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Proxitome profiling reveals a conserved SGT1- NSL1 signaling module that activates NLRmediated immunity

Molecular plant 2024年第9期17卷 1369-1391页

作者： Dingliang Zhang Xinxin Yang Zhiyan Wen Zhen Li Xinyu Zhang Chenchen Zhong Jiajie She Qianshen Zhang He Zhang Wenli Li Xiaoyun Zhao Mingliang Xu Zhen Su Dawei Li Savithramma P.Dinesh-Kumar Yongliang Zhang State Key Laboratory of plant Environmental Resilience College of Biological SciencesChina Agricultural UniversityBejing 100193China Department of plant biology and The Genome Center College of Biological SciencesUniversity of CaliforniaDavisDavisCA 95616USA State Key Laboratory of plant Environmental Resilience College of Agronomy and BiotechnologyChina Agricultural UniversityBejing 100193China

Suppressor of G2 allele of skp1(SGT1)is a highly conserved eukaryotic protein that plays a vital role in growth,development,and immunity in both animals and *** some SGT1 interactors have been identified,the molecular regulatory network of SGT1 remains ***1 serves as a co-chaperone to stabilize protein complexes such as the nucleotide-binding leucine-rich repeat(NLR)class of immune receptors,thereby positively regulating plant ***1 has also been found to be asso-ciated with the SKP1-Cullin-F-box(SCF)E3 ubiquitin ligase ***,whether SGT1 targets im-mune repressors to coordinate plant immune activation remains *** this study,we constructed a toolbox for TurbolD-and split-TurbolD-based proximity labeling(PL)assays in Nicotiana benthamiana and used the PL toolbox to explore the SGT1 interactome during pre-and post-immune *** comprehensive SGT1 interactome network we identified highlights a dynamic shift from proteins associ-ated with plant development to those linked with plant immune *** found that SGT1 interacts with Necrotic Spotted Lesion1(NSL1),which negatively regulates salicylic acid-mediated defenseby inter-fering with the nucleocytoplasmic trafficking of non-expressor of pathogenesis-related genes 1(NPR1)during N NLR-mediated response to tobacco mosaic ***1 promotes the SCF-dependent degrada-tion of NSL1 to facilitate immune activation,while salicylate-induced protein kinase-mediated phosphory-lation of SGT1further potentiates this *** NNLR,NSL1also functions in several other NLR-mediated ***,our study unveils the regulatory landscape of SGT1 and reveals a novel SGT1-NSL1 signaling module that orchestrates plant innate immunity.

关键词： suppressor of G2 allele of skp1 SGT1 proximity labeling N NLR immune receptor Necrotic Spotted Lesion 1 NSL1 salicylic acid ubiquitination

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High-quality assembled and annotated genomes of Nicotiana tabacum and Nicotiana benthamiana reveal chromosome evolution and changes in defense arsenals

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Molecular plant 2024年第3期17卷 423-437页

作者： Jubin Wang Qingling Zhang Jeffrey Tung Xi Zhang Dan Liu Yingtian Deng Zhendong Tian Huilan Chen Taotao Wang Weixiao Yin Bo Lij Zhibing Lai Savithramma P.Dinesh-Kumar Barbara Baker Feng Li National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanHubei 430070China plant Gene Expression Center Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyBerkeleyCA 94706USA college of plant Science and Technology Huazhong Agricultural UniversityWuhanHubei 430070China college of Life Science and Technology Huazhong Agricultural UniversityWuhanHubei 430070China Department of plant biology and The Genome Center College of Biological SciencesUniversity of CalforniaDavisDavisCA 95616USA The Key Laboratory of Horticultural plant Genetic and Improvement of Jiangxi Province Institute of Biological ResourcesJiangxi Academy of SciencesNanchang 330299China institute of Vegetables and Flowers Jiangxi Academy of Agricultural SciencesNanchang 330200Chin Hubei Hongshan Laboratory WuhanHubei 430070China

Nicotiana tabacum and Nicotiana benthamiana are widely used models in plant biology ***,genomic studies of these species have *** we report the chromosome-level reference genome assemblies for *** and *** with an estimated 99.5%and 99.8%completeness,*** transcription start and termination site sequencing methods were developed and used for accurate gene annotation in *** analyses revealed evidence for the parental origins and chromosome structural changes,leading to hybrid genome formation of each ***,theantiviral silencinggenesRDR1,RDR6,DCL2,DCL3,andAGO2were lost from one or both subgenomes in ***,while both homeologs were kept in ***,the *** genome encodes fewer immune receptors and signaling components than that of *** find-ings uncover possible reasons underlying the hypersusceptible nature of *** developed the user-friendly Nicomics(http:/***/Nicomics/)web server to facilitate better use of Nicotiana genomic resources as well as gene structure and expression analyses.

关键词： Nicotiana tabacum Nicotiana benthamiana genomics evolution disease resistance NLR

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Predicting changes in the suitable habitats of six halophytic plant species in the arid areas of Northwest China

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Journal of Arid Land 2024年第10期16卷 1380-1408页

作者： YANG Ao TU Wenqin YIN Benfeng ZHANG Shujun ZHANG Xinyu ZHANG Qing HUANG Yunjie HAN Zhili YANG Ziyue ZHOU Xiaobing ZHUANG Weiwei ZHANG Yuanming college of Life sciences Xinjiang Normal University/Xinjiang Key Laboratory of Special Species Conservation andRegulatory Biology/Key Laboratory of Special Environment Biodiversity Application and Regulation in Xinjiang/KeyLaboratory of Plant Stress Biology in Arid LandUrumqi 830054China State Key Laboratory of Desert and Oasis Ecology Key Laboratory of Ecological Safety and Sustainable Development in AridLandsXinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqi 830011China Xinjiang Key Laboratory of Biodiversity Conservation and Application in Arid Lands Xinjiang Institute of Ecology andGeographyChinese Academy of SciencesUrumqi 830011China Xinjiang Field Scientific Observation Research Station of Tianshan Wild Fruit Forest Ecosystem Yili Botanical GardenXinjiang Institute of Ecology and GeographyChinese Academy of SciencesXinyuan 835800China State Key Laboratory of Earth Surface Processes and Resource Ecology College of Life SciencesBeijing Normal UniversityBeijing 100875China university of Chinese Academy of sciences Beijing 100049China college of biological sciences University of California DavisDavisCA 95616USA college of Ecology and Environment Xinjiang UniversityUrumqi 830017China college of Resources and Environment/Xinjiang Key Laboratory of Soil and plant Ecological Processes Xinjiang AgriculturalUniversityUrumqi 830052China college of Grassland Science Xinjiang Agricultural UniversityUrumqi 830052China

In the context of changes in global climate and land uses,biodiversity patterns and plant species distributions have been significantly *** salinization is a growing problem,particularly in the arid areas of Northwest *** are ideal for restoring soil salinization because of their adaptability to salt *** this study,we collected the current and future bioclimatic data released by the WorldClim database,along with soil data from the Harmonized World Soil Database(v1.2)and A Big Earth Data Platform for Three *** the maximum entropy(MaxEnt)model,the potential suitable habitats of six halophytic plant species(Halostachys caspica(Bieb.)***.,Halogeton glomeratus(Bieb.)***.,Kalidium foliatum(Pall.)Moq.,Halocnemum strobilaceum(Pall.)Bieb.,Salicornia europaea L.,and Suaeda salsa(L.)Pall.)were assessed under the current climate conditions(average for 1970-2000)and future(2050s,2070s,and 2090s)climate scenarios(SSP245 and SSP585,where SSP is the Shared Socio-economic Pathway).The results revealed that all six halophytic plant species exhibited the area under the receiver operating characteristic curve values higher than 0.80 based on the MaxEnt model,indicating the excellent performance of the MaxEnt *** suitability of the six halophytic plant species significantly varied across regions in the arid areas of Northwest *** different future climate change scenarios,the suitable habitat areas for the six halophytic plant species are expected to increase or decrease to varying *** global warming progresses,the suitable habitat areas of ***,***,and *** exhibited an increasing *** contrast,the suitable habitat areas of ***,***,and *** showed an opposite ***,considering the ongoing global warming trend,the centroids of the suitable habitat areas for various halophytic plant species would migrate to different degrees,and four halophytic plant species,namely,S.

关键词： halophytes climate change global warming maximum entropy(MaxEnt)model soil salinization suitable habitats Northwest China

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plant Vascular biology and Agriculture

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Journal of Integrative plant biology 2010年第1期52卷 4-7页

作者： William J. Lucas The Editor of this Special Issue dept. of plant biology college of biological sciences university of california davis

The evolution of animal and plant vascular systems played a pivotal role in the advancement from simple to complex organisms, through the provision of a delivery system for the distribution of components essential for both metabolism and growth. Interestingly, although these two vascular systems conform to the same general rules of fluid dynamics （Murray 1926; McCulloh et al. 2003）, the developmental mechanisms adopted by plants and animals, to generate these long-distance transport systems,

关键词： plant Vascular biology and Agriculture

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AtGGM2014, an Arabidopsis gene co-expression network for functional studies

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Science China(Life sciences) 2015年第3期58卷 276-286页

作者： MA ShiSong BOHNERT Hans J DINESH-KUMAR Savithramma P Department of plant biology and the Genome Center College of Biological Sciences University of California Departments of plant biology and of Crop sciences University of Illinois at Urbana-Champaign

Gene co-expression networks provide an important tool for systems biology studies. Using microarray data from the Array Express database, we constructed an Arabidopsis gene co-expression network, termed At GGM2014, based on the graphical Gaussian model, which contains 102,644 co-expression gene pairs among 18,068 genes. The network was grouped into 622 gene co-expression modules. These modules function in diverse house-keeping, cell cycle, development, hormone response, metabolism, and stress response pathways. We developed a tool to facilitate easy visualization of the expression patterns of these modules either in a tissue context or their regulation under different treatment conditions. The results indicate that at least six modules with tissue-specific expression pattern failed to record modular regulation under various stress conditions. This discrepancy could be best explained by the fact that experiments to study plant stress responses focused mainly on leaves and less on roots, and thus failed to recover specific regulation pattern in other tissues. Overall, the modular structures revealed by our network provide extensive information to generate testable hypotheses about diverse plant signaling pathways. At GGM2014 offers a constructive tool for plant systems biology studies.

关键词： Arabidopsis gene co-expression network graphical Gaussian model plant development stress response hormone response

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Distribution of a kinesin-related protein on Golgi apparatus of tobacco pollen tubes

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Chinese Science Bulletin 2005年第19期50卷 2175-2181页

作者： WEI Liqin LIU Bo LI Yan State Key Laboratory of plant Physiology and Biochemistry College of Biological Sciences China Agricultural University Beijing 100094 China Section of plant biology University of California-Davis Davis CA 95616-8537 USA

Previous study has shown that the internal mo-tor kinesin AtKinesin-13A is associated with Golgi stacks in various Arabidopsis cells. With degenerate primers, a seg-ment of 2067 bp was cloned from tobacco by RT-PCR. The polypeptide coded by the segment has 77.33% similarities with the corresponding part of AtKinesin-13A from Arabi-dopsis; and antibody of AtKinesin-13A recognized specifi-cally the expressed products of the segment in bacteria. Us-ing the anti-AtKinesin-13A antibodies, a 120 kD polypeptide was detected from protein extracts of various organs from Nicotiana tabacum, indicating that a homologue of AtKine-sin-13A protein, NtKinesin-13A, is expressed in Nicotiana tabacum. Immunofluorescence staining showed that the to-bacco NtKinesin-13A protein appeared in particles in pollen tubes by confocal microscopy. Immunofluorescence double labeling showed that the NtKinesin-13A protein particles partially co-distributed with 58K protein, indicating that NtKinesin-13A is located on Golgi apparatus. Immuno-gold labeling and electron microscopy observation revealed that the NtKinesin-13A was associated with Golgi-associated vesi-cles membranes in tobacco pollen tubes. These results sug-gest that the NtKinesin-13A may probably play an important role in controlling Golgi stacks, and/or in transporting Golgi- derived vesicles in pollen tubes.

关键词： Golgi器械花粉管蛋白质烟草微生物

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A Light-Independent Allele of Phytochrome B Faithfully Recapitulates Photomorphogenic Transcriptional Networks

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Molecular plant 2009年第1期2卷 166-182页

作者： Wei Hu Yi-Shin Su J. Clark Lagarias Department of Molecular and Cellular biology College of Biological Sciences University of California Davis CA 95616 USA Present address: Carnegie Institution of Washington -Department of Plant Biology Stanford CA 94305 USA

Dominant gain-of-function alleles of Arabidopsis phytochrome B were recently shown to confer lightindependent, constitutive photomorphogenic （cop） phenotypes to transgenic plants （Su and Lagarias, 2007）. In the present study, comparative transcription profiling experiments were performed to assess whether the pattern of gene expression regulated by these alleles accurately reflects the process of photomorphogenesis in wild-type Arabidopsis. Whole- genome transcription profiles of dark-grown phyAphyB seedlings expressing the Y^276H mutant of phyB （YHB） revealed that YHB reprograms about 13% of the Arabidopsis transcriptome in a light-independent manner. The YHB-regulated transcriptome proved qualitatively similar to but quantitatively greater than those of wild-type seedlings grown under 15 or 50 μmol m^-2 m^-1 continuous red light （Rc）. Among the 2977 genes statistically significant two-fold （SSTF） regulated by YHB in the absence of light include those encoding components of the photosynthetic apparatus, tetrapyrrole/pigment biosynthetic pathways, and early light-responsive signaling factors. Approximately 80% of genes SSTF regulated by Rc were also YHB-regulated. Expression of a notable subset of 346 YHB-regulated genes proved to be strongly attenuated by Rc, indicating compensating regulation by phyC-E and/or other Rc-dependent processes. Since the majority of these 346 genes are regulated by the circadian clock, these results suggest that phyA- and phyB-independent light signaling pathway（s） strongly influence clock output. Together with the unique plastid morphology of dark-grown YHB seedlings, these analyses indicate that the YHB mutant induces constitutive photomorphogenesis via faithful reconstruction of phyB signaling pathways in a light-independent fashion.

关键词： light signaling signal transduction transcriptome analysis photomorphogenesis Arabidopsis phytochrome.

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The Development of Protein Microarrays and Their Applications in DNA-Protein and Protein-Protein Interaction Analyses of Arabidopsis Transcription Factors

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Molecular plant 2008年第1期1卷 27-41页

作者： Wei Gong Kun He Mike Covington S. R Dinesh-Kumar Michael Snyder Stacey L. Harmer Yu-Xian Zhu Xing Wang Denga Peking-Yale Joint Center for plant Molecular Genetics and Agrobiotechnology Co and Plant Genetic Engineering Peking University Beijing 100871 China Department of Molecular Cellular and Developmental Biology Yale University New Haven Connecticut 06520 USA Section of plant biology College of Biological Sciences University of California Davis 95616 USA

We used our collection of Arabidopsis transcription factor （TF） ORFeome clones to construct protein microarrays containing as many as 802 TF proteins. These protein microarrays were used for both protein-DNA and proteinprotein interaction analyses. For protein-DNA interaction studies, we examined AP2/ERF family TFs and their cognate cis-elements. By careful comparison of the DNA-binding specificity of 13 TFs on the protein microarray with previous non-microarray data, we showed that protein microarrays provide an efficient and high throughput tool for genome-wide analysis of TF-DNA interactions. This microarray protein-DNA interaction analysis allowed us to derive a comprehensive view of DNA-binding profiles of AP2/ERF family proteins in Arabidopsis. It also revealed four TFs that bound the EE （evening element） and had the expected phased gene expression under clock-regulation, thus providing a basis for further functional analysis of their roles in clock regulation of gene expression. We also developed procedures for detecting protein interactions using this TF protein microarray and discovered four novel partners that interact with HY5, which can be validated by yeast two-hybrid assays. Thus, plant TF protein microarrays offer an attractive high-throughput alternative to traditional techniques for TF functional characterization on a global scale.

关键词： transcription factor (TF) TF-DNA EE (evening element)

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nitiation of ER Body Formation and Indole Glucosinolate Metabolism by the Plastidia Retrograde Signaling Metabolite, MEcPP

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Molecular plant 2017年第11期10卷 1400-1416页

作者： Jin-Zheng Wang Baohua Li Yanmei Xiao Yu Ni Haiyan Ke Panyu Yang Amancio de Souza Marta Bjornson Xiang He Zhouxin Shen Gerd Ulrich Balcke Steve P. Briggs Alain Tissier Daniel J. Kliebenstein Katayoon Dehesh Institute for Integrative Genome biology and Department of Botany and plant sciences University of California Riverside CA 92521 USA Department of plant biology University of California Davis CA 95616 USA Department of plant sciences University of California Davis CA 95616 USA Division of biological sciences University of California San Diego La Jolla CA 92093 USA Department of Cell and Metabolic biology Leibniz-lnstitute of Plant Biochemistry Halle Germany Present address: college of Agronomy and Biotechnology Southwest University Chongqing P.R. China Present address: Rice Research Institute Sichuan Agricultural University Changdu Sichuan 611130 China

plants have evolved tightly regulated signaling networks to respond and adapt to environmental perturbations, but the nature of the signaling hub（s） involved have remained an enigma. We have previously established that methylerythritol cyclodiphosphate （MEcPP）, a precursor of plastidial isoprenoids and a stress- specific retrograde signaling metabolite, enables cellular readjustments for high-order adaptive functions. Here, we specifically show that MEcPP promotes two Brassicaceae-specific traits, namely endoplasmic reticulum （ER） body formation and induction of indole glucosinolate （IGs） metabolism selectively, via tran- scriptional regulation of key regulators NAIl for ER body formation and MYB51/122 for IGs biosynthesis）. The specificity of MEcPP is further confirmed by the lack of induction of wound-inducible ER body genes as well as IGs by other altered methylerythritol phosphate pathway enzymes. Genetic analyses revealed MEcPP-mediated COil-dependent induction of these traits. Moreover, MEcPP signaling integrates the biosynthesis and hydrolysis of IGs through induction of nitrile-specifier protein1 and reduction of the sup- pressor, ESM1, and production of simple nitriles as the bioactive end product. The findings position the plastidial metabolite, MEcPP, as the initiation hub, transducing signals to adjust the activity of hard- wired gene circuitry to expand phytochemical diversity and alter the associated subcellular structure required for functionality of the secondary metabolites, thereby tailoring plant stress responses.

关键词： glucosinolates ER body retrograde signaling MEP pathway MEcPP stress

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A plant Immune Receptor Adopts a Two-Step Recognition Mechanism to Enhance Viral Effector Perception

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Molecular plant 2019年第2期12卷 248-262页

作者： Jia Li Haining Huang Min Zhu Shen Huang Wenhua Zhang Savithramma P. Dinesh-Kumar Xiaorong Tao Department of plant Pathology Nanjing Agricultural University Nanjing 210095 P. R. China college of Life Science Nanjing Agricultural University Nanjing 210095 P. R. China Department of plant biology and The Genome Center College of Biological Sciences University of California Davis CA USA

plant intracellular nucleotide binding leucine-rich repeat (NLR) immune receptors play critical roles in pathoge n surveillance. Most plant NLRs characterized so far were found to use a single domain/sensor to recognize pathogen effectors. Here we report that the Sw-5b NLR immune receptor uses two distinct domains to detect the viral movement protein NSm encoded by tospovirus. In addition to its leucine-rich repeat (LRR) domain that has been previously reported, the N-terminal Solanaceae domain (SD) of Sw- 5b also interacts with NSm and a conserved 21-amino-acid region of NSm (NSm^21). The specific interaction between Sw-5b SD and NSm is required for releasing the inhibitory effect of coiled-coil domain on the NBARC- LRR region. Furthermore, we found that the binding of NSm affects the nucleotide binding activity of the NB-ARC-LRR in vitro, while Sw-5b NB-ARC-LRR is activated only when NSm and NSm^21 levels are high. Interestingly, Sw-5b SD could significantly enhanee the ability of the NB-ARC-LRR to detect low levels of NSm effector and facilitate its activation and induction of defense response. An Sw-5b SD mutant that is disrupted in NSm recognition failed to enhance the ability of the NB-ARC-LRR to sense low levels of NSm and NSm^21 . Taken together, our results suggest that Sw-5b SD functions as an extra sensor and the NB-ARC-LRR as an activator, and that Sw-5b NLR adopts a two-step recog nition mechanism to enhance viral effector perception.

关键词： plant innate immunity nucleotide binding leucine-rich repeat (NLR) immune receptors Solanaceae domain (SD) pathogen perception two-step recognition defense response

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