1
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Bose D, Singh RK, Robertson ES. KSHV-encoded LANA bypasses transcriptional block through the stabilization of RNA Pol II in hypoxia. mBio 2024; 15:e0277423. [PMID: 38095447 PMCID: PMC10790784 DOI: 10.1128/mbio.02774-23] [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: 10/13/2023] [Accepted: 11/07/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Hypoxia can induce the reactivation of Kaposi sarcoma-associated virus (KSHV), which necessitates the synthesis of critical structural proteins. Despite the unfavorable energetic conditions of hypoxia, KSHV utilizes mechanisms to prevent the degradation of essential cellular machinery required for successful reactivation. Our study provides new insights on strategies employed by KSHV-infected cells to maintain steady-state transcription by overcoming hypoxia-mediated metabolic stress to enable successful reactivation. Our discovery that the interaction of latency-associated nuclear antigen with HIF1α and NEDD4 inhibits its polyubiquitination activity, which blocks the degradation of RNA Pol II during hypoxia, is a significant contribution to our understanding of KSHV biology. This newfound knowledge provides new leads in the development of novel therapies for KSHV-associated diseases.
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Affiliation(s)
- Dipayan Bose
- Tumor Virology Program, Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rajnish Kumar Singh
- Tumor Virology Program, Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Erle S. Robertson
- Tumor Virology Program, Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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2
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Felgines L, Rymen B, Martins LM, Xu G, Matteoli C, Himber C, Zhou M, Eis J, Coruh C, Böhrer M, Kuhn L, Chicher J, Pandey V, Hammann P, Wohlschlegel J, Waltz F, Law JA, Blevins T. CLSY docking to Pol IV requires a conserved domain critical for small RNA biogenesis and transposon silencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.26.573199. [PMID: 38234754 PMCID: PMC10793415 DOI: 10.1101/2023.12.26.573199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Eukaryotes must balance the need for gene transcription by RNA polymerase II (Pol II) against the danger of mutations caused by transposable element (TE) proliferation. In plants, these gene expression and TE silencing activities are divided between different RNA polymerases. Specifically, RNA polymerase IV (Pol IV), which evolved from Pol II, transcribes TEs to generate small interfering RNAs (siRNAs) that guide DNA methylation and block TE transcription by Pol II. While the Pol IV complex is recruited to TEs via SNF2-like CLASSY (CLSY) proteins, how Pol IV partners with the CLSYs remains unknown. Here we identified a conserved CYC-YPMF motif that is specific to Pol IV and is positioned on the complex exterior. Furthermore, we found that this motif is essential for the co-purification of all four CLSYs with Pol IV, but that only one CLSY is present in any given Pol IV complex. These findings support a "one CLSY per Pol IV" model where the CYC-YPMF motif acts as a CLSY-docking site. Indeed, mutations in and around this motif phenocopy pol iv null mutants. Together, these findings provide structural and functional insights into a critical protein feature that distinguishes Pol IV from other RNA polymerases, allowing it to promote genome stability by targeting TEs for silencing.
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3
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Choudhury A, Gachet B, Dixit Z, Faure R, Gill RT, Tenaillon O. Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs. Nat Commun 2023; 14:6319. [PMID: 37813857 PMCID: PMC10562459 DOI: 10.1038/s41467-023-41882-7] [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: 02/23/2023] [Accepted: 09/21/2023] [Indexed: 10/11/2023] Open
Abstract
RNA polymerase (RNAP) is emblematic of complex biological systems that control multiple traits involving trade-offs such as growth versus maintenance. Laboratory evolution has revealed that mutations in RNAP subunits, including RpoB, are frequently selected. However, we lack a systems view of how mutations alter the RNAP molecular functions to promote adaptation. We, therefore, measured the fitness of thousands of mutations within a region of rpoB under multiple conditions and genetic backgrounds, to find that adaptive mutations cluster in two modules. Mutations in one module favor growth over maintenance through a partial loss of an interaction associated with faster elongation. Mutations in the other favor maintenance over growth through a destabilized RNAP-DNA complex. The two molecular handles capture the versatile RNAP-mediated adaptations. Combining both interaction losses simultaneously improved maintenance and growth, challenging the idea that growth-maintenance tradeoff resorts only from limited resources, and revealing how compensatory evolution operates within RNAP.
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Affiliation(s)
- Alaksh Choudhury
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France.
- Laboratoire Biophysique et Évolution (LBE), UMR Chimie Biologie Innovation 8231, ESPCI Paris, Université PSL, CNRS, 75005, Paris, France.
| | - Benoit Gachet
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France
| | - Zoya Dixit
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France
- Université de Paris Cité, INSERM, CNRS, Institut Cochin, UMR 1016, 75014, Paris, France
| | - Roland Faure
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France
- Université de Rennes, INRIA RBA, CNRS UMR 6074, Rennes, France
- Service Evolution Biologique et Ecologie, Université libre de Bruxelles (ULB), 1050, Brussels, Belgium
| | - Ryan T Gill
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado-Boulder, Boulder, CO, 80309-0027, USA
- Novo Nordisk Foundation, Denmark Technical University, 2800 Kgs, Lyngby, Denmark
| | - Olivier Tenaillon
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France.
- Université de Paris Cité, INSERM, CNRS, Institut Cochin, UMR 1016, 75014, Paris, France.
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4
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Woodgate J, Zenkin N. Transcription-translation coupling: Recent advances and future perspectives. Mol Microbiol 2023; 120:539-546. [PMID: 37856403 PMCID: PMC10953045 DOI: 10.1111/mmi.15076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/01/2023] [Accepted: 05/05/2023] [Indexed: 10/21/2023]
Abstract
The flow of genetic information from the chromosome to protein in all living organisms consists of two steps: (1) copying information coded in DNA into an mRNA intermediate via transcription by RNA polymerase, followed by (2) translation of this mRNA into a polypeptide by the ribosome. Unlike eukaryotes, where transcription and translation are separated by a nuclear envelope, in bacterial cells, these two processes occur within the same compartment. This means that a pioneering ribosome starts translation on nascent mRNA that is still being actively transcribed by RNA polymerase. This tethering via mRNA is referred to as 'coupling' of transcription and translation (CTT). CTT raises many questions regarding physical interactions and potential mutual regulation between these large (ribosome is ~2.5 MDa and RNA polymerase is 0.5 MDa) and powerful molecular machines. Accordingly, we will discuss some recently discovered structural and functional aspects of CTT.
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Affiliation(s)
- Jason Woodgate
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUK
| | - Nikolay Zenkin
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUK
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5
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Calil Brondani J, Afful D, Nune H, Hart J, Cook S, Momany C. Overproduction, purification, and transcriptional activity of recombinant Acinetobacter baylyi ADP1 RNA polymerase holoenzyme. Protein Expr Purif 2023; 206:106254. [PMID: 36804950 DOI: 10.1016/j.pep.2023.106254] [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: 01/05/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023]
Abstract
Acinetobacter baylyi is an interesting model organism to investigate bacterial metabolism due to its vast repertoire of metabolic enzymes and ease of genetic manipulation. However, the study of gene expression in vitro is dependent on the availability of its RNA polymerase (RNAp), an essential enzyme in transcription. In this work, we developed a convenient method of producing the recombinant A. baylyi ADP1 RNA polymerase holoenzyme (RNApholo) in E. coli that yields 22 mg of a >96% purity protein from a 1-liter shake flask culture. We further characterized the A. baylyi ADP1 RNApholo kinetic profile using T7 Phage DNA as template and demonstrated that it is a highly transcriptionally active enzyme with an elongation rate of 24 nt/s and a termination efficiency of 94%. Moreover, the A. baylyi ADP1 RNApholo has a substantial sequence identity (∼95%) with the RNApholo from the human pathogen Acinetobacter baumannii. This protein can serve as a source of material for structural and biological studies towards advancing our understanding of genome expression and regulation in Acinetobacter species.
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Affiliation(s)
- Juliana Calil Brondani
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Derrick Afful
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Hanna Nune
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Jesse Hart
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Shelby Cook
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Cory Momany
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA.
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6
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Li X, Chou T. Stochastic dynamics and ribosome-RNAP interactions in transcription-translation coupling. Biophys J 2023; 122:254-266. [PMID: 36199250 PMCID: PMC9822797 DOI: 10.1016/j.bpj.2022.09.041] [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: 06/23/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 01/11/2023] Open
Abstract
Under certain cellular conditions, transcription and mRNA translation in prokaryotes appear to be "coupled," in which the formation of mRNA transcript and production of its associated protein are temporally correlated. Such transcription-translation coupling (TTC) has been evoked as a mechanism that speeds up the overall process, provides protection against premature termination, and/or regulates the timing of transcript and protein formation. What molecular mechanisms underlie ribosome-RNAP coupling and how they can perform these functions have not been explicitly modeled. We develop and analyze a continuous-time stochastic model that incorporates ribosome and RNAP elongation rates, initiation and termination rates, RNAP pausing, and direct ribosome and RNAP interactions (exclusion and binding). Our model predicts how distributions of delay times depend on these molecular features of transcription and translation. We also propose additional measures for TTC: a direct ribosome-RNAP binding probability and the fraction of time the translation-transcription process is "protected" from attack by transcription-terminating proteins. These metrics quantify different aspects of TTC and differentially depend on parameters of known molecular processes. We use our metrics to reveal how and when our model can exhibit either acceleration or deceleration of transcription, as well as protection from termination. Our detailed mechanistic model provides a basis for designing new experimental assays that can better elucidate the mechanisms of TTC.
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Affiliation(s)
- Xiangting Li
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, California
| | - Tom Chou
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, California; Department of Mathematics, University of California, Los Angeles, Los Angeles, California.
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7
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Unarta IC, Goonetilleke EC, Wang D, Huang X. Nucleotide addition and cleavage by RNA polymerase II: Coordination of two catalytic reactions using a single active site. J Biol Chem 2022; 299:102844. [PMID: 36581202 PMCID: PMC9860460 DOI: 10.1016/j.jbc.2022.102844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
RNA polymerase II (Pol II) incorporates complementary ribonucleotides into the growing RNA chain one at a time via the nucleotide addition cycle. The nucleotide addition cycle, however, is prone to misincorporation of noncomplementary nucleotides. Thus, to ensure transcriptional fidelity, Pol II backtracks and then cleaves the misincorporated nucleotides. These two reverse reactions, nucleotide addition and cleavage, are catalyzed in the same active site of Pol II, which is different from DNA polymerases or other endonucleases. Recently, substantial progress has been made to understand how Pol II effectively performs its dual role in the same active site. Our review highlights these recent studies and provides an overall model of the catalytic mechanisms of Pol II. In particular, RNA extension follows the two-metal-ion mechanism, and several Pol II residues play important roles to facilitate the catalysis. In sharp contrast, the cleavage reaction is independent of any Pol II residues. Interestingly, Pol II relies on its residues to recognize the misincorporated nucleotides during the backtracking process, prior to cleavage. In this way, Pol II efficiently compartmentalizes its two distinct catalytic functions using the same active site. Lastly, we also discuss a new perspective on the potential third Mg2+ in the nucleotide addition and intrinsic cleavage reactions.
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Affiliation(s)
- Ilona Christy Unarta
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Eshani C Goonetilleke
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Dong Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA; Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA.
| | - Xuhui Huang
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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8
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Stephanie F, Tambunan USF, Siahaan TJ. M. tuberculosis Transcription Machinery: A Review on the Mycobacterial RNA Polymerase and Drug Discovery Efforts. Life (Basel) 2022; 12:1774. [PMID: 36362929 PMCID: PMC9695777 DOI: 10.3390/life12111774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/24/2022] [Accepted: 11/01/2022] [Indexed: 09/08/2023] Open
Abstract
Mycobacterium tuberculosis (MTB) is the main source of tuberculosis (TB), one of the oldest known diseases in the human population. Despite the drug discovery efforts of past decades, TB is still one of the leading causes of mortality and claimed more than 1.5 million lives worldwide in 2020. Due to the emergence of drug-resistant strains and patient non-compliance during treatments, there is a pressing need to find alternative therapeutic agents for TB. One of the important areas for developing new treatments is in the inhibition of the transcription step of gene expression; it is the first step to synthesize a copy of the genetic material in the form of mRNA. This further translates to functional protein synthesis, which is crucial for the bacteria living processes. MTB contains a bacterial DNA-dependent RNA polymerase (RNAP), which is the key enzyme for the transcription process. MTB RNAP has been targeted for designing and developing antitubercular agents because gene transcription is essential for the mycobacteria survival. Initiation, elongation, and termination are the three important sequential steps in the transcription process. Each step is complex and highly regulated, involving multiple transcription factors. This review is focused on the MTB transcription machinery, especially in the nature of MTB RNAP as the main enzyme that is regulated by transcription factors. The mechanism and conformational dynamics that occur during transcription are discussed and summarized. Finally, the current progress on MTB transcription inhibition and possible drug target in mycobacterial RNAP are also described to provide insight for future antitubercular drug design and development.
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Affiliation(s)
- Filia Stephanie
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Usman Sumo Friend Tambunan
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Teruna J. Siahaan
- Department of Pharmaceutical Chemistry, School of Pharmacy, The University of Kansas, Lawrence, KS 66045, USA
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9
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Johnson RS, Strausbauch M, McCloud C. An NTP-driven mechanism for the nucleotide addition cycle of Escherichia coli RNA polymerase during transcription. PLoS One 2022; 17:e0273746. [PMID: 36282801 PMCID: PMC9595533 DOI: 10.1371/journal.pone.0273746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/15/2022] [Indexed: 11/06/2022] Open
Abstract
The elementary steps of transcription as catalyzed by E. coli RNA polymerase during one and two rounds of the nucleotide addition cycle (NAC) were resolved in rapid kinetic studies. Modelling of stopped-flow kinetic data of pyrophosphate release in a coupled enzyme assay during one round of the NAC indicates that the rate of pyrophosphate release is significantly less than that for nucleotide incorporation. Upon modelling of the stopped-flow kinetic data for pyrophosphate release during two rounds of the NAC, it was observed that the presence of the next nucleotide for incorporation increases the rate of release of the first pyrophosphate equivalent; incorrect nucleotides for incorporation had no effect on the rate of pyrophosphate release. Although the next nucleotide for incorporation increases the rate of pyrophosphate release, it is still significantly less than the rate of incorporation of the first nucleotide. The results from the stopped-flow kinetic studies were confirmed by using quench-flow followed by thin-layer chromatography (QF-TLC) with only the first nucleotide for incorporation labeled on the gamma phosphate with 32P to monitor pyrophosphate release. Collectively, the results are consistent with an NTP-driven model for the NAC in which the binding of the next cognate nucleotide for incorporation causes a synergistic conformational change in the enzyme that triggers the more rapid release of pyrophosphate, translocation of the enzyme along the DNA template strand and nucleotide incorporation.
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Affiliation(s)
- Ronald S. Johnson
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
- * E-mail:
| | - Mark Strausbauch
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Christopher McCloud
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
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10
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McLean EK, Nye TM, Lowder FC, Simmons LA. The Impact of RNA-DNA Hybrids on Genome Integrity in Bacteria. Annu Rev Microbiol 2022; 76:461-480. [PMID: 35655343 PMCID: PMC9527769 DOI: 10.1146/annurev-micro-102521-014450] [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] [Indexed: 09/10/2023]
Abstract
During the essential processes of DNA replication and transcription, RNA-DNA hybrid intermediates are formed that pose significant risks to genome integrity when left unresolved. To manage RNA-DNA hybrids, all cells rely on RNase H family enzymes that specifically cleave the RNA portion of the many different types of hybrids that form in vivo. Recent experimental advances have provided new insight into how RNA-DNA hybrids form and the consequences to genome integrity that ensue when persistent hybrids remain unresolved. Here we review the types of RNA-DNA hybrids, including R-loops, RNA primers, and ribonucleotide misincorporations, that form during DNA replication and transcription and discuss how each type of hybrid can contribute to genome instability in bacteria. Further, we discuss how bacterial RNase HI, HII, and HIII and bacterial FEN enzymes contribute to genome maintenance through the resolution of hybrids.
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Affiliation(s)
- Emma K McLean
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA;
| | - Taylor M Nye
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA;
- Current affiliation: Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Frances C Lowder
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA;
| | - Lyle A Simmons
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA;
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11
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Kirsch SH, Haeckl FPJ, Müller R. Beyond the approved: target sites and inhibitors of bacterial RNA polymerase from bacteria and fungi. Nat Prod Rep 2022; 39:1226-1263. [PMID: 35507039 DOI: 10.1039/d1np00067e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: 2016 to 2022RNA polymerase (RNAP) is the central enzyme in bacterial gene expression representing an attractive and validated target for antibiotics. Two well-known and clinically approved classes of natural product RNAP inhibitors are the rifamycins and the fidaxomycins. Rifampicin (Rif), a semi-synthetic derivative of rifamycin, plays a crucial role as a first line antibiotic in the treatment of tuberculosis and a broad range of bacterial infections. However, more and more pathogens such as Mycobacterium tuberculosis develop resistance, not only against Rif and other RNAP inhibitors. To overcome this problem, novel RNAP inhibitors exhibiting different target sites are urgently needed. This review includes recent developments published between 2016 and today. Particular focus is placed on novel findings concerning already known bacterial RNAP inhibitors, the characterization and development of new compounds isolated from bacteria and fungi, and providing brief insights into promising new synthetic compounds.
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Affiliation(s)
- Susanne H Kirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - F P Jake Haeckl
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.,Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
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12
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Ni H, Kwan-wai Chan B, Cheng Q, Chen K, Xie M, Wang H, Wai-chi Chan E, Chen S. A novel clinical therapy to combat infections caused by Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae. J Infect 2022; 85:174-211. [DOI: 10.1016/j.jinf.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/29/2022]
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13
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Ragab A, Ammar YA, Ezzat A, Mahmoud AM, Mohamed MBI, El-Tabl AS, Farag RS. Synthesis, characterization, thermal properties, antimicrobial evaluation, ADMET study, and molecular docking simulation of new mono Cu (II) and Zn (II) complexes with 2-oxoindole derivatives. Comput Biol Med 2022; 145:105473. [PMID: 35395516 DOI: 10.1016/j.compbiomed.2022.105473] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/10/2022] [Accepted: 03/29/2022] [Indexed: 12/14/2022]
Abstract
One of the interesting research fields is developing and assessing novel metal-containing medications. A new isatin-3-thiosemicarbazone derivative 4 was synthesized by two different methods based on hydrazone derivatives 2 and 3. Additionally, the chelation of thiosemicarbazone with copper (II) and zinc (II) forms a monobasic tridentate (ONS) complex with two five-member rings and a tetrahedral geometry structure. The structure of synthesized complexes was characterized using elemental analysis, FT-IR, mass spectra, and 1H/13C NMR. Thermogravimetric analysis revealed the upgrading of the thermal stability of metal complexes compared to their thiosemicarbazone ligand. The stoichiometric ratio of the coordination confirmed the formation of 1:1 (M: L) stoichiometry. In vitro antimicrobial activity was screened against two gram-positive, two gram-negative, and one fungal strain. Both ligand 4 and Zn complex 6 displayed high antimicrobial activity compared with copper complex 5 based on the zone of inhibition. Further, MIC and MBC were determined for both zinc and ligand. The zinc complex 6 displayed excellent antimicrobial activity with (MIC = 3.9-27.77 μg/mL) against bacterial strains and (MIC = 7.81 μg/mL) against C. albicans, as well as exhibited MBC values ranging between (MBC = 6.51-45.58 μg/mL) and (MFC = 13.58 μg/mL), respectively, and demonstrated bactericidal and fungicidal behavior. The in-silico ADMET study for ligand and two complexes were determined and showed non-AMES toxicity, non-carcinogenic, and obey the rule of five. A comparative docking study provided more insight into the binding mechanisms and suggested that antimicrobial activity may be due to inhibition of different targets.
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Affiliation(s)
- Ahmed Ragab
- Department of Chemistry, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo, 11884, Egypt.
| | - Yousry A Ammar
- Department of Chemistry, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo, 11884, Egypt
| | - Ahmed Ezzat
- Department of Chemistry, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo, 11884, Egypt
| | - Ammar M Mahmoud
- Department of Chemistry, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo, 11884, Egypt
| | - Mahmoud Basseem I Mohamed
- Department of Chemistry, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo, 11884, Egypt
| | - Abdou S El-Tabl
- Department of Chemistry, Faculty of Science, El-Menoufia University, Shebin El-Kom, Egypt
| | - Rabie S Farag
- Department of Chemistry, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo, 11884, Egypt
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14
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Benda M, Woelfel S, Faßhauer P, Gunka K, Klumpp S, Poehlein A, Kálalová D, Šanderová H, Daniel R, Krásný L, Stülke J. Quasi-essentiality of RNase Y in Bacillus subtilis is caused by its critical role in the control of mRNA homeostasis. Nucleic Acids Res 2021; 49:7088-7102. [PMID: 34157109 PMCID: PMC8266666 DOI: 10.1093/nar/gkab528] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 05/28/2021] [Accepted: 06/08/2021] [Indexed: 01/18/2023] Open
Abstract
RNA turnover is essential in all domains of life. The endonuclease RNase Y (rny) is one of the key components involved in RNA metabolism of the model organism Bacillus subtilis. Essentiality of RNase Y has been a matter of discussion, since deletion of the rny gene is possible, but leads to severe phenotypic effects. In this work, we demonstrate that the rny mutant strain rapidly evolves suppressor mutations to at least partially alleviate these defects. All suppressor mutants had acquired a duplication of an about 60 kb long genomic region encompassing genes for all three core subunits of the RNA polymerase—α, β, β′. When the duplication of the RNA polymerase genes was prevented by relocation of the rpoA gene in the B. subtilis genome, all suppressor mutants carried distinct single point mutations in evolutionary conserved regions of genes coding either for the β or β’ subunits of the RNA polymerase that were not tolerated by wild type bacteria. In vitro transcription assays with the mutated polymerase variants showed a severe decrease in transcription efficiency. Altogether, our results suggest a tight cooperation between RNase Y and the RNA polymerase to establish an optimal RNA homeostasis in B. subtilis cells.
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Affiliation(s)
- Martin Benda
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Simon Woelfel
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Patrick Faßhauer
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Katrin Gunka
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Stefan Klumpp
- Institute for the Dynamics of Complex Systems, Georg-August-University Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Debora Kálalová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Šanderová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jörg Stülke
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
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15
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Bokolia NP, Khan IA. Regulation of polyphosphate glucokinase gene expression through co-transcriptional processing in Mycobacterium tuberculosis H37Rv. J Biochem 2021; 170:593-609. [PMID: 34247237 DOI: 10.1093/jb/mvab080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/01/2021] [Indexed: 11/14/2022] Open
Abstract
Transcription is a molecular process that involves the synthesis of RNA chain into the 5'-3' direction, and simultaneously nascent RNA chain tends to form geometric structures, known as co-transcriptional folding. This folding determines the functional properties of RNA molecules and possibly has a critical role during the synthesis. This functioning includes the characterized properties of riboswitches and ribozymes, which are significant when the transcription rate is comparable to the cellular environment. This study reports a novel non-coding region important in the genetic expression of polyphosphate glucokinase (ppgk) in Mycobacterium tuberculosis. This non-coding element of ppgk gene undergoes cleavage activity during the transcriptional process in Mycobacterium tuberculosis. We revealed that cleavage occurs within the nascent RNA, and the resultant cleaved 3'RNA fragment carries the Shine- Dalgarno (SD) sequence and expression platform. We concluded co-transcriptional processing at the non-coding region as the required mechanism for ppgk expression that remains constitutive within the bacterial environment. This study defines the molecular mechanism dependent on the transient but highly active structural features of the nascent RNA.
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Affiliation(s)
- Naveen Prakash Bokolia
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Inshad Ali Khan
- Department of Microbiology, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India
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16
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Elghondakly A, Wu CH, Klupt S, Goodson J, Winkler WC. A NusG Specialized Paralog That Exhibits Specific, High-Affinity RNA-Binding Activity. J Mol Biol 2021; 433:167100. [PMID: 34119489 DOI: 10.1016/j.jmb.2021.167100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/17/2021] [Accepted: 06/05/2021] [Indexed: 10/21/2022]
Abstract
Bacterial NusG associates with RNA polymerase (RNAP) through its N-terminal domain, while the C-terminal domain (CTD) forms dynamic interactions with Rho, S10, NusB and NusA to affect transcription elongation. While virtually all bacteria encode for a core NusG, many also synthesize paralogs that transiently bind RNAP to alter expression of targeted genes. Yet, despite the importance of the genes they regulate, most of the subfamilies of NusG paralogs (e.g., UpxY, TaA, ActX and LoaP) have not been investigated in depth. Herein, we discover that LoaP requires a small RNA hairpin located within the 5' leader region of its targeted operons. LoaP binds the RNA element with nanomolar affinity and high specificity, in contrast to other NusG proteins, which have not been shown to exhibit RNA-binding activity. These data reveal a sequence feature that can be used to identify LoaP-regulated operons. This discovery also expands the repertoire of macromolecular interactions exhibited by the NusG CTD during transcription elongation to include an RNA ligand.
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Affiliation(s)
- Amr Elghondakly
- The University of Maryland, Department of Chemistry and Biochemistry, College Park, MD, United States
| | - Chih Hao Wu
- The University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD, United States
| | - Steven Klupt
- The University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD, United States
| | - Jonathan Goodson
- The University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD, United States
| | - Wade C Winkler
- The University of Maryland, Department of Chemistry and Biochemistry, College Park, MD, United States; The University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD, United States.
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17
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Lang KS, Merrikh H. Topological stress is responsible for the detrimental outcomes of head-on replication-transcription conflicts. Cell Rep 2021; 34:108797. [PMID: 33657379 PMCID: PMC7986047 DOI: 10.1016/j.celrep.2021.108797] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/14/2020] [Accepted: 02/05/2021] [Indexed: 12/18/2022] Open
Abstract
Conflicts between the replication and transcription machineries have profound effects on chromosome duplication, genome organization, and evolution across species. Head-on conflicts (lagging-strand genes) are significantly more detrimental than codirectional conflicts (leading-strand genes). The fundamental reason for this difference is unknown. Here, we report that topological stress significantly contributes to this difference. We find that head-on, but not codirectional, conflict resolution requires the relaxation of positive supercoils by the type II topoisomerases DNA gyrase and Topo IV, at least in the Gram-positive model bacterium Bacillus subtilis. Interestingly, our data suggest that after positive supercoil resolution, gyrase introduces excessive negative supercoils at head-on conflict regions, driving pervasive R-loop formation. Altogether, our results reveal a fundamental mechanistic difference between the two types of encounters, addressing a long-standing question in the field of replication-transcription conflicts. Lang and Merrikh show that resolution of head-on, but not codirectional, conflicts between replication and transcription machineries requires type II topoisomerases, suggesting that a fundamental difference between the two types of conflicts is supercoil buildup in DNA. Furthermore, they show that supercoil resolution at head-on conflict regions drives R-loop formation.
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Affiliation(s)
- Kevin S Lang
- Department of Biochemistry, Light Hall, Vanderbilt University, Nashville, TN, USA
| | - Houra Merrikh
- Department of Biochemistry, Light Hall, Vanderbilt University, Nashville, TN, USA.
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18
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Arba M, Wahyudi ST, Brunt DJ, Paradis N, Wu C. Mechanistic insight on the remdesivir binding to RNA-Dependent RNA polymerase (RdRp) of SARS-cov-2. Comput Biol Med 2021; 129:104156. [PMID: 33260103 PMCID: PMC7691827 DOI: 10.1016/j.compbiomed.2020.104156] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 01/18/2023]
Abstract
The RNA-dependent RNA polymerase (RdRp) is a key enzyme which regulates the viral replication of SARS-CoV-2. Remdesivir (RDV) is clinically used drug which targets RdRp, however its mechanism of action remains elusive. This study aims to find out the binding dynamics of active Remdesivir-triphosphate (RDV-TP) to RdRp by means of molecular dynamics (MD) simulation. We built a homology model of RdRp along with RNA and manganese ion using RdRp hepatitis C virus and recent SARS-CoV-2 structures. We determined that the model was stable during the 500 ns MD simulations. We then employed the model to study the binding of RDV-TP to RdRp during three independent 500 ns MD simulations. It was revealed that the interactions of protein and template-primer RNA were dominated by salt bridge interactions with phosphate groups of RNA, while interactions with base pairs of template-primer RNA were minimal. The binding of RDV-TP showed that the position of phosphate groups was at the entry of the NTP channel and it was stabilized by the interactions with K551, R553, and K621, while the adenosine group on RDV-TP was pairing with U2 of the template strand. The manganese ion was located close to D618, D760, and D761, and helps in stabilization of the phosphate groups of RDV-TP. Further we identified three hits from the natural product database that pose similar to RDV-TP while having lower binding energies than that of RDV-TP, and that SN00359915 had binding free energy about three times lower than that of RDV-TP.
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Affiliation(s)
- Muhammad Arba
- Faculty of Pharmacy, Universitas Halu Oleo, Kendari, 93232, Indonesia.
| | | | - Dylan J Brunt
- Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, NJ, 08028, United States
| | - Nicholas Paradis
- Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, NJ, 08028, United States
| | - Chun Wu
- Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, NJ, 08028, United States.
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19
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Swift RP, Rajaram K, Keutcha C, Liu HB, Kwan B, Dziedzic A, Jedlicka AE, Prigge ST. The NTP generating activity of pyruvate kinase II is critical for apicoplast maintenance in Plasmodium falciparum. eLife 2020; 9:e50807. [PMID: 32815516 PMCID: PMC7556864 DOI: 10.7554/elife.50807] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 08/20/2020] [Indexed: 12/20/2022] Open
Abstract
The apicoplast of Plasmodium falciparum parasites is believed to rely on the import of three-carbon phosphate compounds for use in organelle anabolic pathways, in addition to the generation of energy and reducing power within the organelle. We generated a series of genetic deletions in an apicoplast metabolic bypass line to determine which genes involved in apicoplast carbon metabolism are required for blood-stage parasite survival and organelle maintenance. We found that pyruvate kinase II (PyrKII) is essential for organelle maintenance, but that production of pyruvate by PyrKII is not responsible for this phenomenon. Enzymatic characterization of PyrKII revealed activity against all NDPs and dNDPs tested, suggesting that it may be capable of generating a broad range of nucleotide triphosphates. Conditional mislocalization of PyrKII resulted in decreased transcript levels within the apicoplast that preceded organelle disruption, suggesting that PyrKII is required for organelle maintenance due to its role in nucleotide triphosphate generation.
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Affiliation(s)
- Russell P Swift
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Krithika Rajaram
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Cyrianne Keutcha
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Hans B Liu
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Bobby Kwan
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Amanda Dziedzic
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Anne E Jedlicka
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Sean T Prigge
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
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20
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Panchal VV, Griffiths C, Mosaei H, Bilyk B, Sutton JAF, Carnell OT, Hornby DP, Green J, Hobbs JK, Kelley WL, Zenkin N, Foster SJ. Evolving MRSA: High-level β-lactam resistance in Staphylococcus aureus is associated with RNA Polymerase alterations and fine tuning of gene expression. PLoS Pathog 2020; 16:e1008672. [PMID: 32706832 PMCID: PMC7380596 DOI: 10.1371/journal.ppat.1008672] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 06/02/2020] [Indexed: 12/21/2022] Open
Abstract
Most clinical MRSA (methicillin-resistant S. aureus) isolates exhibit low-level β-lactam resistance (oxacillin MIC 2-4 μg/ml) due to the acquisition of a novel penicillin binding protein (PBP2A), encoded by mecA. However, strains can evolve high-level resistance (oxacillin MIC ≥256 μg/ml) by an unknown mechanism. Here we have developed a robust system to explore the basis of the evolution of high-level resistance by inserting mecA into the chromosome of the methicillin-sensitive S. aureus SH1000. Low-level mecA-dependent oxacillin resistance was associated with increased expression of anaerobic respiratory and fermentative genes. High-level resistant derivatives had acquired mutations in either rpoB (RNA polymerase subunit β) or rpoC (RNA polymerase subunit β') and these mutations were shown to be responsible for the observed resistance phenotype. Analysis of rpoB and rpoC mutants revealed decreased growth rates in the absence of antibiotic, and alterations to, transcription elongation. The rpoB and rpoC mutations resulted in decreased expression to parental levels, of anaerobic respiratory and fermentative genes and specific upregulation of 11 genes including mecA. There was however no direct correlation between resistance and the amount of PBP2A. A mutational analysis of the differentially expressed genes revealed that a member of the S. aureus Type VII secretion system is required for high level resistance. Interestingly, the genomes of two of the high level resistant evolved strains also contained missense mutations in this same locus. Finally, the set of genetically matched strains revealed that high level antibiotic resistance does not incur a significant fitness cost during pathogenesis. Our analysis demonstrates the complex interplay between antibiotic resistance mechanisms and core cell physiology, providing new insight into how such important resistance properties evolve.
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Affiliation(s)
- Viralkumar V. Panchal
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, United Kingdom
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
| | - Caitlin Griffiths
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Hamed Mosaei
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Bohdan Bilyk
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, United Kingdom
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
| | - Joshua A. F. Sutton
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, United Kingdom
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
| | - Oliver T. Carnell
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, United Kingdom
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
| | - David P. Hornby
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Jeffrey Green
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Jamie K. Hobbs
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
| | - William L. Kelley
- Department of Microbiology and Molecular Medicine, University Hospital and Medical School of Geneva, Geneva, Switzerland
| | - Nikolay Zenkin
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Simon J. Foster
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, United Kingdom
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
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21
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Krishna A, Liu B, Peacock SJ, Wigneshweraraj S. The prevalence and implications of single nucleotide polymorphisms in genes encoding the RNA polymerase of clinical isolates of Staphylococcus aureus. Microbiologyopen 2020; 9:e1058. [PMID: 32419302 PMCID: PMC7349150 DOI: 10.1002/mbo3.1058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/23/2020] [Accepted: 04/25/2020] [Indexed: 01/22/2023] Open
Abstract
Central to the regulation of bacterial gene expression is the multisubunit enzyme RNA polymerase (RNAP), which is responsible for catalyzing transcription. As all adaptive processes are underpinned by changes in gene expression, the RNAP can be considered the major mediator of any adaptive response in the bacterial cell. In bacterial pathogens, theoretically, single nucleotide polymorphisms (SNPs) in genes that encode subunits of the RNAP and associated factors could mediate adaptation and confer a selective advantage to cope with biotic and abiotic stresses. We investigated this possibility by undertaking a systematic survey of SNPs in genes encoding the RNAP and associated factors in a collection of 1,429 methicillin-resistant Staphylococcus aureus (MRSA) clinical isolates. We present evidence for the existence of several, hitherto unreported, nonsynonymous SNPs in genes encoding the RNAP and associated factors of MRSA ST22 clinical isolates and propose that the acquisition of amino acid substitutions in the RNAP could represent an adaptive strategy that contributes to the pathogenic success of MRSA.
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Affiliation(s)
- Aishwarya Krishna
- MRC Centre for Molecular Bacteriology and InfectionImperial College LondonLondonUK
| | - Bing Liu
- MRC Centre for Molecular Bacteriology and InfectionImperial College LondonLondonUK
| | - Sharon J. Peacock
- Department of MedicineAddenbrooke's HospitalUniversity of CambridgeCambridgeUK
- Cambridge University Hospitals NHS Foundation TrustCambridgeUK
- Wellcome Trust Sanger InstituteCambridgeUK
- London School of Hygiene and Tropical MedicineLondonUK
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22
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Cheng X, Redanz S, Treerat P, Qin H, Choi D, Zhou X, Xu X, Merritt J, Kreth J. Magnesium-Dependent Promotion of H 2O 2 Production Increases Ecological Competitiveness of Oral Commensal Streptococci. J Dent Res 2020; 99:847-854. [PMID: 32197054 PMCID: PMC7313347 DOI: 10.1177/0022034520912181] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The pyruvate oxidase (SpxB)-dependent production of H2O2 is widely distributed among oral commensal streptococci. Several studies confirmed the ability of H2O2 to antagonize susceptible oral bacterial species, including caries-associated Streptococcus mutans as well as several periodontal pathobionts. Here we report a potential mechanism to bolster oral commensal streptococcal H2O2 production by magnesium (Mg2+) supplementation. Magnesium is a cofactor for SpxB catalytic activity, and supplementation increases the production of H2O2 in vitro. We demonstrate that Mg2+ affects spxB transcription and SpxB abundance in Streptococcus sanguinis and Streptococcus gordonii. The competitiveness of low-passage commensal streptococcal clinical isolates is positively influenced in antagonism assays against S. mutans. In growth conditions normally selective for S. mutans, Mg2+ supplementation is able to increase the abundance of S. sanguinis in dual-species biofilms. Using an in vivo biophotonic imaging platform, we further demonstrate that dietary Mg2+ supplementation significantly improves S. gordonii oral colonization in mice. In summary, our results support a role for Mg2+ supplementation as a potential prebiotic to promote establishment of oral health-associated commensal streptococci.
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Affiliation(s)
- X. Cheng
- The State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China,Department of Geriatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - S. Redanz
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
| | - P. Treerat
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
| | - H. Qin
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
| | - D. Choi
- Department of Community Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR, USA,School of Public Health, Oregon Health & Science University, Portland, OR, USA
| | - X. Zhou
- The State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China,Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - X. Xu
- The State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China,Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - J. Merritt
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA,Department of Restorative Dentistry, Oregon Health and Science University, Portland, OR, USA
| | - J. Kreth
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA,Department of Restorative Dentistry, Oregon Health and Science University, Portland, OR, USA,J. Kreth, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd., MRB433, Portland, OR 97239, USA.
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23
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Núñez-Villanueva D, Hunter CA. Molecular replication using covalent base-pairs with traceless linkers. Org Biomol Chem 2019; 17:9660-9665. [PMID: 31691702 DOI: 10.1039/c9ob02336d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A unique feature of kinetically inert covalent base-pairing is that the nature of the chemical information that is transferred can be modulated by changing the chemical connectivity between the two bases. Formation of esters between phenols and benzoic acids has been used as a base-pairing strategy for sequence information transfer in template-directed synthesis of linear oligomers, but the copy strand produced by this process has the complementary sequence to the template strand. It is possible to form a base-pair between two benzoic acids by using a hydroquinone linker, which is eliminated when the product duplex is hydrolysed. Using this approach, covalent template-directed synthesis was carried out using a benzoic acid 3-mer template to produce an identical copy. This direct replication process was used in iterative rounds of replication leading to an increase of the population of the copied oligomer.
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Affiliation(s)
- Diego Núñez-Villanueva
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Christopher A Hunter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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24
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Organization and regulation of gene transcription. Nature 2019; 573:45-54. [PMID: 31462772 DOI: 10.1038/s41586-019-1517-4] [Citation(s) in RCA: 332] [Impact Index Per Article: 66.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/30/2019] [Indexed: 12/18/2022]
Abstract
The regulated transcription of genes determines cell identity and function. Recent structural studies have elucidated mechanisms that govern the regulation of transcription by RNA polymerases during the initiation and elongation phases. Microscopy studies have revealed that transcription involves the condensation of factors in the cell nucleus. A model is emerging for the transcription of protein-coding genes in which distinct transient condensates form at gene promoters and in gene bodies to concentrate the factors required for transcription initiation and elongation, respectively. The transcribing enzyme RNA polymerase II may shuttle between these condensates in a phosphorylation-dependent manner. Molecular principles are being defined that rationalize transcriptional organization and regulation, and that will guide future investigations.
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25
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Ragheb M, Merrikh H. The enigmatic role of Mfd in replication-transcription conflicts in bacteria. DNA Repair (Amst) 2019; 81:102659. [PMID: 31311770 PMCID: PMC6892258 DOI: 10.1016/j.dnarep.2019.102659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Conflicts between replication and transcription can have life-threatening consequences. RNA polymerase (RNAP) is the major impediment to replication progression, and its efficient removal from DNA should mitigate the consequences of collisions with replication. Cells have various proteins that can resolve conflicts by removing stalled (or actively translocating) RNAP from DNA. It would therefore seem logical that RNAP-associated factors, such as the bacterial DNA translocase Mfd, would minimize the effects of conflicts. Despite seemingly conclusive statements in most textbooks, the role of Mfd in conflicts remains an enigma. In this review, we will discuss the different physical states of RNAP during transcription, and how each distinct state can influence conflict severity and potentially trigger the involvement of Mfd. We propose models to explain the contradictory conclusions from published studies on the potential role of Mfd in resolving conflicts.
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Affiliation(s)
- Mark Ragheb
- Molecular and Cellular Biology Graduate Program and Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Houra Merrikh
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37205, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
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26
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Ciaccia M, Núñez-Villanueva D, Hunter CA. Capping Strategies for Covalent Template-Directed Synthesis of Linear Oligomers Using CuAAC. J Am Chem Soc 2019; 141:10862-10875. [PMID: 31251047 DOI: 10.1021/jacs.9b04973] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Covalent templating provides an attractive solution to the controlled synthesis of linear oligomers because a template oligomer can be used to define the precise length and sequence of the product. If the monomer units are attached to the template using kinetically inert covalent bonds it should be possible to operate at high dilution to favor intramolecular over intermolecular reaction. However, for oligomerization reactions using copper-catalyzed azide alkyne cycloaddition (CuAAC) this is not the case. The rate-limiting step is formation of an activated copper complex, so any alkyne that is activated by copper reacts rapidly with the nearest available azide. As a result, every time a chain end alkyne is activated, rapid intermolecular reaction takes place with a different oligomer leading to the formation of higher order products. It proved possible to block these intermolecular reactions by adding an excess of an azide capping agent that intercepts the chain end of the growing oligomer on the template. By adjusting the concentration of the capping agent to compete effectively with the unwanted intermolecular reactions without interfering with the desired intramolecular reactions, it was possible to obtain quantitative yields of copy strands from covalent template-directed oligomerization reactions. Remarkably, the capping agent could also be used to control the stereochemistry of the duplex formed in the templated oligomerization reaction to give exclusively the antiparallel product.
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Affiliation(s)
- Maria Ciaccia
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Diego Núñez-Villanueva
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Christopher A Hunter
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
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27
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Abstract
In all living organisms, the flow of genetic information is a two-step process: first DNA is transcribed into RNA, which is subsequently used as template for protein synthesis during translation. In bacteria, archaea and eukaryotes, transcription is carried out by multi-subunit RNA polymerases (RNAPs) sharing a conserved architecture of the RNAP core. RNAPs catalyse the highly accurate polymerisation of RNA from NTP building blocks, utilising DNA as template, being assisted by transcription factors during the initiation, elongation and termination phase of transcription. The complexity of this highly dynamic process is reflected in the intricate network of protein-protein and protein-nucleic acid interactions in transcription complexes and the substantial conformational changes of the RNAP as it progresses through the transcription cycle.In this chapter, we will first briefly describe the early work that led to the discovery of multisubunit RNAPs. We will then discuss the three-dimensional organisation of RNAPs from the bacterial, archaeal and eukaryotic domains of life, highlighting the conserved nature, but also the domain-specific features of the transcriptional apparatus. Another section will focus on transcription factors and their role in regulating the RNA polymerase throughout the different phases of the transcription cycle. This includes a discussion of the molecular mechanisms and dynamic events that govern transcription initiation, elongation and termination.
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Núñez-Villanueva D, Ciaccia M, Iadevaia G, Sanna E, Hunter CA. Sequence information transfer using covalent template-directed synthesis. Chem Sci 2019; 10:5258-5266. [PMID: 31191881 PMCID: PMC6540929 DOI: 10.1039/c9sc01460h] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 04/22/2019] [Indexed: 12/14/2022] Open
Abstract
Kinetically inert ester bonds were used to attach monomers to a template, dictating the sequence of the polymer product.
Template-directed synthesis is the biological method for the assembly of oligomers of defined sequence, providing the molecular basis for replication and the process of evolution. To apply analogous processes to synthetic oligomeric molecules, methods are required for the transfer of sequence information from a template to a daughter strand. We show that covalent template-directed synthesis is a promising approach for the molecular replication of sequence information in synthetic oligomers. Two monomer building blocks were synthesized: a phenol monomer and a benzoic acid monomer, each bearing an alkyne and an azide for oligomerization via copper catalyzed azide alkyne cycloaddition (CuAAC) reactions. Stepwise synthesis was used to prepare oligomers, where information was encoded as the sequence of phenol (P) and benzoic acid (A) units. Ester base-pairing was used to attach monomers to a mixed sequence template, and CuAAC was used to zip up the backbone. Hydrolysis of the ester base-pairs gave back the starting template and the sequence complementary copy. When the AAP trimer was used as the template, the complementary sequence PPA was obtained as the major product, with a small amount of scrambling resulting in PAP as a side-product. This covalent base-pairing strategy represents a general approach that can be implemented in different formats for the replication of sequence information in synthetic oligomers.
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Affiliation(s)
- Diego Núñez-Villanueva
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Maria Ciaccia
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Giulia Iadevaia
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Elena Sanna
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Christopher A Hunter
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
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Sauguet L. The Extended "Two-Barrel" Polymerases Superfamily: Structure, Function and Evolution. J Mol Biol 2019; 431:4167-4183. [PMID: 31103775 DOI: 10.1016/j.jmb.2019.05.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 01/14/2023]
Abstract
DNA and RNA polymerases (DNAP and RNAP) play central roles in genome replication, maintenance and repair, as well as in the expression of genes through their transcription. Multisubunit RNAPs carry out transcription and are represented, without exception, in all cellular life forms as well as in nucleo-cytoplasmic DNA viruses. Since their discovery, multisubunit RNAPs have been the focus of intense structural and functional studies revealing that they all share a well-conserved active-site region called the two-barrel catalytic core. The two-barrel core hosts the polymerase active site, which is located at the interface between two double-psi β-barrel domains that contribute distinct amino acid residues to the active site in an asymmetrical fashion. Recently, sequencing and structural studies have added a surprising variety of DNA and RNA to the two-barrel superfamily, including the archaeal replicative DNAP (PolD), which extends the family to DNA-dependent DNAPs involved in replication. While all these polymerases share a minimal core that must have been present in their common ancestor, the two-barrel polymerase superfamily now encompasses a remarkable diversity of enzymes, including DNA-dependent RNAPs, RNA-dependent RNAPs, and DNA-dependent DNAPs, which participate in critical biological processes such as DNA transcription, DNA replication, and gene silencing. The present review will discuss both common features and differences among the extended two-barrel polymerase superfamily, focusing on the newly discovered members. Comparing their structures provides insights into the molecular mechanisms evolved by the contemporary two-barrel polymerases to accomplish their different biological functions.
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Affiliation(s)
- Ludovic Sauguet
- Institut Pasteur, Unité de Dynamique Structurale des Macromolécules, 75015 Paris, France.
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30
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Single-molecule FRET method to investigate the dynamics of transcription elongation through the nucleosome by RNA polymerase II. Methods 2019; 159-160:51-58. [PMID: 30660864 DOI: 10.1016/j.ymeth.2019.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/07/2019] [Accepted: 01/14/2019] [Indexed: 12/27/2022] Open
Abstract
Transcription elongation through the nucleosome is a precisely coordinated activity to ensure timely production of RNA and accurate regulation of co-transcriptional histone modifications. Nucleosomes actively participate in transcription regulation at various levels and impose physical barriers to RNA polymerase II (RNAPII) during transcription elongation. Despite its high significance, the detailed dynamics of how RNAPII translocates along nucleosomal DNA during transcription elongation and how the nucleosome structure dynamically conforms to the changes necessary for RNAPII progression remain poorly understood. Transcription elongation through the nucleosome is a complex process and investigating the changes of the nucleosome structure during this process by ensemble measurements is daunting. This is because it is nearly impossible to synchronize elongation complexes within a nucleosome or a sub-nucleosome to a designated location at a high enough efficiency for desired sample homogeneity. Here we review our recently developed single-molecule FRET experimental system and method that has fulfilled this deficiency. With our method, one can follow the changes in the structure of individual nucleosomes during transcription elongation. We demonstrated that this method enables the detailed measurements of the kinetics of transcription elongation through the nucleosome and its regulation by a transcription factor, which can be easily extended to investigations of the roles of environmental variables and histone post-translational modifications in regulating transcription elongation.
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31
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Núñez-Villanueva D, Ciaccia M, Hunter CA. Cap control: cyclic versus linear oligomerisation in covalent template-directed synthesis. RSC Adv 2019; 9:29566-29569. [PMID: 35531529 PMCID: PMC9071899 DOI: 10.1039/c9ra07233k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/10/2019] [Indexed: 12/17/2022] Open
Abstract
Covalent template-directed synthesis was used to oligomerise monomer building blocks in a controlled manner to give exclusively the linear trimer. Competing reaction pathways were blocked by addition of a large excess of a monomeric capping agent. At a concentration of 1 mM, the cap selectively prevented further reaction of the product chain ends to give polymeric and macrocyclic products, but did not interfere with the templating process. The right concentration of capping agent is required to control the product distribution in covalent template-directed synthesis of linear oligomers using CuAAC.![]()
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Affiliation(s)
| | - Maria Ciaccia
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
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32
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Smith LG, Tan Z, Spasic A, Dutta D, Salas-Estrada LA, Grossfield A, Mathews DH. Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations. J Chem Theory Comput 2018; 14:6598-6612. [PMID: 30375860 DOI: 10.1021/acs.jctc.8b00633] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
To benchmark RNA force fields, we compared the folding stabilities of three 12-nucleotide hairpin stem loops estimated by simulation to stabilities determined by experiment. We used umbrella sampling and a reaction coordinate of end-to-end (5' to 3' hydroxyl oxygen) distance to estimate the free energy change of the transition from the native conformation to a fully extended conformation with no hydrogen bonds between non-neighboring bases. Each simulation was performed four times using the AMBER FF99+bsc0+χOL3 force field, and each window, spaced at 1 Å intervals, was sampled for 1 μs, for a total of 552 μs of simulation. We compared differences in the simulated free energy changes to analogous differences in free energies from optical melting experiments using thermodynamic cycles where the free energy change between stretched and random coil sequences is assumed to be sequence-independent. The differences between experimental and simulated ΔΔ G° are, on average, 0.98 ± 0.66 kcal/mol, which is chemically accurate and suggests that analogous simulations could be used predictively. We also report a novel method to identify where replica free energies diverge along a reaction coordinate, thus indicating where additional sampling would most improve convergence. We conclude by discussing methods to more economically perform these simulations.
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Affiliation(s)
- Louis G Smith
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States.,Center for RNA Biology , University of Rochester , Rochester , New York 14642 , United States
| | - Zhen Tan
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States.,Center for RNA Biology , University of Rochester , Rochester , New York 14642 , United States
| | - Aleksandar Spasic
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States.,Center for RNA Biology , University of Rochester , Rochester , New York 14642 , United States
| | - Debapratim Dutta
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States.,Center for RNA Biology , University of Rochester , Rochester , New York 14642 , United States
| | - Leslie A Salas-Estrada
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States
| | - Alan Grossfield
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States
| | - David H Mathews
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States.,Department of Biostatistics and Computational Biology , University of Rochester , Rochester , New York 14642 , United States.,Center for RNA Biology , University of Rochester , Rochester , New York 14642 , United States
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33
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Krogh TJ, Møller-Jensen J, Kaleta C. Impact of Chromosomal Architecture on the Function and Evolution of Bacterial Genomes. Front Microbiol 2018; 9:2019. [PMID: 30210483 PMCID: PMC6119826 DOI: 10.3389/fmicb.2018.02019] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/09/2018] [Indexed: 12/14/2022] Open
Abstract
The bacterial nucleoid is highly condensed and forms compartment-like structures within the cell. Much attention has been devoted to investigating the dynamic topology and organization of the nucleoid. In contrast, the specific nucleoid organization, and the relationship between nucleoid structure and function is often neglected with regard to importance for adaption to changing environments and horizontal gene acquisition. In this review, we focus on the structure-function relationship in the bacterial nucleoid. We provide an overview of the fundamental properties that shape the chromosome as a structured yet dynamic macromolecule. These fundamental properties are then considered in the context of the living cell, with focus on how the informational flow affects the nucleoid structure, which in turn impacts on the genetic output. Subsequently, the dynamic living nucleoid will be discussed in the context of evolution. We will address how the acquisition of foreign DNA impacts nucleoid structure, and conversely, how nucleoid structure constrains the successful and sustainable chromosomal integration of novel DNA. Finally, we will discuss current challenges and directions of research in understanding the role of chromosomal architecture in bacterial survival and adaptation.
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Affiliation(s)
- Thøger J Krogh
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christoph Kaleta
- Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
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34
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Abstract
During transcription, the nascent transcript behind an elongating RNA polymerase (RNAP) can invade the DNA duplex and hybridize with the complementary DNA template strand, generating a three-stranded "R-loop" structure, composed of an RNA:DNA duplex and an unpaired non-template DNA strand. R-loops can be strongly associated with actively transcribed loci by all RNAPs including the mitochondrial RNA polymerase (mtRNAP). In this chapter, we describe two protocols for the detection of RNA:DNA hybrids in living budding yeast cells, one that uses conventional chromatin immunoprecipitation (ChIP-qPCR) and one that uses DNA:RNA immunoprecipitation (DRIP-qPCR). Both protocols make use of the S9.6 antibody, which is believed to recognize the intermediate A/B helical RNA:DNA duplex conformation, with no sequence specificity.
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Affiliation(s)
- Aziz El Hage
- Wellcome Centre for Cell Biology, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK.
| | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
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35
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Da LT, E C, Shuai Y, Wu S, Su XD, Yu J. T7 RNA polymerase translocation is facilitated by a helix opening on the fingers domain that may also prevent backtracking. Nucleic Acids Res 2017; 45:7909-7921. [PMID: 28575393 PMCID: PMC5737862 DOI: 10.1093/nar/gkx495] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/24/2017] [Indexed: 12/04/2022] Open
Abstract
Here, we studied the complete process of a viral T7 RNA polymerase (RNAP) translocation on DNA during transcription elongation by implementing extensive all-atom molecular dynamics (MD) simulations to construct a Markov state model (MSM). Our studies show that translocation proceeds in a Brownian motion, and the RNAP thermally transits among multiple metastable states. We observed non-synchronized backbone movements of the nucleic acid (NA) chains with the RNA translocation accomplished first, while the template DNA lagged. Notably, both the O-helix and Y-helix on the fingers domain play key roles in facilitating NA translocation through the helix opening. The helix opening allows a key residue Tyr639 to become inserted into the active site, which pushes the RNA–DNA hybrid forward. Another key residue, Phe644, coordinates the downstream template DNA motions by stacking and un-stacking with a transition nucleotide (TN) and its adjacent nucleotide. Moreover, the O-helix opening at pre-translocation (pre-trans) likely resists backtracking. To test this hypothesis, we computationally designed mutants of T7 RNAP by replacing the amino acids on the O-helix with counterpart residues from a mitochondrial RNAP that is capable of backtracking. The current experimental results support the hypothesis.
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Affiliation(s)
- Lin-Tai Da
- Beijing Computational Science Research Center, Beijing 100193, China.,Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Chao E
- Beijing Computational Science Research Center, Beijing 100193, China
| | - Yao Shuai
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Shaogui Wu
- Beijing Computational Science Research Center, Beijing 100193, China
| | - Xiao-Dong Su
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Jin Yu
- Beijing Computational Science Research Center, Beijing 100193, China
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36
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Alhadid Y, Chung S, Lerner E, Taatjes DJ, Borukhov S, Weiss S. Studying transcription initiation by RNA polymerase with diffusion-based single-molecule fluorescence. Protein Sci 2017; 26:1278-1290. [PMID: 28370550 PMCID: PMC5477543 DOI: 10.1002/pro.3160] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/11/2017] [Accepted: 03/13/2017] [Indexed: 01/30/2023]
Abstract
Over the past decade, fluorescence-based single-molecule studies significantly contributed to characterizing the mechanism of RNA polymerase at different steps in transcription, especially in transcription initiation. Transcription by bacterial DNA-dependent RNA polymerase is a multistep process that uses genomic DNA to synthesize complementary RNA molecules. Transcription initiation is a highly regulated step in E. coli, but it has been challenging to study its mechanism because of its stochasticity and complexity. In this review, we describe how single-molecule approaches have contributed to our understanding of transcription and have uncovered mechanistic details that were not observed in conventional assays because of ensemble averaging.
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Affiliation(s)
- Yazan Alhadid
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, California, 90095
| | - SangYoon Chung
- Department of Chemistry & Biochemistry, University of California, Los Angeles, California, 90095
| | - Eitan Lerner
- Department of Chemistry & Biochemistry, University of California, Los Angeles, California, 90095
| | - Dylan J Taatjes
- Department of Chemistry & Biochemistry, University of Colorado, Boulder, Colorado, 80303
| | - Sergei Borukhov
- Rowan University School of Osteopathic Medicine, Stratford, New Jersey, 08084
| | - Shimon Weiss
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, California, 90095
- Department of Chemistry & Biochemistry, University of California, Los Angeles, California, 90095
- Molecular Biology Institute (MBI), University of California, Los Angeles, California, 90095
- California NanoSystems Institute, University of California, Los Angeles, California, 90095
- Department of Physiology, University of California, Los Angeles, California, 90095
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37
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Maji S, Shahoei R, Schulten K, Frank J. Quantitative Characterization of Domain Motions in Molecular Machines. J Phys Chem B 2017; 121:3747-3756. [PMID: 28199113 PMCID: PMC5479934 DOI: 10.1021/acs.jpcb.6b10732] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The work of molecular machines such as the ribosome is accompanied by conformational changes, often characterized by relative motions of their domains. The method we have developed seeks to quantify these motions in a general way, facilitating comparisons of results obtained by different researchers. Typically there are multiple snapshots of a structure in the form of pdb coordinates resulting from flexible fitting of low-resolution density maps, from X-ray crystallography, or from molecular dynamics simulation trajectories. Our objective is to characterize the motion of each domain as a coordinate transformation using moments of inertia tensor, a method we developed earlier. What has been missing until now are ancillary tools that make this task practical, general, and biologically informative. We have provided a comprehensive solution to this task with a set of tools implemented on the VMD platform. These tools address the need for reproducible segmentation of domains, and provide a generalized description of their motions using principal axes of inertia. Although this methodology has been specifically developed for studying ribosome motion, it is applicable to any molecular machine.
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Affiliation(s)
- Suvrajit Maji
- Department of Biochemistry and Molecular Biophysics, Columbia University
| | - Rezvan Shahoei
- Department of Physics, University of Illinois at Urbana-Champaign
- Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana-Champaign
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign
| | - Klaus Schulten
- Department of Physics, University of Illinois at Urbana-Champaign
- Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana-Champaign
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University
- Howard Hughes Medical Institute, Columbia University
- Department of Biological Sciences, Columbia University
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38
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Gomez D, Klumpp S. Facilitated diffusion in the presence of obstacles on the DNA. Phys Chem Chem Phys 2017; 18:11184-92. [PMID: 27048915 DOI: 10.1039/c6cp00307a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Biological functions of DNA depend on the sequence-specific binding of DNA-binding proteins to their corresponding binding sites. Binding of these proteins to their binding sites occurs through a facilitated diffusion process that combines three-dimensional diffusion in the cytoplasm with one-dimensional diffusion (sliding) along the DNA. In this work, we use a lattice model of facilitated diffusion to study how the dynamics of binding of a protein to a specific site (e.g., binding of an RNA polymerase to a promoter or of a transcription factor to its operator site) is affected by the presence of other proteins bound to the DNA, which act as 'obstacles' in the sliding process. Different types of these obstacles with different dynamics are implemented. While all types impair facilitated diffusion, the extent of the hindrance depends on the type of obstacle. As a consequence of hindrance by obstacles, more excursions into the cytoplasm are required for optimal target binding compared to the case without obstacles.
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Affiliation(s)
- David Gomez
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany.
| | - Stefan Klumpp
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany. and Institute for Nonlinear Dynamics, Georg-August University Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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39
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Dynamics of GreB-RNA polymerase interaction allow a proofreading accessory protein to patrol for transcription complexes needing rescue. Proc Natl Acad Sci U S A 2017; 114:E1081-E1090. [PMID: 28137878 DOI: 10.1073/pnas.1616525114] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The secondary channel (SC) of multisubunit RNA polymerases (RNAPs) allows access to the active site and is a nexus for the regulation of transcription. Multiple regulatory proteins bind in the SC and reprogram the catalytic activity of RNAP, but the dynamics of these factors' interactions with RNAP and how they function without cross-interference are unclear. In Escherichia coli, GreB is an SC protein that promotes proofreading by transcript cleavage in elongation complexes backtracked by nucleotide misincorporation. Using multiwavelength single-molecule fluorescence microscopy, we observed the dynamics of GreB interactions with elongation complexes. GreB binds to actively elongating complexes at nearly diffusion-limited rates but remains bound for only 0.3-0.5 s, longer than the duration of the nucleotide addition cycle but far shorter than the time needed to synthesize a complete mRNA. Bound GreB inhibits transcript elongation only partially. To test whether GreB preferentially binds backtracked complexes, we reconstituted complexes stabilized in backtracked and nonbacktracked configurations. By verifying the functional state of each molecular complex studied, we could exclude models in which GreB is selectively recruited to backtracked complexes or is ejected from RNAP by catalytic turnover. Instead, GreB binds rapidly and randomly to elongation complexes, patrolling for those requiring nucleolytic rescue, and its short residence time minimizes RNAP inhibition. The results suggest a general mechanism by which SC factors may cooperate to regulate RNAP while minimizing mutual interference.
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40
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Lee J, Borukhov S. Bacterial RNA Polymerase-DNA Interaction-The Driving Force of Gene Expression and the Target for Drug Action. Front Mol Biosci 2016; 3:73. [PMID: 27882317 PMCID: PMC5101437 DOI: 10.3389/fmolb.2016.00073] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/24/2016] [Indexed: 11/17/2022] Open
Abstract
DNA-dependent multisubunit RNA polymerase (RNAP) is the key enzyme of gene expression and a target of regulation in all kingdoms of life. It is a complex multifunctional molecular machine which, unlike other DNA-binding proteins, engages in extensive and dynamic interactions (both specific and nonspecific) with DNA, and maintains them over a distance. These interactions are controlled by DNA sequences, DNA topology, and a host of regulatory factors. Here, we summarize key recent structural and biochemical studies that elucidate the fine details of RNAP-DNA interactions during initiation. The findings of these studies help unravel the molecular mechanisms of promoter recognition and open complex formation, initiation of transcript synthesis and promoter escape. We also discuss most current advances in the studies of drugs that specifically target RNAP-DNA interactions during transcription initiation and elongation.
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Affiliation(s)
- Jookyung Lee
- Department of Cell Biology, Rowan University School of Osteopathic Medicine Stratford, NJ, USA
| | - Sergei Borukhov
- Department of Cell Biology, Rowan University School of Osteopathic Medicine Stratford, NJ, USA
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41
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Control of transcriptional pausing by biased thermal fluctuations on repetitive genomic sequences. Proc Natl Acad Sci U S A 2016; 113:E7409-E7417. [PMID: 27830653 DOI: 10.1073/pnas.1607760113] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the process of transcription elongation, RNA polymerase (RNAP) pauses at highly nonrandom positions across genomic DNA, broadly regulating transcription; however, molecular mechanisms responsible for the recognition of such pausing positions remain poorly understood. Here, using a combination of statistical mechanical modeling and high-throughput sequencing and biochemical data, we evaluate the effect of thermal fluctuations on the regulation of RNAP pausing. We demonstrate that diffusive backtracking of RNAP, which is biased by repetitive DNA sequence elements, causes transcriptional pausing. This effect stems from the increased microscopic heterogeneity of an elongation complex, and thus is entropy-dominated. This report shows a linkage between repetitive sequence elements encoded in the genome and regulation of RNAP pausing driven by thermal fluctuations.
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42
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Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue. Nat Commun 2016; 7:11244. [PMID: 27091704 PMCID: PMC4838855 DOI: 10.1038/ncomms11244] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 03/03/2016] [Indexed: 12/19/2022] Open
Abstract
The dynamics of the RNA polymerase II (Pol II) backtracking process is poorly understood. We built a Markov State Model from extensive molecular dynamics simulations to identify metastable intermediate states and the dynamics of backtracking at atomistic detail. Our results reveal that Pol II backtracking occurs in a stepwise mode where two intermediate states are involved. We find that the continuous bending motion of the Bridge helix (BH) serves as a critical checkpoint, using the highly conserved BH residue T831 as a sensing probe for the 3′-terminal base paring of RNA:DNA hybrid. If the base pair is mismatched, BH bending can promote the RNA 3′-end nucleotide into a frayed state that further leads to the backtracked state. These computational observations are validated by site-directed mutagenesis and transcript cleavage assays, and provide insights into the key factors that regulate the preferences of the backward translocation. RNA Polymerase II can detect and cleave mis-incorporated nucleotides by a proofreading mechanism that requires backtracking of the enzyme. Here the authors show that Pol II backtracking occurs in a stepwise mode that involves two intermediate states where the fraying of the terminal RNA nucleotide is a prerequisite.
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43
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Bacterial Transcription as a Target for Antibacterial Drug Development. Microbiol Mol Biol Rev 2016; 80:139-60. [PMID: 26764017 DOI: 10.1128/mmbr.00055-15] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Transcription, the first step of gene expression, is carried out by the enzyme RNA polymerase (RNAP) and is regulated through interaction with a series of protein transcription factors. RNAP and its associated transcription factors are highly conserved across the bacterial domain and represent excellent targets for broad-spectrum antibacterial agent discovery. Despite the numerous antibiotics on the market, there are only two series currently approved that target transcription. The determination of the three-dimensional structures of RNAP and transcription complexes at high resolution over the last 15 years has led to renewed interest in targeting this essential process for antibiotic development by utilizing rational structure-based approaches. In this review, we describe the inhibition of the bacterial transcription process with respect to structural studies of RNAP, highlight recent progress toward the discovery of novel transcription inhibitors, and suggest additional potential antibacterial targets for rational drug design.
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Esyunina D, Turtola M, Pupov D, Bass I, Klimašauskas S, Belogurov G, Kulbachinskiy A. Lineage-specific variations in the trigger loop modulate RNA proofreading by bacterial RNA polymerases. Nucleic Acids Res 2016; 44:1298-308. [PMID: 26733581 PMCID: PMC4756841 DOI: 10.1093/nar/gkv1521] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 12/20/2015] [Indexed: 02/01/2023] Open
Abstract
RNA cleavage by bacterial RNA polymerase (RNAP) has been implicated in transcriptional proofreading and reactivation of arrested transcription elongation complexes but its molecular mechanism is less understood than the mechanism of nucleotide addition, despite both reactions taking place in the same active site. RNAP from the radioresistant bacterium Deinococcus radiodurans is characterized by highly efficient intrinsic RNA cleavage in comparison with Escherichia coli RNAP. We find that the enhanced RNA cleavage activity largely derives from amino acid substitutions in the trigger loop (TL), a mobile element of the active site involved in various RNAP activities. The differences in RNA cleavage between these RNAPs disappear when the TL is deleted, or in the presence of GreA cleavage factors, which replace the TL in the active site. We propose that the TL substitutions modulate the RNA cleavage activity by altering the TL folding and its contacts with substrate RNA and that the resulting differences in transcriptional proofreading may play a role in bacterial stress adaptation.
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Affiliation(s)
- Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov square 2, Moscow 123182, Russia
| | - Matti Turtola
- Department of Biochemistry, University of Turku, Turku 20014, Finland
| | - Danil Pupov
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov square 2, Moscow 123182, Russia
| | - Irina Bass
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov square 2, Moscow 123182, Russia
| | | | - Georgiy Belogurov
- Department of Biochemistry, University of Turku, Turku 20014, Finland
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov square 2, Moscow 123182, Russia
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Arimbasseri AG, Maraia RJ. A high density of cis-information terminates RNA Polymerase III on a 2-rail track. RNA Biol 2015; 13:166-71. [PMID: 26636900 DOI: 10.1080/15476286.2015.1116677] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Transcription termination delineates the 3' ends of transcripts, prevents otherwise runaway RNA polymerase (RNAP) from intruding into downstream genes and regulatory elements, and enables release of the RNAP for recycling. While other eukaryotic RNAPs require complex cis-signals and/or accessory factors to achieve these activities, RNAP III does so autonomously with high efficiency and precision at a simple oligo(dT) stretch of 5-6 bp. A basis for this high density cis-information is that both template and nontemplate strands of the RNAP III terminator carry distinct signals for different stages of termination. High-density cis-information is a feature of the RNAP III system that is also reflected by dual functionalities of the tRNA promoters as both DNA and RNA elements. We review emerging developments in RNAP III termination and single strand nontemplate DNA use by other RNAPs. Use of nontemplate signals by RNAPs and associated transcription factors may be prevalent in gene regulation.
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Affiliation(s)
- Aneeshkumar G Arimbasseri
- a Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development , Bethesda , MD , USA
| | - Richard J Maraia
- a Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development , Bethesda , MD , USA.,b Commissioned Corps, U. S. Public Health Service , Washington, DC
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Esyunina DM, Kulbachinskiy AV. Purification and characterization of recombinant Deinococcus radiodurans RNA Polymerase. BIOCHEMISTRY (MOSCOW) 2015; 80:1271-8. [DOI: 10.1134/s0006297915100077] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Zhang N, Schäfer J, Sharma A, Rayner L, Zhang X, Tuma R, Stockley P, Buck M. Mutations in RNA Polymerase Bridge Helix and Switch Regions Affect Active-Site Networks and Transcript-Assisted Hydrolysis. J Mol Biol 2015; 427:3516-3526. [PMID: 26365052 PMCID: PMC4641871 DOI: 10.1016/j.jmb.2015.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 09/02/2015] [Accepted: 09/03/2015] [Indexed: 11/21/2022]
Abstract
In bacterial RNA polymerase (RNAP), the bridge helix and switch regions form an intricate network with the catalytic active centre and the main channel. These interactions are important for catalysis, hydrolysis and clamp domain movement. By targeting conserved residues in Escherichia coli RNAP, we are able to show that functions of these regions are differentially required during σ70-dependent and the contrasting σ54-dependent transcription activations and thus potentially underlie the key mechanistic differences between the two transcription paradigms. We further demonstrate that the transcription factor DksA directly regulates σ54-dependent activation both positively and negatively. This finding is consistent with the observed impacts of DksA on σ70-dependent promoters. DksA does not seem to significantly affect RNAP binding to a pre-melted promoter DNA but affects extensively activity at the stage of initial RNA synthesis on σ54-regulated promoters. Strikingly, removal of the σ54 Region I is sufficient to invert the action of DksA (from stimulation to inhibition or vice versa) at two test promoters. The RNAP mutants we generated also show a strong propensity to backtrack. These mutants increase the rate of transcript-hydrolysis cleavage to a level comparable to that seen in the Thermus aquaticus RNAP even in the absence of a non-complementary nucleotide. These novel phenotypes imply an important function of the bridge helix and switch regions as an anti-backtracking ratchet and an RNA hydrolysis regulator. The bridge helix and switch regions form an intricate network in RNAP. The σ70 and σ54 transcription systems differentially use this interaction network. Transcription factor DksA and σ54 Region I also contribute to this network. Disruption of this network enhances backtracking and intrinsic RNA hydrolysis.
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Affiliation(s)
- Nan Zhang
- Division of Cell and Molecular Biology, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, London SW7 2AZ, United Kingdom.
| | - Jorrit Schäfer
- Division of Cell and Molecular Biology, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Amit Sharma
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Lucy Rayner
- Division of Cell and Molecular Biology, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Xiaodong Zhang
- Division of Macromolecular Structure and Function, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Peter Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Martin Buck
- Division of Cell and Molecular Biology, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, London SW7 2AZ, United Kingdom.
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Imashimizu M, Takahashi H, Oshima T, McIntosh C, Bubunenko M, Court DL, Kashlev M. Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo. Genome Biol 2015; 16:98. [PMID: 25976475 PMCID: PMC4457086 DOI: 10.1186/s13059-015-0666-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 05/05/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Transcription elongation is frequently interrupted by pausing signals in DNA, with downstream effects on gene expression. Transcription errors also induce prolonged pausing, which can lead to a destabilized genome by interfering with DNA replication. Mechanisms of pausing associated with translocation blocks and misincorporation have been characterized in vitro, but not in vivo. RESULTS We investigate the pausing pattern of RNA polymerase (RNAP) in Escherichia coli by a novel approach, combining native elongating transcript sequencing (NET-seq) with RNase footprinting of the transcripts (RNET-seq). We reveal that the G-dC base pair at the 5' end of the RNA-DNA hybrid interferes with RNAP translocation. The distance between the 5' G-dC base pair and the 3' end of RNA fluctuates over a three-nucleotide width. Thus, the G-dC base pair can induce pausing in post-translocated, pre-translocated, and backtracked states of RNAP. Additionally, a CpG sequence of the template DNA strand spanning the active site of RNAP inhibits elongation and induces G-to-A errors, which leads to backtracking of RNAP. Gre factors efficiently proofread the errors and rescue the backtracked complexes. We also find that pausing events are enriched in the 5' untranslated region and antisense transcription of mRNA genes and are reduced in rRNA genes. CONCLUSIONS In E. coli, robust transcriptional pausing involves RNAP interaction with G-dC at the upstream end of the RNA-DNA hybrid, which interferes with translocation. CpG DNA sequences induce transcriptional pausing and G-to-A errors.
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Affiliation(s)
- Masahiko Imashimizu
- Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| | - Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan.
| | - Taku Oshima
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5, Ikoma, Nara, 630-0192, Japan.
| | - Carl McIntosh
- Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| | - Mikhail Bubunenko
- Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| | - Donald L Court
- Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| | - Mikhail Kashlev
- Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
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Ccr4-Not and TFIIS Function Cooperatively To Rescue Arrested RNA Polymerase II. Mol Cell Biol 2015; 35:1915-25. [PMID: 25776559 DOI: 10.1128/mcb.00044-15] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/11/2015] [Indexed: 12/13/2022] Open
Abstract
Expression of the genome requires RNA polymerase II (RNAPII) to transcribe across many natural and unnatural barriers, and this transcription across barriers is facilitated by protein complexes called elongation factors (EFs). Genetic studies in Saccharomyces cerevisiae yeast suggest that multiple EFs collaborate to assist RNAPII in completing the transcription of genes, but the molecular mechanisms of how they cooperate to promote elongation are not well understood. The Ccr4-Not complex participates in multiple steps of mRNA metabolism and has recently been shown to be an EF. Here we describe how Ccr4-Not and TFIIS cooperate to stimulate elongation. We find that Ccr4-Not and TFIIS mutations show synthetically enhanced phenotypes, and biochemical analyses indicate that Ccr4-Not and TFIIS work synergistically to reactivate arrested RNAPII. Ccr4-Not increases the recruitment of TFIIS into elongation complexes and enhances the cleavage of the displaced transcript in backtracked RNAPII. This is mediated by an interaction between Ccr4-Not and the N terminus of TFIIS. In addition to revealing insights into how these two elongation factors cooperate to promote RNAPII elongation, our study extends the growing body of evidence suggesting that the N terminus of TFIIS acts as a docking/interacting site that allows it to synergize with other EFs to promote RNAPII transcription.
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50
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Mejia YX, Nudler E, Bustamante C. Trigger loop folding determines transcription rate of Escherichia coli's RNA polymerase. Proc Natl Acad Sci U S A 2015; 112:743-8. [PMID: 25552559 PMCID: PMC4311812 DOI: 10.1073/pnas.1421067112] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Two components of the RNA polymerase (RNAP) catalytic center, the bridge helix and the trigger loop (TL), have been linked with changes in elongation rate and pausing. Here, single molecule experiments with the WT and two TL-tip mutants of the Escherichia coli enzyme reveal that tip mutations modulate RNAP's pause-free velocity, identifying TL conformational changes as one of two rate-determining steps in elongation. Consistent with this observation, we find a direct correlation between helix propensity of the modified amino acid and pause-free velocity. Moreover, nucleotide analogs affect transcription rate, suggesting that their binding energy also influences TL folding. A kinetic model in which elongation occurs in two steps, TL folding on nucleoside triphosphate (NTP) binding followed by NTP incorporation/pyrophosphate release, quantitatively accounts for these results. The TL plays no role in pause recovery remaining unfolded during a pause. This model suggests a finely tuned mechanism that balances transcription speed and fidelity.
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Affiliation(s)
- Yara X Mejia
- Jason L. Choy Laboratory of Single-Molecule Biophysics, the California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology and Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016
| | - Carlos Bustamante
- Jason L. Choy Laboratory of Single-Molecule Biophysics, the California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720; Department of Molecular and Cell Biology, Department of Physics, Department of Chemistry, Biophysics Graduate Group and Howard Hughes Medical Institute, University of California, Berkeley, CA 94720; and Kavli Energy Nanosciences Institute at Berkeley, Berkeley, CA 94720
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