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DNA chip-based expression profile analysis indicates involvement of the phosphatidylinositol signaling pathway in multiple plant responses to hormone and abiotic treatments

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Cell Research 2004年第1期14卷 34-45页

作者： Wen Hui LIN, Rui YE, Hui MA, Zhi Hong XU, Hong Wei XUE National Laboratory of plant molecular Genetics, institute of plant physiology and Ecology, Shanghai institutes for Biological Sciences (SIBS), Chinese Academy of Sciences and Partner Group of max-planck-institute of molecular plant physiology (MPI-MP) on 'plant molecular physiology and Signal Transduction', 300 Fenglin Road, 200032 Shanghai, China National Laboratory of plant molecular Genetics Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences (SIBS) Chinese Academy of Sciences Partner Group of max-planck-institute of molecular plant physiology (MPI-MP) on “plant molecular physiology and Signal Transduction” Shanghai China

The phosphatidylinositol (PI) metabolic pathway is considered critical in plant responses to many environmental factors, and previous studies have indicated the involvement of multiple PI-related gene families during cellular responses. Through a detailed analysis of the Arabidopsis thaliana genome, 82 polypeptides were identified as being involved in PI signaling. These could be grouped into different families including PI synthases (PIS), PI-phosphate kinases (PIPK), phospholipases (PL), inositol polyphosphate phosphatases (IPPase), inositol polyphosphate kinases (IPK), PI transfer proteins and putative inositol polyphosphate receptors. The presence of more than 10 isoforms of PIPK, PLC, PLD and IPPase suggested that these genes might be differentially expressed during plant cellular responses or growth and development. Accordingly, DNA chip technology was employed to study the expression patterns of various isoforms. In total, 79 mRNA clones were amplified and used for DNA chip generation. Expression

关键词： phosphatidylinositol signal transduction DNA chip expression profile.

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Isolation and functional characterization of the C-terminus of rice phos- phatidylinositol 4-kinase in vitro

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Cell Research 2003年第2期13卷 131-139页

作者： XIANG FENG KONG, ZHI HONG XU, HONG WEI XUE,National Laboratory of plant molecular Genetics, institute of plant physiology and Ecology, Shanghai institutes for Biological Science (SIBS), The Chinese Academy of Sciences Partner Group of max-planck-institute of molecular plant physiology (MPI-MP) on 'plant molecular physiology and Signal Transduction', 300 Fenglin Road, 200032 Shanghai, China National Laboratory of plant molecular Genetics Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Science (SIBS) The Chinese Academy of Sciences Partner Group el max-planck-institute of molecular plant physiology (MPI-MP) on “plant molecular physiology and Signal Transduction” Shanghai China

A partial rice (Oryza sativa L.) cDNA clone. OsPMK1c, was isolated through screening of a cDNA library constructed from tillering materials. OsPI4Klc encoded a peptide of 608 amino acids with a calculated molecular mass of 68.4 kDa. The OsPI4Klc peptide shared high homology and possessed the highly conserved domains present in most isolated cloned PI4-kinases, i.e. a lipid kinase unique (LKU) domain and a catalytic (CAT) domain. A region with similarity to pleckstrin homology (PH) domain was present in OsPI4K1c as well. Further comparison with genomic sequences in databases revealed that OsPI4K1c is located at the 3’-end of a putative rice PI 4-kinase coding gene OsPI4K1, and its coding region corresponded to the C-terminal half of OsPI4Kl protein. Twelve exons (49-562 bp in size) and 11 introns (77-974 bp in size) were identified in OsPI4K1c. The recombinant protein expressed in Escherichia coli phosphorylates phosphatidylinositol at the D4 position of the inositol ring. OsPI4K1 transcript levels were

关键词： Oryza sativa phosphatidylinositol 4-kinase.

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Cellulose Synthases and Synthesis in Arabidopsis

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molecular plant 2011年第2期4卷 199-211页

作者： Anne Endler Staffan Persson max-planck-institute for molecular plant physiology Am M6hlenberg 1 14476 Potsdam Germany

plant cell walls are complex structures composed of high-molecular-weight polysaccharides, proteins, and lignins. Among the wall polysaccharides, cellulose, a hydrogen-bonded β-1,4-1inked glucan microfibril, is the main load-bearing wall component and a key precursor for industrial applications. Cellulose is synthesized by large multi-meric cellulose synthase （CesA） complexes, tracking along cortical microtubules at the plasma membrane. The only known components of these complexes are the cellulose synthase proteins. Recent studies have identified tentative interaction partners for the CesAs and shown that the migratory patterns of the CesA complexes depend on phosphorylation status. These advances may become good platforms for expanding our knowledge about cellulose synthesis in the near future. In addition, our current understanding of cellulose chain polymerization in the context of the CesA complex is discussed.

关键词： Cell expansion cell walls cytoskeleton-cell wall interactions Arabidopsis.

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At Long Last： Evidence for Pexophagy in plants

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molecular plant 2014年第8期7卷 1257-1260页

作者： Tamar Avin-Wittenberg Alisdair R. Fernie max-planck-institute of molecular plant physiology Am Mühlenberg 1 14476 Potsdam-Golm Germany

Peroxisomes are highly dynamic single-membrane-bound eukaryotic organelles displaying great variability in enzymatic content （Platta and Erdmann, 2007）. plant peroxisomes function in a plethora of crucial development and stress ameliorating processes. Among the functions of plant peroxisomes are 13-oxidation of fatty acids, phytohormone production, participation in photorespiration, the glyoxyalte cycle, detoxification processes, and signal molecule generation （Hu et al., 2012）.

关键词： AUTOPHAGY PEROXISOMES ARABIDOPSIS DEGRADATION

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Natural variations of OsAUX5,a target gene of OsWRKY78,control the neutral essential amino acid content in rice grains

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molecular plant 2023年第2期16卷 322-336页

作者： Yuheng Shi Yuanyuan Zhang Yangyang Sun Ziyang Xie Yu Luo Qiyuan Long Jiahui Feng Xueqing Liu Bi Wang Dujun He Junxia Ren Peizhen Guo Junwei Xing Liqiang He Alisdair RFernie Wei Chen Xianqing Liu Yuehua Luo Cheng Jin Jie Luo Sanya Nanfan Research institute of Hainan University Hainan Yazhou Bay Seed LaboratorySanya 572025China College of Tropical Crops Hainan UniversityHaikou 570228China max planck institute of molecular plant physiology 14476 Potsdam-GolmGermany National Key Laboratory of Crop Genetic Improvement and National Center of plant Gene Research(Wuhan) Huazhong Agricultural UniversityWuhan 430070China

Grain essential amino acid(EAA)levels contribute to rice nutritional quality.However,the molecular mechanisms underlying EAA accumulation and natural variation in rice grains remain unclear.Here we report the identification of a previously unrecognized auxin influx carrier subfamily gene,OsAUX5,which encodes an amino acid transporter that functions in uptake of multiple amino acids.We identified an elite haplotype of Pro::OsAUX5^(Hap2) that enhances grain EAA accumulation without an apparent negative effect on agronomic traits.Natural variations of OsAUX5 occur in the cis elements of its promoter,which are differentially activated because of the different binding affinity between OsWRKY78 and the W-box,contributing to grain EAA variation among rice varieties.The two distinct haplotypes were shown to have originated from different Oryza rufipogon progenitors,which contributed to the divergence between japonica and indica.Introduction of the indica-type Pro::OsAUX5^(Hap2) genotype into japonica could significantly increase EAA levels,indicating that indica-type Pro::OsAUX5^(Hap2) can be utilized to increase grain EAAs of japonica varieties.Collectively,our study uncovers an WRKY78–OsAUX5-based regulatory mechanism controlling grain EAA accumulation and provides a potential target for breeding EAA-rich rice.

关键词： amino acid natural variation transcriptional regulation Oryza sativa

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Transcriptional Wiring of Cell Wall-Related Genes in Arabidopsis

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molecular plant 2009年第5期2卷 1015-1024页

作者： Marek Mutwil Colin Ruprecht Federico M. Giorgi Martin Bringmann Bjorn Usadel Staffan Persson max-planck-lnstitute for molecular plant physiology Am Muhlenberg 1 14476 Potsdam Germany

Transcriptional coordination, or co-expression, of genes may signify functional relatedness of the corresponding proteins. For example, several genes involved in secondary cell wall cellulose biosynthesis are co-expressed with genes engaged in the synthesis of xylan, which is a major component of the secondary cell wall. To extend these types of analyses, we investigated the co-expression relationships of all Carbohydrate-Active enZYmes （CAZy）-related genes for Arabidopsis thaliana. Thus, the intention was to transcriptionally link different cell wall-related processes to each other, and also to other biological functions. To facilitate easy manual inspection, we have displayed these interactions as networks and matrices, and created a web-based interface （http：llaranet.***.mpg.delcorecarb） containing downloadable files for all the transcriptional associations.

关键词： Cell walls bioinformatics Arabidopsis co-expression.

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The Potato Sucrose Transporter StSUT1 Interacts with a DRM-Associated Protein Disulfide Isomerase

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molecular plant 2012年第1期5卷 43-62页

作者： Undine Krugel Hong-Xia He Konstanze Gier Jana Reins Izabela Chincinska Bernhard Grimm Waltraud X. Schulze Christina Kuhn institute of Biology Department of Plant Physiology Humboldt University 10115 Berlin Germany max planck institute of molecular plant physiology Am MGhlenberg 1 14476 Potsdam-Golm Germany

Organization of proteins into complexes is crucial for many cellular functions. Recently, the SUT1 protein was shown to form homodimeric complexes, to be associated with lipid raft-like microdomains in yeast as well as in plants and to undergo endocytosis in response to brefeldin A. We therefore aimed to identify SUTl-interacting proteins that might be involved in dimerization, endocytosis, or targeting of SUT1 to raft-like microdomains. Therefore, we identified potato membrane proteins, which are associated with the detergent-resistant membrane （DRM） fraction. Among the proteins identified, we clearly confirmed StSUT1 as part of DRM in potato source leaves. We used the yeast two-hybrid split ubiq- uitin system （SUS） to systematically screen for interaction between the sucrose transporter StSUT1 and other membrane- associated or soluble proteins in vivo. The SUS screen was followed by immunoprecipitation using affinity-purified StSUTl-specific peptide antibodies and mass spectrometric analysis of co-precipitated proteins. A large overlap was ob- served between the StSUTl-interacting proteins identified in the co-immunoprecipitation and the detergent-resistant membrane fraction. One of the SUTl-interacting proteins, a protein disulfide isomerase （PDI）, interacts also with other sucrose transporter proteins. A potential role of the PDI as escort protein is discussed.

关键词： Protein-protein interactions phloem proteins vesicle trafficking endocytosis.

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Integration of rhythmic metabolome and transcriptome provides insights into the transmission of rhythmic fluctuations and temporal diversity of metabolism in rice

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Science China(Life Sciences) 2022年第9期65卷 1794-1810页

作者： Junjie Zhou Chengyuan Liu Qiyu Chen Ling Liu Shuying Niu Ridong Chen Kang Li Yangyang Sun Yuheng Shi Chenkun Yang Shuangqian Shen Yufei Li Junwei Xing Honglun Yuan Xianqing Liu Chuanying Fang Alisdair R.Fernie Jie Luo College of Tropical Crops Hainan UniversityHaikou 570288China National Key Laboratory of Crop Genetic Improvement and National Center of plant Gene Research(Wuhan) Huazhong Agricultural UniversityWuhan 430070China Sanya Nanfan Research institute of Hainan University Hainan Yazhou Bay Seed LaboratorySanya 572025China max-planck-institute of molecular plant physiology Potsdam-Golm 144776Germany Center of plant System Biology and Biotechnology Plovdiv 4000Bulgaria

Various aspects of the organisms adapt to cyclically changing environmental conditions via transcriptional regulation.However,the role of rhythmicity in altering the global aspects of metabolism is poorly characterized.Here,we subjected four rice(Oryza sativa)varieties to a range of metabolic profiles and RNA-seq to investigate the temporal relationships of rhythm between transcription and metabolism.More than 40%of the rhythmic genes and a quarter of metabolites conservatively oscillated across four rice accessions.Compared with the metabolome,the transcriptome was more strongly regulated by rhythm;however,the rhythm of metabolites had an obvious opposite trend between day and night.Through association analysis,the time delay of rhythmic transmission from the transcript to the metabolite level was~4 h under long-day conditions,although the transmission was nearly synchronous for carbohydrate and nucleotide metabolism.The rhythmic accumulation of metabolites maintained highly coordinated temporal relationships in the metabolic network,whereas the correlation of some rhythmic metabolites,such as branched-chain amino acids(BCAAs),was significantly different intervariety.We further demonstrated that the cumulative diversity of BCAAs was due to the differential expression of branched-chain aminotransferase 2 at dawn.Our research reveals the flexible pattern of rice metabolic rhythm existing with conservation and diversity.

关键词： Oryza sativa diurnal cycle metabolome time delay rhythmic diversity

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Characterization of PetM cytochrome b6f subunit 7 domain-containing protein in tomato

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Horticulture Research 2023年第12期10卷 14-25页

作者： Mustafa Bulut Adriano Nunes-Nesi Alisdair R.Fernie Saleh Alseekh Root Biology and Symbiosis Max-Planck-Institute of Molecular Plant PhysiologyAm Mühlenberg 114476 PotsdamGermany Departamento de Biologia Vegetal Universidade Federal de ViçosaViçosa 36570-900 MGBrazil plant Metabolomics The Center for Plant Systems Biology and Biotechnology4000 PlovdivBulgaria

In recent years,multiple advances have been made in understanding the photosynthetic machinery in model organisms.Knowledge transfer to horticultural important fruit crops is challenging and time-consuming due to restrictions in gene editing tools and prolonged life cycles.Here,we characterize a gene encoding a PetM domain-containing protein in tomato.The CRISPR/Cas9 knockout lines of the PetM showed impairment in the chloroplastic electron transport rate(ETR),reduced CO_(2) assimilation,and reduction of carotenoids and chlorophylls(Chl)under several light conditions.Further,growth-condition-dependent elevation or repression of Chl a/b ratios and de-epoxidation states were identified,underlining possible impairment compensation mechanisms.However,under low light and glasshouse conditions,there were basal levels in CO_(2) assimilation and ETR,indicating a potential role of the PetM domain in stabilizing the cytochrome b6f complex(Cb6f)under higher light irradiance and increasing its quantum efficiency.This suggests a potential evolutionary role in which this domain might stabilize the site of the Cb6f regulating ratios of cyclic and linear electron transport and its potential importance during the conquest of terrestrial ecosystems during which plants were exposed to higher irradiance.Finally,the results are discussed with regard to metabolism and their implication to photosynthesis from an agronomic perspective.

关键词： assimilation metabolism consuming

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Development of a widely targeted volatilomics method for profiling volatilomes in plants

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molecular plant 2022年第1期15卷 189-202页

作者： Honglun Yuan Guangping Cao Xiaodong Hou Menglan Huang Pengmeng Du Tingting Tan Youjin Zhang Haihong Zhou Xianqing Liu Ling Liu Yiding Jiangfang Yufei Li Zhenhuan Liu Chuanying Fang Liqing Zhao Alisdair R.Fernie Jie Luo College of Tropical Crops Hainan UniversityHaikou 570288China Sanya Nanfan Research institute of Hainan University Hainan Yazhou Bay Seed LaboratorySanya572025China College of Chemistry and Environmental Engineering Shenzhen UniversityShenzhen 518060China National Key Laboratory of Crop Genetic Improvement and National Center of plant Gene Research(Wuhan) Huazhong Agricultural UniversityWuhan 430070China Department of molecular physiology Max-Planck-lnstitute of Molecular Plant PhysiologyAm Muhlenberg 114476 Potsdam-GolmGermany

Volatile organic compounds play essential roles in plant environment interactions as well as determining the fragrance of plants.Although gas chromatography-mass spectrometry-based untargeted metabolo-mics is commonly used to assess plant volatiles,it suffers from high spectral convolution,low detection sensitivity,a limited number of annotated metabolites,and relatively poor reproducibility.Here,we report a widely targeted volatilomics(WTV)method that involves using a“targeted spectra extraction”algorithm to address spectral convolution,constructing a high-coverage MS2 spectral tag library to expand volatile annotation,adapting a multiple reaction monitoring mode to improve sensitivity,and using regression models to adjust for signal drift.The newly developed method was used to profile the volatilome of rice grains.Compared with the untargeted method,the newly developed WTV method shows higher sensitivity(for example,the signal-to-noise ratio of guaicol increased from 4.1 to 18.8),high annotation coverage(the number of annotated volatiles increased from 43 to 132),and better reproducibility(the number of volatiles in quality control samples with relative standard deviation value below 30.0%increased from 14 to 92 after normalization).Using the WTV method,we studied the metabolic responses of tomato to environmental stimuli and profiled the volatilomes of different rice accessions.The results identified benzothiazole as a potential airborne signal priming tomato plants for enhanced defense and 2-nonanone and 2-heptanone as novel aromatic compounds contributing to rice fragrance.These case studies suggest that the widely targeted volatilomics method is more efficient than those currently used and may considerably promote plant volatilomics studies.

关键词： widely targeted volatilomics GC-MS MS2T library plant volatilome rice tomato

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