51
|
Jouan L, Szatmari G. Interactions of the Caulobacter crescentus XerC and XerD recombinases with the E. coli dif site. FEMS Microbiol Lett 2003; 222:257-62. [PMID: 12770716 DOI: 10.1016/s0378-1097(03)00311-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In most bacteria, chromosome dimers arise from homologous recombination between replicated chromosomes. These dimers are then resolved by the action of the XerC and XerD recombinases, which act on the chromosomal dif site in the presence of the FtsK cell division protein. We have cloned the xerC and xerD genes from Caulobacter crescentus, and overexpressed them as maltose-binding protein fusion proteins. These fusion proteins were purified and used in in vitro DNA-binding assays to the Escherichia coli dif site with each protein individually, and in combination with each other. In addition, combinations of Xer proteins from E. coli were also tested for cooperativity with the corresponding C. crescentus proteins.
Collapse
Affiliation(s)
- Loubna Jouan
- Département de Microbiologie et Immunologie, Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montréal, QC, Canada H3C3J7
| | | |
Collapse
|
52
|
Lee L, Sadowski PD. Sequence of the loxP site determines the order of strand exchange by the Cre recombinase. J Mol Biol 2003; 326:397-412. [PMID: 12559909 DOI: 10.1016/s0022-2836(02)01429-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Conservative site-specific recombinases of the integrase family carry out recombination via a Holliday intermediate. The Cre recombinase, a member of the integrase family, was previously shown to initiate recombination by cleaving and exchanging preferentially on the bottom strand of its loxP target sequence. We have confirmed this strand bias for an intermolecular recombination reaction that used wild-type loxP sites and Cre protein. We have examined the sequence determinants for this strand preference by selectively mutating the two asymmetric scissile base-pairs in the lox site (those immediately adjacent to the sites of cleavage by Cre). We found that the initial strand exchange occurs preferentially next to the scissile G residue. Resolution of the Holliday intermediate thus formed takes place preferentially next to the scissile A residue. Lys86, which contacts the scissile nucleotides in the Cre-lox crystal structures, was important for establishing the strand preference in the resolution of the loxP-Holliday intermediate, but not for the initiation of recombination between loxP sites.
Collapse
Affiliation(s)
- Linda Lee
- Department of Medical Genetics and Microbiology, Faculty of Medicine, University of Toronto, 4284 Medical Science Building, Toronto, Ont., Canada M5S 1A
| | | |
Collapse
|
53
|
Abstract
Recent studies have made great strides toward our understanding of the mechanisms of microbial chromosome segregation and partitioning. This review first describes the mechanisms that function to segregate newly replicated chromosomes, generating daughter molecules that are viable substrates for partitioning. Then experiments that address the mechanisms of bulk chromosome movement are summarized. Recent evidence indicates that a stationary DNA replication factory may be responsible for supplying the force necessary to move newly duplicated DNA toward the cell poles. Some factors contributing to the directionality of chromosome movement probably include centromere-like-binding proteins, DNA condensation proteins, and DNA translocation proteins.
Collapse
Affiliation(s)
- Geoffrey C Draper
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 90095-1569, USA
| | | |
Collapse
|
54
|
Åkerlund T, Gullbrand B, Nordström K. Effects of the Min system on nucleoid segregation in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2002; 148:3213-3222. [PMID: 12368455 DOI: 10.1099/00221287-148-10-3213] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Min system of Escherichia coli directs cell division to the mid-cell by a mechanism that involves the dynamic localization of all of its three constituent proteins, MinC, MinD and MinE. Both the Min system and the nucleoid regulate cell division negatively and strains of E. coli lacking a functional Min system can divide at nucleoid-free cell poles in addition to the nucleoid-free region between newly segregated nucleoids. Interestingly, E. coli strains with a defective Min system have disturbed nucleoid segregation and the cause for this disturbance is not known. It is reported here that growth conditions promoting a higher frequency of polar divisions also lead to a more pronounced disturbance in nucleoid segregation. In strains with an intact Min system, expression of MinE, but not of MinD, from an inducible promoter was followed by impaired nucleoid segregation. These results suggest that the disturbed nucleoid segregation in min mutants is not caused by polar divisions per se, nor by impaired resolution of chromosome dimers in min mutants, leaving open the possibility that the Min system has a direct effect on nucleoid segregation. It is also shown how the disturbed nucleoid segregation can explain in part the unexpected finding that the clear majority of cells in min mutant populations contain 2(n) (n=0, 1, 2.) origins of replication.
Collapse
Affiliation(s)
- Thomas Åkerlund
- Department of Bacteriology, Swedish Institute for Infectious Disease Control, 171 82, Solna, Sweden1
| | - Björn Gullbrand
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, S-751 24, Uppsala, Sweden2
| | - Kurt Nordström
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, S-751 24, Uppsala, Sweden2
| |
Collapse
|
55
|
Rigden DJ, Setlow P, Setlow B, Bagyan I, Stein RA, Jedrzejas MJ. PrfA protein of Bacillus species: prediction and demonstration of endonuclease activity on DNA. Protein Sci 2002; 11:2370-81. [PMID: 12237459 PMCID: PMC2373696 DOI: 10.1110/ps.0216802] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The prfA gene product of Gram-positive bacteria is unusual in being implicated in several cellular processes; cell wall synthesis, chromosome segregation, and DNA recombination and repair. However, no homology of PrfA with other proteins has been evident. Here we report a structural relationship between PrfA and the restriction enzyme PvuII, and thereby produce models that predict that PrfA binds DNA. Indeed, wild-type Bacillus stearothermophilus PrfA, but not a catalytic site mutant, nicked one strand of supercoiled plasmid templates leaving 5'-phosphate and 3'-hydroxyl termini. This activity, much lower on linear or relaxed circular double-stranded DNA or on single-stranded DNA, is consistent with a role for this protein in chromosome segregation, DNA recombination, or DNA repair.
Collapse
Affiliation(s)
- Daniel J Rigden
- National Centre of Genetic Resources and Biotechnology, Cenargen/Embrapa, Brasília, Brazil, D.F. 70770-900.
| | | | | | | | | | | |
Collapse
|
56
|
Corre J, Louarn JM. Evidence from terminal recombination gradients that FtsK uses replichore polarity to control chromosome terminus positioning at division in Escherichia coli. J Bacteriol 2002; 184:3801-7. [PMID: 12081949 PMCID: PMC135174 DOI: 10.1128/jb.184.14.3801-3807.2002] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chromosome dimers in Escherichia coli are resolved at the dif locus by two recombinases, XerC and XerD, and the septum-anchored FtsK protein. Chromosome dimer resolution (CDR) is subject to strong spatiotemporal control: it takes place at the time of cell division, and it requires the dif resolution site to be located at the junction between the two polarized chromosome arms or replichores. Failure of CDR results in trapping of DNA by the septum and RecABCD recombination (terminal recombination). We had proposed that dif sites of a dimer are first moved to the septum by mechanisms based on local polarity and that normally CDR then occurs as the septum closes. To determine whether FtsK plays a role in the mobilization process, as well as in the recombination reaction, we characterized terminal recombination in an ftsK mutant. The frequency of recombination at various points in the terminus region of the chromosome was measured and compared with the recombination frequency on a xerC mutant chromosome with respect to intensity, the region affected, and response to polarity distortion. The use of a prophage excision assay, which allows variation of the site of recombination and interference with local polarity, allowed us to find that cooperating FtsK-dependent and -independent processes localize dif at the septum and that DNA mobilization by FtsK is oriented by the polarity probably due to skewed sequence motifs of the mobilized material.
Collapse
Affiliation(s)
- Jacqueline Corre
- Laboratoire de Microbiologie et de Génétique Moléculaires, CNRS, 31062 Toulouse Cedex, France
| | | |
Collapse
|
57
|
Capiaux H, Lesterlin C, Pérals K, Louarn JM, Cornet F. A dual role for the FtsK protein in Escherichia coli chromosome segregation. EMBO Rep 2002; 3:532-6. [PMID: 12034757 PMCID: PMC1084150 DOI: 10.1093/embo-reports/kvf116] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
FtsK is a multifunctional protein that acts in Escherichia coli cell division and chromosome segregation. Its C-terminal domain is required for XerCD-mediated recombination between dif sites that resolve chromosome dimers formed by recombination between sister chromosomes. We report the construction and analysis of a set of strains carrying different Xer recombination sites in place of dif, some of which recombine in an FtsK-independent manner. The results show that FtsK-independent Xer recombination does not support chromosome dimer resolution. Furthermore, resolution of dimers by the Cre/loxP system also requires FtsK. These findings reveal a second role for FtsK during chromosome dimer resolution in addition to XerCD activation. We propose that FtsK acts to position the dif regions, thus allowing a productive synapse between dif sites.
Collapse
Affiliation(s)
- Hervé Capiaux
- Laboratoire de Microbiologie et de Génétique Moléculaire du CNRS, 118, route de Narbonne, 31062 Toulouse Cedex, France
| | | | | | | | | |
Collapse
|
58
|
Gomis-Rüth FX, Moncalían G, de la Cruz F, Coll M. Conjugative plasmid protein TrwB, an integral membrane type IV secretion system coupling protein. Detailed structural features and mapping of the active site cleft. J Biol Chem 2002; 277:7556-66. [PMID: 11748238 DOI: 10.1074/jbc.m110462200] [Citation(s) in RCA: 63] [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
Bacterial conjugation is an example of macromolecular trafficking between cells and responsible for the spreading of antibiotic resistance among bacteria. It involves translocation of single-stranded DNA across membranes through a type IV secretion system. A coupling protein links the DNA-processing nucleoprotein complex, the relaxosome, with the transport apparatus during cell mating. In Escherichia coli plasmid R388 such a protein is TrwB, a basic integral inner-membrane nucleoside-triphosphate-binding protein. TrwB is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells and export. The structure of a soluble TrwB variant unveils an elongated molecule with six equivalent protein units featuring a spherical quaternary structure, leaving a central channel. The structures of the non-liganded protein and four different complexes with substrate analogues and products allow the precise description of the active site architecture. The active sites are located at the interface between protomers, each of them shaped mainly by residues of one monomer, but including two crucial arginine residues belonging to the adjacent molecule. Upon substrate binding and putative hydrolysis, conformational changes are transferred from the external surface to the interior central channel.
Collapse
Affiliation(s)
- F Xavier Gomis-Rüth
- Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, c/Jordi Girona, 18-26, 08034 Barcelona, Spain.
| | | | | | | |
Collapse
|
59
|
Abstract
FtsK, which links chromosome segregation and cell division in E. coli, has now been shown to be an ATP-dependent DNA translocase. It also activates XerCD-dependent recombination, converting chromosome dimers into monomers, by switching the order of strand cleavage by the recombinase subunits.
Collapse
Affiliation(s)
- William D Donachie
- Institute of Cell and Molecular Biology, University of Edinburgh, Scotland
| |
Collapse
|
60
|
Aussel L, Barre FX, Aroyo M, Stasiak A, Stasiak AZ, Sherratt D. FtsK Is a DNA motor protein that activates chromosome dimer resolution by switching the catalytic state of the XerC and XerD recombinases. Cell 2002; 108:195-205. [PMID: 11832210 DOI: 10.1016/s0092-8674(02)00624-4] [Citation(s) in RCA: 248] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
FtsK acts at the bacterial division septum to couple chromosome segregation with cell division. We demonstrate that a truncated FtsK derivative, FtsK(50C), uses ATP hydrolysis to translocate along duplex DNA as a multimer in vitro, consistent with FtsK having an in vivo role in pumping DNA through the closing division septum. FtsK(50C) also promotes a complete Xer recombination reaction between dif sites by switching the state of activity of the XerCD recombinases so that XerD makes the first pair of strand exchanges to form Holliday junctions that are then resolved by XerC. The reaction between directly repeated dif sites in circular DNA leads to the formation of uncatenated circles and is equivalent to the formation of chromosome monomers from dimers.
Collapse
Affiliation(s)
- Laurent Aussel
- Division of Molecular Genetics, Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, United Kingdom
| | | | | | | | | | | |
Collapse
|
61
|
Chen JC, Beckwith J. FtsQ, FtsL and FtsI require FtsK, but not FtsN, for co-localization with FtsZ during Escherichia coli cell division. Mol Microbiol 2001; 42:395-413. [PMID: 11703663 DOI: 10.1046/j.1365-2958.2001.02640.x] [Citation(s) in RCA: 155] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
During cell division in Gram-negative bacteria, the cell envelope invaginates and constricts at the septum, eventually severing the cell into two compartments, and separating the replicated genetic materials. In Escherichia coli, at least nine essential gene products participate directly in septum formation: FtsA, FtsI, FtsL, FtsK, FtsN, FtsQ, FtsW, FtsZ and ZipA. All nine proteins have been localized to the septal ring, an equatorial ring structure at the division site. We used translational fusions to green fluorescent protein (GFP) to demonstrate that FtsQ, FtsL and FtsI localize to potential division sites in filamentous cells depleted of FtsN, but not in those depleted of FtsK. We also constructed translational fusions of FtsZ, FtsA, FtsQ, FtsL and FtsI to enhanced cyan or yellow fluorescent protein (ECFP or EYFP respectively), GFP variants with different fluorescence spectra. Examination of cells expressing different combinations of the fusions indicated that FtsA, FtsQ, FtsL and FtsI co-localize with FtsZ in filaments depleted of FtsN. These localization results support the model that E. coli cell division proteins assemble sequentially as a multimeric complex at the division site: first FtsZ, then FtsA and ZipA independently of each other, followed successively by FtsK, FtsQ, FtsL, FtsW, FtsI and FtsN.
Collapse
Affiliation(s)
- J C Chen
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | | |
Collapse
|
62
|
Kobayashi G, Moriya S, Wada C. Deficiency of essential GTP-binding protein ObgE in Escherichia coli inhibits chromosome partition. Mol Microbiol 2001; 41:1037-51. [PMID: 11555285 DOI: 10.1046/j.1365-2958.2001.02574.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
GTP-binding proteins are involved in cell proliferation, development, signal transduction, protein elongation, etc. and construct the GTPase superfamily, whose structures and sequence motifs (G-1 to G-5) are highly conserved from prokaryote to eukaryote. Obg of Bacillus subtilis and Obg homologues of other bacteria belong to the GTPase superfamily and have been suggested as being essential for cell growth, development and monitoring of intracellular levels of GTP. We identified the Obg homologue in Escherichia coli, a protein previously known as YhbZ, which we have renamed ObgE. Double cross-over experiments showed that the obgE gene is essential for growth in E. coli. From characterization of the obgE temperature-sensitive mutant, we found that DNA replication was not inhibited, that the nucleoids did not partition and instead remained in the middle of cell, and that the cells elongated. Overproduction of ObgE also resulted in aberrant chromosome segregation. These data suggested that ObgE is involved directly or indirectly in E. coli chromosome partitioning. Characterization studies showed that ObgE is abundant in normal cells, partially associated with the membrane and does not associate with ribosomes such as in Obg of B. subtilis. We purified ObgE protein from a cell extract of E. coli, and the purified ObgE had GTPase activity and DNA-binding ability.
Collapse
Affiliation(s)
- G Kobayashi
- The Institute for Virus Research, Kyoto University, Shogoin-Kawaracho, Sakyo-Ku, Kyoto 606-8507, Japan
| | | | | |
Collapse
|
63
|
Lee L, Sadowski PD. Directional resolution of synthetic holliday structures by the Cre recombinase. J Biol Chem 2001; 276:31092-8. [PMID: 11406627 DOI: 10.1074/jbc.m103739200] [Citation(s) in RCA: 28] [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
The Cre recombinase of bacteriophage P1 cleaves its target site, loxP, in a defined order. Recombination is initiated on one pair of strands to form a Holliday intermediate, which is then resolved by cleavage and exchange of the other pair of strands to yield recombinant products. To investigate the influence of the loxP sequence on the directionality of resolution, we constructed synthetic Holliday (chi) structures containing either wild-type or mutant lox sites. We found that Cre preferentially resolved the synthetic wild-type chi structures on a particular pair of strands. The bias in the direction of resolution was dictated by the asymmetric loxP sequence since the resolution bias was abolished with symmetric lox sites. Systematic substitutions of the loxP site revealed that the bases immediately 5' to the scissile phosphodiester bonds were primarily responsible for the directionality of resolution. Interchanging these base pairs was sufficient to reverse the resolution bias. The Cre-lox co-crystal structures show that Lys(86) makes a base-specific contact with guanine immediately 5' to one of the scissile phosphates. Substituting Lys(86) with alanine resulted in a reduction of the resolution bias, indicating that this amino acid is important for establishing the bias in resolution.
Collapse
Affiliation(s)
- L Lee
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | | |
Collapse
|
64
|
Affiliation(s)
- K P Lemon
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | | |
Collapse
|
65
|
Barre FX, Søballe B, Michel B, Aroyo M, Robertson M, Sherratt D. Circles: the replication-recombination-chromosome segregation connection. Proc Natl Acad Sci U S A 2001; 98:8189-95. [PMID: 11459952 PMCID: PMC37420 DOI: 10.1073/pnas.111008998] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Crossing over by homologous recombination between monomeric circular chromosomes generates dimeric circular chromosomes that cannot be segregated to daughter cells during cell division. In Escherichia coli, homologous recombination is biased so that most homologous recombination events generate noncrossover monomeric circular chromosomes. This bias is lost in ruv mutants. A novel protein, RarA, which is highly conserved in eubacteria and eukaryotes and is related to the RuvB and the DnaX proteins, gamma and tau, may influence the formation of crossover recombinants. Those dimeric chromosomes that do form are converted to monomers by Xer site-specific recombination at the recombination site dif, located in the replication terminus region of the E. coli chromosome. The septum-located FtsK protein, which coordinates cell division with chromosome segregation, is required for a complete Xer recombination reaction at dif. Only correctly positioned dif sites present in a chromosomal dimer are able to access septum-located FtsK. FtsK acts by facilitating a conformational change in the Xer recombination Holliday junction intermediate formed by XerC recombinase. This change provides a substrate for XerD, which then completes the recombination reaction.
Collapse
Affiliation(s)
- F X Barre
- Department of Biochemistry, Division of Molecular Genetics, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | | | | | | | | | | |
Collapse
|
66
|
Kuzminov A. DNA replication meets genetic exchange: chromosomal damage and its repair by homologous recombination. Proc Natl Acad Sci U S A 2001; 98:8461-8. [PMID: 11459990 PMCID: PMC37458 DOI: 10.1073/pnas.151260698] [Citation(s) in RCA: 159] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Proceedings of the National Academy of Sciences Colloquium on the roles of homologous recombination in DNA replication are summarized. Current findings in experimental systems ranging from bacteriophages to mammalian cell lines substantiate the idea that homologous recombination is a system supporting DNA replication when either the template DNA is damaged or the replication machinery malfunctions. There are several lines of supporting evidence: (i) DNA replication aggravates preexisting DNA damage, which then blocks subsequent replication; (ii) replication forks abandoned by malfunctioning replisomes become prone to breakage; (iii) mutants with malfunctioning replisomes or with elevated levels of DNA damage depend on homologous recombination; and (iv) homologous recombination primes DNA replication in vivo and can restore replication fork structures in vitro. The mechanisms of recombinational repair in bacteriophage T4, Escherichia coli, and Saccharomyces cerevisiae are compared. In vitro properties of the eukaryotic recombinases suggest a bigger role for single-strand annealing in the eukaryotic recombinational repair.
Collapse
Affiliation(s)
- A Kuzminov
- Department of Microbiology, University of Illinois, Urbana-Champaign, B103, Chemical and Life Sciences Laboratory, 601 South Goodwin Avenue, Urbana, IL 61801-3709, USA.
| |
Collapse
|
67
|
McCool JD, Sandler SJ. Effects of mutations involving cell division, recombination, and chromosome dimer resolution on a priA2::kan mutant. Proc Natl Acad Sci U S A 2001; 98:8203-10. [PMID: 11459954 PMCID: PMC37422 DOI: 10.1073/pnas.121007698] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recombinational repair of replication forks can occur either to a crossover (XO) or noncrossover (non-XO) depending on Holliday junction resolution. Once the fork is repaired by recombination, PriA is important for restarting these forks in Escherichia coli. PriA mutants are Rec(-) and UV sensitive and have poor viability and 10-fold elevated basal levels of SOS expression. PriA sulB mutant cells and their nucleoids were studied by differential interference contrast and fluorescence microscopy of 4',6-diamidino-2-phenylindole-stained log phase cells. Two populations of cells were seen. Eighty four percent appeared like wild type, and 16% of the cells were filamented and had poorly partitioned chromosomes (Par(-)). To probe potential mechanisms leading to the two populations of cells, mutations were added to the priA sulB mutant. Mutating sulA or introducing lexA3 decreased, but did not eliminate filamentation or defects in partitioning. Mutating either recA or recB virtually eliminated the Par(-) phenotype. Filamentation in the recB mutant decreased to 3%, but increased to 28% in the recA mutant. The ability to resolve and/or branch migrate Holliday junctions also appeared crucial in the priA mutant because removing either recG or ruvC was lethal. Lastly, it was tested whether the ability to resolve chromosome dimers caused by XOs was important in a priA mutant by mutating dif and the C-terminal portion of ftsK. Mutation of dif showed no change in phenotype whereas ftsK1cat was lethal with priA2kan. A model is proposed where the PriA-independent pathway of replication restart functions at forks that have been repaired to non-XOs.
Collapse
Affiliation(s)
- J D McCool
- Department of Microbiology, University of Massachusetts, 203 Morrill Science Center IVN, Amherst, MA 01003, USA
| | | |
Collapse
|
68
|
Abstract
DNA transport is important in various biological contexts--particularly chromosome segregation and intercellular gene transfer. Recently, progress has been made in understanding the function of a family of bacterial proteins involved in DNA transfer, and we focus here on one of the best-understood members, SpoIIIE. Studies of SpoIIIE-like proteins show that they might couple DNA transport to processes such as cell division, conjugation (mating) and the resolution of chromosome dimers.
Collapse
Affiliation(s)
- J Errington
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
| | | | | |
Collapse
|
69
|
Abstract
A discussion of some aspects of the regulation of chromosome replication, segregation and cell division in Escherichia coli.
Collapse
Affiliation(s)
- W D Donachie
- Department of Molecular Biology, University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh, UK
| |
Collapse
|
70
|
Abstract
Recent years have witnessed a resurgence of interest in how the bacterial chromosome is organized and how newly replicated chromosomes are faithfully segregated into daughter cells on cell division. In the past, the problem with studying bacterial chromosomes was their lack of any obvious morphology, combined with the lack of ability to readily separate DNA replication and segregation functions into distinct stages like those observed in eukaryotic cells. This was due to the overlapping nature of these events in most bacterial systems used in the laboratory. The situation has now changed as new tools have become available that enable chromosomes and specific chromosomal sites to be labelled and monitored throughout the cell cycle, and this has led to rapid progress and the discovery of many unexpected results. Historically, chromosome segregation was thought to be achieved through passive processes where chromosomes were separated through some kind of membrane/cell wall attachment and were moved apart as the cell grew (Jacob et al., 1963). We now know that this is not the case and that there are specific mechanisms to actively partition chromosomes. This review will focus principally on the Gram-positive sporulating bacterium Bacillus subtilis, but will also cover work carried out on Escherichia coli, in which valuable information has been obtained, and will cover the events that occur on termination of chromosome replication, chromosome decatenation and chromosome separation.
Collapse
Affiliation(s)
- Peter J Lewis
- School of Biological and Chemical Sciences, University of Newcastle, Callaghan, NSW 2308, Australia1
| |
Collapse
|
71
|
Abstract
Segregation of DNA in bacterial cells is an efficient process that assures that every daughter cell receives a copy of genomic and plasmid DNA. In this review, we focus primarily on observations in recent years, including the visualization of DNA and proteins at the subcellular level, that have begun to define the events that separate DNA molecules. Unlike the process of chromosome segregation in higher cells, segregation of the bacterial chromosome is a continuous process in which chromosomes are separated as they are replicated. Essential to separation is the initial movement of sister origins to opposite ends of the cell. Subsequent replication and controlled condensation of DNA are the driving forces that move sister chromosomes toward their respective origins, which establishes the polarity required for segregation. Final steps in the resolution and separation of sister chromosomes occur at the replication terminus, which is localized at the cell center. In contrast to the chromosome, segregation of low-copy plasmids, such as Escherichia coli F, P1, and R1, is by mechanisms that resemble those used in eukaryotic cells. Each plasmid has a centromere-like site to which plasmid-specified partition proteins bind to promote segregation. Replication of plasmid DNA, which occurs at the cell center, is followed by rapid partition protein-mediated separation of sister plasmids, which become localized at distinct sites on either side of the division plane. The fundamental similarity between chromosome and plasmid segregation-placement of DNA to specific cell sites-implies an underlying cellular architecture to which both DNA and proteins refer.
Collapse
Affiliation(s)
- G S Gordon
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts 02111, USA.
| | | |
Collapse
|
72
|
Sciochetti SA, Piggot PJ, Blakely GW. Identification and characterization of the dif Site from Bacillus subtilis. J Bacteriol 2001; 183:1058-68. [PMID: 11208805 PMCID: PMC94974 DOI: 10.1128/jb.183.3.1058-1068.2001] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria with circular chromosomes have evolved systems that ensure multimeric chromosomes, formed by homologous recombination between sister chromosomes during DNA replication, are resolved to monomers prior to cell division. The chromosome dimer resolution process in Escherichia coli is mediated by two tyrosine family site-specific recombinases, XerC and XerD, and requires septal localization of the division protein FtsK. The Xer recombinases act near the terminus of chromosome replication at a site known as dif (Ecdif). In Bacillus subtilis the RipX and CodV site-specific recombinases have been implicated in an analogous reaction. We present here genetic and biochemical evidence that a 28-bp sequence of DNA (Bsdif), lying 6 degrees counterclockwise from the B. subtilis terminus of replication (172 degrees ), is the site at which RipX and CodV catalyze site-specific recombination reactions required for normal chromosome partitioning. Bsdif in vivo recombination did not require the B. subtilis FtsK homologues, SpoIIIE and YtpT. We also show that the presence or absence of the B. subtilis SPbeta-bacteriophage, and in particular its yopP gene product, appears to strongly modulate the extent of the partitioning defects seen in codV strains and, to a lesser extent, those seen in ripX and dif strains.
Collapse
Affiliation(s)
- S A Sciochetti
- Department of Microbiology and Immunology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, USA
| | | | | |
Collapse
|
73
|
Pérals K, Capiaux H, Vincourt JB, Louarn JM, Sherratt DJ, Cornet F. Interplay between recombination, cell division and chromosome structure during chromosome dimer resolution in Escherichia coli. Mol Microbiol 2001; 39:904-13. [PMID: 11251811 DOI: 10.1046/j.1365-2958.2001.02277.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Chromosome dimers form in bacteria by recombination between circular chromosomes. Resolution of dimers is a highly integrated process involving recombination between dif sites catalysed by the XerCD recombinase, cell division and the integrity of the division septum-associated FtsK protein and the presence of dif inside a restricted region of the chromosome terminus, the dif activity zone (DAZ). We analyse here how these phenomena collaborate. We show that (i) both inter- and intrachromosomal recombination between dif sites are activated by their presence inside the DAZ; (ii) the DAZ-specific activation only occurs in conditions supporting the formation of chromosome dimers; (iii) overexpression of FtsK leads to a general increase in dif recombination irrespective of dif location; (iv) overexpression of FtsK does not improve the ability of dif sites inserted outside the DAZ to resolve chromosome dimers. Our results suggest that the formation of an active XerCD-FtsK-dif complex is restricted to when a dimer is present, the features of chromosome organization that determine the DAZ playing a central role in this control.
Collapse
Affiliation(s)
- K Pérals
- Laboratoire de Microbiologie et de Génétique Moléculaire du CNRS, 118 route de Narbonne, 31062 Toulouse Cedex, France
| | | | | | | | | | | |
Collapse
|
74
|
Effects of replication termination mutants on chromosome partitioning in Bacillus subtilis. Proc Natl Acad Sci U S A 2001. [PMID: 11134515 PMCID: PMC14570 DOI: 10.1073/pnas.011506098] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many circular genomes have replication termination systems, yet disruption of these systems does not cause an obvious defect in growth or viability. We have found that the replication termination system of Bacillus subtilis contributes to accurate chromosome partitioning. Partitioning of the terminus region requires that chromosome dimers, that have formed as a result of RecA-mediated homologous recombination, be resolved to monomers by the site-specific recombinase encoded by ripX. In addition, the chromosome must be cleared from the region of formation of the division septum. This process is facilitated by the spoIIIE gene product which is required for movement of a chromosome out of the way of the division septum during sporulation. We found that deletion of rtp, which encodes the replication termination protein, in combination with mutations in ripX or spoIIIE, led to an increase in production of anucleate cells. This increase in production of anucleate cells depended on recA, indicating that there is probably an increase in chromosome dimer formation in the absence of the replication termination system. Our results also indicate that SpoIIIE probably enhances the function of the RipX recombinase system. We also determined the subcellular location of the replication termination protein and found that it is a good marker for the position of the chromosome terminus.
Collapse
|
75
|
Lemon KP, Kurtser I, Grossman AD. Effects of replication termination mutants on chromosome partitioning in
Bacillus subtilis. Proc Natl Acad Sci U S A 2001; 98:212-7. [PMID: 11134515 PMCID: PMC14570 DOI: 10.1073/pnas.98.1.212] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many circular genomes have replication termination systems, yet
disruption of these systems does not cause an obvious defect in growth
or viability. We have found that the replication termination system of
Bacillus subtilis
contributes to accurate chromosome
partitioning. Partitioning of the terminus region requires that
chromosome dimers, that have formed as a result of RecA-mediated
homologous recombination, be resolved to monomers by the site-specific
recombinase encoded by
ripX
. In addition, the chromosome
must be cleared from the region of formation of the division septum.
This process is facilitated by the
spoIIIE
gene product
which is required for movement of a chromosome out of the way of the
division septum during sporulation. We found that deletion of
rtp
, which encodes the replication termination protein,
in combination with mutations in
ripX
or
spoIIIE
, led to an increase in production of anucleate
cells. This increase in production of anucleate cells depended on
recA
, indicating that there is probably an increase in
chromosome dimer formation in the absence of the replication
termination system. Our results also indicate that SpoIIIE probably
enhances the function of the RipX recombinase system. We also
determined the subcellular location of the replication termination
protein and found that it is a good marker for the position of the
chromosome terminus.
Collapse
Affiliation(s)
- K P Lemon
- Department of Biology, Building 68-530, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | |
Collapse
|
76
|
Barre FX, Aroyo M, Colloms SD, Helfrich A, Cornet F, Sherratt DJ. FtsK functions in the processing of a Holliday junction intermediate during bacterial chromosome segregation. Genes Dev 2000; 14:2976-88. [PMID: 11114887 PMCID: PMC317095 DOI: 10.1101/gad.188700] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In bacteria with circular chromosomes, homologous recombination can generate chromosome dimers that cannot be segregated to daughter cells at cell division. Xer site-specific recombination at dif, a 28-bp site located in the replication terminus region of the chromosome, converts dimers to monomers through the sequential action of the XerC and XerD recombinases. Chromosome dimer resolution requires that dif is positioned correctly in the chromosome, and the activity of FtsK, a septum-located protein that coordinates cell division with chromosome segregation. Here, we show that cycles of XerC-mediated strand exchanges form and resolve Holliday junction intermediates back to substrate irrespective of whether conditions support a complete recombination reaction. The C-terminal domain of FtsK is sufficient to activate the exchange of the second pair of strands by XerD, allowing both intra- and intermolecular recombination reactions to go to completion. Proper positioning of dif in the chromosome and of FtsK at the septum is required to sense the multimeric state of newly replicated chromosomes and restrict complete Xer reactions to dimeric chromosomes.
Collapse
Affiliation(s)
- F X Barre
- Division of Molecular Genetics, Department of Biochemistry, University of Oxford, OX1 3QU, UK
| | | | | | | | | | | |
Collapse
|
77
|
Kinscherf TG, Hirano SS, Willis DK. Transposon insertion in the ftsK gene impairs in planta growth and lesion-forming abilities in Pseudomonas syringae pv. syringae B728a. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2000; 13:1263-1265. [PMID: 11059493 DOI: 10.1094/mpmi.2000.13.11.1263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A Tn5 insertion in the ftsK gene of Pseudomonas syringae pv. syringae B728a impaired brown spot lesion formation on Phaseolus vulgaris, the ability to grow within bean leaves, and swarming ability on semisolid agar. Plasmids containing the ftsK gene were sufficient to complement the original Tn5 mutant for lesion formation and swarming and partially restored in planta growth.
Collapse
Affiliation(s)
- T G Kinscherf
- Department of Plant Pathology, University of Wisconsin-Madison, 53706, USA
| | | | | |
Collapse
|
78
|
Dorazi R, Dewar SJ. The SOS promoter dinH is essential for ftsK transcription during cell division. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 11):2891-2899. [PMID: 11065367 DOI: 10.1099/00221287-146-11-2891] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The formation of the Escherichia coli division septum has been well characterized and the majority of the genes involved have been shown to map to the dcw cluster. One exception is ftsK, which lies at 20 minutes, immediately downstream of the global response regulatory gene, lrp. The promoter for ftsK has not yet been assigned. Here, it is reported that ftsK is transcribed from two promoters; the first is located within the lrp reading frame and is dispensable whilst the second is essential and corresponds to dinH, previously characterized as an SOS promoter regulated by LexA. ftsK is the first essential gene to be described that is controlled by an SOS-inducible promoter. A possible mechanism by which dinH may be activated in recA minus strains, or in strains with uncleavable LexA, is discussed.
Collapse
Affiliation(s)
- Robert Dorazi
- Department of Biological Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK1
| | - Susan J Dewar
- Department of Biological Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK1
| |
Collapse
|
79
|
Abstract
The Holliday junction is a central intermediate in homologous recombination. It consists of a four-way structure that can be resolved by cleavage to give either the crossover or noncrossover products observed. We show here that the formation of these products is controlled by the E. coli resolvasome (RuvABC) in such way that double-strand break repair (DSBR) leads to crossing over and single-strand gap repair (SSGR) does not lead to crossing over. We argue that the positioning of the RuvABC complex and its consequent direction of junction-cleavage is not random. In fact, the action of the RuvABC complex avoids crossing over in the most commonly predicted situations where Holliday junctions are encountered in DNA replication and repair. Our observations suggest that the positioning of the resolvasome may provide a general biochemical mechanism by which cells can control crossing over in recombination.
Collapse
Affiliation(s)
- G A Cromie
- Institute of Cell and Molecular Biology, University of Edinburgh, United Kingdom
| | | |
Collapse
|
80
|
Sciochetti SA, Piggot PJ. A tale of two genomes: resolution of dimeric chromosomes in Escherichia coli and Bacillus subtilis. Res Microbiol 2000; 151:503-11. [PMID: 11037128 DOI: 10.1016/s0923-2508(00)00220-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dimeric chromosomes can be formed during replication of circular bacterial chromosomes by an odd number of homologous recombination events between sister chromosomes. In the absence of a compensating recombination reaction such dimers cannot be segregated from each other as the cell divides. This review highlights the shared and divergent mechanisms employed by Escherichia coli and Bacillus subtilis in their effort to resolve and partition dimeric chromosomes safely. In particular, we discuss the Xer-type recombinases, RecA, FtsK/SpoIIIE, and dif.
Collapse
Affiliation(s)
- S A Sciochetti
- Department of Microbiology & Immunology, Temple University School of Medicine, Philadelphia, PA, USA
| | | |
Collapse
|
81
|
Boyle DS, Grant D, Draper GC, Donachie WD. All major regions of FtsK are required for resolution of chromosome dimers. J Bacteriol 2000; 182:4124-7. [PMID: 10869097 PMCID: PMC94604 DOI: 10.1128/jb.182.14.4124-4127.2000] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Resolution of chromosome dimers, by site-specific recombination between dif sites, is carried out in Escherichia coli by XerCD recombinase in association with the FtsK protein. We show here that a variety of altered FtsK polypeptides, consisting of the N-terminal (cell division) domain alone or with deletions in the proline-glutamine-rich part of the protein, or polypeptides consisting of the C-terminal domain alone are all unable to carry out dif recombination. Alteration of the putative nucleotide-binding site also abolishes the ability of FtsK to carry out recombination between dif sites.
Collapse
Affiliation(s)
- D S Boyle
- Institute of Cell & Molecular Biology, University of Edinburgh, Scotland.
| | | | | | | |
Collapse
|
82
|
Michel B, Recchia GD, Penel-Colin M, Ehrlich SD, Sherratt DJ. Resolution of holliday junctions by RuvABC prevents dimer formation in rep mutants and UV-irradiated cells. Mol Microbiol 2000; 37:180-91. [PMID: 10931315 DOI: 10.1046/j.1365-2958.2000.01989.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In this work, we present evidence that indicates that RuvABC proteins resolve Holliday junctions in a way that prevents dimer formation in vivo. First, although arrested replication forks are rescued by recombinational repair in cells deficient for the Rep helicase, rep mutants do not require the XerCD proteins or the dif site for viability. This shows that the recombination events at arrested replication forks are generally not accompanied by the formation of chromosome dimers. Secondly, resolution of dimers into monomers is essential in the rep ruv strain because of an increased frequency of RecFOR recombination events in the chromosome of this mutant. This suggests that, in the absence of the Ruv proteins, chromosomal recombination leads to frequent dimerization. Thirdly, dif or xerC mutations increase the UV sensitivity of ruv-deficient cells 100-fold, whereas they do not confer UV sensitivity to ruv+ cells. This shows that recombinational repair of UV lesions is not accompanied by dimer formation provided that the RuvABC proteins are active. The requirement for dimer resolution in ruv strains is suppressed by the expression of the RusA Holliday junction resolvase; therefore, RusA also prevents dimer formation. We conclude that the inviability arising from a high frequency of dimer formation in rep or UV-irradiated cells is only observed in the absence of known enzymes that resolve Holliday junctions.
Collapse
Affiliation(s)
- B Michel
- Génétique Microbienne, INRA, 78352 Jouy en Josas Cedex, France
| | | | | | | | | |
Collapse
|
83
|
Arciszewska LK, Baker RA, Hallet B, Sherratt DJ. Coordinated control of XerC and XerD catalytic activities during Holliday junction resolution. J Mol Biol 2000; 299:391-403. [PMID: 10860747 DOI: 10.1006/jmbi.2000.3762] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Site-specific recombinases XerC and XerD function in the segregation of circular bacterial replicons. In a recombining nucleoprotein complex containing two molecules each of XerC and XerD, coordinated reciprocal switches in recombinase activity ensure that only XerC or XerD is active at any one time. Mutated recombinases that carry sub?stitutions of a catalytic arginine residue stimulate cleavage and strand exchange mediated by the partner recombinase on DNA substrates that are normally recombined poorly by the partner. This is associated with a reciprocal impairment of the recombinase's own ability to initiate catalysis. The extent of this switch in catalysis is modulated by changes in recombination site sequence and is not a direct consequence of any catalytic defect. We propose that altered interactions between the mutated proteins and their wild-type partners lead to an increased level of an alternative Holliday junction intermediate that has a conformation appropriate for resolution by the partner recombinase. The results indicate how subtle changes in protein-DNA architecture at a Holliday junction can redirect recombination outcome.
Collapse
Affiliation(s)
- L K Arciszewska
- Division of Molecular Genetics Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | | | | | | |
Collapse
|
84
|
Diez A, Gustavsson N, Nyström T. The universal stress protein A of Escherichia coli is required for resistance to DNA damaging agents and is regulated by a RecA/FtsK-dependent regulatory pathway. Mol Microbiol 2000; 36:1494-503. [PMID: 10931298 DOI: 10.1046/j.1365-2958.2000.01979.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The link between cell division defects and the induction of the universal stress response is demonstrated to operate via the RecA regulator of the SOS response. An insertion in the cell division gene ftsK upregulates uspA in a recA-dependent manner. Unlike true SOS response genes, this upregulation only occurs in growth-arrested cells and is LexA independent. Thus, besides ppGpp-dependent starvation signals, DNA aberrations transduce RecA-dependent signals to the uspA promoter, which only affect the promoter during stasis. Further, we show that ftsK itself, like uspA, is induced in stationary phase and that this induction requires the stringent control modulon rather than activated RecA. Thus, ftsK, like uspA, is regulated by at least two global regulators: ppGpp of the stringent control network and RecA of the SOS modulon. We suggest that UspA is a new bona fide member of the RecA-dependent DNA protection and repair system, as mutants lacking functional UspA were found to be sensitive to UV irradiation and mitomycin C exposure. Moreover, the UV sensitivity of uspA mutants is enhanced in an additive manner by the ftsK1 mutation.
Collapse
Affiliation(s)
- A Diez
- Department of Cell and Molecular Biology--Microbiology, Göteborg University, Sweden
| | | | | |
Collapse
|
85
|
Blakely GW, Davidson AO, Sherratt DJ. Sequential strand exchange by XerC and XerD during site-specific recombination at dif. J Biol Chem 2000; 275:9930-6. [PMID: 10744667 DOI: 10.1074/jbc.275.14.9930] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Successful segregation of circular chromosomes in Escherichia coli requires that dimeric replicons, produced by homologous recombination, are converted to monomers prior to cell division. The Xer site-specific recombination system uses two related tyrosine recombinases, XerC and XerD, to catalyze resolution of circular dimers at the chromosomal site, dif. A 33-base pair DNA fragment containing the 28-base pair minimal dif site is sufficient for the recombinases to mediate both inter- and intramolecular site-specific recombination in vivo. We show that Xer-mediated intermolecular recombination in vitro between nicked linear dif "suicide" substrates and supercoiled plasmid DNA containing dif is initiated by XerC. Furthermore, on the appropriate substrate, the nicked Holliday junction intermediate formed by XerC is converted to a linear product by a subsequent single XerD-mediated strand exchange. We also demonstrate that a XerC homologue from Pseudomonas aeruginosa stimulates strand cleavage by XerD on a nicked linear substrate and promotes initiation of strand exchange by XerD in an intermolecular reaction between linear and supercoiled DNA, thereby reversing the normal order of strand exchanges.
Collapse
Affiliation(s)
- G W Blakely
- Division of Molecular Genetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | | | | |
Collapse
|
86
|
Cox MM, Goodman MF, Kreuzer KN, Sherratt DJ, Sandler SJ, Marians KJ. The importance of repairing stalled replication forks. Nature 2000; 404:37-41. [PMID: 10716434 DOI: 10.1038/35003501] [Citation(s) in RCA: 810] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The bacterial SOS response to unusual levels of DNA damage has been recognized and studied for several decades. Pathways for re-establishing inactivated replication forks under normal growth conditions have received far less attention. In bacteria growing aerobically in the absence of SOS-inducing conditions, many replication forks encounter DNA damage, leading to inactivation. The pathways for fork reactivation involve the homologous recombination systems, are nonmutagenic, and integrate almost every aspect of DNA metabolism. On a frequency-of-use basis, these pathways represent the main function of bacterial DNA recombination systems, as well as the main function of a number of other enzymatic systems that are associated with replication and site-specific recombination.
Collapse
Affiliation(s)
- M M Cox
- Department of Biochemistry, University of Wisconsin-Madison, 53706-1544, USA
| | | | | | | | | | | |
Collapse
|
87
|
Hallet B, Arciszewska LK, Sherratt DJ. Reciprocal control of catalysis by the tyrosine recombinases XerC and XerD: an enzymatic switch in site-specific recombination. Mol Cell 1999; 4:949-59. [PMID: 10635320 DOI: 10.1016/s1097-2765(00)80224-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
In Xer site-specific recombination, sequential DNA strand exchange reactions are catalyzed by a heterotetrameric complex composed of two recombinases, XerC and XerD. It is demonstrated that XerC and XerD catalytic activity is controlled by an interaction involving the C-terminal end of each protein (the donor region) and an internal region close to the active site (the acceptor region). Mutations in these regions reciprocally alter the relative activity of XerC and XerD, with their combination producing synergistic effects on catalysis. The data support a model in which C-terminal intersubunit interactions contribute to coupled protein-DNA conformational changes that lead to sequential activation and reciprocal inhibition of pairs of active sites in the recombinase tetramer during recombination.
Collapse
Affiliation(s)
- B Hallet
- Department of Biochemistry, University of Oxford, United Kingdom
| | | | | |
Collapse
|