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Resolvase

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https://www.readbyqxmd.com/read/29403466/the-novel-phages-phicd5763-and-phicd2955-represent-two-groups-of-big-plasmidial-siphoviridae-phages-of-clostridium-difficile
#1
Gabriel Ramírez-Vargas, Shan Goh, César Rodríguez
Until recently, Clostridium difficile phages were limited to Myoviruses and Siphoviruses of medium genome length (32-57 kb). Here we report the finding of phiCD5763, a Siphovirus with a large extrachromosomal circular genome (132.5 kb, 172 ORFs) and a large capsid (205.6 ± 25.6 nm in diameter) infecting MLST Clade 1 strains of C. difficile. Two subgroups of big phage genomes similar to phiCD5763 were identified in 32 NAPCR1/RT012/ST-54 C. difficile isolates from Costa Rica and in whole genome sequences (WGS) of 41 C...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29348327/genome-instability-as-a-consequence-of-defects-in-the-resolution-of-recombination-intermediates
#2
Stephen C West, Ying Wai Chan
The efficient processing of homologous recombination (HR) intermediates, which often contain four-way structures known as Holliday junctions (HJs), is required for proper chromosome segregation at mitosis. Eukaryotic cells possess three distinct pathways of resolution: (i) HJ dissolution mediated by BLM-topoisomerase IIIα-RMI1-RMI2 (BTR) complex, and HJ resolution catalyzed by either (ii) SLX1-SLX4-MUS81-EME1-XPF-ERCC1 (SMX complex) or (iii) GEN1. The BTR pathway acts at all times throughout the cell cycle, whereas the actions of SMX and GEN1 are restrained in S phase and become elevated late in the cell cycle to ensure the resolution of persistent recombination intermediates before mitotic division...
January 18, 2018: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/29247687/genotypic-variations-between-wild-type-and-small-colony-variants-of-staphylococcus-aureus-in-prosthetic-valve-infectious-endocarditis-a-comparative-genomic-and-transcriptomic-analysis
#3
Hongbin Chen, Qi Wang, Yuyao Yin, Shuguang Li, Deng-Ke Niu, Hui Wang
Staphylococcus aureus small colony variants (SCVs) can cause persistent infections. However, the genomes and transcriptomes of S. aureus SCVs remain poorly understood. We isolated a pair of isogenic wild-type and SCV methicillin-resistant S. aureus (MRSA) strains (IE1 and IE2, respectively) from a patient with prosthetic valve infectious endocarditis. The SCV IE2 strain grew more slowly than the wild-type strain, and serum killing and mouse lethality assays revealed that the virulence of the SCV strain IE2 was decreased...
December 13, 2017: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/29247012/loss-of-drosophila-mei-41-atr-alters-meiotic-crossover-patterning
#4
Morgan M Brady, Susan McMahan, Jeff Sekelsky
Meiotic crossovers must be properly patterned to ensure accurate disjunction of homologous chromosomes during meiosis I. Disruption of the spatial distribution of crossovers can lead to nondisjunction, aneuploidy, gamete dysfunction, miscarriage, or birth defects. One of the earliest identified genes involved in proper crossover patterning is Drosophilamei-41, which encodes the ortholog of the checkpoint kinase ATR. Analysis of hypomorphic mutants suggested the existence of crossover patterning defects, but it was not possible to assess this in null mutants because of maternal-effect embryonic lethality...
December 15, 2017: Genetics
https://www.readbyqxmd.com/read/29129742/the-sequence-preference-of-dna-cleavage-by-t4-endonuclease-vii
#5
Megan E Hardie, Vincent Murray
The enzyme T4 endonuclease VII is a resolvase that acts on branched DNA intermediates during genetic recombination, by cleaving DNA with staggered cuts approximately 3-6 bp apart. In this paper, we investigated the sequence preference of this cleavage reaction utilising two different DNA sequences. For the first time, the DNA sequence preference of T4 endonuclease VII cleavage sites has been examined without the presence of a known DNA substrate to mask any inherent nucleotide preference. The use of the ABI3730 platform enables the cleavage site to be determined at nucleotide resolution...
November 9, 2017: Biochimie
https://www.readbyqxmd.com/read/29038281/putative-integrative-mobile-elements-that-exploit-the-xer-recombination-machinery-carrying-blaimi-type-carbapenemase-genes-in-the-enterobacter-cloacae-complex-in-singapore
#6
Tse H Koh, Nurdyana Binte Abdul Rahman, Jeanette W P Teo, My-Van La, Balamurugan Periaswamy, Swaine L Chen
Whole genome sequencing was performed on 16 isolates of carbapenemase-producing Enterobacter cloacae complex to determine the flanking regions of blaIMI-type genes. Phylogenetic analysis of MLST targets separated the isolates into 4 clusters. The blaIMI-type genes were all found on IMEX elements. The IMEX elements of 5 isolates were similar to those described in Canada, while the remainder were novel. Five isolates had IMEX elements lacking a resolvase and recombinase.
October 16, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29018417/molecular-mechanisms-that-contribute-to-horizontal-transfer-of-plasmids-by-the-bacteriophage-spp1
#7
Ana Valero-Rello, María López-Sanz, Alvaro Quevedo-Olmos, Alexei Sorokin, Silvia Ayora
Natural transformation and viral-mediated transduction are the main avenues of horizontal gene transfer in Firmicutes. Bacillus subtilis SPP1 is a generalized transducing bacteriophage. Using this lytic phage as a model, we have analyzed how viral replication and recombination systems contribute to the transfer of plasmid-borne antibiotic resistances. Phage SPP1 DNA replication relies on essential phage-encoded replisome organizer (G38P), helicase loader (G39P), hexameric replicative helicase (G40P), recombinase (G35P) and in less extent on the partially dispensable 5'→3' exonuclease (G34...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28961460/bacillus-subtilis-disa-helps-to-circumvent-replicative-stress-during-spore-revival
#8
Marina Raguse, Rubén Torres, Elena M Seco, Carolina Gándara, Silvia Ayora, Ralf Moeller, Juan C Alonso
The mechanisms that allow to circumvent replicative stress, and to resume DNA synthesis are poorly understood in Bacillus subtilis. To study the role of the diadenylate cyclase DisA and branch migration translocase (BMT) RadA/Sms in restarting a stalled replication fork, we nicked and broke the circular chromosome of an inert mature haploid spore, damaged the bases, and measured survival of reviving spores. During undisturbed ripening, nicks and breaks should be repaired by pathways that do not invoke long-range end resection or genetic exchange by homologous recombination, after which DNA replication might be initiated...
September 22, 2017: DNA Repair
https://www.readbyqxmd.com/read/28934297/molecular-and-biological-characterization-of-%C3%AF-rs551-a-filamentous-bacteriophage-isolated-from-a-race-3-biovar-2-strain-of-ralstonia-solanacearum
#9
Abdelmonim Ali Ahmad, Michael J Stulberg, John Patrick Mershon, Dimitre S Mollov, Qi Huang
A filamentous bacteriophage, designated ϕRs551, was isolated and purified from the quarantine and select agent phytopathogen Ralstonia solanacearum race 3 biovar 2 strain UW551 (phylotype IIB sequevar 1) grown under normal culture conditions. Electron microscopy suggested that ϕRs551 is a member of the family Inoviridae, and is about 1200 nm long and 7 nm wide. ϕRs551 has a genome of 7929 nucleotides containing 14 open reading frames, and is the first isolated virion that contains a resolvase (ORF13) and putative type-2 phage repressor (ORF14)...
2017: PloS One
https://www.readbyqxmd.com/read/28922417/lingering-single-strand-breaks-trigger-rad51-independent-homology-directed-repair-of-collapsed-replication-forks-in-the-polynucleotide-kinase-phosphatase-mutant-of-fission-yeast
#10
Arancha Sanchez, Mariana C Gadaleta, Oliver Limbo, Paul Russell
The DNA repair enzyme polynucleotide kinase/phosphatase (PNKP) protects genome integrity by restoring ligatable 5'-phosphate and 3'-hydroxyl termini at single-strand breaks (SSBs). In humans, PNKP mutations underlie the neurological disease known as MCSZ, but these individuals are not predisposed for cancer, implying effective alternative repair pathways in dividing cells. Homology-directed repair (HDR) of collapsed replication forks was proposed to repair SSBs in PNKP-deficient cells, but the critical HDR protein Rad51 is not required in PNKP-null (pnk1Δ) cells of Schizosaccharomyces pombe...
September 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28805810/trf2-binds-branched-dna-to-safeguard-telomere-integrity
#11
Isabelle Schmutz, Leonid Timashev, Wei Xie, Dinshaw J Patel, Titia de Lange
Although t-loops protect telomeres, they are at risk of cleavage by Holliday junction (HJ) resolvases if branch migration converts the three-way t-loop junction into four-way HJs. T-loop cleavage is repressed by the TRF2 basic domain, which binds three- and four-way junctions and protects HJs in vitro. By replacing the basic domain with bacterial-protein domains binding three- and four-way junctions, we demonstrated the in vivo relevance of branched-DNA binding. Branched-DNA binding also repressed PARP1, presumably by masking the PARP1 site in the t-loop junction...
September 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28532385/erratum-to-the-holliday-junction-resolvase-recu-is-required-for-chromosome-segregation-and-dna-damage-repair-in-staphylococcus-aureus
#12
Ana R Pereira, Patricia Reed, Helena Veiga, Mariana G Pinho
No abstract text is available yet for this article.
May 22, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28511132/activity-and-in-vivo-dynamics-of-bacillus-subtilis-disa-are-affected-by-rada-sms-and-by-holliday-junction-processing-proteins
#13
Carolina Gándara, Daniella K C de Lucena, Rubén Torres, Ester Serrano, Stephan Altenburger, Peter L Graumann, Juan C Alonso
Bacillus subtilis c-di-AMP synthase DisA and RecA-related RadA/Sms are involved in the repair of DNA damage in exponentially growing cells. We provide genetic evidence that DisA or RadA/Sms is epistatic to the branch migration translocase (BMT) RecG and the Holliday junction (HJ) resolvase RecU in response to DNA damage. We provide genetic evidence damage. Functional DisA-YFP formed dynamic foci in exponentially growing cells, which moved through the nucleoids at a speed compatible with a DNA-scanning mode...
July 2017: DNA Repair
https://www.readbyqxmd.com/read/28495749/holliday-junction-resolvases-mediate-chloroplast-nucleoid-segregation
#14
Yusuke Kobayashi, Osami Misumi, Masaki Odahara, Kota Ishibashi, Masafumi Hirono, Kumi Hidaka, Masayuki Endo, Hiroshi Sugiyama, Hiroshi Iwasaki, Tsuneyoshi Kuroiwa, Toshiharu Shikanai, Yoshiki Nishimura
Holliday junctions, four-stranded DNA structures formed during homologous recombination, are disentangled by resolvases that have been found in prokaryotes and eukaryotes but not in plant organelles. Here, we identify monokaryotic chloroplast 1 (MOC1) as a Holliday junction resolvase in chloroplasts by analyzing a green alga Chlamydomonas reinhardtii mutant defective in chloroplast nucleoid (DNA-protein complex) segregation. MOC1 is structurally similar to a bacterial Holliday junction resolvase, resistance to ultraviolet (Ruv) C, and genetically conserved among green plants...
May 12, 2017: Science
https://www.readbyqxmd.com/read/28453523/the-mismatch-repair-and-meiotic-recombination-endonuclease-mlh1-mlh3-is-activated-by-polymer-formation-and-can-cleave-dna-substrates-in-trans
#15
COMPARATIVE STUDY
Carol M Manhart, Xiaodan Ni, Martin A White, Joaquin Ortega, Jennifer A Surtees, Eric Alani
Crossing over between homologs is initiated in meiotic prophase by the formation of DNA double-strand breaks that occur throughout the genome. In the major interference-responsive crossover pathway in baker's yeast, these breaks are resected to form 3' single-strand tails that participate in a homology search, ultimately forming double Holliday junctions (dHJs) that primarily include both homologs. These dHJs are resolved by endonuclease activity to form exclusively crossovers, which are critical for proper homolog segregation in Meiosis I...
April 2017: PLoS Biology
https://www.readbyqxmd.com/read/28393832/structural-insights-into-pot1-tpp1-interaction-and-pot1-c-terminal-mutations-in-human-cancer
#16
Cong Chen, Peili Gu, Jian Wu, Xianyun Chen, Shuangshuang Niu, Hong Sun, Lijie Wu, Na Li, Junhui Peng, Shaohua Shi, Cuiying Fan, Min Huang, Catherine C L Wong, Qingguo Gong, Chandan Kumar-Sinha, Rongguang Zhang, Lajos Pusztai, Rekha Rai, Sandy Chang, Ming Lei
Mammalian shelterin proteins POT1 and TPP1 form a stable heterodimer that protects chromosome ends and regulates telomerase-mediated telomere extension. However, how POT1 interacts with TPP1 remains unknown. Here we present the crystal structure of the C-terminal portion of human POT1 (POT1C) complexed with the POT1-binding motif of TPP1. The structure shows that POT1C contains two domains, a third OB fold and a Holliday junction resolvase-like domain. Both domains are essential for binding to TPP1. Notably, unlike the heart-shaped structure of ciliated protozoan Oxytricha nova TEBPα-β complex, POT1-TPP1 adopts an elongated V-shaped conformation...
April 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28393830/structural-and-functional-analysis-of-the-human-pot1-tpp1-telomeric-complex
#17
Cory Rice, Prashanth Krishna Shastrula, Andrew V Kossenkov, Robert Hills, Duncan M Baird, Louise C Showe, Tzanko Doukov, Susan Janicki, Emmanuel Skordalakes
POT1 and TPP1 are part of the shelterin complex and are essential for telomere length regulation and maintenance. Naturally occurring mutations of the telomeric POT1-TPP1 complex are implicated in familial glioma, melanoma and chronic lymphocytic leukaemia. Here we report the atomic structure of the interacting portion of the human telomeric POT1-TPP1 complex and suggest how several of these mutations contribute to malignant cancer. The POT1 C-terminus (POT1C) forms a bilobal structure consisting of an OB-fold and a holiday junction resolvase domain...
April 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28362374/a-g-quadruplex-dna-affinity-approach-for-purification-of-enzymatically-active-g4-resolvase1
#18
Eric D Routh, Steven D Creacy, Peter E Beerbower, Steven A Akman, James P Vaughn, Philip J Smaldino
Higher-order nucleic acid structures called G-quadruplexes (G4s, G4 structures) can form in guanine-rich regions of both DNA and RNA and are highly thermally stable. There are >375,000 putative G4-forming sequences in the human genome, and they are enriched in promoter regions, untranslated regions (UTRs), and within the telomeric repeat. Due to the potential for these structures to affect cellular processes, such as replication and transcription, the cell has evolved enzymes to manage them. One such enzyme is G4 Resolvase 1 (G4R1), which was biochemically co-characterized by our laboratory and Nagamine et al...
March 18, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28357386/a-new-role-for-holliday-junction-resolvase-yen1-in-processing-dna-replication-intermediates-exposes-dna2-as-an-accessory-replicative-helicase
#19
COMMENT
Benoît Falquet, Ulrich Rass
DNA replication is mediated by a multi-protein complex known as the replisome. With the hexameric MCM (minichromosome maintenance) replicative helicase at its core, the replisome splits the parental DNA strands, forming replication forks (RFs), where it catalyses coupled leading and lagging strand DNA synthesis. While replication is a highly effective process, intrinsic and oncogene-induced replication stress impedes the progression of replisomes along chromosomes. As a consequence, RFs stall, arrest, and collapse, jeopardizing genome stability...
January 2, 2017: Microbial Cell
https://www.readbyqxmd.com/read/28355180/dhx9-suppresses-rna-processing-defects-originating-from-the-alu-invasion-of-the-human-genome
#20
Tuğçe Aktaş, İbrahim Avşar Ilık, Daniel Maticzka, Vivek Bhardwaj, Cecilia Pessoa Rodrigues, Gerhard Mittler, Thomas Manke, Rolf Backofen, Asifa Akhtar
Transposable elements are viewed as 'selfish genetic elements', yet they contribute to gene regulation and genome evolution in diverse ways. More than half of the human genome consists of transposable elements. Alu elements belong to the short interspersed nuclear element (SINE) family of repetitive elements, and with over 1 million insertions they make up more than 10% of the human genome. Despite their abundance and the potential evolutionary advantages they confer, Alu elements can be mutagenic to the host as they can act as splice acceptors, inhibit translation of mRNAs and cause genomic instability...
April 6, 2017: Nature
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