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Karataş I, Öztürk L, Demir Y, Unlükara A, Kurunç A, Düzdemir O. Alterations in antioxidant enzyme activities and proline content in pea leaves under long-term drought stress. Toxicol Ind Health 2014; 30:693-700. [PMID: 23047611 DOI: 10.1177/0748233712462471] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
The effects of long-term drought stress on chlorophyll, proline, protein and hydrogen peroxide (H2O2) contents, malondialdehyde (MDA) in terms of lipid peroxidation and on the changes in the activities of antioxidant enzymes such as superoxide dismutase (SOD, EC 1.15.1.1), ascorbate peroxidase (APX, EC 1.11.1.11), catalase (CAT, EC 1.11.1.6) and peroxidase (POX; EC 1.11.1.7) in the leaves of pea (Pisum sativum L.) were studied in field conditions. Chlorophyll and protein contents in leaves decreased significantly with increased drought stress. The proline content increased markedly under water deficit. MDA amounts were elevated as a result of water shortage, whereas H(2)O(2) content changed slightly in pea leaves exposed to drought stress. Drought stress markedly enhanced the activities of SOD, CAT and POX but slightly changed the activity of APX. We conclude that in field conditions, long-term water shortage increased the susceptibility to drought in peas.
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Affiliation(s)
- Ilhami Karataş
- Faculty of Science and Arts, Department of Biology, Gaziosmanpaşa University, Tokat, Turkey
| | - Lokman Öztürk
- Faculty of Science and Arts, Department of Biology, Gaziosmanpaşa University, Tokat, Turkey
| | - Yavuz Demir
- Faculty of Education, Department of Biology, Ataturk University, Erzurum, Turkey
| | - Ali Unlükara
- Faculty of Agriculture, Department of Agricultural Structures and Irrigation, Erciyes University, Kayseri, Turkey
| | - Ahmet Kurunç
- Faculty of Agriculture, Department of Agricultural Structures and Irrigation, Akdeniz University, Antalya, Turkey
| | - Oral Düzdemir
- Faculty of Science, Department of Biology, Karatekin University, Çankırı, Turkey
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152
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Bayramov S, Guliyev N. Changes in Rubisco activase gene expression and polypeptide content in Brachypodium distachyon. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 81:61-6. [PMID: 24521715 DOI: 10.1016/j.plaphy.2014.01.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 01/20/2014] [Indexed: 05/08/2023]
Abstract
Regulation of Rubisco (D-ribulose-1,5-bisphosphate carboxylase/oxygenase activase (RCA) gene expression and polypeptide content were determined in Brachypodium distachyon leaves, stems and ear elements at different developmental stages under optimal growth conditions as well as under drought and salt stress conditions. B. distachyon leaf contains a much greater amount of Rubisco activase small (RCAS) isoform than the large one (RCAL) under optimal growth conditions. Increased levels of the RCAL isoform compared with the RCAS isoform were found in leaves and in green stems under salt and drought stress, respectively. Transcriptional levels of RCA are almost identical in different leaf positions. Short-term drought and salt stresses did not cause the impairment of RCA gene expression in early seedlings. But gradually increasing drought stress significantly decreased gene expression in early seedling samples. Amounts of the RCAS isoform were found to be more in different leaves of the plant compared with the RCAL isoform and their ratio was constant under normal condition. In green stems gene expression of RCA decreased under salt and drought stresses, although as it was in green leaves protein amounts of RCAL isoform increased compared with the RCAS isoform. All of the above described results clearly indicate that the accumulation of each RCA isoform is differentially regulated by developmental and environmental cues.
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Affiliation(s)
- Shahniyar Bayramov
- Institute of Botany, Azerbaijan National Academy of Sciences, 40 Patamdar Shosse, AZ-1073 Baku, Azerbaijan.
| | - Novruz Guliyev
- Institute of Botany, Azerbaijan National Academy of Sciences, 40 Patamdar Shosse, AZ-1073 Baku, Azerbaijan
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153
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Degu A, Hochberg U, Sikron N, Venturini L, Buson G, Ghan R, Plaschkes I, Batushansky A, Chalifa-Caspi V, Mattivi F, Delledonne M, Pezzotti M, Rachmilevitch S, Cramer GR, Fait A. Metabolite and transcript profiling of berry skin during fruit development elucidates differential regulation between Cabernet Sauvignon and Shiraz cultivars at branching points in the polyphenol pathway. BMC PLANT BIOLOGY 2014; 14:188. [PMID: 25064275 PMCID: PMC4222437 DOI: 10.1186/s12870-014-0188-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 07/11/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Grapevine berries undergo complex biochemical changes during fruit maturation, many of which are dependent upon the variety and its environment. In order to elucidate the varietal dependent developmental regulation of primary and specialized metabolism, berry skins of Cabernet Sauvignon and Shiraz were subjected to gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) based metabolite profiling from pre-veraison to harvest. The generated dataset was augmented with transcript profiling using RNAseq. RESULTS The analysis of the metabolite data revealed similar developmental patterns of change in primary metabolites between the two cultivars. Nevertheless, towards maturity the extent of change in the major organic acid and sugars (i.e. sucrose, trehalose, malate) and precursors of aromatic and phenolic compounds such as quinate and shikimate was greater in Shiraz compared to Cabernet Sauvignon. In contrast, distinct directional projections on the PCA plot of the two cultivars samples towards maturation when using the specialized metabolite profiles were apparent, suggesting a cultivar-dependent regulation of the specialized metabolism. Generally, Shiraz displayed greater upregulation of the entire polyphenol pathway and specifically higher accumulation of piceid and coumaroyl anthocyanin forms than Cabernet Sauvignon from veraison onwards. Transcript profiling revealed coordinated increased transcript abundance for genes encoding enzymes of committing steps in the phenylpropanoid pathway. The anthocyanin metabolite profile showed F3'5'H-mediated delphinidin-type anthocyanin enrichment in both varieties towards maturation, consistent with the transcript data, indicating that the F3'5'H-governed branching step dominates the anthocyanin profile at late berry development. Correlation analysis confirmed the tightly coordinated metabolic changes during development, and suggested a source-sink relation between the central and specialized metabolism, stronger in Shiraz than Cabernet Sauvignon. RNAseq analysis also revealed that the two cultivars exhibited distinct pattern of changes in genes related to abscisic acid (ABA) biosynthesis enzymes. CONCLUSIONS Compared with CS, Shiraz showed higher number of significant correlations between metabolites, which together with the relatively higher expression of flavonoid genes supports the evidence of increased accumulation of coumaroyl anthocyanins in that cultivar. Enhanced stress related metabolism, e.g. trehalose, stilbene and ABA in Shiraz berry-skin are consistent with its relatively higher susceptibility to environmental cues.
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Affiliation(s)
- Asfaw Degu
- The Albert Katz International School, Beer-Sheva, Israel
- The French Associates Institute for Agriculture and Biotechnology of Drylands, the Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boqer 84990, Israel
| | - Uri Hochberg
- The Albert Katz International School, Beer-Sheva, Israel
- The French Associates Institute for Agriculture and Biotechnology of Drylands, the Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boqer 84990, Israel
| | - Noga Sikron
- The French Associates Institute for Agriculture and Biotechnology of Drylands, the Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boqer 84990, Israel
| | - Luca Venturini
- Biotechnology Department, University of Verona, Strada Le Grazie 15, Verona, Italy
| | - Genny Buson
- Biotechnology Department, University of Verona, Strada Le Grazie 15, Verona, Italy
| | - Ryan Ghan
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno 9557, NV, USA
| | - Inbar Plaschkes
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Albert Batushansky
- The Albert Katz International School, Beer-Sheva, Israel
- The French Associates Institute for Agriculture and Biotechnology of Drylands, the Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boqer 84990, Israel
| | - Vered Chalifa-Caspi
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Fulvio Mattivi
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Massimo Delledonne
- Biotechnology Department, University of Verona, Strada Le Grazie 15, Verona, Italy
| | - Mario Pezzotti
- Biotechnology Department, University of Verona, Strada Le Grazie 15, Verona, Italy
| | - Shimon Rachmilevitch
- The French Associates Institute for Agriculture and Biotechnology of Drylands, the Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boqer 84990, Israel
| | - Grant R Cramer
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno 9557, NV, USA
| | - Aaron Fait
- The French Associates Institute for Agriculture and Biotechnology of Drylands, the Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boqer 84990, Israel
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154
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Liu CW, Chang TS, Hsu YK, Wang AZ, Yen HC, Wu YP, Wang CS, Lai CC. Comparative proteomic analysis of early salt stress responsive proteins in roots and leaves of rice. Proteomics 2014; 14:1759-75. [PMID: 24841874 DOI: 10.1002/pmic.201300276] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 04/01/2014] [Accepted: 05/15/2014] [Indexed: 11/11/2022]
Abstract
Growth and productivity of rice (Oryza sativa L.) are severely affected by salinity. Understanding the mechanisms that protect rice and other important cereal crops from salt stress will help in the development of salt-stress-tolerant strains. In this study, rice seedlings of the same genetic species with various salt tolerances were studied. We first used 2DE to resolve the expressed proteome in rice roots and leaves and then used nanospray liquid chromatography/tandem mass spectrometry to identify the differentially expressed proteins in rice seedlings after salt treatment. The 2DE assays revealed that there were 104 differentially expressed protein spots in rice roots and 59 in leaves. Then, we identified 83 proteins in rice roots and 61 proteins in rice leaves by MS analysis. Functional classification analysis revealed that the differentially expressed proteins from roots could be classified into 18 functional categories while those from leaves could be classified into 11 functional categories. The proteins from rice seedlings that most significantly contributed to a protective effect against increased salinity were cysteine synthase, adenosine triphosphate synthase, quercetin 3-O-methyltransferase 1, and lipoxygenase 2. Further analysis demonstrated that the primary mechanisms underlying the ability of rice seedlings to tolerate salt stress were glycolysis, purine metabolism, and photosynthesis. Thus, we suggest that differentially expressed proteins may serve as marker group for the salt tolerance of rice.
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Affiliation(s)
- Chih-Wei Liu
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
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155
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Meyer E, Aspinwall MJ, Lowry DB, Palacio-Mejía JD, Logan TL, Fay PA, Juenger TE. Integrating transcriptional, metabolomic, and physiological responses to drought stress and recovery in switchgrass (Panicum virgatum L.). BMC Genomics 2014; 15:527. [PMID: 24964784 PMCID: PMC4122788 DOI: 10.1186/1471-2164-15-527] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 06/05/2014] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND In light of the changes in precipitation and soil water availability expected with climate change, understanding the mechanisms underlying plant responses to water deficit is essential. Toward that end we have conducted an integrative analysis of responses to drought stress in the perennial C4 grass and biofuel crop, Panicum virgatum (switchgrass). Responses to soil drying and re-watering were measured at transcriptional, physiological, and metabolomic levels. To assess the interaction of soil moisture with diel light: dark cycles, we profiled gene expression in drought and control treatments under pre-dawn and mid-day conditions. RESULTS Soil drying resulted in reduced leaf water potential, gas exchange, and chlorophyll fluorescence along with differential expression of a large fraction of the transcriptome (37%). Many transcripts responded differently depending on time of day (e.g. up-regulation pre-dawn and down-regulation mid-day). Genes associated with C4 photosynthesis were down-regulated during drought, while C4 metabolic intermediates accumulated. Rapid changes in gene expression were observed during recovery from drought, along with increased water use efficiency and chlorophyll fluorescence. CONCLUSIONS Our findings demonstrate that drought responsive gene expression depends strongly on time of day and that gene expression is extensively modified during the first few hours of drought recovery. Analysis of covariation in gene expression, metabolite abundance, and physiology among plants revealed non-linear relationships that suggest critical thresholds in drought stress responses. Future studies may benefit from evaluating these thresholds among diverse accessions of switchgrass and other C4 grasses.
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Affiliation(s)
- Eli Meyer
- />Department of Integrative Biology, Oregon State University, Cordley Hall 3029, Corvallis, OR 97331 USA
- />Department of Integrative Biology, University of Texas at Austin, 1 University Station C0930, Austin, TX 78712 USA
| | - Michael J Aspinwall
- />Department of Integrative Biology, University of Texas at Austin, 1 University Station C0930, Austin, TX 78712 USA
- />Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, NSW 2751 Australia
| | - David B Lowry
- />Department of Integrative Biology, University of Texas at Austin, 1 University Station C0930, Austin, TX 78712 USA
| | - Juan Diego Palacio-Mejía
- />Department of Integrative Biology, University of Texas at Austin, 1 University Station C0930, Austin, TX 78712 USA
| | - Tierney L Logan
- />Department of Integrative Biology, University of Texas at Austin, 1 University Station C0930, Austin, TX 78712 USA
| | - Philip A Fay
- />USDA-ARS Grassland Soil and Water Research Laboratory, Temple, TX 76502 USA
| | - Thomas E Juenger
- />Department of Integrative Biology, University of Texas at Austin, 1 University Station C0930, Austin, TX 78712 USA
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156
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Integrating transcriptional, metabolomic, and physiological responses to drought stress and recovery in switchgrass (Panicum virgatum L.). BMC Genomics 2014. [PMID: 24964784 DOI: 10.1186/1471‐2164‐15‐527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In light of the changes in precipitation and soil water availability expected with climate change, understanding the mechanisms underlying plant responses to water deficit is essential. Toward that end we have conducted an integrative analysis of responses to drought stress in the perennial C4 grass and biofuel crop, Panicum virgatum (switchgrass). Responses to soil drying and re-watering were measured at transcriptional, physiological, and metabolomic levels. To assess the interaction of soil moisture with diel light: dark cycles, we profiled gene expression in drought and control treatments under pre-dawn and mid-day conditions. RESULTS Soil drying resulted in reduced leaf water potential, gas exchange, and chlorophyll fluorescence along with differential expression of a large fraction of the transcriptome (37%). Many transcripts responded differently depending on time of day (e.g. up-regulation pre-dawn and down-regulation mid-day). Genes associated with C4 photosynthesis were down-regulated during drought, while C4 metabolic intermediates accumulated. Rapid changes in gene expression were observed during recovery from drought, along with increased water use efficiency and chlorophyll fluorescence. CONCLUSIONS Our findings demonstrate that drought responsive gene expression depends strongly on time of day and that gene expression is extensively modified during the first few hours of drought recovery. Analysis of covariation in gene expression, metabolite abundance, and physiology among plants revealed non-linear relationships that suggest critical thresholds in drought stress responses. Future studies may benefit from evaluating these thresholds among diverse accessions of switchgrass and other C4 grasses.
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157
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Physiological aspects of fruit ripening: the mitochondrial connection. Mitochondrion 2014; 17:1-6. [PMID: 24769052 DOI: 10.1016/j.mito.2014.04.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 04/08/2014] [Accepted: 04/14/2014] [Indexed: 11/23/2022]
Abstract
Fruit ripening is a genetically programmed process which leads to an assortment of physiological and metabolic changes that irreversibly alter its characteristics. Depending on the species, fruit maturation can be either climacteric or non-climacteric. In both cases there is a metabolic shift from normal development conditions toward the fully mature state, but climacteric fruit is characterized by a sharp increase in respiration. In non-climacteric fruit, that generally does not display this feature, respiration changes can be affected by processes related to postharvest storage. This review describes some of the many ways in which mitochondrial metabolism is implicated in this crucial reproductive stage, such as the connection between ethylene production and respiration rate, the involvement of alternative oxidase (AOX) and plant uncoupling mitochondrial protein (PUMP) during the ripening and the common alterations of this organelle in fruits affected by different stress conditions.
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158
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Wang L, Zhu W, Fang L, Sun X, Su L, Liang Z, Wang N, Londo JP, Li S, Xin H. Genome-wide identification of WRKY family genes and their response to cold stress in Vitis vinifera. BMC PLANT BIOLOGY 2014; 14:103. [PMID: 24755338 PMCID: PMC4021059 DOI: 10.1186/1471-2229-14-103] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 04/11/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND WRKY transcription factors are one of the largest families of transcriptional regulators in plants. WRKY genes are not only found to play significant roles in biotic and abiotic stress response, but also regulate growth and development. Grapevine (Vitis vinifera) production is largely limited by stressful climate conditions such as cold stress and the role of WRKY genes in the survival of grapevine under these conditions remains unknown. RESULTS We identified a total of 59 VvWRKYs from the V. vinifera genome, belonging to four subgroups according to conserved WRKY domains and zinc-finger structure. The majority of VvWRKYs were expressed in more than one tissue among the 7 tissues examined which included young leaves, mature leaves, tendril, stem apex, root, young fruits and ripe fruits. Publicly available microarray data suggested that a subset of VvWRKYs was activated in response to diverse stresses. Quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 36 VvWRKYs are changed following cold exposure. Comparative analysis was performed on data from publicly available microarray experiments, previous global transcriptome analysis studies, and qRT-PCR. We identified 15 VvWRKYs in at least two of these databases which may relate to cold stress. Among them, the transcription of three genes can be induced by exogenous ABA application, suggesting that they can be involved in an ABA-dependent signaling pathway in response to cold stress. CONCLUSIONS We identified 59 VvWRKYs from the V. vinifera genome and 15 of them showed cold stress-induced expression patterns. These genes represented candidate genes for future functional analysis of VvWRKYs involved in the low temperature-related signal pathways in grape.
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MESH Headings
- Abscisic Acid/pharmacology
- Amino Acid Sequence
- Chromosomes, Plant/genetics
- Cluster Analysis
- Cold Temperature
- Conserved Sequence/genetics
- Crosses, Genetic
- Databases, Genetic
- Gene Expression Profiling
- Gene Expression Regulation, Plant/drug effects
- Genes, Plant
- Molecular Sequence Data
- Multigene Family
- Oligonucleotide Array Sequence Analysis
- Phylogeny
- Protein Structure, Tertiary
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Real-Time Polymerase Chain Reaction
- Stress, Physiological/drug effects
- Stress, Physiological/genetics
- Transcription Factors/chemistry
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
- Vitis/drug effects
- Vitis/genetics
- Vitis/physiology
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Affiliation(s)
- Lina Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Wei Zhu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Linchuan Fang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Xiaoming Sun
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Lingye Su
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, PR China
| | - Nian Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, PR China
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, PR China
| | - Jason P Londo
- United States Department of Agriculture–Agriculture Research Service, Grape Genetics Research Unit, Geneva, NY, USA
| | - Shaohua Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, PR China
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, PR China
| | - Haiping Xin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, PR China
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, PR China
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159
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Wang X, Kayesh E, Han J, Liu C, Wang C, Song C, Ge A, Fang J. Microarray analysis of differentially expressed genes engaged in fruit development between table and wine grape. Mol Biol Rep 2014; 41:4397-412. [PMID: 24728608 DOI: 10.1007/s11033-014-3311-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 02/17/2014] [Indexed: 10/25/2022]
Abstract
Microarray analysis of genes can provide individual gene-expression profiles and new insights for elucidating biological mechanisms responsible for fruit development. To obtain an overall view on expression profiles of metabolism-related genes involved in fruit development of table and wine grapes, a microarray system comprising 15,403 ESTs was used to compare the expressed genes. The expression patterns from the microarray analysis were validated with quantitative real-time polymerase chain reaction analysis of 18 selected genes of interest. During the entire fruit development stage, 2,493 genes exhibited at least 2.0-fold differences in expression levels with 1,244 genes being up-regulated and 1,249 being down-regulated. Following gene ontology analysis, only 929 differentially expressed (including 403 up-regulated and 526 down-regulated) genes were annotated in table and wine grapes. These differentially expressed genes were found to be mainly involved in carbohydrate metabolism, biosynthesis of secondary metabolites as well as energy, lipid and amino acid metabolism via KEGG. Our results provide new insights into the molecular mechanisms and expression profiles of genes in the fruit development stage of table and wine grapes.
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Affiliation(s)
- Xicheng Wang
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, Jiangsu, People's Republic of China,
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160
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Liu J, Chen N, Chen F, Cai B, Dal Santo S, Tornielli GB, Pezzotti M, Cheng ZMM. Genome-wide analysis and expression profile of the bZIP transcription factor gene family in grapevine (Vitis vinifera). BMC Genomics 2014; 15:281. [PMID: 24725365 PMCID: PMC4023599 DOI: 10.1186/1471-2164-15-281] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 03/31/2014] [Indexed: 01/27/2023] Open
Abstract
Background Basic leucine zipper (bZIP) transcription factor gene family is one of the largest and most diverse families in plants. Current studies have shown that the bZIP proteins regulate numerous growth and developmental processes and biotic and abiotic stress responses. Nonetheless, knowledge concerning the specific expression patterns and evolutionary history of plant bZIP family members remains very limited. Results We identified 55 bZIP transcription factor-encoding genes in the grapevine (Vitis vinifera) genome, and divided them into 10 groups according to the phylogenetic relationship with those in Arabidopsis. The chromosome distribution and the collinearity analyses suggest that expansion of the grapevine bZIP (VvbZIP) transcription factor family was greatly contributed by the segment/chromosomal duplications, which may be associated with the grapevine genome fusion events. Nine intron/exon structural patterns within the bZIP domain and the additional conserved motifs were identified among all VvbZIP proteins, and showed a high group-specificity. The predicted specificities on DNA-binding domains indicated that some highly conserved amino acid residues exist across each major group in the tree of land plant life. The expression patterns of VvbZIP genes across the grapevine gene expression atlas, based on microarray technology, suggest that VvbZIP genes are involved in grapevine organ development, especially seed development. Expression analysis based on qRT-PCR indicated that VvbZIP genes are extensively involved in drought- and heat-responses, with possibly different mechanisms. Conclusions The genome-wide identification, chromosome organization, gene structures, evolutionary and expression analyses of grapevine bZIP genes provide an overall insight of this gene family and their potential involvement in growth, development and stress responses. This will facilitate further research on the bZIP gene family regarding their evolutionary history and biological functions.
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Affiliation(s)
| | | | | | | | | | | | | | - Zong-Ming Max Cheng
- College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, Jiangsu, China.
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161
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Genome-wide identification, evolution and expression analysis of the grape (Vitis vinifera L.) zinc finger-homeodomain gene family. Int J Mol Sci 2014; 15:5730-48. [PMID: 24705465 PMCID: PMC4013592 DOI: 10.3390/ijms15045730] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 03/15/2014] [Accepted: 03/25/2014] [Indexed: 12/30/2022] Open
Abstract
Plant zinc finger-homeodomain (ZHD) genes encode a family of transcription factors that have been demonstrated to play an important role in the regulation of plant growth and development. In this study, we identified a total of 13 ZHD genes (VvZHD) in the grape genome that were further classified into at least seven groups. Genome synteny analysis revealed that a number of VvZHD genes were present in the corresponding syntenic blocks of Arabidopsis, indicating that they arose before the divergence of these two species. Gene expression analysis showed that the identified VvZHD genes displayed distinct spatiotemporal expression patterns, and were differentially regulated under various stress conditions and hormone treatments, suggesting that the grape VvZHDs might be also involved in plant response to a variety of biotic and abiotic insults. Our work provides insightful information and knowledge about the ZHD genes in grape, which provides a framework for further characterization of their roles in regulation of stress tolerance as well as other aspects of grape productivity.
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162
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Chitarra W, Balestrini R, Vitali M, Pagliarani C, Perrone I, Schubert A, Lovisolo C. Gene expression in vessel-associated cells upon xylem embolism repair in Vitis vinifera L. petioles. PLANTA 2014; 239:887-99. [PMID: 24402563 DOI: 10.1007/s00425-013-2017-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/20/2013] [Indexed: 05/11/2023]
Abstract
In this work, the involvement of vessel-associated cells in embolism recovery was investigated by studying leaf petiole hydraulics and expression profiles of aquaporins and genes related to sugar metabolism. Two different stress treatments were imposed onto grapevines to induce xylem embolism: one involved a pressure collar applied to the stems, while the other consisted of water deprivation (drought). Embolism formation and repair were monitored during stress application and release (recovery). At the same time, stomatal conductance (g(s)), leaf water potential (Ψ(leaf)) and leaf abscisic acid (ABA) concentration were measured. For each treatment, gene transcript levels were assessed on vessel-associated cells (isolated from leaf petioles by laser microdissection technique) and whole petioles. Both treatments induced severe xylem embolism formation and drops in g s and Ψ (leaf) at a lesser degree and with faster recovery in the case of application of the pressure collar. Leaf ABA concentration only increased upon drought and subsequent recovery. Transcripts linked to sugar mobilisation (encoding a β-amylase and a glucose-6-P transporter) were over-expressed upon stress or recovery, both in vessel-associated cells and whole petioles. However, two aquaporin genes (VvPIP2;1 and VvPIP2;4N) were activated upon stress or recovery only in vessel-associated cells, suggesting a specific effect on embolism refilling. Furthermore, the latter gene was only activated upon drought and subsequent recovery, suggesting that either severe water stress or ABA is required for its regulation.
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Affiliation(s)
- Walter Chitarra
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Via Leonardo da Vinci 44, 10095, Grugliasco, TO, Italy
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Abstract
The availability of many genomic resources such as genome sequences, functional genomics resources including microarrays and RNA-seq, sufficient numbers of molecular markers, express sequence tags (ESTs) and high-density genetic maps is causing a rapid acceleration of genetics and genomic research of many fruit plants. This is leading to an increase in our knowledge of the genes that are linked to many horticultural and agronomically important traits. Recently, some progress has also been made on the identification and functional analysis of miRNAs in some fruit plants. This is one of the most active research fields in plant sciences. The last decade has witnessed development of genomic resources in many fruit plants such as apple, banana, citrus, grapes, papaya, pears, strawberry etc.; however, many of them are still not being exploited. Furthermore, owing to lack of resources, infrastructure and research facilities in many lesser-developed countries, development of genomic resources in many underutilized or less-studied fruit crops, which grow in these countries, is limited. Thus, research emphasis should be given to those fruit crops for which genomic resources are relatively scarce. The development of genomic databases of these less-studied fruit crops will enable biotechnologists to identify target genes that underlie key horticultural and agronomical traits. This review presents an overview of the current status of the development of genomic resources in fruit plants with the main emphasis being on genome sequencing, EST resources, functional genomics resources including microarray and RNA-seq, identification of quantitative trait loci and construction of genetic maps as well as efforts made on the identification and functional analysis of miRNAs in fruit plants.
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Affiliation(s)
- Manoj K Rai
- a Department of Botany , Biotechnology Centre, Jai Narain Vyas University , Jodhpur , Rajasthan , India
| | - N S Shekhawat
- a Department of Botany , Biotechnology Centre, Jai Narain Vyas University , Jodhpur , Rajasthan , India
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164
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The gene family of dehydration responsive element-binding transcription factors in grape (Vitis vinifera): genome-wide identification and analysis, expression profiles, and involvement in abiotic stress resistance. Mol Biol Rep 2014; 41:1577-90. [PMID: 24402876 DOI: 10.1007/s11033-013-3004-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 12/30/2013] [Indexed: 10/25/2022]
Abstract
The dehydration responsive element-binding (DREB) proteins play a critical role in plant development and abiotic stress-mediated gene expression. Therefore, they represent one of the most attractive regulons for breeding programs. However, no comprehensive summary of grapevine DREB family genes is available. During this study, 38 VvDREB members were identified from the entire grapevine genome and its expression sequence tag assembly. These were organized into the same subgroups, A1 through A6, as for Arabidopsis DREBs. The VvDREB genes were distributed in 15 out of 19 chromosomes in grapevine. Multiple sequence alignments were performed and a three-dimensional structure was created to demonstrate sequence conservation. Microarray analysis showed potential regulatory roles for VvDREBs in responses to various abiotic stresses, hormone treatments, berry ripening, exposure to light, and bud development. Cis-acting regulatory elements, such as W-box, MYB-binding site, and light-responsive elements, were the most frequently found in the putative promoter regions. Furthermore, microarray transcriptional profiling of grapevine plants that over-expressed VvDREB23 revealed 248 up-regulated and 229 down-regulated genes, with fold-changes of >1.5 when compared with the empty vector control. Gene ontology classifications showed that different genes function in cellular glucan metabolism, lipid transport, the endomembrane system, cell wall structure, and other important metabolic and developmental processes, as well as in the regulation of molecular functions. Our report provides an overview and constitutes a foundation for further study of this VvDREB gene family. All the microarray data and transcription profiling of transgenic versus empty-vector control transformant grapevines were retrieved from the online resources.
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165
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Naithani S, Raja R, Waddell EN, Elser J, Gouthu S, Deluc LG, Jaiswal P. VitisCyc: a metabolic pathway knowledgebase for grapevine (Vitis vinifera). FRONTIERS IN PLANT SCIENCE 2014; 5:644. [PMID: 25538713 PMCID: PMC4260676 DOI: 10.3389/fpls.2014.00644] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Accepted: 11/01/2014] [Indexed: 05/23/2023]
Abstract
We have developed VitisCyc, a grapevine-specific metabolic pathway database that allows researchers to (i) search and browse the database for its various components such as metabolic pathways, reactions, compounds, genes and proteins, (ii) compare grapevine metabolic networks with other publicly available plant metabolic networks, and (iii) upload, visualize and analyze high-throughput data such as transcriptomes, proteomes, metabolomes etc. using OMICs-Viewer tool. VitisCyc is based on the genome sequence of the nearly homozygous genotype PN40024 of Vitis vinifera "Pinot Noir" cultivar with 12X v1 annotations and was built on BioCyc platform using Pathway Tools software and MetaCyc reference database. Furthermore, VitisCyc was enriched for plant-specific pathways and grape-specific metabolites, reactions and pathways. Currently VitisCyc harbors 68 super pathways, 362 biosynthesis pathways, 118 catabolic pathways, 5 detoxification pathways, 36 energy related pathways and 6 transport pathways, 10,908 enzymes, 2912 enzymatic reactions, 31 transport reactions and 2024 compounds. VitisCyc, as a community resource, can aid in the discovery of candidate genes and pathways that are regulated during plant growth and development, and in response to biotic and abiotic stress signals generated from a plant's immediate environment. VitisCyc version 3.18 is available online at http://pathways.cgrb.oregonstate.edu.
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Affiliation(s)
- Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
- *Correspondence: Sushma Naithani, Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR-97331, USA e-mail:
| | - Rajani Raja
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
| | - Elijah N. Waddell
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
| | | | - Laurent G. Deluc
- Department of Horticulture, Oregon State UniversityCorvallis, OR, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
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166
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George IS, Haynes PA. Current perspectives in proteomic analysis of abiotic stress in Grapevines. FRONTIERS IN PLANT SCIENCE 2014; 5:686. [PMID: 25538720 PMCID: PMC4258992 DOI: 10.3389/fpls.2014.00686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 11/18/2014] [Indexed: 05/21/2023]
Abstract
Grapes are an important crop plant which forms the basis of a globally important industry. Grape and wine production is particularly vulnerable to environmental and climatic fluctuations, which makes it essential for us to develop a greater understanding of the molecular level responses of grape plants to various abiotic stresses. The completion of the initial grape genome sequence in 2007 has led to a significant increase in research on grapes using proteomics approaches. In this article, we discuss some of the current research on abiotic stress in grapevines, in the context of abiotic stress research in other plant species. We also highlight some of the current limitations in grapevine proteomics and identify areas with promising scope for potential future research.
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Affiliation(s)
| | - Paul A. Haynes
- *Correspondence: Paul A. Haynes, Department of Chemistry and Biomolecular Sciences, Macquarie University, F7B 331, North Ryde, NSW 2109, Australia e-mail:
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167
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Hatmi S, Trotel-Aziz P, Villaume S, Couderchet M, Clément C, Aziz A. Osmotic stress-induced polyamine oxidation mediates defence responses and reduces stress-enhanced grapevine susceptibility to Botrytis cinerea. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:75-88. [PMID: 24170740 DOI: 10.1093/jxb/ert351] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Abiotic factors inducing osmotic stress can influence the plant immune response and resistance to pathogen infections. In this study, the effect of polyethylene glycol (PEG)- and sucrose-induced osmotic stress on polyamine (PA) homeostasis and the basal immune response in grapevine plantlets before and after Botrytis cinerea infection was determined. Pharmacological approaches were also addressed to assess the contribution of osmotic stress-induced PA oxidation to the regulation of defence responses and the susceptibility of grapevine to B. cinerea. Following osmotic stress or pathogen infection, PA homeostasis was linked to enhanced activity of diamine oxidases (CuAO) and PA oxidases (PAO) and the production of 1,3-diaminopropane. These responses paralleled the accumulation of the main stilbenic phytoalexins, resveratrol and ε-viniferin and upregulation of gene transcripts including STS (a stilbene synthase), PR-2 (a β-1,3-glucanase), PR3-4c (acidic chitinase IV), and PR-5 (a thaumatin-like protein), as well as NCED2 involved in abscisic acid biosynthesis. It was also demonstrated that leaves pre-exposed to osmotic stress and later inoculated with B. cinerea showed enhanced PA accumulation and attenuation of CuAO and PAO activities. This was consistent with the impaired production of phytoalexins and transcript levels of defence- and stress-related genes following infection, and the enhanced susceptibility to B. cinerea. Pharmacological experiments revealed that, under osmotic stress conditions, CuAO and PAO were involved in PA homeostasis and in the regulation of defence responses. Specific inhibition of CuAO and PAO in osmotically stressed leaves strongly attenuated the induction of defence responses triggered by B. cinerea infection and enhanced susceptibility to the pathogen. Taken together, this study reveals a contribution of PA catabolism to the resistance state through modulation of immune response in grapevine following osmotic stress and/or after B. cinerea infection.
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Affiliation(s)
- Saloua Hatmi
- URVVC EA 4707, University of Reims Champagne-Ardenne, UFR Sciences, Bp. 1039, 51687 Reims Cedex 02, France
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168
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Analysis of the anticancer phytochemicals in Andrographis paniculata Nees. under salinity stress. BIOMED RESEARCH INTERNATIONAL 2013; 2013:319047. [PMID: 24371819 PMCID: PMC3858962 DOI: 10.1155/2013/319047] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 10/14/2013] [Indexed: 01/01/2023]
Abstract
Salinity causes the adverse effects in all physiological processes of plants. The present study aimed to investigate the potential of salt stress to enhance the accumulation of the anticancer phytochemicals in Andrographis paniculata accessions. For this purpose, 70-day-old plants were grown in different salinity levels (0.18, 4, 8, 12, and 16 dSm−1) on sand medium. After inducing a period of 30-day salinity stress and before flowering, all plants were harvested and the data on morphological traits, proline content and the three anticancer phytochemicals, including andrographolide (AG), neoandrographolide (NAG), and 14-deoxy-11,12-didehydroandrographolide (DDAG), were measured. The results indicated that salinity had a significant effect on the aforementioned three anticancer phytochemicals. In addition, the salt tolerance index (STI) was significantly decreased, while, except for DDAG, the content of proline, the AG, and NAG was significantly increased (P ≤ 0.01). Furthermore, it was revealed that significant differences among accessions could happen based on the total dry weight, STI, AG, and NAG. Finally, we noticed that the salinity at 12 dSm−1 led to the maximum increase in the quantities of AG, NAG, and DDAG. In other words, under salinity stress, the tolerant accessions were capable of accumulating the higher amounts of proline, AG, and NAG than the sensitive accessions.
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169
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Hochberg U, Degu A, Toubiana D, Gendler T, Nikoloski Z, Rachmilevitch S, Fait A. Metabolite profiling and network analysis reveal coordinated changes in grapevine water stress response. BMC PLANT BIOLOGY 2013; 13:184. [PMID: 24256338 PMCID: PMC4225576 DOI: 10.1186/1471-2229-13-184] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 11/06/2013] [Indexed: 05/19/2023]
Abstract
BACKGROUND Grapevine metabolism in response to water deficit was studied in two cultivars, Shiraz and Cabernet Sauvignon, which were shown to have different hydraulic behaviors (Hochberg et al. Physiol. Plant. 147:443-453, 2012). RESULTS Progressive water deficit was found to effect changes in leaf water potentials accompanied by metabolic changes. In both cultivars, but more intensively in Shiraz than Cabernet Sauvignon, water deficit caused a shift to higher osmolality and lower C/N ratios, the latter of which was also reflected in marked increases in amino acids, e.g., Pro, Val, Leu, Thr and Trp, reductions of most organic acids, and changes in the phenylpropanoid pathway. PCA analysis showed that changes in primary metabolism were mostly associated with water stress, while diversification of specialized metabolism was mostly linked to the cultivars. In the phloem sap, drought was characterized by higher ABA concentration and major changes in benzoate levels coinciding with lower stomatal conductance and suberinization of vascular bundles. Enhanced suberin biosynthesis in Shiraz was reflected by the higher abundance of sap hydroxybenzoate derivatives. Correlation-based network analysis revealed that compared to Cabernet Sauvignon, Shiraz had considerably larger and highly coordinated stress-related changes, reflected in its increased metabolic network connectivity under stress. Network analysis also highlighted the structural role of major stress related metabolites, e.g., Pro, quercetin and ascorbate, which drastically altered their connectedness in the Shiraz network under water deficit. CONCLUSIONS Taken together, the results showed that Vitis vinifera cultivars possess a common metabolic response to water deficit. Central metabolism, and specifically N metabolism, plays a significant role in stress response in vine. At the cultivar level, Cabernet Sauvignon was characterized by milder metabolic perturbations, likely due to a tighter regulation of stomata upon stress induction. Network analysis was successfully implemented to characterize plant stress molecular response and to identify metabolites with a significant structural and biological role in vine stress response.
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Affiliation(s)
- Uri Hochberg
- Albert Katz International School, Ben-Gurion University of the Negev, 84990 Sede Boqer, Israel
- the French Associates Institute for Agriculture and Biotechnology of Drylands (FAAB), the Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990 Sede Boqer, Israel
| | - Asfaw Degu
- Albert Katz International School, Ben-Gurion University of the Negev, 84990 Sede Boqer, Israel
- the French Associates Institute for Agriculture and Biotechnology of Drylands (FAAB), the Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990 Sede Boqer, Israel
| | - David Toubiana
- the French Associates Institute for Agriculture and Biotechnology of Drylands (FAAB), the Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990 Sede Boqer, Israel
| | - Tanya Gendler
- the French Associates Institute for Agriculture and Biotechnology of Drylands (FAAB), the Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990 Sede Boqer, Israel
| | - Zoran Nikoloski
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Golm, Germany
| | - Shimon Rachmilevitch
- the French Associates Institute for Agriculture and Biotechnology of Drylands (FAAB), the Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990 Sede Boqer, Israel
| | - Aaron Fait
- the French Associates Institute for Agriculture and Biotechnology of Drylands (FAAB), the Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990 Sede Boqer, Israel
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170
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Sanchez DH. Physiological and biotechnological implications of transcript-level variation under abiotic stress. PLANT BIOLOGY (STUTTGART, GERMANY) 2013; 15:925-930. [PMID: 24033916 DOI: 10.1111/plb.12075] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 06/09/2013] [Indexed: 06/02/2023]
Abstract
The discovery of genes that can be used to increase plant tolerance to environmental stress has practical implications for agriculture, since knowledge at the molecular level can potentially be translated from model plants to crops or from tolerant to sensitive cultivars. For more than a decade, researchers have attempted to identify transcriptional and metabolic pathways involved in stress tolerance using functional genomics tools. In some cases, promising results were obtained when a clear causal link was found between transcripts and tolerance/sensitivity to stress. However, recent reports question the global translational power of functional genomics for biotechnological applications, as one of the main limitations seems to be the large variability in gene expression. Transcript-level variability under stress has not been considered of interest in the scientific literature because it is intuitively obvious, but most reports seem to naively overlook the consequences. Here, three case situations are reviewed (variability between genotypes, variability due to environmental interactions and variability between stressors) in support of the concept that inherent transcript-level variation in biological systems may limit our knowledge of environmental plant tolerance and of functional genomics in molecular stress physiology.
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Affiliation(s)
- D H Sanchez
- Laboratory of Plant Genetics-Sciences III, University of Geneva, Geneva, Switzerland
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171
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Guo R, Xu X, Carole B, Li X, Gao M, Zheng Y, Wang X. Genome-wide identification, evolutionary and expression analysis of the aspartic protease gene superfamily in grape. BMC Genomics 2013; 14:554. [PMID: 23945092 PMCID: PMC3751884 DOI: 10.1186/1471-2164-14-554] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 08/06/2013] [Indexed: 12/15/2022] Open
Abstract
Background Aspartic proteases (APs) are a large family of proteolytic enzymes found in almost all organisms. In plants, they are involved in many biological processes, such as senescence, stress responses, programmed cell death, and reproduction. Prior to the present study, no grape AP gene(s) had been reported, and their research on woody species was very limited. Results In this study, a total of 50 AP genes (VvAP) were identified in the grape genome, among which 30 contained the complete ASP domain. Synteny analysis within grape indicated that segmental and tandem duplication events contributed to the expansion of the grape AP family. Additional analysis between grape and Arabidopsis demonstrated that several grape AP genes were found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the divergence of grape and Arabidopsis. Phylogenetic relationships of the 30 VvAPs with the complete ASP domain and their Arabidopsis orthologs, as well as their gene and protein features were analyzed and their cellular localization was predicted. Moreover, expression profiles of VvAP genes in six different tissues were determined, and their transcript abundance under various stresses and hormone treatments were measured. Twenty-seven VvAP genes were expressed in at least one of the six tissues examined; nineteen VvAPs responded to at least one abiotic stress, 12 VvAPs responded to powdery mildew infection, and most of the VvAPs responded to SA and ABA treatments. Furthermore, integrated synteny and phylogenetic analysis identified orthologous AP genes between grape and Arabidopsis, providing a unique starting point for investigating the function of grape AP genes. Conclusions The genome-wide identification, evolutionary and expression analyses of grape AP genes provide a framework for future analysis of AP genes in defining their roles during stress response. Integrated synteny and phylogenetic analyses provide novel insight into the functions of less well-studied genes using information from their better understood orthologs.
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Affiliation(s)
- Rongrong Guo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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172
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Peñuelas J, Sardans J, Estiarte M, Ogaya R, Carnicer J, Coll M, Barbeta A, Rivas-Ubach A, Llusià J, Garbulsky M, Filella I, Jump AS. Evidence of current impact of climate change on life: a walk from genes to the biosphere. GLOBAL CHANGE BIOLOGY 2013; 19:2303-38. [PMID: 23505157 DOI: 10.1111/gcb.12143] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 12/31/2012] [Accepted: 01/14/2013] [Indexed: 05/19/2023]
Abstract
We review the evidence of how organisms and populations are currently responding to climate change through phenotypic plasticity, genotypic evolution, changes in distribution and, in some cases, local extinction. Organisms alter their gene expression and metabolism to increase the concentrations of several antistress compounds and to change their physiology, phenology, growth and reproduction in response to climate change. Rapid adaptation and microevolution occur at the population level. Together with these phenotypic and genotypic adaptations, the movement of organisms and the turnover of populations can lead to migration toward habitats with better conditions unless hindered by barriers. Both migration and local extinction of populations have occurred. However, many unknowns for all these processes remain. The roles of phenotypic plasticity and genotypic evolution and their possible trade-offs and links with population structure warrant further research. The application of omic techniques to ecological studies will greatly favor this research. It remains poorly understood how climate change will result in asymmetrical responses of species and how it will interact with other increasing global impacts, such as N eutrophication, changes in environmental N : P ratios and species invasion, among many others. The biogeochemical and biophysical feedbacks on climate of all these changes in vegetation are also poorly understood. We here review the evidence of responses to climate change and discuss the perspectives for increasing our knowledge of the interactions between climate change and life.
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Affiliation(s)
- Josep Peñuelas
- CSIC, Global Ecology Unit CREAF-CEAB-CSIC-UAB, Cerdanyola del Vallès, Catalonia, Spain.
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173
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Modifications of Kyoho grape berry quality under long-term NaCl treatment. Food Chem 2013; 139:931-7. [DOI: 10.1016/j.foodchem.2013.02.038] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 01/03/2013] [Accepted: 02/11/2013] [Indexed: 11/20/2022]
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174
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Lemoine R, Camera SL, Atanassova R, Dédaldéchamp F, Allario T, Pourtau N, Bonnemain JL, Laloi M, Coutos-Thévenot P, Maurousset L, Faucher M, Girousse C, Lemonnier P, Parrilla J, Durand M. Source-to-sink transport of sugar and regulation by environmental factors. FRONTIERS IN PLANT SCIENCE 2013; 4:272. [PMID: 23898339 PMCID: PMC3721551 DOI: 10.3389/fpls.2013.00272] [Citation(s) in RCA: 526] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 07/02/2013] [Indexed: 05/18/2023]
Abstract
Source-to-sink transport of sugar is one of the major determinants of plant growth and relies on the efficient and controlled distribution of sucrose (and some other sugars such as raffinose and polyols) across plant organs through the phloem. However, sugar transport through the phloem can be affected by many environmental factors that alter source/sink relationships. In this paper, we summarize current knowledge about the phloem transport mechanisms and review the effects of several abiotic (water and salt stress, mineral deficiency, CO2, light, temperature, air, and soil pollutants) and biotic (mutualistic and pathogenic microbes, viruses, aphids, and parasitic plants) factors. Concerning abiotic constraints, alteration of the distribution of sugar among sinks is often reported, with some sinks as roots favored in case of mineral deficiency. Many of these constraints impair the transport function of the phloem but the exact mechanisms are far from being completely known. Phloem integrity can be disrupted (e.g., by callose deposition) and under certain conditions, phloem transport is affected, earlier than photosynthesis. Photosynthesis inhibition could result from the increase in sugar concentration due to phloem transport decrease. Biotic interactions (aphids, fungi, viruses…) also affect crop plant productivity. Recent breakthroughs have identified some of the sugar transporters involved in these interactions on the host and pathogen sides. The different data are discussed in relation to the phloem transport pathways. When possible, the link with current knowledge on the pathways at the molecular level will be highlighted.
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Affiliation(s)
- Remi Lemoine
- Unités Mixtes de Recherche, Ecologie et Biologie des Interactions, Université of Poitiers/Centre National de la Recherche ScientifiquePoitiers, France
| | - Sylvain La Camera
- Unités Mixtes de Recherche, Ecologie et Biologie des Interactions, Université of Poitiers/Centre National de la Recherche ScientifiquePoitiers, France
| | - Rossitza Atanassova
- Unités Mixtes de Recherche, Ecologie et Biologie des Interactions, Université of Poitiers/Centre National de la Recherche ScientifiquePoitiers, France
| | - Fabienne Dédaldéchamp
- Unités Mixtes de Recherche, Ecologie et Biologie des Interactions, Université of Poitiers/Centre National de la Recherche ScientifiquePoitiers, France
| | - Thierry Allario
- Unités Mixtes de Recherche, Ecologie et Biologie des Interactions, Université of Poitiers/Centre National de la Recherche ScientifiquePoitiers, France
| | - Nathalie Pourtau
- Unités Mixtes de Recherche, Ecologie et Biologie des Interactions, Université of Poitiers/Centre National de la Recherche ScientifiquePoitiers, France
| | - Jean-Louis Bonnemain
- Unités Mixtes de Recherche, Ecologie et Biologie des Interactions, Université of Poitiers/Centre National de la Recherche ScientifiquePoitiers, France
| | - Maryse Laloi
- Unités Mixtes de Recherche, Ecologie et Biologie des Interactions, Université of Poitiers/Centre National de la Recherche ScientifiquePoitiers, France
| | - Pierre Coutos-Thévenot
- Unités Mixtes de Recherche, Ecologie et Biologie des Interactions, Université of Poitiers/Centre National de la Recherche ScientifiquePoitiers, France
| | - Laurence Maurousset
- Unités Mixtes de Recherche, Ecologie et Biologie des Interactions, Université of Poitiers/Centre National de la Recherche ScientifiquePoitiers, France
| | - Mireille Faucher
- Unités Mixtes de Recherche, Ecologie et Biologie des Interactions, Université of Poitiers/Centre National de la Recherche ScientifiquePoitiers, France
| | - Christine Girousse
- Diversité et Ecophysiologie des Céréales, Unités Mixtes de RechercheClermont Ferrand, France
| | - Pauline Lemonnier
- Unités Mixtes de Recherche, Ecologie et Biologie des Interactions, Université of Poitiers/Centre National de la Recherche ScientifiquePoitiers, France
| | - Jonathan Parrilla
- Unités Mixtes de Recherche, Ecologie et Biologie des Interactions, Université of Poitiers/Centre National de la Recherche ScientifiquePoitiers, France
| | - Mickael Durand
- Unités Mixtes de Recherche, Ecologie et Biologie des Interactions, Université of Poitiers/Centre National de la Recherche ScientifiquePoitiers, France
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175
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Fotakis C, Christodouleas D, Kokkotou K, Zervou M, Zoumpoulakis P, Moulos P, Liouni M, Calokerinos A. NMR metabolite profiling of Greek grape marc spirits. Food Chem 2013; 138:1837-46. [DOI: 10.1016/j.foodchem.2012.11.128] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 11/12/2012] [Accepted: 11/17/2012] [Indexed: 01/11/2023]
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176
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Choi HK, Iandolino A, da Silva FG, Cook DR. Water deficit modulates the response of Vitis vinifera to the Pierce's disease pathogen Xylella fastidiosa. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:643-57. [PMID: 23425100 DOI: 10.1094/mpmi-09-12-0217-r] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Pierce's disease, caused by the bacterium Xylella fastidiosa, is one of the most devastating diseases of cultivated grape, currently restricted to the Americas. To test the long-standing hypothesis that Pierce's disease results from pathogen-induced drought stress, we used the Affymetrix Vitis GeneChip to compare the transcriptional response of Vitis vinifera to Xylella infection, water deficit, or a combination of the two stresses. The results reveal a redirection of gene transcription involving 822 genes with a minimum twofold change (P < 0.05), including the upregulation of transcripts for phenylpropanoid and flavonoid biosynthesis, pathogenesis-related proteins, abscisic acid- and jasmonic acid-responsive biosynthesis, and downregulation of transcripts related to photosynthesis, growth, and nutrition. Although the transcriptional response of plants to Xylella infection was largely distinct from the response of healthy plants to water stress, we find that 138 of the pathogen-induced genes exhibited a significantly stronger transcriptional response when plants were simultaneously exposed to infection and drought stress, suggesting a strong interaction between disease and water deficit. This interaction between drought stress and disease was mirrored in planta at the physiological level for aspects of water relations and photosynthesis and in terms of the severity of disease symptoms and the extent of pathogen colonization, providing a molecular correlate of the classical concept of the disease triangle in which environment impacts disease severity.
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Affiliation(s)
- Hong-Kyu Choi
- Department of Genetic Engineering, Dong-A University, Bussan, Republic of Korea
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177
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Degenkolbe T, Do PT, Kopka J, Zuther E, Hincha DK, Köhl KI. Identification of drought tolerance markers in a diverse population of rice cultivars by expression and metabolite profiling. PLoS One 2013; 8:e63637. [PMID: 23717458 PMCID: PMC3661581 DOI: 10.1371/journal.pone.0063637] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 04/04/2013] [Indexed: 11/18/2022] Open
Abstract
Rice provides about half of the calories consumed in Asian countries, but its productivity is often reduced by drought, especially when grown under rain-fed conditions. Cultivars with increased drought tolerance have been bred over centuries. Slow selection for drought tolerance on the basis of phenotypic traits may be accelerated by using molecular markers identified through expression and metabolic profiling. Previously, we identified 46 candidate genes with significant genotype × environment interaction in an expression profiling study on four cultivars with contrasting drought tolerance. These potential markers and in addition GC-MS quantified metabolites were tested in 21 cultivars from both indica and japonica background that varied in drought tolerance. Leaf blades were sampled from this population of cultivars grown under control or long-term drought condition and subjected to expression analysis by qRT-PCR and metabolite profiling. Under drought stress, metabolite levels correlated mainly negatively with performance parameters, but eight metabolites correlated positively. For 28 genes, a significant correlation between expression level and performance under drought was confirmed. Negative correlations were predominant. Among those with significant positive correlation was the gene coding for a cytosolic fructose-1,6-bisphosphatase. This enzyme catalyzes a highly regulated step in C-metabolism. The metabolic and transcript marker candidates for drought tolerance were identified in a highly diverse population of cultivars. Thus, these markers may be used to select for tolerance in a wide range of rice germplasms.
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Affiliation(s)
- Thomas Degenkolbe
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Brandenburg, Germany
| | - Phuc T. Do
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Brandenburg, Germany
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Brandenburg, Germany
| | - Ellen Zuther
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Brandenburg, Germany
| | - Dirk K. Hincha
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Brandenburg, Germany
| | - Karin I. Köhl
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Brandenburg, Germany
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178
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Hochberg U, Degu A, Fait A, Rachmilevitch S. Near isohydric grapevine cultivar displays higher photosynthetic efficiency and photorespiration rates under drought stress as compared with near anisohydric grapevine cultivar. PHYSIOLOGIA PLANTARUM 2013; 147:443-52. [PMID: 22901023 DOI: 10.1111/j.1399-3054.2012.01671.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 05/29/2012] [Accepted: 06/01/2012] [Indexed: 05/21/2023]
Abstract
Drought stress is known to limit photosynthesis rates and to inflict photo-oxidative damage in grapevines. Grapevines, which are considered drought-tolerant plants, are characterized by diverse hydraulic and photosynthetic behaviors, depending on the cultivar. This research compared the photosynthesis and the photorespiration of Cabernet Sauvignon (Cs) (isohydric) and Shiraz (anisohydric) in an attempt to acquire a wider perspective on the iso/anisohydric phenomenon and its implications. Shiraz and Cs were subjected to terminal drought in the greenhouse. Soil water content (θ), leaf water potential (Ψl ) and stomata conductance (gs ) were measured to determine the cultivars' hydraulic behavior. Gas exchange and fluorometry measurements were taken at 21 and 2% O2 to acquire photosynthesis and photorespiration characteristics. Cs was found to behave in a near isohydric manner whereas Shiraz behaved in a near anisohydric manner. Compared to Shiraz, the reduced stomata conductance values of Cs were accompanied by higher water use efficiency and photorespiration rates, as well as photosystem II photochemical potential (Fv /Fm ). As compared with Shiraz, Cs compensated for lower stomata conductance by higher photosynthesis and photorespiration. These two processes contributed to higher electron flow rates that might have a role in photoinhibition avoidance, which was observed in the stability of Fv /Fm under drought stress.
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Affiliation(s)
- Uri Hochberg
- Albert Katz International School of Desert Studies, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Negev, Israel
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179
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Cramer GR, Van Sluyter SC, Hopper DW, Pascovici D, Keighley T, Haynes PA. Proteomic analysis indicates massive changes in metabolism prior to the inhibition of growth and photosynthesis of grapevine (Vitis vinifera L.) in response to water deficit. BMC PLANT BIOLOGY 2013; 13:49. [PMID: 23514573 PMCID: PMC3608200 DOI: 10.1186/1471-2229-13-49] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 03/14/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Cabernet Sauvignon grapevines were exposed to a progressive, increasing water defict over 16 days. Shoot elongation and photosynthesis were measured for physiological responses to water deficit. The effect of water deficit over time on the abundance of individual proteins in growing shoot tips (including four immature leaves) was analyzed using nanoflow liquid chromatography - tandem mass spectrometry (nanoLC-MS/MS). RESULTS Water deficit progressively decreased shoot elongation, stomatal conductance and photosynthesis after Day 4; 2277 proteins were identified by shotgun proteomics with an average CV of 9% for the protein abundance of all proteins. There were 472 out of 942 (50%) proteins found in all samples that were significantly affected by water deficit. The 472 proteins were clustered into four groups: increased and decreased abundance of early- and late-responding protein profiles. Vines sensed the water deficit early, appearing to acclimate to stress, because the abundance of many proteins changed before decreases in shoot elongation, stomatal conductance and photosynthesis. Predominant functional categories of the early-responding proteins included photosynthesis, glycolysis, translation, antioxidant defense and growth-related categories (steroid metabolism and water transport), whereas additional proteins for late-responding proteins were largely involved with transport, photorespiration, antioxidants, amino acid and carbohydrate metabolism. CONCLUSIONS Proteomic responses to water deficit were dynamic with early, significant changes in abundance of proteins involved in translation, energy, antioxidant defense and steroid metabolism. The abundance of these proteins changed prior to any detectable decreases in shoot elongation, stomatal conductance or photosynthesis. Many of these early-responding proteins are known to be regulated by post-transcriptional modifications such as phosphorylation. The proteomics analysis indicates massive and substantial changes in plant metabolism that appear to funnel carbon and energy into antioxidant defenses in the very early stages of plant response to water deficit before any significant injury.
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Affiliation(s)
- Grant R Cramer
- Department of Biochemistry and Molecular Biology, University of Nevada Reno, Reno, NV 89557, USA
| | - Steve C Van Sluyter
- Present address: Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Daniel W Hopper
- Department of Biochemistry and Molecular Biology, University of Nevada Reno, Reno, NV 89557, USA
| | - Dana Pascovici
- Present address: Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Tim Keighley
- Present address: Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Paul A Haynes
- Present address: Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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180
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Hill CB, Jha D, Bacic A, Tester M, Roessner U. Characterization of ion contents and metabolic responses to salt stress of different Arabidopsis AtHKT1;1 genotypes and their parental strains. MOLECULAR PLANT 2013; 6:350-68. [PMID: 23132143 DOI: 10.1093/mp/sss125] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Plants employ several strategies to maintain cellular ion homeostasis under salinity stress, including mediating ion fluxes by transmembrane transport proteins and adjusting osmotic pressure by accumulating osmolytes. The HKT (high-affinity potassium transporter) gene family comprises Na(+) and Na(+)/K(+) transporters in diverse plant species, with HKT1;1 as the only member in Arabidopsis thaliana. Cell-type-specific overexpression of AtHKT1;1 has been shown to prevent shoot Na(+) overaccumulation under salinity stress. Here, we analyzed a broad range of metabolites and elements in shoots and roots of different AtHKT1;1 genotypes and their parental strains before and after salinity stress, revealing a reciprocal relationship of metabolite differences between an AtHKT1;1 knockout line (hkt1;1) and the AtHKT1;1 overexpressing lines (E2586 UAS GAL4 :HKT1;1 and J2731*UAS GAL4 :HKT1;1). Although levels of root sugars were increased after salt stress in both AtHKT1;1 overexpressing lines, E2586 UAS GAL4 :HKT1;1 showed higher accumulation of the osmoprotectants trehalose, gentiobiose, and melibiose, whereas J2731*UAS GAL4 :HKT1;1 showed higher levels of sucrose and raffinose, compared with their parental lines, respectively. In contrast, the knockout line hkt1;1 showed strong increases in the levels of the tricarboxylic acid (TCA) cycle intermediates in the shoots after salt treatment. This coincided with a significant depletion of sugars, suggesting that there is an increased rate of carbon influx into the TCA cycle at a constant rate of C-efflux from the cycle, which might be needed to support plant survival during salt stress. Using correlation analysis, we identified associations between the Na(+) content and several sugars, suggesting that regulation of sugar metabolism is important in plant responses to salinity stress.
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Affiliation(s)
- Camilla B Hill
- Australian Centre for Plant Functional Genomics, School of Botany, University of Melbourne, Victoria 3010, Australia
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181
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Tak H, Mhatre M. Cloning and molecular characterization of a putative bZIP transcription factor VvbZIP23 from Vitis vinifera. PROTOPLASMA 2013; 250:333-45. [PMID: 22610648 DOI: 10.1007/s00709-012-0417-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 05/02/2012] [Indexed: 05/16/2023]
Abstract
The proteins harboring bZIP domains comprise a large family and play key roles in many cellular processes, one of them being tolerance to biotic and abiotic stresses in plants. In the present study, we characterize a putative bZIP transcription factor from Vitis vinifera namely VvbZIP23. Our studies revealed that a GFP fusion of VvbZIP23 is localized in the nucleus showing VvbZIP23 codes for a nuclear localized protein. VvbZIP23 identified by in silico approaches from grapevine DNA databases available in the public domain NCBI is present in a single copy in the grapevine genome as shown by Southern blot analysis. Expression of VvbZIP23 is induced by a wide spectrum of abiotic stresses, including drought, salt, and cold. Exogenous application of signaling chemicals like abscisic acid, methyl viologen, salicylic acid, jasmonic acid, and ethephon also induced expression of VvbZIP23. This shows that VvbZIP23 is involved in regulating a number of stress responses in V. vinifera. The 5' proximal region of VvbZIP23 contains many cis-acting elements, which show induction of VvbZIP23 expression in multiple stress responses. Transcripts of VvbZIP23 were found in many parts of the grapevine plant with the highest expression detected in leaves. Further in silico analysis shows that the open reading frame of VvbZIP23 is 822 bp long and codes for a 273 amino acid long protein having a characteristic bZIP domain in its N-terminal end. Overexpression of VvbZIP23-GFP fusion protein in grapevine callus leads to enhanced transcript levels of genes, homologues of which are reported to be important in regulating many stress conditions.
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Affiliation(s)
- Himanshu Tak
- Plant Cell Culture Technology Section, Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India.
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182
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Gambino G, Cuozzo D, Fasoli M, Pagliarani C, Vitali M, Boccacci P, Pezzotti M, Mannini F. Co-evolution between Grapevine rupestris stem pitting-associated virus and Vitis vinifera L. leads to decreased defence responses and increased transcription of genes related to photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:5919-33. [PMID: 22987838 DOI: 10.1093/jxb/ers244] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Grapevine rupestris stem pitting-associated virus (GRSPaV) is a widespread virus infecting Vitis spp. Although it has established a compatible viral interaction in Vitis vinifera without the development of phenotypic alterations, it can occur as distinct variants that show different symptoms in diverse Vitis species. The changes induced by GRSPaV in V. vinifera cv 'Bosco', an Italian white grape variety, were investigated by combining agronomic, physiological, and molecular approaches, in order to provide comprehensive information about the global effects of GRSPaV. In two years, this virus caused a moderate decrease in physiological efficiency, yield performance, and sugar content in berries associated with several transcriptomic alterations. Transcript profiles were analysed by a microarray technique in petiole, leaf, and berry samples collected at véraison and by real-time RT-PCR in a time course carried out at five grapevine developmental stages. Global gene expression analyses showed that transcriptomic changes were highly variable among the different organs and the different phenological phases. GRSPaV triggers some unique responses in the grapevine at véraison, never reported before for other plant-virus interactions. These responses include an increase in transcripts involved in photosynthesis and CO(2) fixation, a moderate reduction in the photosynthesis rate and some defence mechanisms, and an overlap with responses to water and salinity stresses. It is hypothesized that the long co-existence of grapevine and GRSPaV has resulted in the evolution of a form of mutual adaptation between the virus and its host. This study contributes to elucidating alternative mechanisms used by infected plants to contend with viruses.
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Affiliation(s)
- Giorgio Gambino
- Plant Virology Institute, National Research Council (IVV-CNR), UOS Grugliasco, Via L. da Vinci 44, 10095 Grugliasco-TO, Italy.
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183
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Liu GT, Wang JF, Cramer G, Dai ZW, Duan W, Xu HG, Wu BH, Fan PG, Wang LJ, Li SH. Transcriptomic analysis of grape (Vitis vinifera L.) leaves during and after recovery from heat stress. BMC PLANT BIOLOGY 2012; 12:174. [PMID: 23016701 PMCID: PMC3497578 DOI: 10.1186/1471-2229-12-174] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 09/24/2012] [Indexed: 05/20/2023]
Abstract
BACKGROUND Grapes are a major fruit crop around the world. Heat stress can significantly reduce grape yield and quality. Changes at the molecular level in response to heat stress and subsequent recovery are poorly understood. To elucidate the effect of heat stress and subsequent recovery on expression of genes by grape leaves representing the classic heat stress response and thermotolerance mechanisms, transcript abundance of grape (Vitis vinifera L.) leaves was quantified using the Affymetrix Grape Genome oligonucleotide microarray (15,700 transcripts), followed by quantitative Real-Time PCR validation for some transcript profiles. RESULTS We found that about 8% of the total probe sets were responsive to heat stress and/or to subsequent recovery in grape leaves. The heat stress and recovery responses were characterized by different transcriptional changes. The number of heat stress-regulated genes was almost twice the number of recovery-regulated genes. The responsive genes identified in this study belong to a large number of important traits and biological pathways, including cell rescue (i.e., antioxidant enzymes), protein fate (i.e., HSPs), primary and secondary metabolism, transcription factors, signal transduction, and development. We have identified some common genes and heat shock factors (HSFs) that were modulated differentially by heat stress and recovery. Most HSP genes were upregulated by heat stress but were downregulated by the recovery. On the other hand, some specific HSP genes or HSFs were uniquely responsive to heat stress or recovery. CONCLUSION The effect of heat stress and recovery on grape appears to be associated with multiple processes and mechanisms including stress-related genes, transcription factors, and metabolism. Heat stress and recovery elicited common up- or downregulated genes as well as unique sets of responsive genes. Moreover, some genes were regulated in opposite directions by heat stress and recovery. The results indicated HSPs, especially small HSPs, antioxidant enzymes (i.e., ascorbate peroxidase), and galactinol synthase may be important to thermotolerance of grape. HSF30 may be a key regulator for heat stress and recovery, while HSF7 and HSF1 may only be specific to recovery. The identification of heat stress or recovery responsive genes in this study provides novel insights into the molecular basis for heat tolerance in grape leaves.
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Affiliation(s)
- Guo-Tian Liu
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. of China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. of China
| | - Jun-Fang Wang
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. of China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. of China
| | - Grant Cramer
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, 89557, USA
| | - Zhan-Wu Dai
- INRA, ISVV, UMR 1287 EGFV, Villenave d'Ornon, 33882, France
| | - Wei Duan
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. of China
| | - Hong-Guo Xu
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. of China
| | - Ben-Hong Wu
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. of China
| | - Pei-Ge Fan
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. of China
| | - Li-Jun Wang
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. of China
| | - Shao-Hua Li
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. of China
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, P.R. of China
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184
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Zhang Y, Gao M, Singer SD, Fei Z, Wang H, Wang X. Genome-wide identification and analysis of the TIFY gene family in grape. PLoS One 2012; 7:e44465. [PMID: 22984514 PMCID: PMC3439424 DOI: 10.1371/journal.pone.0044465] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 08/02/2012] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The TIFY gene family constitutes a plant-specific group of genes with a broad range of functions. This family encodes four subfamilies of proteins, including ZML, TIFY, PPD and JASMONATE ZIM-Domain (JAZ) proteins. JAZ proteins are targets of the SCF(COI1) complex, and function as negative regulators in the JA signaling pathway. Recently, it has been reported in both Arabidopsis and rice that TIFY genes, and especially JAZ genes, may be involved in plant defense against insect feeding, wounding, pathogens and abiotic stresses. Nonetheless, knowledge concerning the specific expression patterns and evolutionary history of plant TIFY family members is limited, especially in a woody species such as grape. METHODOLOGY/PRINCIPAL FINDINGS A total of two TIFY, four ZML, two PPD and 11 JAZ genes were identified in the Vitis vinifera genome. Phylogenetic analysis of TIFY protein sequences from grape, Arabidopsis and rice indicated that the grape TIFY proteins are more closely related to those of Arabidopsis than those of rice. Both segmental and tandem duplication events have been major contributors to the expansion of the grape TIFY family. In addition, synteny analysis between grape and Arabidopsis demonstrated that homologues of several grape TIFY genes were found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the divergence of lineages that led to grape and Arabidopsis. Analyses of microarray and quantitative real-time RT-PCR expression data revealed that grape TIFY genes are not a major player in the defense against biotrophic pathogens or viruses. However, many of these genes were responsive to JA and ABA, but not SA or ET. CONCLUSION The genome-wide identification, evolutionary and expression analyses of grape TIFY genes should facilitate further research of this gene family and provide new insights regarding their evolutionary history and regulatory control.
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Affiliation(s)
- Yucheng Zhang
- College of Horticulture, Northwest A&F University, Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P. R. China
- College of Enology, Northwest A&F University, Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, Shaanxi, P. R. China
| | - Min Gao
- College of Horticulture, Northwest A&F University, Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P. R. China
- State Key Laboratory of Crop Stress Biology in Arid Areas (Northwest A&F University), Yangling, Shaanxi, P. R. China
| | - Stacy D. Singer
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, United States of America
- USDA Robert W. Holley Center for Agriculture and Health, Ithaca, New York, United States of America
| | - Hua Wang
- College of Enology, Northwest A&F University, Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, Shaanxi, P. R. China
| | - Xiping Wang
- College of Horticulture, Northwest A&F University, Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P. R. China
- State Key Laboratory of Crop Stress Biology in Arid Areas (Northwest A&F University), Yangling, Shaanxi, P. R. China
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185
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Obata T, Fernie AR. The use of metabolomics to dissect plant responses to abiotic stresses. Cell Mol Life Sci 2012; 69:3225-43. [PMID: 22885821 PMCID: PMC3437017 DOI: 10.1007/s00018-012-1091-5] [Citation(s) in RCA: 451] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Revised: 07/09/2012] [Accepted: 07/09/2012] [Indexed: 12/15/2022]
Abstract
Plant metabolism is perturbed by various abiotic stresses. As such the metabolic network of plants must be reconfigured under stress conditions in order to allow both the maintenance of metabolic homeostasis and the production of compounds that ameliorate the stress. The recent development and adoption of metabolomics and systems biology approaches enable us not only to gain a comprehensive overview, but also a detailed analysis of crucial components of the plant metabolic response to abiotic stresses. In this review we introduce the analytical methods used for plant metabolomics and describe their use in studies related to the metabolic response to water, temperature, light, nutrient limitation, ion and oxidative stresses. Both similarity and specificity of the metabolic responses against diverse abiotic stress are evaluated using data available in the literature. Classically discussed stress compounds such as proline, γ-amino butyrate and polyamines are reviewed, and the widespread importance of branched chain amino acid metabolism under stress condition is discussed. Finally, where possible, mechanistic insights into metabolic regulatory processes are discussed.
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Affiliation(s)
- Toshihiro Obata
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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186
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Yang Y, He M, Zhu Z, Li S, Xu Y, Zhang C, Singer SD, Wang Y. Identification of the dehydrin gene family from grapevine species and analysis of their responsiveness to various forms of abiotic and biotic stress. BMC PLANT BIOLOGY 2012; 12:140. [PMID: 22882870 PMCID: PMC3460772 DOI: 10.1186/1471-2229-12-140] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 08/02/2012] [Indexed: 05/02/2023]
Abstract
BACKGROUND Dehydrins (DHNs) protect plant cells from desiccation damage during environmental stress, and also participate in host resistance to various pathogens. In this study, we aimed to identify and characterize the DHN gene families from Vitis vinifera and wild V. yeshanensis, which is tolerant to both drought and cold, and moderately resistant to powdery mildew. RESULTS Four DHN genes were identified in both V. vinifera and V. yeshanensis, which shared a high sequence identity between the two species but little homology between the genes themselves. These genes were designated DHN1, DHN2, DHN3 and DHN4. All four of the DHN proteins were highly hydrophilic and were predicted to be intrinsically disordered, but they differed in their isoelectric points, kinase selectivities and number of functional motifs. Also, the expression profiles of each gene differed appreciably from one another. Grapevine DHN1 was not expressed in vegetative tissues under normal growth conditions, but was induced by drought, cold, heat, embryogenesis, as well as the application of abscisic acid (ABA), salicylic acid (SA), and methyl jasmonate (MeJA). It was expressed earlier in V. yeshanensis under drought conditions than in V. vinifera, and also exhibited a second round of up-regulation in V. yeshanensis following inoculation with Erysiphe necator, which was not apparent in V. vinifera. Like DHN1, DHN2 was induced by cold, heat, embryogenesis and ABA; however, it exhibited no responsiveness to drought, E. necator infection, SA or MeJA, and was also expressed constitutively in vegetative tissues under normal growth conditions. Conversely, DHN3 was only expressed during seed development at extremely low levels, and DHN4 was expressed specifically during late embryogenesis. Neither DHN3 nor DHN4 exhibited responsiveness to any of the treatments carried out in this study. Interestingly, the presence of particular cis-elements within the promoter regions of each gene was positively correlated with their expression profiles. CONCLUSIONS The grapevine DHN family comprises four divergent members. While it is likely that their functions overlap to some extent, it seems that DHN1 provides the main stress-responsive function. In addition, our results suggest a close relationship between expression patterns, physicochemical properties, and cis-regulatory elements in the promoter regions of the DHN genes.
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Affiliation(s)
- Yazhou Yang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mingyang He
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ziguo Zhu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shuxiu Li
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yan Xu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chaohong Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Stacy D Singer
- Department of Agricultural, Food and Nutritional Science, 4–10 Agriculture/Forestry Centre, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Yuejin Wang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China
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187
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Takahashi K, Tokuoka M, Kohno H, Sawamura N, Myoken Y, Mizuno A. Comprehensive analysis of dipeptides in alcoholic beverages by tag-based separation and determination using liquid chromatography/electrospray ionization tandem mass spectrometry and quadrupole-time-of-flight mass spectrometry. J Chromatogr A 2012; 1242:17-25. [DOI: 10.1016/j.chroma.2012.03.076] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 02/28/2012] [Accepted: 03/26/2012] [Indexed: 11/29/2022]
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188
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Mastrobuoni G, Irgang S, Pietzke M, Assmus HE, Wenzel M, Schulze WX, Kempa S. Proteome dynamics and early salt stress response of the photosynthetic organism Chlamydomonas reinhardtii. BMC Genomics 2012; 13:215. [PMID: 22651860 PMCID: PMC3444938 DOI: 10.1186/1471-2164-13-215] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 05/31/2012] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The cellular proteome and metabolome are underlying dynamic regulation allowing rapid adaptation to changes in the environment. System-wide analysis of these dynamics will provide novel insights into mechanisms of stress adaptation for higher photosynthetic organisms. We applied pulsed-SILAC labeling to a photosynthetic organism for the first time and we established a method to study proteome dynamics in the green alga Chlamydomonas reinhardtii, an emerging model system for plant biology. In addition, we combined the analysis of protein synthesis with metabolic profiling to study the dynamic changes of metabolism and proteome turnover under salt stress conditions. RESULTS To study de novo protein synthesis an arginine auxotroph Chlamydomonas strain was cultivated in presence of stable isotope-labeled arginine for 24 hours. From the time course experiment in 3 salt concentrations we could identify more than 2500 proteins and their H/L ratio in at least one experimental condition; for 998 protiens at least 3 ratio counts were detected in the 24 h time point (0 mM NaCl). After fractionation we could identify 3115 proteins and for 1765 of them we determined their de novo synthesis rate. Consistently with previous findings we showed that RuBisCO is among the most prominent proteins in the cell; and similar abundance and turnover for the small and large RuBisCO subunit could be calculated. The D1 protein was identified among proteins with a high synthesis rates. A global median half-life of 45 h was calculated for Chlamydomonas proteins under the chosen conditions. CONCLUSION To investigate the temporal co-regulation of the proteome and metabolome, we applied salt stress to Chlamydomonas and studied the time dependent regulation of protein expression and changes in the metabolome. The main metabolic response to salt stress was observed within the amino acid metabolism. In particular, proline was up-regulated manifold and according to that an increased carbon flow within the proline biosynthetic pathway could be measured. In parallel the analysis of abundance and de novo synthesis of the corresponding enzymes revealed that metabolic rearrangements precede adjustments of protein abundance.
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Affiliation(s)
- Guido Mastrobuoni
- Max Delbrück Center for Molecular Medicine Berlin, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
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189
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Grimplet J, Van Hemert J, Carbonell-Bejerano P, Díaz-Riquelme J, Dickerson J, Fennell A, Pezzotti M, Martínez-Zapater JM. Comparative analysis of grapevine whole-genome gene predictions, functional annotation, categorization and integration of the predicted gene sequences. BMC Res Notes 2012; 5:213. [PMID: 22554261 PMCID: PMC3419625 DOI: 10.1186/1756-0500-5-213] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 05/03/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The first draft assembly and gene prediction of the grapevine genome (8X base coverage) was made available to the scientific community in 2007, and functional annotation was developed on this gene prediction. Since then additional Sanger sequences were added to the 8X sequences pool and a new version of the genomic sequence with superior base coverage (12X) was produced. RESULTS In order to more efficiently annotate the function of the genes predicted in the new assembly, it is important to build on as much of the previous work as possible, by transferring 8X annotation of the genome to the 12X version. The 8X and 12X assemblies and gene predictions of the grapevine genome were compared to answer the question, "Can we uniquely map 8X predicted genes to 12X predicted genes?" The results show that while the assemblies and gene structure predictions are too different to make a complete mapping between them, most genes (18,725) showed a one-to-one relationship between 8X predicted genes and the last version of 12X predicted genes. In addition, reshuffled genomic sequence structures appeared. These highlight regions of the genome where the gene predictions need to be taken with caution. Based on the new grapevine gene functional annotation and in-depth functional categorization, twenty eight new molecular networks have been created for VitisNet while the existing networks were updated. CONCLUSIONS The outcomes of this study provide a functional annotation of the 12X genes, an update of VitisNet, the system of the grapevine molecular networks, and a new functional categorization of genes. Data are available at the VitisNet website (http://www.sdstate.edu/ps/research/vitis/pathways.cfm).
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Affiliation(s)
- Jérôme Grimplet
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), CCT, C/Madre de Dios 51, Logroño, España.
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190
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Li H, Hu T, Fu J. Identification of genes associated with adaptation to NaCl toxicity in perennial ryegrass (Lolium perenne L.). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2012; 79:153-162. [PMID: 22277775 DOI: 10.1016/j.ecoenv.2011.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2011] [Revised: 12/20/2011] [Accepted: 12/24/2011] [Indexed: 05/31/2023]
Abstract
Perennial ryegrass (Lolium perenne L.) is a popular turfgrass species. To understand the molecular mechanisms of salinity tolerance, a suppression subtractive cDNA library was constructed for a salinity-tolerant ryegrass accession, with NaCl-treated (255 mM) plants as the tester. Differentially expressed cDNA fragments were cloned and screened. BLAST search revealed that 268 clones exhibited significant homologies to known genes. These genes could be categorized into 11 different functional groups, including metabolism, energy transfer, detoxification, compatible solute, cellular transport, transcription, signal transduction, etc. The salinity-regulated expression of selected genes was confirmed by RT-PCR analysis. The results suggested that these putatively salinity up-regulated genes may play a vital role in the salinity tolerance of perennial ryegrass. They can be used as candidate genes for creating stress-tolerant grasses and for understanding molecular mechanisms of plant adaptation to salinity stress.
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Affiliation(s)
- Huiying Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Wuhan Institute of Botany, Chinese Academy of Sciences, Lumo street, Wuhan 430074, Hubei, PR China
| | - Tao Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Wuhan Institute of Botany, Chinese Academy of Sciences, Lumo street, Wuhan 430074, Hubei, PR China
| | - Jinmin Fu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Wuhan Institute of Botany, Chinese Academy of Sciences, Lumo street, Wuhan 430074, Hubei, PR China.
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191
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Mandal R, Kathiria P, Psychogios N, Bouatra S, Krishnamurthy R, Wishart D, Kovalchuk I. Progeny of tobacco mosaic virus-infected Nicotiana tabacum plants exhibit trans-generational changes in metabolic profiles. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2012. [DOI: 10.1016/j.bcab.2012.01.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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192
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Zagorchev L, Seal CE, Kranner I, Odjakova M. Redox state of low-molecular-weight thiols and disulphides during somatic embryogenesis of salt-treated suspension cultures of Dactylis glomerata L. Free Radic Res 2012; 46:656-64. [PMID: 22348546 DOI: 10.3109/10715762.2012.667565] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The tripeptide antioxidant γ-L-glutamyl-L-cysteinyl-glycine, or glutathione (GSH), serves a central role in ROS scavenging and oxidative signalling. Here, GSH, glutathione disulphide (GSSG), and other low-molecular-weight (LMW) thiols and their corresponding disulphides were studied in embryogenic suspension cultures of Dactylis glomerata L. subjected to moderate (0.085 M NaCl) or severe (0.17 M NaCl) salt stress. Total glutathione (GSH + GSSG) concentrations and redox state were associated with growth and development in control cultures and in moderately salt-stressed cultures and were affected by severe salt stress. The redox state of the cystine (CySS)/2 cysteine (Cys) redox couple was also affected by developmental stage and salt stress. The glutathione half-cell reduction potential (E(GSSG/2 GSH)) increased with the duration of culturing and peaked when somatic embryos were formed, as did the half-cell reduction potential of the CySS/2 Cys redox couple (E(CySS/2 Cys)). The most noticeable relationship between cellular redox state and developmental state was found when all LMW thiols and disulphides present were mathematically combined into a 'thiol-disulphide redox environment' (E(thiol-disulphide)), whereby reducing conditions accompanied proliferation, resulting in the formation of pro-embryogenic masses (PEMs), and oxidizing conditions accompanied differentiation, resulting in the formation of somatic embryos. The comparatively high contribution of E(CySS/2 Cys) to E(thiol-disulphide) in cultures exposed to severe salt stress suggests that Cys and CySS may be important intracellular redox regulators with a potential role in stress signalling.
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193
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Daldoul S, Mliki A, Höfer MU. Suppressive subtractive hybridization method analysis and its application to salt stress in grapevine (Vitis vinifera L.). RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412010061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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194
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Merewitz EB, Du H, Yu W, Liu Y, Gianfagna T, Huang B. Elevated cytokinin content in ipt transgenic creeping bentgrass promotes drought tolerance through regulating metabolite accumulation. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:1315-28. [PMID: 22131157 PMCID: PMC3276099 DOI: 10.1093/jxb/err372] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 10/04/2011] [Accepted: 10/18/2011] [Indexed: 05/18/2023]
Abstract
Increased endogenous plant cytokinin (CK) content through transformation with an adenine isopentyl transferase (ipt) gene has been associated with improved plant drought tolerance. The objective of this study is to determine metabolic changes associated with elevated CK production in ipt transgenic creeping bentgrass (Agrostis stolonifera L.) with improved drought tolerance. Null transformants (NTs) and plants transformed with ipt controlled by a stress- or senescence-activated promoter (SAG12-ipt) were exposed to well-watered conditions or drought stress by withholding irrigation in an environmental growth chamber. Physiological analysis confirmed that the SAG12-ipt line (S41) had improved drought tolerance compared with the NT plants. Specific metabolite changes over the course of drought stress and differential accumulation of metabolites in SAG12-ipt plants compared with NT plants at the same level of leaf relative water content (47% RWC) were identified using gas chromatography-mass spectroscopy. The metabolite profiling analysis detected 45 metabolites differentially accumulated in response to ipt expression or drought stress, which included amino acids, carbohydrates, organic acids, and organic alcohols. The enhanced drought tolerance of SAG12-ipt plants was associated with the maintenance of accumulation of several metabolites, particularly amino acids (proline, γ-aminobutyric acid, alanine, and glycine) carbohydrates (sucrose, fructose, maltose, and ribose), and organic acids that are mainly involved in the citric acid cycle. The accumulation of these metabolites could contribute to improved drought tolerance due to their roles in the stress response pathways such as stress signalling, osmotic adjustment, and respiration for energy production.
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Affiliation(s)
- Emily B. Merewitz
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Hongmei Du
- Center of Turfgrass Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Wenjuan Yu
- Instrumental Analysis Center of Shanghai Jiao Tong University, Shanghai, China
| | - Yimin Liu
- Instrumental Analysis Center of Shanghai Jiao Tong University, Shanghai, China
| | - Thomas Gianfagna
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Bingru Huang
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ 08901, USA
- To whom correspondence should be addressed. E-mail:
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195
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Krasensky J, Jonak C. Drought, salt, and temperature stress-induced metabolic rearrangements and regulatory networks. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:1593-608. [PMID: 22291134 PMCID: PMC4359903 DOI: 10.1093/jxb/err460] [Citation(s) in RCA: 969] [Impact Index Per Article: 80.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plants regularly face adverse growth conditions, such as drought, salinity, chilling, freezing, and high temperatures. These stresses can delay growth and development, reduce productivity, and, in extreme cases, cause plant death. Plant stress responses are dynamic and involve complex cross-talk between different regulatory levels, including adjustment of metabolism and gene expression for physiological and morphological adaptation. In this review, information about metabolic regulation in response to drought, extreme temperature, and salinity stress is summarized and the signalling events involved in mediating stress-induced metabolic changes are presented.
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Affiliation(s)
- Julia Krasensky
- GMI–Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Claudia Jonak
- GMI–Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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196
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Guillaumie S, Fouquet R, Kappel C, Camps C, Terrier N, Moncomble D, Dunlevy JD, Davies C, Boss PK, Delrot S. Transcriptional analysis of late ripening stages of grapevine berry. BMC PLANT BIOLOGY 2011; 11:165. [PMID: 22098939 PMCID: PMC3233516 DOI: 10.1186/1471-2229-11-165] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 11/18/2011] [Indexed: 05/03/2023]
Abstract
BACKGROUND The composition of grapevine berry at harvest is a major determinant of wine quality. Optimal oenological maturity of berries is characterized by a high sugar/acidity ratio, high anthocyanin content in the skin, and low astringency. However, harvest time is still mostly determined empirically, based on crude biochemical composition and berry tasting. In this context, it is interesting to identify genes that are expressed/repressed specifically at the late stages of ripening and which may be used as indicators of maturity. RESULTS Whole bunches and berries sorted by density were collected in vineyard on Chardonnay (white cultivar) grapevines for two consecutive years at three stages of ripening (7-days before harvest (TH-7), harvest (TH), and 10-days after harvest (TH+10)). Microvinification and sensory analysis indicate that the quality of the wines made from the whole bunches collected at TH-7, TH and TH+10 differed, TH providing the highest quality wines.In parallel, gene expression was studied with Qiagen/Operon microarrays using two types of samples, i.e. whole bunches and berries sorted by density. Only 12 genes were consistently up- or down-regulated in whole bunches and density sorted berries for the two years studied in Chardonnay. 52 genes were differentially expressed between the TH-7 and TH samples. In order to determine whether these genes followed a similar pattern of expression during the late stages of berry ripening in a red cultivar, nine genes were selected for RT-PCR analysis with Cabernet Sauvignon grown under two different temperature regimes affecting the precocity of ripening. The expression profiles and their relationship to ripening were confirmed in Cabernet Sauvignon for seven genes, encoding a carotenoid cleavage dioxygenase, a galactinol synthase, a late embryogenesis abundant protein, a dirigent-like protein, a histidine kinase receptor, a valencene synthase and a putative S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase. CONCLUSIONS This set of up- and down-regulated genes characterize the late stages of berry ripening in the two cultivars studied, and are indirectly linked to wine quality. They might be used directly or indirectly to design immunological, biochemical or molecular tools aimed at the determination of optimal ripening in these cultivars.
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Affiliation(s)
- Sabine Guillaumie
- Univ. Bordeaux, ISVV, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, F-33140 Villenave d'Ornon, France
- INRA, ISVV, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, F-33140 Villenave d'Ornon, France
| | - Romain Fouquet
- Univ. Bordeaux, ISVV, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, F-33140 Villenave d'Ornon, France
- INRA, ISVV, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, F-33140 Villenave d'Ornon, France
| | - Christian Kappel
- Univ. Bordeaux, ISVV, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, F-33140 Villenave d'Ornon, France
- INRA, ISVV, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, F-33140 Villenave d'Ornon, France
| | - Céline Camps
- Univ. Bordeaux, ISVV, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, F-33140 Villenave d'Ornon, France
- INRA, ISVV, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, F-33140 Villenave d'Ornon, France
| | - Nancy Terrier
- INRA, UMR1083 Science Pour l'Oenologie, 2 Place Viala, 34060 Montpellier, Cedex 01, France
| | - Dominique Moncomble
- Comité Interprofessionel du Vin de Champagne, 5 rue Henri Martin, 51204 Epernay, France
| | - Jake D Dunlevy
- Flinders University of South Australia, School of Biological Science, GPO Box 2100, SA 5001, Australia
| | - Christopher Davies
- CSIRO Plant Industry, Waite Campus, Hartley Grove, PO Box 350, Glen Osmond SA 5064, Australia
| | - Paul K Boss
- CSIRO Plant Industry, Waite Campus, Hartley Grove, PO Box 350, Glen Osmond SA 5064, Australia
| | - Serge Delrot
- Univ. Bordeaux, ISVV, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, F-33140 Villenave d'Ornon, France
- INRA, ISVV, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, F-33140 Villenave d'Ornon, France
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197
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Cramer GR, Urano K, Delrot S, Pezzotti M, Shinozaki K. Effects of abiotic stress on plants: a systems biology perspective. BMC PLANT BIOLOGY 2011; 11:163. [PMID: 22094046 PMCID: PMC3252258 DOI: 10.1186/1471-2229-11-163] [Citation(s) in RCA: 527] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 11/17/2011] [Indexed: 05/18/2023]
Abstract
The natural environment for plants is composed of a complex set of abiotic stresses and biotic stresses. Plant responses to these stresses are equally complex. Systems biology approaches facilitate a multi-targeted approach by allowing one to identify regulatory hubs in complex networks. Systems biology takes the molecular parts (transcripts, proteins and metabolites) of an organism and attempts to fit them into functional networks or models designed to describe and predict the dynamic activities of that organism in different environments. In this review, research progress in plant responses to abiotic stresses is summarized from the physiological level to the molecular level. New insights obtained from the integration of omics datasets are highlighted. Gaps in our knowledge are identified, providing additional focus areas for crop improvement research in the future.
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Affiliation(s)
- Grant R Cramer
- Department of Biochemistry and Molecular Biology, Mail Stop 330, University of Nevada, Reno, Nevada 89557, USA
| | - Kaoru Urano
- Gene Discovery Research Group, RIKEN Plant Science Center, 3-1-1 Koyadai, Tsukuba 305-0074, Japan
| | - Serge Delrot
- Univ. Bordeaux, ISVV, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, F-33882 Villenave d'Ornon, France
| | - Mario Pezzotti
- Dipartimento di Biotecnologie, Università di Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Plant Science Center, 3-1-1 Koyadai, Tsukuba 305-0074, Japan
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198
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Jacoby RP, Taylor NL, Millar AH. The role of mitochondrial respiration in salinity tolerance. TRENDS IN PLANT SCIENCE 2011; 16:614-23. [PMID: 21903446 DOI: 10.1016/j.tplants.2011.08.002] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 07/29/2011] [Accepted: 08/05/2011] [Indexed: 05/20/2023]
Abstract
NaCl is the most abundant salt in salinity-affected land. The ability of plants to sift the water table, limit NaCl uptake, compartmentalise Na⁺/Cl⁻ ions and prevent negative ionic and osmotic effects on cell function, are the foundations of salinity tolerance mechanisms. In this review, we show that although the quantitative response of respiratory rate to changes in salt concentration is complex, the properties of respiratory processes are crucial for tolerance during ion exclusion and tissue tolerance. We consider whole-plant gas exchange and carbon balance analysis alongside the salt responses of mitochondrial properties and genetic studies manipulating respiratory processes. We showcase the importance of efficient ATP generation, dampened reactive oxygen species and mitochondrial osmolytes for salinity tolerance in plants.
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Affiliation(s)
- Richard P Jacoby
- ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, M316, The University of Western Australia, Crawley, WA 6009, Australia
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199
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Cao J, Huang J, Yang Y, Hu X. Analyses of the oligopeptide transporter gene family in poplar and grape. BMC Genomics 2011; 12:465. [PMID: 21943393 PMCID: PMC3188535 DOI: 10.1186/1471-2164-12-465] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Accepted: 09/26/2011] [Indexed: 11/12/2022] Open
Abstract
Background Oligopeptide transporters (OPTs) are a group of membrane-localized proteins that have a broad range of substrate transport capabilities and that are thought to contribute to many biological processes. The OPT proteins belong to a small gene family in plants, which includes about 25 members in Arabidopsis and rice. However, no comprehensive study incorporating phylogeny, chromosomal location, gene structure, expression profiling, functional divergence and selective pressure analysis has been reported thus far for Populus and Vitis. Results In the present study, a comprehensive analysis of the OPT gene family in Populus (P. trichocarpa) and Vitis (V. vinifera) was performed. A total of 20 and 18 full-length OPT genes have been identified in Populus and Vitis, respectively. Phylogenetic analyses indicate that these OPT genes consist of two classes that can be further subdivided into 11 groups. Gene structures are considerably conserved among the groups. The distribution of OPT genes was found to be non-random across chromosomes. A high proportion of the genes are preferentially clustered, indicating that tandem duplications may have contributed significantly to the expansion of the OPT gene family. Expression patterns based on our analyses of microarray data suggest that many OPT genes may be important in stress response and functional development of plants. Further analyses of functional divergence and adaptive evolution show that, while purifying selection may have been the main force driving the evolution of the OPTs, some of critical sites responsible for the functional divergence may have been under positive selection. Conclusions Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the Populus and Vitis OPT gene family and of the function and evolution of the OPT gene family in higher plants.
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Affiliation(s)
- Jun Cao
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Institute of Tibet Plateau Research at Kunming, Chinese Academy of Sciences, Kunming, 650204, China
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200
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The effect of scale on gene expression: commercial versus laboratory wine fermentations. Appl Microbiol Biotechnol 2011; 93:1207-19. [PMID: 21931974 DOI: 10.1007/s00253-011-3564-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 08/10/2011] [Accepted: 08/29/2011] [Indexed: 10/17/2022]
Abstract
Molecular and cellular processes that are responsible for industrially relevant phenotypes of fermenting microorganisms are a central focus of biotechnological research. Such research intends to generate insights and solutions for fermentation-based industries with regards to issues such as improving product yield or the quality of the final fermentation product. For logistical reasons, and to ensure data reproducibility, such research is mostly carried out in defined or synthetic media and in small-scale fermentation vessels. Two questions are frequently raised regarding the applicability of this approach to solve problems experienced in industrial fermentations: (1) Is synthetic medium a sufficiently accurate approximation of the generally more complex natural (and frequently highly variable) substrates that are employed in most fermentation-based industries, and (2) can results obtained in small-scale laboratory fermentations be extrapolated to large-scale industrial environments? Here, we address the second question through a comparative transcriptomic approach by assessing the response of an industrial wine yeast strain fermenting a natural grape juice in small-scale laboratory and large-scale industrial conditions. In yeast, transcriptome analysis is arguably the best available tool to holistically assess the physiological state of a population and its response to changing environmental conditions. The data suggest that scale does indeed impact on some environmental parameters such as oxygen availability. However, the data show that small-scale fermentations nevertheless accurately reflect general molecular processes and adaptations during large-scale fermentation and that extrapolation of laboratory datasets to real industrial processes can be justified.
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