Resolution of Holliday Structures by Endonuclease VII As Observed in Interactions with Cruciform DNA

Kemper, Börries; Jensch, F.; Depka-Prondzynski, M.v.; Fritz, Hans-Joachim; Borgmeyer, Uwe; Mizuuchi, Kiyoshi

doi:10.1101/sqb.1984.049.01.092

Cited by 60 publications

(26 citation statements)

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“…Heteroduplex (or mismatch) repair of T4 DNA in vivo and in vitro is mediated by EndoVII, the enzyme that cuts Holliday junctions (522,526,793), not by MutHLS-like enzymes. The specificity of this activity is thought to contribute to the exclu- …”

Section: Dna Repairmentioning

confidence: 99%

Bacteriophage T4 Genome

Miller

Kutter

Mosig

et al. 2003

Microbiol Mol Biol Rev

704

801

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SUMMARY Phage T4 has provided countless contributions to the paradigms of genetics and biochemistry. Its complete genome sequence of 168,903 bp encodes about 300 gene products. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics. Variations on gene expression, including overlapping genes, internal translation initiation, spliced genes, translational bypassing, and RNA processing, alert us to the caveats of purely computational methods. The T4 transcriptional pattern reflects its dependence on the host RNA polymerase and the use of phage-encoded proteins that sequentially modify RNA polymerase; transcriptional activator proteins, a phage sigma factor, anti-sigma, and sigma decoy proteins also act to specify early, middle, and late promoter recognition. Posttranscriptional controls by T4 provide excellent systems for the study of RNA-dependent processes, particularly at the structural level. The redundancy of DNA replication and recombination systems of T4 reveals how phage and other genomes are stably replicated and repaired in different environments, providing insight into genome evolution and adaptations to new hosts and growth environments. Moreover, genomic sequence analysis has provided new insights into tail fiber variation, lysis, gene duplications, and membrane localization of proteins, while high-resolution structural determination of the “cell-puncturing device,” combined with the three-dimensional image reconstruction of the baseplate, has revealed the mechanism of penetration during infection. Despite these advances, nearly 130 potential T4 genes remain uncharacterized. Current phage-sequencing initiatives are now revealing the similarities and differences among members of the T4 family, including those that infect bacteria other than Escherichia coli. T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening our understanding of the complex evolution and ecology of phages—the most abundant and among the most ancient biological entities on Earth.

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Section: Dna Repairmentioning

confidence: 99%

Bacteriophage T4 Genome

Miller

Kutter

Mosig

et al. 2003

Microbiol Mol Biol Rev

704

801

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“…1 and 3, can contribute to DNA repair and explain ''homing'' of intron DNA (15,18,19). Most of the proteins involved in these pathways have been biochemically characterized in exquisite detail (2,12,(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35).…”

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confidence: 99%

Two recombination-dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and horizontal gene transfer

Mosig

Gewin

Luder

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

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. In wild-type T4, timing of these pathways is integrated with the developmental program and related to transcription and packaging of DNA. In primase mutants, which are defective in origin-dependent lagging-strand DNA synthesis, the late pathway can bypass the lack of primers for lagging-strand DNA synthesis. The exquisitely regulated synthesis of endo VII, and of two proteins from its gene, explains the delay of recombination-dependent DNA replication in primase (as well as topoisomerase) mutants, and the temperature-dependence of the delay. Other proteins (e.g., the singlestranded DNA binding protein and the products of genes 46 and 47) are important in all recombination pathways, but they interact differently with other proteins in different pathways. These homologous recombination pathways contribute to evolution because they facilitate acquisition of any foreign DNA with limited sequence homology during horizontal gene transfer, without requiring transposition or site-specific recombination functions. Partial heteroduplex repair can generate what appears to be multiple mutations from a single recombinational intermediate. The resulting sequence divergence generates barriers to formation of viable recombinants. The multiple sequence changes can also lead to erroneous estimates in phylogenetic analyses.The purpose of looking back is not, of course, merely to obtain satisfaction from reflecting on past triumphs; rather, it is to discover as many clues as possible to the likely developments of the future.Glenn T. Seaborg T he tight interrelationship between homologous recombination and DNA replication was first evident in T4 and the related T-even phages. Because DNA of T4 and its host E. coli differ in base composition and modifications and because the host DNA is rapidly degraded after phage infection, molecular aspects of T4 replication and recombination could be readily investigated by biochemical, biophysical, and genetic methods. Early characterization of mutations in most essential genes (1) and the almost complete dependence of replication and recombination on phage-encoded proteins (2) allowed analyses of recombination and replication proteins, as well as ''reality checks'' of results obtained with genetic and biochemical methods (3). The following idiosyncrasies of T4 chromosomes revealed the importance of DNA ends and recombination-dependent DNA replication. Ends of T4 chromosomes are cut during packaging from branched concatemers, which are generated by recombination-dependent replication. A ''headful mechanism'' packages a complete genome and Ϸ3% DNA repeated at each end as ''terminal redundancy,'' thereby generating the random circular permutation of chromosomal ends (4). Some smaller T4 particles, formed because of assembly errors, package incomplete genomes whose ends are also randomly circularly permuted (5). Multifactor crosses revealed stimulation of recombination by their DNA ends, regardless of map positions (5, 6). Moreover, different segregation patterns of alleles in patch vs. splice re...

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“…Several nucleases have been shown to cleave synthetic Holliday junctions (46). Among these, T4 endonuclease VII has the poorest DNA sequence specificity and also exhibits general activity on (26). T4 endonuclease VII cleaved SDR molecules into linear duplex products of size n. Resolution of the SDR molecules into linear duplex products of size n supports the idea that they consist of Holliday junctions or T4 endonuclease VII-sensitive hemicatenanes.…”

Section: Discussionmentioning

confidence: 66%

“…The classical intermediate during homologous recombination is a Holliday junction (21). Previous studies showed that T4 endonuclease VII cleaves synthetic Holliday junctions efficiently but also recognizes and processes other related DNA structures (24,26,27), including replication intermediates (17). While T4 endonuclease VII converts replicating molecules into doublestranded fragments of size n and smaller, the cleavage of Holliday junction-like structure should generate only n-sized minichromosomes (Fig.…”

Section: Discrimination Of 2n Molecules By Two-dimensional Gel Electrmentioning

confidence: 99%

Rad52-Independent Accumulation of Joint Circular Minichromosomes during S Phase in Saccharomyces cerevisiae

Wellinger

Schär²,

Sogo

2003

Molecular and Cellular Biology

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We investigated the formation of X-shaped molecules consisting of joint circular minichromosomes (joint molecules) in Saccharomyces cerevisiae by two-dimensional neutral/neutral gel electrophoresis of psoralencross-linked DNA. The appearance of joint molecules was found to be replication dependent. The joint molecules had physical properties reminiscent of Holliday junctions or hemicatenanes, as monitored by strand displacement, branch migration, and nuclease digestion. Physical linkage of the joint molecules was detected along the entire length of the minichromosome and most likely involved newly replicated sister chromatids. Surprisingly, the formation of joint molecules was found to be independent of Rad52p as well as of other factors associated with a function in homologous recombination or in the resolution of stalled replication intermediates. These findings thus imply the existence of a nonrecombinational pathway(s) for the formation of joint molecules during the process of DNA replication or minichromosome segregation.DNA replication is a highly coordinated process providing an accurate duplication of the chromosomes required for faithful transmission of the genomic information from mother to daughter cells. Studies of mitotic cells have led to a unified model for DNA replication involving three distinct steps; initiation, elongation, and termination (for a review, see reference 57). Several studies seem to corroborate the general features of the bidirectional replication model, which proposes that pairs of divergent replication forks travel away from their origins until they meet the forks coming from opposite directions from the neighboring replicons (22, 42). When two replication forks converge at the end of DNA synthesis, the leading-end polymerases advance toward each other, melting the remaining duplex region, and finish the replication by producing catenated DNA molecules (50,51). An alternative model for termination proposed that one of the advancing polymerases dislodges from the template by accumulated torsional stress, so that only one fork can advance. In subsequent reaction steps, including strand displacement and branch migration, hemicatenated DNA is formed and resolved by type I topoisomerases (31).DNA recombination is an integral part of DNA replication and contributes to the structural integrity of the newly replicated genome (for recent reviews, see references 3, 10, and 30). In replicating DNA, X-shaped molecules (xDNA) with properties of Holliday junction intermediates of homologous recombination (21) can be distinguished physically from replicating molecules by two-dimensional gel electrophoresis (5, 43). The formation of such joint molecules was recently studied within the Saccharomyces cerevisiae ribosomal DNA (rDNA) locus (60) and various loci of Physarum polycephalum (6). In both organisms, Holliday junction-like xDNA molecules were more abundant in S phase. Interestingly, mutations in polymerases ␣ and ␦ stimulated the formation of Holliday junctions in the S. cerevisiae rDNA l...

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Resolution of Holliday Structures by Endonuclease VII As Observed in Interactions with Cruciform DNA

Cited by 60 publications

References 0 publications

Bacteriophage T4 Genome

Bacteriophage T4 Genome

Two recombination-dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and horizontal gene transfer

Rad52-Independent Accumulation of Joint Circular Minichromosomes during S Phase in Saccharomyces cerevisiae

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