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cis-trans Engineering： Advances and Perspectives on Customized Transcriptional Regulation in Plants

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Molecular Plant 2018年第7期11卷 886-898页

作者： Ankita Shrestha Ahamed Khan Nrisingha Dey Division of Microbial and Plant Biotechnology Institute of Life Sciences Department of Biotechnology Government of India Chandrasekharpur Bhubaneswar Odisha India these authors contributed equally to this article.

Coordinated transcriptional control employing synthetic promoters and transcription factors （TFs） can be used to achieve customized regulation of gene expression in planta. Synthetic promoter technology has yielded a series of promoters with modified cis-regulatory elements that provide useful tools for efficient modulation of gene expression. In addition, the use of zinc fingers （ZFs）, transcription activator-like effectors （TALEs）, and catalytically inactive clustered regularly interspaced short palindromic repeats （CRISPR）-associated protein 9 （dCas9） has made it feasible to engineer TFs that can produce targeted gene expression regulation; these approaches are particularly effective when artificial TFs are coupled with transcriptional activators or repressors. This review focuses on strategies used to engineer both promoters and TFs in the context of targeted transcriptional regulation. We also discuss the creation of synthetic inducible platforms, which can be used to impart stress tolerance to plants. We propose that combinatorial ＂cis-trans engineering＂ using a CRISPR-dCas9-based bipartite module could be used to regulate the expression of multiple target genes. This approach provides an attractive tool for introduction of specific qualitative traits into plants, thus enhancing their overall environmental adaptability.

关键词： cis engineering trans engineering synthetic TFs dCas9 bipartite module

A New Year’s spotlight on two years of publication

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Plant Communications 2022年第1期3卷 1-5页

作者： Wenjia Wang Lexuan Gao Xiaofeng Cui Editors Plant Communications These authors contributed equally to this article

With this first issue of 2022,Plant Communications enters its third *** the past 2 years,the activities of plant researchers worldwide have been affected by the COVID-19 pandemic,which has hindered the progress of many ongoing plant science *** the pandemic is not yet over and we currently face many other grand challenges,such as climate change,we have witnessed the global scientific community working boldly together to find solutions for ending the COVID-19 pandemic and tackling other *** change threatens global food security and sustainable development.

关键词： hough global light

Crop Epigenomics： Identifying, Unlocking, and Harnessing Cryptic Variation in Crop Genomes

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Molecular Plant 2015年第6期8卷 860-870页

作者： Lexiang Ji Drexel A. Neumann Robert J. Schmitz Department of Genetics University of Georgia Athens GA 30602 USA Institute of Bioinformatics University of Georgia Athens GA 30602 USA these authors contributed equally to this article.

DNA methylation is a key chromatin modification in plant genomes that is meiotically and mitotically her- itable, and at times is associated with gene expression and morphological variation. Benefiting from the increased availability of high-quality reference genome assemblies and methods to profile single-base res- olution DNA methylation states, DNA methylomes for many crop species are available. These efforts are making it possible to begin answering crucial questions, including understanding the role of DNA methyl- ation in developmental processes, its role in crop species evolution, and whether DNA methylation is dynamically altered and heritable in response to changes in the environment. These genome-wide maps provide evidence for the existence of silent epialleles in plant genomes which, once identified, can be tar- geted for reactivation leading to phenotypic variation.

关键词： epigenomics DNA methylation whole-genome bisulfite sequencing (WGBS) crops comparativegenomics

Jasmonic Acid Oxidase 2 Hydroxylates Jasmonic Acid and Represses Basal Defense and Resistance Responses against Botrytis cinerea Infection

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Molecular Plant 2017年第9期10卷 1159-1173页

作者： Ekaterina Smirnova Laboratoire de Chimie Organique Synthétique Institut de Chimie Université de Strasbourg CNRS Strasbourg France [∗]Corresponding authorthese authors contributed equally to this article.

Jasmonates （JAs） orchestrate immune responses upon wound/herbivore injury or infection by necrotro- phic pathogens. Elucidation of catabolic routes has revealed new complexity in jasmonate metabolism. Two integrated pathways attenuate signaling by turning over the active hormone jasmonoyl-isoleucine （JA-Ile） through w-oxidation or deconjugation, and define an indirect route forming the derivative 12OH-JA. Here, we provide evidence for a second 12OH-JA formation pathway by direct jasmonic acid （JA） oxidation. Three jasmonic acid oxidases （JAOs） of the 2-oxoglutarate dioxygenase family catalyze spe- cific oxidation of JA to 12OH-JA, and their genes are induced by wounding or infection by the fungus Botrytis cinerea. JA02 exhibits the highest basal expression, and its deficiency in jao2 mutants strongly enhanced antifungal resistance. The resistance phenotype resulted from constitutive expression of antimi- crobial markers rather than from their higher induction in infected jao2 plants and could be reversed by ectopic expression of any of the three JAOs injao2. Elevated defense injao2 was dependent on the activity of JASMONATE RESPONSE 1 （JAR1） and CORONATINE-INSENSITIVE 1 （COI1） but was not correlated with erihanced JA-Ile accumulation. Instead, jao2 mutant lines displayed altered accumulation of several JA species in healthy and challenged plants, suggesting elevated metabolic flux through JA-Ile. Collectively, these data identify the missing enzymes hydroxylating JA and uncover an important metabolic diversion mechanism for repressing basal JA defense responses.

关键词： 2-oxoglutarate oxygenase jasmonic acid defense regulation hormone metabolism Botrytis

The CUL3A–LFH1–UBC15 ubiquitin ligase complex mediates SHORT VEGETATIVE PHASE degradation to accelerate flowering at high ambient temperature

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Plant Communications 2024年第4期5卷 224-238页

作者： Suhyun Jin Geummin Youn Sun Young Kim Taewook Kang Hyun-young Shin Ji-Yul Jung Pil Joon Seo Ji Hoon Ahn Department of Life Sciences Korea UniversitySeoul 02841Republic of Korea Department of Chemistry Seoul National UniversitySeoul 08826Republic of Korea these authors contributed equally to this article.

Ambient temperature affects flowering time in plants,and the MADS-box transcription factor SHORT VEGETATIVE PHASE(SVP)plays a crucial role in the response to changes in ambient *** protein stability is regulated by the 26S proteasome pathway and decreases at high ambient temperature,but the details of SVP degradation are ***,we show that SVP degradation at high ambient temperature is mediated by the CULLIN3–RING E3 ubiquitin ligase(CRL3)complex in Arabidopsis *** identified a previously uncharacterized protein that interacts with SVP at high ambient temperature and contains a BTB/POZ *** named this protein LATE FLOWERING AT HIGH TEMPERATURE 1(LFH1).Single mutants of LFH1 or CULLIN3A(CUL3A)showed late flowering specifically at 27***1 protein levels increased at high ambient *** found that LFH1 interacts with CUL3A in the cytoplasm and is important for SVP–CUL3A complex *** in CUL3A and/or LFH1 led to increased SVP protein stability at high ambient temperature,suggesting that the CUL3–LFH1 complex functions in SVP *** E2 ubiquitin-conjugating enzymes(UBCs)using RING-BOX PROTEIN 1(RBX1),a component of the CRL3 complex,as bait identified ***15 mutants also showed late flowering at high ambient *** vitro and in vivo ubiquitination assays using recombinant CUL3A,LFH1,RBX1,and UBC15 showed that SVP is highly ubiquitinated in an ATP-dependent ***,these results indicate that the degradation of SVP at high ambient temperature is mediated by a CRL3 complex comprising CUL3A,LFH1,and UBC15.

关键词： temperature-responsive flowering SVP CUL3 proteasomal degradation ubiquitination

Modulation of Guard Cell Turgor and Drought Folerance by a Peroxisomal Acetate-Malate Shunt

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Molecular Plant 2018年第10期11卷 1278-1291页

作者： Huan Dong Ling Bai Yu Zhang Guozeng Zhang Yanqing Mao Lulu Min Fuyou Xiang Dongdong Qian Xiaohong Zhu Chun-Peng Song Institute of Plant Stress Biology State Key Laboratory of Cotton Biology Department of Biology Henan University 85 Mingiun Street Kaifeng 475001 China these authors contributed equally to this article.

In plants, stomatal movements are tightly controlled by changes in cellular turgor pressure. Carbohydrates produced by glycolysis and the tricarboxylic acid cycle play an important role in regulating turgor pressure. Here, we describe anArabidopsis mutant, bzul, isolated in a screen for elevated leaf temperature in response to drought stress, which displays smaller stomatal pores and higher drought resistance than wild-type plants. BZU1 encodes a known acetyl-coenzyme A synthetase, ACN1, which acts in the first step of a metabolic pathway converting acetate to malate in peroxisomes. We showed that BZUl/ACNl-mediated acetate-to-malate conversion provides a shunt that plays an important role in osmoregulation of stomatal turgor. We found that the smaller stomatal pores in the bzul mutant are a consequence of reduced accumu- lation of malate, which acts as an osmoticum and/or a signaling molecule in the control of turgor pressure within guard cells, and these results provided new genetic evidence for malate-regulated stomatal movement. Collectively, our results indicate that a peroxisomal BZUl/ACNl-mediated acetate--malate shunt regulates drought resistance by controlling the turgor pressure of guard cells in Arabidopsis.

关键词： acetate-malate shunt acetyl-CoA synthetase BZU1/ACN1 guard cell turgor pressure

Soybean miR172a Improves Salt Tolerance and Can Function as a Long-Distance Signal

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Molecular Plant 2016年第9期9卷 1337-1340页

作者： Wen-Jia Pan Jian-Jun Tao Tong Cheng Xiao-Hua Bian Wei Wei Wan-Ke Zhang Biao Ma Shou-Yi Chen Jin-Song Zhang State Key Lab of Plant Genomics Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China These authors contributed equally to the article.

Dear Editor Soybean is an important crop for oil and protein resources but its growth and development may e6counter various abiotic stresses, including high salinity, that can hinder soybean production. Manipulation of soybean stress tolerance requires a thorough understanding of the mechanisms underlying plant response to stresses. Evolutionarily, plants have developed multiple gene regulatory mechanisms to adjust cellular activities for better survival under stress conditions, and one of these is microRNA （miRNA）-medi- ated gene silencing （Zhang, 2015）. Many conserved and novel miRNAs have been identified in different organs of soybean and in different processes during soybean development （Song et al., 2011）. However, these soybean miRNAs were seldom studied in stress response. Previously, we have identified multiple stressresponsive transcription factor genes from soybean and analyzed their functions in stress response （Wei et al., 2009; Wang et al., 2015）. Now we intend to explore the role of miRNAs in the regulation of soybean response to stresses. Among our previously identified miRNAs from soybean （Song et al., 2011）, the gma-miR172a can be induced by salt and other stresses, and so was selected for further investigation.

关键词： SOYBEAN genetics MICRORNA genetics GENES

Expanding the Range of CRISPR/Cas9 Genome Editing in Rice

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Molecular Plant 2016年第6期9卷 943-945页

作者： Xixun Hu Chun Wang Yaping FU Qing Liu Xiaozhen Jiao Kejian Wang State Key Laboratory of Rice Biology China National Rice Research Institute Chinese Academy of Agricultural Sciences Hangzhou 310006 China these authors contributed equally to this article.

Dear Editor The CRISPR/Cas9 system has emerged as a versatile molecular tool for genome editing in various organisms, including plants. In this system, the specificity of Cas9-directed DNA cleavage strictly requires the presence of a chimeric single guide RNA （sgRNA） and a short trinucleotide protospacer adjacent motif （PAM） in the genome （Anders et al., 2014; Sternberg et al., 2014）. To date, the Cas9 used in plants has only been shown to recognize PAM sequences in the canonical form NGG （Li et al., 2013; Miao et al., 2013; Shan et al., 2013; Ma et al., 2015b）. As such, the range of sequences for genome editing in plants is limited to sites containing an NGG motif. Many attempts have been made to overcome this constraint, and recent work has revealed that Cas9 can be modified to recognize alternative PAM sequences in zebrafish and human cells （Kleinstiver et al., 2015）. However, the targeting range limitations of the CRISPR/ Cas9 systems in plants have yet to be resolved. The widely cultivated plant rice is not only an important food crop but also a model crop plant because of its relatively small genome and relative ease of transformation. To expand the range of genome editing in rice, we generated two Cas9 variants as reported （Kleinstiver et al., 2015） and investigated their genome editing performance in rice. We demonstrate that Cas9 can be engineered to target sites containing alternative non-canonical PAMs in rice, which significantly broadens the range of genorne editing.

关键词： GENOME editing RICE CRISPRS (Genetics)

Distant eQTLs and Non-coding Sequences Play Critical Roles in Regulating Gene Expression and Quantitative Trait Variation in Maize

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Molecular Plant 2017年第3期10卷 414-426页

作者： Haijun Liu Xin Luo Luyao Niu Yingjie Xiao Lu Chen Jie Liu Xiaqing Wang Minliang Jin Wenqiang Li Qinghua Zhang Jianbing Yan National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University Wuhan 430070 China These authors contributed equally to this article

A detailed understanding of genetic architecture of mRNA expression by millions of genetic variants is important for studying quantitative trait variation. In this study, we identified 1.25M SNPs with a minor allele frequency greater than 0.05 by combining reduced genome sequencing （GBS）, high- density array technologies （600K）, and previous deep RNA-sequencing data from 368 diverse inbred lines of maize. The balanced allelic frequencies and distributions in a relatively large and diverse natural panel helped to identify expression quantitative trait loci （eQTLs） associated with more than 18 000 genes （63.4% of tested genes）. We found that distant eQTLs were more frequent （~75% of all eQTLs） across the whole genome. Thirteen novel associated loci affecting maize kernel oil concentration were identified using the new dataset, among which one intergenic locus affected the kernel oil variation by controlling expression of three other known oil-related genes. Altogether, this study provides resources for expanding our understanding of cellular regulatory mechanisms of transcriptome variation and the landscape of functional variants within the maize genome, thereby enhancing the understanding of quantitative variations.

关键词： eQTL RNA-seq GBS GWAS non-coding regulation Zea mays