1
|
Charman RJ, Kad NM. Single molecule iSCAT imaging reveals a fast, energy efficient search mode for the DNA repair protein UvrA. NANOSCALE 2022; 14:5174-5184. [PMID: 35311869 PMCID: PMC8969456 DOI: 10.1039/d1nr06913f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Exposure to UV radiation results in numerous DNA lesions, which threaten genome integrity. The nucleotide excision DNA repair pathway detects and repairs a range of such UV-induced DNA lesions. In bacteria, initial damage detection and verification is carried out by two proteins: UvrA and UvrB. Despite decades of study, the process of how these proteins locate damage remains unclear. Here we use high-speed interferometric scattering (iSCAT) microscopy, in combination with a surface-bound-DNA assay, to investigate early damage detection by UvrA. We have discovered that UvrA interacts with DNA in two phases; a slow phase (∼1.3 s-1) that correlates with an ATP-consuming state previously identified, and a second, much faster search mode. These faster interactions persist for ∼130 ms and using ATP analogues we determine this phase does not require ATP consumption. Including this new fast-search state in a model of the DNA search process reveals that only with this state is it possible for basal levels of UvrA to explore 99% of the E. coli genome within a single division cycle. Altogether, this work uncovers the presence of a rapid, energy efficient search mechanism, which allows UvrA alone to search the entirety of the E. coli genome within a single division cycle.
Collapse
Affiliation(s)
- Robert J Charman
- School of Biological Sciences, Division of Natural Sciences, University of Kent, Canterbury CT2 7NH, UK.
| | - Neil M Kad
- School of Biological Sciences, Division of Natural Sciences, University of Kent, Canterbury CT2 7NH, UK.
| |
Collapse
|
2
|
Deaconescu AM. Mfd - at the crossroads of bacterial DNA repair, transcriptional regulation and molecular evolvability. Transcription 2021; 12:156-170. [PMID: 34674614 PMCID: PMC8632110 DOI: 10.1080/21541264.2021.1982628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/06/2021] [Accepted: 09/14/2021] [Indexed: 12/21/2022] Open
Abstract
For survival, bacteria need to continuously evolve and adapt to complex environments, including those that may impact the integrity of the DNA, the repository of genetic information to be passed on to future generations. The multiple factors of DNA repair share the substrate on which they operate with other key cellular machineries, principally those of replication and transcription, implying a high degree of coordination of DNA-based activities. In this review, I focus on progress made in the understanding of the protein factors operating at the crossroads of these three fundamental processes, with emphasis on the mutation frequency decline protein (Mfd, aka TRCF). Although Mfd research has a rich history that goes back in time for more than half a century, recent reports hint that much remains to be uncovered. I argue that besides being a transcription-repair coupling factor (TRCF), Mfd is also a global regulator of transcription and a pro-mutagenic factor, and that the way it interfaces with transcription, replication and nucleotide excision repair makes it an attractive candidate for the development of strategies to curb molecular evolution, hence, antibiotic resistance.
Collapse
Affiliation(s)
- Alexandra M. Deaconescu
- CONTACT Alexandra M. Deaconescu Molecular Biology, Cell Biology and Biochemistry, Laboratories of Molecular Medicine, Brown University, 70 Ship St. G-E4, Providence, RI02903, USA
| |
Collapse
|
3
|
Kraithong T, Hartley S, Jeruzalmi D, Pakotiprapha D. A Peek Inside the Machines of Bacterial Nucleotide Excision Repair. Int J Mol Sci 2021; 22:ijms22020952. [PMID: 33477956 PMCID: PMC7835731 DOI: 10.3390/ijms22020952] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/13/2022] Open
Abstract
Double stranded DNA (dsDNA), the repository of genetic information in bacteria, archaea and eukaryotes, exhibits a surprising instability in the intracellular environment; this fragility is exacerbated by exogenous agents, such as ultraviolet radiation. To protect themselves against the severe consequences of DNA damage, cells have evolved at least six distinct DNA repair pathways. Here, we review recent key findings of studies aimed at understanding one of these pathways: bacterial nucleotide excision repair (NER). This pathway operates in two modes: a global genome repair (GGR) pathway and a pathway that closely interfaces with transcription by RNA polymerase called transcription-coupled repair (TCR). Below, we discuss the architecture of key proteins in bacterial NER and recent biochemical, structural and single-molecule studies that shed light on the lesion recognition steps of both the GGR and the TCR sub-pathways. Although a great deal has been learned about both of these sub-pathways, several important questions, including damage discrimination, roles of ATP and the orchestration of protein binding and conformation switching, remain to be addressed.
Collapse
Affiliation(s)
- Thanyalak Kraithong
- Doctor of Philosophy Program in Biochemistry (International Program), Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Silas Hartley
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA;
- Doctor of Philosophy Programs in Biochemistry, Biology and Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - David Jeruzalmi
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA;
- Doctor of Philosophy Programs in Biochemistry, Biology and Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
- Correspondence: (D.J.); (D.P.)
| | - Danaya Pakotiprapha
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Correspondence: (D.J.); (D.P.)
| |
Collapse
|
4
|
Kraithong T, Sucharitakul J, Buranachai C, Jeruzalmi D, Chaiyen P, Pakotiprapha D. Real-time investigation of the roles of ATP hydrolysis by UvrA and UvrB during DNA damage recognition in nucleotide excision repair. DNA Repair (Amst) 2020; 97:103024. [PMID: 33302090 DOI: 10.1016/j.dnarep.2020.103024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 08/25/2020] [Accepted: 11/09/2020] [Indexed: 10/22/2022]
Abstract
Nucleotide excision repair (NER) stands out among other DNA repair systems for its ability to process a diverse set of unrelated DNA lesions. In bacteria, NER damage detection is orchestrated by the UvrA and UvrB proteins, which form the UvrA2-UvrB2 (UvrAB) damage sensing complex. The highly versatile damage recognition is accomplished in two ATP-dependent steps. In the first step, the UvrAB complex samples the DNA in search of lesion. Subsequently, the presence of DNA damage is verified within the UvrB-DNA complex after UvrA has dissociated. Although the mechanism of bacterial NER damage detection has been extensively investigated, the role of ATP binding and hydrolysis by UvrA and UvrB during this process remains incompletely understood. Here, we report a pre-steady state kinetics Förster resonance energy transfer (FRET) study of the real-time interaction between UvrA, UvrB, and damaged DNA during lesion detection. By using UvrA and UvrB mutants harboring site-specific mutations in the ATP binding sites, we show for the first time that the dissociation of UvrA from the UvrAB-DNA complex does not require ATP hydrolysis by UvrB. We find that ATP hydrolysis by UvrA is not essential, but somehow facilitates the formation of UvrB-DNA complex, with ATP hydrolysis at the proximal site of UvrA playing a more critical role. Consistent with previous reports, our results indicated that the ATPase activity of UvrB is essential for the formation of UvrB-DNA complex but is not required for the binding of the UvrAB complex to DNA.
Collapse
Affiliation(s)
- Thanyalak Kraithong
- Doctor of Philosophy Program in Biochemistry (International Program), Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Jeerus Sucharitakul
- Research Unit in Integrative Immuno-Microbial Biochemistry and Bioresponsive Nanomaterials, Thailand; Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand
| | - Chittanon Buranachai
- Department of Physics, Faculty of Science, Prince of Songkla University, Hat-Yai, Songkhla 90110, Thailand; Center of Excellence for Trace Analysis and Biosensor, Faculty of Science, Prince of Songkla University, Hat-Yai, Songkhla 90110, Thailand
| | - David Jeruzalmi
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA; Doctor of Philosophy Programs in Biochemistry, Biology, and Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Pimchai Chaiyen
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Danaya Pakotiprapha
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
| |
Collapse
|
5
|
Ghodke H, Ho HN, van Oijen AM. Single-molecule live-cell imaging visualizes parallel pathways of prokaryotic nucleotide excision repair. Nat Commun 2020; 11:1477. [PMID: 32198385 PMCID: PMC7083872 DOI: 10.1038/s41467-020-15179-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 02/23/2020] [Indexed: 01/01/2023] Open
Abstract
In the model organism Escherichia coli, helix distorting lesions are recognized by the UvrAB damage surveillance complex in the global genomic nucleotide excision repair pathway (GGR). Alternately, during transcription-coupled repair (TCR), UvrA is recruited to Mfd at sites of RNA polymerases stalled by lesions. Ultimately, damage recognition is mediated by UvrA, followed by verification by UvrB. Here we characterize the differences in the kinetics of interactions of UvrA with Mfd and UvrB by following functional, fluorescently tagged UvrA molecules in live TCR-deficient or wild-type cells. The lifetimes of UvrA in Mfd-dependent or Mfd-independent interactions in the absence of exogenous DNA damage are comparable in live cells, and are governed by UvrB. Upon UV irradiation, the lifetimes of UvrA strongly depended on, and matched those of Mfd. Overall, we illustrate a non-perturbative, imaging-based approach to quantify the kinetic signatures of damage recognition enzymes participating in multiple pathways in cells. In Escherichia coli, the UvrAB damage sensor recognizes helix-distorting lesions by itself or via Mfd bound to stalled RNA polymerase. Here authors use single-molecule fluorescence imaging to quantify the kinetic signatures of interactions of UvrA with Mfd and UvrB in live cells.
Collapse
Affiliation(s)
- Harshad Ghodke
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, 2522, Australia. .,Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia.
| | - Han Ngoc Ho
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| |
Collapse
|
6
|
Thakur M, Muniyappa K. Deciphering the essentiality and function of SxSx motif in Mycobacterium tuberculosis UvrB. Biochimie 2020; 170:94-105. [PMID: 31923481 DOI: 10.1016/j.biochi.2020.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/06/2020] [Indexed: 10/25/2022]
Abstract
The UvrB subunit is a central component of the UvrABC incision complex and plays a pivotal role in damage recognition, strand excision and repair synthesis. A conserved structural motif (the SxSx motif) present in UvrB is analogous to a similar motif (TxGx) in the helicases of superfamily 2, whose function is not fully understood. To elucidate the significance of the SxSx (Ser143-Val144-Ser145-Cys146) motif in Mycobacterium tuberculosis UvrB (MtUvrB), different variants of MtUvrB subunit were constructed and characterized. The SxSx motif indeed was found to be essential for MtUvrB function: while Ser143 and Cys146 residues within this motif were crucial for MtUvrB function, Ser145 plays an important but less essential role. The SxSx motif-deleted mutant was drastically attenuated and three single (S143A, S145A and C146A) mutants and a double (S143A/S145A) mutant exhibited various degrees of severity in their DNA-binding, DNA helicase and ATPase activities. Taken together, these results highlight a hitherto unrecognized role for SxSx motif in the catalytic activities of UvrB.
Collapse
Affiliation(s)
- Manoj Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India.
| |
Collapse
|
7
|
Case BC, Hartley S, Osuga M, Jeruzalmi D, Hingorani MM. The ATPase mechanism of UvrA2 reveals the distinct roles of proximal and distal ATPase sites in nucleotide excision repair. Nucleic Acids Res 2019; 47:4136-4152. [PMID: 30892613 PMCID: PMC6486640 DOI: 10.1093/nar/gkz180] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/02/2019] [Accepted: 03/18/2019] [Indexed: 01/20/2023] Open
Abstract
The UvrA2 dimer finds lesions in DNA and initiates nucleotide excision repair. Each UvrA monomer contains two essential ATPase sites: proximal (P) and distal (D). The manner whereby their activities enable UvrA2 damage sensing and response remains to be clarified. We report three key findings from the first pre-steady state kinetic analysis of each site. Absent DNA, a P2ATP-D2ADP species accumulates when the low-affinity proximal sites bind ATP and enable rapid ATP hydrolysis and phosphate release by the high-affinity distal sites, and ADP release limits catalytic turnover. Native DNA stimulates ATP hydrolysis by all four sites, causing UvrA2 to transition through a different species, P2ADP-D2ADP. Lesion-containing DNA changes the mechanism again, suppressing ATP hydrolysis by the proximal sites while distal sites cycle through hydrolysis and ADP release, to populate proximal ATP-bound species, P2ATP-Dempty and P2ATP-D2ATP. Thus, damaged and native DNA trigger distinct ATPase site activities, which could explain why UvrA2 forms stable complexes with UvrB on damaged DNA compared with weaker, more dynamic complexes on native DNA. Such specific coupling between the DNA substrate and the ATPase mechanism of each site provides new insights into how UvrA2 utilizes ATP for lesion search, recognition and repair.
Collapse
Affiliation(s)
- Brandon C Case
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Silas Hartley
- Department of Chemistry and Biochemistry, City College of New York of the City University of New York, New York, NY 10031, USA.,Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Memie Osuga
- Department of Chemistry and Biochemistry, City College of New York of the City University of New York, New York, NY 10031, USA.,Hunter College High School, New York, NY 10128, USA
| | - David Jeruzalmi
- Department of Chemistry and Biochemistry, City College of New York of the City University of New York, New York, NY 10031, USA.,Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA.,Ph.D. Programs in Chemistry and Biology, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Manju M Hingorani
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| |
Collapse
|
8
|
Thakur M, Badugu S, Muniyappa K. UvrA and UvrC subunits of the Mycobacterium tuberculosis UvrABC excinuclease interact independently of UvrB and DNA. FEBS Lett 2019; 594:851-863. [PMID: 31705809 DOI: 10.1002/1873-3468.13671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/31/2019] [Accepted: 10/31/2019] [Indexed: 11/10/2022]
Abstract
The UvrABC excinuclease plays a vital role in bacterial nucleotide excision repair. While UvrA and UvrB subunits associate to form a UvrA2 B2 complex, interaction between UvrA and UvrC has not been demonstrated or quantified in any bacterial species. Here, using Mycobacterium tuberculosis UvrA (MtUvrA), UvrB (MtUvrB) and UvrC (MtUvrC) subunits, we show that MtUvrA binds to MtUvrB and equally well to MtUvrC with submicromolar affinity. Furthermore, MtUvrA forms a complex with MtUvrC both in vivo and in vitro, independently of DNA and UvrB. Collectively, these findings reveal new insights into the pairwise relationships between the subunits of the UvrABC incision complex.
Collapse
Affiliation(s)
- Manoj Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sugith Badugu
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| |
Collapse
|
9
|
Springall L, Hughes CD, Simons M, Azinas S, Van Houten B, Kad NM. Recruitment of UvrBC complexes to UV-induced damage in the absence of UvrA increases cell survival. Nucleic Acids Res 2019; 46:1256-1265. [PMID: 29240933 PMCID: PMC5814901 DOI: 10.1093/nar/gkx1244] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 12/01/2017] [Indexed: 02/05/2023] Open
Abstract
Nucleotide excision repair (NER) is the primary mechanism for removal of ultraviolet light (UV)-induced DNA photoproducts and is mechanistically conserved across all kingdoms of life. Bacterial NER involves damage recognition by UvrA2 and UvrB, followed by UvrC-mediated incision either side of the lesion. Here, using a combination of in vitro and in vivo single-molecule studies we show that a UvrBC complex is capable of lesion identification in the absence of UvrA. Single-molecule analysis of eGFP-labelled UvrB and UvrC in living cells showed that UV damage caused these proteins to switch from cytoplasmic diffusion to stable complexes on DNA. Surprisingly, ectopic expression of UvrC in a uvrA deleted strain increased UV survival. These data provide evidence for a previously unrealized mechanism of survival that can occur through direct lesion recognition by a UvrBC complex.
Collapse
Affiliation(s)
- Luke Springall
- School of Biological Sciences, University of Kent, Canterbury CT2 7NH, UK
| | - Craig D Hughes
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Michelle Simons
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Stavros Azinas
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | | | - Neil M Kad
- School of Biological Sciences, University of Kent, Canterbury CT2 7NH, UK
| |
Collapse
|
10
|
Barnett JT, Kad NM. Understanding the coupling between DNA damage detection and UvrA's ATPase using bulk and single molecule kinetics. FASEB J 2018; 33:763-769. [PMID: 30020831 PMCID: PMC6355085 DOI: 10.1096/fj.201800899r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Nucleotide excision repair (NER) protects cells against diverse types of DNA damage, principally UV irradiation. In Escherichia coli, damage is recognized by 2 key enzymes: UvrA and UvrB. Despite extensive investigation, the role of UvrA’s 2 ATPase domains in NER remains elusive. Combining single-molecule fluorescence microscopy and classic biochemical methods, we have investigated the role of nucleotide binding in UvrA’s kinetic cycle. Measurement of UvrA’s steady-state ATPase activity shows it is stimulated upon binding DNA (kcat 0.71–1.07/s). Despite UvrA’s ability to discriminate damage, we find UV-damaged DNA does not alter the steady-state ATPase. To understand how damage affects UvrA, we studied its binding to DNA under various nucleotide conditions at the single molecule level. We have found that both UV damage and nucleotide cofactors affect the attached lifetime of UvrA. In the presence of ATP and UV damage, the lifetime is significantly greater compared with undamaged DNA. To reconcile these observations, we suggest that UvrA uses negative cooperativity between its ATPase sites that is gated by damage recognition. Only in the presence of damage is the second site activated, most likely in a sequential manner.—Barnett, J. T., Kad, N. M. Understanding the coupling between DNA damage detection and UvrA’s ATPase using bulk and single molecule kinetics.
Collapse
Affiliation(s)
- Jamie T Barnett
- School of Biological Sciences, University of Kent, Canterbury, United Kingdom
| | - Neil M Kad
- School of Biological Sciences, University of Kent, Canterbury, United Kingdom
| |
Collapse
|
11
|
Lahiri S, Rizzi M, Rossi F, Miggiano R. Mycobacterium tuberculosis
UvrB forms dimers in solution and interacts with UvrA in the absence of ligands. Proteins 2017; 86:98-109. [DOI: 10.1002/prot.25412] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 10/19/2017] [Accepted: 10/27/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Samarpita Lahiri
- DSF-Dipartimento di Scienze del Farmaco; University of Piemonte Orientale; Novara Italy
| | - Menico Rizzi
- DSF-Dipartimento di Scienze del Farmaco; University of Piemonte Orientale; Novara Italy
| | - Franca Rossi
- DSF-Dipartimento di Scienze del Farmaco; University of Piemonte Orientale; Novara Italy
| | - Riccardo Miggiano
- DSF-Dipartimento di Scienze del Farmaco; University of Piemonte Orientale; Novara Italy
| |
Collapse
|
12
|
Abstract
Ubiquitous conserved processes that repair DNA damage are essential for the maintenance and propagation of genomes over generations. Then again, inaccuracies in DNA transactions and failures to remove mutagenic lesions cause heritable genome changes. Building on decades of research using genetics and biochemistry, unprecedented quantitative insight into DNA repair mechanisms has come from the new-found ability to measure single proteins in vitro and inside individual living cells. This has brought together biologists, chemists, engineers, physicists, and mathematicians to solve long-standing questions about the way in which repair enzymes search for DNA lesions and form protein complexes that act in DNA repair pathways. Furthermore, unexpected discoveries have resulted from capabilities to resolve molecular heterogeneity and cell subpopulations, provoking new questions about the role of stochastic processes in DNA repair and mutagenesis. These studies are leading to new technologies that will find widespread use in basic research, biotechnology, and medicine.
Collapse
Affiliation(s)
- Stephan Uphoff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; ,
| | - David J Sherratt
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; ,
| |
Collapse
|
13
|
Thakur M, Kumar MBJ, Muniyappa K. Mycobacterium tuberculosis UvrB Is a Robust DNA-Stimulated ATPase That Also Possesses Structure-Specific ATP-Dependent DNA Helicase Activity. Biochemistry 2016; 55:5865-5883. [PMID: 27618337 DOI: 10.1021/acs.biochem.6b00558] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Much is known about the Escherichia coli nucleotide excision repair (NER) pathway; however, very little is understood about the proteins involved and the molecular mechanism of NER in mycobacteria. In this study, we show that Mycobacterium tuberculosis UvrB (MtUvrB), which exists in solution as a monomer, binds to DNA in a structure-dependent manner. A systematic examination of MtUvrB substrate specificity reveals that it associates preferentially with single-stranded DNA, duplexes with 3' or 5' overhangs, and linear duplex DNA with splayed arms. Whereas E. coli UvrB (EcUvrB) binds weakly to undamaged DNA and has no ATPase activity, MtUvrB possesses intrinsic ATPase activity that is greatly stimulated by both single- and double-stranded DNA. Strikingly, we found that MtUvrB, but not EcUvrB, possesses the DNA unwinding activity characteristic of an ATP-dependent DNA helicase. The helicase activity of MtUvrB proceeds in the 3' to 5' direction and is strongly modulated by a nontranslocating 5' single-stranded tail, indicating that in addition to the translocating strand it also interacts with the 5' end of the substrate. The fraction of DNA unwound by MtUvrB decreases significantly as the length of the duplex increases: it fails to unwind duplexes longer than 70 bp. These results, on one hand, reveal significant mechanistic differences between MtUvrB and EcUvrB and, on the other, support an alternative role for UvrB in the processing of key DNA replication intermediates. Altogether, our findings provide insights into the catalytic functions of UvrB and lay the foundation for further understanding of the NER pathway in M. tuberculosis.
Collapse
Affiliation(s)
- Manoj Thakur
- Department of Biochemistry, Indian Institute of Science , Bangalore 560012, India
| | - Mohan B J Kumar
- Department of Biochemistry, Indian Institute of Science , Bangalore 560012, India
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science , Bangalore 560012, India
| |
Collapse
|
14
|
Stracy M, Jaciuk M, Uphoff S, Kapanidis AN, Nowotny M, Sherratt DJ, Zawadzki P. Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli. Nat Commun 2016; 7:12568. [PMID: 27562541 PMCID: PMC5007444 DOI: 10.1038/ncomms12568] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 07/14/2016] [Indexed: 11/19/2022] Open
Abstract
Nucleotide excision repair (NER) removes chemically diverse DNA lesions in all domains of life. In Escherichia coli, UvrA and UvrB initiate NER, although the mechanistic details of how this occurs in vivo remain to be established. Here, we use single-molecule fluorescence imaging to provide a comprehensive characterization of the lesion search, recognition and verification process in living cells. We show that NER initiation involves a two-step mechanism in which UvrA scans the genome and locates DNA damage independently of UvrB. Then UvrA recruits UvrB from solution to the lesion. These steps are coordinated by ATP binding and hydrolysis in the ‘proximal' and ‘distal' UvrA ATP-binding sites. We show that initial UvrB-independent damage recognition by UvrA requires ATPase activity in the distal site only. Subsequent UvrB recruitment requires ATP hydrolysis in the proximal site. Finally, UvrA dissociates from the lesion complex, allowing UvrB to orchestrate the downstream NER reactions. Nucleotide excision repair is able to identify and remove a wide range of DNA helix distorting lesions from the genome. Here the authors use single molecule imaging of UvrA and UvrB molecules and suggest a two-step ‘scan and recruit' model for UvrA function.
Collapse
Affiliation(s)
- Mathew Stracy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.,Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Marcin Jaciuk
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Ksiecia Trojdena Street, 02-109 Warsaw, Poland
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Ksiecia Trojdena Street, 02-109 Warsaw, Poland
| | - David J Sherratt
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Pawel Zawadzki
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| |
Collapse
|
15
|
Van Houten B, Kad N. Investigation of bacterial nucleotide excision repair using single-molecule techniques. DNA Repair (Amst) 2014; 20:41-48. [PMID: 24472181 PMCID: PMC5053424 DOI: 10.1016/j.dnarep.2013.10.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 10/31/2013] [Indexed: 12/23/2022]
Abstract
Despite three decades of biochemical and structural analysis of the prokaryotic nucleotide excision repair (NER) system, many intriguing questions remain with regard to how the UvrA, UvrB, and UvrC proteins detect, verify and remove a wide range of DNA lesions. Single-molecule techniques have begun to allow more detailed understanding of the kinetics and action mechanism of this complex process. This article reviews how atomic force microscopy and fluorescence microscopy have captured new glimpses of how these proteins work together to mediate NER.
Collapse
Affiliation(s)
- Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Neil Kad
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| |
Collapse
|
16
|
Abstract
Nucleotide excision repair (NER) has allowed bacteria to flourish in many different niches around the globe that inflict harsh environmental damage to their genetic material. NER is remarkable because of its diverse substrate repertoire, which differs greatly in chemical composition and structure. Recent advances in structural biology and single-molecule studies have given great insight into the structure and function of NER components. This ensemble of proteins orchestrates faithful removal of toxic DNA lesions through a multistep process. The damaged nucleotide is recognized by dynamic probing of the DNA structure that is then verified and marked for dual incisions followed by excision of the damage and surrounding nucleotides. The opposite DNA strand serves as a template for repair, which is completed after resynthesis and ligation.
Collapse
Affiliation(s)
- Caroline Kisker
- Rudolf-Virchow-Center for Experimental Biomedicine, University of Wuerzburg, 97080 Wuerzburg, Germany.
| | | | | |
Collapse
|
17
|
Couvé S, Ishchenko AA, Fedorova OS, Ramanculov EM, Laval J, Saparbaev M. Direct DNA Lesion Reversal and Excision Repair in Escherichia coli. EcoSal Plus 2013; 5. [PMID: 26442931 DOI: 10.1128/ecosalplus.7.2.4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2012] [Indexed: 06/05/2023]
Abstract
Cellular DNA is constantly challenged by various endogenous and exogenous genotoxic factors that inevitably lead to DNA damage: structural and chemical modifications of primary DNA sequence. These DNA lesions are either cytotoxic, because they block DNA replication and transcription, or mutagenic due to the miscoding nature of the DNA modifications, or both, and are believed to contribute to cell lethality and mutagenesis. Studies on DNA repair in Escherichia coli spearheaded formulation of principal strategies to counteract DNA damage and mutagenesis, such as: direct lesion reversal, DNA excision repair, mismatch and recombinational repair and genotoxic stress signalling pathways. These DNA repair pathways are universal among cellular organisms. Mechanistic principles used for each repair strategies are fundamentally different. Direct lesion reversal removes DNA damage without need for excision and de novo DNA synthesis, whereas DNA excision repair that includes pathways such as base excision, nucleotide excision, alternative excision and mismatch repair, proceeds through phosphodiester bond breakage, de novo DNA synthesis and ligation. Cell signalling systems, such as adaptive and oxidative stress responses, although not DNA repair pathways per se, are nevertheless essential to counteract DNA damage and mutagenesis. The present review focuses on the nature of DNA damage, direct lesion reversal, DNA excision repair pathways and adaptive and oxidative stress responses in E. coli.
Collapse
|
18
|
Felício DF, Vidal LDS, Irineu RS, Leitão AC, von Kruger WA, Britto CDP, Cardoso A, Cardoso JS, Lage C. Overexpression of Escherichia coli nucleotide excision repair genes after cisplatin-induced damage. DNA Repair (Amst) 2013; 12:63-72. [DOI: 10.1016/j.dnarep.2012.10.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 10/25/2012] [Accepted: 10/30/2012] [Indexed: 12/12/2022]
|
19
|
Pakotiprapha D, Jeruzalmi D. Small-angle X-ray scattering reveals architecture and A2
B2
stoichiometry of the UvrA-UvrB DNA damage sensor. Proteins 2012; 81:132-9. [DOI: 10.1002/prot.24170] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Revised: 08/10/2012] [Accepted: 08/15/2012] [Indexed: 11/09/2022]
|
20
|
UvrD Participation in Nucleotide Excision Repair Is Required for the Recovery of DNA Synthesis following UV-Induced Damage in Escherichia coli. J Nucleic Acids 2012; 2012:271453. [PMID: 23056919 PMCID: PMC3465929 DOI: 10.1155/2012/271453] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 07/17/2012] [Indexed: 11/27/2022] Open
Abstract
UvrD is a DNA helicase that participates in nucleotide excision repair and several replication-associated processes, including methyl-directed mismatch repair and recombination. UvrD is capable of displacing oligonucleotides from synthetic forked DNA structures in vitro and is essential for viability in the absence of Rep, a helicase associated with processing replication forks. These observations have led others to propose that UvrD may promote fork regression and facilitate resetting of the replication fork following arrest. However, the molecular activity of UvrD at replication forks in vivo has not been directly examined. In this study, we characterized the role UvrD has in processing and restoring replication forks following arrest by UV-induced DNA damage. We show that UvrD is required for DNA synthesis to recover. However, in the absence of UvrD, the displacement and partial degradation of the nascent DNA at the arrested fork occur normally. In addition, damage-induced replication intermediates persist and accumulate in uvrD mutants in a manner that is similar to that observed in other nucleotide excision repair mutants. These data indicate that, following arrest by DNA damage, UvrD is not required to catalyze fork regression in vivo and suggest that the failure of uvrD mutants to restore DNA synthesis following UV-induced arrest relates to its role in nucleotide excision repair.
Collapse
|
21
|
Webster MPJ, Jukes R, Zamfir VS, Kay CWM, Bagnéris C, Barrett T. Crystal structure of the UvrB dimer: insights into the nature and functioning of the UvrAB damage engagement and UvrB-DNA complexes. Nucleic Acids Res 2012; 40:8743-58. [PMID: 22753105 PMCID: PMC3458569 DOI: 10.1093/nar/gks633] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
UvrB has a central role in the highly conserved UvrABC pathway functioning not only as a damage recognition element but also as an essential component of the lesion tracking machinery. While it has been recently confirmed that the tracking assembly comprises a UvrA2B2 heterotetramer, the configurations of the damage engagement and UvrB–DNA handover complexes remain obscure. Here, we present the first crystal structure of a UvrB dimer whose biological significance has been verified using both chemical cross-linking and electron paramagnetic resonance spectroscopy. We demonstrate that this dimeric species stably associates with UvrA and forms a UvrA2B2–DNA complex. Our studies also illustrate how signals are transduced between the ATP and DNA binding sites to generate the helicase activity pivotal to handover and formation of the UvrB2–DNA complex, providing key insights into the configurations of these important repair intermediates.
Collapse
Affiliation(s)
- Matthew P J Webster
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, UK
| | | | | | | | | | | |
Collapse
|
22
|
Pakotiprapha D, Samuels M, Shen K, Hu JH, Jeruzalmi D. Structure and mechanism of the UvrA-UvrB DNA damage sensor. Nat Struct Mol Biol 2012; 19:291-8. [PMID: 22307053 DOI: 10.1038/nsmb.2240] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 12/12/2011] [Indexed: 01/12/2023]
Abstract
Nucleotide excision repair (NER) is used by all organisms to eliminate DNA lesions. We determined the structure of the Geobacillus stearothermophilus UvrA-UvrB complex, the damage-sensor in bacterial NER and a new structure of UvrA. We observe that the DNA binding surface of UvrA, previously found in an open shape that binds damaged DNA, also exists in a closed groove shape compatible with native DNA only. The sensor contains two UvrB molecules that flank the UvrA dimer along the predicted path for DNA, ~80 Å from the lesion. We show that the conserved signature domain II of UvrA mediates a nexus of contacts among UvrA, UvrB and DNA. Further, in our new structure of UvrA, this domain adopts an altered conformation while an adjacent nucleotide binding site is vacant. Our findings raise unanticipated questions about NER and also suggest a revised picture of its early stages.
Collapse
Affiliation(s)
- Danaya Pakotiprapha
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | | | | | | | | |
Collapse
|
23
|
Ganesan A, Spivak G, Hanawalt PC. Transcription-coupled DNA repair in prokaryotes. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 110:25-40. [PMID: 22749141 DOI: 10.1016/b978-0-12-387665-2.00002-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Transcription-coupled repair (TCR) is a subpathway of nucleotide excision repair (NER) that acts specifically on lesions in the transcribed strand of expressed genes. First reported in mammalian cells, TCR was then documented in Escherichia coli. In this organism, an RNA polymerase arrested at a lesion is displaced by the transcription repair coupling factor, Mfd. This protein recruits the NER lesion-recognition factor UvrA, and then dissociates from the DNA. UvrA binds UvrB, and the assembled UvrAB* complex initiates repair. In mutants lacking active Mfd, TCR is absent. A gene transcribed by the bacteriophage T7 RNA polymerase in E. coli also requires Mfd for TCR. The CSB protein (missing or defective in cells of patients with Cockayne syndrome, complementation group B) is essential for TCR in humans. CSB and its homologs in higher eukaryotes are likely functional equivalents of Mfd.
Collapse
Affiliation(s)
- Ann Ganesan
- Department of Biology, Stanford University, Stanford, California, USA
| | | | | |
Collapse
|
24
|
Dynamics of lesion processing by bacterial nucleotide excision repair proteins. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 110:1-24. [PMID: 22749140 DOI: 10.1016/b978-0-12-387665-2.00001-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Single-molecule approaches permit an unrivalled view of how complex systems operate and have recently been used to understand DNA-protein interactions. These tools have enabled advances in a particularly challenging problem, the search for damaged sites on DNA. DNA repair proteins are present at the level of just a few hundred copies in bacterial cells to just a few thousand in human cells, and they scan the entire genome in search of their specific substrates. How do these proteins achieve this herculean task when their targets may differ from undamaged DNA by only a single hydrogen bond? Here we examine, using single-molecule approaches, how the prokaryotic nucleotide excision repair system balances the necessity for speed against specificity. We discuss issues at a theoretical, biological, and technical level and finally pose questions for future research.
Collapse
|
25
|
Rossi F, Khanduja JS, Bortoluzzi A, Houghton J, Sander P, Güthlein C, Davis EO, Springer B, Böttger EC, Relini A, Penco A, Muniyappa K, Rizzi M. The biological and structural characterization of Mycobacterium tuberculosis UvrA provides novel insights into its mechanism of action. Nucleic Acids Res 2011; 39:7316-28. [PMID: 21622956 PMCID: PMC3167621 DOI: 10.1093/nar/gkr271] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Mycobacterium tuberculosis is an extremely well adapted intracellular human pathogen that is exposed to multiple DNA damaging chemical assaults originating from the host defence mechanisms. As a consequence, this bacterium is thought to possess highly efficient DNA repair machineries, the nucleotide excision repair (NER) system amongst these. Although NER is of central importance to DNA repair in M. tuberculosis, our understanding of the processes in this species is limited. The conserved UvrABC endonuclease represents the multi-enzymatic core in bacterial NER, where the UvrA ATPase provides the DNA lesion-sensing function. The herein reported genetic analysis demonstrates that M. tuberculosis UvrA is important for the repair of nitrosative and oxidative DNA damage. Moreover, our biochemical and structural characterization of recombinant M. tuberculosis UvrA contributes new insights into its mechanism of action. In particular, the structural investigation reveals an unprecedented conformation of the UvrB-binding domain that we propose to be of functional relevance. Taken together, our data suggest UvrA as a potential target for the development of novel anti-tubercular agents and provide a biochemical framework for the identification of small-molecule inhibitors interfering with the NER activity in M. tuberculosis.
Collapse
Affiliation(s)
- Franca Rossi
- DiSCAFF, University of Piemonte Orientale Amedeo Avogadro, Via Bovio 6, 28100 Novara, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Bichara M, Meier M, Wagner J, Cordonnier A, Lambert IB. Postreplication repair mechanisms in the presence of DNA adducts in Escherichia coli. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2011; 727:104-22. [DOI: 10.1016/j.mrrev.2011.04.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 04/25/2011] [Accepted: 04/26/2011] [Indexed: 02/02/2023]
|
27
|
Manelyte L, Kim YIT, Smith AJ, Smith RM, Savery NJ. Regulation and rate enhancement during transcription-coupled DNA repair. Mol Cell 2011; 40:714-24. [PMID: 21145481 PMCID: PMC3025350 DOI: 10.1016/j.molcel.2010.11.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 08/03/2010] [Accepted: 09/14/2010] [Indexed: 11/22/2022]
Abstract
Transcription-coupled DNA repair (TCR) is a subpathway of nucleotide excision repair (NER) that is triggered when RNA polymerase is stalled by DNA damage. Lesions targeted by TCR are repaired more quickly than lesions repaired by the transcription-independent “global” NER pathway, but the mechanism underlying this rate enhancement is not understood. Damage recognition during bacterial NER depends upon UvrA, which binds to the damage and loads UvrB onto the DNA. Bacterial TCR additionally requires the Mfd protein, a DNA translocase that removes the stalled transcription complexes. We have determined the properties of Mfd, UvrA, and UvrB that are required for the elevated rate of repair observed during TCR. We show that TCR and global NER differ in their requirements for damage recognition by UvrA, indicating that Mfd acts at the very earliest stage of the repair process and extending the functional similarities between TCR in bacteria and eukaryotes.
Collapse
Affiliation(s)
- Laura Manelyte
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | | | | | | | | |
Collapse
|
28
|
Wagner K, Moolenaar GF, Goosen N. Role of the two ATPase domains of Escherichia coli UvrA in binding non-bulky DNA lesions and interaction with UvrB. DNA Repair (Amst) 2010; 9:1176-86. [PMID: 20864419 DOI: 10.1016/j.dnarep.2010.08.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Revised: 08/24/2010] [Accepted: 08/27/2010] [Indexed: 01/20/2023]
Abstract
The UvrA protein is the initial DNA damage-sensing protein in bacterial nucleotide excision repair and detects a wide variety of structurally unrelated lesions. After initial recognition of DNA damage, UvrA loads the UvrB protein onto the DNA. This protein then verifies the presence of a lesion, after which UvrA is released from the DNA. UvrA contains two ATPase domains, both belonging to the ABC ATPase superfamily. We have determined the activities of two mutants, in which a single domain was deactivated. Inactivation of either one ATPase domain in Escherichia coli UvrA results in a complete loss of ATPase activity, indicating that both domains function in a cooperative way. We could show that this ATPase activity is not required for the recognition of bulky lesions by UvrA, but it does promote the specific binding to the less distorting cyclobutane-pyrimidine dimer (CPD). The two ATPase mutants also show a difference in UvrB-loading, depending on the length of the DNA substrate. The ATPase domain I mutant was capable of loading UvrB on a lesion in a 50 bp fragment, but this loading was reduced on a longer substrate. For the ATPase domain II mutant the opposite was found: UvrB could not be loaded on a 50 bp substrate, but this loading was rescued when the length of the fragment was increased. This differential loading of UvrB by the two ATPase mutants could be related to different interactions between the UvrA and UvrB subunits.
Collapse
Affiliation(s)
- Koen Wagner
- Leiden Institute of Chemistry, Leiden University, The Netherlands
| | | | | |
Collapse
|
29
|
Ganesan AK, Hanawalt PC. Transcription-coupled nucleotide excision repair of a gene transcribed by bacteriophage T7 RNA polymerase in Escherichia coli. DNA Repair (Amst) 2010; 9:958-63. [PMID: 20638914 DOI: 10.1016/j.dnarep.2010.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 05/28/2010] [Accepted: 06/22/2010] [Indexed: 11/17/2022]
Abstract
Transcription-coupled nucleotide excision repair (TC-NER) removes certain kinds of lesions from the transcribed strand of expressed genes. The signal for TC-NER is thought to be RNA polymerase stalled at a lesion in the DNA template. In Escherichia coli, the stalled polymerase is dissociated from the lesion by the transcription repair coupling factor (Mfd protein), which also recruits excision repair proteins to the site resulting in efficient removal of the lesion. TC-NER has been documented in cells from a variety of organisms ranging from bacteria to humans. In each case, the RNA polymerase involved has been a multimeric protein complex. To ascertain whether a gene transcribed by the monomeric RNA polymerase of bacteriophage T7 could be repaired by TC-NER, we constructed strains of E. coli in which the chromosomal lacZ gene is controlled by a T7 promoter. In the absence of T7 RNA polymerase, little or no beta-galactosidase is produced, indicating that the E. coli RNA polymerase does not transcribe lacZ efficiently, if at all, in these strains. By introducing a plasmid (pAR1219) carrying the T7 gene 1 under control of the E. coli lac UV5 promoter into these strains, we obtained derivatives in which the level of T7 RNA polymerase could be regulated. In cultures containing upregulated levels of the polymerase, beta-galactosidase was actively produced indicating that the T7 RNA polymerase transcribes the lacZ gene efficiently. Under these conditions, we observed that UV-induced cyclobutane pyrimidine dimers were removed more rapidly from the transcribed strand of lacZ than from the nontranscribed strand, supporting the conclusion that TC-NER occurred in this gene. This response was absent in an mfd-1 mutant, indicating that the underlying mechanism may be similar to that for the bacterial RNA polymerase.
Collapse
Affiliation(s)
- Ann K Ganesan
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA.
| | | |
Collapse
|
30
|
Chang X, Yang L, Zhao Q, Fu W, Chen H, Qiu Z, Chen JA, Hu R, Shu W. Involvement of recF in 254 nm Ultraviolet Radiation Resistance in Deinococcus radiodurans and Escherichia coli. Curr Microbiol 2010; 61:458-64. [DOI: 10.1007/s00284-010-9638-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 03/24/2010] [Indexed: 11/28/2022]
|
31
|
Kad NM, Wang H, Kennedy GG, Warshaw DM, Van Houten B. Collaborative dynamic DNA scanning by nucleotide excision repair proteins investigated by single- molecule imaging of quantum-dot-labeled proteins. Mol Cell 2010; 37:702-13. [PMID: 20227373 DOI: 10.1016/j.molcel.2010.02.003] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 10/14/2009] [Accepted: 12/23/2009] [Indexed: 11/29/2022]
Abstract
How DNA repair proteins sort through a genome for damage is one of the fundamental unanswered questions in this field. To address this problem, we uniquely labeled bacterial UvrA and UvrB with differently colored quantum dots and visualized how they interacted with DNA individually or together using oblique-angle fluorescence microscopy. UvrA was observed to utilize a three-dimensional search mechanism, binding transiently to the DNA for short periods (7 s). UvrA also was observed jumping from one DNA molecule to another over approximately 1 microm distances. Two UvrBs can bind to a UvrA dimer and collapse the search dimensionality of UvrA from three to one dimension by inducing a substantial number of UvrAB complexes to slide along the DNA. Three types of sliding motion were characterized: random diffusion, paused motion, and directed motion. This UvrB-induced change in mode of searching permits more rapid and efficient scanning of the genome for damage.
Collapse
Affiliation(s)
- Neil M Kad
- Department of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK.
| | | | | | | | | |
Collapse
|
32
|
Goosen N. Scanning the DNA for damage by the nucleotide excision repair machinery. DNA Repair (Amst) 2010; 9:593-6. [PMID: 20335079 DOI: 10.1016/j.dnarep.2010.02.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 02/12/2010] [Accepted: 02/24/2010] [Indexed: 11/28/2022]
Abstract
Damage detection during nucleotide excision repair requires the action of multiple proteins that probe the DNA for different parameters like disruption of basepairing, DNA bendability and presence of chemical modifications. In a recent study it has been shown that two of these probing events can be spatially separated on the DNA. Upon initial binding of the XPC protein to a region with disrupted basepairing a complex of XPC, TFIIH and XPA is translocated to a CPD lesion even when this chemical modification is located up to 160 nucleotides from the mispaired region.
Collapse
Affiliation(s)
- Nora Goosen
- Laboratory of Molecular Genetics, Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
| |
Collapse
|
33
|
Jia L, Kropachev K, Ding S, Van Houten B, Geacintov NE, Broyde S. Exploring damage recognition models in prokaryotic nucleotide excision repair with a benzo[a]pyrene-derived lesion in UvrB. Biochemistry 2009; 48:8948-57. [PMID: 19681599 DOI: 10.1021/bi9010072] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The UvrB protein is a central unit for damage recognition in the prokaryotic nucleotide excision repair system, which excises bulky DNA lesions. We have utilized molecular modeling and MD simulations based on crystal structures, mutagenesis, and fluorescence data, to model the 10R-(+)-cis-anti-B[a]P-N2-dG lesion, derived from the tumorigenic (+)-anti-B[a]PDE metabolite of benzo[a]pyrene, at different locations on the inner and outer strand in UvrB. Our results suggest that this lesion is accommodated on the inner strand where it might translocate through the tunnel created by the beta-hairpin and UvrB domain 1B and ultimately could be housed in the pocket behind the beta-hairpin prior to excision by UvrC. Lesions that vary in size and shape may be stopped at the gate to the tunnel, within the tunnel, or in the pocket when UvrC initiates excision. Common features of beta-hairpin intrusion between the two DNA strands and nucleotide flipping manifested in structures of prokaryotic and eukaryotic NER lesion recognition proteins are consistent with common recognition mechanisms, based on lesion-induced local thermodynamic distortion/destabilization and nucleotide flipping.
Collapse
Affiliation(s)
- Lei Jia
- Department of Biology, New York University, 100 Washington Square East, Room 1009, New York, New York 10003, USA
| | | | | | | | | | | |
Collapse
|
34
|
Pruteanu M, Baker TA. Proteolysis in the SOS response and metal homeostasis in Escherichia coli. Res Microbiol 2009; 160:677-83. [PMID: 19747971 DOI: 10.1016/j.resmic.2009.08.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 08/15/2009] [Accepted: 08/17/2009] [Indexed: 10/20/2022]
Abstract
Proteolysis is used by all forms of life for shaping the proteome in response to adverse environmental conditions in order to ensure optimal survival. Here we will address the role of proteolysis in helping cells respond to environmental stress, with a focus on the impact of proteolysis under DNA-damaging conditions and in maintenance of cellular homeostasis in response to metal exposure in bacteria.
Collapse
Affiliation(s)
- Mihaela Pruteanu
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Building 68-523, 77 Massachusetts Ave, Cambridge, MA 02139, USA.
| | | |
Collapse
|
35
|
Pakotiprapha D, Liu Y, Verdine GL, Jeruzalmi D. A structural model for the damage-sensing complex in bacterial nucleotide excision repair. J Biol Chem 2009; 284:12837-44. [PMID: 19287003 DOI: 10.1074/jbc.m900571200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nucleotide excision repair is distinguished from other DNA repair pathways by its ability to process a wide range of structurally unrelated DNA lesions. In bacteria, damage recognition is achieved by the UvrA.UvrB ensemble. Here, we report the structure of the complex between the interaction domains of UvrA and UvrB. These domains are necessary and sufficient for full-length UvrA and UvrB to associate and thereby form the DNA damage-sensing complex of bacterial nucleotide excision repair. The crystal structure and accompanying biochemical analyses suggest a model for the complete damage-sensing complex.
Collapse
Affiliation(s)
- Danaya Pakotiprapha
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | | | | | | |
Collapse
|
36
|
Atkinson J, Guy CP, Cadman CJ, Moolenaar GF, Goosen N, McGlynn P. Stimulation of UvrD helicase by UvrAB. J Biol Chem 2009; 284:9612-23. [PMID: 19208629 DOI: 10.1074/jbc.m808030200] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Helicases play critical roles in all aspects of nucleic acid metabolism by catalyzing the remodeling of DNA and RNA structures. UvrD is an abundant helicase in Escherichia coli with well characterized functions in mismatch and nucleotide excision repair and a possible role in displacement of proteins such as RecA from single-stranded DNA. The mismatch repair protein MutL is known to stimulate UvrD. Here we show that the nucleotide excision repair proteins UvrA and UvrB can together stimulate UvrD-catalyzed unwinding of a range of DNA substrates containing strand discontinuities, including forked DNA substrates. The stimulation is specific for UvrD, as UvrAB failed to stimulate Rep helicase, a UvrD homologue. Moreover, although UvrAB can promote limited strand displacement, stimulation of UvrD did not require the strand displacement function of UvrAB. We conclude that UvrAB, like MutL, modulate UvrD helicase activity. This stimulation likely plays a role in DNA strand and protein displacement by UvrD in nucleotide excision repair. Promotion of UvrD-catalyzed unwinding of nicked duplexes by UvrAB may also explain the need for UvrAB and UvrD in Okazaki fragment processing in cells lacking DNA polymerase I. More generally, these data support the idea that helicase activity is regulated in vivo, with helicases acting as part of multisubunit complexes rather than in isolation.
Collapse
Affiliation(s)
- John Atkinson
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | | | | | | | | | | |
Collapse
|
37
|
Wagner K, Moolenaar G, van Noort J, Goosen N. Single-molecule analysis reveals two separate DNA-binding domains in the Escherichia coli UvrA dimer. Nucleic Acids Res 2009; 37:1962-72. [PMID: 19208636 PMCID: PMC2665241 DOI: 10.1093/nar/gkp071] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The UvrA protein is the initial damage-recognizing factor in bacterial nucleotide excision repair. Each monomer of the UvrA dimer contains two ATPase sites. Using single-molecule analysis we show that dimerization of UvrA in the presence of ATP is significantly higher than with ADP or nonhydrolyzable ATPγS, suggesting that the active UvrA dimer contains a mixture of ADP and ATP. We also show that the UvrA dimer has a high preference of binding the end of a linear DNA fragment, independent on the presence or type of cofactor. Apparently ATP binding or hydrolysis is not needed to discriminate between DNA ends and internal sites. A significant number of complexes could be detected where one UvrA dimer bridges two DNA ends implying the presence of two separate DNA-binding domains, most likely present in each monomer. On DNA containing a site-specific lesion the damage-specific binding is much higher than DNA-end binding, but only in the absence of cofactor or with ATP. With ATPγS no discrimination between a DNA end and a DNA damage could be observed. We present a model where damage recognition of UvrA depends on the ability of both UvrA monomers to interact with the DNA flanking the lesion.
Collapse
Affiliation(s)
- Koen Wagner
- Laboratory of Molecular Genetics, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | | | | | | |
Collapse
|
38
|
Pruteanu M, Baker TA. Controlled degradation by ClpXP protease tunes the levels of the excision repair protein UvrA to the extent of DNA damage. Mol Microbiol 2008; 71:912-24. [PMID: 19183285 DOI: 10.1111/j.1365-2958.2008.06574.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
UV irradiation damages DNA and activates expression of genes encoding proteins helpful for survival under DNA stress. These proteins are often deleterious in the absence of DNA damage. Here, we investigate mechanisms used to regulate the levels of DNA-repair proteins during recovery by studying control of the nucleotide excision repair (NER) protein UvrA. We show that UvrA is induced after UV irradiation and reaches maximum levels between approximately 20 and 120 min post UV. During post-UV recovery, UvrA levels decrease principally as a result of ClpXP-dependent protein degradation. The rate of UvrA degradation depends on the amount of unrepaired pyrimidine dimers present; this degradation rate is initially slow shortly after UV, but increases as damage is repaired. This increase in UvrA degradation as repair progresses is also influenced by protein-protein interactions. Genetic and in vitro experiments support the conclusion that UvrA-UvrB interactions antagonize degradation. In contrast, Mfd appears to act as an enhancer of UvrA turnover. Thus, our results reveal that a complex network of interactions contribute to tuning the level of UvrA in the cell in response to the extent of DNA damage and nicely mirror findings with excision repair proteins from eukaryotes, which are controlled by proteolysis in a similar manner.
Collapse
Affiliation(s)
- Mihaela Pruteanu
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | |
Collapse
|
39
|
Goosen N, Moolenaar GF. Repair of UV damage in bacteria. DNA Repair (Amst) 2008; 7:353-79. [DOI: 10.1016/j.dnarep.2007.09.002] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Accepted: 09/06/2007] [Indexed: 10/22/2022]
|