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uz-Zaman MH, D’Alton S, Barrick JE, Ochman H. Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with Escherichia coli. PLoS Biol 2024; 22:e3002418. [PMID: 38713714 PMCID: PMC11101190 DOI: 10.1371/journal.pbio.3002418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 05/17/2024] [Accepted: 04/18/2024] [Indexed: 05/09/2024] Open
Abstract
The phenomenon of de novo gene birth-the emergence of genes from non-genic sequences-has received considerable attention due to the widespread occurrence of genes that are unique to particular species or genomes. Most instances of de novo gene birth have been recognized through comparative analyses of genome sequences in eukaryotes, despite the abundance of novel, lineage-specific genes in bacteria and the relative ease with which bacteria can be studied in an experimental context. Here, we explore the genetic record of the Escherichia coli long-term evolution experiment (LTEE) for changes indicative of "proto-genic" phases of new gene birth in which non-genic sequences evolve stable transcription and/or translation. Over the time span of the LTEE, non-genic regions are frequently transcribed, translated and differentially expressed, with levels of transcription across low-expressed regions increasing in later generations of the experiment. Proto-genes formed downstream of new mutations result either from insertion element activity or chromosomal translocations that fused preexisting regulatory sequences to regions that were not expressed in the LTEE ancestor. Additionally, we identified instances of proto-gene emergence in which a previously unexpressed sequence was transcribed after formation of an upstream promoter, although such cases were rare compared to those caused by recruitment of preexisting promoters. Tracing the origin of the causative mutations, we discovered that most occurred early in the history of the LTEE, often within the first 20,000 generations, and became fixed soon after emergence. Our findings show that proto-genes emerge frequently within evolving populations, can persist stably, and can serve as potential substrates for new gene formation.
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Affiliation(s)
- Md. Hassan uz-Zaman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Simon D’Alton
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Jeffrey E. Barrick
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Howard Ochman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
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2
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Meier D, Rauch C, Wagner M, Klemm P, Blumenkamp P, Müller R, Ellenberger E, Karia KM, Vecchione S, Serrania J, Lechner M, Fritz G, Goesmann A, Becker A. A MoClo-Compatible Toolbox of ECF Sigma Factor-Based Regulatory Switches for Proteobacterial Chassis. BIODESIGN RESEARCH 2024; 6:0025. [PMID: 38384496 PMCID: PMC10880074 DOI: 10.34133/bdr.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/04/2023] [Indexed: 02/23/2024] Open
Abstract
The construction of complex synthetic gene circuits with predetermined and reliable output depends on orthogonal regulatory parts that do not inadvertently interfere with the host machinery or with other circuit components. Previously, extracytoplasmic function sigma factors (ECFs), a diverse group of alternative sigma factors with distinct promoter specificities, were shown to have great potential as context-independent regulators, but so far, they have only been used in a few model species. Here, we show that the alphaproteobacterium Sinorhizobium meliloti, which has been proposed as a plant-associated bacterial chassis for synthetic biology, has a similar phylogenetic ECF acceptance range as the gammaproteobacterium Escherichia coli. A common set of orthogonal ECF-based regulators that can be used in both bacterial hosts was identified and used to create 2-step delay circuits. The genetic circuits were implemented in single copy in E. coli by chromosomal integration using an established method that utilizes bacteriophage integrases. In S. meliloti, we demonstrated the usability of single-copy pABC plasmids as equivalent carriers of the synthetic circuits. The circuits were either implemented on a single pABC or modularly distributed on 3 such plasmids. In addition, we provide a toolbox containing pABC plasmids compatible with the Golden Gate (MoClo) cloning standard and a library of basic parts that enable the construction of ECF-based circuits in S. meliloti and in E. coli. This work contributes to building a context-independent and species-overarching ECF-based toolbox for synthetic biology applications.
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Affiliation(s)
- Doreen Meier
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Christian Rauch
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Marcel Wagner
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Paul Klemm
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Patrick Blumenkamp
- Bioinformatics and Systems Biology,
Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Raphael Müller
- Bioinformatics and Systems Biology,
Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Eric Ellenberger
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Kinnari M. Karia
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Stefano Vecchione
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Javier Serrania
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Marcus Lechner
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Georg Fritz
- The University of Western Australia, School of Molecular Sciences, Perth, Australia
| | - Alexander Goesmann
- Bioinformatics and Systems Biology,
Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
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Uz-Zaman MH, D'Alton S, Barrick JE, Ochman H. Promoter capture drives the emergence of proto-genes in Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.15.567300. [PMID: 38013999 PMCID: PMC10680751 DOI: 10.1101/2023.11.15.567300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The phenomenon of de novo gene birth-the emergence of genes from non-genic sequences-has received considerable attention due to the widespread occurrence of genes that are unique to particular species or genomes. Most instances of de novo gene birth have been recognized through comparative analyses of genome sequences in eukaryotes, despite the abundance of novel, lineage-specific genes in bacteria and the relative ease with which bacteria can be studied in an experimental context. Here, we explore the genetic record of the Escherichia coli Long-Term Evolution Experiment (LTEE) for changes indicative of "proto-genic" phases of new gene birth in which non-genic sequences evolve stable transcription and/or translation. Over the time-span of the LTEE, non-genic regions are frequently transcribed, translated and differentially expressed, thereby serving as raw material for new gene emergence. Most proto-genes result either from insertion element activity or chromosomal translocations that fused pre-existing regulatory sequences to regions that were not expressed in the LTEE ancestor. Additionally, we identified instances of proto-gene emergence in which a previously unexpressed sequence was transcribed after formation of an upstream promoter. Tracing the origin of the causative mutations, we discovered that most occurred early in the history of the LTEE, often within the first 20,000 generations, and became fixed soon after emergence. Our findings show that proto-genes emerge frequently within evolving populations, persist stably, and can serve as potential substrates for new gene formation.
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4
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Zehentner B, Scherer S, Neuhaus K. Non-canonical transcriptional start sites in E. coli O157:H7 EDL933 are regulated and appear in surprisingly high numbers. BMC Microbiol 2023; 23:243. [PMID: 37653502 PMCID: PMC10469882 DOI: 10.1186/s12866-023-02988-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/21/2023] [Indexed: 09/02/2023] Open
Abstract
Analysis of genome wide transcription start sites (TSSs) revealed an unexpected complexity since not only canonical TSS of annotated genes are recognized by RNA polymerase. Non-canonical TSS were detected antisense to, or within, annotated genes as well new intergenic (orphan) TSS, not associated with known genes. Previously, it was hypothesized that many such signals represent noise or pervasive transcription, not associated with a biological function. Here, a modified Cappable-seq protocol allows determining the primary transcriptome of the enterohemorrhagic E. coli O157:H7 EDL933 (EHEC). We used four different growth media, both in exponential and stationary growth phase, replicated each thrice. This yielded 19,975 EHEC canonical and non-canonical TSS, which reproducibly occurring in three biological replicates. This questions the hypothesis of experimental noise or pervasive transcription. Accordingly, conserved promoter motifs were found upstream indicating proper TSSs. More than 50% of 5,567 canonical and between 32% and 47% of 10,355 non-canonical TSS were differentially expressed in different media and growth phases, providing evidence for a potential biological function also of non-canonical TSS. Thus, reproducible and environmentally regulated expression suggests that a substantial number of the non-canonical TSSs may be of unknown function rather than being the result of noise or pervasive transcription.
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Affiliation(s)
- Barbara Zehentner
- Chair for Microbial Ecology, TUM School of Life Sciences, Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany
| | - Siegfried Scherer
- Chair for Microbial Ecology, TUM School of Life Sciences, Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany
- ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Klaus Neuhaus
- ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany.
- Core Facility Microbiome, ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany.
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Zhao L, Tabari E, Rong H, Dong X, Xue D, Su Z. Antisense transcription and its roles in adaption to environmental stress in E. coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.23.533988. [PMID: 36993172 PMCID: PMC10055363 DOI: 10.1101/2023.03.23.533988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
UNLABELLED It has been reported that a highly varying proportion (1% ∼ 93%) of genes in various prokaryotes have antisense RNA (asRNA) transcription. However, the extent of the pervasiveness of asRNA transcription in the well-studied E. coli K12 strain has thus far been an issue of debate. Furthermore, very little is known about the expression patterns and functions of asRNAs under various conditions. To fill these gaps, we determined the transcriptomes and proteomes of E. coli K12 at multiple time points in five culture conditions using strand-specific RNA-seq, differential RNA-seq, and quantitative mass spectrometry methods. To reduce artifacts of possible transcriptional noise, we identified asRNA using stringent criteria with biological replicate verification and transcription start sites (TSSs) information included. We identified a total of 660 asRNAs, which were generally short and largely condition-dependently transcribed. We found that the proportions of the genes which had asRNA transcription highly depended on the culture conditions and time points. We classified the transcriptional activities of the genes in six transcriptional modes according to their relative levels of asRNA to mRNA. Many genes changed their transcriptional modes at different time points of the culture conditions, and such transitions can be described in a well-defined manner. Intriguingly, the protein levels and mRNA levels of genes in the sense-only/sense-dominant mode were moderately correlated, but the same was not true for genes in the balanced/antisense-dominant mode, in which asRNAs were at a comparable or higher level to mRNAs. These observations were further validated by western blot on candidate genes, where an increase in asRNA transcription diminished gene expression in one case and enhanced it in another. These results suggest that asRNAs may directly or indirectly regulate translation by forming duplexes with cognate mRNAs. Thus, asRNAs may play an important role in the bacterium's responses to environmental changes during growth and adaption to different environments. IMPORTANCE The cis -antisense RNA (asRNA) is a type of understudied RNA molecules in prokaryotes, which is believed to be important in regulating gene expression. Our current understanding of asRNA is constrained by inconsistent reports about its identification and properties. These discrepancies are partially caused by a lack of sufficient samples, biological replicates, and culture conditions. This study aimed to overcome these disadvantages and identified 660 putative asRNAs using integrated information from strand-specific RNA-seq, differential RNA-seq, and mass spectrometry methods. In addition, we explored the relative expression between asRNAs and sense RNAs and investigated asRNA regulated transcriptional activity changes over different culture conditions and time points. Our work strongly suggests that asRNAs may play a crucial role in bacterium's responses to environmental changes during growth and adaption to different environments.
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Cheah HL, Ahmed SA, Tang TH. Transcription start site mapping and small RNA profiling of Leptospira biflexa serovar Patoc. World J Microbiol Biotechnol 2023; 39:104. [PMID: 36808011 DOI: 10.1007/s11274-023-03540-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/03/2023] [Indexed: 02/23/2023]
Abstract
Leptospirosis is an emerging zoonotic disease caused by bacterial species of the genus Leptospira. However, the regulatory mechanisms and pathways underlying the adaptation of pathogenic and non-pathogenic Leptospira spp. in different environmental conditions remain elusive. Leptospira biflexa is a non-pathogenic species of Leptospira that lives exclusively in a natural environment. It is an ideal model not only for exploring molecular mechanisms underlying the environmental survival of Leptospira species but also for identifying virulence factors unique to Leptospira's pathogenic species. In this study, we aim to establish the transcription start site (TSS) landscape and the small RNA (sRNA) profile of L. biflexa serovar Patoc grown to exponential and stationary phases via differential RNA-seq (dRNA-seq) and small RNA-seq (sRNA-seq) analyses, respectively. Our dRNA-seq analysis uncovered a total of 2726 TSSs, which are also used to identify other elements, e.g., promoter and untranslated regions (UTRs). Besides, our sRNA-seq analysis revealed a total of 603 sRNA candidates, comprising 16 promoter-associated sRNAs, 184 5'UTR-derived sRNAs, 230 true intergenic sRNAs, 136 5'UTR-antisense sRNAs, and 130 open reading frame (ORF)-antisense sRNAs. In summary, these findings reflect the transcriptional complexity of L. biflexa serovar Patoc under different growth conditions and help to facilitate our understanding of regulatory networks in L. biflexa. To the best of our knowledge, this is the first study reporting the TSS landscape of L. biflexa. The TSS and sRNA landscapes of L. biflexa can also be compared with its pathogenic counterparts, e.g., L. borgpetersenii and L. interrogans, to identify features contributing to their environmental survival and virulence.
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Affiliation(s)
- Hong-Leong Cheah
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Siti Aminah Ahmed
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Thean-Hock Tang
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
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Sun Y, Chen H, Xu M, He L, Mao H, Yang S, Qiao X, Yang D. Exopolysaccharides metabolism and cariogenesis of Streptococcus mutans biofilm regulated by antisense vicK RNA. J Oral Microbiol 2023; 15:2204250. [PMID: 37138664 PMCID: PMC10150615 DOI: 10.1080/20002297.2023.2204250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
Background Streptococcus mutans (S. mutans) is a pivotal cariogenic pathogen contributing to its multiple virulence factors, one of which is synthesizing exopolysaccharides (EPS). VicK, a sensor histidine kinase, plays a major role in regulating genes associated with EPS synthesis and adhesion. Here we first identified an antisense vicK RNA (ASvicK) bound with vicK into double-stranded RNA (dsRNA). Objective This study aims to investigate the effect and mechanism of ASvicK in the EPS metabolism and cariogenesis of S. mutans. Methods The phenotypes of biofilm were detected by scanning electron microscopy (SEM), gas chromatography-mass spectrometery (GC-MS) , gel permeation chromatography (GPC) , transcriptome analysis and Western blot. Co-immunoprecipitation (Co-ip) assay and enzyme activity experiment were adopted to investigate the mechanism of ASvicK regulation. Caries animal models were developed to study the relationship between ASvicK and cariogenicity of S. mutans. Results Overexpression of ASvicK can inhibit the growth of biofilm, reduce the production of EPS and alter genes and protein related to EPS metabolism. ASvicK can adsorb RNase III to regulate vicK and affect the cariogenicity of S. mutans. Conclusions ASvicK regulates vicK at the transcriptional and post-transcriptional levels, effectively inhibits EPS synthesis and biofilm formation and reduces its cariogenicity in vivo.
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Affiliation(s)
- Yuting Sun
- Department of Endodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Hong Chen
- Department of Endodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Mengmeng Xu
- Department of Endodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Liwen He
- Department of Endodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Hongchen Mao
- Department of Endodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Shiyao Yang
- Department of Endodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Xin Qiao
- Department of Endodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Deqin Yang
- Department of Endodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
- CONTACT Deqin Yang Department of Endodontics, Stomatological Hospital of Chongqing Medical University, Chongqing4404100, China
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Ali A, Salem M. Genome-wide identification of antisense lncRNAs and their association with susceptibility to Flavobacterium psychrophilum in rainbow trout. Front Immunol 2022; 13:1050722. [PMID: 36561762 PMCID: PMC9763276 DOI: 10.3389/fimmu.2022.1050722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic genomes encode long noncoding natural antisense transcripts (lncNATs) that have been increasingly recognized as regulatory members of gene expression. Recently, we identified a few antisense transcripts correlating in expression with immune-related genes. However, a systematic genome-wide analysis of lncNATs in rainbow trout is lacking. This study used 134 RNA-Seq datasets from five different projects to identify antisense transcripts. A total of 13,503 lncNATs were identified genome-wide. About 75% of lncNATs showed multiple exons compared to 36.5% of the intergenic lncRNAs. RNA-Seq datasets from resistant, control, and susceptible rainbow trout genetic lines with significant differences in survival rate following Flavobacterium psychrophilum (Fp) infection were analyzed to investigate the potential role of the lncNATs during infection. Twenty-four pairwise comparisons between the different genetic lines, infectious status, and time points revealed 581 differentially expressed (DE) lncNATs and 179 differentially used exons (DUEs). Most of the DE lncNATs strongly and positively correlated in expression with their corresponding sense transcripts across 24 RNA-Seq datasets. LncNATs complementary to genes related to immunity, muscle contraction, proteolysis, and iron/heme metabolism were DE following infection. LncNATs complementary to hemolysis-related genes were DE in the resistant fish compared to susceptible fish on day 5 post-infection, suggesting enhanced clearance of free hemoglobin (Hb) and heme and increased erythropoiesis. LncNATs complementary to hepcidin, a master negative regulator of the plasma iron concentration, were the most downregulated lncNATs on day 5 of bacterial infection in the resistant fish. Ninety-four DE lncNAT, including five complementary to hepcidin, are located within 26 QTL regions previously identified in association with bacterial cold water disease (BCWD) in rainbow trout. Collectively, lncNATs are involved in the molecular architecture of fish immunity and should be further investigated for potential applications in genomic selection and genetic manipulation in aquaculture.
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Anand D, Jakkala K, Nair RR, Sharan D, Pradhan A, Mukkayyan N, Ajitkumar P. Complete identity and expression of StfZ, the cis-antisense RNA to the mRNA of the cell division gene ftsZ, in Escherichia coli. Front Microbiol 2022; 13:920117. [PMID: 36338044 PMCID: PMC9628754 DOI: 10.3389/fmicb.2022.920117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Bacteria regulate FtsZ protein levels through transcriptional and translational mechanisms for proper cell division. A cis-antisense RNA, StfZ, produced from the ftsA-ftsZ intergenic region, was proposed to regulate FtsZ level in Escherichia coli. However, its structural identity remained unknown. In this study, we determined the complete sequence of StfZ and identified the isoforms and its promoters. We find that under native physiological conditions, StfZ is expressed at a 1:6 ratio of StfZ:ftsZ mRNA at all growth phases from three promoters as three isoforms of 366, 474, and 552 nt RNAs. Overexpression of StfZ reduces FtsZ protein level, increases cell length, and blocks cell division without affecting the ftsZ mRNA stability. We did not find differential expression of StfZ under the stress conditions of heat shock, cold shock, or oxidative stress, or at any growth phase. These data indicated that the cis-encoded StfZ antisense RNA to ftsZ mRNA may be involved in the fine tuning of ftsZ mRNA levels available for translation as per the growth-phase-specific requirement at all phases of growth and cell division.
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Affiliation(s)
- Deepak Anand
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Department of Biology, Lund University, Lund, Sweden
- *Correspondence: Deepak Anand,
| | - Kishor Jakkala
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, United States
| | - Rashmi Ravindran Nair
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Deepti Sharan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Department of Microbiology, The University of Chicago, Chicago, IL, United States
| | - Atul Pradhan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, United States
| | - Nagaraja Mukkayyan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, MD, United States
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Scholz SA, Lindeboom CD, Freddolino PL. Genetic context effects can override canonical cis regulatory elements in Escherichia coli. Nucleic Acids Res 2022; 50:10360-10375. [PMID: 36134716 PMCID: PMC9561378 DOI: 10.1093/nar/gkac787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 08/10/2022] [Accepted: 09/02/2022] [Indexed: 11/12/2022] Open
Abstract
Recent experiments have shown that in addition to control by cis regulatory elements, the local chromosomal context of a gene also has a profound impact on its transcription. Although this chromosome-position dependent expression variation has been empirically mapped at high-resolution, the underlying causes of the variation have not been elucidated. Here, we demonstrate that 1 kb of flanking, non-coding synthetic sequences with a low frequency of guanosine and cytosine (GC) can dramatically reduce reporter expression compared to neutral and high GC-content flanks in Escherichia coli. Natural and artificial genetic context can have a similarly strong effect on reporter expression, regardless of cell growth phase or medium. Despite the strong reduction in the maximal expression level from the fully-induced reporter, low GC synthetic flanks do not affect the time required to reach the maximal expression level after induction. Overall, we demonstrate key determinants of transcriptional propensity that appear to act as tunable modulators of transcription, independent of regulatory sequences such as the promoter. These findings provide insight into the regulation of naturally occurring genes and an independent control for optimizing expression of synthetic biology constructs.
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Affiliation(s)
- Scott A Scholz
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Chase D Lindeboom
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Peter L Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
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11
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Regulatory Interplay between RNase III and Antisense RNAs in E. coli: the Case of AsflhD and FlhD, Component of the Master Regulator of Motility. mBio 2022; 13:e0098122. [PMID: 36000733 PMCID: PMC9600491 DOI: 10.1128/mbio.00981-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In order to respond to ever-changing environmental cues, bacteria display resilient regulatory mechanisms controlling gene expression. At the post-transcriptional level, this is achieved by a combination of RNA-binding proteins, such as ribonucleases (RNases), and regulatory RNAs, including antisense RNAs (asRNAs). Bound to their complementary mRNA, asRNAs are primary targets for the double-strand-specific endoribonuclease, RNase III. Taking advantage of our own and previously published transcriptomic data sets obtained in strains inactivated for RNase III, we selected several candidate asRNAs and confirmed the existence of RNase III-sensitive asRNAs for crp, ompR, phoP, and flhD genes, all encoding global regulators of gene expression in Escherichia coli. Using FlhD, a component of the master regulator of motility (FlhD4C2), as our model, we demonstrate that the asRNA AsflhD, transcribed from the coding sequence of flhD, is involved in the fine-tuning of flhD expression and thus participates in the control of motility.
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12
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Martinez B, Bharati BK, Epshtein V, Nudler E. Pervasive Transcription-coupled DNA repair in E. coli. Nat Commun 2022; 13:1702. [PMID: 35354807 PMCID: PMC8967931 DOI: 10.1038/s41467-022-28871-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/14/2022] [Indexed: 11/18/2022] Open
Abstract
Global Genomic Repair (GGR) and Transcription-Coupled Repair (TCR) have been viewed, respectively, as major and minor sub-pathways of the nucleotide excision repair (NER) process that removes bulky lesions from the genome. Here we applied a next generation sequencing assay, CPD-seq, in E. coli to measure the levels of cyclobutane pyrimidine dimer (CPD) lesions before, during, and after UV-induced genotoxic stress, and, therefore, to determine the rate of genomic recovery by NER at a single nucleotide resolution. We find that active transcription is necessary for the repair of not only the template strand (TS), but also the non-template strand (NTS), and that the bulk of TCR is independent of Mfd – a DNA translocase that is thought to be necessary and sufficient for TCR in bacteria. We further show that repair of both TS and NTS is enhanced by increased readthrough past Rho-dependent terminators. We demonstrate that UV-induced genotoxic stress promotes global antitermination so that TCR is more accessible to the antisense, intergenic, and other low transcribed regions. Overall, our data suggest that GGR and TCR are essentially the same process required for complete repair of the bacterial genome. Transcription-Coupled DNA repair has been classically defined as the preferential repair of the template strand (TS) over the non-template strand (NTS). Here the authors challenge this classic model of TCR by using a genome-wide repair assay, CPD-seq, as well as RNA-seq, to show that TCR occurs across the entire E. coli genome – including NTS and intergenic regions.
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Affiliation(s)
- Britney Martinez
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Binod K Bharati
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA.,Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Vitaly Epshtein
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA. .,Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, New York, 10016, USA.
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13
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Abstract
Despite their ubiquitous nature, few antisense RNAs have been functionally characterized, and this class of RNAs is considered by some to be transcriptional noise. Here, we report that an antisense RNA (asRNA), aMEF (antisense mazEF), functions as a dual regulator for the type II toxin-antitoxin (TA) system mazEF. Unlike type I TA systems and many other regulatory asRNAs, aMEF stimulates the synthesis and translation of mazEF rather than inhibition and degradation. Our data indicate that a double-stranded RNA intermediate and RNase III are not necessary for aMEF-dependent regulation of mazEF expression. The lack of conservation of asRNA promoters has been used to support the hypothesis that asRNAs are spurious transcriptional noise and nonfunctional. We demonstrate that the aMEF promoter is active and functional in Escherichia coli despite poor sequence conservation, indicating that the lack of promoter sequence conservation should not be correlated with functionality. IMPORTANCE Next-generation RNA sequencing of numerous organisms has revealed that transcription is widespread across the genome, termed pervasive transcription, and does not adhere to annotated gene boundaries. The function of pervasive transcription is enigmatic and has generated considerable controversy as to whether it is transcriptional noise or biologically relevant. Antisense transcription is one class of pervasive transcription that occurs from the DNA strand opposite an annotated gene. Relatively few pervasively transcribed asRNAs have been functionally characterized, and their regulatory roles or lack thereof remains unknown. It is important to study examples of these asRNAs and determine if they are functional regulators. In this study, we elucidate the function of an asRNA (aMEF) demonstrating that pervasive transcripts can be functional.
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14
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Pinatel E, Calcagnile M, Talà A, Damiano F, Siculella L, Peano C, De Benedetto GE, Pennetta A, De Bellis G, Alifano P. Interplay between non-coding RNA transcription, stringent phenotype and antibiotic production in Streptomyces. J Biotechnol 2022:S0168-1656(22)00029-3. [PMID: 35182607 DOI: 10.1016/j.jbiotec.2022.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/12/2022] [Indexed: 11/26/2022]
Abstract
While in recent years the key role of non-coding RNAs (ncRNAs) in regulation of gene expression has become increasingly evident, their interaction with the global regulatory circuits is still obscure. Here we analyzed the structure and organization of the transcriptome of Streptomyces ambofaciens, the producer of spiramycin. We identified ncRNAs including 45 small-RNAs (sRNAs) and 119 antisense-RNAs (asRNAs I) that appear transcribed from dedicated promoters. Some sRNAs and asRNAs are unprecedented in Streptomyces, and were predicted to target mRNAs encoding proteins involved in transcription, translation, ribosomal structure and biogenesis, and regulation of morphological and biochemical differentiation. We then compared ncRNA expression in three strains: i.) the wild type strain; ii.) an isogenic pirA-defective mutant with central carbon metabolism imbalance, "relaxed" phenotype, and repression of antibiotic production; iii.) a pirA-derivative strain harboring a "stringent" RNA polymerase that suppresses pirA-associated phenotypes. Data indicated that expression of most ncRNAs was correlated to the stringent/relaxed phenotype suggesting novel effector mechanisms of the stringent response.
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Affiliation(s)
- Eva Pinatel
- Institute of Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - Matteo Calcagnile
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Adelfia Talà
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Fabrizio Damiano
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Luisa Siculella
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Clelia Peano
- Genomic Unit, IRCCS Humanitas Clinical and Research Center, Rozzano, Milan, Italy; Institute of Genetic and Biomedical Research, UoS of Milan, National Research Council, Rozzano, Milan, Italy
| | | | - Antonio Pennetta
- Department of Cultural Heritage, University of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Gianluca De Bellis
- Institute of Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - Pietro Alifano
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Monteroni, 73100 Lecce, Italy.
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15
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Regulation of Heterogenous LexA Expression in Staphylococcus aureus by an Antisense RNA Originating from Transcriptional Read-Through upon Natural Mispairings in the sbrB Intrinsic Terminator. Int J Mol Sci 2022; 23:ijms23010576. [PMID: 35009002 PMCID: PMC8745188 DOI: 10.3390/ijms23010576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/30/2021] [Accepted: 01/01/2022] [Indexed: 12/10/2022] Open
Abstract
Bacterial genomes are pervasively transcribed, generating a wide variety of antisense RNAs (asRNAs). Many of them originate from transcriptional read-through events (TREs) during the transcription termination process. Previous transcriptome analyses revealed that the lexA gene from Staphylococcus aureus, which encodes the main SOS response regulator, is affected by the presence of an asRNA. Here, we show that the lexA antisense RNA (lexA-asRNA) is generated by a TRE on the intrinsic terminator (TTsbrB) of the sbrB gene, which is located downstream of lexA, in the opposite strand. Transcriptional read-through occurs by a natural mutation that destabilizes the TTsbrB structure and modifies the efficiency of the intrinsic terminator. Restoring the mispairing mutation in the hairpin of TTsbrB prevented lexA-asRNA transcription. The level of lexA-asRNA directly correlated with cellular stress since the expressions of sbrB and lexA-asRNA depend on the stress transcription factor SigB. Comparative analyses revealed strain-specific nucleotide polymorphisms within TTsbrB, suggesting that this TT could be prone to accumulating natural mutations. A genome-wide analysis of TREs suggested that mispairings in TT hairpins might provide wider transcriptional connections with downstream genes and, ultimately, transcriptomic variability among S. aureus strains.
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16
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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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17
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Abstract
Conventional bacterial genome annotation provides information about coding sequences but ignores untranslated regions and operons. However, untranslated regions contain important regulatory elements as well as targets for many regulatory factors, such as small RNAs. Operon maps are also essential for functional gene analysis. In the last decade, considerable progress has been made in the study of bacterial transcriptomes through transcriptome sequencing (RNA-seq). Given the compact nature of bacterial genomes, many challenges still cannot be resolved through short reads generated using classical RNA-seq because of fragmentation and loss of the full-length information. Direct RNA sequencing is a technology that sequences the native RNA directly without information loss or bias. Here, we employed direct RNA sequencing to annotate the Vibrio parahaemolyticus transcriptome with its full features, including transcription start sites (TSSs), transcription termination sites, and operon maps. A total of 4,103 TSSs were identified. In comparison to short-read sequencing, full-length information provided a deeper view of TSS classification, showing that most internal and antisense TSSs were actually a result of gene overlap. Sequencing the transcriptome of V. parahaemolyticus grown with bile allowed us to study the landscape of pathogenicity island Vp-PAI. Some genes in this region were reannotated, providing more accurate annotation to increase precision in their characterization. Quantitative detection of operons in V. parahaemolyticus showed high complexity in some operons, shedding light on a greater extent of regulation within the same operon. Our study using direct RNA sequencing provides a quantitative and high-resolution landscape of the V. parahaemolyticus transcriptome. IMPORTANCEVibrio parahaemolyticus is a halophilic bacterium found in the marine environment. Outbreaks of gastroenteritis resulting from seafood poisoning by these pathogens have risen over the past 2 decades. Upon ingestion by humans—often through the consumption of raw or undercooked seafood—V. parahaemolyticus senses the host environment and expresses numerous genes, the products of which synergize to synthesize and secrete toxins that can cause acute gastroenteritis. To understand the regulation of such adaptive response, mRNA transcripts must be mapped accurately. However, due to the limitations of common sequencing methods, not all features of bacterial transcriptomes are always reported. We applied direct RNA sequencing to analyze the V. parahaemolyticus transcriptome. Mapping the full features of the transcriptome is anticipated to enhance our understanding of gene regulation in this bacterium and provides a data set for future work. Additionally, this study reveals a deeper view of a complicated transcriptome landscape, demonstrating the importance of applying such methods to other bacterial models.
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18
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Interplay between Non-Coding RNA Transcription, Stringent/Relaxed Phenotype and Antibiotic Production in Streptomyces ambofaciens. Antibiotics (Basel) 2021; 10:antibiotics10080947. [PMID: 34438997 PMCID: PMC8388888 DOI: 10.3390/antibiotics10080947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/28/2021] [Accepted: 08/02/2021] [Indexed: 11/25/2022] Open
Abstract
While in recent years the key role of non-coding RNAs (ncRNAs) in the regulation of gene expression has become increasingly evident, their interaction with the global regulatory circuits is still obscure. Here we analyzed the structure and organization of the transcriptome of Streptomyces ambofaciens, the producer of spiramycin. We identified ncRNAs including 45 small-RNAs (sRNAs) and 119 antisense-RNAs (asRNAs I) that appear transcribed from dedicated promoters. Some sRNAs and asRNAs are unprecedented in Streptomyces and were predicted to target mRNAs encoding proteins involved in transcription, translation, ribosomal structure and biogenesis, and regulation of morphological and biochemical differentiation. We then compared ncRNA expression in three strains: (i) the wild-type strain; (ii) an isogenic pirA-defective mutant with central carbon metabolism imbalance, “relaxed” phenotype, and repression of antibiotic production; and (iii) a pirA-derivative strain harboring a “stringent” RNA polymerase that suppresses pirA-associated phenotypes. Data indicated that the expression of most ncRNAs was correlated to the stringent/relaxed phenotype suggesting novel effector mechanisms of the stringent response.
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19
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Li R, Sklutuis R, Groebner JL, Romerio F. HIV-1 Natural Antisense Transcription and Its Role in Viral Persistence. Viruses 2021; 13:v13050795. [PMID: 33946840 PMCID: PMC8145503 DOI: 10.3390/v13050795] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/11/2022] Open
Abstract
Natural antisense transcripts (NATs) represent a class of RNA molecules that are transcribed from the opposite strand of a protein-coding gene, and that have the ability to regulate the expression of their cognate protein-coding gene via multiple mechanisms. NATs have been described in many prokaryotic and eukaryotic systems, as well as in the viruses that infect them. The human immunodeficiency virus (HIV-1) is no exception, and produces one or more NAT from a promoter within the 3’ long terminal repeat. HIV-1 antisense transcripts have been the focus of several studies spanning over 30 years. However, a complete appreciation of the role that these transcripts play in the virus lifecycle is still lacking. In this review, we cover the current knowledge about HIV-1 NATs, discuss some of the questions that are still open and identify possible areas of future research.
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Affiliation(s)
- Rui Li
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA;
| | - Rachel Sklutuis
- HIV Dynamics and Replication Program, Host-Virus Interaction Branch, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; (R.S.); (J.L.G.)
| | - Jennifer L. Groebner
- HIV Dynamics and Replication Program, Host-Virus Interaction Branch, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; (R.S.); (J.L.G.)
| | - Fabio Romerio
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA;
- Correspondence:
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20
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Chia JY, Khoo KS, Ling TC, Croft L, Manickam S, Yap YJ, Show PL. Description and detection of excludons as transcriptional regulators in gram-positive, gram-negative and archaeal strains of prokaryotes. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.101933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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21
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Millar JA, Raghavan R. Modulation of Bacterial Fitness and Virulence Through Antisense RNAs. Front Cell Infect Microbiol 2021; 10:596277. [PMID: 33747974 PMCID: PMC7968456 DOI: 10.3389/fcimb.2020.596277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/30/2020] [Indexed: 01/22/2023] Open
Abstract
Regulatory RNAs contribute to gene expression control in bacteria. Antisense RNAs (asRNA) are a class of regulatory RNAs that are transcribed from opposite strands of their target genes. Typically, these untranslated transcripts bind to cognate mRNAs and rapidly regulate gene expression at the post-transcriptional level. In this article, we review asRNAs that modulate bacterial fitness and increase virulence. We chose examples that underscore the variety observed in nature including, plasmid- and chromosome-encoded asRNAs, a riboswitch-regulated asRNA, and asRNAs that require other RNAs or RNA-binding proteins for stability and activity. We explore how asRNAs improve bacterial fitness and virulence by modulating plasmid acquisition and maintenance, regulating transposon mobility, increasing resistance against bacteriophages, controlling flagellar production, and regulating nutrient acquisition. We conclude with a brief discussion on how this knowledge is helping to inform current efforts to develop new therapeutics.
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Affiliation(s)
- Jess A Millar
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, United States.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Rahul Raghavan
- Department of Biology and Center for Life in Extreme Environments, Portland State University, Portland, OR, United States.,Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States
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22
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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: 82] [Impact Index Per Article: 20.5] [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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23
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Whitworth DE, Swain MT. A survey of non-coding RNAs in the social and predatory myxobacterium Myxococcus xanthus DK1622. Mol Omics 2020; 16:492-502. [PMID: 32780046 DOI: 10.1039/d0mo00068j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Prokaryotic ncRNAs are important regulators of gene expression, and can be involved in complex signalling networks. The myxobacteria are model organisms for studies into multicellular development and microbial predation, being particularly renowned for their large genomes and exceptionally sophisticated signalling networks. However, apart from two specific examples, little is known about their regulatory ncRNAs. Here, we integrate bioinformatic predictions and transcriptome sequence data to provide a comprehensive survey of the ncRNAs made by the exemplar myxobacterium M. xanthus DK1622. M. xanthus RNA-seq data from four experimental conditions was interrogated to identify transcripts mapping outside coding sequences and to known ncRNAs. The resulting 37 ncRNAs were clustered on the genome and most (30/37) were conserved across the myxobacteria. A majority of ncRNAs (22/37) were intergenic, while 13 were at least partially antisense to protein-coding genes. Predicted promoter and terminator sequences explained the start/stop sites of 18 ncRNAs. mRNA targets for the ncRNAs were predicted, including plausible candidates for a known regulatory ncRNA. 22 ncRNAs were differentially expressed by nutrient availability and expression of 25 predicted targets was found to correlate strongly with that of their regulatory ncRNAs. Sharing of predicted mRNA targets by multiple ncRNAs suggests that some ncRNAs might regulate each other within signalling networks. This genomic survey of M. xanthus ncRNA biology provides a starting point for further studies of myxobacterial ncRNAs, which are likely to have important functions in these industrially important and sophisticated organisms.
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Affiliation(s)
- David E Whitworth
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, SY23 3DD, UK.
| | - Martin T Swain
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, SY23 3DD, UK.
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24
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Narra HP, Sahni A, Alsing J, Schroeder CLC, Golovko G, Nia AM, Fofanov Y, Khanipov K, Sahni SK. Comparative transcriptomic analysis of Rickettsia conorii during in vitro infection of human and tick host cells. BMC Genomics 2020; 21:665. [PMID: 32977742 PMCID: PMC7519539 DOI: 10.1186/s12864-020-07077-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/17/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Pathogenic Rickettsia species belonging to the spotted fever group are arthropod-borne, obligate intracellular bacteria which exhibit preferential tropism for host microvascular endothelium in the mammalian hosts, resulting in disease manifestations attributed primarily to endothelial damage or dysfunction. Although rickettsiae are known to undergo evolution through genomic reduction, the mechanisms by which these pathogens regulate their transcriptome to ensure survival in tick vectors and maintenance by transovarial/transstadial transmission, in contrast to their ability to cause debilitating infections in human hosts remain unknown. In this study, we compare the expression profiles of rickettsial sRNAome/transcriptome and determine the transcriptional start sites (TSSs) of R. conorii transcripts during in vitro infection of human and tick host cells. RESULTS We performed deep sequencing on total RNA from Amblyomma americanum AAE2 cells and human microvascular endothelial cells (HMECs) infected with R. conorii. Strand-specific RNA sequencing of R. conorii transcripts revealed the expression 32 small RNAs (Rc_sR's), which were preferentially expressed above the limit of detection during tick cell infection, and confirmed the expression of Rc_sR61, sR71, and sR74 by quantitative RT-PCR. Intriguingly, a total of 305 and 132 R. conorii coding genes were differentially upregulated (> 2-fold) in AAE2 cells and HMECs, respectively. Further, enrichment for primary transcripts by treatment with Terminator 5'-Phosphate-dependent Exonuclease resulted in the identification of 3903 and 2555 transcription start sites (TSSs), including 214 and 181 primary TSSs in R. conorii during the infection to tick and human host cells, respectively. Seventy-five coding genes exhibited different TSSs depending on the host environment. Finally, we also observed differential expression of 6S RNA during host-pathogen and vector-pathogen interactions in vitro, implicating an important role for this noncoding RNA in the regulation of rickettsial transcriptome depending on the supportive host niche. CONCLUSIONS In sum, the findings of this study authenticate the presence of novel Rc_sR's in R. conorii, reveal the first evidence for differential expression of coding transcripts and utilization of alternate transcriptional start sites depending on the host niche, and implicate a role for 6S RNA in the regulation of coding transcriptome during tripartite host-pathogen-vector interactions.
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Affiliation(s)
- Hema P Narra
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
| | - Abha Sahni
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jessica Alsing
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Casey L C Schroeder
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - George Golovko
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Anna M Nia
- Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Sanjeev K Sahni
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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25
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Ardern Z, Neuhaus K, Scherer S. Are Antisense Proteins in Prokaryotes Functional? Front Mol Biosci 2020; 7:187. [PMID: 32923454 PMCID: PMC7457138 DOI: 10.3389/fmolb.2020.00187] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/16/2020] [Indexed: 12/16/2022] Open
Abstract
Many prokaryotic RNAs are transcribed from loci outside of annotated protein coding genes. Across bacterial species hundreds of short open reading frames antisense to annotated genes show evidence of both transcription and translation, for instance in ribosome profiling data. Determining the functional fraction of these protein products awaits further research, including insights from studies of molecular interactions and detailed evolutionary analysis. There are multiple lines of evidence, however, that many of these newly discovered proteins are of use to the organism. Condition-specific phenotypes have been characterized for a few. These proteins should be added to genome annotations, and the methods for predicting them standardized. Evolutionary analysis of these typically young sequences also may provide important insights into gene evolution. This research should be prioritized for its exciting potential to uncover large numbers of novel proteins with extremely diverse potential practical uses, including applications in synthetic biology and responding to pathogens.
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Affiliation(s)
- Zachary Ardern
- Chair for Microbial Ecology, Technical University of Munich, Munich, Germany
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26
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Narra HP, Sahni A, Walker DH, Sahni SK. Recent research milestones in the pathogenesis of human rickettsioses and opportunities ahead. Future Microbiol 2020; 15:753-765. [PMID: 32691620 DOI: 10.2217/fmb-2019-0266] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Infections caused by pathogenic Rickettsia species continue to scourge human health across the globe. From the point of entry at the site of transmission by arthropod vectors, hematogenous dissemination of rickettsiae occurs to diverse host tissues leading to 'rickettsial vasculitis' as the salient feature of pathogenesis. This perspective article accentuates recent breakthrough developments in the context of host-pathogen-vector interactions during rickettsial infections. The subtopics include potential exploitation of circulating macrophages for spread, identification of new entry mechanisms and regulators of actin-based motility, appreciation of metabolites acquired from and effectors delivered into the host, importance of the toxin-antitoxin module in host-cell interactions, effects of the vector microbiome on rickettsial transmission, and niche-specific riboregulation and adaptation. Further research on these aspects will advance our understanding of the biology of rickettsiae as intracellular pathogens and should enable design and development of new approaches to counter rickettsioses in humans and other hosts.
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Affiliation(s)
- Hema P Narra
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Abha Sahni
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - David H Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Sanjeev K Sahni
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
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27
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Dual RNA-seq of Orientia tsutsugamushi informs on host-pathogen interactions for this neglected intracellular human pathogen. Nat Commun 2020; 11:3363. [PMID: 32620750 PMCID: PMC7335160 DOI: 10.1038/s41467-020-17094-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 06/11/2020] [Indexed: 12/12/2022] Open
Abstract
Studying emerging or neglected pathogens is often challenging due to insufficient information and absence of genetic tools. Dual RNA-seq provides insights into host-pathogen interactions, and is particularly informative for intracellular organisms. Here we apply dual RNA-seq to Orientia tsutsugamushi (Ot), an obligate intracellular bacterium that causes the vector-borne human disease scrub typhus. Half the Ot genome is composed of repetitive DNA, and there is minimal collinearity in gene order between strains. Integrating RNA-seq, comparative genomics, proteomics, and machine learning to study the transcriptional architecture of Ot, we find evidence for wide-spread post-transcriptional antisense regulation. Comparing the host response to two clinical isolates, we identify distinct immune response networks for each strain, leading to predictions of relative virulence that are validated in a mouse infection model. Thus, dual RNA-seq can provide insight into the biology and host-pathogen interactions of a poorly characterized and genetically intractable organism such as Ot.
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28
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Glaub A, Huptas C, Neuhaus K, Ardern Z. Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data. J Biol Chem 2020; 295:8999-9011. [PMID: 32385111 PMCID: PMC7335797 DOI: 10.1074/jbc.ra119.012161] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 05/05/2020] [Indexed: 02/03/2023] Open
Abstract
Ribosome profiling (RIBO-Seq) has improved our understanding of bacterial translation, including finding many unannotated genes. However, protocols for RIBO-Seq and corresponding data analysis are not yet standardized. Here, we analyzed 48 RIBO-Seq samples from nine studies of Escherichia coli K12 grown in lysogeny broth medium and particularly focused on the size-selection step. We show that for conventional expression analysis, a size range between 22 and 30 nucleotides is sufficient to obtain protein-coding fragments, which has the advantage of removing many unwanted rRNA and tRNA reads. More specific analyses may require longer reads and a corresponding improvement in rRNA/tRNA depletion. There is no consensus about the appropriate sequencing depth for RIBO-Seq experiments in prokaryotes, and studies vary significantly in total read number. Our analysis suggests that 20 million reads that are not mapping to rRNA/tRNA are required for global detection of translated annotated genes. We also highlight the influence of drug-induced ribosome stalling, which causes bias at translation start sites. The resulting accumulation of reads at the start site may be especially useful for detecting weakly expressed genes. As different methods suit different questions, it may not be possible to produce a "one-size-fits-all" ribosome profiling data set. Therefore, experiments should be carefully designed in light of the scientific questions of interest. We propose some basic characteristics that should be reported with any new RIBO-Seq data sets. Careful attention to the factors discussed should improve prokaryotic gene detection and the comparability of ribosome profiling data sets.
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Affiliation(s)
- Alina Glaub
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany
| | - Christopher Huptas
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany
| | - Klaus Neuhaus
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany; Core Facility Microbiome, ZIEL Institute for Food and Health, Technical University of Munich, Freising, Germany
| | - Zachary Ardern
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany.
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29
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Riboregulation in Nitrogen-Fixing Endosymbiotic Bacteria. Microorganisms 2020; 8:microorganisms8030384. [PMID: 32164262 PMCID: PMC7143759 DOI: 10.3390/microorganisms8030384] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 01/21/2023] Open
Abstract
Small non-coding RNAs (sRNAs) are ubiquitous components of bacterial adaptive regulatory networks underlying stress responses and chronic intracellular infection of eukaryotic hosts. Thus, sRNA-mediated regulation of gene expression is expected to play a major role in the establishment of mutualistic root nodule endosymbiosis between nitrogen-fixing rhizobia and legume plants. However, knowledge about this level of genetic regulation in this group of plant-interacting bacteria is still rather scarce. Here, we review insights into the rhizobial non-coding transcriptome and sRNA-mediated post-transcriptional regulation of symbiotic relevant traits such as nutrient uptake, cell cycle, quorum sensing, or nodule development. We provide details about the transcriptional control and protein-assisted activity mechanisms of the functionally characterized sRNAs involved in these processes. Finally, we discuss the forthcoming research on riboregulation in legume symbionts.
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30
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Hwang S, Lee N, Jeong Y, Lee Y, Kim W, Cho S, Palsson BO, Cho BK. Primary transcriptome and translatome analysis determines transcriptional and translational regulatory elements encoded in the Streptomyces clavuligerus genome. Nucleic Acids Res 2020; 47:6114-6129. [PMID: 31131406 PMCID: PMC6614810 DOI: 10.1093/nar/gkz471] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/10/2019] [Accepted: 05/17/2019] [Indexed: 02/06/2023] Open
Abstract
Determining transcriptional and translational regulatory elements in GC-rich Streptomyces genomes is essential to elucidating the complex regulatory networks that govern secondary metabolite biosynthetic gene cluster (BGC) expression. However, information about such regulatory elements has been limited for Streptomyces genomes. To address this limitation, a high-quality genome sequence of β-lactam antibiotic-producing Streptomyces clavuligerus ATCC 27 064 is completed, which contains 7163 newly annotated genes. This provides a fundamental reference genome sequence to integrate multiple genome-scale data types, including dRNA-Seq, RNA-Seq and ribosome profiling. Data integration results in the precise determination of 2659 transcription start sites which reveal transcriptional and translational regulatory elements, including −10 and −35 promoter components specific to sigma (σ) factors, and 5′-untranslated region as a determinant for translation efficiency regulation. Particularly, sequence analysis of a wide diversity of the −35 components enables us to predict potential σ-factor regulons, along with various spacer lengths between the −10 and −35 elements. At last, the primary transcriptome landscape of the β-lactam biosynthetic pathway is analyzed, suggesting temporal changes in metabolism for the synthesis of secondary metabolites driven by transcriptional regulation. This comprehensive genetic information provides a versatile genetic resource for rational engineering of secondary metabolite BGCs in Streptomyces.
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Affiliation(s)
- Soonkyu Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Namil Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yujin Jeong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yongjae Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Woori Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.,Novo Nordisk Foundation Center for Biosustainability, 2800 Kongens Lyngby, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,Intelligent Synthetic Biology Center, Daejeon 34141, Republic of Korea
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31
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Abstract
This study systematically evaluated the global patterns of microbial antisense expression across various environments and provides a bird’s-eye view of general patterns observed across data sets, which can provide guidelines in our understanding of antisense expression as well as interpretation of metatranscriptomic data in general. This analysis highlights that in some environments, antisense expression from microbial communities can dominate over regular gene expression. We explored some potential drivers of antisense transcription, but more importantly, this study serves as a starting point, highlighting topics for future research and providing guidelines to include antisense expression in generic bioinformatic pipelines for metatranscriptomic data. High-throughput sequencing has allowed unprecedented insight into the composition and function of complex microbial communities. With metatranscriptomics, it is possible to interrogate the transcriptomes of multiple organisms simultaneously to get an overview of the gene expression of the entire community. Studies have successfully used metatranscriptomics to identify and describe relationships between gene expression levels and community characteristics. However, metatranscriptomic data sets contain a rich suite of additional information that is just beginning to be explored. Here, we focus on antisense expression in metatranscriptomics, discuss the different computational strategies for handling it, and highlight the strengths but also potentially detrimental effects on downstream analysis and interpretation. We also analyzed the antisense transcriptomes of multiple genomes and metagenome-assembled genomes (MAGs) from five different data sets and found high variability in the levels of antisense transcription for individual species, which were consistent across samples. Importantly, we challenged the conceptual framework that antisense transcription is primarily the product of transcriptional noise and found mixed support, suggesting that the total observed antisense RNA in complex communities arises from the combined effect of unknown biological and technical factors. Antisense transcription can be highly informative, including technical details about data quality and novel insight into the biology of complex microbial communities. IMPORTANCE This study systematically evaluated the global patterns of microbial antisense expression across various environments and provides a bird’s-eye view of general patterns observed across data sets, which can provide guidelines in our understanding of antisense expression as well as interpretation of metatranscriptomic data in general. This analysis highlights that in some environments, antisense expression from microbial communities can dominate over regular gene expression. We explored some potential drivers of antisense transcription, but more importantly, this study serves as a starting point, highlighting topics for future research and providing guidelines to include antisense expression in generic bioinformatic pipelines for metatranscriptomic data.
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32
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Harden TT, Herlambang KS, Chamberlain M, Lalanne JB, Wells CD, Li GW, Landick R, Hochschild A, Kondev J, Gelles J. Alternative transcription cycle for bacterial RNA polymerase. Nat Commun 2020; 11:448. [PMID: 31974358 PMCID: PMC6978322 DOI: 10.1038/s41467-019-14208-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 12/10/2019] [Indexed: 11/18/2022] Open
Abstract
RNA polymerases (RNAPs) transcribe genes through a cycle of recruitment to promoter DNA, initiation, elongation, and termination. After termination, RNAP is thought to initiate the next round of transcription by detaching from DNA and rebinding a new promoter. Here we use single-molecule fluorescence microscopy to observe individual RNAP molecules after transcript release at a terminator. Following termination, RNAP almost always remains bound to DNA and sometimes exhibits one-dimensional sliding over thousands of basepairs. Unexpectedly, the DNA-bound RNAP often restarts transcription, usually in reverse direction, thus producing an antisense transcript. Furthermore, we report evidence of this secondary initiation in live cells, using genome-wide RNA sequencing. These findings reveal an alternative transcription cycle that allows RNAP to reinitiate without dissociating from DNA, which is likely to have important implications for gene regulation.
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Affiliation(s)
- Timothy T Harden
- Department of Physics, Brandeis University, Waltham, MA, 02454, USA
| | | | | | - Jean-Benoît Lalanne
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Christopher D Wells
- Department of Microbiology, Blavatnick Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Robert Landick
- Department of Biochemistry and Department of Bacteriology, University of Wisconsin, Madison, WI, 53706, USA
| | - Ann Hochschild
- Department of Microbiology, Blavatnick Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Jane Kondev
- Department of Physics, Brandeis University, Waltham, MA, 02454, USA.
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, MA, 02454, USA.
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33
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Lejars M, Hajnsdorf E. The world of asRNAs in Gram-negative and Gram-positive bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194489. [PMID: 31935527 DOI: 10.1016/j.bbagrm.2020.194489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/09/2020] [Indexed: 12/19/2022]
Abstract
Bacteria exhibit an amazing diversity of mechanisms controlling gene expression to both maintain essential functions and modulate accessory functions in response to environmental cues. Over the years, it has become clear that bacterial regulation of gene expression is still far from fully understood. This review focuses on antisense RNAs (asRNAs), a class of RNA regulators defined by their location in cis and their perfect complementarity with their targets, as opposed to small RNAs (sRNAs) which act in trans with only short regions of complementarity. For a long time, only few functional asRNAs in bacteria were known and were almost exclusively found on mobile genetic elements (MGEs), thus, their importance among the other regulators was underestimated. However, the extensive application of transcriptomic approaches has revealed the ubiquity of asRNAs in bacteria. This review aims to present the landscape of studied asRNAs in bacteria by comparing 67 characterized asRNAs from both Gram-positive and Gram-negative bacteria. First we describe the inherent ambiguity in the existence of asRNAs in bacteria, second, we highlight their diversity and their involvement in all aspects of bacterial life. Finally we compare their location and potential mode of action toward their target between Gram-negative and Gram-positive bacteria and present tendencies and exceptions that could lead to a better understanding of asRNA functions.
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Affiliation(s)
- Maxence Lejars
- UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 75005 Paris, France.
| | - Eliane Hajnsdorf
- UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 75005 Paris, France.
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34
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Abstract
Bacteria participate in a wide diversity of symbiotic associations with eukaryotic hosts that require precise interactions for bacterial recognition and persistence. Most commonly, host-associated bacteria interfere with host gene expression to modulate the immune response to the infection. However, many of these bacteria also interfere with host cellular differentiation pathways to create a hospitable niche, resulting in the formation of novel cell types, tissues, and organs. In both of these situations, bacterial symbionts must interact with eukaryotic regulatory pathways. Here, we detail what is known about how bacterial symbionts, from pathogens to mutualists, control host cellular differentiation across the central dogma, from epigenetic chromatin modifications, to transcription and mRNA processing, to translation and protein modifications. We identify four main trends from this survey. First, mechanisms for controlling host gene expression appear to evolve from symbionts co-opting cross-talk between host signaling pathways. Second, symbiont regulatory capacity is constrained by the processes that drive reductive genome evolution in host-associated bacteria. Third, the regulatory mechanisms symbionts exhibit correlate with the cost/benefit nature of the association. And, fourth, symbiont mechanisms for interacting with host genetic regulatory elements are not bound by native bacterial capabilities. Using this knowledge, we explore how the ubiquitous intracellular Wolbachia symbiont of arthropods and nematodes may modulate host cellular differentiation to manipulate host reproduction. Our survey of the literature on how infection alters gene expression in Wolbachia and its hosts revealed that, despite their intermediate-sized genomes, different strains appear capable of a wide diversity of regulatory manipulations. Given this and Wolbachia's diversity of phenotypes and eukaryotic-like proteins, we expect that many symbiont-induced host differentiation mechanisms will be discovered in this system.
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Affiliation(s)
- Shelbi L Russell
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.
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35
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Gophna U. The unbearable ease of expression-how avoidance of spurious transcription can shape G+C content in bacterial genomes. FEMS Microbiol Lett 2019; 365:5181332. [PMID: 30423131 DOI: 10.1093/femsle/fny267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/11/2018] [Indexed: 12/28/2022] Open
Affiliation(s)
- Uri Gophna
- Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Levanon Street, Tel Aviv 69000, Israel
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36
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Nadiras C, Eveno E, Schwartz A, Figueroa-Bossi N, Boudvillain M. A multivariate prediction model for Rho-dependent termination of transcription. Nucleic Acids Res 2019; 46:8245-8260. [PMID: 29931073 PMCID: PMC6144790 DOI: 10.1093/nar/gky563] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/08/2018] [Indexed: 11/13/2022] Open
Abstract
Bacterial transcription termination proceeds via two main mechanisms triggered either by simple, well-conserved (intrinsic) nucleic acid motifs or by the motor protein Rho. Although bacterial genomes can harbor hundreds of termination signals of either type, only intrinsic terminators are reliably predicted. Computational tools to detect the more complex and diversiform Rho-dependent terminators are lacking. To tackle this issue, we devised a prediction method based on Orthogonal Projections to Latent Structures Discriminant Analysis [OPLS-DA] of a large set of in vitro termination data. Using previously uncharacterized genomic sequences for biochemical evaluation and OPLS-DA, we identified new Rho-dependent signals and quantitative sequence descriptors with significant predictive value. Most relevant descriptors specify features of transcript C>G skewness, secondary structure, and richness in regularly-spaced 5'CC/UC dinucleotides that are consistent with known principles for Rho-RNA interaction. Descriptors collectively warrant OPLS-DA predictions of Rho-dependent termination with a ∼85% success rate. Scanning of the Escherichia coli genome with the OPLS-DA model identifies significantly more termination-competent regions than anticipated from transcriptomics and predicts that regions intrinsically refractory to Rho are primarily located in open reading frames. Altogether, this work delineates features important for Rho activity and describes the first method able to predict Rho-dependent terminators in bacterial genomes.
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Affiliation(s)
- Cédric Nadiras
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France.,ED 549, Sciences Biologiques & Chimie du Vivant, Université d'Orléans, France
| | - Eric Eveno
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France
| | - Annie Schwartz
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France
| | - Nara Figueroa-Bossi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University of Paris-Sud, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Marc Boudvillain
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France
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37
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Haryono M, Cho ST, Fang MJ, Chen AP, Chou SJ, Lai EM, Kuo CH. Differentiations in Gene Content and Expression Response to Virulence Induction Between Two Agrobacterium Strains. Front Microbiol 2019; 10:1554. [PMID: 31354658 PMCID: PMC6629968 DOI: 10.3389/fmicb.2019.01554] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/21/2019] [Indexed: 01/15/2023] Open
Abstract
Agrobacterium tumefaciens is important in biotechnology due to its ability to transform eukaryotic cells. Although the molecular mechanisms have been studied extensively, previous studies were focused on the model strain C58. Consequently, nearly all of the commonly used strains for biotechnology application were derived from C58 and share similar host ranges. To overcome this limitation, better understanding of the natural genetic variation could provide valuable insights. In this study, we conducted comparative analysis between C58 and 1D1609. These two strains belong to different genomospecies within the species complex and have distinct infectivity profiles. Genome comparisons revealed that each strain has >1,000 unique genes in addition to the 4,115 shared genes. Furthermore, the divergence in gene content and sequences vary among replicons. The circular chromosome is much more conserved compared to the linear chromosome. To identify the genes that may contribute to their differentiation in virulence, we compared the transcriptomes to screen for genes differentially expressed in response to the inducer acetosyringone. Based on the RNA-Seq results with three biological replicates, ∼100 differentially expressed genes were identified in each strain. Intriguingly, homologous genes with the same expression pattern account for <50% of these differentially expressed genes. This finding indicated that phenotypic variation may be partially explained by divergence in expression regulation. In summary, this study characterized the genomic and transcriptomic differences between two representative Agrobacterium strains. Moreover, the short list of differentially expressed genes are promising candidates for future characterization, which could improve our understanding of the genetic mechanisms for phenotypic divergence.
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Affiliation(s)
- Mindia Haryono
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Mei-Jane Fang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ai-Ping Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Shu-Jen Chou
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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38
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The Primary Antisense Transcriptome of Halobacterium salinarum NRC-1. Genes (Basel) 2019; 10:genes10040280. [PMID: 30959844 PMCID: PMC6523106 DOI: 10.3390/genes10040280] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 12/17/2022] Open
Abstract
Antisense RNAs (asRNAs) are present in diverse organisms and play important roles in gene regulation. In this work, we mapped the primary antisense transcriptome in the halophilic archaeon Halobacterium salinarum NRC-1. By reanalyzing publicly available data, we mapped antisense transcription start sites (aTSSs) and inferred the probable 3′ ends of these transcripts. We analyzed the resulting asRNAs according to the size, location, function of genes on the opposite strand, expression levels and conservation. We show that at least 21% of the genes contain asRNAs in H. salinarum. Most of these asRNAs are expressed at low levels. They are located antisense to genes related to distinctive characteristics of H. salinarum, such as bacteriorhodopsin, gas vesicles, transposases and other important biological processes such as translation. We provide evidence to support asRNAs in type II toxin–antitoxin systems in archaea. We also analyzed public Ribosome profiling (Ribo-seq) data and found that ~10% of the asRNAs are ribosome-associated non-coding RNAs (rancRNAs), with asRNAs from transposases overrepresented. Using a comparative transcriptomics approach, we found that ~19% of the asRNAs annotated in H. salinarum belong to genes with an ortholog in Haloferax volcanii, in which an aTSS could be identified with positional equivalence. This shows that most asRNAs are not conserved between these halophilic archaea.
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39
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Transcriptional noise and exaptation as sources for bacterial sRNAs. Biochem Soc Trans 2019; 47:527-539. [PMID: 30837318 DOI: 10.1042/bst20180171] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/01/2019] [Accepted: 02/01/2019] [Indexed: 11/17/2022]
Abstract
Understanding how new genes originate and integrate into cellular networks is key to understanding evolution. Bacteria present unique opportunities for both the natural history and experimental study of gene origins, due to their large effective population sizes, rapid generation times, and ease of genetic manipulation. Bacterial small non-coding RNAs (sRNAs), in particular, many of which operate through a simple antisense regulatory logic, may serve as tractable models for exploring processes of gene origin and adaptation. Understanding how and on what timescales these regulatory molecules arise has important implications for understanding the evolution of bacterial regulatory networks, in particular, for the design of comparative studies of sRNA function. Here, we introduce relevant concepts from evolutionary biology and review recent work that has begun to shed light on the timescales and processes through which non-functional transcriptional noise is co-opted to provide regulatory functions. We explore possible scenarios for sRNA origin, focusing on the co-option, or exaptation, of existing genomic structures which may provide protected spaces for sRNA evolution.
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40
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Abstract
Bacterial regulatory RNAs are key players in adaptation to changing environmental conditions and response to diverse cellular stresses. However, while regulatory RNAs of bacterial pathogens have been intensely studied under defined conditions in vitro, characterization of their role during the infection of eukaryotic host organisms is lagging behind. This review summarizes our current understanding of the contribution of the different classes of regulatory RNAs and RNA-binding proteins to bacterial virulence and illustrates their role in infection by reviewing the mechanisms of some prominent representatives of each class. Emerging technologies are described that bear great potential for global, unbiased studies of virulence-related RNAs in bacterial model and nonmodel pathogens in the future. The review concludes by deducing common principles of RNA-mediated gene expression control of virulence programs in different pathogens, and by defining important open questions for upcoming research in the field.
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41
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Junges R, Salvadori G, Chen T, Morrison DA, Petersen FC. Hidden Gems in the Transcriptome Maps of Competent Streptococci. Front Mol Biosci 2019; 5:116. [PMID: 30662898 PMCID: PMC6328492 DOI: 10.3389/fmolb.2018.00116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 12/11/2018] [Indexed: 11/22/2022] Open
Abstract
Natural transformation is regarded as an important mechanism in bacteria that allows for adaptation to different environmental stressors by ensuring genome plasticity. Since the discovery of this phenomenon in Streptococcus pneumoniae, remarkable progress has been made in the understanding of the molecular mechanisms and pathways coordinating this process. Recently, the advent of high-throughput sequencing allows the posing of questions that address the system at a larger scale but also allow for the creation of high-resolution maps of transcription. Thus, while much is already known about genetic competence in streptococci, recent studies continue to reveal intricate novel regulation pathways and components. In this perspective article, we highlight the use of transcriptional profiling and mapping as a valuable resource in the identification and characterization of “hidden gems” pertinent to the natural transformation system. Such strategies have recently been employed in a variety of different species. In S. mutans, for example, genome editing combined with the power of promoter mapping and RNA-Seq allowed for the identification of a link between the ComCDE and the ComRS systems, a ComR positive feedback loop mediated by SigX, and the XrpA peptide, encoded within sigX, which inhibits competence. In S. pneumoniae, a novel member of the competence regulon termed BriC was found to be directly under control of ComE and to promote biofilm formation and nasopharyngeal colonization but not competence. Together these new technologies enable us to discover new links and to revisit old pathways in the compelling study of natural genetic transformation.
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Affiliation(s)
- Roger Junges
- Faculty of Dentistry, Institute of Oral Biology, University of Oslo, Oslo, Norway
| | - Gabriela Salvadori
- Faculty of Dentistry, Institute of Oral Biology, University of Oslo, Oslo, Norway
| | - Tsute Chen
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, United States
| | - Donald A Morrison
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Fernanda C Petersen
- Faculty of Dentistry, Institute of Oral Biology, University of Oslo, Oslo, Norway
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42
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The novel EHEC gene asa overlaps the TEGT transporter gene in antisense and is regulated by NaCl and growth phase. Sci Rep 2018; 8:17875. [PMID: 30552341 PMCID: PMC6294744 DOI: 10.1038/s41598-018-35756-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/08/2018] [Indexed: 12/02/2022] Open
Abstract
Only a few overlapping gene pairs are known in the best-analyzed bacterial model organism Escherichia coli. Automatic annotation programs usually annotate only one out of six reading frames at a locus, allowing only small overlaps between protein-coding sequences. However, both RNAseq and RIBOseq show signals corresponding to non-trivially overlapping reading frames in antisense to annotated genes, which may constitute protein-coding genes. The transcription and translation of the novel 264 nt gene asa, which overlaps in antisense to a putative TEGT (Testis-Enhanced Gene Transfer) transporter gene is detected in pathogenic E. coli, but not in two apathogenic E. coli strains. The gene in E. coli O157:H7 (EHEC) was further analyzed. An overexpression phenotype was identified in two stress conditions, i.e. excess in salt or arginine. For this, EHEC overexpressing asa was grown competitively against EHEC with a translationally arrested asa mutant gene. RT-qPCR revealed conditional expression dependent on growth phase, sodium chloride, and arginine. Two potential promoters were computationally identified and experimentally verified by reporter gene expression and determination of the transcription start site. The protein Asa was verified by Western blot. Close homologues of asa have not been found in protein databases, but bioinformatic analyses showed that it may be membrane associated, having a largely disordered structure.
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43
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Mehrotra R, Loake G, Mehrotra S. Promoter choice: Selection vs. rejection. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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44
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Charubin K, Bennett RK, Fast AG, Papoutsakis ET. Engineering Clostridium organisms as microbial cell-factories: challenges & opportunities. Metab Eng 2018; 50:173-191. [DOI: 10.1016/j.ymben.2018.07.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 11/25/2022]
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45
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Kröger C, MacKenzie KD, Alshabib EY, Kirzinger MWB, Suchan DM, Chao TC, Akulova V, Miranda-CasoLuengo AA, Monzon VA, Conway T, Sivasankaran SK, Hinton JCD, Hokamp K, Cameron ADS. The primary transcriptome, small RNAs and regulation of antimicrobial resistance in Acinetobacter baumannii ATCC 17978. Nucleic Acids Res 2018; 46:9684-9698. [PMID: 29986115 PMCID: PMC6182133 DOI: 10.1093/nar/gky603] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 06/21/2018] [Accepted: 06/26/2018] [Indexed: 12/12/2022] Open
Abstract
We present the first high-resolution determination of transcriptome architecture in the priority pathogen Acinetobacter baumannii. Pooled RNA from 16 laboratory conditions was used for differential RNA-seq (dRNA-seq) to identify 3731 transcriptional start sites (TSS) and 110 small RNAs, including the first identification in A. baumannii of sRNAs encoded at the 3' end of coding genes. Most sRNAs were conserved among sequenced A. baumannii genomes, but were only weakly conserved or absent in other Acinetobacter species. Single nucleotide mapping of TSS enabled prediction of -10 and -35 RNA polymerase binding sites and revealed an unprecedented base preference at position +2 that hints at an unrecognized transcriptional regulatory mechanism. To apply functional genomics to the problem of antimicrobial resistance, we dissected the transcriptional regulation of the drug efflux pump responsible for chloramphenicol resistance, craA. The two craA promoters were both down-regulated >1000-fold when cells were shifted to nutrient limited medium. This conditional down-regulation of craA expression renders cells sensitive to chloramphenicol, a highly effective antibiotic for the treatment of multidrug resistant infections. An online interface that facilitates open data access and visualization is provided as 'AcinetoCom' (http://bioinf.gen.tcd.ie/acinetocom/).
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Affiliation(s)
- Carsten Kröger
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Keith D MacKenzie
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
- Department of Biology, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Ebtihal Y Alshabib
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
- Department of Biology, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Morgan W B Kirzinger
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Danae M Suchan
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
- Department of Biology, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Tzu-Chiao Chao
- Department of Biology, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
- Institute of Environmental Change and Society, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Valentyna Akulova
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Aleksandra A Miranda-CasoLuengo
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Vivian A Monzon
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Tyrrell Conway
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Sathesh K Sivasankaran
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Jay C D Hinton
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Karsten Hokamp
- Department of Genetics, School of Genetics & Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Andrew D S Cameron
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
- Department of Biology, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
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46
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Ralston MT, Papoutsakis ET. RNAseq‐based transcriptome assembly of
Clostridium acetobutylicum
for functional genome annotation and discovery. AIChE J 2018. [DOI: 10.1002/aic.16396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Matthew T. Ralston
- Molecular Biotechnology Laboratory, Delaware Biotechnology Institute University of Delaware Newark DE 19711
- Center for Bioinformatics and Computational Biology University of Delaware Newark DE 19711
| | - Eleftherios T. Papoutsakis
- Dept. of Chemical and Biomolecular Engineering University of Delaware Newark DE 19711
- Molecular Biotechnology Laboratory, Delaware Biotechnology Institute University of Delaware Newark DE 19711
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Abstract
ABSTRACT
Although bacterial genomes are usually densely protein-coding, genome-wide mapping approaches of transcriptional start sites revealed that a significant fraction of the identified promoters drive the transcription of noncoding RNAs. These can be
trans
-acting RNAs, mainly originating from intergenic regions and, in many studied examples, possessing regulatory functions. However, a significant fraction of these noncoding RNAs consist of natural antisense transcripts (asRNAs), which overlap other transcriptional units. Naturally occurring asRNAs were first observed to play a role in bacterial plasmid replication and in bacteriophage λ more than 30 years ago. Today’s view is that asRNAs abound in all three domains of life. There are several examples of asRNAs in bacteria with clearly defined functions. Nevertheless, many asRNAs appear to result from pervasive initiation of transcription, and some data point toward global functions of such widespread transcriptional activity, explaining why the search for a specific regulatory role is sometimes futile. In this review, we give an overview about the occurrence of antisense transcription in bacteria, highlight particular examples of functionally characterized asRNAs, and discuss recent evidence pointing at global relevance in RNA processing and transcription-coupled DNA repair.
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48
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Cheah HL, Raabe CA, Lee LP, Rozhdestvensky TS, Citartan M, Ahmed SA, Tang TH. Bacterial regulatory RNAs: complexity, function, and putative drug targeting. Crit Rev Biochem Mol Biol 2018; 53:335-355. [PMID: 29793351 DOI: 10.1080/10409238.2018.1473330] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Over the past decade, RNA-deep sequencing has uncovered copious non-protein coding RNAs (npcRNAs) in bacteria. Many of them are key players in the regulation of gene expression, taking part in various regulatory circuits, such as metabolic responses to different environmental stresses, virulence, antibiotic resistance, and host-pathogen interactions. This has contributed to the high adaptability of bacteria to changing or even hostile environments. Their mechanisms include the regulation of transcriptional termination, modulation of translation, and alteration of messenger RNA (mRNA) stability, as well as protein sequestration. Here, the mechanisms of gene expression by regulatory bacterial npcRNAs are comprehensively reviewed and supplemented with well-characterized examples. This class of molecules and their mechanisms of action might be useful targets for the development of novel antibiotics.
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Affiliation(s)
- Hong-Leong Cheah
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| | - Carsten A Raabe
- b Institute of Experimental Pathology, Centre for Molecular Biology of Inflammation , University of Münster , Münster , Germany.,c Brandenburg Medical School (MHB) , Neuruppin , Germany.,d Institute of Medical Biochemistry, Centre for Molecular Biology of Inflammation , University of Münster , Münster , Germany
| | - Li-Pin Lee
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| | - Timofey S Rozhdestvensky
- e Medical Faculty, Transgenic Mouse and Genome Engineering Model Core Facility (TRAM) , University of Münster , Münster , Germany
| | - Marimuthu Citartan
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| | - Siti Aminah Ahmed
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| | - Thean-Hock Tang
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
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49
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Lo WS, Kuo CH. Horizontal Acquisition and Transcriptional Integration of Novel Genes in Mosquito-Associated Spiroplasma. Genome Biol Evol 2018; 9:3246-3259. [PMID: 29177479 PMCID: PMC5726471 DOI: 10.1093/gbe/evx244] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2017] [Indexed: 12/20/2022] Open
Abstract
Genetic differentiation among symbiotic bacteria is important in shaping biodiversity. The genus Spiroplasma contains species occupying diverse niches and is a model system for symbiont evolution. Previous studies have established that two mosquito-associated species have diverged extensively in their carbohydrate metabolism genes despite having a close phylogenetic relationship. Notably, although the commensal Spiroplasma diminutum lacks identifiable pathogenicity factors, the pathogenic Spiroplasma taiwanense was found to have acquired a virulence factor glpO and its associated genes through horizontal transfer. However, it is unclear if these acquired genes have been integrated into the regulatory network. In this study, we inferred the gene content evolution in these bacteria, as well as examined their transcriptomes in response to glucose availability. The results indicated that both species have many more gene acquisitions from the Mycoides-Entomoplasmataceae clade, which contains several important pathogens of ruminants, than previously thought. Moreover, several acquired genes have higher expression levels than the vertically inherited homologs, indicating possible functional replacement. Finally, the virulence factor and its functionally linked genes in S. taiwanense were up-regulated in response to glucose starvation, suggesting that these acquired genes are under expression regulation and the pathogenicity may be a stress response. In summary, although differential gene losses are a major process for symbiont divergence, gene gains are critical in counteracting genome degradation and driving diversification among facultative symbionts.
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Affiliation(s)
- Wen-Sui Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan.,Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan.,Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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50
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Fitzgerald DM, Smith C, Lapierre P, Wade JT. The evolutionary impact of intragenic FliA promoters in proteobacteria. Mol Microbiol 2018; 108:361-378. [PMID: 29476659 PMCID: PMC5943157 DOI: 10.1111/mmi.13941] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2018] [Indexed: 12/12/2022]
Abstract
In Escherichia coli, one sigma factor recognizes the majority of promoters, and six 'alternative' sigma factors recognize specific subsets of promoters. The alternative sigma factor FliA (σ28 ) recognizes promoters upstream of many flagellar genes. We previously showed that most E. coli FliA binding sites are located inside genes. However, it was unclear whether these intragenic binding sites represent active promoters. Here, we construct and assay transcriptional promoter-lacZ fusions for all 52 putative FliA promoters previously identified by ChIP-seq. These experiments, coupled with integrative analysis of published genome-scale transcriptional datasets, strongly suggest that most intragenic FliA binding sites are active promoters that transcribe highly unstable RNAs. Additionally, we show that widespread intragenic FliA-dependent transcription may be a conserved phenomenon, but that specific promoters are not themselves conserved. We conclude that intragenic FliA-dependent promoters and the resulting RNAs are unlikely to have important regulatory functions. Nonetheless, one intragenic FliA promoter is broadly conserved and constrains evolution of the overlapping protein-coding gene. Thus, our data indicate that intragenic regulatory elements can influence bacterial protein evolution and suggest that the impact of intragenic regulatory sequences on genome evolution should be considered more broadly.
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Affiliation(s)
- Devon M. Fitzgerald
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
| | - Carol Smith
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Joseph T. Wade
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
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