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Holliday junction

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https://www.readbyqxmd.com/read/29348327/genome-instability-as-a-consequence-of-defects-in-the-resolution-of-recombination-intermediates
#1
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/29295984/rad54-n-terminal-domain-is-a-dna-sensor-that-couples-atp-hydrolysis-with-branch-migration-of-holliday-junctions
#2
Nadish Goyal, Matthew J Rossi, Olga M Mazina, Yong Chi, Robert L Moritz, Bruce E Clurman, Alexander V Mazin
In eukaryotes, RAD54 catalyzes branch migration (BM) of Holliday junctions, a basic process during DNA repair, replication, and recombination. RAD54 also stimulates RAD51 recombinase and has other activities. Here, we investigate the structural determinants for different RAD54 activities. We find that the RAD54 N-terminal domain (NTD) is responsible for initiation of BM through two coupled, but distinct steps; specific binding to Holliday junctions and RAD54 oligomerization. Furthermore, we find that the RAD54 oligomeric state can be controlled by NTD phosphorylation at S49, a CDK2 consensus site, which inhibits RAD54 oligomerization and, consequently, BM...
January 2, 2018: Nature Communications
https://www.readbyqxmd.com/read/29290614/topoisomerase-3%C3%AE-is-required-for-decatenation-and-segregation-of-human-mtdna
#3
Thomas J Nicholls, Cristina A Nadalutti, Elisa Motori, Ewen W Sommerville, Gráinne S Gorman, Swaraj Basu, Emily Hoberg, Doug M Turnbull, Patrick F Chinnery, Nils-Göran Larsson, Erik Larsson, Maria Falkenberg, Robert W Taylor, Jack D Griffith, Claes M Gustafsson
How mtDNA replication is terminated and the newly formed genomes are separated remain unknown. We here demonstrate that the mitochondrial isoform of topoisomerase 3α (Top3α) fulfills this function, acting independently of its nuclear role as a component of the Holliday junction-resolving BLM-Top3α-RMI1-RMI2 (BTR) complex. Our data indicate that mtDNA replication termination occurs via a hemicatenane formed at the origin of H-strand replication and that Top3α is essential for resolving this structure. Decatenation is a prerequisite for separation of the segregating unit of mtDNA, the nucleoid, within the mitochondrial network...
December 14, 2017: Molecular Cell
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
#4
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/29177740/synthesis-of-hemicatenanes-for-the-study-of-type-ia-topoisomerases
#5
Shun-Hsiao Lee, Tao-Shih Hsieh, Grace Ee-Lu Siaw
Hemicatenane is a structure that forms when two DNA duplexes are physically linked through a single-stranded crossover. It is proposed to be an intermediate resulting from double Holliday junction (dHJ) dissolution, repair of replication stalled forks and late stage replication. Our previous study has shown that hemicatenane can be synthesized and dissolved in vitro by hyperthermophilic type IA topoisomerases. Here we present the protocol of hemicatenane synthesis and its structure detection by 2D agarose gel electrophoresis...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29091094/dna-nanotubes-assembled-from-tensegrity-triangle-tiles-with-circular-dna-scaffolds
#6
Noshin Afshan, Mashooq Ali, Meng Wang, Mirza Muhammad Faran Ashraf Baig, Shou-Jun Xiao
Using small circular DNA molecules of different lengths as scaffolds, we successfully synthesised DNA nanotubes consisting of Mao's DNA tensegrity triangle tiles with four-arm junctions (Holliday junctions) at all vertices. Due to the intrinsic curvature of the triangle tile and the consecutive tile alignment, the 2D arrays are organised in the form of nanotubes. Two sized triangle tiles with equilateral side lengths of 1.5 and 2.5 full helical turns are connected by the sticky ended cohesion of a duplex with a length of 2...
November 16, 2017: Nanoscale
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/28922417/lingering-single-strand-breaks-trigger-rad51-independent-homology-directed-repair-of-collapsed-replication-forks-in-the-polynucleotide-kinase-phosphatase-mutant-of-fission-yeast
#9
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/28918480/sgs1-helicase-is-required-for-efficient-pcna-monoubiquitination-and-translesion-dna-synthesis-in-saccharomyces-cerevisiae
#10
Fangfang Li, Lindsay G Ball, Li Fan, Michelle Hanna, Wei Xiao
DNA-damage tolerance (DDT) is employed by eukaryotes to deal with replication blocks on the template strand, and is divided into two parallel pathways that are activated by sequential ubiquitination of proliferating cell nuclear antigen (PCNA) at the Lys164 residue. Rad6-Rad18-mediated PCNA monoubiquitination promotes translesion DNA synthesis (TLS) and the monoubiquitinated PCNA can be further polyubiquitinated by an Mms2-Ubc13-Rad5 complex, leading to error-free lesion bypass. We previously reported that the DNA helicase Sgs1 is required for error-free lesion bypass, probably through the double-Holliday junction migration and subsequent resolution...
September 16, 2017: Current Genetics
https://www.readbyqxmd.com/read/28911104/synthesis-and-incorporation-of-13c-labeled-dna-building-blocks-to-probe-structural-dynamics-of-dna-by-nmr
#11
Felix Nußbaumer, Michael Andreas Juen, Catherina Gasser, Johannes Kremser, Thomas Müller, Martin Tollinger, Christoph Kreutz
We report the synthesis of atom-specifically 13C-modified building blocks that can be incorporated into DNA via solid phase synthesis to facilitate investigations on structural and dynamic features via NMR spectroscopy. In detail, 6-13C-modified pyrimidine and 8-13C purine DNA phosphoramidites were synthesized and incorporated into a polypurine tract DNA/RNA hybrid duplex to showcase the facile resonance assignment using site-specific labeling. We also addressed micro- to millisecond dynamics in the mini-cTAR DNA...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28842529/structure-of-the-holliday-junction-applications-beyond-recombination
#12
REVIEW
P Shing Ho
The Holliday junction (HJ) is an essential element in recombination and related mechanisms. The structure of this four-stranded DNA assembly, which is now well-defined alone and in complex with proteins, has led to its applications in areas well outside of molecular recombination, including nanotechnology and biophysics. This minireview explores some interesting recent research on the HJ, as it has been adapted to design regular two- or three-dimensional lattices for crystal engineering, and more complex systems through DNA origami...
October 15, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28834211/archaeal-muts5-tightly-binds-to-holliday-junction-similarly-to-eukaryotic-muts%C3%AE
#13
Koki Ohshita, Kenji Fukui, Mizuki Sato, Takashi Morisawa, Yuichi Hakumai, Yuki Morono, Fumio Inagaki, Takato Yano, Makoto Ashiuchi, Taisuke Wakamatsu
Archaeal DNA recombination mechanism and the related proteins are similar to those in eukaryotes. However, no functional homolog of eukaryotic MutSγ, which recognizes Holliday junction to promote homologous recombination, has been identified in archaea. Hence, the whole molecular mechanism of archaeal homologous recombination has not yet been revealed. In this study, to identify the archaeal functional homolog of MutSγ, we focused on a functionally uncharacterized MutS homolog, MutS5, from a hyperthermophilic archaeon Pyrococcus horikoshii (phMutS5)...
October 2017: FEBS Journal
https://www.readbyqxmd.com/read/28827832/mlh3-mutations-in-baker-s-yeast-alter-meiotic-recombination-outcomes-by-increasing-noncrossover-events-genome-wide
#14
Najla Al-Sweel, Vandana Raghavan, Abhishek Dutta, V P Ajith, Luigi Di Vietro, Nabila Khondakar, Carol M Manhart, Jennifer A Surtees, K T Nishant, Eric Alani
Mlh1-Mlh3 is an endonuclease hypothesized to act in meiosis to resolve double Holliday junctions into crossovers. It also plays a minor role in eukaryotic DNA mismatch repair (MMR). To understand how Mlh1-Mlh3 functions in both meiosis and MMR, we analyzed in baker's yeast 60 new mlh3 alleles. Five alleles specifically disrupted MMR, whereas one (mlh3-32) specifically disrupted meiotic crossing over. Mlh1-mlh3 representatives for each class were purified and characterized. Both Mlh1-mlh3-32 (MMR+, crossover-) and Mlh1-mlh3-45 (MMR-, crossover+) displayed wild-type endonuclease activities in vitro...
August 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28819432/silencing-of-hjurp-induces-dysregulation-of-cell-cycle-and-ros-metabolism-in-bladder-cancer-cells-via-ppar%C3%AE-sirt1-feedback-loop
#15
Rui Cao, Gang Wang, Kaiyu Qian, Liang Chen, Guofeng Qian, Conghua Xie, Han C Dan, Wei Jiang, Min Wu, Chin-Lee Wu, Yu Xiao, Xinghuan Wang
Holliday Junction Recognition Protein (HJURP) is a centromeric histone chaperone involving in de novo histone H3 variant CenH3 (CENP-A) recruitment. Our transcriptome and in vivo study revealed that HJURP is significantly upregulated in bladder cancer (BCa) tissues at both mRNA and protein levels. Knockdown of HJURP inhibited proliferation and viability of BCa cell lines revealed by CCK-8, colony formation and Ki-67-staining assays, and induced apoptosis and reactive oxygen species (ROS) production, as well as triggered cell cycle arrest at G0/G1 phase possibly via loss of CENP-A...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28805810/trf2-binds-branched-dna-to-safeguard-telomere-integrity
#16
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/28731332/tuning-the-cavity-size-and-chirality-of-self-assembling-3d-dna-crystals
#17
Chad R Simmons, Fei Zhang, Tara MacCulloch, Noureddine Fahmi, Nicholas Stephanopoulos, Yan Liu, Nadrian C Seeman, Hao Yan
The foundational goal of structural DNA nanotechnology-the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems-was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold...
August 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28645372/analysis-of-structure-selective-endonuclease-activities-from-yeast-and-human-extracts
#18
Joao Matos, Stephen C West
The efficient separation of two equal DNA masses to the daughter cells is an essential step in mitosis. This process is dependent upon the removal of any remaining recombination or replication intermediates that link sister chromatids, and a failure to resolve these intermediates leads to genome instability. Similarly, a failure to resolve meiotic recombination intermediates that link homologous chromosomes can cause chromosome nondisjunction and aneuploidy. Cleavage of these potentially toxic replication/recombination intermediates requires the Mus81 endonuclease, which is active upon flaps, forks, and more complex secondary structures in DNA such as Holliday junctions...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28642366/saccharomyces-cerevisiae-red1-protein-exhibits-nonhomologous-dna-end-joining-activity-and-potentiates-hop1-promoted-pairing-of-double-stranded-dna
#19
COMPARATIVE STUDY
Rucha Kshirsagar, Indrajeet Ghodke, K Muniyappa
Elucidation of the function of synaptonemal complex (SC) in Saccharomyces cerevisiae has mainly focused on in vivo analysis of recombination-defective meiotic mutants. Consequently, significant gaps remain in the mechanistic understanding of the activities of various SC proteins and the functional relationships among them. S. cerevisiae Hop1 and Red1 are essential structural components of the SC axial/lateral elements. Previous studies have demonstrated that Hop1 is a structure-selective DNA-binding protein exhibiting high affinity for the Holliday junction and promoting DNA bridging, condensation, and pairing between double-stranded DNA molecules...
August 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28640495/control-of-mus81-nuclease-during-the-cell-cycle
#20
REVIEW
Boris Pfander, Joao Matos
DNA replication and homologous recombination involve the formation of branched DNA structures that physically link chromosomes. Such DNA-based connections, which arise during S-phase, are typically disengaged prior to entry into mitosis, in order to ensure proper chromosome segregation. Exceptions can, however, occur: replication stress, or elevated levels of DNA damage, may cause cells to enter mitosis with unfinished replication as well as carrying recombination intermediates, such as Holliday junctions. Hence, cells are equipped with pathways that recognize and process branched DNA structures, and evolved mechanisms to enhance their function when on the verge of undergoing cell division...
July 2017: FEBS Letters
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