201
|
Li J, Wu Z, Cui L, Zhang T, Guo Q, Xu J, Jia L, Lou Q, Huang S, Li Z, Chen J. Transcriptome comparison of global distinctive features between pollination and parthenocarpic fruit set reveals transcriptional phytohormone cross-talk in cucumber (Cucumis sativus L.). PLANT & CELL PHYSIOLOGY 2014; 55:1325-42. [PMID: 24733865 DOI: 10.1093/pcp/pcu051] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Parthenocarpy is an important trait determining yield and quality of fruit crops. However, the understanding of the mechanisms underlying parthenocarpy induction is limited. Cucumber (Cucumis sativus L.) is abundant in parthenocarpic germplasm resources and is an excellent model organism for parthenocarpy studies. In this study, the transcriptome of cucumber fruits was studied using RNA sequencing (RNA-Seq). Differentially expressed genes (DEGs) of set fruits were compared against aborted fruits. Distinctive features of parthenocarpic and pollinated fruits were revealed by combining the analysis of the transcriptome together with cytomorphological and physiological analysis. Cell division and the transcription of cell division genes were found to be more active in parthenocarpic fruit. The study also indicated that parthenocarpic fruit set is a high sugar-consuming process which is achieved via enhanced carbohydrate degradation through transcription of genes that lead to the breakdown of carbohydrates. Furthermore, the evidence provided by this work supports a hypothesis that parthenocarpic fruit set is induced by mimicking the processes of pollination/fertilization at the transcriptional level, i.e. by performing the same transcriptional patterns of genes inducing pollination and gametophyte development as in pollinated fruit. Based on the RNA-Seq and ovary transient expression results, 14 genes were predicted as putative parthenocarpic genes. The transcription analysis of these candidate genes revealed auxin, cytokinin and gibberellin cross-talk at the transcriptional level during parthenocarpic fruit set.
Collapse
Affiliation(s)
- Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, ChinaThese authors contributed equally to this work
| | - Zhe Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Horticulture, Shanxi Agricultural University, Shanxi 030801, ChinaThese authors contributed equally to this work
| | - Li Cui
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, ChinaThese authors contributed equally to this work
| | - Tinglin Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Qinwei Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Li Jia
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Sanwen Huang
- Key Laboratory of Horticultural Crops Genetic Improvement of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics Technology, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhengguo Li
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
202
|
Morphological and proteomic analysis reveal the role of pistil under pollination in Liriodendron chinense (Hemsl.) Sarg. PLoS One 2014; 9:e99970. [PMID: 24924488 PMCID: PMC4055720 DOI: 10.1371/journal.pone.0099970] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 05/21/2014] [Indexed: 11/19/2022] Open
Abstract
Pollination is an important physiological process during which interaction between pollen and pistil occurs. This interaction could determine whether or not fertilization will occur and hence the ratio of plant seed setting. Liriodendron chinense (Hemsl.) Sarg. (L. chinense) exhibits a distinct phenomenon where seed setting ratio is not more than 10% in natural environment. To explore the origin of this phenomenon, we conducted a comparative morphological and proteomic analysis on L. chinense pistils upon pollination. The morphological analysis showed that pollen grows well in vitro, but much slower on pistil or nutrient medium containing pistil extract. Proteomic analysis showed that 493 proteins had changed the expression after pollination. Among them, 468 and 51 proteins were identified by isobaric tags for relative and absolute quantitation and two-dimensional gel electrophoresis respectively, and 26 proteins were common in the two methods. After proteins functional categorization, 66 differentially expressed proteins that are involved in reproduction process were found. Further analysis showed that among the reproductive process related proteins, protein disulfide-isomerase A6 and four embryo-defective proteins showed closer relations with the low seed setting phenomenon. The results indicated that the element from pistil might be the main reason leading to low seed setting in L. chinense, which will provide new insights in the mechanisms underlying L. chinense reproduction process.
Collapse
|
203
|
Sorin C, Declerck M, Christ A, Blein T, Ma L, Lelandais-Brière C, Njo MF, Beeckman T, Crespi M, Hartmann C. A miR169 isoform regulates specific NF-YA targets and root architecture in Arabidopsis. THE NEW PHYTOLOGIST 2014; 202:1197-1211. [PMID: 24533947 DOI: 10.1111/nph.12735] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 01/21/2014] [Indexed: 05/20/2023]
Abstract
In plants, roots are essential for water and nutrient acquisition. MicroRNAs (miRNAs) regulate their target mRNAs by transcript cleavage and/or inhibition of protein translation and are known as major post-transcriptional regulators of various developmental pathways and stress responses. In Arabidopsis thaliana, four isoforms of miR169 are encoded by 14 different genes and target diverse mRNAs, encoding subunits A of the NF-Y transcription factor complex. These miRNA isoforms and their targets have previously been linked to nutrient signalling in plants. By using mimicry constructs against different isoforms of miR169 and miR-resistant versions of NF-YA genes we analysed the role of specific miR169 isoforms in root growth and branching. We identified a regulatory node involving the particular miR169defg isoform and NF-YA2 and NF-YA10 genes that acts in the control of primary root growth. The specific expression of MIM169defg constructs altered specific cell type numbers and dimensions in the root meristem. Preventing miR169defg-regulation of NF-YA2 indirectly affected laterial root initiation. We also showed that the miR169defg isoform affects NF-YA2 transcripts both at mRNA stability and translation levels. We propose that a specific miR169 isoform and the NF-YA2 target control root architecture in Arabidopsis.
Collapse
Affiliation(s)
- Céline Sorin
- Institut des Sciences du Végétal (ISV), CNRS, UPR2355, Saclay Plant Sciences, F-91198, Gif-sur-Yvette Cedex, France
- Université Paris Diderot, Sorbonne Paris Cité, F-75205, Paris Cedex 13, France
| | - Marie Declerck
- Institut des Sciences du Végétal (ISV), CNRS, UPR2355, Saclay Plant Sciences, F-91198, Gif-sur-Yvette Cedex, France
| | - Aurélie Christ
- Institut des Sciences du Végétal (ISV), CNRS, UPR2355, Saclay Plant Sciences, F-91198, Gif-sur-Yvette Cedex, France
| | - Thomas Blein
- Institut des Sciences du Végétal (ISV), CNRS, UPR2355, Saclay Plant Sciences, F-91198, Gif-sur-Yvette Cedex, France
- INRA, Institut JP Bourgin, Route de Saint-Cyr, 78026, Versailles Cedex, France
| | - Linnan Ma
- Institut des Sciences du Végétal (ISV), CNRS, UPR2355, Saclay Plant Sciences, F-91198, Gif-sur-Yvette Cedex, France
| | - Christine Lelandais-Brière
- Institut des Sciences du Végétal (ISV), CNRS, UPR2355, Saclay Plant Sciences, F-91198, Gif-sur-Yvette Cedex, France
- Université Paris Diderot, Sorbonne Paris Cité, F-75205, Paris Cedex 13, France
| | - Maria Fransiska Njo
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, Technologiepark 927, 9052, Ghent, Belgium
- Department Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, Technologiepark 927, 9052, Ghent, Belgium
- Department Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Martin Crespi
- Institut des Sciences du Végétal (ISV), CNRS, UPR2355, Saclay Plant Sciences, F-91198, Gif-sur-Yvette Cedex, France
| | - Caroline Hartmann
- Institut des Sciences du Végétal (ISV), CNRS, UPR2355, Saclay Plant Sciences, F-91198, Gif-sur-Yvette Cedex, France
- Université Paris Diderot, Sorbonne Paris Cité, F-75205, Paris Cedex 13, France
| |
Collapse
|
204
|
Qin Y, Ma X, Yu G, Wang Q, Wang L, Kong L, Kim W, Wang HW. Evolutionary history of trihelix family and their functional diversification. DNA Res 2014; 21:499-510. [PMID: 24864043 PMCID: PMC4195496 DOI: 10.1093/dnares/dsu016] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
In this study, we carried out an evolutionary, transcriptional, and functional analyses of the trihelix transcription factor family. A total of 319 trihelix members, identified from 11 land plant species, were classified into five clades. The results of phylogeny indicate the binding domains of GT1 and GT2 diverged early in the existence of land plants. Genomic localization revealed that the trihelix family members were highly conserved among cereal species, even though some homeologs generated during the tetraploidy of maize were lost. Three-dimensional structural analyses and an examination of subcellular localization of this family supported the involvement of all five clades in transcriptional regulation. Furthermore, the family members from all clades in sorghum and rice showed a broad and dynamic expression pattern in response to abiotic stresses, indicating regulatory subfunctionalization of their original functions. This finding is further supported by the phenotypes of enhanced tolerance to cold, salt, and drought in transgenic plants overexpressing Sb06g023980 and Sb06g024110. In contrast, few Arobidopsis genes showed inducible expression under abiotic stress conditions, which may indicate a functional shift. Finally, our co-expression analysis points to the involvement of this family in various metabolic processes, implying their further functional divergence.
Collapse
Affiliation(s)
- Yao Qin
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong 271018, People's Republic of China Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-713, Republic of Korea
| | - Xin Ma
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong 271018, People's Republic of China
| | - Guanghui Yu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong 271018, People's Republic of China
| | - Qi Wang
- Agronomy College, Sichuan Agricultural University, No. 211, Huiming Road, Wenjiang Region, Chengdu 611130, PR China
| | - Liang Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong 271018, People's Republic of China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong 271018, People's Republic of China
| | - Wook Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-713, Republic of Korea
| | - Hong Wei Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong 271018, People's Republic of China
| |
Collapse
|
205
|
Paul P, Simm S, Mirus O, Scharf KD, Fragkostefanakis S, Schleiff E. The complexity of vesicle transport factors in plants examined by orthology search. PLoS One 2014; 9:e97745. [PMID: 24844592 PMCID: PMC4028247 DOI: 10.1371/journal.pone.0097745] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 04/24/2014] [Indexed: 11/18/2022] Open
Abstract
Vesicle transport is a central process to ensure protein and lipid distribution in eukaryotic cells. The current knowledge on the molecular components and mechanisms of this process is majorly based on studies in Saccharomyces cerevisiae and Arabidopsis thaliana, which revealed 240 different proteinaceous factors either experimentally proven or predicted to be involved in vesicle transport. In here, we performed an orthologue search using two different algorithms to identify the components of the secretory pathway in yeast and 14 plant genomes by using the 'core-set' of 240 factors as bait. We identified 4021 orthologues and (co-)orthologues in the discussed plant species accounting for components of COP-II, COP-I, Clathrin Coated Vesicles, Retromers and ESCRTs, Rab GTPases, Tethering factors and SNAREs. In plants, we observed a significantly higher number of (co-)orthologues than yeast, while only 8 tethering factors from yeast seem to be absent in the analyzed plant genomes. To link the identified (co-)orthologues to vesicle transport, the domain architecture of the proteins from yeast, genetic model plant A. thaliana and agriculturally relevant crop Solanum lycopersicum has been inspected. For the orthologous groups containing (co-)orthologues from yeast, A. thaliana and S. lycopersicum, we observed the same domain architecture for 79% (416/527) of the (co-)orthologues, which documents a very high conservation of this process. Further, publically available tissue-specific expression profiles for a subset of (co-)orthologues found in A. thaliana and S. lycopersicum suggest that some (co-)orthologues are involved in tissue-specific functions. Inspection of localization of the (co-)orthologues based on available proteome data or localization predictions lead to the assignment of plastid- as well as mitochondrial localized (co-)orthologues of vesicle transport factors and the relevance of this is discussed.
Collapse
Affiliation(s)
- Puneet Paul
- Department of Biosciences Molecular Cell Biology of Plants
| | - Stefan Simm
- Department of Biosciences Molecular Cell Biology of Plants
| | - Oliver Mirus
- Department of Biosciences Molecular Cell Biology of Plants
| | | | | | - Enrico Schleiff
- Department of Biosciences Molecular Cell Biology of Plants
- Cluster of Excellence Frankfurt
- Center of Membrane Proteomics; Goethe University Frankfurt, Frankfurt/Main, Germany
- * E-mail:
| |
Collapse
|
206
|
Wang H, Liu R, Wang J, Wang P, Shen Y, Liu G. The Arabidopsis kinesin gene AtKin-1 plays a role in the nuclear division process during megagametogenesis. PLANT CELL REPORTS 2014; 33:819-828. [PMID: 24667993 DOI: 10.1007/s00299-014-1594-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 01/15/2014] [Accepted: 02/26/2014] [Indexed: 06/03/2023]
Abstract
Atkin - 1 , the only Kinesin-1 member of Arabidopsis thaliana , plays a role during female gametogenesis through regulation of nuclear division cycles. Kinesins are microtubule-dependent motor proteins found in eukaryotic organisms. They constitute a superfamily that can be further classified into at least 14 families. In the Kinesin-1 family, members from animal and fungi play roles in long-distance transport of organelles and vesicles. Although Kinesin-1-like sequences have been identified in higher plants, little is known about their function in plant cells, other than in a recently identified Kinesin-1-like protein in a rice pollen semi-sterile mutant. In this study, the gene encoding the only Kinesin-1 member in Arabidopsis, AtKin-1 was found to be specifically expressed in ovules and anthers. AtKin-1 loss-of-function mutants showed substantially aborted ovules in siliques, and this finding was supported by complementation testing. Reciprocal crossing between mutant and wild-type plants indicated that a defect in AtKin-1 results in partially aborted megagametophytes, with no observable effects on pollen fertility. Further observation of ovule development in the mutant pistils indicated that the enlargement of the megaspore was blocked and nuclear division arrested at the one-nucleate stage during embryo sac formation. Our data suggest that AtKin-1 plays a role in the nuclear division cycles during megagametogenesis.
Collapse
Affiliation(s)
- Haiqing Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, 23 Xinning Road, Xining, 810001, China,
| | | | | | | | | | | |
Collapse
|
207
|
You J, Zong W, Du H, Hu H, Xiong L. A special member of the rice SRO family, OsSRO1c, mediates responses to multiple abiotic stresses through interaction with various transcription factors. PLANT MOLECULAR BIOLOGY 2014; 84:693-705. [PMID: 24337801 DOI: 10.1007/s11103-013-0163-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 12/05/2013] [Indexed: 05/09/2023]
Abstract
SIMILAR TO RCD ONE (SRO) is a plant-specific gene family involved in development and abiotic stress responses. SRO proteins are characterized by containing poly (ADP-ribose) polymerase catalytic (PARP) and C-terminal RCD1-SRO-TAF4 domains, and can be classified into two groups and five subgroups on the basis of their PARP domain. Expression analysis of rice SRO genes in response to various abiotic stresses showed that OsSRO1c, a rice SRO gene which functions downstream of the stress-responsive transcription factor SNAC1, is the major stress-responsive gene in the rice SRO family. The ossro1c-1 mutant showed resistance not only to chloroplastic oxidative stress, but also to apoplastic oxidative stress. However, the ossro1c-1 mutant and artificial microRNA-OsSRO1c transgenic rice were significantly impaired in cold tolerance. When compared with the well-characterized Arabidopsis SRO protein radical-induced cell death 1 (RCD1), OsSRO1c has considerable variation in the protein sequence, and the two genes exhibit different expression profiles under abiotic stresses. Furthermore, ossro1c-1 and rcd1 showed different responses to multiple abiotic stresses. By screening an Arabidopsis transcription factor library, 29 transcription factors interacted with OsSRO1c in yeast, but only two of these transcription factors were reported to interact with RCD1, which may partly explain the different responses of the two mutants under various stresses. The data presented in this report provide important clues for further elucidating the molecular and biochemical mechanisms of OsSRO1c in mediating responses to multiple abiotic stresses.
Collapse
Affiliation(s)
- Jun You
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | | | | | | | | |
Collapse
|
208
|
Fu WQ, Zhao ZG, Ge XH, Ding L, Li ZY. Anatomy and transcript profiling of gynoecium development in female sterile Brassica napus mediated by one alien chromosome from Orychophragmus violaceus. BMC Genomics 2014; 15:61. [PMID: 24456102 PMCID: PMC3930543 DOI: 10.1186/1471-2164-15-61] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 01/21/2014] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The gynoecium is one of the most complex organs of angiosperms specialized for seed production and dispersal, but only several genes important for ovule or embryo sac development were identified by using female sterile mutants. The female sterility in oilseed rape (Brassica napus) was before found to be related with one alien chromosome from another crucifer Orychophragmus violaceus. Herein, the developmental anatomy and comparative transcript profiling (RNA-seq) for the female sterility were performed to reveal the genes and possible metabolic pathways behind the formation of the damaged gynoecium. RESULTS The ovules in the female sterile Brassica napus with two copies of the alien chromosomes (S1) initiated only one short integument primordium which underwent no further development and the female gametophyte development was blocked after the tetrad stage but before megagametogenesis initiation. Using Brassica_ 95k_ unigene as the reference genome, a total of 28,065 and 27,653 unigenes were identified to be transcribed in S1 and donor B. napus (H3), respectively. Further comparison of the transcript abundance between S1 and H3 revealed that 4540 unigenes showed more than two fold expression differences. Gene ontology and pathway enrichment analysis of the Differentially Expressed Genes (DEGs) showed that a number of important genes and metabolism pathways were involved in the development of gynoecium, embryo sac, ovule, integuments as well as the interactions between pollen and pistil. CONCLUSIONS DEGs for the ovule development were detected to function in the metabolism pathways regulating brassinosteroid (BR) biosynthesis, adaxial/abaxial axis specification, auxin transport and signaling. A model was proposed to show the possible roles and interactions of these pathways for the sterile gynoecium development. The results provided new information for the molecular mechanisms behind the gynoecium development at early stage in B. napus.
Collapse
Affiliation(s)
| | | | | | | | - Zai-yun Li
- National Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, P, R, China.
| |
Collapse
|
209
|
Belda-Palazón B, Nohales MA, Rambla JL, Aceña JL, Delgado O, Fustero S, Martínez MC, Granell A, Carbonell J, Ferrando A. Biochemical quantitation of the eIF5A hypusination in Arabidopsis thaliana uncovers ABA-dependent regulation. FRONTIERS IN PLANT SCIENCE 2014; 5:202. [PMID: 24904603 PMCID: PMC4032925 DOI: 10.3389/fpls.2014.00202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 04/24/2014] [Indexed: 05/08/2023]
Abstract
The eukaryotic translation elongation factor eIF5A is the only protein known to contain the unusual amino acid hypusine which is essential for its biological activity. This post-translational modification is achieved by the sequential action of the enzymes deoxyhypusine synthase (DHS) and deoxyhypusine hydroxylase (DOHH). The crucial molecular function of eIF5A during translation has been recently elucidated in yeast and it is expected to be fully conserved in every eukaryotic cell, however the functional description of this pathway in plants is still sparse. The genetic approaches with transgenic plants for either eIF5A overexpression or antisense have revealed some activities related to the control of cell death processes but the molecular details remain to be characterized. One important aspect of fully understanding this pathway is the biochemical description of the hypusine modification system. Here we have used recombinant eIF5A proteins either modified by hypusination or non-modified to establish a bi-dimensional electrophoresis (2D-E) profile for the three eIF5A protein isoforms and their hypusinated or unmodified proteoforms present in Arabidopsis thaliana. The combined use of the recombinant 2D-E profile together with 2D-E/western blot analysis from whole plant extracts has provided a quantitative approach to measure the hypusination status of eIF5A. We have used this information to demonstrate that treatment with the hormone abscisic acid produces an alteration of the hypusine modification system in Arabidopsis thaliana. Overall this study presents the first biochemical description of the post-translational modification of eIF5A by hypusination which will be functionally relevant for future studies related to the characterization of this pathway in Arabidopsis thaliana.
Collapse
Affiliation(s)
- Borja Belda-Palazón
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de ValenciaValencia, Spain
| | - María A. Nohales
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de ValenciaValencia, Spain
| | - José L. Rambla
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de ValenciaValencia, Spain
| | - José L. Aceña
- Centro de Investigación Príncipe FelipeValencia, Spain
| | - Oscar Delgado
- Centro de Investigación Príncipe FelipeValencia, Spain
| | - Santos Fustero
- Centro de Investigación Príncipe FelipeValencia, Spain
- Departamento de Química Orgánica, Universidad de ValenciaValencia, Spain
| | - M. Carmen Martínez
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de BarcelonaBarcelona, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de ValenciaValencia, Spain
| | - Juan Carbonell
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de ValenciaValencia, Spain
| | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de ValenciaValencia, Spain
- *Correspondence: Alejandro Ferrando, Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de Valencia, C/Ingeniero Fausto Elio, s/n, 46022 Valencia, Spain e-mail:
| |
Collapse
|
210
|
Shen Y, Conde e Silva N, Audonnet L, Servet C, Wei W, Zhou DX. Over-expression of histone H3K4 demethylase gene JMJ15 enhances salt tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2014; 5:290. [PMID: 25009544 PMCID: PMC4068201 DOI: 10.3389/fpls.2014.00290] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 06/04/2014] [Indexed: 05/20/2023]
Abstract
Histone H3 lysine 4 trimethylation (H3K4me3) has been shown to be involved in stress-responsive gene expression and gene priming in plants. However, the role of H3K4me3 resetting in the processes is not clear. In this work we studied the expression and function of Arabidopsis H3K4 demethylase gene JMJ15. We show that the expression of JMJ15 was relatively low and was limited to a number of tissues during vegetative growth but was higher in young floral organs. Over-expression of the gene in gain-of-function mutants reduced the plant height with accumulation of lignin in stems, while the loss-of-function mutation did not produce any visible phenotype. The gain-of-function mutants showed enhanced salt tolerance, whereas the loss-of-function mutant was more sensitive to salt compared to the wild type. Transcriptomic analysis revealed that over-expression of JMJ15 down-regulated many genes which are preferentially marked by H3K4me3 and H3K4me2. Many of the down-regulated genes encode transcription regulators involved in stress responses. The data suggest that increased JMJ15 levels may regulate the gene expression program that enhances stress tolerance.
Collapse
Affiliation(s)
- Yuan Shen
- Saclay Plant Science, Institut de Biologie des Plantes, Université Paris-Sud 11Orsay, France
| | - Natalia Conde e Silva
- Saclay Plant Science, Institut de Biologie des Plantes, Université Paris-Sud 11Orsay, France
- UMR 8618, CNRSOrsay, France
| | - Laure Audonnet
- Saclay Plant Science, Institut de Biologie des Plantes, Université Paris-Sud 11Orsay, France
| | | | - Wei Wei
- Interdisciplinary Scientific Research Institute, Jianghan UniversityWuhan, China
| | - Dao-Xiu Zhou
- Saclay Plant Science, Institut de Biologie des Plantes, Université Paris-Sud 11Orsay, France
- UMR 8618, CNRSOrsay, France
- *Correspondence: Dao-Xiu Zhou, Institut de Biologie des Plantes, Université Paris-Sud 11, B630, 91405 Orsay, France e-mail:
| |
Collapse
|
211
|
Galland M, Huguet R, Arc E, Cueff G, Job D, Rajjou L. Dynamic proteomics emphasizes the importance of selective mRNA translation and protein turnover during Arabidopsis seed germination. Mol Cell Proteomics 2014; 13:252-68. [PMID: 24198433 PMCID: PMC3879618 DOI: 10.1074/mcp.m113.032227] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 10/23/2013] [Indexed: 01/02/2023] Open
Abstract
During seed germination, the transition from a quiescent metabolic state in a dry mature seed to a proliferative metabolic state in a vigorous seedling is crucial for plant propagation as well as for optimizing crop yield. This work provides a detailed description of the dynamics of protein synthesis during the time course of germination, demonstrating that mRNA translation is both sequential and selective during this process. The complete inhibition of the germination process in the presence of the translation inhibitor cycloheximide established that mRNA translation is critical for Arabidopsis seed germination. However, the dynamics of protein turnover and the selectivity of protein synthesis (mRNA translation) during Arabidopsis seed germination have not been addressed yet. Based on our detailed knowledge of the Arabidopsis seed proteome, we have deepened our understanding of seed mRNA translation during germination by combining two-dimensional gel-based proteomics with dynamic radiolabeled proteomics using a radiolabeled amino acid precursor, namely [(35)S]-methionine, in order to highlight de novo protein synthesis, stability, and turnover. Our data confirm that during early imbibition, the Arabidopsis translatome keeps reflecting an embryonic maturation program until a certain developmental checkpoint. Furthermore, by dividing the seed germination time lapse into discrete time windows, we highlight precise and specific patterns of protein synthesis. These data refine and deepen our knowledge of the three classical phases of seed germination based on seed water uptake during imbibition and reveal that selective mRNA translation is a key feature of seed germination. Beyond the quantitative control of translational activity, both the selectivity of mRNA translation and protein turnover appear as specific regulatory systems, critical for timing the molecular events leading to successful germination and seedling establishment.
Collapse
Affiliation(s)
- Marc Galland
- From ‡INRA, Jean-Pierre Bourgin Institute (IJPB, UMR1318 INRA-AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences” (LabEx SPS), F-78026 Versailles, France
- §AgroParisTech, Chair of Plant Physiology, F-75231 Paris, France
| | - Romain Huguet
- ¶CNRS/Bayer CropScience Joint Laboratory (UMR5240), F-69263 Lyon, France
| | - Erwann Arc
- From ‡INRA, Jean-Pierre Bourgin Institute (IJPB, UMR1318 INRA-AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences” (LabEx SPS), F-78026 Versailles, France
- §AgroParisTech, Chair of Plant Physiology, F-75231 Paris, France
| | - Gwendal Cueff
- From ‡INRA, Jean-Pierre Bourgin Institute (IJPB, UMR1318 INRA-AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences” (LabEx SPS), F-78026 Versailles, France
- §AgroParisTech, Chair of Plant Physiology, F-75231 Paris, France
| | - Dominique Job
- §AgroParisTech, Chair of Plant Physiology, F-75231 Paris, France
- ¶CNRS/Bayer CropScience Joint Laboratory (UMR5240), F-69263 Lyon, France
| | - Loïc Rajjou
- From ‡INRA, Jean-Pierre Bourgin Institute (IJPB, UMR1318 INRA-AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences” (LabEx SPS), F-78026 Versailles, France
- §AgroParisTech, Chair of Plant Physiology, F-75231 Paris, France
| |
Collapse
|
212
|
Rocheta M, Sobral R, Magalhães J, Amorim MI, Ribeiro T, Pinheiro M, Egas C, Morais-Cecílio L, Costa MMR. Comparative transcriptomic analysis of male and female flowers of monoecious Quercus suber. FRONTIERS IN PLANT SCIENCE 2014; 5:599. [PMID: 25414713 PMCID: PMC4222140 DOI: 10.3389/fpls.2014.00599] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 10/14/2014] [Indexed: 05/03/2023]
Abstract
Monoecious species provide a comprehensive system to study the developmental programs underlying the establishment of female and male organs in unisexual flowers. However, molecular resources for most monoecious non-model species are limited, hampering our ability to study the molecular mechanisms involved in flower development of these species. The objective of this study was to identify differentially expressed genes during the development of male and female flowers of the monoecious species Quercus suber, an economically important Mediterranean tree. Total RNA was extracted from different developmental stages of Q. suber flowers. Non-normalized cDNA libraries of male and female flowers were generated using 454 pyrosequencing technology producing a total of 962,172 high-quality reads with an average length of 264 nucleotides. The assembly of the reads resulted in 14,488 contigs for female libraries and 10,438 contigs for male libraries. Comparative analysis of the transcriptomes revealed genes differentially expressed in early and late stages of development of female and male flowers, some of which have been shown to be involved in pollen development, in ovule formation and in flower development of other species with a monoecious, dioecious, or hermaphroditic sexual system. Moreover, we found differentially expressed genes that have not yet been characterized and others that have not been previously shown to be implicated in flower development. This transcriptomic analysis constitutes a major step toward the characterization of the molecular mechanisms involved in flower development in a monoecious tree with a potential contribution toward the knowledge of conserved developmental mechanisms in other species.
Collapse
Affiliation(s)
- Margarida Rocheta
- Departamento de Recursos Naturais Ambiente e Território, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
| | - Rómulo Sobral
- Centre for Biodiversity, Functional & Integrative Genomics, Plant Functional Biology Centre, University of MinhoBraga, Portugal
| | - Joana Magalhães
- Centre for Biodiversity, Functional & Integrative Genomics, Plant Functional Biology Centre, University of MinhoBraga, Portugal
| | - Maria I. Amorim
- Departamento de Biologia, Faculdade de Ciências da Universidade do PortoPorto, Portugal
| | - Teresa Ribeiro
- Departamento de Recursos Naturais Ambiente e Território, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
| | - Miguel Pinheiro
- Biocant, Parque Tecnológico de CantanhedeCantanhede, Portugal
| | - Conceição Egas
- Biocant, Parque Tecnológico de CantanhedeCantanhede, Portugal
| | - Leonor Morais-Cecílio
- Departamento de Recursos Naturais Ambiente e Território, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
- *Correspondence: Leonor Morais-Cecílio, Departamento de Recursos Naturais Ambiente e Território, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisboa, Portugal e-mail:
| | - Maria M. R. Costa
- Centre for Biodiversity, Functional & Integrative Genomics, Plant Functional Biology Centre, University of MinhoBraga, Portugal
- Maria M. R. Costa, Centre for Biodiversity, Functional & Integrative Genomics, Plant Functional Biology Centre, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal e-mail:
| |
Collapse
|
213
|
Siriwardana CL, Kumimoto RW, Jones DS, Holt BF. Gene Family Analysis of the Arabidopsis NF-YA Transcription Factors Reveals Opposing Abscisic Acid Responses During Seed Germination. PLANT MOLECULAR BIOLOGY REPORTER 2014; 32:971-986. [PMID: 25190903 PMCID: PMC4149875 DOI: 10.1007/s11105-014-0704-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
In the plant kingdom, each of the NUCLEAR FACTOR-Y (NF-Y) transcription factor families, NF-YA, NF-YB, and NF-YC, has undergone a great expansion compared to the animal kingdom. For example, Arabidopsis thaliana has 10 members of each gene family compared to only one in humans. Progress towards understanding the significance of this expansion is limited due to a lack of studies looking at the complete gene family during plant development. In the current study, transgenic overexpression lines were created for all 10 Arabidopsis NF-YA genes and examined for general development and alterations in abscisic acid (ABA)-mediated seed germination. NF-YA overexpression typically led to severe growth retardation and developmental defects, which extended from embryogenesis through to adult plants. Although overexpression of all NF-YA family members consistently led to growth retardation, some transgenic lines were hypersensitive to ABA during germination while others were hyposensitive. The opposing germination phenotypes were associated with the phylogenetic relationships between the NF-YA members. In addition, ABA marker genes were misregulated and ABA induction of gene expression was reduced in the overexpressors. Collectively, this study demonstrates that although NF-Ys have retained high degrees of similarity, they have evolved unique and sometimes opposing roles during plant development.
Collapse
Affiliation(s)
- Chamindika L. Siriwardana
- Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, GLCH, Room 43, Norman, OK 73019 USA
| | - Roderick W. Kumimoto
- Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, GLCH, Room 43, Norman, OK 73019 USA
| | - Daniel S. Jones
- Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, GLCH, Room 43, Norman, OK 73019 USA
| | - Ben F. Holt
- Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, GLCH, Room 43, Norman, OK 73019 USA
| |
Collapse
|
214
|
Terrasson E, Buitink J, Righetti K, Ly Vu B, Pelletier S, Zinsmeister J, Lalanne D, Leprince O. An emerging picture of the seed desiccome: confirmed regulators and newcomers identified using transcriptome comparison. FRONTIERS IN PLANT SCIENCE 2013; 4:497. [PMID: 24376450 PMCID: PMC3859232 DOI: 10.3389/fpls.2013.00497] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 11/18/2013] [Indexed: 05/19/2023]
Abstract
Desiccation tolerance (DT) is the capacity to withstand total loss of cellular water. It is acquired during seed filling and lost just after germination. However, in many species, a germinated seed can regain DT under adverse conditions such as osmotic stress. The genes, proteins and metabolites that are required to establish this DT is referred to as the desiccome. It includes both a range of protective mechanisms and underlying regulatory pathways that remain poorly understood. As a first step toward the identification of the seed desiccome of Medicago truncatula, using updated microarrays we characterized the overlapping transcriptomes associated with acquisition of DT in developing seeds and the re-establishment of DT in germinated seeds using a polyethylene glycol treatment (-1.7 MPa). The resulting list contained 740 and 2829 transcripts whose levels, respectively, increased and decreased with DT. Fourty-eight transcription factors (TF) were identified including MtABI3, MtABI5 and many genes regulating flowering transition and cell identity. A promoter enrichment analysis revealed a strong over-representation of ABRE elements together with light-responsive cis-acting elements. In Mtabi5 Tnt1 insertion mutants, DT could no longer be re-established by an osmotic stress. Transcriptome analysis on Mtabi5 radicles during osmotic stress revealed that 13 and 15% of the up-regulated and down-regulated genes, respectively, are mis-regulated in the mutants and might be putative downstream targets of MtABI5 implicated in the re-establishment of DT. Likewise, transcriptome comparisons of the desiccation sensitive Mtabi3 mutants and hairy roots ectopically expressing MtABI3 revealed that 35 and 23% of the up-regulated and down-regulated genes are acting downstream of MtABI3. Our data suggest that ABI3 and ABI5 have complementary roles in DT. Whether DT evolved by co-opting existing pathways regulating flowering and cellular phase transition and cell identity is discussed.
Collapse
Affiliation(s)
- Emmanuel Terrasson
- Université d'Angers, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAVAngers, France
| | - Julia Buitink
- Institut National de la Recherche Agronomique, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAVAngers, France
| | - Karima Righetti
- Institut National de la Recherche Agronomique, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAVAngers, France
| | - Benoit Ly Vu
- Agrocampus Ouest, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAVAngers, France
| | - Sandra Pelletier
- Institut National de la Recherche Agronomique, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAVAngers, France
| | - Julia Zinsmeister
- Agrocampus Ouest, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAVAngers, France
| | - David Lalanne
- Institut National de la Recherche Agronomique, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAVAngers, France
| | - Olivier Leprince
- Agrocampus Ouest, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAVAngers, France
| |
Collapse
|
215
|
Burroughs AM, Ando Y, Aravind L. New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:141-81. [PMID: 24311560 DOI: 10.1002/wrna.1210] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/03/2013] [Accepted: 11/01/2013] [Indexed: 12/19/2022]
Abstract
Our understanding of the pervasive involvement of small RNAs in regulating diverse biological processes has been greatly augmented by recent application of deep-sequencing technologies to small RNA across diverse eukaryotes. We review the currently known small RNA classes and place them in context of the reconstructed evolutionary history of the RNA interference (RNAi) protein machinery. This synthesis indicates that the earliest versions of eukaryotic RNAi systems likely utilized small RNA processed from three types of precursors: (1) sense-antisense transcriptional products, (2) genome-encoded, imperfectly complementary hairpin sequences, and (3) larger noncoding RNA precursor sequences. Structural dissection of PIWI proteins along with recent discovery of novel families (including Med13 of the Mediator complex) suggest that emergence of a distinct architecture with the N-terminal domains (also occurring separately fused to endoDNases in prokaryotes) formed via duplication of an ancestral unit was key to their recruitment as primary RNAi effectors and use of small RNAs of certain preferred lengths. Prokaryotic PIWI proteins are typically components of several RNA-directed DNA restriction or CRISPR/Cas systems. However, eukaryotic versions appear to have emerged from a subset that evolved RNA-directed RNAi. They were recruited alongside RNaseIII domains and RNA-dependent RNA polymerase (RdRP) domains, also from prokaryotic systems, to form the core eukaryotic RNAi system. Like certain regulatory systems, RNAi diversified into two distinct but linked arms concomitant with eukaryotic nucleocytoplasmic compartmentalization. Subsequent elaboration of RNAi proceeded via diversification of the core protein machinery through lineage-specific expansions and recruitment of new components from prokaryotes (nucleases and small RNA-modifying enzymes), allowing for diversification of associating small RNAs.
Collapse
Affiliation(s)
- Alexander Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | | |
Collapse
|
216
|
Kourmpetli S, Lee K, Hemsley R, Rossignol P, Papageorgiou T, Drea S. Bidirectional promoters in seed development and related hormone/stress responses. BMC PLANT BIOLOGY 2013; 13:187. [PMID: 24261334 PMCID: PMC4222868 DOI: 10.1186/1471-2229-13-187] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 11/15/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND Bidirectional promoters are common in genomes but under-studied experimentally, particularly in plants. We describe a targeted identification and selection of a subset of putative bidirectional promoters to identify genes involved in seed development and to investigate possible coordinated responses of gene pairs to conditions important in seed maturation such as desiccation and ABA-regulation. RESULTS We combined a search for 100-600 bp intergenic regions in the Arabidopsis genome with a cis-element based selection for those containing multiple copies of the G-box motif, CACGTG. One of the putative bidirectional promoters identified also contained a CE3 coupling element 5 bp downstream of one G-box and is identical to that characterized previously in the HVA1 promoter of barley. CE3 elements are significantly under-represented and under-studied in Arabidopsis. We further characterized the pair of genes associated with this promoter and uncovered roles for two small, previously uncharacterized, plant-specific proteins in Arabidopsis seed development and stress responses. CONCLUSIONS Using bioinformatics we identified putative bidirectional promoters involved in seed development and analysed expression patterns for a pair of plant-specific genes in various tissues and in response to hormones/stress. We also present preliminary functional analysis of these genes that is suggestive of roles in seed development.
Collapse
Affiliation(s)
- Sofia Kourmpetli
- Department of Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Kate Lee
- Bioinformatics and Biostatistics Analysis Support Hub (BBASH), College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, UK
| | - Rachel Hemsley
- Current address UCL Business PLC, The Network Building, 97 Tottenham Court Road, London W1T 4TP, UK
| | - Pascale Rossignol
- Current address Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Thaleia Papageorgiou
- Department of Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Sinéad Drea
- Department of Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| |
Collapse
|
217
|
Zhao C, Beers EP. Alternative splicing of Myb-related genes MYR1 and MYR2 may modulate activities through changes in dimerization, localization, or protein folding. PLANT SIGNALING & BEHAVIOR 2013; 8:e27325. [PMID: 24309816 PMCID: PMC4091541 DOI: 10.4161/psb.27325] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Arabidopsis genes MYR1 and MYR2 are regulators of flowering time under low light intensity. These Myb-related genes are expressed as alternative splice variants affected in their coiled-coil and DNA-binding domains. We tested whether alternative splicing could affect dimerization and localization of MYR1 and MYR2, thereby potentially affecting their activity. Using MYR1 as a model for variants within the coiled-coil region, we detected 2 types of homodimers. For MYR2, alternative splicing in the DNA-binding Myb-like domain abolished the ability of MYR2 to dimerize. Alternative splicing in the coiled-coil domain did not affect nuclear localization, as determined by transient expression in tobacco, while alternative splicing in the DNA-binding domain of MYR2 yielded a distinct intranuclear localization pattern that may reflect changes in phosphorylation-dependent protein folding. Thus alternative splicing of these genes may result in changes in dimerization or protein folding resulting in changes in activity and abundance of MYR1 or MYR2 protein.
Collapse
|
218
|
Yuen CYL, Matsumoto KO, Christopher DA. Variation in the Subcellular Localization and Protein Folding Activity among Arabidopsis thaliana Homologs of Protein Disulfide Isomerase. Biomolecules 2013; 3:848-69. [PMID: 24970193 PMCID: PMC4030966 DOI: 10.3390/biom3040848] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/27/2013] [Accepted: 10/12/2013] [Indexed: 12/18/2022] Open
Abstract
Protein disulfide isomerases (PDIs) catalyze the formation, breakage, and rearrangement of disulfide bonds to properly fold nascent polypeptides within the endoplasmic reticulum (ER). Classical animal and yeast PDIs possess two catalytic thioredoxin-like domains (a, a') and two non-catalytic domains (b, b'), in the order a-b-b'-a'. The model plant, Arabidopsis thaliana, encodes 12 PDI-like proteins, six of which possess the classical PDI domain arrangement (AtPDI1 through AtPDI6). Three additional AtPDIs (AtPDI9, AtPDI10, AtPDI11) possess two thioredoxin domains, but without intervening b-b' domains. C-terminal green fluorescent protein (GFP) fusions to each of the nine dual-thioredoxin PDI homologs localized predominantly to the ER lumen when transiently expressed in protoplasts. Additionally, expression of AtPDI9:GFP-KDEL and AtPDI10: GFP-KDDL was associated with the formation of ER bodies. AtPDI9, AtPDI10, and AtPDI11 mediated the oxidative folding of alkaline phosphatase when heterologously expressed in the Escherichia coli protein folding mutant, dsbA-. However, only three classical AtPDIs (AtPDI2, AtPDI5, AtPDI6) functionally complemented dsbA-. Interestingly, chemical inducers of the ER unfolded protein response were previously shown to upregulate most of the AtPDIs that complemented dsbA-. The results indicate that Arabidopsis PDIs differ in their localization and protein folding activities to fulfill distinct molecular functions in the ER.
Collapse
Affiliation(s)
- Christen Y L Yuen
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
| | - Kristie O Matsumoto
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
| | - David A Christopher
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
| |
Collapse
|
219
|
Martín MV, Distefano AM, Zabaleta EJ, Pagnussat GC. New insights into the functional roles of reactive oxygen species during embryo sac development and fertilization in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2013; 8:doi: 10.4161/psb.25714. [PMID: 23887494 PMCID: PMC4091057 DOI: 10.4161/psb.25714] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Previously considered as toxic by-products of aerobic metabolism, reactive oxygen species (ROS) are emerging as essential signaling molecules in eukaryotes. Recent evidence showed that maintenance of ROS homeostasis during female gametophyte development is crucial for embryo sac patterning and fertilization. Although ROS are exclusively detected in the central cell of mature embryo sacs, the study of mutants deficient in ROS homeostasis suggests that controlled oxidative bursts might take place earlier during gametophyte development. Also, a ROS burst that depends on pollination takes place inside the embryo sac. This oxidative response might be required for pollen tube growth arrest and for sperm cell release. In this mini-review, we will focus on new insights into the role of ROS during female gametophyte development and fertilization. Special focus will be made on the mitochondrial Mn-Superoxide dismutase (MSD1), which has been recently reported to be essential for maintaining ROS homeostasis during embryo sac formation.
Collapse
|
220
|
Murcha MW, Wang Y, Narsai R, Whelan J. The plant mitochondrial protein import apparatus - the differences make it interesting. Biochim Biophys Acta Gen Subj 2013; 1840:1233-45. [PMID: 24080405 DOI: 10.1016/j.bbagen.2013.09.026] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/17/2013] [Accepted: 09/18/2013] [Indexed: 12/25/2022]
Abstract
BACKGROUND Mitochondria play essential roles in the life and death of almost all eukaryotic cells, ranging from single-celled to multi-cellular organisms that display tissue and developmental differentiation. As mitochondria only arose once in evolution, much can be learned from studying single celled model systems such as yeast and applying this knowledge to other organisms. However, two billion years of evolution have also resulted in substantial divergence in mitochondrial function between eukaryotic organisms. SCOPE OF REVIEW Here we review our current understanding of the mechanisms of mitochondrial protein import between plants and yeast (Saccharomyces cerevisiae) and identify a high level of conservation for the essential subunits of plant mitochondrial import apparatus. Furthermore, we investigate examples whereby divergence and acquisition of functions have arisen and highlight the emerging examples of interactions between the import apparatus and components of the respiratory chain. MAJOR CONCLUSIONS After more than three decades of research into the components and mechanisms of mitochondrial protein import of plants and yeast, the differences between these systems are examined. Specifically, expansions of the small gene families that encode the mitochondrial protein import apparatus in plants are detailed, and their essential role in seed viability is revealed. GENERAL SIGNIFICANCE These findings point to the essential role of the inner mitochondrial protein translocases in Arabidopsis, establishing their necessity for seed viability and the crucial role of mitochondrial biogenesis during germination. This article is part of a Special Issue entitled Frontiers of Mitochondrial Research.
Collapse
Affiliation(s)
- Monika W Murcha
- ARC Centre of Excellence in Plant Energy Biology, Bayliss Building M316, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia.
| | - Yan Wang
- ARC Centre of Excellence in Plant Energy Biology, Bayliss Building M316, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Reena Narsai
- ARC Centre of Excellence in Plant Energy Biology, Bayliss Building M316, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia; Computational Systems Biology, Bayliss Building M316, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
| | - James Whelan
- ARC Centre of Excellence in Plant Energy Biology, Bayliss Building M316, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia; Department of Botany, School of Life Science, La Trobe University, Bundoora 3086, Victoria, Australia
| |
Collapse
|
221
|
Xiang H, Li X, Dai F, Xu X, Tan A, Chen L, Zhang G, Ding Y, Li Q, Lian J, Willden A, Guo Q, Xia Q, Wang J, Wang W. Comparative methylomics between domesticated and wild silkworms implies possible epigenetic influences on silkworm domestication. BMC Genomics 2013; 14:646. [PMID: 24059350 PMCID: PMC3852238 DOI: 10.1186/1471-2164-14-646] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 09/04/2013] [Indexed: 11/13/2022] Open
Abstract
Background In contrast to wild species, which have typically evolved phenotypes over long periods of natural selection, domesticates rapidly gained human-preferred agronomic traits in a relatively short-time frame via artificial selection. Under domesticated conditions, many traits can be observed that cannot only be due to environmental alteration. In the case of silkworms, aside from genetic divergence, whether epigenetic divergence played a role in domestication is an unanswered question. The silkworm is still an enigma in that it has two DNA methyltransferases (DNMT1 and DNMT2) but their functionality is unknown. Even in particular the functionality of the widely distributed DNMT1 remains unknown in insects in general. Results By embryonic RNA interference, we reveal that knockdown of silkworm Dnmt1 caused decreased hatchability, providing the first direct experimental evidence of functional significance of insect Dnmt1. In the light of this fact and those that DNA methylation is correlated with gene expression in silkworms and some agronomic traits in domesticated organisms are not stable, we comprehensively compare silk gland methylomes of 3 domesticated (Bombyx mori) and 4 wild (Bombyx mandarina) silkworms to identify differentially methylated genes between the two. We observed 2-fold more differentiated methylated cytosinces (mCs) in domesticated silkworms as compared to their wild counterparts, suggesting a trend of increasing DNA methylation during domestication. Further study of more domesticated and wild silkworms narrowed down the domesticates’ epimutations, and we were able to identify a number of differential genes. One such gene showing demethyaltion in domesticates correspondently displays lower gene expression, and more interestingly, has experienced selective sweep. A methylation-increased gene seems to result in higher expression in domesticates and the function of its Drosophila homolog was previously found to be essential for cell volume regulation, indicating a possible correlation with the enlargement of silk glands in domesticated silkworms. Conclusions Our results imply epigenetic influences at work during domestication, which gives insight into long time historical controversies regarding acquired inheritance.
Collapse
Affiliation(s)
- Hui Xiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming, Yunnan Province 650223, China.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
222
|
Okada T, Hu Y, Tucker MR, Taylor JM, Johnson SD, Spriggs A, Tsuchiya T, Oelkers K, Rodrigues JC, Koltunow AM. Enlarging cells initiating apomixis in Hieracium praealtum transition to an embryo sac program prior to entering mitosis. PLANT PHYSIOLOGY 2013; 163:216-31. [PMID: 23864557 PMCID: PMC3762643 DOI: 10.1104/pp.113.219485] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 07/08/2013] [Indexed: 05/19/2023]
Abstract
Hieracium praealtum forms seeds asexually by apomixis. During ovule development, sexual reproduction initiates with megaspore mother cell entry into meiosis and formation of a tetrad of haploid megaspores. The sexual pathway ceases when a diploid aposporous initial (AI) cell differentiates, enlarges, and undergoes mitosis, forming an aposporous embryo sac that displaces sexual structures. Embryo and endosperm development in aposporous embryo sacs is fertilization independent. Transcriptional data relating to apomixis initiation in Hieracium spp. ovules is scarce and the functional identity of the AI cell relative to other ovule cell types is unclear. Enlarging AI cells with undivided nuclei, early aposporous embryo sacs containing two to four nuclei, and random groups of sporophytic ovule cells not undergoing these events were collected by laser capture microdissection. Isolated amplified messenger RNA samples were sequenced using the 454 pyrosequencing platform and comparatively analyzed to establish indicative roles of the captured cell types. Transcriptome and protein motif analyses showed that approximately one-half of the assembled contigs identified homologous sequences in Arabidopsis (Arabidopsis thaliana), of which the vast majority were expressed during early Arabidopsis ovule development. The sporophytic ovule cells were enriched in signaling functions. Gene expression indicative of meiosis was notably absent in enlarging AI cells, consistent with subsequent aposporous embryo sac formation without meiosis. The AI cell transcriptome was most similar to the early aposporous embryo sac transcriptome when comparing known functional annotations and both shared expressed genes involved in gametophyte development, suggesting that the enlarging AI cell is already transitioning to an embryo sac program prior to mitotic division.
Collapse
|
223
|
Tanaka Y, Nishimura K, Kawamukai M, Oshima A, Nakagawa T. Redundant function of two Arabidopsis COPII components, AtSec24B and AtSec24C, is essential for male and female gametogenesis. PLANTA 2013; 238:561-75. [PMID: 23779001 DOI: 10.1007/s00425-013-1913-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 06/05/2013] [Indexed: 05/08/2023]
Abstract
Anterograde vesicle transport from the endoplasmic reticulum to the Golgi apparatus is the start of protein transport through the secretory pathway, in which the transport is mediated by coat protein complex II (COPII)-coated vesicles. Therefore, most proteins synthesized on the endoplasmic reticulum are loaded as cargo into COPII vesicles. The COPII is composed of the small GTPase Sar1 and two types of protein complexes (Sec23/24 and Sec13/31). Of these five COPII components, Sec24 is thought to recognize cargo that is incorporated into COPII vesicles by directly interacting with the cargo. The Arabidopsis genome encodes three types of Sec24 homologs (AtSec24A, AtSec24B, and AtSec24C). The subcellular dynamics and function of AtSec24A have been characterized. The intracellular distributions and functions of other AtSec24 proteins are not known, and the functional differences among the three AtSec24s remain unclear. Here, we found that all three AtSec24s were expressed in similar parts of the plant body and showed the same subcellular localization pattern. AtSec24B knockout plant, but not AtSec24C knockdown plant, showed mild male sterility with reduction of pollen germination. Significant decrease of AtSec24B and AtSec24C expression affected male and female gametogenesis in Arabidopsis thaliana. Our results suggested that the redundant function of AtSec24B and AtSec24C is crucial for the development of plant reproductive cells. We propose that the COPII transport is involved in male and female gametogenesis in planta.
Collapse
Affiliation(s)
- Yuji Tanaka
- Department of Molecular and Functional Genomics, Center for Integrated Research in Science, Shimane University, Nishikawatsu 1060, Matsue, 690-8504, Japan
| | | | | | | | | |
Collapse
|
224
|
Nie DM, Ouyang YD, Wang X, Zhou W, Hu CG, Yao J. Genome-wide analysis of endosperm-specific genes in rice. Gene 2013; 530:236-47. [PMID: 23948082 DOI: 10.1016/j.gene.2013.07.088] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 07/24/2013] [Accepted: 07/26/2013] [Indexed: 12/31/2022]
Abstract
The endosperm of the cereal crop is an important nutrient source for humans. It also acts as a critical integrator of plant seed growth and development. Despite its importance, the comprehensive understanding in regulating of endosperm development in rice remains elusive. Here, we performed a genomic survey comprising the identification and functional characterization of the endosperm-specific genes (OsEnS) in rice using Affymetrix microarray data and Gene Ontology (GO) analysis. A total of 151 endosperm-specific genes were identified, and the expression patterns of 13 selected genes were confirmed by qRT-PCR analysis. Promoter regions of the endosperm-specific expression genes were analyzed by PLACE Signal Scan Search. The results indicated that some motifs were involved in endosperm-specific expression regulation, and some cis-elements were responsible for hormone regulation. The bootstrap analysis indicated that the RY repeat (CATGCA box) was over-represented in promoter regions of endosperm-specific expression genes. GO analysis indicated that these genes could be classified into 12 groups, namely, transcription factor, stress/defense, seed storage protein (SSP), carbohydrate and energy metabolism, seed maturation, protein metabolism, lipid metabolism, transport, cell wall related, hormone related, signal transduction, and one unclassified group. Taken together, our results provide informative clues for further functional characterization of the endosperm-specific genes, which facilitate the understanding of the molecular mechanism in rice endosperm development.
Collapse
Affiliation(s)
- Dong-Ming Nie
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | | | | | | | | | | |
Collapse
|
225
|
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.
Collapse
|
226
|
Zhuang Y, Zhang H, Lin S. Polyadenylation of 18S rRNA in algae(1). JOURNAL OF PHYCOLOGY 2013; 49:570-579. [PMID: 27007045 DOI: 10.1111/jpy.12068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 12/23/2012] [Indexed: 06/05/2023]
Abstract
Polyadenylation is best known for occurring to mRNA of eukaryotes transcribed by RNA polymerase II to stabilize mRNA molecules and promote their translation. rRNAs transcribed by RNA polymerase I or III are typically believed not to be polyadenylated. However, there is increasing evidence that polyadenylation occurs to nucleus-encoded rRNAs as part of the RNA degradation pathway. To examine whether the same polyadenylation-assisted degradation pathway occurs in algae, we surveyed representative species of algae including diatoms, chlorophytes, dinoflagellates and pelagophytes using oligo (dT)-primed reversed transcription PCR (RT-PCR). In all the algal species examined, truncated 18S rRNA or its precursor molecules with homo- or hetero-polymeric poly(A) tails were detected. Mining existing algal expressed sequence tag (EST) data revealed polyadenylated truncated 18S rRNA in four additional phyla of algae. rRNA polyadenylation occurred at various internal positions along the 18S rRNA and its precursor sequences. Moreover, putative homologs of noncanonical poly(A) polymerase (ncPAP) Trf4p, which is responsible for polyadenylating nuclear-encoded RNA and targeting it for degradation, were detected from the genomes and transcriptomes of five phyla of algae. Our results suggest that polyadenylation-assisted RNA degradation mechanism widely exists in algae, particularly for the nucleus-encoded rRNA and its precursors.
Collapse
Affiliation(s)
- Yunyun Zhuang
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
- Marine Biodiversity and Global Change Research Center and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, China
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
- Marine Biodiversity and Global Change Research Center and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, China
| |
Collapse
|
227
|
Martin MV, Fiol DF, Sundaresan V, Zabaleta EJ, Pagnussat GC. oiwa, a female gametophytic mutant impaired in a mitochondrial manganese-superoxide dismutase, reveals crucial roles for reactive oxygen species during embryo sac development and fertilization in Arabidopsis. THE PLANT CELL 2013; 25:1573-91. [PMID: 23653473 PMCID: PMC3694693 DOI: 10.1105/tpc.113.109306] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Reactive oxygen species (ROS) can function as signaling molecules, regulating key aspects of plant development, or as toxic compounds leading to oxidative damage. In this article, we show that the regulation of ROS production during megagametogenesis is largely dependent on MSD1, a mitochondrial Mn-superoxide dismutase. Wild-type mature embryo sacs show ROS exclusively in the central cell, which appears to be the main source of ROS before pollination. Accordingly, MSD1 shows a complementary expression pattern. MSD1 expression is elevated in the egg apparatus at maturity but is downregulated in the central cell. The oiwa mutants are characterized by high levels of ROS detectable in both the central cell and the micropylar cells. Remarkably, egg apparatus cells in oiwa show central cell features, indicating that high levels of ROS result in the expression of central cell characteristic genes. Notably, ROS are detected in synergid cells after pollination. This ROS burst depends on stigma pollination but precedes fertilization, suggesting that embryo sacs sense the imminent arrival of pollen tubes and respond by generating an oxidative environment. Altogether, we show that ROS play a crucial role during female gametogenesis and fertilization. MSD1 activity seems critical for maintaining ROS localization and important for embryo sac patterning.
Collapse
Affiliation(s)
- María Victoria Martin
- Instituto de Investigaciones Biológicas IIB-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Diego Fernando Fiol
- Instituto de Investigaciones Biológicas IIB-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Venkatesan Sundaresan
- Department of Plant Biology, University of California, Davis, California 95616
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Eduardo Julián Zabaleta
- Instituto de Investigaciones Biológicas IIB-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Gabriela Carolina Pagnussat
- Instituto de Investigaciones Biológicas IIB-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
- Address correspondence to
| |
Collapse
|
228
|
Jia M, Wu H, Clay KL, Jung R, Larkins BA, Gibbon BC. Identification and characterization of lysine-rich proteins and starch biosynthesis genes in the opaque2 mutant by transcriptional and proteomic analysis. BMC PLANT BIOLOGY 2013; 13:60. [PMID: 23586588 PMCID: PMC3762070 DOI: 10.1186/1471-2229-13-60] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Accepted: 04/05/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND The opaque2 mutant is valuable for producing maize varieties with enhanced nutritional value. However, the exact mechanisms by which it improves protein quality and creates a soft endosperm texture are unclear. Given the importance of improving nutritional quality in grain crops, a better understanding of the physiological basis for these traits is necessary. RESULTS In this study, we combined transcript profiling and proteomic analysis to better understand which genes and proteins are altered by opaque2 in the W64A inbred line. These analyses showed that the accumulation of some lysine-rich proteins, such as sorbitol dehydrogenase and glyceraldehyde3-phosphate dehydrogenase, was increased in mature kernels and may contribute substantially to the lysine content of opaque2 endosperm. Some defense proteins such as beta-glucosidase aggregating factor were strongly down regulated and may be regulated directly by opaque2. The mutant also had altered expression of a number of starch biosynthesis genes and this was associated with a more highly crystalline starch. CONCLUSIONS The results of these studies revealed specific target genes that can be investigated to further improve nutritional quality and agronomic performance of high lysine maize lines, particularly those based on the presence of the opaque2 mutation. Alteration of amylopectin branching patterns in opaque2 starch could contribute to generation of the soft, starchy endosperm.
Collapse
Affiliation(s)
- Mo Jia
- Department of Biology, Baylor University, One Bear place #97388, Waco, TX 76798, USA
| | - Hao Wu
- Department of Biology, Baylor University, One Bear place #97388, Waco, TX 76798, USA
| | - Kasi L Clay
- Department of Biology, Baylor University, One Bear place #97388, Waco, TX 76798, USA
| | - Rudolf Jung
- Pioneer Hi-Bred International, Inc., Johnston, IA 50131, USA
| | - Brian A Larkins
- Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Bryan C Gibbon
- Department of Biology, Baylor University, One Bear place #97388, Waco, TX 76798, USA
| |
Collapse
|
229
|
Mühlhausen A, Lenser T, Mummenhoff K, Theißen G. Evidence that an evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae) was caused by a change in the control of valve margin identity genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:824-35. [PMID: 23173897 DOI: 10.1111/tpj.12079] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 11/05/2012] [Accepted: 11/09/2012] [Indexed: 05/08/2023]
Abstract
In the Brassicaceae, indehiscent fruits evolved from dehiscent fruits several times independently. Here we use closely related wild species of the genus Lepidium as a model system to analyse the underlying developmental genetic mechanisms in a candidate gene approach. ALCATRAZ (ALC), INDEHISCENT (IND), SHATTERPROOF1 (SHP1) and SHATTERPROOF2 (SHP2) are known fruit developmental genes of Arabidopsis thaliana that are expressed in the fruit valve margin governing dehiscence zone formation. Comparative expression analysis by quantitative RT-PCR, Northern blot and in situ hybridization show that their orthologues from Lepidium campestre (dehiscent fruits) are similarly expressed at valve margins. In sharp contrast, expression of the respective orthologues is abolished in the corresponding tissue of indehiscent Lepidium appelianum fruits, indicating that changes in the genetic pathway identified in A. thaliana caused the transition from dehiscent to indehiscent fruits in the investigated species. As parallel mutations in different genes are quite unlikely, we conclude that the changes in gene expression patterns are probably caused by changes in upstream regulators of ALC, IND and SHP1/2, possible candidates from A. thaliana being FRUITFULL (FUL), REPLUMLESS (RPL) and APETALA2 (AP2). However, neither expression analyses nor functional tests in transgenic plants provided any evidence that the FUL or RPL orthologues of Lepidium were involved in evolution of fruit indehiscence in Lepidium. In contrast, stronger expression of AP2 in indehiscent compared to dehiscent fruits identifies AP2 as a candidate gene that deserves further investigation.
Collapse
Affiliation(s)
- Andreas Mühlhausen
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, D-49076 Osnabrück, Germany
| | | | | | | |
Collapse
|
230
|
De Wilde K, De Buck S, Vanneste K, Depicker A. Recombinant antibody production in Arabidopsis seeds triggers an unfolded protein response. PLANT PHYSIOLOGY 2013; 161:1021-33. [PMID: 23188806 PMCID: PMC3561000 DOI: 10.1104/pp.112.209718] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 11/26/2012] [Indexed: 05/07/2023]
Abstract
Among the many plant-based production systems that are being tested for molecular farming, seeds are very attractive, as they provide a stable environment in which the accumulating recombinant proteins can be stored. However, it is not known exactly how high production levels of recombinant antibodies influence the endogenous transcriptome and proteome of the developing seed. To address this question, we studied the transcriptomic status in developing Arabidopsis (Arabidopsis thaliana) seeds 13 d post anthesis of three transgenic lines, producing varying levels of recombinant VHH or single-chain Fv antibody fragments fused to the human immunoglobulin G1-derived Fc fragment under the control of the β-PHASEOLIN seed-specific promoter. Using genome-wide Tiling arrays, we demonstrated that only a small proportion of the transcriptome was significantly changed in each of the lines compared with the wild type. Strikingly, in all three lines, we found a large overlap of up-regulated genes corresponding to protein folding, glycosylation/modification, translocation, vesicle transport, and protein degradation, suggestive of a state of cellular stress called the unfolded protein response. Moreover, the gene up-regulation amplitude was similar in all three lines. We hypothesize that the production of recombinant antibodies in the endoplasmic reticulum triggers endoplasmic reticulum stress, causing a disturbance of the normal cellular homeostasis.
Collapse
Affiliation(s)
- Kirsten De Wilde
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.); and Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.)
| | - Sylvie De Buck
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.); and Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.)
| | - Kevin Vanneste
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.); and Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.)
| | - Ann Depicker
- Department of Plant Systems Biology, VIB, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.); and Department of Plant Biotechnology and Bioinformatics, Ghent University, B–9052 Ghent, Belgium (K.D.W., S.D.B., K.V., A.D.)
| |
Collapse
|
231
|
Aiese Cigliano R, Sanseverino W, Cremona G, Ercolano MR, Conicella C, Consiglio FM. Genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles. BMC Genomics 2013; 14:57. [PMID: 23356725 PMCID: PMC3567966 DOI: 10.1186/1471-2164-14-57] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 01/22/2013] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Histone post-translational modifications (HPTMs) including acetylation and methylation have been recognized as playing a crucial role in epigenetic regulation of plant growth and development. Although Solanum lycopersicum is a dicot model plant as well as an important crop, systematic analysis and expression profiling of histone modifier genes (HMs) in tomato are sketchy. RESULTS Based on recently released tomato whole-genome sequences, we identified in silico 32 histone acetyltransferases (HATs), 15 histone deacetylases (HDACs), 52 histone methytransferases (HMTs) and 26 histone demethylases (HDMs), and compared them with those detected in Arabidopsis (Arabidopsis thaliana), maize (Zea mays) and rice (Oryza sativa) orthologs. Comprehensive analysis of the protein domain architecture and phylogeny revealed the presence of non-canonical motifs and new domain combinations, thereby suggesting for HATs the existence of a new family in plants. Due to species-specific diversification during evolutionary history tomato has fewer HMs than Arabidopsis. The transcription profiles of HMs within tomato organs revealed a broad functional role for some HMs and a more specific activity for others, suggesting key HM regulators in tomato development. Finally, we explored S. pennellii introgression lines (ILs) and integrated the map position of HMs, their expression profiles and the phenotype of ILs. We thereby proved that the strategy was useful to identify HM candidates involved in carotenoid biosynthesis in tomato fruits. CONCLUSIONS In this study, we reveal the structure, phylogeny and spatial expression of members belonging to the classical families of HMs in tomato. We provide a framework for gene discovery and functional investigation of HMs in other Solanaceae species.
Collapse
Affiliation(s)
- Riccardo Aiese Cigliano
- CNR, National Research Council of Italy, Institute of Plant Genetics, Research Division Portici, Via Università 133, 80055 Portici, Italy
| | | | | | | | | | | |
Collapse
|
232
|
Luo JL, Zhao N, Lu CM. [Plant Trihelix transcription factors family]. YI CHUAN = HEREDITAS 2012; 34:1551-60. [PMID: 23262102 DOI: 10.3724/sp.j.1005.2012.01551] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The Trihelix transcription factor family has raised great concerns only in recent years. It was named after its conserved DNA binding domain containing three tandem helix (helix-loop-helix-loop-helix), which could bind specifically with GT element, a light-responsive DNA element. So, this family is also known as GT factors. At the early stage of study, the knowledge of this family was only confined to their functions in regulation of light-responsive genes. However, recent researches indicated that Trihelix family also plays important roles in different growth and development processes involving flowers, stomata, trichomes, embryos, and seeds, as well as roles in response to abiotic and biotic stresses. This review mainly focused on the structural characteristics, classification, and the latest functional research progresses on the Trihelix family.
Collapse
Affiliation(s)
- Jun-Ling Luo
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.
| | | | | |
Collapse
|
233
|
Hosseinpour B, HajiHoseini V, Kashfi R, Ebrahimie E, Hemmatzadeh F. Protein interaction network of Arabidopsis thaliana female gametophyte development identifies novel proteins and relations. PLoS One 2012; 7:e49931. [PMID: 23239973 PMCID: PMC3519845 DOI: 10.1371/journal.pone.0049931] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 10/17/2012] [Indexed: 01/01/2023] Open
Abstract
Although the female gametophyte in angiosperms consists of just seven cells, it has a complex biological network. In this study, female gametophyte microarray data from Arabidopsis thaliana were integrated into the Arabidopsis interactome database to generate a putative interaction map of the female gametophyte development including proteome map based on biological processes and molecular functions of proteins. Biological and functional groups as well as topological characteristics of the network were investigated by analyzing phytohormones, plant defense, cell death, transporters, regulatory factors, and hydrolases. This approach led to the prediction of critical members and bottlenecks of the network. Seventy-four and 24 upregulated genes as well as 171 and 3 downregulated genes were identified in subtracted networks based on biological processes and molecular function respectively, including novel genes such as the pathogenesis-related protein 4, ER type Ca(2+) ATPase 3, dihydroflavonol reductase, and ATP disulfate isomerase. Biologically important relationships between genes, critical nodes, and new essential proteins such as AT1G26830, AT5G20850, CYP74A, AT1G42396, PR4 and MEA were found in the interactome's network. The positions of novel genes, both upregulated and downregulated, and their relationships with biological pathways, in particular phytohormones, were highlighted in this study.
Collapse
Affiliation(s)
- Batool Hosseinpour
- Institute of Agriculture, Iranian Research Organization for Science and Technology, Tehran, Iran
| | - Vahid HajiHoseini
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Rafieh Kashfi
- Department of Crop Production & Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Esmaeil Ebrahimie
- Department of Crop Production & Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, South Australia, Australia
- * E-mail: (EE); (FH)
| | - Farhid Hemmatzadeh
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- * E-mail: (EE); (FH)
| |
Collapse
|
234
|
Petroni K, Kumimoto RW, Gnesutta N, Calvenzani V, Fornari M, Tonelli C, Holt BF, Mantovani R. The promiscuous life of plant NUCLEAR FACTOR Y transcription factors. THE PLANT CELL 2012; 24:4777-92. [PMID: 23275578 PMCID: PMC3556957 DOI: 10.1105/tpc.112.105734] [Citation(s) in RCA: 218] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 11/23/2012] [Accepted: 12/10/2012] [Indexed: 05/18/2023]
Abstract
The CCAAT box is one of the most common cis-elements present in eukaryotic promoters and is bound by the transcription factor NUCLEAR FACTOR Y (NF-Y). NF-Y is composed of three subunits, NF-YA, NF-YB, and NF-YC. Unlike animals and fungi, plants have significantly expanded the number of genes encoding NF-Y subunits. We provide a comprehensive classification of NF-Y genes, with a separation of closely related, but distinct, histone fold domain proteins. We additionally review recent experiments that have placed NF-Y at the center of many developmental stress-responsive processes in the plant lineage.
Collapse
Affiliation(s)
- Katia Petroni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Roderick W. Kumimoto
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019
| | - Nerina Gnesutta
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Valentina Calvenzani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Monica Fornari
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Chiara Tonelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Ben F. Holt
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
- Address correspondence to
| |
Collapse
|
235
|
Hwang IS, Kim NH, Choi DS, Hwang BK. Overexpression of Xanthomonas campestris pv. vesicatoria effector AvrBsT in Arabidopsis triggers plant cell death, disease and defense responses. PLANTA 2012; 236:1191-1204. [PMID: 22678032 DOI: 10.1007/s00425-012-1672-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Accepted: 05/19/2012] [Indexed: 06/01/2023]
Abstract
Recognition of bacterial effector proteins by plant cells is crucial for plant disease and defense response signaling. The Xanthomonas campestris pv. vesicatoria (Xcv) type III effector protein, AvrBsT, is secreted into plant cells from Xcv strain Bv5-4a. Here, we demonstrate that dexamethasone (DEX): avrBsT overexpression triggers cell death signaling in healthy transgenic Arabidopsis plants. AvrBsT overexpression in Arabidopsis also reduced susceptibility to infection with the obligate biotrophic oomycete Hyaloperonospora arabidopsidis. Overexpression of avrBsT significantly induced some defense-related genes in Arabidopsis leaves. A high-throughput in planta proteomics screen identified TCP-1 chaperonin, SEC7-like guanine nucleotide exchange protein and calmodulin-like protein, which were differentially expressed in DEX:avrBsT-overexpression (OX) Arabidopsis plants during Hp. arabidopsidis infection. Treatment with purified GST-tagged AvrBsT proteins distinctly inhibited the growth and sporulation of Hp. arabidopsidis on Arabdiopsis cotyledons. In contrast, DEX:avrBsT-OX plants exhibited enhanced susceptibility to Pseudomonas syringae pv. tomato (Pst) DC3000 infection. Notably, susceptible cell death and enhanced electrolyte leakage were significantly induced in the Pst-infected leaves of DEX:avrBsT-OX plants. Together, these results suggest that Xcv effector AvrBsT overexpression triggers plant cell death, disease and defense signaling leading to both disease and defense responses to microbial pathogens of different lifestyles.
Collapse
Affiliation(s)
- In Sun Hwang
- Laboratory of Molecular Plant Pathology, School of Life Sciences and Biotechnology, Korea University, Anam-dong, Sungbuk-ku, Seoul 136-713, Republic of Korea
| | | | | | | |
Collapse
|
236
|
Deng W, Chen G, Peng F, Truksa M, Snyder CL, Weselake RJ. Transparent testa16 plays multiple roles in plant development and is involved in lipid synthesis and embryo development in canola. PLANT PHYSIOLOGY 2012; 160:978-89. [PMID: 22846192 PMCID: PMC3461570 DOI: 10.1104/pp.112.198713] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Transparent Testa16 (TT16), a transcript regulator belonging to the B(sister) MADS box proteins, regulates proper endothelial differentiation and proanthocyanidin accumulation in the seed coat. Our understanding of its other physiological roles, however, is limited. In this study, the physiological and developmental roles of TT16 in an important oil crop, canola (Brassica napus), were dissected by a loss-of-function approach. RNA interference (RNAi)-mediated down-regulation of tt16 in canola caused dwarf phenotypes with a decrease in the number of inflorescences, flowers, siliques, and seeds. Fluorescence microscopy revealed that tt16 deficiency affects pollen tube guidance, resulting in reduced fertility and negatively impacting embryo and seed development. Moreover, Bntt16 RNAi plants had reduced oil content and altered fatty acid composition. Transmission electron microscopy showed that the seeds of the RNAi plants had fewer oil bodies than the nontransgenic plants. In addition, tt16 RNAi transgenic lines were more sensitive to auxin. Further analysis by microarray showed that tt16 down-regulation alters the expression of genes involved in gynoecium and embryo development, lipid metabolism, auxin transport, and signal transduction. The broad regulatory function of TT16 at the transcriptional level may explain the altered phenotypes observed in the transgenic lines. Overall, the results uncovered important biological roles of TT16 in plant development, especially in fatty acid synthesis and embryo development.
Collapse
|
237
|
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.
Collapse
|
238
|
Schippers JHM, Nguyen HM, Lu D, Schmidt R, Mueller-Roeber B. ROS homeostasis during development: an evolutionary conserved strategy. Cell Mol Life Sci 2012; 69:3245-57. [PMID: 22842779 PMCID: PMC11114851 DOI: 10.1007/s00018-012-1092-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Revised: 07/09/2012] [Accepted: 07/09/2012] [Indexed: 12/22/2022]
Abstract
The balance between cellular proliferation and differentiation is a key aspect of development in multicellular organisms. Recent studies on Arabidopsis roots revealed distinct roles for different reactive oxygen species (ROS) in these processes. Modulation of the balance between ROS in proliferating cells and elongating cells is controlled at least in part at the transcriptional level. The effect of ROS on proliferation and differentiation is not specific for plants but appears to be conserved between prokaryotic and eukaryotic life forms. The ways in which ROS is received and how it affects cellular functioning is discussed from an evolutionary point of view. The different redox-sensing mechanisms that evolved ultimately result in the activation of gene regulatory networks that control cellular fate and decision-making. This review highlights the potential common origin of ROS sensing, indicating that organisms evolved similar strategies for utilizing ROS during development, and discusses ROS as an ancient universal developmental regulator.
Collapse
Affiliation(s)
- Jos H. M. Schippers
- Department of Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Hung M. Nguyen
- Department of Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Dandan Lu
- Department of Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Romy Schmidt
- Department of Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Bernd Mueller-Roeber
- Department of Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| |
Collapse
|
239
|
Valencia-Morales MDP, Camas-Reyes JA, Cabrera-Ponce JL, Alvarez-Venegas R. The Arabidopsis thaliana SET-domain-containing protein ASHH1/SDG26 interacts with itself and with distinct histone lysine methyltransferases. JOURNAL OF PLANT RESEARCH 2012; 125:679-692. [PMID: 22438063 DOI: 10.1007/s10265-012-0485-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 02/23/2012] [Indexed: 05/31/2023]
Abstract
Polycomb group (PcG) and trithorax group (trxG) proteins are key regulators of homeotic genes and have central roles in cell proliferation, growth and development. In animals, PcG and trxG proteins form higher order protein complexes that contain SET domain proteins with histone methyltransferase activity, and are responsible for the different types of lysine methylation at the N-terminal tails of the core histone proteins. However, whether H3K4 methyltransferase complexes exist in Arabidopsis thaliana remains unknown. Here, we make use of the yeast two-hybrid system and the bimolecular fluorescence complementation assay to provide evidence for the self-association of the Arabidopsis thaliana SET-domain-containing protein SET DOMAIN GROUP 26 (SDG26), also known as ABSENT, SMALL, OR HOMEOTIC DISCS 1 HOMOLOG 1 (ASHH1). In addition, we show that the ASHH1 protein associates with SET-domain-containing sequences from two distinct histone lysine methyltransferases, the ARABIDOPSIS HOMOLOG OF TRITHORAX-1 (ATX1) and ASHH2 proteins. Furthermore, after screening a cDNA library we found that ASHH1 interacts with two proteins from the heat shock protein 40 kDa (Hsp40/DnaJ) superfamily, thus connecting the epigenetic network with a system sensing external cues. Our findings suggest that trxG complexes in Arabidopsis thaliana could involve different sets of histone lysine methyltransferases, and that these complexes may be engaged in multiple developmental processes in Arabidopsis.
Collapse
Affiliation(s)
- María del Pilar Valencia-Morales
- Departamento de Ingeniería Genética, CINVESTAV Unidad Irapuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, C.P. 36821, Irapuato, Guanajuato, Mexico
| | | | | | | |
Collapse
|
240
|
Abstract
An abundant class of E3 ubiquitin ligases encodes the RING-finger domain. The RING finger binds to the E2 ubiquitin-conjugating enzyme and brings together both the E2 and substrate. It is predicted that 477 RING finger E3 ligases exist in Arabidopsis thaliana. A particular family among them, named Arabidopsis Tóxicos en Levadura (ATL), consists of 91 members that contain the RING-H2 variation and a hydrophobic domain located at the N-terminal end. Transmembrane E3 ligases are important in several biological processes. For instance, some transmembrane RING finger E3 ligases are main participants in the endoplasmic reticulum-associated degradation pathway that targets misfolded proteins. Functional analysis of a number of ATLs has shown that some of them regulate distinct pathways in plants. Several ATLs have been shown to participate in defense responses, while others play a role in the regulation of the carbon/nitrogen response during post-germinative seedling growth transition, in the regulation of cell death during root development, in endosperm development, or in the transition to flowering under short day conditions. The ATL family has also been instrumental in evolution studies for showing how gene families are expanded in plant genomes.
Collapse
Affiliation(s)
- Plinio Guzmán
- Departamento de Ingeniería Genética de Plantas Centro de Investigación y de Estudios Avanzados, Unidad Irapuato, Irapuato, México.
| |
Collapse
|
241
|
Niedojadło K, Pięciński S, Smoliński DJ, Bednarska-Kozakiewicz E. Ribosomal RNA of Hyacinthus orientalis L. female gametophyte cells before and after fertilization. PLANTA 2012; 236:171-84. [PMID: 22398640 PMCID: PMC3382635 DOI: 10.1007/s00425-012-1618-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 02/16/2012] [Indexed: 05/25/2023]
Abstract
The nucleolar activity of Hyacinthus orientalis L. embryo sac cells was investigated. The distributions of nascent pre-rRNA (ITS1), 26S rRNA and of the 5S rRNA and U3 snoRNA were determined using fluorescence in situ hybridization (FISH). Our results indicated the different rRNA metabolism of the H. orientalis female gametophyte cells before and after fertilization. In the target cells for the male gamete, i.e., the egg cell and the central cell whose activity is silenced in the mature embryo sac (Pięciński et al. in Sex Plant Reprod 21:247-257, 2008; Niedojadło et al. in Planta doi: 10.1007/s00425-012-1599-9 , 2011), rRNA metabolism is directed at the accumulation of rRNPs in the cytoplasm and immature transcripts in the nucleolus. In both cells, fertilization initiates the maturation of the maternal pre-rRNA and the expression of zygotic rDNA. The resumption of rRNA transcription observed in the hyacinth zygote indicates that in plants, there is a different mechanism for the regulation of RNA Pol I activity than in animals. In synergids and antipodal cells, which have somatic functions, the nucleolar activity is correlated with the metabolic activity of these cells and changes in successive stages of embryo sac development.
Collapse
Affiliation(s)
- Katarzyna Niedojadło
- Department of Cell Biology, Institute of General and Molecular Biology, Nicolaus Copernicus University, Gagarina 9, 87-100, Toruń, Poland.
| | | | | | | |
Collapse
|
242
|
Yang H, Mo H, Fan D, Cao Y, Cui S, Ma L. Overexpression of a histone H3K4 demethylase, JMJ15, accelerates flowering time in Arabidopsis. PLANT CELL REPORTS 2012; 31:1297-1308. [PMID: 22555401 DOI: 10.1007/s00299-012-1249-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 02/26/2012] [Accepted: 03/17/2012] [Indexed: 05/28/2023]
Abstract
UNLABELLED The methylation of histone 3 lysine 4 (H3K4) is essential for gene activation. Flowering Locus C (FLC), an important flowering repressor, quantitatively regulates flowering time in Arabidopsis and its expression level is coincident with H3K4 trimethylation (H3K4me3) dynamics. The methylation state of FLC chromatin is determined by the balance between methylation and demethylation, which is mediated by histone methyltransferases and demethylases, respectively. However, little is known about the role of histone demethylase(s) in FLC regulation. Here, we characterized the biochemical activity and biological function of a novel JmjC domain-containing H3K4 demethylase, JMJ15, in Arabidopsis. JMJ15, which is a member of the H3K4 demethylase JARID1 family, displayed H3K4me3 demethylase activity both in vitro and in vivo. The mutation of JMJ15 did not produce an obvious phenotype; however, overexpression JMJ15 resulted in an obvious early flowering phenotype, which was associated with the repression of FLC level and reduction in H3K4me3 at the FLC locus, resulting in increased FT expression. Our results suggest that JMJ15 is a novel H3K4 demethylase, involved in the control of flowering time by demethylating H3K4me3 at FLC chromatin when it was overexpressed in Arabidopsis. KEY MESSAGE Overexpression of a histone H3K4 demethylase, JMJ15, represses FLC expression by decreasing its chromatin H3K4me3 level, thereby controlling flowering time in Arabidopsis.
Collapse
Affiliation(s)
- Hongchun Yang
- Hebei Key Laboratory of Molecular Cell Biology, College of Biological Sciences, Hebei Normal University, Shijiazhuang 050016, Hebei, China
| | | | | | | | | | | |
Collapse
|
243
|
Niedojadło K, Pięciński S, Smoliński DJ, Bednarska-Kozakiewicz E. Transcriptional activity of Hyacinthus orientalis L. female gametophyte cells before and after fertilization. PLANTA 2012; 236:153-69. [PMID: 22293855 PMCID: PMC3382649 DOI: 10.1007/s00425-012-1599-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 01/05/2012] [Indexed: 05/19/2023]
Abstract
We characterized three phases of Hyacinthus orientalis L. embryo sac development, in which the transcriptional activity of the cells differed using immunolocalization of incorporated 5′-bromouracil, the total RNA polymerase II pool and the hypo- (initiation) and hyperphosphorylated (elongation) forms of RNA Pol II. The first stage, which lasts from the multinuclear stage to cellularization, is a period of high transcriptional activity, probably related to the maturation of female gametophyte cells. The second stage, encompassing the period of embryo sac maturity and the progamic phase, involves the transcriptional silencing of cells that will soon undergo fusion with male gametes. During this period in the hyacinth egg cell, there are almost no newly formed transcripts, and only a small pool of RNA Pol II is present in the nucleus. The transcriptional activity of the central cell is only slightly higher than that observed in the egg cell. The post-fertilization stage is related to the transcriptional activation of the zygote and the primary endosperm cell. The rapid increase in the pool of newly formed transcripts in these cells is accompanied by an increase in the pool of RNA Pol II, and the pattern of enzyme distribution in the zygote nucleus is similar to that observed in the somatic cells of the ovule. Our data, together with the earlier results of Pięciński et al. (2008), indicate post-fertilization synthesis and the maturation of numerous mRNA transcripts, suggesting that fertilization in H. orientalis induces the activation of the zygote and endosperm genomes.
Collapse
Affiliation(s)
- Katarzyna Niedojadło
- Department of Cell Biology, Institute of General and Molecular Biology, Nicolaus Copernicus University, Gagarina 9, 87-100 Toruń, Poland.
| | | | | | | |
Collapse
|
244
|
Sánchez-León N, Arteaga-Vázquez M, Alvarez-Mejía C, Mendiola-Soto J, Durán-Figueroa N, Rodríguez-Leal D, Rodríguez-Arévalo I, García-Campayo V, García-Aguilar M, Olmedo-Monfil V, Arteaga-Sánchez M, de la Vega OM, Nobuta K, Vemaraju K, Meyers BC, Vielle-Calzada JP. Transcriptional analysis of the Arabidopsis ovule by massively parallel signature sequencing. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:3829-42. [PMID: 22442422 PMCID: PMC3388818 DOI: 10.1093/jxb/ers075] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The life cycle of flowering plants alternates between a predominant sporophytic (diploid) and an ephemeral gametophytic (haploid) generation that only occurs in reproductive organs. In Arabidopsis thaliana, the female gametophyte is deeply embedded within the ovule, complicating the study of the genetic and molecular interactions involved in the sporophytic to gametophytic transition. Massively parallel signature sequencing (MPSS) was used to conduct a quantitative large-scale transcriptional analysis of the fully differentiated Arabidopsis ovule prior to fertilization. The expression of 9775 genes was quantified in wild-type ovules, additionally detecting >2200 new transcripts mapping to antisense or intergenic regions. A quantitative comparison of global expression in wild-type and sporocyteless (spl) individuals resulted in 1301 genes showing 25-fold reduced or null activity in ovules lacking a female gametophyte, including those encoding 92 signalling proteins, 75 transcription factors, and 72 RNA-binding proteins not reported in previous studies based on microarray profiling. A combination of independent genetic and molecular strategies confirmed the differential expression of 28 of them, showing that they are either preferentially active in the female gametophyte, or dependent on the presence of a female gametophyte to be expressed in sporophytic cells of the ovule. Among 18 genes encoding pentatricopeptide-repeat proteins (PPRs) that show transcriptional activity in wild-type but not spl ovules, CIHUATEOTL (At4g38150) is specifically expressed in the female gametophyte and necessary for female gametogenesis. These results expand the nature of the transcriptional universe present in the ovule of Arabidopsis, and offer a large-scale quantitative reference of global expression for future genomic and developmental studies.
Collapse
Affiliation(s)
- Nidia Sánchez-León
- Laboratorio Nacional de Genómica para la Biodiversidad y Departamento de Ingeniería Genética de Plantas, Cinvestav Irapuato CP36821 México
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
245
|
Su N, Hu ML, Wu DX, Wu FQ, Fei GL, Lan Y, Chen XL, Shu XL, Zhang X, Guo XP, Cheng ZJ, Lei CL, Qi CK, Jiang L, Wang H, Wan JM. Disruption of a rice pentatricopeptide repeat protein causes a seedling-specific albino phenotype and its utilization to enhance seed purity in hybrid rice production. PLANT PHYSIOLOGY 2012; 159:227-38. [PMID: 22430843 PMCID: PMC3366715 DOI: 10.1104/pp.112.195081] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Accepted: 03/15/2012] [Indexed: 05/18/2023]
Abstract
The pentatricopeptide repeat (PPR) gene family represents one of the largest gene families in higher plants. Accumulating data suggest that PPR proteins play a central and broad role in modulating the expression of organellar genes in plants. Here we report a rice (Oryza sativa) mutant named young seedling albino (ysa) derived from the rice thermo/photoperiod-sensitive genic male-sterile line Pei'ai64S, which is a leading male-sterile line for commercial two-line hybrid rice production. The ysa mutant develops albino leaves before the three-leaf stage, but the mutant gradually turns green and recovers to normal green at the six-leaf stage. Further investigation showed that the change in leaf color in ysa mutant is associated with changes in chlorophyll content and chloroplast development. Map-based cloning revealed that YSA encodes a PPR protein with 16 tandem PPR motifs. YSA is highly expressed in young leaves and stems, and its expression level is regulated by light. We showed that the ysa mutation has no apparent negative effects on several important agronomic traits, such as fertility, stigma extrusion rate, selfed seed-setting rate, hybrid seed-setting rate, and yield heterosis under normal growth conditions. We further demonstrated that ysa can be used as an early marker for efficient identification and elimination of false hybrids in commercial hybrid rice production, resulting in yield increases by up to approximately 537 kg ha(-1).
Collapse
MESH Headings
- Amino Acid Motifs
- Amino Acid Sequence
- Biomarkers
- Chimera/genetics
- Chimera/metabolism
- Chlorophyll/metabolism
- Chloroplasts/metabolism
- Chloroplasts/ultrastructure
- Chromosome Mapping
- Chromosomes, Plant/genetics
- Chromosomes, Plant/metabolism
- Cloning, Molecular
- Crosses, Genetic
- Fertility
- Genes, Plant
- Hybrid Vigor
- Microscopy, Electron, Transmission
- Molecular Sequence Data
- Mutation
- Oryza/anatomy & histology
- Oryza/genetics
- Oryza/metabolism
- Phenotype
- Photoperiod
- Plant Leaves/anatomy & histology
- Plant Leaves/metabolism
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plant Stems/metabolism
- Plant Stems/physiology
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Seedlings/genetics
- Seedlings/metabolism
- Seeds/genetics
- Seeds/metabolism
- Transcription, Genetic
Collapse
|
246
|
Waduwara-Jayabahu I, Oppermann Y, Wirtz M, Hull ZT, Schoor S, Plotnikov AN, Hell R, Sauter M, Moffatt BA. Recycling of methylthioadenosine is essential for normal vascular development and reproduction in Arabidopsis. PLANT PHYSIOLOGY 2012; 158:1728-44. [PMID: 22345506 PMCID: PMC3320181 DOI: 10.1104/pp.111.191072] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
5'-Methylthioadenosine (MTA) is the common by-product of polyamine (PA), nicotianamine (NA), and ethylene biosynthesis in Arabidopsis (Arabidopsis thaliana). The methylthiol moiety of MTA is salvaged by 5'-methylthioadenosine nucleosidase (MTN) in a reaction producing methylthioribose (MTR) and adenine. The MTN double mutant, mtn1-1mtn2-1, retains approximately 14% of the MTN enzyme activity present in the wild type and displays a pleiotropic phenotype that includes altered vasculature and impaired fertility. These abnormal traits were associated with increased MTA levels, altered PA profiles, and reduced NA content. Exogenous feeding of PAs partially recovered fertility, whereas NA supplementation improved fertility and also reversed interveinal chlorosis. The analysis of PA synthase crystal structures containing bound MTA suggests that the corresponding enzyme activities are sensitive to available MTA. Mutant plants that expressed either MTN or human methylthioadenosine phosphorylase (which metabolizes MTA without producing MTR) appeared wild type, proving that the abnormal traits of the mutant are due to MTA accumulation rather than reduced MTR. Based on our results, we propose that the key targets affected by increased MTA content are thermospermine synthase activity and spermidine-dependent posttranslational modification of eukaryotic initiation factor 5A.
Collapse
|
247
|
Li CH, Fu SX, Chen XJ, Qi CK. Phenotypic characterization and genetic analysis of a partially female-sterile mutant in Brassica napus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 185-186:112-117. [PMID: 22325872 DOI: 10.1016/j.plantsci.2011.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 09/23/2011] [Accepted: 09/24/2011] [Indexed: 05/31/2023]
Abstract
mfs is a partially female-sterile Brassica napus mutant derived from a spontaneous mutation. When the mutant is crossed as a female, very poor seed set is obtained, whereas it is fertile as a pollen donor. The floret of the mutant consisted of almost equal-length stamens, a short pistil, a flat style and ovary, and the stigma was chapped. Measures of pollen viability and pollen tube growth in vitro indicated that the mutation enhanced pollen viability. The papillae of mfs consisted of two conjoint bilobed domes, and the papillar cells were sparse, oblate and large at anthesis, but become withered and senesced quickly afterward. Pollen grains could germinate over the papillar cells, but pollen tubes could not penetrate into it. After flower opening, the number of organelles in mfs papillar cell decreased, the structure of it distinctly degenerated, and vacuolization was abnormally high. Genetic analysis of 3 F2 populations and 3 BC1F1 populations suggested that the mutant trait was controlled by two recessive genes.
Collapse
Affiliation(s)
- Chun-Hong Li
- Nanjing Sub-Center of National Rapeseed Development Center, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, PR China
| | | | | | | |
Collapse
|
248
|
Sakai T, Mochizuki S, Haga K, Uehara Y, Suzuki A, Harada A, Wada T, Ishiguro S, Okada K. The wavy growth 3 E3 ligase family controls the gravitropic response in Arabidopsis roots. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:303-14. [PMID: 22122664 DOI: 10.1111/j.1365-313x.2011.04870.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Regulation of the root growth pattern is an important control mechanism during plant growth and propagation. To better understand alterations in root growth direction in response to environmental stimuli, we have characterized an Arabidopsis thaliana mutant, wavy growth 3 (wav3), whose roots show a short-pitch pattern of wavy growth on inclined agar medium. The wav3 mutant shows a greater curvature of root bending in response to gravity, but a smaller curvature in response to light, suggesting that it is a root gravitropism-enhancing mutation. This wav3 phenotype also suggests that enhancement of the gravitropic response in roots strengthens root tip impedance after contact with the agar surface and/or causes an increase in subsequent root bending in response to obstacle-touching stimulus in these mutants. WAV3 encodes a protein with a RING finger domain, and is mainly expressed in root tips. RING-containing proteins often function as an E3 ubiquitin ligase, and the WAV3 protein shows such activity in vitro. There are three genes homologous to WAV3 in the Arabidopsis genome [EMBRYO SAC DEVELOPMENT ARREST 40 (EDA40), WAVH1 and WAVH2 ], and wav3 wavh1 wavh2 triple mutants show marked root gravitropism abnormalities. This genetic study indicates that WAV3 functions positively rather than negatively in root gravitropism, and that enhancement of the gravitropic response in wav3 roots is dependent upon the function of WAVH2 in the absence of WAV3. Hence, our results demonstrate that the WAV3 family of proteins are E3 ligases that are required for root gravitropism in Arabidopsis.
Collapse
Affiliation(s)
- Tatsuya Sakai
- Graduate School of Science and Technology, Niigata University, Nishi-ku, Niigata 950-2181, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
249
|
Genome-wide evaluation of histone methylation changes associated with leaf senescence in Arabidopsis. PLoS One 2012; 7:e33151. [PMID: 22427974 PMCID: PMC3299739 DOI: 10.1371/journal.pone.0033151] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 02/10/2012] [Indexed: 01/05/2023] Open
Abstract
Leaf senescence is the orderly dismantling of older tissue that allows recycling of nutrients to developing portions of the plant and is accompanied by major changes in gene expression. Histone modifications correlate to levels of gene expression, and this study utilizes ChIP-seq to classify activating H3K4me3 and silencing H3K27me3 marks on a genome-wide scale for soil-grown mature and naturally senescent Arabidopsis leaves. ChIPnorm was used to normalize data sets and identify genomic regions with significant differences in the two histone methylation patterns, and the differences were correlated to changes in gene expression. Genes that showed an increase in the H3K4me3 mark in older leaves were senescence up-regulated, while genes that showed a decrease in the H3K4me3 mark in the older leaves were senescence down-regulated. For the H3K27me3 modification, genes that lost the H3K27me3 mark in older tissue were senescence up-regulated. Only a small number of genes gained the H3K27me3 mark, and these were senescence down-regulated. Approximately 50% of senescence up-regulated genes lacked the H3K4me3 mark in both mature and senescent leaf tissue. Two of these genes, SAG12 and At1g73220, display strong senescence up-regulation without the activating H3K4me3 histone modification. This study provides an initial epigenetic framework for the developmental transition into senescence.
Collapse
|
250
|
Schmitz RJ, Ecker JR. Epigenetic and epigenomic variation in Arabidopsis thaliana. TRENDS IN PLANT SCIENCE 2012; 17:149-54. [PMID: 22342533 PMCID: PMC3645451 DOI: 10.1016/j.tplants.2012.01.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 12/23/2011] [Accepted: 01/04/2012] [Indexed: 05/04/2023]
Abstract
Arabidopsis thaliana (Arabidopsis) is ideally suited for studies of natural phenotypic variation. This species has also provided an unparalleled experimental system to explore the mechanistic link between genetic and epigenetic variation, especially with regard to cytosine methylation. Using high-throughput sequencing methods, genotype to epigenotype to phenotype observations can now be extended to plant populations. We review the evidence for induced and spontaneous epigenetic variants that have been identified in Arabidopsis in the laboratory and discuss how these experimental observations could explain existing variation in the wild.
Collapse
Affiliation(s)
- Robert J Schmitz
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | |
Collapse
|