1
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Sinha PR, Balasubramanian R, Hegde SR. Integrated sequence and -omic features reveal novel small proteome of Mycobacterium tuberculosis. Front Microbiol 2024; 15:1335310. [PMID: 38812687 PMCID: PMC11133741 DOI: 10.3389/fmicb.2024.1335310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/15/2024] [Indexed: 05/31/2024] Open
Abstract
Bioinformatic studies on small proteins are under-represented due to difficulties in annotation posed by their small size. However, recent discoveries emphasize the functional significance of small proteins in cellular processes including cell signaling, metabolism, and adaptation to stress. In this study, we utilized a Random Forest classifier trained on sequence features, RNA-Seq, and Ribo-Seq data to uncover small proteins (smORFs) in M. tuberculosis. Independent predictions for the exponential and starvation conditions resulted in 695 potential smORFs. We examined the functional implications of these smORFs using homology searches, LC-MS/MS, and ChIP-seq data, testing their expression in diverse growth conditions, and identifying protein domains. We provide evidence that some of these smORFs could be part of operons, or exist as upstream ORFs. This expanded data resource for the proteins of M. tuberculosis would aid in fine-tuning the existing protein and gene regulatory networks, thereby improving system-wide studies. The primary goal of this study was to uncover and characterize smORFs in M. tuberculosis through bioinformatic analysis, shedding light on their functional roles and genomic organization. Further investigation of these potential smORFs would provide valuable insights into the genome organization and functional diversity of the M. tuberculosis proteome.
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Affiliation(s)
| | | | - Shubhada R. Hegde
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, India
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2
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Chauvier A, Dandpat SS, Romero R, Walter NG. A nascent riboswitch helix orchestrates robust transcriptional regulation through signal integration. Nat Commun 2024; 15:3955. [PMID: 38729929 PMCID: PMC11087558 DOI: 10.1038/s41467-024-48409-8] [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: 01/09/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
Widespread manganese-sensing transcriptional riboswitches effect the dependable gene regulation needed for bacterial manganese homeostasis in changing environments. Riboswitches - like most structured RNAs - are believed to fold co-transcriptionally, subject to both ligand binding and transcription events; yet how these processes are orchestrated for robust regulation is poorly understood. Through a combination of single-molecule and bulk approaches, we discover how a single Mn2+ ion and the transcribing RNA polymerase (RNAP), paused immediately downstream by a DNA template sequence, are coordinated by the bridging switch helix P1.1 in the representative Lactococcus lactis riboswitch. This coordination achieves a heretofore-overlooked semi-docked global conformation of the nascent RNA, P1.1 base pair stabilization, transcription factor NusA ejection, and RNAP pause extension, thereby enforcing transcription readthrough. Our work demonstrates how a central, adaptable RNA helix functions analogous to a molecular fulcrum of a first-class lever system to integrate disparate signals for finely balanced gene expression control.
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Affiliation(s)
- Adrien Chauvier
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Shiba S Dandpat
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
- Intel Corporation, Hillsboro, OR, USA
| | - Rosa Romero
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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3
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Walter N, Chauvier A, Dandpat S, Romero R. A nascent riboswitch helix orchestrates robust transcriptional regulation through signal integration. RESEARCH SQUARE 2024:rs.3.rs-3849447. [PMID: 38352525 PMCID: PMC10862961 DOI: 10.21203/rs.3.rs-3849447/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Widespread manganese-sensing transcriptional riboswitches effect the dependable gene regulation needed for bacterial manganese homeostasis in changing environments. Riboswitches - like most structured RNAs - are believed to fold co-transcriptionally, subject to both ligand binding and transcription events; yet how these processes are orchestrated for robust regulation is poorly understood. Through a combination of single molecule and bulk approaches, we discovered how a single Mn 2+ ion and the transcribing RNA polymerase (RNAP), paused immediately downstream by a DNA template sequence, are coordinated by the bridging switch helix P1.1 in the paradigmatic Lactococcus lactis riboswitch. This coordination achieves a heretofore-overlooked semi-docked global conformation of the nascent RNA, P1.1 base pair stabilization, transcription factor NusA ejection, and RNAP pause extension, thereby enforcing transcription readthrough. Our work demonstrates how a central, adaptable RNA helix functions analogous to a molecular fulcrum of a first-class lever system to integrate disparate signals for finely balanced gene expression control.
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4
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Bharati BK, Gowder M, Zheng F, Alzoubi K, Svetlov V, Kamarthapu V, Weaver JW, Epshtein V, Vasilyev N, Shen L, Zhang Y, Nudler E. Crucial role and mechanism of transcription-coupled DNA repair in bacteria. Nature 2022; 604:152-159. [PMID: 35355008 PMCID: PMC9370829 DOI: 10.1038/s41586-022-04530-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 02/07/2022] [Indexed: 01/11/2023]
Abstract
Transcription-coupled DNA repair (TCR) is presumed to be a minor sub-pathway of nucleotide excision repair (NER) in bacteria. Global genomic repair is thought to perform the bulk of repair independently of transcription. TCR is also believed to be mediated exclusively by Mfd-a DNA translocase of a marginal NER phenotype1-3. Here we combined in cellulo cross-linking mass spectrometry with structural, biochemical and genetic approaches to map the interactions within the TCR complex (TCRC) and to determine the actual sequence of events that leads to NER in vivo. We show that RNA polymerase (RNAP) serves as the primary sensor of DNA damage and acts as a platform for the recruitment of NER enzymes. UvrA and UvrD associate with RNAP continuously, forming a surveillance pre-TCRC. In response to DNA damage, pre-TCRC recruits a second UvrD monomer to form a helicase-competent UvrD dimer that promotes backtracking of the TCRC. The weakening of UvrD-RNAP interactions renders cells sensitive to genotoxic stress. TCRC then recruits a second UvrA molecule and UvrB to initiate the repair process. Contrary to the conventional view, we show that TCR accounts for the vast majority of chromosomal repair events; that is, TCR thoroughly dominates over global genomic repair. We also show that TCR is largely independent of Mfd. We propose that Mfd has an indirect role in this process: it participates in removing obstructive RNAPs in front of TCRCs and also in recovering TCRCs from backtracking after repair has been completed.
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Affiliation(s)
- Binod K Bharati
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.,Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA
| | - Manjunath Gowder
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.,Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA
| | - Fangfang Zheng
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Khaled Alzoubi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Venu Kamarthapu
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.,Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA
| | - Jacob W Weaver
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Vitaly Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Liqiang Shen
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA. .,Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA.
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5
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Dynamic competition between a ligand and transcription factor NusA governs riboswitch-mediated transcription regulation. Proc Natl Acad Sci U S A 2021; 118:2109026118. [PMID: 34782462 DOI: 10.1073/pnas.2109026118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2021] [Indexed: 11/18/2022] Open
Abstract
Cotranscriptional RNA folding is widely assumed to influence the timely control of gene expression, but our understanding remains limited. In bacteria, the fluoride (F-)-sensing riboswitch is a transcriptional control element essential to defend against toxic F- levels. Using this model riboswitch, we find that its ligand F- and essential bacterial transcription factor NusA compete to bind the cotranscriptionally folding RNA, opposing each other's modulation of downstream pausing and termination by RNA polymerase. Single-molecule fluorescence assays probing active transcription elongation complexes discover that NusA unexpectedly binds highly reversibly, frequently interrogating the complex for emerging, cotranscriptionally folding RNA duplexes. NusA thus fine-tunes the transcription rate in dependence of the ligand-responsive higher-order structure of the riboswitch. At the high NusA concentrations found intracellularly, this dynamic modulation is expected to lead to adaptive bacterial transcription regulation with fast response times.
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6
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Du C, Wang Y, Gong S. Regulation of the ThiM riboswitch is facilitated by the trapped structure formed during transcription of the wild-type sequence. FEBS Lett 2021; 595:2816-2828. [PMID: 34644399 DOI: 10.1002/1873-3468.14202] [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: 06/18/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 11/09/2022]
Abstract
The ThiM riboswitch from Escherichia coli is a typical mRNA device that modulates downstream gene expression by sensing TPP. The helix-based RNA folding theory is used to investigate its detailed regulatory behaviors in cells. This RNA molecule is transcriptionally trapped in a state with the unstructured SD sequence in the absence of TPP, which induces downstream gene expression. As a key step to turn on gene expression, formation of this trapped state (the genetic ON state) highly depends on the co-transcriptional folding of its wild-type sequence. Instead of stabilities of the genetic ON and OFF states, the transcription rate, pause, and ligand levels are combined to affect the ThiM riboswitch-mediated gene regulation, which is consistent with a kinetic control model.
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Affiliation(s)
- Chengyi Du
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, China
| | - Yujie Wang
- Department of Physics and Telecommunication Engineering, Zhoukou Normal University, China
| | - Sha Gong
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, China
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7
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Mandell ZF, Oshiro RT, Yakhnin AV, Vishwakarma R, Kashlev M, Kearns DB, Babitzke P. NusG is an intrinsic transcription termination factor that stimulates motility and coordinates gene expression with NusA. eLife 2021; 10:e61880. [PMID: 33835023 PMCID: PMC8060035 DOI: 10.7554/elife.61880] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 04/08/2021] [Indexed: 12/21/2022] Open
Abstract
NusA and NusG are transcription factors that stimulate RNA polymerase pausing in Bacillus subtilis. While NusA was known to function as an intrinsic termination factor in B. subtilis, the role of NusG in this process was unknown. To examine the individual and combinatorial roles that NusA and NusG play in intrinsic termination, Term-seq was conducted in wild type, NusA depletion, ΔnusG, and NusA depletion ΔnusG strains. We determined that NusG functions as an intrinsic termination factor that works alone and cooperatively with NusA to facilitate termination at 88% of the 1400 identified intrinsic terminators. Our results indicate that NusG stimulates a sequence-specific pause that assists in the completion of suboptimal terminator hairpins with weak terminal A-U and G-U base pairs at the bottom of the stem. Loss of NusA and NusG leads to global misregulation of gene expression and loss of NusG results in flagella and swimming motility defects.
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Affiliation(s)
- Zachary F Mandell
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
| | - Reid T Oshiro
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Alexander V Yakhnin
- NCI RNA Biology Laboratory, Center for Cancer Research, NCIFrederickUnited States
| | - Rishi Vishwakarma
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
| | - Mikhail Kashlev
- NCI RNA Biology Laboratory, Center for Cancer Research, NCIFrederickUnited States
| | - Daniel B Kearns
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
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8
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Guo H, Yu X, Liu Z, Li J, Ye J, Zha Z. Deltamethrin transformation by Bacillus thuringiensis and the associated metabolic pathways. ENVIRONMENT INTERNATIONAL 2020; 145:106167. [PMID: 33035892 DOI: 10.1016/j.envint.2020.106167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/08/2020] [Accepted: 09/25/2020] [Indexed: 05/22/2023]
Abstract
The biological toxicity of deltamethrin at molecular level has been investigated, whereas, the proteome responsive mechanisms of cells under deltamethrin stress at the phylogenetic level are not clear. The proteome expression, transformation-related pathway and regulatory network of Bacillus thuringiensis during the process of deltamethrin transformation were explored using proteomics and metabolomics approaches in the present study. The results showed that deltamethrin was effectively removed by B. thuringiensis within 48 h. The stress responses of B. thuringiensis were activated to resist deltamethrin stress, with significant differential expression of proteins that were primarily involved in the synthesis of DNA and shock proteins, endospore formation, carbon metabolism. The expression patterns of ribosomal proteins confirmed that the transcription and translation of DNA, and biosynthesis of heat shock proteins were inhibited as deltamethrin transformation. The synthesis of oxaloacetate and acetyl-CoA were also hindered, resulting in downregulated expression of carbohydrate metabolism, TCA cycle and energy metabolism. Meanwhile, endospore formation and germination were promoted to resist oxidative stress induced by deltamethrin. These findings imparted novel insight to elucidate underlying stress response mechanisms of the organism under target contaminants stress, and the interaction between deltamethrin transformation and cellular metabolism at the pathway and network levels.
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Affiliation(s)
- Huiying Guo
- Institute of Orthopedic Diseases and Department of Bone and Joint Surgery, The First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Xiaolong Yu
- Guangdong Provincial Key Laboratory of Petrochemical Pollution Processes and Control, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming 525000, China
| | - Ziyi Liu
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Jieruo Li
- Institute of Orthopedic Diseases and Department of Bone and Joint Surgery, The First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Jinshao Ye
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China.
| | - Zhengang Zha
- Institute of Orthopedic Diseases and Department of Bone and Joint Surgery, The First Affiliated Hospital, Jinan University, Guangzhou 510630, China.
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9
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Control of ribosome synthesis in bacteria: the important role of rRNA chain elongation rate. SCIENCE CHINA-LIFE SCIENCES 2020; 64:795-802. [DOI: 10.1007/s11427-020-1742-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/26/2020] [Indexed: 10/23/2022]
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10
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Kim S, Beltran B, Irnov I, Jacobs-Wagner C. Long-Distance Cooperative and Antagonistic RNA Polymerase Dynamics via DNA Supercoiling. Cell 2020; 179:106-119.e16. [PMID: 31539491 DOI: 10.1016/j.cell.2019.08.033] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 06/14/2019] [Accepted: 08/16/2019] [Indexed: 12/12/2022]
Abstract
Genes are often transcribed by multiple RNA polymerases (RNAPs) at densities that can vary widely across genes and environmental conditions. Here, we provide in vitro and in vivo evidence for a built-in mechanism by which co-transcribing RNAPs display either collaborative or antagonistic dynamics over long distances (>2 kb) through transcription-induced DNA supercoiling. In Escherichia coli, when the promoter is active, co-transcribing RNAPs translocate faster than a single RNAP, but their average speed is not altered by large variations in promoter strength and thus RNAP density. Environmentally induced promoter repression reduces the elongation efficiency of already-loaded RNAPs, causing premature termination and quick synthesis arrest of no-longer-needed proteins. This negative effect appears independent of RNAP convoy formation and is abrogated by topoisomerase I activity. Antagonistic dynamics can also occur between RNAPs from divergently transcribed gene pairs. Our findings may be broadly applicable given that transcription on topologically constrained DNA is the norm across organisms.
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Affiliation(s)
- Sangjin Kim
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA.
| | - Bruno Beltran
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA
| | - Irnov Irnov
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA.
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11
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NusA directly interacts with antitermination factor Q from phage λ. Sci Rep 2020; 10:6607. [PMID: 32313022 PMCID: PMC7171158 DOI: 10.1038/s41598-020-63523-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/27/2020] [Indexed: 12/03/2022] Open
Abstract
Antitermination (AT) is a ubiquitous principle in the regulation of bacterial transcription to suppress termination signals. In phage λ antiterminator protein Q controls the expression of the phage’s late genes with loading of λQ onto the transcription elongation complex halted at a σ-dependent pause requiring a specific DNA element. The molecular basis of λQ-dependent AT and its dependence on N-utilization substance (Nus) A is so far only poorly understood. Here we used solution-state nuclear magnetic resonance spectroscopy to show that the solution structure of λQ is in agreement with the crystal structure of an N-terminally truncated variant and that the 60 residues at the N-terminus are unstructured. We also provide evidence that multidomain protein NusA interacts directly with λQ via its N-terminal domain (NTD) and the acidic repeat (AR) 2 domain, with the λQ:NusA-AR2 interaction being able to release NusA autoinhibition. The binding sites for NusA-NTD and NusA-AR2 on λQ overlap and the interactions are mutually exclusive with similar affinities, suggesting distinct roles during λQ-dependent AT, e.g. the λQ:NusA-NTD interaction might position NusA-NTD in a way to suppress termination, making NusA-NTD repositioning a general scheme in AT mechanisms.
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12
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Chen M, Fredrick K. RNA Polymerase's Relationship with the Ribosome: Not So Physical, Most of the Time. J Mol Biol 2020; 432:3981-3986. [PMID: 32198117 DOI: 10.1016/j.jmb.2020.03.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/03/2020] [Accepted: 03/11/2020] [Indexed: 01/19/2023]
Abstract
In bacteria, the rates of transcription elongation and translation elongation are coordinated, changing together in response to growth conditions. It has been proposed that this is due to physical coupling of RNA polymerase and the lead ribosome on nascent mRNA, an interaction important for preventing premature transcription termination by Rho factor. Recent studies challenge this view and provide evidence that coordination is indirect, mediated in Escherichia coli by the alarmone (p)ppGpp. Here, we discuss these new findings and how they shape our understanding of the functional relationship between RNA polymerase and the ribosome as well as the basis of transcriptional polarity.
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Affiliation(s)
- Menglin Chen
- Department of Microbiology, Ohio State Biochemistry Program, and Center for RNA Biology, The Ohio State University, 484 W. 12(th) Ave, Columbus, OH, 43210, USA
| | - Kurt Fredrick
- Department of Microbiology, Ohio State Biochemistry Program, and Center for RNA Biology, The Ohio State University, 484 W. 12(th) Ave, Columbus, OH, 43210, USA.
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13
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Dudenhoeffer BR, Schneider H, Schweimer K, Knauer SH. SuhB is an integral part of the ribosomal antitermination complex and interacts with NusA. Nucleic Acids Res 2020; 47:6504-6518. [PMID: 31127279 PMCID: PMC6614797 DOI: 10.1093/nar/gkz442] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 12/20/2022] Open
Abstract
The synthesis of ribosomal RNA (rRNA) is a tightly regulated central process in all cells. In bacteria efficient expression of all seven rRNA operons relies on the suppression of termination signals (antitermination) and the proper maturation of the synthesized rRNA. These processes depend on N-utilization substance (Nus) factors A, B, E and G, as well as ribosomal protein S4 and inositol monophosphatase SuhB, but their structural basis is only poorly understood. Combining nuclear magnetic resonance spectroscopy and biochemical approaches we show that Escherichia coli SuhB can be integrated into a Nus factor-, and optionally S4-, containing antitermination complex halted at a ribosomal antitermination signal. We further demonstrate that SuhB specifically binds to the acidic repeat 2 (AR2) domain of the multi-domain protein NusA, an interaction that may be involved in antitermination or posttranscriptional processes. Moreover, we show that SuhB interacts with RNA and weakly associates with RNA polymerase (RNAP). We finally present evidence that SuhB, the C-terminal domain of the RNAP α-subunit, and the N-terminal domain of NusG share binding sites on NusA-AR2 and that all three can release autoinhibition of NusA, indicating that NusA-AR2 serves as versatile recruitment platform for various factors in transcription regulation.
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Affiliation(s)
| | - Hans Schneider
- Biopolymers, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Kristian Schweimer
- Biopolymers, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Stefan H Knauer
- Biopolymers, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
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14
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Ami VKG, Balasubramanian R, Hegde SR. Genome-wide identification of the context-dependent sRNA expression in Mycobacterium tuberculosis. BMC Genomics 2020; 21:167. [PMID: 32070281 PMCID: PMC7029489 DOI: 10.1186/s12864-020-6573-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/10/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Tuberculosis remains one of the leading causes of morbidity and mortality worldwide. Therefore, understanding the pathophysiology of Mycobacterium tuberculosis is imperative for developing new drugs. Post-transcriptional regulation plays a significant role in microbial adaptation to different growth conditions. While the proteins associated with gene expression regulation have been extensively studied in the pathogenic strain M. tuberculosis H37Rv, post-transcriptional regulation involving small RNAs (sRNAs) remains poorly understood. RESULTS We developed a novel moving-window based approach to detect sRNA expression using RNA-Seq data. Overlaying ChIP-seq data of RNAP (RNA Polymerase) and NusA suggest that these putative sRNA coding regions are significantly bound by the transcription machinery. Besides capturing many experimentally validated sRNAs, we observe the context-dependent expression of novel sRNAs in the intergenic regions of M. tuberculosis genome. For example, ncRv11806 shows expression only in the stationary phase, suggesting its role in mycobacterial latency which is a key attribute to long term pathogenicity. Also, ncRv11875C showed expression in the iron-limited condition, which is prevalent inside the macrophages of the host cells. CONCLUSION The systems level analysis of sRNA highlights the condition-specific expression of sRNAs which might enable the pathogen survival by rewiring regulatory circuits.
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Affiliation(s)
- Vimla Kany G Ami
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560 100, India
| | - Rami Balasubramanian
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560 100, India
| | - Shubhada R Hegde
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560 100, India.
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15
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Spatial organization of RNA polymerase and its relationship with transcription in Escherichia coli. Proc Natl Acad Sci U S A 2019; 116:20115-20123. [PMID: 31527272 DOI: 10.1073/pnas.1903968116] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent studies have shown that RNA polymerase (RNAP) is organized into distinct clusters in Escherichia coli and Bacillus subtilis cells. Spatially organized molecular components in prokaryotic systems imply compartmentalization without the use of membranes, which may offer insights into unique functions and regulations. It has been proposed that the formation of RNAP clusters is driven by active ribosomal RNA (rRNA) transcription and that RNAP clusters function as factories for highly efficient transcription. In this work, we examined these hypotheses by investigating the spatial organization and transcription activity of RNAP in E. coli cells using quantitative superresolution imaging coupled with genetic and biochemical assays. We observed that RNAP formed distinct clusters that were engaged in active rRNA synthesis under a rich medium growth condition. Surprisingly, a large fraction of RNAP clusters persisted in the absence of high rRNA transcription activities or when the housekeeping σ70 was sequestered, and was only significantly diminished when all RNA transcription was inhibited globally. In contrast, the cellular distribution of RNAP closely followed the morphology of the underlying nucleoid under all conditions tested irrespective of the corresponding transcription activity, and RNAP redistributed into dispersed, smaller clusters when the supercoiling state of the nucleoid was perturbed. These results suggest that RNAP was organized into active transcription centers under the rich medium growth condition; its spatial arrangement at the cellular level, however, was not dependent on rRNA synthesis activity and was likely organized by the underlying nucleoid.
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16
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Kang JY, Mishanina TV, Landick R, Darst SA. Mechanisms of Transcriptional Pausing in Bacteria. J Mol Biol 2019; 431:4007-4029. [PMID: 31310765 DOI: 10.1016/j.jmb.2019.07.017] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 12/21/2022]
Abstract
Pausing by RNA polymerase (RNAP) during transcription regulates gene expression in all domains of life. In this review, we recap the history of transcriptional pausing discovery, summarize advances in our understanding of the underlying causes of pausing since then, and describe new insights into the pausing mechanisms and pause modulation by transcription factors gained from structural and biochemical experiments. The accumulated evidence to date suggests that upon encountering a pause signal in the nucleic-acid sequence being transcribed, RNAP rearranges into an elemental, catalytically inactive conformer unable to load NTP substrate. The conformation, and as a consequence lifetime, of an elemental paused RNAP is modulated by backtracking, nascent RNA structure, binding of transcription regulators, or a combination of these mechanisms. We conclude the review by outlining open questions and directions for future research in the field of transcriptional pausing.
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Affiliation(s)
- Jin Young Kang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejon 34141, Republic of Korea.
| | - Tatiana V Mishanina
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Seth A Darst
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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17
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Fouqueau T, Blombach F, Cackett G, Carty AE, Matelska DM, Ofer S, Pilotto S, Phung DK, Werner F. The cutting edge of archaeal transcription. Emerg Top Life Sci 2018; 2:517-533. [PMID: 33525828 PMCID: PMC7289017 DOI: 10.1042/etls20180014] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 10/01/2018] [Accepted: 10/04/2018] [Indexed: 12/26/2022]
Abstract
The archaeal RNA polymerase (RNAP) is a double-psi β-barrel enzyme closely related to eukaryotic RNAPII in terms of subunit composition and architecture, promoter elements and basal transcription factors required for the initiation and elongation phase of transcription. Understanding archaeal transcription is, therefore, key to delineate the universally conserved fundamental mechanisms of transcription as well as the evolution of the archaeo-eukaryotic transcription machineries. The dynamic interplay between RNAP subunits, transcription factors and nucleic acids dictates the activity of RNAP and ultimately gene expression. This review focusses on recent progress in our understanding of (i) the structure, function and molecular mechanisms of known and less characterized factors including Elf1 (Elongation factor 1), NusA (N-utilization substance A), TFS4, RIP and Eta, and (ii) their evolution and phylogenetic distribution across the expanding tree of Archaea.
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Affiliation(s)
- Thomas Fouqueau
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Fabian Blombach
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Gwenny Cackett
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Alice E Carty
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Dorota M Matelska
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Sapir Ofer
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Simona Pilotto
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Duy Khanh Phung
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Finn Werner
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
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18
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Gourse RL, Chen AY, Gopalkrishnan S, Sanchez-Vazquez P, Myers A, Ross W. Transcriptional Responses to ppGpp and DksA. Annu Rev Microbiol 2018; 72:163-184. [PMID: 30200857 PMCID: PMC6586590 DOI: 10.1146/annurev-micro-090817-062444] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The stringent response to nutrient deprivation is a stress response found throughout the bacterial domain of life. Although first described in proteobacteria for matching ribosome synthesis to the cell's translation status and for preventing formation of defective ribosomal particles, the response is actually much broader, regulating many hundreds of genes-some positively, some negatively. Utilization of the signaling molecules ppGpp and pppGpp for this purpose is ubiquitous in bacterial evolution, although the mechanisms employed vary. In proteobacteria, the signaling molecules typically bind to two sites on RNA polymerase, one at the interface of the β' and ω subunits and one at the interface of the β' secondary channel and the transcription factor DksA. The β' secondary channel is targeted by other transcription regulators as well. Although studies on the transcriptional outputs of the stringent response date back at least 50 years, the mechanisms responsible are only now coming into focus.
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Affiliation(s)
- Richard L Gourse
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , , , ,
| | - Albert Y Chen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , , , ,
| | - Saumya Gopalkrishnan
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , , , ,
| | - Patricia Sanchez-Vazquez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , , , ,
| | | | - Wilma Ross
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , , , ,
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19
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Guo X, Myasnikov AG, Chen J, Crucifix C, Papai G, Takacs M, Schultz P, Weixlbaumer A. Structural Basis for NusA Stabilized Transcriptional Pausing. Mol Cell 2018; 69:816-827.e4. [PMID: 29499136 PMCID: PMC5842316 DOI: 10.1016/j.molcel.2018.02.008] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/22/2018] [Accepted: 02/02/2018] [Indexed: 12/12/2022]
Abstract
Transcriptional pausing by RNA polymerases (RNAPs) is a key mechanism to regulate gene expression in all kingdoms of life and is a prerequisite for transcription termination. The essential bacterial transcription factor NusA stimulates both pausing and termination of transcription, thus playing a central role. Here, we report single-particle electron cryo-microscopy reconstructions of NusA bound to paused E. coli RNAP elongation complexes with and without a pause-enhancing hairpin in the RNA exit channel. The structures reveal four interactions between NusA and RNAP that suggest how NusA stimulates RNA folding, pausing, and termination. An asymmetric translocation intermediate of RNA and DNA converts the active site of the enzyme into an inactive state, providing a structural explanation for the inhibition of catalysis. Comparing RNAP at different stages of pausing provides insights on the dynamic nature of the process and the role of NusA as a regulatory factor.
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Affiliation(s)
- Xieyang Guo
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Cedex, France; Université de Strasbourg, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale (Inserm), U964, 67404 Illkirch Cedex, France
| | - Alexander G Myasnikov
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Cedex, France; Université de Strasbourg, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale (Inserm), U964, 67404 Illkirch Cedex, France
| | - James Chen
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Corinne Crucifix
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Cedex, France; Université de Strasbourg, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale (Inserm), U964, 67404 Illkirch Cedex, France
| | - Gabor Papai
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Cedex, France; Université de Strasbourg, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale (Inserm), U964, 67404 Illkirch Cedex, France
| | - Maria Takacs
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Cedex, France; Université de Strasbourg, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale (Inserm), U964, 67404 Illkirch Cedex, France
| | - Patrick Schultz
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Cedex, France; Université de Strasbourg, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale (Inserm), U964, 67404 Illkirch Cedex, France
| | - Albert Weixlbaumer
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Cedex, France; Université de Strasbourg, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale (Inserm), U964, 67404 Illkirch Cedex, France.
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20
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Tan L, Moriel DG, Totsika M, Beatson SA, Schembri MA. Differential Regulation of the Surface-Exposed and Secreted SslE Lipoprotein in Extraintestinal Pathogenic Escherichia coli. PLoS One 2016; 11:e0162391. [PMID: 27598999 PMCID: PMC5012682 DOI: 10.1371/journal.pone.0162391] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 08/22/2016] [Indexed: 11/19/2022] Open
Abstract
Extra-intestinal pathogenic Escherichia coli (ExPEC) are responsible for diverse infections including meningitis, sepsis and urinary tract infections. The alarming rise in anti-microbial resistance amongst ExPEC complicates treatment and has highlighted the need for alternative preventive measures. SslE is a lipoprotein secreted by a dedicated type II secretion system in E. coli that was first identified as a potential vaccine candidate using reverse genetics. Although the function and protective efficacy of SslE has been studied, the molecular mechanisms that regulate SslE expression remain to be fully elucidated. Here, we show that while the expression of SslE can be detected in E. coli culture supernatants, different strains express and secrete different amounts of SslE when grown under the same conditions. While the histone-like transcriptional regulator H-NS strongly represses sslE at ambient temperatures, the variation in SslE expression at human physiological temperature suggested a more complex mode of regulation. Using a genetic screen to identify novel regulators of sslE in the high SslE-expressing strain UTI89, we defined a new role for the nucleoid-associated regulator Fis and the ribosome-binding GTPase TypA as positive regulators of sslE transcription. We also showed that Fis-mediated enhancement of sslE transcription is dependent on a putative Fis-binding sequence located upstream of the -35 sequence in the core promoter element, and provide evidence to suggest that Fis may work in complex with H-NS to control SslE expression. Overall, this study has defined a new mechanism for sslE regulation and increases our understanding of this broadly conserved E. coli vaccine antigen.
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Affiliation(s)
- Lendl Tan
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, QLD 4072, Brisbane, Australia
| | - Danilo G. Moriel
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, QLD 4072, Brisbane, Australia
| | - Makrina Totsika
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, QLD 4059, Brisbane, Australia
| | - Scott A. Beatson
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, QLD 4072, Brisbane, Australia
| | - Mark A. Schembri
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, QLD 4072, Brisbane, Australia
- * E-mail:
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21
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Wells CD, Deighan P, Brigham M, Hochschild A. Nascent RNA length dictates opposing effects of NusA on antitermination. Nucleic Acids Res 2016; 44:5378-89. [PMID: 27025650 PMCID: PMC4914094 DOI: 10.1093/nar/gkw198] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/15/2016] [Indexed: 12/31/2022] Open
Abstract
The NusA protein is a universally conserved bacterial transcription elongation factor that binds RNA polymerase (RNAP). When functioning independently, NusA enhances intrinsic termination. Paradoxically, NusA stimulates the function of the N and Q antiterminator proteins of bacteriophage λ. The mechanistic basis for NusA's functional plasticity is poorly understood. Here we uncover an effect of nascent RNA length on the ability of NusA to collaborate with Q. Ordinarily, Q engages RNAP during early elongation when it is paused at a specific site just downstream of the phage late-gene promoter. NusA facilitates this engagement process and both proteins remain associated with the transcription elongation complex (TEC) as it escapes the pause and transcribes the late genes. We show that the λ-related phage 82 Q protein (82Q) can also engage RNAP that is paused at a promoter-distal position and thus contains a nascent RNA longer than that associated with the natively positioned TEC. However, the effect of NusA in this context is antagonistic rather than stimulatory. Moreover, cleaving the long RNA associated with the promoter-distal TEC restores NusA's stimulatory effect. Our findings reveal a critical role for nascent RNA in modulating NusA's effect on 82Q-mediated antitermination, with implications for understanding NusA's functional plasticity.
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Affiliation(s)
| | - Padraig Deighan
- Department of Microbiology and Immunobiology, Boston, MA 02115, USA Department of Biology, Emmanuel College, Boston, MA 02115, USA
| | | | - Ann Hochschild
- Department of Microbiology and Immunobiology, Boston, MA 02115, USA
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22
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Abstract
UNLABELLED A complex of highly conserved proteins consisting of NusB, NusE, NusA, and NusG is required for robust expression of rRNA in Escherichia coli. This complex is proposed to prevent Rho-dependent transcription termination by a process known as "antitermination." The mechanism of this antitermination in rRNA is poorly understood but requires association of NusB and NusE with a specific RNA sequence in rRNA known as BoxA. Here, we identify a novel member of the rRNA antitermination machinery: the inositol monophosphatase SuhB. We show that SuhB associates with elongating RNA polymerase (RNAP) at rRNA in a NusB-dependent manner. Although we show that SuhB is required for BoxA-mediated antitermination in a reporter system, our data indicate that the major function of the NusB/E/A/G/SuhB complex is not to prevent Rho-dependent termination of rRNA but rather to promote correct rRNA maturation. This occurs through formation of a SuhB-mediated loop between NusB/E/BoxA and RNAP/NusA/G. Thus, we have reassigned the function of these proteins at rRNA and identified another key player in this complex. IMPORTANCE As RNA polymerase transcribes the rRNA operons in E. coli, it complexes with a set of proteins called Nus that confer enhanced rates of transcription elongation, correct folding of rRNA, and rRNA assembly with ribosomal proteins to generate a fully functional ribosome. Four Nus proteins were previously known, NusA, NusB, NusE, and NusG; here, we discover and describe a fifth, SuhB, that is an essential component of this complex. We demonstrate that the main function of this SuhB-containing complex is not to prevent premature transcription termination within the rRNA operon, as had been long claimed, but to enable rRNA maturation and a functional ribosome fully competent for translation.
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23
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Smith AD, Yan X, Chen C, Dawson HD, Bhagwat AA. Understanding the host-adapted state of Citrobacter rodentium by transcriptomic analysis. Arch Microbiol 2016; 198:353-62. [PMID: 26837900 DOI: 10.1007/s00203-016-1191-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/17/2015] [Accepted: 01/12/2016] [Indexed: 12/18/2022]
Abstract
Citrobacter rodentium (Cr) is a mouse pathogen that mimics many aspects of enteropathogenic Escherichia coli infections including producing attaching and effacing (A/E) lesions. Host-adapted (HA) Cr cells that are shed at the peak of infection have been reported to be hyper-infective. The exact mechanism underlying this phenomenon has remained elusive since the pathogen loses its HA 'status' immediately upon subculturing in laboratory media. We sequenced the entire transcriptome of Cr directly from the feces of infected mice and analyzed the gene expression pattern. We observed that the entire transcriptional machinery as well as several transcriptional regulators to be differentially expressed when compared with the transcriptome of cells grown on laboratory media. Major adhesion and effector genes, tir and eae, were highly expressed in HA along with many genes located on all five loci of enterocyte effacement regions (LEE 1-5). Notable absent among the HA expressed genes were 19 fimbrial operons and non-fimbrial adhesions and several non-LEE encoded effectors. These results demonstrate that host-adapted Cr has a unique transcriptome that is associated with increased host transmission.
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Affiliation(s)
- Allen D Smith
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, USDA-ARS, 10300 Baltimore Ave., B307C, Rm. 228, BARC-E, Beltsville, MD, 20705, USA.
| | - Xianghe Yan
- Environmental, Microbial, and Food Safety Laboratory, Beltsville Agriculture Research Center, USDA-ARS, Beltsville, MD, USA
| | - Celine Chen
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, USDA-ARS, 10300 Baltimore Ave., B307C, Rm. 228, BARC-E, Beltsville, MD, 20705, USA
| | - Harry D Dawson
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, USDA-ARS, 10300 Baltimore Ave., B307C, Rm. 228, BARC-E, Beltsville, MD, 20705, USA
| | - Arvind A Bhagwat
- Environmental, Microbial, and Food Safety Laboratory, Beltsville Agriculture Research Center, USDA-ARS, Beltsville, MD, USA
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24
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Mondal S, Yakhnin AV, Sebastian A, Albert I, Babitzke P. NusA-dependent transcription termination prevents misregulation of global gene expression. Nat Microbiol 2016; 1:15007. [PMID: 27571753 DOI: 10.1038/nmicrobiol.2015.7] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/09/2015] [Indexed: 01/28/2023]
Abstract
Intrinsic transcription terminators consist of an RNA hairpin followed by a U-rich tract, and these signals can trigger termination without the involvement of additional factors. Although NusA is known to stimulate intrinsic termination in vitro, the in vivo targets and global impact of NusA are not known because it is essential for viability. Using genome-wide 3' end-mapping on an engineered Bacillus subtilis NusA depletion strain, we show that weak suboptimal terminators are the principle NusA substrates. Moreover, a subclass of weak non-canonical terminators was identified that completely depend on NusA for effective termination. NusA-dependent terminators tend to have weak hairpins and/or distal U-tract interruptions, supporting a model in which NusA is directly involved in the termination mechanism. Depletion of NusA altered global gene expression directly and indirectly via readthrough of suboptimal terminators. Readthrough of NusA-dependent terminators caused misregulation of genes involved in essential cellular functions, especially DNA replication and metabolism. We further show that nusA is autoregulated by a transcription attenuation mechanism that does not rely on antiterminator structures. Instead, NusA-stimulated termination in its 5' UTR dictates the extent of transcription into the operon, thereby ensuring tight control of cellular NusA levels.
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Affiliation(s)
- Smarajit Mondal
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Alexander V Yakhnin
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Aswathy Sebastian
- Bioinformatics Consulting Center, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Istvan Albert
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Bioinformatics Consulting Center, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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25
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Gong S, Wang Y, Zhang W. Kinetic regulation mechanism of pbuE riboswitch. J Chem Phys 2015; 142:015103. [DOI: 10.1063/1.4905214] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Sha Gong
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
| | - Yujie Wang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
| | - Wenbing Zhang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
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26
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Davis L, Gedeon T, Gedeon J, Thorenson J. A traffic flow model for bio-polymerization processes. J Math Biol 2013; 68:667-700. [PMID: 23404039 DOI: 10.1007/s00285-013-0651-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 11/27/2012] [Indexed: 11/25/2022]
Abstract
Bio-polymerization processes like transcription and translation are central to proper function of a cell. The speed at which the bio-polymer grows is affected both by the number of pauses of elongation machinery, as well the number of bio-polymers due to crowding effects. In order to quantify these effects in fast transcribing ribosome genes, we rigorously show that a classical traffic flow model is the limit of a mean occupancy ODE model. We compare the simulation of this model to a stochastic model and evaluate the combined effect of the polymerase density and the existence of pauses on the instantaneous transcription rate of ribosomal genes.
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Affiliation(s)
- Lisa Davis
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, 59717-2400, USA
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27
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Bubunenko M, Court DL, Refaii AA, Saxena S, Korepanov A, Friedman DI, Gottesman ME, Alix JH. Nus transcription elongation factors and RNase III modulate small ribosome subunit biogenesis in Escherichia coli. Mol Microbiol 2013; 87:382-93. [PMID: 23190053 PMCID: PMC3545037 DOI: 10.1111/mmi.12105] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2012] [Indexed: 01/02/2023]
Abstract
Escherichia coli NusA and NusB proteins bind specific sites, such as those in the leader and spacer sequences that flank the 16S region of the ribosomal RNA transcript, forming a complex with RNA polymerase that suppresses Rho-dependent transcription termination. Although antitermination has long been the accepted role for Nus factors in rRNA synthesis, we propose that another major role for the Nus-modified transcription complex in rrn operons is as an RNA chaperone insuring co-ordination of 16S rRNA folding and RNase III processing that results in production of proper 30S ribosome subunits. This contrarian proposal is based on our studies of nusA and nusB cold-sensitive mutations that have altered translation and at low temperature accumulate 30S subunit precursors. Both phenotypes are suppressed by deletion of RNase III. We argue that these results are consistent with the idea that the nus mutations cause altered rRNA folding that leads to abnormal 30S subunits and slow translation. According to this idea, functional Nus proteins stabilize an RNA loop between their binding sites in the 5' RNA leader and on the transcribing RNA polymerase, providing a topological constraint on the RNA that aids normal rRNA folding and processing.
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Affiliation(s)
- Mikhail Bubunenko
- Frederick National Laboratory for Cancer Research, Basic Research Program, SAIC-Frederick, Inc., Frederick, Maryland 21702, USA
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Donald L. Court
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Abdalla Al Refaii
- CNRS UPR9073, associated with University of Paris Diderot, Sorbonne Paris Cite Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005 Paris
| | - Shivalika Saxena
- Columbia University Medical Center, Departments of Microbiology and Biochemistry and Molecular Biophysics, New York, New York 10032, USA
| | - Alexey Korepanov
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - David I. Friedman
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Max E. Gottesman
- Columbia University Medical Center, Departments of Microbiology and Biochemistry and Molecular Biophysics, New York, New York 10032, USA
| | - Jean-Hervé Alix
- CNRS UPR9073, associated with University of Paris Diderot, Sorbonne Paris Cite Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005 Paris
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28
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Uplekar S, Rougemont J, Cole ST, Sala C. High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis. Nucleic Acids Res 2012; 41:961-77. [PMID: 23222129 PMCID: PMC3553938 DOI: 10.1093/nar/gks1260] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To construct a regulatory map of the genome of the human pathogen, Mycobacterium tuberculosis, we applied two complementary high-resolution approaches: strand-specific RNA-seq, to survey the global transcriptome, and ChIP-seq, to monitor the genome-wide dynamics of RNA polymerase (RNAP) and the anti-terminator NusA. Although NusA does not bind directly to DNA, but rather to RNAP and/or to the nascent transcript, we demonstrate that NusA interacts with RNAP ubiquitously throughout the chromosome, and that its profile mirrors RNAP distribution in both the exponential and stationary phases of growth. Generally, promoter-proximal peaks for RNAP and NusA were observed, followed by a decrease in signal strength reflecting transcriptional polarity. Differential binding of RNAP and NusA in the two growth conditions correlated with transcriptional activity as reflected by RNA abundance. Indeed, a significant association between expression levels and the presence of NusA throughout the gene body was detected, confirming the peculiar transcription-promoting role of NusA. Integration of the data sets pinpointed transcriptional units, mapped promoters and uncovered new anti-sense and non-coding transcripts. Highly expressed transcriptional units were situated mainly on the leading strand, despite the relatively unbiased distribution of genes throughout the genome, thus helping the replicative and transcriptional complexes to align.
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Affiliation(s)
- Swapna Uplekar
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, CH-1015 Lausanne, Switzerland
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29
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Zhou J, Ha KS, La Porta A, Landick R, Block SM. Applied force provides insight into transcriptional pausing and its modulation by transcription factor NusA. Mol Cell 2012; 44:635-46. [PMID: 22099310 DOI: 10.1016/j.molcel.2011.09.018] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 08/22/2011] [Accepted: 09/15/2011] [Indexed: 10/15/2022]
Abstract
Transcriptional pausing by RNA polymerase (RNAP) plays an essential role in gene regulation. Pausing is modified by various elongation factors, including prokaryotic NusA, but the mechanisms underlying pausing and NusA function remain unclear. Alternative models for pausing invoke blockade events that precede translocation (on-pathway), enzyme backtracking (off-pathway), or isomerization to a nonbacktracked, elemental pause state (off-pathway). We employed an optical trapping assay to probe the motions of individual RNAP molecules transcribing a DNA template carrying tandem repeats encoding the his pause, subjecting these enzymes to controlled forces. NusA significantly decreased the pause-free elongation rate of RNAP while increasing the probability of entry into short- and long-lifetime pauses, in a manner equivalent to exerting a ~19 pN force opposing transcription. The effects of force and NusA on pause probabilities and lifetimes support a reaction scheme where nonbacktracked, elemental pauses branch off the elongation pathway from the pretranslocated state of RNAP.
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Affiliation(s)
- Jing Zhou
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
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30
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SigN is responsible for differentiation and stress responses based on comparative proteomic analyses of Streptomyces coelicolor wild-type and sigN deletion strains. Microbiol Res 2010; 165:221-31. [DOI: 10.1016/j.micres.2009.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Revised: 05/12/2009] [Accepted: 05/16/2009] [Indexed: 11/17/2022]
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31
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Nord S, Bylund GO, Lövgren JM, Wikström PM. The RimP Protein Is Important for Maturation of the 30S Ribosomal Subunit. J Mol Biol 2009; 386:742-53. [DOI: 10.1016/j.jmb.2008.12.076] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Revised: 12/18/2008] [Accepted: 12/29/2008] [Indexed: 01/21/2023]
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32
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Abstract
Physiological changes that result in changes in bacterial gene expression are often accompanied by changes in the growth rate for fast adapting enteric bacteria. Because the availability of RNA polymerase (RNAP) in cells depends on the growth rate, transcriptional control involves not only the regulation of promoters, but also depends on the available (or free) RNAP concentration, which is difficult to quantify directly. Here, we develop a simple physical model describing the partitioning of cellular RNAP into different classes: RNAPs transcribing mRNA and ribosomal RNA (rRNA), RNAPs nonspecifically bound to DNA, free RNAP, and immature RNAP. Available experimental data for Escherichia coli allow us to determine the 2 unknown parameters of the model and hence deduce the free RNAP concentration at different growth rates. The results allow us to predict the growth-rate dependence of the activities of constitutive (unregulated) promoters, and to disentangle the growth-rate-dependent regulation of promoters (e.g., the promoters of rRNA operons) from changes in transcription due to changes in the free RNAP concentration at different growth rates. Our model can quantitatively account for the observed changes in gene expression patterns in mutant E. coli strains with altered levels of RNAP expression without invoking additional parameters. Applying our model to the case of the stringent response after amino acid starvation, we can evaluate the plausibility of various scenarios of passive transcriptional control proposed to account for the observed changes in the expression of rRNA and biosynthetic operons.
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33
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Abstract
The elongation phase of transcription by RNA polymerase is highly regulated and modulated. Both general and operon-specific elongation factors determine the local rate and extent of transcription to coordinate the appearance of transcript with its use as a messenger or functional ribonucleoprotein or regulatory element, as well as to provide operon-specific gene regulation.
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Affiliation(s)
- Jeffrey W Roberts
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.
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34
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Stochasticity and traffic jams in the transcription of ribosomal RNA: Intriguing role of termination and antitermination. Proc Natl Acad Sci U S A 2008; 105:18159-64. [PMID: 19017803 DOI: 10.1073/pnas.0806084105] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In fast-growing bacteria, ribosomal RNA (rRNA) is required to be transcribed at very high rates to sustain the high cellular demand on ribosome synthesis. This results in dense traffic of RNA polymerases (RNAP). We developed a stochastic model, integrating results of single-molecule and quantitative in vivo studies of Escherichia coli, to evaluate the quantitative effect of pausing, termination, and antitermination (AT) on rRNA transcription. Our calculations reveal that in dense RNAP traffic, spontaneous pausing of RNAP can lead to severe "traffic jams," as manifested in the broad distribution of inter-RNAP distances and can be a major factor limiting transcription and hence growth. Our results suggest the suppression of these pauses by the ribosomal AT complex to be essential at fast growth. Moreover, unsuppressed pausing by even a few nonantiterminated RNAPs can already reduce transcription drastically under dense traffic. However, the termination factor Rho can remove the nonantiterminated RNAPs and restore fast transcription. The results thus suggest an intriguing role by Rho to enhance rather than attenuate rRNA transcription.
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35
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Abstract
Transcription antitermination in the ribosomal operons of Escherichia coli results in the modification of RNA polymerase by specific proteins, altering its basic properties. For such alterations to occur, signal sequences in rrn operons are required as well as individual interacting proteins. In this study we tested putative rrn transcription antitermination-inducing sequences from five different bacteria for their abilities to function in E. coli. We further examined their response to the lack of one known rrn transcription antitermination protein from E. coli, NusB. We monitored antitermination activity by assessing the ability of RNA polymerase to read through a factor-dependent terminator. We found that, in general, the closer the regulatory sequence matched that of E. coli, the more likely there was to be a successful antitermination-proficient modification of the transcription complex. The rrn leader sequences from Pseudomonas aeruginosa, Bacillus subtilis, and Caulobacter crescentus all provided various levels of, but functionally significant antitermination properties to, RNA polymerase, while those of Mycobacterium tuberculosis and Thermotoga maritima did not. Possible RNA folding structures of presumed antitermination sequences and specific critical bases are discussed in light of our results. An unexpected finding was that when using the Caulobacter crescentus rrn leader sequence, there was little effect on terminator readthrough in the absence of NusB. All other hybrid antitermination system activities required this factor. Possible reasons for this finding are discussed.
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36
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Shankar S, Hatoum A, Roberts JW. A transcription antiterminator constructs a NusA-dependent shield to the emerging transcript. Mol Cell 2007; 27:914-27. [PMID: 17889665 PMCID: PMC2075354 DOI: 10.1016/j.molcel.2007.07.025] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2007] [Revised: 06/15/2007] [Accepted: 07/24/2007] [Indexed: 10/22/2022]
Abstract
The universal bacterial transcription elongation factor NusA mediates elongation activities of RNA polymerase. By itself, NusA induces transcription pausing and facilitates intrinsic termination, but NusA also is a cofactor of antiterminators that antagonize pausing and prevent termination. We show that NusA is required for lambda-related phage 82 antiterminator Q(82) to construct a stable complex in which RNA-based termination mechanisms have restricted access to the emerging transcript; this result suggests a locale for both Q(82) and NusA near the beta flap domain of RNA polymerase. Furthermore, as NusA is not required for the antipausing activity of Q(82) in vitro, we distinguish two distinct activities of antiterminators, namely antipausing and RNA occlusion, and discuss their roles in Q(82) function.
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Affiliation(s)
- Smita Shankar
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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37
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Bubunenko M, Baker T, Court DL. Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli. J Bacteriol 2007; 189:2844-53. [PMID: 17277072 PMCID: PMC1855809 DOI: 10.1128/jb.01713-06] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Accepted: 01/18/2007] [Indexed: 11/20/2022] Open
Abstract
We describe here details of the method we used to identify and distinguish essential from nonessential genes on the bacterial Escherichia coli chromosome. Three key features characterize our method: high-efficiency recombination, precise replacement of just the open reading frame of a chromosomal gene, and the presence of naturally occurring duplications within the bacterial genome. We targeted genes encoding functions critical for processes of transcription and translation. Proteins from three complexes were evaluated to determine if they were essential to the cell by deleting their individual genes. The transcription elongation Nus proteins and termination factor Rho, which are involved in rRNA antitermination, the ribosomal proteins of the small 30S ribosome subunit, and minor ribosome-associated proteins were analyzed. It was concluded that four of the five bacterial transcription antitermination proteins are essential, while all four of the minor ribosome-associated proteins examined (RMF, SRA, YfiA, and YhbH), unlike most ribosomal proteins, are dispensable. Interestingly, although most 30S ribosomal proteins were essential, the knockouts of six ribosomal protein genes, rpsF (S6), rpsI (S9), rpsM (S13), rpsO (S15), rpsQ (S17), and rpsT (S20), were viable.
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Affiliation(s)
- Mikhail Bubunenko
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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38
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Coleman SA, Fischer ER, Cockrell DC, Voth DE, Howe D, Mead DJ, Samuel JE, Heinzen RA. Proteome and antigen profiling of Coxiella burnetii developmental forms. Infect Immun 2006; 75:290-8. [PMID: 17088354 PMCID: PMC1828411 DOI: 10.1128/iai.00883-06] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A biphasic developmental cycle whereby highly resistant small-cell variants (SCVs) are generated from large-cell variants (LCVs) is considered fundamental to the virulence of Coxiella burnetii, the causative agent of human Q fever. In this study a proteome analysis of C. burnetii developmental forms was conducted to provide insight into their unique biological and immunological properties. Silver-stained gels of SCV and LCV lysates separated by two-dimensional (2-D) gel electrophoresis resolved over 675 proteins in both developmental forms. Forty-eight proteins were greater than twofold more abundant in LCVs than in SCVs, with six proteins greater than twofold more abundant in SCVs than in LCVs. Four and 15 upregulated proteins of SCVs and LCVs, respectively, were identified by mass spectrometry, and their predicted functional roles are consistent with a metabolically active LCV and a structurally resistant SCV. One-dimensional and 2-D immunoblots of cell form lysates probed with sera from infected/vaccinated guinea pigs and convalescent-phase serum from human patients who had recovered from acute Q fever, respectively, revealed both unique SCV/LCV antigens and common SCV/LCV antigens that were often differentially synthesized. Antigens recognized during human infection were identified by mass spectroscopy and included both previously described immunodominant proteins of C. burnetii and novel immunogenic proteins that may be important in the pathophysiology of clinical Q fever and/or the induction of protective immunity.
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Affiliation(s)
- Sherry A Coleman
- Coxiella Pathogenesis Section, Research Technology Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana 59840, USA
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39
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Abstract
Rho-dependent transcription terminators participate in sophisticated genetic regulatory mechanisms, in both bacteria and phages; they occur in regulatory regions preceding the coding sequences of genes and within coding sequences, as well as at the end of transcriptional units, to prevent readthrough transcription. Most Rho-dependent terminators have been found in enteric bacteria, but they also occur in Gram-positive bacteria and may be widespread among bacteria. Rho-dependent termination requires both cis-acting elements, on the mRNA, and trans-acting factors. The only cis-acting element common to Rho-dependent terminators is richness in rC residues. Additional sequence elements have been observed at different Rho termination sites. These 'auxiliary elements' may assist in the termination process; they differ among terminators, their occurrence possibly depending on the function and sequence context of the terminator. Specific nucleotides required for termination have also been identified at Rho sites. Rho is the main factor required for termination; it is a ring-shaped hexameric protein with ATPase and helicase activities. NusG, NusA and NusB are additional factors participating in the termination process. Rho-dependent termination occurs by binding of Rho to ribosome-free mRNA, C-rich sites being good candidates for binding. Rho's ATPase is activated by Rho-mRNA binding, and provides the energy for Rho translocation along the mRNA; translocation requires sliding of the message into the central hole of the hexamer. When a polymerase pause site is encountered, the actual termination occurs, and the transcript is released by Rho's helicase activity. Many aspects of this process are still being studied. The isolation of mutants suppressing termination, site-directed mutagenesis of cis-acting elements in Rho-dependent termination, and biochemistry, are and will be contributing to unravelling the still undefined aspects of the Rho termination machinery. Analysis of the more sophisticated regulatory mechanisms relying on Rho-dependent termination may be crucial in identifying new essential elements for termination.
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Affiliation(s)
- M Sofia Ciampi
- Dipartimento di Genetica e Microbiologia, Università di Bari, Via Amendola 165/A, 70126 Bari, Italy
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40
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Nyström T. Growth versus maintenance: a trade-off dictated by RNA polymerase availability and sigma factor competition? Mol Microbiol 2005; 54:855-62. [PMID: 15522072 DOI: 10.1111/j.1365-2958.2004.04342.x] [Citation(s) in RCA: 166] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The regulatory design of higher organisms is proposed to comprise a trade-off between activities devoted to reproduction and those devoted to cellular maintenance and repair. Excessive reproduction will inevitably limit the organism's ability to resist stress whereas excessively devoted stress defence systems may increase lifespan but reduce Darwinian fitness. The trade-off is arguably a consequence of limited resources in any one organism but the nature and identity of such limiting resources are ambiguous. Analysis of global control of gene expression in Escherichia coli suggests that reproduction and maintenance activities are also at odds in bacteria and that this antagonism may be a consequence of a battle between transcription factors for limiting RNA polymerase. The outcome of this battle is regulated and depends on the nutritional status of the environment, the levels of the alarmone ppGpp, and RNA polymerase availability. This paper reviews how the concentration of RNA polymerase available for transcription initiation may vary upon shifts between growth and growth-arrest conditions and how this adjustment may differentially affect genes whose functions relate to reproduction and maintenance.
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Affiliation(s)
- Thomas Nyström
- Department of Cell and Molecular Biology - Microbiology, Göteborg University, Medicinaregatan 9C, 413 90 Göteborg, Sweden.
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41
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Abstract
The small nucleotide ppGpp acts as a global regulator of gene expression in bacteria. Proteomic analysis of cells lacking ppGpp has shown that this nucleotide might affect many more genes than previously anticipated. These findings and others suggest that ppGpp causes a redirection of transcription so that genes important for starvation survival and virulence are favoured at the expense of those required for growth and proliferation. In addition, new insights into the mechanism by which ppGpp affects gene expression have been achieved owing to in vitro studies of ppGpp function, complemented by structural studies of the ppGpp-RNA polymerase complex.
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Affiliation(s)
- Lisa U Magnusson
- Department of Cell and Molecular Biology-Microbiology, Göteborg University, Box 462, 405 30 Göteborg, Sweden
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42
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Greive SJ, von Hippel PH. Thinking quantitatively about transcriptional regulation. Nat Rev Mol Cell Biol 2005; 6:221-32. [PMID: 15714199 DOI: 10.1038/nrm1588] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
By thinking about the chemical and physical mechanisms that are involved in the stepwise elongation of RNA transcripts, we can begin to understand the way that these mechanisms are controlled within the cell to reflect the different requirements for transcription that are posed by various metabolic, developmental and disease states. Here, we focus on the mechanistic details of the single-nucleotide addition (or excision) cycle in the transcription process, as this is the level at which many regulatory mechanisms function and can be explained in quantitative terms.
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Affiliation(s)
- Sandra J Greive
- Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, Oregon 97403, USA
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43
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Abstract
Ribosomal RNA transcription is the rate-limiting step in ribosome synthesis in bacteria and has been investigated intensely for over half a century. Multiple mechanisms ensure that rRNA synthesis rates are appropriate for the cell's particular growth condition. Recently, important advances have been made in our understanding of rRNA transcription initiation in Escherichia coli. These include (a) a model at the atomic level of the network of protein-DNA and protein-protein interactions that recruit RNA polymerase to rRNA promoters, accounting for their extraordinary strength; (b) discovery of the nonredundant roles of two small molecule effectors, ppGpp and the initiating NTP, in regulation of rRNA transcription initiation; and (c) identification of a new component of the transcription machinery, DksA, that is absolutely required for regulation of rRNA promoter activity. Together, these advances provide clues important for our molecular understanding not only of rRNA transcription, but also of transcription in general.
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Affiliation(s)
- Brian J Paul
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA.
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44
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Quan S, Zhang N, French S, Squires CL. Transcriptional polarity in rRNA operons of Escherichia coli nusA and nusB mutant strains. J Bacteriol 2005; 187:1632-8. [PMID: 15716433 PMCID: PMC1063997 DOI: 10.1128/jb.187.5.1632-1638.2005] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Synthesis of ribosomes in Escherichia coli requires an antitermination system that modifies RNA polymerase to achieve efficient transcription of the genes specifying 16S, 23S, and 5S rRNA. This modification requires nucleotide signals in the RNA and specific transcription factors, such as NusA and NusB. Transcription of rrn operons in strains lacking the ability to produce either NusA or NusB was examined by electron microscopy. The distribution and numbers of RNA polymerase molecules on rrn operons were determined for each mutant. Compared to the wild type, the 16S gene in the nusB mutant strain had an equivalent number of RNA polymerase molecules, but the number of RNA polymerase molecules was reduced 1.4-fold for the nusA mutant. For both mutant strains, there were twofold-fewer RNA polymerase molecules on the 23S RNA gene than for the wild type. Overall, the mutant strains each had 1.6-fold-fewer RNA polymerase molecules on their rrn operons than did the wild type. To determine if decreased transcription of the 23S gene observed by electron microscopy also affected the 30S/50S ribosomal subunit ratio, ribosome profiles were examined by sucrose gradient analysis. The 30S/50S ratio increased 2.5- to 3-fold for the nus mutant strains over that for wild-type cells. Thus, strains carrying either a nusA mutation or a nusB mutation have defects in transcription of 23S rRNA.
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Affiliation(s)
- Selwyn Quan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Ave., Boston, MA 02111, USA
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45
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Kemp P, Gupta M, Molineux IJ. Bacteriophage T7 DNA ejection into cells is initiated by an enzyme-like mechanism. Mol Microbiol 2004; 53:1251-65. [PMID: 15306026 DOI: 10.1111/j.1365-2958.2004.04204.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In a normal infection about 850 bp of the bacteriophage T7 genome is ejected into the cell, the remainder of the genome is internalized through transcription by Escherichia coli and then T7 RNA polymerase. Rates of T7 DNA internalization by the E. coli enzyme in vivo are constant across the whole genome. As expected for an enzyme-catalysed reaction, rates vary with temperature and can be fitted to Arrhenius kinetics. Phage virions containing a mutant gp16, a protein known to be ejected from the phage capsid into the cell at the initiation of infection, allow complete entry of the T7 genome in the absence of transcription. The kinetics of DNA ejection from such a mutant virion into the bacterial cytoplasm have also been measured at different temperatures in vivo. Between 15 and 43 degrees C the entire 40 kb T7 genome is translocated into the cell at a constant rate that is characteristic for each temperature, and the temperature-dependence of DNA translocation rates can be fitted to Arrhenius kinetics. The data are consistent with the idea that transcription-independent DNA translocation from the T7 virion is also enzyme-catalysed. The proton motive force is necessary for this mode of DNA translocation, because collapsing the membrane potential while the T7 genome is entering the cell abruptly halts further DNA transfer.
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Affiliation(s)
- Priscilla Kemp
- Section of Molecular Genetics and Microbiology, and Institute for Cell and Molecular Biology, University of Texas, Austin, TX 78712-1095, USA
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46
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Arnvig KB, Pennell S, Gopal B, Colston MJ. A high-affinity interaction between NusA and the rrn nut site in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2004; 101:8325-30. [PMID: 15159542 PMCID: PMC420393 DOI: 10.1073/pnas.0401287101] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bacterial NusA protein enhances transcriptional pausing and termination and is known to play an essential role in antitermination. Antitermination is signaled by a nut-like cis-acting RNA sequence comprising boxB, boxA, and boxC. In the present study, we demonstrate a direct, specific high-affinity interaction between the rrn leader nut-like sites and the NusA proteins of Mycobacterium tuberculosis and Escherichia coli. This NusA-RNA interaction relies on the conserved region downstream of boxA, the boxC region, thus demonstrating a key function of this element. We have established an in vivo assay for antitermination in mycobacteria and use this to show that the M. tuberculosis rrn nut-like site enhances transcriptional read-through of untranslated RNA consistent with an antitermination signal within this site. Finally, we present evidence that this NusA-RNA interaction affects transcriptional events further downstream.
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Affiliation(s)
- Kristine B Arnvig
- Division of Mycobacterial Research, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom.
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47
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Torres M, Balada JM, Zellars M, Squires C, Squires CL. In vivo effect of NusB and NusG on rRNA transcription antitermination. J Bacteriol 2004; 186:1304-10. [PMID: 14973028 PMCID: PMC344418 DOI: 10.1128/jb.186.5.1304-1310.2004] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Similarities between lambda and rRNA transcription antitermination have led to suggestions that they involve the same Nus factors. However, direct in vivo confirmation that rRNA antitermination requires all of the lambda Nus factors is lacking. We have therefore analyzed the in vivo role of NusB and NusG in rRNA transcription antitermination and have established that both are essential for it. We used a plasmid test system in which reporter gene mRNA was measured to monitor rRNA antiterminator-dependent bypass of a Rho-dependent terminator. A comparison of terminator read-through in a wild-type Escherichia coli strain and that in a nusB::IS10 mutant strain determined the requirement for NusB. In the absence of NusB, antiterminator-dependent terminator read-through was not detected, showing that NusB is necessary for rRNA transcription antitermination. The requirement for NusG was determined by comparing rRNA antiterminator-dependent terminator read-through in a strain overexpressing NusG with that in a strain depleted of NusG. In NusG-depleted cells, termination levels were unchanged in the presence or absence of the antiterminator, demonstrating that NusG, like NusB, is necessary for rRNA transcription antitermination. These results imply that NusB and NusG are likely to be part of an RNA-protein complex formed with RNA polymerase during transcription of the rRNA antiterminator sequences that is required for rRNA antiterminator-dependent terminator read-through.
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Affiliation(s)
- Martha Torres
- King Faisal Specialist Hospital and Research Centre, Radiation Biology Laboratory, Biomedical Physics Department, Riyadh 11211, Saudi Arabia
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48
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Abstract
In bacteria, conditions that uncouple translation from transcription activate intragenic terminators located within cistrons. We analyzed the function of NusA in intragenic termination, making use of two tandem terminators located within the hisG cistron, GTTE1 and GTTE2. GTTE2 is a canonical Rho site, capable to terminate with Rho alone in vitro. By contrast, GTTE1 is a suboptimal terminator, featuring a boxA element and requiring a functional NusB to terminate efficiently in vivo. We found that a functional NusA is necessary for efficient termination events to occur at both GTTE1 and 2. To enhance termination at GTTE1 in conditions in which the transcript is free of ribosomes, NusA acts at the same step as NusB and NusE/S10. In the presence of concomitant translation, termination at GTTE1 is dependent on the relative position of the translation stop codon and boxA. If translation stops upstream of boxA, NusA acts at the same step as NusB enhance termination. Ribosomes terminating translation at boxA influence termination at GTTE1. Interactions of NusA and/or NusB with ribosomal components, including NusE/S10, might facilitate termination. Differently from what observed at GTTE1, the NusA-stimulated pausing seems to be sufficient for the occurrence of complete termination events at GTTE2. A functional NusA is also necessary to prevent premature termination of normally translated transcripts. Our data support the hypothesis that NusA may program a fraction of the RNA polymerase to terminate transcription upon interactions with specific sites on the nascent mRNA and either other Nuses or ribosomes.
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Affiliation(s)
- M Stella Carlomagno
- Dipartimento di Biologia e Patologia Cellulare e Molecolare L. Califano, Università degli Studi di Napoli Federico II, Via S. Pansini 5, 80131 Naples, Italy.
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49
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Magnusson LU, Nystrom T, Farewell A. Underproduction of sigma 70 mimics a stringent response. A proteome approach. J Biol Chem 2003; 278:968-73. [PMID: 12421813 DOI: 10.1074/jbc.m209881200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
When Escherichia coli cells enter stationary phase due to carbon starvation the synthesis of ribosomal proteins is rapidly repressed. In a DeltarelA DeltaspoT mutant, defective in the production of the alarmone guanosine tetraphosphate (ppGpp), this regulation of the levels of the protein synthesizing system is abolished. Using a proteomic approach we demonstrate that the production of the vast majority of detected E. coli proteins are decontrolled during carbon starvation in the DeltarelA DeltaspoT strain and that the starved cells behave as if they were growing exponentially. In addition we show that the inhibition of ribosome synthesis by the stringent response can be qualitatively mimicked by artificially lowering the levels of the housekeeping sigma factor, sigma(70). In other words, genes encoding the protein-synthesizing system are especially sensitive to reduced availability of sigma(70) programmed RNA polymerase. This effect is not dependent on ppGpp since lowering the levels of sigma(70) gives a similar but less pronounced effect in a ppGpp(0) strain. The data is discussed in view of the models advocating for a passive control of gene expression during stringency based on alterations in RNA polymerase availability.
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Affiliation(s)
- Lisa U Magnusson
- Department of Cell and Molecular Biology-Microbiology, Göteborg University, Box 462, Sweden
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Affiliation(s)
- Catherine L Squires
- Department of Molecular Biology and Microbiology, Tufts University, School of Medicine, Boston, Massachusetts 02111-1800, USA
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