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Jaworska K, Konarska J, Gomza P, Rożen P, Nieckarz M, Krawczyk-Balska A, Brzostek K, Raczkowska A. Interplay between the RNA Chaperone Hfq, Small RNAs and Transcriptional Regulator OmpR Modulates Iron Homeostasis in the Enteropathogen Yersinia enterocolitica. Int J Mol Sci 2023; 24:11157. [PMID: 37446335 DOI: 10.3390/ijms241311157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Iron is both essential for and potentially toxic to bacteria, so the precise maintenance of iron homeostasis is necessary for their survival. Our previous study indicated that in the human enteropathogen Yersinia enterocolitica, the regulator OmpR directly controls the transcription of the fur, fecA and fepA genes, encoding the ferric uptake repressor and two transporters of ferric siderophores, respectively. This study was undertaken to determine the significance of the RNA chaperone Hfq and the small RNAs OmrA and RyhB1 in the post-transcriptional control of the expression of these OmpR targets. We show that Hfq silences fur, fecA and fepA expression post-transcriptionally and negatively affects the production of FLAG-tagged Fur, FecA and FepA proteins. In addition, we found that the fur gene is under the negative control of the sRNA RyhB1, while fecA and fepA are negatively regulated by the sRNA OmrA. Finally, our data revealed that the role of OmrA results from a complex interplay of transcriptional and post-transcriptional effects in the feedback circuit between the regulator OmpR and the sRNA OmrA. Thus, the expression of fur, fecA and fepA is subject to complex transcriptional and post-transcriptional regulation in order to maintain iron homeostasis in Y. enterocolitica.
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Affiliation(s)
- Karolina Jaworska
- Department of Molecular Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Julia Konarska
- Department of Molecular Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Patrycja Gomza
- Department of Molecular Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Paula Rożen
- Department of Molecular Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Marta Nieckarz
- Department of Molecular Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Agata Krawczyk-Balska
- Department of Molecular Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Katarzyna Brzostek
- Department of Molecular Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Adrianna Raczkowska
- Department of Molecular Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
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2
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Ghandour R, Papenfort K. Small regulatory RNAs in Vibrio cholerae. MICROLIFE 2023; 4:uqad030. [PMID: 37441523 PMCID: PMC10335731 DOI: 10.1093/femsml/uqad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023]
Abstract
Vibrio cholerae is a major human pathogen causing the diarrheal disease, cholera. Regulation of virulence in V. cholerae is a multifaceted process involving gene expression changes at the transcriptional and post-transcriptional level. Whereas various transcription factors have been reported to modulate virulence in V. cholerae, small regulatory RNAs (sRNAs) have now been established to also participate in virulence control and the regulation of virulence-associated processes, such as biofilm formation, quorum sensing, stress response, and metabolism. In most cases, these sRNAs act by base-pairing with multiple target transcripts and this process typically requires the aid of an RNA-binding protein, such as the widely conserved Hfq protein. This review article summarizes the functional roles of sRNAs in V. cholerae, their underlying mechanisms of gene expression control, and how sRNAs partner with transcription factors to modulate complex regulatory programs. In addition, we will discuss regulatory principles discovered in V. cholerae that not only apply to other Vibrio species, but further extend into the large field of RNA-mediated gene expression control in bacteria.
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Affiliation(s)
- Rabea Ghandour
- Friedrich Schiller University Jena, Institute of Microbiology, 07745 Jena, Germany
| | - Kai Papenfort
- Corresponding author. Institute of Microbiology, General Microbiology, Friedrich Schiller University Jena, Winzerlaer Straße 2, 07745 Jena, Germany. Tel: +49-3641-949-311; E-mail:
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3
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Kuo CH, Lin WF, Liu CJ, Wang ZC, Liu TY, Peng HL. Role of the stress-responsive two-component system CpxAR in regulating fimbriae expression in Klebsiella pneumoniae CG43. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2023:S1684-1182(23)00040-3. [PMID: 36898943 DOI: 10.1016/j.jmii.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 02/06/2023] [Accepted: 02/18/2023] [Indexed: 02/27/2023]
Abstract
BACKGROUND CpxAR is a two-component system that allows bacteria to reorganize envelope structures in response to extracellular stimuli. CpxAR negatively affects type 1 fimbriae expression in Klebsiella pneumoniae CG43, a hypervirulent strain. The involvement of CpxAR in the regulation of type 3 fimbriae expression was investigated. METHODS cpxAR, cpxA, and cpxR gene-specific deletion mutants were generated. The deletion effects on the expression of type 1 and type 3 fimbriae were analyzed via measuring the promoter activity, mannose sensitive yeast agglutination activity, biofilm formation, and the production of the major pilins FimA and MrkA respectively. RNA sequencing analysis of CG43S3, ΔcpxAR, ΔcpxR and Δfur was employed to study the regulatory mechanism influencing the expression of type 3 fimbriae. RESULTS Deletion of cpxAR increased type 1 and type 3 fimbrial expression. Comparative transcriptomic analysis showed that the expression of oxidative stress-responsive enzymes, type 1 and type 3 fimbriae, and iron acquisition and homeostasis control systems were differentially affected by cpxAR or cpxR deletion. Subsequent analysis revealed that the small RNA RyhB negatively affects the expression of type 3 fimbriae, while CpxAR positively controls ryhB expression. Finally, the site-directed mutation of the predicted interacting sequences of RyhB with the mRNA of MrkA attenuated the RyhB repression of type 3 fimbriae. CONCLUSION CpxAR negatively regulates the expression of type 3 fimbriae by modulating cellular iron levels thereafter activating the expression of RyhB. The activated RyhB represses the expression of type 3 fimbriae by base-pairing binding to the 5'region of mrkA mRNA.
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Affiliation(s)
- Chih-Hao Kuo
- Department of Biological Science and Technology, School of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsin Chu, Taiwan
| | - Wei-Feng Lin
- Institute of Molecular Medicine and Bioengineering, School of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsin Chu, Taiwan
| | - Chia-Jui Liu
- Department of Biological Science and Technology, School of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsin Chu, Taiwan
| | - Zhe-Chong Wang
- Department of Biological Science and Technology, School of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsin Chu, Taiwan
| | - Ting-Yi Liu
- Institute of Molecular Medicine and Bioengineering, School of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsin Chu, Taiwan
| | - Hwei-Ling Peng
- Department of Biological Science and Technology, School of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsin Chu, Taiwan; Institute of Molecular Medicine and Bioengineering, School of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsin Chu, Taiwan.
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4
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Liu L, Liu W, He Y, Liu Y, Zhang Y. The cyclic AMP receptor protein (CRP) controls expression of the ferric uptake regulator (Fur) in Yersinia pestis. Can J Microbiol 2022; 68:501-506. [PMID: 35801716 DOI: 10.1139/cjm-2021-0314] [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: 11/22/2022]
Abstract
Yersinia pestis, the causative agent of plague, is one of the most dangerous pathogens in the world. Both the cyclic AMP receptor protein (CRP) and ferric uptake regulator (Fur) are global regulators that control the expression of a great deal of genes involved in a variety of cellular functions in Y. pestis. In this work, two CRP box-like deoxyribonucleic acid (DNA) sequences were detected in the upstream DNA region of fur, suggesting that the transcription of fur might be directly regulated by CRP in Y. pestis. Thus, transcriptional regulation of fur by CRP was investigated by primer extension, quantitative real-time PCR, LacZ fusion, and electrophoretic mobility shift assays. The results demonstrated that CRP was able to bind the regulatory DNA region of fur to activate its transcription. The data presented here not only suggested that the CRP and Fur regulons were bridged together via the direct regulation of fur by CRP, but also provided us a deeper understanding of the transcriptional regulation of fur in Y. pestis.
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Affiliation(s)
- Lei Liu
- Department of Transfusion Medicine, General Hospital of Central Theater Command of the PLA, Wuhan 430070, Hubei, China.,The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Wanbing Liu
- Department of Transfusion Medicine, General Hospital of Central Theater Command of the PLA, Wuhan 430070, Hubei, China
| | - Yingyu He
- The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Yan Liu
- The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, Guangdong, China
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5
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Teschler JK, Nadell CD, Drescher K, Yildiz FH. Mechanisms Underlying Vibrio cholerae Biofilm Formation and Dispersion. Annu Rev Microbiol 2022; 76:503-532. [PMID: 35671532 DOI: 10.1146/annurev-micro-111021-053553] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Biofilms are a widely observed growth mode in which microbial communities are spatially structured and embedded in a polymeric extracellular matrix. Here, we focus on the model bacterium Vibrio cholerae and summarize the current understanding of biofilm formation, including initial attachment, matrix components, community dynamics, social interactions, molecular regulation, and dispersal. The regulatory network that orchestrates the decision to form and disperse from biofilms coordinates various environmental inputs. These cues are integrated by several transcription factors, regulatory RNAs, and second-messenger molecules, including bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP). Through complex mechanisms, V. cholerae weighs the energetic cost of forming biofilms against the benefits of protection and social interaction that biofilms provide. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Jennifer K Teschler
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA;
| | - Carey D Nadell
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | | | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA;
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6
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Boutet E, Djerroud S, Perreault J. Small RNAs beyond Model Organisms: Have We Only Scratched the Surface? Int J Mol Sci 2022; 23:ijms23084448. [PMID: 35457265 PMCID: PMC9029176 DOI: 10.3390/ijms23084448] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 01/27/2023] Open
Abstract
Small RNAs (sRNAs) are essential regulators in the adaptation of bacteria to environmental changes and act by binding targeted mRNAs through base complementarity. Approximately 550 distinct families of sRNAs have been identified since their initial characterization in the 1980s, accelerated by the emergence of RNA-sequencing. Small RNAs are found in a wide range of bacterial phyla, but they are more prominent in highly researched model organisms compared to the rest of the sequenced bacteria. Indeed, Escherichia coli and Salmonella enterica contain the highest number of sRNAs, with 98 and 118, respectively, with Enterobacteriaceae encoding 145 distinct sRNAs, while other bacteria families have only seven sRNAs on average. Although the past years brought major advances in research on sRNAs, we have perhaps only scratched the surface, even more so considering RNA annotations trail behind gene annotations. A distinctive trend can be observed for genes, whereby their number increases with genome size, but this is not observable for RNAs, although they would be expected to follow the same trend. In this perspective, we aimed at establishing a more accurate representation of the occurrence of sRNAs in bacteria, emphasizing the potential for novel sRNA discoveries.
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7
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Lee KW, Wen Y, Park NY, Kim KS. Quorum sensing and iron-dependent coordinated control of autoinducer-2 production via small RNA RyhB in Vibrio vulnificus. Sci Rep 2022; 12:831. [PMID: 35039556 PMCID: PMC8764119 DOI: 10.1038/s41598-021-04757-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 12/29/2021] [Indexed: 12/12/2022] Open
Abstract
Roles for the non-coding small RNA RyhB in quorum-sensing and iron-dependent gene modulation in the human pathogen V. vulnificus were assessed in this study. Both the quorum sensing master regulator SmcR and the Fur-iron complex were observed to bind to the region upstream of the non-coding small RNA RyhB gene to repress expression, which suggests that RyhB is associated with both quorum-sensing and iron-dependent signaling in this pathogen. We found that expression of LuxS, which is responsible for the biosynthesis of autoinducer-2 (AI-2), was higher in wild type than in a ryhB-deletion isotype. RyhB binds directly to the 5′-UTR (untranslated region) of the luxS transcript to form a heteroduplex, which not only stabilizes luxS mRNA but also disrupts the secondary structure that normally obscures the translational start codon and thereby allows translation of LuxS to begin. The binding of RyhB to luxS mRNA requires the chaperone protein Hfq, which stabilizes RyhB. These results demonstrate that the small RNA RyhB is a key element associated with feedback control of AI-2 production, and that it inhibits quorum-sensing signaling in an iron-dependent manner. This study, taken together with previous studies, shows that iron availability and cell density signals are funneled to SmcR and RyhB, and that these regulators coordinate cognate signal pathways that result in the proper balance of protein expression in response to environmental conditions.
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Affiliation(s)
- Keun-Woo Lee
- Department of Life Sciences, Sogang University, Baekbeom-Ro, Mapo-Gu, Seoul, 121-742, Korea
| | - Yancheng Wen
- Department of Life Sciences, Sogang University, Baekbeom-Ro, Mapo-Gu, Seoul, 121-742, Korea.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer Research Center for Molecular Medicine, Fujian Medical University, Fuzhou, Fujian, People's Republic of China
| | - Na-Young Park
- Department of Life Sciences, Sogang University, Baekbeom-Ro, Mapo-Gu, Seoul, 121-742, Korea
| | - Kun-Soo Kim
- Department of Life Sciences, Sogang University, Baekbeom-Ro, Mapo-Gu, Seoul, 121-742, Korea.
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8
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Djapgne L, Oglesby AG. Impacts of Small RNAs and Their Chaperones on Bacterial Pathogenicity. Front Cell Infect Microbiol 2021; 11:604511. [PMID: 34322396 PMCID: PMC8311930 DOI: 10.3389/fcimb.2021.604511] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 06/07/2021] [Indexed: 12/25/2022] Open
Abstract
Bacterial small RNAs (sRNAs) are critical post-transcriptional regulators that exert broad effects on cell physiology. One class of sRNAs, referred to as trans-acting sRNAs, base-pairs with mRNAs to cause changes in their stability or translation. Another class of sRNAs sequesters RNA-binding proteins that in turn modulate mRNA expression. RNA chaperones play key roles in these regulatory events by promoting base-pairing of sRNAs to mRNAs, increasing the stability of sRNAs, inducing conformational changes on mRNA targets upon binding, or by titrating sRNAs away from their primary targets. In pathogenic bacteria, sRNAs and their chaperones exert broad impacts on both cell physiology and virulence, highlighting the central role of these systems in pathogenesis. This review provides an overview of the growing number and roles of these chaperone proteins in sRNA regulation, highlighting how these proteins contribute to bacterial pathogenesis.
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Affiliation(s)
- Louise Djapgne
- Department of Chemistry, Georgetown College, Washington, DC, United States
| | - Amanda G Oglesby
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States.,Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, MD, United States
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9
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Gao H, Wang H, Qin Q, Gao Y, Qiu Y, Zhang J, Li J, Lou J, Diao B, Zhang Y, Kan B. Transcriptional regulation of the mannitol phosphotransferase system operon by the ferric uptake regulator (Fur) in Vibrio cholerae El Tor serogroup O1. Res Microbiol 2021; 172:103848. [PMID: 34089838 DOI: 10.1016/j.resmic.2021.103848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 04/22/2021] [Accepted: 05/24/2021] [Indexed: 11/17/2022]
Abstract
The phosphoenolpyruvate (PEP): carbohydrate phosphotransferase system (PTS) allows bacteria to use various carbohydrates as energy resources including mannitol. The mannitol-specific PTS transporter in Vibrio cholerae is encoded by the mtlADR operon. Expression of the mtl operon has been shown to be strictly regulated by CRP, MtlS, and MtlR. In the present study, we investigated the regulation of mtlADR by the ferric uptake regulator (Fur). The results showed that Fur binds to the promoter-proximal DNA region of mtlADR to repress its transcription independent of iron, in mannitol-containing growth medium. The capacity for mannitol fermentation was significantly increased in Δfur relative to that of WT for normal and iron-replete growth media. The level of organic acids produced by Δfur was significantly enhanced relative to that produced by the WT strain in the normal and iron-replete media but not in an iron-starved medium. The results provided for a deeper understanding of the regulation of mtlADR in V. cholerae.
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Affiliation(s)
- He Gao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Han Wang
- Department of Clinical Diagnostic Centre, The Fifth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
| | - Qin Qin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yue Gao
- First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Yue Qiu
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Jingyun Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jie Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jing Lou
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Baowei Diao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yiquan Zhang
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China; Wuxi School of Medicine, Jiangnan University, Wuxi 214122, Jiangsu, China.
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
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10
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Toward a Comprehensive Analysis of Posttranscriptional Regulatory Networks: a New Tool for the Identification of Small RNA Regulators of Specific mRNAs. mBio 2021; 12:mBio.03608-20. [PMID: 33622723 PMCID: PMC8545128 DOI: 10.1128/mbio.03608-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A number of computational or experimental tools have been developed to identify targets of small RNA (sRNA) regulation. Here, we modified one of these methods, based on in vivo proximity ligation of sRNAs bound to their targets, referred to as rGRIL-seq, that can be used to capture sRNA regulators of a gene of interest. Intracellular expression of bacteriophage T4 RNA ligase leads to a covalent linking of sRNAs base-paired with mRNAs, and the chimeras are captured using oligonucleotides complementary to the mRNA, followed by sequencing. This allows the identification of known as well as novel sRNAs. We applied rGRIL-seq toward finding sRNA regulators of expression of the stress response sigma factor RpoS in Escherichia coli, Pseudomonas aeruginosa, and Vibrio cholerae. In E. coli, we confirmed the regulatory role of known sRNAs and discovered a new negative regulator, asYbiE. When applied to P. aeruginosa and V. cholerae, we identified two novel sRNAs (s03661 and s0223) in P. aeruginosa and two known sRNAs (TfoR and Vcr043) in V. cholerae as direct regulators of rpoS. The use of rGRIL-seq for defining multiple posttranscriptional regulatory inputs into individual mRNAs represents a step toward a more comprehensive understanding of the workings of bacterial regulatory networks.
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11
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Gao H, Ma L, Qin Q, Qiu Y, Zhang J, Li J, Lou J, Diao B, Zhao H, Shi Q, Zhang Y, Kan B. Fur Represses Vibrio cholerae Biofilm Formation via Direct Regulation of vieSAB, cdgD, vpsU, and vpsA-K Transcription. Front Microbiol 2020; 11:587159. [PMID: 33193241 PMCID: PMC7641913 DOI: 10.3389/fmicb.2020.587159] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/25/2020] [Indexed: 12/21/2022] Open
Abstract
Attached Vibrio cholerae biofilms are essential for environmental persistence and infectivity. The vps loci (vpsU, vpsA-K, and vpsL-Q) are required for mature biofilm formation and are responsible for the synthesis of exopolysaccharide. Transcription of vps genes is activated by the signaling molecule bis-(3'-5')-cyclic di-GMP (c-di-GMP), whose metabolism is controlled by the proteins containing the GGDEF and/or EAL domains. The ferric uptake regulator (Fur) plays key roles in the transcription of many genes involved in iron metabolism and non-iron functions. However, roles for Fur in Vibrio biofilm production have not been documented. In this study, phenotypic assays demonstrated that Fur, independent of iron, decreases in vivo c-di-GMP levels and inhibits in vitro biofilm formation by Vibrio cholerae. The Fur box-like sequences were detected within the promoter-proximal DNA regions of vpsU, vpsA-K, vieSAB, and cdgD, suggesting that transcription of these genes may be under the direct control of Fur. Indeed, the results of luminescence, quantitative PCR (qPCR), electrophoretic mobility shift assay (EMSA), and DNase I footprinting assays demonstrated Fur to bind to the promoter-proximal DNA regions of vpsU, vpsA-K, and cdgD to repress their transcription. In contrast, Fur activates the transcription of vieSAB in a direct manner. The cdgD and vieSAB encode proteins with GGDEF and EAL domains, respectively. Thus, data presented here highlight a new physiological role for Fur wherein it acts as a repressor of V. cholerae biofilm formation mediated by decreasing the production of exopolysaccharide and the intracellular levels of c-di-GMP.
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Affiliation(s)
- He Gao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lizhi Ma
- Third Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Qin Qin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yue Qiu
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Jingyun Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jie Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jing Lou
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Baowei Diao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hongqun Zhao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qiannan Shi
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yiquan Zhang
- School of Medicine, Jiangsu University, Zhenjiang, China.,Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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12
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Acuña LG, Barros MJ, Montt F, Peñaloza D, Núñez P, Valdés I, Gil F, Fuentes JA, Calderón IL. Participation of two sRNA RyhB homologs from the fish pathogen Yersinia ruckeri in bacterial physiology. Microbiol Res 2020; 242:126629. [PMID: 33153884 DOI: 10.1016/j.micres.2020.126629] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 09/11/2020] [Accepted: 10/13/2020] [Indexed: 01/19/2023]
Abstract
Small noncoding RNAs (sRNAs) are important regulators of gene expression and physiology in bacteria. RyhB is an iron-responsive sRNA well characterized in Escherichia coli and conserved in other Enterobacteriaceae. In this study, we identified and characterized two RyhB homologs (named RyhB-1 and RyhB-2) in the fish pathogen Yersinia ruckeri. We found that, as in other Enterobacteriaceae, both RyhB-1 and RyhB-2 are induced under iron starvation, repressed by the Fur regulator, and depend on Hfq for stability. Despite these similarities in expression, the mutant strains of Y. ruckeri lacking RyhB-1 (ΔryhB-1) or RyhB-2 (ΔryhB-2) exhibited differential phenotypes. In comparison with the wild type, the ΔryhB-1 strain showed a hypermotile phenotype, reduced biofilm formation, increased replication rate, faster growth, and increased ATP levels in bacterial cultures. By contrast, in salmon cell cultures, the ΔryhB-1 strain exhibited an increased survival. On the other hand, the ΔryhB-2 strain was non-motile and showed augmented biofilm formation as compared to the wild type. The expression of a subset of RyhB conserved targets, selected from different bacterial species, was analyzed by quantitative RT-PCR in wild type, ΔryhB-1, ΔryhB-2, and ΔryhB-1 ΔryhB-2 strains cultured in iron-depleted media. RyhB-1 negatively affected the expression of most analyzed genes (sodB, acnA, sdhC, bfr, fliF, among others), whose functions are related to metabolism and motility, involving iron-containing proteins. Among the genes analyzed, only sdhC and bfr appeared as targets for RyhB-2. Taken together, these results indicate that Y. ruckeri RyhB homologs participate in the modulation of the bacterial physiology with non-redundant roles.
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Affiliation(s)
- Lillian G Acuña
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - M José Barros
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Fernanda Montt
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Diego Peñaloza
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Paula Núñez
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Iván Valdés
- Desarrollo de Biológicos, Veterquímica S.A., Santiago, Chile.
| | - Fernando Gil
- Microbiota-Host Interactions and Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Juan A Fuentes
- Laboratorio de Genética y Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Iván L Calderón
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
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IurV, Encoded by ORF VCA0231, Is Involved in the Regulation of Iron Uptake Genes in Vibrio cholerae. Genes (Basel) 2020; 11:genes11101184. [PMID: 33053678 PMCID: PMC7600106 DOI: 10.3390/genes11101184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 11/16/2022] Open
Abstract
The pathogen Vibrio cholerae has multiple iron acquisition systems which allow bacteria to exploit a variety of iron sources across the different environments on which it thrives. The expression of such iron uptake systems is highly regulated, mainly by the master iron homeostasis regulator Fur but also by other mechanisms. Recently, we documented that the expression of many of the iron-responsive genes is also modulated by riboflavin. Among them, the open reading frame VCA0231, repressed both by riboflavin and iron, encodes a putative transcriptional regulator of the AraC/XylS family. Nonetheless, the genes or functions affected by this factor are unknown. In the present study, a series of in silico analyses was performed in order to identify the putative functions associated with the product of VCA0231. The STRING database predicted many iron uptake genes as functional partners for the product of VCA0231. In addition, a genomic neighborhood analysis with the Enzyme Function Initiative tools detected many Pfam families involved in iron homeostasis genetically associated with VCA0231. Moreover, a phylogenetic tree showed that other AraC/XylS members known to regulate siderophore utilization in bacteria clustered together and the product of VCA0231 localized in this cluster. This suggested that the product of VCA0231, here named IurV, is involved in the regulation of iron uptake processes. RNAseq was performed to determine the transcriptional effects of a deletion in VCA0231. A total of 52 genes were overexpressed and 21 genes were downregulated in response to the iurV deletion. Among these, several iron uptake genes and other iron homeostasis-related genes were found. Six gene ontology (GO) functional terms were enriched in the upregulated genes, of which five were related to iron metabolism. The regulatory pattern observed in the transcriptomics of a subset of genes was independently confirmed by quantitative real time PCR analysis. The results indicate that IurV is a novel regulator of the AraC/XylS family involved in the repression of iron uptake genes. Whether this effect is direct or indirect remains to be determined.
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The Endoribonuclease RNase E Coordinates Expression of mRNAs and Small Regulatory RNAs and Is Critical for the Virulence of Brucella abortus. J Bacteriol 2020; 202:JB.00240-20. [PMID: 32747427 DOI: 10.1128/jb.00240-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/27/2020] [Indexed: 12/19/2022] Open
Abstract
RNases are key regulatory components in prokaryotes, responsible for the degradation and maturation of specific RNA molecules at precise times. Specifically, RNases allow cells to cope with changes in their environment through rapid alteration of gene expression. To date, few RNases have been characterized in the mammalian pathogen Brucella abortus In the present work, we sought to investigate several RNases in B. abortus and determine what role, if any, they have in pathogenesis. Of the 4 RNases reported in this study, the highly conserved endoribonuclease, RNase E, was found to play an integral role in the virulence of B. abortus Although rne, which encodes RNase E, is essential in B. abortus, we were able to generate a strain encoding a defective version of RNase E lacking the C-terminal portion of the protein, and this strain (rne-tnc) was attenuated in a mouse model of Brucella infection. RNA-sequencing analysis revealed massive RNA dysregulation in B. abortus rne-tnc, with 122 upregulated and 161 downregulated transcripts compared to the parental strain. Interestingly, several mRNAs related to metal homeostasis were significantly decreased in the rne-tnc strain. We also identified a small regulatory RNA (sRNA), called Bsr4, that exhibited significantly elevated levels in rne-tnc, demonstrating an important role for RNase E in sRNA-mediated regulatory pathways in Brucella Overall, these data highlight the importance of RNase E in B. abortus, including the role of RNase E in properly controlling mRNA levels and contributing to virulence in an animal model of infection.IMPORTANCE Brucellosis is a debilitating disease of humans and animals globally, and there is currently no vaccine to combat human infection by Brucella spp. Moreover, effective antibiotic treatment in humans is extremely difficult and can lead to disease relapse. Therefore, it is imperative that systems and pathways be identified and characterized in the brucellae so new vaccines and therapies can be generated. In this study, we describe the impact of the endoribonuclease RNase E on the control of mRNA and small regulatory RNA (sRNA) levels in B. abortus, as well as the importance of RNase E for the full virulence of B. abortus This work greatly enhances our understanding of ribonucleases in the biology and pathogenesis of Brucella spp.
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Gao H, Zhang J, Lou J, Li J, Qin Q, Shi Q, Zhang Y, Kan B. Direct Binding and Regulation by Fur and HapR of the Intermediate Regulator and Virulence Factor Genes Within the ToxR Virulence Regulon in Vibrio cholerae. Front Microbiol 2020; 11:709. [PMID: 32362889 PMCID: PMC7181404 DOI: 10.3389/fmicb.2020.00709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/26/2020] [Indexed: 01/30/2023] Open
Abstract
Cholera toxin (CT) and toxin coregulated pilus (TCP, TcpA is the major subunit) are two major virulence factors of Vibrio cholerae, both of which play critical roles in developing severe diarrhea in human. Expression of CT and TCP is under the tight control of the regulatory cascade known as the ToxR virulence regulon, which is composed of three regulators ToxR, TcpP, and ToxT. Besides, their expression is also regulated by the quorum sensing (QS) master regulator HapR and the regulatory protein Fur. Though transcription of tcpP, toxT, and/or tcpA are reported to be regulated by HapR and Fur, to date there are no studies to verify their direct regulations. In the present study, we showed that HapR directly repress the transcription of tcpP and tcpA by binding to their promoter regions, and possibly repress toxT transcription in an indirect manner. Fur directly activated the transcription of tcpP, toxT, and tcpA by binding to their promoters. Taking account of the sequential expression of hapR, fur, tcpP, toxT, and tcpA in the different growth phases of V. cholerae, we deduce that at the early mid-logarithmic growth phase, Fur binds to the promoters of tcpP, toxT, and tcpA to activate their transcription; while at the later mid-logarithmic growth phase, HapR can bind to the promoters of tcpP and tcpA to repress their transcription. Our study reveals the new recognition in the virulence regulatory pathways in V. cholerae and suggests the complicated and subtle regulation network with the growth density dependence.
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Affiliation(s)
- He Gao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jingyun Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jing Lou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jie Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qin Qin
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qiannan Shi
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yiquan Zhang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Biao Kan
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Abstract
Hfq (host factor for phage Q beta) is key for posttranscriptional gene regulation in many bacteria. Hfq's function is to stabilize sRNAs and to facilitate base-pairing with trans-encoded target mRNAs. Loss of Hfq typically results in pleiotropic phenotypes, and, in the major human pathogen Vibrio cholerae, Hfq inactivation has been linked to reduced virulence, failure to produce biofilms, and impaired intercellular communication. However, the RNA ligands of Hfq in V. cholerae are currently unknown. Here, we used RIP-seq (RNA immunoprecipitation followed by high-throughput sequencing) analysis to identify Hfq-bound RNAs in V. cholerae Our work revealed 603 coding and 85 noncoding transcripts associated with Hfq, including 44 sRNAs originating from the 3' end of mRNAs. Detailed investigation of one of these latter transcripts, named FarS (fatty acid regulated sRNA), showed that this sRNA is produced by RNase E-mediated maturation of the fabB 3'UTR, and, together with Hfq, inhibits the expression of two paralogous fadE mRNAs. The fabB and fadE genes are antagonistically regulated by the major fatty acid transcription factor, FadR, and we show that, together, FadR, FarS, and FadE constitute a mixed feed-forward loop regulating the transition between fatty acid biosynthesis and degradation in V. cholerae Our results provide the molecular basis for studies on Hfq in V. cholerae and highlight the importance of a previously unrecognized sRNA for fatty acid metabolism in this major human pathogen.
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17
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Lambrecht SJ, Steglich C, Hess WR. A minimum set of regulators to thrive in the ocean. FEMS Microbiol Rev 2020; 44:232-252. [DOI: 10.1093/femsre/fuaa005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/19/2020] [Indexed: 12/25/2022] Open
Abstract
ABSTRACT
Marine cyanobacteria of the genus Prochlorococcus thrive in high cell numbers throughout the euphotic zones of the world's subtropical and tropical oligotrophic oceans, making them some of the most ecologically relevant photosynthetic microorganisms on Earth. The ecological success of these free-living phototrophs suggests that they are equipped with a regulatory system competent to address many different stress situations. However, Prochlorococcus genomes are compact and streamlined, with the majority encoding only five different sigma factors, five to six two-component systems and eight types of other transcriptional regulators. Here, we summarize the existing information about the functions of these protein regulators, about transcriptomic responses to defined stress conditions, and discuss the current knowledge about riboswitches, RNA-based regulation and the roles of certain metabolites as co-regulators. We focus on the best-studied isolate, Prochlorococcus MED4, but extend to other strains and ecotypes when appropriate, and we include some information gained from metagenomic and metatranscriptomic analyses.
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Affiliation(s)
- S Joke Lambrecht
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Claudia Steglich
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
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Jelínek J, Hoksza D, Hajič J, Pešek J, Drozen J, Hladík T, Klimpera M, Vohradský J, Pánek J. rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5479229. [PMID: 31032840 PMCID: PMC6482342 DOI: 10.1093/database/baz047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/01/2019] [Accepted: 03/21/2019] [Indexed: 12/11/2022]
Abstract
Secondary data structure of RNA molecules provides insights into the identity and function of RNAs. With RNAs readily sequenced, the question of their structural characterization is increasingly important. However, RNA structure is difficult to acquire. Its experimental identification is extremely technically demanding, while computational prediction is not accurate enough, especially for large structures of long sequences. We address this difficult situation with rPredictorDB, a predictive database of RNA secondary structures that aims to form a middle ground between experimentally identified structures in PDB and predicted consensus secondary structures in Rfam. The database contains individual secondary structures predicted using a tool for template-based prediction of RNA secondary structure for the homologs of the RNA families with at least one homolog with experimentally solved structure. Experimentally identified structures are used as the structural templates and thus the prediction has higher reliability than de novo predictions in Rfam. The sequences are downloaded from public resources. So far rPredictorDB covers 7365 RNAs with their secondary structures. Plots of the secondary structures use the Traveler package for readable display of RNAs with long sequences and complex structures, such as ribosomal RNAs. The RNAs in the output of rPredictorDB are extensively annotated and can be viewed, browsed, searched and downloaded according to taxonomic, sequence and structure data. Additionally, structure of user-provided sequences can be predicted using the templates stored in rPredictorDB.
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Affiliation(s)
- Jan Jelínek
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha.,Laboratory of Bioinformatics, Institute of Microbiology, The Czech Academy of Sciences, Videnska, Praha
| | - David Hoksza
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha.,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, avenue du Swing, Belvaux
| | - Jan Hajič
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha
| | - Jan Pešek
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha
| | - Jan Drozen
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha
| | - Tomáš Hladík
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha
| | - Michal Klimpera
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha
| | - Jiří Vohradský
- Laboratory of Bioinformatics, Institute of Microbiology, The Czech Academy of Sciences, Videnska, Praha
| | - Josef Pánek
- Laboratory of Bioinformatics, Institute of Microbiology, The Czech Academy of Sciences, Videnska, Praha
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Gao H, Xu J, Lu X, Li J, Lou J, Zhao H, Diao B, Shi Q, Zhang Y, Kan B. Expression of Hemolysin Is Regulated Under the Collective Actions of HapR, Fur, and HlyU in Vibrio cholerae El Tor Serogroup O1. Front Microbiol 2018; 9:1310. [PMID: 29971055 PMCID: PMC6018088 DOI: 10.3389/fmicb.2018.01310] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 05/29/2018] [Indexed: 12/19/2022] Open
Abstract
The biotype El Tor of serogroup O1 and most of the non-O1/non-O139 strains of Vibrio cholerae can produce an extracellular pore-forming toxin known as cholera hemolysin (HlyA). Expression of HlyA has been previously reported to be regulated by the quorum sensing (QS) and the regulatory proteins HlyU and Fur, but lacks the direct evidence for their binding to the promoter of hlyA. In the present work, we showed that the QS regulator HapR, along with Fur and HlyU, regulates the transcription of hlyA in V. cholerae El Tor biotype. At the late mid-logarithmic growth phase, HapR binds to the three promoters of fur, hlyU, and hlyA to repress their transcription. At the early mid-logarithmic growth phase, Fur binds to the promoters of hlyU and hlyA to repress their transcription; meanwhile, HlyU binds to the promoter of hlyA to activate its transcription, but it manifests direct inhibition of its own gene. The highest transcriptional level of hlyA occurs at an OD600 value of around 0.6–0.7, which may be due to the subtle regulation of HapR, Fur, and HlyU. The complex regulation of HapR, Fur, and HlyU on hlyA would be beneficial to the invasion and pathogenesis of V. cholerae during the different infection stages.
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Affiliation(s)
- He Gao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jialiang Xu
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, School of Food and Chemical Engineering, Beijing Technology and Business University, Beijing, China
| | - Xin Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jie Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jing Lou
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hongqun Zhao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Baowei Diao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qiannan Shi
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yiquan Zhang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Krin E, Pierlé SA, Sismeiro O, Jagla B, Dillies MA, Varet H, Irazoki O, Campoy S, Rouy Z, Cruveiller S, Médigue C, Coppée JY, Mazel D. Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation. BMC Genomics 2018; 19:373. [PMID: 29783948 PMCID: PMC5963079 DOI: 10.1186/s12864-018-4716-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/23/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicting LexA binding box consensus and in vitro validation. Here, we perform whole transcriptome sequencing from Vibrio cholerae treated with mitomycin C as an SOS inducer to characterize the SOS regulon and other pathways affected by this treatment. RESULTS Comprehensive transcriptional profiling allowed us to define the full landscape of promoters and transcripts active in V. cholerae. We performed extensive transcription start site (TSS) mapping as well as detection/quantification of the coding and non-coding RNA (ncRNA) repertoire in strain N16961. To improve TSS detection, we developed a new technique to treat RNA extracted from cells grown in various conditions. This allowed for identification of 3078 TSSs with an average 5'UTR of 116 nucleotides, and peak distribution between 16 and 64 nucleotides; as well as 629 ncRNAs. Mitomycin C treatment induced transcription of 737 genes and 28 ncRNAs at least 2 fold, while it repressed 231 genes and 17 ncRNAs. Data analysis revealed that in addition to the core genes known to integrate the SOS regulon, several metabolic pathways were induced. This study allowed for expansion of the Vibrio SOS regulon, as twelve genes (ubiEJB, tatABC, smpA, cep, VC0091, VC1190, VC1369-1370) were found to be co-induced with their adjacent canonical SOS regulon gene(s), through transcriptional read-through. Characterization of UV and mitomycin C susceptibility for mutants of these newly identified SOS regulon genes and other highly induced genes and ncRNAs confirmed their role in DNA damage rescue and protection. CONCLUSIONS We show that genotoxic stress induces a pervasive transcriptional response, affecting almost 20% of the V. cholerae genes. We also demonstrate that the SOS regulon is larger than previously known, and its syntenic organization is conserved among Vibrio species. Furthermore, this specific co-localization is found in other γ-proteobacteria for genes recN-smpA and rmuC-tatABC, suggesting SOS regulon conservation in this phylum. Finally, we comment on the limitations of widespread NGS approaches for identification of all RNA species in bacteria.
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Affiliation(s)
- Evelyne Krin
- 0000 0001 2353 6535grid.428999.7Département Génomes et Génétique, Institut Pasteur, Unité de Plasticité du Génome Bactérien, Paris, France
- 0000 0001 2112 9282grid.4444.0CNRS, UMR 3525, Paris, France
| | - Sebastian Aguilar Pierlé
- 0000 0001 2353 6535grid.428999.7Département Génomes et Génétique, Institut Pasteur, Unité de Plasticité du Génome Bactérien, Paris, France
- 0000 0001 2112 9282grid.4444.0CNRS, UMR 3525, Paris, France
| | - Odile Sismeiro
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
| | - Bernd Jagla
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
- Present adress: Institut Pasteur, Biomarker Discovery Platform, UtechS CB and Hub Bioinformatique et Biostatistique – C3BI, USR 3756 IP CNRS, Paris, France
| | - Marie-Agnès Dillies
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
- Present adress: Institut Pasteur, Hub Bioinformatique et Biostatistique – C3BI, USR 3756 IP CNRS, Paris, France
| | - Hugo Varet
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
| | - Oihane Irazoki
- grid.7080.fDepartament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, Spain
| | - Susana Campoy
- grid.7080.fDepartament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, Spain
| | - Zoé Rouy
- 0000 0001 2180 5818grid.8390.2UMR 8030, CNRS, CEA, Institut de Biologie François Jacob - Genoscope, Laboratoire d’Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Evry-Val-d’Essonne, Evry, France
| | - Stéphane Cruveiller
- 0000 0001 2180 5818grid.8390.2UMR 8030, CNRS, CEA, Institut de Biologie François Jacob - Genoscope, Laboratoire d’Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Evry-Val-d’Essonne, Evry, France
| | - Claudine Médigue
- 0000 0001 2180 5818grid.8390.2UMR 8030, CNRS, CEA, Institut de Biologie François Jacob - Genoscope, Laboratoire d’Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Evry-Val-d’Essonne, Evry, France
| | - Jean-Yves Coppée
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
| | - Didier Mazel
- 0000 0001 2353 6535grid.428999.7Département Génomes et Génétique, Institut Pasteur, Unité de Plasticité du Génome Bactérien, Paris, France
- 0000 0001 2112 9282grid.4444.0CNRS, UMR 3525, Paris, France
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Abstract
ABSTRACT
While iron is essential to sustain growth, its excess can be detrimental to the cell by generating highly toxic reactive oxygen species. Regulation of iron homeostasis thus plays a vital role in almost all living organisms. During the last 15 years, the small RNA (sRNA) RyhB has been shown to be a key actor of iron homeostasis regulation in bacteria. Through multiple molecular mechanisms, RyhB represses expendable iron-utilizing proteins, promotes siderophore production, and coordinates Fe-S cluster cofactor biogenesis, thereby establishing a so-called iron-sparing response. In this review, we will summarize knowledge on how sRNAs control iron homeostasis mainly through studies on RyhB in
Escherichia coli
. The parallel roles and modes of action of other sRNAs in different bacteria will also be described. Finally, we will discuss what questions remain to be answered concerning this important stress response regulation by sRNAs.
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Ha S, Shin B, Park W. Lack of glyoxylate shunt dysregulates iron homeostasis in Pseudomonas aeruginosa. MICROBIOLOGY-SGM 2018; 164:587-599. [PMID: 29465342 DOI: 10.1099/mic.0.000623] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The aceA and glcB genes, encoding isocitrate lyase (ICL) and malate synthase, respectively, are not in an operon in many bacteria, including Pseudomonas aeruginosa, unlike in Escherichia coli. Here, we show that expression of aceA in P. aeruginosa is specifically upregulated under H2O2-induced oxidative stress and under iron-limiting conditions. In contrast, the addition of exogenous redox active compounds or antibiotics increases the expression of glcB. The transcriptional start sites of aceA under iron-limiting conditions and in the presence of iron were found to be identical by 5' RACE. Interestingly, the enzymatic activities of ICL and isocitrate dehydrogenase had opposite responses under different iron conditions, suggesting that the glyoxylate shunt (GS) might be important under iron-limiting conditions. Remarkably, the intracellular iron concentration was lower while the iron demand was higher in the GS-activated cells growing on acetate compared to cells growing on glucose. Absence of GS dysregulated iron homeostasis led to changes in the cellular iron pool, with higher intracellular chelatable iron levels. In addition, GS mutants were found to have higher cytochrome c oxidase activity on iron-supplemented agar plates of minimal media, which promoted the growth of the GS mutants. However, deletion of the GS genes resulted in higher sensitivity to a high concentration of H2O2, presumably due to iron-mediated killing. In conclusion, the GS system appears to be tightly linked to iron homeostasis in the promotion of P. aeruginosa survival under oxidative stress.
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Affiliation(s)
- Sunhee Ha
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Bora Shin
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
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Gans J, Osborne J, Cheng J, Djapgne L, Oglesby-Sherrouse AG. Sequence-Specific Affinity Chromatography of Bacterial Small Regulatory RNA-Binding Proteins from Bacterial Cells. Methods Mol Biol 2018; 1737:341-350. [PMID: 29484602 DOI: 10.1007/978-1-4939-7634-8_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Bacterial small RNA molecules (sRNAs) are increasingly recognized as central regulators of bacterial stress responses and pathogenesis. In many cases, RNA-binding proteins are critical for the stability and function of sRNAs. Previous studies have adopted strategies to genetically tag an sRNA of interest, allowing isolation of RNA-protein complexes from cells. Here we present a sequence-specific affinity purification protocol that requires no prior genetic manipulation of bacterial cells, allowing isolation of RNA-binding proteins bound to native RNA molecules.
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Affiliation(s)
- Jonathan Gans
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, MD, USA
| | - Jonathan Osborne
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, MD, USA
| | - Juliet Cheng
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, MD, USA
| | - Louise Djapgne
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, MD, USA
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Thode SK, Bækkedal C, Söderberg JJ, Hjerde E, Hansen H, Haugen P. Construction of a fur null mutant and RNA-sequencing provide deeper global understanding of the Aliivibrio salmonicida Fur regulon. PeerJ 2017; 5:e3461. [PMID: 28717590 PMCID: PMC5511505 DOI: 10.7717/peerj.3461] [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: 01/09/2017] [Accepted: 05/24/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The ferric uptake regulator (Fur) is a transcription factor and the main regulator of iron acquisition in prokaryotes. When bound to ferric iron, Fur recognizes its DNA binding site and generally executes its function by repressing transcription of its target genes. Due to its importance in virulence, the Fur regulon is well studied for several model bacteria. In our previous work, we used computational predictions and microarray to gain insights into Fur-regulation in Aliivibrio salmonicida, and have identified a number of genes and operons that appear to be under direct control of Fur. To provide a more accurate and deeper global understanding of the biological role of Fur we have now generated an A. salmonicida fur knock-out strain and used RNA-sequencing to compare gene expression between the wild-type and fur null mutant strains. RESULTS An A. salmonicida fur null mutant strain was constructed. Biological assays demonstrate that deletion of fur results in loss of fitness, with reduced growth rates, and reduced abilities to withstand low-iron conditions, and oxidative stress. When comparing expression levels in the wild-type and the fur null mutant we retrieved 296 differentially expressed genes distributed among 18 of 21 functional classes of genes. A gene cluster encoding biosynthesis of the siderophore bisucaberin represented the highest up-regulated genes in the fur null mutant. Other highly up-regulated genes all encode proteins important for iron acquisition. Potential targets for the RyhB sRNA was predicted from the list of down-regulated genes, and significant complementarities were found between RyhB and mRNAs of the fur, sodB, cysN and VSAL_I0422 genes. Other sRNAs with potential functions in iron homeostasis were identified. CONCLUSION The present work provides by far the most comprehensive and deepest understanding of the Fur regulon in A. salmonicida to date. Our data also contribute to a better understanding of how Fur plays a key role in iron homeostasis in bacteria in general, and help to show how Fur orchestrates iron uptake when iron levels are extremely low.
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Affiliation(s)
- Sunniva Katharina Thode
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiTThe Arctic University of Norway, Tromsø, Norway
| | - Cecilie Bækkedal
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiTThe Arctic University of Norway, Tromsø, Norway
| | - Jenny Johansson Söderberg
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiTThe Arctic University of Norway, Tromsø, Norway
| | - Erik Hjerde
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiTThe Arctic University of Norway, Tromsø, Norway
| | - Hilde Hansen
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiTThe Arctic University of Norway, Tromsø, Norway
| | - Peik Haugen
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiTThe Arctic University of Norway, Tromsø, Norway
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25
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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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26
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Meyer MM. The role of mRNA structure in bacterial translational regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27301829 DOI: 10.1002/wrna.1370] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 01/08/2023]
Abstract
The characteristics of bacterial messenger RNAs (mRNAs) that influence translation efficiency provide many convenient handles for regulation of gene expression, especially when coupled with the processes of transcription termination and mRNA degradation. An mRNA's structure, especially near the site of initiation, has profound consequences for how readily it is translated. This property allows bacterial gene expression to be altered by changes to mRNA structure induced by temperature, or interactions with a wide variety of cellular components including small molecules, other RNAs (such as sRNAs and tRNAs), and RNA-binding proteins. This review discusses the links between mRNA structure and translation efficiency, and how mRNA structure is manipulated by conditions and signals within the cell to regulate gene expression. The range of RNA regulators discussed follows a continuum from very complex tertiary structures such as riboswitch aptamers and ribosomal protein-binding sites to thermosensors and mRNA:sRNA interactions that involve only base-pairing interactions. Furthermore, the high degrees of diversity observed for both mRNA structures and the mechanisms by which inhibition of translation occur have significant consequences for understanding the evolution of bacterial translational regulation. WIREs RNA 2017, 8:e1370. doi: 10.1002/wrna.1370 For further resources related to this article, please visit the WIREs website.
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27
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Kim JN. Roles of two RyhB paralogs in the physiology of Salmonella enterica. Microbiol Res 2016; 186-187:146-52. [PMID: 27242152 DOI: 10.1016/j.micres.2016.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/07/2016] [Accepted: 04/10/2016] [Indexed: 11/18/2022]
Abstract
Salmonella has evolved complicated regulatory systems to regulate the expression of virulence determinants that are acquired by horizontal gene transfer in response to various environmental niches. Among these, small RNA (sRNA)-mediated regulation exhibits unique features, distinct from those of protein factor-mediated regulation, which may provide benefits for a pathogen coping with the complex stress conditions encountered during host infection. Specifically, iron acquisition by this pathogenic bacterium is important for cellular processes such as energy metabolism and DNA replication. Many studies on the role of RyhB sRNA have begun to unveil the essential nature of iron acquisition in allowing the organism to persist and develop pathogenicity. The Salmonella genome encodes two RyhB paralogs, RyhB-1 and RyhB-2, which are known to act singularly or together on target expression. Based on the mechanism of Escherichia coli RyhB function, this review proposes a possible model to show how two Salmonella RyhB paralogs regulate the level of target mRNAs by sensing environmental inputs or conditions. This review also describes the involvement of Salmonella RyhBs in diverse functions including nitrate homeostasis, adaptive system to oxidative stress, and intracellular survival. Thus, the two Salmonella RyhBs play a critical role in the regulation of gene expression that appears to be essential for persistence and pathogenesis of Salmonella spp.
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Affiliation(s)
- Jeong Nam Kim
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610, United States.
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28
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Kazi MI, Conrado AR, Mey AR, Payne SM, Davies BW. ToxR Antagonizes H-NS Regulation of Horizontally Acquired Genes to Drive Host Colonization. PLoS Pathog 2016; 12:e1005570. [PMID: 27070545 PMCID: PMC4829181 DOI: 10.1371/journal.ppat.1005570] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 03/22/2016] [Indexed: 02/04/2023] Open
Abstract
The virulence regulator ToxR initiates and coordinates gene expression needed by Vibrio cholerae to colonize the small intestine and cause disease. Despite its prominence in V. cholerae virulence, our understanding of the direct ToxR regulon is limited to four genes: toxT, ompT, ompU and ctxA. Here, we determine ToxR’s genome-wide DNA-binding profile and demonstrate that ToxR is a global regulator of both progenitor genome-encoded genes and horizontally acquired islands that encode V. cholerae’s major virulence factors and define pandemic lineages. We show that ToxR shares more than a third of its regulon with the histone-like nucleoid structuring protein H-NS, and antagonizes H-NS binding at shared binding locations. Importantly, we demonstrate that this regulatory interaction is the critical function of ToxR in V. cholerae colonization and biofilm formation. In the absence of H-NS, ToxR is no longer required for V. cholerae to colonize the infant mouse intestine or for robust biofilm formation. We further illustrate a dramatic difference in regulatory scope between ToxR and other prominent virulence regulators, despite similar predicted requirements for DNA binding. Our results suggest that factors in addition to primary DNA structure influence the ability of ToxR to recognize its target promoters. The transcription factor ToxR initiates a virulence regulatory cascade required for V. cholerae to express essential host colonization factors and cause disease. Genome-wide expression studies suggest that ToxR regulates many genes important for V. cholerae pathogenesis, yet our knowledge of the direct regulon controlled by ToxR is limited to just four genes. Here, we determine ToxR’s genome-wide DNA-binding profile and show that ToxR is a global regulator of both progenitor genome-encoded genes and horizontally acquired islands that encode V. cholerae’s major virulence factors. Our results suggest that ToxR has gained regulatory control over important acquired elements that not only drive V. cholerae pathogenesis, but also define the major transitions of V. cholerae pandemic lineages. We demonstrate that ToxR shares more than a third of its regulon with the histone-like nucleoid structuring protein H-NS, and antagonizes H-NS for control of critical colonization functions. This regulatory interaction is the major role of ToxR in V. cholerae colonization, since deletion of hns abrogates the need for ToxR in V. cholerae host colonization. By comparing the genome-wide binding profiles of ToxR and other critical virulence regulators, we show that, despite similar predicted DNA binding requirements, ToxR is unique in its global control of progenitor-encoded and acquired genes. Our results suggest that factors in addition to primary DNA structure determine selection of ToxR binding sites.
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Affiliation(s)
- Misha I. Kazi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Aaron R. Conrado
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Alexandra R. Mey
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Shelley M. Payne
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
- Institute of Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Bryan W. Davies
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
- Institute of Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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29
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Payne SM, Mey AR, Wyckoff EE. Vibrio Iron Transport: Evolutionary Adaptation to Life in Multiple Environments. Microbiol Mol Biol Rev 2016; 80:69-90. [PMID: 26658001 PMCID: PMC4711184 DOI: 10.1128/mmbr.00046-15] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Iron is an essential element for Vibrio spp., but the acquisition of iron is complicated by its tendency to form insoluble ferric complexes in nature and its association with high-affinity iron-binding proteins in the host. Vibrios occupy a variety of different niches, and each of these niches presents particular challenges for acquiring sufficient iron. Vibrio species have evolved a wide array of iron transport systems that allow the bacteria to compete for this essential element in each of its habitats. These systems include the secretion and uptake of high-affinity iron-binding compounds (siderophores) as well as transport systems for iron bound to host complexes. Transporters for ferric and ferrous iron not complexed to siderophores are also common to Vibrio species. Some of the genes encoding these systems show evidence of horizontal transmission, and the ability to acquire and incorporate additional iron transport systems may have allowed Vibrio species to more rapidly adapt to new environmental niches. While too little iron prevents growth of the bacteria, too much can be lethal. The appropriate balance is maintained in vibrios through complex regulatory networks involving transcriptional repressors and activators and small RNAs (sRNAs) that act posttranscriptionally. Examination of the number and variety of iron transport systems found in Vibrio spp. offers insights into how this group of bacteria has adapted to such a wide range of habitats.
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Affiliation(s)
- Shelley M Payne
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Alexandra R Mey
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Elizabeth E Wyckoff
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
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30
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Sabharwal D, Song T, Papenfort K, Wai SN. The VrrA sRNA controls a stationary phase survival factor Vrp of Vibrio cholerae. RNA Biol 2015; 12:186-96. [PMID: 25826569 PMCID: PMC4615753 DOI: 10.1080/15476286.2015.1017211] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Small non-coding RNAs (sRNAs) are emerging regulatory elements in bacteria. The Vibrio cholerae sRNA VrrA has previously been shown to down-regulate outer membrane proteins (OmpA and OmpT) and biofilm matrix protein (RbmC) by base-pairing with the 5′ region of the corresponding mRNAs. In this study, we present an additional target of VrrA in V. cholerae, the mRNA coding for the ribosome binding protein Vrp. Vrp is homologous to ribosome-associated inhibitor A (RaiA) of Escherichia coli which facilitates stationary phase survival through ribosome hibernation. We show that VrrA down-regulates Vrp protein synthesis by base-pairing to the 5′ region of vrp mRNA and that the regulation requires the RNA chaperone protein, Hfq. We further demonstrate that Vrp is highly expressed during stationary phase growth and associates with the ribosome of V. cholerae. The effect of the Vrp protein in starvation survival is synergistic with that of the VC2530 protein, a homolog of the E. coli hibernation promoting factor HPF, suggesting a combined role for these proteins in ribosome hibernation in V. cholerae. Vrp and VC2530 are important for V. cholerae starvation survival under nutrient deficient conditions. While VC2530 is down-regulated in cells lacking vrrA, mutation of vrp results in VC2530 activation. This is the first report indicating a regulatory role for an sRNA, modulating stationary factors involved in bacterial ribosome hibernation.
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Affiliation(s)
- Dharmesh Sabharwal
- a Department of Molecular Biology; The Laboratory for Molecular Infection Medicine Sweden (MIMS) , Umeå Centre for Microbial Research (UCMR); Umeå University , Umeå , Sweden
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31
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Ryan D, Pati NB, Ojha UK, Padhi C, Ray S, Jaiswal S, Singh GP, Mannala GK, Schultze T, Chakraborty T, Suar M. Global transcriptome and mutagenic analyses of the acid tolerance response of Salmonella enterica serovar Typhimurium. Appl Environ Microbiol 2015; 81:8054-65. [PMID: 26386064 PMCID: PMC4651094 DOI: 10.1128/aem.02172-15] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 09/01/2015] [Indexed: 01/18/2023] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is one of the leading causative agents of food-borne bacterial gastroenteritis. Swift invasion through the intestinal tract and successful establishment in systemic organs are associated with the adaptability of S. Typhimurium to different stress environments. Low-pH stress serves as one of the first lines of defense in mammalian hosts, which S. Typhimurium must efficiently overcome to establish an infection. Therefore, a better understanding of the molecular mechanisms underlying the adaptability of S. Typhimurium to acid stress is highly relevant. In this study, we have performed a transcriptome analysis of S. Typhimurium under the acid tolerance response (ATR) and found a large number of genes (∼47%) to be differentially expressed (more than 1.5-fold or less than -1.5-fold; P < 0.01). Functional annotation revealed differentially expressed genes to be associated with regulation, metabolism, transport and binding, pathogenesis, and motility. Additionally, our knockout analysis of a subset of differentially regulated genes facilitated the identification of proteins that contribute to S. Typhimurium ATR and virulence. Mutants lacking genes encoding the K(+) binding and transport protein KdpA, hypothetical protein YciG, the flagellar hook cap protein FlgD, and the nitrate reductase subunit NarZ were significantly deficient in their ATRs and displayed varied in vitro virulence characteristics. This study offers greater insight into the transcriptome changes of S. Typhimurium under the ATR and provides a framework for further research on the subject.
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Affiliation(s)
- Daniel Ryan
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India
| | - Niladri Bhusan Pati
- Institute of Medical Microbiology, German Centre of Infection Research, Site Giessen-Marburg-Langen, Justus-Liebig-University Giessen, Giessen, Germany
| | - Urmesh K Ojha
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India
| | | | - Shilpa Ray
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India
| | - Sangeeta Jaiswal
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India
| | - Gajinder P Singh
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India
| | - Gopala K Mannala
- Institute of Medical Microbiology, German Centre of Infection Research, Site Giessen-Marburg-Langen, Justus-Liebig-University Giessen, Giessen, Germany
| | - Tilman Schultze
- Institute of Medical Microbiology, German Centre of Infection Research, Site Giessen-Marburg-Langen, Justus-Liebig-University Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, German Centre of Infection Research, Site Giessen-Marburg-Langen, Justus-Liebig-University Giessen, Giessen, Germany
| | - Mrutyunjay Suar
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India
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32
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Kaushik MS, Singh P, Tiwari B, Mishra AK. Ferric Uptake Regulator (FUR) protein: properties and implications in cyanobacteria. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1134-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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33
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Updegrove TB, Shabalina SA, Storz G. How do base-pairing small RNAs evolve? FEMS Microbiol Rev 2015; 39:379-91. [PMID: 25934120 DOI: 10.1093/femsre/fuv014] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2015] [Indexed: 01/12/2023] Open
Abstract
The increasing numbers of characterized base-pairing small RNAs (sRNAs) and the identification of these regulators in a broad range of bacteria are allowing comparisons between species and explorations of sRNA evolution. In this review, we describe some examples of trans-encoded base-pairing sRNAs that are species-specific and others that are more broadly distributed. We also describe examples of sRNA orthologs where different features are conserved. These examples provide the background for a discussion of mechanisms of sRNA evolution and selective pressures on the sRNAs and their mRNA target(s).
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Affiliation(s)
- Taylor B Updegrove
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institutes of Health, Bethesda, MD 20892, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Gisela Storz
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institutes of Health, Bethesda, MD 20892, USA
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34
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Wang Y, Ke Y, Xu J, Wang L, Wang T, Liang H, Zhang W, Gong C, Yuan J, Zhuang Y, An C, Lei S, Du X, Wang Z, Li W, Yuan X, Huang L, Yang X, Chen Z. Identification of a Novel Small Non-Coding RNA Modulating the Intracellular Survival of Brucella melitensis. Front Microbiol 2015; 6:164. [PMID: 25852653 PMCID: PMC4365724 DOI: 10.3389/fmicb.2015.00164] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 02/02/2015] [Indexed: 12/20/2022] Open
Abstract
Bacterial small non-coding RNAs (sRNAs) are gene expression modulators respond to environmental changes, stressful conditions, and pathogenesis. In this study, by using a combined bioinformatic and experimental approach, eight novel sRNA genes were identified in intracellular pathogen Brucella melitensis. BSR0602, one sRNA that was highly induced in stationary phase, was further examined and found to modulate the intracellular survival of B. melitensis. BSR0602 was present at very high levels in vitro under stresses similar to those encountered during infection in host macrophages. Furthermore, BSR0602 was found to be highly expressed in the spleens of infected mice, suggesting its potential role in the control of pathogenesis. BSR0602 targets the mRNAs coding for gntR, a global transcriptional regulator, which is required for B. melitensis virulence. Overexpression of BSR0602 results in distinct reduction in the gntR mRNA level. B. melitensis with high level of BSR0602 is defective in bacteria intracellular survival in macrophages and defective in growth in the spleens of infected mice. Therefore, BSR0602 may directly inhibit the expression of gntR, which then impairs Brucellae intracellular survival and contributes to Brucella infection. Our findings suggest that BSR0602 is responsible for bacterial adaptation to stress conditions and thus modulate B. melitensis intracellular survival.
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Affiliation(s)
- Yufei Wang
- Department of Laboratory Medicine, The General Hospital of Chinese People's Armed Police Forces , Beijing , China
| | - Yuehua Ke
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Jie Xu
- Laboratory of Clinical Immunology in Jiangsu Province, Department of Clinical Laboratory, The First Affiliated Hospital of Soochow University , Suzhou , China
| | - Ligui Wang
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Tongkun Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing , China
| | - Hui Liang
- Department of Laboratory Medicine, The General Hospital of Chinese People's Armed Police Forces , Beijing , China
| | - Wei Zhang
- Department of Laboratory Medicine, The General Hospital of Chinese People's Armed Police Forces , Beijing , China
| | - Chunli Gong
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Jiuyun Yuan
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Yubin Zhuang
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Chang An
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Shuangshuang Lei
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Xinying Du
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Zhoujia Wang
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Wenna Li
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Xitong Yuan
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Liuyu Huang
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Xiaoli Yang
- Department of Laboratory Medicine, The General Hospital of Chinese People's Armed Police Forces , Beijing , China
| | - Zeliang Chen
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
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Thode SK, Kahlke T, Robertsen EM, Hansen H, Haugen P. The immediate global responses of Aliivibrio salmonicida to iron limitations. BMC Microbiol 2015; 15:9. [PMID: 25649684 PMCID: PMC4324432 DOI: 10.1186/s12866-015-0342-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 01/09/2015] [Indexed: 01/15/2023] Open
Abstract
Background Iron is an essential micronutrient for all living organisms, and virulence and sequestration of iron in pathogenic bacteria are believed to be correlated. As a defence mechanism, potential hosts therefore keep the level of free iron inside the body to a minimum. In general, iron metabolism is well studied for some bacteria (mostly human or animal pathogens). However, this area is still under-investigated for a number of important bacterial pathogens. Aliivibrio salmonicida is a fish pathogen, and previous studies of this bacterium have shown that production of siderophores is temperature regulated and dependent on low iron conditions. In this work we studied the immediate changes in transcription in response to a sudden decrease in iron levels in cultures of A. salmonicida. In addition, we compared our results to studies performed with Vibrio cholerae and Vibrio vulnificus using a pan-genomic approach. Results Microarray technology was used to monitor global changes in transcriptional levels. Cultures of A. salmonicida were grown to mid log phase before the iron chelator 2,2’-dipyridyl was added and samples were collected after 15 minutes of growth. Using our statistical cut-off values, we retrieved thirty-two differentially expressed genes where the most up-regulated genes belong to an operon encoding proteins responsible for producing the siderophore bisucaberin. A subsequent pan-transcriptome analysis revealed that nine of the up-regulated genes from our dataset were also up-regulated in datasets from similar experiments using V. cholerae and V. vulnificus, thus indicating that these genes are involved in a shared strategy to mitigate low iron conditions. Conclusions The present work highlights the effect of iron limitation on the gene regulatory network of the fish pathogen A. salmonicida, and provides insights into common and unique strategies of Vibrionaceae species to mitigate low iron conditions. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0342-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sunniva Katharina Thode
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiT - The Arctic University of Norway, Tromsø, 9037, Norway.
| | - Tim Kahlke
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiT - The Arctic University of Norway, Tromsø, 9037, Norway. .,Current address: Environmental Genomics Team, CSIRO Marine and Atmospheric Research, Castray Esplanade, Hobart, 7000, TAS, Australia.
| | - Espen Mikal Robertsen
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiT - The Arctic University of Norway, Tromsø, 9037, Norway.
| | - Hilde Hansen
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiT - The Arctic University of Norway, Tromsø, 9037, Norway.
| | - Peik Haugen
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiT - The Arctic University of Norway, Tromsø, 9037, Norway.
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Peng X, Dong H, Wu Q. A new cis-encoded sRNA, BsrH, regulating the expression of hemH gene in Brucella abortus 2308. FEMS Microbiol Lett 2014; 362:1-7. [DOI: 10.1093/femsle/fnu017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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The small RNA RyhB contributes to siderophore production and virulence of uropathogenic Escherichia coli. Infect Immun 2014; 82:5056-68. [PMID: 25245805 DOI: 10.1128/iai.02287-14] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In Escherichia coli, the small regulatory noncoding RNA (sRNA) RyhB and the global ferric uptake regulator (Fur) mediate iron acquisition and storage control. Iron is both essential and potentially toxic for most living organisms, making the precise maintenance of iron homeostasis necessary for survival. While the roles of these regulators in iron homeostasis have been well studied in a nonpathogenic E. coli strain, their impact on the production of virulence-associated factors is still unknown for a pathogenic E. coli strain. We thus investigated the roles of RyhB and Fur in iron homeostasis and virulence of the uropathogenic E. coli (UPEC) strain CFT073. In a murine model of urinary tract infection (UTI), deletion of fur alone did not attenuate virulence, whereas a ΔryhB mutant and a Δfur ΔryhB double mutant showed significantly reduced bladder colonization. The Δfur mutant was more sensitive to oxidative stress and produced more of the siderophores enterobactin, salmochelins, and aerobactin than the wild-type strain. In contrast, while RyhB was not implicated in oxidative stress resistance, the ΔryhB mutant produced lower levels of siderophores. This decrease was correlated with the downregulation of shiA (encoding a transporter of shikimate, a precursor of enterobactin and salmochelin biosynthesis) and iucD (involved in aerobactin biosynthesis) in this mutant grown in minimal medium or in human urine. iucD was also downregulated in bladders infected with the ΔryhB mutant compared to those infected with the wild-type strain. Our results thus demonstrate that the sRNA RyhB is involved in production of iron acquisition systems and colonization of the urinary tract by pathogenic E. coli.
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McClure R, Tjaden B, Genco C. Identification of sRNAs expressed by the human pathogen Neisseria gonorrhoeae under disparate growth conditions. Front Microbiol 2014; 5:456. [PMID: 25221548 PMCID: PMC4148029 DOI: 10.3389/fmicb.2014.00456] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 08/11/2014] [Indexed: 01/17/2023] Open
Abstract
In the last several years, bacterial gene regulation via small RNAs (sRNAs) has been recognized as an important mechanism controlling expression of essential proteins that are critical to bacterial growth and metabolism. Technologies such as RNA-seq are rapidly expanding the field of sRNAs and are enabling a global view of the “sRNAome” of several bacterial species. While numerous sRNAs have been identified in a variety of both Gram-negative and Gram-positive bacteria, only a very small number have been fully characterized in the human pathogen Neisseria gonorrhoeae, the etiological agent of the STD gonorrhea. Here we present the first analysis of N. gonorrhoeae specifically focused on the identification of sRNAs through RNA-seq analysis of the organism cultured under different in vitro growth conditions. Using a new computational program, Rockhopper, to analyze prokaryotic RNA-seq data obtained from N. gonorrhoeae we identified several putative sRNAs and confirmed their expression and size through Northern blot analysis. In addition, RNA was collected from four different growth conditions (iron replete and deplete, as well as with and without co-culture with human endocervical cells). Many of the putative sRNAs identified shoed varying expression levels relative to the different growth conditions examine or were detected only under certain conditions but not others. Comparisons of identified sRNAs with the regulatory pattern of putative mRNA targets revealed possible functional roles for these sRNAs. These studies are the first to carry out a global analysis of N. gonorrhoeae specifically focused on sRNAs and show that RNA-mediated regulation may be an important mechanism of gene control in this human pathogen.
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Affiliation(s)
- Ryan McClure
- Department of Medicine Section of Infectious Disease, Boston University School of Medicine Boston, MA, USA ; Department of Microbiology, Boston University School of Medicine Boston, MA, USA
| | - Brian Tjaden
- Department of Computer Science, Wellesley College Wellesley, MA, USA
| | - Caroline Genco
- Department of Medicine Section of Infectious Disease, Boston University School of Medicine Boston, MA, USA ; Department of Microbiology, Boston University School of Medicine Boston, MA, USA
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HrrF is the Fur-regulated small RNA in nontypeable Haemophilus influenzae. PLoS One 2014; 9:e105644. [PMID: 25157846 PMCID: PMC4144887 DOI: 10.1371/journal.pone.0105644] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/21/2014] [Indexed: 02/06/2023] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) are Gram-negative commensal bacteria that reside in the nasopharynx. NTHi can also cause multiple upper and lower respiratory tract diseases that include sinusitis, conjunctivitis, bronchitis, and otitis media. In numerous bacterial species the ferric uptake regulator (Fur) acts as a global regulator of iron homeostasis by negatively regulating the expression of iron uptake systems. However in NTHi strain 86-028NP and numerous other bacterial species there are multiple instances where Fur positively affects gene expression. It is known that many instances of positive regulation by Fur occur indirectly through a small RNA intermediate. However, no examples of small RNAs have been described in NTHi. Therefore we used RNA-Seq analysis to analyze the transcriptome of NTHi strain 86-028NPrpsL and an isogenic 86-028NPrpsLΔfur strain to identify Fur-regulated intergenic transcripts. From this analysis we identified HrrF, the first small RNA described in any Haemophilus species. Orthologues of this small RNA exist only among other Pasteurellaceae. Our analysis showed that HrrF is maximally expressed when iron levels are low. Additionally, Fur was shown to bind upstream of the hrrF promoter. RNA-Seq analysis was used to identify targets of HrrF which include genes whose products are involved in molybdate uptake, deoxyribonucleotide synthesis, and amino acid biosynthesis. The stability of HrrF is not dependent on the RNA chaperone Hfq. This study is the first step in an effort to investigate the role small RNAs play in altering gene expression in response to iron limitation in NTHi.
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Peer A, Margalit H. Evolutionary patterns of Escherichia coli small RNAs and their regulatory interactions. RNA (NEW YORK, N.Y.) 2014; 20:994-1003. [PMID: 24865611 PMCID: PMC4114697 DOI: 10.1261/rna.043133.113] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 03/23/2014] [Indexed: 06/03/2023]
Abstract
Most bacterial small RNAs (sRNAs) are post-transcriptional regulators of gene expression, exerting their regulatory function by base-pairing with their target mRNAs. While it has become evident that sRNAs play central regulatory roles in the cell, little is known about their evolution and the evolution of their regulatory interactions. Here we used the prokaryotic phylogenetic tree to reconstruct the evolutionary history of Escherichia coli sRNAs and their binding sites on target mRNAs. We discovered that sRNAs currently present in E. coli mainly accumulated inside the Enterobacteriales order, succeeding the appearance of other types of noncoding RNAs and concurrently with the evolution of a variant of the Hfq protein exhibiting a longer C-terminal region. Our analysis of the evolutionary ages of sRNA-mRNA interactions revealed that while all sRNAs were evolutionarily older than most of their known binding sites on mRNA targets, for quite a few sRNAs there was at least one binding site that coappeared with or preceded them. It is conceivable that the establishment of these first interactions forced selective pressure on the sRNAs, after which additional targets were acquired by fitting a binding site to the active region of the sRNA. This conjecture is supported by the appearance of many binding sites on target mRNAs only after the sRNA gain, despite the prior presence of the target gene in ancestral genomes. Our results suggest a selective mechanism that maintained the sRNAs across the phylogenetic tree, and shed light on the evolution of E. coli post-transcriptional regulatory network.
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Yu C, Lopez CA, Hu H, Xia Y, Freedman DS, Reddington AP, Daaboul GG, Ünlü MS, Genco CA. A high-throughput method to examine protein-nucleotide interactions identifies targets of the bacterial transcriptional regulatory protein fur. PLoS One 2014; 9:e96832. [PMID: 24811061 PMCID: PMC4014563 DOI: 10.1371/journal.pone.0096832] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/13/2014] [Indexed: 11/19/2022] Open
Abstract
The Ferric uptake regulatory protein (Fur) is a transcriptional regulatory protein that functions to control gene transcription in response to iron in a number of pathogenic bacteria. In this study, we applied a label-free, quantitative and high-throughput analysis method, Interferometric Reflectance Imaging Sensor (IRIS), to rapidly characterize Fur-DNA interactions in vitro with predicted Fur binding sequences in the genome of Neisseria gonorrhoeae, the causative agent of the sexually transmitted disease gonorrhea. IRIS can easily be applied to examine multiple protein-protein, protein-nucleotide and nucleotide-nucleotide complexes simultaneously and demonstrated here that seventy percent of the predicted Fur boxes in promoter regions of iron-induced genes bound to Fur in vitro with a range of affinities as observed using this microarray screening technology. Combining binding data with mRNA expression levels in a gonococcal fur mutant strain allowed us to identify five new gonococcal genes under Fur-mediated direct regulation.
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Affiliation(s)
- Chunxiao Yu
- Department of Medicine, Section of Infectious Diseases, Boston University School of Medicine, Boston University, Boston, Massachusetts, United States of America
| | - Carlos A. Lopez
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Han Hu
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, United States of America
| | - Yu Xia
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, United States of America
| | - David S. Freedman
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Alexander P. Reddington
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, United States of America
| | - George G. Daaboul
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - M. Selim Ünlü
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, United States of America
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Physics Department, Boston University, Boston, Massachusetts, United States of America
| | - Caroline Attardo Genco
- Department of Medicine, Section of Infectious Diseases, Boston University School of Medicine, Boston University, Boston, Massachusetts, United States of America
- Department of Microbiology, Boston University School of Medicine, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
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α-fur, an antisense RNA gene to fur in the extreme acidophile Acidithiobacillus ferrooxidans. Microbiology (Reading) 2014; 160:514-524. [DOI: 10.1099/mic.0.073171-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A large non-coding RNA, termed α-Fur, of ~1000 nt has been detected in the extreme acidophile Acidithiobacillus ferrooxidans encoded on the antisense strand to the iron-responsive master regulator fur (ferric uptake regulator) gene. A promoter for α-fur was predicted bioinformatically and validated using gene fusion experiments. The promoter is situated within the coding region and in the same sense as proB, potentially encoding a glutamate 5-kinase. The 3′ termination site of the α-fur transcript was determined by 3′ rapid amplification of cDNA ends to lie 7 nt downstream of the start of transcription of fur. Thus, α-fur is antisense to the complete coding region of fur, including its predicted ribosome-binding site. The genetic context of α-fur is conserved in several members of the genus Acidithiobacillus but not in all acidophiles, indicating that it is monophyletic but not niche specific. It is hypothesized that α-Fur regulates the cellular level of Fur. This is the fourth example of an antisense RNA to fur, although it is the first in an extreme acidophile, and underscores the growing importance of cis-encoded non-coding RNAs as potential regulators involved in the microbial iron-responsive stimulon.
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Nguyen AN, Jacq A. Small RNAs in the Vibrionaceae: an ocean still to be explored. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:381-92. [PMID: 24458378 DOI: 10.1002/wrna.1218] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 12/13/2013] [Accepted: 12/16/2013] [Indexed: 11/09/2022]
Abstract
In bacteria, the discovery of noncoding small RNAs (sRNAs) as modulators of gene expression in response to environmental signals has brought new insights into bacterial gene regulation, including control of pathogenicity. The Vibrionaceae constitute a family of marine bacteria of which many are responsible for infections affecting not only humans, such as Vibrio cholerae but also fish and marine invertebrates, representing the major cause of mortality in farmed marine species. They are able to colonize many habitats, existing as planktonic forms, in biofilms or associated with various hosts. This high adaptability is linked to their capacity to generate genetic diversity, in part through lateral gene transfer, but also by varying gene expression control. In the recent years, several major studies have illustrated the importance of small regulatory sRNAs in the Vibrionaceae for the control of pathogenicity and adaptation to environment and nutrient sources such as chitin, especially in V. cholerae and Vibrio harveyi. The existence of a complex regulatory network controlled by quorum sensing has been demonstrated in which sRNAs play central roles. This review covers major advances made in the discovery and elucidation of functions of Vibrionaceae sRNAs within the last 10 years.
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Affiliation(s)
- An Ngoc Nguyen
- Institut de Génétique et Microbiologie, UMR 8621 CNRS-Université Paris-Sud, 91405 Orsay Cedex, France
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Venkataramanan KP, Jones SW, McCormick KP, Kunjeti SG, Ralston MT, Meyers BC, Papoutsakis ET. The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum. BMC Genomics 2013; 14:849. [PMID: 24299206 PMCID: PMC3879012 DOI: 10.1186/1471-2164-14-849] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 11/14/2013] [Indexed: 01/01/2023] Open
Abstract
Background Small non-coding RNAs (sRNA) are emerging as major components of the cell’s regulatory network, several possessing their own regulons. A few sRNAs have been reported as being involved in general or toxic-metabolite stress, mostly in Gram- prokaryotes, but hardly any in Gram+ prokaryotes. Significantly, the role of sRNAs in the stress response remains poorly understood at the genome-scale level. It was previously shown that toxic-metabolite stress is one of the most comprehensive and encompassing stress responses in the cell, engaging both the general stress (or heat-shock protein, HSP) response as well as specialized metabolic programs. Results Using RNA deep sequencing (RNA-seq) we examined the sRNome of C. acetobutylicum in response to the native but toxic metabolites, butanol and butyrate. 7.5% of the RNA-seq reads mapped to genome outside annotated ORFs, thus demonstrating the richness and importance of the small RNome. We used comparative expression analysis of 113 sRNAs we had previously computationally predicted, and of annotated mRNAs to set metrics for reliably identifying sRNAs from RNA-seq data, thus discovering 46 additional sRNAs. Under metabolite stress, these 159 sRNAs displayed distinct expression patterns, a select number of which was verified by Northern analysis. We identified stress-related expression of sRNAs affecting transcriptional (6S, S-box & solB) and translational (tmRNA & SRP-RNA) processes, and 65 likely targets of the RNA chaperone Hfq. Conclusions Our results support an important role for sRNAs for understanding the complexity of the regulatory network that underlies the stress response in Clostridium organisms, whether related to normophysiology, pathogenesis or biotechnological applications.
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Troxell B, Hassan HM. Transcriptional regulation by Ferric Uptake Regulator (Fur) in pathogenic bacteria. Front Cell Infect Microbiol 2013; 3:59. [PMID: 24106689 PMCID: PMC3788343 DOI: 10.3389/fcimb.2013.00059] [Citation(s) in RCA: 290] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 09/18/2013] [Indexed: 12/16/2022] Open
Abstract
In the ancient anaerobic environment, ferrous iron (Fe2+) was one of the first metal cofactors. Oxygenation of the ancient world challenged bacteria to acquire the insoluble ferric iron (Fe3+) and later to defend against reactive oxygen species (ROS) generated by the Fenton chemistry. To acquire Fe3+, bacteria produce low-molecular weight compounds, known as siderophores, which have extremely high affinity for Fe3+. However, during infection the host restricts iron from pathogens by producing iron- and siderophore-chelating proteins, by exporting iron from intracellular pathogen-containing compartments, and by limiting absorption of dietary iron. Ferric Uptake Regulator (Fur) is a transcription factor which utilizes Fe2+ as a corepressor and represses siderophore synthesis in pathogens. Fur, directly or indirectly, controls expression of enzymes that protect against ROS damage. Thus, the challenges of iron homeostasis and defense against ROS are addressed via Fur. Although the role of Fur as a repressor is well-documented, emerging evidence demonstrates that Fur can function as an activator. Fur activation can occur through three distinct mechanisms (1) indirectly via small RNAs, (2) binding at cis regulatory elements that enhance recruitment of the RNA polymerase holoenzyme (RNAP), and (3) functioning as an antirepressor by removing or blocking DNA binding of a repressor of transcription. In addition, Fur homologs control defense against peroxide stress (PerR) and control uptake of other metals such as zinc (Zur) and manganese (Mur) in pathogenic bacteria. Fur family members are important for virulence within bacterial pathogens since mutants of fur, perR, or zur exhibit reduced virulence within numerous animal and plant models of infection. This review focuses on the breadth of Fur regulation in pathogenic bacteria.
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Affiliation(s)
- Bryan Troxell
- Department of Immunology and Microbiology, Indiana University School of Medicine Indianapolis, IN, USA
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Oglesby-Sherrouse AG, Murphy ER. Iron-responsive bacterial small RNAs: variations on a theme. Metallomics 2013; 5:276-86. [PMID: 23340911 DOI: 10.1039/c3mt20224k] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
For most living organisms, iron is both essential and potentially toxic, making the precise maintenance of iron homeostasis necessary for survival. To manage this paradox, bacteria regulate the acquisition, utilization, and storage of iron in response to its availability. The iron-dependent ferric uptake repressor (Fur) often mediates this iron-responsive regulation by both direct and indirect mechanisms. In 2002, Masse and Gottesman identified a novel target of Fur-mediated regulation in Escherichia coli: a gene encoding a small regulatory RNA (sRNA) termed RyhB. Under conditions of iron-limitation, RyhB is produced and functions to regulate the expression of several target genes encoding iron-utilizing enzymes, iron acquisition systems, and iron storage factors. This pivotal finding provided the missing link between environmental iron-limitation and previously observed decreases in certain iron-dependent metabolic pathways, a phenomenon now referred to as an "iron-sparing" response. The discovery of RyhB opened the door to the rapidly expanding field of bacterial iron-regulated sRNAs, which continue to be identified and described in numerous bacterial species. Most striking are findings that the impact of iron-responsive sRNA regulation often extends beyond iron homeostasis, particularly with regard to production of virulence-associated factors by pathogenic bacteria. This review discusses trends in the collective body of work on iron-regulated sRNAs, highlighting both the regulatory mechanisms they utilize to control target gene expression and the impact of this regulation on basic processes controlling bacterial physiology and virulence.
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Affiliation(s)
- Amanda G Oglesby-Sherrouse
- Department of Pharmaceutical Sciences, School of Pharmacy, Department of Microbiology and Immunology, School of Medicine, University of Maryland Baltimore, 20 Penn Street, Baltimore, MD, USA.
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The Vibrio parahaemolyticus small RNA RyhB promotes production of the siderophore vibrioferrin by stabilizing the polycistronic mRNA. J Bacteriol 2013; 195:3692-703. [PMID: 23772063 DOI: 10.1128/jb.00162-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
High-affinity iron acquisition in Vibrio parahaemolyticus is mediated by the cognate siderophore vibrioferrin. We have previously reported that the vibrioferrin biosynthesis operon (pvsOp) is regulated at the transcriptional level by the iron-responsive repressor Fur (T. Tanabe, T. Funahashi, H. Nakao, S. Miyoshi, S. Shinoda, and S. Yamamoto, J. Bacteriol. 185:6938-6949, 2003). In this study, we identified the Fur-regulated small RNA RyhB and the RNA chaperone Hfq protein as additional regulatory proteins of vibrioferrin biosynthesis. We found that vibrioferrin production was greatly impaired in both the ryhB and hfq deletion mutants, and a TargetRNA search (http://snowwhite.wellesley.edu/targetRNA/index2.html) revealed that the 5'-untranslated region of pvsOp mRNA (pvsOp 5'-UTR) contains a potential base-pairing region required for the formation of the RyhB-pvsOp 5'-UTR duplex. An electrophoresis mobility shift assay indicated that RyhB can directly bind to the pvsOp 5'-UTR with the aid of Hfq. Rifampin chase experiments indicated that the half-life of pvsOp mRNA in the ryhB and hfq mutants was approximately 3-fold shorter than that in the parental strain, suggesting that both RyhB and Hfq are engaged in the stabilization of pvsOp mRNA. Chrome azurol S assays followed by electrophoresis mobility shift assays and rifampin chase experiments carried out for mutant strains indicated that base pairing between RyhB and the pvsOp 5'-UTR results in an increase in the stability of pvsOp mRNA, thereby leading to the promotion of vibrioferrin production. It is unprecedented that RyhB confers increased stability on a polycistronic mRNA involved in siderophore biosynthesis as a direct target.
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Hoe CH, Raabe CA, Rozhdestvensky TS, Tang TH. Bacterial sRNAs: regulation in stress. Int J Med Microbiol 2013; 303:217-29. [PMID: 23660175 DOI: 10.1016/j.ijmm.2013.04.002] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/26/2013] [Accepted: 04/07/2013] [Indexed: 11/28/2022] Open
Abstract
Bacteria are often exposed to a hostile environment and have developed a plethora of cellular processes in order to survive. A burgeoning list of small non-coding RNAs (sRNAs) has been identified and reported to orchestrate crucial stress responses in bacteria. Among them, cis-encoded sRNA, trans-encoded sRNA, and 5'-untranslated regions (UTRs) of the protein coding sequence are influential in the bacterial response to environmental cues, such as fluctuation of temperature and pH as well as other stress conditions. This review summarizes the role of bacterial sRNAs in modulating selected stress conditions and highlights the alliance between stress response and clustered regularly interspaced short palindromic repeats (CRISPR) in bacterial defense.
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Affiliation(s)
- Chee-Hock Hoe
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Kepala Batas, 13200 Penang, Malaysia.
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Harrison A, Santana EA, Szelestey BR, Newsom DE, White P, Mason KM. Ferric uptake regulator and its role in the pathogenesis of nontypeable Haemophilus influenzae. Infect Immun 2013; 81:1221-33. [PMID: 23381990 PMCID: PMC3639608 DOI: 10.1128/iai.01227-12] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 01/21/2013] [Indexed: 11/20/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) is a commensal microorganism of the human nasopharynx, and yet is also an opportunistic pathogen of the upper and lower respiratory tracts. Host microenvironments influence gene expression patterns, likely critical for NTHi persistence. The host sequesters iron as a mechanism to control microbial growth, and yet iron limitation influences gene expression and subsequent production of proteins involved in iron homeostasis. Careful regulation of iron uptake, via the ferric uptake regulator Fur, is essential in multiple bacteria, including NTHi. We hypothesized therefore that Fur contributes to iron homeostasis in NTHi, is critical for bacterial persistence, and likely regulates expression of virulence factors. Toward this end, fur was deleted in the prototypic NTHi clinical isolate, 86-028NP, and we assessed gene expression regulated by Fur. As expected, expression of the majority of genes that encode proteins with predicted roles in iron utilization was repressed by Fur. However, 14 Fur-regulated genes encode proteins with no known function, and yet may contribute to iron utilization or other biological functions. In a mammalian model of human otitis media, we determined that Fur was critical for bacterial persistence, indicating an important role for Fur-mediated iron homeostasis in disease progression. These data provide a profile of genes regulated by Fur in NTHi and likely identify additional regulatory pathways involved in iron utilization. Identification of such pathways will increase our understanding of how this pathogen can persist within host microenvironments, as a common commensal and, importantly, as a pathogen with significant clinical impact.
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Affiliation(s)
- Alistair Harrison
- The Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, The Center for Microbial Interface Biology, and Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA.
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