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Somers J, Nelms B. The sporophyte-to-gametophyte transition: The haploid generation comes of age. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102416. [PMID: 37441836 DOI: 10.1016/j.pbi.2023.102416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/02/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023]
Abstract
Flowering plants alternate between two multicellular generations: the diploid sporophyte and haploid gametophyte. Despite its small size, the gametophyte has significant impacts on plant genetics, evolution, and breeding. Each male pollen grain and female embryo sac is a multicellular organism with independent gene expression, a functioning metabolism, and specialized cell types. In this review, we describe recent progress in understanding the process in which the haploid genome takes over expression from its diploid parent - the sporophyte-to-gametophyte transition. The focus is on pollen, but similar concepts may also apply to the female gametophyte. Technological advances in single-cell genomics offer the opportunity to characterize haploid gene expression in unprecedented detail, positioning the field to make rapid progress.
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Affiliation(s)
- Julian Somers
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Brad Nelms
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
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2
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Pedroletti L, Moseler A, Meyer AJ. Assembly, transfer, and fate of mitochondrial iron-sulfur clusters. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3328-3344. [PMID: 36846908 DOI: 10.1093/jxb/erad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/13/2023] [Indexed: 06/08/2023]
Abstract
Since the discovery of an autonomous iron-sulfur cluster (Fe-S) assembly machinery in mitochondria, significant efforts to examine the nature of this process have been made. The assembly of Fe-S clusters occurs in two distinct steps with the initial synthesis of [2Fe-2S] clusters by a first machinery followed by a subsequent assembly into [4Fe-4S] clusters by a second machinery. Despite this knowledge, we still have only a rudimentary understanding of how Fe-S clusters are transferred and distributed among their respective apoproteins. In particular, demand created by continuous protein turnover and the sacrificial destruction of clusters for synthesis of biotin and lipoic acid reveal possible bottlenecks in the supply chain of Fe-S clusters. Taking available information from other species into consideration, this review explores the mitochondrial assembly machinery of Arabidopsis and provides current knowledge about the respective transfer steps to apoproteins. Furthermore, this review highlights biotin synthase and lipoyl synthase, which both utilize Fe-S clusters as a sulfur source. After extraction of sulfur atoms from these clusters, the remains of the clusters probably fall apart, releasing sulfide as a highly toxic by-product. Immediate refixation through local cysteine biosynthesis is therefore an essential salvage pathway and emphasizes the physiological need for cysteine biosynthesis in plant mitochondria.
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Affiliation(s)
- Luca Pedroletti
- INRES-Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113 Bonn, Germany
| | - Anna Moseler
- INRES-Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113 Bonn, Germany
| | - Andreas J Meyer
- INRES-Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113 Bonn, Germany
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3
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Robinson R, Sprott D, Couroux P, Routly E, Labbé N, Xing T, Robert LS. The triticale mature pollen and stigma proteomes - assembling the proteins for a productive encounter. J Proteomics 2023; 278:104867. [PMID: 36870675 DOI: 10.1016/j.jprot.2023.104867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023]
Abstract
Triticeae crops are major contributors to global food production and ensuring their capacity to reproduce and generate seeds is critical. However, despite their importance our knowledge of the proteins underlying Triticeae reproduction is severely lacking and this is not only true of pollen and stigma development, but also of their pivotal interaction. When the pollen grain and stigma are brought together they have each accumulated the proteins required for their intended meeting and accordingly studying their mature proteomes is bound to reveal proteins involved in their diverse and complex interactions. Using triticale as a Triticeae representative, gel-free shotgun proteomics was used to identify 11,533 and 2977 mature stigma and pollen proteins respectively. These datasets, by far the largest to date, provide unprecedented insights into the proteins participating in Triticeae pollen and stigma development and interactions. The study of the Triticeae stigma has been particularly neglected. To begin filling this knowledge gap, a developmental iTRAQ analysis was performed revealing 647 proteins displaying differential abundance as the stigma matures in preparation for pollination. An in-depth comparison to an equivalent Brassicaceae analysis divulged both conservation and diversification in the makeup and function of proteins involved in the pollen and stigma encounter. SIGNIFICANCE: Successful pollination brings together the mature pollen and stigma thus initiating an intricate series of molecular processes vital to crop reproduction. In the Triticeae crops (e.g. wheat, barley, rye, triticale) there persists a vast deficit in our knowledge of the proteins involved which needs to be addressed if we are to face the many upcoming challenges to crop production such as those associated with climate change. At maturity, both the pollen and stigma have acquired the protein complement necessary for their forthcoming encounter and investigating their proteomes will inevitably provide unprecedented insights into the proteins enabling their interactions. By combining the analysis of the most comprehensive Triticeae pollen and stigma global proteome datasets to date with developmental iTRAQ investigations, proteins implicated in the different phases of pollen-stigma interaction enabling pollen adhesion, recognition, hydration, germination and tube growth, as well as those underlying stigma development were revealed. Extensive comparisons between equivalent Triticeae and Brassiceae datasets highlighted both the conservation of biological processes in line with the shared goal of activating the pollen grain and promoting pollen tube invasion of the pistil to effect fertilization, as well as the significant distinctions in their proteomes consistent with the considerable differences in their biochemistry, physiology and morphology.
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Affiliation(s)
- Reneé Robinson
- Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada; Carleton University, Department of Biology, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - David Sprott
- Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada
| | - Philippe Couroux
- Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada
| | - Elizabeth Routly
- Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada
| | - Natalie Labbé
- Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada
| | - Tim Xing
- Carleton University, Department of Biology, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Laurian S Robert
- Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada.
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4
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Nogués I, Sekula B, Angelaccio S, Grzechowiak M, Tramonti A, Contestabile R, Ruszkowski M. Arabidopsis thaliana serine hydroxymethyltransferases: functions, structures, and perspectives. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 187:37-49. [PMID: 35947902 DOI: 10.1016/j.plaphy.2022.07.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/12/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Serine hydroxymethyltransferase (SHM) is one of the hallmarks of one-carbon metabolism. In plants, isoforms of SHM participate in photorespiration and/or transfer the one-carbon unit from L-serine to tetrahydrofolate (THF), hence producing 5,10-CH2-THF that is needed, e.g., for biosynthesis of methionine, thymidylate, and purines. These links highlight the importance of SHM activity in DNA biogenesis, its epigenetic methylations, and in stress responses. Plant genomes encode several SHM isoforms that localize to cytosol, mitochondria, plastids, and nucleus. In this work, we present a thorough functional and structural characterization of all seven SHM isoforms from Arabidopsis thaliana (AtSHM1-7). In particular, we analyzed tissue-specific expression profiles of the AtSHM genes. We also compared catalytic properties of the active AtSHM1-4 in terms of catalytic efficiency in both directions and inhibition by the THF substrate. Despite numerous attempts to rescue the SHM activity of AtSHM5-7, we failed, which points towards different physiological functions of these isoforms. Comparative analysis of experimental and predicted three-dimensional structures of AtSHM1-7 proteins indicated differences in regions that surround the entrance to the active site cavity.
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Affiliation(s)
- Isabel Nogués
- Research Institute on Terrestrial Ecosystems, Italian National Research Council, Monterotondo Scalo, Rome, Italy
| | - Bartosz Sekula
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL, USA; Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Lodz, Poland
| | - Sebastiana Angelaccio
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Marta Grzechowiak
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Angela Tramonti
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Roberto Contestabile
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Milosz Ruszkowski
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL, USA; Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
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5
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Qi X, Guo S, Wang D, Zhong Y, Chen M, Chen C, Cheng D, Liu Z, An T, Li J, Jiao Y, Wang Y, Liu J, Zhang Y, Chen S, Liu C. ZmCOI2a and ZmCOI2b redundantly regulate anther dehiscence and gametophytic male fertility in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:849-862. [PMID: 35167149 DOI: 10.1111/tpj.15708] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
In higher plants, the generation and release of viable pollen from anthers is vital for double fertilization and the initiation of seed development. Thus, the characterization of genes related to pollen development and anther dehiscence in plants is of great significance. The F-box protein COI1 plays a crucial role in the jasmonate (JA) signaling pathway and interacts with many JAZ family proteins in the presence of jasmonoyl-isoleucine (JA-Ile) or coronatine (COR). The mutation of AtCOI1 in Arabidopsis leads to defective anther dehiscence and male sterility (MS), although COI has not been shown to affect fertility in Zea mays (maize). Here we identified two genes, ZmCOI2a and ZmCOI2b, that redundantly regulate gametophytic male fertility. Both ZmCOI2a and ZmCOI2b are highly homologous and constitutively expressed in all tissues tested. Subcellular localization revealed that ZmCOI2a and ZmCOI2b were located in the nucleus. The coi2a coi2b double mutant, generated by CRISPR/Cas9, had non-dehiscent anthers, delayed anther development and MS. In addition, coi2a coi2b male gametes could not be transmitted to the next generation because of severe defects in pollen germination. The JA content of coi2a coi2b anthers was unaltered compared with those of the wild type, and the exogenous application of JA could not rescue the fertility defects of coi2a coi2b. Transcriptome analysis showed that the expression of genes involving the JA signaling transduction pathway, including ZmJAZ3, ZmJAZ4, ZmJAZ5 and ZmJAZ15, was affected in coi2a coi2b. However, yeast two-hybrid assays showed that ZmJAZs interacted with ZmCOI1s, but not with ZmCOI2s. In conclusion, ZmCOI2a and ZmCOI2b redundantly regulate anther dehiscence and gametophytic male fertility in maize.
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Affiliation(s)
- Xiaolong Qi
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Shuwei Guo
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Dong Wang
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Yu Zhong
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Ming Chen
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Chen Chen
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Dehe Cheng
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Zongkai Liu
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Tai An
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Jinlong Li
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Yanyan Jiao
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Yuwen Wang
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Jinchu Liu
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Yuling Zhang
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Shaojiang Chen
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Chenxu Liu
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
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6
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Li X, Tang C, Li X, Zhu X, Cai Y, Wang P, Zhang S, Wu J. Cellulose accumulation mediated by PbrCSLD5, a cellulose synthase-like protein, results in cessation of pollen tube growth in Pyrus bretschneideri. PHYSIOLOGIA PLANTARUM 2022; 174:e13700. [PMID: 35526262 DOI: 10.1111/ppl.13700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 04/21/2022] [Accepted: 05/05/2022] [Indexed: 06/14/2023]
Abstract
Cellulose, a key component of the cell wall, plays an important role in maintaining the growth of pollen tubes. However, the molecular mechanism of cellulose participating in the cessation of pear pollen tube growth remains unclear. Here, we reported that at 15 h post-cultured (HPC), the slow-growth pear pollen tubes showed thickened cell walls and cellulose accumulation in the inner wall. Transcriptome data and quantitative real-time PCR analysis showed that PbrCSLD5, a cellulose synthesis-like gene, was highly expressed in the 15 HPC pear pollen tubes. Knockdown of PbrCSLD5 caused a decrease in cellulose content in pear pollen tubes. Moreover, PbrCSLD5 overexpression in Arabidopsis resulted in the accumulation of cellulose and disruption of normal pollen tube growth. Transcription factor PbrMADS52 was found to bind to the promoter of PbrCSLD5 and enhanced its expression. Our results suggested that the PbrMADS52-PbrCSLD5 signaling pathway led to increased cellulose content in the pear pollen tube cell wall, thereby inhibiting pollen tube growth. These results provided new insights into the regulation of pollen tube growth.
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Affiliation(s)
- Xian Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Chao Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Hainan Yazhou Bay Seed Lab, Sanya, China
- Sanya Institute of Nanjing Agricultural University, Sanya, China
| | - Xiaoqiang Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xiaoxuan Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Yiling Cai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Peng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Shaoling Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Juyou Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Hainan Yazhou Bay Seed Lab, Sanya, China
- Sanya Institute of Nanjing Agricultural University, Sanya, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
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7
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Chen H, Yang Q, Fu H, Chen K, Zhao S, Zhang C, Cai T, Wang L, Lu W, Dang H, Gao M, Li H, Yuan X, Varshney RK, Zhuang W. Identification of Key Gene Networks and Deciphering Transcriptional Regulators Associated With Peanut Embryo Abortion Mediated by Calcium Deficiency. FRONTIERS IN PLANT SCIENCE 2022; 13:814015. [PMID: 35386666 PMCID: PMC8978587 DOI: 10.3389/fpls.2022.814015] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Peanut embryo development is easily affected by a variety of nutrient elements in the soil, especially the calcium level. Peanut produces abortive embryos in calcium-deficient soil, but underlying mechanism remains unclear. Thus, identifying key transcriptional regulators and their associated regulatory networks promises to contribute to a better understanding of this process. In this study, cellular biology and gene expression analyses were performed to investigate peanut embryo development with the aim to discern the global architecture of gene regulatory networks underlying peanut embryo abortion under calcium deficiency conditions. The endomembrane systems tended to disintegrate, impairing cell growth and starch, protein and lipid body accumulation, resulting in aborted seeds. RNA-seq analysis showed that the gene expression profile in peanut embryos was significantly changed under calcium deficiency. Further analysis indicated that multiple signal pathways were involved in the peanut embryo abortion. Differential expressed genes (DEGs) related to cytoplasmic free Ca2+ were significantly altered. DEGs in plant hormone signaling pathways tended to be associated with increased IAA and ethylene but with decreased ABA, gibberellin, cytokinin, and brassinosteroid levels. Certain vital genes, including apoptosis-inducing factor, WRKYs and ethylene-responsive transcription factors, were up-regulated, while key regulators of embryo development, such as TCP4, WRI1, FUS3, ABI3, and GLK1 were down-regulated. Weighted gene co-expression network analysis (WGCNA) identified 16 significant modules associated with the plant hormone signaling, MAPK signaling, ubiquitin mediated proteolysis, reserve substance biosynthesis and metabolism pathways to decipher regulatory network. The most significant module was darkolivegreen2 and FUS3 (AH06G23930) had the highest connectivity among this module. Importantly, key transcription factors involved in embryogenesis or ovule development including TCP4, GLK1, ABI3, bHLH115, MYC2, etc., were also present in this module and down regulated under calcium deficiency. This study presents the first global view of the gene regulatory network involved in peanut embryo abortion under calcium deficiency conditions and lays foundation for improving peanut tolerances to calcium deficiency by a targeted manipulation of molecular breeding.
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Affiliation(s)
- Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiang Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huiwen Fu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kun Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shanshan Zhao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tiecheng Cai
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lihui Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenzhi Lu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hao Dang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Meijia Gao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Agricultural Biotechnology Center, Center for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Huaqi Li
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Agricultural Biotechnology Center, Center for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Xinyi Yuan
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rajeev K. Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Agricultural Biotechnology Center, Center for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
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8
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Abstract
Flowering plants alternate between multicellular haploid (gametophyte) and diploid (sporophyte) generations. Pollen actively transcribes its haploid genome, providing phenotypic diversity even among pollen grains from a single plant. In this study, we used allele-specific RNA sequencing of single pollen precursors to follow the shift to haploid expression in maize pollen. We observed widespread biallelic expression for 11 days after meiosis, indicating that transcripts synthesized by the diploid sporophyte persist long into the haploid phase. Subsequently, there was a rapid and global conversion to monoallelic expression at pollen mitosis I, driven by active new transcription from the haploid genome. Genes showed evidence of increased purifying selection if they were expressed after (but not before) pollen mitosis I. This work establishes the timing during which haploid selection may act in pollen.
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Affiliation(s)
- Brad Nelms
- Department of Plant Biology, University of Georgia, Athens, GA 30606, USA
| | - Virginia Walbot
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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9
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Chen Y, Zhu W, Shi S, Wu L, Du S, Jin L, Yang K, Zhao W, Yang J, Guo L, Wang Z, Zhang Y. Use of RNAi With OsMYB76R as a Reporter for Candidate Genes Can Efficiently Create and Verify Gametophytic Male Sterility in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:728193. [PMID: 34552609 PMCID: PMC8451479 DOI: 10.3389/fpls.2021.728193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Gametophytic male sterility (GMS) plays an important role in the study of pollen development and seed propagation of recessive nuclear male sterile lines insensitive to the environmental conditions in hybrid rice breeding. Since the inherent phenotypic and genetic characteristics of GMS, it is very difficult to find and identify the GMS mutants. However, due to the abundance of gene transcription data, a large number of pollen-specific genes have been found, and most of them may be associated with GMS. To promote the study of these genes in pollen development and heterosis utilization, in this study, an easy and efficient method of creating and identifying GMS was established using RNAi and OsMYB76R as a reporter. First, the OsC1/OsMYB76 gene involved in anthocyanin synthesis was modified, and we have validated that the modified OsMYB76R is workable as the same as the pre-modified OsMYB76 gene. Then, the ascorbic acid oxidase gene OsPTD1 was downregulated using RNAi, driven by its own promoter that resulted in abnormal pollen tube growth. Finally, the RNAi elements were linked with OsMYB76R and transformed into an osmyb76 mutant, and the distortion of purple color segregation was found in T1 and F1 generations. This indicates that the OsPTD1 GMS was prepared successfully. Compared to current methods, there are several advantages to this method. First, time is saved in material preparation, as one generation less needs to be compared than in the conventional method, and mutation screening can be avoided. In addition, for identification, the cost is lower; PCR, electrophoresis, and other processes are not needed; and no expensive chemicals or instruments are required. Finally, the results are more accurate, with much lower background effects, and no damage to the plant. The result is an easy, efficient, low-cost, and accurate method of preparing and identifying GMS genes.
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Affiliation(s)
- Yun Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Wenping Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Shudan Shi
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Lina Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Shuanglin Du
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Liangshen Jin
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Kuan Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Wenjia Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Jiaxin Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhongwei Wang
- Biotechnology Research Center, Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Yi Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, Kunming, China
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10
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Xu S, Ding Y, Sun J, Zhang Z, Wu Z, Yang T, Shen F, Xue G. A high-quality genome assembly of Jasminum sambac provides insight into floral trait formation and Oleaceae genome evolution. Mol Ecol Resour 2021; 22:724-739. [PMID: 34460989 DOI: 10.1111/1755-0998.13497] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 11/29/2022]
Abstract
As one of the most economically significant Oleaceae family members, Jasminum sambac is renowned for its distinct sweet, heady fragrance. Using Illumina reads, Nanopore long reads, and HiC-sequencing, we efficiently assembled and annotated the J. sambac genome. The high-quality genome assembly consisted of a total of 507 Mb sequence (contig N50 = 17.6 Mb) with 13 pseudomolecules. A total of 21,143 protein-coding genes and 303 Mb repeat sequences were predicted. An ancient whole-genome triplication event at the base of Oleaceae (~66 million years ago [Ma], Late Cretaceous) was identified and this may have contributed to the diversification of the Oleaceae ancestor and its divergence from the Lamiales. Stress-related (e.g., WRKY) and flowering-related (e.g., MADS-box) genes were located in the triplicated regions, suggesting that the polyploidy event might have contributed adaptive potential. Genes related to terpenoid biosynthesis, for example, FTA and TPS, were observed to be duplicated to a great extent in the J. sambac genome, perhaps explaining the strong fragrance of the flowers. Copy number changes in distinct phylogenetic clades of the MADS-box family were observed in J. sambac genome, for example, AGL6- and Mα- were lost and SOC- expanded, features that might underlie the long flowering period of J. sambac. The structural genes implicated in anthocyanin biosynthesis were depleted and this may explain the absence of vivid colours in jasmine. Collectively, assembling the J. sambac genome provides new insights into the genome evolution of the Oleaceae family and provides mechanistic insights into floral properties.
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Affiliation(s)
- Shixiao Xu
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| | - Yongle Ding
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| | - Juntao Sun
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| | - Zhiqiang Zhang
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| | - Zhaoyun Wu
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| | - Tiezhao Yang
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China
| | - Fei Shen
- Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Gang Xue
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
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11
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Przybyla-Toscano J, Christ L, Keech O, Rouhier N. Iron-sulfur proteins in plant mitochondria: roles and maturation. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2014-2044. [PMID: 33301571 DOI: 10.1093/jxb/eraa578] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/05/2020] [Indexed: 05/22/2023]
Abstract
Iron-sulfur (Fe-S) clusters are prosthetic groups ensuring electron transfer reactions, activating substrates for catalytic reactions, providing sulfur atoms for the biosynthesis of vitamins or other cofactors, or having protein-stabilizing effects. Hence, metalloproteins containing these cofactors are essential for numerous and diverse metabolic pathways and cellular processes occurring in the cytoplasm. Mitochondria are organelles where the Fe-S cluster demand is high, notably because the activity of the respiratory chain complexes I, II, and III relies on the correct assembly and functioning of Fe-S proteins. Several other proteins or complexes present in the matrix require Fe-S clusters as well, or depend either on Fe-S proteins such as ferredoxins or on cofactors such as lipoic acid or biotin whose synthesis relies on Fe-S proteins. In this review, we have listed and discussed the Fe-S-dependent enzymes or pathways in plant mitochondria including some potentially novel Fe-S proteins identified based on in silico analysis or on recent evidence obtained in non-plant organisms. We also provide information about recent developments concerning the molecular mechanisms involved in Fe-S cluster synthesis and trafficking steps of these cofactors from maturation factors to client apoproteins.
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Affiliation(s)
- Jonathan Przybyla-Toscano
- Université de Lorraine, INRAE, IAM, Nancy, France
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Loïck Christ
- Université de Lorraine, INRAE, IAM, Nancy, France
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
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12
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Cascallares M, Setzes N, Marchetti F, López GA, Distéfano AM, Cainzos M, Zabaleta E, Pagnussat GC. A Complex Journey: Cell Wall Remodeling, Interactions, and Integrity During Pollen Tube Growth. FRONTIERS IN PLANT SCIENCE 2020; 11:599247. [PMID: 33329663 PMCID: PMC7733995 DOI: 10.3389/fpls.2020.599247] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/02/2020] [Indexed: 05/05/2023]
Abstract
In flowering plants, pollen tubes undergo a journey that starts in the stigma and ends in the ovule with the delivery of the sperm cells to achieve double fertilization. The pollen cell wall plays an essential role to accomplish all the steps required for the successful delivery of the male gametes. This extended path involves female tissue recognition, rapid hydration and germination, polar growth, and a tight regulation of cell wall synthesis and modification, as its properties change not only along the pollen tube but also in response to guidance cues inside the pistil. In this review, we focus on the most recent advances in elucidating the molecular mechanisms involved in the regulation of cell wall synthesis and modification during pollen germination, pollen tube growth, and rupture.
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Affiliation(s)
| | | | | | | | | | | | | | - Gabriela Carolina Pagnussat
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
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13
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Beaudry FE, Rifkin JL, Barrett SC, Wright SI. Evolutionary Genomics of Plant Gametophytic Selection. PLANT COMMUNICATIONS 2020; 1:100115. [PMID: 33367268 PMCID: PMC7748008 DOI: 10.1016/j.xplc.2020.100115] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/17/2020] [Accepted: 10/22/2020] [Indexed: 05/26/2023]
Abstract
It has long been recognized that natural selection during the haploid gametophytic phase of the plant life cycle may have widespread importance for rates of evolution and the maintenance of genetic variation. Recent theoretical advances have further highlighted the significance of gametophytic selection for diverse evolutionary processes. Genomic approaches offer exciting opportunities to address key questions about the extent and effects of gametophytic selection on plant evolution and adaptation. Here, we review the progress and prospects for integrating functional and evolutionary genomics to test theoretical predictions, and to examine the importance of gametophytic selection on genetic diversity and rates of evolution. There is growing evidence that selection during the gametophyte phase of the plant life cycle has important effects on both gene and genome evolution and is likely to have important pleiotropic effects on the sporophyte. We discuss the opportunities to integrate comparative population genomics, genome-wide association studies, and experimental approaches to further distinguish how differential selection in the two phases of the plant life cycle contributes to genetic diversity and adaptive evolution.
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Affiliation(s)
- Felix E.G. Beaudry
- Department of Ecology and Evolutionary Biology, The University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Joanna L. Rifkin
- Department of Ecology and Evolutionary Biology, The University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Spencer C.H. Barrett
- Department of Ecology and Evolutionary Biology, The University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Stephen I. Wright
- Department of Ecology and Evolutionary Biology, The University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
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14
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Lopez-Hernandez F, Tryfona T, Rizza A, Yu XL, Harris MOB, Webb AAR, Kotake T, Dupree P. Calcium Binding by Arabinogalactan Polysaccharides Is Important for Normal Plant Development. THE PLANT CELL 2020; 32:3346-3369. [PMID: 32769130 PMCID: PMC7534474 DOI: 10.1105/tpc.20.00027] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 06/17/2020] [Accepted: 07/31/2020] [Indexed: 05/19/2023]
Abstract
Arabinogalactan proteins (AGPs) are a family of plant extracellular proteoglycans involved in many physiological events. AGPs are often anchored to the extracellular side of the plasma membrane and are highly glycosylated with arabinogalactan (AG) polysaccharides, but the molecular function of this glycosylation remains largely unknown. The β-linked glucuronic acid (GlcA) residues in AG polysaccharides have been shown in vitro to bind to calcium in a pH-dependent manner. Here, we used Arabidopsis (Arabidopsis thaliana) mutants in four AG β-glucuronyltransferases (GlcAT14A, -B, -D, and -E) to understand the role of glucuronidation of AG. AG isolated from glcat14 triple mutants had a strong reduction in glucuronidation. AG from a glcat14a/b/d triple mutant had lower calcium binding capacity in vitro than AG from wild-type plants. Some mutants had multiple developmental defects such as reduced trichome branching. glcat14a/b/e triple mutant plants had severely limited seedling growth and were sterile, and the propagation of calcium waves was perturbed in roots. Several of the developmental phenotypes were suppressed by increasing the calcium concentration in the growth medium. Our results show that AG glucuronidation is crucial for multiple developmental processes in plants and suggest that a function of AGPs might be to bind and release cell-surface apoplastic calcium.
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Affiliation(s)
| | - Theodora Tryfona
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Annalisa Rizza
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Xiaolan L Yu
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Matthew O B Harris
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Alex A R Webb
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Toshihisa Kotake
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
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15
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Adhikari PB, Liu X, Kasahara RD. Fertilization-Defective Gametophytic Mutant Screening: A Novel Approach. FRONTIERS IN PLANT SCIENCE 2020; 11:967. [PMID: 32714355 PMCID: PMC7340155 DOI: 10.3389/fpls.2020.00967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Gametophytic mutants share very small proportion of the total mutants generated by any mutagenic approach; even rarer are the fertilization-defective gametophytic mutants. They require an efficient and targeted strategy instead of 'brute force' screening approach. The classical gametophyte mutant screening method, mainly based on the segregation distortion, can distinguish gametophytic mutants from the others. However, the mutants pooled after the screening constitute both fertilization-defective and developmental-defective gametophytic mutants. Until recently, there has not been any straightforward way to screen the former from the latter. Additionally, most of the mutations affecting both gametes are lost during the screening process. The novel gametophyte screening approach tends to circumvent those shortcomings. This review discusses on the classical approach of gametophytic mutant screening and focuses on the novel approach on distinguishing fertilization-/developmental-defective gametophytic mutants (both male and female). It offers an empirical basis of screening such mutants by taking in the consideration of earlier studies on fertilization failure, initiation of seed coat formation, and fertilization recovery system in plants.
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Affiliation(s)
- Prakash Babu Adhikari
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Horticultural Plant Biology and Metabolomics Center (HBMC), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoyan Liu
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Horticultural Plant Biology and Metabolomics Center (HBMC), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ryushiro D. Kasahara
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Horticultural Plant Biology and Metabolomics Center (HBMC), Fujian Agriculture and Forestry University, Fuzhou, China
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16
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Meinke DW. Genome-wide identification of EMBRYO-DEFECTIVE (EMB) genes required for growth and development in Arabidopsis. THE NEW PHYTOLOGIST 2020; 226:306-325. [PMID: 31334862 DOI: 10.1111/nph.16071] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/10/2019] [Indexed: 05/20/2023]
Abstract
With the emergence of high-throughput methods in plant biology, the importance of long-term projects characterized by incremental advances involving multiple laboratories can sometimes be overlooked. Here, I highlight my 40-year effort to isolate and characterize the most common class of mutants encountered in Arabidopsis (Arabidopsis thaliana): those defective in embryo development. I present an updated dataset of 510 EMBRYO-DEFECTIVE (EMB) genes identified throughout the Arabidopsis community; include important details on 2200 emb mutants and 241 pigment-defective embryo (pde) mutants analyzed in my laboratory; provide curated datasets with key features and publication links for each EMB gene identified; revisit past estimates of 500-1000 total EMB genes in Arabidopsis; document 83 double mutant combinations reported to disrupt embryo development; emphasize the importance of following established nomenclature guidelines and acknowledging allele history in research publications; and consider how best to extend community-based curation and screening efforts to approach saturation for this diverse class of mutants in the future. Continued advances in identifying EMB genes and characterizing their loss-of-function mutant alleles are needed to understand genotype-to-phenotype relationships in Arabidopsis on a broad scale, and to document the contributions of large numbers of essential genes to plant growth and development.
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Affiliation(s)
- David W Meinke
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK, 74078, USA
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17
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Zhang L, Jia X, Zhao J, Hasi A, Niu Y. Molecular characterisation and expression analysis of NAC transcription factor genes in wild Medicago falcata under abiotic stresses. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:327-341. [PMID: 32092285 DOI: 10.1071/fp19199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/19/2019] [Indexed: 06/10/2023]
Abstract
The No apical meristem-Arabidopsis transcription activation factor-Cup-shaped cotyledon (NAC) proteins play vital roles in plant development processes and responses to abiotic stress. In this study, 146 unigenes were identified as NAC genes from wild Medicago falcata L. by RNA sequencing. Among these were 30 full-length NACs, which, except for MfNAC63, MfNAC64 and MfNAC91, contained a complete DNA-binding domain and a variable transcriptional activation region. Sequence analyses of MfNACs along with their Arabidopsis thaliana (L.) Heynh. counterparts allowed these proteins to be phylogenetically classified into nine groups. MfNAC35, MfNAC88, MfNAC79, MfNAC26 and MfNAC95 were found to be stress-responsive genes. The eight MfNAC genes that were chosen for further analysis had different expression abilities in the leaves, stems and roots of M. falcata. Additionally, their expression levels were regulated by salinity, drought and cold stress, and ABA. This study will be useful for understanding the roles of MfNACs in wild M. falcata and could provide important information for the selection of candidate genes associated with stress tolerance.
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Affiliation(s)
- Liquan Zhang
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, P.R. China; and State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, P.R.China; and Corresponding authors. Emails: ;
| | - Xuhui Jia
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, P.R. China
| | - Jingwei Zhao
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, P.R. China
| | - Agula Hasi
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, P.R. China
| | - Yiding Niu
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, P.R. China; and State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, P.R.China; and Corresponding authors. Emails: ;
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18
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Devani RS, Chirmade T, Sinha S, Bendahmane A, Dholakia BB, Banerjee AK, Banerjee J. Flower bud proteome reveals modulation of sex-biased proteins potentially associated with sex expression and modification in dioecious Coccinia grandis. BMC PLANT BIOLOGY 2019; 19:330. [PMID: 31337343 PMCID: PMC6651928 DOI: 10.1186/s12870-019-1937-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/11/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND Dioecy is an important sexual system wherein, male and female flowers are borne on separate unisexual plants. Knowledge of sex-related differences can enhance our understanding in molecular and developmental processes leading to unisexual flower development. Coccinia grandis is a dioecious species belonging to Cucurbitaceae, a family well-known for diverse sexual forms. Male and female plants have 22A + XY and 22A + XX chromosomes, respectively. Previously, we have reported a gynomonoecious form (22A + XX) of C. grandis bearing morphologically hermaphrodite flowers (GyM-H) and female flowers (GyM-F). Also, we have showed that foliar spray of AgNO3 on female plant induces morphologically hermaphrodite bud development (Ag-H) despite the absence of Y-chromosome. RESULTS To identify sex-related differences, total proteomes from male, female, GyM-H and Ag-H flower buds at early and middle stages of development were analysed by label-free proteomics. Protein search against the cucumber protein sequences (Phytozome) as well as in silico translated C. grandis flower bud transcriptome database, resulted in the identification of 2426 and 3385 proteins (FDR ≤ 1%), respectively. The latter database was chosen for further analysis as it led to the detection of higher number of proteins. Identified proteins were annotated using BLAST2GO pipeline. SWATH-MS-based comparative abundance analysis between Female_Early_vs_Male_Early, Ag_Early_vs_Female_Early, GyM-H_Middle_vs_Male_Middle and Ag_Middle_vs_ Male_Middle led to the identification of 650, 1108, 905 and 805 differentially expressed proteins, respectively, at fold change ≥1.5 and P ≤ 0.05. Ethylene biosynthesis-related candidates as highlighted in protein interaction network were upregulated in female buds compared to male buds. AgNO3 treatment on female plant induced proteins related to pollen development in Ag-H buds. Additionally, a few proteins governing pollen germination and tube growth were highly enriched in male buds compared to Ag-H and GyM-H buds. CONCLUSION Overall, current proteomic analysis provides insights in the identification of key proteins governing dioecy and unisexual flower development in cucurbitaceae, the second largest horticultural family in terms of economic importance. Also, our results suggest that the ethylene-mediated stamen inhibition might be conserved in dioecious C. grandis similar to its monoecious cucurbit relatives. Further, male-biased proteins associated with pollen germination and tube growth identified here can help in understanding pollen fertility.
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Affiliation(s)
- Ravi Suresh Devani
- Biology Division, Indian Institute of Science Education and Research (IISER), Pune, 411008 India
- IPS2, INRA, CNRS, University Paris Sud, University of Evry, University of Paris Diderot, University of Paris Saclay, Batiment 630, 91405 Orsay, France
| | - Tejas Chirmade
- Biochemical Science Division National Chemical laboratory (CSIR-NCL), Pune, 411008 India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Sangram Sinha
- Department of Botany, Tripura University, Suryamaninagar, Tripura 799022 India
| | - Abdelhafid Bendahmane
- IPS2, INRA, CNRS, University Paris Sud, University of Evry, University of Paris Diderot, University of Paris Saclay, Batiment 630, 91405 Orsay, France
| | - Bhushan B. Dholakia
- Biology Division, Indian Institute of Science Education and Research (IISER), Pune, 411008 India
- Biochemical Science Division National Chemical laboratory (CSIR-NCL), Pune, 411008 India
- Department of Molecular Biology & Bioinformatics, Tripura University, Suryamaninagar, Tripura 799022 India
| | - Anjan Kumar Banerjee
- Biology Division, Indian Institute of Science Education and Research (IISER), Pune, 411008 India
| | - Jayeeta Banerjee
- Biology Division, Indian Institute of Science Education and Research (IISER), Pune, 411008 India
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19
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Tunsagool P, Jutidamrongphan W, Phaonakrop N, Jaresitthikunchai J, Roytrakul S, Leelasuphakul W. Insights into stress responses in mandarins triggered by Bacillus subtilis cyclic lipopeptides and exogenous plant hormones upon Penicillium digitatum infection. PLANT CELL REPORTS 2019; 38:559-575. [PMID: 30715581 DOI: 10.1007/s00299-019-02386-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/25/2019] [Indexed: 05/11/2023]
Abstract
Bacillus subtilis CLP extract activates defense gene expression and increases the unique protein production involving in pathways of ISR, SAR, ubiquitin-proteasome system, and glycolysis for stress responses in flavedo tissues. Cyclic lipopeptides (CLPs) of Bacillus subtilis ABS-S14 had ability to activate plant defensive pathways, increase resistance and control green mold rot caused by Penicillium digitatum in mandarin fruit. The current study investigated transcriptional and proteomic data to highlight the unique induction effect of CLPs produced by B. subtilis ABS-S14 on the defense mechanism of mandarins in response to P. digitatum attack, and their differences from those following the exogenous plant hormone application. The proteomic patterns of the flavedo tissues as affected by Bacillus CLP extract, salicylic acid (SA), methyl jasmonate (MeJA), and ethephon (Et) were explored. qPCR analysis revealed the great effects of CLP extract in enhancing the transcription of PAL, ACS1, GLU, POD, and PR1. Tryptic peptides by LC-MS analysis between treatments with and without fungal infection were compared. B. subtilis CLP extract empowered the plant's immune response to wound stress by the significant production of calmodulin-binding receptor-like cytoplasmic kinase 2, molybdenum cofactor sulfurase, and NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase. Ubiquitin carrier protein abundance was developed only in the treated flavedo with CLP extract coupled with P. digitatum infection. The gene expression and overall proteome findings involving pathways of ubiquitin proteasome system, ISR, SAR, and energy production provide a new insight into the molecular mechanisms of the antagonist B. subtilis ABS-S14 inducing resistance against green mold in mandarins.
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Affiliation(s)
- Paiboon Tunsagool
- Department of Biochemistry, Prince of Songkla University, Songkhla, 90112, Thailand
| | | | - Narumon Phaonakrop
- Proteomics Research Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Thailand Science Park (TSP), Pathum Thani, 12120, Thailand
| | - Janthima Jaresitthikunchai
- Proteomics Research Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Thailand Science Park (TSP), Pathum Thani, 12120, Thailand
| | - Sittiruk Roytrakul
- Proteomics Research Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Thailand Science Park (TSP), Pathum Thani, 12120, Thailand
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Shen X, Xu L, Liu Y, Dong H, Zhou D, Zhang Y, Lin S, Cao J, Huang L. Comparative transcriptome analysis and ChIP-sequencing reveals stage-specific gene expression and regulation profiles associated with pollen wall formation in Brassica rapa. BMC Genomics 2019; 20:264. [PMID: 30943898 PMCID: PMC6446297 DOI: 10.1186/s12864-019-5637-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 03/24/2019] [Indexed: 12/05/2022] Open
Abstract
Background Genic male sterility (GMS) line is an important approach to utilize heterosis in Brassica rapa, one of the most widely cultivated vegetable crops in Northeast Asia. However, the molecular genetic mechanisms of GMS remain to be largely unknown. Results Detailed phenotypic observation of ‘Bcajh97-01A/B’, a B. rapa genic male sterile AB line in this study revealed that the aberrant meiotic cytokinesis and premature tapetal programmed cell death occurring in the sterile line ultimately resulted in microspore degeneration and pollen wall defect. Further gene expression profile of the sterile and fertile floral buds of ‘Bcajh97-01A/B’ at five typical developmental stages during pollen development supported the result of phenotypic observation and identified stage-specific genes associated with the main events associated with pollen wall development, including tapetum development or functioning, callose metabolism, pollen exine formation and cell wall modification. Additionally, by using ChIP-sequencing, the genomic and gene-level distribution of trimethylated histone H3 lysine 4 (H3K4) and H3K27 were mapped on the fertile floral buds, and a great deal of pollen development-associated genes that were covalently modified by H3K4me3 and H3K27me3 were identified. Conclusions Our study provids a deeper understanding into the gene expression and regulation network during pollen development and pollen wall formation in B. rapa, and enabled the identification of a set of candidate genes for further functional annotation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5637-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiuping Shen
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.,Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture / Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Liai Xu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.,Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture / Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Yanhong Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.,Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture / Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Heng Dong
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.,Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture / Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Dong Zhou
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.,Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture / Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Yuzhi Zhang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.,Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture / Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Sue Lin
- Institute of Life Sciences, Wenzhou University, Wenzhou, 325000, China
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.,Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture / Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China. .,Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture / Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China.
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HSFA2 Functions in the Physiological Adaptation of Undifferentiated Plant Cells to Spaceflight. Int J Mol Sci 2019; 20:ijms20020390. [PMID: 30658467 PMCID: PMC6359015 DOI: 10.3390/ijms20020390] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/29/2018] [Accepted: 01/11/2019] [Indexed: 11/16/2022] Open
Abstract
Heat Shock Factor A2 (HsfA2) is part of the Heat Shock Factor (HSF) network, and plays an essential role beyond heat shock in environmental stress responses and cellular homeostatic control. Arabidopsis thaliana cell cultures derived from wild type (WT) ecotype Col-0 and a knockout line deficient in the gene encoding HSFA2 (HSFA2 KO) were grown aboard the International Space Station (ISS) to ascertain whether the HSF network functions in the adaptation to the novel environment of spaceflight. Microarray gene expression data were analyzed using a two-part comparative approach. First, genes differentially expressed between the two environments (spaceflight to ground) were identified within the same genotype, which represented physiological adaptation to spaceflight. Second, gene expression profiles were compared between the two genotypes (HSFA2 KO to WT) within the same environment, which defined genes uniquely required by each genotype on the ground and in spaceflight-adapted states. Results showed that the endoplasmic reticulum (ER) stress and unfolded protein response (UPR) define the HSFA2 KO cells' physiological state irrespective of the environment, and likely resulted from a deficiency in the chaperone-mediated protein folding machinery in the mutant. Results further suggested that additional to its universal stress response role, HsfA2 also has specific roles in the physiological adaptation to spaceflight through cell wall remodeling, signal perception and transduction, and starch biosynthesis. Disabling HsfA2 altered the physiological state of the cells, and impacted the mechanisms induced to adapt to spaceflight, and identified HsfA2-dependent genes that are important to the adaption of wild type cells to spaceflight. Collectively these data indicate a non-thermal role for the HSF network in spaceflight adaptation.
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Dehors J, Mareck A, Kiefer-Meyer MC, Menu-Bouaouiche L, Lehner A, Mollet JC. Evolution of Cell Wall Polymers in Tip-Growing Land Plant Gametophytes: Composition, Distribution, Functional Aspects and Their Remodeling. FRONTIERS IN PLANT SCIENCE 2019; 10:441. [PMID: 31057570 PMCID: PMC6482432 DOI: 10.3389/fpls.2019.00441] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/22/2019] [Indexed: 05/22/2023]
Abstract
During evolution of land plants, the first colonizing species presented leafy-dominant gametophytes, found in non-vascular plants (bryophytes). Today, bryophytes include liverworts, mosses, and hornworts. In the first seedless vascular plants (lycophytes), the sporophytic stage of life started to be predominant. In the seed producing plants, gymnosperms and angiosperms , the gametophytic stage is restricted to reproduction. In mosses and ferns, the haploid spores germinate and form a protonema, which develops into a leafy gametophyte producing rhizoids for anchorage, water and nutrient uptakes. The basal gymnosperms (cycads and Ginkgo) reproduce by zooidogamy. Their pollen grains develop a multi-branched pollen tube that penetrates the nucellus and releases flagellated sperm cells that swim to the egg cell. The pollen grain of other gymnosperms (conifers and gnetophytes) as well as angiosperms germinates and produces a pollen tube that directly delivers the sperm cells to the ovule (siphonogamy). These different gametophytes, which are short or long-lived structures, share a common tip-growing mode of cell expansion. Tip-growth requires a massive cell wall deposition to promote cell elongation, but also a tight spatial and temporal control of the cell wall remodeling in order to modulate the mechanical properties of the cell wall. The growth rate of these cells is very variable depending on the structure and the species, ranging from very slow (protonemata, rhizoids, and some gymnosperm pollen tubes), to a slow to fast-growth in other gymnosperms and angiosperms. In addition, the structural diversity of the female counterparts in angiosperms (dry, semi-dry vs wet stigmas, short vs long, solid vs hollow styles) will impact the speed and efficiency of sperm delivery. As the evolution and diversity of the cell wall polysaccharides accompanied the diversification of cell wall structural proteins and remodeling enzymes, this review focuses on our current knowledge on the biochemistry, the distribution and remodeling of the main cell wall polymers (including cellulose, hemicelluloses, pectins, callose, arabinogalactan-proteins and extensins), during the tip-expansion of gametophytes from bryophytes, pteridophytes (lycophytes and monilophytes), gymnosperms and the monocot and eudicot angiosperms.
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23
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Forsthoefel NR, Klag KA, McNichol SR, Arnold CE, Vernon CR, Wood WW, Vernon DM. Arabidopsis PIRL6 Is Essential for Male and Female Gametogenesis and Is Regulated by Alternative Splicing. PLANT PHYSIOLOGY 2018; 178:1154-1169. [PMID: 30206104 PMCID: PMC6236607 DOI: 10.1104/pp.18.00329] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/29/2018] [Indexed: 05/07/2023]
Abstract
Plant intracellular Ras-group leucine-rich repeat (LRR) proteins (PIRLs) are related to Ras-interacting animal LRR proteins that participate in developmental cell signaling. Systematic knockout analysis has implicated some members of the Arabidopsis (Arabidopsis thaliana) PIRL family in pollen development. However, for PIRL6, no bona fide knockout alleles have been recovered, suggesting that it may have an essential function in both male and female gametophytes. To test this hypothesis, we investigated PIRL6 expression and induced knockdown by RNA interference. Knockdown triggered defects in gametogenesis, resulting in abnormal pollen and early developmental arrest in the embryo sac. Consistent with this, PIRL6 was expressed in gametophytes: functional transcripts were detected in wild-type flowers but not in sporocyteless (spl) mutant flowers, which do not produce gametophytes. A genomic PIRL6-GFP fusion construct confirmed expression in both pollen and the embryo sac. Interestingly, PIRL6 is part of a convergent overlapping gene pair, a scenario associated with an increased likelihood of alternative splicing. We detected multiple alternative PIRL6 mRNAs in vegetative organs and spl mutant flowers, tissues that lacked the functionally spliced transcript. cDNA sequencing revealed that all contained intron sequences and premature termination codons. These alternative mRNAs accumulated in the nonsense-mediated decay mutant upf3, indicating that they are normally subjected to degradation. Together, these results demonstrate that PIRL6 is required in both male and female gametogenesis and suggest that sporophytic expression is negatively regulated by unproductive alternative splicing. This posttranscriptional mechanism may function to minimize PIRL6 protein expression in sporophyte tissues while allowing the overlapping adjacent gene to remain widely transcribed.
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Affiliation(s)
- Nancy R Forsthoefel
- Program in Biochemistry, Biophysics, and Molecular Biology, Whitman College, Walla Walla, Washington 99362
| | - Kendra A Klag
- Program in Biochemistry, Biophysics, and Molecular Biology, Whitman College, Walla Walla, Washington 99362
| | - Savannah R McNichol
- Program in Biochemistry, Biophysics, and Molecular Biology, Whitman College, Walla Walla, Washington 99362
| | - Claire E Arnold
- Program in Biochemistry, Biophysics, and Molecular Biology, Whitman College, Walla Walla, Washington 99362
| | - Corina R Vernon
- Program in Biochemistry, Biophysics, and Molecular Biology, Whitman College, Walla Walla, Washington 99362
| | - Whitney W Wood
- Program in Biochemistry, Biophysics, and Molecular Biology, Whitman College, Walla Walla, Washington 99362
| | - Daniel M Vernon
- Program in Biochemistry, Biophysics, and Molecular Biology, Whitman College, Walla Walla, Washington 99362
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Huang L, Dong H, Zhou D, Li M, Liu Y, Zhang F, Feng Y, Yu D, Lin S, Cao J. Systematic identification of long non-coding RNAs during pollen development and fertilization in Brassica rapa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:203-222. [PMID: 29975432 DOI: 10.1111/tpj.14016] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/18/2018] [Accepted: 06/26/2018] [Indexed: 05/21/2023]
Abstract
The importance of long non-coding RNAs (lncRNAs) in plant development has been established, but a systematic analysis of lncRNAs expressed during pollen development and fertilization has been elusive. We performed a time series of RNA-seq experiments at five developmental stages during pollen development and three different time points after pollination in Brassica rapa and identified 12 051 putative lncRNAs. A comprehensive view of dynamic lncRNA expression networks underpinning pollen development and fertilization was provided. B. rapa lncRNAs share many common characteristics of lncRNAs: relatively short length, low expression but specific in narrow time windows, and low evolutionary conservation. Gene modules and key lncRNAs regulating reproductive development such as exine formation were uncovered. Forty-seven cis-acting lncRNAs and 451 trans-acting lncRNAs were revealed to be highly coexpressed with their target protein-coding genes. Of particular importance are the discoveries of 14 lncRNAs that were highly coexpressed with 10 function-known pollen-associated coding genes. Fifteen lncRNAs were predicted as endogenous target mimics for 13 miRNAs, and two lncRNAs were proved to be functional target mimics for miR160 after experimental verification and shown to function in pollen development. Our study provides the systematic identification of lncRNAs during pollen development and fertilization in B. rapa and forms the foundation for future genetic, genomic, and evolutionary studies.
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Affiliation(s)
- Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Heng Dong
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Dong Zhou
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Ming Li
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Yanhong Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Fang Zhang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Yaoyao Feng
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Dongliang Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Sue Lin
- Institute of Life Sciences, Wenzhou University, Wenzhou, 325000, China
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
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25
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Chen L, Ding X, Zhang H, He T, Li Y, Wang T, Li X, Jin L, Song Q, Yang S, Gai J. Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing. BMC Genomics 2018; 19:663. [PMID: 30208848 PMCID: PMC6134632 DOI: 10.1186/s12864-018-5054-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 09/03/2018] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Cytoplasmic male sterility (CMS) is a natural phenomenon of pollen abortion caused by the interaction between cytoplasmic genes and nuclear genes. CMS is a simple and effective pollination control system, and plays an important role in crop heterosis utilization. Circular RNAs (circRNAs) are a vital type of non-coding RNAs, which play crucial roles in microRNAs (miRNAs) function and post-transcription control. To explore the expression profile and possible functions of circRNAs in the soybean CMS line NJCMS1A and its maintainer NJCMS1B, high-throughput deep sequencing coupled with RNase R enrichment strategy was conducted. RESULTS CircRNA libraries were constructed from flower buds of NJCMS1A and its maintainer NJCMS1B with three biological replicates. A total of 2867 circRNAs were identified, with 1009 circRNAs differentially expressed between NJCMS1A and NJCMS1B based on analysis of high-throughput sequencing. Of the 12 randomly selected circRNAs with different expression levels, 10 showed consistent expression patterns based on high-throughput sequencing and quantitative real-time PCR analyses. Tissue specific expression patterns were also verified with two circRNAs by quantitative real-time PCR. Most parental genes of differentially expressed circRNAs were mainly involved in biological processes such as metabolic process, biological regulation, and reproductive process. Moreover, 83 miRNAs were predicted from the differentially expressed circRNAs, some of which were strongly related to pollen development and male fertility; The functions of miRNA targets were analyzed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and the target mRNAs were significantly enriched in signal transduction and programmed cell death. Furthermore, a total of 165 soybean circRNAs were predicted to contain at least one internal ribosome entry site (IRES) element and an open reading frame, indicating their potential to encode polypeptides or proteins. CONCLUSIONS Our study indicated that the circRNAs might participate in the regulation of flower and pollen development, which could provide a new insight into the molecular mechanisms of CMS in soybean.
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Affiliation(s)
- Linfeng Chen
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xianlong Ding
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Hao Zhang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Tingting He
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yanwei Li
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Tanliu Wang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xiaoqiang Li
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Ling Jin
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, USDA-ARS, Beltsville, MD 20705 USA
| | - Shouping Yang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Junyi Gai
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
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Singh MK, Jürgens G. Specificity of plant membrane trafficking - ARFs, regulators and coat proteins. Semin Cell Dev Biol 2017; 80:85-93. [PMID: 29024759 DOI: 10.1016/j.semcdb.2017.10.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 09/29/2017] [Accepted: 10/09/2017] [Indexed: 11/27/2022]
Abstract
Approximately one-third of all eukaryotic proteins are delivered to their destination by trafficking within the endomembrane system. Such cargo proteins are incorporated into forming membrane vesicles on donor compartments and delivered to acceptor compartments by vesicle fusion. How cargo proteins are sorted into forming vesicles is still largely unknown. Here we review the roles of small GTPases of the ARF/SAR1 family, their regulators designated ARF guanine-nucleotide exchange factors (ARF-GEFs) and ARF GTPase-activating proteins (ARF-GAPs) as well as coat protein complexes during membrane vesicle formation. Although conserved across eukaryotes, these four functional groups of proteins display plant-specific modifications in composition, structure and function.
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Affiliation(s)
- Manoj K Singh
- Centre for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Gerd Jürgens
- Centre for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany.
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Competitive Ability of Maize Pollen Grains Requires Paralogous Serine Threonine Protein Kinases STK1 and STK2. Genetics 2017; 207:1361-1370. [PMID: 28986443 DOI: 10.1534/genetics.117.300358] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/03/2017] [Indexed: 11/18/2022] Open
Abstract
serine threonine kinase1 (stk1) and serine threonine kinase2 (stk2) are closely related maize paralogous genes predicted to encode serine/threonine protein kinases. Pollen mutated in stk1 or stk2 competes poorly with normal pollen, pointing to a defect in pollen tube germination or growth. Both genes are expressed in pollen, but not in most other tissues. In germination media, STK1 and STK2 fluorescent fusion proteins localize to the plasma membrane of the vegetative cell. RNA-seq experiments identified 534 differentially expressed genes in stk1 mutant pollen relative to wild type. Gene ontology (GO) molecular functional analysis uncovered several differentially expressed genes with putative ribosome initiation and elongation functions, suggesting that stk1 might affect ribosome function. Of the two paralogs, stk1 may play a more important role in pollen development than stk2, as stk2 mutations have a smaller pollen transmission effect. However, stk2 does act as an enhancer of stk1 because the double mutant combination is only infrequently pollen-transmitted in double heterozygotes. We conclude that the stk paralogs play an essential role in pollen development.
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Dissecting Pistil Responses to Incompatible and Compatible Pollen in Self-Incompatibility Brassica oleracea Using Comparative Proteomics. Protein J 2017; 36:123-137. [PMID: 28299594 DOI: 10.1007/s10930-017-9697-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Angiosperms have developed self-incompatibility (SI) systems to reject self-pollen, thereby promoting outcrossing. The Brassicaceae belongs to typical sporophytic system, having a single S-locus controlled SI response, and was chosen as a model system to study SI-related intercellular signal transduction. In this regard, the downstream factor of EXO70A1 was unknown. Here, protein two-dimensional electrophoresis (2-DE) method and coupled with matrix-assisted laser desorption ionization/time of flight of flight mass spectrometry (MALDI-TOF -MS) and peptide mass fingerprinting (PMF) was used to further explore the mechanism of SI responses in Brassica oleracea L. var. capitata L. at protein level. To further confirm the time point of protein profile change, total proteins were collected from B. oleracea pistils at 0 min, 1 h, and 2 h after self-pollination. In total 902, 1088 and 1023 protein spots were separated in 0 min, 1 h and 2 h 2-DE maps, respectively. Our analyses of self-pollination profiles indicated that proteins mainly changed at 1 h post-pollination in B. oleracea. Moreover, 1077 protein spots were separated in cross-pollinated 1 h (CP) pistil 2-DE map. MALDI-TOF-MS and PMF successfully identified 34 differentially-expressed proteins (DEPs) in SP and CP 1 h 2-DE maps. Gene ontology and KEGG analysis revealed an array of proteins grouped in the following categories: stress and defense response (35%), protein metabolism (18%), carbohydrate and energy metabolism (12%), regulation of translation (9%), pollen tube development (12%), transport (9%) and cytoskeletal (6%). Sets of DEPs identified specifically in SP or only up-regulated expressed in CP pistils were chosen for funther investigating in floral organs and during the process of self- and cross-pollination. The function of these DEPs in terms of their potential involvement in SI in B. oleracea is discussed.
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Abstract
Flowering plants, like placental mammals, have an extensive maternal contribution toward progeny development. Plants are distinguished from animals by a genetically active haploid phase of growth and development between meiosis and fertilization, called the gametophyte. Flowering plants are further distinguished by the process of double fertilization that produces sister progeny, the endosperm and the embryo, of the seed. Because of this, there is substantial gene expression in the female gametophyte that contributes to the regulation of growth and development of the seed. A primary function of the endosperm is to provide growth support to its sister embryo. Several mutations in Zea mays subsp. mays have been identified that affect the contribution of the mother gametophyte to the seed. The majority affect both the endosperm and the embryo, although some embryo-specific effects have been observed. Many alter the pattern of expression of a marker for the basal endosperm transfer layer, a tissue that transports nutrients from the mother plant to the developing seed. Many of them cause abnormal development of the female gametophyte prior to fertilization, revealing potential cellular mechanisms of maternal control of seed development. These effects include reduced central cell size, abnormal architecture of the central cell, abnormal numbers and morphology of the antipodal cells, and abnormal egg cell morphology. These mutants provide insight into the logic of seed development, including necessary features of the gametes and supporting cells prior to fertilization, and set up future studies on the mechanisms regulating maternal contributions to the seed.
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30
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Wu FY, Tang CY, Guo YM, Yang MK, Yang RW, Lu GH, Yang YH. Comparison of miRNAs and Their Targets in Seed Development between Two Maize Inbred Lines by High-Throughput Sequencing and Degradome Analysis. PLoS One 2016; 11:e0159810. [PMID: 27463682 PMCID: PMC4962988 DOI: 10.1371/journal.pone.0159810] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/10/2016] [Indexed: 11/21/2022] Open
Abstract
MicroRNAs (miRNAs) play an important role in plant growth, development, and response to environment. For identifying and comparing miRNAs and their targets in seed development between two maize inbred lines (i.e. PH6WC and PH4CV), two sRNAs and two degradome libraries were constructed. Through high-throughput sequencing and miRNA identification, 55 conserved and 24 novel unique miRNA sequences were identified in two sRNA libraries; moreover, through degradome sequencing and analysis, 137 target transcripts corresponding to 38 unique miRNA sequences were identified in two degradome libraries. Subsequently, 16 significantly differentially expressed miRNA sequences were verified by qRT-PCR, in which 9 verified sequences obviously target 30 transcripts mainly involved with regulation in flowering and development in embryo. Therefore, the results suggested that some miRNAs (e.g. miR156, miR171, miR396 and miR444) related reproductive development might differentially express in seed development between the PH6WC and PH4CV maize inbred lines in this present study.
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Affiliation(s)
- Feng-Yao Wu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Cheng-Yi Tang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- * E-mail: (YY); (CT); (GL)
| | - Yu-Min Guo
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Min-Kai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Rong-Wu Yang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Gui-Hua Lu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- * E-mail: (YY); (CT); (GL)
| | - Yong-Hua Yang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- * E-mail: (YY); (CT); (GL)
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Abstract
The genetic regulation of cell patterning within plant gametophytes remains poorly understood. Now, two new studies in the liverwort Marchantia polymorpha shed light on the conserved function of an RKD transcription factor as a key regulator of egg cell fate in the land plant lineage.
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Affiliation(s)
- Leonor C Boavida
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Jörg D Becker
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal.
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32
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Lampugnani ER, Ho YY, Moller IE, Koh PL, Golz JF, Bacic A, Newbigin E. A Glycosyltransferase from Nicotiana alata Pollen Mediates Synthesis of a Linear (1,5)-α-L-Arabinan When Expressed in Arabidopsis. PLANT PHYSIOLOGY 2016; 170:1962-74. [PMID: 26850276 PMCID: PMC4825119 DOI: 10.1104/pp.15.02005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 02/04/2016] [Indexed: 05/09/2023]
Abstract
The walls of Nicotiana alata pollen tubes contain a linear arabinan composed of (1,5)-α-linked arabinofuranose residues. Although generally found as a side chain on the backbone of the pectic polysaccharide rhamnogalacturonan I, the arabinan in N. alata pollen tubes is considered free, as there is no detectable rhamnogalacturonan I in these walls. Carbohydrate-specific antibodies detected arabinan epitopes at the tip and along the shank of N. alata pollen tubes that are predominantly part of the primary layer of the bilayered wall. A sequence related to ARABINAN DEFICIENT1 (AtARAD1), a presumed arabinan arabinosyltransferase from Arabidopsis (Arabidopsis thaliana), was identified by searching an N alata pollen transcriptome. Transcripts for this ARAD1-like sequence, which we have named N. alata ARABINAN DEFICIENT-LIKE1 (NaARADL1), accumulate in various tissues, most abundantly in the pollen grain and tube, and encode a protein that is a type II membrane protein with its catalytic carboxyl terminus located in the Golgi lumen. The NaARADL1 protein can form homodimers when transiently expressed in Nicotiana benthamiana leaves and heterodimers when coexpressed with AtARAD1 The expression of NaARADL1 in Arabidopsis led to plants with more arabinan in their walls and that also exuded a guttation fluid rich in arabinan. Chemical and enzymatic characterization of the guttation fluid showed that a soluble, linear α-(1,5)-arabinan was the most abundant polymer present. These results are consistent with NaARADL1 having an arabinan (1,5)-α-arabinosyltransferase activity.
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Affiliation(s)
- Edwin R Lampugnani
- Plant Cell Biology Research Centre, School of BioSciences (E.R.L., Y.Y.H., I.E.M., P.-L.K., A.B., E.N.), and School of BioSciences (J.F.G.), University of Melbourne, Melbourne, Victoria, 3010 Australia; andAustralian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (E.R.L., Y.Y.H., I.E.M., A.B.)
| | - Yin Ying Ho
- Plant Cell Biology Research Centre, School of BioSciences (E.R.L., Y.Y.H., I.E.M., P.-L.K., A.B., E.N.), and School of BioSciences (J.F.G.), University of Melbourne, Melbourne, Victoria, 3010 Australia; andAustralian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (E.R.L., Y.Y.H., I.E.M., A.B.)
| | - Isabel E Moller
- Plant Cell Biology Research Centre, School of BioSciences (E.R.L., Y.Y.H., I.E.M., P.-L.K., A.B., E.N.), and School of BioSciences (J.F.G.), University of Melbourne, Melbourne, Victoria, 3010 Australia; andAustralian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (E.R.L., Y.Y.H., I.E.M., A.B.)
| | - Poh-Ling Koh
- Plant Cell Biology Research Centre, School of BioSciences (E.R.L., Y.Y.H., I.E.M., P.-L.K., A.B., E.N.), and School of BioSciences (J.F.G.), University of Melbourne, Melbourne, Victoria, 3010 Australia; andAustralian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (E.R.L., Y.Y.H., I.E.M., A.B.)
| | - John F Golz
- Plant Cell Biology Research Centre, School of BioSciences (E.R.L., Y.Y.H., I.E.M., P.-L.K., A.B., E.N.), and School of BioSciences (J.F.G.), University of Melbourne, Melbourne, Victoria, 3010 Australia; andAustralian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (E.R.L., Y.Y.H., I.E.M., A.B.)
| | - Antony Bacic
- Plant Cell Biology Research Centre, School of BioSciences (E.R.L., Y.Y.H., I.E.M., P.-L.K., A.B., E.N.), and School of BioSciences (J.F.G.), University of Melbourne, Melbourne, Victoria, 3010 Australia; andAustralian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (E.R.L., Y.Y.H., I.E.M., A.B.)
| | - Ed Newbigin
- Plant Cell Biology Research Centre, School of BioSciences (E.R.L., Y.Y.H., I.E.M., P.-L.K., A.B., E.N.), and School of BioSciences (J.F.G.), University of Melbourne, Melbourne, Victoria, 3010 Australia; andAustralian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (E.R.L., Y.Y.H., I.E.M., A.B.)
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33
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Yue Y, Peng H, Sun J, Yang Z, Yang H, Liu G, Hu H. Characterization of two CYP77 gene family members related to development of ornamental organs in petunia. J Genet 2016; 95:177-81. [PMID: 27019447 DOI: 10.1007/s12041-015-0603-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuanzheng Yue
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of
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34
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Madison SL, Buchanan ML, Glass JD, McClain TF, Park E, Nebenführ A. Class XI Myosins Move Specific Organelles in Pollen Tubes and Are Required for Normal Fertility and Pollen Tube Growth in Arabidopsis. PLANT PHYSIOLOGY 2015; 169:1946-60. [PMID: 26358416 PMCID: PMC4634091 DOI: 10.1104/pp.15.01161] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/10/2015] [Indexed: 05/18/2023]
Abstract
Pollen tube growth is an essential aspect of plant reproduction because it is the mechanism through which nonmotile sperm cells are delivered to ovules, thus allowing fertilization to occur. A pollen tube is a single cell that only grows at the tip, and this tip growth has been shown to depend on actin filaments. It is generally assumed that myosin-driven movements along these actin filaments are required to sustain the high growth rates of pollen tubes. We tested this conjecture by examining seed set, pollen fitness, and pollen tube growth for knockout mutants of five of the six myosin XI genes expressed in pollen of Arabidopsis (Arabidopsis thaliana). Single mutants had little or no reduction in overall fertility, whereas double mutants of highly similar pollen myosins had greater defects in pollen tube growth. In particular, myo11c1 myo11c2 pollen tubes grew more slowly than wild-type pollen tubes, which resulted in reduced fitness compared with the wild type and a drastic reduction in seed set. Golgi stack and peroxisome movements were also significantly reduced, and actin filaments were less organized in myo11c1 myo11c2 pollen tubes. Interestingly, the movement of yellow fluorescent protein-RabA4d-labeled vesicles and their accumulation at pollen tube tips were not affected in the myo11c1 myo11c2 double mutant, demonstrating functional specialization among myosin isoforms. We conclude that class XI myosins are required for organelle motility, actin organization, and optimal growth of pollen tubes.
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Affiliation(s)
- Stephanie L Madison
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840
| | - Matthew L Buchanan
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840
| | - Jeremiah D Glass
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840
| | - Tarah F McClain
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840
| | - Eunsook Park
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840
| | - Andreas Nebenführ
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840
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35
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Hayashi-Tsugane M, Maekawa M, Tsugane K. A gain-of-function Bushy dwarf tiller 1 mutation in rice microRNA gene miR156d caused by insertion of the DNA transposon nDart1. Sci Rep 2015; 5:14357. [PMID: 26403301 PMCID: PMC4585910 DOI: 10.1038/srep14357] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/26/2015] [Indexed: 12/22/2022] Open
Abstract
A non-autonomous DNA transposon in rice, nDart1, is actively transposed in the presence of an autonomous element, aDart1, under natural conditions. The nDart1-promoted gene tagging line was developed using the endogenous nDart1/aDart1 system to generate various rice mutants effectively. While the dominant mutants were occasionally isolated from the tagging line, it was unclear what causes dominant mutations. A semidominant mutant, Bushy dwarf tiller1 (Bdt1), which has the valuable agronomic traits of multiple tillering and dwarfism, was obtained from the tagging line. Bdt1 mutant carried a newly inserted nDart1 at 38-bp upstream of transcription initiation site of a non-protein-coding gene, miR156d. This insertion caused an upstream shift of the miR156d transcription initiation site and, consequently, increased the functional transcripts producing mature microRNAs. These results indicate that the total amount of miR156d is controlled not only by transcript quantity but also by transcript quality. Furthermore, transgenic lines introduced an miR156d fragment that flanked the nDart1 sequence at the 5′ region, suggesting that insertion of nDart1 in the gene promoter region enhances gene expression as a cis-element. This study demonstrates the ability of nDart1 to produce gain-of-function mutants as well as further insights into the function of transposable elements in genome evolution.
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Affiliation(s)
| | - Masahiko Maekawa
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Kazuo Tsugane
- National Institute for Basic Biology, Okazaki 444-8585, Japan.,The Graduate University for Advanced Studies [SOKENDAI], Okazaki 444-8585, Japan
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36
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Dong X, Nou IS, Yi H, Hur Y. Suppression of ASKβ (AtSK32), a Clade III Arabidopsis GSK3, Leads to the Pollen Defect during Late Pollen Development. Mol Cells 2015; 38:506-17. [PMID: 25997736 PMCID: PMC4469908 DOI: 10.14348/molcells.2015.2323] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/23/2015] [Accepted: 02/23/2015] [Indexed: 11/27/2022] Open
Abstract
Arabidopsis Shaggy-like protein kinases (ASKs) are Arabidopsis thaliana homologs of glycogen synthase kinase 3/SHAGGY-like kinases (GSK3/SGG), which are comprised of 10 genes with diverse functions. To dissect the function of ASKβ (AtSK32), ASKβ antisense transgenic plants were generated, revealing the effects of ASKβ down-regulation in Arabidopsis. Suppression of ASKβ expression specifically interfered with pollen development and fertility without altering the plants' vegetative phenotypes, which differed from the phenotypes reported for Arabidopsis plants defective in other ASK members. The strength of these phenotypes showed an inverse correlation with the expression levels of ASKβ and its co-expressed genes. In the aborted pollen of ASKβ antisense plants, loss of nuclei and shrunken cytoplasm began to appear at the bicellular stage of microgametogenesis. The in silico analysis of promoter and the expression characteristics implicate ASKβ is associated with the expression of genes known to be involved in sperm cell differentiation. We speculate that ASKβ indirectly affects the transcription of its co-expressed genes through the phosphorylation of its target proteins during late pollen development.
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Affiliation(s)
- Xiangshu Dong
- Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 305-764,
Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Jeonnam 540-742,
Korea
| | - Hankuil Yi
- Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 305-764,
Korea
| | - Yoonkang Hur
- Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 305-764,
Korea
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37
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Lafleur E, Kapfer C, Joly V, Liu Y, Tebbji F, Daigle C, Gray-Mitsumune M, Cappadocia M, Nantel A, Matton DP. The FRK1 mitogen-activated protein kinase kinase kinase (MAPKKK) from Solanum chacoense is involved in embryo sac and pollen development. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1833-43. [PMID: 25576576 PMCID: PMC4378624 DOI: 10.1093/jxb/eru524] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The fertilization-related kinase 1 (ScFRK1), a nuclear-localized mitogen-activated protein kinase kinase kinase (MAPKKK) from the wild potato species Solanum chacoense, belongs to a small group of pMEKKs that do not possess an extended N- or C-terminal regulatory domain. Initially selected based on its highly specific expression profile following fertilization, in situ expression analyses revealed that the ScFRK1 gene is also expressed early on during female gametophyte development in the integument and megaspore mother cell and, later, in the synergid and egg cells of the embryo sac. ScFRK1 mRNAs are also detected in pollen mother cells. Transgenic plants with lower or barely detectable levels of ScFRK1 mRNAs lead to the production of small fruits with severely reduced seed set, resulting from a concomitant decline in the number of normal embryo sacs produced. Megagametogenesis and microgametogenesis were affected, as megaspores did not progress beyond the functional megaspore (FG1) stage and the microspore collapsed around the first pollen mitosis. As for other mutants that affect embryo sac development, pollen tube guidance was severely affected in the ScFRK1 transgenic lines. Gametophyte to sporophyte communication was also affected, as observed from a marked change in the transcriptomic profiles of the sporophytic tissues of the ovule. The ScFRK1 MAPKKK is thus involved in a signalling cascade that regulates both male and female gamete development.
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Affiliation(s)
- Edith Lafleur
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Christelle Kapfer
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Valentin Joly
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Yang Liu
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Faiza Tebbji
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC H1X 2B2, Canada Institut de recherche en biotechnologie, Conseil national de recherches du Canada, 6100 Avenue Royalmount, Montréal, QC H4P 2R2, Canada
| | - Caroline Daigle
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Madoka Gray-Mitsumune
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Mario Cappadocia
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - André Nantel
- Institut de recherche en biotechnologie, Conseil national de recherches du Canada, 6100 Avenue Royalmount, Montréal, QC H4P 2R2, Canada
| | - Daniel P Matton
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
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38
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Chettoor AM, Givan SA, Cole RA, Coker CT, Unger-Wallace E, Vejlupkova Z, Vollbrecht E, Fowler JE, Evans MM. Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes. Genome Biol 2014; 15:414. [PMID: 25084966 PMCID: PMC4309534 DOI: 10.1186/s13059-014-0414-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 07/15/2014] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Plant gametophytes play central roles in sexual reproduction. A hallmark of the plant life cycle is that gene expression is required in the haploid gametophytes. Consequently, many mutant phenotypes are expressed in this phase. RESULTS We perform a quantitative RNA-seq analysis of embryo sacs, comparator ovules with the embryo sacs removed, mature pollen, and seedlings to assist the identification of gametophyte functions in maize. Expression levels were determined for annotated genes in both gametophytes, and novel transcripts were identified from de novo assembly of RNA-seq reads. Transposon-related transcripts are present in high levels in both gametophytes, suggesting a connection between gamete production and transposon expression in maize not previously identified in any female gametophytes. Two classes of small signaling proteins and several transcription factor gene families are enriched in gametophyte transcriptomes. Expression patterns of maize genes with duplicates in subgenome 1 and subgenome 2 indicate that pollen-expressed genes in subgenome 2 are retained at a higher rate than subgenome 2 genes with other expression patterns. Analysis of available insertion mutant collections shows a statistically significant deficit in insertions in gametophyte-expressed genes. CONCLUSIONS This analysis, the first RNA-seq study to compare both gametophytes in a monocot, identifies maize gametophyte functions, gametophyte expression of transposon-related sequences, and unannotated, novel transcripts. Reduced recovery of mutations in gametophyte-expressed genes is supporting evidence for their function in the gametophytes. Expression patterns of extant, duplicated maize genes reveals that selective pressures based on male gametophytic function have likely had a disproportionate effect on plant genomes.
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39
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Ma X, Sukiran NL, Ma H, Su Z. Moderate drought causes dramatic floral transcriptomic reprogramming to ensure successful reproductive development in Arabidopsis. BMC PLANT BIOLOGY 2014; 14:164. [PMID: 24928551 PMCID: PMC4067085 DOI: 10.1186/1471-2229-14-164] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 05/29/2014] [Indexed: 05/02/2023]
Abstract
BACKGROUND Drought is a major constraint that leads to extensive losses to agricultural yield worldwide. The potential yield is largely determined during inflorescence development. However, to date, most investigations on plant response to drought have focused on vegetative development. This study describes the morphological changes of reproductive development and the comparison of transcriptomes under various drought conditions. RESULTS The plants grown were studied under two drought conditions: minimum for successful reproduction (45-50% soil water content, moderate drought, MD) and for survival (30-35%, severe drought, SD). MD plants can produce similar number of siliques on the main stem and similar number of seeds per silique comparing with well-water plants. The situation of SD plants was much worse than MD plants. The transcriptomes of inflorescences were further investigated at molecular level using microarrays. Our results showed more than four thousands genes with differential expression under severe drought and less than two thousand changed under moderate drought condition (with 2-fold change and q-value < 0.01). We found a group of genes with increased expression as the drought became more severe, suggesting putative adaptation to the dehydration. Interestingly, we also identified genes with alteration only under the moderate but not the severe drought condition, indicating the existence of distinct sets of genes responsive to different levels of water availability. Further cis-element analyses of the putative regulatory sequences provided more information about the underlying mechanisms for reproductive responses to drought, suggesting possible novel candidate genes that protect those developing flowers under drought stress. CONCLUSIONS Different pathways may be activated in response to moderate and severe drought in reproductive tissues, potentially helping plant to maximize its yield and balance the resource consumption between vegetative and reproductive development under dehydration stresses.
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Affiliation(s)
- Xuan Ma
- Department of Biology and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA 16802, USA
- Intercollege Graduate Program in Cell and Developmental Biology, the Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Noor Liyana Sukiran
- Department of Biology and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA 16802, USA
- Current address: School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Institute of Plant Biology, Institute of Genetics, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Zhao Su
- Department of Biology and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA 16802, USA
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40
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Guan Y, Lu J, Xu J, McClure B, Zhang S. Two Mitogen-Activated Protein Kinases, MPK3 and MPK6, Are Required for Funicular Guidance of Pollen Tubes in Arabidopsis. PLANT PHYSIOLOGY 2014; 165:528-533. [PMID: 24717717 PMCID: PMC4044831 DOI: 10.1104/pp.113.231274] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Double fertilization in flowering plants requires the delivery of two immotile sperm cells to the female gametes by a pollen tube, which perceives guidance cues, modifies its tip growth direction, and eventually enters the micropyle of the ovule. In spite of the recent progress, so far, little is known about the signaling events in pollen tubes in response to the guidance cues. Here, we show that MPK3 and MPK6, two Arabidopsis (Arabidopsis thaliana) mitogen-activated protein kinases, mediate the guidance response in pollen tubes. Genetic analysis revealed that mpk3 mpk6 double mutant pollen has reduced transmission. However, direct observation of mpk3 mpk6 mutant pollen phenotype was hampered by the embryo lethality of double homozygous mpk3-/- mpk6-/- plants. Utilizing a fluorescent reporter-tagged complementation method, we showed that the mpk3 mpk6 mutant pollen had normal pollen tube growth but impaired pollen tube guidance. In vivo pollination assays revealed that the mpk3 mpk6 mutant pollen tubes were defective in the funicular guidance phase. By contrast, semi-in vitro guidance assay showed that the micropylar guidance of the double mutant pollen tube was normal. Our results provide direct evidence to support that the funicular guidance phase of the pollen tube requires an in vivo signaling mechanism distinct from the micropyle guidance. Moreover, our finding opened up the possibility that the MPK3/MPK6 signaling pathway may link common signaling networks in plant stress response and pollen-pistil interaction.
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Affiliation(s)
- Yuefeng Guan
- Division of Biochemistry, University of Missouri, Columbia, Missouri 65211 (Y.G., B.M., S.Z.);College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China (J.L., J.X.); andShanghai Center for Plant Stress Biology, Shanghai 201602, China (Y.G.)
| | - Jianping Lu
- Division of Biochemistry, University of Missouri, Columbia, Missouri 65211 (Y.G., B.M., S.Z.);College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China (J.L., J.X.); andShanghai Center for Plant Stress Biology, Shanghai 201602, China (Y.G.)
| | - Juan Xu
- Division of Biochemistry, University of Missouri, Columbia, Missouri 65211 (Y.G., B.M., S.Z.);College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China (J.L., J.X.); andShanghai Center for Plant Stress Biology, Shanghai 201602, China (Y.G.)
| | - Bruce McClure
- Division of Biochemistry, University of Missouri, Columbia, Missouri 65211 (Y.G., B.M., S.Z.);College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China (J.L., J.X.); andShanghai Center for Plant Stress Biology, Shanghai 201602, China (Y.G.)
| | - Shuqun Zhang
- Division of Biochemistry, University of Missouri, Columbia, Missouri 65211 (Y.G., B.M., S.Z.);College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China (J.L., J.X.); andShanghai Center for Plant Stress Biology, Shanghai 201602, China (Y.G.)
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Endo S, Shinohara H, Matsubayashi Y, Fukuda H. A Novel Pollen-Pistil Interaction Conferring High-Temperature Tolerance during Reproduction via CLE45 Signaling. Curr Biol 2013; 23:1670-6. [DOI: 10.1016/j.cub.2013.06.060] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 06/05/2013] [Accepted: 06/26/2013] [Indexed: 10/26/2022]
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The Arabidopsis Plant Intracellular Ras-group LRR (PIRL) Family and the Value of Reverse Genetic Analysis for Identifying Genes that Function in Gametophyte Development. PLANTS 2013; 2:507-20. [PMID: 27137390 PMCID: PMC4844374 DOI: 10.3390/plants2030507] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 07/02/2013] [Accepted: 07/24/2013] [Indexed: 12/31/2022]
Abstract
Arabidopsis thaliana has proven a powerful system for developmental genetics, but identification of gametophytic genes with developmental mutants can be complicated by factors such as gametophyte-lethality, functional redundancy, or poor penetrance. These issues are exemplified by the Plant Intracellular Ras-group LRR (PIRL) genes, a family of nine genes encoding a class of leucine-rich repeat proteins structurally related to animal and fungal LRR proteins involved in developmental signaling. Previous analysis of T-DNA insertion mutants showed that two of these genes, PIRL1 and PIRL9, have an essential function in pollen formation but are functionally redundant. Here, we present evidence implicating three more PIRLs in gametophyte development. Scanning electron microscopy revealed that disruption of either PIRL2 or PIRL3 results in a low frequency of pollen morphological abnormalities. In addition, molecular analysis of putative pirl6 insertion mutants indicated that knockout alleles of this gene are not represented in current Arabidopsis mutant populations, suggesting gametophyte lethality may hinder mutant recovery. Consistent with this, available microarray and RNA-seq data have documented strongest PIRL6 expression in developing pollen. Taken together, these results now implicate five PIRLs in gametophyte development. Systematic reverse genetic analysis of this novel LRR family has therefore identified gametophytically active genes that otherwise would likely be missed by forward genetic screens.
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Mollet JC, Leroux C, Dardelle F, Lehner A. Cell Wall Composition, Biosynthesis and Remodeling during Pollen Tube Growth. PLANTS 2013; 2:107-47. [PMID: 27137369 PMCID: PMC4844286 DOI: 10.3390/plants2010107] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/19/2013] [Accepted: 02/19/2013] [Indexed: 01/01/2023]
Abstract
The pollen tube is a fast tip-growing cell carrying the two sperm cells to the ovule allowing the double fertilization process and seed setting. To succeed in this process, the spatial and temporal controls of pollen tube growth within the female organ are critical. It requires a massive cell wall deposition to promote fast pollen tube elongation and a tight control of the cell wall remodeling to modify the mechanical properties. In addition, during its journey, the pollen tube interacts with the pistil, which plays key roles in pollen tube nutrition, guidance and in the rejection of the self-incompatible pollen. This review focuses on our current knowledge in the biochemistry and localization of the main cell wall polymers including pectin, hemicellulose, cellulose and callose from several pollen tube species. Moreover, based on transcriptomic data and functional genomic studies, the possible enzymes involved in the cell wall remodeling during pollen tube growth and their impact on the cell wall mechanics are also described. Finally, mutant analyses have permitted to gain insight in the function of several genes involved in the pollen tube cell wall biosynthesis and their roles in pollen tube growth are further discussed.
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Affiliation(s)
- Jean-Claude Mollet
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, EA4358, IRIB, Normandy University, University of Rouen, 76821 Mont Saint-Aignan, France.
| | - Christelle Leroux
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, EA4358, IRIB, Normandy University, University of Rouen, 76821 Mont Saint-Aignan, France.
| | - Flavien Dardelle
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, EA4358, IRIB, Normandy University, University of Rouen, 76821 Mont Saint-Aignan, France.
| | - Arnaud Lehner
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, EA4358, IRIB, Normandy University, University of Rouen, 76821 Mont Saint-Aignan, France.
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Shi T, Gao Z, Wang L, Zhang Z, Zhuang W, Sun H, Zhong W. Identification of differentially-expressed genes associated with pistil abortion in Japanese apricot by genome-wide transcriptional analysis. PLoS One 2012; 7:e47810. [PMID: 23091648 PMCID: PMC3472986 DOI: 10.1371/journal.pone.0047810] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 09/17/2012] [Indexed: 12/05/2022] Open
Abstract
The phenomenon of pistil abortion widely occurs in Japanese apricot, and imperfect flowers with pistil abortion seriously decrease the yield in production. Although transcriptome analyses have been extensively studied in the past, a systematic study of differential gene expression has not been performed in Japanese apricot. To investigate genes related to the pistil development of Japanese apricot, high-throughput sequencing technology (Illumina) was employed to survey gene expression profiles from perfect and imperfect Japanese apricot flower buds. 3,476,249 and 3,580,677 tags were sequenced from two libraries constructed from perfect and imperfect flower buds of Japanese apricot, respectively. There were 689 significant differentially-expressed genes between the two libraries. GO annotation revealed that highly ranked genes were those implicated in small molecule metabolism, cellular component organisation or biogenesis at the cellular level and fatty acid metabolism. According to the results, we assumed that late embryogenesis abundant protein (LEA), Dicer-like 3 (DCL3) Xyloglucan endotransglucosylase/hydrolase 2 (XTH2), Pectin lyase-like superfamily protein (PPME1), Lipid transfer protein 3 (LTP3), Fatty acid biosynthesis 1 (FAB1) and Fatty acid desaturase 5 (FAD5) might have relationships with the pistil abortion in Japanese apricot. The expression patterns of 36 differentially expressed genes were confirmed by real-time (RT)-PCR. This is the first report of the Illumina RNA-seq technique being used for the analysis of differentially-expressed gene profiles related to pistil abortion that both computationally and experimentally provides valuable information for the further functional characterisation of genes associated with pistil development in woody plants.
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Affiliation(s)
- Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
- * E-mail:
| | - Liangju Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
| | - Zhen Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
| | - Weibing Zhuang
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
| | - Hailong Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
| | - Wenjun Zhong
- College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China
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Nikolovski N, Rubtsov D, Segura MP, Miles GP, Stevens TJ, Dunkley TP, Munro S, Lilley KS, Dupree P. Putative glycosyltransferases and other plant Golgi apparatus proteins are revealed by LOPIT proteomics. PLANT PHYSIOLOGY 2012; 160:1037-51. [PMID: 22923678 PMCID: PMC3461528 DOI: 10.1104/pp.112.204263] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 08/22/2012] [Indexed: 05/18/2023]
Abstract
The Golgi apparatus is the central organelle in the secretory pathway and plays key roles in glycosylation, protein sorting, and secretion in plants. Enzymes involved in the biosynthesis of complex polysaccharides, glycoproteins, and glycolipids are located in this organelle, but the majority of them remain uncharacterized. Here, we studied the Arabidopsis (Arabidopsis thaliana) membrane proteome with a focus on the Golgi apparatus using localization of organelle proteins by isotope tagging. By applying multivariate data analysis to a combined data set of two new and two previously published localization of organelle proteins by isotope tagging experiments, we identified the subcellular localization of 1,110 proteins with high confidence. These include 197 Golgi apparatus proteins, 79 of which have not been localized previously by a high-confidence method, as well as the localization of 304 endoplasmic reticulum and 208 plasma membrane proteins. Comparison of the hydrophobic domains of the localized proteins showed that the single-span transmembrane domains have unique properties in each organelle. Many of the novel Golgi-localized proteins belong to uncharacterized protein families. Structure-based homology analysis identified 12 putative Golgi glycosyltransferase (GT) families that have no functionally characterized members and, therefore, are not yet assigned to a Carbohydrate-Active Enzymes database GT family. The substantial numbers of these putative GTs lead us to estimate that the true number of plant Golgi GTs might be one-third above those currently annotated. Other newly identified proteins are likely to be involved in the transport and interconversion of nucleotide sugar substrates as well as polysaccharide and protein modification.
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Muralla R, Lloyd J, Meinke D. Molecular foundations of reproductive lethality in Arabidopsis thaliana. PLoS One 2011; 6:e28398. [PMID: 22164284 PMCID: PMC3229588 DOI: 10.1371/journal.pone.0028398] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 11/07/2011] [Indexed: 11/23/2022] Open
Abstract
The SeedGenes database (www.seedgenes.org) contains information on more than 400 genes required for embryo development in Arabidopsis. Many of these EMBRYO-DEFECTIVE (EMB) genes encode proteins with an essential function required throughout the life cycle. This raises a fundamental question. Why does elimination of an essential gene in Arabidopsis often result in embryo lethality rather than gametophyte lethality? In other words, how do mutant (emb) gametophytes survive and participate in fertilization when an essential cellular function is disrupted? Furthermore, why do some mutant embryos proceed further in development than others? To address these questions, we first established a curated dataset of genes required for gametophyte development in Arabidopsis based on information extracted from the literature. This provided a basis for comparison with EMB genes obtained from the SeedGenes dataset. We also identified genes that exhibited both embryo and gametophyte defects when disrupted by a loss-of-function mutation. We then evaluated the relationship between mutant phenotype, gene redundancy, mutant allele strength, gene expression pattern, protein function, and intracellular protein localization to determine what factors influence the phenotypes of lethal mutants in Arabidopsis. After removing cases where continued development potentially resulted from gene redundancy or residual function of a weak mutant allele, we identified numerous examples of viable mutant (emb) gametophytes that required further explanation. We propose that the presence of gene products derived from transcription in diploid (heterozygous) sporocytes often enables mutant gametophytes to survive the loss of an essential gene in Arabidopsis. Whether gene disruption results in embryo or gametophyte lethality therefore depends in part on the ability of residual, parental gene products to support gametophyte development. We also highlight here 70 preglobular embryo mutants with a zygotic pattern of inheritance, which provide valuable insights into the maternal-to-zygotic transition in Arabidopsis and the timing of paternal gene activation during embryo development.
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Affiliation(s)
- Rosanna Muralla
- Department of Botany, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Johnny Lloyd
- Department of Botany, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - David Meinke
- Department of Botany, Oklahoma State University, Stillwater, Oklahoma, United States of America
- * E-mail:
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Palanivelu R, Tsukamoto T. Pathfinding in angiosperm reproduction: pollen tube guidance by pistils ensures successful double fertilization. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2011; 1:96-113. [PMID: 23801670 DOI: 10.1002/wdev.6] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Sexual reproduction in flowering plants is unique in multiple ways. Distinct multicellular gametophytes contain either a pair of immotile, haploid male gametes (sperm cells) or a pair of female gametes (haploid egg cell and homodiploid central cell). After pollination, the pollen tube, a cellular extension of the male gametophyte, transports both male gametes at its growing tip and delivers them to the female gametes to affect double fertilization. The pollen tube travels a long path and sustains its growth over a considerable amount of time in the female reproductive organ (pistil) before it reaches the ovule, which houses the female gametophyte. The pistil facilitates the pollen tube's journey by providing multiple, stage-specific, nutritional, and guidance cues along its path. The pollen tube interacts with seven different pistil cell types prior to completing its journey. Consequently, the pollen tube has a dynamic gene expression program allowing it to continuously reset and be receptive to multiple pistil signals as it migrates through the pistil. Here, we review the studies, including several significant recent advances, that led to a better understanding of the multitude of cues generated by the pistil tissues to assist the pollen tube in delivering the sperm cells to the female gametophyte. We also highlight the outstanding questions, draw attention to opportunities created by recent advances and point to approaches that could be undertaken to unravel the molecular mechanisms underlying pollen tube-pistil interactions.
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Bolle C, Schneider A, Leister D. Perspectives on Systematic Analyses of Gene Function in Arabidopsis thaliana: New Tools, Topics and Trends. Curr Genomics 2011; 12:1-14. [PMID: 21886450 PMCID: PMC3129038 DOI: 10.2174/138920211794520187] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 10/28/2010] [Accepted: 11/23/2010] [Indexed: 11/22/2022] Open
Abstract
Since the sequencing of the nuclear genome of Arabidopsis thaliana ten years ago, various large-scale analyses of gene function have been performed in this model species. In particular, the availability of collections of lines harbouring random T-DNA or transposon insertions, which include mutants for almost all of the ~27,000 A. thaliana genes, has been crucial for the success of forward and reverse genetic approaches. In the foreseeable future, genome-wide phenotypic data from mutant analyses will become available for Arabidopsis, and will stimulate a flood of novel in-depth gene-function analyses. In this review, we consider the present status of resources and concepts for systematic studies of gene function in A. thaliana. Current perspectives on the utility of loss-of-function and gain-of-function mutants will be discussed in light of the genetic and functional redundancy of many A. thaliana genes.
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Affiliation(s)
- C Bolle
- Lehrstuhl für Molekularbiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, D-82152 Planegg-Martinsried, Germany
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Narsai R, Law SR, Carrie C, Xu L, Whelan J. In-depth temporal transcriptome profiling reveals a crucial developmental switch with roles for RNA processing and organelle metabolism that are essential for germination in Arabidopsis. PLANT PHYSIOLOGY 2011; 157:1342-62. [PMID: 21908688 PMCID: PMC3252162 DOI: 10.1104/pp.111.183129] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 09/05/2011] [Indexed: 05/20/2023]
Abstract
Germination represents a rapid transition from dormancy to a high level of metabolic activity. In-depth transcriptomic profiling at 10 time points in Arabidopsis (Arabidopsis thaliana), including fresh seed, ripened seed, during stratification, germination, and postgermination per se, revealed specific temporal expression patterns that to our knowledge have not previously been identified. Over 10,000 transcripts were differentially expressed during cold stratification, with subequal numbers up-regulated as down-regulated, revealing an active period in preparing seeds for germination, where transcription and RNA degradation both play important roles in regulating the molecular sequence of events. A previously unidentified transient expression pattern was observed for a group of genes, whereby a significant rise in expression was observed at the end of stratification and significantly lower expression was observed 6 h later. These genes were further defined as germination specific, as they were most highly expressed at this time in germination, in comparison with all developmental tissues in the AtGenExpress data set. Functional analysis of these genes using genetic inactivation revealed that they displayed a significant enrichment for embryo-defective or -arrested phenotype. This group was enriched in genes encoding mitochondrial and nuclear RNA-processing proteins, including more than 45% of all pentatricopeptide domain-containing proteins expressed during germination. The presence of mitochondrial DNA replication factors and RNA-processing functions in this germination-specific subset represents the earliest events in organelle biogenesis, preceding any changes associated with energy metabolism. Green fluorescent protein analysis also confirmed organellar localization for 65 proteins, largely showing germination-specific expression. These results suggest that mitochondrial biogenesis involves a two-step process to produce energetically active organelles: an initial phase at the end of stratification involving mitochondrial DNA synthesis and RNA processing, and a later phase for building the better-known energetic functions. This also suggests that signals with a mitochondrial origin and retrograde signals may be crucial for successful germination.
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Affiliation(s)
- Reena Narsai
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia.
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50
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Alandete-Saez M, Ron M, Leiboff S, McCormick S. Arabidopsis thaliana GEX1 has dual functions in gametophyte development and early embryogenesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 68:620-32. [PMID: 21831199 DOI: 10.1111/j.1365-313x.2011.04713.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
GEX1 is a plasma membrane protein that is conserved among plant species, and has previously been shown to be expressed in sperm cells and some sporophytic tissues. Here we show that GEX1 is also expressed in the embryo sac before cellularization, in the egg cell after cellularization, in the zygote/embryo immediately after fertilization and in the pollen vegetative cell. We functionally characterize GEX1 in Arabidopsis thaliana, and show that it is a versatile protein that performs functions during male and female gametophyte development, and during early embryogenesis. gex1-1/+ plants, which synthesize a truncated GEX1 mRNA encoding a protein lacking the predicted cytoplasmic domain, but still targeted to the plasma membrane, had embryos that arrested before the pre-globular stage. gex1-3/+ plants, carrying a null GEX1 allele, had defects during male and female gametophyte development, and during early embryogenesis. Using an antisense GEX1 transgenic line we demonstrate that the predicted GEX1 extracellular domain is sufficient and necessary for GEX1 function during the development of both gametophytes. The predicted cytoplasmic domain is necessary for correct early embryogenesis and mediates homodimer formation at the plasma membrane. We propose that dimerization of GEX1 in the zygote might be an upstream step in a signaling cascade regulating early embryogenesis.
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Affiliation(s)
- Monica Alandete-Saez
- Plant Gene Expression Center and Department of Plant and Microbial Biology, USDA/ARS-UC-Berkeley, Albany, CA 94710, USA
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