1
|
Warren Norris MAH, Plaskon DM, Tamayo R. Phase Variation of Flagella and Toxins in Clostridioides difficile is Mediated by Selective Rho-dependent Termination. J Mol Biol 2024; 436:168456. [PMID: 38278436 PMCID: PMC10942720 DOI: 10.1016/j.jmb.2024.168456] [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: 10/26/2023] [Revised: 01/16/2024] [Accepted: 01/20/2024] [Indexed: 01/28/2024]
Abstract
Clostridioides difficile is an intestinal pathogen that exhibits phase variation of flagella and toxins through inversion of the flagellar (flg) switch controlling flagellar and toxin gene expression. The transcription termination factor Rho preferentially inhibits swimming motility of bacteria with the 'flg-OFF' switch sequence. How C. difficile Rho mediates this selectivity was unknown. C. difficile Rho contains an N-terminal insertion domain (NID) which is found in a subset of Rho orthologues and confers diverse functions. Here we determined how Rho distinguishes between flg-ON and -OFF mRNAs and the roles of the NID and other domains of C. difficile Rho. Using in vitro ATPase assays, we determined that Rho specifically binds a region containing the left inverted repeat of the flg switch, but only of flg-OFF mRNA, indicating that differential termination is mediated by selective Rho binding. Using a suite of in vivo and in vitro assays in C. difficile, we determined that the NID is essential for Rho termination of flg-OFF mRNA, likely by influencing the ability to form stable hexamers, and the RNA binding domain is critical for flg-OFF specific termination. This work gives insight into the novel mechanism by which Rho interacts with flg mRNA to mediate phase variation of flagella and toxins in C. difficile and broadens our understanding of Rho-mediated termination in an organism with an AT-rich genome.
Collapse
Affiliation(s)
- Mercedes A H Warren Norris
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Dylan M Plaskon
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
| |
Collapse
|
2
|
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: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [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.
Collapse
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, USA
| | - 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
| |
Collapse
|
3
|
Cryo-EM structure of transcription termination factor Rho from Mycobacterium tuberculosis reveals bicyclomycin resistance mechanism. Commun Biol 2022; 5:120. [PMID: 35140348 PMCID: PMC8828861 DOI: 10.1038/s42003-022-03069-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/21/2022] [Indexed: 01/17/2023] Open
Abstract
The bacterial Rho factor is a ring-shaped motor triggering genome-wide transcription termination and R-loop dissociation. Rho is essential in many species, including in Mycobacterium tuberculosis where rho gene inactivation leads to rapid death. Yet, the M. tuberculosis Rho [MtbRho] factor displays poor NTPase and helicase activities, and resistance to the natural Rho inhibitor bicyclomycin [BCM] that remain unexplained. To address these issues, we solved the cryo-EM structure of MtbRho at 3.3 Å resolution. The MtbRho hexamer is poised into a pre-catalytic, open-ring state wherein specific contacts stabilize ATP in intersubunit ATPase pockets, thereby explaining the cofactor preference of MtbRho. We reveal a leucine-to-methionine substitution that creates a steric bulk in BCM binding cavities near the positions of ATP γ-phosphates, and confers resistance to BCM at the expense of motor efficiency. Our work contributes to explain the unusual features of MtbRho and provides a framework for future antibiotic development. Cryo-EM shows that M. tuberculosis Rho-factor adopts an open, ring-shaped hexamer conformation and a steric bulk in the cavity for bicyclomycin binding, which explains resistance to the antibiotic.
Collapse
|
4
|
Simon I, Delaleau M, Schwartz A, Boudvillain M. A Large Insertion Domain in the Rho Factor From a Low G + C, Gram-negative Bacterium is Critical for RNA Binding and Transcription Termination Activity. J Mol Biol 2021; 433:167060. [PMID: 34023400 DOI: 10.1016/j.jmb.2021.167060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/30/2021] [Accepted: 05/16/2021] [Indexed: 10/21/2022]
Abstract
Rho-dependent termination of transcription (RDTT) is a critical regulatory mechanism specific to bacteria. In a subset of species including most Actinobacteria and Bacteroidetes, the Rho factor contains a large, poorly conserved N-terminal insertion domain (NID) of cryptic function. To date, only two NID-bearing Rho factors from high G + C Actinobacteria have been thoroughly characterized. Both can trigger RDTT at promoter-proximal sites or with structurally constrained transcripts that are unsuitable for the archetypal, NID-less Rho factor of Escherichia coli (EcRho). Here, we provide the first biochemical characterization of a NID-bearing Rho factor from a low G + C bacterium. We show that Bacteroides fragilis Rho (BfRho) is a bona fide RNA-dependent NTPase motor able to unwind long RNA:DNA duplexes and to disrupt transcription complexes. The large NID (~40% of total mass) strongly increases BfRho affinity for RNA, is strictly required for RDTT, but does not promote RDTT at promoter-proximal sites or with a structurally constrained transcript. Furthermore, the NID does not preclude modulation of RDTT by transcription factors NusA and NusG or by the Rho inhibitor bicyclomycin. Although the NID contains a prion-like Q/N-rich motif, it does not spontaneously trigger formation of β-amyloids. Thus, despite its unusually large RNA binding domain, BfRho behaves more like the NID-less EcRho than NID-bearing counterparts from high G + C Actinobacteria. Our data highlight the evolutionary plasticity of Rho's N-terminal region and illustrate how RDTT is adapted to distinct genomic contents.
Collapse
Affiliation(s)
- Isabelle Simon
- Centre de Biophysique Moléculaire, CNRS UPR4301, Rue Charles Sadron, 45071 Orléans cedex 2, France; ED 549, Santé, Sciences Biologiques & Chimie du Vivant, Université d'Orléans, France
| | - Mildred Delaleau
- 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
| | - Marc Boudvillain
- Centre de Biophysique Moléculaire, CNRS UPR4301, Rue Charles Sadron, 45071 Orléans cedex 2, France.
| |
Collapse
|
5
|
Bossi L, Figueroa-Bossi N, Bouloc P, Boudvillain M. Regulatory interplay between small RNAs and transcription termination factor Rho. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194546. [PMID: 32217107 DOI: 10.1016/j.bbagrm.2020.194546] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/12/2020] [Accepted: 03/20/2020] [Indexed: 12/14/2022]
Abstract
The largest and best studied group of regulatory small RNAs (sRNAs) in bacteria act by modulating translation or turnover of messenger RNAs (mRNAs) through base-pairing interactions that typically take place near the 5' end of the mRNA. This allows the sRNA to bind the complementary target sequence while the remainder of the mRNA is still being made, creating conditions whereby the action of the sRNA can extend to transcriptional steps, most notably transcription termination. Increasing evidence corroborates the existence of a functional interplay between sRNAs and termination factor Rho. Two general mechanisms have emerged. One mechanism operates in translated regions subjected to sRNA repression. By inhibiting ribosome binding co-transcriptionally, the sRNA uncouples translation from transcription, allowing Rho to bind the nascent RNA and promote termination. In the second mechanism, which functions in 5' untranslated regions, the sRNA antagonizes termination directly by interfering with Rho binding to the RNA or the subsequent translocation along the RNA. Here, we review the above literature in the context of other mechanisms that underlie the participation of Rho-dependent transcription termination in gene regulation. This article is part of a Special Issue entitled: RNA and gene control in bacteria edited by Dr. M. Guillier and F. Repoila.
Collapse
Affiliation(s)
- Lionello Bossi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Nara Figueroa-Bossi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Philippe Bouloc
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Marc Boudvillain
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
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
| |
Collapse
|
8
|
D'Heygère F, Schwartz A, Coste F, Castaing B, Boudvillain M. ATP-dependent motor activity of the transcription termination factor Rho from Mycobacterium tuberculosis. Nucleic Acids Res 2015; 43:6099-111. [PMID: 25999346 PMCID: PMC4499133 DOI: 10.1093/nar/gkv505] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 05/04/2015] [Indexed: 11/13/2022] Open
Abstract
The bacterial transcription termination factor Rho-a ring-shaped molecular motor displaying directional, ATP-dependent RNA helicase/translocase activity-is an interesting therapeutic target. Recently, Rho from Mycobacterium tuberculosis (MtbRho) has been proposed to operate by a mechanism uncoupled from molecular motor action, suggesting that the manner used by Rho to dissociate transcriptional complexes is not conserved throughout the bacterial kingdom. Here, however, we demonstrate that MtbRho is a bona fide molecular motor and directional helicase which requires a catalytic site competent for ATP hydrolysis to disrupt RNA duplexes or transcription elongation complexes. Moreover, we show that idiosyncratic features of the MtbRho enzyme are conferred by a large, hydrophilic insertion in its N-terminal 'RNA binding' domain and by a non-canonical R-loop residue in its C-terminal 'motor' domain. We also show that the 'motor' domain of MtbRho has a low apparent affinity for the Rho inhibitor bicyclomycin, thereby contributing to explain why M. tuberculosis is resistant to this drug. Overall, our findings support that, in spite of adjustments of the Rho motor to specific traits of its hosting bacterium, the basic principles of Rho action are conserved across species and could thus constitute pertinent screening criteria in high-throughput searches of new Rho inhibitors.
Collapse
Affiliation(s)
- François D'Heygère
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France Ecole doctorale Santé, Sciences Biologiques et Chimie du Vivant (ED 549), Université d'Orléans, Orléans, France
| | - Annie Schwartz
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France
| | - Franck Coste
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France ITP Sciences Biologiques & Chimie du Vivant, Université d'Orléans, Orléans, France
| | - Marc Boudvillain
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France ITP Sciences Biologiques & Chimie du Vivant, Université d'Orléans, Orléans, France
| |
Collapse
|
9
|
Gocheva V, Le Gall A, Boudvillain M, Margeat E, Nollmann M. Direct observation of the translocation mechanism of transcription termination factor Rho. Nucleic Acids Res 2015; 43:2367-77. [PMID: 25662222 PMCID: PMC4344519 DOI: 10.1093/nar/gkv085] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Rho is a ring-shaped, ATP-fueled motor essential for remodeling transcriptional complexes and R-loops in bacteria. Despite years of research on this fundamental model helicase, key aspects of its mechanism of translocation remain largely unknown. Here, we used single-molecule manipulation and fluorescence methods to directly monitor the dynamics of RNA translocation by Rho. We show that the efficiency of Rho activation is strongly dependent on the force applied on the RNA but that, once active, Rho is able to translocate against a large opposing force (at least 7 pN) by a mechanism involving ‘tethered tracking’. Importantly, the ability to directly measure dynamics at the single-molecule level allowed us to determine essential motor properties of Rho. Hence, Rho translocates at a rate of ∼56 nt per second under our experimental conditions, which is 2–5 times faster than velocities measured for RNA polymerase under similar conditions. Moreover, the processivity of Rho (∼62 nt at a 7 pN opposing force) is large enough for Rho to reach termination sites without dissociating from its RNA loading site, potentially increasing the efficiency of transcription termination. Our findings unambiguously establish ‘tethered tracking’ as the main pathway for Rho translocation, support ‘kinetic coupling’ between Rho and RNA polymerase during Rho-dependent termination, and suggest that forces applied on the nascent RNA transcript by cellular substructures could have important implications for the regulation of transcription and its coupling to translation in vivo.
Collapse
Affiliation(s)
- Veronika Gocheva
- CNRS UMR5048, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090 Montpellier, France INSERM U554, 34090 Montpellier, France Universités Montpellier 1 et 2, 34090 Montpellier, France
| | - Antoine Le Gall
- CNRS UMR5048, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090 Montpellier, France INSERM U554, 34090 Montpellier, France Universités Montpellier 1 et 2, 34090 Montpellier, France
| | - Marc Boudvillain
- CNRS, Centre de Biophysique Moléculaire, rue Charles Sadron, 45071 Orléans, France ITP Sciences Biologiques & Chimie du Vivant, Université d'Orléans, France
| | - Emmanuel Margeat
- CNRS UMR5048, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090 Montpellier, France INSERM U554, 34090 Montpellier, France Universités Montpellier 1 et 2, 34090 Montpellier, France
| | - Marcelo Nollmann
- CNRS UMR5048, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090 Montpellier, France INSERM U554, 34090 Montpellier, France Universités Montpellier 1 et 2, 34090 Montpellier, France
| |
Collapse
|
10
|
D'Heygère F, Schwartz A, Coste F, Castaing B, Boudvillain M. Monitoring RNA unwinding by the transcription termination factor Rho from Mycobacterium tuberculosis. Methods Mol Biol 2015; 1259:293-311. [PMID: 25579593 DOI: 10.1007/978-1-4939-2214-7_18] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Transcription termination factor Rho is a ring-shaped, homo-hexamieric RNA translocase that dissociates transcription elongation complexes and transcriptional RNA-DNA duplexes (R-loops) in bacteria. The molecular mechanisms underlying these biological functions have been essentially studied with Rho enzymes from Escherichia coli or close Gram-negative relatives. However, phylo-divergent Rho factors may have distinct properties. Here, we describe methods for the preparation and in vitro characterization (ATPase and helicase activities) of the Rho factor from Mycobacterium tuberculosis, a specimen with uncharacteristic molecular and enzymatic features. These methods set the stage for future studies aimed at better defining the diversity of enzymatic properties of Rho across the bacterial kingdom.
Collapse
Affiliation(s)
- François D'Heygère
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique (CNRS), Rue Charles Sadron, 45071, Orléans, cedex 2, France
| | | | | | | | | |
Collapse
|
11
|
Mitra A, Misquitta R, Nagaraja V. Mycobacterium tuberculosis Rho is an NTPase with distinct kinetic properties and a novel RNA-binding subdomain. PLoS One 2014; 9:e107474. [PMID: 25229539 PMCID: PMC4167861 DOI: 10.1371/journal.pone.0107474] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 08/18/2014] [Indexed: 11/29/2022] Open
Abstract
Two mechanisms--factor independent and dependent termination--ensure the completion of RNA synthesis in eubacteria. Factor-dependent mechanism relies on the Rho protein to terminate transcription by interacting with RNA polymerase. Although well studied in Escherichia coli, the properties of the Rho homologs from most bacteria are not known. The rho gene is unusually large in genus Mycobacterium and other members of actinobacteria, having ∼150 additional residues towards the amino terminal end. We describe the distinct properties of Rho from Mycobacterium tuberculosis. It is an NTPase with a preference for purine nucleoside triphosphates with kinetic properties different from E. coli homolog and an ability to use various RNA substrates. The N-terminal subdomain of MtbRho can bind to RNA by itself, and appears to contribute to the interaction of the termination factor with RNAs. Furthermore, the interaction with RNA induces changes in conformation and oligomerization of MtbRho.
Collapse
Affiliation(s)
- Anirban Mitra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Rachel Misquitta
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| |
Collapse
|
12
|
D’Heygère F, Rabhi M, Boudvillain M. Phyletic distribution and conservation of the bacterial transcription termination factor Rho. Microbiology (Reading) 2013; 159:1423-1436. [DOI: 10.1099/mic.0.067462-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- François D’Heygère
- Ecole doctorale Santé, Sciences Biologiques et Chimie du Vivant (ED 549), Université d’Orléans, France
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France
| | - Makhlouf Rabhi
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France
| | - Marc Boudvillain
- ITP Sciences Biologiques et Chimie du Vivant, Université d’Orléans, France
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France
| |
Collapse
|
13
|
Rabhi M, Rahmouni AR, Boudvillain M. Transcription Termination Factor Rho: A Ring-Shaped RNA Helicase from Bacteria. RNA HELICASES 2010. [DOI: 10.1039/9781849732215-00243] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Makhlouf Rabhi
- Centre de Biophysique Moléculaire (UPR4301) CNRS rue Charles Sadron 45071 Orléans cedex 2 France
- Ecole doctorale Sciences et Technologies, Université d’Orléans France
| | - A. Rachid Rahmouni
- Centre de Biophysique Moléculaire (UPR4301) CNRS rue Charles Sadron 45071 Orléans cedex 2 France
| | - Marc Boudvillain
- Centre de Biophysique Moléculaire (UPR4301) CNRS rue Charles Sadron 45071 Orléans cedex 2 France
| |
Collapse
|
14
|
The Structure of RNA-Free Rho Termination Factor Indicates a Dynamic Mechanism of Transcript Capture. J Mol Biol 2010; 400:16-23. [DOI: 10.1016/j.jmb.2010.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 04/15/2010] [Accepted: 05/03/2010] [Indexed: 11/21/2022]
|
15
|
Haga S, Hirano Y, Murayama O, Millar BC, Moore JE, Matsuda M. Structural analysis and genetic variation of the 16S-23S rDNA internal spacer region from Micrococcus luteus strains. Lett Appl Microbiol 2003; 37:314-7. [PMID: 12969495 DOI: 10.1046/j.1472-765x.2003.01399.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS To clone and sequence the 16S-23S ribosomal DNA (rDNA) internal spacer region (ISR) from Micrococcus luteus. METHODS AND RESULTS The primer pair for 16S-23S rDNA ISR amplified a fragment of about 850 bp in length for two strains, JCM3347 and JCM3348 and a fragment of about 790 bp for a strain, ATCC9341. After sequencing the ISRs were identified by the comparison of the ISRs and the flanking regions of ISR. CONCLUSIONS Although the sequence difference of the ISR occurred at only one position between the two JCM strains, the highly variable length (440 and 370 bp) and sequence similarity (about 40%) were demonstrated between the ISRs of the two JCM strains and a ATCC strain. SIGNIFICANCE AND IMPACT OF THE STUDY A CCTCCT sequence was first detected at the 3'-end of the 16S rDNA of the three strains. Moreover, highly similar sequence to the 21-bp region containing a putative rRNA processing site was observed in the ISR of the three strains. Interestingly, no intercistronic tRNAs were demonstrated in the ISRs from the three strains.
Collapse
Affiliation(s)
- S Haga
- Laboratory of Molecular Biology, School of Environmental Health Sciences, Azabu University, Sagamihara, Japan
| | | | | | | | | | | |
Collapse
|
16
|
Ingham CJ. Characterisation of the enzymatic and RNA-binding properties of the Rhodobacter sphaeroides 2.4.1. Rho homologue. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1446:115-25. [PMID: 10395924 DOI: 10.1016/s0167-4781(99)00082-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The Escherichia coli Rho is a transcription termination factor with complex enzymatic properties. Rho is a near-universal prokaryotic transcription factor, but very few non-enteric Rho factors have been studied. The expression and enzymatic activity of Rho from the GC-rich, Gram-negative bacterium Rhodobacter sphaeroides was characterised. Poly(C)-activated ATP hydrolysis, multimerisation and the abundance of the R. sphaeroides Rho were similar to the E. coli Rho. The R. sphaeroides Rho was a DNA:RNA helicase. The R. sphaeroides Rho was unique in Rho factors characterised to date in that it did not interact with the lambdatR1 terminator transcript and ATP hydrolysis was unusually weakly activated by poly(U) RNA. A chimeric Rho (RhoER), with the RNA-binding domain from the E. coli Rho and the ATPase domain of the R. sphaeroides Rho, was activated by RNA co-factors in a similar fashion to the E. coli Rho. The activity of RhoER suggests functional interactions between the N- and C-terminal domains of Rho monomers are highly conserved between Rho factors. The main differences between Rho factors from different bacteria is in the specificity of RNA binding although this does not appear to be necessarily dependent on the GC bias of target RNA as has been previously suggested.
Collapse
Affiliation(s)
- C J Ingham
- School of Biological Sciences, University Park, Nottingham University, Nottingham, NG7 2RD, UK.
| |
Collapse
|
17
|
Burns CM, Nowatzke WL, Richardson JP. Activation of Rho-dependent transcription termination by NusG. Dependence on terminator location and acceleration of RNA release. J Biol Chem 1999; 274:5245-51. [PMID: 9988775 DOI: 10.1074/jbc.274.8.5245] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
There is a kinetic limitation to Rho function at the first intragenic terminator in the lacZ gene (tiZ1) which can be overcome by NusG: Rho can terminate transcription with slowly moving, but not rapidly moving, RNA polymerase unless NusG is also present. Here we report further studies with two other Rho-dependent terminators that are not kinetically limited (tiZ2 and lambda tR1) which show that the requirement for NusG depends on the properties of the terminator and its location in the transcription unit. NusG is also shown to increase the rate of Rho-mediated dissociation of transcription complexes arrested at a specific termination stop point in the tiZ1 region and the rates of dissociation with three different Rho factors and two different terminators correlated with their sensitivity to RNA polymerase elongation kinetics. These results suggest a model of NusG function which involves an alteration in the susceptibility of the transcription complex to Rho action which allows termination to occur within the short kinetic window when RNA polymerase is traversing the termination region.
Collapse
Affiliation(s)
- C M Burns
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | | | | |
Collapse
|
18
|
Ingham CJ, Dennis J, Furneaux PA. Autogenous regulation of transcription termination factor Rho and the requirement for Nus factors in Bacillus subtilis. Mol Microbiol 1999; 31:651-63. [PMID: 10027981 DOI: 10.1046/j.1365-2958.1999.01205.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The expression and activity of transcription termination factor Rho and the requirement for transcription elongation factors NusA and NusG was investigated in Bacillus subtilis. Rho was present at < 5% of the level found in Escherichia coli, but Rho factors from these two bacteria had similar properties as RNA-activated ATPases and in vitro termination of transcription on the lambda tR1 terminator. The B. subtilis rho gene was autoregulated at the level of transcription; autoregulation required sequences within the rho mRNA leader region and gene. To date, the B. subtilis rho is the only gene from a Gram-positive bacterium found to be regulated by Rho. Rho was not involved in bulk mRNA decay in B. subtilis. The E. coli elongation factors NusA and NusG target Rho, and the importance of these proteins in B. subtilis was examined by gene disruption. The B. subtilis NusG was inessential for both the viability and the autoregulation of Rho, whereas NusA was essential, and the requirement for NusA was independent of Rho. This contrasts with E. coli in which NusG is essential but NusA becomes dispensable if Rho terminates transcription less efficiently.
Collapse
Affiliation(s)
- C J Ingham
- School of Biological Sciences, Nottingham University, UK.
| | | | | |
Collapse
|
19
|
Allison TJ, Wood TC, Briercheck DM, Rastinejad F, Richardson JP, Rule GS. Crystal structure of the RNA-binding domain from transcription termination factor rho. NATURE STRUCTURAL BIOLOGY 1998; 5:352-6. [PMID: 9586995 DOI: 10.1038/nsb0598-352] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Transcription termination factor rho is an ATP-dependent hexameric helicase found in most eubacterial species. The Escherichia coli rho monomer consists of two domains, an RNA-binding domain (residues 1-130) and an ATPase domain (residues 131-419). The ATPase domain is homologous to the beta subunit of F1-ATPase. Here, we report that the crystal structure of the RNA-binding domain of rho (rho130) at 1.55 A confirms that rho130 contains the oligosaccharide/oligonucleotide-binding (OB) fold, a five stranded beta-barrel. The beta-barrel of rho130 is also surprisingly similar to the N-terminal beta-barrel of F1 ATPase, extending the applicability of F1 ATPase as a structural model for hexameric rho.
Collapse
|
20
|
Nowatzke WL, Keller E, Koch G, Richardson JP. Transcription termination factor Rho is essential for Micrococcus luteus. J Bacteriol 1997; 179:5238-40. [PMID: 9260971 PMCID: PMC179387 DOI: 10.1128/jb.179.16.5238-5240.1997] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The growth of Micrococcus luteus, a soil microorganism that belongs to the high-G+C gram-positive phylogenetic group, is prevented by bicyclomycin, an antibiotic that inhibits the activity of the M. luteus transcription termination factor Rho. A mutant that can grow in 0.3 mM bicyclomycin has a Rho that is insensitive to bicyclomycin and has the single amino acid residue change of Asp474 to Gly. These results indicate that the function of its Rho factor is essential for M. luteus and that growth of a gram-positive organism can be blocked by bicyclomycin.
Collapse
Affiliation(s)
- W L Nowatzke
- Department of Chemistry, Indiana University, Bloomington 47405, USA
| | | | | | | |
Collapse
|