201
|
Ma N, Sargent EH, Kelley SO. Biotemplated nanostructures: directed assembly of electronic and optical materials using nanoscale complementarity. ACTA ACUST UNITED AC 2008. [DOI: 10.1039/b711764g] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
202
|
Leuba SH, Anand SP, Harp JM, Khan SA. Expedient placement of two fluorescent dyes for investigating dynamic DNA protein interactions in real time. Chromosome Res 2008; 16:451-67. [PMID: 18461484 PMCID: PMC2413326 DOI: 10.1007/s10577-008-1235-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Many questions in molecular and cellular biology can be reduced to questions about 'who talks to whom, when and how frequently'. Here, we review approaches we have used with single-pair fluorescence resonance energy transfer (spFRET) to follow the motions between two well-placed fluorescent probes to ask similar questions. We describe two systems. We have used a nucleosomal system in which the naked DNA molecule has the acceptor and donor dyes too far apart for FRET to occur whereas the dyes are close enough in the reconstituted nucleosome for FRET. As these individual nucleosomes were tethered on a surface, we could follow dynamics in the repositioning of these two dyes, inferring that nucleosomes stochastically and reversibly open and close. These results imply that most of the DNA on the nucleosome can be sporadically accessible to regulatory proteins and proteins that track the DNA double helix. In the case of following the binding of recombination protein RecA to double-stranded DNA (dsDNA) and the RecA filament displacement by DNA helicase motor PcrA, the dsDNA template is prepared with the two dyes close enough to each other to generate high FRET. Binding of the RecA molecules to form a filament lengthens the dsDNA molecule 1.5-fold and reduces the FRET accordingly. Once added, DNA motor protein helicase PcrA can displace the RecA filament with concomitant return of the DNA molecule to its original B-form and high FRET state. Thus, appropriately placed fluorescent dyes can be used to monitor conformational changes occurring in DNA and or proteins and provide increased sensitivity for investigating dynamic DNA-protein interactions in real time.
Collapse
Affiliation(s)
- Sanford H Leuba
- Department of Cell Biology, University of Pittsburgh School of Medicine and Swanson School of Engineering, Petersen Institute of NanoScience and Engineering and University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA.
| | | | | | | |
Collapse
|
203
|
Sarma R, Mulder DW, Brecht E, Szilagyi RK, Seefeldt LC, Tsuruta H, Peters JW. Probing the MgATP-bound conformation of the nitrogenase Fe protein by solution small-angle X-ray scattering. Biochemistry 2007; 46:14058-66. [PMID: 18001132 PMCID: PMC3289971 DOI: 10.1021/bi700446s] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The MgATP-bound conformation of the Fe protein of nitrogenase from Azotobacter vinelandii has been examined in solution by small-angle X-ray scattering (SAXS) and compared to existing crystallographically characterized Fe protein conformations. The results of the analysis of the crystal structure of an Fe protein variant with a Switch II single-amino acid deletion recently suggested that the MgATP-bound state of the Fe protein may exist in a conformation that involves a large-scale reorientation of the dimer subunits, resulting in an overall elongated structure relative to the more compact structure of the MgADP-bound state. It was hypothesized that the Fe protein variant may be a conformational mimic of the MgATP-bound state of the native Fe protein largely on the basis of the observation that the spectroscopic properties of the [4Fe-4S] cluster of the variant mimicked in part the spectroscopic signatures of the native nitrogenase Fe protein in the MgATP-bound state. In this work, SAXS studies reveal that the large-scale conformational differences between the native Fe protein and the variant observed by X-ray crystallography are also observed in solution. In addition, comparison of the SAXS curves of the Fe protein nucleotide-bound states to the nucleotide-free states indicates that the conformation of the MgATP-bound state in solution does not resemble the structure of the variant as initially proposed, but rather, at the resolution of this experiment, it resembles the structure of the nucleotide-free state. These results provide insights into the Fe protein conformations that define the role of MgATP in nitrogenase catalysis.
Collapse
Affiliation(s)
- Ranjana Sarma
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | - David W. Mulder
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | - Eric Brecht
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | - Robert K. Szilagyi
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | | | | | - John W. Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| |
Collapse
|
204
|
Bannister LA, Pezza RJ, Donaldson JR, de Rooij DG, Schimenti KJ, Camerini-Otero RD, Schimenti JC. A dominant, recombination-defective allele of Dmc1 causing male-specific sterility. PLoS Biol 2007; 5:e105. [PMID: 17425408 PMCID: PMC1847842 DOI: 10.1371/journal.pbio.0050105] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2006] [Accepted: 02/14/2007] [Indexed: 11/18/2022] Open
Abstract
DMC1 is a meiosis-specific homolog of bacterial RecA and eukaryotic RAD51 that can catalyze homologous DNA strand invasion and D-loop formation in vitro. DMC1-deficient mice and yeast are sterile due to defective meiotic recombination and chromosome synapsis. The authors identified a male dominant sterile allele of Dmc1, Dmc1Mei11, encoding a missense mutation in the L2 DNA binding domain that abolishes strand invasion activity. Meiosis in male heterozygotes arrests in pachynema, characterized by incomplete chromosome synapsis and no crossing-over. Young heterozygous females have normal litter sizes despite having a decreased oocyte pool, a high incidence of meiosis I abnormalities, and susceptibility to premature ovarian failure. Dmc1Mei11 exposes a sex difference in recombination in that a significant portion of female oocytes can compensate for DMC1 deficiency to undergo crossing-over and complete gametogenesis. Importantly, these data demonstrate that dominant alleles of meiosis genes can arise and propagate in populations, causing infertility and other reproductive consequences due to meiotic prophase I defects. About 10%–15% of couples are infertile due to defects in meiosis (the process by which egg or sperm cells containing a single copy of each chromosome are produced). Because studying the genetics of meiosis in humans is difficult, we performed genetic screens in mice and identified a novel mutation in Dmc1 that causes male-specific infertility due to defects in meiosis. Dmc1 encodes a key protein required for meiotic recombination; the mutation causes a single amino acid change that prevents genetic exchange, or crossing-over, in males, abolishes its recombination activity, and abrogates the production of sperm. Though heterozygous females are fertile, they have fewer oocytes due to a high incidence of meiosis I abnormalities, and show susceptibility to premature ovarian failure. Importantly, these data demonstrate that dominant alleles of meiosis genes can arise and propagate in populations, and produce meiotic prophase I defects that cause infertility and other reproductive abnormalities. Meiosis occurs in both the male and female germ lines; here the authors describe a mutation that affects only male meiosis, causing sterility.
Collapse
Affiliation(s)
- Laura A Bannister
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Roberto J Pezza
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Janet R Donaldson
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Dirk G de Rooij
- Department of Endocrinology, Utrecht University, Utrecht, The Netherlands
- Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kerry J Schimenti
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - R. Daniel Camerini-Otero
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John C Schimenti
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
205
|
Sequence characterization and comparative analysis of three plasmids isolated from environmental Vibrio spp. Appl Environ Microbiol 2007; 73:7703-10. [PMID: 17921277 DOI: 10.1128/aem.01577-07] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The horizontal transfer of genes by mobile genetic elements such as plasmids and phages can accelerate genome diversification of Vibrio spp., affecting their physiology, pathogenicity, and ecological character. In this study, sequence analysis of three plasmids from Vibrio spp. previously isolated from salt marsh sediment revealed the remarkable diversity of these elements. Plasmids p0908 (81.4 kb), p23023 (52.5 kb), and p09022 (31.0 kb) had a predicted 99, 64, and 32 protein-coding sequences and G+C contents of 49.2%, 44.7%, and 42.4%, respectively. A phylogenetic tree based on concatenation of the host 16S rRNA and rpoA nucleotide sequences indicated p23023 and p09022 were isolated from strains most closely related to V. mediterranei and V. campbellii, respectively, while the host of p0908 forms a clade with V. fluvialis and V. furnissii. Many predicted proteins had amino acid identities to proteins of previously characterized phages and plasmids (24 to 94%). Predicted proteins with similarity to chromosomally encoded proteins included RecA, a nucleoid-associated protein (NdpA), a type IV helicase (UvrD), and multiple hypothetical proteins. Plasmid p0908 had striking similarity to enterobacteria phage P1, sharing genetic organization and amino acid identity for 23 predicted proteins. This study provides evidence of genetic exchange between Vibrio plasmids, phages, and chromosomes among diverse Vibrio spp.
Collapse
|
206
|
Parsons JA, Bannam TL, Devenish RJ, Rood JI. TcpA, an FtsK/SpoIIIE homolog, is essential for transfer of the conjugative plasmid pCW3 in Clostridium perfringens. J Bacteriol 2007; 189:7782-90. [PMID: 17720795 PMCID: PMC2168741 DOI: 10.1128/jb.00783-07] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The conjugative tetracycline resistance plasmid pCW3 is the paradigm conjugative plasmid in the anaerobic gram-positive pathogen Clostridium perfringens. Two closely related FtsK/SpoIIIE homologs, TcpA and TcpB, are encoded on pCW3, which is significant since FtsK domains are found in coupling proteins of gram-negative conjugation systems. To develop an understanding of the mechanism of conjugative transfer in C. perfringens, we determined the role of these proteins in the conjugation process. Mutation and complementation analysis was used to show that the tcpA gene was essential for the conjugative transfer of pCW3 and that the tcpB gene was not required for transfer. Furthermore, complementation of a pCW3DeltatcpA mutant with divergent tcpA homologs provided experimental evidence that all of the known conjugative plasmids from C. perfringens use a similar transfer mechanism. Functional genetic analysis of the TcpA protein established the essential role in conjugative transfer of its Walker A and Walker B ATP-binding motifs and its FtsK-like RAAG motif. It is postulated that TcpA is the essential DNA translocase or coupling protein encoded by pCW3 and as such represents a key component of the unique conjugation process in C. perfringens.
Collapse
Affiliation(s)
- Jennifer A Parsons
- Department of Microbiology, Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton Campus, Victoria 3800, Australia
| | | | | | | |
Collapse
|
207
|
Nishiwaki T, Satomi Y, Kitayama Y, Terauchi K, Kiyohara R, Takao T, Kondo T. A sequential program of dual phosphorylation of KaiC as a basis for circadian rhythm in cyanobacteria. EMBO J 2007; 26:4029-37. [PMID: 17717528 PMCID: PMC1994132 DOI: 10.1038/sj.emboj.7601832] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2007] [Accepted: 07/23/2007] [Indexed: 11/09/2022] Open
Abstract
The circadian phosphorylation cycle of the cyanobacterial clock protein KaiC has been reconstituted in vitro. The phosphorylation profiles of two phosphorylation sites in KaiC, serine 431 (S431) and threonine 432 (T432), revealed that the phosphorylation cycle contained four steps: (i) T432 phosphorylation; (ii) S431 phosphorylation to generate the double-phosphorylated form of KaiC; (iii) T432 dephosphorylation; and (iv) S431 dephosphorylation. We then examined the effects of mutations introduced at one KaiC phosphorylation site on the intact phosphorylation site. We found that the product of each step in the phosphorylation cycle regulated the reaction in the next step, and that double phosphorylation converted KaiC from an autokinase to an autophosphatase, whereas complete dephosphorylation had the opposite effect. These mechanisms serve as the basis for cyanobacterial circadian rhythm generation. We also found that associations among KaiA, KaiB, and KaiC result from S431 phosphorylation, and these interactions would maintain the amplitude of the rhythm.
Collapse
Affiliation(s)
- Taeko Nishiwaki
- Division of Biological Science, Graduate School of Science, Nagoya University and SORST, Japan Science and Technology Agency (JST), Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Yoshinori Satomi
- Institute for Protein Research, Osaka University, Suita-shi, Osaka, Japan
| | - Yohko Kitayama
- Division of Biological Science, Graduate School of Science, Nagoya University and SORST, Japan Science and Technology Agency (JST), Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Kazuki Terauchi
- Division of Biological Science, Graduate School of Science, Nagoya University and SORST, Japan Science and Technology Agency (JST), Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Reiko Kiyohara
- Division of Biological Science, Graduate School of Science, Nagoya University and SORST, Japan Science and Technology Agency (JST), Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Toshifumi Takao
- Institute for Protein Research, Osaka University, Suita-shi, Osaka, Japan
| | - Takao Kondo
- Division of Biological Science, Graduate School of Science, Nagoya University and SORST, Japan Science and Technology Agency (JST), Furo-cho, Chikusa-ku, Nagoya, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, and SORST, Japan Science and Technology Agency (JST), Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan. Tel.: +81 52 789 2498; Fax: +81 52 789 2963; E-mail:
| |
Collapse
|
208
|
Grycova L, Lansky Z, Friedlova E, Vlachova V, Kubala M, Obsilova V, Obsil T, Teisinger J. ATP binding site on the C-terminus of the vanilloid receptor. Arch Biochem Biophys 2007; 465:389-98. [PMID: 17706589 DOI: 10.1016/j.abb.2007.06.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Revised: 06/29/2007] [Accepted: 06/30/2007] [Indexed: 10/23/2022]
Abstract
Transient receptor potential channel vanilloid receptor subunit 1 (TRPV1) is a thermosensitive cation channel activated by noxious heat as well as a wide range of chemical stimuli. Although ATP by itself does not directly activate TRPV1, it was shown that intracellular ATP increases its activity by directly interacting with the Walker A motif residing on the C-terminus of TRPV1. In order to identify the amino acid residues that are essential for the binding of ATP to the TRPV1 channel, we performed the following point mutations of the Walker A motif: P732A, D733A, G734A, K735A, D736A, and D737A. Employing bulk fluorescence measurements, namely a TNP-ATP competition assay and FITC labelling and quenching experiments, we identified the key role of the K735 residue in the binding of the nucleotide. Experimental data was interpreted according to our molecular modelling simulations.
Collapse
Affiliation(s)
- Lenka Grycova
- Institute of Physiology, Academy of Sciences of the Czech Republic, Vídenská 1083, 14220 Prague, Czech Republic
| | | | | | | | | | | | | | | |
Collapse
|
209
|
Bailey S, Eliason WK, Steitz TA. The crystal structure of the Thermus aquaticus DnaB helicase monomer. Nucleic Acids Res 2007; 35:4728-36. [PMID: 17606462 PMCID: PMC1950529 DOI: 10.1093/nar/gkm507] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The ring-shaped hexameric DnaB helicase unwinds duplex DNA at the replication fork of eubacteria. We have solved the crystal structure of the full-length Thermus aquaticus DnaB monomer, or possibly dimer, at 2.9 A resolution. DnaB is a highly flexible two domain protein. The C-terminal domain exhibits a RecA-like core fold and contains all the conserved sequence motifs that are characteristic of the DnaB helicase family. The N-terminal domain contains an additional helical hairpin that makes it larger than previously appreciated. Several DnaB mutations that modulate its interaction with primase are found in this hairpin. The similarity in the fold of the DnaB N-terminal domain with that of the C-terminal helicase-binding domain (HBD) of the DnaG primase also includes this hairpin. Comparison of hexameric homology models of DnaB with the structure of the papillomavirus E1 helicase suggests the two helicases may function through different mechanisms despite their sharing a common ancestor.
Collapse
Affiliation(s)
- Scott Bailey
- Department of Molecular Biophysics and Biochemistry, Department of Chemistry and Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA
| | - William K. Eliason
- Department of Molecular Biophysics and Biochemistry, Department of Chemistry and Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA
| | - Thomas A. Steitz
- Department of Molecular Biophysics and Biochemistry, Department of Chemistry and Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA
- *To whom correspondence should be addressed.+1 203 432 5619+1 203 432 3282
| |
Collapse
|
210
|
Abstract
The RecA protein is a recombinase functioning in recombinational DNA repair in bacteria. RecA is regulated at many levels. The expression of the recA gene is regulated within the SOS response. The activity of the RecA protein itself is autoregulated by its own C-terminus. RecA is also regulated by the action of other proteins. To date, these include the RecF, RecO, RecR, DinI, RecX, RdgC, PsiB, and UvrD proteins. The SSB protein also indirectly affects RecA function by competing for ssDNA binding sites. The RecO and RecR, and possibly the RecF proteins, all facilitate RecA loading onto SSB-coated ssDNA. The RecX protein blocks RecA filament extension, and may have other effects on RecA activity. The DinI protein stabilizes RecA filaments. The RdgC protein binds to dsDNA and blocks RecA access to dsDNA. The PsiB protein, encoded by F plasmids, is uncharacterized, but may inhibit RecA in some manner. The UvrD helicase removes RecA filaments from RecA. All of these proteins function in a network that determines where and how RecA functions. Additional regulatory proteins may remain to be discovered. The elaborate regulatory pattern is likely to be reprised for RecA homologues in archaeans and eukaryotes.
Collapse
Affiliation(s)
- Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA.
| |
Collapse
|
211
|
Lanzov VA. RecA homologous DNA transferase: Functional activities and a search for homology by recombining DNA molecules. Mol Biol 2007. [DOI: 10.1134/s0026893307030077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
212
|
Nishinaka T, Doi Y, Hara R, Yashima E. Elastic behavior of RecA-DNA helical filaments. J Mol Biol 2007; 370:837-45. [PMID: 17559876 DOI: 10.1016/j.jmb.2007.05.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Revised: 05/09/2007] [Accepted: 05/10/2007] [Indexed: 10/23/2022]
Abstract
Escherichia coli RecA protein forms a right-handed helical filament with DNA molecules and has an ATP-dependent activity that exchanges homologous strands between single-stranded DNA (ssDNA) and duplex DNA. We show that the RecA-ssDNA filamentous complex is an elastic helical molecule whose length is controlled by the binding and release of nucleotide cofactors. RecA-ssDNA filaments were fluorescently labelled and attached to a glass surface inside a flow chamber. When the chamber solution was replaced by a buffer solution without nucleotide cofactors, the RecA-ssDNA filament rapidly contracted approximately 0.68-fold with partial filament dissociation. The contracted filament elongated up to 1.25-fold when a buffer solution containing ATPgammaS was injected, and elongated up to 1.17-fold when a buffer solution containing ATP or dATP was injected. This contraction-elongation behavior was able to be repeated by the successive injection of dATP and non-nucleotide buffers. We propose that this elastic motion couples to the elastic motion and/or the twisting rotation of DNA strands within the filament by adjusting their helical phases.
Collapse
Affiliation(s)
- Taro Nishinaka
- Yashima Super-structured Helix Project, ERATO, Japan Science and Technology Agency, 101 Creation Core Nagoya, 2266-22 Anagahora, Shimoshidami, Nagoya 463-0003, Japan.
| | | | | | | |
Collapse
|
213
|
Barnes RL, McCulloch R. Trypanosoma brucei homologous recombination is dependent on substrate length and homology, though displays a differential dependence on mismatch repair as substrate length decreases. Nucleic Acids Res 2007; 35:3478-93. [PMID: 17478508 PMCID: PMC1904282 DOI: 10.1093/nar/gkm249] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Homologous recombination functions universally in the maintenance of genome stability through the repair of DNA breaks and in ensuring the completion of replication. In some organisms, homologous recombination can perform more specific functions. One example of this is in antigenic variation, a widely conserved mechanism for the evasion of host immunity. Trypanosoma brucei, the causative agent of sleeping sickness in Africa, undergoes antigenic variation by periodic changes in its variant surface glycoprotein (VSG) coat. VSG switches involve the activation of VSG genes, from an enormous silent archive, by recombination into specialized expression sites. These reactions involve homologous recombination, though they are characterized by an unusually high rate of switching and by atypical substrate requirements. Here, we have examined the substrate parameters of T. brucei homologous recombination. We show, first, that the reaction is strictly dependent on substrate length and that it is impeded by base mismatches, features shared by homologous recombination in all organisms characterized. Second, we identify a pathway of homologous recombination that acts preferentially on short substrates and is impeded to a lesser extent by base mismatches and the mismatch repair machinery. Finally, we show that mismatches during T. brucei recombination may be repaired by short-patch mismatch repair.
Collapse
Affiliation(s)
| | - Richard McCulloch
- *To whom correspondence should be addressed. Tel: 0044 141 330 5946; Fax: 0044 141 330 5422;
| |
Collapse
|
214
|
Cline DJ, Holt SL, Singleton SF. Inhibition of Escherichia coli RecA by rationally redesigned N-terminal helix. Org Biomol Chem 2007; 5:1525-8. [PMID: 17571180 DOI: 10.1039/b703159a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Bacterial RecA promotes the development and transmission of antibiotic resistance genes by self-assembling into an ATP-hydrolyzing filamentous homopolymer on single-stranded DNA. We report the design of a 29mer peptide based on the RecA N-terminal domain involved in intermonomer contact that inhibits RecA filament assembly with an IC50 of 3 microM.
Collapse
Affiliation(s)
- Daniel J Cline
- School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7360, USA
| | | | | |
Collapse
|
215
|
Draper B, Rao VB. An ATP hydrolysis sensor in the DNA packaging motor from bacteriophage T4 suggests an inchworm-type translocation mechanism. J Mol Biol 2007; 369:79-94. [PMID: 17428497 DOI: 10.1016/j.jmb.2007.03.019] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Revised: 03/04/2007] [Accepted: 03/05/2007] [Indexed: 12/01/2022]
Abstract
Tailed bacteriophages and large eukaryotic viruses employ powerful molecular motors to translocate dsDNA into a preassembled capsid shell. The phage T4 motor is composed of a dodecameric portal and small and large terminase subunits assembled at the special head-tail connector vertex of the prohead. The motor pumps DNA through the portal channel, utilizing ATP hydrolysis energy provided by an ATPase present in the large terminase subunit. We report that the ATPase motors of terminases, helicases, translocating restriction enzymes, and protein translocases possess a common coupling motif (C-motif). Mutations in the phage T4 terminase C-motif lead to loss of stimulated ATPase and DNA translocation activities. Surprisingly, the mutants can catalyze at least one ATP hydrolysis event but are unable to turn over and reset the motor. This is the first report of a catalytic block in translocating ATPase motor after ATP hydrolysis occurred. We suggest that the C-motif is an ATP hydrolysis sensor, linking product release to mechanical motion. A novel terminase-driven mechanism is proposed for translocation of dsDNA in viruses.
Collapse
Affiliation(s)
- Bonnie Draper
- Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | | |
Collapse
|
216
|
Chen LT, Ko TP, Chang YC, Lin KA, Chang CS, Wang AHJ, Wang TF. Crystal structure of the left-handed archaeal RadA helical filament: identification of a functional motif for controlling quaternary structures and enzymatic functions of RecA family proteins. Nucleic Acids Res 2007; 35:1787-801. [PMID: 17329376 PMCID: PMC1874592 DOI: 10.1093/nar/gkl1131] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The RecA family of proteins mediates homologous recombination, an evolutionarily conserved pathway that maintains genomic stability by protecting against DNA double strand breaks. RecA proteins are thought to facilitate DNA strand exchange reactions as closed-rings or as right-handed helical filaments. Here, we report the crystal structure of a left-handed Sulfolobus solfataricus RadA helical filament. Each protomer in this left-handed filament is linked to its neighbour via interactions of a β-strand polymerization motif with the neighbouring ATPase domain. Immediately following the polymerization motif, we identified an evolutionarily conserved hinge region (a subunit rotation motif) in which a 360° clockwise axial rotation accompanies stepwise structural transitions from a closed ring to the AMP–PNP right-handed filament, then to an overwound right-handed filament and finally to the left-handed filament. Additional structural and functional analyses of wild-type and mutant proteins confirmed that the subunit rotation motif is crucial for enzymatic functions of RecA family proteins. These observations support the hypothesis that RecA family protein filaments may function as rotary motors.
Collapse
Affiliation(s)
- Li-Tzu Chen
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Institute of Biological Chemistry and Institute of Physics, Academia Sinica, Taipei 115, Taiwan
| | - Tzu-Ping Ko
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Institute of Biological Chemistry and Institute of Physics, Academia Sinica, Taipei 115, Taiwan
| | - Yuan-Chih Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Institute of Biological Chemistry and Institute of Physics, Academia Sinica, Taipei 115, Taiwan
| | - Kuei-An Lin
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Institute of Biological Chemistry and Institute of Physics, Academia Sinica, Taipei 115, Taiwan
| | - Chia-Seng Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Institute of Biological Chemistry and Institute of Physics, Academia Sinica, Taipei 115, Taiwan
| | - Andrew H.-J. Wang
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Institute of Biological Chemistry and Institute of Physics, Academia Sinica, Taipei 115, Taiwan
| | - Ting-Fang Wang
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Institute of Biological Chemistry and Institute of Physics, Academia Sinica, Taipei 115, Taiwan
- *To whom correspondence should be addressed. +886-2-27855696+886-2-27889759
| |
Collapse
|
217
|
Egel R. RecA-DNA filament topology: the overlooked alternative of an unconventional syn-syn duplex intermediate. DNA Repair (Amst) 2007; 6:669-75. [PMID: 17317338 DOI: 10.1016/j.dnarep.2006.12.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Revised: 12/17/2006] [Accepted: 12/21/2006] [Indexed: 10/23/2022]
Abstract
The helical filaments of RecA protein mediate strand exchange for homologous recombination, but the paths of the interacting DNAs have yet to be determined. Although this interaction is commonly limited to three strands, it is reasoned here that the intrinsic symmetry relationships of quadruplex topology are superior in explaining a range of observations. In particular, this topology suggests the potential of post-exchange base pairing in the unorthodox configuration of syn-syn glycosidic bonds between the nucleotide bases and the pentose rings in the sugar-phosphate backbone, which would transiently be stabilized by the external scaffolding of the RecA protein filament.
Collapse
Affiliation(s)
- Richard Egel
- Institute of Molecular Biology and Physiology, University of Copenhagen, Ole Maaløe Vej 5, DK-2100 Copenhagen Ø, Denmark.
| |
Collapse
|
218
|
Abbani MA, Papagiannis CV, Sam MD, Cascio D, Johnson RC, Clubb RT. Structure of the cooperative Xis-DNA complex reveals a micronucleoprotein filament that regulates phage lambda intasome assembly. Proc Natl Acad Sci U S A 2007; 104:2109-14. [PMID: 17287355 PMCID: PMC1893000 DOI: 10.1073/pnas.0607820104] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The DNA architectural protein Xis regulates the construction of higher-order nucleoprotein intasomes that integrate and excise the genome of phage lambda from the Escherichia coli chromosome. Xis modulates the directionality of site-specific recombination by stimulating phage excision 10(6)-fold, while simultaneously inhibiting phage reintegration. Control is exerted by cooperatively assembling onto a approximately 35-bp DNA regulatory element, which it distorts to preferentially stabilize an excisive intasome. Here, we report the 2.6-A crystal structure of the complex between three cooperatively bound Xis proteins and a 33-bp DNA containing the regulatory element. Xis binds DNA in a head-to-tail orientation to generate a micronucleoprotein filament. Although each protomer is anchored to the duplex by a similar set of nonbase specific contacts, malleable protein-DNA interactions enable binding to sites that differ in nucleotide sequence. Proteins at the ends of the duplex sequence specifically recognize similar binding sites and participate in cooperative binding via protein-protein interactions with a bridging Xis protomer that is bound in a less specific manner. Formation of this polymer introduces approximately 72 degrees of curvature into the DNA with slight positive writhe, which functions to connect disparate segments of DNA bridged by integrase within the excisive intasome.
Collapse
Affiliation(s)
- Mohamad A. Abbani
- *Department of Chemistry and Biochemistry and University of California–Department of Energy Institute of Genomics and Proteomics, and
| | - Christie V. Papagiannis
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, 10833 Le Conte Avenue, Los Angeles, CA 90095-1737
| | - My D. Sam
- *Department of Chemistry and Biochemistry and University of California–Department of Energy Institute of Genomics and Proteomics, and
| | - Duilio Cascio
- *Department of Chemistry and Biochemistry and University of California–Department of Energy Institute of Genomics and Proteomics, and
| | - Reid C. Johnson
- Molecular Biology Institute, University of California, 611 Charles Young Drive East, Los Angeles, CA 90095-1570; and
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, 10833 Le Conte Avenue, Los Angeles, CA 90095-1737
- To whom correspondence may be addressed. E-mail:
or
| | - Robert T. Clubb
- *Department of Chemistry and Biochemistry and University of California–Department of Energy Institute of Genomics and Proteomics, and
- Molecular Biology Institute, University of California, 611 Charles Young Drive East, Los Angeles, CA 90095-1570; and
- To whom correspondence may be addressed. E-mail:
or
| |
Collapse
|
219
|
Champier G, Hantz S, Couvreux A, Stuppfler S, Mazeron MC, Bouaziz S, Denis F, Alain S. New Functional Domains of Human Cytomegalovirus pUL89 predicted by Sequence Analysis and Three-Dimensional Modelling of the Catalytic Site DEXDc. Antivir Ther 2007. [DOI: 10.1177/135965350701200209] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Introduction Benzimidazole d-ribonucleosides inhibit DNA packaging during human cytomegalovirus (HCMV) replication. Although they have been shown to target pUL56 and pUL89, the large and small subunits of the HCMV terminase respectively, their mechanism of action is not yet fully understood. Methods and results To better understand HCMV DNA maturation and the mechanism of action of benzimidazole derivatives, we studied the HCMV pUL89 protein by a genetic approach combined with primary structure analysis. The pUL89 sequence analysis of 25 HCMV strains and counterparts among herpesviruses allowed identification of 12 conserved regions. We also built a three-dimensional model of the pUL89 ATPasic catalytic site, including ATPase motor motifs I, II and III, that may facilitate the development of future antiviral drugs active against HCMV. Finally, we identified several putative functional domains in pUL89, such as pUL89 zinc finger (pUL89-ZF), DNA cutting sites and portal binding sites, that are probably involved in CMV DNA cleavage and packaging.
Collapse
Affiliation(s)
- Gaël Champier
- EA MENRT 3175 Faculté de Médecine de Limoges et Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire Dupuytren, Limoges, France
| | - Sébastien Hantz
- EA MENRT 3175 Faculté de Médecine de Limoges et Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire Dupuytren, Limoges, France
| | - Anthony Couvreux
- Département de Pharmacologie Chimique et Génétique, UFR des Sciences Pharmaceutiques et Biologiques, Paris, France
| | - Stéphanie Stuppfler
- EA MENRT 3175 Faculté de Médecine de Limoges et Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire Dupuytren, Limoges, France
| | - Marie-Christine Mazeron
- Service de Bactériologie-Virologie, Hôpital Lariboisière, Assistance Publique-Hôpitaux de Paris, Paris, France
- Centre National de Référence Cytomégalovirus, Laboratoire de Bacteriologie-Virologie, Centre Hospitalier Universitaire Dupuytren, Limoges, France
| | - Serge Bouaziz
- Département de Pharmacologie Chimique et Génétique, UFR des Sciences Pharmaceutiques et Biologiques, Paris, France
| | - François Denis
- EA MENRT 3175 Faculté de Médecine de Limoges et Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire Dupuytren, Limoges, France
| | - Sophie Alain
- EA MENRT 3175 Faculté de Médecine de Limoges et Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire Dupuytren, Limoges, France
- Centre National de Référence Cytomégalovirus, Laboratoire de Bacteriologie-Virologie, Centre Hospitalier Universitaire Dupuytren, Limoges, France
| |
Collapse
|
220
|
Centore RC, Sandler SJ. UvrD limits the number and intensities of RecA-green fluorescent protein structures in Escherichia coli K-12. J Bacteriol 2007; 189:2915-20. [PMID: 17259317 PMCID: PMC1855782 DOI: 10.1128/jb.01777-06] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RecA is important for recombination, DNA repair, and SOS induction. In Escherichia coli, RecBCD, RecFOR, and RecJQ prepare DNA substrates onto which RecA binds. UvrD is a 3'-to-5' helicase that participates in methyl-directed mismatch repair and nucleotide excision repair. uvrD deletion mutants are sensitive to UV irradiation, hypermutable, and hyper-rec. In vitro, UvrD can dissociate RecA from single-stranded DNA. Other experiments suggest that UvrD removes RecA from DNA where it promotes unproductive reactions. To test if UvrD limits the number and/or the size of RecA-DNA structures in vivo, an uvrD mutation was combined with recA-gfp. This recA allele allows the number of RecA structures and the amount of RecA at these structures to be assayed in living cells. uvrD mutants show a threefold increase in the number of RecA-GFP foci, and these foci are, on average, nearly twofold higher in relative intensity. The increased number of RecA-green fluorescent protein foci in the uvrD mutant is dependent on recF, recO, recR, recJ, and recQ. The increase in average relative intensity is dependent on recO and recQ. These data support an in vivo role for UvrD in removing RecA from the DNA.
Collapse
Affiliation(s)
- Richard C Centore
- Department of Microbiology, Morrill Science Center IV N203, University of Massachusetts at Amherst, Amherst, MA 01003, USA
| | | |
Collapse
|
221
|
Krishna R, Prabu JR, Manjunath GP, Datta S, Chandra NR, Muniyappa K, Vijayan M. Snapshots of RecA protein involving movement of the C-domain and different conformations of the DNA-binding loops: crystallographic and comparative analysis of 11 structures of Mycobacterium smegmatis RecA. J Mol Biol 2007; 367:1130-44. [PMID: 17306300 DOI: 10.1016/j.jmb.2007.01.058] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Revised: 01/17/2007] [Accepted: 01/22/2007] [Indexed: 10/23/2022]
Abstract
Mycobacterium smegmatis RecA and its nucleotide complexes crystallize in three different, but closely related, forms characterized by specific ranges of unit cell dimensions. The six crystals reported here and five reported earlier, all grown under the same or very similar conditions, belong to these three forms, all in space group P6(1). They include one obtained by reducing relative humidity around the crystal. In all crystals, RecA monomers form filaments around a 6(1) screw axis. Thus, the c-dimension of the crystal corresponds to the pitch of the RecA filament. As reported for Escherichia coli RecA, the variation in the pitch among the three forms correlates well with the motion of the C-terminal domain of the RecA monomers with respect to the main domain. The domain motion is compatible with formation of inactive as well as active RecA filaments involving monomers with a fully ordered C domain. It does not appear to influence the movement upon nucleotide-binding of the switch residue, which is believed to provide the trigger for transmitting the effect of nucleotide binding to the DNA-binding region. Interestingly, partial dehydration of the crystal results in the movement of the residue similar to that caused by nucleotide binding. The ordering of the DNA-binding loops, which present ensembles of conformations, is also unaffected by domain motion. The conformation of loop L2 appears to depend upon nucleotide binding, presumably on account of the movement of the switch residue that forms part of the loop. The conformations of loops L1 and L2 are correlated and have implications for intermolecular communications within the RecA filament. The structures resulting from different orientations of the C domain and different conformations of the DNA-binding loops appear to represent snapshots of the RecA at different phases of activity, and provide insights into the mechanism of action of RecA.
Collapse
Affiliation(s)
- R Krishna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India
| | | | | | | | | | | | | |
Collapse
|
222
|
Abstract
The recombinases of the RecA family are often viewed only as DNA-pairing proteins - they bind to one DNA segment, align it with homologous sequences in another DNA segment, promote an exchange of DNA strands and then dissociate. To a first approximation, this description seems to fit the eukaryotic (Rad51 and Dmc1) and archaeal (RadA) RecA homologues. However, the bacterial RecA protein does much more, coupling ATP hydrolysis with DNA-strand exchange in a manner that greatly expands its repertoire of activities. This article explores the protein activities and experimental results that have identified RecA as a motor protein.
Collapse
Affiliation(s)
- Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706-1544, USA.
| |
Collapse
|
223
|
|
224
|
Nishinaka T, Doi Y, Hashimoto M, Hara R, Shibata T, Harada Y, Kinosita K, Noji H, Yashima E. Visualization of RecA filaments and DNA by fluorescence microscopy. J Biochem 2007; 141:147-56. [PMID: 17202195 DOI: 10.1093/jb/mvm033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have developed two experimental methods for observing Escherichia coli RecA-DNA filament under a fluorescence microscope. First, RecA-DNA filaments were visualized by immunofluorescence staining with anti-RecA monoclonal antibody. Although the detailed filament structures below submicron scale were unable to be measured accurately due to optical resolution limit, this method has an advantage to analyse a large number of RecA-DNA filaments in a single experiment. Thus, it provides a reliable statistical distribution of the filament morphology. Moreover, not only RecA filament, but also naked DNA region was visualized separately in combination with immunofluorescence staining using anti-DNA monoclonal antibody. Second, by using cysteine derivative RecA protein, RecA-DNA filament was directly labelled by fluorescent reagent, and was able to observe directly under a fluorescence microscope with its enzymatic activity maintained. We showed that the RecA-DNA filament disassembled in the direction from 5' to 3' of ssDNA as dATP hydrolysis proceeded.
Collapse
Affiliation(s)
- Taro Nishinaka
- Yashima Super-structured Helix Project, ERATO, Japan Science and Technology Agency, 101 Creation Core Nagoya, 2266-22 Anagahora, Nagoya 463-0003, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
225
|
Fonseca MM, Alarcon FJ, Vasconcelos ATD, Agnez-Lima LF. A model for the RecA protein of Mycoplasma synoviae. Genet Mol Biol 2007. [DOI: 10.1590/s1415-47572007000200018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
226
|
|
227
|
The bacterial RecA protein: structure, function, and regulation. MOLECULAR GENETICS OF RECOMBINATION 2007. [DOI: 10.1007/978-3-540-71021-9_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
228
|
Okoshi K, Nishinaka T, Doi Y, Hara R, Hashimoto M, Yashima E. Liquid crystal formation of RecA–DNA filamentous complexes. Chem Commun (Camb) 2007:2022-4. [PMID: 17713065 DOI: 10.1039/b702982a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Spontaneous optical birefringence of RecA-bound linear and closed circular single-stranded DNA filaments, as well as RecA self-assembled polymer, was observed in aqueous buffer solutions, which demonstrates the formation of lyotropic liquid crystalline phases.
Collapse
Affiliation(s)
- Kento Okoshi
- Yashima Super-structured Helix Project, Exploratory Research for Advanced Technology (ERA TO), Japan Science and Technology Agency (JST), Shimoshidami, Moriyama-ku, Nagoya 463-0003, Japan.
| | | | | | | | | | | |
Collapse
|
229
|
Petukhov M, Lebedev D, Shalguev V, Islamov A, Kuklin A, Lanzov V, Isaev-Ivanov V. Conformational flexibility of RecA protein filament: transitions between compressed and stretched states. Proteins 2006; 65:296-304. [PMID: 16909421 DOI: 10.1002/prot.21116] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
RecA protein is a central enzyme in homologous DNA recombination, repair and other forms of DNA metabolism in bacteria. It functions as a flexible helix-shaped filament bound on stretched single-stranded or double-stranded DNA in the presence of ATP. In this work, we present an atomic level model for conformational transitions of the RecA filament. The model describes small movements of the RecA N-terminal domain due to coordinated rotation of main chain dihedral angles of two amino acid residues (Psi/Lys23 and Phi/Gly24), while maintaining unchanged the RecA intersubunit interface. The model is able to reproduce a wide range of observed helix pitches in transitions between compressed and stretched conformations of the RecA filament. Predictions of the model are in agreement with Small Angle Neutron Scattering (SANS) measurements of the filament helix pitch in RecA::ADP-AlF(4) complex at various salt concentrations.
Collapse
Affiliation(s)
- Michael Petukhov
- Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, the Russian Academy of Sciences, Gatchina/St. Petersburg, Russia.
| | | | | | | | | | | | | |
Collapse
|
230
|
Morimatsu K, Takahashi M. Structural analysis of RecA protein–DNA complexes by fluorescence-detected linear dichroism: Absence of structural change of filament for pairing of complementary DNA strands. Anal Biochem 2006; 358:192-8. [DOI: 10.1016/j.ab.2006.08.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Revised: 08/21/2006] [Accepted: 08/28/2006] [Indexed: 10/24/2022]
|
231
|
Qian X, He Y, Ma X, Fodje MN, Grochulski P, Luo Y. Calcium stiffens archaeal Rad51 recombinase from Methanococcus voltae for homologous recombination. J Biol Chem 2006; 281:39380-7. [PMID: 17050545 DOI: 10.1074/jbc.m607785200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Archaeal RadA or Rad51 recombinases are close homologues of eukaryal Rad51 and DMC1. These and bacterial RecA orthologues play a key role in DNA repair by forming helical nucleoprotein filaments in which a hallmark strand exchange reaction between homologous DNA substrates occurs. Recent studies have discovered the stimulatory role by calcium on human and yeast recombinases. Here we report that the strand exchange activity but not the ATPase activity of an archaeal RadA/Rad51 recombinase from Methanococcus voltae (MvRadA) is also subject to calcium stimulation. Crystallized MvRadA filaments in the presence of CaCl(2) resemble that of the recently reported ATPase active form in the presence of an activating dose of KCl. At the ATPase center, one Ca(2+) ion takes the place of two K(+) ions in the K(+)-bound form. The terminal phosphate of the nonhydrolyzable ATP analogue is in a staggered conformation in the Ca(2+)-bound form. In comparison, an eclipsed conformation was seen in the K(+)-bound form. Despite the changes in the ATPase center, both forms harbor largely ordered L2 regions in essentially identical conformations. These data suggest a unified stimulation mechanism by potassium and calcium because of the existence of a conserved ATPase center promiscuous in binding cations.
Collapse
Affiliation(s)
- Xinguo Qian
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | | | | | | | | | | |
Collapse
|
232
|
Sattin BD, Goh MC. Novel polymorphism of RecA fibrils revealed by atomic force microscopy. J Biol Phys 2006; 32:153-68. [PMID: 19669458 DOI: 10.1007/s10867-006-9010-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
RecA fibrils in physiological conditions have been successfully imaged using Tapping Mode atomic force microscopy. This represents the first time images of recA have been obtained without drying, freezing and/or exposure to high vacuum conditions. While previously observed structures - the monomer, the hexamer, the short rod - were seen, a new type of fibril was also observed. This protofibril is narrower in diameter than the standard fibril, and occurs in three distinct morphologies: aperiodic, 100-nm periodic, and 150-nm periodic. In addition, much longer rods were observed, and appear curved and even circular.
Collapse
Affiliation(s)
- Bernie D Sattin
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | | |
Collapse
|
233
|
Joo C, McKinney SA, Nakamura M, Rasnik I, Myong S, Ha T. Real-time observation of RecA filament dynamics with single monomer resolution. Cell 2006; 126:515-27. [PMID: 16901785 DOI: 10.1016/j.cell.2006.06.042] [Citation(s) in RCA: 252] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 05/16/2006] [Accepted: 06/20/2006] [Indexed: 11/27/2022]
Abstract
RecA and its homologs help maintain genomic integrity through recombination. Using single-molecule fluorescence assays and hidden Markov modeling, we show the most direct evidence that a RecA filament grows and shrinks primarily one monomer at a time and only at the extremities. Both ends grow and shrink, contrary to expectation, but a higher binding rate at one end is responsible for directional filament growth. Quantitative rate determination also provides insights into how RecA might control DNA accessibility in vivo. We find that about five monomers are sufficient for filament nucleation. Although ordinarily single-stranded DNA binding protein (SSB) prevents filament nucleation, single RecA monomers can easily be added to an existing filament and displace SSB from DNA at the rate of filament extension. This supports the proposal for a passive role of RecA-loading machineries in SSB removal.
Collapse
Affiliation(s)
- Chirlmin Joo
- Howard Hughes Medical Institute and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | | | | | | | | |
Collapse
|
234
|
Baitin DM, Bakhlanova IV, Kil YV, Cox MM, Lanzov VA. Distinguishing characteristics of hyperrecombinogenic RecA protein from Pseudomonas aeruginosa acting in Escherichia coli. J Bacteriol 2006; 188:5812-20. [PMID: 16885449 PMCID: PMC1540092 DOI: 10.1128/jb.00358-06] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Escherichia coli, a relatively low frequency of recombination exchanges (FRE) is predetermined by the activity of RecA protein, as modulated by a complex regulatory program involving both autoregulation and other factors. The RecA protein of Pseudomonas aeruginosa (RecA(Pa)) exhibits a more robust recombinase activity than its E. coli counterpart (RecA(Ec)). Low-level expression of RecA(Pa) in E. coli cells results in hyperrecombination (an increase of FRE) even in the presence of RecA(Ec). This genetic effect is supported by the biochemical finding that the RecA(Pa) protein is more efficient in filament formation than RecA K72R, a mutant protein with RecA(Ec)-like DNA-binding ability. Expression of RecA(Pa) also partially suppresses the effects of recF, recO, and recR mutations. In concordance with the latter, RecA(Pa) filaments initiate recombination equally from both the 5' and 3' ends. Besides, these filaments exhibit more resistance to disassembly from the 5' ends that makes the ends potentially appropriate for initiation of strand exchange. These comparative genetic and biochemical characteristics reveal that multiple levels are used by bacteria for a programmed regulation of their recombination activities.
Collapse
Affiliation(s)
- Dmitry M Baitin
- Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina/St. Petersburg 188300, Russia
| | | | | | | | | |
Collapse
|
235
|
Sarai N, Kagawa W, Kinebuchi T, Kagawa A, Tanaka K, Miyagawa K, Ikawa S, Shibata T, Kurumizaka H, Yokoyama S. Stimulation of Dmc1-mediated DNA strand exchange by the human Rad54B protein. Nucleic Acids Res 2006; 34:4429-37. [PMID: 16945962 PMCID: PMC1636354 DOI: 10.1093/nar/gkl562] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The process of homologous recombination is indispensable for both meiotic and mitotic cell division, and is one of the major pathways for double-strand break (DSB) repair. The human Rad54B protein, which belongs to the SWI2/SNF2 protein family, plays a role in homologous recombination, and may function with the Dmc1 recombinase, a meiosis-specific Rad51 homolog. In the present study, we found that Rad54B enhanced the DNA strand-exchange activity of Dmc1 by stabilizing the Dmc1–single-stranded DNA (ssDNA) complex. Therefore, Rad54B may stimulate the Dmc1-mediated DNA strand exchange by stabilizing the nucleoprotein filament, which is formed on the ssDNA tails produced at DSB sites during homologous recombination.
Collapse
Affiliation(s)
- Naoyuki Sarai
- RIKEN Genomic Sciences Center1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Wataru Kagawa
- RIKEN Genomic Sciences Center1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Takashi Kinebuchi
- RIKEN Genomic Sciences Center1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Ako Kagawa
- RIKEN Genomic Sciences Center1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Kozo Tanaka
- School of Life Sciences, University of Dundee, Wellcome Trust BiocentreDundee DD1 5EH, UK
| | - Kiyoshi Miyagawa
- Center for Disease Biology and Integrative Medicine, Faculty of Medicine, University of Tokyo7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shukuko Ikawa
- RIKEN Discovery Research Institute, Wako-shiSaitama 351-0198, Japan
| | - Takehiko Shibata
- RIKEN Discovery Research Institute, Wako-shiSaitama 351-0198, Japan
| | - Hitoshi Kurumizaka
- RIKEN Genomic Sciences Center1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Graduate School of Science and Engineering, Waseda University3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- To whom correspondence should be addressed. Tel: +81 3 5286 8189; Fax: +81 3 5292 9211;
| | - Shigeyuki Yokoyama
- RIKEN Genomic Sciences Center1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- RIKEN Harima Institute at SPring-8, 1-1-1 KohtoMikazuki-cho, Sayo, Hyogo 679-5148, Japan
- Correspondence may also be addressed to Shigeyuki Yokoyama. Tel: +81 3 5841 4413; Fax: +81 3 5841 8057;
| |
Collapse
|
236
|
Killoran MP, Keck JL. Sit down, relax and unwind: structural insights into RecQ helicase mechanisms. Nucleic Acids Res 2006; 34:4098-105. [PMID: 16935877 PMCID: PMC1616949 DOI: 10.1093/nar/gkl538] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Revised: 06/29/2006] [Accepted: 07/13/2006] [Indexed: 01/25/2023] Open
Abstract
Helicases are specialized molecular motors that separate duplex nucleic acids into single strands. The RecQ family of helicases functions at the interface of DNA replication, recombination and repair in bacterial and eukaryotic cells. They are key, multifunctional enzymes that have been linked to three human diseases: Bloom's, Werner's and Rothmund-Thomson's syndromes. This review summarizes recent studies that relate the structures of RecQ proteins to their biochemical activities.
Collapse
Affiliation(s)
- Michael P. Killoran
- Department of Biomolecular Chemistry, 550 Medical Science Center, 1300 University Avenue, University of Wisconsin School of Medicine and Public HealthMadison, WI 53706-1532, USA
| | - James L. Keck
- Department of Biomolecular Chemistry, 550 Medical Science Center, 1300 University Avenue, University of Wisconsin School of Medicine and Public HealthMadison, WI 53706-1532, USA
| |
Collapse
|
237
|
Sung P, Klein H. Mechanism of homologous recombination: mediators and helicases take on regulatory functions. Nat Rev Mol Cell Biol 2006; 7:739-50. [PMID: 16926856 DOI: 10.1038/nrm2008] [Citation(s) in RCA: 479] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Homologous recombination (HR) is an important mechanism for the repair of damaged chromosomes, for preventing the demise of damaged replication forks, and for several other aspects of chromosome maintenance. As such, HR is indispensable for genome integrity, but it must be regulated to avoid deleterious events. Mutations in the tumour-suppressor protein BRCA2, which has a mediator function in HR, lead to cancer formation. DNA helicases, such as Bloom's syndrome protein (BLM), regulate HR at several levels, in attenuating unwanted HR events and in determining the outcome of HR. Defects in BLM are also associated with the cancer phenotype. The past several years have witnessed dramatic advances in our understanding of the mechanism and regulation of HR.
Collapse
Affiliation(s)
- Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
| | | |
Collapse
|
238
|
Prasad TK, Yeykal CC, Greene EC. Visualizing the assembly of human Rad51 filaments on double-stranded DNA. J Mol Biol 2006; 363:713-28. [PMID: 16979659 DOI: 10.1016/j.jmb.2006.08.046] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Revised: 08/13/2006] [Accepted: 08/16/2006] [Indexed: 10/24/2022]
Abstract
Rad51 is the core component of the eukaryotic homologous recombination machinery and assembles into extended nucleoprotein filaments on DNA. To study the dynamic behavior of Rad51 we have developed a single-molecule assay that relies on a combination of hydrodynamic force and microscale diffusion barriers to align individual DNA molecules on the surface of a microfluidic sample chamber that is coated with a lipid bilayer. When visualized with total internal reflection fluorescence microscopy (TIRFM), these "molecular curtains" allow for the direct visualization of hundreds of individual DNA molecules. Using this approach, we have analyzed the binding of human Rad51 to single molecules of double-stranded DNA under a variety of different reaction conditions by monitoring the extension of the fluorescently labeled DNA, which coincides with assembly of the nucleoprotein filament. We have also generated several mutants in conserved regions of Rad51 implicated in DNA binding, and tested them for their ability to assemble into extended filaments. We show that proteins with mutations within the DNA-binding surface located on the N-terminal domain still retain the ability to form extended nucleoprotein filaments. Mutations in the L1 loop, which projects towards the central axis of the filament, completely abolish assembly of extended filaments. In contrast, most mutations within or near the L2 DNA-binding loop, which is also located near the central axis of the filament, do not affect the ability of the protein to assemble into extended filaments on double-stranded (ds)DNA. Taken together, these results demonstrate that the L1-loop plays a crucial role in the assembly of extended nucleoprotein filaments on dsDNA, but the N-terminal domain and the L2 DNA-binding loop have significantly less impact on this process. The results presented here also provide an important initial framework for beginning to study the biochemical behaviors of Rad51 nucleoprotein filaments using our novel experimental system.
Collapse
Affiliation(s)
- Tekkatte Krishnamurthy Prasad
- Department of Biochemistry and Molecular Biophysics, Columbia University, College of Physicians and Surgeons, Black Building Room 536, 650 West 168th Street, New York, NY 10032, USA
| | | | | |
Collapse
|
239
|
|
240
|
Rudolph MG, Heissmann R, Wittmann JG, Klostermeier D. Crystal structure and nucleotide binding of the Thermus thermophilus RNA helicase Hera N-terminal domain. J Mol Biol 2006; 361:731-43. [PMID: 16890241 DOI: 10.1016/j.jmb.2006.06.065] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Revised: 06/20/2006] [Accepted: 06/26/2006] [Indexed: 02/06/2023]
Abstract
DEAD box RNA helicases use the energy of ATP hydrolysis to unwind double-stranded RNA regions or to disrupt RNA/protein complexes. A minimal RNA helicase comprises nine conserved motifs distributed over two RecA-like domains. The N-terminal domain contains all motifs involved in nucleotide binding, namely the Q-motif, the DEAD box, and the P-loop, as well as the SAT motif, which has been implicated in the coordination of ATP hydrolysis and RNA unwinding. We present here the crystal structure of the N-terminal domain of the Thermus thermophilus RNA helicase Hera in complex with adenosine monophosphate (AMP). Upon binding of AMP the P-loop adopts a partially collapsed or half-open conformation that is still connected to the DEAD box motif, and the DEAD box in turn is linked to the SAT motif via hydrogen bonds. This network of interactions communicates changes in the P-loop conformation to distant parts of the helicase. The affinity of AMP is comparable to that of ADP and ATP, substantiating that the binding energy from additional phosphate moieties is directly converted into conformational changes of the entire helicase. Importantly, the N-terminal Hera domain forms a dimer in the crystal similar to that seen in another thermophilic prokaryote. It is possible that this mode of dimerization represents the prototypic architecture in RNA helicases of thermophilic origin.
Collapse
Affiliation(s)
- Markus G Rudolph
- Department of Molecular Structural Biology, University of Göttingen, D-37077 Göttingen, Germany
| | | | | | | |
Collapse
|
241
|
Bennett MJ, Sawaya MR, Eisenberg D. Deposition diseases and 3D domain swapping. Structure 2006; 14:811-24. [PMID: 16698543 DOI: 10.1016/j.str.2006.03.011] [Citation(s) in RCA: 170] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Revised: 02/21/2006] [Accepted: 03/01/2006] [Indexed: 12/30/2022]
Abstract
Protein aggregation is a feature of both normal cellular assemblies and pathological protein depositions. Although the limited order of aggregates has often impeded their structural characterization, 3D domain swapping has been implicated in the formation of several protein aggregates. Here, we review known structures displaying 3D domain swapping in the context of amyloid and related fibrils, prion proteins, and macroscopic aggregates, and we discuss the possible involvement of domain swapping in protein deposition diseases.
Collapse
Affiliation(s)
- Melanie J Bennett
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
| | | | | |
Collapse
|
242
|
Wu Z, Xing X, Bohl CE, Wisler JW, Dalton JT, Bell CE. Domain structure and DNA binding regions of beta protein from bacteriophage lambda. J Biol Chem 2006; 281:25205-14. [PMID: 16820360 PMCID: PMC1950251 DOI: 10.1074/jbc.m512450200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
beta protein from bacteriophage lambda promotes a single-strand annealing reaction that is central to Red-mediated recombination at double-strand DNA breaks and chromosomal ends. beta protein binds most tightly to an intermediate of annealing formed by the sequential addition of two complementary oligonucleotides. Here we have characterized the domain structure of beta protein in the presence and absence of DNA using limited proteolysis. Residues 1-130 form an N-terminal "core" domain that is resistant to proteases in the absence of DNA, residues 131-177 form a central region with enhanced resistance to proteases upon DNA complex formation, and the C-terminal residues 178-261 of beta protein are sensitive to proteases in both the presence and absence of DNA. We probed the DNA binding regions of beta protein further using biotinylation of lysine residues and mass spectrometry. Several lysine residues within the first 177 residues of beta protein are protected from biotinylation in the DNA complex, whereas none of the lysine residues in the C-terminal portion are protected. The results lead to a model for the domain structure and DNA binding of beta protein in which a stable N-terminal core and a more flexible central domain come together to bind DNA, whereas a C-terminal tail remains disordered. A fragment consisting of residues 1-177 of beta protein maintains normal binding to sequentially added complementary oligonucleotides and has significantly enhanced binding to single-strand DNA.
Collapse
Affiliation(s)
- Zengru Wu
- Division of Pharmaceutics, College of Pharmacy, Ohio State University, Columbus, Ohio 43210
| | - Xu Xing
- Department of Molecular and Cellular Biochemistry, College of Medicine, Ohio State University, Columbus, Ohio 43210
| | - Casey E. Bohl
- Division of Pharmaceutics, College of Pharmacy, Ohio State University, Columbus, Ohio 43210
| | - James W. Wisler
- Department of Molecular and Cellular Biochemistry, College of Medicine, Ohio State University, Columbus, Ohio 43210
| | - James T. Dalton
- Division of Pharmaceutics, College of Pharmacy, Ohio State University, Columbus, Ohio 43210
- To whom correspondence may be addressed: Division of Pharmaceutics, College of Pharmacy, The Ohio State University, 500 West 12th Ave., Columbus OH 43210. Tel.: 614-688-3797; Fax: 614-292-7766; E-Mail:
| | - Charles E. Bell
- Department of Molecular and Cellular Biochemistry, College of Medicine, Ohio State University, Columbus, Ohio 43210
| |
Collapse
|
243
|
Keramisanou D, Biris N, Gelis I, Sianidis G, Karamanou S, Economou A, Kalodimos CG. Disorder-order folding transitions underlie catalysis in the helicase motor of SecA. Nat Struct Mol Biol 2006; 13:594-602. [PMID: 16783375 DOI: 10.1038/nsmb1108] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2005] [Accepted: 05/12/2006] [Indexed: 01/01/2023]
Abstract
SecA is a helicase-like motor that couples ATP hydrolysis with the translocation of extracytoplasmic protein substrates. As in most helicases, this process is thought to occur through nucleotide-regulated rigid-body movement of the motor domains. NMR, thermodynamic and biochemical data show that SecA uses a novel mechanism wherein conserved regions lining the nucleotide cleft undergo cycles of disorder-order transitions while switching among functional catalytic states. The transitions are regulated by interdomain interactions mediated by crucial 'arginine finger' residues located on helicase motifs. Furthermore, we show that the nucleotide cleft allosterically communicates with the preprotein substrate-binding domain and the regulatory, membrane-inserting C domain, thereby allowing for the coupling of the ATPase cycle to the translocation activity. The intrinsic plasticity and functional disorder-order folding transitions coupled to ligand binding seem to provide a precise control of the catalytic activation process and simple regulation of allosteric mechanisms.
Collapse
|
244
|
Matsuo Y, Sakane I, Takizawa Y, Takahashi M, Kurumizaka H. Roles of the human Rad51 L1 and L2 loops in DNA binding. FEBS J 2006; 273:3148-59. [PMID: 16780572 DOI: 10.1111/j.1742-4658.2006.05323.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The human Rad51 protein, a eukaryotic ortholog of the bacterial RecA protein, is a key enzyme that functions in homologous recombination and recombinational repair of double strand breaks. The Rad51 protein contains two flexible loops, L1 and L2, which are proposed to be sites for DNA binding, based on a structural comparison with RecA. In the present study, we performed mutational and fluorescent spectroscopic analyses on the L1 and L2 loops to examine their role in DNA binding. Gel retardation and DNA-dependent ATP hydrolysis measurements revealed that the substitution of the tyrosine residue at position 232 (Tyr232) within the L1 loop with alanine, a short side chain amino acid, significantly decreased the DNA-binding ability of human Rad51, without affecting the protein folding or the salt-induced, DNA-independent ATP hydrolysis. Even the conservative replacement with tryptophan affected the DNA binding, indicating that Tyr232 is involved in DNA binding. The importance of the L1 loop was confirmed by the fluorescence change of a tryptophan residue, replacing the Asp231, Ser233, or Gly236 residue, upon DNA binding. The alanine replacement of phenylalanine at position 279 (Phe279) within the L2 loop did not affect the DNA-binding ability of human Rad51, unlike the Phe203 mutation of the RecA L2 loop. The Phe279 side chain may not be directly involved in the interaction with DNA. However, the fluorescence intensity of the tryptophan replacing the Rad51-Phe279 residue was strongly reduced upon DNA binding, indicating that the L2 loop is also close to the DNA-binding site.
Collapse
Affiliation(s)
- Yusuke Matsuo
- Graduate School of Science and Engineering, Waseda University, Tokyo, Japan
| | | | | | | | | |
Collapse
|
245
|
Qian X, He Y, Wu Y, Luo Y. Asp302 determines potassium dependence of a RadA recombinase from Methanococcus voltae. J Mol Biol 2006; 360:537-47. [PMID: 16782126 DOI: 10.1016/j.jmb.2006.05.058] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Revised: 04/12/2006] [Accepted: 05/23/2006] [Indexed: 12/20/2022]
Abstract
Archaeal RadA/Rad51 are close homologues of eukaryal Rad51/DMC1. Such recombinases, as well as their bacterial RecA orthologues, form helical nucleoprotein filaments in which a hallmark strand exchange reaction occurs between homologous DNA substrates. Our recent ATPase and structure studies on RadA recombinase from Methanococcus voltae have suggested that not only magnesium but also potassium ions are absorbed at the ATPase center. Potassium, but not sodium, stimulates the ATP hydrolysis reaction with an apparent dissociation constant of approximately 40 mM. The minimal inhibitory effect by 40 mM NaCl further suggests that the protein does not have adequate affinity for sodium. The wild-type protein's strand exchange activity is also stimulated by potassium with an apparent dissociation constant of approximately 35 mM. We made site-directed mutations at the potassium-contacting residues Glu151 and Asp302. The mutant proteins are expectedly defective in promoting ATP hydrolysis. Similar potassium preference in strand exchange is observed for the E151D and E151K proteins. The D302K protein, however, shows comparable strand exchange efficiencies in the presence of either potassium or sodium. Crystallized E151D filaments reveal a potassium-dependent conformational change similar to what has previously been observed with the wild-type protein. We interpret these data as suggesting that both ATP hydrolysis and DNA strand exchange requires accessibility to an "active" conformation similar to the crystallized ATPase-active form in the presence of ATP, Mg2+ and K+.
Collapse
Affiliation(s)
- Xinguo Qian
- Department of Biochemistry, University of Saskatchewan, A3 Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada S7N 5E5
| | | | | | | |
Collapse
|
246
|
Galkin VE, Wu Y, Zhang XP, Qian X, He Y, Yu X, Heyer WD, Luo Y, Egelman EH. The Rad51/RadA N-Terminal Domain Activates Nucleoprotein Filament ATPase Activity. Structure 2006; 14:983-92. [PMID: 16765891 DOI: 10.1016/j.str.2006.04.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2006] [Revised: 04/08/2006] [Accepted: 04/10/2006] [Indexed: 10/24/2022]
Abstract
Proteins in the RecA/RadA/Rad51 family form helical filaments on DNA that function in homologous recombination. While these proteins all have the same highly conserved ATP binding core, the RadA/Rad51 proteins have an N-terminal domain that shows no homology with the C-terminal domain found in RecA. Both the Rad51 N-terminal and RecA C-terminal domains have been shown to bind DNA, but no role for these domains has been established. We show that RadA filaments can be trapped in either an inactive or active conformation with respect to the ATPase and that activation involves a large rotation of the subunit aided by the N-terminal domain. The G103E mutation within the yeast Rad51 N-terminal domain inactivates the filament by failing to make proper contacts between the N-terminal domain and the core. These results show that the N-terminal domains play a regulatory role in filament activation and highlight the modular architecture of the recombination proteins.
Collapse
Affiliation(s)
- Vitold E Galkin
- Department of Biochemistry and Molecular Genetics, University of Virginia, Box 800733, Charlottesville, Virginia 22908, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
247
|
Wiese C, Hinz JM, Tebbs RS, Nham PB, Urbin SS, Collins DW, Thompson LH, Schild D. Disparate requirements for the Walker A and B ATPase motifs of human RAD51D in homologous recombination. Nucleic Acids Res 2006; 34:2833-43. [PMID: 16717288 PMCID: PMC1464408 DOI: 10.1093/nar/gkl366] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In vertebrates, homologous recombinational repair (HRR) requires RAD51 and five RAD51 paralogs (XRCC2, XRCC3, RAD51B, RAD51C and RAD51D) that all contain conserved Walker A and B ATPase motifs. In human RAD51D we examined the requirement for these motifs in interactions with XRCC2 and RAD51C, and for survival of cells in response to DNA interstrand crosslinks (ICLs). Ectopic expression of wild-type human RAD51D or mutants having a non-functional A or B motif was used to test for complementation of a rad51d knockout hamster CHO cell line. Although A-motif mutants complement very efficiently, B-motif mutants do not. Consistent with these results, experiments using the yeast two- and three-hybrid systems show that the interactions between RAD51D and its XRCC2 and RAD51C partners also require a functional RAD51D B motif, but not motif A. Similarly, hamster Xrcc2 is unable to bind to the non-complementing human RAD51D B-motif mutants in co-immunoprecipitation assays. We conclude that a functional Walker B motif, but not A motif, is necessary for RAD51D's interactions with other paralogs and for efficient HRR. We present a model in which ATPase sites are formed in a bipartite manner between RAD51D and other RAD51 paralogs.
Collapse
Affiliation(s)
- Claudia Wiese
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | | | | | | | | | | | | | | |
Collapse
|
248
|
Hare S, Bayliss R, Baron C, Waksman G. A large domain swap in the VirB11 ATPase of Brucella suis leaves the hexameric assembly intact. J Mol Biol 2006; 360:56-66. [PMID: 16730027 DOI: 10.1016/j.jmb.2006.04.060] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Revised: 04/25/2006] [Accepted: 04/26/2006] [Indexed: 11/28/2022]
Abstract
VirB11 ATPases are hexameric assemblies that power type IV secretion systems in bacteria. The hexamer of Brucella suis VirB11 (BsB11), like that of the Helicobacter pylori VirB11 (Hp0525), consists of a double ring structure formed by the N-terminal and C-terminal domains of each monomer. However, the monomer differs dramatically from that of Hp0525 by a large domain swap that leaves the hexameric assembly intact but profoundly alters the nucleotide-binding site and the interface between subunits.
Collapse
Affiliation(s)
- Stephen Hare
- School of Crystallography, Birkbeck College, Malet Street, London, WC1E 7HX, UK
| | | | | | | |
Collapse
|
249
|
Rajan R, Wisler JW, Bell CE. Probing the DNA sequence specificity of Escherichia coli RECA protein. Nucleic Acids Res 2006; 34:2463-71. [PMID: 16684994 PMCID: PMC1459065 DOI: 10.1093/nar/gkl302] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Escherichia coli RecA protein catalyzes the central DNA strand-exchange step of homologous recombination, which is essential for the repair of double-stranded DNA breaks. In this reaction, RecA first polymerizes on single-stranded DNA (ssDNA) to form a right-handed helical filament with one monomer per 3 nt of ssDNA. RecA generally binds to any sequence of ssDNA but has a preference for GT-rich sequences, as found in the recombination hot spot Chi (5′-GCTGGTGG-3′). When this sequence is located within an oligonucleotide, binding of RecA is phased relative to it, with a periodicity of three nucleotides. This implies that there are three separate nucleotide-binding sites within a RecA monomer that may exhibit preferences for the four different nucleotides. Here we have used a RecA coprotease assay to further probe the ssDNA sequence specificity of E.coli RecA protein. The extent of self-cleavage of a λ repressor fragment in the presence of RecA, ADP-AlF4 and 64 different trinucleotide-repeating 15mer oligonucleotides was determined. The coprotease activity of RecA is strongly dependent on the ssDNA sequence, with TGG-repeating sequences giving by far the highest coprotease activity, and GC and AT-rich sequences the lowest. For selected trinucleotide-repeating sequences, the DNA-dependent ATPase and DNA-binding activities of RecA were also determined. The DNA-binding and coprotease activities of RecA have the same sequence dependence, which is essentially opposite to that of the ATPase activity of RecA. The implications with regard to the biological mechanism of RecA are discussed.
Collapse
Affiliation(s)
| | | | - Charles E. Bell
- To whom correspondence should be addressed. Tel: +1 614 688 3115; Fax: +1 614 292 4118;
| |
Collapse
|
250
|
Meinke G, Bullock PA, Bohm A. Crystal structure of the simian virus 40 large T-antigen origin-binding domain. J Virol 2006; 80:4304-12. [PMID: 16611889 PMCID: PMC1472039 DOI: 10.1128/jvi.80.9.4304-4312.2006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The origins of replication of DNA tumor viruses have a highly conserved feature, namely, multiple binding sites for their respective initiator proteins arranged as inverted repeats. In the 1.45-angstroms crystal structure of the simian virus 40 large T-antigen (T-ag) origin-binding domain (obd) reported herein, T-ag obd monomers form a left-handed spiral with an inner channel of 30 angstroms having six monomers per turn. The inner surface of the spiral is positively charged and includes residues known to bind DNA. Residues implicated in hexamerization of full-length T-ag are located at the interface between adjacent T-ag obd monomers. These data provide a high-resolution model of the hexamer of origin-binding domains observed in electron microscopy studies and allow the obd's to be oriented relative to the hexamer of T-ag helicase domains to which they are connected.
Collapse
MESH Headings
- Amino Acid Sequence
- Antigens, Viral, Tumor/chemistry
- Antigens, Viral, Tumor/genetics
- Antigens, Viral, Tumor/metabolism
- Base Sequence
- Binding Sites
- Crystallography, X-Ray
- DNA, Viral/chemistry
- DNA, Viral/genetics
- DNA, Viral/metabolism
- Models, Molecular
- Molecular Sequence Data
- Protein Binding
- Protein Structure, Quaternary
- Protein Structure, Tertiary
- Replication Origin/genetics
- Simian virus 40/chemistry
- Simian virus 40/genetics
Collapse
Affiliation(s)
- Gretchen Meinke
- Tufts University School of Medicine, Department of Biochemistry, 136 Harrison Avenue, Boston, Massachusetts 02111, USA
| | | | | |
Collapse
|