1
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Chauvier A, Walter NG. Beyond ligand binding: Single molecule observation reveals how riboswitches integrate multiple signals to balance bacterial gene regulation. Curr Opin Struct Biol 2024; 88:102893. [PMID: 39067113 DOI: 10.1016/j.sbi.2024.102893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/26/2024] [Accepted: 07/09/2024] [Indexed: 07/30/2024]
Abstract
Riboswitches are specialized RNA structures that orchestrate gene expression in response to sensing specific metabolite or ion ligands, mostly in bacteria. Upon ligand binding, these conformationally dynamic RNA motifs undergo structural changes that control critical gene expression processes such as transcription termination and translation initiation, thereby enabling cellular homeostasis and adaptation. Because RNA folds rapidly and co-transcriptionally, riboswitches make use of the low complexity of RNA sequences to adopt alternative, transient conformations on the heels of the transcribing RNA polymerase (RNAP), resulting in kinetic partitioning that defines the regulatory outcome. This review summarizes single molecule microscopy evidence that has begun to unveil a sophisticated network of dynamic, kinetically balanced interactions between riboswitch architecture and the gene expression machinery that, together, integrate diverse cellular signals.
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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. https://twitter.com/adrienchauvier
| | - 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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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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Ghosh T, Jahangirnejad S, Chauvier A, Stringer AM, Korepanov AP, Côté JP, Wade JT, Lafontaine DA. Direct and indirect control of Rho-dependent transcription termination by the Escherichia coli lysC riboswitch. RNA (NEW YORK, N.Y.) 2024; 30:381-391. [PMID: 38253429 PMCID: PMC10946432 DOI: 10.1261/rna.079779.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024]
Abstract
Bacterial riboswitches are molecular structures that play a crucial role in controlling gene expression to maintain cellular balance. The Escherichia coli lysC riboswitch has been previously shown to regulate gene expression through translation initiation and mRNA decay. Recent research suggests that lysC gene expression is also influenced by Rho-dependent transcription termination. Through a series of in silico, in vitro, and in vivo experiments, we provide experimental evidence that the lysC riboswitch directly and indirectly modulates Rho transcription termination. Our study demonstrates that Rho-dependent transcription termination plays a significant role in the cotranscriptional regulation of lysC expression. Together with previous studies, our work suggests that lysC expression is governed by a lysine-sensing riboswitch that regulates translation initiation, transcription termination, and mRNA degradation. Notably, both Rho and RNase E target the same region of the RNA molecule, implying that RNase E may degrade Rho-terminated transcripts, providing a means to selectively eliminate these incomplete messenger RNAs. Overall, this study sheds light on the complex regulatory mechanisms used by bacterial riboswitches, emphasizing the role of transcription termination in the control of gene expression and mRNA stability.
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Affiliation(s)
- Tithi Ghosh
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1K 2R1
| | - Shirin Jahangirnejad
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1K 2R1
| | - Adrien Chauvier
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1K 2R1
| | - Anne M Stringer
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA
| | - Alexey P Korepanov
- Expression Génétique Microbienne, UMR8261 CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jean Phillippe Côté
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1K 2R1
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York 12201, USA
| | - Daniel A Lafontaine
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1K 2R1
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4
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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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5
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Chauvier A, Walter NG. Regulation of bacterial gene expression by non-coding RNA: It is all about time! Cell Chem Biol 2024; 31:71-85. [PMID: 38211587 DOI: 10.1016/j.chembiol.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024]
Abstract
Commensal and pathogenic bacteria continuously evolve to survive in diverse ecological niches by efficiently coordinating gene expression levels in their ever-changing environments. Regulation through the RNA transcript itself offers a faster and more cost-effective way to adapt than protein-based mechanisms and can be leveraged for diagnostic or antimicrobial purposes. However, RNA can fold into numerous intricate, not always functional structures that both expand and obscure the plethora of roles that regulatory RNAs serve within the cell. Here, we review the current knowledge of bacterial non-coding RNAs in relation to their folding pathways and interactions. We posit that co-transcriptional folding of these transcripts ultimately dictates their downstream functions. Elucidating the spatiotemporal folding of non-coding RNAs during transcription therefore provides invaluable insights into bacterial pathogeneses and predictive disease diagnostics. Finally, we discuss the implications of co-transcriptional folding andapplications of RNAs for therapeutics and drug targets.
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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
| | - 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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Gupta S, Padmashali N, Pal D. INTERPIN: A repository for intrinsic transcription termination hairpins in bacteria. Biochimie 2023; 214:228-236. [PMID: 37499897 DOI: 10.1016/j.biochi.2023.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
The large-scale detection of putative intrinsic transcription terminators is limited to only a few bacteria currently. We discovered a group of hairpins, called cluster hairpins, present within 15 nucleotides from each other. These are expected to work in tandem to cause intrinsic transcription termination (ITT), while the single hairpin can do the same alone. Therefore, exploring these ITT sites and the hairpins across bacterial genomes becomes highly desirable. INTERPIN is the largest archived collection of in silico inferred ITT hairpins in bacteria, covering 12745 bacterial genomes and encompassing ten bacterial phyla for ∼25 million hairpins. Users can obtain details on operons, individual cluster, and single ITT hairpins that were screened therein. Integrated Genome Viewer (IGV) software interactively visualizes hairpin secondary and tertiary structures in the genomic context. We also discuss statistics for the occurrence of cluster or single hairpins and other termination alternatives while showing the validation of predicted hairpins against in vivo detected hairpins. The database is freely available at http://pallab.cds.iisc.ac.in/INTERPIN/. INTERPIN (database and software) can make predictions for both AT and GC-rich genomes, which has not been achieved by any other program so far. It can also be used to improve genome annotation as well as to get predictions to improve the understanding of the ITT pathway by further analysis.
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Affiliation(s)
- Swati Gupta
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, 560012, Karnataka, India
| | - Namrata Padmashali
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, 560012, Karnataka, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, 560012, Karnataka, India.
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Krypotou E, Townsend GE, Gao X, Tachiyama S, Liu J, Pokorzynski ND, Goodman AL, Groisman EA. Bacteria require phase separation for fitness in the mammalian gut. Science 2023; 379:1149-1156. [PMID: 36927025 PMCID: PMC10148683 DOI: 10.1126/science.abn7229] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/10/2023] [Indexed: 03/18/2023]
Abstract
Therapeutic manipulation of the gut microbiota holds great potential for human health. The mechanisms bacteria use to colonize the gut therefore present valuable targets for clinical intervention. We now report that bacteria use phase separation to enhance fitness in the mammalian gut. We establish that the intrinsically disordered region (IDR) of the broadly and highly conserved transcription termination factor Rho is necessary and sufficient for phase separation in vivo and in vitro in the human commensal Bacteroides thetaiotaomicron. Phase separation increases transcription termination by Rho in an IDR-dependent manner. Moreover, the IDR is critical for gene regulation in the gut. Our findings expose phase separation as vital for host-commensal bacteria interactions and relevant for novel clinical applications.
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Affiliation(s)
- Emilia Krypotou
- Department of Microbial Pathogenesis, Yale School of Medicine; 295 Congress Avenue, New Haven, CT 06536, USA
- Yale Microbial Sciences Institute; P.O. Box 27389, West Haven, CT, 06516, USA
| | - Guy E. Townsend
- Department of Microbial Pathogenesis, Yale School of Medicine; 295 Congress Avenue, New Haven, CT 06536, USA
- Yale Microbial Sciences Institute; P.O. Box 27389, West Haven, CT, 06516, USA
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, 700 HMC Crescent Road, Hershey, PA 17033
| | - Xiaohui Gao
- Department of Microbial Pathogenesis, Yale School of Medicine; 295 Congress Avenue, New Haven, CT 06536, USA
| | - Shoichi Tachiyama
- Department of Microbial Pathogenesis, Yale School of Medicine; 295 Congress Avenue, New Haven, CT 06536, USA
- Yale Microbial Sciences Institute; P.O. Box 27389, West Haven, CT, 06516, USA
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale School of Medicine; 295 Congress Avenue, New Haven, CT 06536, USA
- Yale Microbial Sciences Institute; P.O. Box 27389, West Haven, CT, 06516, USA
| | - Nick D. Pokorzynski
- Department of Microbial Pathogenesis, Yale School of Medicine; 295 Congress Avenue, New Haven, CT 06536, USA
| | - Andrew L. Goodman
- Department of Microbial Pathogenesis, Yale School of Medicine; 295 Congress Avenue, New Haven, CT 06536, USA
- Yale Microbial Sciences Institute; P.O. Box 27389, West Haven, CT, 06516, USA
| | - Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine; 295 Congress Avenue, New Haven, CT 06536, USA
- Yale Microbial Sciences Institute; P.O. Box 27389, West Haven, CT, 06516, USA
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Song E, Hwang S, Munasingha PR, Seo YS, Kang J, Kang C, Hohng S. Transcriptional pause extension benefits the stand-by rather than catch-up Rho-dependent termination. Nucleic Acids Res 2023; 51:2778-2789. [PMID: 36762473 PMCID: PMC10085680 DOI: 10.1093/nar/gkad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/30/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
Transcriptional pause is essential for all types of termination. In this single-molecule study on bacterial Rho factor-dependent terminators, we confirm that the three Rho-dependent termination routes operate compatibly together in a single terminator, and discover that their termination efficiencies depend on the terminational pauses in unexpected ways. Evidently, the most abundant route is that Rho binds nascent RNA first and catches up with paused RNA polymerase (RNAP) and this catch-up Rho mediates simultaneous releases of transcript RNA and template DNA from RNAP. The fastest route is that the catch-up Rho effects RNA-only release and leads to 1D recycling of RNAP on DNA. The slowest route is that the RNAP-prebound stand-by Rho facilitates only the simultaneous rather than sequential releases. Among the three routes, only the stand-by Rho's termination efficiency positively correlates with pause duration, contrary to a long-standing speculation, invariably in the absence or presence of NusA/NusG factors, competitor RNAs or a crowding agent. Accordingly, the essential terminational pause does not need to be long for the catch-up Rho's terminations, and long pauses benefit only the stand-by Rho's terminations. Furthermore, the Rho-dependent termination of mgtA and ribB riboswitches is controlled mainly by modulation of the stand-by rather than catch-up termination.
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Affiliation(s)
- Eunho Song
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul 08826, Republic of Korea
| | - Seungha Hwang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Palinda Ruvan Munasingha
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yeon-Soo Seo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jin Young Kang
- Correspondence may also be addressed to Jin Young Kang. Tel: +82 42 350 2831;
| | - Changwon Kang
- Correspondence may also be addressed to Changwon Kang. Tel: +82 42 350 2610;
| | - Sungchul Hohng
- To whom correspondence should be addressed. Tel: +82 2 880 6593;
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Failure of Translation Initiation of the Next Gene Decouples Transcription at Intercistronic Sites and the Resultant mRNA Generation. mBio 2022; 13:e0128722. [PMID: 35695461 PMCID: PMC9239205 DOI: 10.1128/mbio.01287-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Escherichia coli, transcription is coupled with translation. The polar gal operon is transcribed galE-galT-galK-galM; however, about 10% of transcription terminates at the end of galE because of Rho-dependent termination (RDT). When galE translation is complete, galT translation should begin immediately. It is unclear whether RDT at the end of galE is due to decoupling of translation termination and transcription at the cistron junction. In this study, we show that RDT at the galE/galT cistron junction is linked to the failure of translation initiation at the start of galT, rather than translation termination at the end of galE. We also show that transcription pauses 130 nucleotides downstream from the site of galE translation termination, and this pause is required for RDT. IMPORTANCE Transcription of operons is initiated at the promoter of the first gene in the operon, continues through cistron junctions, and terminates at the end of the operon, generating a full-length mRNA. Here, we show that Rho-dependent termination of transcription occurs stochastically at a cistron junction, generating a stable mRNA that is shorter than the full-length mRNA. We further show that stochastic failure in translation initiation of the next gene, rather than the failure of translation termination of the preceding gene, causes the Rho-dependent termination. Thus, stochastic failure in translation initiation at the cistron junction causes the promoter-proximal gene to be transcribed more than promoter-distal genes within the operon.
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Rho-dependent transcription termination proceeds via three routes. Nat Commun 2022; 13:1663. [PMID: 35351884 PMCID: PMC8964686 DOI: 10.1038/s41467-022-29321-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 03/09/2022] [Indexed: 01/26/2023] Open
Abstract
Rho is a general transcription termination factor in bacteria, but many aspects of its mechanism of action are unclear. Diverse models have been proposed for the initial interaction between the RNA polymerase (RNAP) and Rho (catch-up and stand-by pre-terminational models); for the terminational release of the RNA transcript (RNA shearing, RNAP hyper-translocation or displacing, and allosteric models); and for the post-terminational outcome (whether the RNAP dissociates or remains bound to the DNA). Here, we use single-molecule fluorescence assays to study those three steps in transcription termination mediated by E. coli Rho. We find that different mechanisms previously proposed for each step co-exist, but apparently occur on various timescales and tend to lead to specific outcomes. Our results indicate that three kinetically distinct routes take place: (1) the catch-up mode leads first to RNA shearing for RNAP recycling on DNA, and (2) later to RNAP displacement for decomposition of the transcriptional complex; (3) the last termination usually follows the stand-by mode with displacing for decomposing. This three-route model would help reconcile current controversies on the mechanisms. Rho is a general transcription termination factor in bacteria. Here, Song et al. use single-molecule fluorescence assays to provide evidence that Rho-mediated transcription termination can occur via three kinetically different routes.
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11
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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: 20] [Impact Index Per Article: 6.7] [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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12
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Abstract
To exert their functions, RNAs adopt diverse structures, ranging from simple secondary to complex tertiary and quaternary folds. In vivo, RNA folding starts with RNA transcription, and a wide variety of processes are coupled to co-transcriptional RNA folding events, including the regulation of fundamental transcription dynamics, gene regulation by mechanisms like attenuation, RNA processing or ribonucleoprotein particle formation. While co-transcriptional RNA folding and associated co-transcriptional processes are by now well accepted as pervasive regulatory principles in all organisms, investigations into the role of the transcription machinery in co-transcriptional folding processes have so far largely focused on effects of the order in which RNA regions are produced and of transcription kinetics. Recent structural and structure-guided functional analyses of bacterial transcription complexes increasingly point to an additional role of RNA polymerase and associated transcription factors in supporting co-transcriptional RNA folding by fostering or preventing strategic contacts to the nascent transcripts. In general, the results support the view that transcription complexes can act as RNA chaperones, a function that has been suggested over 30 years ago. Here, we discuss transcription complexes as RNA chaperones based on recent examples from bacterial transcription.
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Affiliation(s)
- Nelly Said
- Freie Universität Berlin, Department Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Berlin, Germany
| | - Markus C Wahl
- Freie Universität Berlin, Department Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Berlin, Germany.,Helmholtz-Zentrum Berlin Für Materialien Und Energie, Macromolecular Crystallography, Berlin, Germany
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13
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Abstract
Mg2+ is the most abundant divalent cation in living cells. It is essential for charge neutralization, macromolecule stabilization, and the assembly and activity of ribosomes and as a cofactor for enzymatic reactions. When experiencing low cytoplasmic Mg2+, bacteria adopt two main strategies: They increase the abundance and activity of Mg2+ importers and decrease the abundance of Mg2+-chelating ATP and rRNA. These changes reduce regulated proteolysis by ATP-dependent proteases and protein synthesis in a systemic fashion. In many bacterial species, the transcriptional regulator PhoP controls expression of proteins mediating these changes. The 5' leader region of some mRNAs responds to low cytoplasmic Mg2+ or to disruptions in translation of open reading frames in the leader regions by furthering expression of the associated coding regions, which specify proteins mediating survival when the cytoplasmic Mg2+ concentration is low. Microbial species often utilize similar adaptation strategies to cope with low cytoplasmic Mg2+ despite relying on different genes to do so.
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Affiliation(s)
- Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, USA; .,Yale Microbial Sciences Institute, West Haven, Connecticut 06516, USA
| | - Carissa Chan
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, USA;
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Abstract
Cellular life depends on transcription of DNA by RNA polymerase to express genetic information. RNA polymerase has evolved not just to read information from DNA and write it to RNA but also to sense and process information from the cellular and extracellular environments. Much of this information processing occurs during transcript elongation, when transcriptional pausing enables regulatory decisions. Transcriptional pauses halt RNA polymerase in response to DNA and RNA sequences and structures at locations and times that help coordinate interactions with small molecules and transcription factors important for regulation. Four classes of transcriptional pause signals are now evident after decades of study: elemental pauses, backtrack pauses, hairpin-stabilized pauses, and regulator-stabilized pauses. In this review, I describe current understanding of the molecular mechanisms of these four classes of pause signals, remaining questions about how RNA polymerase responds to pause signals, and the many exciting directions now open to understand pausing and the regulation of transcript elongation on a genome-wide scale. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Robert Landick
- Department of Biochemistry and Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
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15
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Trzilova D, Anjuwon-Foster BR, Torres Rivera D, Tamayo R. Rho factor mediates flagellum and toxin phase variation and impacts virulence in Clostridioides difficile. PLoS Pathog 2020; 16:e1008708. [PMID: 32785266 PMCID: PMC7446863 DOI: 10.1371/journal.ppat.1008708] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 08/24/2020] [Accepted: 06/16/2020] [Indexed: 12/17/2022] Open
Abstract
The intestinal pathogen Clostridioides difficile exhibits heterogeneity in motility and toxin production. This phenotypic heterogeneity is achieved through phase variation by site-specific recombination via the DNA recombinase RecV, which reversibly inverts the "flagellar switch" upstream of the flgB operon. A recV mutation prevents flagellar switch inversion and results in phenotypically locked strains. The orientation of the flagellar switch influences expression of the flgB operon post-transcription initiation, but the specific molecular mechanism is unknown. Here, we report the isolation and characterization of spontaneous suppressor mutants in the non-motile, non-toxigenic recV flg OFF background that regained motility and toxin production. The restored phenotypes corresponded with increased expression of flagellum and toxin genes. The motile suppressor mutants contained single-nucleotide polymorphisms (SNPs) in rho, which encodes the bacterial transcription terminator Rho factor. Analyses using transcriptional reporters indicate that Rho contributes to heterogeneity in flagellar gene expression by preferentially terminating transcription of flg OFF mRNA within the 5' leader sequence. Additionally, Rho is important for initial colonization of the intestine in a mouse model of infection, which may in part be due to the sporulation and growth defects observed in the rho mutants. Together these data implicate Rho factor as a regulator of gene expression affecting phase variation of important virulence factors of C. difficile.
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Affiliation(s)
- Dominika Trzilova
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Brandon R. Anjuwon-Foster
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Dariana Torres Rivera
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
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16
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Bédard ASV, Hien EDM, Lafontaine DA. Riboswitch regulation mechanisms: RNA, metabolites and regulatory proteins. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194501. [PMID: 32036061 DOI: 10.1016/j.bbagrm.2020.194501] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/05/2020] [Accepted: 02/06/2020] [Indexed: 12/17/2022]
Abstract
Riboswitches are RNA sensors that have been shown to modulate the expression of downstream genes by altering their structure upon metabolite binding. Riboswitches are unique among cellular regulators in that metabolite detection is strictly performed using RNA interactions with the sensed metabolite and in which no regulatory protein is needed to mediate the interaction. However, recent studies have shed light on riboswitch control mechanisms relying on protein regulators to harness metabolite binding for the mediation of gene expression, thereby increasing the range of cellular factors involved in riboswitch regulation. The interaction between riboswitches and proteins adds another level of evolutionary pressure as riboswitches must maintain key residues for metabolite detection, structural switching and protein binding sites. Here, we review regulatory mechanisms involving Escherichia coli riboswitches that have recently been shown to rely on regulatory proteins. We also discuss the implication of such protein-based riboswitch regulatory mechanisms for genetic regulation.
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Affiliation(s)
- Anne-Sophie Vézina Bédard
- Department of biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Elsa D M Hien
- Department of biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Daniel A Lafontaine
- Department of biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada.
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17
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Nadiras C, Eveno E, Schwartz A, Figueroa-Bossi N, Boudvillain M. A multivariate prediction model for Rho-dependent termination of transcription. Nucleic Acids Res 2019; 46:8245-8260. [PMID: 29931073 PMCID: PMC6144790 DOI: 10.1093/nar/gky563] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/08/2018] [Indexed: 11/13/2022] Open
Abstract
Bacterial transcription termination proceeds via two main mechanisms triggered either by simple, well-conserved (intrinsic) nucleic acid motifs or by the motor protein Rho. Although bacterial genomes can harbor hundreds of termination signals of either type, only intrinsic terminators are reliably predicted. Computational tools to detect the more complex and diversiform Rho-dependent terminators are lacking. To tackle this issue, we devised a prediction method based on Orthogonal Projections to Latent Structures Discriminant Analysis [OPLS-DA] of a large set of in vitro termination data. Using previously uncharacterized genomic sequences for biochemical evaluation and OPLS-DA, we identified new Rho-dependent signals and quantitative sequence descriptors with significant predictive value. Most relevant descriptors specify features of transcript C>G skewness, secondary structure, and richness in regularly-spaced 5'CC/UC dinucleotides that are consistent with known principles for Rho-RNA interaction. Descriptors collectively warrant OPLS-DA predictions of Rho-dependent termination with a ∼85% success rate. Scanning of the Escherichia coli genome with the OPLS-DA model identifies significantly more termination-competent regions than anticipated from transcriptomics and predicts that regions intrinsically refractory to Rho are primarily located in open reading frames. Altogether, this work delineates features important for Rho activity and describes the first method able to predict Rho-dependent terminators in bacterial genomes.
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Affiliation(s)
- Cédric Nadiras
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France.,ED 549, Sciences Biologiques & Chimie du Vivant, Université d'Orléans, France
| | - Eric Eveno
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France
| | - Annie Schwartz
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France
| | - Nara Figueroa-Bossi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University of Paris-Sud, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Marc Boudvillain
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France
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18
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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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19
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Regulation of Bacterial Gene Expression by Transcription Attenuation. Microbiol Mol Biol Rev 2019; 83:83/3/e00019-19. [PMID: 31270135 DOI: 10.1128/mmbr.00019-19] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A wide variety of mechanisms that control gene expression in bacteria are based on conditional transcription termination. Generally, in these mechanisms, a transcription terminator is located between a promoter and a downstream gene(s), and the efficiency of the terminator is controlled by a regulatory effector that can be a metabolite, protein, or RNA. The most common type of regulation involving conditional termination is transcription attenuation, in which the primary regulatory target is an essential element of a single terminator. The terminator can be either intrinsic or Rho dependent, with each presenting unique regulatory targets. Transcription attenuation mechanisms can be divided into five classes based primarily on the manner in which transcription termination is rendered conditional. This review summarizes each class of control mechanisms from a historical perspective, describes important examples in a physiological context and the current state of knowledge, highlights major advances, and discusses expectations of future discoveries.
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20
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Gupta A, Swati D. Riboswitches in Archaea. Comb Chem High Throughput Screen 2019; 22:135-149. [DOI: 10.2174/1386207322666190425143301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 03/15/2019] [Accepted: 04/13/2019] [Indexed: 12/15/2022]
Abstract
Background:
Riboswitches are cis-acting, non-coding RNA elements found in the
5’UTR of bacterial mRNA and 3’ UTR of eukaryotic mRNA, that fold in a complex manner to act
as receptors for specific metabolites hence altering their conformation in response to the change in
concentrations of a ligand or metabolite. Riboswitches function as gene regulators in numerous
bacteria, archaea, fungi, algae and plants.
Aim and Objective:
This study identifies different classes of riboswitches in the Archaeal domain
of life. Previous studies have suggested that riboswitches carry a conserved aptameric domain in
different domains of life. Since Archaea are considered to be the most idiosyncratic organisms it
was interesting to look for the conservation pattern of riboswitches in these obviously strange
microorganisms.
Materials and Methods:
Completely sequenced Archaeal Genomes present in the NCBI repository
were used for studying riboswitches and other ncRNAs. The sequence files in FASTA format were
downloaded from NCBI Genome database and information related to these genomes was retrieved
from GenBank. Three bioinformatics approaches were used namely, ab initio, consensus structure
prediction and statistical model-based prediction for identifying riboswitches.
Results:
Archaeal genomes have a sporadic distribution of putative riboswitches like the TPP,
FMN, Guanidine, Lysine and c-di-AMP riboswitches, which are known to occur in bacteria. Also,
a class of riboswitch sensing c-di-GMP, a second messenger, has been identified in a few Archaeal
organisms.
Conclusion:
This study clearly reveals that bioinformatics methods are likely to play a major role
in identifying conserved riboswitches and in establishing how widespread these classes are in all
domains of life, even though the final confirmation may come from wet lab methods.
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Affiliation(s)
- Angela Gupta
- Department of Bioinformatics, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi, India
| | - D. Swati
- Department of Bioinformatics, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi, India
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21
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Roberts JW. Mechanisms of Bacterial Transcription Termination. J Mol Biol 2019; 431:4030-4039. [PMID: 30978344 DOI: 10.1016/j.jmb.2019.04.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/28/2019] [Accepted: 04/02/2019] [Indexed: 01/28/2023]
Abstract
Bacterial transcription termination, described mostly for Escherichia coli, occurs in three recognized ways: intrinsic termination, an activity only of the core RNAP enzyme and transcript sequences that encode an RNA hairpin and terminal uridine-rich segment; termination by the enzyme Rho, an ATP-dependent RNA translocase that releases RNA by forcing uncharacterized structural changes in the elongating complex; and Mfd-dependent termination, the activity of an ATP-dependent DNA translocase that is thought to dissociate the elongation complex by exerting torque on a stalled RNAP. Intrinsic termination can be described in terms of the nucleic acid movements in the process, whereas the enzymatic mechanisms have been illuminated importantly by definitive structural and biochemical analysis of their activity.
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Affiliation(s)
- Jeffrey W Roberts
- Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA.
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22
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Kim S, Jacobs-Wagner C. Effects of mRNA Degradation and Site-Specific Transcriptional Pausing on Protein Expression Noise. Biophys J 2019; 114:1718-1729. [PMID: 29642040 DOI: 10.1016/j.bpj.2018.02.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/30/2018] [Accepted: 02/07/2018] [Indexed: 12/20/2022] Open
Abstract
Genetically identical cells exhibit diverse phenotypes even when experiencing the same environment. This phenomenon in part originates from cell-to-cell variability (noise) in protein expression. Although various kinetic schemes of stochastic transcription initiation are known to affect gene expression noise, how posttranscription initiation events contribute to noise at the protein level remains incompletely understood. To address this question, we developed a stochastic simulation-based model of bacterial gene expression that integrates well-known dependencies between transcription initiation, transcription elongation dynamics, mRNA degradation, and translation. We identified realistic conditions under which mRNA lifetime and transcriptional pauses modulate the protein expression noise initially introduced by the promoter architecture. For instance, we found that the short lifetime of bacterial mRNAs facilitates the production of protein bursts. Conversely, RNA polymerase (RNAP) pausing at specific sites during transcription elongation can attenuate protein bursts by fluidizing the RNAP traffic to the point of erasing the effect of a bursty promoter. Pause-prone sites, if located close to the promoter, can also affect noise indirectly by reducing both transcription and translation initiation due to RNAP and ribosome congestion. Our findings highlight how the interplay between transcription initiation, transcription elongation, translation, and mRNA degradation shapes the distribution in protein numbers. They also have implications for our understanding of gene evolution and suggest combinatorial strategies for modulating phenotypic variability by genetic engineering.
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Affiliation(s)
- Sangjin Kim
- Microbial Sciences Institute, West Haven, Connecticut; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut; Howard Hughes Medical Institute, New Haven, Connecticut
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, West Haven, Connecticut; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut; Howard Hughes Medical Institute, New Haven, Connecticut; Department of Microbial Pathogenesis, Yale School of Medicine, Yale University, New Haven, Connecticut.
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23
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Hou YM, Masuda I, Gamper H. Codon-Specific Translation by m 1G37 Methylation of tRNA. Front Genet 2019; 9:713. [PMID: 30687389 PMCID: PMC6335274 DOI: 10.3389/fgene.2018.00713] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 12/20/2018] [Indexed: 12/31/2022] Open
Abstract
Although the genetic code is degenerate, synonymous codons for the same amino acid are not translated equally. Codon-specific translation is important for controlling gene expression and determining the proteome of a cell. At the molecular level, codon-specific translation is regulated by post-transcriptional epigenetic modifications of tRNA primarily at the wobble position 34 and at position 37 on the 3'-side of the anticodon. Modifications at these positions determine the quality of codon-anticodon pairing and the speed of translation on the ribosome. Different modifications operate in distinct mechanisms of codon-specific translation, generating a diversity of regulation that is previously unanticipated. Here we summarize recent work that demonstrates codon-specific translation mediated by the m1G37 methylation of tRNA at CCC and CCU codons for proline, an amino acid that has unique features in translation.
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Affiliation(s)
- Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, United States
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24
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Kang JY, Mishanina TV, Bellecourt MJ, Mooney RA, Darst SA, Landick R. RNA Polymerase Accommodates a Pause RNA Hairpin by Global Conformational Rearrangements that Prolong Pausing. Mol Cell 2019; 69:802-815.e5. [PMID: 29499135 DOI: 10.1016/j.molcel.2018.01.018] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/27/2017] [Accepted: 01/12/2018] [Indexed: 01/10/2023]
Abstract
Sequence-specific pausing by RNA polymerase (RNAP) during transcription plays crucial and diverse roles in gene expression. In bacteria, RNA structures are thought to fold within the RNA exit channel of the RNAP and can increase pause lifetimes significantly. The biophysical mechanism of pausing is uncertain. We used single-particle cryo-EM to determine structures of paused complexes, including a 3.8-Å structure of an RNA hairpin-stabilized, paused RNAP that coordinates RNA folding in the his operon attenuation control region of E. coli. The structures revealed a half-translocated pause state (RNA post-translocated, DNA pre-translocated) that can explain transcriptional pausing and a global conformational change of RNAP that allosterically inhibits trigger loop folding and can explain pause hairpin action. Pause hairpin interactions with the RNAP RNA exit channel suggest how RNAP guides the formation of nascent RNA structures.
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Affiliation(s)
- Jin Young Kang
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Tatiana V Mishanina
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Michael J Bellecourt
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Rachel Anne Mooney
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Seth A Darst
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, 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.
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25
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Ray S, Chauvier A, Walter NG. Kinetics coming into focus: single-molecule microscopy of riboswitch dynamics. RNA Biol 2018; 16:1077-1085. [PMID: 30328748 DOI: 10.1080/15476286.2018.1536594] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Riboswitches are dynamic RNA motifs that are mostly embedded in the 5'-untranslated regions of bacterial mRNAs, where they regulate gene expression transcriptionally or translationally by undergoing conformational changes upon binding of a small metabolite or ion. Due to the small size of typical ligands, relatively little free energy is available from ligand binding to overcome the often high energetic barrier of reshaping RNA structure. Instead, most riboswitches appear to take advantage of the directional and hierarchical folding of RNA by employing the ligand as a structural 'linchpin' to adjust the kinetic partitioning between alternate folds. In this model, even small, local structural and kinetic effects of ligand binding can cascade into global RNA conformational changes affecting gene expression. Single-molecule (SM) microscopy tools are uniquely suited to study such kinetically controlled RNA folding since they avoid the ensemble averaging of bulk techniques that loses sight of unsynchronized, transient, and/or multi-state kinetic behavior. This review summarizes how SM methods have begun to unravel riboswitch-mediated gene regulation.
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Affiliation(s)
- Sujay Ray
- a Single Molecule Analysis Group, Department of Chemistry, University of Michigan , Ann Arbor , MI , USA
| | - Adrien Chauvier
- a Single Molecule Analysis Group, Department of Chemistry, University of Michigan , Ann Arbor , MI , USA
| | - Nils G Walter
- a Single Molecule Analysis Group, Department of Chemistry, University of Michigan , Ann Arbor , MI , USA
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26
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Hua B, Panja S, Wang Y, Woodson SA, Ha T. Mimicking Co-Transcriptional RNA Folding Using a Superhelicase. J Am Chem Soc 2018; 140:10067-10070. [PMID: 30063835 DOI: 10.1021/jacs.8b03784] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Vectorial folding of RNA during transcription can produce intermediates with distinct biochemical activities. Here, we design an artificial minimal system to mimic cotranscriptional RNA folding in vitro. In this system, a presynthesized RNA molecule begins to fold from its 5'-end, as it is released from a heteroduplex by an engineered helicase that translocates on the complementary DNA strand in the 3'-to-5' direction. This chemically stabilized "superhelicase" Rep-X processively unwinds thousands of base pairs of DNA. The presynthesized RNA enables us to flexibly position fluorescent labels on the RNA for single-molecule fluorescence resonance energy transfer analysis and allows us to study real-time conformational dynamics during the vectorial folding process. We observed distinct signatures of the maiden secondary and tertiary folding of the Oryza sativa twister ribozyme. The maiden vectorial tertiary folding transitions occurred faster than Mg2+-induced refolding, but were also more prone to misfolding, likely due to sequential formation of alternative secondary structures. This novel assay can be applied to studying other kinetically controlled processes, such as riboswitch control and RNA-protein assembly.
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Affiliation(s)
- Boyang Hua
- Department of Biophysics and Biophysical Chemistry , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States
| | - Subrata Panja
- T. C. Jenkins Department of Biophysics , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Yanbo Wang
- Department of Biophysics and Biophysical Chemistry , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States
| | - Sarah A Woodson
- T. C. Jenkins Department of Biophysics , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States.,T. C. Jenkins Department of Biophysics , Johns Hopkins University , Baltimore , Maryland 21218 , United States.,Department of Biomedical Engineering , Johns Hopkins University , Baltimore , Maryland 21218 , United States.,Howard Hughes Medical Institute , Baltimore , Maryland 21205 , United States
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27
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Raghunathan N, Kapshikar RM, Leela JK, Mallikarjun J, Bouloc P, Gowrishankar J. Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli. Nucleic Acids Res 2018; 46:3400-3411. [PMID: 29474582 PMCID: PMC5909445 DOI: 10.1093/nar/gky118] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/30/2018] [Accepted: 02/09/2018] [Indexed: 12/22/2022] Open
Abstract
Transcription termination by Rho is essential for viability in various bacteria, including some major pathogens. Since Rho acts by targeting nascent RNAs that are not simultaneously translated, it also regulates antisense transcription. Here we show that RNase H-deficient mutants of Escherichia coli exhibit heightened sensitivity to the Rho inhibitor bicyclomycin, and that Rho deficiency provokes increased formation of RNA-DNA hybrids (R-loops) which is ameliorated by expression of the phage T4-derived R-loop helicase UvsW. We also provide evidence that in Rho-deficient cells, R-loop formation blocks subsequent rounds of antisense transcription at more than 500 chromosomal loci. Hence these antisense transcripts, which can extend beyond 10 kb in their length, are only detected when Rho function is absent or compromised and the UvsW helicase is concurrently expressed. Thus the potential for antisense transcription in bacteria is much greater than hitherto recognized; and the cells are able to retain viability even when nearly one-quarter of their total non-rRNA abundance is accounted for by antisense transcripts, provided that R-loop formation from them is curtailed.
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Affiliation(s)
- Nalini Raghunathan
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Rajvardhan M Kapshikar
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Jakku K Leela
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
| | - Jillella Mallikarjun
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Philippe Bouloc
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France
| | - Jayaraman Gowrishankar
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
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28
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Mustoe AM, Busan S, Rice GM, Hajdin CE, Peterson BK, Ruda VM, Kubica N, Nutiu R, Baryza JL, Weeks KM. Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing. Cell 2018; 173:181-195.e18. [PMID: 29551268 DOI: 10.1016/j.cell.2018.02.034] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/02/2018] [Accepted: 02/15/2018] [Indexed: 11/25/2022]
Abstract
mRNAs can fold into complex structures that regulate gene expression. Resolving such structures de novo has remained challenging and has limited our understanding of the prevalence and functions of mRNA structure. We use SHAPE-MaP experiments in living E. coli cells to derive quantitative, nucleotide-resolution structure models for 194 endogenous transcripts encompassing approximately 400 genes. Individual mRNAs have exceptionally diverse architectures, and most contain well-defined structures. Active translation destabilizes mRNA structure in cells. Nevertheless, mRNA structure remains similar between in-cell and cell-free environments, indicating broad potential for structure-mediated gene regulation. We find that the translation efficiency of endogenous genes is regulated by unfolding kinetics of structures overlapping the ribosome binding site. We discover conserved structured elements in 35% of UTRs, several of which we validate as novel protein binding motifs. RNA structure regulates every gene studied here in a meaningful way, implying that most functional structures remain to be discovered.
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Affiliation(s)
- Anthony M Mustoe
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA.
| | - Steven Busan
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Greggory M Rice
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA; Novartis Institutes for Biomedical Research, Inc., Cambridge, MA, USA
| | | | - Brant K Peterson
- Novartis Institutes for Biomedical Research, Inc., Cambridge, MA, USA
| | - Vera M Ruda
- Novartis Institutes for Biomedical Research, Inc., Cambridge, MA, USA
| | - Neil Kubica
- Novartis Institutes for Biomedical Research, Inc., Cambridge, MA, USA
| | - Razvan Nutiu
- Novartis Institutes for Biomedical Research, Inc., Cambridge, MA, USA
| | - Jeremy L Baryza
- Novartis Institutes for Biomedical Research, Inc., Cambridge, MA, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA.
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29
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Gong S, Wang Y, Wang Z, Zhang W. Computational Methods for Modeling Aptamers and Designing Riboswitches. Int J Mol Sci 2017; 18:E2442. [PMID: 29149090 PMCID: PMC5713409 DOI: 10.3390/ijms18112442] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/12/2017] [Accepted: 11/14/2017] [Indexed: 02/04/2023] Open
Abstract
Riboswitches, which are located within certain noncoding RNA region perform functions as genetic "switches", regulating when and where genes are expressed in response to certain ligands. Understanding the numerous functions of riboswitches requires computation models to predict structures and structural changes of the aptamer domains. Although aptamers often form a complex structure, computational approaches, such as RNAComposer and Rosetta, have already been applied to model the tertiary (three-dimensional (3D)) structure for several aptamers. As structural changes in aptamers must be achieved within the certain time window for effective regulation, kinetics is another key point for understanding aptamer function in riboswitch-mediated gene regulation. The coarse-grained self-organized polymer (SOP) model using Langevin dynamics simulation has been successfully developed to investigate folding kinetics of aptamers, while their co-transcriptional folding kinetics can be modeled by the helix-based computational method and BarMap approach. Based on the known aptamers, the web server Riboswitch Calculator and other theoretical methods provide a new tool to design synthetic riboswitches. This review will represent an overview of these computational methods for modeling structure and kinetics of riboswitch aptamers and for designing riboswitches.
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Affiliation(s)
- 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, Huanggang 438000, China.
| | - Yanli Wang
- Department of Physics, Wuhan University, Wuhan 430072, China.
| | - Zhen Wang
- Department of Physics, Wuhan University, Wuhan 430072, China.
| | - Wenbing Zhang
- Department of Physics, Wuhan University, Wuhan 430072, China.
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30
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González-González A, Hug SM, Rodríguez-Verdugo A, Patel JS, Gaut BS. Adaptive Mutations in RNA Polymerase and the Transcriptional Terminator Rho Have Similar Effects on Escherichia coli Gene Expression. Mol Biol Evol 2017; 34:2839-2855. [PMID: 28961910 PMCID: PMC5815632 DOI: 10.1093/molbev/msx216] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Modifications to transcriptional regulators play a major role in adaptation. Here, we compared the effects of multiple beneficial mutations within and between Escherichia coli rpoB, the gene encoding the RNA polymerase β subunit, and rho, which encodes a transcriptional terminator. These two genes have harbored adaptive mutations in numerous E. coli evolution experiments but particularly in our previous large-scale thermal stress experiment, where the two genes characterized alternative adaptive pathways. To compare the effects of beneficial mutations, we engineered four advantageous mutations into each of the two genes and measured their effects on fitness, growth, gene expression and transcriptional termination at 42.2 °C. Among the eight mutations, two rho mutations had no detectable effect on relative fitness, suggesting they were beneficial only in the context of epistatic interactions. The remaining six mutations had an average relative fitness benefit of ∼20%. The rpoB mutations affected the expression of ∼1,700 genes; rho mutations affected the expression of fewer genes but most (83%) were a subset of those altered by rpoB mutants. Across the eight mutants, relative fitness correlated with the degree to which a mutation restored gene expression back to the unstressed, 37.0 °C state. The beneficial mutations in the two genes did not have identical effects on fitness, growth or gene expression, but they caused parallel phenotypic effects on gene expression and genome-wide transcriptional termination.
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Affiliation(s)
- Andrea González-González
- Department of Ecology and Evolutionary Biology, University of California,
Irvine, CA
- Department of Biological Sciences, University of Idaho, Moscow, ID
| | - Shaun M. Hug
- Department of Ecology and Evolutionary Biology, University of California,
Irvine, CA
| | - Alejandra Rodríguez-Verdugo
- Department of Environmental Systems Sciences, ETH Zürich, Zürich,
Switzerland
- Department of Environmental Microbiology, Eawag, Dübendorf,
Switzerland
| | | | - Brandon S. Gaut
- Department of Ecology and Evolutionary Biology, University of California,
Irvine, CA
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31
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Abstract
At the end of the multistep transcription process, the elongating RNA polymerase (RNAP) is dislodged from the DNA template either at specific DNA sequences, called the terminators, or by a nascent RNA-dependent helicase, Rho. In Escherichia coli, about half of the transcription events are terminated by the Rho protein. Rho utilizes its RNA-dependent ATPase activities to translocate along the mRNA and eventually dislodges the RNAP via an unknown mechanism. The transcription elongation factor NusG facilitates this termination process by directly interacting with Rho. In this review, we discuss current models describing the mechanism of action of this hexameric transcription terminator, its regulation by different cis and trans factors, and the effects of the termination process on physiological processes in bacterial cells, particularly E. coli and Salmonella enterica Typhimurium.
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Affiliation(s)
- Pallabi Mitra
- Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad-500001, India; , , ,
| | - Gairika Ghosh
- Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad-500001, India; , , , .,Department of Graduate Studies, Manipal University, Manipal, Karnataka-576104, India
| | - Md Hafeezunnisa
- Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad-500001, India; , , , .,Department of Graduate Studies, Manipal University, Manipal, Karnataka-576104, India
| | - Ranjan Sen
- Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad-500001, India; , , ,
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32
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Sherwood AV, Henkin TM. Riboswitch-Mediated Gene Regulation: Novel RNA Architectures Dictate Gene Expression Responses. Annu Rev Microbiol 2017; 70:361-74. [PMID: 27607554 DOI: 10.1146/annurev-micro-091014-104306] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Riboswitches are RNA elements that act on the mRNA with which they are cotranscribed to modulate expression of that mRNA. These elements are widely found in bacteria, where they have a broad impact on gene expression. The defining feature of riboswitches is that they directly recognize a physiological signal, and the resulting shift in RNA structure affects gene regulation. The majority of riboswitches respond to cellular metabolites, often in a feedback loop to repress synthesis of the enzymes used to produce the metabolite. Related elements respond to the aminoacylation status of a specific tRNA or to a physical parameter, such as temperature or pH. Recent studies have identified new classes of riboswitches and have revealed new insights into the molecular mechanisms of signal recognition and gene regulation. Application of structural and biophysical approaches has complemented previous genetic and biochemical studies, yielding new information about how different riboswitches operate.
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Affiliation(s)
- Anna V Sherwood
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210; .,Molecular, Cellular and Developmental Graduate Program, The Ohio State University, Columbus, Ohio 43210
| | - Tina M Henkin
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210;
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33
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Hou YM, Matsubara R, Takase R, Masuda I, Sulkowska JI. TrmD: A Methyl Transferase for tRNA Methylation With m 1G37. Enzymes 2017; 41:89-115. [PMID: 28601227 DOI: 10.1016/bs.enz.2017.03.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
TrmD is an S-adenosyl methionine (AdoMet)-dependent methyl transferase that synthesizes the methylated m1G37 in tRNA. TrmD is specific to and essential for bacterial growth, and it is fundamentally distinct from its eukaryotic and archaeal counterpart Trm5. TrmD is unusual by using a topological protein knot to bind AdoMet. Despite its restricted mobility, the TrmD knot has complex dynamics necessary to transmit the signal of AdoMet binding to promote tRNA binding and methyl transfer. Mutations in the TrmD knot block this intramolecular signaling and decrease the synthesis of m1G37-tRNA, prompting ribosomes to +1-frameshifts and premature termination of protein synthesis. TrmD is unique among AdoMet-dependent methyl transferases in that it requires Mg2+ in the catalytic mechanism. This Mg2+ dependence is important for regulating Mg2+ transport to Salmonella for survival of the pathogen in the host cell. The strict conservation of TrmD among bacterial species suggests that a better characterization of its enzymology and biology will have a broad impact on our understanding of bacterial pathogenesis.
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Affiliation(s)
- Ya-Ming Hou
- Thomas Jefferson University, Philadelphia, PA, United States.
| | - Ryuma Matsubara
- Thomas Jefferson University, Philadelphia, PA, United States
| | - Ryuichi Takase
- Thomas Jefferson University, Philadelphia, PA, United States
| | - Isao Masuda
- Thomas Jefferson University, Philadelphia, PA, United States
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34
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Wang B. Human Skin RNases Offer Dual Protection against Invading Bacteria. Front Microbiol 2017; 8:624. [PMID: 28443087 PMCID: PMC5386971 DOI: 10.3389/fmicb.2017.00624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/27/2017] [Indexed: 12/25/2022] Open
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35
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Transcriptional pausing at the translation start site operates as a critical checkpoint for riboswitch regulation. Nat Commun 2017; 8:13892. [PMID: 28071751 PMCID: PMC5234074 DOI: 10.1038/ncomms13892] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 11/10/2016] [Indexed: 11/24/2022] Open
Abstract
On the basis of nascent transcript sequencing, it has been postulated but never demonstrated that transcriptional pausing at translation start sites is important for gene regulation. Here we show that the Escherichia coli thiamin pyrophosphate (TPP) thiC riboswitch contains a regulatory pause site in the translation initiation region that acts as a checkpoint for thiC expression. By biochemically probing nascent transcription complexes halted at defined positions, we find a narrow transcriptional window for metabolite binding, in which the downstream boundary is delimited by the checkpoint. We show that transcription complexes at the regulatory pause site favour the formation of a riboswitch intramolecular lock that strongly prevents TPP binding. In contrast, cotranscriptional metabolite binding increases RNA polymerase pausing and induces Rho-dependent transcription termination at the checkpoint. Early transcriptional pausing may provide a general mechanism, whereby transient transcriptional windows directly coordinate the sensing of environmental cues and bacterial mRNA regulation. Riboswitches are non-coding RNA elements that detect metabolites and control expression by regulating mRNA levels or translation. Here, the authors provide evidence that the E. coli thiC riboswitch has a pause site in the translation initiation region that acts as a checkpoint for thiC expression.
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36
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Kriner MA, Groisman EA. RNA secondary structures regulate three steps of Rho-dependent transcription termination within a bacterial mRNA leader. Nucleic Acids Res 2016; 45:631-642. [PMID: 28123036 PMCID: PMC5314796 DOI: 10.1093/nar/gkw889] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 09/20/2016] [Accepted: 09/30/2016] [Indexed: 11/14/2022] Open
Abstract
Transcription termination events in bacteria often require the RNA helicase Rho. Typically, Rho promotes termination at the end of coding sequences, but it can also terminate transcription within leader regions to implement regulatory decisions. Rho-dependent termination requires initial recognition of a Rho utilization (rut) site on a nascent RNA by Rho's primary binding surface. However, it is presently unclear what factors determine the location of transcription termination, how RNA secondary structures influence this process and whether mechanistic differences distinguish constitutive from regulated Rho-dependent terminators. We previously demonstrated that the 5′ leader mRNA of the Salmonella corA gene can adopt two mutually exclusive conformations that dictate accessibility of a rut site to Rho. We now report that the corA leader also controls two subsequent steps of Rho-dependent termination. First, the RNA conformation that presents an accessible rut site promotes pausing of RNA polymerase (RNAP) at a single Rho-dependent termination site over 100 nt downstream. Second, an additional RNA stem-loop promotes Rho activity and controls the location at which Rho-dependent termination occurs, despite having no effect on initial Rho binding to the corA leader. Thus, the multi-step nature of Rho-dependent termination may facilitate regulation of a given coding region by multiple cytoplasmic signals.
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Affiliation(s)
- Michelle A Kriner
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA.,Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA
| | - Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA .,Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA
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37
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Learning from the Leaders: Gene Regulation by the Transcription Termination Factor Rho. Trends Biochem Sci 2016; 41:690-699. [PMID: 27325240 DOI: 10.1016/j.tibs.2016.05.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/18/2016] [Accepted: 05/25/2016] [Indexed: 01/23/2023]
Abstract
The RNA helicase Rho triggers 20-30% of transcription termination events in bacteria. While Rho is associated with most transcription elongation complexes, it only promotes termination of a subset. Recent studies of individual Rho-dependent terminators located within the 5' leader regions of bacterial mRNAs have identified novel mechanisms that govern Rho target specificity and have revealed unanticipated physiological functions for Rho. In particular, the multistep nature of Rho-dependent termination enables regulatory input from determinants beyond the sequence of the Rho loading site, and allows a given Rho-dependent terminator to respond to multiple signals. Further, the unique position of Rho as a sensor of cellular translation has been exploited to regulate the transcription of genes required for protein synthesis, including those specifying Mg(2+) transporters.
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38
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Mäder U, Nicolas P, Depke M, Pané-Farré J, Debarbouille M, van der Kooi-Pol MM, Guérin C, Dérozier S, Hiron A, Jarmer H, Leduc A, Michalik S, Reilman E, Schaffer M, Schmidt F, Bessières P, Noirot P, Hecker M, Msadek T, Völker U, van Dijl JM. Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions. PLoS Genet 2016; 12:e1005962. [PMID: 27035918 PMCID: PMC4818034 DOI: 10.1371/journal.pgen.1005962] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 03/04/2016] [Indexed: 11/18/2022] Open
Abstract
Staphylococcus aureus is a major pathogen that colonizes about 20% of the human population. Intriguingly, this Gram-positive bacterium can survive and thrive under a wide range of different conditions, both inside and outside the human body. Here, we investigated the transcriptional adaptation of S. aureus HG001, a derivative of strain NCTC 8325, across experimental conditions ranging from optimal growth in vitro to intracellular growth in host cells. These data establish an extensive repertoire of transcription units and non-coding RNAs, a classification of 1412 promoters according to their dependence on the RNA polymerase sigma factors SigA or SigB, and allow identification of new potential targets for several known transcription factors. In particular, this study revealed a relatively low abundance of antisense RNAs in S. aureus, where they overlap only 6% of the coding genes, and only 19 antisense RNAs not co-transcribed with other genes were found. Promoter analysis and comparison with Bacillus subtilis links the small number of antisense RNAs to a less profound impact of alternative sigma factors in S. aureus. Furthermore, we revealed that Rho-dependent transcription termination suppresses pervasive antisense transcription, presumably originating from abundant spurious transcription initiation in this A+T-rich genome, which would otherwise affect expression of the overlapped genes. In summary, our study provides genome-wide information on transcriptional regulation and non-coding RNAs in S. aureus as well as new insights into the biological function of Rho and the implications of spurious transcription in bacteria. The major human pathogen Staphylococcus aureus can survive under a wide range of conditions, both inside and outside the human body. The goal of this study was to determine how S. aureus adapts to such different conditions and, additionally, we wanted to identify general factors governing the staphylococcal transcriptome architecture. Therefore, we performed a precise analysis of all RNA transcripts of S. aureus across experimental conditions ranging from in vitro growth in different media to internalization by eukaryotic host cells. We systematically mapped all transcription units, annotated non-coding RNAs, and assigned promoters controlled by particular RNA polymerase sigma factors and transcription factors. By a comparison with data available for the related Gram-positive bacterium Bacillus subtilis, we made key observations concerning the abundance and origin of antisense RNAs. Intriguingly, these findings support the view that many antisense RNAs in a bacterium like B. subtilis could be byproducts of spurious promoter recognition by condition-specific alternative sigma factors. We also report that the transcription termination factor Rho prevents widespread antisense transcription, presumably caused by pervasive transcription initiation in the A+T-rich genome of S. aureus. Altogether our study presents new perspectives on the biological significance of antisense and pervasive transcription in bacteria.
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Affiliation(s)
- Ulrike Mäder
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Pierre Nicolas
- MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Maren Depke
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jan Pané-Farré
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Michel Debarbouille
- Biology of Gram-Positive Pathogens, Department of Microbiology, Institut Pasteur and CNRS ERL 3526, Paris, France
| | - Magdalena M. van der Kooi-Pol
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cyprien Guérin
- MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sandra Dérozier
- MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Aurelia Hiron
- Biology of Gram-Positive Pathogens, Department of Microbiology, Institut Pasteur and CNRS ERL 3526, Paris, France
| | - Hanne Jarmer
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Aurélie Leduc
- MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Stephan Michalik
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Ewoud Reilman
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marc Schaffer
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Frank Schmidt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | | | - Philippe Noirot
- Institut Micalis, INRA and AgroParisTech, Jouy-en-Josas, France
| | - Michael Hecker
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Tarek Msadek
- Biology of Gram-Positive Pathogens, Department of Microbiology, Institut Pasteur and CNRS ERL 3526, Paris, France
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
- * E-mail: (UV); (JMvD)
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- * E-mail: (UV); (JMvD)
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39
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Ray-Soni A, Bellecourt MJ, Landick R. Mechanisms of Bacterial Transcription Termination: All Good Things Must End. Annu Rev Biochem 2016; 85:319-47. [PMID: 27023849 DOI: 10.1146/annurev-biochem-060815-014844] [Citation(s) in RCA: 227] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Transcript termination is essential for accurate gene expression and the removal of RNA polymerase (RNAP) at the ends of transcription units. In bacteria, two mechanisms are responsible for proper transcript termination: intrinsic termination and Rho-dependent termination. Intrinsic termination is mediated by signals directly encoded within the DNA template and nascent RNA, whereas Rho-dependent termination relies upon the adenosine triphosphate-dependent RNA translocase Rho, which binds nascent RNA and dissociates the elongation complex. Although significant progress has been made in understanding these pathways, fundamental details remain undetermined. Among those that remain unresolved are the existence of an inactivated intermediate in the intrinsic termination pathway, the role of Rho-RNAP interactions in Rho-dependent termination, and the mechanisms by which accessory factors and nucleoid-associated proteins affect termination. We describe current knowledge, discuss key outstanding questions, and highlight the importance of defining the structural rearrangements of RNAP that are involved in the two mechanisms of transcript termination.
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Affiliation(s)
- Ananya Ray-Soni
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706; ,
| | - Michael J Bellecourt
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706; ,
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706; , .,Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706;
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40
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Grylak-Mielnicka A, Bidnenko V, Bardowski J, Bidnenko E. Transcription termination factor Rho: a hub linking diverse physiological processes in bacteria. Microbiology (Reading) 2016; 162:433-447. [DOI: 10.1099/mic.0.000244] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Aleksandra Grylak-Mielnicka
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
- Institute of Biochemistry and Biophysics PAS, 02-106 Warsaw, Poland
| | - Vladimir Bidnenko
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Jacek Bardowski
- Institute of Biochemistry and Biophysics PAS, 02-106 Warsaw, Poland
| | - Elena Bidnenko
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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41
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Zhang J, Landick R. A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure. Trends Biochem Sci 2016; 41:293-310. [PMID: 26822487 DOI: 10.1016/j.tibs.2015.12.009] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/21/2015] [Accepted: 12/22/2015] [Indexed: 02/06/2023]
Abstract
The vectorial (5'-to-3' at varying velocity) synthesis of RNA by cellular RNA polymerases (RNAPs) creates a rugged kinetic landscape, demarcated by frequent, sometimes long-lived, pauses. In addition to myriad gene-regulatory roles, these pauses temporally and spatially program the co-transcriptional, hierarchical folding of biologically active RNAs. Conversely, these RNA structures, which form inside or near the RNA exit channel, interact with the polymerase and adjacent protein factors to influence RNA synthesis by modulating pausing, termination, antitermination, and slippage. Here, we review the evolutionary origin, mechanistic underpinnings, and regulatory consequences of this interplay between RNAP and nascent RNA structure. We categorize and rationalize the extensive linkage between the transcriptional machinery and its product, and provide a framework for future studies.
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Affiliation(s)
- Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA.
| | - Robert Landick
- Departments of Biochemistry and Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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42
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The unmasking of 'junk' RNA reveals novel sRNAs: from processed RNA fragments to marooned riboswitches. Curr Opin Microbiol 2016; 30:16-21. [PMID: 26771674 DOI: 10.1016/j.mib.2015.12.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/17/2015] [Accepted: 12/09/2015] [Indexed: 11/22/2022]
Abstract
While the notion that RNAs can function as regulators dates back to early molecular studies of gene regulation of the lac operon, it is only over the last decade that the ubiquity and diversity of regulatory RNAs are being realized. Advancements in high throughput sequencing and the adoption of these approaches to rapidly sequence genomes and transcriptomes and to examine gene expression and RNA binding protein specificity have revealed an ever-expanding RNA world. In this review, we focus on recent studies revealing that RNA fragments cleaved from larger coding or noncoding RNAs can have regulatory functions. Additionally, we discuss examples of riboswitches that function in trans as mRNA or protein-binding sRNAs, upending the traditional thinking that these are exclusively cis-acting elements.
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43
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Perez-Gonzalez C, Grondin JP, Lafontaine DA, Carlos Penedo J. Biophysical Approaches to Bacterial Gene Regulation by Riboswitches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 915:157-91. [PMID: 27193543 DOI: 10.1007/978-3-319-32189-9_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The last decade has witnessed the discovery of a variety of non-coding RNA sequences that perform a broad range of crucial biological functions. Among these, the ability of certain RNA sequences, so-called riboswitches, has attracted considerable interest. Riboswitches control gene expression in response to the concentration of particular metabolites to which they bind without the need for any protein. These RNA switches not only need to adopt a very specific tridimensional structure to perform their function, but also their sequence has been evolutionary optimized to recognize a particular metabolite with high affinity and selectivity. Thus, riboswitches offer a unique opportunity to get fundamental insights into RNA plasticity and how folding dynamics and ligand recognition mechanisms have been efficiently merged to control gene regulation. Because riboswitch sequences have been mostly found in bacterial organisms controlling the expression of genes associated to the synthesis, degradation or transport of crucial metabolites for bacterial survival, they offer exciting new routes for antibiotic development in an era where bacterial resistance is more than ever challenging conventional drug discovery strategies. Here, we give an overview of the architecture, diversity and regulatory mechanisms employed by riboswitches with particular emphasis on the biophysical methods currently available to characterise their structure and functional dynamics.
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Affiliation(s)
- Cibran Perez-Gonzalez
- SUPA School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK
| | - Jonathan P Grondin
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Daniel A Lafontaine
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
| | - J Carlos Penedo
- SUPA School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK. .,Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, KY16 9ST, UK.
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44
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Hug SM, Gaut BS. The phenotypic signature of adaptation to thermal stress in Escherichia coli. BMC Evol Biol 2015; 15:177. [PMID: 26329930 PMCID: PMC4557228 DOI: 10.1186/s12862-015-0457-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 08/19/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the short-term, organisms acclimate to stress through phenotypic plasticity, but in the longer term they adapt to stress genetically. The mutations that accrue during adaptation may contribute to completely novel phenotypes, or they may instead act to restore the phenotype from a stressed to a pre-stress condition. To better understand the influence of evolution on the diversity and direction of phenotypic change, we used Biolog microarrays to assay 94 phenotypes of 115 Escherichia coli clones that had adapted to high temperature (42.2 °C). We also assayed these same phenotypes in the clones' ancestor under non-stress (37.0 °C) and stress (42.2 °C) conditions. We explored associations between Biolog phenotypes and genotypes, and we also investigated phenotypic differences between clones that have one of two adaptive genetic trajectories: one that is typified by mutations in the RNA polymerase β-subunit (rpoB) and another that is defined by mutations in the rho termination factor. RESULTS Most (54 %) phenotypic variation was restorative, shifting the phenotype from the acclimated state back toward the unstressed state. Novel phenotypes were more rare, comprising between 5 and 18 % of informative phenotypic variation. Phenotypic variation associated statistically with genetic variation, demonstrating a genetic basis for phenotypic change. Finally, clones with rpoB mutations differed in phenotype from those with rho mutations, largely due to differences in chemical sensitivity. CONCLUSIONS Our results contribute to previous observations showing that a major component of adaptation in microbial evolution experiments is toward restoration to the unstressed state. In addition, we found that a large deletion strongly affected phenotypic variation. Finally, we demonstrated that the two genetic trajectories leading to thermal adaptation encompass different phenotypes.
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Affiliation(s)
- Shaun M Hug
- Department of Ecology and Evolutionary Biology, UC Irvine, 321 Steinhaus Hall, Irvine, CA, 92697, USA.
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, 321 Steinhaus Hall, Irvine, CA, 92697, USA.
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45
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When Too Much ATP Is Bad for Protein Synthesis. J Mol Biol 2015; 427:2586-2594. [PMID: 26150063 DOI: 10.1016/j.jmb.2015.06.021] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 06/30/2015] [Accepted: 06/30/2015] [Indexed: 01/17/2023]
Abstract
Adenosine triphosphate (ATP) is the energy currency of living cells. Even though ATP powers virtually all energy-dependent activities, most cellular ATP is utilized in protein synthesis via tRNA aminoacylation and guanosine triphosphate regeneration. Magnesium (Mg(2+)), the most common divalent cation in living cells, plays crucial roles in protein synthesis by maintaining the structure of ribosomes, participating in the biochemistry of translation initiation and functioning as a counterion for ATP. A non-physiological increase in ATP levels hinders growth in cells experiencing Mg(2+) limitation because ATP is the most abundant nucleotide triphosphate in the cell, and Mg(2+) is also required for the stabilization of the cytoplasmic membrane and as a cofactor for essential enzymes. We propose that organisms cope with Mg(2+) limitation by decreasing ATP levels and ribosome production, thereby reallocating Mg(2+) to indispensable cellular processes.
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Mellin JR, Cossart P. Unexpected versatility in bacterial riboswitches. Trends Genet 2015; 31:150-6. [PMID: 25708284 DOI: 10.1016/j.tig.2015.01.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 01/23/2015] [Accepted: 01/23/2015] [Indexed: 12/11/2022]
Abstract
Bacterial riboswitches are elements present in the 5'-untranslated regions (UTRs) of mRNA molecules that bind to ligands and regulate the expression of downstream genes. Riboswitches typically regulate the expression of protein-coding genes. However, mechanisms of riboswitch-mediated regulation have recently been shown to be more diverse than originally thought, with reports showing that riboswitches can regulate the expression of noncoding RNAs and control the access of proteins, such as transcription termination factor Rho and RNase E, to a nascent RNA. Riboswitches are also increasingly used in biotechnology, with advances in the engineering of synthetic riboswitches and the development of riboswitch-based sensors. In this review we address the emerging roles and mechanisms of riboswitch-mediated regulation in natura and recent progress in the development of riboswitch-based technology.
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Affiliation(s)
- J R Mellin
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, 75015 Paris, France; Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 604, 75015 Paris, France; Institut National de la Recherche Agronomique (INRA) Unité USC2020, 75015 Paris, France
| | - Pascale Cossart
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, 75015 Paris, France; Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 604, 75015 Paris, France; Institut National de la Recherche Agronomique (INRA) Unité USC2020, 75015 Paris, France.
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Gehring AM, Santangelo TJ. Manipulating archaeal systems to permit analyses of transcription elongation-termination decisions in vitro. Methods Mol Biol 2015; 1276:263-79. [PMID: 25665569 DOI: 10.1007/978-1-4939-2392-2_15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transcription elongation by multisubunit RNA polymerases (RNAPs) is processive, but neither uniform nor continuous. Regulatory events during elongation include pausing, backtracking, arrest, and transcription termination, and it is critical to determine whether the absence of continued synthesis is transient or permanent. Here we describe mechanisms to generate large quantities of stable archaeal elongation complexes on a solid support to permit (1) single-round transcription, (2) walking of RNAP to any defined template position, and (3) discrimination of transcripts that are associated with RNAP from those that are released to solution. This methodology is based on untagged proteins transcribing biotin- and digoxigenin-labeled DNA templates in association with paramagnetic particles.
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Affiliation(s)
- Alexandra M Gehring
- Department of Biochemistry and Molecular Biology, 383 MRB, Colorado State University, Fort Collins, CO, 80523, USA
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Windgassen TA, Mooney RA, Nayak D, Palangat M, Zhang J, Landick R. Trigger-helix folding pathway and SI3 mediate catalysis and hairpin-stabilized pausing by Escherichia coli RNA polymerase. Nucleic Acids Res 2014; 42:12707-21. [PMID: 25336618 PMCID: PMC4227799 DOI: 10.1093/nar/gku997] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The conformational dynamics of the polymorphous trigger loop (TL) in RNA polymerase (RNAP) underlie multiple steps in the nucleotide addition cycle and diverse regulatory mechanisms. These mechanisms include nascent RNA hairpin-stabilized pausing, which inhibits TL folding into the trigger helices (TH) required for rapid nucleotide addition. The nascent RNA pause hairpin forms in the RNA exit channel and promotes opening of the RNAP clamp domain, which in turn stabilizes a partially folded, paused TL conformation that disfavors TH formation. We report that inhibiting TH unfolding with a disulfide crosslink slowed multiround nucleotide addition only modestly but eliminated hairpin-stabilized pausing. Conversely, a substitution that disrupts the TH folding pathway and uncouples establishment of key TH–NTP contacts from complete TH formation and clamp movement allowed rapid catalysis and eliminated hairpin-stabilized pausing. We also report that the active-site distal arm of the TH aids TL folding, but that a 188-aa insertion in the Escherichia coli TL (sequence insertion 3; SI3) disfavors TH formation and stimulates pausing. The effect of SI3 depends on the jaw domain, but not on downstream duplex DNA. Our results support the view that both SI3 and the pause hairpin modulate TL folding in a constrained pathway of intermediate states.
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Affiliation(s)
- Tricia A Windgassen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Rachel Anne Mooney
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Dhananjaya Nayak
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Murali Palangat
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jinwei Zhang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, 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
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Closed for business: exit-channel coupling to active site conformation in bacterial RNA polymerase. Nat Struct Mol Biol 2014; 21:741-2. [DOI: 10.1038/nsmb.2883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Different tradeoffs result from alternate genetic adaptations to a common environment. Proc Natl Acad Sci U S A 2014; 111:12121-6. [PMID: 25092325 DOI: 10.1073/pnas.1406886111] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Fitness tradeoffs are often assumed by evolutionary theory, yet little is known about the frequency of fitness tradeoffs during stress adaptation. Even less is known about the genetic factors that confer these tradeoffs and whether alternative adaptive mutations yield contrasting tradeoff dynamics. We addressed these issues using 114 clones of Escherichia coli that were evolved independently for 2,000 generations under thermal stress (42.2 °C). For each clone, we measured their fitness relative to the ancestral clone at 37 °C and 20 °C. Tradeoffs were common at 37 °C but more prevalent at 20 °C, where 56% of clones were outperformed by the ancestor. We also characterized the upper and lower thermal boundaries of each clone. All clones shifted their upper boundary to at least 45 °C; roughly half increased their lower niche boundary concomitantly, representing a shift of thermal niche. The remaining clones expanded their thermal niche by increasing their upper limit without a commensurate increase of lower limit. We associated these niche dynamics with genotypes and confirmed associations by engineering single mutations in the rpoB gene, which encodes the beta subunit of RNA polymerase, and the rho gene, which encodes a termination factor. Single mutations in the rpoB gene exhibit antagonistic pleiotropy, with fitness tradeoffs at 18 °C and fitness benefits at 42.2 °C. In contrast, a mutation within the rho transcriptional terminator, which defines an alternative adaptive pathway from that of rpoB, had no demonstrable effect on fitness at 18 °C. This study suggests that two different genetic pathways toward high-temperature adaptation have contrasting effects with respect to thermal tradeoffs.
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