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CRISPR AND Plant

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https://www.readbyqxmd.com/read/30538157/histone-acetylation-cooperating-with-areb1-transcription-factor-regulates-drought-response-and-tolerance-in-populus-trichocarpa
#1
Shuang Li, Ying-Chung Jimmy Lin, Pengyu Wang, Baofeng Zhang, Meng Li, Su Chen, Rui Shi, Sermsawat Tunlaya-Anukit, Xinying Liu, Zhifeng Wang, Xiufang Dai, Jing Yu, Chenguang Zhou, Baoguang Liu, Jack P Wang, Vincent L Chiang, Wei Li
Plants develop tolerance to drought by activating genes with altered levels of epigenetic modifications. Specific transcription factors (TFs) are involved in this activation, but the molecular connections within the regulatory system are unclear. Here, we analyzed genome-wide H3K9ac enrichment and examined its association with transcriptomes in Populus trichocarpa under drought stress. We revealed that ABA-Responsive Element (ABRE) motifs in promoters of the drought-responsive genes, PtrNAC006, 007, and 120, are involved in H3K9ac enhancement and activation of these genes...
December 11, 2018: Plant Cell
https://www.readbyqxmd.com/read/30537191/developing-a-highly-efficient-and-wildly-adaptive-crispr-sacas9-toolset-for-plant-genome-editing
#2
Ruying Qin, Juan Li, Hao Li, Yuandi Zhang, Xiaoshuang Liu, Yuxin Miao, Xiuqing Zhang, Pengcheng Wei
The CRISPR- Streptococcus pyogenes Cas9 (SpCas9) system offers a rapid, simple and flexible genome editing approach. However, the targeting scope of the SpCas9 system is limited by the canonical NGG PAM. To broaden the editing range of the CRISPR system, several Cas orthologs recognized different PAM were isolated from diverse microbes and were engineered as powerful genome editing tools in eukaryotic cells (Murovec et al., 2017). One Cas9 ortholog, Staphylococcus aureus Cas9 (SaCas9), has a smaller size and comparable activity compared to SpCas9 (Kleinstiver et al...
December 10, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30537089/a-crispr-cas9-deletion-into-the-phosphate-transporter-slypho1-1-reveals-its-role-in-phosphate-nutrition-of-tomato-seedlings
#3
Panfeng Zhao, Qiuye You, Mingguang Lei
In vascular (Arabidopsis thaliana) and nonvascular (Physcomitrella patens) plants, PHOSPHATE 1 (PHO1) homologs play important roles in the acquisition and transfer of phosphate. The tomato genome contains six genes (SlPHO1;1-SlPHO1;6) homologous to AtPHO1. The six proteins have typical characteristics of the plant PHO1 family, such as the three SPX sub domains in the N-terminal portion and one EXS domain in the C-terminal portion. Phylogenetic analysis revealed that the SlPHO1 family is subdivided into three clusters...
December 8, 2018: Physiologia Plantarum
https://www.readbyqxmd.com/read/30531939/genome-editing-in-plants-by-engineered-crispr-cas9-recognizing-ng-pam
#4
Masaki Endo, Masafumi Mikami, Akira Endo, Hidetaka Kaya, Takeshi Itoh, Hiroshi Nishimasu, Osamu Nureki, Seiichi Toki
Streptococcus pyogenes Cas9 (SpCas9) is widely used for genome editing and requires NGG as a protospacer adjacent motif (PAM). Here, we show that the engineered SpCas9 (SpCas9-NGv1) can efficiently mutagenize endogenous target sites with NG PAMs in the rice and Arabidopsis genomes. Furthermore, we demonstrate that the SpCas9-NGv1 nickase fused to cytidine deaminase mediates C-to-T substitutions near the 5' end of the target sequence.
December 10, 2018: Nature Plants
https://www.readbyqxmd.com/read/30530297/characterization-of-the-secondary-metabolite-biosynthetic-gene-clusters-in-archaea
#5
Shengqin Wang, Zhihong Zheng, Huixi Zou, Nan Li, Mingjiang Wu
Secondary metabolites are a range of bioactive compounds yielded by bacteria, fungi and plants, etc. The published archaea genomic data provide the opportunity for efficient identification of secondary metabolite biosynthetic gene clusters (BGCs) by genome mining. However, the study of secondary metabolites in archaea is still rare. By using the antiSMASH, we found two main putative secondary metabolite BGCs, bacteriocin and terpene in 203 Archaea genomes. Compared with the genomes of Euryarchaeota that usually lives in less complexity of environment, the genomes of Crenarchaeota usually contained more abundant bacteriocin...
November 20, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/30530202/rice-big-gene-is-required-for-seedling-viability
#6
Rui Cheng, Luping Gong, Zhengzheng Li, Yun-Kuan Liang
Arabidopsis BIG (AtBIG) gene encodes an enormous protein that is required for auxin transport. Loss of AtBIG function not only profoundly changes plant architecture but also alters plant adaptability to environmental stimuli. A putative homolog of AtBIG exists in the rice genome, but no function has been ascribed to it. In this study, we focus on the characterization of the gene structure and function of OsBIG. Sequence and phylogenetic analysis shows that the homologs of OsBIG have high amino acid conservation in several domains across species...
November 10, 2018: Journal of Plant Physiology
https://www.readbyqxmd.com/read/30526490/comparative-genomics-of-84-pectobacterium-genomes-reveals-the-variations-related-to-a-pathogenic-lifestyle
#7
Xiaoying Li, Yali Ma, Shuqing Liang, Yu Tian, Sanjun Yin, Sisi Xie, Hua Xie
BACKGROUND: Pectobacterium spp. are necrotrophic bacterial plant pathogens of the family Pectobacteriaceae, responsible for a wide spectrum of diseases of important crops and ornamental plants including soft rot, blackleg, and stem wilt. P. carotovorum is a genetically heterogeneous species consisting of three valid subspecies, P. carotovorum subsp. brasiliense (Pcb), P. carotovorum subsp. carotovorum (Pcc), and P. carotovorum subsp. odoriferum (Pco). RESULTS: Thirty-two P...
December 7, 2018: BMC Genomics
https://www.readbyqxmd.com/read/30521608/crispr-cas9-mediated-knockout-of-the-abdominal-a-homeotic-gene-in-fall-armyworm-moth-spodoptera-frugiperda
#8
Ke Wu, Paul D Shirk, Caitlin E Taylor, Richard B Furlong, Bryce D Shirk, Daniele H Pinheiro, Blair D Siegfried
The fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith), is an important pest of maize in the Americas and has recently been introduced into Africa. Fall armyworm populations have developed resistance to control strategies that depend on insecticides and transgenic plants expressing Bacillus thuringiensis toxins. The study of various resistance mechanisms at the molecular level and the development novel control strategies have been hampered by a lack of functional genomic tools such as gene editing in this pest...
2018: PloS One
https://www.readbyqxmd.com/read/30521567/the-dfr-locus-a-smart-landing-pad-for-targeted-transgene-insertion-in-tomato
#9
Benoit Danilo, Laura Perrot, Emmanuel Botton, Fabien Nogué, Marianne Mazier
Targeted insertion of transgenes in plants is still challenging and requires further technical innovation. In the present study, we chose the tomato DFR gene involved in anthocyanin biosynthesis as a landing pad for targeted transgene insertion using CRISPR-Cas9 in a two-step strategy. First, a 1013 bp was deleted in the endogenous DFR gene. Hypocotyls and callus of in vitro regenerated plantlets homozygous for the deletion were green instead of the usual anthocyanin produced purple colour. Next, standard Agrobacterium-mediated transformation was used to target transgene insertion at the DFR landing pad in the dfr deletion line...
2018: PloS One
https://www.readbyqxmd.com/read/30511631/crispr-cas9-a-robust-technology-for-producing-genetically-engineered-plants
#10
Rimsha Farooq, Khadim Hussain, Shahid Nazir, Muhammad Rizwan Javed, Nazish Masood
CRISPR/Cas9 is a technology evolved from modified type II immune system of bacteria and archaea. Exploitation of this bacterial immune system in all eukaryotes including plants may lead to site-specific targeted genome engineering. Genome engineering is objectively utilized to express/silence a trait harbouring gene in the plant genome. In this review, different genetic engineering techniques including classical breeding, RNAi and genetic transformation and synthetic sequence-specific nucleases (zinc finger nucleases; ZFNs and transcription activator-like effector nuclease; TALENs) techniques have been described and compared with advanced genome editing technique CRISPR/Cas9, on the basis of their merits and drawbacks...
November 30, 2018: Cellular and Molecular Biology
https://www.readbyqxmd.com/read/30509166/identification-and-characterization-of-gmmyb118-responses-to-drought-and-salt-stress
#11
Yong-Tao Du, Meng-Jie Zhao, Chang-Tao Wang, Yuan Gao, Yan-Xia Wang, Yong-Wei Liu, Ming Chen, Jun Chen, Yong-Bin Zhou, Zhao-Shi Xu, You-Zhi Ma
BACKGROUND: Abiotic stress severely influences plant growth and development. MYB transcription factors (TFs), which compose one of the largest TF families, play an important role in abiotic stress responses. RESULT: We identified 139 soybean MYB-related genes; these genes were divided into six groups based on their conserved domain and were distributed among 20 chromosomes (Chrs). Quantitative real-time PCR (qRT-PCR) indicated that GmMYB118 highly responsive to drought, salt and high temperature stress; thus, this gene was selected for further analysis...
December 3, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/30508644/participation-of-vitamin-d-upregulated-protein-1-txnip-ask1-jnk1-signalosome-in-the-enhancement-of-aml-cell-death-by-a-post-cytotoxic-differentiation-regimen
#12
X Wang, M Nachliely, J S Harrison, M Danilenko, G P Studzinski
Standard therapy for Acute Myeloid Leukemia (AML) is rarely curative, and several suggested improvements have had little success so far. We have reported that in an in vitro model of a potential therapeutic regimen for AML, the activity of cytarabine (AraC) is enhanced by a sequential treatment with a combination of the vitamin D2 analog Doxercalciferol (D2) and the plant-derived antioxidant carnosic acid (CA) Importantly, the enhancement occurred selectively in patient-derived AML blasts, but not in the normal bone marrow cells...
November 30, 2018: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/30508598/a-plant-immune-receptor-degraded-by-selective-autophagy
#13
Fan Yang, Athen N Kimberlin, Christian G Elowsky, Yunfeng Liu, Ariadna Gonzalez-Solis, Edgar B Cahoon, James R Alfano
Plants recycle non-activated immune receptors to maintain a functional immune system. The Arabidopsis immune receptor kinase FLAGELLIN-SENSING 2 (FLS2) recognizes bacterial flagellin. Arabidopsis orosomucoid (ORM) proteins are negative regulators of sphingolipid biosynthesis, but the mechanism by which they do this is not well understood. Here, we provide evidence that ORM proteins act as selective autophagy receptors to degrade FLS2. Arabidopsis plants over-expressing ORM1 or ORM2 lack or have greatly diminished FLS2 levels, lack FLS2 signaling, and are more susceptible to the bacterial pathogen Pseudomonas syringae...
November 30, 2018: Molecular Plant
https://www.readbyqxmd.com/read/30500879/crispr-local-a-local-single-guide-rna-sgrna-design-tool-for-non-reference-plant-genomes
#14
Jiamin Sun, Hao Liu, Jianxiao Liu, Shikun Cheng, Yong Peng, Qinghua Zhang, Jianbing Yan, Hai-Jun Liu, Ling-Ling Chen
Summary: CRISPR-Local is a high-throughput local tool for designing sgRNAs in plants and other organisms that factors in genetic variation and is optimized to generate genome-wide sgRNAs. CRISPR-Local outperforms other sgRNA design tools in the following respects: (1) designing sgRNAs suitable for non-reference varieties; (2) screening for sgRNAs that are capable of simultaneously targeting multiple genes; (3) saving computational resources by avoiding repeated calculations from multiple submissions; and (4) running offline, with both command-line and graphical user interface modes, and the ability to export multiple formats for further batch analysis or visualization...
November 30, 2018: Bioinformatics
https://www.readbyqxmd.com/read/30499032/purine-nucleotide-biosynthetic-gene-gars-controls-early-chloroplast-development-in-rice-oryza-sativa-l
#15
Penghui Cao, Yakun Ren, Xi Liu, Tianyu Zhang, Ping Zhang, Lianjie Xiao, Fulin Zhang, Shijia Liu, Ling Jiang, Jianmin Wan
GARS encodes an enzyme catalyzing the second step of purine nucleotide biosynthesis and plays an important role to maintain the development of chloroplasts in juvenile plants by affecting the expression of plastid-encoded genes. A series of rice white striped mutants were previously described. In this research, we characterized a novel gars mutant with white striped leaves at the seedling stage. By positional cloning, we identified the mutated gene, which encodes a glycinamide ribonucleotide synthetase (GARS) that catalyzes the second step of purine nucleotide biosynthesis...
November 29, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/30483283/genome-editing-for-crop-improvement-applications-in-clonally-propagated-polyploids-with-a-focus-on-potato-solanum-tuberosum-l
#16
Satya Swathi Nadakuduti, C Robin Buell, Daniel F Voytas, Colby G Starker, David S Douches
Genome-editing has revolutionized biology. When coupled with a recently streamlined regulatory process by the U.S. Department of Agriculture and the potential to generate transgene-free varieties, genome-editing provides a new avenue for crop improvement. For heterozygous, polyploid and vegetatively propagated crops such as cultivated potato, Solanum tuberosum Group Tuberosum L., genome-editing presents tremendous opportunities for trait improvement. In potato, traits such as improved resistance to cold-induced sweetening, processing efficiency, herbicide tolerance, modified starch quality and self-incompatibility have been targeted utilizing CRISPR/Cas9 and TALEN reagents in diploid and tetraploid clones...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/30481169/genome-wide-crispr-screens-for-shiga-toxins-and-ricin-reveal-golgi-proteins-critical-for-glycosylation
#17
Songhai Tian, Khaja Muneeruddin, Mei Yuk Choi, Liang Tao, Robiul H Bhuiyan, Yuhsuke Ohmi, Keiko Furukawa, Koichi Furukawa, Sebastian Boland, Scott A Shaffer, Rosalyn M Adam, Min Dong
Glycosylation is a fundamental modification of proteins and membrane lipids. Toxins that utilize glycans as their receptors have served as powerful tools to identify key players in glycosylation processes. Here, we carried out Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9-mediated genome-wide loss-of-function screens using two related bacterial toxins, Shiga-like toxins (Stxs) 1 and 2, which use a specific glycolipid, globotriaosylceramide (Gb3), as receptors, and the plant toxin ricin, which recognizes a broad range of glycans...
November 2018: PLoS Biology
https://www.readbyqxmd.com/read/30477421/targeted-mutagenesis-using-the-agrobacterium-tumefaciens-mediated-crispr-cas9-system-in-common-wheat
#18
Shujuan Zhang, Rongzhi Zhang, Guoqi Song, Jie Gao, Wei Li, Xiaodong Han, Mingli Chen, Yulian Li, Genying Li
BACKGROUND: Recently, the CRISPR/Cas9 system has been widely used to precisely edit plant genomes. Due to the difficulty in Agrobacterium-mediated genetic transformation of wheat, the reported applications in CRISPR/Cas9 system were all based on the biolistic transformation. RESULTS: In the present study, we efficiently applied targeted mutagenesis in common wheat (Triticum aestivum L.) protoplasts and transgenic T0 plants using the CRISPR/Cas9 system delivered via Agrobacterium tumefaciens...
November 26, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/30467959/genes-regulating-gland-development-in-the-cotton-plant
#19
Madhusudhana R Janga, Devendra Pandeya, LeAnne M Campbell, Kranti Konganti, Stephany Toinga Villafuerte, Lorraine Puckhaber, Alan Pepper, Robert D Stipanovic, Jodi A Scheffler, Keerti S Rathore
In seeds and other parts of cultivated, tetraploid cotton (Gossypium hirsutum L.), multicellular groups of cells lysigenously form dark glands containing toxic terpenoids such as gossypol that defend the plant against pests and pathogens. Using RNA-seq analysis of embryos from near-isogenic glanded (Gl2 Gl2 Gl3 Gl3 ) versus glandless (gl2 gl2 gl3 gl3 ) plants, we identified 33 genes that expressed exclusively or at higher levels in embryos just prior to gland formation in glanded plants. Virus Induced Gene Silencing against three gene pairs led to significant reductions in the number of glands in the leaves, and significantly lower levels of gossypol and related terpenoids...
November 22, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30466578/in-vivo-promoter-engineering-in-plants-are-we-ready
#20
REVIEW
Ramakrishnan Pandiarajan, Anil Grover
Engineering plant promoter sequence for optimal expression of a gene has been a long standing goal for plant scientists. In recent times, Sequence Specific Nucleases (SSNs) like CRISPR/Cas9 are enabling researchers to achieve this goal, in vivo in the genome. It is well known that SSNs have met with unprecedented success in rapid transgene free crop improvement largely by targeting the coding sequence. Here, we discuss the strategies being employed by plant scientists in targeting SSNs to non-coding promoter regions/Cis Regulatory Elements (CRE)...
December 2018: Plant Science: An International Journal of Experimental Plant Biology
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