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Mejía-Almonte C, Busby SJW, Wade JT, van Helden J, Arkin AP, Stormo GD, Eilbeck K, Palsson BO, Galagan JE, Collado-Vides J. Redefining fundamental concepts of transcription initiation in bacteria. Nat Rev Genet 2020; 21:699-714. [PMID: 32665585 PMCID: PMC7990032 DOI: 10.1038/s41576-020-0254-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2020] [Indexed: 12/15/2022]
Abstract
Despite enormous progress in understanding the fundamentals of bacterial gene regulation, our knowledge remains limited when compared with the number of bacterial genomes and regulatory systems to be discovered. Derived from a small number of initial studies, classic definitions for concepts of gene regulation have evolved as the number of characterized promoters has increased. Together with discoveries made using new technologies, this knowledge has led to revised generalizations and principles. In this Expert Recommendation, we suggest precise, updated definitions that support a logical, consistent conceptual framework of bacterial gene regulation, focusing on transcription initiation. The resulting concepts can be formalized by ontologies for computational modelling, laying the foundation for improved bioinformatics tools, knowledge-based resources and scientific communication. Thus, this work will help researchers construct better predictive models, with different formalisms, that will be useful in engineering, synthetic biology, microbiology and genetics.
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Affiliation(s)
- Citlalli Mejía-Almonte
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México
| | | | - Joseph T Wade
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Jacques van Helden
- Aix-Marseille University, INSERM UMR S 1090, Theory and Approaches of Genome Complexity (TAGC), Marseille, France
- CNRS, Institut Français de Bioinformatique, IFB-core, UMS 3601, Evry, France
| | - Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Gary D Stormo
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - James E Galagan
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Julio Collado-Vides
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
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2
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Sheehan LM, Caswell CC. An account of evolutionary specialization: the AbcR small RNAs in the Rhizobiales. Mol Microbiol 2017; 107:24-33. [PMID: 29076560 DOI: 10.1111/mmi.13869] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2017] [Indexed: 01/26/2023]
Abstract
The AbcR small RNAs (sRNAs) are a fascinating example of two highly conserved sRNAs that differ tremendously at the functional level among organisms. From their transcriptional activation to their regulatory capabilities, the AbcR sRNAs exhibit varying characteristics in three well-studied bacteria belonging to the Rhizobiales order: the plant symbiont Sinorhizobium meliloti, the plant pathogen Agrobacterium tumefaciens, and the animal pathogen Brucella abortus. This review outlines the similarities and differences of the AbcR sRNAs between each of these organisms, and discusses reasons as to why this group of sRNAs has diverged in their genetic organization and regulatory functions across species. In the end, this review will shed light on how regulatory systems, although seemingly conserved among bacteria, can vary based on the environmental niche and lifestyle of an organism.
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Affiliation(s)
- Lauren M Sheehan
- Department of Biomedical Sciences and Pathobiology, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Clayton C Caswell
- Department of Biomedical Sciences and Pathobiology, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
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3
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Wang L, Yang G, Qi L, Li X, Jia L, Xie J, Qiu S, Li P, Hao R, Wu Z, Du X, Li W, Song H. A Novel Small RNA Regulates Tolerance and Virulence in Shigella flexneri by Responding to Acidic Environmental Changes. Front Cell Infect Microbiol 2016; 6:24. [PMID: 27014636 PMCID: PMC4782007 DOI: 10.3389/fcimb.2016.00024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/12/2016] [Indexed: 12/20/2022] Open
Abstract
Shigella flexneri is an important cause of bacillary dysentery in developing countries. Small regulatory RNAs (sRNAs) play essential roles in diverse cellular processes. We found a novel sRNA Ssr1 based on RT-PCR, northern blot, and 5′RACE in S. flexneri. Ssr1 responds to acidic environmental changes, as shown by a strong linear correlation between the pH value and Ssr1 expression (R = 0.785, P < 0.05) using the qRT-PCR method. Deletion of Ssr1 results in growth retardation at pH values ranging from 5.0 to 7.0 (P < 0.05), and the survival rate was reduced by 22% in acidic conditions (pH 3.0). Additionally, virulence was significantly increased in an Ssr1 mutant strain, as revealed in a murine lung invasion model and survival model assays. By using the sTarPicker method and proteomic analysis, we considered that DnaK, which is a major factor that confers acidic stress tolerance, may be a direct target of Ssr1. We also found that Ssr1 may enhance virulence by directly targeting OmpA; this leads to altered expression of genes in the type three secretion system (T3SS). This work provides new insight into the mechanism of adaptation to environmental stress and into the pathogenesis of Shigella.
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Affiliation(s)
- Ligui Wang
- Institute of Disease Control and Prevention, Academy of Military Medical SciencesBeijing, China; Center of Computational Biology, Beijing Institute of Basic Medical SciencesBeijing, China
| | - Guang Yang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Lihua Qi
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Xiang Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Leili Jia
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Jing Xie
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Shaofu Qiu
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Peng Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - RongZhang Hao
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Zhihao Wu
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Xinying Du
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Wuju Li
- Center of Computational Biology, Beijing Institute of Basic Medical Sciences Beijing, China
| | - Hongbin Song
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
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4
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Mondragón E, Maher LJ. Anti-Transcription Factor RNA Aptamers as Potential Therapeutics. Nucleic Acid Ther 2015; 26:29-43. [PMID: 26509637 PMCID: PMC4753637 DOI: 10.1089/nat.2015.0566] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Transcription factors (TFs) are DNA-binding proteins that play critical roles in regulating gene expression. These proteins control all major cellular processes, including growth, development, and homeostasis. Because of their pivotal role, cells depend on proper TF function. It is, therefore, not surprising that TF deregulation is linked to disease. The therapeutic drug targeting of TFs has been proposed as a frontier in medicine. RNA aptamers make interesting candidates for TF modulation because of their unique characteristics. The products of in vitro selection, aptamers are short nucleic acids (DNA or RNA) that bind their targets with high affinity and specificity. Aptamers can be expressed on demand from transgenes and are intrinsically amenable to recognition by nucleic acid-binding proteins such as TFs. In this study, we review several natural prokaryotic and eukaryotic examples of RNAs that modulate the activity of TFs. These examples include 5S RNA, 6S RNA, 7SK, hepatitis delta virus-RNA (HDV-RNA), neuron restrictive silencer element (NRSE)-RNA, growth arrest-specific 5 (Gas5), steroid receptor RNA activator (SRA), trophoblast STAT utron (TSU), the 3' untranslated region of caudal mRNA, and heat shock RNA-1 (HSR1). We then review examples of unnatural RNA aptamers selected to inhibit TFs nuclear factor-kappaB (NF-κB), TATA-binding protein (TBP), heat shock factor 1 (HSF1), and runt-related transcription factor 1 (RUNX1). The field of RNA aptamers for DNA-binding proteins continues to show promise.
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Affiliation(s)
- Estefanía Mondragón
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine , Rochester, Minnesota
| | - Louis James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine , Rochester, Minnesota
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5
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A versatile framework for microbial engineering using synthetic non-coding RNAs. Nat Rev Microbiol 2014; 12:341-54. [DOI: 10.1038/nrmicro3244] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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6
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Chappell J, Takahashi MK, Meyer S, Loughrey D, Watters KE, Lucks J. The centrality of RNA for engineering gene expression. Biotechnol J 2013; 8:1379-95. [PMID: 24124015 PMCID: PMC4033574 DOI: 10.1002/biot.201300018] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/19/2013] [Accepted: 08/15/2013] [Indexed: 12/25/2022]
Abstract
Synthetic biology holds promise as both a framework for rationally engineering biological systems and a way to revolutionize how we fundamentally understand them. Essential to realizing this promise is the development of strategies and tools to reliably and predictably control and characterize sophisticated patterns of gene expression. Here we review the role that RNA can play towards this goal and make a case for why this versatile, designable, and increasingly characterizable molecule is one of the most powerful substrates for engineering gene expression at our disposal. We discuss current natural and synthetic RNA regulators of gene expression acting at key points of control – transcription, mRNA degradation, and translation. We also consider RNA structural probing and computational RNA structure predication tools as a way to study RNA structure and ultimately function. Finally, we discuss how next-generation sequencing methods are being applied to the study of RNA and to the characterization of RNA's many properties throughout the cell.
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Affiliation(s)
- James Chappell
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
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7
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Mujahid S, Bergholz TM, Oliver HF, Boor KJ, Wiedmann M. Exploration of the role of the non-coding RNA SbrE in L. monocytogenes stress response. Int J Mol Sci 2012; 14:378-93. [PMID: 23263668 PMCID: PMC3565269 DOI: 10.3390/ijms14010378] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 12/11/2012] [Accepted: 12/14/2012] [Indexed: 12/30/2022] Open
Abstract
SbrE is a ncRNA in Listeria monocytogenes, reported to be up-regulated by the alternative sigma factor σB. Initial quantitative RT-PCR (qRT-PCR) experiments on parent strains and isogenic ΔsigB strains demonstrated σB-dependent expression of SbrE across the four L. monocytogenes lineages and in L. innocua. Microarray and proteomics (MDLC/MS/MS with iTRAQ labeling) experiments with the L. monocytogenes parent strain and an isogenic ΔsbrE strain identified a single gene (lmo0636) and two proteins (Lmo0637 and Lmo2094) that showed lower expression levels in the ΔsbrE strain. qRT-PCR demonstrated an increase in SbrE transcript levels in stationary phase L. monocytogenes and in bacteria exposed to oxidative stress (mean log2 transcript levels 7.68 ± 0.57 and 1.70 ± 0.71 greater than in mid-log phase cells, respectively). However, no significant differences in growth or survival between the parent strain and ΔsbrE strain were confirmed under a variety of environmental stress conditions tested. Our data suggest that σB-dependent transcription of SbrE represents a conserved mechanism that contributes, across Listeria species, to fine-tuning of gene expression under specific environmental conditions that remain to be defined.
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Affiliation(s)
- Sana Mujahid
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA; E-Mails: (S.M.); (T.M.B.); (H.F.O.); (K.J.B.)
| | - Teresa M. Bergholz
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA; E-Mails: (S.M.); (T.M.B.); (H.F.O.); (K.J.B.)
| | - Haley F. Oliver
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA; E-Mails: (S.M.); (T.M.B.); (H.F.O.); (K.J.B.)
- Department of Food Science, Purdue University, West Lafayette, IN 47907, USA
| | - Kathryn J. Boor
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA; E-Mails: (S.M.); (T.M.B.); (H.F.O.); (K.J.B.)
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA; E-Mails: (S.M.); (T.M.B.); (H.F.O.); (K.J.B.)
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8
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Goodson MS, Lynch JA, Lamkin T, Kramer R. Elucidation of small RNAs that activate transcription in bacteria. ACS Synth Biol 2012; 1:181-9. [PMID: 23651156 DOI: 10.1021/sb2000275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small non-coding RNA (sRNA) control of gene expression has been shown to play a prominent role in genetic regulation. While the majority of identified bacterial sRNAs exert their control at the translational level, a few examples of bacterial sRNAs that inhibit transcription have also been identified. Using an engineered combinatorial RNA library, we have elucidated bacterial sRNAs that activate transcription of a target gene in E. coli to varying degrees. Mutation of the strongest activator modified its activation potential. Our results suggest that transcriptional activation of our target gene results from recruitment of the bacterial RNA polymerase complex to the promoter region. These data, coupled with the malleability of RNA, provide a context to define synthetic control of genes in bacteria at the transcriptional level.
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Affiliation(s)
- Michael S. Goodson
- 711th Human Performance Wing, Air
Force Research Laboratory, 2510 Fifth Street, Building 840, Wright-Patterson
Air Force Base, Ohio 45433, United States
| | - John A. Lynch
- Department of Chemistry, University of Cincinnati,
Cincinnati, Ohio 45267, United States
| | - Thomas Lamkin
- 711th Human Performance Wing, Air Force Research Laboratory, University
of Cincinnati, 231 Albert Sabin Way, Medical Sciences Building, Cincinnati,
Ohio 45221, United States
| | - Ryan Kramer
- 711th Human Performance Wing, Air Force Research Laboratory, University
of Cincinnati, 231 Albert Sabin Way, Medical Sciences Building, Cincinnati,
Ohio 45221, United States
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9
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Gong H, Vu GP, Bai Y, Chan E, Wu R, Yang E, Liu F, Lu S. A Salmonella small non-coding RNA facilitates bacterial invasion and intracellular replication by modulating the expression of virulence factors. PLoS Pathog 2011; 7:e1002120. [PMID: 21949647 PMCID: PMC3174252 DOI: 10.1371/journal.ppat.1002120] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 04/29/2011] [Indexed: 12/17/2022] Open
Abstract
Small non-coding RNAs (sRNAs) that act as regulators of gene expression have been identified in all kingdoms of life, including microRNA (miRNA) and small interfering RNA (siRNA) in eukaryotic cells. Numerous sRNAs identified in Salmonella are encoded by genes located at Salmonella pathogenicity islands (SPIs) that are commonly found in pathogenic strains. Whether these sRNAs are important for Salmonella pathogenesis and virulence in animals has not been reported. In this study, we provide the first direct evidence that a pathogenicity island-encoded sRNA, IsrM, is important for Salmonella invasion of epithelial cells, intracellular replication inside macrophages, and virulence and colonization in mice. IsrM RNA is expressed in vitro under conditions resembling those during infection in the gastrointestinal tract. Furthermore, IsrM is found to be differentially expressed in vivo, with higher expression in the ileum than in the spleen. IsrM targets the mRNAs coding for SopA, a SPI-1 effector, and HilE, a global regulator of the expression of SPI-1 proteins, which are major virulence factors essential for bacterial invasion. Mutations in IsrM result in disregulation of expression of HilE and SopA, as well as other SPI-1 genes whose expression is regulated by HilE. Salmonella with deletion of isrM is defective in bacteria invasion of epithelial cells and intracellular replication/survival in macrophages. Moreover, Salmonella with mutations in isrM is attenuated in killing animals and defective in growth in the ileum and spleen in mice. Our study has shown that IsrM sRNA functions as a pathogenicity island-encoded sRNA directly involved in Salmonella pathogenesis in animals. Our results also suggest that sRNAs may represent a distinct class of virulence factors that are important for bacterial infection in vivo. Regulated expression of virulence factors is essential for infection by human pathogens such as Salmonella. Small non-coding RNAs (sRNAs) that act as regulators of gene expression have been identified in all kingdoms of life, and many sRNAs in Salmonella are encoded by genes located at Salmonella pathogenicity islands commonly found in pathogenic strains. In this study, we demonstrated that a pathogenicity island-encoded sRNA directly targets the expression of both a global regulator of virulence genes as well as a specific virulence factor critical for Salmonella pathogenesis. The sRNA is important for Salmonella invasion of epithelial cells, replication inside macrophages, and virulence/colonization in mice, representing the first example of a pathogenicity island-encoded sRNA that is directly involved in Salmonella pathogenesis in vivo. Our study suggests that sRNA may function as a distinct class of virulence factors that significantly contribute to bacterial infection in vivo. Furthermore, our results raise the possibility of developing new strategies against bacterial infection by preventing the expression of regulatory sRNAs.
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MESH Headings
- 5' Untranslated Regions
- Animals
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- Epithelial Cells/microbiology
- Epithelial Cells/pathology
- Female
- Gastrointestinal Tract/cytology
- Gastrointestinal Tract/microbiology
- Gene Expression Regulation, Bacterial
- Genomic Islands
- Ileum/cytology
- Macrophages/microbiology
- Mice
- Mice, Inbred BALB C
- Mice, SCID
- Promoter Regions, Genetic
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/genetics
- RNA, Small Untranslated/genetics
- RNA, Small Untranslated/metabolism
- Salmonella Infections, Animal/microbiology
- Salmonella Infections, Animal/pathology
- Salmonella typhimurium/genetics
- Salmonella typhimurium/growth & development
- Salmonella typhimurium/metabolism
- Salmonella typhimurium/pathogenicity
- Sequence Alignment
- Sequence Analysis
- Spleen/cytology
- Virulence Factors/biosynthesis
- Virulence Factors/genetics
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Affiliation(s)
- Hao Gong
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, United States of America
| | - Gia-Phong Vu
- Program in Comparative Biochemistry, University of California, Berkeley, California, United States of America
| | - Yong Bai
- Program in Comparative Biochemistry, University of California, Berkeley, California, United States of America
| | - Elton Chan
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, United States of America
| | - Ruobin Wu
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, United States of America
| | - Edward Yang
- Program in Comparative Biochemistry, University of California, Berkeley, California, United States of America
| | - Fenyong Liu
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, United States of America
- Program in Comparative Biochemistry, University of California, Berkeley, California, United States of America
- * E-mail: (FL); (SL)
| | - Sangwei Lu
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, United States of America
- Program in Comparative Biochemistry, University of California, Berkeley, California, United States of America
- * E-mail: (FL); (SL)
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Shinhara A, Matsui M, Hiraoka K, Nomura W, Hirano R, Nakahigashi K, Tomita M, Mori H, Kanai A. Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli. BMC Genomics 2011; 12:428. [PMID: 21864382 PMCID: PMC3175480 DOI: 10.1186/1471-2164-12-428] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2011] [Accepted: 08/24/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In Escherichia coli, approximately 100 regulatory small RNAs (sRNAs) have been identified experimentally and many more have been predicted by various methods. To provide a comprehensive overview of sRNAs, we analysed the low-molecular-weight RNAs (< 200 nt) of E. coli with deep sequencing, because the regulatory RNAs in bacteria are usually 50-200 nt in length. RESULTS We discovered 229 novel candidate sRNAs (≥ 50 nt) with computational or experimental evidence of transcription initiation. Among them, the expression of seven intergenic sRNAs and three cis-antisense sRNAs was detected by northern blot analysis. Interestingly, five novel sRNAs are expressed from prophage regions and we note that these sRNAs have several specific characteristics. Furthermore, we conducted an evolutionary conservation analysis of the candidate sRNAs and summarised the data among closely related bacterial strains. CONCLUSIONS This comprehensive screen for E. coli sRNAs using a deep sequencing approach has shown that many as-yet-undiscovered sRNAs are potentially encoded in the E. coli genome. We constructed the Escherichia coli Small RNA Browser (ECSBrowser; http://rna.iab.keio.ac.jp/), which integrates the data for previously identified sRNAs and the novel sRNAs found in this study.
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Affiliation(s)
- Atsuko Shinhara
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
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Genomes of the most dangerous epidemic bacteria have a virulence repertoire characterized by fewer genes but more toxin-antitoxin modules. PLoS One 2011; 6:e17962. [PMID: 21437250 PMCID: PMC3060909 DOI: 10.1371/journal.pone.0017962] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 02/22/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND We conducted a comparative genomic study based on a neutral approach to identify genome specificities associated with the virulence capacity of pathogenic bacteria. We also determined whether virulence is dictated by rules, or if it is the result of individual evolutionary histories. We systematically compared the genomes of the 12 most dangerous pandemic bacteria for humans ("bad bugs") to their closest non-epidemic related species ("controls"). METHODOLOGY/PRINCIPAL FINDINGS We found several significantly different features in the "bad bugs", one of which was a smaller genome that likely resulted from a degraded recombination and repair system. The 10 Cluster of Orthologous Group (COG) functional categories revealed a significantly smaller number of genes in the "bad bugs", which lacked mostly transcription, signal transduction mechanisms, cell motility, energy production and conversion, and metabolic and regulatory functions. A few genes were identified as virulence factors, including secretion system proteins. Five "bad bugs" showed a greater number of poly (A) tails compared to the controls, whereas an elevated number of poly (A) tails was found to be strongly correlated to a low GC% content. The "bad bugs" had fewer tandem repeat sequences compared to controls. Moreover, the results obtained from a principal component analysis (PCA) showed that the "bad bugs" had surprisingly more toxin-antitoxin modules than did the controls. CONCLUSIONS/SIGNIFICANCE We conclude that pathogenic capacity is not the result of "virulence factors" but is the outcome of a virulent gene repertoire resulting from reduced genome repertoires. Toxin-antitoxin systems could participate in the virulence repertoire, but they may have developed independently of selfish evolution.
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12
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When one is better than two: RNA with dual functions. Biochimie 2010; 93:633-44. [PMID: 21111023 DOI: 10.1016/j.biochi.2010.11.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 11/17/2010] [Indexed: 11/23/2022]
Abstract
The central dogma of biology, until not long ago, held that genetic information stored on DNA molecules was translated into the final protein products through RNA as intermediate molecules. Then, an additional level of complexity in the regulation of genome expression was added, implicating new classes of RNA molecules called non-coding RNA (ncRNA). These ncRNA are also often referred to as functional RNA in that, although they do not contain the capacity to encode proteins, do have a function as RNA molecules. They have been thus far considered as truly non-coding RNA since no ORF long enough to be considered, nor protein, have been associated with them. However, the recent identification and characterization of bifunctional RNA, i.e. RNA for which both coding capacity and activity as functional RNA have been reported, suggests that a definite categorization of some RNA molecules is far from being straightforward. Indeed, several RNA primarily classified as non-protein-coding RNA has been showed to hold coding capacities and associated peptides. Conversely, mRNA, usually regarded as strictly protein-coding, may act as functional RNA molecules. Here, we describe several examples of these bifunctional RNA that have been already characterized from bacteria to mammals. We also extend this concept to fortuitous acquisition of dual function in pathological conditions and to the recently highlighted duality between information carried by a gene and its pseudogenes counterparts.
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13
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Smith AM, Fuchs RT, Grundy FJ, Henkin TM. Riboswitch RNAs: regulation of gene expression by direct monitoring of a physiological signal. RNA Biol 2010; 7:104-10. [PMID: 20061810 DOI: 10.4161/rna.7.1.10757] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Riboswitches are cis-encoded, cis-acting RNA elements that directly sense a physiological signal. Signal response results in a change in RNA structure that impacts gene expression. Elements of this type play an important role in bacteria, where they regulate a variety of fundamental cellular pathways. Riboswitch-mediated gene regulation most commonly occurs by effects on transcription attenuation, to control whether a full-length transcript is synthesized, or on translation initiation, in which case the transcript is constitutively synthesized but binding of the translation initiation complex is modulated. An overview of the role of riboswitch RNAs in bacterial gene expression will be provided, and a few examples are described in more detail to illustrate the types of mechanisms that have been uncovered.
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Affiliation(s)
- Angela M Smith
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, OH, USA
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14
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Busby S, Kolb A, Buc H. Where it all Begins: An Overview of Promoter Recognition and Open Complex Formation. RNA POLYMERASES AS MOLECULAR MOTORS 2009. [DOI: 10.1039/9781847559982-00013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Stephen Busby
- School of Biosciences, University of Birmingham Birmingham B15 2TT United Kingdom
| | - Annie Kolb
- Institut Pasteur, Molecular Genetics Unit and CNRS URA 2172 25 rue du Dr. Roux 75724 Paris Cedex 15 France
| | - Henri Buc
- CIS Institut Pasteur75724Paris Cedex 15France
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15
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Dambach MD, Winkler WC. Expanding roles for metabolite-sensing regulatory RNAs. Curr Opin Microbiol 2009; 12:161-9. [PMID: 19250859 DOI: 10.1016/j.mib.2009.01.012] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Accepted: 01/23/2009] [Indexed: 12/28/2022]
Abstract
Metabolite-sensing regulatory RNAs, oft referred to as riboswitches, are widely used among eubacteria for control of diverse biochemical pathways and transport mechanisms. Great strides have been made in understanding the general structure and biochemistry of individual riboswitch classes. However, along with these advancements, it has become clear that metabolite-sensing riboswitches respond to an increasingly structurally diverse range of metabolite and metal ligands. Moreover, the recent accruement of new riboswitches has uncovered individual examples and classes that utilize unique regulatory strategies or employ a regulatory logic other than simple feedback inhibition.
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Affiliation(s)
- Michael D Dambach
- The University of Texas Southwestern Medical Center, Department of Biochemistry, Dallas, 75390-9038, United States
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Abstract
Riboswitches are RNA elements that undergo a shift in structure in response to binding of a regulatory molecule. These elements are encoded within the transcript they regulate, and act in cis to control expression of the coding sequence(s) within that transcript; their function is therefore distinct from that of small regulatory RNAs (sRNAs) that act in trans to regulate the activity of other RNA transcripts. Riboswitch RNAs control a broad range of genes in bacterial species, including those involved in metabolism or uptake of amino acids, cofactors, nucleotides, and metal ions. Regulation occurs as a consequence of direct binding of an effector molecule, or through sensing of a physical parameter such as temperature. Here we review the global role of riboswitch RNAs in bacterial cell metabolism.
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Affiliation(s)
- Tina M Henkin
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA.
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André G, Even S, Putzer H, Burguière P, Croux C, Danchin A, Martin-Verstraete I, Soutourina O. S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum. Nucleic Acids Res 2008; 36:5955-69. [PMID: 18812398 PMCID: PMC2566862 DOI: 10.1093/nar/gkn601] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The ubiGmccBA operon of Clostridium acetobutylicum is involved in methionine to cysteine conversion. We showed that its expression is controlled by a complex regulatory system combining several RNA-based mechanisms. Two functional convergent promoters associated with transcriptional antitermination systems, a cysteine-specific T-box and an S-box riboswitch, are located upstream of and downstream from the ubiG operon, respectively. Several antisense RNAs were synthesized from the downstream S-box-dependent promoter, resulting in modulation of the level of ubiG transcript and of MccB activity. In contrast, the upstream T-box system did not appear to play a major role in regulation, leaving antisense transcription as the major regulatory mechanism for the ubiG operon. The abundance of sense and antisense transcripts was inversely correlated with the sulfur source availability. Deletion of the downstream promoter region completely abolished the sulfur-dependent control of the ubiG operon, and the expression of antisense transcripts in trans did not restore the regulation of the operon. Our data revealed important insights into the molecular mechanism of cis-antisense-mediated regulation, a control system only rarely observed in prokaryotes. We proposed a regulatory model in which the antisense RNA controlled the expression of the ubiG operon in cis via transcriptional interference at the ubiG locus.
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Affiliation(s)
- Gaëlle André
- Genetics of Bacterial Genomes, Pasteur Institute, CNRS URA2171, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
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Richards J, Sundermeier T, Svetlanov A, Karzai AW. Quality control of bacterial mRNA decoding and decay. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2008; 1779:574-82. [PMID: 18342642 DOI: 10.1016/j.bbagrm.2008.02.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Accepted: 02/05/2008] [Indexed: 11/19/2022]
Abstract
Studies in eukaryotes and prokaryotes have revealed that gene expression is not only controlled through altering the rate of transcription but also through varying rates of translation and mRNA decay. Indeed, the expression level of a protein is strongly affected by the steady state level of its mRNA. RNA decay can, along with transcription, play an important role in regulating gene expression by fine-tuning the steady state level of a given transcript and affecting its subsequent decoding during translation. Alterations in mRNA stability can in turn have dramatic effects on cell physiology and as a consequence the fitness and survival of the organism. Recent evidence suggests that mRNA decay can be regulated in response to environmental cues in order to enable the organism to adapt to its changing surroundings. Bacteria have evolved unique post transcriptional control mechanisms to enact such adaptive responses through: 1) general mRNA decay, 2) differential mRNA degradation using small non-coding RNAs (sRNAs), and 3) selective mRNA degradation using the tmRNA quality control system. Here, we review our current understanding of these molecular mechanisms, gleaned primarily from studies of the model gram negative organism Escherichia coli, that regulate the stability and degradation of normal and defective transcripts.
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Affiliation(s)
- Jamie Richards
- Department of Biochemistry and Cell Biology, Center for Infectious Diseases of Stony Brook University, Stony Brook, NY 11794, USA
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Zemanová M, Kaderábková P, Pátek M, Knoppová M, Silar R, Nesvera J. Chromosomally encoded small antisense RNA in Corynebacterium glutamicum. FEMS Microbiol Lett 2007; 279:195-201. [PMID: 18093135 DOI: 10.1111/j.1574-6968.2007.01024.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The first observation of chromosomally encoded small antisense RNA in Corynebacterium glutamicum is reported. Transcription oriented in the reverse direction to the transcription of the genes cg1934 and cg1935 was demonstrated within the chromosomal cg1934-cg1935 intergenic region. The transcription was found to be increased after heat shock. The transcriptional start point of this RNA designated ArnA was localized 21 bp upstream of the cg1935 translational start point by primer extension analysis, when the total RNA was isolated from cells grown at 30 degrees C. After heat shock, the transcriptional start point of an additional species of ArnA RNA was detected 19 bp upstream of the cg1935 translational start point. The stress-response sigma factor SigH was found to be involved in the synthesis of ArnA RNAs. The 3' end of the ArnA RNAs was identified using the 3'-rapid amplification of cDNA ends technique. The length of the two ArnA RNA species was thus determined to be 129 and 131 nt, respectively. The ArnA RNAs were found to overlap the 5'-untranslated region of the transcript of the cg1935 gene coding for a transcriptional regulator of the GntR family. These results suggest that the noncoding ArnA RNAs have a regulatory function.
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Affiliation(s)
- Martina Zemanová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Videnská 1083, 20 Prague 4, Czech Republic
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Roberts F, Allison GE, Verma NK. Transcription-termination-mediated immunity and its prevention in bacteriophage SfV of Shigella flexneri. J Gen Virol 2007; 88:3187-3197. [PMID: 17947546 DOI: 10.1099/vir.0.83062-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The temperate phage SfV encodes the genes responsible for the serotype conversion of Shigella flexneri strains from serotype Y to 5a. Bacteriophages often encode proteins that prevent subsequent infection by homologous phages; the mechanism by which this is accomplished is referred to as superinfection immunity. The serotype conversion mediated following lysogenization of SfV is one such mechanism. Another mechanism is the putative lambda-like CI protein within SfV. This study reports the characterization of a third superinfection mechanism, transcription termination, in SfV. The presence of a small immunity-mediating RNA molecule, called CI RNA, and its essential role in the establishment of immunity, is shown. The novel role of the gene orf77, located immediately downstream from the transcription termination region, in inhibiting the establishment of CI RNA-mediated immunity is also presented.
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Affiliation(s)
- Fleur Roberts
- School of Biochemistry and Molecular Biology, College of Science, The Australian National University, Canberra, ACT 0200, Australia
| | - Gwen E Allison
- Australian National University Medical School, The Australian National University, Canberra, ACT 0200, Australia.,School of Biochemistry and Molecular Biology, College of Science, The Australian National University, Canberra, ACT 0200, Australia
| | - Naresh K Verma
- School of Biochemistry and Molecular Biology, College of Science, The Australian National University, Canberra, ACT 0200, Australia
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Wakeman CA, Winkler WC, Dann CE. Structural features of metabolite-sensing riboswitches. Trends Biochem Sci 2007; 32:415-24. [PMID: 17764952 PMCID: PMC2933830 DOI: 10.1016/j.tibs.2007.08.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Revised: 06/18/2007] [Accepted: 08/17/2007] [Indexed: 12/30/2022]
Abstract
Riboswitches, metabolite-sensing RNA elements that are present in untranslated regions of the transcripts that they regulate, possess extensive tertiary structure to couple metabolite binding to genetic control. Here we discuss recently published structures from four riboswitch classes and compare these natural RNA structures to those of in-vitro-selected RNA aptamers, which bind ligands similar to those of the riboswitches. In addition, we examine the glmS riboswitch - the first example of a ribozyme-based riboswitch. This RNA provides the latest twist in the riboswitch field and portends exciting advances in the coming years. Our knowledge of the mechanisms underlying genetic regulation by riboswitches has increased mightily in recent years and will continue to grow as new riboswitch classes and ligands are discovered and structurally characterized.
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Affiliation(s)
- Catherine A. Wakeman
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9038, USA
| | - Wade C. Winkler
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9038, USA
| | - Charles E. Dann
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9038, USA
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Abstract
The past decade has seen an explosion in discovery of small, non-coding RNAs in all organisms. As functions for many of the small RNAs have been identified, it has become increasingly clear that they are important components in regulating gene expression. A multitude of RNAs target mRNAs for regulation at the level of translation or stability, including the microRNAs in higher eukaryotes and the Hfq binding RNAs in bacteria. Other RNAs regulate transcription, such as murine B2 RNA, mammalian 7SK RNA and the bacterial 6S RNA, which will be the focus of this review. Details of 6S RNA interactions with RNA polymerase, how 6S RNA regulates transcription, and how 6S RNA function contributes to cellular survival are discussed.
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Affiliation(s)
- Karen M Wassarman
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr., Madison, WI 53706, USA.
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Wassarman KM. 6S RNA: a small RNA regulator of transcription. Curr Opin Microbiol 2007; 10:164-8. [PMID: 17383220 DOI: 10.1016/j.mib.2007.03.008] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2006] [Accepted: 03/12/2007] [Indexed: 11/16/2022]
Abstract
Appreciation for the prevalence and diversity of noncoding, small RNAs (sRNAs) has grown enormously in the past decade. A major role for sRNAs in all organisms is to regulate gene expression, often at the level of mRNA translation or stability. However, a few sRNAs have been shown to function by regulating transcription. The bacterial 6S RNA was the first sRNA shown to inhibit transcription by binding directly to the housekeeping holoenzyme form of RNA polymerase (i.e. sigma70-RNA polymerase in E. coli). It resides within the active site of RNA polymerase, blocks access to promoter DNA and, surprisingly, is used as a template for RNA synthesis. 6S RNA regulation of transcription leads to altered cell survival, perhaps by redirecting resource utilization under nutrient-limiting conditions.
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Affiliation(s)
- Karen M Wassarman
- Department of Bacteriology, University of Wisconsin-Madison, 420 Henry Mall, Madison, WI 53706, USA.
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