica serovar Typhimurium. J Microbiol 2020; 58:499-506. [PMID: 32279276 DOI: 10.1007/s12275-020-0027-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/13/2020] [Accepted: 03/05/2020] [Indexed: 12/26/2022]
Abstract
RaoN is a Salmonella-specific small RNA that is encoded in the cspH-envE intergenic region on Salmonella pathogenicity island-11. We previously reported that RaoN is induced under conditions of acid and oxidative stress combined with nutrient limitation, contributing to the intramacrophage growth of Salmonella enterica serovar Typhimurium. However, the role of RaoN in nitrosative stress response and virulence has not yet been elucidated. Here we show that the raoN mutant strain has increased susceptibility to nitrosative stress by using a nitric oxide generating acidified nitrite. Extending previous research on the role of RaoN in oxidative stress resistance, we found that NADPH oxidase inhibition restores the growth of the raoN mutant in LPS-treated J774A.1 macrophages. Flow cytometry analysis further revealed that the inactivation of raoN leads to an increase in the intracellular level of reactive oxygen species (ROS) in Salmonella-infected macrophages, suggesting that RaoN is involved in the inhibition of NADPH oxidase-mediated ROS production by mechanisms not yet resolved. Moreover, we evaluated the effect of raoN mutation on the virulence in murine systemic infection and determined that the raoN mutant is less virulent than the wild-type strain following oral inoculation. In conclusion, small regulatory RNA RaoN controls nitrosative-oxidative stress resistance and is required for virulence of Salmonella in mice.
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Affiliation(s)
- Sinyeon Kim
- School of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Yong Heon Lee
- Department of Biomedical Laboratory Science, Dongseo University, Busan, 47011, Republic of Korea.
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10
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Cameron TA, Matz LM, Sinha D, De Lay NR. Polynucleotide phosphorylase promotes the stability and function of Hfq-binding sRNAs by degrading target mRNA-derived fragments. Nucleic Acids Res 2019; 47:8821-8837. [PMID: 31329973 PMCID: PMC7145675 DOI: 10.1093/nar/gkz616] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 07/02/2019] [Accepted: 07/11/2019] [Indexed: 01/14/2023] Open
Abstract
In many Gram-negative and some Gram-positive bacteria, small regulatory RNAs (sRNAs) that bind the RNA chaperone Hfq have a pivotal role in modulating virulence, stress responses, metabolism and biofilm formation. These sRNAs recognize transcripts through base-pairing, and sRNA–mRNA annealing consequently alters the translation and/or stability of transcripts leading to changes in gene expression. We have previously found that the highly conserved 3′-to-5′ exoribonuclease polynucleotide phosphorylase (PNPase) has an indispensable role in paradoxically stabilizing Hfq-bound sRNAs and promoting their function in gene regulation in Escherichia coli. Here, we report that PNPase contributes to the degradation of specific short mRNA fragments, the majority of which bind Hfq and are derived from targets of sRNAs. Specifically, we found that these mRNA-derived fragments accumulate in the absence of PNPase or its exoribonuclease activity and interact with PNPase. Additionally, we show that mutations in hfq or in the seed pairing region of some sRNAs eliminated the requirement of PNPase for their stability. Altogether, our results are consistent with a model that PNPase degrades mRNA-derived fragments that could otherwise deplete cells of Hfq-binding sRNAs through pairing-mediated decay.
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Affiliation(s)
- Todd A Cameron
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Lisa M Matz
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Dhriti Sinha
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Nicholas R De Lay
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, The University of Texas Health Science Center, Houston, TX 77030, USA
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11
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Meng X, Meng X, Wang J, Wang H, Zhu C, Ni J, Zhu G. Small non-coding RNA STnc640 regulates expression of fimA fimbrial gene and virulence of Salmonella enterica serovar Enteritidis. BMC Vet Res 2019; 15:319. [PMID: 31488137 PMCID: PMC6727533 DOI: 10.1186/s12917-019-2066-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 08/27/2019] [Indexed: 12/25/2022] Open
Abstract
Background Small non-coding RNAs (sRNAs) regulate bacterial gene expression at the post-transcriptional level. STnc640 is a type of sRNA that was identified in Salmonella Typhimurium. Results In this study, STnc640 in Salmonella Enteritidis was confirmed to be an Hfq-dependent sRNA. TargetRNA software analysis showed that fimbrial genes fimA and bcfA were likely to be the target genes of STnc640. To investigate the target mRNAs and function of STnc640 in pathogenicity, we constructed the deletion mutant strain 50336△stnc640 and the complemented strain 50336△stnc640/pstnc640 in Salmonella Enteritidis 50336. The RT-qPCR results showed that the mRNA level of fimA was decreased, while bcfA was unchanged in 50336△stnc640 compared with that in the wild type (WT) strain. The adhesion ability of 50336△stnc640 to Caco-2 cells was increased compared to the 50336 WT strain. The virulence of 50336△stnc640 was enhanced in a one-day-old chicken model of S. Enteritidis disease as determined by quantifying the 50% lethal dose (LD50) of the bacterial strains. Conclusions The results demonstrate that STnc640 contributes to the virulence of Salmonella Enteritidis.
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Affiliation(s)
- Xia Meng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
| | - Xianchen Meng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Jinqiu Wang
- Department of Animal Husbandry and Veterinary Medicine, Beijing Vocational College of Agriculture, Beijing, 102442, China
| | - Heng Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Chunhong Zhu
- Jiangsu provincial key lab for genetics and breeding of poultry, Jiangsu Institute of Poultry Science, Yangzhou, 225125, China
| | - Jie Ni
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
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12
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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: 9] [Impact Index Per Article: 1.8] [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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13
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YshB Promotes Intracellular Replication and Is Required for Salmonella Virulence. J Bacteriol 2019; 201:JB.00314-19. [PMID: 31182500 DOI: 10.1128/jb.00314-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 06/07/2019] [Indexed: 11/20/2022] Open
Abstract
Salmonella virulence requires the initial invasion of host cells, followed by modulation of the intracellular environment for survival and replication. In an effort to characterize the role of small RNAs in Salmonella pathogenesis, we inadvertently identified a 5-kDa protein named YshB that is involved in the intracellular survival of Salmonella We show here that yshB expression is upregulated upon entry into macrophages. When yshB expression is upregulated before bacterial entry, invasion efficiency is inhibited. Lack of YshB resulted in reduced bacterial survival within the macrophages and led to reduced virulence in a mouse model of infection.IMPORTANCE Salmonella gastroenteritis is one of the most common causes of foodborne disease, possibly affecting millions of people globally each year. Here we characterize the role of a novel small protein, YshB, in mediating Salmonella intracellular survival. This elucidation adds to the body of knowledge regarding how this bacterium achieves intracellular survival.
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14
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Sinha D, Matz LM, Cameron TA, De Lay NR. Poly(A) polymerase is required for RyhB sRNA stability and function in Escherichia coli. RNA (NEW YORK, N.Y.) 2018; 24:1496-1511. [PMID: 30061117 PMCID: PMC6191717 DOI: 10.1261/rna.067181.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/24/2018] [Indexed: 05/05/2023]
Abstract
Small regulatory RNAs (sRNAs) are an important class of bacterial post-transcriptional regulators that control numerous physiological processes, including stress responses. In Gram-negative bacteria including Escherichia coli, the RNA chaperone Hfq binds many sRNAs and facilitates pairing to target transcripts, resulting in changes in mRNA transcription, translation, or stability. Here, we report that poly(A) polymerase (PAP I), which promotes RNA degradation by exoribonucleases through the addition of poly(A) tails, has a crucial role in the regulation of gene expression by Hfq-dependent sRNAs. Specifically, we show that deletion of pcnB, encoding PAP I, paradoxically resulted in an increased turnover of certain Hfq-dependent sRNAs, including RyhB. RyhB instability in the pcnB deletion strain was suppressed by mutations in hfq or ryhB that disrupt pairing of RyhB with target RNAs, by mutations in the 3' external transcribed spacer of the glyW-cysT-leuZ transcript (3'ETSLeuZ) involved in pairing with RyhB, or an internal deletion in rne, which encodes the endoribonuclease RNase E. Finally, the reduced stability of RyhB in the pcnB deletion strain resulted in impaired regulation of some of its target mRNAs, specifically sodB and sdhCDAB. Altogether our data support a model where PAP I plays a critical role in ensuring the efficient decay of the 3'ETSLeuZ In the absence of PAP I, the 3'ETSLeuZ transcripts accumulate, bind Hfq, and pair with RyhB, resulting in its depletion via RNase E-mediated decay. This ultimately leads to a defect in RyhB function in a PAP I deficient strain.
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Affiliation(s)
- Dhriti Sinha
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Lisa M Matz
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Todd A Cameron
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Nicholas R De Lay
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas 77030, USA
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15
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Transcriptome-Wide Analysis of Protein-RNA and RNA-RNA Interactions in Pathogenic Bacteria. Methods Enzymol 2018; 612:467-488. [PMID: 30502953 DOI: 10.1016/bs.mie.2018.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Regulatory RNAs and RNA-binding proteins (RBPs) play critical roles in virulence gene expression in pathogenic bacteria. A wealth of regulatory RNAs have been identified in bacterial pathogens using RNA-seq and recent technical advances are uncovering their mRNA targets. UV-crosslinking is a powerful tool for identifying protein binding sites throughout the transcriptome providing base-pair resolution of sites in vivo. With minor modifications to the protocol, RNA-RNA interactions can also be captured by proximity-dependent ligation of RNA pairs on the protein. Here, we described a high-stringency UV-crosslinking method for recovery of both protein-RNA interactions (CRAC) and RNA-RNA interactions occurring on the bait protein (CLASH). These analyses provide complementary data that provide insights into RBP, and regulatory RNA function.
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16
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Malabirade A, Habier J, Heintz-Buschart A, May P, Godet J, Halder R, Etheridge A, Galas D, Wilmes P, Fritz JV. The RNA Complement of Outer Membrane Vesicles From Salmonella enterica Serovar Typhimurium Under Distinct Culture Conditions. Front Microbiol 2018; 9:2015. [PMID: 30214435 PMCID: PMC6125333 DOI: 10.3389/fmicb.2018.02015] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/09/2018] [Indexed: 12/20/2022] Open
Abstract
Bacterial outer membrane vesicles (OMVs), as well as OMV-associated small RNAs, have been demonstrated to play a role in host-pathogen interactions. The presence of larger RNA transcripts in OMVs has been less studied and their potential role in host-pathogen interactions remains largely unknown. Here we analyze RNA from OMVs secreted by Salmonella enterica serovar Typhimurium (S. Typhimurium) cultured under different conditions, which mimic host-pathogen interactions. S. Typhimurium was grown to exponential and stationary growth phases in minimal growth control medium (phosphate-carbon-nitrogen, PCN), as well as in acidic and phosphate-depleted PCN, comparable to the macrophage environment and inducing therefore the expression of Salmonella pathogenicity island 2 (SPI-2) genes. Moreover, Salmonella pathogenicity island 1 (SPI-1), which is required for virulence during the intestinal phase of infection, was induced by culturing S. Typhimurium to the stationary phase in Lysogeny Broth (LB). For each condition, we identified OMV-associated RNAs that are enriched in the extracellular environment relative to the intracellular space. All RNA classes could be observed, but a vast majority of rRNA was exported in all conditions in variable proportions with a notable decrease in LB SPI-1 inducing media. Several mRNAs and ncRNAs were specifically enriched in/on OMVs dependent on the growth conditions. Important to note is that some RNAs showed identical read coverage profiles intracellularly and extracellularly, whereas distinct coverage patterns were observed for other transcripts, suggesting a specific processing or degradation. Moreover, PCR experiments confirmed that distinct RNAs were present in or on OMVs as full-length transcripts (IsrB-1/2; IsrA; ffs; SsrS; CsrC; pSLT035; 10Sa; rnpB; STM0277; sseB; STM0972; STM2606), whereas others seemed to be rather present in a processed or degraded form. Finally, we show by a digestion protection assay that OMVs are able to prevent enzymatic degradation of given full-length transcripts (SsrS, CsrC, 10Sa, and rnpB). In summary, we show that OMV-associated RNA is clearly different in distinct culture conditions and that at least a fraction of the extracellular RNA is associated as a full-length transcripts with OMVs, indicating that some RNAs are protected by OMVs and thereby leaving open the possibility that those might be functionally active.
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Affiliation(s)
- Antoine Malabirade
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Janine Habier
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Anna Heintz-Buschart
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Julien Godet
- UMR CNRS 7021, Laboratoire de BioImagerie et Pathologies, Université de Strasbourg, Strasbourg, France
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Alton Etheridge
- Pacific Northwest Research Institute, Seattle, WA, United States
| | - David Galas
- Pacific Northwest Research Institute, Seattle, WA, United States
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Joëlle V Fritz
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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17
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Small RNA profiling in Mycobacterium tuberculosis identifies MrsI as necessary for an anticipatory iron sparing response. Proc Natl Acad Sci U S A 2018; 115:6464-6469. [PMID: 29871950 PMCID: PMC6016810 DOI: 10.1073/pnas.1718003115] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
This work describes the most extensive discovery and functional characterization of small regulatory RNAs (sRNAs) in Mycobacterium tuberculosis to date. We comprehensively define the sRNAs expressed in M. tuberculosis under five host-like stress conditions. This reference dataset comprehensively defines the expression patterns and boundaries of mycobacterial sRNAs. We perform in-depth characterization of one sRNA, mycobacterial regulatory sRNA in iron (MrsI), which is induced in M. tuberculosis in multiple stress conditions. MrsI is critical for the iron-sparing response in mycobacteria by binding directly to mRNAs encoding nonessential iron-containing proteins to repress their expression. Interestingly, MrsI acts in an anticipatory manner, in which its induction by a variety of stresses primes M. tuberculosis to enter an iron-sparing state more rapidly upon iron deprivation. One key to the success of Mycobacterium tuberculosis as a pathogen is its ability to reside in the hostile environment of the human macrophage. Bacteria adapt to stress through a variety of mechanisms, including the use of small regulatory RNAs (sRNAs), which posttranscriptionally regulate bacterial gene expression. However, very little is currently known about mycobacterial sRNA-mediated riboregulation. To date, mycobacterial sRNA discovery has been performed primarily in log-phase growth, and no direct interaction between any mycobacterial sRNA and its targets has been validated. Here, we performed large-scale sRNA discovery and expression profiling in M. tuberculosis during exposure to five pathogenically relevant stresses. From these data, we identified a subset of sRNAs that are highly induced in multiple stress conditions. We focused on one of these sRNAs, ncRv11846, here renamed mycobacterial regulatory sRNA in iron (MrsI). We characterized the regulon of MrsI and showed in mycobacteria that it regulates one of its targets, bfrA, through a direct binding interaction. MrsI mediates an iron-sparing response that is required for optimal survival of M. tuberculosis under iron-limiting conditions. However, MrsI is induced by multiple host-like stressors, which appear to trigger MrsI as part of an anticipatory response to impending iron deprivation in the macrophage environment.
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18
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Biological and regulatory roles of acid-induced small RNA RyeC in Salmonella Typhimurium. Biochimie 2018; 150:48-56. [PMID: 29730297 DOI: 10.1016/j.biochi.2018.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/01/2018] [Indexed: 12/23/2022]
Abstract
Salmonella Typhimurium is an enteric pathogen that has evolved masterful strategies to enable survival under stress conditions both within and outside a host. The acid tolerance response (ATR) is one such mechanism that enhances the viability of acid adapted bacteria to lethal pH levels. While numerous studies exist on the protein coding components of this response, there is very little data on the roles of small RNAs (sRNAs). These non-coding RNA molecules have recently been shown to play roles as regulators of bacterial stress response and virulence pathways. They function through complementary base pairing interactions with target mRNAs and affect their translation and/or stability. There are also a few that directly bind to proteins by mimicking their respective targets. Here, we identify several sRNAs expressed during the ATR of S. Typhimurium and characterize one highly induced candidate, RyeC. Further, we identify ptsI as a trans-encoded target that is directly regulated by this sRNA. From a functional perspective, over-expression of RyeC in Salmonella produced a general attenuation of several in vitro phenotypes including acid survival, motility, adhesion and invasion of epithelial cell lines as well as replication within macrophages. Together, this study highlights the diverse roles played by sRNAs in acid tolerance and virulence of S. Typhimurium.
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19
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Zhang S, Liu S, Wu N, Yuan Y, Zhang W, Zhang Y. Small Non-coding RNA RyhB Mediates Persistence to Multiple Antibiotics and Stresses in Uropathogenic Escherichia coli by Reducing Cellular Metabolism. Front Microbiol 2018; 9:136. [PMID: 29467745 PMCID: PMC5808207 DOI: 10.3389/fmicb.2018.00136] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/22/2018] [Indexed: 11/25/2022] Open
Abstract
As dormant phenotypic variants of bacteria, persisters account for many chronic infections affecting human health. Despite numerous studies, the role of small non-coding RNA (sRNA) in bacterial persistence has not been reported. To investigate the role of Hfq-interacting sRNA in persistence, we constructed the deletion mutants of 20 Hfq-interacting sRNAs (RyhB, GcvB, MgrR, RybB, MicF, SgrS, RprA, DicF, SsrS, FnrS, GadY, DsrA, OmrB, ArcZ, RyeB, RydC, OmrA, MicA, MicC, and ChiX) to assess their persistence capacity in uropathogenic Escherichia coli strain UTI89 and identified a new sRNA RyhB being involved in persister formation. The ryhB-knockout mutant had significant defect in persistence to a diverse range of antibiotics (levofloxacin, cefotaxime, gentamicin) and stresses (hyperosmosis, acid, and heat) in both exponential phase and stationary phase. In addition, the effect of RyhB on persistence was synergistic with ppGpp and Fur protein. RNA-Seq analysis indicated that the ryhB-knockout mutant had a hyperactive metabolic state compared with the parent strain. Interestingly, increased adenosine triphosphate (ATP) levels and altered NAD+/NADH ratios were observed in the ryhB-knockout mutant. Our findings represent a new level of persistence regulation via sRNA and may provide novel therapeutic targets for interventions.
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Affiliation(s)
- Shanshan Zhang
- Key Lab of Molecular Virology, Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Shuang Liu
- Key Lab of Molecular Virology, Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Nan Wu
- Key Lab of Molecular Virology, Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Youhua Yuan
- Key Lab of Molecular Virology, Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Key Lab of Molecular Virology, Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Ying Zhang
- Key Lab of Molecular Virology, Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.,Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
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20
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Barquist L, Westermann AJ, Vogel J. Molecular phenotyping of infection-associated small non-coding RNAs. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2016.0081. [PMID: 27672158 DOI: 10.1098/rstb.2016.0081] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2016] [Indexed: 02/07/2023] Open
Abstract
Infection is a complicated balance, with both pathogen and host struggling to tilt the result in their favour. Bacterial infection biology has relied on forward genetics for many of its advances, defining phenotype in terms of replication in model systems. However, many known virulence factors fail to produce robust phenotypes, particularly in the systems most amenable to genetic manipulation, such as cell-culture models. This has particularly been limiting for the study of the bacterial regulatory small RNAs (sRNAs) in infection. We argue that new sequencing-based technologies can work around this problem by providing a 'molecular phenotype', defined in terms of the specific transcriptional dysregulation in the infection system induced by gene deletion. We illustrate this using the example of our recent study of the PinT sRNA using dual RNA-seq, that is, simultaneous RNA sequencing of host and pathogen during infection. We additionally discuss how other high-throughput technologies, in particular genetic interaction mapping using transposon insertion sequencing, may be used to further dissect molecular phenotypes. We propose a strategy for how high-throughput technologies can be integrated in the study of non-coding regulators as well as bacterial virulence factors, enhancing our ability to rapidly generate hypotheses with regards to their function.This article is part of the themed issue 'The new bacteriology'.
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Affiliation(s)
- Lars Barquist
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany
| | - Alexander J Westermann
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany Research Centre for Infectious Diseases (ZINF), University of Würzburg, 97070 Würzburg, Germany
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21
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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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Ren J, Sang Y, Qin R, Cui Z, Yao YF. 6S RNA is involved in acid resistance and invasion of epithelial cells in Salmonella enterica serovar Typhimurium. Future Microbiol 2017; 12:1045-1057. [PMID: 28796533 DOI: 10.2217/fmb-2017-0055] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
AIM Acid is an important environmental condition encountered frequently by Salmonella enterica serovar Typhimurium during its pathogenesis, but the role of small-noncoding RNAs (sRNAs) in response to acid stress is poorly understood. METHODS We used RNA sequencing to explore acid-responsive sRNAs in S. Typhimurium. RESULTS It identified that 6S RNA encoded by the ssrS was significantly upregulated at pH 3.0. The 6S RNA knockout strain showed a reduced ability to survive at pH 3.0. Additionally, genes in Salmonella pathogenicity island-1 were downregulated in the 6S RNA knockout strain. The loss of 6S RNA significantly reduced S. Typhimurium invasion ability in HeLa cells and virulence in a mouse model. CONCLUSION These findings demonstrate that 6S RNA plays an important role in S. Typhimurium survival under extremely acid conditions and for invasion of epithelial cells.
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Affiliation(s)
- Jie Ren
- Department of Microbiology & Immunology, Laboratory of Bacterial Pathogenesis, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu Sang
- Department of Microbiology & Immunology, Laboratory of Bacterial Pathogenesis, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ran Qin
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu-Feng Yao
- Department of Microbiology & Immunology, Laboratory of Bacterial Pathogenesis, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
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Abstract
Bacterial pathogens must endure or adapt to different environments and stresses during transmission and infection. Posttranscriptional gene expression control by regulatory RNAs, such as small RNAs and riboswitches, is now considered central to adaptation in many bacteria, including pathogens. The study of RNA-based regulation (riboregulation) in pathogenic species has provided novel insight into how these bacteria regulate virulence gene expression. It has also uncovered diverse mechanisms by which bacterial small RNAs, in general, globally control gene expression. Riboregulators as well as their targets may also prove to be alternative targets or provide new strategies for antimicrobials. In this article, we present an overview of the general mechanisms that bacteria use to regulate with RNA, focusing on examples from pathogens. In addition, we also briefly review how deep sequencing approaches have aided in opening new perspectives in small RNA identification and the study of their functions. Finally, we discuss examples of riboregulators in two model pathogens that control virulence factor expression or survival-associated phenotypes, such as stress tolerance, biofilm formation, or cell-cell communication, to illustrate how riboregulation factors into regulatory networks in bacterial pathogens.
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Nawaz MZ, Jian H, He Y, Xiong L, Xiao X, Wang F. Genome-Wide Detection of Small Regulatory RNAs in Deep-Sea Bacterium Shewanella piezotolerans WP3. Front Microbiol 2017; 8:1093. [PMID: 28663744 PMCID: PMC5471319 DOI: 10.3389/fmicb.2017.01093] [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] [Received: 03/06/2017] [Accepted: 05/30/2017] [Indexed: 11/13/2022] Open
Abstract
Shewanella are one of the most abundant Proteobacteria in the deep-sea and are renowned for their versatile electron accepting capacities. The molecular mechanisms involved in their adaptation to diverse and extreme environments are not well understood. Small non-coding RNAs (sRNAs) are known for modulating the gene expression at transcriptional and posttranscriptional levels, subsequently playing a key role in microbial adaptation. To understand the potential roles of sRNAs in the adaptation of Shewanella toward deep-sea environments, here an in silico approach was utilized to detect the sRNAs in the genome of Shewanella piezotolerans WP3, a piezotolerant and psychrotolerant deep-sea iron reducing bacterium. After scanning 3673 sets of 5' and 3' UTRs of orthologous genes, 209 sRNA candidates were identified with high confidence in S. piezotolerans WP3. About 92% (193 out of 209) of these putative sRNAs belong to the class trans-encoded RNAs, suggesting that trans-regulatory RNAs are the dominant class of sRNAs in S. piezotolerans WP3. The remaining 16 cis-regulatory RNAs were validated through quantitative polymerase chain reaction. Five cis-sRNAs were further shown to act as cold regulated sRNAs. Our study provided additional evidence at the transcriptional level to decipher the microbial adaptation mechanisms to extreme environmental conditions.
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Affiliation(s)
- Muhammad Z Nawaz
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China.,State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong UniversityShanghai, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China
| | - Ying He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China.,State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong UniversityShanghai, China
| | - Lei Xiong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China.,State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong UniversityShanghai, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China.,State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong UniversityShanghai, China
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InvS Coordinates Expression of PrgH and FimZ and Is Required for Invasion of Epithelial Cells by Salmonella enterica serovar Typhimurium. J Bacteriol 2017; 199:JB.00824-16. [PMID: 28439039 DOI: 10.1128/jb.00824-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 04/20/2017] [Indexed: 11/20/2022] Open
Abstract
Deep sequencing has revolutionized our understanding of the bacterial RNA world and has facilitated the identification of 280 small RNAs (sRNAs) in Salmonella Despite the suspicions that sRNAs may play important roles in Salmonella pathogenesis, the functions of most sRNAs remain unknown. To advance our understanding of RNA biology in Salmonella virulence, we searched for sRNAs required for bacterial invasion into nonphagocytic cells. After screening 75 sRNAs, we discovered that the ablation of InvS caused a significant decrease of Salmonella invasion into epithelial cells. A proteomic analysis showed that InvS modulated the levels of several type III secreted Salmonella proteins. The level of PrgH, a type III secretion apparatus protein, was significantly lower in the absence of InvS, consistent with the known roles of PrgH in effector secretion and bacterial invasion. We discovered that InvS modulates fimZ expression and hence flagellar gene expression and motility. We propose that InvS coordinates the increase of PrgH and decrease in FimZ that promote efficient Salmonella invasion into nonphagocytic cells.IMPORTANCE Salmonellosis continues to be the most common foodborne infection reported by the CDC in the United States. Central to Salmonella pathogenesis is the ability to invade nonphagocytic cells and to replicate inside host cells. Invasion genes are known to be regulated by protein transcriptional networks, but little is known about the role played by small RNAs (sRNAs) in this process. We have identified a novel sRNA, InvS, that is involved in Salmonella invasion. Our result will likely provide an opportunity to better understand the fundamental question of how Salmonella regulates invasion gene expression and may inform strategies for therapeutic intervention.
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Ryan D, Mukherjee M, Suar M. The expanding targetome of small RNAs in Salmonella Typhimurium. Biochimie 2017; 137:69-77. [DOI: 10.1016/j.biochi.2017.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 03/10/2017] [Indexed: 10/20/2022]
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Novel DNA Binding and Regulatory Activities for σ 54 (RpoN) in Salmonella enterica Serovar Typhimurium 14028s. J Bacteriol 2017; 199:JB.00816-16. [PMID: 28373272 DOI: 10.1128/jb.00816-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 03/27/2017] [Indexed: 01/13/2023] Open
Abstract
The variable sigma (σ) subunit of the bacterial RNA polymerase (RNAP) holoenzyme, which is responsible for promoter specificity and open complex formation, plays a strategic role in the response to environmental changes. Salmonella enterica serovar Typhimurium utilizes the housekeeping σ70 and five alternative sigma factors, including σ54 The σ54-RNAP differs from other σ-RNAP holoenzymes in that it forms a stable closed complex with the promoter and requires ATP hydrolysis by an activated cognate bacterial enhancer binding protein (bEBP) to transition to an open complex and initiate transcription. In S. Typhimurium, σ54-dependent promoters normally respond to one of 13 different bEBPs, each of which is activated under a specific growth condition. Here, we utilized a constitutively active, promiscuous bEBP to perform a genome-wide identification of σ54-RNAP DNA binding sites and the transcriptome of the σ54 regulon of S. Typhimurium. The position and context of many of the identified σ54 RNAP DNA binding sites suggest regulatory roles for σ54-RNAP that connect the σ54 regulon to regulons of other σ factors to provide a dynamic response to rapidly changing environmental conditions.IMPORTANCE The alternative sigma factor σ54 (RpoN) is required for expression of genes involved in processes with significance in agriculture, bioenergy production, bioremediation, and host-microbe interactions. The characterization of the σ54 regulon of the versatile pathogen S. Typhimurium has expanded our understanding of the scope of the σ54 regulon and how it links to other σ regulons within the complex regulatory network for gene expression in bacteria.
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Pérez-Reytor D, Plaza N, Espejo RT, Navarrete P, Bastías R, Garcia K. Role of Non-coding Regulatory RNA in the Virulence of Human Pathogenic Vibrios. Front Microbiol 2017; 7:2160. [PMID: 28123382 PMCID: PMC5225090 DOI: 10.3389/fmicb.2016.02160] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/22/2016] [Indexed: 12/22/2022] Open
Abstract
In recent decades, the identification of small non-coding RNAs in bacteria has revealed an important regulatory mechanism of gene expression involved in the response to environmental signals and to the control of virulence. In the family Vibrionaceae, which includes several human and animal pathogens, small non-coding RNAs (sRNAs) are closely related to important processes including metabolism, quorum sensing, virulence, and fitness. Studies conducted in silico and experiments using microarrays and high-throughput RNA sequencing have led to the discovery of an unexpected number of sRNAs in Vibrios. The present review discusses the most relevant reports regarding the mechanisms of action of sRNAs and their implications in the virulence of the main human pathogens in the family Vibrionaceae: Vibrio parahaemolyticus, V. vulnificus and V. cholerae.
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Affiliation(s)
- Diliana Pérez-Reytor
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile San Miguel, Chile
| | - Nicolás Plaza
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de ChileSan Miguel, Chile; Institute of Nutrition and Food Technology, University of ChileSantiago, Chile
| | - Romilio T Espejo
- Institute of Nutrition and Food Technology, University of Chile Santiago, Chile
| | - Paola Navarrete
- Institute of Nutrition and Food Technology, University of Chile Santiago, Chile
| | - Roberto Bastías
- Laboratory of Microbiology, Institute of Biology, Pontificia Universidad Católica de Valparaíso Valparaíso, Chile
| | - Katherine Garcia
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile San Miguel, Chile
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Ryan D, Ojha UK, Jaiswal S, Padhi C, Suar M. The Small RNA DsrA Influences the Acid Tolerance Response and Virulence of Salmonella enterica Serovar Typhimurium. Front Microbiol 2016; 7:599. [PMID: 27199929 PMCID: PMC4844625 DOI: 10.3389/fmicb.2016.00599] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/11/2016] [Indexed: 01/05/2023] Open
Abstract
The Gram-negative, enteropathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) is exposed to various stress conditions during pathogenesis, of which acid stress serves as a major defense mechanism in the host. Such environments are encountered in the stomach and Salmonella containing vacuole of phagocytic and non-phagocytic cells. It is only recently that small RNAs (sRNAs) have come to the forefront as major regulators of stress response networks. Consequently, the sRNA DsrA which regulates acid resistance in Escherichia coli, has not been characterized in the acid tolerance response (ATR) of Salmonella. In this study, we show dsrA to be induced two and threefold under adaptation and challenge phases of the ATR, respectively. Additionally, an isogenic mutant lacking dsrA (ΔDsrA) displayed lower viability under the ATR along with reduced motility, feeble adhesion and defective invasion efficacy in vitro. Expression analysis revealed down regulation of several Salmonella pathogenicity island-1 (SPI-1) effectors in ΔDsrA compared to the wild-type, under SPI-1 inducing conditions. Additionally, our in vivo data revealed ΔDsrA to be unable to cause gut inflammation in C57BL/6 mice at 72 h post infection, although intracellular survival and systemic dissemination remained unaffected. A possible explanation may be the significantly reduced expression of flagellin structural genes fliC and fljB in ΔDsrA, which have been implicated as major proinflammatory determinants. This study serves to highlight the role of sRNAs such as DsrA in both acid tolerance and virulence of S. Typhimurium. Additionally the robust phenotype of non-invasiveness could be exploited in developing SPI-I attenuated S. Typhimurium strains without disrupting SPI-I genes.
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Affiliation(s)
- Daniel Ryan
- Infection Biology Laboratory, School of Biotechnology, KIIT University Bhubaneswar, India
| | - Urmesh K Ojha
- Infection Biology Laboratory, School of Biotechnology, KIIT University Bhubaneswar, India
| | - Sangeeta Jaiswal
- Infection Biology Laboratory, School of Biotechnology, KIIT University Bhubaneswar, India
| | - Chandrashekhar Padhi
- Infection Biology Laboratory, School of Biotechnology, KIIT University Bhubaneswar, India
| | - Mrutyunjay Suar
- Infection Biology Laboratory, School of Biotechnology, KIIT University Bhubaneswar, India
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30
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Gifsy-1 Prophage IsrK with Dual Function as Small and Messenger RNA Modulates Vital Bacterial Machineries. PLoS Genet 2016; 12:e1005975. [PMID: 27057757 PMCID: PMC4825925 DOI: 10.1371/journal.pgen.1005975] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 03/14/2016] [Indexed: 11/20/2022] Open
Abstract
While an increasing number of conserved small regulatory RNAs (sRNAs) are known to function in general bacterial physiology, the roles and modes of action of sRNAs from horizontally acquired genomic regions remain little understood. The IsrK sRNA of Gifsy-1 prophage of Salmonella belongs to the latter class. This regulatory RNA exists in two isoforms. The first forms, when a portion of transcripts originating from isrK promoter reads-through the IsrK transcription-terminator producing a translationally inactive mRNA target. Acting in trans, the second isoform, short IsrK RNA, binds the inactive transcript rendering it translationally active. By switching on translation of the first isoform, short IsrK indirectly activates the production of AntQ, an antiterminator protein located upstream of isrK. Expression of antQ globally interferes with transcription termination resulting in bacterial growth arrest and ultimately cell death. Escherichia coli and Salmonella cells expressing AntQ display condensed chromatin morphology and localization of UvrD to the nucleoid. The toxic phenotype of AntQ can be rescued by co-expression of the transcription termination factor, Rho, or RNase H, which protects genomic DNA from breaks by resolving R-loops. We propose that AntQ causes conflicts between transcription and replication machineries and thus promotes DNA damage. The isrK locus represents a unique example of an island-encoded sRNA that exerts a highly complex regulatory mechanism to tune the expression of a toxic protein.
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Holmqvist E, Wright PR, Li L, Bischler T, Barquist L, Reinhardt R, Backofen R, Vogel J. Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo. EMBO J 2016; 35:991-1011. [PMID: 27044921 PMCID: PMC5207318 DOI: 10.15252/embj.201593360] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/26/2016] [Indexed: 12/22/2022] Open
Abstract
The molecular roles of many RNA‐binding proteins in bacterial post‐transcriptional gene regulation are not well understood. Approaches combining in vivo UV crosslinking with RNA deep sequencing (CLIP‐seq) have begun to revolutionize the transcriptome‐wide mapping of eukaryotic RNA‐binding protein target sites. We have applied CLIP‐seq to chart the target landscape of two major bacterial post‐transcriptional regulators, Hfq and CsrA, in the model pathogen Salmonella Typhimurium. By detecting binding sites at single‐nucleotide resolution, we identify RNA preferences and structural constraints of Hfq and CsrA during their interactions with hundreds of cellular transcripts. This reveals 3′‐located Rho‐independent terminators as a universal motif involved in Hfq–RNA interactions. Additionally, Hfq preferentially binds 5′ to sRNA‐target sites in mRNAs, and 3′ to seed sequences in sRNAs, reflecting a simple logic in how Hfq facilitates sRNA–mRNA interactions. Importantly, global knowledge of Hfq sites significantly improves sRNA‐target predictions. CsrA binds AUGGA sequences in apical loops and targets many Salmonella virulence mRNAs. Overall, our generic CLIP‐seq approach will bring new insights into post‐transcriptional gene regulation by RNA‐binding proteins in diverse bacterial species.
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Affiliation(s)
- Erik Holmqvist
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Patrick R Wright
- Bioinformatics Group, Department of Computer Science, Albert Ludwig University Freiburg, Freiburg, Germany
| | - Lei Li
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Thorsten Bischler
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Lars Barquist
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Richard Reinhardt
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, Albert Ludwig University Freiburg, Freiburg, Germany BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
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Suar M, Ryan D. Small RNA in the acid tolerance response of Salmonella and their role in virulence. Virulence 2016; 6:105-6. [PMID: 25853732 DOI: 10.4161/21505594.2014.988543] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Mrutyunjay Suar
- a School of Biotechnology ; KIIT University ; Bhubaneswar , Odisha , India
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Feliciano JR, Grilo AM, Guerreiro SI, Sousa SA, Leitão JH. Hfq: a multifaceted RNA chaperone involved in virulence. Future Microbiol 2015; 11:137-51. [PMID: 26685037 DOI: 10.2217/fmb.15.128] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hfq has emerged in recent years as a master regulator of gene expression in bacteria, mainly due to its ability to mediate the interaction of small noncoding RNAs with their mRNA targets, including those related to virulence in Gram-negative bacteria. In this work, we review current knowledge on the involvement of Hfq in the regulation of virulence traits related to secretion systems, alternative sigma factors, outer membrane proteins, polysaccharides and iron metabolism. Recent data from transcriptomics and proteomics studies performed for major pathogens are included. We also summarize and correlate current knowledge on how Hfq protein impacts pathogenicity of bacterial pathogens.
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Affiliation(s)
- Joana R Feliciano
- iBB - Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa. Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | | | - Soraia I Guerreiro
- iBB - Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa. Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Sílvia A Sousa
- iBB - Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa. Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Jorge H Leitão
- iBB - Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa. Av. Rovisco Pais, 1049-001 Lisboa, Portugal.,Departamento de Bioengenharia, Instituto Superior Técnico, Universidade de Lisboa. Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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Srikumar S, Kröger C, Hébrard M, Colgan A, Owen SV, Sivasankaran SK, Cameron ADS, Hokamp K, Hinton JCD. RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella Typhimurium. PLoS Pathog 2015; 11:e1005262. [PMID: 26561851 PMCID: PMC4643027 DOI: 10.1371/journal.ppat.1005262] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 10/17/2015] [Indexed: 11/18/2022] Open
Abstract
Salmonella enterica serovar Typhimurium is arguably the world’s best-understood bacterial pathogen. However, crucial details about the genetic programs used by the bacterium to survive and replicate in macrophages have remained obscure because of the challenge of studying gene expression of intracellular pathogens during infection. Here, we report the use of deep sequencing (RNA-seq) to reveal the transcriptional architecture and gene activity of Salmonella during infection of murine macrophages, providing new insights into the strategies used by the pathogen to survive in a bactericidal immune cell. We characterized 3583 transcriptional start sites that are active within macrophages, and highlight 11 of these as candidates for the delivery of heterologous antigens from Salmonella vaccine strains. A majority (88%) of the 280 S. Typhimurium sRNAs were expressed inside macrophages, and SPI13 and SPI2 were the most highly expressed pathogenicity islands. We identified 31 S. Typhimurium genes that were strongly up-regulated inside macrophages but expressed at very low levels during in vitro growth. The SalComMac online resource allows the visualisation of every transcript expressed during bacterial replication within mammalian cells. This primary transcriptome of intra-macrophage S.-Typhimurium describes the transcriptional start sites and the transcripts responsible for virulence traits, and catalogues the sRNAs that may play a role in the regulation of gene expression during infection. The burden of Salmonellosis remains unacceptably high throughout the world and control measures have had limited success. Because Salmonella bacteria can be transmitted from the wider environment to animals and humans, the bacteria encounter diverse environments that include food, water, plant surfaces and the extracellular and intracellular phases of infection of eukaryotic hosts. An intricate transcriptional network has evolved to respond to a variety of environmental signals and control the “right time/ right place” expression of virulence genes. To understand how transcription is rewired during intracellular infection, we determined the primary transcriptome of Salmonella enterica serovar Typhimurium within murine macrophages. We report the coding genes, sRNAs and transcriptional start sites that are expressed within macrophages at 8 hours after infection, and use these to infer gene function. We identified gene promoters that are specifically expressed within macrophages and could drive the intracellular delivery of antigens by S. Typhimurium vaccine strains. These data contribute to our understanding of the mechanisms used by Salmonella to regulate virulence gene expression whilst replicating inside mammalian cells.
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Affiliation(s)
- Shabarinath Srikumar
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Carsten Kröger
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Magali Hébrard
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland
| | - Aoife Colgan
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland
| | - Siân V. Owen
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Sathesh K. Sivasankaran
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland
| | | | - Karsten Hokamp
- Department of Genetics, School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College, Dublin, Ireland
| | - Jay C. D. Hinton
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- * E-mail:
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Wang J, Liu T, Zhao B, Lu Q, Wang Z, Cao Y, Li W. sRNATarBase 3.0: an updated database for sRNA-target interactions in bacteria. Nucleic Acids Res 2015; 44:D248-53. [PMID: 26503244 PMCID: PMC4702819 DOI: 10.1093/nar/gkv1127] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 10/13/2015] [Indexed: 12/14/2022] Open
Abstract
Bacterial sRNAs are a class of small regulatory RNAs of about 40–500 nt in length; they play multiple biological roles through binding to their target mRNAs or proteins. Therefore, elucidating sRNA targets is very important. However, only targets of a few sRNAs have been described. To facilitate sRNA functional studies such as developing sRNA target prediction models, we updated the sRNATarBase database, which was initially developed in 2010. The new version (recently moved to http://ccb1.bmi.ac.cn/srnatarbase/) contains 771 sRNA-target entries manually collected from 213 papers, and 23 290 and 11 750 predicted targets from sRNATarget and sTarPicker, respectively. Among the 771 entries, 475 and 17 were involved in validated sRNA–mRNA and sRNA–protein interactions, respectively, while 279 had no reported interactions. We also presented detailed information for 316 binding regions of sRNA-target mRNA interactions and related mutation experiments, as well as new features, including NCBI sequence viewer, sRNA regulatory network, target prediction-based GO and pathway annotations, and error report system. The new version provides a comprehensive annotation of validated sRNA-target interactions, and will be a useful resource for bacterial sRNA studies.
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Affiliation(s)
- Jiang Wang
- Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Haidian district, Beijing 100850, China
| | - Tao Liu
- Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Haidian district, Beijing 100850, China
| | - Bo Zhao
- Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Haidian district, Beijing 100850, China
| | - Qixuan Lu
- Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Haidian district, Beijing 100850, China
| | - Zheng Wang
- Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Haidian district, Beijing 100850, China
| | - Yuan Cao
- Department of Laboratory Medicine, Jinan Military General Hospital, Jinan, Shandong 250031, China
| | - Wuju Li
- Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Haidian district, Beijing 100850, China
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Barquist L, Vogel J. Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies. Annu Rev Genet 2015; 49:367-94. [PMID: 26473381 DOI: 10.1146/annurev-genet-112414-054804] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past decade, bacterial small RNAs (sRNAs) have gone from a biological curiosity to being recognized as a major class of regulatory molecules. High-throughput methods for sampling the transcriptional output of bacterial cells demonstrate that sRNAs are universal features of bacterial transcriptomes, are plentiful, and appear to vary extensively over evolutionary time. With ever more bacteria coming under study, the question becomes how can we accelerate the discovery and functional characterization of sRNAs in diverse organisms. New technologies built on high-throughput sequencing are emerging that can rapidly provide global insight into the numbers and functions of sRNAs in bacteria of interest, providing information that can shape hypotheses and guide research. In this review, we describe recent developments in transcriptomics (RNA-seq) and functional genomics that we expect to help us develop an integrated, systems-level view of sRNA biology in bacteria.
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Affiliation(s)
- Lars Barquist
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany; ,
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany; ,
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Elfenbein JR, Knodler LA, Nakayasu ES, Ansong C, Brewer HM, Bogomolnaya L, Adams LG, McClelland M, Adkins JN, Andrews-Polymenis HL. Multicopy Single-Stranded DNA Directs Intestinal Colonization of Enteric Pathogens. PLoS Genet 2015; 11:e1005472. [PMID: 26367458 PMCID: PMC4569332 DOI: 10.1371/journal.pgen.1005472] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 07/28/2015] [Indexed: 01/10/2023] Open
Abstract
Multicopy single-stranded DNAs (msDNAs) are hybrid RNA-DNA molecules encoded on retroelements called retrons and produced by the action of retron reverse transcriptases. Retrons are widespread in bacteria but the natural function of msDNA has remained elusive despite 30 years of study. The major roadblock to elucidation of the function of these unique molecules has been the lack of any identifiable phenotypes for mutants unable to make msDNA. We report that msDNA of the zoonotic pathogen Salmonella Typhimurium is necessary for colonization of the intestine. Similarly, we observed a defect in intestinal persistence in an enteropathogenic E. coli mutant lacking its retron reverse transcriptase. Under anaerobic conditions in the absence of msDNA, proteins of central anaerobic metabolism needed for Salmonella colonization of the intestine are dysregulated. We show that the msDNA-deficient mutant can utilize nitrate, but not other alternate electron acceptors in anaerobic conditions. Consistent with the availability of nitrate in the inflamed gut, a neutrophilic inflammatory response partially rescued the ability of a mutant lacking msDNA to colonize the intestine. These findings together indicate that the mechanistic basis of msDNA function during Salmonella colonization of the intestine is proper production of proteins needed for anaerobic metabolism. We further conclude that a natural function of msDNA is to regulate protein abundance, the first attributable function for any msDNA. Our data provide novel insight into the function of this mysterious molecule that likely represents a new class of regulatory molecules.
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Affiliation(s)
- Johanna R. Elfenbein
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University Health Science Center, Bryan, Texas, United States of America
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Leigh A. Knodler
- Paul G. Allen School of Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Ernesto S. Nakayasu
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Charles Ansong
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Heather M. Brewer
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Lydia Bogomolnaya
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University Health Science Center, Bryan, Texas, United States of America
| | - L. Garry Adams
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Michael McClelland
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California-Irvine, Irvine, California, United States of America
| | - Joshua N. Adkins
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Helene L. Andrews-Polymenis
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University Health Science Center, Bryan, Texas, United States of America
- * E-mail:
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sRNA-Mediated Regulation of P-Fimbriae Phase Variation in Uropathogenic Escherichia coli. PLoS Pathog 2015; 11:e1005109. [PMID: 26291711 PMCID: PMC4546395 DOI: 10.1371/journal.ppat.1005109] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 07/24/2015] [Indexed: 12/21/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) are capable of occupying physiologically distinct intracellular and extracellular niches within the urinary tract. This feat requires the timely regulation of gene expression and small RNAs (sRNAs) are known to mediate such rapid adjustments in response to changing environmental cues. This study aimed to uncover sRNA-mediated gene regulation in the UPEC strain UTI89, during infection of bladder epithelial cells. Hfq is an RNA chaperone known to facilitate and stabilize sRNA and target mRNA interactions with bacterial cells. The co-immunoprecipitation and high throughput RNA sequencing of Hfq bound sRNAs performed in this study, revealed distinct sRNA profiles in UPEC in the extracellular and intracellular environments. Our findings emphasize the importance of studying regulatory sRNAs in a biologically relevant niche. This strategy also led to the discovery of a novel virulence-associated trans-acting sRNA—PapR. Deletion of papR was found to enhance adhesion of UTI89 to both bladder and kidney cell lines in a manner independent of type-1 fimbriae. We demonstrate PapR mediated posttranscriptional repression of the P-fimbriae phase regulator gene papI and postulate a role for such regulation in fimbrial cross-talk at the population level in UPEC. Our results further implicate the Leucine responsive protein (LRP) as a transcriptional activator regulating PapR expression. Our study reports, for the first time, a role for sRNAs in regulation of P-fimbriae phase variation and emphasizes the importance of studying pathogenesis-specific sRNAs within a relevant biological niche. Recent years have seen an increasing emphasis placed on the role of small RNAs (sRNAs) in the regulation of bacterial gene expression and stress adaptation. The advent of high-throughput sequencing methods has now made it possible to directly monitor the appearance of potentially virulence-associated sRNAs that may contribute to rapid adaptation of the pathogen to a changing environment during infection. Uropathogenic Escherichia coli (UPEC) are presumably exposed to a deluge of stimuli from epithelial cell contact, urine and host immune factors and we asked if any regulatory sRNAs would play a role in the transition of UPEC from the extracellular niche to the intracellular one. This study employs co-immunoprecipitation using the RNA chaperone Hfq to identify novel virulence-associated sRNAs in intracellular UPEC, followed by high-throughput RNA-seq. We report the identification of a novel sRNA that we designate PapR (P-fimbriae regulator) and elaborate on this discovery by demonstrating a role for PapR in regulation of P-fimbriae—a UPEC surface virulence factor. The results presented in this study offer new insights into the molecular mechanisms of UPEC pathogenesis and a role for sRNA mediated regulation of virulence factors.
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Haning K, Cho SH, Contreras LM. Small RNAs in mycobacteria: an unfolding story. Front Cell Infect Microbiol 2014; 4:96. [PMID: 25105095 PMCID: PMC4109619 DOI: 10.3389/fcimb.2014.00096] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/03/2014] [Indexed: 01/10/2023] Open
Abstract
Mycobacteria represent a class of powerful pathogens, including those causing tuberculosis and leprosy, which continue to be worldwide health challenges. In the last 20 years, an abundance of non-coding, small RNAs (sRNAs) have been discovered in model bacteria and gained significant attention as regulators of cellular responses, including pathogenesis. Naturally, a search in mycobacteria followed, revealing over 200 sRNAs thus far. Characterization of these sRNAs is only beginning, but differential expression under environmental stresses suggests relevance to mycobacterial pathogenesis. This review provides a comprehensive overview of the current knowledge of sRNAs in mycobacteria, including historical perspective and techniques used for identification and characterization.
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Affiliation(s)
- Katie Haning
- McKetta Department of Chemical Engineering, Cockrell School of Engineering, The University of Texas at AustinAustin, TX, USA
| | - Seung Hee Cho
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at AustinAustin, TX, USA
| | - Lydia M. Contreras
- McKetta Department of Chemical Engineering, Cockrell School of Engineering, The University of Texas at AustinAustin, TX, USA
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at AustinAustin, TX, USA
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Kröger C, Colgan A, Srikumar S, Händler K, Sivasankaran SK, Hammarlöf DL, Canals R, Grissom JE, Conway T, Hokamp K, Hinton JCD. An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium. Cell Host Microbe 2014; 14:683-95. [PMID: 24331466 DOI: 10.1016/j.chom.2013.11.010] [Citation(s) in RCA: 333] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 11/13/2013] [Accepted: 11/21/2013] [Indexed: 11/15/2022]
Abstract
Bacterial transcriptional networks consist of hundreds of transcription factors and thousands of promoters. However, the true complexity of transcription in a bacterial pathogen and the effect of the environments encountered during infection remain to be established. We present a simplified approach for global promoter identification in bacteria using RNA-seq-based transcriptomic analyses of 22 distinct infection-relevant environmental conditions. Individual RNA samples were combined to identify most of the 3,838 Salmonella enterica serovar Typhimurium promoters in just two RNA-seq runs. Individual in vitro conditions stimulated characteristic transcriptional signatures, and the suite of 22 conditions induced transcription of 86% of all S. Typhimurium genes. We highlight the environmental conditions that induce the Salmonella pathogenicity islands and present a small RNA expression landscape of 280 sRNAs. This publicly available compendium of environmentally controlled expression of every transcriptional feature of S. Typhimurium constitutes a useful resource for the bacterial research community.
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Affiliation(s)
- Carsten Kröger
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Aoife Colgan
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Shabarinath Srikumar
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Kristian Händler
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Sathesh K Sivasankaran
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Disa L Hammarlöf
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Rocío Canals
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Joe E Grissom
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Tyrrell Conway
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Karsten Hokamp
- Department of Genetics, School of Genetics & Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Jay C D Hinton
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland; Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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42
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Lowery CA, Matamouros S, Niessen S, Zhu J, Scolnick J, Lively JM, Cravatt BF, Miller SI, Kaufmann GF, Janda KD. A chemical biology approach to interrogate quorum-sensing regulated behaviors at the molecular and cellular level. ACTA ACUST UNITED AC 2014; 20:903-11. [PMID: 23890008 DOI: 10.1016/j.chembiol.2013.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 05/08/2013] [Accepted: 05/29/2013] [Indexed: 10/26/2022]
Abstract
Small molecule probes have been used extensively to explore biologic systems and elucidate cellular signaling pathways. In this study, we use an inhibitor of bacterial communication to monitor changes in the proteome of Salmonella enterica serovar Typhimurium with the aim of discovering unrecognized processes regulated by AI-2-based quorum-sensing (QS), a mechanism of bacterial intercellular communication that allows for the coordination of gene expression in a cell density-dependent manner. In S. typhimurium, this system regulates the uptake and catabolism of intercellular signals and has been implicated in pathogenesis, including the invasion of host epithelial cells. We demonstrate that our QS antagonist is capable of selectively inhibiting the expression of known QS-regulated proteins in S. typhimurium, thus attesting that QS inhibitors may be used to confirm proposed and elucidate previously unidentified QS pathways without relying on genetic manipulation.
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Affiliation(s)
- Colin A Lowery
- The Skaggs Institute for Chemical Biology, Departments of Chemistry, Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Calderón PF, Morales EH, Acuña LG, Fuentes DN, Gil F, Porwollik S, McClelland M, Saavedra CP, Calderón IL. The small RNA RyhB homologs from Salmonella typhimurium participate in the response to S-nitrosoglutathione-induced stress. Biochem Biophys Res Commun 2014; 450:641-5. [PMID: 24937451 DOI: 10.1016/j.bbrc.2014.06.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 06/06/2014] [Indexed: 12/25/2022]
Abstract
Typically, the expression of sRNAs is activated in response to environmental stimuli in order to regulate gene expression through post-transcriptional mechanisms. In the present work we show that the Salmonellatyphimurium paralogous sRNAs RyhB-1 and RyhB-2 are induced in response to the nitrosating agent S-nitrosoglutathione (GSNO). Inactivation of these sRNAs decreased S. typhimurium resistance to GSNO and increased the levels of nitrosylated proteins. These results prompted us to evaluate a possible role of these sRNAs in nitrosative stress resistance. RNA profiling was used as a screen to identify novel RyhB-1 and RyhB-2 regulated targets. A subset of genes was filtered based on their potential role in the response to nitrosative stress and their expression was analyzed by quantitative RT-PCR in wild type, single and double mutant strains (ΔryhB1, ΔryhB2 and ΔryhB1 ΔryhB2) treated with GSNO. In response to GSNO RyhB-1 and RyhB-2 negatively regulate the expression of the genes cyoABC (cytochrome bo oxidase), cydB (cytochrome bd oxidase), cybC (cytochrome b-562), and positively regulate the nirBCD operon (nitrite reductase system). Together, these results suggest that RyhB-1 and RyhB-2 finely tune the expression of genes coding for cytochrome oxidases and the nitrate reductase system, allowing the cell to cope with GSNO-induced stress.
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Affiliation(s)
- Paulina F Calderón
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
| | - Eduardo H Morales
- Great Lakes Bioenergy Research Center and Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Lillian G Acuña
- Laboratorio de Ecofisiología Microbiana, Fundación Ciencia & Vida, Santiago, Chile.
| | - Danitza N Fuentes
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
| | - Fernando Gil
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
| | - S Porwollik
- Department of Microbiology and Molecular Genetics, B240 Medical Sciences Building, University of California, Irvine, CA 92697, USA.
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, B240 Medical Sciences Building, University of California, Irvine, CA 92697, USA.
| | - Claudia P Saavedra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
| | - Iván L Calderón
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
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Zeng Q, Sundin GW. Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function. BMC Genomics 2014; 15:414. [PMID: 24885615 PMCID: PMC4070566 DOI: 10.1186/1471-2164-15-414] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/09/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Erwinia amylovora is a phytopathogenic bacterium and causal agent of fire blight disease in apples and pears. Although many virulence factors have been characterized, the coordination of expression of these virulence factors in E. amylovora is still not clear. Regulatory small RNAs (sRNAs) are important post-transcriptional regulatory components in bacteria. A large number of sRNAs require the RNA chaperone Hfq for both stability and functional activation. In E. amylovora, Hfq was identified as a major regulator of virulence and various virulence traits. However, information is still lacking about Hfq-dependent sRNAs on a genome scale, including the virulence regulatory functions of these sRNAs in E. amylovora. RESULTS Using both an RNA-seq analysis and a Rho-independent terminator search, 40 candidate Hfq-dependent sRNAs were identified in E. amylovora. The expression and sizes of 12 sRNAs and the sequence boundaries of seven sRNAs were confirmed by Northern blot and 5' RACE assay respectively. Sequence conservation analysis identified sRNAs conserved only in the Erwinia genus as well as E. amylovora species-specific sRNAs. In addition, a dynamic re-patterning of expression of Hfq-dependent sRNAs was observed at 6 and 12 hours after induction in Hrp-inducing minimal medium. Furthermore, sRNAs that control virulence traits were characterized, among which ArcZ positively controls the type III secretion system (T3SS), amylovoran exopolysaccahride production, biofilm formation, and motility, and negatively modulates attachment while RmaA (Hrs6) and OmrAB both negatively regulate amylovoran production and positively regulate motility. CONCLUSIONS This study has significantly enhanced our understanding of the Hfq-dependent sRNAs in E. amylovora at the genome level. The identification of multiple virulence-regulating sRNAs also suggests that post-transcriptional regulation by sRNAs may play a role in the deployment of virulence factors needed during varying stages of pathogenesis during host invasion by E. amylovora.
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Affiliation(s)
- Quan Zeng
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
| | - George W Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
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Lévi-Meyrueis C, Monteil V, Sismeiro O, Dillies MA, Monot M, Jagla B, Coppée JY, Dupuy B, Norel F. Expanding the RpoS/σS-network by RNA sequencing and identification of σS-controlled small RNAs in Salmonella. PLoS One 2014; 9:e96918. [PMID: 24810289 PMCID: PMC4014581 DOI: 10.1371/journal.pone.0096918] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 04/13/2014] [Indexed: 12/31/2022] Open
Abstract
The RpoS/σS sigma subunit of RNA polymerase (RNAP) controls a global adaptive response that allows many Gram-negative bacteria to survive starvation and various stresses. σS also contributes to biofilm formation and virulence of the food-borne pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium). In this study, we used directional RNA-sequencing and complementary assays to explore the σS-dependent transcriptome of S. Typhimurium during late stationary phase in rich medium. This study confirms the large regulatory scope of σS and provides insights into the physiological functions of σS in Salmonella. Extensive regulation by σS of genes involved in metabolism and membrane composition, and down-regulation of the respiratory chain functions, were important features of the σS effects on gene transcription that might confer fitness advantages to bacterial cells and/or populations under starving conditions. As an example, we show that arginine catabolism confers a competitive fitness advantage in stationary phase. This study also provides a firm basis for future studies to address molecular mechanisms of indirect regulation of gene expression by σS. Importantly, the σS-controlled downstream network includes small RNAs that might endow σS with post-transcriptional regulatory functions. Of these, four (RyhB-1/RyhB-2, SdsR, SraL) were known to be controlled by σS and deletion of the sdsR locus had a competitive fitness cost in stationary phase. The σS-dependent control of seven additional sRNAs was confirmed in Northern experiments. These findings will inspire future studies to investigate molecular mechanisms and the physiological impact of post-transcriptional regulation by σS.
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Affiliation(s)
- Corinne Lévi-Meyrueis
- Institut Pasteur, Unité de Génétique Moléculaire, Département de Microbiologie, Paris, France
- CNRS, ERL3526, Paris, France
- Université Paris Sud XI, Orsay, France
| | - Véronique Monteil
- Institut Pasteur, Unité de Génétique Moléculaire, Département de Microbiologie, Paris, France
- CNRS, ERL3526, Paris, France
| | - Odile Sismeiro
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et génétique, Paris, France
| | - Marie-Agnès Dillies
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et génétique, Paris, France
| | - Marc Monot
- Institut Pasteur, Laboratoire Pathogenèse des bactéries anaérobies, Département de Microbiologie, Paris, France
| | - Bernd Jagla
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et génétique, Paris, France
| | - Jean-Yves Coppée
- Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et génétique, Paris, France
| | - Bruno Dupuy
- Institut Pasteur, Laboratoire Pathogenèse des bactéries anaérobies, Département de Microbiologie, Paris, France
| | - Françoise Norel
- Institut Pasteur, Unité de Génétique Moléculaire, Département de Microbiologie, Paris, France
- CNRS, ERL3526, Paris, France
- * E-mail:
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46
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Gonzalo-Asensio J, Ortega ÁD, Rico-Pérez G, Pucciarelli MG, García-del Portillo F. A novel antisense RNA from the Salmonella virulence plasmid pSLT expressed by non-growing bacteria inside eukaryotic cells. PLoS One 2013; 8:e77939. [PMID: 24205037 PMCID: PMC3815029 DOI: 10.1371/journal.pone.0077939] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 09/05/2013] [Indexed: 12/21/2022] Open
Abstract
Bacterial small RNAs (sRNAs) are regulatory molecules playing relevant roles in response to environmental changes, stressful conditions and pathogenesis. The intracellular bacterial pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) is known to regulate expression of some sRNAs during colonization of fibroblasts. Here, we characterize a previously unknown sRNA encoded in the S. Typhimurium pSLT virulence plasmid that is specifically up-regulated by non-growing dormant bacteria persisting inside fibroblasts. This sRNA was inferred in microarray expression analyses, which unraveled enhanced transcriptional activity in the PSLT047- PSLT046 (mig5) intergenic region. The sRNA transcript was further identified as a 597-nucleotide molecule, which we named IesR-1, for ‘Intracellular-expressed-sRNA-1′. IesR-1 expression is low in bacteria growing in axenic cultures across a variety of experimental conditions but displays a marked increase (∼200–300 fold) following bacterial entry into fibroblasts. Remarkably, induction of IesR-1 expression is not prominent in bacteria proliferating within epithelial cells. IesR-1 deletion affects the control of bacterial growth in defined fibroblast cell lines and impairs virulence in a mouse infection model. Expression analyses performed in the PSLT047-iesR-1-PSLT046 (mig5) region support a cis-acting regulatory mechanism of IesR-1 as antisense RNA over the PSLT047 transcript involving interaction at their respective 3′ ends and modulation of PSLT047 protein levels. This model is sustained by the scarce production of PSLT047 protein observed in non-growing intracellular bacteria and the high amount of PSLT047 protein produced by bacteria carrying a truncated IesR-1 version with separated 5′ and 3′ regions. Taken together, these data reveal that S. Typhimurium sRNAs encoded in the pSLT virulence plasmid respond to a state of persistence inside the host cell. As exemplified by IesR-1, some of these sRNAs may contribute to diminish the relative levels of proteins, such as PSLT047, which are probably dispensable for the intracellular lifestyle.
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Affiliation(s)
- Jesús Gonzalo-Asensio
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Álvaro D. Ortega
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Gadea Rico-Pérez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - M. Graciela Pucciarelli
- Departamento de Biología Molecular, Universidad Autónoma de Madrid. Centro de Biología Molecular ‘Severo Ochoa’ (CBMSO-CSIC), Madrid, Spain
| | - Francisco García-del Portillo
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
- * E-mail:
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47
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Faner MA, Feig AL. Identifying and characterizing Hfq-RNA interactions. Methods 2013; 63:144-59. [PMID: 23707622 DOI: 10.1016/j.ymeth.2013.04.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 04/24/2013] [Accepted: 04/25/2013] [Indexed: 11/15/2022] Open
Abstract
To regulate stress responses and virulence, bacteria use small regulatory RNAs (sRNAs). These RNAs can up or down regulate target mRNAs through base pairing by influencing ribosomal access and RNA decay. A large class of these sRNAs, called trans-encoded sRNAs, requires the RNA binding protein Hfq to facilitate base pairing between the regulatory RNA and its target mRNA. The resulting network of regulation is best characterized in Escherichia coli and Salmonella typhimurium, but the importance of Hfq dependent sRNA regulation is recognized in a diverse population of bacteria. In this review we present the approaches and methods used to discover Hfq binding RNAs, characterize their interactions and elucidate their functions.
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Affiliation(s)
- M A Faner
- Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI, United States
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48
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Barquist L, Langridge GC, Turner DJ, Phan MD, Turner AK, Bateman A, Parkhill J, Wain J, Gardner PP. A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium. Nucleic Acids Res 2013; 41:4549-64. [PMID: 23470992 PMCID: PMC3632133 DOI: 10.1093/nar/gkt148] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Salmonella Typhi and Typhimurium diverged only ∼50 000 years ago, yet have very different host ranges and pathogenicity. Despite the availability of multiple whole-genome sequences, the genetic differences that have driven these changes in phenotype are only beginning to be understood. In this study, we use transposon-directed insertion-site sequencing to probe differences in gene requirements for competitive growth in rich media between these two closely related serovars. We identify a conserved core of 281 genes that are required for growth in both serovars, 228 of which are essential in Escherichia coli. We are able to identify active prophage elements through the requirement for their repressors. We also find distinct differences in requirements for genes involved in cell surface structure biogenesis and iron utilization. Finally, we demonstrate that transposon-directed insertion-site sequencing is not only applicable to the protein-coding content of the cell but also has sufficient resolution to generate hypotheses regarding the functions of non-coding RNAs (ncRNAs) as well. We are able to assign probable functions to a number of cis-regulatory ncRNA elements, as well as to infer likely differences in trans-acting ncRNA regulatory networks.
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Affiliation(s)
- Lars Barquist
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
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49
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Park SH, Butcher BG, Anderson Z, Pellegrini N, Bao Z, D’Amico K, Filiatrault MJ. Analysis of the small RNA P16/RgsA in the plant pathogen Pseudomonas syringae pv. tomato strain DC3000. MICROBIOLOGY-SGM 2012; 159:296-306. [PMID: 23258266 PMCID: PMC3709562 DOI: 10.1099/mic.0.063826-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Bacteria contain small non-coding RNAs (ncRNAs) that are responsible for altering transcription, translation or mRNA stability. ncRNAs are important because they regulate virulence factors and susceptibility to various stresses. Here, the regulation of a recently described ncRNA of Pseudomonas syringae pv. tomato DC3000, P16, was investigated. We determined that RpoS regulates the expression of P16. We found that deletion of P16 results in increased sensitivity to hydrogen peroxide compared to the wild-type strain, suggesting that P16 plays a role in the bacteria’s susceptibility to oxidative stress. Additionally the P16 mutant displayed enhanced resistance to heat stress. Our findings provide new information on the regulation and role of this ncRNA in P. syringae.
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Affiliation(s)
- So Hae Park
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Bronwyn G. Butcher
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Zoe Anderson
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Nola Pellegrini
- Plant–Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA
| | - Zhongmeng Bao
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Katherine D’Amico
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
- Plant–Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA
| | - Melanie J. Filiatrault
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
- Plant–Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA
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