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homologous dependent recombination

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https://www.readbyqxmd.com/read/29680900/a-novel-enzyme-of-type-vi-sulfide-quinone-oxidoreductases-in-purple-sulfur-photosynthetic-bacteria
#1
Ágnes Duzs, András Tóth, Brigitta Németh, Tímea Balogh, Péter B Kós, Gábor Rákhely
Sulfide detoxification can be catalyzed by ancient membrane-bound flavoproteins, sulfide:quinone oxidoreductases (Sqr), which have important roles in sulfide homeostasis and sulfide-dependent energy conservation processes by transferring electrons from sulfide to respiratory or photosynthetic membrane electron flow. Sqr enzymes have been categorized into six groups. Several members of the groups I, II, III, and V are well-known, but type IV and VI Sqrs are, as yet, uncharacterized or hardly characterized at all...
April 21, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29675001/-leishmania-infantum-lipophosphoglycan-deficient-mutants-a-tool-to-study-host-cell-parasite-interplay
#2
Milena Lázaro-Souza, Christine Matte, Jonilson B Lima, Guillermo Arango Duque, Graziele Quintela-Carvalho, Áislan de Carvalho Vivarini, Sara Moura-Pontes, Cláudio P Figueira, Flávio H Jesus-Santos, Ulisses Gazos Lopes, Leonardo P Farias, Théo Araújo-Santos, Albert Descoteaux, Valéria M Borges
Lipophosphoglycan (LPG) is the major surface glycoconjugate of metacyclic Leishmania promastigotes and is associated with virulence in various species of this parasite. Here, we generated a LPG-deficient mutant of Leishmania infantum , the foremost etiologic agent of visceral leishmaniasis in Brazil. The L. infantum LPG-deficient mutant (Δ lpg1 ) was obtained by homologous recombination and complemented via episomal expression of LPG1 (Δ lpg1 + LPG1 ). Deletion of LPG1 had no observable effect on parasite morphology or on the presence of subcellular organelles, such as lipid droplets...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29669960/a-highly-efficient-targeted-recombination-system-for-engineering-linear-chromosomes-of-industrial-bacteria-streptomyces
#3
Hung-Yin Pan, Carton W Chen, Chih-Hung Huang
Soil bacteria Streptomyces are the most important producers of secondary metabolites, including most known antibiotics. These bacteria and their close relatives are unique in possessing linear chromosomes, which typically harbor 20 to 30 biosynthetic gene clusters of tens to hundreds of kb in length. Many Streptomyces chromosomes are accompanied by linear plasmids with sizes ranging from several to several hundred kb. The large linear plasmids also often contain biosynthetic gene clusters. We have developed a targeted recombination procedure for arm exchanges between a linear plasmid and a linear chromosome...
April 17, 2018: Journal of General and Applied Microbiology
https://www.readbyqxmd.com/read/29667244/the-effects-of-atrad52-overexpression-on-homologous-recombination-in-arabidopsis
#4
Aviva Samach, Vyacheslav Gurevich, Naomi Avivi-Ragolsky, Avraham A Levy
AtRad52 homologs are involved in DNA recombination and repair but their precise functions in different homologous recombination pathways or in gene-targeting have not been analyzed. In order to facilitate our analyses, we generated an AtRad52-1A variant that had a stronger nuclear localization than the native gene thanks to the removal of the transit peptide for mitochondrial localization and to the addition of a nuclear localization signal. Overexpression of this variant increased homologous recombination in the nucleus, compared to the native AtRad52-1A: it increased Intra-Chromosomal Recombination and Synthesis-Dependent Strand-Annealing homologous recombination repair rates; but conversely, it repressed the Single-Strand Annealing pathway...
April 18, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29659985/grapevine-fatty-acid-hydroperoxide-lyase-generates-actin-disrupting-volatiles-and-promotes-defence-related-cell-death
#5
Sahar Akaberi, Hao Wang, Patricia Claudel, Michael Riemann, Bettina Hause, Philippe Hugueney, Peter Nick
Fatty acid hydroperoxides can generate short-chained volatile aldehydes that may participate in plant defence. A grapevine Hydroperoxide lyase (VvHPL1) clustering to the CYP74B class was functionally characterised with respect to a role in defence. In grapevine leaves, transcripts of this gene accumulated rapidly to high abundance in response to wounding. Cellular functions of VvHPL1 were investigated upon heterologous expression in tobacco BY-2 cells. A C-terminal GFP fusion of VvHPL1 was located in plastids...
April 5, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29659762/activation-of-%C3%AF-20-dependent-recombination-and-horizontal-gene-transfer-in-mycoplasma-genitalium
#6
Sergi Torres-Puig, Carlos Martínez-Torró, Ignasi Granero-Moya, Enrique Querol, Jaume Piñol, Oscar Q Pich
In the human pathogen Mycoplasma genitalium, homologous recombination is under the control of σ20, an alternative sigma factor that boosts the generation of genetic and antigenic diversity in the population. Under laboratory growth conditions, σ20 activation is rare and the factors governing its intermittent activity are unknown. Two σ20-regulated genes, rrlA and rrlB, showed to be important for recombination of homologous DNA sequences in this bacterium. Herein, we demonstrate that rrlA and rrlB code for two small proteins that participate in a feed-forward loop essential for σ20 function...
April 11, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29656238/terminal-deoxynucleotidyltransferase-the-story-of-an-untemplated-dna-polymerase-capable-of-dna-bridging-and-templated-synthesis-across-strands
#7
REVIEW
Jérôme Loc'h, Marc Delarue
Terminal deoxynucleotidyltransferase (TdT) is a member of the polX family which is involved in DNA repair. It has been known for years as an untemplated DNA polymerase used during V(D)J recombination to generate diversity at the CDR3 region of immunoglobulins and T-cell receptors. Recently, however, TdT was crystallized in the presence of a complete DNA synapsis made of two double-stranded DNA (dsDNA), each with a 3' protruding end, and overlapping with only one micro-homology base-pair, thus giving structural insight for the first time into DNA synthesis across strands...
April 12, 2018: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/29627866/replication-timing-of-large-sorex-granarius-soricidae-eulipotyphla-telomeres
#8
Julia M Minina, Tatjana V Karamysheva, Nicolaj B Rubtsov, Natalia S Zhdanova
Previously, we described the unique feature of telomeric regions in Iberian shrew Sorex granarius: its telomeres have two ranges of size, very small (3.8 kb of telomeric repeats on average) and very large discontinuous telomeres (213 kb) interrupted with 18S rDNA. In this study, we have demonstrated extraordinary replication pattern of S. granarius large telomeres that have not been shown before in other studied mammal. Using the ReD-FISH procedure, we observed prolonged, through S period, large telomere replication...
April 7, 2018: Protoplasma
https://www.readbyqxmd.com/read/29621557/crispr-cas9-an-efficient-tool-for-precise-plant-genome-editing
#9
REVIEW
Waqar Islam
Efficient plant genome editing is dependent upon induction of double stranded DNA breaks (DSBs) through site specified nucleases. These DSBs initiate the process of DNA repair which can either base upon homologous recombination (HR) or non-homologous end jointing (NHEJ). Recently, CRISPR-Cas9 mechanism got highlighted as revolutionizing genetic tool due to its simpler frame work along with the broad range of adaptability and applications. So, in this review, we have tried to sum up the application of this biotechnological tool in plant genome editing...
April 2, 2018: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/29619377/roles-of-nucks1-in-diseases-susceptibility-potential-biomarker-and-regulatory-mechanisms
#10
REVIEW
Pengru Huang, Yujie Cai, Bin Zhao, Lili Cui
Nuclear casein kinase and cyclin-dependent kinase substrate 1 (NUCKS1) is a 27 kD chromosomal, highly conserved, and vertebrate-specific protein. NUCKS1 gene encodes a nuclear protein and the conserved regions of NUCKS1 contain several consensus phosphorylation sites for casein kinase II (CK2) and cyclin-dependent kinases (Cdk) and a basic DNA-binding domain. NUCKS1 is similar to the high mobility group (HMG) family which dominates chromatin remodeling and regulates gene transcription. Meanwhile, NUCKS1 is a RAD51 associated protein 1 (RAD51AP1) paralog that is significant for homologous recombination (HR) and genome stability and also a transcriptional regulator of the insulin signaling components...
2018: BioMed Research International
https://www.readbyqxmd.com/read/29618374/transient-reduction-of-dna-methylation-at-the-onset-of-meiosis-in-male-mice
#11
Valeriya Gaysinskaya, Brendan F Miller, Chiara De Luca, Godfried W van der Heijden, Kasper D Hansen, Alex Bortvin
BACKGROUND: Meiosis is a specialized germ cell cycle that generates haploid gametes. In the initial stage of meiosis, meiotic prophase I (MPI), homologous chromosomes pair and recombine. Extensive changes in chromatin in MPI raise an important question concerning the contribution of epigenetic mechanisms such as DNA methylation to meiosis. Interestingly, previous studies concluded that in male mice, genome-wide DNA methylation patters are set in place prior to meiosis and remain constant subsequently...
April 4, 2018: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29595473/topoisomerase-vi-senses-and-exploits-both-dna-crossings-and-bends-to-facilitate-strand-passage
#12
Timothy J Wendorff, James M Berger
Type II topoisomerases manage DNA supercoiling and aid chromosome segregation using a complex, ATP-dependent duplex strand passage mechanism. Type IIB topoisomerases and their homologs support both archaeal/plant viability and meiotic recombination. Topo VI, a prototypical type IIB topoisomerase, comprises two Top6A and two Top6B protomers; how these subunits cooperate to engage two DNA segments and link ATP turnover to DNA transport is poorly understood. Using multiple biochemical approaches, we show that Top6B, which harbors the ATPase activity of topo VI, recognizes and exploits the DNA crossings present in supercoiled DNA to stimulate subunit dimerization by ATP...
March 29, 2018: ELife
https://www.readbyqxmd.com/read/29592899/synthetic-lethality-of-parp-inhibition-and-ionizing-radiation-is-p53-dependent
#13
Steven T Sizemore, Rahman Mohammed, Gina M Sizemore, Somaira Nowsheen, Hao Yu, Michael C Ostrowski, Arnab Chakravarti, Fen Xia
PARP inhibitors (PARPi) are potentially effective therapeutic agents capable of inducing synthetic lethality in tumors with deficiencies in homologous recombination (HR)-mediated DNA repair such as those carrying BRCA1 mutations. However, BRCA mutations are rare, the majority of tumors are proficient in HR repair, and thus most tumors are resistant to PARPi. Previously, we observed that ionizing radiation (IR) initiates cytoplasmic translocation of BRCA1 leading to suppression of HR-mediated DNA repair and induction of synthetic PARPi lethality in wild-type BRCA1 and HR-proficient tumor cells...
March 28, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29590434/an-e2f7-dependent-transcriptional-program-modulates-dna-damage-repair-and-genomic-stability
#14
Jone Mitxelena, Aintzane Apraiz, Jon Vallejo-Rodríguez, Iraia García-Santisteban, Asier Fullaondo, Mónica Alvarez-Fernández, Marcos Malumbres, Ana M Zubiaga
The cellular response to DNA damage is essential for maintaining the integrity of the genome. Recent evidence has identified E2F7 as a key player in DNA damage-dependent transcriptional regulation of cell-cycle genes. However, the contribution of E2F7 to cellular responses upon genotoxic damage is still poorly defined. Here we show that E2F7 represses the expression of genes involved in the maintenance of genomic stability, both throughout the cell cycle and upon induction of DNA lesions that interfere with replication fork progression...
March 24, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29590107/novel-function-of-hats-and-hdacs-in-homologous-recombination-through-acetylation-of-human-rad52-at-double-strand-break-sites
#15
Takeshi Yasuda, Wataru Kagawa, Tomoo Ogi, Takamitsu A Kato, Takehiro Suzuki, Naoshi Dohmae, Kazuya Takizawa, Yuka Nakazawa, Matthew D Genet, Mika Saotome, Michio Hama, Teruaki Konishi, Nakako Izumi Nakajima, Masaharu Hazawa, Masanori Tomita, Manabu Koike, Katsuko Noshiro, Kenichi Tomiyama, Chizuka Obara, Takaya Gotoh, Ayako Ui, Akira Fujimori, Fumiaki Nakayama, Fumio Hanaoka, Kaoru Sugasawa, Ryuichi Okayasu, Penny A Jeggo, Katsushi Tajima
The p300 and CBP histone acetyltransferases are recruited to DNA double-strand break (DSB) sites where they induce histone acetylation, thereby influencing the chromatin structure and DNA repair process. Whether p300/CBP at DSB sites also acetylate non-histone proteins, and how their acetylation affects DSB repair, remain unknown. Here we show that p300/CBP acetylate RAD52, a human homologous recombination (HR) DNA repair protein, at DSB sites. Using in vitro acetylated RAD52, we identified 13 potential acetylation sites in RAD52 by a mass spectrometry analysis...
March 28, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29582426/prevalence-of-brca1-2-large-genomic-rearrangements-in-chinese-women-with-sporadic-triple-negative-or-familial-breast-cancer
#16
L Su, J Zhang, H Meng, T Ouyang, J Li, T Wang, Z Fan, T Fan, B Lin, Y Xie
The prevalence of BRCA1/2 large genomic rearrangements (LGRs) and their underlying mechanisms have not been fully evaluated in Chinese women with breast cancer. In this study, we determined the prevalence of BRCA1/2 LGRs in 834 patients with familial breast cancer and 660 patients with sporadic triple-negative breast cancer who were negative for BRCA1/2 small-range mutations using the multiplex ligation-dependent probe amplification method. We found that twenty index patients (2.4%) in the familial breast cancer group carried a BRCA1 or BRCA2 LGR, and the frequencies of BRCA1 and BRCA2 LGRs were 1...
March 27, 2018: Clinical Genetics
https://www.readbyqxmd.com/read/29580618/transcriptional-control-of-the-phenol-hydroxylase-gene-phe-of-corynebacterium-glutamicum-by-the-arac-type-regulator-pher
#17
Can Chen, Yaoling Zhang, Lei Xu, Kaixiang Zhu, Yanyan Feng, Junfeng Pan, Meiru Si, Lei Zhang, Xihui Shen
Corynebacterium glutamicum can degrade phenol by a meta-cleavage pathway, which depends on ncgl2588 (phe) of the phe operon encoding phenol hydroxylase. An additional gene, ncgl2587 (pheR), is located upstream of phe. The pheR encodes an AraC/XylR-type regulator protein with 377 amino acid residues and is transcribed in the same direction as phe. Disruption of pheR by homologous recombination resulted in the accumulation of phenol in C. glutamicum. PheR demonstrates a low type of constitutive expression where phenol induces phe expression...
April 2018: Microbiological Research
https://www.readbyqxmd.com/read/29573495/efficient-in-planta-gene-targeting-in-arabidopsis-using-egg-cell-specific-expression-of-the-cas9-nuclease-of-s-aureus
#18
Felix Wolter, Jeanette Klemm, Holger Puchta
Gene targeting (GT), the programmed change of genomic sequences by homologous recombination (HR), is still a major challenge in plants. We previously developed an in planta GT strategy by simultaneously releasing from the genome a dsDNA donor molecule and creating a DSB at a specific site within the targeted gene. Using Cas9 form S. pyogenes (SpCas9) under the control of a ubiquitin gene promoter, we obtained seeds harbouring GT events, although at a low frequency. In the present research we tested different developmentally controlled promotors and different kinds of DNA lesions for their ability to enhance GT of the acetolactate synthase (ALS) gene of Arabidopsis...
March 24, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29564828/genes-proteins-and-biological-pathways-preventing-chromothripsis
#19
Martin Poot
The highly complex structural genome variations chromothripsis, chromoanasynthesis, and chromoplexy are subsumed under the term chromoanagenesis, which means chromosome rebirth. Precipitated by numerous DNA double-strand breaks, they differ in number of and distances between breakpoints, associated copy number variations, order and orientation of segments, and flanking sequences at joining points. Results from patients with the autosomal dominant cancer susceptibility disorder Li-Fraumeni syndrome implicated somatic TP53 mutations in chromothripsis...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29556040/ctip-fusion-to-cas9-enhances-transgene-integration-by-homology-dependent-repair
#20
M Charpentier, A H Y Khedher, S Menoret, A Brion, K Lamribet, E Dardillac, C Boix, L Perrouault, L Tesson, S Geny, A De Cian, J M Itier, I Anegon, B Lopez, C Giovannangeli, J P Concordet
In genome editing with CRISPR-Cas9, transgene integration often remains challenging. Here, we present an approach for increasing the efficiency of transgene integration by homology-dependent repair (HDR). CtIP, a key protein in early steps of homologous recombination, is fused to Cas9 and stimulates transgene integration by HDR at the human AAVS1 safe harbor locus. A minimal N-terminal fragment of CtIP, designated HE for HDR enhancer, is sufficient to stimulate HDR and this depends on CDK phosphorylation sites and the multimerization domain essential for CtIP activity in homologous recombination...
March 19, 2018: Nature Communications
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