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https://www.readbyqxmd.com/read/29348170/crispr-rna-and-anti-crispr-protein-binding-to-the-xanthomonas-albilineans-csy1-csy2-heterodimer-in-the-type-i-f-crispr-cas-system
#1
Suji Hong, Donghyun Ka, Seo Jeong Yoon, Nayoung Suh, Migyeong Jeong, Jeong-Yong Suh, Euiyoung Bae
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide microbial adaptive immunity against bacteriophages. In type I-F CRISPR-Cas systems, multiple Cas proteins (Csy1-4) comprise a surveillance complex (Csy complex) with CRISPR RNA (crRNA) for target recognition. Here, we report the biochemical characterization of the Csy1-Csy2 subcomplex from Xanthomonas albilineans, including the analysis of its interaction with crRNA and also AcrF2, an anti-CRISPR (Acr) protein from a phage that infects Pseudomonas aeruginosa The X...
January 18, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29346415/acute-multi-sgrna-knockdown-of-keops-complex-genes-reproduces-the-microcephaly-phenotype-of-the-stable-knockout-zebrafish-model
#2
Tilman Jobst-Schwan, Johanna Magdalena Schmidt, Ronen Schneider, Charlotte A Hoogstraten, Jeremy F P Ullmann, David Schapiro, Amar J Majmundar, Amy Kolb, Kaitlyn Eddy, Shirlee Shril, Daniela A Braun, Annapurna Poduri, Friedhelm Hildebrandt
Until recently, morpholino oligonucleotides have been widely employed in zebrafish as an acute and efficient loss-of-function assay. However, off-target effects and reproducibility issues when compared to stable knockout lines have compromised their further use. Here we employed an acute CRISPR/Cas approach using multiple single guide RNAs targeting simultaneously different positions in two exemplar genes (osgep or tprkb) to increase the likelihood of generating mutations on both alleles in the injected F0 generation and to achieve a similar effect as morpholinos but with the reproducibility of stable lines...
2018: PloS One
https://www.readbyqxmd.com/read/29345746/history-of-genome-editing-in-yeast
#3
Marcin G Fraczek, Samina Naseeb, Daniela Delneri
For thousands of years humans have used the budding yeast Saccharomyces cerevisiae for production of bread and alcohol, however only for the last 30-40 years our understanding of the yeast biology has dramatically increased enabling us to modify its genome. Although S. cerevisiae has been the main focus of many research groups, other non-conventional yeasts have also been studied and exploited for biotechnological purposes. Our experiments and knowledge have evolved from recombination, to high-throughput PCR based transformations, to highly accurate CRISPR methods, in order to alter yeast traits for either research of industrial purposes...
January 18, 2018: Yeast
https://www.readbyqxmd.com/read/29344267/break-breast-cancer-addiction-by-crispr-cas9-genome-editing
#4
REVIEW
Haitao Yang, MariaLynn Jaeger, Averi Walker, Daniel Wei, Katie Leiker, Tao Weitao
Breast cancer is the leading diagnosed cancer for women globally. Evolution of breast cancer in tumorigenesis, metastasis and treatment resistance appears to be driven by the aberrant gene expression and protein degradation encoded by the cancer genomes. The uncontrolled cancer growth relies on these cellular events, thus constituting the cancerous programs and rendering the addiction towards them. These programs are likely the potential anticancer biomarkers for Personalized Medicine of breast cancer. This review intends to delineate the impact of the CRSPR/Cas-mediated genome editing in identification and validation of these anticancer biomarkers...
2018: Journal of Cancer
https://www.readbyqxmd.com/read/29337866/crispr-cas-targeting-of-host-genes-as-an-antiviral-strategy
#5
REVIEW
Shuliang Chen, Xiao Yu, Deyin Guo
Currently, a new gene editing tool-the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) associated (Cas) system-is becoming a promising approach for genetic manipulation at the genomic level. This simple method, originating from the adaptive immune defense system in prokaryotes, has been developed and applied to antiviral research in humans. Based on the characteristics of virus-host interactions and the basic rules of nucleic acid cleavage or gene activation of the CRISPR-Cas system, it can be used to target both the virus genome and host factors to clear viral reservoirs and prohibit virus infection or replication...
January 16, 2018: Viruses
https://www.readbyqxmd.com/read/29335550/the-peg-responding-desiccome-of-the-alder-microsymbiont-frankia-alni
#6
Kais Ghedira, Emna Harigua-Souiai, Cherif Ben Hamda, Pascale Fournier, Petar Pujic, Sihem Guesmi, Ikram Guizani, Guylaine Miotello, Jean Armengaud, Philippe Normand, Haïtham Sghaier
Actinorhizal plants are ecologically and economically important. Symbiosis with nitrogen-fixing bacteria allows these woody dicotyledonous plants to colonise soils under nitrogen deficiency, water-stress or other extreme conditions. However, proteins involved in xerotolerance of symbiotic microorganisms have yet to be identified. Here we characterise the polyethylene glycol (PEG)-responding desiccome from the most geographically widespread Gram-positive nitrogen-fixing plant symbiont, Frankia alni, by next-generation proteomics, taking advantage of a Q-Exactive HF tandem mass spectrometer equipped with an ultra-high-field Orbitrap analyser...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29331410/implementing-crispr-cas-technologies-in-conventional-and-non-conventional-yeasts-current-state-and-future-prospects
#7
REVIEW
Hana Raschmanova, Astrid Weninger, Anton Glieder, Karin Kovar, Thomas Vogl
Within five years, the CRISPR-Cas system has emerged as the dominating tool for genome engineering, while also changing the speed and efficiency of metabolic engineering in conventional (Saccharomyces cerevisiae and Schizosaccharomyces pombe) and non-conventional (Yarrowia lipolytica, Pichia pastoris syn. Komagataella phaffii, Kluyveromyces lactis, Candida albicans and C. glabrata) yeasts. Especially in S. cerevisiae, an extensive toolbox of advanced CRISPR-related applications has been established, including crisprTFs and gene drives...
January 10, 2018: Biotechnology Advances
https://www.readbyqxmd.com/read/29331077/optimized-paired-sgrna-cas9-cloning-and-expression-cassette-triggers-high-efficiency-multiplex-genome-editing-in-kiwifruit
#8
Zupeng Wang, Shuaibin Wang, Dawei Li, Qiong Zhang, Li Li, Caihong Zhong, Yifei Liu, Hongwen Huang
Kiwifruit is an important fruit crop; however, technologies for its functional genomic and molecular improvement are limited. The clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system has been successfully applied to genetic improvement in many crops, but its editing capability is variable depending on the different combinations of the synthetic guide RNA (sgRNA) and Cas9 protein expression devices. Optimizing conditions for its use within a particular species is therefore needed to achieve highly efficient genome editing...
January 13, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29328063/immune-loss-as-a-driver-of-coexistence-during-host-phage-coevolution
#9
Jake L Weissman, Rayshawn Holmes, Rodolphe Barrangou, Sylvain Moineau, William F Fagan, Bruce Levin, Philip L F Johnson
Bacteria and their viral pathogens face constant pressure for augmented immune and infective capabilities, respectively. Under this reciprocally imposed selective regime, we expect to see a runaway evolutionary arms race, ultimately leading to the extinction of one species. Despite this prediction, in many systems host and pathogen coexist with minimal coevolution even when well-mixed. Previous work explained this puzzling phenomenon by invoking fitness tradeoffs, which can diminish an arms race dynamic. Here we propose that the regular loss of immunity by the bacterial host can also produce host-phage coexistence...
January 12, 2018: ISME Journal
https://www.readbyqxmd.com/read/29327920/generation-of-optogenetically-modified-adenovirus-vector-for-spatiotemporally-controllable-gene-therapy
#10
Kazuo Takayama, Hiroyuki Mizuguchi
Gene therapy is expected to be utilized for the treatment of various diseases. However, the spatiotemporal resolution of current gene therapy technology is not high enough. In this study, we generated a new technology for spatiotemporally controllable gene therapy. We introduced optogenetic and CRISPR/Cas9 techniques into a recombinant adenovirus (Ad) vector, which is widely used in clinical trials and exhibits high gene transfer efficiency, to generate an illumination-dependent spatiotemporally controllable gene regulation system (designated the Opt/Cas-Ad system)...
January 12, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29327679/natural-and-artificial-strategies-to-control-the-conjugative-transmission-of-plasmids
#11
María Getino, Fernando de la Cruz
Conjugative plasmids are the main carriers of transmissible antibiotic resistance (AbR) genes. For that reason, strategies to control plasmid transmission have been proposed as potential solutions to prevent AbR dissemination. Natural mechanisms that bacteria employ as defense barriers against invading genomes, such as restriction-modification or CRISPR-Cas systems, could be exploited to control conjugation. Besides, conjugative plasmids themselves display mechanisms to minimize their associated burden or to compete with related or unrelated plasmids...
January 2018: Microbiology Spectrum
https://www.readbyqxmd.com/read/29327438/establishing-rna-virus-resistance-in-plants-by-harnessing-crispr-immune-system
#12
Tong Zhang, Qiufeng Zheng, Xin Yi, Hong An, Yaling Zhao, Siqi Ma, Guohui Zhou
Recently, CRISPR-Cas (clustered, regularly interspaced short palindromic repeats-CRISPR associated proteins) system has been used to produce plants resistant to DNA virus infections. However, there is no RNA virus control method in plants that uses CRISPR-Cas system to target the viral genome directly. Here we reprogrammed the CRISPR-Cas9 system from Francisella novicida to confer molecular immunity against RNA viruses in Nicotiana benthamiana and Arabidopsis plants. Plants expressing FnCas9 and sgRNA specific for the cucumber mosaic virus (CMV) or tobacco mosaic virus (TMV) exhibited significantly attenuated virus infection symptoms and reduced viral RNA accumulation...
January 11, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29326299/targeting-mutant-kras-with-crispr-cas9-controls-tumor-growth
#13
Hyongbum Henry Kim, Wonjoo Kim, Sangeun Lee, Han Sang Kim, Minjung Song, Yong Hoon Cha, Young-Hoon Kim, Jeonghong Shin, Eun-Seo Lee, Yeonsoo Joo, Jae J Song, Eun Ju Choi, Jae W Choi, Jinu Lee, Moonkyung Kang, Jong In Yook, Min Goo Lee, Yeon-Soo Kim, Soonmyung Paik
KRAS is the most frequently mutated oncogene in human tumors and its activating mutations represents important therapeutic targets. The combination of Cas9 and guide RNA from the CRISPR-Cas system recognizes a specific DNA sequence and makes a double-strand break, which enables editing of the relevant genes. Here we harnessed CRISPR to specifically target mutant KRAS alleles in cancer cells. We screened guide RNAs using a reporter system and validated them in cancer cells after lentiviral delivery of Cas9 and guide RNA...
January 11, 2018: Genome Research
https://www.readbyqxmd.com/read/29326210/complete-genome-sequencing-of-acinetobacter-sp-strain-logew2-3-isolated-from-the-pellet-of-a-white-stork-reveals-a-novel-class-d-beta-lactamase-gene
#14
Ulrike Blaschke, Evelyn Skiebe, Michael Kaatz, Paul G Higgins, Yvonne Pfeifer, Gottfried Wilharm
Whole-genome sequencing of Acinetobacter sp. strain LoGeW2-3, isolated from the pellet of a white stork (Ciconia ciconia), reveals the presence of a plasmid of 179,399 bp encoding a CRISPR-Cas (clustered regularly interspaced short palindromic repeats and associated genes) system of the I-F type, and the chromosomally encoded novel class D beta-lactamase OXA-568.
January 11, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29325038/the-crispr-cas-system-in-enterobacteriaceae
#15
Liliana Medina-Aparicio, Sonia Dávila, Javier E Rebollar-Flores, Edmundo Calva, Ismael Hernández-Lucas
In nature, microorganisms are constantly exposed to multiple viral infections and thus have developed many strategies to survive phage attack and invasion by foreign DNA. One of such strategies is the CRISPR-Cas bacterial immunological system. This defense mechanism is widespread in prokaryotes including several families such as Enterobacteriaceae. Much knowledge about the CRISPR-Cas system has been generated, including its biological functions, transcriptional regulation, distribution, utility as a molecular marker, and as a tool for specific genome editing...
January 9, 2018: Pathogens and Disease
https://www.readbyqxmd.com/read/29320733/dna-unwinding-is-the-primary-determinant-of-crispr-cas9-activity
#16
Shanzhong Gong, Helen Hong Yu, Kenneth A Johnson, David W Taylor
Bacterial adaptive immunity utilizes RNA-guided surveillance complexes comprising Cas proteins together with CRISPR RNAs (crRNAs) to target foreign nucleic acids for destruction. Cas9, a type II CRISPR-Cas effector complex, can be programed with a single-guide RNA that base pairs with the target strand of dsDNA, displacing the non-target strand to create an R-loop, where the HNH and the RuvC nuclease domains cleave opposing strands. While many structural and biochemical studies have shed light on the mechanism of Cas9 cleavage, a clear unifying model has yet to emerge...
January 9, 2018: Cell Reports
https://www.readbyqxmd.com/read/29316264/heme-oxygenase-1-affects-generation-and-spontaneous-cardiac-differentiation-of-induced-pluripotent-stem-cells
#17
Jacek Stepniewski, Tomasz Pacholczak, Aniela Skrzypczyk, Maciej Ciesla, Agata Szade, Krzysztof Szade, Romain Bidanel, Agnieszka Langrzyk, Radoslaw Grochowski, Felix Vandermeeren, Neli Kachamakova-Trojanowska, Mateusz Jez, Grazyna Drabik, Mahito Nakanishi, Alicja Jozkowicz, Jozef Dulak
Cellular stress can influence efficiency of iPSCs generation and their differentiation. However, the role of intracellular cytoprotective factors in these processes is still not well known. Therefore, we investigated the effect of HO-1 (Hmox1) or Nrf2 (Nfe2l2), two major cytoprotective genes. Hmox1-/- fibroblasts demonstrated decreased reprogramming efficiency in comparison to Hmox1+/+ cells. Reversely, pharmacological enhancement of HO-1 resulted in higher number of iPSCs colonies. Importantly, elevated level of both p53 and p53-regulated miR-34a and 14-3-3σ was observed in HO-1-deficient fibroblasts whereas downregulation of p53 in these cells markedly increased their reprogramming efficiency...
January 9, 2018: IUBMB Life
https://www.readbyqxmd.com/read/29305085/engineering-the-delivery-system-for-crispr-based-genome-editing
#18
REVIEW
Zachary Glass, Matthew Lee, Yamin Li, Qiaobing Xu
Clustered regularly interspaced short palindromic repeat-CRISPR-associated protein (CRISPR-Cas) systems, found in nature as microbial adaptive immune systems, have been repurposed into an important tool in biological engineering and genome editing, providing a programmable platform for precision gene targeting. These tools have immense promise as therapeutics that could potentially correct disease-causing mutations. However, CRISPR-Cas gene editing components must be transported directly to the nucleus of targeted cells to exert a therapeutic effect...
January 2, 2018: Trends in Biotechnology
https://www.readbyqxmd.com/read/29304331/rapid-and-scalable-characterization-of-crispr-technologies-using-an-e-%C3%A2-coli-cell-free-transcription-translation-system
#19
Ryan Marshall, Colin S Maxwell, Scott P Collins, Thomas Jacobsen, Michelle L Luo, Matthew B Begemann, Benjamin N Gray, Emma January, Anna Singer, Yonghua He, Chase L Beisel, Vincent Noireaux
CRISPR-Cas systems offer versatile technologies for genome engineering, yet their implementation has been outpaced by ongoing discoveries of new Cas nucleases and anti-CRISPR proteins. Here, we present the use of E. coli cell-free transcription-translation (TXTL) systems to vastly improve the speed and scalability of CRISPR characterization and validation. TXTL can express active CRISPR machinery from added plasmids and linear DNA, and TXTL can output quantitative dynamics of DNA cleavage and gene repression-all without protein purification or live cells...
January 4, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29303478/rna-dependent-rna-targeting-by-crispr-cas9
#20
Steven C Strutt, Rachel M Torrez, Emine Kaya, Oscar A Negrete, Jennifer A Doudna
Double-stranded DNA (dsDNA) binding and cleavage by Cas9 is a hallmark of type II CRISPR-Cas bacterial adaptive immunity. All known Cas9 enzymes are thought to recognize DNA exclusively as a natural substrate, providing protection against DNA phage and plasmids. Here we show that Cas9 enzymes from both subtypes II-A and II-C can recognize and cleave single-stranded RNA (ssRNA) by an RNA-guided mechanism that is independent of a protospacer-adjacent motif (PAM) sequence in the target RNA. RNA-guided RNA cleavage is programmable and site-specific, and we find that this activity can be exploited to reduce infection by single-stranded RNA phage in vivo...
January 5, 2018: ELife
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