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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

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

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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

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

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： PROTEIN microarrays plant physiology PROTEINS plant genetics ARABIDOPSIS thaliana TRANSCRIPTION factors

Proximity labeling: an emerging tool for probing in planta molecular interactions

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plant Communications 2021年第2期2卷 1-15页

作者： Xinxin Yang Zhiyan Wen Dingliang Zhang Zhen Li Dawei Li Ugrappa Nagalakshmi Savithramma P.Dinesh-Kumar Yongliang Zhang State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology College of Biological SciencesChina Agricultural UniversityBeijing 100193P.R.China State Key Laboratory of plant Physiology and Biochemistry College of Biological SciencesChina Agricultural UniversityBeijing 100193China Department of plant biology and the Genome Center College of Biological SciencesUniversity of CaliforniaDavisDavisCA 95616USA

Protein–protein interaction(PPI)networks are key to nearly all aspects of cellular ***,the identification of PPIs is important for understanding a specific biological process in an *** with conventional methods for probing PPIs,the recently described proximity labeling(PL)approach combined with mass spectrometry(MS)-based quantitative proteomics hasemerged as apowerful approach for characterizing ***,the application of PL in planta remains in its ***,we summarize recent progress in PL and its potential utilization in plant *** specifically summarize advances in PL,including the development and comparison of different PL enzymes and the application of PL for deciphering various molecular interactions in different organisms with an emphasis on plant systems.

关键词： protein interactions proximity labeling biotin ligase plant membrane contact sites organelles

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

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

The tea plant CsLHT1 and CsLHT6 transporters take up amino acids, as a nitrogen source, from the soil of organic tea plantations

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Horticulture Research 2021年第1期8卷 2333-2344页

作者： Fang Li Chunxia Dong Tianyuan Yang Shilai Bao Wanping Fang William J.Lucas Zhaoliang Zhang State Key Laboratory of Tea plant biology and Utilization Anhui Agricultural university HefeiAnhui 230036China college of Horticulture Nanjing Agricultural university Nanjing 210095China State Key Laboratory of Molecular Developmental biology Institute of Genetics and Developmental Biology Chinese Academy of SciencesBeijing 100101China Department of plant biology College of Biological Sciences University of CaliforniaDavisCA 95616USA

Organic tea is more popular than conventional tea that originates from fertilized *** acids inorganic soils constitute a substantial pool nitrogen(N)available for ***,the amino-acid contents in soils of tea plantations and how tea plants take up these amino acids remain largely *** this study,we show that the amino-acid content in the soil of an organic tea plantation is significantly higher than that of a conventional tea ***,alanine,valine,and leucine were the most abundant amino acids in the soil of this tea *** 15 N-glutamate was fed to tea plants,it was efficiently absorbed and significantly increased the contents of other amino acids in the *** cloned seven CsLHT genes encoding amino-acid transporters and found that the expression of CsLHT1,CsLHT2,and CsLHT6 in the roots significantly increased upon glutamate ***,the expression of CsLHT1 or CsLHT6 in a yeast amino-acid uptake-defective mutant,22Δ10α,enabled growth on media with amino acids constituting the sole N ***-acid uptake assays indicated that CsLHT1 and CsLHT6 are H^(+)-dependent high-and low-affinity amino-acid transporters,*** further demonstrated that CsLHT1 and CsLHT6 are highly expressed in the roots and are localized to the plasma ***,overexpression of CsLHT1 and CsLHT6 in Arabidopsis significantly improved the uptake of exogenously supplied 15 N-glutamate and 15 *** together,our findings are consistent with the involvement of CsLHT1 and CsLHT6 in amino-acid uptake from the soil,which is particularly important for tea plants grown inorganic tea plantations.

关键词： roots inorganic const

CLE25 peptide regulates phloem initiation in Arabidopsis through a CLERK-CLV2 receptor complex

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Journal of Integrative plant biology 2019年第10期61卷 1043-1061页

作者： Shi-Chao Ren Xiu-Fen Song Wen-Qiang Chen Ran Lu William J. Lucas Chun-Ming Liu Key Laboratory of plant Molecular Physiology Institute of Botany Chinese Academy of Sciences Nanxincun 20 Fragrant Hill Beiing 100093 China university of Chinese Academy of sciences Beiing 100049 China Department of plant biology College of Biological Sciences University of California Davis CA 95616 USA Institute of Crop sciences Chinese Academy of Agricultural Sciences Beiing 100081 China

The phloem, located within the vascular system, is critical for delivery of nutrients and signaling molecules throughout the plant body. Although the morphological process and several factors regulating phloem differentiation have been reported, the molecular mechanism underlying its initiation remains largely unknown. Here, we report that the small peptide-coding gene, CLAVATA 3 (CLV3)/EMBEYO SURROUNDING REGION 25 (CLE25), the expression of which begins in provascular initial cells of 64-cell-staged embryos, and continues in sieve element-procambium stem cells and phloem lineage cells, during postembryonic root development, facilitates phloem initiation in Arabidopsis. Knockout of CLE25 led to delayed protophloem formation, and in situ expression of an antagonistic CLE25G6T peptide compromised the fate-determining periclinal division of the sieve element precursor cell and the continuity of the phloem in roots. In stems of CLE25G6T plants the phloem formation was also compromised, and procambial cells were over-accumulated. Genetic and biochemical analyses indicated that a complex, consisting of the CLE-RESISTANT RECEPTOR KINASE (CLERK) leucinerich repeat (LRR) receptor kinase and the CLV2 LRR receptor- like protein, is involved in perceiving the CLE25 peptide. Similar to CLE25, CLERK was also expressed during early embryogenesis. Taken together, our findings suggest that CLE25 regulates phloem initiation in Arabidopsis through a CLERK-CLV2 receptor complex.

关键词： CLE25 peptide CLERK-CLV2 receptor complex