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Rice Protein Tagging Project:A call for International collaborations on Genome-wide In-Locus Tagging of Rice Proteins

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Molecular Plant 2020年第12期13卷 1663-1665页

作者： Yuming Lu pamela c.ronald Bin Han Jiayang Li Jian-Kang Zhu Shanghai center for Plant Stress Biology CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina Department of Plant Pathology and the Genome center University of CaliforniaDavisCAUSA National center for Gene Research CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina State Key Laboratory of Plant Genomics and National Center for Plant Gene Research(Beijing)Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijingChina Department of Horticulture and Landscape Architecture Purdue UniversityWest LafayetteINUSA

In September 1997,the International Rice Genome Sequencing Project was *** initiative pooled the resources of ten nations to obtain the first complete rice genome sequence,and promoted rice research and breeding into the post-genomics era(Li et al.,2018).In 2008,an internationally coordinated project named "RIcE2020" was proposed to systematically and fully characterize all rice genes,transcripts,and proteins(Zhang et al.,2008).While genes and their transcripts can be readily characterized by sequencing-and PcR-based methods,the characterization of protein dynamics including protein levels,subcellular localizations,post-transla-tional modifications,and interactions with macromolecules(e.g.,proteins,DNA,RNA,carbohydrates,and lipids)and small molecules(e.g.,metabolites and ligands)is much more challenging and usually requires antibodies that specifically recognize the protein of *** it is very difficult to systematically produce reliable antibodies for the specific recognition of individual plant proteins,a common practice is to transform a tag-fused open reading frame(ORF)of a gene to the corresponding loss-of-function mutant ***,such an ectopically expressed tagged protein may not fully reca-pitulate the properties of the endogenous protein due to the random insertion of the transgene,even when the transgene is expressed under the endogenous gene promoter.A preferred so-lution is to genetically label the coding sequence of the gene of interest,at its in vivo locus,with a sequence encoding a fluores-cent protein tag or an affinity tag such as FLAG or *** "in-locus" protein tagging,as we are naming it here,has been carried out genome-wide in yeast,caenorhabditis elegans,fly,and mammalian cultured cells,greatly facilitating the characterization of proteins in these organisms(Jiang et al.,2018).In 2017,a Genome Tagging Project was launched in mice,aiming to label every protein using a cRISPR/cas9-based "artificial spermatids"method(

关键词： breeding Genome endogenous

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OsSERK1 regulates rice development but not immunity to Xanthomonas oryzae pv. oryzae or Magnaporthe oryzae

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Journal of Integrative Plant Biology 2014年第12期56卷 1179-1192页

作者： Shimin Zuo Xiaogang Zhou Mawsheng chen Shilu Zhang Benjamin Schwessinger Deling Ruan can Yuan Jing Wang Xuewei chen pamela c.ronald Department of Plant Pathology and the Genome center University of California Joint Bioenergy Institute Emeryville California 94710 USA Key Laboratory of crop Genetics and Physiology of Jiangsu Province College of Agriculture Yangzhou University Key Laboratory of Plant Functional Genomics of the Ministry of Education College of Agriculture Yangzhou University Rice Research Institute Sichuan Agricultural University at Wenjiang

Somatic embryogenesis receptor kinase（SERK）proteins play pivotal roles in regulation of plant development and immunity. The rice genome contains two SERK genes,OsSerk1 and OsSerk2. We previously demonstrated that OsSerk2 is required for rice Xa21-mediated resistance to Xanthomonas oryzae pv. oryzae（Xoo） and for normal development. Here we report the molecular characterization of OsSerk1. Overexpression of OsSerk1 results in a semi-dwarf phenotype whereas silencing of OsSerk1 results in a reduced angle of the lamina joint. OsSerk1 is not required for rice resistance to Xoo or Magnaporthe oryzae. Overexpression of Os Serk1 in OsSerk2-silenced lines complements phenotypes associated with brassinosteroid（BR） signaling defects, but not the disease resistance phenotype mediated by Xa21. In yeast, OsSERK1 interacts with itself forming homodimers, and also interacts with the kinase domains of OsSERK2 and BRI1, ***1 is a functional protein kinase capable of auto-phosphorylation in vitro. We conclude that, whereas OsSERK2 regulates both rice development and immunity, OsSERK1 functions in rice development but not immunity to Xoo and M. oryzae.

关键词： Oryza sativa OsSERK1 somatic embryogenesis receptor kinase Xanthomonas oryzae pv.Oryzae Magnaporthe oryzae

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The Receptor Kinase XAK1 Regulates the Early Signaling of the Pattern-recognition Receptor XA21-mediated Innate Immunity

The Receptor Kinase XAK1 Regulates the Early Signaling of th...

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中国植物病理学会2011年学术年会

作者： Mawsheng chern Patrick E.canlas pamela c.ronald Department of Plant Pathology University of CaliforniaDavisCalifornia 95616USA Department of Plant Molecular Systems Biotechnology and crop Biotech Institute Kyung Hee UniversityYongin 446-701Korea Department of Genetics Scripps Research Institute10550 North Torrey Pines RoadLa JollaCalifornia 92037USA

＜正＞Plants sense potential microbial invaders by using pattern-recognition receptors to recognize pathogen-associated molecular patterns（PAMPs）.In rice,the leucine-rich repeat receptor kinase XA21 act as pattern-recognition receptor for the bacterial PAMP Ax21 （Activator of XA21-mediated immunity） and contribute to innate immunity against Xanthomonas oryzae ***（Xoo）,the causal bacterial pathogen to *** is known about the early signaling in XA21-mediated innate immune *** we show that XAK1（XA21-associated receptor kinase 1）,one of rice somatic embryogenesis receptor kinases（SERKs） is essential for XA21-mediated innate ***21 plants silenced for XAK1 show deeply compromised resistance to Xoo indicating that XAK1 acts as a positive regulator in *** provide evidence that XAK1 interacts with XA21 in yeast in a kinase-dependent *** association of XAK1 with XA21 in vivo is *** addition,we found that XAK1 is associated with developmental regulation through the plant hormone brassinolide（BL）.Thus,XAK1 is not only associated with PRR-dependent signaling,which initiates innate immunity but also regulates development through the hormone BL.

关键词： Rice innate immunity Xoo development brassinolide

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The receptor kinase XAK1 regulates the early signaling of the pattern-recognition receptor XA21-mediated innate immunity

The receptor kinase XAK1 regulates the early signaling of th...

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中国作物学会50周年庆祝会暨2011年学术年会

作者： Mawsheng chern Patrick E. canlas pamela c.ronald Department of Plant Pathology University of CaliforniaDavisCalifornia 95616USA Department of Plant Molecular Systems Biotechnology and crop Biotech Institute Kyung Hee UniversityYongin 446-701Korea Department of Genetics Scripps Research Institute10550 North Torrey Pines RoadLa JollaCalifornia 92037USA

Plants sense potential microbial invaders by using pattern-recognition receptors to recognize pathogen-associated molecular patterns(PAMPs).In rice,the leucine-rich repeat receptor kinase XA21 acts as pattern-recognition receptor for the bacterial PAMP Ax21(Activator of XA21-mediated immunity) and contribute to innate immunity against Xanthomonas oryzae ***(Xoo),the causal bacterial pathogen to *** is known about the early signaling in XA21 -mediated innate immune *** we show that XAK1(XA21-associated receptor kinase 1),one of rice somatic embryogenesis receptor kinases(SERKs) is essential for XA21-mediated innate ***21 plants silenced for XAK1 show deeply compromised resistance to Xoo indicating that XAK1 acts as a positive regulator in *** provide evidence that XAK1 interacts with XA21 in yeast in a kinase-dependent *** association of XAK1 with XA21 in vivo is *** addition,we found that XAK1 is associated with developmental regulation through the plant hormone brassinolide(BL).Thus,XAK1 is not only associated with PRR-dependent signaling,which initiates innate immunity but also regulates development through the hormone BL.

关键词： Rice innate immunity Xoo development brassinolide

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Dissect the rice immune system using a whole-genome sequenced mutant population

Dissect the rice immune system using a whole-genome sequence...

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第十九届中国作物学会学术年会

作者：沙干 Rashmi Jain Juan Zhao Xiaojing Kong Qiping Sun Lei Yang Jerry Jenkins Mawsheng chern Joel A.Martin Feng Xing Weibo Xie Qiang Li Liang Guo Rod A.Wing Jeremy Schmutz pamela c.ronald 李国田 college of Plant Science and Technology Huazhong Agricultural University Department of Plant Pathology University of California Joint Bioenergy Institute Lawrence Berkeley National Laboratory U.S.Department of Energy Joint Genome Institute HudsonAlpha Institute for Biotechnology National Key Laboratory of crop Genetic Improvement National Center of Plant Gene Research (Wuhan) Huazhong Agricultural University Arizona Genomics Institute School of Plant Sciences University of Arizona BIO5 Institute School of Plant Sciences University of Arizona

Background: The availability of thousands of sequenced rice genomes from diverse varieties and accessions provides a rich genetic resource for in-depth exploration in rice function genomics. One drawback to these collections is that most of these rice varieties have long life cycles, and/or low transformation efficiencies, which limits their usefulness as model organisms for biological studies. In contrast, the rice variety Kitaake has a rapid life cycle(9 weeks seed to seed) and is easy to transform and propagate. For these reasons, Kitaake has emerged as a model for studies of diverse monocotyledonous species. Results: We report the de novo genome sequencing and analysis of an early flowering Geng/japonica variety KitaakeX. Our KitaakeX sequence assembly contains 377.6 Mb, consisting of 33 scaffolds(476 contigs) with a contig N50 of 1.4 Mb. complementing the assembly are detailed gene annotations of 35,594 protein coding genes. To further facilitate rice research, we generated and sequenced a fast-neutron-induced mutant population. We sequenced 1,504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. We have screened this mutant population for lines altered in plant immunity and identified multiple mutant candidates. One of them named rbl1 showed enhanced resistance to the rice blast fungus Magnaporthe oryzae. We cloned the target gene that is involved in phospholipid biosynthesis and plasma membrane integrity. RBL1 is mainly located in endoplasmic reticulum(ER). Lipidomics assays show that the phosphatidylinositol(PI) level is significantly reduced in the rbl1 mutant. We have used RNA-seq assays to analyze genes with altered expression levels and identified multiple downstream candidate genes, including receptor-like cytoplasmic kinases(

关键词： Rice Kitaake Lesion mimic mutant Blast resistance Lipidomics

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A single transcription factor promotes both yield and immunity in rice

A single transcription factor promotes both yield and immuni...

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2018全国植物生物学大会

作者： Jing Wang Lian Zhou Hui Shi Mawsheng chern Hong Yu Hong Yi Min He Junjie Yin Xiaobo Zhu Yan Li Weitao Li Jiali Liu Jichun Wang Xiaoqiong chen Hai Qing Yuping Wang Guifu Liu Wenming Wang Ping Li Xianjun Wu Lihuang Zhu Jian-Min Zhou pamela c.ronald Shigui Li Jiayang Li Xuewei chen State Key Laboratory of crop Genetics of Disease Resistance and Disease control State Key Laboratory of Hybrid RiceKey Laboratory of Major Crop Diseases and Collaborative Innovation Center for Hybrid Rice in Yangtze River BasinRice Research InstituteSichuan Agricultural University at Wenjiang Department of Plant Pathology and the Genome center University of California State Key Laboratory of Plant Genomics and National center for Plant Gene Research Beijing Institute of Genetics and Developmental BiologyChinese Academy of Sciences University of the chinese Academy of Sciences

Plant immunity often penalizes growth and *** transcription factor Ideal Plant Architecture 1(IPA1) reducesunproductivetillers and increases grains per panicle,which results in improved rice *** we report that higher IPA1 levels enhance ***,phosphorylation of IPAl at amino acid S163 within its DNA-binding domain occurs in response to infection by the fungus Magnaporthe oryzae,and alters the DNA binding specificity of *** IPAl binds to the promoter of the pathogen defense gene WRKY45 and activates its expression,leading to enhanced disease ***1 returns to a non-phosphorylated state within 48 hours after infection,resuming support of the growth needed for high *** IPA1 promotes both yield and disease resistance by sustaining a balancebetween growth and immunity.

关键词： Transcriptional Factor IPA1 Yield Immunity Rice

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A rice TPR domain protein BSR-K1 negatively regulates broad-spectrum resistance via binding OsPAL1 mRNA

A rice TPR domain protein BSR-K1 negatively regulates broad-...

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中国植物病理学会2019年学术年会

作者： Zhou Xiaogang Liao Haicheng chern Mawsheng Yin Junjie chen Yufei Wang Jianping Zhu Xiaobo chen Zhixiong Yuan can Zhao Wen Wang Jing Li Weitao He Min Ma Bingtian Wang Jichun Qin Peng chen Weilan Wang Yuping Liu Jiali Qian Yangwen Wang Wenming Wu Xianjun Li Ping Zhu Lihuang Li Shigui pamela c.ronald chen Xuewei Key Laboratory of Major crop Diseases Sichuan Agricultural University State Key Laboratory of Hybrid Rice Sichuan Agricultural University

crops carrying broad-spectrum resistance loci provide an effective strategy for controlling infectious disease because these loci typically confer resistance to diverse races of a pathogen or even multiple species of *** their importance,only a few crop broad-spectrum resistance loci have been ***,we report the identification and characterization of the ricebsr-kl(broad-spectrum resistance Kitaake-1) mutant,which confers broad-spectrum resistance against Magnaporthe oryzae and Xanthomonas oryzae *** with no major penalty on key agronomic ***-based cloning reveals that Bsr-k1 encodes a tetratricopeptide repeats(TPRs)-containing protein,which binds to mRNAs of multiple OsPAL(OsPAL1-7) genes and promotes their *** of function of the Bsr-k1 gene leads to accumulation of OsPAL1-7 mRNAs in the bsr-k1 ***,overexpression of OsPAL1 in wild-type rice TP309 confers resistance to ***,supporting the role of *** discovery of the bsr-k1 allele constitutes a significant conceptual advancement and provides a valuable tool for breeding broad-spectrum resistant rice.

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Genome Editing of a Rice cDP-DAG Synthase confers Multi-pathogen Resistance

Genome Editing of a Rice CDP-DAG Synthase Confers Multi-path...

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中国植物病理学会2023年学术年会

作者： SHA Gan SUN Peng KONG Xiaojing HAN Xinyu SUN Qiping LAETITIA Fouillen ZHAO Juan LI Yun YANG Lei WANG Yin GONG Qiuwen ZHOU Yarn ZHOU Wenqing JAIN Rashmi GAO Jie HUANG Renliang cHEN Xiaoyang ZHENG Lu ZHANG Wanying QIN Ziting ZHOU Qi ZENG Qingdong XIE Kabin XU Jiandi TSAN-Yu chiu GUO Liang Jenny c.Mortimer YOHANN Boutté LI Qiang KANG Zhensheng pamela c.ronald LI Guotian Department of Plant Pathology and the Genome center University of CaliforniaDavis National Key Laboratory of crop Genetic Improvement Huazhong Agricultural University BGI-Shenzhen State Key Laboratory of crop Stress Biology for Arid Areas Northwest A&F University School of Agriculture Food and WineUniversity of Adelaide Innovative Genomics Institute University of CaliforniaBerkeley

The discovery and application of genome editing introduce a new era of plant breeding,giving researchers efficient tools for the precise engineering of crop ***, we demonstrate the power of genome editing for engineering broad-spectrum disease resistance in rice( Oryza sativa).We first isolated a lesion mimic mutant( LMM) from a mutagenized rice population, demonstrated that a29-bp deletion in a gene we named RESISTANcE TO BLAST1( RBL1) caused this phenotype and showed that this mutation caused a ca.20-fold reduction in *** encodes a cytidine diphosphate diacylglycerol(cDP-DAG) synthase required for phospholipid *** of RBL1 results in reduced levels of phosphatidylinositol(P1) and its derivative PI(4, 5) *** PI(4, 5) P is enriched in cellular structures specifically associated with effector secretion and fungal infection, suggesting a role as a disease susceptibility *** targeted genome editing, we obtained an allele of RBL1, named RBL1, which confers broad-spectrum resistance but does not decrease yield in a model rice variety as assessed in small-scale field *** study has demonstrated the usefulness of editing of an LMM gene, a strategy relevant to diverse LMM genes and crops.

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Recent Advances in Dissecting Stress-Regulatory crosstalk in Rice

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Molecular Plant 2013年第2期6卷 250-260页

作者： Rita Sharma David De Vleesschauwer Manoj K. Sharma pamela c. ronald Department of Plant Pathology and Genome center University of California Davis CA 95616 USA Joint BioEnergy Institute Emeryville CA 94710 USA Laboratory of Phytopathology Faculty of Bioscience Engineering Ghent University B-9000 Ghent Belgium Department of Plant Molecular Systems Biotechnology and crop Biotech Institute Kyung Hee University Yongin 446-701 Korea

Biotic and abiotic stresses impose a serious limitation on crop productivity worldwide. Prior or simultaneous exposure to one type of stress often affects the plant response to other stresses, indicating extensive overlap and cross-talk between stress-response signaling pathways. Systems biology approaches that integrate large genomic and prot-eomic data sets have facilitated identification of candidate genes that govern this stress-regulatory crosstalk. Recently, we constructed a yeast two-hybrid map around three rice proteins that control the response to biotic and abiotic stresses, namely the immune receptor XA21, which confers resistance to the Gram-negative bacterium, Xanthomonas oryzae pv. oryzae; NH1, the rice ortholog of NPR1, a key regulator of systemic acquired resistance; and the ethylene-responsive transcription factor, SUBIA, which confers tolerance to submergence stress. These studies coupled with transcriptional profiling and co-expression analyses identified a suite of proteins that are positioned at the interface of biotic and abiotic stress responses, including mitogen-activated protein kinase 5 （OsMPK5）, wall-associated kinase 25 （WAK25）, sucrose non-fermenting-l-related protein kinase-1 （SnRK1）, SUBIA binding protein 23 （SAB23）, and several WRKY family tran- scription factors. Emerging evidence suggests that these genes orchestrate crosstalk between biotic and abiotic stresses through a variety of mechanisms, including regulation of cellular energy homeostasis and modification of synergistic and/or antagonistic interactions between the stress hormones salicylic acid, ethylene, jasmonic acid, and abscisic acid.

关键词： abiotic biotic crosstalk defense response hormone systems biology stress.

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Strong Suppression of Systemic Acquired Resistance in Arabidopsis by NRR is Dependent on its Ability to Interact with NPRland its Putative Repression Domain

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Molecular Plant 2008年第3期1卷 552-559页

作者： Mawsheng chern Patrick E. canlas pamela c. ronald Department of Plant Pathology University of California Davis CA 95616 USA

Systemic Acquired Resistance （SAR） in plants confers lasting broad-spectrum resistance to pathogens and requires the phytohormone salicylic acid （SA）. Arabidopsis NPR1/NIM1 is a key regulator of the SAR response. Studies attempting to reveal the function of NPR1 and how it mediates SA signaling have led to isolation of two classes of proteins that interact with NPRI＂ the first class includes rice NRR, Arabidopsis NIMIN1, NIMIN2, and NIMIN3, and tobacco NIMIN2-1ike proteins; the second class belongs to TGA transcription factors. We have previously shown that overexpression of N RR in rice suppresses both basal and Xa21-mediated resistance. In order to test whether NRR affects SA-induced, NPRl-mediated SAR, we have transformed Arabidopsis with the rice NRR gene and tested its effects on the defense response. Expression of NRR in Arabidopsis results in suppression of PR gene induction by SAR inducer and resistance to pathogens. These phenotypes are even more severe than those of the nprl-1 mutant. The ability of NRR to suppress PR gene induction and disease resistance is correlated with its ability to bind to NPR1 because two point mutations in NRR, which reduce NPR1 binding, fail to suppress NPR1. In contrast, wild-type and a mutant NRR, which still binds to NPR1 strongly, retain the ability to suppress the SAR response. Replacing the c-terminal 79 amino acids of NRR with the VP16 activation domain turns the fusion protein into a transcriptional co-activator. These results indicate that NRR binds to NPR1 in vivo in a protein complex to inhibit transcriptional activation of PR genes and that NRR contains a transcription repression domain for active repression.

关键词： NRR NPR1 SA SAR disease resistance.

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