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https://www.readbyqxmd.com/read/27914284/applying-crispr-cas-for-genome-engineering-in-plants-the-best-is-yet-to-come
#1
REVIEW
Holger Puchta
Less than 5 years ago the CRISPR/Cas nuclease was first introduced into eukaryotes, shortly becoming the most efficient and widely used tool for genome engineering. For plants, efforts were centred on obtaining heritable changes in most transformable crop species by inducing mutations into open reading frames of interest, via non-homologous end joining. Now it is important to take the next steps and further develop the technology to reach its full potential. For breeding, besides using DNA-free editing and avoiding off target effects, it will be desirable to apply the system for the mutation of regulatory elements and for more complex genome rearrangements...
November 30, 2016: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/27912110/structures-and-mechanisms-of-crispr-rna-guided-effector-nucleases
#2
REVIEW
Hiroshi Nishimasu, Osamu Nureki
In the prokaryotic CRISPR-Cas adaptive immune systems, a CRISPR RNA (crRNA) assembles with multiple or single Cas proteins to form crRNA ribonucleoprotein (crRNP) effector complexes, responsible for the destruction of invading genetic elements. Although the mechanisms of target recognition and cleavage by the crRNP effectors are quite diverse among the different types of CRISPR-Cas systems, the basic action principles of these crRNA-guided effector nucleases are highly conserved. In all of the crRNP effectors, the repeat-derived invariant and spacer-derived variable segments of the crRNA are recognized by the Cas protein(s) in sequence-dependent and sequence-independent manners, respectively, with the spacer-derived guide segment available for base pairing with target nucleic acids...
November 29, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27911718/attacking-hiv-1-rna-versus-dna-by-sequence-specific-approaches-rnai-versus-crispr-cas
#3
REVIEW
Elena Herrera-Carrillo, Ben Berkhout
Human immunodeficiency virus type 1 (HIV-1) infection can be effectively controlled by potent antiviral drugs, but this never results in a cure. The patient should therefore take these drugs for the rest of his/her life, which can cause drug-resistance and adverse effects. Therefore, more durable therapeutic strategies should be considered, such as a stable gene therapy to protect the target T cells against HIV-1 infection. The development of potent therapeutic regimens based on the RNA interference (RNAi) and clustered regularly interspaced short palindromic repeats (CRISPR-Cas) mechanisms will be described, which can be delivered by lentiviral vectors...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27908725/par3l-enhances-colorectal-cancer-cell-survival-by-inhibiting-lkb1-ampk-signaling-pathway
#4
Taiyuan Li, Dongning Liu, Xiong Lei, Qunguang Jiang
Partitioning defective 3-like protein (Par3L) is a recently identified cell polarity protein that plays an important role in mammary stem cell maintenance. Previously, we showed that high expression of Par3L is associated with poor survival in malignant colorectal cancer (CRC), but the underlying mechanism remained unknown. To this end, we established a Par3L knockout colorectal cancer cell line using the CRISPR/Cas system. Interestingly, reduced proliferation, enhanced cell death and caspase-3 activation were observed in Par3L knockout (KO) cells as compared with wildtype (WT) cells...
November 28, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27904648/editing-of-the-urease-gene-by-crispr-cas-in-the-diatom-thalassiosira-pseudonana
#5
Amanda Hopes, Vladimir Nekrasov, Sophien Kamoun, Thomas Mock
BACKGROUND: CRISPR-Cas is a recent and powerful addition to the molecular toolbox which allows programmable genome editing. It has been used to modify genes in a wide variety of organisms, but only two alga to date. Here we present a methodology to edit the genome of Thalassiosira pseudonana, a model centric diatom with both ecological significance and high biotechnological potential, using CRISPR-Cas. RESULTS: A single construct was assembled using Golden Gate cloning...
2016: Plant Methods
https://www.readbyqxmd.com/read/27900888/using-the-crispr-cas9-system-to-eliminate-native-plasmids-of-zymomonas-mobilis-zm4
#6
Qing-Hua Cao, Huan-Huan Shao, Hui Qiu, Tao Li, Yi-Zheng Zhang, Xue-Mei Tan
The CRISPR/Cas system can be used to simply and efficiently edit the genomes of various species, including animals, plants, and microbes. Zymomonas mobilis ZM4 is a highly efficient, ethanol-producing bacterium that contains five native plasmids. Here, we constructed the pSUZM2a-Cas9 plasmid and a single-guide RNA expression plasmid. The pSUZM2a-Cas9 plasmid was used to express the Cas9 gene cloned from Streptococcus pyogenes CICC 10464. The single-guide RNA expression plasmid pUC-T7sgRNA, with a T7 promoter, can be used for the in vitro synthesis of single-guide RNAs...
November 30, 2016: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/27899566/asymmetric-positioning-of-cas1-2-complex-and-integration-host-factor-induced-dna-bending-guide-the-unidirectional-homing-of-protospacer-in-crispr-cas-type-i-e-system
#7
K N R Yoganand, R Sivathanu, Siddharth Nimkar, B Anand
CRISPR-Cas system epitomizes prokaryote-specific quintessential adaptive defense machinery that limits the genome invasion of mobile genetic elements. It confers adaptive immunity to bacteria by capturing a protospacer fragment from invading foreign DNA, which is later inserted into the leader proximal end of CRIPSR array and serves as immunological memory to recognize recurrent invasions. The universally conserved Cas1 and Cas2 form an integration complex that is known to mediate the protospacer invasion into the CRISPR array...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27896818/coupling-immunity-and-programmed-cell-suicide-in-prokaryotes-life-or-death-choices
#8
Eugene V Koonin, Feng Zhang
Host-pathogen arms race is a universal, central aspect of the evolution of life. Most organisms evolved several distinct yet interacting strategies of anti-pathogen defense including resistance to parasite invasion, innate and adaptive immunity, and programmed cell death (PCD). The PCD is the means of last resort, a suicidal response to infection that is activated when resistance and immunity fail. An infected cell faces a decision between active defense and altruistic suicide or dormancy induction, depending on whether immunity is "deemed" capable of preventing parasite reproduction and consequent infection of other cells...
November 29, 2016: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/27895053/utilising-polymorphisms-to-achieve-allele-specific-genome-editing-in-zebrafish
#9
Samuel J Capon, Gregory J Baillie, Neil I Bower, Jason A da Silva, Scott Paterson, Benjamin M Hogan, Cas Simons, Kelly A Smith
The advent of genome editing has significantly altered genetic research, including research using the zebrafish model. To better understand the selectivity of the commonly used CRISPR/Cas9 system, we investigated single base pair mismatches in target sites and examined how they affect genome editing in the zebrafish model. Using two different zebrafish strains that have been deep sequenced, CRISPR/Cas9 target sites containing polymorphisms between the two strains were identified. These strains were crossed (creating heterozygotes at polymorphic sites) and CRISPR/Cas9 complexes that perfectly complement one strain injected...
November 28, 2016: Biology Open
https://www.readbyqxmd.com/read/27894274/gene-cassette-knock-in-in-mammalian-cells-and-zygotes-by-enhanced-mmej
#10
Tomomi Aida, Shota Nakade, Tetsushi Sakuma, Yayoi Izu, Ayu Oishi, Keiji Mochida, Harumi Ishikubo, Takako Usami, Hidenori Aizawa, Takashi Yamamoto, Kohichi Tanaka
BACKGROUND: Although CRISPR/Cas enables one-step gene cassette knock-in, assembling targeting vectors containing long homology arms is a laborious process for high-throughput knock-in. We recently developed the CRISPR/Cas-based precise integration into the target chromosome (PITCh) system for a gene cassette knock-in without long homology arms mediated by microhomology-mediated end-joining. RESULTS: Here, we identified exonuclease 1 (Exo1) as an enhancer for PITCh in human cells...
November 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27890921/bacterial-physiology-quorum-sensing-controls-the-cost-of-crispr-cas
#11
Ursula Hofer
No abstract text is available yet for this article.
November 28, 2016: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/27875019/generation-of-targeted-mutant-rice-using-a-crispr-cpf1-system
#12
Rongfang Xu, Ruiying Qin, Hao Li, Dongdong Li, Li Li, Pengcheng Wei, Jianbo Yang
CRISPR-Cpf1 is a newly identified CRISPR-Cas system, and Cpf1 was recently engineered as a molecular tool for targeted genome editing in mammalian cells. To test whether the engineered CRISPR-Cpf1 system could induce the production of rice mutants, we selected two genome targets in the OsPDS and OsBEL genes. Our results show that both targets could be efficiently mutated in transgenic rice plants using CRISPR-Cpf1. We found that pre-crRNAs with a full-length direct repeat sequence exhibited considerably increased efficiencies compared with mature crRNAs...
November 22, 2016: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/27874856/in-vivo-editing-of-the-human-mutant-rhodopsin-gene-by-electroporation-of-plasmid-based-crispr-cas9-in-the-mouse-retina
#13
Maria Carmela Latella, Maria Teresa Di Salvo, Fabienne Cocchiarella, Daniela Benati, Giulia Grisendi, Antonella Comitato, Valeria Marigo, Alessandra Recchia
The bacterial CRISPR/Cas system has proven to be an efficient tool for genetic manipulation in various organisms. Here we show the application of CRISPR-Cas9 technology to edit the human Rhodopsin (RHO) gene in a mouse model for autosomal dominant Retinitis Pigmentosa. We designed single or double sgRNAs to knock-down mutant RHO expression by targeting exon 1 of the RHO gene carrying the P23H dominant mutation. By delivering Cas9 and sgRNAs in a single plasmid we induced an efficient gene editing in vitro, in HeLa cells engineered to constitutively express the P23H mutant RHO allele...
November 22, 2016: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/27871367/conformational-control-of-cascade-interference-and-priming-activities-in-crispr-immunity
#14
Chaoyou Xue, Natalie R Whitis, Dipali G Sashital
During type I-E CRISPR-Cas immunity, the Cascade surveillance complex utilizes CRISPR-derived RNAs to target complementary invasive DNA for destruction. When invader mutation blocks this interference activity, Cascade instead triggers rapid primed adaptation against the invader. The molecular basis for this dual Cascade activity is poorly understood. Here we show that the conformation of the Cse1 subunit controls Cascade activity. Using FRET, we find that Cse1 exists in a dynamic equilibrium between "open" and "closed" conformations, and the extent to which the open conformation is favored directly correlates with the attenuation of interference and relative increase in priming activity upon target mutation...
November 17, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27867047/assessing-the-intra-species-genetic-variability-in-the-clonal-pathogen-campylobacter-fetus-crisprs-are-highly-polymorphic-dna-markers
#15
Lucía Calleros, Laura Betancor, Gregorio Iraola, Alejandra Méndez, Claudia Morsella, Fernando Paolicchi, Silvia Silveyra, Alejandra Velilla, Ruben Pérez
Campylobacter fetus is a Gram-negative, microaerophilic bacterium that infects animals and humans. The subspecies Campylobacter fetus subsp. fetus (Cff) affects a broad range of vertebrate hosts and induces abortion in cows and sheep. Campylobacter fetus subsp. venerealis (Cfv) is restricted to cattle and causes the endemic disease bovine genital campylobacteriosis, which triggers reproductive problems and is responsible for major economic losses. Campylobacter fetus subsp. testudinum (Cft) has been isolated mostly from apparently healthy reptiles belonging to different species but also from ill snakes and humans...
November 17, 2016: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/27867010/quorum-sensing-controls-adaptive-immunity-through-the-regulation-of-multiple-crispr-cas-systems
#16
Adrian G Patterson, Simon A Jackson, Corinda Taylor, Gary B Evans, George P C Salmond, Rita Przybilski, Raymond H J Staals, Peter C Fineran
Bacteria commonly exist in high cell density populations, making them prone to viral predation and horizontal gene transfer (HGT) through transformation and conjugation. To combat these invaders, bacteria possess an arsenal of defenses, such as CRISPR-Cas adaptive immunity. Many bacterial populations coordinate their behavior as cell density increases, using quorum sensing (QS) signaling. In this study, we demonstrate that QS regulation results in increased expression of the type I-E, I-F, and III-A CRISPR-Cas systems in Serratia cells in high-density populations...
November 16, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27863223/memory-upgrade-insights-into-primed-adaptation-by-crispr-cas-immune-systems
#17
Anita Ramachandran, Scott Bailey
Recently, Künne et al. (2016) demonstrated that degradation products of Cas3 obtained during CRISPR interference fuel priming. In this issue of Molecular Cell, Xue et al. (2016) highlight the conformational changes in Cascade that underpin the priming process when interference is blocked.
November 17, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27862566/host-diversity-limits-the-evolution-of-parasite-local-adaptation
#18
Daniel Morley, Jenny M Broniewski, Edze R Westra, Angus Buckling, Stineke van Houte
Specificity in the interactions between hosts and their parasites can lead to local adaptation. However, the degree of local adaptation is predicted to depend upon the diversity of resistance alleles within the host population; increasing host diversity should decrease mean parasite infectivity and hence reduce local adaptation. In this study we empirically test this prediction using the highly specific interactions between bacteria with CRISPR-Cas immunity and their bacteriophage. Bacteria acquire immunity to phage by incorporating a phage-derived spacer sequence into CRISPR loci on the host genome, and phage can escape the CRISPR-mediated immunity of a specific clone by mutating the targeted sequence...
November 14, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27857054/type-i-crispr-cas-targets-endogenous-genes-and-regulates-virulence-to-evade-mammalian-host-immunity
#19
Rongpeng Li, Lizhu Fang, Shirui Tan, Min Yu, Xuefeng Li, Sisi He, Yuquan Wei, Guoping Li, Jianxin Jiang, Min Wu
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) systems in bacteria and archaea provide adaptive immunity against invading foreign nucleic acids. Previous studies suggest that certain bacteria employ their Type II CRISPR-Cas systems to target their own genes, thus evading host immunity. However, whether other CRISPR-Cas systems have similar functions during bacterial invasion of host cells remains unknown. Here we identify a novel role for Type I CRISPR-Cas systems in evading host defenses in Pseudomonas aeruginosa strain UCBPP-PA14...
December 2016: Cell Research
https://www.readbyqxmd.com/read/27849583/quorum-sensing-controls-the-pseudomonas-aeruginosa-crispr-cas-adaptive-immune-system
#20
Nina M Høyland-Kroghsbo, Jon Paczkowski, Sampriti Mukherjee, Jenny Broniewski, Edze Westra, Joseph Bondy-Denomy, Bonnie L Bassler
CRISPR-Cas are prokaryotic adaptive immune systems that provide protection against bacteriophage (phage) and other parasites. Little is known about how CRISPR-Cas systems are regulated, preventing prediction of phage dynamics in nature and manipulation of phage resistance in clinical settings. Here, we show that the bacterium Pseudomonas aeruginosa PA14 uses the cell-cell communication process, called quorum sensing, to activate cas gene expression, to increase CRISPR-Cas targeting of foreign DNA, and to promote CRISPR adaptation, all at high cell density...
November 14, 2016: Proceedings of the National Academy of Sciences of the United States of America
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