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Abstract
Small RNAs (sRNAs) are important gene regulators in bacteria, but it is unclear how new sRNAs originate and become part of regulatory networks that coordinate bacterial response to environmental stimuli. Using a covariance modeling-based approach, we analyzed the presence of hundreds of sRNAs in more than a thousand genomes across Enterobacterales, a bacterial order with a confluence of factors that allows robust genome-scale sRNA analyses: several well-studied organisms with fairly conserved genome structures, an established phylogeny, and substantial nucleotide diversity within a narrow evolutionary space. We discovered that a majority of sRNAs arose recently, and uncovered protein-coding genes as a potential source from which new sRNAs arise. A detailed investigation of the emergence of OxyS, a peroxide-responding sRNA, revealed that it evolved from a fragment of a peroxidase messenger RNA. Importantly, although it replaced the ancestral peroxidase, OxyS continues to be part of the ancestral peroxide-response regulon, indicating that an sRNA that arises from a protein-coding gene would inherently be part of the parental protein's regulatory network. This new insight provides a fresh framework for understanding sRNA origin and regulatory integration in bacteria.
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Affiliation(s)
- Madeline C Krieger
- Department of Biology, Portland State University, Portland, OR, USA
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, OR, USA
| | - H Auguste Dutcher
- Department of Biology, Portland State University, Portland, OR, USA
- Laboratory of Genetics and Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
| | - Andrew J Ashford
- Department of Biology, Portland State University, Portland, OR, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Rahul Raghavan
- Department of Biology, Portland State University, Portland, OR, USA
- Department of Molecular Microbiology and Immunology, The University of Texas at San Antonio, San Antonio, TX, USA
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2
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Svensson SL, Sharma CM. Small RNAs that target G-rich sequences are generated by diverse biogenesis pathways in Epsilonproteobacteria. Mol Microbiol 2021; 117:215-233. [PMID: 34818434 DOI: 10.1111/mmi.14850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 11/30/2022]
Abstract
Bacterial small RNAs (sRNAs) are widespread post-transcriptional regulators controlling bacterial stress responses and virulence. Nevertheless, little is known about how they arise and evolve. Homologues can be difficult to identify beyond the strain level using sequence-based approaches, and similar functionalities can arise by convergent evolution. Here, we found that the virulence-associated CJnc190 sRNA of the foodborne pathogen Campylobacter jejuni resembles the RepG sRNA from the gastric pathogen Helicobacter pylori. However, while both sRNAs bind G-rich sites in their target mRNAs using a C/U-rich loop, they largely differ in their biogenesis. RepG is transcribed from a stand-alone gene and does not require processing, whereas CJnc190 is transcribed from two promoters as precursors that are processed by RNase III and also has a cis-encoded antagonist, CJnc180. By comparing CJnc190 homologues in diverse Campylobacter species, we show that RNase III-dependent processing of CJnc190 appears to be a conserved feature even outside of C. jejuni. We also demonstrate the CJnc180 antisense partner is expressed in C. coli, yet here might be derived from the 3'UTR of the upstream flagella-related gene. Our analysis of G-tract targeting sRNAs in Epsilonproteobacteria demonstrates that similar sRNAs can have markedly different biogenesis pathways.
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Affiliation(s)
- Sarah L Svensson
- Department of Molecular Infection Biology II, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Bavaria, 97080, Germany
| | - Cynthia M Sharma
- Department of Molecular Infection Biology II, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Bavaria, 97080, Germany
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3
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Burning the Candle at Both Ends: Have Exoribonucleases Driven Divergence of Regulatory RNA Mechanisms in Bacteria? mBio 2021; 12:e0104121. [PMID: 34372700 PMCID: PMC8406224 DOI: 10.1128/mbio.01041-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Regulatory RNAs have emerged as ubiquitous gene regulators in all bacterial species studied to date. The combination of sequence-specific RNA interactions and malleable RNA structure has allowed regulatory RNA to adopt different mechanisms of gene regulation in a diversity of genetic backgrounds. In the model GammaproteobacteriaEscherichia coli and Salmonella, the regulatory RNA chaperone Hfq appears to play a global role in gene regulation, directly controlling ∼20 to 25% of the entire transcriptome. While the model FirmicutesBacillus subtilis and Staphylococcus aureus encode a Hfq homologue, its role has been significantly depreciated. These bacteria also have marked differences in RNA turnover. E. coli and Salmonella degrade RNA through internal endonucleolytic and 3′→5′ exonucleolytic cleavage that appears to allow transient accumulation of mRNA 3′ UTR cleavage fragments that contain stabilizing 3′ structures. In contrast, B. subtilis and S. aureus are able to exonucleolytically attack internally cleaved RNA from both the 5′ and 3′ ends, efficiently degrading mRNA 3′ UTR fragments. Here, we propose that the lack of 5′→3′ exoribonuclease activity in Gammaproteobacteria has allowed the accumulation of mRNA 3′ UTR ends as the “default” setting. This in turn may have provided a larger pool of unconstrained RNA sequences that has fueled the expansion of Hfq function and small RNA (sRNA) regulation in E. coli and Salmonella. Conversely, the exoribonuclease RNase J may be a significant barrier to the evolution of 3′ UTR sRNAs in B. subtilis and S. aureus that has limited the pool of RNA ligands available to Hfq and other sRNA chaperones, depreciating their function in these model Firmicutes.
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4
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Thairu MW, Meduri VRS, Degnan PH, Hansen AK. Natural selection shapes maintenance of orthologous sRNAs in divergent host-restricted bacterial genomes. Mol Biol Evol 2021; 38:4778-4791. [PMID: 34213555 PMCID: PMC8557413 DOI: 10.1093/molbev/msab202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Historically it has been difficult to study the evolution of bacterial small RNAs (sRNAs) across distantly related species. For example, identifying homologs of sRNAs is often difficult in genomes that have undergone multiple structural rearrangements. Also, some types of regulatory sRNAs evolve at rapid rates. The high degree of genomic synteny among divergent host-restricted bacterial lineages, including intracellular symbionts, is conducive to sRNA maintenance and homolog identification. In turn, symbiont genomes can provide us with novel insights into sRNA evolution. Here, we examine the sRNA expression profile of the obligate symbiont of psyllids, Carsonella ruddii, which has one of the smallest cellular genomes described. Using RNA-seq, we identified 36 and 32 antisense sRNAs (asRNAs) expressed by Carsonella from the psyllids Bactericera cockerelli (Carsonella-BC) and Diaphorina citri (Carsonella-DC), respectively. The majority of these asRNAs were associated with genes that are involved in essential amino acid biosynthetic pathways. Eleven of the asRNAs were conserved in both Carsonella lineages and the majority were maintained by selection. Notably, five of the corresponding coding sequences are also the targets of conserved asRNAs in a distantly related insect symbiont, Buchnera. We detected differential expression of two asRNAs for genes involved in arginine and leucine biosynthesis occurring between two distinct Carsonella-BC life stages. Using asRNAs identified in Carsonella, Buchnera, and Profftella which are all endosymbionts, and Escherichia coli, we determined that regions upstream of these asRNAs encode unique conserved patterns of AT/GC richness, GC skew, and sequence motifs which may be involved in asRNA regulation.
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Affiliation(s)
- Margaret W Thairu
- Department of Entomology, University of California, Riverside, Riverside, CA.,Department of Bacteriology, University of Wisconsin, Madison, Madison, WI
| | | | - Patrick H Degnan
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Allison K Hansen
- Department of Entomology, University of California, Riverside, Riverside, CA
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Madikonda AK, Shaikh A, Khanra S, Yakkala H, Yellaboina S, Lin-Chao S, Siddavattam D. Metabolic remodeling in Escherichia coli MG1655. A prophage e14-encoded small RNA, co293, post-transcriptionally regulates transcription factors HcaR and FadR. FEBS J 2020; 287:4767-4782. [PMID: 32061118 DOI: 10.1111/febs.15247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/10/2019] [Accepted: 02/12/2020] [Indexed: 11/26/2022]
Abstract
In previous studies, we have shown the existence of metabolic remodeling in glucose-grown Escherichia coli MG1655 cells expressing the esterase Orf306 from the opd island of Sphingobium fuliginis. We now show that Orf306-dependent metabolic remodeling is due to regulation of a novel small RNA (sRNA). Endogenous propionate, produced due to the esterase/lipase activity of Orf306, repressed expression of a novel E. coli sRNA, co293. This sRNA post-transcriptionally regulates expression of the transcription factors HcaR and FadR either by inhibiting translation or by destabilizing their transcripts. Hence, repression of co293 expression elevates the levels of HcaR and FadR with consequent activation of alternative carbon catabolic pathways. HcaR activates the hca and MHP operons leading to upregulation of the phenyl propionate and hydroxy phenyl propionate (HPP) degradation pathways. Similarly, FadR stimulates the expression of the transcription factor IclR which negatively regulates the glyoxylate bypass pathway genes, aceBAK.
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Affiliation(s)
- Ashok Kumar Madikonda
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, India
| | - Akbarpasha Shaikh
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, India
| | - Sonali Khanra
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, India
| | - Harshita Yakkala
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, India
| | - Sailu Yellaboina
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, India
| | - Sue Lin-Chao
- Institute of Molecular Biology, Academia Sinica, Nangang, Taiwan
| | - Dayananda Siddavattam
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, India
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6
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Diallo I, Provost P. RNA-Sequencing Analyses of Small Bacterial RNAs and their Emergence as Virulence Factors in Host-Pathogen Interactions. Int J Mol Sci 2020; 21:E1627. [PMID: 32120885 PMCID: PMC7084465 DOI: 10.3390/ijms21051627] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/22/2020] [Accepted: 02/25/2020] [Indexed: 12/14/2022] Open
Abstract
Proteins have long been considered to be the most prominent factors regulating so-called invasive genes involved in host-pathogen interactions. The possible role of small non-coding RNAs (sRNAs), either intracellular, secreted or packaged in outer membrane vesicles (OMVs), remained unclear until recently. The advent of high-throughput RNA-sequencing (RNA-seq) techniques has accelerated sRNA discovery. RNA-seq radically changed the paradigm on bacterial virulence and pathogenicity to the point that sRNAs are emerging as an important, distinct class of virulence factors in both gram-positive and gram-negative bacteria. The potential of OMVs, as protectors and carriers of these functional, gene regulatory sRNAs between cells, has also provided an additional layer of complexity to the dynamic host-pathogen relationship. Using a non-exhaustive approach and through examples, this review aims to discuss the involvement of sRNAs, either free or loaded in OMVs, in the mechanisms of virulence and pathogenicity during bacterial infection. We provide a brief overview of sRNA origin and importance, and describe the classical and more recent methods of identification that have enabled their discovery, with an emphasis on the theoretical lower limit of RNA sizes considered for RNA sequencing and bioinformatics analyses.
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Affiliation(s)
| | - Patrick Provost
- CHUQ Research Center/CHUL, Department of Microbiology-Infectious Disease and Immunity, Faculty of Medicine, Université Laval, Quebec, QC G1V 0A6, Canada;
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Hu G, Hu T, Zhan Y, Lu W, Lin M, Huang Y, Yan Y. NfiS, a species-specific regulatory noncoding RNA of Pseudomonas stutzeri, enhances oxidative stress tolerance in Escherichia coli. AMB Express 2019; 9:156. [PMID: 31555995 PMCID: PMC6761216 DOI: 10.1186/s13568-019-0881-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/17/2019] [Indexed: 12/20/2022] Open
Abstract
Noncoding RNAs (ncRNAs) can finely control the expression of target genes at the posttranscriptional level in prokaryotes. Regulatory small RNAs (sRNAs) designed to control target gene expression for applications in metabolic engineering and synthetic biology have been successfully developed and used. However, the effect on the heterologous expression of species- or strain-specific ncRNAs in other bacterial strains remains poorly understood. In this work, a Pseudomonas stutzeri species-specific regulatory ncRNA, NfiS, which has been shown to play an important role in the response to oxidative stress as well as osmotic stress in P. stutzeri A1501, was cloned and transferred to the Escherichia coli strain Trans10. Recombinant NfiS-expressing E. coli, namely, Trans10-nfiS, exhibited significant enhancement of tolerance to oxidative stress. To map the possible gene regulatory networks mediated by NfiS in E. coli under oxidative stress, a microarray assay was performed to delineate the transcriptomic differences between Trans10-nfiS and wild-type E. coli under H2O2 shock treatment conditions. In all, 1184 genes were found to be significantly altered, and these genes were divided into mainly five functional categories: stress response, regulation, metabolism related, transport or membrane protein and unknown function. Our results suggest that the P. stutzeri species-specific ncRNA NfiS acts as a regulator that integrates adaptation to H2O2 with other cellular stress responses and helps protect E. coli cells against oxidative damage.
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8
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Abstract
Despite the central role of bacterial noncoding small RNAs (sRNAs) in posttranscriptional regulation, little is understood about their evolution. Here we compile what has been studied to date and trace a life cycle of sRNAs-from their mechanisms of emergence, through processes of change and frequent neofunctionalization, to their loss from bacterial lineages. Because they possess relatively unrestrictive structural requirements, we find that sRNA origins are varied, and include de novo emergence as well as formation from preexisting genetic elements via duplication events and horizontal gene transfer. The need for only partial complementarity to their mRNA targets facilitates apparent rapid change, which also contributes to significant challenges in tracing sRNAs across broad evolutionary distances. We document that recently emerged sRNAs in particular evolve quickly, mirroring dynamics observed in microRNAs, their functional analogs in eukaryotes. Mutations in mRNA-binding regions, transcriptional regulator or sigma factor binding sites, and protein-binding regions are all likely sources of shifting regulatory roles of sRNAs. Finally, using examples from the few evolutionary studies available, we examine cases of sRNA loss and describe how these may be the result of adaptive in addition to neutral processes. We highlight the need for more-comprehensive analyses of sRNA evolutionary patterns as a means to improve novel sRNA detection, enhance genome annotation, and deepen our understanding of regulatory networks in bacteria.
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9
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Wolf IR, Paschoal AR, Quiroga C, Domingues DS, de Souza RF, Pretto-Giordano LG, Vilas-Boas LA. Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes. BMC Genomics 2018; 19:556. [PMID: 30055586 PMCID: PMC6064168 DOI: 10.1186/s12864-018-4951-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/22/2018] [Indexed: 01/08/2023] Open
Abstract
Background Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a Gram-positive bacterium that colonizes the gastrointestinal and genitourinary tract of humans. This bacterium has also been isolated from various animals, such as fish and cattle. Non-coding RNAs (ncRNAs) can act as regulators of gene expression in bacteria, such as Streptococcus pneumoniae and Streptococcus pyogenes. However, little is known about the genomic distribution of ncRNAs and RNA families in S. agalactiae. Results Comparative genome analysis of 27 S. agalactiae strains showed more than 5 thousand genomic regions identified and classified as Core, Exclusive, and Shared genome sequences. We identified 27 to 89 RNA families per genome distributed over these regions, from these, 25 were in Core regions while Shared and Exclusive regions showed variations amongst strains. We propose that the amount and type of ncRNA present in each genome can provide a pattern to contribute in the identification of the clonal types. Conclusions The identification of RNA families provides an insight over ncRNAs, sRNAs and ribozymes function, that can be further explored as targets for antibiotic development or studied in gene regulation of cellular processes. RNA families could be considered as markers to determine infection capabilities of different strains. Lastly, pan-genome analysis of GBS including the full range of functional transcripts provides a broader approach in the understanding of this pathogen. Electronic supplementary material The online version of this article (10.1186/s12864-018-4951-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ivan Rodrigo Wolf
- Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| | - Alexandre Rossi Paschoal
- Universidade Tecnológica Federal do Paraná, Campus Cornélio Procópio, Cornélio Procópio, Paraná, Brazil.
| | - Cecilia Quiroga
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - Douglas Silva Domingues
- Departamento de Botânica, Instituto de Biociências de Rio Claro, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, São Paulo, Brazil
| | - Rogério Fernandes de Souza
- Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | | | - Laurival Antonio Vilas-Boas
- Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
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Cerutti F, Mallet L, Painset A, Hoede C, Moisan A, Bécavin C, Duval M, Dussurget O, Cossart P, Gaspin C, Chiapello H. Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria. BMC Genomics 2017; 18:882. [PMID: 29145803 PMCID: PMC5689173 DOI: 10.1186/s12864-017-4242-0] [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: 06/26/2017] [Accepted: 10/29/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Small regulatory RNAs (sRNAs) are widely found in bacteria and play key roles in many important physiological and adaptation processes. Studying their evolution and screening for events of coevolution with other genomic features is a powerful way to better understand their origin and assess a common functional or adaptive relationship between them. However, evolution and coevolution of sRNAs with coding genes have been sparsely investigated in bacterial pathogens. RESULTS We designed a robust and generic phylogenomics approach that detects correlated evolution between sRNAs and protein-coding genes using their observed and inferred patterns of presence-absence in a set of annotated genomes. We applied this approach on 79 complete genomes of the Listeria genus and identified fifty-two accessory sRNAs, of which most were present in the Listeria common ancestor and lost during Listeria evolution. We detected significant coevolution between 23 sRNA and 52 coding genes and inferred the Listeria sRNA-coding genes coevolution network. We characterized a main hub of 12 sRNAs that coevolved with genes encoding cell wall proteins and virulence factors. Among them, an sRNA specific to L. monocytogenes species, rli133, coevolved with genes involved either in pathogenicity or in interaction with host cells, possibly acting as a direct negative post-transcriptional regulation. CONCLUSIONS Our approach allowed the identification of candidate sRNAs potentially involved in pathogenicity and host interaction, consistent with recent findings on known pathogenicity actors. We highlight four sRNAs coevolving with seven internalin genes, some of which being important virulence factors in Listeria.
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Affiliation(s)
- Franck Cerutti
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France
| | - Ludovic Mallet
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France
| | - Anaïs Painset
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France.,Present address: Public Health England, 61 Colindale Avenue, London, NW9 5EQ, England
| | - Claire Hoede
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France
| | - Annick Moisan
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France
| | - Christophe Bécavin
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, F-75015, Paris, France.,INSERM, U604,F-75015, Paris, France.,INRA, USC2020, F-75015, Paris, France.,Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France
| | - Mélodie Duval
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, F-75015, Paris, France.,INSERM, U604,F-75015, Paris, France.,INRA, USC2020, F-75015, Paris, France
| | - Olivier Dussurget
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, F-75015, Paris, France.,INSERM, U604,F-75015, Paris, France.,INRA, USC2020, F-75015, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, F-75013, Paris, France
| | - Pascale Cossart
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, F-75015, Paris, France.,INSERM, U604,F-75015, Paris, France.,INRA, USC2020, F-75015, Paris, France
| | - Christine Gaspin
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France
| | - Hélène Chiapello
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France.
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11
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Chen ICK, Velicer GJ, Yu YTN. Divergence of functional effects among bacterial sRNA paralogs. BMC Evol Biol 2017; 17:199. [PMID: 28830343 PMCID: PMC5568312 DOI: 10.1186/s12862-017-1037-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/04/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Non-coding small RNAs (sRNAs) regulate a variety of important biological processes across all life domains, including bacteria. However, little is known about the functional evolution of sRNAs in bacteria, which might occur via changes in sRNA structure and/or stability or changes in interactions between sRNAs and their associated regulatory networks, including target mRNAs. The sRNA Pxr functions as a developmental gatekeeper in the model cooperative bacterium Myxococcus xanthus. Specifically, Pxr prevents the initiation of fruiting body development when nutrients are abundant. Previous work has shown that Pxr appears to have a recent origin within a sub-clade of the myxobacteria, which allowed us to infer the most recent common ancestor of pxr and examine the divergence of Pxr since its origin. RESULTS To test for inter-specific divergence in functional effects, extant pxr homologs from several species and their inferred ancestor were introduced into an M. xanthus deletion mutant lacking pxr. Both the inferred ancestral pxr and all extant alleles from species containing only one copy of pxr were found to control development in M. xanthus in a qualitatively similar manner to the native M. xanthus allele. However, multiple paralogs present in Cystobacter species exhibited divergent effects, with two paralogs controlling M. xanthus development but two others failing to do so. These differences may have occurred through changes in gene expression caused by apparent structural differences in the sRNA variants encoded by these paralogs. CONCLUSIONS Taken together, our results suggest that Pxr plays a common fundamental role in developmental gene regulation across diverse species of myxobacteria but also that the functional effects of some Pxr variants may be evolving in some lineages.
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Affiliation(s)
- I-Chen Kimberly Chen
- Department of Biology, Indiana University, Bloomington, IN47405, USA. .,Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland. .,Present address: School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30332, USA.
| | - Gregory J Velicer
- Department of Biology, Indiana University, Bloomington, IN47405, USA.,Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Yuen-Tsu Nicco Yu
- Department of Biology, Indiana University, Bloomington, IN47405, USA.,Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland
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Kacharia FR, Millar JA, Raghavan R. Emergence of New sRNAs in Enteric Bacteria is Associated with Low Expression and Rapid Evolution. J Mol Evol 2017; 84:204-213. [PMID: 28405712 DOI: 10.1007/s00239-017-9793-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/07/2017] [Indexed: 10/19/2022]
Abstract
Non-coding small RNAs (sRNAs) are critical to post-transcriptional gene regulation in bacteria. However, unlike for protein-coding genes, the evolutionary forces that shape sRNAs are not understood. We investigated sRNAs in enteric bacteria and discovered that recently emerged sRNAs evolve at significantly faster rates than older sRNAs. Concomitantly, younger sRNAs are expressed at significantly lower levels than older sRNAs. This process could potentially facilitate the integration of newly emerged sRNAs into bacterial regulatory networks. Furthermore, it has previously been difficult to trace the evolutionary histories of sRNAs because rapid evolution obscures their original sources. We overcame this challenge by identifying a recently evolved sRNA in Escherichia coli, which allowed us to determine that novel sRNAs could emerge from vestigial bacteriophage genes, the first known source for sRNA origination.
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Affiliation(s)
- Fenil R Kacharia
- Department of Biology and Center for Life in Extreme Environments, Portland State University, Portland, OR, 97201, USA
| | - Jess A Millar
- Department of Biology and Center for Life in Extreme Environments, Portland State University, Portland, OR, 97201, USA
| | - Rahul Raghavan
- Department of Biology and Center for Life in Extreme Environments, Portland State University, Portland, OR, 97201, USA.
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13
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Noro E, Mori M, Makino G, Takai Y, Ohnuma S, Sato A, Tomita M, Nakahigashi K, Kanai A. Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth. RNA Biol 2016; 14:206-218. [PMID: 27981881 PMCID: PMC5324740 DOI: 10.1080/15476286.2016.1270001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A new screening system for artificial small RNAs (sRNAs) that inhibit the growth of Escherichia coli was constructed. In this system, we used a plasmid library to express RNAs of ∼120 nucleotides, each with a random 30-nucleotide sequence that can recognize its target mRNA(s). After approximately 60,000 independent colonies were screened, several plasmids that inhibited bacterial growth were isolated. To understand the inhibitory mechanism, we focused on one sRNA, S-20, that exerted a strong inhibitory effect. A time-course analysis of the proteome of S-20-expressing E. coli and a bioinformatic analysis were used to identify potential S-20 target mRNAs, and suggested that S-20 binds the translation initiation sites of several mRNAs encoding enzymes such as peroxiredoxin (osmC), glycyl-tRNA synthetase α subunit (glyQ), uncharacterized protein ygiM, and tryptophan synthase β chain (trpB). An in vitro translation analysis of chimeric luciferase-encoding mRNAs, each containing a potential S-20 target sequence, indicated that the translation of these mRNAs was inhibited in the presence of S-20. A gel shift analysis combined with the analysis of a series of S-20 mutants suggested that S-20 targets multiple mRNAs that are responsible for inhibiting E. coli growth. These data also suggest that S-20 acts like an endogenous sRNA and that E. coli can utilize artificial sRNAs.
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Affiliation(s)
- Emiko Noro
- a Institute for Advanced Biosciences, Keio University , Tsuruoka , Japan
| | - Masaru Mori
- a Institute for Advanced Biosciences, Keio University , Tsuruoka , Japan.,b Systems Biology Program, Graduate School of Media and Governance, Keio University , Fujisawa , Japan
| | - Gakuto Makino
- a Institute for Advanced Biosciences, Keio University , Tsuruoka , Japan.,c Faculty of Environment and Information Studies, Keio University , Fujisawa , Japan
| | - Yuki Takai
- a Institute for Advanced Biosciences, Keio University , Tsuruoka , Japan
| | - Sumiko Ohnuma
- a Institute for Advanced Biosciences, Keio University , Tsuruoka , Japan
| | - Asako Sato
- a Institute for Advanced Biosciences, Keio University , Tsuruoka , Japan
| | - Masaru Tomita
- a Institute for Advanced Biosciences, Keio University , Tsuruoka , Japan.,b Systems Biology Program, Graduate School of Media and Governance, Keio University , Fujisawa , Japan.,c Faculty of Environment and Information Studies, Keio University , Fujisawa , Japan
| | - Kenji Nakahigashi
- a Institute for Advanced Biosciences, Keio University , Tsuruoka , Japan.,b Systems Biology Program, Graduate School of Media and Governance, Keio University , Fujisawa , Japan
| | - Akio Kanai
- a Institute for Advanced Biosciences, Keio University , Tsuruoka , Japan.,b Systems Biology Program, Graduate School of Media and Governance, Keio University , Fujisawa , Japan.,c Faculty of Environment and Information Studies, Keio University , Fujisawa , Japan
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Abstract
Small regulatory RNAs comprise critically important modulators of gene expression in bacteria, yet very little is known about their prevalence and functions in Rickettsia species. R. conorii, the causative agent of Mediterranean spotted fever, is a tick-borne pathogen that primarily infects microvascular endothelium in humans. We have determined the transcriptional landscape of R. conorii during infection of Human Microvascular Endothelial Cells (HMECs) by strand-specific RNA sequencing to identify 4 riboswitches, 13 trans-acting (intergenic), and 22 cis-acting (antisense) small RNAs (termed ‘Rc_sR’s). Independent expression of four novel trans-acting sRNAs (Rc_sR31, Rc_sR33, Rc_sR35, and Rc_sR42) and known bacterial sRNAs (6S, RNaseP_bact_a, ffs, and α-tmRNA) was next confirmed by Northern hybridization. Comparative analysis during infection of HMECs vis-à-vis tick AAE2 cells revealed significantly higher expression of Rc_sR35 and Rc_sR42 in HMECs, whereas Rc_sR31 and Rc_sR33 were expressed at similar levels in both cell types. We further predicted a total of 502 genes involved in all important biological processes as potential targets of Rc_sRs and validated the interaction of Rc_sR42 with cydA (cytochrome d ubiquinol oxidase subunit I). Our findings constitute the first evidence of the existence of post-transcriptional riboregulatory mechanisms in R. conorii and interactions between a novel Rc_sR and its target mRNA.
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Patel S. Drivers of bacterial genomes plasticity and roles they play in pathogen virulence, persistence and drug resistance. INFECTION GENETICS AND EVOLUTION 2016; 45:151-164. [DOI: 10.1016/j.meegid.2016.08.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 08/26/2016] [Accepted: 08/27/2016] [Indexed: 12/11/2022]
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16
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Exploring lateral genetic transfer among microbial genomes using TF-IDF. Sci Rep 2016; 6:29319. [PMID: 27452976 PMCID: PMC4958990 DOI: 10.1038/srep29319] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/13/2016] [Indexed: 11/17/2022] Open
Abstract
Many microbes can acquire genetic material from their environment and incorporate it into their genome, a process known as lateral genetic transfer (LGT). Computational approaches have been developed to detect genomic regions of lateral origin, but typically lack sensitivity, ability to distinguish donor from recipient, and scalability to very large datasets. To address these issues we have introduced an alignment-free method based on ideas from document analysis, term frequency-inverse document frequency (TF-IDF). Here we examine the performance of TF-IDF on three empirical datasets: 27 genomes of Escherichia coli and Shigella, 110 genomes of enteric bacteria, and 143 genomes across 12 bacterial and three archaeal phyla. We investigate the effect of k-mer size, gap size and delineation of groups on the inference of genomic regions of lateral origin, finding an interplay among these parameters and sequence divergence. Because TF-IDF identifies donor groups and delineates regions of lateral origin within recipient genomes, aggregating these regions by gene enables us to explore, for the first time, the mosaic nature of lateral genes including the multiplicity of biological sources, ancestry of transfer and over-writing by subsequent transfers. We carry out Gene Ontology enrichment tests to investigate which biological processes are potentially affected by LGT.
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The novel regulatory ncRNA, NfiS, optimizes nitrogen fixation via base pairing with the nitrogenase gene nifK mRNA in Pseudomonas stutzeri A1501. Proc Natl Acad Sci U S A 2016; 113:E4348-56. [PMID: 27407147 DOI: 10.1073/pnas.1604514113] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Unlike most Pseudomonas, the root-associated bacterium Pseudomonas stutzeri A1501 fixes nitrogen after the horizontal acquisition of a nitrogen-fixing (nif) island. A genome-wide search for small noncoding RNAs (ncRNAs) in P. stutzeri A1501 identified the novel P. stutzeri-specific ncRNA NfiS in the core genome, whose synthesis was significantly induced under nitrogen fixation or sorbitol stress conditions. The expression of NfiS was RNA chaperone Hfq-dependent and activated by the sigma factor RpoN/global nitrogen activator NtrC/nif-specific activator NifA regulatory cascade. The nfiS-deficient mutant displayed reduced nitrogenase activity, as well as increased sensitivity to multiple stresses, such as osmotic and oxidative stresses. Secondary structure prediction and complementation studies confirmed that a stem-loop structure was essential for NfiS to regulate the nitrogenase gene nifK mRNA synthesis and thus nitrogenase activity. Microscale thermophoresis and physiological analysis showed that NfiS directly pairs with nifK mRNA and ultimately enhances nitrogenase activity by increasing the translation efficiency and the half-life of nifK mRNA. Our data also suggest structural and functional divergence of NfiS evolution in diazotrophic and nondiazotrophic backgrounds. It is proposed that NfiS was recruited by nifK mRNA as a novel regulator to integrate the horizontally acquired nif island into host global networks.
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18
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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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Lagares A, Roux I, Valverde C. Phylogenetic distribution and evolutionary pattern of an α-proteobacterial small RNA gene that controls polyhydroxybutyrate accumulation in Sinorhizobium meliloti. Mol Phylogenet Evol 2016; 99:182-193. [DOI: 10.1016/j.ympev.2016.03.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/09/2016] [Accepted: 03/21/2016] [Indexed: 01/26/2023]
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A Prophage-Encoded Small RNA Controls Metabolism and Cell Division in Escherichia coli. mSystems 2016; 1:mSystems00021-15. [PMID: 27822514 PMCID: PMC5069750 DOI: 10.1128/msystems.00021-15] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 01/17/2016] [Indexed: 12/24/2022] Open
Abstract
Hundreds of small RNAs (sRNAs) have been identified in diverse bacterial species, and while the functions of most remain unknown, some regulate key processes, particularly stress responses. The sRNA DicF was identified over 25 years ago as an inhibitor of cell division but since then has remained uncharacterized. DicF consists of 53 nucleotides and is encoded by a gene carried on a prophage (Qin) in the genomes of many Escherichia coli strains. We demonstrated that DicF inhibits cell division via direct base pairing with ftsZ mRNA to repress translation and prevent new synthesis of the bacterial tubulin homolog FtsZ. Systems analysis using computational and experimental methods identified additional mRNA targets of DicF: xylR and pykA mRNAs, encoding the xylose uptake and catabolism regulator and pyruvate kinase, respectively. Genetic analyses showed that DicF directly base pairs with and represses translation of these targets. Phenotypes of cells expressing DicF variants demonstrated that DicF-associated growth inhibition is not solely due to repression of ftsZ, indicating that the physiological consequences of DicF-mediated regulation extend beyond effects on cell division caused by reduced FtsZ synthesis. IMPORTANCE sRNAs are ubiquitous and versatile regulators of bacterial gene expression. A number of well-characterized examples in E. coli are highly conserved and present in the E. coli core genome. In contrast, the sRNA DicF (identified over 20 years ago but remaining poorly characterized) is encoded by a gene carried on a defective prophage element in many E. coli genomes. Here, we characterize DicF in order to better understand how horizontally acquired sRNA regulators impact bacterial gene expression and physiology. Our data confirm the long-hypothesized DicF-mediated regulation of ftsZ, encoding the bacterial tubulin homolog required for cell division. We further uncover DicF-mediated posttranscriptional control of metabolic gene expression. Ectopic production of DicF is highly toxic to E. coli cells, but the toxicity is not attributable to DicF regulation of ftsZ. Further work is needed to reveal the biological roles of and benefits for the host conferred by DicF and other products encoded by defective prophages.
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21
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Fris ME, Murphy ER. Riboregulators: Fine-Tuning Virulence in Shigella. Front Cell Infect Microbiol 2016; 6:2. [PMID: 26858941 PMCID: PMC4728522 DOI: 10.3389/fcimb.2016.00002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 01/08/2016] [Indexed: 11/13/2022] Open
Abstract
Within the past several years, RNA-mediated regulation (ribo-regulation) has become increasingly recognized for its importance in controlling critical bacterial processes. Regulatory RNA molecules, or riboregulators, are perpetually responsive to changes within the micro-environment of a bacterium. Notably, several characterized riboregulators control virulence in pathogenic bacteria, as is the case for each riboregulator characterized to date in Shigella. The timing of virulence gene expression and the ability of the pathogen to adapt to rapidly changing environmental conditions is critical to the establishment and progression of infection by Shigella species; ribo-regulators mediate each of these important processes. This mini review will present the current state of knowledge regarding RNA-mediated regulation in Shigella by detailing the characterization and function of each identified riboregulator in these pathogens.
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Affiliation(s)
- Megan E Fris
- Department of Biological Science, Ohio University Athens, OH, USA
| | - Erin R Murphy
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University Athens, OH, USA
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22
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Bobrovskyy M, Vanderpool CK. Diverse mechanisms of post-transcriptional repression by the small RNA regulator of glucose-phosphate stress. Mol Microbiol 2015; 99:254-73. [PMID: 26411266 DOI: 10.1111/mmi.13230] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2015] [Indexed: 01/17/2023]
Abstract
The Escherichia coli small RNA SgrS controls a metabolic stress response that occurs upon accumulation of certain glycolytic intermediates. SgrS base pairs with and represses translation of ptsG and manXYZ mRNAs, which encode sugar transporters, and activates translation of yigL mRNA, encoding a sugar phosphatase. This study defines four new genes as direct targets of E. coli SgrS. These new targets, asd, adiY, folE and purR, encode transcription factors or enzymes of diverse metabolic pathways, including aspartate semialdehyde dehydrogenase, arginine decarboxylase gene activator, GTP cyclohydrolase I and a repressor of purine biosynthesis, respectively. SgrS represses translation of each of the four target mRNAs via distinct mechanisms. SgrS binding sites overlapping the Shine-Dalgarno sequences of adiY and folE mRNAs suggest that SgrS pairing with these targets directly occludes ribosome binding and prevents translation initiation. SgrS binding within the purR coding sequence recruits the RNA chaperone Hfq to directly repress purR translation. Two separate SgrS binding sites were found on asd mRNA, and both are required for full translational repression. Ectopic overexpression of asd, adiY and folE is specifically detrimental to cells experiencing glucose-phosphate stress, suggesting that SgrS-dependent repression of the metabolic functions encoded by these targets promotes recovery from glucose-phosphate stress.
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Affiliation(s)
- Maksym Bobrovskyy
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave., Urbana, IL, 61801, USA
| | - Carin K Vanderpool
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave., Urbana, IL, 61801, USA
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23
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Thébault P, Bourqui R, Benchimol W, Gaspin C, Sirand-Pugnet P, Uricaru R, Dutour I. Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks. Brief Bioinform 2015; 16:795-805. [PMID: 25477348 PMCID: PMC4570199 DOI: 10.1093/bib/bbu045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 11/05/2014] [Indexed: 12/29/2022] Open
Abstract
The revolution in high-throughput sequencing technologies has enabled the acquisition of gigabytes of RNA sequences in many different conditions and has highlighted an unexpected number of small RNAs (sRNAs) in bacteria. Ongoing exploitation of these data enables numerous applications for investigating bacterial transacting sRNA-mediated regulation networks. Focusing on sRNAs that regulate mRNA translation in trans, recent works have noted several sRNA-based regulatory pathways that are essential for key cellular processes. Although the number of known bacterial sRNAs is increasing, the experimental validation of their interactions with mRNA targets remains challenging and involves expensive and time-consuming experimental strategies. Hence, bioinformatics is crucial for selecting and prioritizing candidates before designing any experimental work. However, current software for target prediction produces a prohibitive number of candidates because of the lack of biological knowledge regarding the rules governing sRNA-mRNA interactions. Therefore, there is a real need to develop new approaches to help biologists focus on the most promising predicted sRNA-mRNA interactions. In this perspective, this review aims at presenting the advantages of mixing bioinformatics and visualization approaches for analyzing predicted sRNA-mediated regulatory bacterial networks.
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Yang G, Wang L, Wang Y, Li P, Zhu J, Qiu S, Hao R, Wu Z, Li W, Song H. hfq regulates acid tolerance and virulence by responding to acid stress in Shigella flexneri. Res Microbiol 2015; 166:476-85. [DOI: 10.1016/j.resmic.2015.06.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/13/2015] [Accepted: 06/17/2015] [Indexed: 11/28/2022]
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25
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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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Discovery of putative small non-coding RNAs from the obligate intracellular bacterium Wolbachia pipientis. PLoS One 2015; 10:e0118595. [PMID: 25739023 PMCID: PMC4349823 DOI: 10.1371/journal.pone.0118595] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 01/21/2015] [Indexed: 12/18/2022] Open
Abstract
Wolbachia pipientis is an endosymbiotic bacterium that induces a wide range of effects in its insect hosts, including manipulation of reproduction and protection against pathogens. Little is known of the molecular mechanisms underlying the insect-Wolbachia interaction, though it is likely to be mediated via the secretion of proteins or other factors. There is an increasing amount of evidence that bacteria regulate many cellular processes, including secretion of virulence factors, using small non-coding RNAs (sRNAs), but sRNAs have not previously been described from Wolbachia. We have used two independent approaches, one based on comparative genomics and the other using RNA-Seq data generated for gene expression studies, to identify candidate sRNAs in Wolbachia. We experimentally characterized the expression of one of these candidates in four Wolbachia strains, and showed that it is differentially regulated in different host tissues and sexes. Given the roles played by sRNAs in other host-associated bacteria, the conservation of the candidate sRNAs between different Wolbachia strains, and the sex- and tissue-specific differential regulation we have identified, we hypothesise that sRNAs may play a significant role in the biology of Wolbachia, and in particular in its interactions with its host.
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27
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Kim T, Bak G, Lee J, Kim KS. Systematic analysis of the role of bacterial Hfq-interacting sRNAs in the response to antibiotics. J Antimicrob Chemother 2015; 70:1659-68. [PMID: 25724987 DOI: 10.1093/jac/dkv042] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/03/2015] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To systematically analyse the interplay between the expression of Hfq-associated small non-coding RNAs (sRNAs) and antibiotic susceptibility in Gram-negative bacteria. METHODS To identify the roles of sRNAs in the antibiotic susceptibility of Escherichia coli and Salmonella species, susceptibility tests, growth analyses and viability assays were performed using E. coli Hfq-associated sRNAs from overexpression libraries. Prediction, susceptibility testing of gene knockouts and expression analysis of target genes under conditions of sRNA overexpression or knockout were performed to identify candidate targets for modulating antibiotic susceptibility. RESULTS The susceptibilities of E. coli strains overexpressing each of the 26 known Hfq-dependent sRNAs to major classes of antibiotics were determined. Induced expression of 17 sRNAs modulated the susceptibility of E. coli to antibiotics. Among them, four sRNA knockout strains partially or completely reversed susceptibility phenotypes of sRNA overexpression. The phenotype of OxyS, RseX or MicF was not entirely dependent on the presence of Hfq protein, in contrast to the dependency of previously characterized roles. The function of eight of nine sRNAs was found to be conserved in the response to antibiotics in Salmonella. Some MicF- or RyeB-mediated cellular target genes and pathways that may be important for the regulation of antibiotic susceptibility were identified. Finally, the overexpression of RyeB potentiated the efficacy of levofloxacin against MDR strains. CONCLUSIONS Our data indicate that Hfq-associated sRNAs potentially enable bacteria to adapt to antibiotic challenges via multifaceted approaches. Therefore, sRNA-based applications will form a new antibiotic arsenal for combating the rise in antibiotic resistance.
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Affiliation(s)
- Taeyeon Kim
- Superbacteria Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Geunu Bak
- Superbacteria Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Juyeon Lee
- Superbacteria Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Kwang-Sun Kim
- Superbacteria Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea Biosystems and Bioengineering program, University of Science and Technology (UST), Daejeon, Korea
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28
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Raghavan R, Kacharia FR, Millar JA, Sislak CD, Ochman H. Genome rearrangements can make and break small RNA genes. Genome Biol Evol 2015; 7:557-66. [PMID: 25601101 PMCID: PMC4350180 DOI: 10.1093/gbe/evv009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Small RNAs (sRNAs) are short, transcribed regulatory elements that are typically encoded in the intergenic regions (IGRs) of bacterial genomes. Several sRNAs, first recognized in Escherichia coli, are conserved among enteric bacteria, but because of the regulatory roles of sRNAs, differences in sRNA repertoires might be responsible for features that differentiate closely related species. We scanned the E. coli MG1655 and Salmonella enterica Typhimurium genomes for nonsyntenic IGRs as a potential source of uncharacterized, species-specific sRNAs and found that genome rearrangements have reconfigured several IGRs causing the disruption and formation of sRNAs. Within an IGR that is present in E. coli but was disrupted in Salmonella by a translocation event is an sRNA that is associated with the FNR/CRP global regulators and influences E. coli biofilm formation. A Salmonella-specific sRNA evolved de novo through point mutations that generated a σ70 promoter sequence in an IGR that arose through genome rearrangement events. The differences in the sRNA pools among bacterial species have previously been ascribed to duplication, deletion, or horizontal acquisition. Here, we show that genomic rearrangements also contribute to this process by either disrupting sRNA-containing IGRs or creating IGRs in which novel sRNAs may evolve.
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Affiliation(s)
- Rahul Raghavan
- Department of Biology and Center for Life in Extreme Environments, Portland State University
| | - Fenil R Kacharia
- Department of Biology and Center for Life in Extreme Environments, Portland State University
| | - Jess A Millar
- Department of Biology and Center for Life in Extreme Environments, Portland State University
| | - Christine D Sislak
- Department of Biology and Center for Life in Extreme Environments, Portland State University
| | - Howard Ochman
- Department of Integrative Biology, The University of Texas at Austin
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30
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Caswell CC, Oglesby-Sherrouse AG, Murphy ER. Sibling rivalry: related bacterial small RNAs and their redundant and non-redundant roles. Front Cell Infect Microbiol 2014; 4:151. [PMID: 25389522 PMCID: PMC4211561 DOI: 10.3389/fcimb.2014.00151] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 10/07/2014] [Indexed: 11/13/2022] Open
Abstract
Small RNA molecules (sRNAs) are now recognized as key regulators controlling bacterial gene expression, as sRNAs provide a quick and efficient means of positively or negatively altering the expression of specific genes. To date, numerous sRNAs have been identified and characterized in a myriad of bacterial species, but more recently, a theme in bacterial sRNAs has emerged: the presence of more than one highly related sRNAs produced by a given bacterium, here termed sibling sRNAs. Sibling sRNAs are those that are highly similar at the nucleotide level, and while it might be expected that sibling sRNAs exert identical regulatory functions on the expression of target genes based on their high degree of relatedness, emerging evidence is demonstrating that this is not always the case. Indeed, there are several examples of bacterial sibling sRNAs with non-redundant regulatory functions, but there are also instances of apparent regulatory redundancy between sibling sRNAs. This review provides a comprehensive overview of the current knowledge of bacterial sibling sRNAs, and also discusses important questions about the significance and evolutionary implications of this emerging class of regulators.
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Affiliation(s)
- Clayton C Caswell
- Department of Biomedical Sciences and Pathobiology, Center for Molecular Medicine and Infectious Diseases, VA-MD Regional College of Veterinary Medicine, Virginia Tech Blacksburg, VA, USA
| | - Amanda G Oglesby-Sherrouse
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, MD, USA ; Department of Microbiology and Immunology, School of Medicine, University of Maryland Baltimore, MD, USA
| | - Erin R Murphy
- Department of Biomedical Sciences, Ohio University Heritage College of Osteopathic Medicine Athens, OH, USA
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31
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Peterman N, Lavi-Itzkovitz A, Levine E. Large-scale mapping of sequence-function relations in small regulatory RNAs reveals plasticity and modularity. Nucleic Acids Res 2014; 42:12177-88. [PMID: 25262352 PMCID: PMC4231740 DOI: 10.1093/nar/gku863] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Two decades into the genomics era the question of mapping sequence to function has evolved from identifying functional elements to characterizing their quantitative properties including, in particular, their specificity and efficiency. Here, we use a large-scale approach to establish a quantitative map between the sequence of a bacterial regulatory RNA and its efficiency in modulating the expression of its targets. Our approach generalizes the sort-seq method, introduced recently to analyze promoter sequences, in order to accurately quantify the efficiency of a large library of sequence variants. We focus on two small RNAs (sRNAs) in E. coli, DsrA and RyhB, and their regulation of both repressed and activated targets. In addition to precisely identifying functional elements in the sRNAs, our data establish quantitative relationships between structural and energetic features of the sRNAs and their regulatory activity, and characterize a large set of direct and indirect interactions between nucleotides. A core of these interactions supports a model where specificity can be enhanced by a rigid molecular structure. Both sRNAs exhibit a modular design with limited cross-interactions, dividing the requirements for structural stability and target binding among modules.
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Affiliation(s)
- Neil Peterman
- Department of Physics and FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Anat Lavi-Itzkovitz
- Department of Physics and FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Erel Levine
- Department of Physics and FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
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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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Vergara-Irigaray M, Fookes MC, Thomson NR, Tang CM. RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri. BMC Genomics 2014; 15:438. [PMID: 24907032 PMCID: PMC4229854 DOI: 10.1186/1471-2164-15-438] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 05/23/2014] [Indexed: 01/03/2023] Open
Abstract
Background Shigella flexneri is an important human pathogen that has to adapt to the anaerobic environment in the gastrointestinal tract to cause dysentery. To define the influence of anaerobiosis on the virulence of Shigella, we performed deep RNA sequencing to identify transcriptomic differences that are induced by anaerobiosis and modulated by the anaerobic Fumarate and Nitrate Reduction regulator, FNR. Results We found that 528 chromosomal genes were differentially expressed in response to anaerobic conditions; of these, 228 genes were also influenced by FNR. Genes that were up-regulated in anaerobic conditions are involved in carbon transport and metabolism (e.g. ptsG, manX, murQ, cysP, cra), DNA topology and regulation (e.g. ygiP, stpA, hns), host interactions (e.g. yciD, nmpC, slyB, gapA, shf, msbB) and survival within the gastrointestinal tract (e.g. shiA, ospI, adiY, cysP). Interestingly, there was a marked effect of available oxygen on genes involved in Type III secretion system (T3SS), which is required for host cell invasion and pathogenesis. These genes, located on the large Shigella virulence plasmid, were down regulated in anaerobiosis in an FNR-dependent manner. We also confirmed anaerobic induction of csrB and csrC small RNAs in an FNR-independent manner. Conclusions Anaerobiosis promotes survival and adaption strategies of Shigella, while modulating virulence plasmid genes involved in T3SS-mediated host cell invasion. The influence of FNR on this process is more extensive than previously appreciated, although aside from the virulence plasmid, this transcriptional regulator does not govern expression of genes on other horizontally acquired sequences on the chromosome such as pathogenicity islands. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-438) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Christoph M Tang
- Sir William Dunn School of Pathology, Oxford University, Oxford, United Kingdom.
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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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Bapteste E, Dupré J. Towards a processual microbial ontology. BIOLOGY & PHILOSOPHY 2013; 28:379-404. [PMID: 23487350 PMCID: PMC3591535 DOI: 10.1007/s10539-012-9350-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 10/17/2012] [Indexed: 05/26/2023]
Abstract
Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely "processually equivalent" entities, "processually versatile" entities, and "stabilized" entities.
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Affiliation(s)
- Eric Bapteste
- />UMR CNRS 7138, Université Pierre et Marie Curie, 75005 Paris, France
| | - John Dupré
- />ESRC Centre for Genomics in Society (Egenis), University of Exeter, Exeter, UK
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Toffano-Nioche C, Nguyen AN, Kuchly C, Ott A, Gautheret D, Bouloc P, Jacq A. Transcriptomic profiling of the oyster pathogen Vibrio splendidus opens a window on the evolutionary dynamics of the small RNA repertoire in the Vibrio genus. RNA (NEW YORK, N.Y.) 2012; 18:2201-2219. [PMID: 23097430 PMCID: PMC3504672 DOI: 10.1261/rna.033324.112] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 09/08/2012] [Indexed: 06/01/2023]
Abstract
Work in recent years has led to the recognition of the importance of small regulatory RNAs (sRNAs) in bacterial regulation networks. New high-throughput sequencing technologies are paving the way to the exploration of an expanding sRNA world in nonmodel bacteria. In the Vibrio genus, compared to the enterobacteriaceae, still a limited number of sRNAs have been characterized, mostly in Vibrio cholerae, where they have been shown to be important for virulence, as well as in Vibrio harveyi. In addition, genome-wide approaches in V. cholerae have led to the discovery of hundreds of potential new sRNAs. Vibrio splendidus is an oyster pathogen that has been recently associated with massive mortality episodes in the French oyster growing industry. Here, we report the first RNA-seq study in a Vibrio outside of the V. cholerae species. We have uncovered hundreds of candidate regulatory RNAs, be it cis-regulatory elements, antisense RNAs, and trans-encoded sRNAs. Conservation studies showed the majority of them to be specific to V. splendidus. However, several novel sRNAs, previously unidentified, are also present in V. cholerae. Finally, we identified 28 trans sRNAs that are conserved in all the Vibrio genus species for which a complete genome sequence is available, possibly forming a Vibrio "sRNA core."
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Affiliation(s)
- Claire Toffano-Nioche
- Institut de Génétique et Microbiologie, CNRS/UMR 8621, IFR115, Université Paris-Sud, Bâtiment 400, 91405 Orsay Cedex, France
| | - An N. Nguyen
- Institut de Génétique et Microbiologie, CNRS/UMR 8621, IFR115, Université Paris-Sud, Bâtiment 400, 91405 Orsay Cedex, France
| | - Claire Kuchly
- Institut de Génétique et Microbiologie, CNRS/UMR 8621, IFR115, Université Paris-Sud, Bâtiment 400, 91405 Orsay Cedex, France
| | - Alban Ott
- Institut de Génétique et Microbiologie, CNRS/UMR 8621, IFR115, Université Paris-Sud, Bâtiment 400, 91405 Orsay Cedex, France
| | - Daniel Gautheret
- Institut de Génétique et Microbiologie, CNRS/UMR 8621, IFR115, Université Paris-Sud, Bâtiment 400, 91405 Orsay Cedex, France
| | - Philippe Bouloc
- Institut de Génétique et Microbiologie, CNRS/UMR 8621, IFR115, Université Paris-Sud, Bâtiment 400, 91405 Orsay Cedex, France
| | - Annick Jacq
- Institut de Génétique et Microbiologie, CNRS/UMR 8621, IFR115, Université Paris-Sud, Bâtiment 400, 91405 Orsay Cedex, France
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Kim D, Hong JSJ, Qiu Y, Nagarajan H, Seo JH, Cho BK, Tsai SF, Palsson BØ. Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling. PLoS Genet 2012; 8:e1002867. [PMID: 22912590 PMCID: PMC3415461 DOI: 10.1371/journal.pgen.1002867] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Accepted: 06/14/2012] [Indexed: 01/08/2023] Open
Abstract
Genome-wide transcription start site (TSS) profiles of the enterobacteria Escherichia coli and Klebsiella pneumoniae were experimentally determined through modified 5′ RACE followed by deep sequencing of intact primary mRNA. This identified 3,746 and 3,143 TSSs for E. coli and K. pneumoniae, respectively. Experimentally determined TSSs were then used to define promoter regions and 5′ UTRs upstream of coding genes. Comparative analysis of these regulatory elements revealed the use of multiple TSSs, identical sequence motifs of promoter and Shine-Dalgarno sequence, reflecting conserved gene expression apparatuses between the two species. In both species, over 70% of primary transcripts were expressed from operons having orthologous genes during exponential growth. However, expressed orthologous genes in E. coli and K. pneumoniae showed a strikingly different organization of upstream regulatory regions with only 20% identical promoters with TSSs in both species. Over 40% of promoters had TSSs identified in only one species, despite conserved promoter sequences existing in the other species. 662 conserved promoters having TSSs in both species resulted in the same number of comparable 5′ UTR pairs, and that regulatory element was found to be the most variant region in sequence among promoter, 5′ UTR, and ORF. In K. pneumoniae, 48 sRNAs were predicted and 36 of them were expressed during exponential growth. Among them, 34 orthologous sRNAs between two species were analyzed in depth, and the analysis showed that many sRNAs of K. pneumoniae, including pleiotropic sRNAs such as rprA, arcZ, and sgrS, may work in the same way as in E. coli. These results reveal a new dimension of comparative genomics such that a comparison of two genomes needs to be comprehensive over all levels of genome organization. In order to investigate similarities and differences of closely related species, most of the comparative genomics studies focus on comparing the gene contents either shared or specific for each genome. However, it is also important to investigate the differences in non-coding regulatory elements because they influence the transcriptional and post-transcriptional processes. Thus, we performed a genome-wide profiling of transcription start sites (TSSs) in two species, E. coli K-12 MG1655 and K. pneumoniae MGH78578. Experimental identification of TSSs is important for precise definition of promoter regions and 5′ untranslated regions upstream of coding genes. Comparative analysis of these regulatory elements revealed the use of multiple TSSs, identical sequence motifs of promoter and Shine-Dalgarno sequence. However, we observed that the upstream regulatory regions of the majority of operons having orthologous genes were organized with different usage of promoters and TSSs, resulting in diverse and complex gene regulation. We also found that the 5′ UTR is the least conserved regulatory element in sequence between the two species. Moreover, 34 orthologous sRNAs between E. coli and K. pneumoniae were analyzed in depth. The analysis suggested many of K. pneumoniae sRNAs might regulate the target genes as in E. coli.
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Affiliation(s)
- Donghyuk Kim
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Jay Sung-Joong Hong
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Yu Qiu
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Harish Nagarajan
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Joo-Hyun Seo
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Byung-Kwan Cho
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Shih-Feng Tsai
- Division of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, Taiwan
| | - Bernhard Ø. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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