Advances in Biophysics最新文献

{"title":"The function of RecQ helicase gene family (especially BLM) in DNA recombination and joining","authors":"Hideo Kaneko,&nbsp;Toshiyuki Fukao,&nbsp;Naomi Kondo","doi":"10.1016/S0065-227X(04)80061-3","DOIUrl":"10.1016/S0065-227X(04)80061-3","url":null,"abstract":"<div><p>Bloom syndrome is a rare autosomal recessive genetic disorder characterized by lupus-like erythematous telangiectasias of the face, sun sensitivity, stunted growth, and immunodeficiency. Chromosome instability syndromes have a common feature, being associated at high frequency with neoplasia. BS is considered as one of the chromosome instability syndromes since the fibroblasts or lymphocytes of BS patients show excessive spontaneous chromosome instability. The causative gene of BS (<em>BLM</em>) was identified as a RecQ helicase homologue. In this review, we showed the characteristic phenotypes of BS, especially two Japanese siblings. In the latter of the review, the functional domains of BLM, those are nuclear localization signal and the interacting proteins such as ATM, are shown. Several lines of reports indicates that BLM helicase is involved in the re-initiation of DNA replication at sites where replication forks have arrested or collapsed. To elucidate the precise function of RecQ helicase in DNA repair and replication aims not only to improve our understanding of the molecular basis for tumorigenesis, but also to extend the range of potential therapeutic targets.</p></div>","PeriodicalId":50880,"journal":{"name":"Advances in Biophysics","volume":"38 ","pages":"Pages 45-64"},"PeriodicalIF":0.0,"publicationDate":"2004-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-227X(04)80061-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"55849772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nijmegen breakage syndrome and DNA double strand break repair by NBS1 complex","authors":"Shinya Matsuura ,&nbsp;Junya Kobayashi ,&nbsp;Hiroshi Tauchi ,&nbsp;Kenshi Komatsu","doi":"10.1016/S0065-227X(04)80076-5","DOIUrl":"10.1016/S0065-227X(04)80076-5","url":null,"abstract":"<div><p>The isolation of the <em>NBS1</em> gene revealed the molecular mechanisms of DSB repair. In response to DNA damage, histone H2AX in the vicinity of DSBs is phosphorylated by ATM. NBS1 then targets the MRE11/RAD50 complex to the sites of DSBs through interaction of the FHA/BRCT domain with γ-H2AX. NBSI complex binds to damaged-DNA directly, and HR repair is initiated. To collaborate DSB repair, ATM also regulates cell cycle checkpoints at GI, G2, and intra-S phases <em>via</em> phosphorylation of SMC, CHK2 and FANCD2. The phosphorylation of these proteins require NBS1 complex. Thus, NBSI has at least two important roles in genome maintenance, as a DNA repair protein in HR pathway and as a signal modifier in intra-S phase checkpoints. NBSI is also known to be involved in maintenance of telomores, which have DSB-like structures and defects here can cause telomcric fusion. Therefore, NBS1 should be a multi-functional protein for the maintenance of genomic integrity. Further studies on NBS1 will provide insights into the mechanisms of DNA damage response and the network of these factors involved in genomic stability.</p></div>","PeriodicalId":50880,"journal":{"name":"Advances in Biophysics","volume":"38 ","pages":"Pages 65-80"},"PeriodicalIF":0.0,"publicationDate":"2004-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-227X(04)80076-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"55849785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transposition mechanisms and biothechnology applications of the medaka fish tol2 transposable element.","authors":"Akihiko Koga","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The Tol2 element of the medaka fish is a member of the hAT (hobo/Activator/Tam3) transposable element family. About 20 copies are present in the medaka fish genome and, unlike many other hAT family elements, virtually all the copies are autonomous or potentially autonomous, containing an intact transposase gene. Excision of Tol2 is not precise at the nucleotide sequence level, excision footprints being heterogeneous. In more than half of excision events, however, breakage and rejoining of DNA molecules occur within the 8-bp target site duplication region, removing the entire Tol2 sequence and retaining parts of the target site duplications. In the reminder of the excision events, either the left or the right terminal region is left and the other end is lost together with its flanking region. Thus, there might be two different mechanisms of excision. Insertion of Tol2 occurs without detectable preference for target sequences and creates a target site duplication of exactly 8 bp. In addition to the medaka fish and related fish species, Tol2 transposes in mammalian cells in culture, including human and mouse examples. Autonomy is also retained in these cases. A gene transfer vector using Tol2 has already been established in fish. Foreign DNA fragements inserted in Tol2 can be efficiently delivered to the chromosomes by transposition. The latest version of the vector contains, between the Tol2 terminal regions, a bacterial drug-resistance gene and a plasmid replication origin. This allows simple recovery of insertion regions, as plasmid DNA, from genomic DNA of transformants. Modification of this system for other vertebrates, especially for mammals, are now in progress.</p>","PeriodicalId":50880,"journal":{"name":"Advances in Biophysics","volume":"38 Complete","pages":"161-180"},"PeriodicalIF":0.0,"publicationDate":"2004-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40913113","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular mechanism of vde-initiated intein homing in yeast nuclear genome","authors":"Tomoyuki Fukuda,&nbsp;Yuri Nagai,&nbsp;Yoshikazu Ohya","doi":"10.1016/S0065-227X(04)80181-3","DOIUrl":"10.1016/S0065-227X(04)80181-3","url":null,"abstract":"<div><p><em>In Saccharomyces cerevisiae, VMAI</em> intein encodes a homing endonuclease termed VDE which is produced by an autocatalytic protein splicing reaction. VDE introduces a DSB at its recognition sequence on intein-minus allele, resulting in the lateral transfer of <em>VMAI</em> intein. In this review, we summarize a decade of <em>in vitro</em> study on VDE and describe our recent study on the <em>in vivo</em> behavior of both VDE and host proteins involved in intein mobility. Meiotic DSBs caused by VDE are repaired in the similar pathway to that working in meiotic recombination induced by Spollp-mediated DSBs. Meiosis-specific DNA cleavage and homing is shown to be guaranteed by the two distinct mechanisms, the subcellular localization of VDE and a requirement of premeiotic DNA replication. Based on these lines of evidence, we present the whole picture of molecular mechanism of VDEinitiated homing in yeast cells.</p></div>","PeriodicalId":50880,"journal":{"name":"Advances in Biophysics","volume":"38 ","pages":"Pages 215-232"},"PeriodicalIF":0.0,"publicationDate":"2004-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-227X(04)80181-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"55849860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure and function of the shufflon in plasmid r64","authors":"Atsuko Gyohda,&nbsp;Nobuhisa Furuya,&nbsp;Akiko Ishiwa,&nbsp;Shujuan Zhu,&nbsp;Teruya Komano","doi":"10.1016/S0065-227X(04)80166-7","DOIUrl":"10.1016/S0065-227X(04)80166-7","url":null,"abstract":"<div><p>Conservative site-specific recombination plays key roles in creating biological diversity in prokaryotes. Most site-specific inversion systems consist of two recombination sites and a recombinase gene. In contrast, the shufflon multiple inversion system of plasmid R64 consists of seven <em>sfx</em> recombination sites, which separate four invertible DNA segments, and the <em>rci</em> gene encoding a site-specific recombinase of the integrase family. The <em>rci</em> product mediates recombination between any two inverted <em>sfx</em> sites, resulting in the inversion of four DNA segments independently or in groups. Random shufflon inversions construct seven <em>pilV</em> genes encoding constant N-terminal segment with different C-terminal segments. The <em>pilV</em> products are tip-located adhesins of the type IV pilus, called the thin pilus, of R64 and recognize lipopolysaccharides of recipient bacterial cells during R64 liquid matings. Thus, the shufflon determines the recipient specificity of liquid matings.</p><p>Rci protein of R64 was overexpressed, purified, and used for <em>in vitro</em> recombination reactions. The cleavage and rejoining of DNA strands in shufflon recombinations were found to take place in the form of a 5′ protruding 7-hp staggered cut within <em>sfx</em> sequences. Thus, the sfx sequence is asymmetric: only the 7-bp spacer sequence and the right arm sequence are conserved among various R64 <em>sfxs</em>, whereas the <em>sfx</em> left arm sequences are not conserved. Rci protein was shown to bind to entire <em>sfx</em> sequences, suggesting that it binds to the right arms of the <em>sfx</em> sequences in a sequence-specific manner and to their left arms in a non-sequence-specific manner. The <em>sfx</em> left arm sequences greatly affected the shufflon inversion frequency. The artificial symmetric <em>sfx</em> sequence, in which the <em>sfx</em> left arm was changed to the inverted repeat sequence of the right arm, exhibited the highest inversion frequency. Rci-dependent deletion of a DNA segment flanked by two symmetric <em>sfx</em> sequences in direct orientation was observed, suggesting that the asymmetry of <em>sfx</em> sequences may prevent recombination between <em>sfx</em> sequences in direct orientation in the R64 shufflon. The Rci C-terminal domain was not required for recombination using the symmetric <em>sfx</em> sequence. A model, where the C-terminal domain of Rci protein plays a key role in the sequence-specific and non-specific binding of Rci to asymmetric <em>sfx</em> sites, was proposed.</p><p>Site-specific recombination in the temperate phage Mx8 of <em>M. xanthus</em> was also described. The Mx8 <em>attP</em> site is located within the coding sequence of the Mx8 <em>intP</em> gene. Therefore, the integration of Mx8 into the <em>M. xanthus</em> chromosome results in the conversion of the <em>intP</em> gene into a new gene, <em>intP</em>. As a result of this conversion, the 112-amino-acid C-termi","PeriodicalId":50880,"journal":{"name":"Advances in Biophysics","volume":"38 ","pages":"Pages 183-213"},"PeriodicalIF":0.0,"publicationDate":"2004-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-227X(04)80166-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"55849850","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The function of RecQ helicase gene family (especially BLM) in DNA recombination and joining.","authors":"Hideo Kaneko,&nbsp;Toshiyuki Fukao,&nbsp;Naomi Kondo","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Bloom syndrome is a rare autosomal recessive genetic disorder characterized by lupus-like erythematous telangiectasias of the face, sun sensitivity, stunted growth, and immunodeficiency. Chromosome instability syndromes have a common feature, being associated at high frequency with neoplasia. BS is considered as one of the chromosome instability syndromes since the fibroblasts or lymphocytes of BS patients show excessive spontaneous chromosome instability. The causative gene of BS (BLM) was identified as a RecQ helicase homologue. In this review, we showed the characteristic phenotypes of BS, especially two Japanese siblings. In the latter of the review, the functional domains of BLM, those are nuclear localization signal and the interacting proteins such as ATM, are shown. Several lines of reports indicates that BLM helicase is involved in the re-initiation of DNA replication at sites where replication forks have arrested or collapsed. To elucidate the precise function of RecQ helicase in DNA repair and replication aims not only to improve our understanding of the molecular basis for tumorigenesis, but also to extend the range of potential therapeutic targets.</p>","PeriodicalId":50880,"journal":{"name":"Advances in Biophysics","volume":"38 Complete","pages":"45-64"},"PeriodicalIF":0.0,"publicationDate":"2004-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40913107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Illegitimate recombination mediated by double-strand break and end-joining in Escherichia coli.","authors":"Hideo Ikeda,&nbsp;Kouya Shiraishi,&nbsp;Yasuyuki Ogata","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The frequency of illegitimate recombination has been measured by a lambda bio transducing phage assay during the induction of the E. coli lambda cI857 lysogen. Illegitimate recombination falls into two classes, short homology-independent and short homology-dependent illegitimate recombination. The former involves sequences with virtually no homology, and is mediated by DNA topoisomerases and controlled by the DNA binding protein HU. The latter is induced by UV irradiation or other DNA damaging agents and requires short regions of homology, usually contain 4 to 13 base pairs, at sites involved in recombination. It has been shown that the RecJ exonuclease promotes short homology-dependent illegitimate recombination, but that the RecQ helicase suppresses it. In addition, we have shown that the overexpression of RecE and RecT enhances the frequencies of spontaneous and UV-induced illegitimate recombination and that the RecJ, RecF, RecO, and RecR functions are required for this RecE-mediated illegitimate recombination. Moreover, we have also indicated that RecQ plays a role in the suppression of RecE-mediated illegitimate recombination, with the participation of DnaB, Fis, ExoI, and H-NS. Models have been proposed for these modes of recombination: the DNA gyrase subunit exchange model for short homology-independent illegitimate recombination and the \"double-strand break and join\" model for short homology-dependent illegitimate recombination. Many features of these models remain to be tested in future studies.</p>","PeriodicalId":50880,"journal":{"name":"Advances in Biophysics","volume":"38 ","pages":"3-20"},"PeriodicalIF":0.0,"publicationDate":"2004-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24768608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preface to volume 38","authors":"Hideo Ikeda,&nbsp;Shigeru Iida,&nbsp;Eiichi Ohtsubo","doi":"10.1016/S0065-227X(04)80016-9","DOIUrl":"10.1016/S0065-227X(04)80016-9","url":null,"abstract":"","PeriodicalId":50880,"journal":{"name":"Advances in Biophysics","volume":"38 ","pages":"Pages v-vi"},"PeriodicalIF":0.0,"publicationDate":"2004-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-227X(04)80016-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"55849734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Illegitimate recombination mediated by double-strand break and end-joining in Escherichia coli","authors":"Hideo Ikeda ,&nbsp;Kouya Shiraishi ,&nbsp;Yasuyuki Ogata","doi":"10.1016/S0065-227X(04)80031-5","DOIUrl":"10.1016/S0065-227X(04)80031-5","url":null,"abstract":"<div><p>The frequency of illegitimate recombination has been measured by a λ<em>bio</em> transducing phage assay during the induction of the <em>E. coli</em> λ <em>c1857</em> lysogen. Illegitimate recombination falls into two classes, short homology-independent and short homology-dependent illegitimate recombination. The former involves sequences with virtually no homology, and is mediated by DNA topoisomerases and controlled by the DNA binding protein HU. The latter is induced by UV irradiation or other DNA damaging agents and requires short regions of homology, usually contain 4 to 13 base pairs, at sites involved in recombination. It has been shown that the RecJ exonuclease promotes short homology-dependent illegitimate recombination, but that the RecQ helicase suppresses it. In addition, we have shown that the overexpression of RecE and RecT enhances the frequencies of spontaneous and UV-induced illegitimate recombination and that the RecJ, RecF, RecO, and RecR functions are required for this RecE-mediated illegitimate recombination. Moreover, we have also indicated that RecQ plays a role in the suppression of RecEmediated illegitimate recombination, with the participation of DnaB, Fis, Exol, and H-NS. Models have been proposed for these modes of recombination: the DNA gyrase subunit exchange model for short homology-independent illegitimate recombination and the “double-strand break and join” model for short homologydependent illegitimate recombination. Many features of these models remain to be tested in future studies.</p></div>","PeriodicalId":50880,"journal":{"name":"Advances in Biophysics","volume":"38 ","pages":"Pages 3-20"},"PeriodicalIF":0.0,"publicationDate":"2004-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-227X(04)80031-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"55849750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Intermediate molecules generated by transposase in the pathways of transposition of bacterial insertion element 1S3","authors":"Eiichi Ohtsubo,&nbsp;Hiroshi Minematsu,&nbsp;Ken Tsuchida,&nbsp;Hisako Ohtsubo,&nbsp;Yasuhiko Sekine","doi":"10.1016/S0065-227X(04)80121-7","DOIUrl":"10.1016/S0065-227X(04)80121-7","url":null,"abstract":"","PeriodicalId":50880,"journal":{"name":"Advances in Biophysics","volume":"38 ","pages":"Pages 125-139"},"PeriodicalIF":0.0,"publicationDate":"2004-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-227X(04)80121-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"55849814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}