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RecA crispr

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https://www.readbyqxmd.com/read/30189098/crispr-cas-adaptation-in-escherichia-coli-requires-recbcd-helicase-but-not-nuclease-activity-is-independent-of-homologous-recombination-and-is-antagonized-by-5-ssdna-exonucleases
#1
Marin Radovcic, Tom Killelea, Ekaterina Savitskaya, Lukas Wettstein, Edward L Bolt, Ivana Ivancic-Bace
Prokaryotic adaptive immunity is established against mobile genetic elements (MGEs) by 'naïve adaptation' when DNA fragments from a newly encountered MGE are integrated into CRISPR-Cas systems. In Escherichia coli, DNA integration catalyzed by Cas1-Cas2 integrase is well understood in mechanistic and structural detail but much less is known about events prior to integration that generate DNA for capture by Cas1-Cas2. Naïve adaptation in E. coli is thought to depend on the DNA helicase-nuclease RecBCD for generating DNA fragments for capture by Cas1-Cas2...
September 5, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29595998/single-molecule-view-of-small-rna-guided-target-search-and-recognition
#2
Viktorija Globyte, Sung Hyun Kim, Chirlmin Joo
Most everyday processes in life involve a necessity for an entity to locate its target. On a cellular level, many proteins have to find their target to perform their function. From gene-expression regulation to DNA repair to host defense, numerous nucleic acid-interacting proteins use distinct target search mechanisms. Several proteins achieve that with the help of short RNA strands known as guides. This review focuses on single-molecule advances studying the target search and recognition mechanism of Argonaute and CRISPR (clustered regularly interspaced short palindromic repeats) systems...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29531845/expression-of-reca-and-cell-penetrating-peptide-cpp-fusion-protein-in-bacteria-and-in-mammalian-cells
#3
Xiubao Chang, Yuexian Hou
Genome editing is a powerful tool to modify a specific gene and to correct a disease-causing mutation. Recently developed new techniques, such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALEN) and clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9), significantly facilitate the progression in this field. However, mutations associated with the double strand DNA breaks (DSBs) introduced by these systems hampered their direct usage in clinic. In order to prevent the mutations caused by DSBs, we have designed a novel mean to induce homology-directed recombination (HDR) without DSBs, i...
2018: International Journal of Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28915012/managing-the-sos-response-for-enhanced-crispr-cas-based-recombineering-in-e-coli-through-transient-inhibition-of-host-reca-activity
#4
Eirik Adim Moreb, Benjamin Hoover, Adam Yaseen, Nisakorn Valyasevi, Zoe Roecker, Romel Menacho-Melgar, Michael D Lynch
Phage-derived "recombineering" methods are utilized for bacterial genome editing. Recombineering results in a heterogeneous population of modified and unmodified chromosomes, and therefore selection methods, such as CRISPR-Cas9, are required to select for edited clones. Cells can evade CRISPR-Cas-induced cell death through recA-mediated induction of the SOS response. The SOS response increases RecA dependent repair as well as mutation rates through induction of the umuDC error prone polymerase. As a result, CRISPR-Cas selection is more efficient in recA mutants...
December 15, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/27833912/sacb-sacr-gene-cassette-as-the-negative-selection-marker-to-suppress-agrobacterium-overgrowth-in-agrobacterium-mediated-plant-transformation
#5
Yiming Liu, Jiamin Miao, Sy Traore, Danyu Kong, Yi Liu, Xunzhong Zhang, Zachary L Nimchuk, Zongrang Liu, Bingyu Zhao
Agrobacterium overgrowth is a common problem in Agrobacterium-mediated plant transformation. To suppress the Agrobacterium overgrowth, various antibiotics have been used during plant tissue culture steps. The antibiotics are expensive and may adversely affect plant cell differentiation and reduce plant transformation efficiency. The SacB-SacR proteins are toxic to most Agrobacterium tumefaciens strains when they are grown on culture medium supplemented with sucrose. Therefore, SacB-SacR genes can be used as negative selection markers to suppress the overgrowth of A...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/25968642/clustered-regularly-interspaced-short-palindromic-repeat-dependent-biofilm-specific-death-of-pseudomonas-aeruginosa-mediated-by-increased-expression-of-phage-related-genes
#6
Gary E Heussler, Kyle C Cady, Katja Koeppen, Sabin Bhuju, Bruce A Stanton, George A O'Toole
UNLABELLED: The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (CRISPR/Cas) system is an adaptive immune system present in many archaea and bacteria. CRISPR/Cas systems are incredibly diverse, and there is increasing evidence of CRISPR/Cas systems playing a role in cellular functions distinct from phage immunity. Previously, our laboratory reported one such alternate function in which the type 1-F CRISPR/Cas system of the opportunistic pathogen Pseudomonas aeruginosa strain UCBPP-PA14 (abbreviated as P...
May 12, 2015: MBio
https://www.readbyqxmd.com/read/25368186/molecular-insights-into-dna-interference-by-crispr-associated-nuclease-helicase-cas3
#7
COMPARATIVE STUDY
Bei Gong, Minsang Shin, Jiali Sun, Che-Hun Jung, Edward L Bolt, John van der Oost, Jeong-Sun Kim
Mobile genetic elements in bacteria are neutralized by a system based on clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. Type I CRISPR-Cas systems use a "Cascade" ribonucleoprotein complex to guide RNA specifically to complementary sequence in invader double-stranded DNA (dsDNA), a process called "interference." After target recognition by Cascade, formation of an R-loop triggers recruitment of a Cas3 nuclease-helicase, completing the interference process by destroying the invader dsDNA...
November 18, 2014: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/24709747/prophage-induction-and-differential-reca-and-umudab-transcriptome-regulation-in-the-dna-damage-responses-of-acinetobacter-baumannii-and-acinetobacter-baylyi
#8
Janelle M Hare, Joshua C Ferrell, Travis A Witkowski, Alison N Grice
The SOS response to DNA damage that induces up to 10% of the prokaryotic genome requires RecA action to relieve LexA transcriptional repression. In Acinetobacter species, which lack LexA, the error-prone polymerase accessory UmuDAb is instead required for ddrR induction after DNA damage, suggesting it might be a LexA analog. RNA-Seq experiments defined the DNA damage transcriptome (mitomycin C-induced) of wild type, recA and umuDAb mutant strains of both A. baylyi ADP1 and A. baumannii ATCC 17978. Of the typical SOS response genes, few were differentially regulated in these species; many were repressed or absent...
2014: PloS One
https://www.readbyqxmd.com/read/24256232/electron-microscopy-studies-of-type-iii-crispr-machines-in-sulfolobus-solfataricus
#9
REVIEW
Giuseppe Cannone, Mariam Webber-Birungi, Laura Spagnolo
The CRISPR (clustered regularly interspaced short palindromic repeats) system is an adaptive immune system that targets viruses and other mobile genetic elements in bacteria and archaea. Cells store information of past infections in their genome in repeat-spacer arrays. After transcription, these arrays are processed into unit-length crRNA (CRISPR RNA) that is loaded into effector complexes encoded by Cas (CRISPR-associated) genes. CRISPR-Cas complexes target invading nucleic acid for degradation. CRISPR effector complexes have been classified into three main types (I-III)...
December 2013: Biochemical Society Transactions
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