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Genome-Wide Identification and Functional Analysis of Genes Expressed Ubiquitously in Rice

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Molecular Plant 2015年第2期8卷 276-289页

作者： Ki-Hong Jung Sung-Ruyl Kim Hoi-Khoanh Giong Minh Xuan Nguyen Hyun-Jung Koh gynheung an Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute Kyung Hee University Yongin 446-701 Korea Graduate School of Biotechnology Kyung Hee University Yongin 446-701 Korea These authors contributed equally to the article.

Genes that are expressed ubiquitously throughout all developmental stages are thought to be necessary for basic biological or cellular functions. Therefore, determining their biological roles is a great challenge. We identified 4034 of these genes in rice after studying the results of Agilent 44K and Affymetrix meta- anatomical expression profiles. Among 105 genes that were characterized by loss-of-function analysis, 79 were classified as members of gene families, the majority of which were predominantly expressed. Using T-DNA insertional mutants, we examined 43 genes and found that loss of expression of six genes caused developing seedor seedling-defective phenotypes. Of these, three are singletons without similar family members and defective phenotypes are expected from mutations. Phylogenomic analyses integrating genome-wide transcriptome data revealed the functional dominance of three ubiquitously expressed fam- ily genes. Among them, we investigated the function of OsO3g19890, which is involved in ATP generation within the mitochondria during endosperm development. We also created and evaluated functional net- works associated with this gene to understand the molecular mechanism. Our study provides a useful strategy for pheonome analysis of ubiquitously expressed genes in rice.

关键词： functional redundancy phylogenomic analysis rice systematic phenotype screening ubiquitouslyexpressed genes

Rice-Specific Mitochondrial Iron-Regulated Gene （MIR） Plays an Important Role in Iron Homeostasis

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Molecular Plant 2009年第5期2卷 1059-1066页

作者： Yasuhiro Ishimaru Khurram Bashir Masaru Fujimoto gynheung an Reiko Nakanishi Itai Nobuhiro Tsutsumi Hiromi Nakanishi Naoko K Nishizawa Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi Bunkyo-Ku Tokyo 113-8657 Japan Department of Life Sciences Pohang University of Science and Technology Pohang 790-784 Republic of Korea Research Institute for Bioresources and Biotechnology Ishikawa Prefectural University Ishikawa 921-8836 Japan

Mitochondria utilize iron （Fe）, but the proteins involved in mitochondrial Fe regulation are not characterized in plants. We cloned and characterized a mitochondrial iron-regulated （MIR） gene in rice involved in Fe homeostasis. MIR, when expressed in tobacco BY-2 cells, was localized to the mitochondria. MIR transcripts were greatly increased in response to Fe deficiency in roots and shoot tissue. MIR is not homologous to any known protein, as homologs were not found in the rice or Arabidopsis genome databases, or in the EST database for other organisms. Growth in the MIR T-DNA knockout rice mutant （mir） was significantly impaired compared to wild-type （WT） plants when grown under Fe-deficient or -sufficient conditions. Furthermore, mir plants accumulated more than twice the amount of Fe in shoot and root tissue compared to WT plants when grown under either Fe-sufficient or -deficient conditions. Despite the high accumulation of Fe in roots and shoots, mir plants triggered the expression of Fe-deficiency-inducible genes, indicating that mir may not be able to utilize Fe for physiological functions. These results clearly suggest that MIR is a rice-specific mitochondrial protein, recently evolved, and plays a significant role in Fe homeostasis.

关键词： Fe-deficiency-regulated gene Fe homeostasis mitochondria Oryza sativa.

Rice Transcription Factor OsDOFll Modulates Sugar Transport by Promoting Expression of Sucrose Transporter and SWEET Genes

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Molecular Plant 2018年第6期11卷 833-845页

作者： Yunfei Wu Sang-Kyu Lee Youngchul Yoo Jinhuan Wei Suk-Yoon Kwon Sang-Won Lee Jong-Seong Jeon gynheung an Crop Biotech Institute and Graduate School of Biotechnology Kyung Hee University Yongin 17104 Korea Plant Systems Engineering Research Center Korea Research Institute of Bioscience and Biotechnology Daejeon 34141 Korea

Sucrose is produced in mesophyll cells and transferred into phloem cells before it is delivered long- distance to sink tissues. However, little is known about how sucrose transport is regulated in plants. Here, we identified a T-DNA insertional mutant of Oryza sativa DNA BINDING WITH ONE FINGER 11 （OsDOF11）, which is expressed in the vascular cells of photosynthetic organs and in various sink tissues. The osdofll mutant plants are semi-dwarf and have fewer tillers and smaller panicles as compared with wild-type （WT） plants. Although sucrose enhanced root elongation in young WT seedlings, this enhance- ment did not occur in osdof11 seedlings due to reduced sucrose uptake. Sugar transport rate analyses revealed that less sugar was transported in osdofll plants than in the WT. Expression of four Sucrose Transporter （SUT） genes-OsSUT1, OsSUT3, OsSUT4, and OsSUT5-as well as two Sugars Will Eventually be Exported Transporters （SWEET） genes, OsSWEETll and OsSWEET14, was altered in various organs of the mutant, including the leaves. Chromatin immunoprecipitation assays showed that OsDOFll directly binds the promoter regions of SUT1, OsSWEETll, and OsSWEET14, indicating that the expression of these transporters responsible for sucrose transport via apopiastic loading is coordinately controlled by OsDOFll. We also observed that osdofll mutant plants were less susceptible to infection byXanthomonas oryzae pathovar oryzae, suggesting that OsDOFll participates in sugar distribution during pathogenic in- vasion. Collectively, these results suggest that OsDOFll modulates sugar transport by regulating the expression of both SUT and SWEET genes in rice.

关键词： OsDOF11 phloem loading rice SUT SWEET Xanthomonas oryzae

A rice tubulin tyrosine ligase-like 12 protein affects the dynamic and orientation of microtubules

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Journal of Integrative Plant Biology 2021年第5期63卷 848-864页

作者： Kunxi Zhang Xin Zhu Steffen Durst Petra Hohenberger Min‐Jung Han gynheung an Vaidurya PSahi Michael Riemann Peter Nick Molecular Cell Biology Botanical InstituteKarlsruhe Institute of TechnologyKarlsruhe 76131Germany Aptamer Initiative Postech Biotech CenterPohang University of Science and TechnologyPohang‐siGyeongsangbuk‐do37673South Korea Department of Plant Molecular Systems Biotech Kyung Hee UniversityYongin 446‐701South Korea

The detyrosination/retyrosination cycle is the most common post-translational modification of α-tubulin.Removal of the conserved C-terminal tyrosine of α-tubulin by a still elusive tubulin tyrosine carboxypeptidase, and religation of this tyrosine by a tubulin tyrosine ligase(TTL), are probably common to all eukaryotes. Interestingly, for plants, the only candidates qualifying as potential TTL homologs are the tubulin tyrosine ligase-like 12 proteins. To get insight into the biological functions of these potential TTL homologs, we cloned the rice TTL-like 12 protein(Os TTLL12)andgeneratedoverexpression Os TTLL12-RFP lines in both rice and tobacco BY-2 cells. We found, unexpectedly, that overexpression of this Os TTLL12-RFP increased the relative abundance of detyrosinated α-tubulin in both coleoptile and seminal root, correlated with more stable microtubules. This was independent of the respective orientation of cortical microtubule, and followed by correspondingly changing growth of coleoptiles and seminal roots. A perturbed organization of phragmoplast microtubules and disoriented cell walls were further characteristics of this phenotype. Thus, the elevated tubulin detyrosination in consequence of Os TTLL12 overexpression affects structural and dynamic features of microtubules, followed by changes in the axiality of cell plate deposition and, consequently, plant growth.

关键词： microtubule phragmoplast rice tobacco BY-2 tubulin detyrosination tubulin tyrosine carboxypeptidase tubulin tyrosine ligase tubulin tyrosine ligase-like 12

Mutation of Oryza sativa CORONATINE INSENSITIVE 1b(OsCOI1b) delays leaf senescence

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Journal of Integrative Plant Biology 2015年第6期57卷 562-576页

作者： Sang-Hwa Lee Yasuhito Sakuraba Taeyoung Lee Kyu-Won Kim gynheung an Han Yong Lee Nam-Chon Paek Department of Plant Science Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesSeoul National University Interdisciplinary Program in Bioinformatics Seoul National University Department of Plant Molecular Systems Biotechnology Crop Biotech InstituteKyung Hee University Department of Agricultural Biotechnology Seoul National University

Jasmonic acid （JA） functions in plant development, including senescence and immunity. Arabidopsis thaliana CORONATINE INSENSITIVE 1 encodes a JA receptor and functions in the JA‐responsive signaling pathway. The Arabidopsis genome harbors a single COI gene, but the rice （Oryza sativa） genome harbors three COI homologs, OsCOI1a, OsCOI1b, and OsCOI2. Thus, it remains unclear whether each OsCOI has distinct, additive, synergistic, or redundant func-tions in development. Here, we use the oscoi1b‐1 knockout mutants to show that OsCOI1b mainly affects leaf senescence under senescence‐promoting conditions. oscoi1b‐1 mutants stayed green during dark‐induced and natural senescence, with substantial retention of chlorophylls and photosyn-thetic capacity. Furthermore, several senescence‐associated genes were downregulated in oscoi1b‐1 mutants, including homologs of Arabidopsis thaliana ETHYLENE INSENSITIVE 3 and ORESARA 1, important regulators of leaf senescence. These results suggest that crosstalk between JA signaling and ethylene signaling affects leaf senescence. The Arabidopsis coi1‐1 plants containing 35S：OsCOI1a or 35S：OsCOI1b rescued the delayed leaf senescence during dark incubation, sug-gesting that both OsCOI1a and OsCOI1b are required for promoting leaf senescence in rice. oscoi1b‐1 mutants showed significant decreases in spikelet fertility and grain weight, leading to severe reduction of grain yield, indicating that OsCOI1‐mediated JA signaling affects spikelet fertility and grain filling.

关键词： Jasmonic acid leaf senescence OsCOI1b rice stay-green

Role of rice cytosolic hexokinase OsHXK7 in sugar signaling and metabolism

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Journal of Integrative Plant Biology 2016年第2期58卷 127-135页

作者： Hyun-Bi Kim Jung-Il Cho Nayeon Ryoo Dong-Ho Shin Youn-Il Park Yong-Sic Hwang Sang-Kyu Lee gynheung an Jong-Seong Jeon Crop Biotech Institute & Graduate School of Biotechnology Kyung Hee University National Academy of Agricultural Science Rural Development Administration Center for Neuroscience Korea Institute of Science and Technology Department of Biology Chungnam National University Department of Bioscience and Biotechnology Konkuk University

We characterized the function of the rice cytosolic hexokinase OsHXK7 （Qryza sativa HexokindseZ）, which is highly upregulated when seeds germinate under O2- deficient conditions. According to transient expression assays that used the promoter：luciferase fusion construct, OsHXK7 enhanced the glucose （Glc）-dependent repression of a rice n-amylase gene （RAmy3D） in the mesophyll protoplasts of maize, but its catalytically inactive mutant alleles did not. Consistently, the expression of OsHXK7, but not its catalytically inactive alleles, complemented the Arabidopsis glucose insensitive2-1 （gin2-1） mutant, thereby resulting in the wild type characteristics of Glc-dependent repression, seedling development, and plant growth. Interestingly, OsHXK7-mediated Glc-dependent repression was abolished in the O2-deficient mesophyll protoplasts of maize. This result provides compelling evidence that OsHXK7 functions in sugar signaling via a glycolysis-dependent manner under normal conditions, but its signaling role is suppressed when O2 is deficient. The germination of two null OsHXK7 mutants, oshxk7-1 and oshxk7-2, was affected by O2 deficiency, but overexpression enhanced germination in rice. This result suggests the distinct role that OsHXK7 plays in sugar metabolism and efficient germination by enforcing glycolysis-mediated fermentation in O2-deficient rice.

关键词： Germination metabolism OsHXK7 O2 deficiency rice signaling sugar

Natural Variation in OsPRR37 Regulates Heading Date and Contributes to Rice Cultivation at a Wide Range of Latitudes

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Molecular Plant 2013年第6期6卷 1877-1888页

作者： Bon-Hyuk Koo Soo-Cheul Yoo Joon-Woo Park Choon-Tak Kwon Byoung-Doo Lee gynheung an Zhanying Zhang linjie Li Zichao Li Nam-Chon Paek Department of Plant Science Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences Seoul National UniversitySeoul 151-921 Korea Department of Plant Systems Biotech and Crop Biotech Institute Kyung Hee University Yongin 446-701 Korea Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement China Agriculture UniversityBeijing 100193 China Institute of Green Bio Science and Technology Seoul National University Pyeongchang 232-916 Korea

Heading date and photoperiod sensitivity are fundamental traits that determine rice adaptation to a wide range of geographic environments. By quantitative trait locus （QTL） mapping and candidate gene analysis using whole- genome re-sequencing, we found that Oryza sativa Pseudo-Response Regulator37 （OsPRR37; hereafter PRR37） is respon- sible for the Early heading7-2 （EH7-2）/Heading date2 （Hd2） QTL which was identified from a cross of late-heading rice ＇Milyang23 （M23）＇ and early-heading rice ＇H143＇. H143 contains a missense mutation of an invariantly conserved amino acid in the CCT （CONSTANS, CO-like, and TOC1） domain of PRR37 protein. In the world rice collection, different types of nonfunctional PRR37 alleles were found in many European and Asian rice cultivars. Notably, the japonica varieties harboring nonfunctional alleles of both Ghd7/Hd4 and PRR37/Hd2 flower extremely early under natural long-day condi- tions, and are adapted to the northernmost regions of rice cultivation, up to 53~ N latitude. Genetic analysis revealed that the effects of PRR37 and Ghd7 alleles on heading date are additive, and PRR37 down-regulates Hd3a expression to suppress flowering under long-day conditions. Our results demonstrate that natural variations in PRR37/Hd2 and GhdT/ Hd4 have contributed to the expansion of rice cultivation to temperate and cooler regions.

关键词： rice heading date quantitative trait locus natural variation Ghd7 OsPRR37.

Photosynthetic activity and expression of genes encoding antioxidant enzymes in the leaves of alanine am inotransferase mutant （Oryza sativa L.） against salt stress

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Photosynthetic activity and expression of genes encoding ant...

过表达玉米转录因子ABP9大幅度提高了转基因水稻的耐旱和耐盐性

The 3rd Asian and Oceanian Conference on Photobiology

作者： Kyoung nam Im gynheung an In Ho Park Chin Bum Lee Department of Biology Dong-eui UniversityBusanKorea National Research Laboratory of Plant Functional Genomics Division of Molecular and Life SciencesPohang University of Science and Technology （POSTECH）Pohang 790-784Republic of Korea Department of Biology Donga University Busan Korea Department of Biology Dong-eui University Busan Korea

＜正＞T-DNA tagging lines in rice, 1C-12812 （Oriza sativa cv. Hwayoung） and 3A-10591 （Oriza sativa cv. Dongjin） in which T-DNA was inserted into the 9th exon （Chr 3） and 4th intron （Chr 10） of OsAlaAT, respectively were isolated from T-DNA mutagenized populations. Two homozygote mutants were selected by genotyping with AlaAT1 and AlaAT-specific primers. In case of seed length and growth of the mutant, 1C-12812 and 3A-10591 showed smaller and weaker phenotypes than wild type. The photosynthetic activities （Fv/Fm and qQ） of 3A-10591 were decreased than control under salt stress （NaCl 300mM, 24h treatment）. However, PSⅡ activity of 1C-12812 was not decreased in comparison with 3A-10591. The mRNA levels of cytosolic ascrobate peroxidase （cAPX） and peroxidase Ⅱ（POX Ⅱ） in the leaves of 1C-12812 were determined by RT-PCR under different salt concentrations. mRNA levels of cAPX were increased against salt treatment in both control and mutant rice. However, mRNA level of POX Ⅱ was decreased dramatically and the total POX activity was also decreased under salt stress （NaCl 300mM, 24h treatment） in the leaves of 1C-12812. These results indicate that the loss of AlaAT activity may affect the photosynthetic activities related to photorespiration and the activities/synthesis of antioxidant enzymes, especially POX Ⅱ.

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过表达玉米转录因子ABP9大幅度提高了转基因水稻的耐旱和耐盐性