101
|
The Role of Pyrophosphorolysis in the Initiation-to-Elongation Transition by E. coli RNA Polymerase. J Mol Biol 2019; 431:2528-2542. [PMID: 31029704 DOI: 10.1016/j.jmb.2019.04.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/13/2019] [Accepted: 04/15/2019] [Indexed: 02/02/2023]
Abstract
RNA polymerase can cleave a phosphodiester bond at the 3' end of a nascent RNA in the presence of pyrophosphate producing NTP. Pyrophosphorolysis has been characterized during elongation steps of transcription where its rate is significantly slower than the forward rate of NMP addition. In contrast, we report here that pyrophosphorolysis can occur in a millisecond time scale during the transition of Escherichia coli RNA polymerase from initiation to elongation at the psbA2 promoter. This rapid pyrophosphorolysis occurs during productive RNA synthesis as opposed to abortive RNA synthesis. Dissociation of σ70 or RNA extension beyond nine nucleotides dramatically reduces the rate of pyrophosphorolysis. We argue that the rapid pyrophosphorolysis allows iterative cycles of cleavage and re-synthesis of the 3' phosphodiester bond by the productive complexes in the early stage of transcription. This iterative process may provide an opportunity for the σ70 to dissociate from the RNA exit channel of the enzyme, enabling RNA to extend through the channel.
Collapse
|
102
|
Pérez Di Giorgio JA, Lepage É, Tremblay-Belzile S, Truche S, Loubert-Hudon A, Brisson N. Transcription is a major driving force for plastid genome instability in Arabidopsis. PLoS One 2019; 14:e0214552. [PMID: 30943245 PMCID: PMC6447228 DOI: 10.1371/journal.pone.0214552] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/15/2019] [Indexed: 12/14/2022] Open
Abstract
Though it is an essential process, transcription can be a source of genomic instability. For instance, it may generate RNA:DNA hybrids as the nascent transcript hybridizes with the complementary DNA template. These hybrids, called R-loops, act as a major cause of replication fork stalling and DNA breaks. In this study, we show that lowering transcription and R-loop levels in plastids of Arabidopsis thaliana reduces DNA rearrangements and mitigates plastid genome instability phenotypes. This effect can be observed on a genome-wide scale, as the loss of the plastid sigma transcription factor SIG6 prevents DNA rearrangements by favoring conservative repair in the presence of ciprofloxacin-induced DNA damage or in the absence of plastid genome maintenance actors such as WHY1/WHY3, RECA1 and POLIB. Additionally, resolving R-loops by the expression of a plastid-targeted exogenous RNAse H1 produces similar results. We also show that highly-transcribed genes are more susceptible to DNA rearrangements, as increased transcription of the psbD operon by SIG5 correlates with more locus-specific rearrangements. The effect of transcription is not specific to Sigma factors, as decreased global transcription levels by mutation of heat-stress-induced factor HSP21, mutation of nuclear-encoded polymerase RPOTp, or treatment with transcription-inhibitor rifampicin all prevent the formation of plastid genome rearrangements, especially under induced DNA damage conditions.
Collapse
Affiliation(s)
| | - Étienne Lepage
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Samuel Tremblay-Belzile
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Sébastien Truche
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Audrey Loubert-Hudon
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Normand Brisson
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| |
Collapse
|
103
|
Qiu Z, Zhu L, He L, Chen D, Zeng D, Chen G, Hu J, Zhang G, Ren D, Dong G, Gao Z, Shen L, Zhang Q, Guo L, Qian Q. DNA damage and reactive oxygen species cause cell death in the rice local lesions 1 mutant under high light and high temperature. THE NEW PHYTOLOGIST 2019; 222:349-365. [PMID: 30449034 DOI: 10.1111/nph.15597] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 11/07/2018] [Indexed: 05/17/2023]
Abstract
High light and high temperature (HLHT) stress may become more frequent and severe as the climate changes, affecting crop growth and resulting in reduced production. However, the mechanism of the response to HLHT stress in rice is not yet fully understood. In the present study, we screened a rice mutant library using HLHT conditions and isolated an HLHT-sensitive mutant, local lesions 1 (ls1), which showed decreased pigment contents, defective stomata and chloroplasts, and a local lesions phenotype under HLHT. We characterized and cloned LS1 by map-based cloning and genetic complementation. LS1 encodes the A subunit of the RNase H2 complex (RNASEH2A). Terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) and comet assays indicated that mutation of LS1 led to severe DNA damage under HLHT stress. Furthermore, we found excessive reactive oxygen species (ROS) accumulation in the ls1 mutant under HLHT stress. Exogenous antioxidants eased the local lesions phenotype of the ls1 mutant under HLHT. DNA damage caused by HLHT stress induces ROS accumulation, which causes the injury and apoptosis of leaf cells in the ls1 mutant. These results enhance our understanding of the regulatory mechanism in the response to HLHT stress in higher plants.
Collapse
Affiliation(s)
- Zhennan Qiu
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Li Zhu
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Lei He
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Dongdong Chen
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Guang Chen
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Deyong Ren
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Lan Shen
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Qiang Zhang
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China, National Rice Research Institute, Hangzhou, 310006, China
| |
Collapse
|
104
|
Myka KK, Küsters K, Washburn R, Gottesman ME. DksA-RNA polymerase interactions support new origin formation and DNA repair in Escherichia coli. Mol Microbiol 2019; 111:1382-1397. [PMID: 30779388 PMCID: PMC6488371 DOI: 10.1111/mmi.14227] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2019] [Indexed: 01/04/2023]
Abstract
The formation of new replication origins (cSDR) and repair of DNA double‐strand breaks (DSBs) in E. coli share a commonality. We find that the two processes require the RNAP‐associated factor, DksA. However, whereas cSDR also relies on (p)ppGpp, the alarmone molecule is dispensable for the repair of topoisomerase type II (Top II) DNA adducts and associated DSBs. The requirement for DksA in repair of nalidixic acid (Nal)‐induced DSBs or for the formation of new origins is not suppressed by a greA deletion mutation, indicating an active role of DksA rather than competition with GreA for insertion into the RNAP secondary channel. Like dksA mutations, transcription termination factor Rho mutations also confer sensitivity to Nal. The rho and dksA mutations are not epistatic, suggesting they involve different repair pathways. The roles of DksA in DSB repair and cSDR differ; certain DksA and RNAP mutants are able to support the first process, but not the latter. We suggest that new origin formation and DNA repair of protein adducts with DSBs may both involve the removal of RNAP without destruction of the RNA:DNA hybrid.
Collapse
Affiliation(s)
- Kamila K Myka
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
| | - Kira Küsters
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
| | - Robert Washburn
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
| | - Max E Gottesman
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
| |
Collapse
|
105
|
Rho-dependent transcription termination in bacteria recycles RNA polymerases stalled at DNA lesions. Nat Commun 2019; 10:1207. [PMID: 30872584 PMCID: PMC6418286 DOI: 10.1038/s41467-019-09146-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 02/14/2019] [Indexed: 01/25/2023] Open
Abstract
In bacteria, transcription-coupled repair of DNA lesions initiates after the Mfd protein removes RNA polymerases (RNAPs) stalled at the lesions. The bacterial RNA helicase, Rho, is a transcription termination protein that dislodges the elongation complexes. Here, we show that Rho dislodges the stalled RNAPs at DNA lesions. Strains defective in both Rho and Mfd are susceptible to DNA-damaging agents and are inefficient in repairing or propagating UV-damaged DNA. In vitro transcription assays show that Rho dissociates the stalled elongation complexes at the DNA lesions. We conclude that Rho-dependent termination recycles stalled RNAPs, which might facilitate DNA repair and other DNA-dependent processes essential for bacterial cell survival. We surmise that Rho might compete with, or augment, the Mfd function. In bacteria, the Rho protein dislodges elongation complexes to terminate transcription, and the Mfd protein removes RNA polymerases (RNAPs) stalled at DNA lesions. Here, Jain et al. show that Rho also dissociates stalled RNAPs at DNA lesions, which may facilitate DNA repair and other DNA-dependent processes.
Collapse
|
106
|
Transcription in cyanobacteria: a distinctive machinery and putative mechanisms. Biochem Soc Trans 2019; 47:679-689. [DOI: 10.1042/bst20180508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/11/2019] [Accepted: 02/04/2019] [Indexed: 02/03/2023]
Abstract
Abstract
Transcription in cyanobacteria involves several fascinating features. Cyanobacteria comprise one of the very few groups in which no proofreading factors (Gre homologues) have been identified. Gre factors increase the efficiency of RNA cleavage, therefore helping to maintain the fidelity of the RNA transcript and assist in the resolution of stalled RNAPs to prevent genome damage. The vast majority of bacterial species encode at least one of these highly conserved factors and so their absence in cyanobacteria is intriguing. Additionally, the largest subunit of bacterial RNAP has undergone a split in cyanobacteria to form two subunits and the SI3 insertion within the integral trigger loop element is roughly 3.5 times larger than in Escherichia coli. The Rho termination factor also appears to be absent, leaving cyanobacteria to rely solely on an intrinsic termination mechanism. Furthermore, cyanobacteria must be able to respond to environment signals such as light intensity and tightly synchronise gene expression and other cell activities to a circadian rhythm.
Collapse
|
107
|
Nadiras C, Delaleau M, Schwartz A, Margeat E, Boudvillain M. A Fluorogenic Assay To Monitor Rho-Dependent Termination of Transcription. Biochemistry 2019; 58:865-874. [PMID: 30624903 DOI: 10.1021/acs.biochem.8b01216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Transcription termination mediated by the ring-shaped, ATP-dependent Rho motor is a multipurpose regulatory mechanism specific to bacteria and constitutes an interesting target for the development of new antibiotics. Although Rho-dependent termination can punctuate gene expression or contribute to the protection of the genome at hundreds of sites within a given bacterium, its exact perimeter and site- or species-specific features remain insufficiently characterized. New advanced approaches are required to explore thoroughly the diversity of Rho-dependent terminators and the complexity of associated mechanisms. Current in vitro analyses of Rho-dependent termination rely on radiolabeling, gel electrophoresis, and phosphorimaging of transcription reaction products and are thus hazardous, inconvenient, and low-throughput. To address these limitations, we have developed the first in vitro assay using a fluorescence detection modality to study Rho-dependent transcription termination. This powerful experimental tool accurately estimates terminator strengths in a matter of minutes and is optimized for a microplate reader format allowing multiplexed characterization of putative terminator sequences and mechanisms or high-throughput screening of new drugs targeting Rho-dependent termination.
Collapse
Affiliation(s)
- Cédric Nadiras
- Centre de Biophysique Moléculaire , CNRS UPR4301 , rue Charles Sadron , 45071 Orléans cedex 2, France.,ED 549, Sciences Biologiques & Chimie du Vivant , Université d'Orléans , 45100 Orléans , France
| | - Mildred Delaleau
- Centre de Biophysique Moléculaire , CNRS UPR4301 , rue Charles Sadron , 45071 Orléans cedex 2, France
| | - Annie Schwartz
- Centre de Biophysique Moléculaire , CNRS UPR4301 , rue Charles Sadron , 45071 Orléans cedex 2, France
| | - Emmanuel Margeat
- Centre de Biochimie Structurale, INSERM U 1054, CNRS UMR 5048, Université de Montpellier , 29 rue de Navacelles , 34090 Montpellier , France
| | - Marc Boudvillain
- Centre de Biophysique Moléculaire , CNRS UPR4301 , rue Charles Sadron , 45071 Orléans cedex 2, France.,ED 549, Sciences Biologiques & Chimie du Vivant , Université d'Orléans , 45100 Orléans , France
| |
Collapse
|
108
|
Crossley MP, Bocek M, Cimprich KA. R-Loops as Cellular Regulators and Genomic Threats. Mol Cell 2019; 73:398-411. [PMID: 30735654 PMCID: PMC6402819 DOI: 10.1016/j.molcel.2019.01.024] [Citation(s) in RCA: 429] [Impact Index Per Article: 85.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/03/2019] [Accepted: 01/15/2019] [Indexed: 12/17/2022]
Abstract
During transcription, the nascent RNA strand can base pair with its template DNA, displacing the non-template strand as ssDNA and forming a structure called an R-loop. R-loops are common across many domains of life and cause DNA damage in certain contexts. In this review, we summarize recent results implicating R-loops as important regulators of cellular processes such as transcription termination, gene regulation, and DNA repair. We also highlight recent work suggesting that R-loops can be problematic to cells as blocks to efficient transcription and replication that trigger the DNA damage response. Finally, we discuss how R-loops may contribute to cancer, neurodegeneration, and inflammatory diseases and compare the available next-generation sequencing-based approaches to map R-loops genome wide.
Collapse
Affiliation(s)
- Madzia P Crossley
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Michael Bocek
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA.
| |
Collapse
|
109
|
Pupov D, Ignatov A, Agapov A, Kulbachinskiy A. Distinct effects of DNA lesions on RNA synthesis by Escherichia coli RNA polymerase. Biochem Biophys Res Commun 2019; 510:122-127. [PMID: 30665719 DOI: 10.1016/j.bbrc.2019.01.062] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/12/2019] [Indexed: 01/08/2023]
Abstract
DNA lesions can severely compromise genome stability and lead to cell death if unrepaired. RNA polymerase (RNAP) is known to serve as a sensor of DNA damage and to attract DNA repair factors to the damaged template sites. Here, we systematically investigated the ability of Escherichia coli RNAP to transcribe DNA templates containing various types of DNA lesions, and analyzed their effects on transcription fidelity. We showed that transcription is strongly inhibited on templates containing cyclobutane thymine dimers, 1,N6-ethenoadenine and abasic sites, while 8-oxoguanine and thymine glycol have mild effects on transcription efficiency. Similarly to many polymerases, E. coli RNAP follows the "A" rule during nucleotide insertion opposite abasic sites and bulky lesions, and can also incorporate and efficiently extend an adenine nucleotide opposite 8-oxoguanine. Mutations in RNAP regions around the templating nucleotide decrease the efficiency of translesion synthesis, likely by altering the RNAP-template contacts in the active site. Thus, DNA lesions can lead to distinct outcomes in transcription, depending on the severity of the damage and contacts of the damaged template with the active site of RNAP.
Collapse
Affiliation(s)
- Danil Pupov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Artem Ignatov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Aleksei Agapov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
| |
Collapse
|
110
|
Esyunina D, Kulbachinskiy A. Interactions in the active site of Deinococcus radiodurans RNA polymerase during RNA proofreading. Biochem Biophys Res Commun 2018; 509:161-166. [PMID: 30579600 DOI: 10.1016/j.bbrc.2018.12.095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 12/13/2018] [Indexed: 11/25/2022]
Abstract
Co-transcriptional RNA proofreading by RNA polymerase (RNAP) is essential for accurate mRNA synthesis and reactivation of stalled transcription complexes, which can otherwise compromise genome integrity. RNAP from the stress-resistant bacterium Deinococcus radiodurans exhibits high levels of RNA cleavage in comparison with RNAP from Escherichia coli, which allows it to remove misincorporated nucleotides with high efficiency. Here, we show that the rate of RNA cleavage by D. radiodurans RNAP depends on the structure of the (mis)matched RNA 3'-nucleotide and its contacts with the active site. These interactions likely position the reactive phosphodiester bond in the cleavage-competent conformation, thus facilitating its hydrolysis catalyzed by metal ions in the active center. The universal RNA cleavage factor GreA largely alleviates defects in RNA cleavage caused by modifications in the RNA 3'-nucleotide or in its binding pocket in RNAP, suggesting that GreA functionally substitutes for these contacts. The results demonstrate that various RNAPs rely on a conserved mechanism for RNA proofreading, which can be modulated by changes in accessory parts of the active center.
Collapse
Affiliation(s)
- Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.
| |
Collapse
|
111
|
Lisitskaya L, Aravin AA, Kulbachinskiy A. DNA interference and beyond: structure and functions of prokaryotic Argonaute proteins. Nat Commun 2018; 9:5165. [PMID: 30514832 PMCID: PMC6279821 DOI: 10.1038/s41467-018-07449-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 10/26/2018] [Indexed: 12/14/2022] Open
Abstract
Recognition and repression of RNA targets by Argonaute proteins guided by small RNAs is the essence of RNA interference in eukaryotes. Argonaute proteins with diverse structures are also found in many bacterial and archaeal genomes. Recent studies revealed that, similarly to their eukaryotic counterparts, prokaryotic Argonautes (pAgos) may function in cell defense against foreign genetic elements but, in contrast, preferably act on DNA targets. Many crucial details of the pAgo action, and the roles of a plethora of pAgos with non-conventional architecture remain unknown. Here, we review available structural and biochemical data on pAgos and discuss their possible functions in host defense and other genetic processes in prokaryotic cells. In this review, Aravin and colleagues examine bacterial and archaeal Argonaute proteins, discuss their diverse architectures and their possible roles in host defense, proposing additional functions for Argonaute proteins in prokaryotic cells.
Collapse
Affiliation(s)
- Lidiya Lisitskaya
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Alexei A Aravin
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia. .,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
| |
Collapse
|
112
|
Turtola M, Mäkinen JJ, Belogurov GA. Active site closure stabilizes the backtracked state of RNA polymerase. Nucleic Acids Res 2018; 46:10870-10887. [PMID: 30256972 PMCID: PMC6237748 DOI: 10.1093/nar/gky883] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/30/2018] [Accepted: 09/19/2018] [Indexed: 01/02/2023] Open
Abstract
All cellular RNA polymerases (RNAP) occasionally backtrack along the template DNA as part of transcriptional proofreading and regulation. Here, we studied the mechanism of RNAP backtracking by one nucleotide using two complementary approaches that allowed us to precisely measure the occupancy and lifetime of the backtracked state. Our data show that the stability of the backtracked state is critically dependent on the closure of the RNAP active site by a mobile domain, the trigger loop (TL). The lifetime and occupancy of the backtracked state measurably decreased by substitutions of the TL residues that interact with the nucleoside triphosphate (NTP) substrate, whereas amino acid substitutions that stabilized the closed active site increased the lifetime and occupancy. These results suggest that the same conformer of the TL closes the active site during catalysis of nucleotide incorporation into the nascent RNA and backtracking by one nucleotide. In support of this hypothesis, we construct a model of the 1-nt backtracked complex with the closed active site and the backtracked nucleotide in the entry pore area known as the E-site. We further propose that 1-nt backtracking mimics the reversal of the NTP substrate loading into the RNAP active site during on-pathway elongation.
Collapse
Affiliation(s)
- Matti Turtola
- University of Turku, Department of Biochemistry, FIN-20014 Turku, Finland
| | - Janne J Mäkinen
- University of Turku, Department of Biochemistry, FIN-20014 Turku, Finland
| | | |
Collapse
|
113
|
Ragheb MN, Thomason MK, Hsu C, Nugent P, Gage J, Samadpour AN, Kariisa A, Merrikh CN, Miller SI, Sherman DR, Merrikh H. Inhibiting the Evolution of Antibiotic Resistance. Mol Cell 2018; 73:157-165.e5. [PMID: 30449724 PMCID: PMC6320318 DOI: 10.1016/j.molcel.2018.10.015] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/17/2018] [Accepted: 10/09/2018] [Indexed: 11/30/2022]
Abstract
Efforts to battle antimicrobial resistance (AMR) are generally focused on developing novel antibiotics. However, history shows that resistance arises regardless of the nature or potency of new drugs. Here, we propose and provide evidence for an alternate strategy to resolve this problem: inhibiting evolution. We determined that the DNA translocase Mfd is an “evolvability factor” that promotes mutagenesis and is required for rapid resistance development to all antibiotics tested across highly divergent bacterial species. Importantly, hypermutator alleles that accelerate AMR development did not arise without Mfd, at least during evolution of trimethoprim resistance. We also show that Mfd’s role in AMR development depends on its interactions with the RNA polymerase subunit RpoB and the nucleotide excision repair protein UvrA. Our findings suggest that AMR development can be inhibited through inactivation of evolvability factors (potentially with “anti-evolution” drugs)—in particular, Mfd—providing an unexplored route toward battling the AMR crisis. The bacterial transcription-coupled repair (TCR) factor Mfd promotes mutagenesis Mfd-driven mutagenesis accelerates the evolution of antimicrobial resistance (AMR) The rapid evolution of AMR requires Mfd’s interaction with RpoB and UvrA Mfd may be an ideal target for “anti-evolution” drugs that inhibit AMR development
Collapse
Affiliation(s)
- Mark N Ragheb
- Department of Microbiology, University of Washington, Seattle, WA, USA; Molecular and Cellular Biology Graduate Program and Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | | | - Chris Hsu
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Patrick Nugent
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - John Gage
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | | | - Ankunda Kariisa
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | | | - Samuel I Miller
- Department of Microbiology, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David R Sherman
- Center for Infectious Disease Research, Seattle, WA, USA; Interdiscipinary Program of Pathobiology, Department of Global Health, University of Washington, Seattle, WA, USA
| | - Houra Merrikh
- Department of Microbiology, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| |
Collapse
|
114
|
Merrikh CN, Merrikh H. Gene inversion potentiates bacterial evolvability and virulence. Nat Commun 2018; 9:4662. [PMID: 30405125 PMCID: PMC6220195 DOI: 10.1038/s41467-018-07110-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 10/15/2018] [Indexed: 12/12/2022] Open
Abstract
Most bacterial genes are encoded on the leading strand, co-orienting the movement of the replication machinery with RNA polymerases. This bias reduces the frequency of detrimental head-on collisions between the two machineries. The negative outcomes of these collisions should lead to selection against head-on alleles, maximizing genome co-orientation. Our findings challenge this model. Using the GC skew calculation, we reveal the evolutionary inversion record of all chromosomally encoded genes in multiple divergent bacterial pathogens. Against expectations, we find that a large number of co-oriented genes have inverted to the head-on orientation, presumably increasing the frequency of head-on replication-transcription conflicts. Furthermore, we find that head-on genes, (including key antibiotic resistance and virulence genes) have higher rates of non-synonymous mutations and are more frequently under positive selection (dN/dS > 1). Based on these results, we propose that spontaneous gene inversions can increase the evolvability and pathogenic capacity of bacteria through head-on replication-transcription collisions. Head-on replication-transcription collisions occur within genes encoded on the lagging DNA strand. Here, the authors show that a large number of originally co-oriented (leading strand) genes have inverted to the head-on orientation, increasing both gene-specific mutation rates, and the overall evolvability of several bacterial pathogens.
Collapse
Affiliation(s)
- Christopher N Merrikh
- Department of Microbiology, University of Washington, Health Sciences Building J-209, Seattle, WA, 98195, USA
| | - Houra Merrikh
- Department of Microbiology, University of Washington, Health Sciences Building J-209, Seattle, WA, 98195, USA. .,Department of Genome Sciences, University of Washington, Seattle, 98195, WA, USA.
| |
Collapse
|
115
|
Belotserkovskii BP, Tornaletti S, D'Souza AD, Hanawalt PC. R-loop generation during transcription: Formation, processing and cellular outcomes. DNA Repair (Amst) 2018; 71:69-81. [PMID: 30190235 PMCID: PMC6340742 DOI: 10.1016/j.dnarep.2018.08.009] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
R-loops are structures consisting of an RNA-DNA duplex and an unpaired DNA strand. They can form during transcription upon nascent RNA "threadback" invasion into the DNA duplex to displace the non-template strand. Although R-loops occur naturally in all kingdoms of life and serve regulatory roles, they are often deleterious and can cause genomic instability. Of particular importance are the disastrous consequences when replication forks or transcription complexes collide with R-loops. The appropriate processing of R-loops is essential to avoid a number of human neurodegenerative and other clinical disorders. We provide a perspective on mechanistic aspects of R-loop formation and their resolution learned from studies in model systems. This should contribute to improved understanding of R-loop biological functions and enable their practical applications. We propose the novel employment of artificially-generated stable R-loops to selectively inactivate tumor cells.
Collapse
Affiliation(s)
- Boris P Belotserkovskii
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, United States
| | - Silvia Tornaletti
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, United States
| | - Alicia D D'Souza
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, United States
| | - Philip C Hanawalt
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, United States.
| |
Collapse
|
116
|
Le TT, Wang MD. Molecular Highways—Navigating Collisions of DNA Motor Proteins. J Mol Biol 2018; 430:4513-4524. [DOI: 10.1016/j.jmb.2018.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/31/2018] [Accepted: 08/03/2018] [Indexed: 01/09/2023]
|
117
|
Nagel A, Michalik S, Debarbouille M, Hertlein T, Gesell Salazar M, Rath H, Msadek T, Ohlsen K, van Dijl JM, Völker U, Mäder U. Inhibition of Rho Activity Increases Expression of SaeRS-Dependent Virulence Factor Genes in Staphylococcus aureus, Showing a Link between Transcription Termination, Antibiotic Action, and Virulence. mBio 2018; 9:e01332-18. [PMID: 30228237 PMCID: PMC6143737 DOI: 10.1128/mbio.01332-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/16/2018] [Indexed: 12/29/2022] Open
Abstract
Staphylococcus aureus causes various diseases ranging from skin and soft tissue infections to life-threatening infections. Adaptation to the different host niches is controlled by a complex network of transcriptional regulators. Global profiling of condition-dependent transcription revealed adaptation of S. aureus HG001 at the levels of transcription initiation and termination. In particular, deletion of the gene encoding the Rho transcription termination factor triggered a remarkable overall increase in antisense transcription and gene expression changes attributable to indirect regulatory effects. The goal of the present study was a detailed comparative analysis of S. aureus HG001 and its isogenic rho deletion mutant. Proteome analysis revealed significant differences in cellular and extracellular protein profiles, most notably increased amounts of the proteins belonging to the SaeR regulon in the Rho-deficient strain. The SaeRS two-component system acts as a major regulator of virulence gene expression in staphylococci. Higher levels of SaeRS-dependent virulence factors such as adhesins, toxins, and immune evasion proteins in the rho mutant resulted in higher virulence in a murine bacteremia model, which was alleviated in a rho complemented strain. Inhibition of Rho activity by bicyclomycin, a specific inhibitor of Rho activity, also induced the expression of SaeRS-dependent genes, at both the mRNA and protein levels, to the same extent as observed in the rho mutant. Taken together, these findings indicate that activation of the Sae system in the absence of Rho is directly linked to Rho's transcription termination activity and establish a new link between antibiotic action and virulence gene expression in S. aureusIMPORTANCE The major human pathogen Staphylococcus aureus is a widespread commensal bacterium but also the most common cause of nosocomial infections. It adapts to the different host niches through a complex gene regulatory network. We show here that the Rho transcription termination factor, which represses pervasive antisense transcription in various bacteria, including S. aureus, plays a role in controlling SaeRS-dependent virulence gene expression. A Rho-deficient strain produces larger amounts of secreted virulence factors in vitro and shows increased virulence in mice. We also show that treatment of S. aureus with the antibiotic bicyclomycin, which inhibits Rho activity and is effective against Gram-negative bacteria, induces the same changes in the proteome as observed in the Rho-deficient strain. Our results reveal for the first time a link between transcription termination and virulence regulation in S. aureus, which implies a novel mechanism by which an antibiotic can modulate the expression of virulence factors.
Collapse
Affiliation(s)
- Anna Nagel
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Stephan Michalik
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Michel Debarbouille
- Biology of Gram-Positive Pathogens, Department of Microbiology, Institut Pasteur and CNRS ERL 3526, Paris, France
| | - Tobias Hertlein
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Manuela Gesell Salazar
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Hermann Rath
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Tarek Msadek
- Biology of Gram-Positive Pathogens, Department of Microbiology, Institut Pasteur and CNRS ERL 3526, Paris, France
| | - Knut Ohlsen
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Ulrike Mäder
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
118
|
Kumar V, Mishra RK, Kaur G, Dutta D. Cobalt and nickel impair DNA metabolism by the oxidative stress independent pathway. Metallomics 2018; 9:1596-1609. [PMID: 29058747 DOI: 10.1039/c7mt00231a] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The oxidative stress that evolves under cobalt and nickel exposure is thought to exert toxicity, though the exact routes of such metal poisoning remain ambiguous. We revisited the metal toxicity in Escherichia coli to show that cobalt and nickel exposure at levels as low as 0.5 and 1 mM, respectively, visibly inhibits growth. We also observed that acidic conditions aggravated, while alkaline conditions alleviated the metal toxicity. Besides, 1 mM manganese, which is non-cytotoxic, as judged by the growth of E. coli, synergistically elevated cobalt and nickel stress. However, the metal toxicity did not lead to oxidative stress in E. coli. On the other hand, we show that cobalt and nickel, but not manganese, reduced the rate of DNA replication to 50% within 2 hours. Interestingly, the metal ions promoted DNA double-strand breaks but did not induce SOS repair pathways, indicating that the metal ions could block SOS induction. To test this, we show that cobalt and nickel, but not manganese, suppressed the nalidixic acid-induced SOS response. Finally, using an in vitro assay system, we demonstrated that cobalt and nickel inhibit RecBCD function, which is essential for SOS induction. Therefore, our data indicate that cobalt and nickel affect DNA replication, damage DNA, and inhibit the SOS repair pathway to exert toxicity.
Collapse
Affiliation(s)
- Vineet Kumar
- CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India.
| | | | | | | |
Collapse
|
119
|
Traverse CC, Ochman H. A Genome-Wide Assay Specifies Only GreA as a Transcription Fidelity Factor in Escherichia coli. G3 (BETHESDA, MD.) 2018; 8:2257-2264. [PMID: 29769292 PMCID: PMC6027873 DOI: 10.1534/g3.118.200209] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 04/28/2018] [Indexed: 02/07/2023]
Abstract
Although mutations are the basis for adaptation and heritable genetic change, transient errors occur during transcription at rates that are orders of magnitude higher than the mutation rate. High rates of transcription errors can be detrimental by causing the production of erroneous proteins that need to be degraded. Two transcription fidelity factors, GreA and GreB, have previously been reported to stimulate the removal of errors that occur during transcription, and a third fidelity factor, DksA, is thought to decrease the error rate through an unknown mechanism. Because the majority of transcription-error assays of these fidelity factors were performed in vitro and on individual genes, we measured the in vivo transcriptome-wide error rates in all possible combinations of mutants of the three fidelity factors. This method expands measurements of these fidelity factors to the full spectrum of errors across the entire genome. Our assay shows that GreB and DksA have no significant effect on transcription error rates, and that GreA only influences the transcription error rate by reducing G-to-A errors.
Collapse
Affiliation(s)
- Charles C Traverse
- Department of Integrative Biology, University of Texas, Austin, Texas 78712
| | - Howard Ochman
- Department of Integrative Biology, University of Texas, Austin, Texas 78712
| |
Collapse
|
120
|
Gordon AJE, Sivaramakrishnan P, Halliday JA, Herman C. Transcription infidelity and genome integrity: the parallax view. Transcription 2018; 9:315-320. [PMID: 29929421 DOI: 10.1080/21541264.2018.1491251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
It was recently shown that removal of GreA, a transcription fidelity factor, enhances DNA break repair. This counterintuitive result, arising from unresolved backtracked RNA polymerase impeding DNA resection and thereby facilitating RecA-loading, leads to an interesting corollary: error-free full-length transcripts and broken chromosomes. Therefore, transcription fidelity may compromise genomic integrity.
Collapse
Affiliation(s)
- Alasdair J E Gordon
- a Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA
| | - Priya Sivaramakrishnan
- a Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA.,b Department of Genetics , Perelman School of Medicine, University of Pennsylvania , Philadelphia , PA , USA
| | - Jennifer A Halliday
- a Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA
| | - Christophe Herman
- a Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA.,c Department of Molecular Virology and Microbiology , Baylor College of Medicine , Houston , TX , USA.,d Dan L. Duncan Cancer Center, Baylor College of Medicine , Houston , TX , USA
| |
Collapse
|
121
|
Bhardwaj A, Ghose D, Thakur KG, Dutta D. Escherichia coli β-clamp slows down DNA polymerase I dependent nick translation while accelerating ligation. PLoS One 2018; 13:e0199559. [PMID: 29924849 PMCID: PMC6010275 DOI: 10.1371/journal.pone.0199559] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 06/08/2018] [Indexed: 11/25/2022] Open
Abstract
The nick translation property of DNA polymerase I (Pol I) ensures the maturation of Okazaki fragments by removing primer RNAs and facilitating ligation. However, prolonged nick translation traversing downstream DNA is an energy wasting futile process, as Pol I simultaneously polymerizes and depolymerizes at the nick sites utilizing energy-rich dNTPs. Using an in vitro assay system, we demonstrate that the β-clamp of the Escherichia coli replisome strongly inhibits nick translation on the DNA substrate. To do so, β-clamp inhibits the strand displacement activity of Pol I by interfering with the interaction between the finger subdomain of Pol I and the downstream primer-template junction. Conversely, β-clamp stimulates the 5’ exonuclease property of Pol I to cleave single nucleotides or shorter oligonucleotide flaps. This single nucleotide flap removal at high frequency increases the probability of ligation between the upstream and downstream DNA strands at an early phase, terminating nick translation. Besides β-clamp-mediated ligation helps DNA ligase to seal the nick promptly during the maturation of Okazaki fragments.
Collapse
Affiliation(s)
- Amit Bhardwaj
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | | | | | - Dipak Dutta
- CSIR-Institute of Microbial Technology, Chandigarh, India
- * E-mail:
| |
Collapse
|
122
|
Lang KS, Merrikh H. The Clash of Macromolecular Titans: Replication-Transcription Conflicts in Bacteria. Annu Rev Microbiol 2018; 72:71-88. [PMID: 29856930 DOI: 10.1146/annurev-micro-090817-062514] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Within the last decade, it has become clear that DNA replication and transcription are routinely in conflict with each other in growing cells. Much of the seminal work on this topic has been carried out in bacteria, specifically, Escherichia coli and Bacillus subtilis; therefore, studies of conflicts in these species deserve special attention. Collectively, the recent findings on conflicts have fundamentally changed the way we think about DNA replication in vivo. Furthermore, new insights on this topic have revealed that the conflicts between replication and transcription significantly influence many key parameters of cellular function, including genome organization, mutagenesis, and evolution of stress response and virulence genes. In this review, we discuss the consequences of replication-transcription conflicts on the life of bacteria and describe some key strategies cells use to resolve them. We put special emphasis on two critical aspects of these encounters: ( a) the consequences of conflicts on replisome stability and dynamics, and ( b) the resulting increase in spontaneous mutagenesis.
Collapse
Affiliation(s)
- Kevin S Lang
- Department of Microbiology, University of Washington, Seattle, Washington 98195, USA;
| | - Houra Merrikh
- Department of Microbiology, University of Washington, Seattle, Washington 98195, USA; .,Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5061, USA
| |
Collapse
|
123
|
McGinty RJ, Puleo F, Aksenova AY, Hisey JA, Shishkin AA, Pearson EL, Wang ET, Housman DE, Moore C, Mirkin SM. A Defective mRNA Cleavage and Polyadenylation Complex Facilitates Expansions of Transcribed (GAA) n Repeats Associated with Friedreich's Ataxia. Cell Rep 2018; 20:2490-2500. [PMID: 28877480 DOI: 10.1016/j.celrep.2017.08.051] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/19/2017] [Accepted: 08/15/2017] [Indexed: 02/03/2023] Open
Abstract
Expansions of microsatellite repeats are responsible for numerous hereditary diseases in humans, including myotonic dystrophy and Friedreich's ataxia. Whereas the length of an expandable repeat is the main factor determining disease inheritance, recent data point to genomic trans modifiers that can impact the likelihood of expansions and disease progression. Detection of these modifiers may lead to understanding and treating repeat expansion diseases. Here, we describe a method for the rapid, genome-wide identification of trans modifiers for repeat expansion in a yeast experimental system. Using this method, we found that missense mutations in the endoribonuclease subunit (Ysh1) of the mRNA cleavage and polyadenylation complex dramatically increase the rate of (GAA)n repeat expansions but only when they are actively transcribed. These expansions correlate with slower transcription elongation caused by the ysh1 mutation. These results reveal an interplay between RNA processing and repeat-mediated genome instability, confirming the validity of our approach.
Collapse
Affiliation(s)
- Ryan J McGinty
- Department of Biology, Tufts University, Medford, MA 02421, USA
| | - Franco Puleo
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Anna Y Aksenova
- Department of Biology, Tufts University, Medford, MA 02421, USA; Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Julia A Hisey
- Department of Biology, Tufts University, Medford, MA 02421, USA
| | - Alexander A Shishkin
- Department of Biology, Tufts University, Medford, MA 02421, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Erika L Pearson
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Eric T Wang
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA; Center for Neurogenetics, University of Florida, Gainesville, FL 32610, USA
| | - David E Housman
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
| | - Claire Moore
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02421, USA.
| |
Collapse
|
124
|
Artsimovitch I. Rebuilding the bridge between transcription and translation. Mol Microbiol 2018; 108:467-472. [PMID: 29608805 DOI: 10.1111/mmi.13964] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2018] [Indexed: 12/21/2022]
Abstract
In Bacteria, ribosomes may bind to the nascent RNA emerging from the transcribing RNA polymerase and initiate translation. Transcription-translation coupling plays diverse roles in cellular physiology, including attenuation control, mRNA surveillance and maintenance of genome integrity. While the existence of coupling is broadly accepted, its mechanism and ubiquity are debated. Structural evidence supports mutually exclusive modes of RNA polymerase-ribosome contacts. In a model based on nuclear magnetic resonance data, NusG binds to a ribosomal protein S10 and acts as an adapter between RNA polymerase and the 30S subunit. Recent single-particle cryo electron microscopy analyses of RNA polymerase bound to 30S and 70S ribosomes revealed extensive, and very distinct, contacts which are incompatible with bridging by NusG. Saxena et al. provide the first evidence for NusG-mediated coupling in vivo. Their results demonstrate that Escherichia coli NusG interacts with the 70S ribosomes through a previously established interface and that these interactions are required for survival when translation elongation is hindered to weaken coupling. Future studies will address a likely possibility that distinct bridging mechanisms underpin context-dependent coupling in the cell.
Collapse
Affiliation(s)
- Irina Artsimovitch
- Department of Microbiology, The Center for RNA Biology, The Ohio State University, Columbus, Ohio, 43210, USA
| |
Collapse
|
125
|
Kotsantis P, Petermann E, Boulton SJ. Mechanisms of Oncogene-Induced Replication Stress: Jigsaw Falling into Place. Cancer Discov 2018; 8:537-555. [PMID: 29653955 DOI: 10.1158/2159-8290.cd-17-1461] [Citation(s) in RCA: 232] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/26/2018] [Accepted: 03/09/2018] [Indexed: 12/31/2022]
Abstract
Oncogene activation disturbs cellular processes and accommodates a complex landscape of changes in the genome that contribute to genomic instability, which accelerates mutation rates and promotes tumorigenesis. Part of this cellular turmoil involves deregulation of physiologic DNA replication, widely described as replication stress. Oncogene-induced replication stress is an early driver of genomic instability and is attributed to a plethora of factors, most notably aberrant origin firing, replication-transcription collisions, reactive oxygen species, and defective nucleotide metabolism.Significance: Replication stress is a fundamental step and an early driver of tumorigenesis and has been associated with many activated oncogenes. Deciphering the mechanisms that contribute to the replication stress response may provide new avenues for targeted cancer treatment. In this review, we discuss the latest findings on the DNA replication stress response and examine the various mechanisms through which activated oncogenes induce replication stress. Cancer Discov; 8(5); 537-55. ©2018 AACR.
Collapse
Affiliation(s)
| | - Eva Petermann
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | | |
Collapse
|
126
|
Saxena S, Myka KK, Washburn R, Costantino N, Court DL, Gottesman ME. Escherichia coli transcription factor NusG binds to 70S ribosomes. Mol Microbiol 2018; 108:495-504. [PMID: 29575154 DOI: 10.1111/mmi.13953] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2018] [Indexed: 10/17/2022]
Abstract
Transcription and translation are coupled processes in bacteria. A role of transcription elongation cofactor NusG in coupling has been suggested by in vitro structural studies. NMR revealed association of the NusG carboxy-terminal domain with S10 (NusE), implying a direct role for NusG as a bridge linking RNAP and the lead ribosome. Here we present the first in vitro and in vivo evidence of full-length NusG association with mature 70S ribosomes. Binding did not require accessory factors in vitro. Mutating the NusG:S10 binding interface at NusG F165 or NusE M88 and D97 residues weakened NusG:S10 association in vivo and completely abolished it in vitro, supporting the specificity of this interaction. Mutations in the binding interface increased sensitivity to chloramphenicol. This phenotype was suppressed by rpoB*35, an RNAP mutation that reduces replisome-RNAP clashes. We propose that weakened NusG:S10 interaction leads to uncoupling when translation is inhibited, with resulting RNAP backtracking, replication blocks and formation of lethal DNA double-strand breaks.
Collapse
Affiliation(s)
- Shivalika Saxena
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Kamila K Myka
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Robert Washburn
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Nina Costantino
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Donald L Court
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Max E Gottesman
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| |
Collapse
|
127
|
Le TT, Yang Y, Tan C, Suhanovsky MM, Fulbright RM, Inman JT, Li M, Lee J, Perelman S, Roberts JW, Deaconescu AM, Wang MD. Mfd Dynamically Regulates Transcription via a Release and Catch-Up Mechanism. Cell 2017; 172:344-357.e15. [PMID: 29224782 DOI: 10.1016/j.cell.2017.11.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 09/21/2017] [Accepted: 11/09/2017] [Indexed: 11/25/2022]
Abstract
The bacterial Mfd ATPase is increasingly recognized as a general transcription factor that participates in the resolution of transcription conflicts with other processes/roadblocks. This function stems from Mfd's ability to preferentially act on stalled RNA polymerases (RNAPs). However, the mechanism underlying this preference and the subsequent coordination between Mfd and RNAP have remained elusive. Here, using a novel real-time translocase assay, we unexpectedly discovered that Mfd translocates autonomously on DNA. The speed and processivity of Mfd dictate a "release and catch-up" mechanism to efficiently patrol DNA for frequently stalled RNAPs. Furthermore, we showed that Mfd prevents RNAP backtracking or rescues a severely backtracked RNAP, allowing RNAP to overcome stronger obstacles. However, if an obstacle's resistance is excessive, Mfd dissociates the RNAP, clearing the DNA for other processes. These findings demonstrate a remarkably delicate coordination between Mfd and RNAP, allowing efficient targeting and recycling of Mfd and expedient conflict resolution.
Collapse
Affiliation(s)
- Tung T Le
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Yi Yang
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Chuang Tan
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Margaret M Suhanovsky
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA
| | | | - James T Inman
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Ming Li
- Department of Chemistry, Cornell University, Ithaca, NY 14853, USA
| | - Jaeyoon Lee
- Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Sarah Perelman
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA
| | - Jeffrey W Roberts
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Alexandra M Deaconescu
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA
| | - Michelle D Wang
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
128
|
Imashimizu M, Lukatsky DB. Transcription pausing: biological significance of thermal fluctuations biased by repetitive genomic sequences. Transcription 2017; 9:196-203. [PMID: 29105534 PMCID: PMC5927657 DOI: 10.1080/21541264.2017.1393492] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Transcription of DNA by RNA polymerase (RNAP) takes place in a cell environment dominated by thermal fluctuations. How are transcription reactions including initiation, elongation, and termination on genomic DNA so well-controlled during such fluctuations? A recent statistical mechanical approach using high-throughput sequencing data reveals that repetitive DNA sequence elements embedded into a genomic sequence provide the key mechanism to functionally bias the fluctuations of transcription elongation complexes. In particular, during elongation pausing, such repetitive sequence elements can increase the magnitude of one-dimensional diffusion of the RNAP enzyme on the DNA upstream of the pausing site, generating a large variation in the dwell times of RNAP pausing under the control of these genomic signals.
Collapse
Affiliation(s)
- Masahiko Imashimizu
- a Institute of Medical Science , University of Tokyo , Minato-ku, Tokyo , Japan
| | - David B Lukatsky
- b Department of Chemistry , Ben-Gurion University of the Negev , Be'er Sheva , Israel
| |
Collapse
|
129
|
Fan H, Conn AB, Williams PB, Diggs S, Hahm J, Gamper HB, Hou YM, O'Leary SE, Wang Y, Blaha GM. Transcription-translation coupling: direct interactions of RNA polymerase with ribosomes and ribosomal subunits. Nucleic Acids Res 2017; 45:11043-11055. [PMID: 28977553 PMCID: PMC5737488 DOI: 10.1093/nar/gkx719] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/09/2017] [Indexed: 11/12/2022] Open
Abstract
In prokaryotes, RNA polymerase and ribosomes can bind concurrently to the same RNA transcript, leading to the functional coupling of transcription and translation. The interactions between RNA polymerase and ribosomes are crucial for the coordination of transcription with translation. Here, we report that RNA polymerase directly binds ribosomes and isolated large and small ribosomal subunits. RNA polymerase and ribosomes form a one-to-one complex with a micromolar dissociation constant. The formation of the complex is modulated by the conformational and functional states of RNA polymerase and the ribosome. The binding interface on the large ribosomal subunit is buried by the small subunit during protein synthesis, whereas that on the small subunit remains solvent-accessible. The RNA polymerase binding site on the ribosome includes that of the isolated small ribosomal subunit. This direct interaction between RNA polymerase and ribosomes may contribute to the coupling of transcription to translation.
Collapse
Affiliation(s)
- Haitian Fan
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Adam B Conn
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Preston B Williams
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Stephen Diggs
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Joseph Hahm
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Howard B Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Seán E O'Leary
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Gregor M Blaha
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| |
Collapse
|
130
|
Schroeder JW, Yeesin P, Simmons LA, Wang JD. Sources of spontaneous mutagenesis in bacteria. Crit Rev Biochem Mol Biol 2017; 53:29-48. [PMID: 29108429 DOI: 10.1080/10409238.2017.1394262] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mutations in an organism's genome can arise spontaneously, that is, in the absence of exogenous stress and prior to selection. Mutations are often neutral or deleterious to individual fitness but can also provide genetic diversity driving evolution. Mutagenesis in bacteria contributes to the already serious and growing problem of antibiotic resistance. However, the negative impacts of spontaneous mutagenesis on human health are not limited to bacterial antibiotic resistance. Spontaneous mutations also underlie tumorigenesis and evolution of drug resistance. To better understand the causes of genetic change and how they may be manipulated in order to curb antibiotic resistance or the development of cancer, we must acquire a mechanistic understanding of the major sources of mutagenesis. Bacterial systems are particularly well-suited to studying mutagenesis because of their fast growth rate and the panoply of available experimental tools, but efforts to understand mutagenic mechanisms can be complicated by the experimental system employed. Here, we review our current understanding of mutagenic mechanisms in bacteria and describe the methods used to study mutagenesis in bacterial systems.
Collapse
Affiliation(s)
- Jeremy W Schroeder
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
| | - Ponlkrit Yeesin
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
| | - Lyle A Simmons
- b Department of Molecular, Cellular, and Developmental Biology , University of Michigan , Ann Arbor , MI , USA
| | - Jue D Wang
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
| |
Collapse
|
131
|
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.
Collapse
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
| |
Collapse
|
132
|
James K, Gamba P, Cockell SJ, Zenkin N. Misincorporation by RNA polymerase is a major source of transcription pausing in vivo. Nucleic Acids Res 2017; 45:1105-1113. [PMID: 28180286 PMCID: PMC5388426 DOI: 10.1093/nar/gkw969] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/07/2016] [Accepted: 10/11/2016] [Indexed: 11/13/2022] Open
Abstract
The transcription error rate estimated from mistakes in end product RNAs is 10−3–10−5. We analyzed the fidelity of nascent RNAs from all actively transcribing elongation complexes (ECs) in Escherichia coli and Saccharomyces cerevisiae and found that 1–3% of all ECs in wild-type cells, and 5–7% of all ECs in cells lacking proofreading factors are, in fact, misincorporated complexes. With the exception of a number of sequence-dependent hotspots, most misincorporations are distributed relatively randomly. Misincorporation at hotspots does not appear to be stimulated by pausing. Since misincorporation leads to a strong pause of transcription due to backtracking, our findings indicate that misincorporation could be a major source of transcriptional pausing and lead to conflicts with other RNA polymerases and replication in bacteria and eukaryotes. This observation implies that physical resolution of misincorporated complexes may be the main function of the proofreading factors Gre and TFIIS. Although misincorporation mechanisms between bacteria and eukaryotes appear to be conserved, the results suggest the existence of a bacteria-specific mechanism(s) for reducing misincorporation in protein-coding regions. The links between transcription fidelity, human disease, and phenotypic variability in genetically-identical cells can be explained by the accumulation of misincorporated complexes, rather than mistakes in mature RNA.
Collapse
Affiliation(s)
- Katherine James
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Bioscience, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle Upon Tyne, UK
| | - Pamela Gamba
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Bioscience, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle Upon Tyne, UK
| | - Simon J Cockell
- Bioinformatics Support Unit, Newcastle University, William Leech Building, Framlington Place, Newcastle Upon Tyne, UK
| | - Nikolay Zenkin
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Bioscience, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle Upon Tyne, UK
| |
Collapse
|
133
|
Transcription fidelity and its roles in the cell. Curr Opin Microbiol 2017; 42:13-18. [PMID: 28968546 PMCID: PMC5904569 DOI: 10.1016/j.mib.2017.08.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/11/2017] [Accepted: 08/18/2017] [Indexed: 12/21/2022]
Abstract
The Trigger Loop is one of the major determinants of transcription fidelity. Intrinsic proofreading occurs via transcript-assisted cleavage. Factor-assisted proofreading takes place via exchange of RNAP active centres. Misincorporation is a major source of transcription pausing. Another role of fidelity is the prevention of conflicts with other cellular processes.
Accuracy of transcription is essential for productive gene expression, and the past decade has brought new understanding of the mechanisms ensuring transcription fidelity. The discovery of a new catalytic domain, the Trigger Loop, revealed that RNA polymerase can actively choose the correct substrates. Also, the intrinsic proofreading activity was found to proceed via a ribozyme-like mechanism, whereby the erroneous nucleoside triphosphate (NTP) helps its own excision. Factor-assisted proofreading was shown to proceed through an exchange of active centres, a unique phenomenon among proteinaceous enzymes. Furthermore, most recent in vivo studies have revised the roles of transcription accuracy and proofreading factors, as not only required for production of errorless RNAs, but also for prevention of frequent misincorporation-induced pausing that may cause conflicts with fellow RNA polymerases and the replication machinery.
Collapse
|
134
|
Genome-Wide Spectra of Transcription Insertions and Deletions Reveal That Slippage Depends on RNA:DNA Hybrid Complementarity. mBio 2017; 8:mBio.01230-17. [PMID: 28851848 PMCID: PMC5574713 DOI: 10.1128/mbio.01230-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Advances in sequencing technologies have enabled direct quantification of genome-wide errors that occur during RNA transcription. These errors occur at rates that are orders of magnitude higher than rates during DNA replication, but due to technical difficulties such measurements have been limited to single-base substitutions and have not yet quantified the scope of transcription insertions and deletions. Previous reporter gene assay findings suggested that transcription indels are produced exclusively by elongation complex slippage at homopolymeric runs, so we enumerated indels across the protein-coding transcriptomes of Escherichia coli and Buchnera aphidicola, which differ widely in their genomic base compositions and incidence of repeat regions. As anticipated from prior assays, transcription insertions prevailed in homopolymeric runs of A and T; however, transcription deletions arose in much more complex sequences and were rarely associated with homopolymeric runs. By reconstructing the relocated positions of the elongation complex as inferred from the sequences inserted or deleted during transcription, we show that continuation of transcription after slippage hinges on the degree of nucleotide complementarity within the RNA:DNA hybrid at the new DNA template location. The high level of mistakes generated during transcription can result in the accumulation of malfunctioning and misfolded proteins which can alter global gene regulation and in the expenditure of energy to degrade these nonfunctional proteins. The transcriptome-wide occurrence of base substitutions has been elucidated in bacteria, but information on transcription insertions and deletions—errors that potentially have more dire effects on protein function—is limited to reporter gene constructs. Here, we capture the transcriptome-wide spectrum of insertions and deletions in Escherichia coli and Buchnera aphidicola and show that they occur at rates approaching those of base substitutions. Knowledge of the full extent of sequences subject to transcription indels supports a new model of bacterial transcription slippage, one that relies on the number of complementary bases between the transcript and the DNA template to which it slipped.
Collapse
|
135
|
Hamperl S, Bocek MJ, Saldivar JC, Swigut T, Cimprich KA. Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses. Cell 2017; 170:774-786.e19. [PMID: 28802045 DOI: 10.1016/j.cell.2017.07.043] [Citation(s) in RCA: 388] [Impact Index Per Article: 55.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 05/09/2017] [Accepted: 07/25/2017] [Indexed: 12/19/2022]
Abstract
Conflicts between transcription and replication are a potent source of DNA damage. Co-transcriptional R-loops could aggravate such conflicts by creating an additional barrier to replication fork progression. Here, we use a defined episomal system to investigate how conflict orientation and R-loop formation influence genome stability in human cells. R-loops, but not normal transcription complexes, induce DNA breaks and orientation-specific DNA damage responses during conflicts with replication forks. Unexpectedly, the replisome acts as an orientation-dependent regulator of R-loop levels, reducing R-loops in the co-directional (CD) orientation but promoting their formation in the head-on (HO) orientation. Replication stress and deregulated origin firing increase the number of HO collisions leading to genome-destabilizing R-loops. Our findings connect DNA replication to R-loop homeostasis and suggest a mechanistic basis for genome instability resulting from deregulated DNA replication, observed in cancer and other disease states.
Collapse
Affiliation(s)
- Stephan Hamperl
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael J Bocek
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joshua C Saldivar
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
136
|
Replication-Transcription Conflicts Generate R-Loops that Orchestrate Bacterial Stress Survival and Pathogenesis. Cell 2017; 170:787-799.e18. [PMID: 28802046 DOI: 10.1016/j.cell.2017.07.044] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 05/09/2017] [Accepted: 07/25/2017] [Indexed: 12/31/2022]
Abstract
Replication-transcription collisions shape genomes, influence evolution, and promote genetic diseases. Although unclear why, head-on transcription (lagging strand genes) is especially disruptive to replication and promotes genomic instability. Here, we find that head-on collisions promote R-loop formation in Bacillus subtilis. We show that pervasive R-loop formation at head-on collision regions completely blocks replication, elevates mutagenesis, and inhibits gene expression. Accordingly, the activity of the R-loop processing enzyme RNase HIII at collision regions is crucial for stress survival in B. subtilis, as many stress response genes are head-on to replication. Remarkably, without RNase HIII, the ability of the intracellular pathogen Listeria monocytogenes to infect and replicate in hosts is weakened significantly, most likely because many virulence genes are head-on to replication. We conclude that the detrimental effects of head-on collisions stem primarily from excessive R-loop formation and that the resolution of these structures is critical for bacterial stress survival and pathogenesis.
Collapse
|
137
|
Abstract
At the end of the multistep transcription process, the elongating RNA polymerase (RNAP) is dislodged from the DNA template either at specific DNA sequences, called the terminators, or by a nascent RNA-dependent helicase, Rho. In Escherichia coli, about half of the transcription events are terminated by the Rho protein. Rho utilizes its RNA-dependent ATPase activities to translocate along the mRNA and eventually dislodges the RNAP via an unknown mechanism. The transcription elongation factor NusG facilitates this termination process by directly interacting with Rho. In this review, we discuss current models describing the mechanism of action of this hexameric transcription terminator, its regulation by different cis and trans factors, and the effects of the termination process on physiological processes in bacterial cells, particularly E. coli and Salmonella enterica Typhimurium.
Collapse
Affiliation(s)
- Pallabi Mitra
- Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad-500001, India; , , ,
| | - Gairika Ghosh
- Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad-500001, India; , , , .,Department of Graduate Studies, Manipal University, Manipal, Karnataka-576104, India
| | - Md Hafeezunnisa
- Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad-500001, India; , , , .,Department of Graduate Studies, Manipal University, Manipal, Karnataka-576104, India
| | - Ranjan Sen
- Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad-500001, India; , , ,
| |
Collapse
|
138
|
Sedlyarova N, Rescheneder P, Magán A, Popitsch N, Rziha N, Bilusic I, Epshtein V, Zimmermann B, Lybecker M, Sedlyarov V, Schroeder R, Nudler E. Natural RNA Polymerase Aptamers Regulate Transcription in E. coli. Mol Cell 2017; 67:30-43.e6. [PMID: 28648779 PMCID: PMC5535762 DOI: 10.1016/j.molcel.2017.05.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 04/10/2017] [Accepted: 05/23/2017] [Indexed: 01/19/2023]
Abstract
In search for RNA signals that modulate transcription via direct interaction with RNA polymerase (RNAP), we deep sequenced an E. coli genomic library enriched for RNAP-binding RNAs. Many natural RNAP-binding aptamers, termed RAPs, were mapped to the genome. Over 60% of E. coli genes carry RAPs in their mRNA. Combining in vitro and in vivo approaches, we characterized a subset of inhibitory RAPs (iRAPs) that promote Rho-dependent transcription termination. A representative iRAP within the coding region of the essential gene, nadD, greatly reduces its transcriptional output in stationary phase and under oxidative stress, demonstrating that iRAPs control gene expression in response to changing environment. The mechanism of iRAPs involves active uncoupling of transcription and translation, making nascent RNA accessible to Rho. iRAPs encoded in the antisense strand also promote gene expression by reducing transcriptional interference. In essence, our work uncovers a broad class of cis-acting RNA signals that globally control bacterial transcription.
Collapse
Affiliation(s)
- Nadezda Sedlyarova
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9/5, 1030 Vienna, Austria
| | - Philipp Rescheneder
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna & Medical University of Vienna, 1030 Vienna, Austria
| | - Andrés Magán
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9/5, 1030 Vienna, Austria
| | - Niko Popitsch
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090 Vienna, Austria
| | - Natascha Rziha
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9/5, 1030 Vienna, Austria
| | - Ivana Bilusic
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9/5, 1030 Vienna, Austria
| | - Vitaly Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Bob Zimmermann
- Department of Molecular Evolution and Development, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Meghan Lybecker
- University of Colorado, 1420 Austin Bluffs Parkway, Colorado Springs, CO 80918, USA
| | - Vitaly Sedlyarov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Renée Schroeder
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9/5, 1030 Vienna, Austria.
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA.
| |
Collapse
|
139
|
Mustaev A, Roberts J, Gottesman M. Transcription elongation. Transcription 2017; 8:150-161. [PMID: 28301288 PMCID: PMC5501382 DOI: 10.1080/21541264.2017.1289294] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/25/2017] [Accepted: 01/26/2017] [Indexed: 12/23/2022] Open
Abstract
This review is focused on recent progress in understanding how Escherichia coli RNAP polymerase translocates along the DNA template and the factors that affect this movement. We discuss the fundamental aspects of RNAP translocation, template signals that influence forward or backward movement, and host or phage factors that modulate translocation.
Collapse
Affiliation(s)
- Arkady Mustaev
- PHRI Center, NJMS, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Jeffrey Roberts
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Max Gottesman
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY, USA
| |
Collapse
|
140
|
Blumenfeld B, Ben-Zimra M, Simon I. Perturbations in the Replication Program Contribute to Genomic Instability in Cancer. Int J Mol Sci 2017; 18:E1138. [PMID: 28587102 PMCID: PMC5485962 DOI: 10.3390/ijms18061138] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/08/2017] [Accepted: 05/21/2017] [Indexed: 12/14/2022] Open
Abstract
Cancer and genomic instability are highly impacted by the deoxyribonucleic acid (DNA) replication program. Inaccuracies in DNA replication lead to the increased acquisition of mutations and structural variations. These inaccuracies mainly stem from loss of DNA fidelity due to replication stress or due to aberrations in the temporal organization of the replication process. Here we review the mechanisms and impact of these major sources of error to the replication program.
Collapse
Affiliation(s)
- Britny Blumenfeld
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
| | - Micha Ben-Zimra
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
- Pharmacology and Experimental Therapeutics Unit, The Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel.
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
| |
Collapse
|
141
|
Conflict Resolution in the Genome: How Transcription and Replication Make It Work. Cell 2017; 167:1455-1467. [PMID: 27912056 DOI: 10.1016/j.cell.2016.09.053] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/20/2016] [Accepted: 09/27/2016] [Indexed: 01/12/2023]
Abstract
The complex machineries involved in replication and transcription translocate along the same DNA template, often in opposing directions and at different rates. These processes routinely interfere with each other in prokaryotes, and mounting evidence now suggests that RNA polymerase complexes also encounter replication forks in higher eukaryotes. Indeed, cells rely on numerous mechanisms to avoid, tolerate, and resolve such transcription-replication conflicts, and the absence of these mechanisms can lead to catastrophic effects on genome stability and cell viability. In this article, we review the cellular responses to transcription-replication conflicts and highlight how these inevitable encounters shape the genome and impact diverse cellular processes.
Collapse
|
142
|
Marnef A, Cohen S, Legube G. Transcription-Coupled DNA Double-Strand Break Repair: Active Genes Need Special Care. J Mol Biol 2017; 429:1277-1288. [PMID: 28363678 DOI: 10.1016/j.jmb.2017.03.024] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/22/2017] [Accepted: 03/23/2017] [Indexed: 12/22/2022]
Abstract
For decades, it has been speculated that specific loci on eukaryotic chromosomes are inherently susceptible to breakage. The advent of high-throughput genomic technologies has now paved the way to their identification. A wealth of data suggests that transcriptionally active loci are particularly fragile and that a specific DNA damage response is activated and dedicated to their repair. Here, we review current understanding of the crosstalk between transcription and double-strand break repair, from the reasons underlying the intrinsic fragility of genes to the mechanisms that restore the integrity of damaged transcription units.
Collapse
Affiliation(s)
- Aline Marnef
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, 118 Route de Narbonne, 31062 Toulouse, France
| | - Sarah Cohen
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, 118 Route de Narbonne, 31062 Toulouse, France
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, 118 Route de Narbonne, 31062 Toulouse, France.
| |
Collapse
|
143
|
Myka KK, Hawkins M, Syeda AH, Gupta MK, Meharg C, Dillingham MS, Savery NJ, Lloyd RG, McGlynn P. Inhibiting translation elongation can aid genome duplication in Escherichia coli. Nucleic Acids Res 2017; 45:2571-2584. [PMID: 27956500 PMCID: PMC5389703 DOI: 10.1093/nar/gkw1254] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/28/2016] [Accepted: 12/01/2016] [Indexed: 12/28/2022] Open
Abstract
Conflicts between replication and transcription challenge chromosome duplication. Escherichia coli replisome movement along transcribed DNA is promoted by Rep and UvrD accessory helicases with Δrep ΔuvrD cells being inviable under rapid growth conditions. We have discovered that mutations in a tRNA gene, aspT, in an aminoacyl tRNA synthetase, AspRS, and in a translation factor needed for efficient proline-proline bond formation, EF-P, suppress Δrep ΔuvrD lethality. Thus replication-transcription conflicts can be alleviated by the partial sacrifice of a mechanism that reduces replicative barriers, namely translating ribosomes that reduce RNA polymerase backtracking. Suppression depends on RelA-directed synthesis of (p)ppGpp, a signalling molecule that reduces replication-transcription conflicts, with RelA activation requiring ribosomal pausing. Levels of (p)ppGpp in these suppressors also correlate inversely with the need for Rho activity, an RNA translocase that can bind to emerging transcripts and displace transcription complexes. These data illustrate the fine balance between different mechanisms in facilitating gene expression and genome duplication and demonstrate that accessory helicases are a major determinant of this balance. This balance is also critical for other aspects of bacterial survival: the mutations identified here increase persistence indicating that similar mutations could arise in naturally occurring bacterial populations facing antibiotic challenge.
Collapse
Affiliation(s)
- Kamila K. Myka
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Michelle Hawkins
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Aisha H. Syeda
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Milind K. Gupta
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Caroline Meharg
- Institute for Global Food Security, Queen's University Belfast, David Keir Building, Malone Road, Belfast BT9 5BN, UK
| | - Mark S. Dillingham
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8, 1TD, UK
| | - Nigel J. Savery
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8, 1TD, UK
| | - Robert G. Lloyd
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Peter McGlynn
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| |
Collapse
|
144
|
Lukačišin M, Landon M, Jajoo R. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One 2017; 12:e0174066. [PMID: 28301878 PMCID: PMC5354634 DOI: 10.1371/journal.pone.0174066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 03/02/2017] [Indexed: 01/22/2023] Open
Abstract
RNA Polymerase II pauses and backtracks during transcription, with many consequences for gene expression and cellular physiology. Here, we show that the energy required to melt double-stranded nucleic acids in the transcription bubble predicts pausing in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do. In addition, the same energy difference also determines when the RNA polymerase backtracks instead of continuing to move forward. This data-driven model corroborates—in a genome wide and quantitative manner—previous evidence that sequence-dependent thermodynamic features of nucleic acids influence both transcriptional pausing and backtracking.
Collapse
Affiliation(s)
- Martin Lukačišin
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America
- IST Austria, Klosterneuburg, Austria
| | - Matthieu Landon
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America
- Department of Genetics, Harvard Medical School, Boston, MA, United States of America
- Ecole des Mines de Paris, Mines Paristech, Paris, France
| | - Rishi Jajoo
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America
- * E-mail:
| |
Collapse
|
145
|
Maraia RJ, Arimbasseri AG. Factors That Shape Eukaryotic tRNAomes: Processing, Modification and Anticodon-Codon Use. Biomolecules 2017; 7:biom7010026. [PMID: 28282871 PMCID: PMC5372738 DOI: 10.3390/biom7010026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 02/24/2017] [Indexed: 01/24/2023] Open
Abstract
Transfer RNAs (tRNAs) contain sequence diversity beyond their anticodons and the large variety of nucleotide modifications found in all kingdoms of life. Some modifications stabilize structure and fit in the ribosome whereas those to the anticodon loop modulate messenger RNA (mRNA) decoding activity more directly. The identities of tRNAs with some universal anticodon loop modifications vary among distant and parallel species, likely to accommodate fine tuning for their translation systems. This plasticity in positions 34 (wobble) and 37 is reflected in codon use bias. Here, we review convergent evidence that suggest that expansion of the eukaryotic tRNAome was supported by its dedicated RNA polymerase III transcription system and coupling to the precursor-tRNA chaperone, La protein. We also review aspects of eukaryotic tRNAome evolution involving G34/A34 anticodon-sparing, relation to A34 modification to inosine, biased codon use and regulatory information in the redundancy (synonymous) component of the genetic code. We then review interdependent anticodon loop modifications involving position 37 in eukaryotes. This includes the eukaryote-specific tRNA modification, 3-methylcytidine-32 (m3C32) and the responsible gene, TRM140 and homologs which were duplicated and subspecialized for isoacceptor-specific substrates and dependence on i6A37 or t6A37. The genetics of tRNA function is relevant to health directly and as disease modifiers.
Collapse
Affiliation(s)
- Richard J Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
- Commissioned Corps, U.S. Public Health Service, Rockville, MD, 20016, USA.
| | - Aneeshkumar G Arimbasseri
- Molecular Genetics Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.
| |
Collapse
|
146
|
Miropolskaya N, Esyunina D, Kulbachinskiy A. Conserved functions of the trigger loop and Gre factors in RNA cleavage by bacterial RNA polymerases. J Biol Chem 2017; 292:6744-6752. [PMID: 28242762 DOI: 10.1074/jbc.m116.766592] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 02/16/2017] [Indexed: 11/06/2022] Open
Abstract
RNA cleavage by RNA polymerase (RNAP) is the central step in co-transcriptional RNA proofreading. Bacterial RNAPs were proposed to rely on the same mobile element of the active site, the trigger loop (TL), for both nucleotide addition and RNA cleavage. RNA cleavage can also be stimulated by universal Gre factors, which should replace the TL to get access to the RNAP active site. The contributions of the TL and Gre factors to RNA cleavage reportedly vary between RNAPs from different bacterial species and, probably, different types of transcription complexes. Here, by comparing RNAPs from Escherichia coli, Deinococcus radiodurans, and Thermus aquaticus, we show that the functions of the TL and Gre factors in RNA cleavage are conserved in various species, with important variations that may be related to extremophilic adaptation. Deletions of the TL strongly impair intrinsic RNA cleavage by all three RNAPs and eliminate the interspecies differences in the reaction rates. GreA factors activate RNA cleavage by wild-type RNAPs to similar levels. The rates of GreA-dependent cleavage are lower for ΔTL RNAP variants, suggesting that the TL contributes to the Gre function. Finally, neither the TL nor GreA can efficiently activate RNA cleavage in certain types of backtracked transcription complexes, suggesting that these complexes adopt a catalytically inactive conformation probably important for transcription regulation.
Collapse
Affiliation(s)
- Nataliya Miropolskaya
- From the Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Square 2, Moscow 123182, Russia
| | - Daria Esyunina
- From the Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Square 2, Moscow 123182, Russia
| | - Andrey Kulbachinskiy
- From the Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Square 2, Moscow 123182, Russia
| |
Collapse
|
147
|
Selby CP. Mfd Protein and Transcription-Repair Coupling in Escherichia coli. Photochem Photobiol 2017; 93:280-295. [PMID: 27864884 DOI: 10.1111/php.12675] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/18/2016] [Indexed: 01/30/2023]
Abstract
In 1989, transcription-repair coupling (TRC) was first described in Escherichia coli, as the transcription-dependent, preferential nucleotide excision repair (NER) of UV photoproducts located in the template DNA strand. This finding led to pioneering biochemical studies of TRC in the laboratory of Professor Aziz Sancar, where, at the time, major contributions were being made toward understanding the roles of the UvrA, UvrB and UvrC proteins in NER. When the repair studies were extended to TRC, template but not coding strand lesions were found to block RNA polymerase (RNAP) in vitro, and unexpectedly, the blocked RNAP inhibited NER. A transcription-repair coupling factor, also called Mfd protein, was found to remove the blocked RNAP, deliver the repair enzyme to the lesion and thereby mediate more rapid repair of the transcription-blocking lesion compared with lesions elsewhere. Structural and functional analyses of Mfd protein revealed helicase motifs responsible for ATP hydrolysis and DNA binding, and regions that interact with RNAP and UvrA. These and additional studies provided a basis upon which other investigators, in following decades, have characterized fascinating and unexpected structural and mechanistic features of Mfd, revealed the possible existence of additional pathways of TRC and discovered additional roles of Mfd in the cell.
Collapse
Affiliation(s)
- Christopher P Selby
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC
| |
Collapse
|
148
|
Mangiameli SM, Merrikh CN, Wiggins PA, Merrikh H. Transcription leads to pervasive replisome instability in bacteria. eLife 2017; 6. [PMID: 28092263 PMCID: PMC5305214 DOI: 10.7554/elife.19848] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 01/15/2017] [Indexed: 12/19/2022] Open
Abstract
The canonical model of DNA replication describes a highly-processive and largely continuous process by which the genome is duplicated. This continuous model is based upon in vitro reconstitution and in vivo ensemble experiments. Here, we characterize the replisome-complex stoichiometry and dynamics with single-molecule resolution in bacterial cells. Strikingly, the stoichiometries of the replicative helicase, DNA polymerase, and clamp loader complexes are consistent with the presence of only one active replisome in a significant fraction of cells (>40%). Furthermore, many of the observed complexes have short lifetimes (<8 min), suggesting that replisome disassembly is quite prevalent, possibly occurring several times per cell cycle. The instability of the replisome complex is conflict-induced: transcription inhibition stabilizes these complexes, restoring the second replisome in many of the cells. Our results suggest that, in contrast to the canonical model, DNA replication is a largely discontinuous process in vivo due to pervasive replication-transcription conflicts. DOI:http://dx.doi.org/10.7554/eLife.19848.001
Collapse
Affiliation(s)
| | | | - Paul A Wiggins
- Department of Physics, University of Washington, Seattle, United States.,Department of Microbiology, University of Washington, Seattle, United States.,Department of Bioengineering, University of Washington, Seattle, United States
| | - Houra Merrikh
- Department of Microbiology, University of Washington, Seattle, United States.,Department of Genome Sciences, University of Washington, Seattle, United States
| |
Collapse
|
149
|
Mangiameli SM, Merrikh CN, Wiggins PA, Merrikh H. Transcription leads to pervasive replisome instability in bacteria. eLife 2017; 6. [PMID: 28092263 DOI: 10.7554/elife.19848.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 01/15/2017] [Indexed: 05/21/2023] Open
Abstract
The canonical model of DNA replication describes a highly-processive and largely continuous process by which the genome is duplicated. This continuous model is based upon in vitro reconstitution and in vivo ensemble experiments. Here, we characterize the replisome-complex stoichiometry and dynamics with single-molecule resolution in bacterial cells. Strikingly, the stoichiometries of the replicative helicase, DNA polymerase, and clamp loader complexes are consistent with the presence of only one active replisome in a significant fraction of cells (>40%). Furthermore, many of the observed complexes have short lifetimes (<8 min), suggesting that replisome disassembly is quite prevalent, possibly occurring several times per cell cycle. The instability of the replisome complex is conflict-induced: transcription inhibition stabilizes these complexes, restoring the second replisome in many of the cells. Our results suggest that, in contrast to the canonical model, DNA replication is a largely discontinuous process in vivo due to pervasive replication-transcription conflicts.
Collapse
Affiliation(s)
| | | | - Paul A Wiggins
- Department of Physics, University of Washington, Seattle, United States
- Department of Microbiology, University of Washington, Seattle, United States
- Department of Bioengineering, University of Washington, Seattle, United States
| | - Houra Merrikh
- Department of Microbiology, University of Washington, Seattle, United States
- Department of Genome Sciences, University of Washington, Seattle, United States
| |
Collapse
|
150
|
Abstract
Pausing by RNA polymerase is a major mechanism that regulates transcription elongation but can cause conflicts with fellow RNA polymerases and other cellular machineries. Here, we summarize our recent finding that misincorporation could be a major source of transcription pausing in vivo, and discuss the role of misincorporation-induced pausing.
Collapse
Affiliation(s)
- Pamela Gamba
- a Centre for Bacterial Cell Biology , Institute for Cell and Molecular Biosciences, Newcastle University , Newcastle upon Tyne , UK
| | - Katherine James
- a Centre for Bacterial Cell Biology , Institute for Cell and Molecular Biosciences, Newcastle University , Newcastle upon Tyne , UK
| | - Nikolay Zenkin
- a Centre for Bacterial Cell Biology , Institute for Cell and Molecular Biosciences, Newcastle University , Newcastle upon Tyne , UK
| |
Collapse
|