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Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA. Structural basis for transcription complex disruption by the Mfd translocase. eLife 2021; 10:62117. [PMID: 33480355 PMCID: PMC7864632 DOI: 10.7554/elife.62117] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/21/2021] [Indexed: 12/30/2022] Open
Abstract
Transcription-coupled repair (TCR) is a sub-pathway of nucleotide excision repair (NER) that preferentially removes lesions from the template-strand (t-strand) that stall RNA polymerase (RNAP) elongation complexes (ECs). Mfd mediates TCR in bacteria by removing the stalled RNAP concealing the lesion and recruiting Uvr(A)BC. We used cryo-electron microscopy to visualize Mfd engaging with a stalled EC and attempting to dislodge the RNAP. We visualized seven distinct Mfd-EC complexes in both ATP and ADP-bound states. The structures explain how Mfd is remodeled from its repressed conformation, how the UvrA-interacting surface of Mfd is hidden during most of the remodeling process to prevent premature engagement with the NER pathway, how Mfd alters the RNAP conformation to facilitate disassembly, and how Mfd forms a processive translocation complex after dislodging the RNAP. Our results reveal an elaborate mechanism for how Mfd kinetically discriminates paused from stalled ECs and disassembles stalled ECs to initiate TCR.
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Affiliation(s)
- Jin Young Kang
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
| | - Eliza Llewellyn
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
| | - James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Joshua Brewer
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
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Olinares PDB, Kang JY, Llewellyn E, Chiu C, Chen J, Malone B, Saecker RM, Campbell EA, Darst SA, Chait BT. Native Mass Spectrometry-Based Screening for Optimal Sample Preparation in Single-Particle Cryo-EM. Structure 2020; 29:186-195.e6. [PMID: 33217329 PMCID: PMC7867593 DOI: 10.1016/j.str.2020.11.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/26/2020] [Accepted: 11/02/2020] [Indexed: 01/19/2023]
Abstract
Recent advances in single-particle cryogenic electron microscopy (cryo-EM) have enabled the structural determination of numerous protein assemblies at high resolution, yielding unprecedented insights into their function. However, despite its extraordinary capabilities, cryo-EM remains time-consuming and resource-intensive. It is therefore beneficial to have a means for rapidly assessing and optimizing the quality of samples prior to lengthy cryo-EM analyses. To do this, we have developed a native mass spectrometry (nMS) platform that provides rapid feedback on sample quality and highly streamlined biochemical screening. Because nMS enables accurate mass analysis of protein complexes, it is well suited to routine evaluation of the composition, integrity, and homogeneity of samples prior to their plunge-freezing on EM grids. We demonstrate the utility of our nMS-based platform for facilitating cryo-EM studies using structural characterizations of exemplar bacterial transcription complexes as well as the replication-transcription assembly from the SARS-CoV-2 virus that is responsible for the COVID-19 pandemic.
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Affiliation(s)
- Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA.
| | - Jin Young Kang
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Eliza Llewellyn
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Courtney Chiu
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Brandon Malone
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Ruth M Saecker
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA.
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Genome-wide transcription-coupled repair in Escherichia coli is mediated by the Mfd translocase. Proc Natl Acad Sci U S A 2017; 114:E2116-E2125. [PMID: 28167766 PMCID: PMC5358382 DOI: 10.1073/pnas.1700230114] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In transcription-coupled repair (TCR), nucleotide excision repair occurs most rapidly in the template strand of actively transcribed genes. TCR has been observed in a limited set of genes directly assayed in Escherichia coli cells. In vitro, Mfd translocase performs reactions necessary to mediate TCR: It removes RNA polymerase blocked by a template strand lesion and rapidly delivers repair enzymes to the lesion. This study applied excision repair sequencing methodology to map the location of repair sites in different E. coli strains. Results showed that Mfd-dependent TCR is widespread in the E. coli genome. Results with UvrD helicase demonstrated its role in basal repair, but no overall role in TCR. We used high-throughput sequencing of short, cyclobutane pyrimidine dimer-containing ssDNA oligos generated during repair of UV-induced damage to study that process at both mechanistic and systemic levels in Escherichia coli. Numerous important insights on DNA repair were obtained, bringing clarity to the respective roles of UvrD helicase and Mfd translocase in repair of UV-induced damage. Mechanistically, experiments showed that the predominant role of UvrD in vivo is to unwind the excised 13-mer from dsDNA and that mutation of uvrD results in remarkable protection of that oligo from exonuclease activity as it remains hybridized to the dsDNA. Genome-wide analysis of the transcribed strand/nontranscribed strand (TS/NTS) repair ratio demonstrated that deletion of mfd globally shifts the distribution of TS/NTS ratios downward by a factor of about 2 on average for the most highly transcribed genes. Even for the least transcribed genes, Mfd played a role in preferential repair of the transcribed strand. On the other hand, mutation of uvrD, if anything, slightly pushed the distribution of TS/NTS ratios to higher ratios. These results indicate that Mfd is the transcription repair-coupling factor whereas UvrD plays a role in excision repair by aiding the catalytic turnover of excision repair proteins.
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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.
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Affiliation(s)
- Christopher P Selby
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC
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Iannone R, Inga A, Luque-Romero FL, Menichini P, Abbondandolo A, Abril N, Pueyo C, Fronza G. Mutation spectra analysis suggests that N-(2-chloroethyl)-N′-cyclohexyl-N-nitrosourea-induced lesions are subject to transcription-coupled repair in Escherichia coli. Mol Carcinog 1997. [DOI: 10.1002/(sici)1098-2744(199705)19:1<39::aid-mc6>3.0.co;2-i] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abstract
Mutation frequency decline is the rapid and irreversible decline in the suppressor mutation frequency of Escherichia coli cells if the cells are kept in nongrowth media immediately following the mutagenic treatment. The gene mfd, which is necessary for mutation frequency decline, encodes a protein of 130 kDa which couples transcription to excision repair by binding to RNA polymerase and to UvrA, which is the damage recognition subunit of the excision repair enzyme. Although current evidence suggests that transcription-repair coupling is the cause of the preferential repair of the transcribed strand of mRNA encoding genes as well as of suppressor tRNA genes, the decline occurs under stringent response conditions in which the tRNA genes are not efficiently transcribed. Thus, the mechanism of strand-specific repair is well understood, but some questions remain regarding the precise mechanism of mutation frequency decline.
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Affiliation(s)
- C P Selby
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill 27599
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Abstract
'Mutation frequency decline' (MFD) was discovered about forty years ago, and described as the disappearance of a particular class of ultraviolet light-induced mutations in Escherichia coli that occurred whenever protein synthesis was briefly inhibited immediately after irradiation. Later, MFD was interpreted as an excision repair anomaly uniquely affecting nonsense suppressor mutations induced in certain tRNA genes. Never fully understood, MFD has recently been linked to the newly discovered transcription-coupled rapid repair of ultraviolet damage on the template strand of active genes. This article recalls the emergence and development of the MFD story, and offers a new way to explain it and its relation to strand-specific excision repair.
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Affiliation(s)
- E M Witkin
- Waksman Institute, Rutgers State University of New Jersey, Piscataway 08855-0759
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Affiliation(s)
- C P Selby
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill 27599
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Abstract
Lesions in the transcribed strand block transcription and are repaired more rapidly than lesions in the nontranscribed (coding) strand which do not block RNA polymerase (RNAP). It has been shown previously that in Escherichia coli the mfd (mutation frequency decline) gene is necessary for strand-specific repair. The mfd gene was cloned and sequenced and the Mfd protein was purified and used to reconstitute strand-specific repair in a completely defined system. The mfd gene encodes a protein of 130 kilodaltons and contains the so-called "helicase motifs," a leucine zipper motif, and regions of sequence similarity to UvrB and RecG proteins. The Mfd protein was shown to (i) displace RNAP stalled at a lesion in an adenosine triphosphate-dependent reaction, (ii) bind to the damage recognition subunit (UvrA) of the excision nuclease, and (iii) stimulate the repair of the transcribed strand only when transcription is taking place. Thus, Mfd appears to target the transcribed strand for repair by recognizing a stalled RNAP and actively recruiting the repair enzyme to the transcription blocking lesion as it dissociates the stalled RNAP.
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Affiliation(s)
- C P Selby
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill 27599
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Abstract
When populations of microorganisms are subjected to certain nonlethal selections, useful mutants arise among the nongrowing cells whereas useless mutants do not. This phenomenon, known as adaptive, directed, or selection-induced mutation, challenges the long-held belief that mutations only arise at random and without regard for utility. In recent years a growing number of studies have examined adaptive mutation in both bacteria and yeast. Although conflicts and controversies remain, the weight of the evidence indicates that adaptive mutation cannot be explained by trivial artifacts and that nondividing cells accumulate mutations in the absence of genomic replication. Because this process tends to produce only useful mutations, the cells appear to have a mechanism for preventing useless genetic changes from occurring or for eliminating them after they occur. The model that most readily explains the evidence is that cells under stress produce genetic variants continuously and at random, but these variants are immortalized as mutations only if they allow the cell to grow.
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Affiliation(s)
- P L Foster
- Department of Environmental Health, Boston University School of Public Health, Massachusetts 02118
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Oller AR, Fijalkowska IJ, Dunn RL, Schaaper RM. Transcription-repair coupling determines the strandedness of ultraviolet mutagenesis in Escherichia coli. Proc Natl Acad Sci U S A 1992; 89:11036-40. [PMID: 1438310 PMCID: PMC50478 DOI: 10.1073/pnas.89.22.11036] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We have analyzed the spectra of UV-induced mutations in the lacI gene of a wild-type and an mfd strain of Escherichia coli. mfd strains have been recently proposed to be deficient in a factor coupling DNA repair and transcription. Analysis of UV-induced mutations occurring at adjacent pyrimidines showed that mutations in the wild-type strain arose largely from the nontranscribed strand but arose predominantly from the transcribed strand in the mfd strain. The overall strand switch was 14-fold. One mutation, G.C-->A.T in the lacI initiation codon, showed a > 300-fold shift. No effect was observed for mutations at non-pyrimidine-pyrimidine sequences. These results provide in vivo evidence for a key role of the mfd gene in controlling the strandedness of mutagenesis and support the proposed role of the mfd gene product in directing DNA excision repair to the transcribed strand of a damaged gene.
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Affiliation(s)
- A R Oller
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709
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Selby CP, Witkin EM, Sancar A. Escherichia coli mfd mutant deficient in "mutation frequency decline" lacks strand-specific repair: in vitro complementation with purified coupling factor. Proc Natl Acad Sci U S A 1991; 88:11574-8. [PMID: 1763073 PMCID: PMC53178 DOI: 10.1073/pnas.88.24.11574] [Citation(s) in RCA: 167] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Mutation frequency decline (MFD) is the rapid decrease in the frequency of certain induced nonsense suppressor mutations occurring when protein synthesis is transiently inhibited immediately after irradiation. MFD is abolished by mutations in the uvrA, -B, or -C genes, which prevent excision repair, or by a mfd mutation, which reduces the rate of excision but does not affect survival. Using an in vitro repair synthesis assay we found that although wild-type cells repair the transcribed (template) strand preferentially, mfd- cells are incapable of strand-specific repair. The deficiency in strand-selective repair of mfd- cell extract was corrected by adding highly purified "transcription-repair coupling factor" to the reaction mixture. We conclude that mfd is, most likely, the gene encoding the transcription-repair coupling factor.
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Affiliation(s)
- C P Selby
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill 27599
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Mellon I, Hanawalt PC. Induction of the Escherichia coli lactose operon selectively increases repair of its transcribed DNA strand. Nature 1989; 342:95-8. [PMID: 2554145 DOI: 10.1038/342095a0] [Citation(s) in RCA: 465] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nucleotide excision repair helps to ameliorate the lethal and mutagenic consequences of DNA damage by removing helix-distorting lesions from cellular genomes. We have previously analysed the removal of ultraviolet-induced cyclobutane pyrimidine dimers from specific DNA sequences in mammalian cells and demonstrated that transcriptionally active genes are preferentially repaired. Additionally, we found that in rodent and human cells only the transcribed strand of the dihydrofolate reductase gene is selectively repaired. Transcription is blocked by pyrimidine dimers in template DNA and the selective removal of these lesions seems to be important for cell survival after irradiation with ultraviolet light. To determine whether this feature of repair is common to prokaryotes and eukaryotes and better to understand its mechanism, we have investigated repair in the two separate DNA strands of the lactose operon of ultraviolet-irradiated Escherichia coli. We find a dramatic difference in the repair of the two strands only when transcription is induced. Most dimers are removed from the transcribed strand of the induced operon within five minutes of irradiation. In the nontranscribed strand, repair is significantly slower and resembles that found in both strands of the uninduced operon. Thus there seems to be a mechanism that couples nucleotide excision repair and transcription.
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Affiliation(s)
- I Mellon
- Department of Biological Sciences, Stanford University, California 94305-5020
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Bridges BA, Sharif F. Mutagenic DNA repair in Escherichia coli. XV. Mutation frequency decline of ochre suppressor mutations in umuC and lexA bacteria occurring between ultraviolet irradiation and delayed photoreversal. Mutat Res 1988; 197:15-22. [PMID: 2827019 DOI: 10.1016/0027-5107(88)90136-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Tryptophan-independent mutations were induced in CM1141 trpE65 umuC122::Tn5 following exposure to ultraviolet light (UV) plus delayed photoreversal. The mutations appeared to be exclusively class 2 ochre suppressors and showed mutation frequency decline (MFD) when the bacteria were incubated in glucose-salts medium after UV and before photoreversal. The phenomenon was similar to MFD after normal UV mutagenesis of umu+ bacteria, being inhibited in the presence of caffeine or in the absence of glucose. Mutations were also induced by UV plus delayed photoreversal in the lexA (Ind-) strain CM561, and the yield was higher than in the umuC strain suggesting that potentially mutagenic configurations might be removed or altered to some extent by the product of a gene under lexA control such that fewer were available for misincorporation events. MFD was also demonstrated in CM561 showing that this process is not dependent on the derepression of any genes under lexA control. MFD could still be demonstrated 23 min after UV at a time when most misincorporations seem to have occurred, but for technical reasons the possibility could not be excluded that the misincorporations in question could have occurred during rather than before the exposure to photoreversing light. Delayed photoreversal mutagenesis of normally non-UV-mutable strains has been interpreted as a first stage (misincorporation) of normal UV mutagenesis. The present results are consistent with this interpretation since MFD of suppressor mutations is a feature of both processes.
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Affiliation(s)
- B A Bridges
- MRC Cell Mutation Unit, University of Sussex, Falmer, Brighton, Great Britain
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