1
|
The Biochemical Mechanism of Fork Regression in Prokaryotes and Eukaryotes—A Single Molecule Comparison. Int J Mol Sci 2022; 23:ijms23158613. [PMID: 35955746 PMCID: PMC9368896 DOI: 10.3390/ijms23158613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 02/04/2023] Open
Abstract
The rescue of stalled DNA replication forks is essential for cell viability. Impeded but still intact forks can be rescued by atypical DNA helicases in a reaction known as fork regression. This reaction has been studied at the single-molecule level using the Escherichia coli DNA helicase RecG and, separately, using the eukaryotic SMARCAL1 enzyme. Both nanomachines possess the necessary activities to regress forks: they simultaneously couple DNA unwinding to duplex rewinding and the displacement of bound proteins. Furthermore, they can regress a fork into a Holliday junction structure, the central intermediate of many fork regression models. However, there are key differences between these two enzymes. RecG is monomeric and unidirectional, catalyzing an efficient and processive fork regression reaction and, in the process, generating a significant amount of force that is used to displace the tightly-bound E. coli SSB protein. In contrast, the inefficient SMARCAL1 is not unidirectional, displays limited processivity, and likely uses fork rewinding to facilitate RPA displacement. Like many other eukaryotic enzymes, SMARCAL1 may require additional factors and/or post-translational modifications to enhance its catalytic activity, whereas RecG can drive fork regression on its own.
Collapse
|
2
|
Bianco PR. OB-fold Families of Genome Guardians: A Universal Theme Constructed From the Small β-barrel Building Block. Front Mol Biosci 2022; 9:784451. [PMID: 35223988 PMCID: PMC8881015 DOI: 10.3389/fmolb.2022.784451] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
The maintenance of genome stability requires the coordinated actions of multiple proteins and protein complexes, that are collectively known as genome guardians. Within this broadly defined family is a subset of proteins that contain oligonucleotide/oligosaccharide-binding folds (OB-fold). While OB-folds are widely associated with binding to single-stranded DNA this view is no longer an accurate depiction of how these domains are utilized. Instead, the core of the OB-fold is modified and adapted to facilitate binding to a variety of DNA substrates (both single- and double-stranded), phospholipids, and proteins, as well as enabling catalytic function to a multi-subunit complex. The flexibility accompanied by distinctive oligomerization states and quaternary structures enables OB-fold genome guardians to maintain the integrity of the genome via a myriad of complex and dynamic, protein-protein; protein-DNA, and protein-lipid interactions in both prokaryotes and eukaryotes.
Collapse
Affiliation(s)
- Piero R. Bianco
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, United States
| |
Collapse
|
3
|
Bianco PR. The mechanism of action of the SSB interactome reveals it is the first OB-fold family of genome guardians in prokaryotes. Protein Sci 2021; 30:1757-1775. [PMID: 34089559 PMCID: PMC8376408 DOI: 10.1002/pro.4140] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 12/28/2022]
Abstract
The single-stranded DNA binding protein (SSB) is essential to all aspects of DNA metabolism in bacteria. This protein performs two distinct, but closely intertwined and indispensable functions in the cell. SSB binds to single-stranded DNA (ssDNA) and at least 20 partner proteins resulting in their regulation. These partners comprise a family of genome guardians known as the SSB interactome. Essential to interactome regulation is the linker/OB-fold network of interactions. This network of interactions forms when one or more PXXP motifs in the linker of SSB bind to an OB-fold in a partner, with interactome members involved in competitive binding between the linker and ssDNA to their OB-fold. Consequently, when linker-binding occurs to an OB-fold in an interactome partner, proteins are loaded onto the DNA. When linker/OB-fold interactions occur between SSB tetramers, cooperative ssDNA-binding results, producing a multi-tetrameric complex that rapidly protects the ssDNA. Within this SSB-ssDNA complex, there is an extensive and dynamic network of linker/OB-fold interactions that involves multiple tetramers bound contiguously along the ssDNA lattice. The dynamic behavior of these tetramers which includes binding mode changes, sliding as well as DNA wrapping/unwrapping events, are likely coupled to the formation and disruption of linker/OB-fold interactions. This behavior is essential to facilitating downstream DNA processing events. As OB-folds are critical to the essence of the linker/OB-fold network of interactions, and they are found in multiple interactome partners, the SSB interactome is classified as the first family of prokaryotic, oligosaccharide/oligonucleotide binding fold (OB-fold) genome guardians.
Collapse
MESH Headings
- Amino Acid Motifs
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Binding, Competitive
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- DNA-Binding Proteins/chemistry
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression Regulation, Bacterial
- Gene Regulatory Networks
- Genome, Bacterial
- Klebsiella pneumoniae/chemistry
- Klebsiella pneumoniae/genetics
- Klebsiella pneumoniae/metabolism
- Models, Molecular
- Oligonucleotides/chemistry
- Oligonucleotides/metabolism
- Oligosaccharides/chemistry
- Oligosaccharides/metabolism
- Protein Binding
- Protein Conformation
- Protein Interaction Mapping
- Protein Multimerization
Collapse
Affiliation(s)
- Piero R. Bianco
- Department of Pharmaceutical Sciences, College of PharmacyUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| |
Collapse
|
4
|
Bianco PR, Lu Y. Single-molecule insight into stalled replication fork rescue in Escherichia coli. Nucleic Acids Res 2021; 49:4220-4238. [PMID: 33744948 PMCID: PMC8096234 DOI: 10.1093/nar/gkab142] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/15/2021] [Accepted: 02/22/2021] [Indexed: 01/05/2023] Open
Abstract
DNA replication forks stall at least once per cell cycle in Escherichia coli. DNA replication must be restarted if the cell is to survive. Restart is a multi-step process requiring the sequential action of several proteins whose actions are dictated by the nature of the impediment to fork progression. When fork progress is impeded, the sequential actions of SSB, RecG and the RuvABC complex are required for rescue. In contrast, when a template discontinuity results in the forked DNA breaking apart, the actions of the RecBCD pathway enzymes are required to resurrect the fork so that replication can resume. In this review, we focus primarily on the significant insight gained from single-molecule studies of individual proteins, protein complexes, and also, partially reconstituted regression and RecBCD pathways. This insight is related to the bulk-phase biochemical data to provide a comprehensive review of each protein or protein complex as it relates to stalled DNA replication fork rescue.
Collapse
Affiliation(s)
- Piero R Bianco
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Yue Lu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA
| |
Collapse
|
5
|
Ding W, Tan HY, Zhang JX, Wilczek LA, Hsieh KR, Mulkin JA, Bianco PR. The mechanism of Single strand binding protein-RecG binding: Implications for SSB interactome function. Protein Sci 2020; 29:1211-1227. [PMID: 32196797 PMCID: PMC7184773 DOI: 10.1002/pro.3855] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 01/10/2023]
Abstract
The Escherichia coli single-strand DNA binding protein (SSB) is essential to viability where it functions to regulate SSB interactome function. Here it binds to single-stranded DNA and to target proteins that comprise the interactome. The region of SSB that links these two essential protein functions is the intrinsically disordered linker. Key to linker function is the presence of three, conserved PXXP motifs that mediate binding to oligosaccharide-oligonucleotide binding folds (OB-fold) present in SSB and its interactome partners. Not surprisingly, partner OB-fold deletions eliminate SSB binding. Furthermore, single point mutations in either the PXXP motifs or, in the RecG OB-fold, obliterate SSB binding. The data also demonstrate that, and in contrast to the view currently held in the field, the C-terminal acidic tip of SSB is not required for interactome partner binding. Instead, we propose the tip has two roles. First, and consistent with the proposal of Dixon, to regulate the structure of the C-terminal domain in a biologically active conformation that prevents linkers from binding to SSB OB-folds until this interaction is required. Second, as a secondary binding domain. Finally, as OB-folds are present in SSB and many of its partners, we present the SSB interactome as the first family of OB-fold genome guardians identified in prokaryotes.
Collapse
Affiliation(s)
- Wenfei Ding
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
- Department of BiochemistryUniversity at BuffaloBuffaloNew YorkUnited States
| | - Hui Yin Tan
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
- Present address:
Department of Chemistry and BiochemistryUniversity of Notre DameSouth BendIndianaUnited States
| | - Jia Xiang Zhang
- Department of BiochemistryUniversity at BuffaloBuffaloNew YorkUnited States
| | - Luke A. Wilczek
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
- Department of BiochemistryUniversity at BuffaloBuffaloNew YorkUnited States
- Present address:
Department of ChemistryBrown UniversityProvidenceRhode IslandUnited States
| | - Karin R. Hsieh
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
| | - Jeffrey A. Mulkin
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
| | - Piero R. Bianco
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
- Department of BiochemistryUniversity at BuffaloBuffaloNew YorkUnited States
| |
Collapse
|
6
|
Bianco PR. DNA Helicase-SSB Interactions Critical to the Regression and Restart of Stalled DNA Replication forks in Escherichia coli. Genes (Basel) 2020; 11:E471. [PMID: 32357475 PMCID: PMC7290993 DOI: 10.3390/genes11050471] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/21/2020] [Accepted: 04/23/2020] [Indexed: 01/25/2023] Open
Abstract
In Escherichia coli, DNA replication forks stall on average once per cell cycle. When this occurs, replisome components disengage from the DNA, exposing an intact, or nearly intact fork. Consequently, the fork structure must be regressed away from the initial impediment so that repair can occur. Regression is catalyzed by the powerful, monomeric DNA helicase, RecG. During this reaction, the enzyme couples unwinding of fork arms to rewinding of duplex DNA resulting in the formation of a Holliday junction. RecG works against large opposing forces enabling it to clear the fork of bound proteins. Following subsequent processing of the extruded junction, the PriA helicase mediates reloading of the replicative helicase DnaB leading to the resumption of DNA replication. The single-strand binding protein (SSB) plays a key role in mediating PriA and RecG functions at forks. It binds to each enzyme via linker/OB-fold interactions and controls helicase-fork loading sites in a substrate-dependent manner that involves helicase remodeling. Finally, it is displaced by RecG during fork regression. The intimate and dynamic SSB-helicase interactions play key roles in ensuring fork regression and DNA replication restart.
Collapse
Affiliation(s)
- Piero R Bianco
- Center for Single Molecule Biophysics, University at Buffalo, SUNY, Buffalo, NY 14221, USA
| |
Collapse
|
7
|
Weaver GM, Mettrick KA, Corocher TA, Graham A, Grainge I. Replication fork collapse at a protein-DNA roadblock leads to fork reversal, promoted by the RecQ helicase. Mol Microbiol 2018; 111:455-472. [PMID: 30466158 DOI: 10.1111/mmi.14166] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2018] [Indexed: 11/27/2022]
Abstract
Proteins that bind DNA are the cause of the majority of impediments to replication fork progression and can lead to subsequent collapse of the replication fork. Failure to deal with fork collapse efficiently leads to mutation or cell death. Several models have been proposed for how a cell processes a stalled or collapsed replication fork; eukaryotes and bacteria are not dissimilar in terms of the general pathways undertaken to deal with these events. This study shows that replication fork regression, the combination of replication fork reversal leading to formation of a Holliday Junction along with exonuclease digestion, is the preferred pathway for dealing with a collapsed fork in Escherichia coli. Direct endo-nuclease activity at the replication fork was not observed. The protein that had the greatest effect on these fork processing events was the RecQ helicase, while RecG and RuvABC, which have previously been implicated in this process, were found to play a lesser role. Eukaryotic RecQ homologues, BLM and WRN, have also been implicated in processing events following replication fork collapse and may reflect a conserved mechanism. Finally, the SOS response was not induced by the protein-DNA roadblock under these conditions, so did not affect fork processing.
Collapse
Affiliation(s)
- Georgia M Weaver
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
| | - Karla A Mettrick
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
| | - Tayla-Ann Corocher
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
| | - Adam Graham
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
| | - Ian Grainge
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
| |
Collapse
|
8
|
Bianco PR, Lyubchenko YL. SSB and the RecG DNA helicase: an intimate association to rescue a stalled replication fork. Protein Sci 2017; 26:638-649. [PMID: 28078722 DOI: 10.1002/pro.3114] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 12/26/2016] [Accepted: 12/28/2016] [Indexed: 12/27/2022]
Abstract
In E. coli, the regression of stalled DNA replication forks is catalyzed by the DNA helicase RecG. One means of gaining access to the fork is by binding to the single strand binding protein or SSB. This interaction occurs via the wedge domain of RecG and the intrinsically disordered linker (IDL) of SSB, in a manner similar to that of SH3 domains binding to PXXP motif-containing ligands in eukaryotic cells. During loading, SSB remodels the wedge domain so that the helicase domains bind to the parental, duplex DNA, permitting the helicase to translocate using thermal energy. This translocation may be used to clear the fork of obstacles, prior to the initiation of fork regression.
Collapse
Affiliation(s)
- Piero R Bianco
- SUNY Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, 321 Cary Hall, 3435 Main St, Buffalo, New York 14214.,Department of Microbiology and Immunology, University at Buffalo, Buffalo, New York.,Department of Biochemistry, University at Buffalo, Buffalo, New York
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska, 68198-6025
| |
Collapse
|
9
|
Moiseeva ED, Bazhulina NP, Gursky YG, Grokhovsky SL, Surovaya AN, Gursky GV. Targeting Holliday junctions by origin DNA-binding protein of herpes simplex virus type 1. J Biomol Struct Dyn 2016; 35:704-723. [PMID: 26987269 DOI: 10.1080/07391102.2016.1161561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
In the present paper, the interactions of the origin binding protein (OBP) of herpes simplex virus type 1 (HSV1) with synthetic four-way Holliday junctions (HJs) were studied using electrophoresis mobility shift assay and the FRET method and compared with the interactions of the protein with duplex and single-stranded DNAs. It has been found that OBP exhibits a strong preference for binding to four-way and three-way DNA junctions and possesses much lower affinities to duplex and single-stranded DNAs. The protein forms three types of complexes with HJs. It forms complexes I and II which are reminiscent of the tetramer and octamer complexes with four-way junction of HJ-specific protein RuvA of Escherichia coli. The binding approaches saturation level when two OBP dimers are bound per junction. In the presence of Mg2+ ions (≥2 mM) OBP also interacts with HJ in the stacked arm form (complex III). In the presence of 5 mM ATP and 10 mM Mg2+ ions OBP catalyzes processing of the HJ in which one of the annealed oligonucleotides has a 3'-terminal tail containing 20 unpaired thymine residues. The observed preference of OBP for binding to the four-way DNA junctions provides a basis for suggestion that OBP induces large DNA structural changes upon binding to Box I and Box II sites in OriS. These changes involve the bending and partial melting of the DNA at A+T-rich spacer and also include the formation of HJ containing Box I and Box II inverted repeats and flanking DNA sequences.
Collapse
Affiliation(s)
- E D Moiseeva
- a Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , ul. Vavilova 32, 119991 Moscow , Russia
| | - N P Bazhulina
- a Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , ul. Vavilova 32, 119991 Moscow , Russia
| | - Y G Gursky
- b Russian Cardiology Research-and-Production Complex , 3ya Cherepkovskaya ul. 15a, 121552 Moscow , Russia
| | - S L Grokhovsky
- a Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , ul. Vavilova 32, 119991 Moscow , Russia
| | - A N Surovaya
- a Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , ul. Vavilova 32, 119991 Moscow , Russia
| | - G V Gursky
- a Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , ul. Vavilova 32, 119991 Moscow , Russia
| |
Collapse
|
10
|
Upton AL, Grove JI, Mahdi AA, Briggs GS, Milner DS, Rudolph CJ, Lloyd RG. Cellular location and activity of Escherichia coli RecG proteins shed light on the function of its structurally unresolved C-terminus. Nucleic Acids Res 2014; 42:5702-14. [PMID: 24692661 PMCID: PMC4027168 DOI: 10.1093/nar/gku228] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
RecG is a DNA translocase encoded by most species of bacteria. The Escherichia coli protein targets branched DNA substrates and drives the unwinding and rewinding of DNA strands. Its ability to remodel replication forks and to genetically interact with PriA protein have led to the idea that it plays an important role in securing faithful genome duplication. Here we report that RecG co-localises with sites of DNA replication and identify conserved arginine and tryptophan residues near its C-terminus that are needed for this localisation. We establish that the extreme C-terminus, which is not resolved in the crystal structure, is vital for DNA unwinding but not for DNA binding. Substituting an alanine for a highly conserved tyrosine near the very end results in a substantial reduction in the ability to unwind replication fork and Holliday junction structures but has no effect on substrate affinity. Deleting or substituting the terminal alanine causes an even greater reduction in unwinding activity, which is somewhat surprising as this residue is not uniformly present in closely related RecG proteins. More significantly, the extreme C-terminal mutations have little effect on localisation. Mutations that do prevent localisation result in only a slight reduction in the capacity for DNA repair.
Collapse
Affiliation(s)
- Amy L Upton
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jane I Grove
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Akeel A Mahdi
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Geoffrey S Briggs
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - David S Milner
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Christian J Rudolph
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK School of Health Sciences and Social Care, Division of Biosciences, Brunel University, Uxbridge, London UB8 3PH, UK
| | - Robert G Lloyd
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| |
Collapse
|
11
|
Bazhulina NP, Surovaya AN, Gursky YG, Andronova VL, Moiseeva ED, Nikitin CACM, Golovkin MV, Galegov GА, Grokhovsky SL, Gursky GV. Complex of the herpes simplex virus type 1 origin binding protein UL9 with DNA as a platform for the design of a new type of antiviral drugs. J Biomol Struct Dyn 2013; 32:1456-73. [PMID: 23879454 PMCID: PMC4066892 DOI: 10.1080/07391102.2013.820110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The herpes simplex virus type 1 origin-binding protein, OBP, is a DNA helicase encoded by the UL9 gene. The protein binds in a sequence-specific manner to the viral origins of replication, two OriS sites and one OriL site. In order to search for efficient inhibitors of the OBP activity, we have obtained a recombinant origin-binding protein expressed in Escherichia coli cells. The UL9 gene has been amplified by PCR and inserted into a modified plasmid pET14 between NdeI and KpnI sites. The recombinant protein binds to Box I and Box II sequences and possesses helicase and ATPase activities. In the presence of ATP and viral protein ICP8 (single-strand DNA-binding protein), the initiator protein induces unwinding of the minimal OriS duplex (≈80 bp). The protein also binds to a single-stranded DNA (OriS*) containing a stable Box I-Box III hairpin and an unstable AT-rich hairpin at the 3'-end. In the present work, new minor groove binding ligands have been synthesized which are capable to inhibit the development of virus-induced cytopathic effect in cultured Vero cells. Studies on binding of these compounds to DNA and synthetic oligonucleotides have been performed by fluorescence methods, gel mobility shift analysis and footprinting assays. Footprinting studies have revealed that Pt-bis-netropsin and related molecules exhibit preferences for binding to the AT-spacer in OriS. The drugs stabilize structure of the AT-rich region and inhibit the fluctuation opening of AT-base pairs which is a prerequisite to unwinding of DNA by OBP. Kinetics of ATP-dependent unwinding of OriS in the presence and absence of netropsin derivatives have been studied by measuring the efficiency of Forster resonance energy transfer (FRET) between fluorophores attached to 5'- and 3'- ends of an oligonucleotide in the minimal OriS duplex. The results are consistent with the suggestion that OBP is the DNA Holiday junction (HJ) binding helicase. The protein induces conformation changes (bending and partial melting) of OriS duplexes and stimulates HJ formation in the absence of ATP. The antiviral activity of bis-netropsins is coupled with their ability to inhibit the fluctuation opening of АТ base pairs in the А + Т cluster and their capacity to stabilize the structure of the АТ-rich hairpin in the single-stranded oligonucleotide corresponding to the upper chain in the minimal duplex OriS. The antiviral activities of bis-netropsins in cell culture and their therapeutic effects on HSV1-infected laboratory animals have been studied.
Collapse
Affiliation(s)
- N P Bazhulina
- a V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , ul. Vavilova 32, 119991 , Moscow , Russia
| | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Killen MW, Stults DM, Wilson WA, Pierce AJ. Escherichia coli RecG functionally suppresses human Bloom syndrome phenotypes. BMC Mol Biol 2012; 13:33. [PMID: 23110454 PMCID: PMC3517418 DOI: 10.1186/1471-2199-13-33] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Accepted: 10/11/2012] [Indexed: 11/10/2022] Open
Abstract
Defects in the human BLM gene cause Bloom syndrome, notable for early development of tumors in a broad variety of tissues. On the basis of sequence similarity, BLM has been identified as one of the five human homologs of RecQ from Escherichia coli. Nevertheless, biochemical characterization of the BLM protein indicates far greater functional similarity to the E. coli RecG protein and there is no known RecG homolog in human cells. To explore the possibility that the shared biochemistries of BLM and RecG may represent an example of convergent evolution of cellular function where in humans BLM has evolved to fulfill the genomic stabilization role of RecG, we determined whether expression of RecG in human BLM-deficient cells could suppress established functional cellular Bloom syndrome phenotypes. We found that RecG can indeed largely suppress both the definitive elevated sister chromatid exchange phenotype and the more recently demonstrated gene cluster instability phenotype of BLM-deficient cells. In contrast, expression of RecG has no impact on either of these phenotypes in human cells with functional BLM protein. These results suggest that the combination of biochemical activities shared by RecG and BLM fill the same evolutionary niche in preserving genomic integrity without requiring exactly identical molecular mechanisms.
Collapse
Affiliation(s)
- Michael W Killen
- Department of Microbiology, Immunology and Molecular Genetics, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | | | | | | |
Collapse
|
13
|
Structural and Functional Characterization of RecG Helicase under Dilute and Molecular Crowding Conditions. J Nucleic Acids 2012; 2012:392039. [PMID: 22919464 PMCID: PMC3420092 DOI: 10.1155/2012/392039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 05/30/2012] [Indexed: 12/04/2022] Open
Abstract
In an ATP-dependent reaction, the Escherichia coli RecG helicase unwinds DNA junctions in vitro. We present evidence of a unique protein conformational change in the RecG helicase from an α-helix to a β-strand upon an ATP binding under dilute conditions using circular dichroism (CD) spectroscopy. In contrast, under molecular crowding conditions, the α-helical conformation was stable even upon an ATP binding. These distinct conformational behaviors were observed to be independent of Na+ and Mg2+. Interestingly, CD measurements demonstrated that the spectra of a frayed duplex decreased with increasing of the RecG concentration both under dilute and molecular crowding conditions in the presence of ATP, suggesting that RecG unwound the frayed duplex. Our findings raise the possibility that the α-helix and β-strand forms of RecG are a preactive and an active structure with the helicase activity, respectively.
Collapse
|
14
|
Atkinson J, McGlynn P. Replication fork reversal and the maintenance of genome stability. Nucleic Acids Res 2009; 37:3475-92. [PMID: 19406929 PMCID: PMC2699526 DOI: 10.1093/nar/gkp244] [Citation(s) in RCA: 181] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The progress of replication forks is often threatened in vivo, both by DNA damage and by proteins bound to the template. Blocked forks must somehow be restarted, and the original blockage cleared, in order to complete genome duplication, implying that blocked fork processing may be critical for genome stability. One possible pathway that might allow processing and restart of blocked forks, replication fork reversal, involves the unwinding of blocked forks to form four-stranded structures resembling Holliday junctions. This concept has gained increasing popularity recently based on the ability of such processing to explain many genetic observations, the detection of unwound fork structures in vivo and the identification of enzymes that have the capacity to catalyse fork regression in vitro. Here, we discuss the contexts in which fork regression might occur, the factors that may promote such a reaction and the possible roles of replication fork unwinding in normal DNA metabolism.
Collapse
Affiliation(s)
- John Atkinson
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | | |
Collapse
|
15
|
Smith AJ, Szczelkun MD, Savery NJ. Controlling the motor activity of a transcription-repair coupling factor: autoinhibition and the role of RNA polymerase. Nucleic Acids Res 2007; 35:1802-11. [PMID: 17329375 PMCID: PMC1874598 DOI: 10.1093/nar/gkm019] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Motor proteins that couple ATP hydrolysis to movement along nucleic acids play a variety of essential roles in DNA metabolism. Often these enzymes function as components of macromolecular complexes, and DNA translocation by the motor protein drives movement of other components of the complex. In order to understand how the activity of motor proteins is regulated within multi-protein complexes we have studied the bacterial transcription-repair coupling factor, Mfd, which is a helicase superfamily 2 member that binds to RNA polymerase (RNAP) and removes stalled transcription complexes from DNA. Using an oligonucleotide displacement assay that monitors protein movement on double-stranded DNA we show that Mfd has little motor activity in isolation, but exhibits efficient oligonucleotide displacement activity when bound to a stalled transcription complex. Deletion of the C-terminal domain of Mfd increases the ATPase activity of the protein and allows efficient oligo-displacement in the absence of RNAP. Our results suggest that an autoinhibitory domain ensures the motor activity of Mfd is only functional within the correct macromolecular context: recruitment of Mfd to a stalled transcription complex relieves the autoinhibition and unmasks the motor activity.
Collapse
Affiliation(s)
| | | | - Nigel J. Savery
- *To whom correspondence should be addressed. +(44) 117 928 9708+(44) 117 928 8274
| |
Collapse
|
16
|
Slocum SL, Buss JA, Kimura Y, Bianco PR. Characterization of the ATPase activity of the Escherichia coli RecG protein reveals that the preferred cofactor is negatively supercoiled DNA. J Mol Biol 2007; 367:647-64. [PMID: 17292398 PMCID: PMC1913479 DOI: 10.1016/j.jmb.2007.01.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2006] [Revised: 12/29/2006] [Accepted: 01/02/2007] [Indexed: 02/07/2023]
Abstract
RecG is a member of the superfamily 2 helicase family. Its possible role in vivo is ATP hydrolysis driven regression of stalled replication forks. To gain mechanistic insight into how this is achieved, a coupled spectrophotometric assay was utilized to characterize the ATPase activity of RecG in vitro. The results demonstrate an overwhelming preference for negatively supercoiled DNA ((-)scDNA) as a cofactor for the hydrolysis of ATP. In the presence of (-)scDNA the catalytic efficiency of RecG and the processivity (as revealed through heparin trapping), were higher than on any other cofactor examined. The activity of RecG on (-)scDNA was not due to the presence of single-stranded regions functioning as loading sites for the enzyme as relaxed circular DNA treated with DNA gyrase, resulted in the highest levels of ATPase activity. Relaxation of (-)scDNA by a topoisomerase resulted in a 12-fold decrease in ATPase activity, comparable to that observed on both linear double-stranded (ds)DNA and (+)scDNA. In addition to the elevated activity in the presence of (-)scDNA, RecG also has high activity on model 4Y-substrates (i.e. chicken foot structures). This is due largely to the high apparent affinity of the enzyme for this DNA substrate, which is 46-fold higher than a 2Y-substrate (i.e. a three-way with two single-stranded (ss)DNA arms). Finally, the enzyme exhibited significant, but lower activity on ssDNA. This activity was enhanced by the Escherichia coli stranded DNA-binding protein (SSB) protein, which occurs through stabilizing of the binding of RecG to ssDNA. Stabilization is not afforded by the bacteriophage gene 32 protein, indicating a species specific, protein-protein interaction is involved. These results combine to provide significant insight into the manner and timing of the interaction of RecG with DNA at stalled replication forks.
Collapse
Affiliation(s)
- Stephen L. Slocum
- Department of Biochemistry, University at Buffalo, Buffalo, NY 14214 USA
| | - Jackson A. Buss
- Center for Single Molecule Biophysics, University at Buffalo, Buffalo, NY 14214 USA
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY 14214 USA
| | - Yuji Kimura
- Center for Single Molecule Biophysics, University at Buffalo, Buffalo, NY 14214 USA
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY 14214 USA
| | - Piero R. Bianco
- Department of Biochemistry, University at Buffalo, Buffalo, NY 14214 USA
- Center for Single Molecule Biophysics, University at Buffalo, Buffalo, NY 14214 USA
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY 14214 USA
| |
Collapse
|
17
|
Bichara M, Pinet I, Origas M, Fuchs RPP. Inactivation of recG stimulates the RecF pathway during lesion-induced recombination in E. coli. DNA Repair (Amst) 2006; 5:129-37. [PMID: 16257588 DOI: 10.1016/j.dnarep.2005.08.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2005] [Revised: 08/01/2005] [Accepted: 08/25/2005] [Indexed: 12/23/2022]
Abstract
Lesions that transiently block DNA synthesis generate replication intermediates with recombinogenic potential. In order to investigate the mechanisms involved in lesion-induced recombination, we developed an homologous recombination assay involving the transfer of genetic information from a plasmid donor molecule to the Escherichia coli chromosome. The replication blocking lesion used in the present assay is formed by covalent binding of the carcinogen N-2-acetylaminofluorene to the C8 position of guanine residues (G-AAF adducts). The frequency of recombination events was monitored as a function of the number of lesions present on the donor plasmid. These DNA adducts are found to trigger high levels of homologous recombination events in a dose-dependent manner. Formation of recombinants is entirely RecA-dependent, the RecF and RecBCD sub-pathways accounting for about 2/3 and 1/3, respectively. Inactivation of recG stimulates recombinant formation about five-fold. In a recG background, the RecF pathway is stimulated about four-fold, while the contribution of the RecBCD pathway remains constant. In addition, in the recG strain, a recombination pathway that accounts for about 30% of the recombinants and requires genes that belong to both RecF and RecBCD pathways is revealed.
Collapse
Affiliation(s)
- Marc Bichara
- Departement Intégrité du Génome, UMR 7100, CNRS, Ecole Supérieure de Biotechnologie de Strasbourg, Boulevard Sebastien Brant, BP 10413, 67412 Illkirch-Cedex, France.
| | | | | | | |
Collapse
|
18
|
Wen Q, Mahdi AA, Briggs GS, Sharples GJ, Lloyd RG. Conservation of RecG activity from pathogens to hyperthermophiles. DNA Repair (Amst) 2005; 4:23-31. [PMID: 15533834 DOI: 10.1016/j.dnarep.2004.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2004] [Accepted: 07/13/2004] [Indexed: 11/24/2022]
Abstract
Maintaining the integrity of the genome is essential for the survival of all organisms. RecG helicase plays an important part in this process in Escherichia coli, promoting recombination and DNA repair, and providing ways to rescue stalled replication forks by way of a Holliday junction intermediate. We purified RecG proteins from three other species: two Gram-positive mesophiles, Bacillus subtilis and Streptococcus pneumoniae, and one extreme thermophile, Aquifex aeolicus. All three proteins bind and unwind replication fork and Holliday junction DNA molecules with efficiencies similar to the E. coli protein. Proteins from the Gram-positive species promote DNA repair in E. coli, indicating either that RecG acts alone or that any necessary protein-protein interactions are conserved. The S. pneumoniae RecG reduces plasmid copy number when expressed in E. coli, indicating that like the E. coli protein it unwinds plasmid R loop structures used to prime replication. This effect is not seen with B. subtilis RecG; the protein either lacks R loop unwinding activity or is compromised by having insufficient ATP. The A. aeolicus protein unwinds DNA well at 60 degrees C but is less efficient at 37 degrees C, explaining its inability to function in E. coli at this temperature. The N-terminal extension present in this protein was investigated and found to be dispensable for activity and thermo-stability. The results presented suggest that the role of RecG in DNA replication and repair is likely to be conserved throughout all bacteria, which underlines the importance of this protein in genome duplication and cell survival.
Collapse
Affiliation(s)
- Qin Wen
- Queens Medical Centre, Institute of Genetics, University of Nottingham, Nottingham NG7 2UH, UK
| | | | | | | | | |
Collapse
|
19
|
Briggs GS, Mahdi AA, Wen Q, Lloyd RG. DNA binding by the substrate specificity (wedge) domain of RecG helicase suggests a role in processivity. J Biol Chem 2005; 280:13921-7. [PMID: 15695524 DOI: 10.1074/jbc.m412054200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RecG differs from most helicases acting on branched DNA in that it is thought to catalyze unwinding via translocation of a monomer on dsDNA, with a wedge domain facilitating strand separation. Conserved phenylalanines in the wedge are shown to be critical for DNA binding. When detached from the helicase domains, the wedge bound a Holliday junction with high affinity but failed to bind a replication fork structure. Further stabilizing contacts are identified in full-length RecG, which may explain fork binding. Detached from the wedge, the helicase region unwound junctions but had extremely low substrate affinity, arguing against the "classical inchworm" mode of translocation. We propose that the processivity of RecG on branched DNA substrates is dependent on the ability of the wedge to establish strong binding at the branch point. This keeps the helicase motor in contact with the substrate, enabling it to drive dsDNA translocation with high efficiency.
Collapse
Affiliation(s)
- Geoffrey S Briggs
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
| | | | | | | |
Collapse
|
20
|
Kang J, Tavakoli D, Tschumi A, Aras RA, Blaser MJ. Effect of host species on recG phenotypes in Helicobacter pylori and Escherichia coli. J Bacteriol 2004; 186:7704-13. [PMID: 15516585 PMCID: PMC524884 DOI: 10.1128/jb.186.22.7704-7713.2004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Recombination is a fundamental mechanism for the generation of genetic variation. Helicobacter pylori strains have different frequencies of intragenomic recombination, arising from deletions and duplications between DNA repeat sequences, as well as intergenomic recombination, facilitated by their natural competence. We identified a gene, hp1523, that influences recombination frequencies in this highly diverse bacterium and demonstrate its importance in maintaining genomic integrity by limiting recombination events. HP1523 shows homology to RecG, an ATP-dependent helicase that in Escherichia coli allows repair of damaged replication forks to proceed without recourse to potentially mutagenic recombination. Cross-species studies done show that hp1523 can complement E. coli recG mutants in trans to the same extent as E. coli recG can, indicating that hp1523 has recG function. The E. coli recG gene only partially complements the hp1523 mutation in H. pylori. Unlike other recG homologs, hp1523 is not involved in DNA repair in H. pylori, although it has the ability to repair DNA when expressed in E. coli. Therefore, host context appears critical in defining the function of recG. The fact that in E. coli recG phenotypes are not constant in other species indicates the diverse roles for conserved recombination genes in prokaryotic evolution.
Collapse
Affiliation(s)
- Josephine Kang
- Department of Microbiology, New York University School of Medicine, VA Medical Center, New York, New York, USA.
| | | | | | | | | |
Collapse
|
21
|
Briggs GS, Mahdi AA, Weller GR, Wen Q, Lloyd RG. Interplay between DNA replication, recombination and repair based on the structure of RecG helicase. Philos Trans R Soc Lond B Biol Sci 2004; 359:49-59. [PMID: 15065656 PMCID: PMC1693295 DOI: 10.1098/rstb.2003.1364] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Recent studies in Escherichia coli indicate that the interconversion of DNA replication fork and Holliday junction structures underpins chromosome duplication and helps secure faithful transmission of the genome from one generation to the next. It facilitates interplay between DNA replication, recombination and repair, and provides means to rescue replication forks stalled by lesions in or on the template DNA. Insight into how this interconversion may be catalysed has emerged from genetic, biochemical and structural studies of RecG protein, a member of superfamily 2 of DNA and RNA helicases. We describe how a single molecule of RecG might target a branched DNA structure and translocate a single duplex arm to drive branch migration of a Holliday junction, interconvert replication fork and Holliday junction structures and displace the invading strand from a D loop formed during recombination at a DNA end. We present genetic evidence suggesting how the latter activity may provide an efficient pathway for the repair of DNA double-strand breaks that avoids crossing over, thus facilitating chromosome segregation at cell division.
Collapse
Affiliation(s)
- Geoffrey S Briggs
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | | | | | | | | |
Collapse
|
22
|
Mahdi AA, Briggs GS, Sharples GJ, Wen Q, Lloyd RG. A model for dsDNA translocation revealed by a structural motif common to RecG and Mfd proteins. EMBO J 2003; 22:724-34. [PMID: 12554672 PMCID: PMC140728 DOI: 10.1093/emboj/cdg043] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
RecG protein differs from other helicases analysed to atomic resolution in that it mediates strand separation via translocation on double-stranded (ds) rather than single-stranded (ss) DNA. We describe a highly conserved helical hairpin motif in RecG and show it to be important for helicase activity. It places two arginines (R609 and R630) in opposing positions within the component helices where they are stabilized by a network of hydrogen bonds involving a glutamate from helicase motif VI. We suggest that disruption of this feature, triggered by ATP hydrolysis, moves an adjacent loop structure in the dsDNA-binding channel and that a swinging arm motion of this loop drives translocation. Substitutions that reverse the charge at R609 or R630 reduce DNA unwinding and ATPase activities, and increase dsDNA binding, but do not affect branched DNA binding. Sequences forming the helical hairpin and loop structures are highly conserved in Mfd protein, a transcription-coupled DNA repair factor that also translocates on dsDNA. The possibility of type I restriction enzymes and chromatin-remodelling factors using similar structures to drive translocation on dsDNA is discussed.
Collapse
Affiliation(s)
| | | | - Gary J. Sharples
- Institute of Genetics, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK
Present address: Centre for Infectious Diseases, Wolfson Research Institute, University of Durham, Queen’s Campus, Stockton-on-Tees TS17 6BH, UK Corresponding author e-mail:
| | | | - Robert G. Lloyd
- Institute of Genetics, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK
Present address: Centre for Infectious Diseases, Wolfson Research Institute, University of Durham, Queen’s Campus, Stockton-on-Tees TS17 6BH, UK Corresponding author e-mail:
| |
Collapse
|
23
|
Tanaka T, Mizukoshi T, Taniyama C, Kohda D, Arai KI, Masai H. DNA binding of PriA protein requires cooperation of the N-terminal D-loop/arrested-fork binding and C-terminal helicase domains. J Biol Chem 2002; 277:38062-71. [PMID: 12151393 DOI: 10.1074/jbc.m204397200] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PriA protein is essential for RecA-dependent DNA replication induced by stalled replication forks in Escherichia coli. PriA is a DEXH-type DNA helicase, ATPase activity of which depends on its binding to structured DNA including a D-loop-like structure. Here, we show that the N-terminal 181-amino acid polypeptide can form a complex with D-loop in gel shift assays and have identified a unique motif present in the N-terminal segment of PriA that plays a role in its DNA binding. We have also identified residues in the C terminus proximal helicase domain essential for D-loop binding. PriA proteins mutated in this domain do not bind to D-loop, despite the presence of the N-terminal DNA-binding motif. Those mutants that cannot bind to D-loop in vitro do not support a recombination-dependent mode of DNA replication in vivo, indicating that binding to a D-loop-like structure is essential for the ability of PriA to initiate DNA replication and repair from stalled replication forks. We propose that binding of the PriA protein to stalled replication forks requires proper configuration of the N-terminal fork-recognition and C-terminal helicase domains and that the latter may stabilize binding and increase binding specificity.
Collapse
Affiliation(s)
- Taku Tanaka
- Department of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | | | | | | | | | | |
Collapse
|
24
|
Abstract
The stalling of DNA replication forks that occurs as a consequence of encountering DNA damage is a critical problem for cells. RecG protein is involved in the processing of stalled replication forks, and acts by reversing the fork past the damage to create a four-way junction that allows template switching and lesion bypass. We have determined the crystal structure of RecG bound to a DNA substrate that mimics a stalled replication fork. The structure not only reveals the elegant mechanism used by the protein to recognize junctions but has also trapped the protein in the initial stage of fork reversal. We propose a mechanism for how forks are processed by RecG to facilitate replication fork restart. In addition, this structure suggests that the mechanism and function of the two largest helicase superfamilies are distinct.
Collapse
Affiliation(s)
- M R Singleton
- ICRF Clare Hall Laboratories, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3LD, United Kingdom
| | | | | |
Collapse
|
25
|
Abstract
We present a summary of recent progress in understanding Escherichia coli K-12 gene and protein functions. New information has come both from classical biological experimentation and from using the analytical tools of functional genomics. The content of the E. coli genome can clearly be seen to contain elements acquired by horizontal transfer. Nevertheless, there is probably a large, stable core of >3500 genes that are shared among all E. coli strains. The gene-enzyme relationship is examined, and, in many cases, it exhibits complexity beyond a simple one-to-one relationship. Also, the E. coli genome can now be seen to contain many multiple enzymes that carry out the same or closely similar reactions. Some are similar in sequence and may share common ancestry; some are not. We discuss the concept of a minimal genome as being variable among organisms and obligatorily linked to their life styles and defined environmental conditions. We also address classification of functions of gene products and avenues of insight into the history of protein evolution.
Collapse
Affiliation(s)
- M Riley
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA. ,
| | | |
Collapse
|
26
|
McGlynn P, Mahdi AA, Lloyd RG. Characterisation of the catalytically active form of RecG helicase. Nucleic Acids Res 2000; 28:2324-32. [PMID: 10871364 PMCID: PMC102718 DOI: 10.1093/nar/28.12.2324] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Replication of DNA is fraught with difficulty and chromosomes contain many lesions which may block movement of the replicative machinery. However, several mechanisms to overcome such problems are beginning to emerge from studies with Escherichia coli. An important enzyme in one or more of these mechanisms is the RecG helicase, which may target stalled replication forks to generate a four-stranded (Holliday) junction, thus facilitating repair and/or bypass of the original lesion. To begin to understand how RecG might catalyse regression of fork structures, we have analysed what the catalytically active form of the enzyme may be. We have found that RecG exists as a monomer in solution as measured by gel filtration but when bound to junction DNA the enzyme forms two distinct protein-DNA complexes that contain one and two protein molecules. However, mutant inhibition studies failed to provide any evidence that RecG acts as a multimer in vitro. Additionally, there was no evidence for cooperativity in the junction DNA-stimulated hydrolysis of ATP. These data suggest that RecG functions as a monomer to unwind junction DNA, which supports an 'inchworm' rather than an 'active rolling' mechanism of DNA unwinding. The observed in vivo inhibition of wild-type RecG by mutant forms of the enzyme was attributed to occlusion of the DNA target and correlates with the very low abundance of replication forks within an E.COLI: cell, even during rapid growth.
Collapse
Affiliation(s)
- P McGlynn
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | | | | |
Collapse
|
27
|
Cox MM. Recombinational DNA repair in bacteria and the RecA protein. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1999; 63:311-66. [PMID: 10506835 DOI: 10.1016/s0079-6603(08)60726-6] [Citation(s) in RCA: 168] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In bacteria, the major function of homologous genetic recombination is recombinational DNA repair. This is not a process reserved only for rare double-strand breaks caused by ionizing radiation, nor is it limited to situations in which the SOS response has been induced. Recombinational DNA repair in bacteria is closely tied to the cellular replication systems, and it functions to repair damage at stalled replication forks, Studies with a variety of rec mutants, carried out under normal aerobic growth conditions, consistently suggest that at least 10-30% of all replication forks originating at the bacterial origin of replication are halted by DNA damage and must undergo recombinational DNA repair. The actual frequency may be much higher. Recombinational DNA repair is both the most complex and the least understood of bacterial DNA repair processes. When replication forks encounter a DNA lesion or strand break, repair is mediated by an adaptable set of pathways encompassing most of the enzymes involved in DNA metabolism. There are five separate enzymatic processes involved in these repair events: (1) The replication fork assembled at OriC stalls and/or collapses when encountering DNA damage. (2) Recombination enzymes provide a complementary strand for a lesion isolated in a single-strand gap, or reconstruct a branched DNA at the site of a double-strand break. (3) The phi X174-type primosome (or repair primosome) functions in the origin-independent reassembly of the replication fork. (4) The XerCD site-specific recombination system resolves the dimeric chromosomes that are the inevitable by-product of frequent recombination associated with recombinational DNA repair. (5) DNA excision repair and other repair systems eliminate lesions left behind in double-stranded DNA. The RecA protein plays a central role in the recombination phase of the process. Among its many activities, RecA protein is a motor protein, coupling the hydrolysis of ATP to the movement of DNA branches.
Collapse
Affiliation(s)
- M M Cox
- Department of Biochemistry, University of Wisconsin-Madison 53706, USA
| |
Collapse
|
28
|
Sharples GJ, Ingleston SM, Lloyd RG. Holliday junction processing in bacteria: insights from the evolutionary conservation of RuvABC, RecG, and RusA. J Bacteriol 1999; 181:5543-50. [PMID: 10482492 PMCID: PMC94071 DOI: 10.1128/jb.181.18.5543-5550.1999] [Citation(s) in RCA: 143] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- G J Sharples
- Institute of Genetics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, United Kingdom.
| | | | | |
Collapse
|
29
|
Whitby MC, Lloyd RG. Targeting Holliday junctions by the RecG branch migration protein of Escherichia coli. J Biol Chem 1998; 273:19729-39. [PMID: 9677403 DOI: 10.1074/jbc.273.31.19729] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RecG protein of Escherichia coli is a junction-specific DNA helicase that drives branch migration of Holliday intermediates in genetic recombination and DNA repair. The reaction was investigated using synthetic X-junctions. RecG dissociates X-junctions to flayed duplex products, although DNA unwinding of the heterologous arms is limited to </=30 base pairs. Junction unwinding requires Mg2+ and the hydrolysis of ATP. X-junction DNA stimulates the ATPase activity of RecG. ATPase activity is also stimulated by linear duplex DNA, although to a lesser extent than by X-DNA, but not by linear single-stranded DNA. In situ 1,10-phenanthroline-copper footprinting shows that RecG binds to the strand cross-over point at the center of the X-junction. Substrate recognition by RecG was investigated using DNAs that represented the various component parts of an X-junction. The minimal DNA structure that RecG forms a stable complex with is a flayed duplex, suggesting that this is the critical feature for junction recognition by RecG. Junction binding and unwinding also depend critically on the concentration of free Mg2+, excess free cation dramatically inhibiting both processes. These inhibitory effects are not mediated specifically by Mg2+; e.g. both Ca2+ and hexamminecobalt(III) chloride also inhibit X-junction binding and unwinding by RecG. The relative abilities of these cations to inhibit RecG-junction binding is correlated with their respective abilities to stack X-junction DNA. From this we conclude that RecG is unable to bind or binds very poorly to fully stacked X-junctions.
Collapse
Affiliation(s)
- M C Whitby
- Microbiology Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
| | | |
Collapse
|