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Chun HJ, Baek D, Cho HM, Jung HS, Jeong MS, Jung WH, Choi CW, Lee SH, Jin BJ, Park MS, Kim HJ, Chung WS, Lee SY, Bohnert HJ, Bressan RA, Yun DJ, Hong YS, Kim MC. Metabolic Adjustment of Arabidopsis Root Suspension Cells During Adaptation to Salt Stress and Mitotic Stress Memory. Plant Cell Physiol 2019; 60:612-625. [PMID: 30496500 DOI: 10.1093/pcp/pcy231] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/22/2018] [Indexed: 05/14/2023]
Abstract
Sessile plants reprogram their metabolic and developmental processes during adaptation to prolonged environmental stresses. To understand the molecular mechanisms underlying adaptation of plant cells to saline stress, we established callus suspension cell cultures from Arabidopsis roots adapted to high salt for an extended period of time. Adapted cells exhibit enhanced salt tolerance compared with control cells. Moreover, acquired salt tolerance is maintained even after the stress is relieved, indicating the existence of a memory of acquired salt tolerance during mitotic cell divisions, known as mitotic stress memory. Metabolite profiling using 1H-nuclear magnetic resonance (NMR) spectroscopy revealed metabolic discrimination between control, salt-adapted and stress-memory cells. Compared with control cells, salt-adapted cells accumulated higher levels of sugars, amino acids and intermediary metabolites in the shikimate pathway, such as coniferin. Moreover, adapted cells acquired thicker cell walls with higher lignin contents, suggesting the importance of adjustments of physical properties during adaptation to elevated saline conditions. When stress-memory cells were reverted to normal growth conditions, the levels of metabolites again readjusted. Whereas most of the metabolic changes reverted to levels intermediate between salt-adapted and control cells, the amounts of sugars, alanine, γ-aminobutyric acid and acetate further increased in stress-memory cells, supporting a view of their roles in mitotic stress memory. Our results provide insights into the metabolic adjustment of plant root cells during adaptation to saline conditions as well as pointing to the function of mitotic memory in acquired salt tolerance.
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Affiliation(s)
- Hyun Jin Chun
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, Korea
| | - Dongwon Baek
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Hyun Min Cho
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Hyun Suk Jung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Korea
| | - Myeong Seon Jeong
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Korea
- Chuncheon Center, Korea Basic Science Institute (KBSI), Chuncheon, Korea
| | - Wook-Hun Jung
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Cheol Woo Choi
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Su Hyeon Lee
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Byung Jun Jin
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Mi Suk Park
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Hyun-Jin Kim
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Woo Sik Chung
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Hans J Bohnert
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ray A Bressan
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Korea
| | - Young-Shick Hong
- Department of Food and Nutrition, Chonnam National University, Gwangju, Korea
| | - Min Chul Kim
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, Korea
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
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Hwang JE, Kim YJ, Shin MH, Hyun HJ, Bohnert HJ, Park HC. A comprehensive analysis of the Korean fir (Abies koreana) genes expressed under heat stress using transcriptome analysis. Sci Rep 2018; 8:10233. [PMID: 29980711 PMCID: PMC6035224 DOI: 10.1038/s41598-018-28552-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 06/22/2018] [Indexed: 11/09/2022] Open
Abstract
Korean fir (Abies koreana), a rare species endemic to South Korea, is sensitive to climate change. Here, we used next-generation massively parallel sequencing technology and de novo transcriptome assembly to gain a comprehensive overview of the Korean fir transcriptome under heat stress. Sequencing control and heat-treated samples of Korean fir, we obtained more than 194,872,650 clean reads from each sample. After de novo assembly and quantitative assessment, 42,056 unigenes were generated with an average length of 908 bp. In total, 6,401 differentially expressed genes were detected, of which 2,958 were up-regulated and 3,443 down-regulated, between the heat-treated and control samples. A gene ontology analysis of these unigenes revealed heat-stress-related terms, such as "response to stimulus". Further, in depth analysis revealed 204 transcription factors and 189 Hsps as differentially expressed. Finally, 12 regulated candidate genes associated with heat stress were examined using quantitative real-time PCR (qRT-PCR). In this study, we present the first comprehensive characterisation of Korean fir subjected to heat stress using transcriptome analysis. It provides an important resource for future studies of Korean fir with the objective of identifying heat stress tolerant lines.
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Affiliation(s)
- Jung Eun Hwang
- Division of Ecological Conservation, Bureau of Ecological Research, National Institute of Ecology, Seocheon, Republic of Korea
| | - Yun Jeong Kim
- Division of Ecological Conservation, Bureau of Ecological Research, National Institute of Ecology, Seocheon, Republic of Korea
| | - Myung Hwan Shin
- Division of Ecological Conservation, Bureau of Ecological Research, National Institute of Ecology, Seocheon, Republic of Korea
| | - Hwa Ja Hyun
- National Institute Forest Science Warm Temperate and Subtropical Forest Research Center, Jeju, Republic of Korea
| | - Hans J Bohnert
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hyeong Cheol Park
- Division of Ecological Conservation, Bureau of Ecological Research, National Institute of Ecology, Seocheon, Republic of Korea.
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Ali A, Raddatz N, Aman R, Kim S, Park HC, Jan M, Baek D, Khan IU, Oh DH, Lee SY, Bressan RA, Lee KW, Maggio A, Pardo JM, Bohnert HJ, Yun DJ. A Single Amino-Acid Substitution in the Sodium Transporter HKT1 Associated with Plant Salt Tolerance. Plant Physiol 2016; 171:2112-26. [PMID: 27208305 PMCID: PMC4936583 DOI: 10.1104/pp.16.00569] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/06/2016] [Indexed: 05/20/2023]
Abstract
A crucial prerequisite for plant growth and survival is the maintenance of potassium uptake, especially when high sodium surrounds the root zone. The Arabidopsis HIGH-AFFINITY K(+) TRANSPORTER1 (HKT1), and its homologs in other salt-sensitive dicots, contributes to salinity tolerance by removing Na(+) from the transpiration stream. However, TsHKT1;2, one of three HKT1 copies in Thellungiella salsuginea, a halophytic Arabidopsis relative, acts as a K(+) transporter in the presence of Na(+) in yeast (Saccharomyces cerevisiae). Amino-acid sequence comparisons indicated differences between TsHKT1;2 and most other published HKT1 sequences with respect to an Asp residue (D207) in the second pore-loop domain. Two additional T salsuginea and most other HKT1 sequences contain Asn (n) in this position. Wild-type TsHKT1;2 and altered AtHKT1 (AtHKT1(N-D)) complemented K(+)-uptake deficiency of yeast cells. Mutant hkt1-1 plants complemented with both AtHKT1(N) (-) (D) and TsHKT1;2 showed higher tolerance to salt stress than lines complemented by the wild-type AtHKT1 Electrophysiological analysis in Xenopus laevis oocytes confirmed the functional properties of these transporters and the differential selectivity for Na(+) and K(+) based on the n/d variance in the pore region. This change also dictated inward-rectification for Na(+) transport. Thus, the introduction of Asp, replacing Asn, in HKT1-type transporters established altered cation selectivity and uptake dynamics. We describe one way, based on a single change in a crucial protein that enabled some crucifer species to acquire improved salt tolerance, which over evolutionary time may have resulted in further changes that ultimately facilitated colonization of saline habitats.
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Affiliation(s)
- Akhtar Ali
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju 660-701, Republic of Korea (A.A., R.A., S.K., M.J., D.B., I.U.K., S.Y.L., K.W.L., H.J.B., D.-J.Y.); Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M-40, km 37.7, E-28223 Pozuelo de Alarcón Madrid (N.R.);Division of Ecological Adaptation Research, National Institute of Ecology (NIE), Seocheon 325-813, Republic of Korea (H.C.P.); Department of Biology, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907-2010 (R.A.B.);Department of Agriculture, University of Naples Federico II, Via Universita` 100, Portici, I-80055, Italy (A.M.);Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Cientificas, 41092 Sevilla, Spain (J.M.P.); College of Science, King Abdulaziz University, Jeddah 21589, KSA (H.J.B.); and Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
| | - Natalia Raddatz
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju 660-701, Republic of Korea (A.A., R.A., S.K., M.J., D.B., I.U.K., S.Y.L., K.W.L., H.J.B., D.-J.Y.); Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M-40, km 37.7, E-28223 Pozuelo de Alarcón Madrid (N.R.);Division of Ecological Adaptation Research, National Institute of Ecology (NIE), Seocheon 325-813, Republic of Korea (H.C.P.); Department of Biology, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907-2010 (R.A.B.);Department of Agriculture, University of Naples Federico II, Via Universita` 100, Portici, I-80055, Italy (A.M.);Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Cientificas, 41092 Sevilla, Spain (J.M.P.); College of Science, King Abdulaziz University, Jeddah 21589, KSA (H.J.B.); and Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
| | - Rashid Aman
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju 660-701, Republic of Korea (A.A., R.A., S.K., M.J., D.B., I.U.K., S.Y.L., K.W.L., H.J.B., D.-J.Y.); Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M-40, km 37.7, E-28223 Pozuelo de Alarcón Madrid (N.R.);Division of Ecological Adaptation Research, National Institute of Ecology (NIE), Seocheon 325-813, Republic of Korea (H.C.P.); Department of Biology, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907-2010 (R.A.B.);Department of Agriculture, University of Naples Federico II, Via Universita` 100, Portici, I-80055, Italy (A.M.);Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Cientificas, 41092 Sevilla, Spain (J.M.P.); College of Science, King Abdulaziz University, Jeddah 21589, KSA (H.J.B.); and Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
| | - Songmi Kim
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju 660-701, Republic of Korea (A.A., R.A., S.K., M.J., D.B., I.U.K., S.Y.L., K.W.L., H.J.B., D.-J.Y.); Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M-40, km 37.7, E-28223 Pozuelo de Alarcón Madrid (N.R.);Division of Ecological Adaptation Research, National Institute of Ecology (NIE), Seocheon 325-813, Republic of Korea (H.C.P.); Department of Biology, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907-2010 (R.A.B.);Department of Agriculture, University of Naples Federico II, Via Universita` 100, Portici, I-80055, Italy (A.M.);Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Cientificas, 41092 Sevilla, Spain (J.M.P.); College of Science, King Abdulaziz University, Jeddah 21589, KSA (H.J.B.); and Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
| | - Hyeong Cheol Park
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju 660-701, Republic of Korea (A.A., R.A., S.K., M.J., D.B., I.U.K., S.Y.L., K.W.L., H.J.B., D.-J.Y.); Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M-40, km 37.7, E-28223 Pozuelo de Alarcón Madrid (N.R.);Division of Ecological Adaptation Research, National Institute of Ecology (NIE), Seocheon 325-813, Republic of Korea (H.C.P.); Department of Biology, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907-2010 (R.A.B.);Department of Agriculture, University of Naples Federico II, Via Universita` 100, Portici, I-80055, Italy (A.M.);Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Cientificas, 41092 Sevilla, Spain (J.M.P.); College of Science, King Abdulaziz University, Jeddah 21589, KSA (H.J.B.); and Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
| | - Masood Jan
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju 660-701, Republic of Korea (A.A., R.A., S.K., M.J., D.B., I.U.K., S.Y.L., K.W.L., H.J.B., D.-J.Y.); Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M-40, km 37.7, E-28223 Pozuelo de Alarcón Madrid (N.R.);Division of Ecological Adaptation Research, National Institute of Ecology (NIE), Seocheon 325-813, Republic of Korea (H.C.P.); Department of Biology, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907-2010 (R.A.B.);Department of Agriculture, University of Naples Federico II, Via Universita` 100, Portici, I-80055, Italy (A.M.);Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Cientificas, 41092 Sevilla, Spain (J.M.P.); College of Science, King Abdulaziz University, Jeddah 21589, KSA (H.J.B.); and Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
| | - Dongwon Baek
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju 660-701, Republic of Korea (A.A., R.A., S.K., M.J., D.B., I.U.K., S.Y.L., K.W.L., H.J.B., D.-J.Y.); Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M-40, km 37.7, E-28223 Pozuelo de Alarcón Madrid (N.R.);Division of Ecological Adaptation Research, National Institute of Ecology (NIE), Seocheon 325-813, Republic of Korea (H.C.P.); Department of Biology, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907-2010 (R.A.B.);Department of Agriculture, University of Naples Federico II, Via Universita` 100, Portici, I-80055, Italy (A.M.);Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Cientificas, 41092 Sevilla, Spain (J.M.P.); College of Science, King Abdulaziz University, Jeddah 21589, KSA (H.J.B.); and Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
| | - Irfan Ullah Khan
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju 660-701, Republic of Korea (A.A., R.A., S.K., M.J., D.B., I.U.K., S.Y.L., K.W.L., H.J.B., D.-J.Y.); Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M-40, km 37.7, E-28223 Pozuelo de Alarcón Madrid (N.R.);Division of Ecological Adaptation Research, National Institute of Ecology (NIE), Seocheon 325-813, Republic of Korea (H.C.P.); Department of Biology, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907-2010 (R.A.B.);Department of Agriculture, University of Naples Federico II, Via Universita` 100, Portici, I-80055, Italy (A.M.);Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Cientificas, 41092 Sevilla, Spain (J.M.P.); College of Science, King Abdulaziz University, Jeddah 21589, KSA (H.J.B.); and Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
| | - Dong-Ha Oh
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju 660-701, Republic of Korea (A.A., R.A., S.K., M.J., D.B., I.U.K., S.Y.L., K.W.L., H.J.B., D.-J.Y.); Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M-40, km 37.7, E-28223 Pozuelo de Alarcón Madrid (N.R.);Division of Ecological Adaptation Research, National Institute of Ecology (NIE), Seocheon 325-813, Republic of Korea (H.C.P.); Department of Biology, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907-2010 (R.A.B.);Department of Agriculture, University of Naples Federico II, Via Universita` 100, Portici, I-80055, Italy (A.M.);Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Cientificas, 41092 Sevilla, Spain (J.M.P.); College of Science, King Abdulaziz University, Jeddah 21589, KSA (H.J.B.); and Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju 660-701, Republic of Korea (A.A., R.A., S.K., M.J., D.B., I.U.K., S.Y.L., K.W.L., H.J.B., D.-J.Y.); Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M-40, km 37.7, E-28223 Pozuelo de Alarcón Madrid (N.R.);Division of Ecological Adaptation Research, National Institute of Ecology (NIE), Seocheon 325-813, Republic of Korea (H.C.P.); Department of Biology, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907-2010 (R.A.B.);Department of Agriculture, University of Naples Federico II, Via Universita` 100, Portici, I-80055, Italy (A.M.);Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Cientificas, 41092 Sevilla, Spain (J.M.P.); College of Science, King Abdulaziz University, Jeddah 21589, KSA (H.J.B.); and Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
| | - Ray A Bressan
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju 660-701, Republic of Korea (A.A., R.A., S.K., M.J., D.B., I.U.K., S.Y.L., K.W.L., H.J.B., D.-J.Y.); Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M-40, km 37.7, E-28223 Pozuelo de Alarcón Madrid (N.R.);Division of Ecological Adaptation Research, National Institute of Ecology (NIE), Seocheon 325-813, Republic of Korea (H.C.P.); Department of Biology, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907-2010 (R.A.B.);Department of Agriculture, University of Naples Federico II, Via Universita` 100, Portici, I-80055, Italy (A.M.);Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Cientificas, 41092 Sevilla, Spain (J.M.P.); College of Science, King Abdulaziz University, Jeddah 21589, KSA (H.J.B.); and Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
| | - Keun Woo Lee
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju 660-701, Republic of Korea (A.A., R.A., S.K., M.J., D.B., I.U.K., S.Y.L., K.W.L., H.J.B., D.-J.Y.); Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M-40, km 37.7, E-28223 Pozuelo de Alarcón Madrid (N.R.);Division of Ecological Adaptation Research, National Institute of Ecology (NIE), Seocheon 325-813, Republic of Korea (H.C.P.); Department of Biology, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907-2010 (R.A.B.);Department of Agriculture, University of Naples Federico II, Via Universita` 100, Portici, I-80055, Italy (A.M.);Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Cientificas, 41092 Sevilla, Spain (J.M.P.); College of Science, King Abdulaziz University, Jeddah 21589, KSA (H.J.B.); and Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
| | - Albino Maggio
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju 660-701, Republic of Korea (A.A., R.A., S.K., M.J., D.B., I.U.K., S.Y.L., K.W.L., H.J.B., D.-J.Y.); Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M-40, km 37.7, E-28223 Pozuelo de Alarcón Madrid (N.R.);Division of Ecological Adaptation Research, National Institute of Ecology (NIE), Seocheon 325-813, Republic of Korea (H.C.P.); Department of Biology, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907-2010 (R.A.B.);Department of Agriculture, University of Naples Federico II, Via Universita` 100, Portici, I-80055, Italy (A.M.);Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Cientificas, 41092 Sevilla, Spain (J.M.P.); College of Science, King Abdulaziz University, Jeddah 21589, KSA (H.J.B.); and Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
| | - Jose M Pardo
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju 660-701, Republic of Korea (A.A., R.A., S.K., M.J., D.B., I.U.K., S.Y.L., K.W.L., H.J.B., D.-J.Y.); Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M-40, km 37.7, E-28223 Pozuelo de Alarcón Madrid (N.R.);Division of Ecological Adaptation Research, National Institute of Ecology (NIE), Seocheon 325-813, Republic of Korea (H.C.P.); Department of Biology, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907-2010 (R.A.B.);Department of Agriculture, University of Naples Federico II, Via Universita` 100, Portici, I-80055, Italy (A.M.);Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Cientificas, 41092 Sevilla, Spain (J.M.P.); College of Science, King Abdulaziz University, Jeddah 21589, KSA (H.J.B.); and Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
| | - Hans J Bohnert
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju 660-701, Republic of Korea (A.A., R.A., S.K., M.J., D.B., I.U.K., S.Y.L., K.W.L., H.J.B., D.-J.Y.); Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M-40, km 37.7, E-28223 Pozuelo de Alarcón Madrid (N.R.);Division of Ecological Adaptation Research, National Institute of Ecology (NIE), Seocheon 325-813, Republic of Korea (H.C.P.); Department of Biology, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907-2010 (R.A.B.);Department of Agriculture, University of Naples Federico II, Via Universita` 100, Portici, I-80055, Italy (A.M.);Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Cientificas, 41092 Sevilla, Spain (J.M.P.); College of Science, King Abdulaziz University, Jeddah 21589, KSA (H.J.B.); and Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
| | - Dae-Jin Yun
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju 660-701, Republic of Korea (A.A., R.A., S.K., M.J., D.B., I.U.K., S.Y.L., K.W.L., H.J.B., D.-J.Y.); Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M-40, km 37.7, E-28223 Pozuelo de Alarcón Madrid (N.R.);Division of Ecological Adaptation Research, National Institute of Ecology (NIE), Seocheon 325-813, Republic of Korea (H.C.P.); Department of Biology, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907-2010 (R.A.B.);Department of Agriculture, University of Naples Federico II, Via Universita` 100, Portici, I-80055, Italy (A.M.);Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Cientificas, 41092 Sevilla, Spain (J.M.P.); College of Science, King Abdulaziz University, Jeddah 21589, KSA (H.J.B.); and Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
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4
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Cha JY, Kim WY, Kang SB, Kim JI, Baek D, Jung IJ, Kim MR, Li N, Kim HJ, Nakajima M, Asami T, Sabir JSM, Park HC, Lee SY, Bohnert HJ, Bressan RA, Pardo JM, Yun DJ. A novel thiol-reductase activity of Arabidopsis YUC6 confers drought tolerance independently of auxin biosynthesis. Nat Commun 2015; 6:8041. [PMID: 26314500 PMCID: PMC4560777 DOI: 10.1038/ncomms9041] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 07/11/2015] [Indexed: 11/10/2022] Open
Abstract
YUCCA (YUC) proteins constitute a family of flavin monooxygenases (FMOs), with an important role in auxin (IAA) biosynthesis. Here we report that Arabidopsis plants overexpressing YUC6 display enhanced IAA-related phenotypes and exhibit improved drought stress tolerance, low rate of water loss and controlled ROS accumulation under drought and oxidative stresses. Co-overexpression of an IAA-conjugating enzyme reduces IAA levels but drought stress tolerance is unaffected, indicating that the stress-related phenotype is not based on IAA overproduction. YUC6 contains a previously unrecognized FAD- and NADPH-dependent thiol-reductase activity (TR) that overlaps with the FMO domain involved in IAA biosynthesis. Mutation of a conserved cysteine residue (Cys-85) preserves FMO but suppresses TR activity and stress tolerance, whereas mutating the FAD- and NADPH-binding sites, that are common to TR and FMO domains, abolishes all outputs. We provide a paradigm for a single protein playing a dual role, regulating plant development and conveying stress defence responses.
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Affiliation(s)
- Joon-Yung Cha
- Division of Applied Life Science (BK21Plus), PMBBRC &IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21Plus), PMBBRC &IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Sun Bin Kang
- Division of Applied Life Science (BK21Plus), PMBBRC &IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Jeong Im Kim
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Dongwon Baek
- Division of Applied Life Science (BK21Plus), PMBBRC &IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - In Jung Jung
- Division of Applied Life Science (BK21Plus), PMBBRC &IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Mi Ri Kim
- Division of Applied Life Science (BK21Plus), PMBBRC &IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Ning Li
- Division of Applied Life Science (BK21Plus), PMBBRC &IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Hyun-Jin Kim
- Division of Applied Life Science (BK21Plus), PMBBRC &IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Masatoshi Nakajima
- Department of Applied Biological Chemistry, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Tadao Asami
- Department of Applied Biological Chemistry, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan.,Department of Biochemistry, King Abdulaziz University, Jeddah 21589, Kingdom of Saudi Arabia
| | - Jamal S M Sabir
- Biotechnology Research Group, Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah 21589, Kingdom of Saudi Arabia
| | - Hyeong Cheol Park
- Department of Ecological Adaptation, National Institute of Ecology, Seocheon 325-813, Republic of Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21Plus), PMBBRC &IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Hans J Bohnert
- Biotechnology Research Group, Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah 21589, Kingdom of Saudi Arabia.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ray A Bressan
- Biotechnology Research Group, Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah 21589, Kingdom of Saudi Arabia.,Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jose M Pardo
- Instituto de Recursos Naturales y Agrobiologia, Consejo Superior de Investigaciones Cientificas, Sevilla 41012, Spain
| | - Dae-Jin Yun
- Division of Applied Life Science (BK21Plus), PMBBRC &IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
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5
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Oh DH, Barkla BJ, Vera-Estrella R, Pantoja O, Lee SY, Bohnert HJ, Dassanayake M. Cell type-specific responses to salinity - the epidermal bladder cell transcriptome of Mesembryanthemum crystallinum. New Phytol 2015; 207:627-44. [PMID: 25944243 DOI: 10.1111/nph.13414] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/08/2015] [Indexed: 05/18/2023]
Abstract
Mesembryanthemum crystallinum (ice plant) exhibits extreme tolerance to salt. Epidermal bladder cells (EBCs), developing on the surface of aerial tissues and specialized in sodium sequestration and other protective functions, are critical for the plant's stress adaptation. We present the first transcriptome analysis of EBCs isolated from intact plants, to investigate cell type-specific responses during plant salt adaptation. We developed a de novo assembled, nonredundant EBC reference transcriptome. Using RNAseq, we compared the expression patterns of the EBC-specific transcriptome between control and salt-treated plants. The EBC reference transcriptome consists of 37 341 transcript-contigs, of which 7% showed significantly different expression between salt-treated and control samples. We identified significant changes in ion transport, metabolism related to energy generation and osmolyte accumulation, stress signalling, and organelle functions, as well as a number of lineage-specific genes of unknown function, in response to salt treatment. The salinity-induced EBC transcriptome includes active transcript clusters, refuting the view of EBCs as passive storage compartments in the whole-plant stress response. EBC transcriptomes, differing from those of whole plants or leaf tissue, exemplify the importance of cell type-specific resolution in understanding stress adaptive mechanisms.
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Affiliation(s)
- Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Bronwyn J Barkla
- Southern Cross Plant Science, Southern Cross University, PO Box 157, Lismore, NSW, 2480, Australia
| | - Rosario Vera-Estrella
- Instituto de Biotecnología, UNAM, A.P. 510-3, Colonia Miraval, Cuernavaca, MOR, 62250, México
| | - Omar Pantoja
- Instituto de Biotecnología, UNAM, A.P. 510-3, Colonia Miraval, Cuernavaca, MOR, 62250, México
| | - Sang-Yeol Lee
- Division of Applied Life Science, Gyeongsang National University, Jinju, 660-701, South Korea
| | - Hans J Bohnert
- Departments of Plant Biology and of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
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6
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Ma S, Bohnert HJ, Dinesh-Kumar SP. AtGGM2014, an Arabidopsis gene co-expression network for functional studies. Sci China Life Sci 2015; 58:276-86. [PMID: 25682393 DOI: 10.1007/s11427-015-4803-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 12/25/2014] [Indexed: 12/19/2022]
Abstract
Gene co-expression networks provide an important tool for systems biology studies. Using microarray data from the ArrayExpress database, we constructed an Arabidopsis gene co-expression network, termed AtGGM2014, 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. AtGGM2014 offers a constructive tool for plant systems biology studies.
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Affiliation(s)
- ShiSong Ma
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California, Davis, CA, 95616, USA,
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7
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Park HC, Lee S, Park B, Choi W, Kim C, Lee S, Chung WS, Lee SY, Sabir J, Bressan RA, Bohnert HJ, Mengiste T, Yun DJ. Pathogen associated molecular pattern (PAMP)-triggered immunity is compromised under C-limited growth. Mol Cells 2015; 38:40-50. [PMID: 25387755 PMCID: PMC4314131 DOI: 10.14348/molcells.2015.2165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 09/24/2013] [Accepted: 10/14/2014] [Indexed: 11/27/2022] Open
Abstract
In the interaction between plants and pathogens, carbon (C) resources provide energy and C skeletons to maintain, among many functions, the plant immune system. However, variations in C availability on pathogen associated molecular pattern (PAMP) triggered immunity (PTI) have not been systematically examined. Here, three types of starch mutants with enhanced susceptibility to Pseudomonas syringae pv. tomato DC3000 hrcC were examined for PTI. In a dark period-dependent manner, the mutants showed compromised induction of a PTI marker, and callose accumulation in response to the bacterial PAMP flagellin, flg22. In combination with weakened PTI responses in wild type by inhibition of the TCA cycle, the experiments determined the necessity of C-derived energy in establishing PTI. Global gene expression analyses identified flg22 responsive genes displaying C supply-dependent patterns. Nutrient recycling-related genes were regulated similarly by C-limitation and flg22, indicating re-arrangements of expression programs to redirect resources that establish or strengthen PTI. Ethylene and NAC transcription factors appear to play roles in these processes. Under C-limitation, PTI appears compromised based on suppression of genes required for continued biosynthetic capacity and defenses through flg22. Our results provide a foundation for the intuitive perception of the interplay between plant nutrition status and pathogen defense.
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Affiliation(s)
- Hyeong Cheol Park
- Division of Applied Life Science (BK21 Plus Program) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
- Bureau of Ecological Conservation Reseach, National Institute of Ecology, Seocheon 325-813,
Korea
| | - Shinyoung Lee
- Division of Applied Life Science (BK21 Plus Program) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907,
USA
| | - Bokyung Park
- Division of Applied Life Science (BK21 Plus Program) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| | - Wonkyun Choi
- Division of Applied Life Science (BK21 Plus Program) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
- Bureau of Ecological Conservation Reseach, National Institute of Ecology, Seocheon 325-813,
Korea
| | - Chanmin Kim
- Division of Applied Life Science (BK21 Plus Program) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| | - Sanghun Lee
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907,
USA
| | - Woo Sik Chung
- Division of Applied Life Science (BK21 Plus Program) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21 Plus Program) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| | - Jamal Sabir
- College of Science, King Abdulaziz University, Jeddah 21589,
Kingdom of Saudi Arabia
| | - Ray A. Bressan
- Division of Applied Life Science (BK21 Plus Program) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907,
USA
- College of Science, King Abdulaziz University, Jeddah 21589,
Kingdom of Saudi Arabia
| | - Hans J. Bohnert
- Division of Applied Life Science (BK21 Plus Program) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
- College of Science, King Abdulaziz University, Jeddah 21589,
Kingdom of Saudi Arabia
- Departments of Plant Biology and of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801,
USA
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907,
USA
| | - Dae-Jin Yun
- Division of Applied Life Science (BK21 Plus Program) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
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8
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Oh DH, Hong H, Lee SY, Yun DJ, Bohnert HJ, Dassanayake M. Genome structures and transcriptomes signify niche adaptation for the multiple-ion-tolerant extremophyte Schrenkiella parvula. Plant Physiol 2014; 164:2123-38. [PMID: 24563282 PMCID: PMC3982767 DOI: 10.1104/pp.113.233551] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Schrenkiella parvula (formerly Thellungiella parvula), a close relative of Arabidopsis (Arabidopsis thaliana) and Brassica crop species, thrives on the shores of Lake Tuz, Turkey, where soils accumulate high concentrations of multiple-ion salts. Despite the stark differences in adaptations to extreme salt stresses, the genomes of S. parvula and Arabidopsis show extensive synteny. S. parvula completes its life cycle in the presence of Na⁺, K⁺, Mg²⁺, Li⁺, and borate at soil concentrations lethal to Arabidopsis. Genome structural variations, including tandem duplications and translocations of genes, interrupt the colinearity observed throughout the S. parvula and Arabidopsis genomes. Structural variations distinguish homologous gene pairs characterized by divergent promoter sequences and basal-level expression strengths. Comparative RNA sequencing reveals the enrichment of ion-transport functions among genes with higher expression in S. parvula, while pathogen defense-related genes show higher expression in Arabidopsis. Key stress-related ion transporter genes in S. parvula showed increased copy number, higher transcript dosage, and evidence for subfunctionalization. This extremophyte offers a framework to identify the requisite adjustments of genomic architecture and expression control for a set of genes found in most plants in a way to support distinct niche adaptation and lifestyles.
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9
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Batelli G, Oh DH, D'Urzo MP, Orsini F, Dassanayake M, Zhu JK, Bohnert HJ, Bressan RA, Maggio A. Using Arabidopsis-related model species (ARMS): growth, genetic transformation, and comparative genomics. Methods Mol Biol 2014; 1062:27-51. [PMID: 24057359 DOI: 10.1007/978-1-62703-580-4_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The Arabidopsis-related model species (ARMS) Thellungiella salsuginea and Thellungiella parvula have generated broad interest in salt stress research. While general growth characteristics of these species are similar to Arabidopsis, some aspects of their life cycle require particular attention in order to obtain healthy plants, with a large production of seeds in a relatively short time. This chapter describes basic procedures for growth, maintenance, and Agrobacterium-mediated transformation of ARMS. Where appropriate, differences in requirements between Thellungiella spp. and Arabidopsis are highlighted, along with basic growth requirements of other less studied candidate model species. Current techniques for comparative genomics analysis between Arabidopsis and ARMS are also described in detail.
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10
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Kim WY, Ali Z, Park HJ, Park SJ, Cha JY, Perez-Hormaeche J, Quintero FJ, Shin G, Kim MR, Qiang Z, Ning L, Park HC, Lee SY, Bressan RA, Pardo JM, Bohnert HJ, Yun DJ. Release of SOS2 kinase from sequestration with GIGANTEA determines salt tolerance in Arabidopsis. Nat Commun 2013; 4:1352. [PMID: 23322040 DOI: 10.1038/ncomms2357] [Citation(s) in RCA: 175] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 12/04/2012] [Indexed: 12/11/2022] Open
Abstract
Environmental challenges to plants typically entail retardation of vegetative growth and delay or cessation of flowering. Here we report a link between the flowering time regulator, GIGANTEA (GI), and adaptation to salt stress that is mechanistically based on GI degradation under saline conditions, thus retarding flowering. GI, a switch in photoperiodicity and circadian clock control, and the SNF1-related protein kinase SOS2 functionally interact. In the absence of stress, the GI:SOS2 complex prevents SOS2-based activation of SOS1, the major plant Na(+)/H(+)-antiporter mediating adaptation to salinity. GI overexpressing, rapidly flowering, plants show enhanced salt sensitivity, whereas gi mutants exhibit enhanced salt tolerance and delayed flowering. Salt-induced degradation of GI confers salt tolerance by the release of the SOS2 kinase. The GI-SOS2 interaction introduces a higher order regulatory circuit that can explain in molecular terms, the long observed connection between floral transition and adaptive environmental stress tolerance in Arabidopsis.
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Affiliation(s)
- Woe-Yeon Kim
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 660-701, South Korea
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11
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Kim WY, Ali Z, Park HJ, Park SJ, Cha JY, Perez-Hormaeche J, Quintero FJ, Shin G, Kim MR, Qiang Z, Ning L, Park HC, Lee SY, Bressan RA, Pardo JM, Bohnert HJ, Yun DJ. Erratum: Corrigendum: Release of SOS2 kinase from sequestration with GIGANTEA determines salt tolerance in Arabidopsis. Nat Commun 2013. [DOI: 10.1038/ncomms2846] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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12
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Kim JI, Baek D, Park HC, Chun HJ, Oh DH, Lee MK, Cha JY, Kim WY, Kim MC, Chung WS, Bohnert HJ, Lee SY, Bressan RA, Lee SW, Yun DJ. Overexpression of Arabidopsis YUCCA6 in potato results in high-auxin developmental phenotypes and enhanced resistance to water deficit. Mol Plant 2013; 6:337-49. [PMID: 22986790 DOI: 10.1093/mp/sss100] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Indole-3-acetic acid (IAA), a major plant auxin, is produced in both tryptophan-dependent and tryptophan-independent pathways. A major pathway in Arabidopsis thaliana generates IAA in two reactions from tryptophan. Step one converts tryptophan to indole-3-pyruvic acid (IPA) by tryptophan aminotransferases followed by a rate-limiting step converting IPA to IAA catalyzed by YUCCA proteins. We identified eight putative StYUC (Solanum tuberosum YUCCA) genes whose deduced amino acid sequences share 50%-70% identity with those of Arabidopsis YUCCA proteins. All include canonical, conserved YUCCA sequences: FATGY motif, FMO signature sequence, and FAD-binding and NADP-binding sequences. In addition, five genes were found with ~50% amino acid sequence identity to Arabidopsis tryptophan aminotransferases. Transgenic potato (Solanum tuberosum cv. Jowon) constitutively overexpressing Arabidopsis AtYUC6 displayed high-auxin phenotypes such as narrow downward-curled leaves, increased height, erect stature, and longevity. Transgenic potato plants overexpressing AtYUC6 showed enhanced drought tolerance based on reduced water loss. The phenotype was correlated with reduced levels of reactive oxygen species in leaves. The results suggest a functional YUCCA pathway of auxin biosynthesis in potato that may be exploited to alter plant responses to the environment.
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Affiliation(s)
- Jeong Im Kim
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
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Baek D, Kim MC, Chun HJ, Kang S, Park HC, Shin G, Park J, Shen M, Hong H, Kim WY, Kim DH, Lee SY, Bressan RA, Bohnert HJ, Yun DJ. Regulation of miR399f transcription by AtMYB2 affects phosphate starvation responses in Arabidopsis. Plant Physiol 2013; 161:362-73. [PMID: 23154535 PMCID: PMC3532267 DOI: 10.1104/pp.112.205922] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 11/12/2012] [Indexed: 05/18/2023]
Abstract
Although a role for microRNA399 (miR399) in plant responses to phosphate (Pi) starvation has been indicated, the regulatory mechanism underlying miR399 gene expression is not clear. Here, we report that AtMYB2 functions as a direct transcriptional activator for miR399 in Arabidopsis (Arabidopsis thaliana) Pi starvation signaling. Compared with untransformed control plants, transgenic plants constitutively overexpressing AtMYB2 showed increased miR399f expression and tissue Pi contents under high Pi growth and exhibited elevated expression of a subset of Pi starvation-induced genes. Pi starvation-induced root architectural changes were more exaggerated in AtMYB2-overexpressing transgenic plants compared with the wild type. AtMYB2 directly binds to a MYB-binding site in the miR399f promoter in vitro, as well as in vivo, and stimulates miR399f promoter activity in Arabidopsis protoplasts. Transcription of AtMYB2 itself is induced in response to Pi deficiency, and the tissue expression patterns of miR399f and AtMYB2 are similar. Both genes are expressed mainly in vascular tissues of cotyledons and in roots. Our results suggest that AtMYB2 regulates plant responses to Pi starvation by regulating the expression of the miR399 gene.
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Affiliation(s)
| | | | | | - Songhwa Kang
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660–701, Korea (D.B., M.C.K., H.J.C., S.K., H.C.P., G.S., J.P., M.S., H.H., W.-Y.K., S.Y.L., D.-J.Y.)
- College of Life Science and Natural Resources, Dong-A University, Busan 604–714, Korea (D.H.K.)
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (R.A.B.)
- Department of Plant Biology and Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
- College of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia (R.A.B., H.J.B.)
| | - Hyeong Cheol Park
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660–701, Korea (D.B., M.C.K., H.J.C., S.K., H.C.P., G.S., J.P., M.S., H.H., W.-Y.K., S.Y.L., D.-J.Y.)
- College of Life Science and Natural Resources, Dong-A University, Busan 604–714, Korea (D.H.K.)
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (R.A.B.)
- Department of Plant Biology and Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
- College of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia (R.A.B., H.J.B.)
| | - Gilok Shin
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660–701, Korea (D.B., M.C.K., H.J.C., S.K., H.C.P., G.S., J.P., M.S., H.H., W.-Y.K., S.Y.L., D.-J.Y.)
- College of Life Science and Natural Resources, Dong-A University, Busan 604–714, Korea (D.H.K.)
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (R.A.B.)
- Department of Plant Biology and Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
- College of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia (R.A.B., H.J.B.)
| | - Jiyoung Park
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660–701, Korea (D.B., M.C.K., H.J.C., S.K., H.C.P., G.S., J.P., M.S., H.H., W.-Y.K., S.Y.L., D.-J.Y.)
- College of Life Science and Natural Resources, Dong-A University, Busan 604–714, Korea (D.H.K.)
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (R.A.B.)
- Department of Plant Biology and Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
- College of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia (R.A.B., H.J.B.)
| | - Mingzhe Shen
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660–701, Korea (D.B., M.C.K., H.J.C., S.K., H.C.P., G.S., J.P., M.S., H.H., W.-Y.K., S.Y.L., D.-J.Y.)
- College of Life Science and Natural Resources, Dong-A University, Busan 604–714, Korea (D.H.K.)
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (R.A.B.)
- Department of Plant Biology and Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
- College of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia (R.A.B., H.J.B.)
| | - Hyewon Hong
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660–701, Korea (D.B., M.C.K., H.J.C., S.K., H.C.P., G.S., J.P., M.S., H.H., W.-Y.K., S.Y.L., D.-J.Y.)
- College of Life Science and Natural Resources, Dong-A University, Busan 604–714, Korea (D.H.K.)
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (R.A.B.)
- Department of Plant Biology and Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
- College of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia (R.A.B., H.J.B.)
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660–701, Korea (D.B., M.C.K., H.J.C., S.K., H.C.P., G.S., J.P., M.S., H.H., W.-Y.K., S.Y.L., D.-J.Y.)
- College of Life Science and Natural Resources, Dong-A University, Busan 604–714, Korea (D.H.K.)
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (R.A.B.)
- Department of Plant Biology and Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
- College of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia (R.A.B., H.J.B.)
| | - Doh Hoon Kim
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660–701, Korea (D.B., M.C.K., H.J.C., S.K., H.C.P., G.S., J.P., M.S., H.H., W.-Y.K., S.Y.L., D.-J.Y.)
- College of Life Science and Natural Resources, Dong-A University, Busan 604–714, Korea (D.H.K.)
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (R.A.B.)
- Department of Plant Biology and Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
- College of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia (R.A.B., H.J.B.)
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660–701, Korea (D.B., M.C.K., H.J.C., S.K., H.C.P., G.S., J.P., M.S., H.H., W.-Y.K., S.Y.L., D.-J.Y.)
- College of Life Science and Natural Resources, Dong-A University, Busan 604–714, Korea (D.H.K.)
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (R.A.B.)
- Department of Plant Biology and Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
- College of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia (R.A.B., H.J.B.)
| | - Ray A. Bressan
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660–701, Korea (D.B., M.C.K., H.J.C., S.K., H.C.P., G.S., J.P., M.S., H.H., W.-Y.K., S.Y.L., D.-J.Y.)
- College of Life Science and Natural Resources, Dong-A University, Busan 604–714, Korea (D.H.K.)
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (R.A.B.)
- Department of Plant Biology and Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
- College of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia (R.A.B., H.J.B.)
| | - Hans J. Bohnert
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660–701, Korea (D.B., M.C.K., H.J.C., S.K., H.C.P., G.S., J.P., M.S., H.H., W.-Y.K., S.Y.L., D.-J.Y.)
- College of Life Science and Natural Resources, Dong-A University, Busan 604–714, Korea (D.H.K.)
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (R.A.B.)
- Department of Plant Biology and Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (H.J.B.)
- College of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia (R.A.B., H.J.B.)
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Abstract
Extremophile plants thrive in places where most plant species cannot survive. Recent developments in high-throughput technologies and comparative genomics are shedding light on the evolutionary mechanisms leading to their adaptation.
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Affiliation(s)
- Dong-Ha Oh
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 61801, USA
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15
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Ma S, Bachan S, Porto M, Bohnert HJ, Snyder M, Dinesh-Kumar SP. Discovery of stress responsive DNA regulatory motifs in Arabidopsis. PLoS One 2012; 7:e43198. [PMID: 22912824 PMCID: PMC3418279 DOI: 10.1371/journal.pone.0043198] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 07/17/2012] [Indexed: 11/25/2022] Open
Abstract
The discovery of DNA regulatory motifs in the sequenced genomes using computational methods remains challenging. Here, we present MotifIndexer - a comprehensive strategy for de novo identification of DNA regulatory motifs at a genome level. Using word-counting methods, we indexed the existence of every 8-mer oligo composed of bases A, C, G, T, r, y, s, w, m, k, n or 12-mer oligo composed of A, C, G, T, n, in the promoters of all predicted genes of Arabidopsis thaliana genome and of selected stress-induced co-expressed genes. From this analysis, we identified number of over-represented motifs. Among these, major critical motifs were identified using a position filter. We used a model based on uniform distribution and the z-scores derived from this model to describe position bias. Interestingly, many motifs showed position bias towards the transcription start site. We extended this model to show biased distribution of motifs in the genomes of both A. thaliana and rice. We also used MotifIndexer to identify conserved motifs in co-expressed gene groups from two Arabidopsis species, A. thaliana and A. lyrata. This new comparative genomics method does not depend on alignments of homologous gene promoter sequences.
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Affiliation(s)
- Shisong Ma
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California Davis, Davis, California, United States of America
- * E-mail: (SPD-K); (SM)
| | - Shawn Bachan
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California Davis, Davis, California, United States of America
| | - Matthew Porto
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California Davis, Davis, California, United States of America
| | - Hans J. Bohnert
- Departements of Plant Biology and Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Michael Snyder
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Savithramma P. Dinesh-Kumar
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California Davis, Davis, California, United States of America
- * E-mail: (SPD-K); (SM)
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16
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17
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Ali Z, Park HC, Ali A, Oh DH, Aman R, Kropornicka A, Hong H, Choi W, Chung WS, Kim WY, Bressan RA, Bohnert HJ, Lee SY, Yun DJ. TsHKT1;2, a HKT1 homolog from the extremophile Arabidopsis relative Thellungiella salsuginea, shows K(+) specificity in the presence of NaCl. Plant Physiol 2012; 158:1463-74. [PMID: 22238420 PMCID: PMC3291249 DOI: 10.1104/pp.111.193110] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 01/08/2012] [Indexed: 05/02/2023]
Abstract
Cellular Na(+)/K(+) ratio is a crucial parameter determining plant salinity stress resistance. We tested the function of plasma membrane Na(+)/K(+) cotransporters in the High-affinity K(+) Transporter (HKT) family from the halophytic Arabidopsis (Arabidopsis thaliana) relative Thellungiella salsuginea. T. salsuginea contains at least two HKT genes. TsHKT1;1 is expressed at very low levels, while the abundant TsHKT1;2 is transcriptionally strongly up-regulated by salt stress. TsHKT-based RNA interference in T. salsuginea resulted in Na(+) sensitivity and K(+) deficiency. The athkt1 mutant lines overexpressing TsHKT1;2 proved less sensitive to Na(+) and showed less K(+) deficiency than lines overexpressing AtHKT1. TsHKT1;2 ectopically expressed in yeast mutants lacking Na(+) or K(+) transporters revealed strong K(+) transporter activity and selectivity for K(+) over Na(+). Altering two amino acid residues in TsHKT1;2 to mimic the AtHKT1 sequence resulted in enhanced sodium uptake and loss of the TsHKT1;2 intrinsic K(+) transporter activity. We consider the maintenance of K(+) uptake through TsHKT1;2 under salt stress an important component supporting the halophytic lifestyle of T. salsuginea.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Dae-Jin Yun
- Division of Applied Life Science (Brain Korea 21 Program) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660–701, Korea (Z.A., H.C.P., A.A., R.A., H.H., W.C., W.S.C., W.-Y.K., R.A.B., H.J.B., S.Y.L., D.-J,Y.); Genomics and Biotechnology Section, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia (Z.A., R.A.B., H.J.B.); Department of Plant Biology (D.-H.O., A.K., H.J.B.) and Department of Crop Sciences (H.J.B.), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (R.A.B.)
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18
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Abstract
The traditional focus on the central dogma of molecular biology, from gene through RNA to protein, has now been replaced by the recognition of an additional mechanism. The new regulatory mechanism, post-translational modifications to proteins, can actively alter protein function or activity introducing additional levels of functional complexity by altering cellular and sub-cellular location, protein interactions and the outcome of biochemical reaction chains. Modifications by ubiquitin (Ub) and ubiquitin-like modifiers systems are conserved in all eukaryotic organisms. One of them, small ubiquitin-like modifier (SUMO) is present in plants. The SUMO mechanism includes several isoforms of proteins that are involved in reactions of sumoylation and de-sumoylation. Sumoylation affects several important processes in plants. Outstanding among those are responses to environmental stresses. These may be abiotic stresses, such as phosphate deficiency, heat, low temperature, and drought, or biotic stressses, as well including defense reactions to pathogen infection. Also, the regulations of flowering time, cell growth and development, and nitrogen assimilation have recently been added to this list. Identification of SUMO targets is material to characterize the function of sumoylation or desumoylation. Affinity purification and mass spectrometric identification have been done lately in plants. Further SUMO noncovalent binding appears to have function in other model organisms and SUMO interacting proteins in plants will be of interest to plant biologists who dissect the dynamic function of SUMO. This review will discuss results of recent insights into the role of sumoylation in plants.
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Affiliation(s)
- Hee Jin Park
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Hyeong Cheol Park
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Hans J. Bohnert
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
- Departments of Plant Biology and of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Dae-Jin Yun
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
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19
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Dassanayake M, Oh DH, Haas JS, Hernandez A, Hong H, Ali S, Yun DJ, Bressan RA, Zhu JK, Bohnert HJ, Cheeseman JM. The genome of the extremophile crucifer Thellungiella parvula. Nat Genet 2011; 43:913-8. [PMID: 21822265 DOI: 10.1038/ng.889] [Citation(s) in RCA: 264] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 06/24/2011] [Indexed: 01/02/2023]
Abstract
Thellungiella parvula is related to Arabidopsis thaliana and is endemic to saline, resource-poor habitats, making it a model for the evolution of plant adaptation to extreme environments. Here we present the draft genome for this extremophile species. Exclusively by next generation sequencing, we obtained the de novo assembled genome in 1,496 gap-free contigs, closely approximating the estimated genome size of 140 Mb. We anchored these contigs to seven pseudo chromosomes without the use of maps. We show that short reads can be assembled to a near-complete chromosome level for a eukaryotic species lacking prior genetic information. The sequence identifies a number of tandem duplications that, by the nature of the duplicated genes, suggest a possible basis for T. parvula's extremophile lifestyle. Our results provide essential background for developing genomically influenced testable hypotheses for the evolution of environmental stress tolerance.
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Affiliation(s)
- Maheshi Dassanayake
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
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20
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Park HC, Choi W, Park HJ, Cheong MS, Koo YD, Shin G, Chung WS, Kim WY, Kim MG, Bressan RA, Bohnert HJ, Lee SY, Yun DJ. Identification and molecular properties of SUMO-binding proteins in Arabidopsis. Mol Cells 2011; 32:143-51. [PMID: 21607647 PMCID: PMC3887670 DOI: 10.1007/s10059-011-2297-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 04/20/2011] [Accepted: 04/28/2011] [Indexed: 10/18/2022] Open
Abstract
Reversible conjugation of the small ubiquitin modifier (SUMO) peptide to proteins (SUMOylation) plays important roles in cellular processes in animals and yeasts. However, little is known about plant SUMO targets. To identify SUMO substrates in Arabidopsis and to probe for biological functions of SUMO proteins, we constructed 6xHis-3xFLAG fused AtSUMO1 (HFAtSUMO1) controlled by the CaMV35S promoter for transformation into Arabidopsis Col-0. After heat treatment, an increased sumoylation pattern was detected in the transgenic plants. SUMO1-modified proteins were selected after two-dimensional gel electrophoresis (2-DE) image analysis and identified using matrix-assisted laser-desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). We identified 27 proteins involved in a variety of processes such as nucleic acid metabolism, signaling, metabolism, and including proteins of unknown functions. Binding and sumoylation patterns were confirmed independently. Surprisingly, MCM3 (At5G46280), a DNA replication licensing factor, only interacted with and became sumoylated by AtSUMO1, but not by SUMO1ΔGG or AtSUMO3. The results suggest specific interactions between sumoylation targets and particular sumoylation enzymes.
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Affiliation(s)
- Hyeong Cheol Park
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
- These authors contributed equally to this work
| | - Wonkyun Choi
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
- These authors contributed equally to this work
| | - Hee Jin Park
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, USA
- These authors contributed equally to this work
| | - Mi Sun Cheong
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Yoon Duck Koo
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Gilok Shin
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Woo Sik Chung
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Min Gab Kim
- Bio-Crops Development Division, Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea
| | - Ray A. Bressan
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, USA
- King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Hans J. Bohnert
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
- Departments of Plant Biology and of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Sang Yeol Lee
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Dae-Jin Yun
- Division of Applied Life Science (Brain Korea 21 Program), and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
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21
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Choi W, Baek D, Oh DH, Park J, Hong H, Kim WY, Bohnert HJ, Bressan RA, Park HC, Yun DJ. NKS1, Na(+)- and K(+)-sensitive 1, regulates ion homeostasis in an SOS-independent pathway in Arabidopsis. Phytochemistry 2011; 72:330-6. [PMID: 21227472 DOI: 10.1016/j.phytochem.2010.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 11/01/2010] [Accepted: 12/06/2010] [Indexed: 05/30/2023]
Abstract
An Arabidopsis thaliana mutant, nks1-1, exhibiting enhanced sensitivity to NaCl was identified in a screen of a T-DNA insertion population in the genetic background of Col-0 gl1sos3-1. Analysis of the genome sequence in the region flanking the T-DNA left border indicated two closely linked mutations in the gene encoded at locus At4g30996. A second allele, nks1-2, was obtained from the Arabidopsis Biological Resource Center. NKS1 mRNA was detected in all parts of wild-type plants but was not detected in plants of either mutant, indicating inactivation by the mutations. Both mutations in NKS1 were associated with increased sensitivity to NaCl and KCl, but not to LiCl or mannitol. NaCl sensitivity was associated with nks1 mutations in Arabidopsis lines expressing either wild type or null alleles of SOS1, SOS2 or SOS3. The NaCl-sensitive phenotype of the nks1-2 mutant was complemented by expression of a full-length NKS1 allele from the CaMV35S promoter. When grown in medium containing NaCl, nks1 mutants accumulated more Na(+) than wild type and K(+)/Na(+) homeostasis was perturbed. It is proposed NKS1, a plant-specific gene encoding a 19kDa endomembrane-localized protein of unknown function, is part of an ion homeostasis regulation pathway that is independent of the SOS pathway.
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Affiliation(s)
- Wonkyun Choi
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
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22
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Bressan RA, Reddy MP, Chung SH, Yun DJ, Hardin LS, Bohnert HJ. Stress-adapted extremophiles provide energy without interference with food production. Food Secur 2011. [DOI: 10.1007/s12571-011-0112-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Miura K, Lee J, Gong Q, Ma S, Jin JB, Yoo CY, Miura T, Sato A, Bohnert HJ, Hasegawa PM. SIZ1 regulation of phosphate starvation-induced root architecture remodeling involves the control of auxin accumulation. Plant Physiol 2011; 155:1000-12. [PMID: 21156857 PMCID: PMC3032448 DOI: 10.1104/pp.110.165191] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 11/26/2010] [Indexed: 05/20/2023]
Abstract
Phosphate (Pi) limitation causes plants to modulate the architecture of their root systems to facilitate the acquisition of Pi. Previously, we reported that the Arabidopsis (Arabidopsis thaliana) SUMO E3 ligase SIZ1 regulates root architecture remodeling in response to Pi limitation; namely, the siz1 mutations cause the inhibition of primary root (PR) elongation and the promotion of lateral root (LR) formation. Here, we present evidence that SIZ1 is involved in the negative regulation of auxin patterning to modulate root system architecture in response to Pi starvation. The siz1 mutations caused greater PR growth inhibition and LR development of seedlings in response to Pi limitation. Similar root phenotypes occurred if Pi-deficient wild-type seedlings were supplemented with auxin. N-1-Naphthylphthalamic acid, an inhibitor of auxin efflux activity, reduced the Pi starvation-induced LR root formation of siz1 seedlings to a level equivalent to that seen in the wild type. Monitoring of the auxin-responsive reporter DR5::uidA indicated that auxin accumulates in PR tips at early stages of the Pi starvation response. Subsequently, DR5::uidA expression was observed in the LR primordia, which was associated with LR elongation. The time-sequential patterning of DR5::uidA expression occurred earlier in the roots of siz1 as compared with the wild type. In addition, microarray analysis revealed that several other auxin-responsive genes, including genes involved in cell wall loosening and biosynthesis, were up-regulated in siz1 relative to wild-type seedlings in response to Pi starvation. Together, these results suggest that SIZ1 negatively regulates Pi starvation-induced root architecture remodeling through the control of auxin patterning.
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Affiliation(s)
- Kenji Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.
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24
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Dassanayake M, Oh DH, Hong H, Bohnert HJ, Cheeseman JM. Transcription strength and halophytic lifestyle. Trends Plant Sci 2011; 16:1-3. [PMID: 21094076 DOI: 10.1016/j.tplants.2010.10.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Revised: 10/25/2010] [Accepted: 10/25/2010] [Indexed: 05/30/2023]
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26
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Park HC, Kim H, Koo SC, Park HJ, Cheong MS, Hong H, Baek D, Chung WS, Kim DH, Bressan RA, Lee SY, Bohnert HJ, Yun DJ. Functional characterization of the SIZ/PIAS-type SUMO E3 ligases, OsSIZ1 and OsSIZ2 in rice. Plant Cell Environ 2010; 33:1923-34. [PMID: 20561251 DOI: 10.1111/j.1365-3040.2010.02195.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Sumoylation is a post-translational regulatory process in diverse cellular processes in eukaryotes, involving conjugation/deconjugation of small ubiquitin-like modifier (SUMO) proteins to other proteins thus modifying their function. The PIAS [protein inhibitor of activated signal transducers and activators of transcription (STAT)] and SAP (scaffold attachment factor A/B/acinus/PIAS)/MIZ (SIZ) proteins exhibit SUMO E3-ligase activity that facilitates the conjugation of SUMO proteins to target substrates. Here, we report the isolation and molecular characterization of Oryza sativa SIZ1 (OsSIZ1) and SIZ2 (OsSIZ2), rice homologs of Arabidopsis SIZ1. The rice SIZ proteins are localized to the nucleus and showed sumoylation activities in a tobacco system. Our analysis showed increased amounts of SUMO conjugates associated with environmental stresses such as high and low temperature, NaCl and abscisic acid (ABA) in rice plants. The expression of OsSIZ1 and OsSIZ2 in siz1-2 Arabidopsis plants partially complemented the morphological mutant phenotype and enhanced levels of SUMO conjugates under heat shock conditions. In addition, ABA-hypersensitivity of siz1-2 seed germination was partially suppressed by OsSIZ1 and OsSIZ2. The results suggest that rice SIZ1 and SIZ2 are able to functionally complement Arabidopsis SIZ1 in the SUMO conjugation pathway. Their effects on the Arabidopsis mutant suggest a function for these genes related to stress responses and stress adaptation.
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Affiliation(s)
- Hyeong Cheol Park
- Division of Applied Life Science (BK21 program), Plant Molecular Biology and Biotechnology Research Center and Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju 660-701, Korea.
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27
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Oh DH, Dassanayake M, Haas JS, Kropornika A, Wright C, d'Urzo MP, Hong H, Ali S, Hernandez A, Lambert GM, Inan G, Galbraith DW, Bressan RA, Yun DJ, Zhu JK, Cheeseman JM, Bohnert HJ. Genome structures and halophyte-specific gene expression of the extremophile Thellungiella parvula in comparison with Thellungiella salsuginea (Thellungiella halophila) and Arabidopsis. Plant Physiol 2010; 154:1040-52. [PMID: 20833729 PMCID: PMC2971586 DOI: 10.1104/pp.110.163923] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The genome of Thellungiella parvula, a halophytic relative of Arabidopsis (Arabidopsis thaliana), is being assembled using Roche-454 sequencing. Analyses of a 10-Mb scaffold revealed synteny with Arabidopsis, with recombination and inversion and an uneven distribution of repeat sequences. T. parvula genome structure and DNA sequences were compared with orthologous regions from Arabidopsis and publicly available bacterial artificial chromosome sequences from Thellungiella salsuginea (previously Thellungiella halophila). The three-way comparison of sequences, from one abiotic stress-sensitive species and two tolerant species, revealed extensive sequence conservation and microcolinearity, but grouping Thellungiella species separately from Arabidopsis. However, the T. parvula segments are distinguished from their T. salsuginea counterparts by a pronounced paucity of repeat sequences, resulting in a 30% shorter DNA segment with essentially the same gene content in T. parvula. Among the genes is SALT OVERLY SENSITIVE1 (SOS1), a sodium/proton antiporter, which represents an essential component of plant salinity stress tolerance. Although the SOS1 coding region is highly conserved among all three species, the promoter regions show conservation only between the two Thellungiella species. Comparative transcript analyses revealed higher levels of basal as well as salt-induced SOS1 expression in both Thellungiella species as compared with Arabidopsis. The Thellungiella species and other halophytes share conserved pyrimidine-rich 5' untranslated region proximal regions of SOS1 that are missing in Arabidopsis. Completion of the genome structure of T. parvula is expected to highlight distinctive genetic elements underlying the extremophile lifestyle of this species.
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Affiliation(s)
- Dong-Ha Oh
- Department of Plant Biology , University of Illinois, Urbana, Illinois 61801, USA.
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Orsini F, D'Urzo MP, Inan G, Serra S, Oh DH, Mickelbart MV, Consiglio F, Li X, Jeong JC, Yun DJ, Bohnert HJ, Bressan RA, Maggio A. A comparative study of salt tolerance parameters in 11 wild relatives of Arabidopsis thaliana. J Exp Bot 2010; 61:3787-98. [PMID: 20595237 PMCID: PMC2921208 DOI: 10.1093/jxb/erq188] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 06/04/2010] [Accepted: 06/04/2010] [Indexed: 05/18/2023]
Abstract
Salinity is an abiotic stress that limits both yield and the expansion of agricultural crops to new areas. In the last 20 years our basic understanding of the mechanisms underlying plant tolerance and adaptation to saline environments has greatly improved owing to active development of advanced tools in molecular, genomics, and bioinformatics analyses. However, the full potential of investigative power has not been fully exploited, because the use of halophytes as model systems in plant salt tolerance research is largely neglected. The recent introduction of halophytic Arabidopsis-Relative Model Species (ARMS) has begun to compare and relate several unique genetic resources to the well-developed Arabidopsis model. In a search for candidates to begin to understand, through genetic analyses, the biological bases of salt tolerance, 11 wild relatives of Arabidopsis thaliana were compared: Barbarea verna, Capsella bursa-pastoris, Hirschfeldia incana, Lepidium densiflorum, Malcolmia triloba, Lepidium virginicum, Descurainia pinnata, Sisymbrium officinale, Thellungiella parvula, Thellungiella salsuginea (previously T. halophila), and Thlaspi arvense. Among these species, highly salt-tolerant (L. densiflorum and L. virginicum) and moderately salt-tolerant (M. triloba and H. incana) species were identified. Only T. parvula revealed a true halophytic habitus, comparable to the better studied Thellungiella salsuginea. Major differences in growth, water transport properties, and ion accumulation are observed and discussed to describe the distinctive traits and physiological responses that can now be studied genetically in salt stress research.
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Affiliation(s)
- Francesco Orsini
- Department of Agro-environmental Sciences and Technologies, University of Bologna, Viale Fanin 44, I-40127 Bologna, Italy
- Department of Agricultural Engineering and Agronomy, University of Naples Federico II, Via Università 100, Portici, I-80055, Italy
| | - Matilde Paino D'Urzo
- Center for Plant Environmental Stress Physiology, Purdue University, 625 Agriculture Mall Drive, West Lafayette, IN 47907-2010, USA
- KAUST–Plant Stress Genomics and Technology Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Gunsu Inan
- Center for Plant Environmental Stress Physiology, Purdue University, 625 Agriculture Mall Drive, West Lafayette, IN 47907-2010, USA
- Institute of Biotechnology, University of Ankara, Tandoan, Ankara, 06100, Turkey
| | - Sara Serra
- Department of Fruit Tree and Woody Plant Sciences, University of Bologna, Viale Fanin 46, I-40127 Bologna, Italy
| | - Dong-Ha Oh
- Division of Applied Life Science (BK21 program) and Environmental Biotechnology National Core Research Center, Graduate School of Gyeongsang National University, Jinju 660-701, Korea
- Department of Plant Biology and Department of Crop Sciences, University of Illinois at Urbana-Champaign, 201 W. Gregory Drive Urbana, IL 61801, USA
| | - Michael V. Mickelbart
- Center for Plant Environmental Stress Physiology, Purdue University, 625 Agriculture Mall Drive, West Lafayette, IN 47907-2010, USA
| | - Federica Consiglio
- Institute of Plant Genetics, Via Universita' 133, I-80055 Portici, Italy
| | - Xia Li
- The Key Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021, China
| | - Jae Cheol Jeong
- Division of Applied Life Science (BK21 program) and Environmental Biotechnology National Core Research Center, Graduate School of Gyeongsang National University, Jinju 660-701, Korea
| | - Dae-Jin Yun
- Center for Plant Environmental Stress Physiology, Purdue University, 625 Agriculture Mall Drive, West Lafayette, IN 47907-2010, USA
- Division of Applied Life Science (BK21 program) and Environmental Biotechnology National Core Research Center, Graduate School of Gyeongsang National University, Jinju 660-701, Korea
| | - Hans J. Bohnert
- Division of Applied Life Science (BK21 program) and Environmental Biotechnology National Core Research Center, Graduate School of Gyeongsang National University, Jinju 660-701, Korea
- Department of Plant Biology and Department of Crop Sciences, University of Illinois at Urbana-Champaign, 201 W. Gregory Drive Urbana, IL 61801, USA
| | - Ray A. Bressan
- Center for Plant Environmental Stress Physiology, Purdue University, 625 Agriculture Mall Drive, West Lafayette, IN 47907-2010, USA
- KAUST–Plant Stress Genomics and Technology Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Division of Applied Life Science (BK21 program) and Environmental Biotechnology National Core Research Center, Graduate School of Gyeongsang National University, Jinju 660-701, Korea
| | - Albino Maggio
- Department of Agricultural Engineering and Agronomy, University of Naples Federico II, Via Università 100, Portici, I-80055, Italy
- To whom correspondence should be addressed: E-mail:
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Abstract
The accumulation of sugar alcohols and other low molecular weight metabolites such as proline and glycine-betaine is a widespread response that may protect against environmental stress that occurs in a diverse range of organisms. Transgenic tobacco plants that synthesize and accumulate the sugar alcohol mannitol were engineered by introduction of a bacterial gene that encodes mannitol 1 -phosphate dehydrogenase. Growth of plants from control and mannitol-containing lines in the absence and presence of added sodium chloride was analyzed. Plants containing mannitol had an increased ability to tolerate high salinity.
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Ernst L, Goodger JQD, Alvarez S, Marsh EL, Berla B, Lockhart E, Jung J, Li P, Bohnert HJ, Schachtman DP. Sulphate as a xylem-borne chemical signal precedes the expression of ABA biosynthetic genes in maize roots. J Exp Bot 2010; 61:3395-405. [PMID: 20566566 DOI: 10.1093/jxb/erq160] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Recent reports suggest that early sensing of soil water stress by plant roots and the concomitant reduction in stomatal conductance may not be mediated by root-sourced abscisic acid (ABA), but that other xylem-borne chemicals may be the primary stress signal(s). To gain more insight into the role of root-sourced ABA, the timing and location of the expression of genes for key enzymes involved in ABA biosynthesis in Zea mays roots was measured and a comprehensive analysis of root xylem sap constituents from the early to the later stages of water stress was conducted. Xylem sap and roots were sampled from plants at an early stage of water stress when only a reduction in leaf conductance was measured, as well as at later stages when leaf xylem pressure potential decreased. It was found that the majority of ABA biosynthetic genes examined were only significantly expressed in the elongation region of roots at a later stage of water stress. Apart from ABA, sulphate was the only xylem-borne chemical that consistently showed significantly higher concentrations from the early to the later stages of stress. Moreover, there was an interactive effect of ABA and sulphate in decreasing maize transpiration rate and Vicia faba stomatal aperture, as compared to ABA alone. The expression of a sulphate transporter gene was also analysed and it was found that it had increased in the elongation region of roots from the early to the later stages of water stress. Our results support the suggestion that in the early stage of water stress, increased levels of ABA in xylem sap may not be due to root biosynthesis, ABA glucose ester catabolism or pH-mediated redistribution, but may be due to shoot biosynthesis and translocation to the roots. The analysis of xylem sap mineral content and bioassays indicate that the anti-transpirant effect of the ABA reaching the stomata at the early stages of water stress may be enhanced by the increased concentrations of sulphate in the xylem which is also transported from the roots to the leaves.
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Affiliation(s)
- Laura Ernst
- Donald Danforth Plant Science Center, 975 North Warson Rd, St Louis, MO 63132, USA
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31
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Zurawski G, Bohnert HJ, Whitfeld PR, Bottomley W. Nucleotide sequence of the gene for the M(r) 32,000 thylakoid membrane protein from Spinacia oleracea and Nicotiana debneyi predicts a totally conserved primary translation product of M(r) 38,950. Proc Natl Acad Sci U S A 2010; 79:7699-703. [PMID: 16593262 PMCID: PMC347415 DOI: 10.1073/pnas.79.24.7699] [Citation(s) in RCA: 217] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The gene for the so-called M(r) 32,000 rapidly labeled photosystem II thylakoid membrane protein (here designated psbA) of spinach (Spinacia oleracea) chloroplasts is located on the chloroplast DNA in the large single-copy region immediately adjacent to one of the inverted repeat sequences. In this paper we show that the size of the mRNA for this protein is approximately 1.25 kilobases and that the direction of transcription is towards the inverted repeat unit. The nucleotide sequence of the gene and its flanking regions is presented. The only large open reading frame in the sequence codes for a protein of M(r) 38,950. The nucleotide sequence of psbA from Nicotiana debneyi also has been determined, and comparison of the sequences from the two species shows them to be highly conserved (>95% homology) throughout the entire reading frame. Conservation of the amino acid sequence is absolute, there being no changes in a total of 353 residues. This leads us to conclude that the primary translation product of psbA must be a protein of M(r) 38,950. The protein is characterized by the complete absence of lysine residues and is relatively rich in hydrophobic amino acids, which tend to be clustered. Transcription of spinach psbA starts about 86 base pairs before the first ATG codon. Immediately upstream from this point there is a sequence typical of that found in E. coli promoters. An almost identical sequence occurs in the equivalent region of N. debneyi DNA.
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Affiliation(s)
- G Zurawski
- Division of Plant Industry, Commonwealth Scientific and Industrial Research Organization, P.O. Box 1600, Canberra City, Australian Capital Territory 2601, Australia
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32
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Oh DH, Ali Z, Hyeong CP, Bressan RA, Dae JY, Bohnert HJ. Consequences of SOS1 deficiency: intracellular physiology and transcription. Plant Signal Behav 2010; 5:766-768. [PMID: 20505347 PMCID: PMC3001585 DOI: 10.4161/psb.5.6.11777] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 03/12/2010] [Indexed: 05/26/2023]
Abstract
As much as there is known about the function of the sodium/proton antiporter SOS1 in plants, recent studies point towards a more general role for this protein. The crucial involvement in salt stress protection is clearly one of its functions -confined to the N-terminus, but the modular structure of the protein includes a segment with several domains that are functionally not studied but comprise more than half of the protein's length. Additional functions of the protein appear to be an influence on vesicle trafficking, vacuolar pH and general ion homeostasis during salt stress. Eliminating SOS1 leads to the expression of genes that are not strictly salinity stress related. Functions that are regulated in sos1 mutants included pathogen responses, and effects on circadian rhythm.
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Affiliation(s)
- Donga Ha Oh
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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33
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Cheong MS, Park HC, Bohnert HJ, Bressan RA, Yun DJ. Structural and functional studies of SIZ1, a PIAS-type SUMO E3 ligase from Arabidopsis. Plant Signal Behav 2010; 5:567-569. [PMID: 20404572 PMCID: PMC7080486 DOI: 10.4161/psb.11426] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 02/05/2010] [Indexed: 05/27/2023]
Abstract
Small ubiquitin-like modifier (SUMO) is a post-translational modifier peptide that is involved in several biological processes in eukaryotes. Arabidopsis SIZ1, a SUMO E3 ligase, is an ortholog of the mammalian PIAS (Protein Inhibitor of Activated STAT) and yeast SIZ (SAP/Miz) proteins. SIZ1 contains all of the typical domains of PIAS/SIZ-type proteins, such as the PINIT, SAP, SP-RING, and plant-specific PHD domains. SIZ1 plays a pivotal role in controlling SUMOylation, and disruption of its function has been reported to affect stress responses, growth, and development. We performed a structural and functional analysis of SIZ1 by determining the phenotypes of siz1 knockout mutants transformed with SIZ1 alleles carrying point mutations in predicted SIZ1 domains. This study establishes that the diverse properties characteristic of SIZ1 are associated with specific domains and that they can be separated.
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34
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Oh DH, Lee SY, Bressan RA, Yun DJ, Bohnert HJ. Intracellular consequences of SOS1 deficiency during salt stress. J Exp Bot 2010; 5:766-8. [PMID: 20054031 PMCID: PMC2826659 DOI: 10.1093/jxb/erp391] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Revised: 12/12/2009] [Accepted: 12/15/2009] [Indexed: 05/18/2023]
Abstract
A mutation of AtSOS1 (Salt Overly Sensitive 1), a plasma membrane Na(+)/H(+)-antiporter in Arabidopsis thaliana, leads to a salt-sensitive phenotype accompanied by the death of root cells under salt stress. Intracellular events and changes in gene expression were compared during a non-lethal salt stress between the wild type and a representative SOS1 mutant, atsos1-1, by confocal microscopy using ion-specific fluorophores and by quantitative RT-PCR. In addition to the higher accumulation of sodium ions, atsos1-1 showed inhibition of endocytosis, abnormalities in vacuolar shape and function, and changes in intracellular pH compared to the wild type in root tip cells under stress. Quantitative RT-PCR revealed a dramatically faster and higher induction of root-specific Ca(2+) transporters, including several CAXs and CNGCs, and the drastic down-regulation of genes involved in pH-homeostasis and membrane potential maintenance. Differential regulation of genes for functions in intracellular protein trafficking in atsos1-1 was also observed. The results suggested roles of the SOS1 protein, in addition to its function as a Na(+)/H(+) antiporter, whose disruption affected membrane traffic and vacuolar functions possibly by controlling pH homeostasis in root cells.
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Affiliation(s)
- Dong-Ha Oh
- Division of Applied Life Science (BK21 program) and Environmental BiotechnologyNational Core Research Center, Graduate School of Gyeongsang NationalUniversity, Jinju 660-701, Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21 program) and Environmental BiotechnologyNational Core Research Center, Graduate School of Gyeongsang NationalUniversity, Jinju 660-701, Korea
| | - Ray A. Bressan
- Department of Horticulture and Landscape Architecture, Purdue University, WestLafayette, IN 47907, USA
- WCU Program, Division of Applied Life Sciences, Gyeongsang National University, Jinju 660--701, Korea
| | - Dae-Jin Yun
- Division of Applied Life Science (BK21 program) and Environmental BiotechnologyNational Core Research Center, Graduate School of Gyeongsang NationalUniversity, Jinju 660-701, Korea
- WCU Program, Division of Applied Life Sciences, Gyeongsang National University, Jinju 660--701, Korea
| | - Hans J. Bohnert
- WCU Program, Division of Applied Life Sciences, Gyeongsang National University, Jinju 660--701, Korea
- Departments of Plant Biology and of Crop Sciences, University of Illinois at UrbanaChampaign, Urbana, IL 61801, USA
- To whom correspondence should be addressed. E-mail:
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35
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Dassanayake M, Haas JS, Bohnert HJ, Cheeseman JM. Comparative transcriptomics for mangrove species: an expanding resource. Funct Integr Genomics 2010; 10:523-32. [PMID: 20107865 DOI: 10.1007/s10142-009-0156-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Revised: 11/30/2009] [Accepted: 12/24/2009] [Indexed: 11/30/2022]
Abstract
We present here the Mangrove Transcriptome Database (MTDB), an integrated, web-based platform providing transcript information from all 28 mangrove species for which information is available. Sequences are annotated, and when possible, GO clustered and assigned to KEGG pathways, making MTDB a valuable resource for approaching mangrove or other extremophile biology from the transcriptomic level. As one example outlining the potential of MTDB, we highlight the analysis of mangrove microRNA (miRNA) precursor sequences, miRNA target sites, and their conservation and divergence compared with model plants. MTDB is available at http://mangrove.illinois.edu .
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Affiliation(s)
- Maheshi Dassanayake
- Department of Plant Biology, University of Illinois, 505 S Goodwin Ave, Urbana, IL 61801, USA
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36
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Cheong MS, Park HC, Hong MJ, Lee J, Choi W, Jin JB, Bohnert HJ, Lee SY, Bressan RA, Yun DJ. Specific domain structures control abscisic acid-, salicylic acid-, and stress-mediated SIZ1 phenotypes. Plant Physiol 2009; 151:1930-42. [PMID: 19837819 PMCID: PMC2785975 DOI: 10.1104/pp.109.143719] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 10/10/2009] [Indexed: 05/20/2023]
Abstract
SIZ1 (for yeast SAP and MIZ1) encodes the sole ortholog of mammalian PIAS (for protein inhibitor of activated STAT) and yeast SIZ SUMO (for small ubiquitin-related modifier) E3 ligases in Arabidopsis (Arabidopsis thaliana). Four conserved motifs in SIZ1 include SAP (for scaffold attachment factor A/B/acinus/PIAS domain), PINIT (for proline-isoleucine-asparagine-isoleucine-threonine), SP-RING (for SIZ/PIAS-RING), and SXS (for serine-X-serine, where X is any amino acid) motifs. SIZ1 contains, in addition, a PHD (for plant homeodomain) typical of plant PIAS proteins. We determined phenotypes of siz1-2 knockout mutants transformed with SIZ1 alleles carrying point mutations in the predicted domains. Domain SP-RING is required for SUMO conjugation activity and nuclear localization of SIZ1. Salicylic acid (SA) accumulation and SA-dependent phenotypes of siz1-2, such as diminished plant size, heightened innate immunity, and abscisic acid inhibition of cotyledon greening, as well as SA-independent basal thermotolerance were not complemented by the altered SP-RING allele of SIZ1. The SXS domain also controlled SA accumulation and was involved in greening and expansion of cotyledons of seedlings germinated in the presence of abscisic acid. Mutations of the PHD zinc finger domain and the PINIT motif affected in vivo SUMOylation. Expression of the PHD and/or PINIT domain mutant alleles of SIZ1 in siz1-2 promoted hypocotyl elongation in response to sugar and light. The various domains of SIZ1 make unique contributions to the plant's ability to cope with its environment.
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37
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Abstract
Much is already known about the function and functioning of the three genes that make up the SOS (Salt-Overly-Sensitive) pathway in plants, but recent studies indicate that the linkage between external increases in salinity and stress protection provided by genes SOS1, SOS2 and SOS3 is more complex than previously appreciated. It has recently been shown that the engineered reduced expression of the sodium/proton antiporter SOS1 affected several pathways indicating a role for SOS1 that exceeds its known function as an antiporter. Interference with expression of SOS1, characterized as a sodium/proton antiporter in the halophyte Thellungiella salsuginea converted Thellungiella into an essentially glycophytic species.
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Affiliation(s)
- Dong-Ha Oh
- Departments of Plant Biology and of Crop Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA
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38
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Mang HG, Laluk KA, Parsons EP, Kosma DK, Cooper BR, Park HC, AbuQamar S, Boccongelli C, Miyazaki S, Consiglio F, Chilosi G, Bohnert HJ, Bressan RA, Mengiste T, Jenks MA. The Arabidopsis RESURRECTION1 gene regulates a novel antagonistic interaction in plant defense to biotrophs and necrotrophs. Plant Physiol 2009; 151:290-305. [PMID: 19625635 PMCID: PMC2735982 DOI: 10.1104/pp.109.142158] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Accepted: 07/17/2009] [Indexed: 05/18/2023]
Abstract
We report a role for the Arabidopsis (Arabidopsis thaliana) RESURRECTION1 (RST1) gene in plant defense. The rst1 mutant exhibits enhanced susceptibility to the biotrophic fungal pathogen Erysiphe cichoracearum but enhanced resistance to the necrotrophic fungal pathogens Botrytis cinerea and Alternaria brassicicola. RST1 encodes a novel protein that localizes to the plasma membrane and is predicted to contain 11 transmembrane domains. Disease responses in rst1 correlate with higher levels of jasmonic acid (JA) and increased basal and B. cinerea-induced expression of the plant defensin PDF1.2 gene but reduced E. cichoracearum-inducible salicylic acid levels and expression of pathogenesis-related genes PR1 and PR2. These results are consistent with rst1's varied resistance and susceptibility to pathogens of different life styles. Cuticular lipids, both cutin monomers and cuticular waxes, on rst1 leaves were significantly elevated, indicating a role for RST1 in the suppression of leaf cuticle lipid synthesis. The rst1 cuticle exhibits normal permeability, however, indicating that the disease responses of rst1 are not due to changes in this cuticle property. Double mutant analysis revealed that the coi1 mutation (causing defective JA signaling) is completely epistatic to rst1, whereas the ein2 mutation (causing defective ethylene signaling) is partially epistatic to rst1, for resistance to B. cinerea. The rst1 mutation thus defines a unique combination of disease responses to biotrophic and necrotrophic fungi in that it antagonizes salicylic acid-dependent defense and enhances JA-mediated defense through a mechanism that also controls cuticle synthesis.
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Affiliation(s)
- Hyung Gon Mang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907-2054, USA
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39
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Oh DH, Leidi E, Zhang Q, Hwang SM, Li Y, Quintero FJ, Jiang X, D'Urzo MP, Lee SY, Zhao Y, Bahk JD, Bressan RA, Yun DJ, Pardo JM, Bohnert HJ. Loss of halophytism by interference with SOS1 expression. Plant Physiol 2009; 151:210-22. [PMID: 19571313 PMCID: PMC2735974 DOI: 10.1104/pp.109.137802] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2009] [Accepted: 06/27/2009] [Indexed: 05/18/2023]
Abstract
The contribution of SOS1 (for Salt Overly Sensitive 1), encoding a sodium/proton antiporter, to plant salinity tolerance was analyzed in wild-type and RNA interference (RNAi) lines of the halophytic Arabidopsis (Arabidopsis thaliana)-relative Thellungiella salsuginea. Under all conditions, SOS1 mRNA abundance was higher in Thellungiella than in Arabidopsis. Ectopic expression of the Thellungiella homolog ThSOS1 suppressed the salt-sensitive phenotype of a Saccharomyces cerevisiae strain lacking sodium ion (Na(+)) efflux transporters and increased salt tolerance of wild-type Arabidopsis. thsos1-RNAi lines of Thellungiella were highly salt sensitive. A representative line, thsos1-4, showed faster Na(+) accumulation, more severe water loss in shoots under salt stress, and slower removal of Na(+) from the root after removal of stress compared with the wild type. thsos1-4 showed drastically higher sodium-specific fluorescence visualized by CoroNa-Green, a sodium-specific fluorophore, than the wild type, inhibition of endocytosis in root tip cells, and cell death in the adjacent elongation zone. After prolonged stress, Na(+) accumulated inside the pericycle in thsos1-4, while sodium was confined in vacuoles of epidermis and cortex cells in the wild type. RNAi-based interference of SOS1 caused cell death in the root elongation zone, accompanied by fragmentation of vacuoles, inhibition of endocytosis, and apoplastic sodium influx into the stele and hence the shoot. Reduction in SOS1 expression changed Thellungiella that normally can grow in seawater-strength sodium chloride solutions into a plant as sensitive to Na(+) as Arabidopsis.
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Affiliation(s)
- Dong-Ha Oh
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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Abstract
The tropical intertidal ecosystem is defined by trees - mangroves - which are adapted to an extreme and extremely variable environment. The genetic basis underlying these adaptations is, however, virtually unknown. Based on advances in pyrosequencing, we present here the first transcriptome analysis for plants for which no prior genomic information was available. We selected the mangroves Rhizophora mangle (Rhizophoraceae) and Heritiera littoralis (Malvaceae) as ecologically important extremophiles employing markedly different physiological and life-history strategies for survival and dominance in this extreme environment. For maximal representation of conditional transcripts, mRNA was obtained from a variety of developmental stages, tissues types, and habitats. For each species, a normalized cDNA library of pooled mRNAs was analysed using GSFLX pyrosequencing. A total of 537,635 sequences were assembled de novo and annotated as > 13,000 distinct gene models for each species. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology annotations highlighted remarkable similarities in the mangrove transcriptome profiles, which differed substantially from the model plants Arabidopsis and Populus. Similarities in the two species suggest a unique mangrove lifestyle overarching the effects of transcriptome size, habitat, tissue type, developmental stage, and biogeographic and phylogenetic differences between them.
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Affiliation(s)
- M Dassanayake
- Department of Plant Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL 61801 USA
| | - J S Haas
- Office of Networked Information Technologies (ONIT), School of Integrative Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL 61801 USA
| | - H J Bohnert
- Department of Plant Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL 61801 USA
| | - J M Cheeseman
- Department of Plant Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL 61801 USA
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41
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Li P, Ainsworth EA, Leakey ADB, Ulanov A, Lozovaya V, Ort DR, Bohnert HJ. Arabidopsis transcript and metabolite profiles: ecotype-specific responses to open-air elevated [CO2]. Plant Cell Environ 2008; 31:1673-87. [PMID: 18721265 DOI: 10.1111/j.1365-3040.2008.01874.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
A Free-Air CO(2) Enrichment (FACE) experiment compared the physiological parameters, transcript and metabolite profiles of Arabidopsis thaliana Columbia-0 (Col-0) and Cape Verde Island (Cvi-0) at ambient (approximately 0.375 mg g(-1)) and elevated (approximately 0.550 mg g(-1)) CO(2) ([CO(2)]). Photoassimilate pool sizes were enhanced in high [CO(2)] in an ecotype-specific manner. Short-term growth at elevated [CO(2)] stimulated carbon gain irrespective of down-regulation of plastid functions and altered expression of genes involved in nitrogen metabolism resembling patterns observed under N-deficiency. The study confirmed well-known characteristics, but the use of a time course, ecotypic genetic differences, metabolite analysis and the focus on clusters of functional categories provided new aspects about responses to elevated [CO(2)]. Longer-term Cvi-0 responded by down-regulating functions favouring carbon accumulation, and both ecotypes showed altered expression of genes for defence, redox control, transport, signalling, transcription and chromatin remodelling. Overall, carbon fixation with a smaller commitment of resources in elevated [CO(2)] appeared beneficial, with the extra C only partially utilized possibly due to disturbance of the C : N ratio. To different degrees, both ecotypes perceived elevated [CO(2)] as a metabolic perturbation that necessitated increased functions consuming or storing photoassimilate, with Cvi-0 emerging as more capable of acclimating. Elevated [CO(2)] in Arabidopsis favoured adjustments in reactive oxygen species (ROS) homeostasis and signalling that defined genotypic markers.
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Affiliation(s)
- Pinghua Li
- Department of Plant Biology, University of Illinois at Urbana - Champaign, Urbana, IL 61801, USA
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42
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Mane SP, Robinet CV, Ulanov A, Schafleitner R, Tincopa L, Gaudin A, Nomberto G, Alvarado C, Solis C, Bolivar LA, Blas R, Ortega O, Solis J, Panta A, Rivera C, Samolski I, Carbajulca DH, Bonierbale M, Pati A, Heath LS, Bohnert HJ, Grene R. Molecular and physiological adaptation to prolonged drought stress in the leaves of two Andean potato genotypes. Funct Plant Biol 2008; 35:669-688. [PMID: 32688822 DOI: 10.1071/fp07293] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Accepted: 07/25/2008] [Indexed: 06/11/2023]
Abstract
Responses to prolonged drought and recovery from drought of two South American potato (Solanum tuberosum L. ssp. andigena (Juz & Buk) Hawkes) landraces, Sullu and Ccompis were compared under field conditions. Physiological and biomass measurements, yield analysis, the results of hybridisation to a potato microarray platform (44 000 probes) and metabolite profiling were used to characterise responses to water deficit. Drought affected shoot and root biomass negatively in Ccompis but not in Sullu, whereas both genotypes maintained tuber yield under water stress. Ccompis showed stronger reduction in maximum quantum yield under stress than Sullu, and less decrease in stomatal resistance. Genes associated with PSII functions were activated during recovery in Sullu only. Evidence for sucrose accumulation in Sullu only during maximum stress and recovery was observed, in addition to increases in cell wall biosynthesis. A depression in the abundance of plastid superoxide dismutase transcripts was observed under maximum stress in Ccompis. Both sucrose and the regulatory molecule trehalose accumulated in the leaves of Sullu only. In contrast, in Ccompis, the raffinose oligosaccharide family pathway was activated, whereas low levels of sucrose and minor stress-mediated changes in trehalose were observed. Proline, and expression of the associated genes, rose in both genotypes under drought, with a 3-fold higher increase in Sullu than in Ccompis. The results demonstrate the presence of distinct molecular and biochemical drought responses in the two potato landraces leading to yield maintenance but differential biomass accumulation in vegetative tissues.
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Affiliation(s)
| | - Cecilia Vasquez Robinet
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Alexander Ulanov
- Biotechnology Center, University of Illinois, Urbana, IL 61801, USA
| | | | | | | | | | | | | | | | - Raul Blas
- Centro Internacional de la Papa, Lima, Peru
| | | | | | - Ana Panta
- Centro Internacional de la Papa, Lima, Peru
| | | | | | | | | | - Amrita Pati
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Hans J Bohnert
- Departments of Plant Biology and of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruth Grene
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA
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Li P, Ma S, Bohnert HJ. Coexpression characteristics of trehalose-6-phosphate phosphatase subfamily genes reveal different functions in a network context. Physiol Plant 2008; 133:544-556. [PMID: 18435695 DOI: 10.1111/j.1399-3054.2008.01101.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Arabidopsis thaliana databases are available that highlight the behavior of the transcriptome under literally hundreds of experimental manipulations, making attempts possible that integrate this information into gene networks. We present and discuss the functioning of a gene network model generated using deposited microarray experiments. Based on a graphical Gaussian model, the network describes conditional coregulation of genes under a variety of external factors and abiotic, biotic and chemical treatments. In this study, we show an aspect of this network that pertains to functions of genes in families where all members appear to carry out the same biochemical reaction. Chosen in this study were 10 genes in the Arabidopsis genome encoding trehalose-6-phosphate phosphatases (TPPs). Nine of these genes were highlighted by the network. Generally, each TPP formed a network associated with genes that identify different functional categories. Thus, network structures were obtained that identified connections to carbon distribution, drought, cold, pathogen responses, calcium and reactive oxygen species/redox signatures, including transcriptional control genes that separated network graphs seeded with different TPP genes. The structure of the transcript coexpression networks, by associating diverse members of gene families into separate clusters, facilitates hypothesis building and in-depth studies of functions of individual genes in families.
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Affiliation(s)
- Pinghua Li
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 1201 West Gregory Drive, Urbana, IL 61801, USA
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44
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Fathinejad S, Steiner JM, Reipert S, Marchetti M, Allmaier G, Burey SC, Ohnishi N, Fukuzawa H, Löffelhardt W, Bohnert HJ. A carboxysomal carbon-concentrating mechanism in the cyanelles of the 'coelacanth' of the algal world, Cyanophora paradoxa? Physiol Plant 2008; 133:27-32. [PMID: 18248510 DOI: 10.1111/j.1399-3054.2007.01030.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Cyanelles are the peculiar plastids of glaucocystophyte algae that retained a peptidoglycan wall from the ancestral cyanobacterial endosymbiont. All cyanobacteria and most algae possess an inorganic carbon-concentrating mechanism (CCM) that involves a microcompartment--carboxysomes in prokaryotes and pyrenoids in eukaryotes--harboring the bulk of cellular (plastidic) Rubisco. In the case of the living fossil, Cyanophora paradoxa, the existence of a CCM was a matter of debate. Microarray data revealing 142 CO(2)-responsive genes (induced or repressed through a shift from high to low CO(2) conditions), gas exchange measurements and measurements of photosynthetic affinity provided strong support for a CCM. We favor a recent hypothesis that glaucocystophyte cyanelles as the closest cousins to cyanobacteria among plastids contain 'eukaryotic carboxysomes': bicarbonate enrichment within cyanelles should be considerably higher than in chloroplasts with their pyrenoid-based CCM. Thus, the stress-bearing function of the peptidoglycan layer, the other unique heritage, would be indispensable. An isolation method for cyanelle 'carboxysomes' was developed and the protein components other than Rubisco analyzed by MS. Rubisco activase was identified and corroborated by western blotting. The well-established cyanelle in vitro import system allows to use them as 'honorary cyanobacteria': assembly processes of supramolecular structures as phycobilisomes and carboxysomes thus can be studied after import of nucleus-encoded precursor proteins and subsequent fractionation. Even minor components can easily be tracked and a surprisingly dynamic view is obtained. Labeled pre-activase was imported into isolated cyanelles and 30% of the mature protein was found to be incorporated into the carboxysome fraction. A final decision between carboxysome or pyrenoid must await the identification of cyanelle carbonic anhydrase and, especially, the demonstration of shell proteins.
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Affiliation(s)
- Sara Fathinejad
- Max F. Perutz Laboratories, University Departments at the Vienna Biocenter, Department of Biochemistry, 1030 Vienna, Austria.
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45
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Spollen WG, Tao W, Valliyodan B, Chen K, Hejlek LG, Kim JJ, LeNoble ME, Zhu J, Bohnert HJ, Henderson D, Schachtman DP, Davis GE, Springer GK, Sharp RE, Nguyen HT. Spatial distribution of transcript changes in the maize primary root elongation zone at low water potential. BMC Plant Biol 2008; 8:32. [PMID: 18387193 PMCID: PMC2364623 DOI: 10.1186/1471-2229-8-32] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2007] [Accepted: 04/03/2008] [Indexed: 05/20/2023]
Abstract
BACKGROUND Previous work showed that the maize primary root adapts to low Psiw (-1.6 MPa) by maintaining longitudinal expansion in the apical 3 mm (region 1), whereas in the adjacent 4 mm (region 2) longitudinal expansion reaches a maximum in well-watered roots but is progressively inhibited at low Psiw. To identify mechanisms that determine these responses to low Psiw, transcript expression was profiled in these regions of water-stressed and well-watered roots. In addition, comparison between region 2 of water-stressed roots and the zone of growth deceleration in well-watered roots (region 3) distinguished stress-responsive genes in region 2 from those involved in cell maturation. RESULTS Responses of gene expression to water stress in regions 1 and 2 were largely distinct. The largest functional categories of differentially expressed transcripts were reactive oxygen species and carbon metabolism in region 1, and membrane transport in region 2. Transcripts controlling sucrose hydrolysis distinguished well-watered and water-stressed states (invertase vs. sucrose synthase), and changes in expression of transcripts for starch synthesis indicated further alteration in carbon metabolism under water deficit. A role for inositols in the stress response was suggested, as was control of proline metabolism. Increased expression of transcripts for wall-loosening proteins in region 1, and for elements of ABA and ethylene signaling were also indicated in the response to water deficit. CONCLUSION The analysis indicates that fundamentally different signaling and metabolic response mechanisms are involved in the response to water stress in different regions of the maize primary root elongation zone.
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Affiliation(s)
- William G Spollen
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
- Research Support Computing, University of Missouri, Columbia, MO 65211, USA
| | - Wenjing Tao
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
- Bio-Rad Laboratories, 2000 Alfred Nobel Drive, Hercules, CA 94547, USA
| | - Babu Valliyodan
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Kegui Chen
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Lindsey G Hejlek
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Jong-Joo Kim
- Department of Animal Science, University of Arizona, Tucson, Arizona 85721, USA
- School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 712749 South Korea
- School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 712749 South Korea
| | - Mary E LeNoble
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Jinming Zhu
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Hans J Bohnert
- Department of Plant Biology and Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - David Henderson
- Department of Animal Science, University of Arizona, Tucson, Arizona 85721, USA
- Insightful Corporation, Seattle, WA 98109, USA
| | | | - Georgia E Davis
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Gordon K Springer
- Department of Computer Science, University of Missouri, Columbia, MO 65211, USA
| | - Robert E Sharp
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
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46
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Abstract
Transcript dynamics of the Arabidopsis genome is captured in a high-confidence, realistic GGM(Graphical Gaussian Model)-based gene network that identifies co-regulation correlation of 22 000 genes across >150 conditions in specific clusters.
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Affiliation(s)
- Shisong Ma
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, Urbana IL 61801, USA
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47
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Vasquez-Robinet C, Mane SP, Ulanov AV, Watkinson JI, Stromberg VK, De Koeyer D, Schafleitner R, Willmot DB, Bonierbale M, Bohnert HJ, Grene R. Physiological and molecular adaptations to drought in Andean potato genotypes. J Exp Bot 2008; 59:2109-23. [PMID: 18535297 PMCID: PMC2413284 DOI: 10.1093/jxb/ern073] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2007] [Revised: 01/17/2008] [Accepted: 02/14/2008] [Indexed: 05/18/2023]
Abstract
The drought stress tolerance of two Solanum tuberosum subsp. andigena landraces, one hybrid (adgxtbr) and Atlantic (S. tuberosum subsp. tuberosum) has been evaluated. Photosynthesis in the Andigena landraces during prolonged drought was maintained significantly longer than in the Tuberosum (Atlantic) line. Among the Andigena landraces, 'Sullu' (SUL) was more drought resistant than 'Negra Ojosa' (NOJ). Microarray analysis and metabolite data from leaf samples taken at the point of maximum stress suggested higher mitochondrial metabolic activity in SUL than in NOJ. A greater induction of chloroplast-localized antioxidant and chaperone genes in SUL compared with NOJ was evident. ABA-responsive TFs were more induced in NOJ compared with SUL, including WRKY1, mediating a response in SA signalling that may give rise to increased ROS. NOJ may be experiencing higher ROS levels than SUL. Metabolite profiles of NOJ were characterized by compounds indicative of stress, for example, proline, trehalose, and GABA, which accumulated to a higher degree than in SUL. The differences between the Andigena lines were not explained by protective roles of compatible solutes; hexoses and complex sugars were similar in both landraces. Instead, lower levels of ROS accumulation, greater mitochondrial activity and active chloroplast defences contributed to a lower stress load in SUL than in NOJ during drought.
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Affiliation(s)
- Cecilia Vasquez-Robinet
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Shrinivasrao P. Mane
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Alexander V. Ulanov
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Verlyn K. Stromberg
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - David De Koeyer
- Agriculture and Agri-Food Canada, New Brunswick, Canada E3B 4Z7
| | | | | | | | - Hans J. Bohnert
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruth Grene
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA
- To whom correspondence should be addressed. E-mail:
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48
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Watkinson JI, Hendricks L, Sioson AA, Heath LS, Bohnert HJ, Grene R. Tuber development phenotypes in adapted and acclimated, drought-stressed Solanum tuberosum ssp. andigena have distinct expression profiles of genes associated with carbon metabolism. Plant Physiol Biochem 2008; 46:34-45. [PMID: 18061466 DOI: 10.1016/j.plaphy.2007.10.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Indexed: 05/10/2023]
Abstract
A drought screen identified accessions of Solanum tuberosum ssp. andigena that showed varying degrees of physiological acclimation or adaptation to repeated drought stress. The accessions also showed variable tuber phenotypes from small tubers that failed to develop in an accession that showed photosynthetic adaptation to normal tubers in an accession with a phenotype showing some degree of photosynthetic adaptation and acclimation. Using microarray data, we correlated the expression of genes associated with carbon metabolism with the tuber development phenotypes under drought. Genes associated with sucrose and starch metabolism showed responses consistent with starch deficiency in the adapted accession and normal starch deposition in the intermediate accession. Starch phosphorylase and glycogen bound starch synthase were induced in the adapted accession, which had abnormal tuber development. Genes associated with trehalose were induced in the intermediate accession with normal tuber development. Genes associated with respiration were also induced in the intermediate accession, and a pattern compatible with the existence of a 3PGA recovery pathway was revealed. Expression of thioredoxin genes also correlated with tuber development phenotypes under drought stress. The data suggest differential regulation of starch deposition in accessions of Andigena with different abilities to respond to drought stress.
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Affiliation(s)
- Jonathan I Watkinson
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA.
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49
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Ma S, Bohnert HJ. Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression. Genome Biol 2007; 8:R49. [PMID: 17408486 PMCID: PMC1896000 DOI: 10.1186/gb-2007-8-4-r49] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2006] [Revised: 01/02/2007] [Accepted: 04/04/2007] [Indexed: 11/18/2022] Open
Abstract
The integration of stress-dependent, tissue- and cell-specific expression profiles and 5'-regulatory sequence motif analysis defines a common stress transcriptome, identifies major motifs for stress response, and places stress response in the context of tissue and cell lineages in the Arabidopsis root. Background Arabidopsis thaliana transcript profiles indicate effects of abiotic and biotic stresses and tissue-specific and cell-specific gene expression. Organizing these datasets could reveal the structure and mechanisms of responses and crosstalk between pathways, and in which cells the plants perceive, signal, respond to, and integrate environmental inputs. Results We clustered Arabidopsis transcript profiles for various treatments, including abiotic, biotic, and chemical stresses. Ubiquitous stress responses in Arabidopsis, similar to those of fungi and animals, employ genes in pathways related to mitogen-activated protein kinases, Snf1-related kinases, vesicle transport, mitochondrial functions, and the transcription machinery. Induced responses to stresses are attributed to genes whose promoters are characterized by a small number of regulatory motifs, although secondary motifs were also apparent. Most genes that are downregulated by stresses exhibited distinct tissue-specific expression patterns and appear to be under developmental regulation. The abscisic acid-dependent transcriptome is delineated in the cluster structure, whereas functions that are dependent on reactive oxygen species are widely distributed, indicating that evolutionary pressures confer distinct responses to different stresses in time and space. Cell lineages in roots express stress-responsive genes at different levels. Intersections of stress-responsive and cell-specific profiles identified cell lineages affected by abiotic stress. Conclusion By analyzing the stress-dependent expression profile, we define a common stress transcriptome that apparently represents universal cell-level stress responses. Combining stress-dependent and tissue-specific and cell-specific expression profiles, and Arabidopsis 5'-regulatory DNA sequences, we confirm known stress-related 5' cis-elements on a genome-wide scale, identify secondary motifs, and place the stress response within the context of tissues and cell lineages in the Arabidopsis root.
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Affiliation(s)
- Shisong Ma
- Physiological and Molecular Plant Biology Graduate Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Hans J Bohnert
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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50
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Burey SC, Poroyko V, Ergen ZN, Fathi-Nejad S, Schüller C, Ohnishi N, Fukuzawa H, Bohnert HJ, Löffelhardt W. Acclimation to low [CO(2)] by an inorganic carbon-concentrating mechanism in Cyanophora paradoxa. Plant Cell Environ 2007; 30:1422-35. [PMID: 17897412 DOI: 10.1111/j.1365-3040.2007.01715.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The glaucocystophyte Cyanophora paradoxa contains cyanelles, plastids with prokaroytic features such as a peptidoglycan wall and a central proteinaceous inclusion body. While this central body includes the majority of the enzyme ribulose 1,5-bisphosphate carboxylase/oxgenase Rubisco), the presence of a carbon-concentrating mechanism (CCM) in C. paradoxa has only been hypothesized. Here, we present physiological data in support of a CCM: CO(2) exchange activity as well as apparent affinity against inorganic carbon were found to increase under CO(2)-limiting stress. Further, expressed sequence tags (ESTs) of C. paradoxa were obtained from two cDNA libraries, one from cells grown in high [CO(2)] conditions and one from cells grown under low [CO(2)] conditions. A cDNA microarray platform assembled from 2378 cDNA sequences revealed that 142 genes significantly responded to a shift from high to low [CO(2)]. Trends in gene expression were comparable to those reported for Chlamydomonas reinhardtii and the cyanobacterium Synechocystis 6803, both possessing a CCM. Among genes regulated by [CO(2)], transcripts were identified encoding carbonic anhydrases (CAs), Rubisco activase and a putative bicarbonate transporter in C. paradoxa, likely functionally involved in the CCM. These results and the polyhedric appearance of the central body further support the hypothesis of a unique 'eukaryotic carboxysome' in Cyanophora.
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Affiliation(s)
- S C Burey
- Max F. Perutz Laboratories, University of Vienna, Department of Biochemistry, Dr. Bohr-Gasse 9/5, A-1030 Vienna, Austria
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