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Audoor S, Bilcke G, Pargana K, Belišová D, Thierens S, Van Bel M, Sterck L, Rijsdijk N, Annunziata R, Ferrante MI, Vandepoele K, Vyverman W. Transcriptional chronology reveals conserved genes involved in pennate diatom sexual reproduction. Mol Ecol 2024; 33:e17320. [PMID: 38506152 DOI: 10.1111/mec.17320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/23/2024] [Accepted: 03/07/2024] [Indexed: 03/21/2024]
Abstract
Sexual reproduction is a major driver of adaptation and speciation in eukaryotes. In diatoms, siliceous microalgae with a unique cell size reduction-restitution life cycle and among the world's most prolific primary producers, sex also acts as the main mechanism for cell size restoration through the formation of an expanding auxospore. However, the molecular regulators of the different stages of sexual reproduction and size restoration are poorly explored. Here, we combined RNA sequencing with the assembly of a 55 Mbp reference genome for Cylindrotheca closterium to identify patterns of gene expression during different stages of sexual reproduction. These were compared with a corresponding transcriptomic time series of Seminavis robusta to assess the degree of expression conservation. Integrative orthology analysis revealed 138 one-to-one orthologues that are upregulated during sex in both species, among which 56 genes consistently upregulated during cell pairing and gametogenesis, and 11 genes induced when auxospores are present. Several early, sex-specific transcription factors and B-type cyclins were also upregulated during sex in other pennate and centric diatoms, pointing towards a conserved core regulatory machinery for meiosis and gametogenesis across diatoms. Furthermore, we find molecular evidence that the pheromone-induced cell cycle arrest is short-lived in benthic diatoms, which may be linked to their active mode of mate finding through gliding. Finally, we exploit the temporal resolution of our comparative analysis to report the first marker genes for auxospore identity called AAE1-3 ("Auxospore-Associated Expression"). Altogether, we introduce a multi-species model of the transcriptional dynamics during size restoration in diatoms and highlight conserved gene expression dynamics during different stages of sexual reproduction.
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Affiliation(s)
- Sien Audoor
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
| | - Gust Bilcke
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Katerina Pargana
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
| | - Darja Belišová
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Sander Thierens
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Michiel Van Bel
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Lieven Sterck
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Nadine Rijsdijk
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | | | - Maria Immacolata Ferrante
- Stazione Zoologica Anton Dohrn, Naples, Italy
- Associate to the National Institute of Oceanography and Applied Geophysics, Trieste, Italy
| | - Klaas Vandepoele
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for AI & Computational Biology, VIB, Ghent, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Ghent, Ghent, Belgium
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Zhang Z, Zhang A, Zhang Y, Zhao J, Wang Y, Zhang L, Zhang S. Ectopic expression of HaPEPC1 from the desert shrub Haloxylon ammodendron confers drought stress tolerance in Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108536. [PMID: 38507839 DOI: 10.1016/j.plaphy.2024.108536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/29/2024] [Accepted: 03/13/2024] [Indexed: 03/22/2024]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) plays a crucial role in the initial carbon fixation process in C4 plants. However, its nonphotosynthetic functions in Haloxylon ammodendron, a C4 perennial xerohalophytic shrub, are still poorly understood. Previous studies have reported the involvement of PEPC in plant responses to abiotic stresses such as drought and salt stress. However, the underlying mechanism of PEPC tolerance to drought stress has not been determined. In this study, we cloned the C4-type PEPC gene HaPEPC1 from H. ammodendron and investigated its biological function by generating transgenic Arabidopsis plants with ectopic expression of HaPEPC1. Our results showed that, compared with WT (wild-type) plants, ectopic expression of HaPEPC1 plants exhibited significantly greater germination rates and chlorophyll contents. Furthermore, under drought stress, the transgenic plants presented increased root length, fresh weight, photosynthetic capacity, and antioxidant enzyme activities, particularly ascorbate peroxidase and peroxidase. Additionally, the transgenic plants exhibited reduced levels of malondialdehyde, H2O2 (hydrogen peroxide), and O2- (superoxide radical). Transcriptome analysis indicated that ectopic expression of HaPEPC1 primarily regulated the expression of genes associated with the stress defence response, glutathione metabolism, and abscisic acid (ABA) synthesis and signalling pathways in response to drought stress. Taken together, these findings suggest that the ectopic expression of HaPEPC1 enhances the reduction of H2O2 and O2- in transgenic plants, thereby improving reactive oxygen species (ROS) scavenging capacity and enhancing drought tolerance. Therefore, the HaPEPC1 gene holds promise as a candidate gene for crop selection aimed at enhancing drought tolerance.
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Affiliation(s)
- Zhilong Zhang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Anna Zhang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yaru Zhang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Juan Zhao
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuanyuan Wang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lingling Zhang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Sheng Zhang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Kim YJ, Kim MH, Hong WJ, Moon S, Kim EJ, Silva J, Lee J, Lee S, Kim ST, Park SK, Jung KH. GORI, encoding the WD40 domain protein, is required for pollen tube germination and elongation in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1645-1664. [PMID: 33345419 DOI: 10.1111/tpj.15139] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 10/30/2020] [Accepted: 11/13/2020] [Indexed: 05/05/2023]
Abstract
Successful delivery of sperm cells to the embryo sac in higher plants is mediated by pollen tube growth. The molecular mechanisms underlying pollen germination and tube growth in crop plants remain rather unclear, although these mechanisms are crucial to plant reproduction and seed formation. By screening pollen-specific gene mutants in rice (Oryza sativa), we identified a T-DNA insertional mutant of Germinating modulator of rice pollen (GORI) that showed a one-to-one segregation ratio for wild type (WT) to heterozygous. GORI encodes a seven-WD40-motif protein that is homologous to JINGUBANG/REN4 in Arabidopsis. GORI is specifically expressed in rice pollen, and its protein is localized in the nucleus, cytosol and plasma membrane. Furthermore, a homozygous mutant, gori-2, created through CRISPR-Cas9 clearly exhibited male sterility with disruption of pollen tube germination and elongation. The germinated pollen tube of gori-2 exhibited decreased actin filaments and altered pectin distribution. Transcriptome analysis revealed that 852 pollen-specific genes were downregulated in gori-2 compared with the WT, and Gene Ontology enrichment analysis indicated that these genes are strongly associated with cell wall modification and clathrin coat assembly. Based on the molecular features of GORI, phenotypical observation of the gori mutant and its interaction with endocytic proteins and Rac GTPase, we propose that GORI plays key roles in forming endo-/exocytosis complexes that could mediate pollen tube growth in rice.
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Affiliation(s)
- Yu-Jin Kim
- Department of Life Science and Environmental Biochemistry, Pusan National University, Miryang, 50463, Republic of Korea
| | - Myung-Hee Kim
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Woo-Jong Hong
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Sunok Moon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Eui-Jung Kim
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Jeniffer Silva
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Jinwon Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Sangho Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, 50463, Republic of Korea
| | - Soon Ki Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
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Weber M, Beyene B, Nagler N, Herfert J, Schempp S, Klecker M, Clemens S. A mutation in the essential and widely conserved DAMAGED DNA BINDING1-Cullin4 ASSOCIATED FACTOR gene OZS3 causes hypersensitivity to zinc excess, cold and UV stress in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:995-1009. [PMID: 32314481 DOI: 10.1111/tpj.14779] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 02/18/2020] [Accepted: 04/01/2020] [Indexed: 05/28/2023]
Abstract
The overly zinc sensitive Arabidopsis thaliana mutant ozs3 shows reduced growth of the primary root, which is exacerbated by an excess specifically of Zn ions. In addition, ozs3 plants display various subtle developmental phenotypes, such as longer petioles and early flowering. Also, ozs3 seedlings are completely but reversibly growth-arrested when shifted to 4°C. The causal mutation was mapped to a gene encoding a putative substrate-recognition receptor of cullin4 E3 ligases. OZS3 orthologous genes can be found in almost all eukaryotic genomes. Most species from Schizosaccharomyces pombe to Homo sapiens, and including A. thaliana, possess one ortholog. No functional data are available for these genes in any of the multicellular model systems. CRISPR-Cas9-mediated knockout demonstrated that a complete loss of OZS3 function is embryo-lethal, indicating essentiality of OZS3 and its orthologs. The OZS3 protein interacts with the adaptor protein DAMAGED DNA BINDING1 (DDB1) in the nucleus. Thus, it is indeed a member of the large yet poorly characterized family of DDB1-cullin4 associated factors in plants. Mutant phenotypes of ozs3 plants are apparently caused by the weakened DDB1-OZS3 interaction as a result of the exchange of a conserved amino acid near the conserved WDxR motif.
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Affiliation(s)
- Michael Weber
- Department of Plant Physiology, University of Bayreuth, Bayreuth, 95440, Germany
| | - Blen Beyene
- Department of Plant Physiology, University of Bayreuth, Bayreuth, 95440, Germany
| | - Nicole Nagler
- Department of Plant Physiology, University of Bayreuth, Bayreuth, 95440, Germany
| | - Jörn Herfert
- Department of Plant Physiology, University of Bayreuth, Bayreuth, 95440, Germany
| | - Stefanie Schempp
- Department of Plant Physiology, University of Bayreuth, Bayreuth, 95440, Germany
| | - Maria Klecker
- Department of Plant Physiology, University of Bayreuth, Bayreuth, 95440, Germany
| | - Stephan Clemens
- Department of Plant Physiology, University of Bayreuth, Bayreuth, 95440, Germany
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Lo S, Muñoz-Amatriaín M, Hokin SA, Cisse N, Roberts PA, Farmer AD, Xu S, Close TJ. A genome-wide association and meta-analysis reveal regions associated with seed size in cowpea [Vigna unguiculata (L.) Walp]. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3079-3087. [PMID: 31367839 PMCID: PMC6791911 DOI: 10.1007/s00122-019-03407-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/24/2019] [Indexed: 05/19/2023]
Abstract
This paper combined GWAS, meta-analysis and sequence homology comparison with common bean to identify regions associated with seed size variation in domesticated cowpea. Seed size is an important trait for yield and commercial value in dry-grain cowpea. Seed size varies widely among different cowpea accessions, and the genetic basis of such variation is not yet well understood. To better decipher the genetic basis of seed size, a genome-wide association study (GWAS) and meta-analysis were conducted on a panel of 368 cowpea diverse accessions from 51 countries. Four traits, including seed weight, length, width and density were evaluated across three locations. Using 51,128 single nucleotide polymorphisms covering the cowpea genome, 17 loci were identified for these traits. One locus was common to weight, width and length, suggesting pleiotropy. By integrating synteny-based analysis with common bean, six candidate genes (Vigun05g036000, Vigun05g039600, Vigun05g204200, Vigun08g217000, Vigun11g187000, and Vigun11g191300) which are implicated in multiple functional categories related to seed size such as endosperm development, embryo development, and cell elongation were identified. These results suggest that a combination of GWAS meta-analysis with synteny comparison in a related plant is an efficient approach to identify candidate gene (s) for complex traits in cowpea. The identified loci and candidate genes provide useful information for improving cowpea varieties and for molecular investigation of seed size.
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Affiliation(s)
- Sassoum Lo
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
| | - María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Samuel A Hokin
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Ndiaga Cisse
- Centre d'Etude Régional pour l'Amélioration de l'Adaptation à la Sècheresse, ISRA/CERAAS, Thies, Senegal
| | - Philip A Roberts
- Department of Nematology, University of California, Riverside, CA, 92521, USA
| | - Andrew D Farmer
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Shizhong Xu
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
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6
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Glöckle B, Urban WJ, Nagahara S, Andersen ED, Higashiyama T, Grini PE, Schnittger A. Pollen differentiation as well as pollen tube guidance and discharge are independent of the presence of gametes. Development 2018; 145:dev.152645. [PMID: 29217755 PMCID: PMC5825867 DOI: 10.1242/dev.152645] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/27/2017] [Indexed: 12/16/2022]
Abstract
After meiosis, an unequal cell division generates the male gamete lineage in flowering plants. The generative cell will undergo a second division, giving rise to the two gametes, i.e. the sperm cells. The other cell will develop into the vegetative cell that plays a crucial role in pollen tube formation and sperm delivery. Recently, the vegetative cell has been suggested to be important for programming of the chromatin state in sperm cells and/or the resulting fertilization products. Blocking the initial unequal division genetically, we first highlight that the default differentiation state after male meiosis is a vegetative fate, which is consistent with earlier work. We find that uni-nucleated mutant microspores differentiated as wild-type vegetative cells, including chromatin remodeling and the transcriptional activation of transposable elements. Moreover, live-cell imaging revealed that this vegetative cell is sufficient for the correct guidance of the pollen tube to the female gametes. Hence, we conclude that vegetative cell differentiation and function does not depend on the formation or presence of the actual gametes but rather on external signals or a cell-autonomous pace keeper. Summary: Cell biological analyses in Arabidopsis show that the vegetative cell differentiates without the presence of the actual gametes, and is solely sufficient for pollen tube germination, guidance, ovule penetration and pollen tube discharge.
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Affiliation(s)
- Barbara Glöckle
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS - UPR2357, Université de Strasbourg, 12 Rue du Général Zimmer, 67084 Strasbourg Cedex, France.,Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Wojciech J Urban
- University of Hamburg, Biozentrum Klein Flottbek, Department of Developmental Biology, 22609 Hamburg, Germany
| | - Shiori Nagahara
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Ellen D Andersen
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.,JST ERATO Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Paul E Grini
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Arp Schnittger
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS - UPR2357, Université de Strasbourg, 12 Rue du Général Zimmer, 67084 Strasbourg Cedex, France .,University of Hamburg, Biozentrum Klein Flottbek, Department of Developmental Biology, 22609 Hamburg, Germany
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7
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Bian S, Li X, Mainali H, Chen L, Dhaubhadel S. Genome-wide analysis of DWD proteins in soybean (Glycine max): Significance of Gm08DWD and GmMYB176 interaction in isoflavonoid biosynthesis. PLoS One 2017; 12:e0178947. [PMID: 28586359 PMCID: PMC5460815 DOI: 10.1371/journal.pone.0178947] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/22/2017] [Indexed: 01/26/2023] Open
Abstract
A subset of WD40 proteins with DWD motif has been proposed to serve as substrate receptor of DDB-CUL4-ROC1 complex, thereby getting involved in protein degradation via ubiquitination pathway. Here, we identified a total of 161 potential DWD proteins in soybean (Glycine max) by searching DWD motif against the genome-wide WD40 repeats, and classified them into 20 groups on the basis of their functional domains and annotations. These putative DWD genes in soybean displayed tissue-specific expression patterns, and their genome localization and analysis of evolutionary relationship identified 48 duplicated gene pairs within 161 GmDWDs. Among the 161 soybean DWD proteins, Gm08DWD was previously found to interact with an isoflavonoid regulator, GmMYB176. Therefore, Gm08DWD and its homologue Gm05DWD were further investigated. Expression profile of both genes in different soybean tissues revealed that Gm08DWD was expressed higher in embryo, while Gm05DWD exhibited maximum transcript accumulation in leaf. Our protein-protein interaction studies demonstrated that Gm08DWD interacts with GmMYB176. Although Gm08DWD was localized both in nucleus and cytoplasm, the resulting complex of Gm08DWD and GmMYB176 was mainly observed in the nucleus. This finding is consistent with the functional localization of CUL4-E3 ligase complex. In conclusion, the survey on soybean potential DWD protein is useful reference for the further functional investigation of their DDB1-binding ability. Based on the functional investigation of Gm08DWD, we speculate that protein-protein interaction between Gm08DWD and GmMYB176 may lead to the degradation of GmMYB176 through CUL4-DDB1complex.
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Affiliation(s)
- Shaomin Bian
- College of Plant Science, Jilin University, Changchun, Jilin, China
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
| | - Xuyan Li
- College of Plant Science, Jilin University, Changchun, Jilin, China
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
| | - Hemanta Mainali
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
| | - Ling Chen
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
| | - Sangeeta Dhaubhadel
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
- Department of Biology, Western University, London, ON, Canada
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Kapolas G, Beris D, Katsareli E, Livanos P, Zografidis A, Roussis A, Milioni D, Haralampidis K. APRF1 promotes flowering under long days in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 253:141-153. [PMID: 27968983 DOI: 10.1016/j.plantsci.2016.09.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 09/23/2016] [Accepted: 09/26/2016] [Indexed: 05/25/2023]
Abstract
Arabidopsis thaliana flowering time mutants revealed the function of numerous genes that regulate the transition from vegetative to reproductive growth. Analyses of their loci have shown that many of them act as chromatin modifiers. In this study, a combination of molecular and genetic approaches have been implemented, to characterize the function of APRF1 (ANTHESIS POMOTING FACTOR 1) gene in A. thaliana and to investigate its role in plant development. APRF1 encodes for a low molecular weight nuclear WDR protein which displays functional homology to the Swd2 protein, an essential subunit of the yeast histone methylation COMPASS complex. Compared to WT plants, total loss-of-function aprf1 mutants exhibited shoot apical meristem (SAM) alterations and increased growth rates. However, the vegetative phase of aprf1 plants was prolonged and bolting was delayed, indicating an impairment in flowering under long days (LD). On the contrary, overexpression of APRF1 accelerates flowering. Consistent with the late flowering phenotype, the molecular data confirmed that FLC and SOC1 expression were significantly altered in the aprf1 mutants. Our data suggest that APRF1 acts upstream of FLC and promotes flowering under LD.
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Affiliation(s)
- Georgios Kapolas
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Despoina Beris
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Efthimia Katsareli
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Pantelis Livanos
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Aris Zografidis
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Andreas Roussis
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Dimitra Milioni
- Agricultural University of Athens, Department of Agricultural Biotechnology, Iera Odos 75, 11855 Athens, Greece.
| | - Kosmas Haralampidis
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
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9
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Maruyama D, Ohtsu M, Higashiyama T. Cell fusion and nuclear fusion in plants. Semin Cell Dev Biol 2016; 60:127-135. [PMID: 27473789 DOI: 10.1016/j.semcdb.2016.07.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/25/2016] [Accepted: 07/26/2016] [Indexed: 10/21/2022]
Abstract
Eukaryotic cells are surrounded by a plasma membrane and have a large nucleus containing the genomic DNA, which is enclosed by a nuclear envelope consisting of the outer and inner nuclear membranes. Although these membranes maintain the identity of cells, they sometimes fuse to each other, such as to produce a zygote during sexual reproduction or to give rise to other characteristically polyploid tissues. Recent studies have demonstrated that the mechanisms of plasma membrane or nuclear membrane fusion in plants are shared to some extent with those of yeasts and animals, despite the unique features of plant cells including thick cell walls and intercellular connections. Here, we summarize the key factors in the fusion of these membranes during plant reproduction, and also focus on "non-gametic cell fusion," which was thought to be rare in plant tissue, in which each cell is separated by a cell wall.
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Affiliation(s)
- Daisuke Maruyama
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
| | - Mina Ohtsu
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Tetsuya Higashiyama
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan; Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan; JST ERATO Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
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10
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Qin X, Huang Q, Xiao H, Zhang Q, Ni C, Xu Y, Liu G, Yang D, Zhu Y, Hu J. The rice DUF1620-containing and WD40-like repeat protein is required for the assembly of the restoration of fertility complex. THE NEW PHYTOLOGIST 2016; 210:934-945. [PMID: 26781807 DOI: 10.1111/nph.13824] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 11/22/2015] [Indexed: 06/05/2023]
Abstract
Cytoplasmic male sterility (CMS) and restoration of fertility (Rf) are widely distributed in plant species utilized by humans. RF5 and GRP162 are subunits of the restoration of fertility complex (RFC) in Hong-Lian rice. Despite the fact that the RFC is 400-500 kDa in size, the other proteins or factors in the complex still remain unknown. Here, we identified RFC subunit 3, which encodes a DUF1620-containing and WD40-like repeat protein (RFC3) that is present in all tissues but highly expressed in leaves. We established that RFC3 interacts with both RF5 and GRP162 in vitro and in vivo, and is transported into the mitochondria as a membrane protein. Furthermore, CMS RNA (atp6-orfH79) and CMS cytotoxic protein (ORFH79) accumulate when RFC3 is silenced in restorer lines. We presented the analysis with blue-native polyacrylamide gel electrophoresis, indicating that RFC is disrupted in the RNAi line. We concluded that RCF3 is indispensable as a scaffold protein for the assembly of the RFC complex. We unveil a new molecular player of the RFC in the Rf pathway in rice and propose the model of RFC based on these data.
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Affiliation(s)
- Xiaojian Qin
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Qi Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Haijun Xiao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Qiannan Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Chenzi Ni
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Yanghong Xu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Gai Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Daichang Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
- Engineering Research Center for Plant Biotechnology and Germplasm, Utilization, Ministry of Education, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, the Ministry of Agriculture, The Yangtze River Valley Hybrid Rice Collaboration & Innovation Center, Wuhan University, Wuhan, Hubei, 430072, China
| | - Yingguo Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
- Engineering Research Center for Plant Biotechnology and Germplasm, Utilization, Ministry of Education, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, the Ministry of Agriculture, The Yangtze River Valley Hybrid Rice Collaboration & Innovation Center, Wuhan University, Wuhan, Hubei, 430072, China
| | - Jun Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
- Engineering Research Center for Plant Biotechnology and Germplasm, Utilization, Ministry of Education, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, the Ministry of Agriculture, The Yangtze River Valley Hybrid Rice Collaboration & Innovation Center, Wuhan University, Wuhan, Hubei, 430072, China
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11
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Ju Y, Liu C, Lu W, Zhang Q, Sodmergen. Arabidopsis mitochondrial protein slow embryo development1 is essential for embryo development. Biochem Biophys Res Commun 2016; 474:371-376. [PMID: 27109472 DOI: 10.1016/j.bbrc.2016.04.114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 04/20/2016] [Indexed: 10/21/2022]
Abstract
The plant seeds formation are crucial parts in reproductive process in seed plants as well as food source for humans. Proper embryo development ensure viable seed formation. Here, we showed an Arabidopsis T-DNA insertion mutant slow embryo development1 (sed1) which exhibited retarded embryogenesis, led to aborted seeds. Embryo without SED1 developed slower compared to normal one and could be recognized at early globular stage by its white appearance. In later development stage, storage accumulated poorly with less protein and lipid body production. In vitro culture did not rescue albino embryo. SED1 encoded a protein targeted to mitochondria. Transmission electron microscopic analysis revealed that mitochondria developed abnormally, and more strikingly plastid failed to construct grana in time in sed1/sed1 embryo. These data indicated that SED1 is indispensable for embryogenesis in Arabidopsis, and the mitochondria may be involved in the regulation of many aspects of seed development.
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Affiliation(s)
- Yan Ju
- Key Laboratory of Cell Proliferation and Differentiation (Ministry of Education), College of Life Sciences, Peking University, Beijing 100871, China
| | - Chunying Liu
- Key Laboratory of Cell Proliferation and Differentiation (Ministry of Education), College of Life Sciences, Peking University, Beijing 100871, China
| | - Wenwen Lu
- Key Laboratory of Cell Proliferation and Differentiation (Ministry of Education), College of Life Sciences, Peking University, Beijing 100871, China
| | - Quan Zhang
- Key Laboratory of Cell Proliferation and Differentiation (Ministry of Education), College of Life Sciences, Peking University, Beijing 100871, China
| | - Sodmergen
- Key Laboratory of Cell Proliferation and Differentiation (Ministry of Education), College of Life Sciences, Peking University, Beijing 100871, China.
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12
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Beris D, Kapolas G, Livanos P, Roussis A, Milioni D, Haralampidis K. RNAi-mediated silencing of the Arabidopsis thaliana ULCS1 gene, encoding a WDR protein, results in cell wall modification impairment and plant infertility. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 245:71-83. [PMID: 26940493 DOI: 10.1016/j.plantsci.2016.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 01/19/2016] [Accepted: 01/23/2016] [Indexed: 05/25/2023]
Abstract
Ubiquitin mediated protein degradation constitutes one of the most complex post translational gene regulation mechanisms in eukaryotes. This fine-tuned proteolytic machinery is based on a vast number of E3 ubiquitin ligase complexes that mark target proteins with ubiquitin. The specificity is accomplished by a number of adaptor proteins that contain functional binding domains, including the WD40 repeat motif (WDRs). To date, only few of these proteins have been identified in plants. An RNAi mediated silencing approach was used here to functionally characterize the Arabidopsis thaliana ULCS1 gene, which encodes for a small molecular weight WDR protein. AtULCS1 interacts with the E3Cullin Ring Ligase subunit DDB1a, regulating most likely the degradation of specific proteins involved in the manifestation of diverse developmental events. Silencing of AtULCS1 results in sterile plants with pleiotropic phenotypes. Detailed analysis revealed that infertility is the outcome of anther indehiscence, which in turn is due to the impairment of the plants to accomplish secondary wall modifications. Furthermore, IREGULAR XYLEM gene expression and lignification is diminished in anther endothecium and the stem vascular tissue of the silenced plants. These data underline the importance of AtULCS1 in plant development and reproduction.
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Affiliation(s)
- Despoina Beris
- University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Georgios Kapolas
- University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Pantelis Livanos
- University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Andreas Roussis
- University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Dimitra Milioni
- Agricultural University of Athens, Department of Agricultural Biotechnology, Iera Odos 75, 11855 Athens, Greece.
| | - Kosmas Haralampidis
- University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
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13
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Tang X, Miao M, Niu X, Zhang D, Cao X, Jin X, Zhu Y, Fan Y, Wang H, Liu Y, Sui Y, Wang W, Wang A, Xiao F, Giovannoni J, Liu Y. Ubiquitin-conjugated degradation of golden 2-like transcription factor is mediated by CUL4-DDB1-based E3 ligase complex in tomato. THE NEW PHYTOLOGIST 2016; 209:1028-39. [PMID: 26352615 DOI: 10.1111/nph.13635] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 08/11/2015] [Indexed: 05/19/2023]
Abstract
CULLIN4-RING ubiquitin ligases (CRL4s) as well as their targets are fundamental regulators functioning in many key developmental and stress responses in eukaryotes. In tomato (Solanum lycopersicum), molecular cloning has revealed that the underlying genes of natural spontaneous mutations high pigment 1 (hp1), high pigment 2 (hp2) and uniform ripening (u) encode UV-DAMAGED DNA BINDING PROTEIN 1 (DDB1), DE-ETIOLATED 1 (DET1) and GOLDEN 2-LIKE (GLK2), respectively. However, the molecular basis of the opposite actions of tomato GLK2 vs CUL4-DDB1-DET1 complex on regulating plastid level and fruit quality remains unknown. Here, we provide molecular evidence showing that the tomato GLK2 protein is a substrate of the CUL4-DDB1-DET1 ubiquitin ligase complex for the proteasome degradation. SlGLK2 is degraded by the ubiquitin-proteasome system, which is mainly determined by two lysine residues (K11 and K253). SlGLK2 associates with the CUL4-DDB1-DET1 E3 complex in plant cells. Genetically impairing CUL4, DDB1 or DET1 results in a retardation of SlGLK2 degradation by the 26S proteasome. These findings are relevant to the potential of nutrient accumulation in tomato fruit by mediating the plastid level and contribute to a deeper understanding of an important regulatory loop, linking protein turnover to gene regulation.
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Affiliation(s)
- Xiaofeng Tang
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
| | - Min Miao
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Xiangli Niu
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Danfeng Zhang
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Xulv Cao
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Xichen Jin
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Yunye Zhu
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Youhong Fan
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Hongtao Wang
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Ying Liu
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Yuan Sui
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Wenjie Wang
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
- Department of Plant, Soil, and Entomological Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Anquan Wang
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
- Boyce Thompson Institute for Plant Research, Cornell University, Tower Road, Ithaca, NY, 14853, USA
| | - Fangming Xiao
- Department of Plant, Soil, and Entomological Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Jim Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University, Tower Road, Ithaca, NY, 14853, USA
| | - Yongsheng Liu
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
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14
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Dutilleul C, Ribeiro I, Blanc N, Nezames CD, Deng XW, Zglobicki P, Palacio Barrera AM, Atehortùa L, Courtois M, Labas V, Giglioli-Guivarc'h N, Ducos E. ASG2 is a farnesylated DWD protein that acts as ABA negative regulator in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:185-98. [PMID: 26147561 DOI: 10.1111/pce.12605] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/23/2015] [Accepted: 06/24/2015] [Indexed: 05/12/2023]
Abstract
The tagging-via-substrate approach designed for the capture of mammal prenylated proteins was adapted to Arabidopsis cell culture. In this way, proteins are in vivo tagged with an azide-modified farnesyl moiety and captured thanks to biotin alkyne Click-iT® chemistry with further streptavidin-affinity chromatography. Mass spectrometry analyses identified four small GTPases and ASG2 (ALTERED SEED GERMINATION 2), a protein previously associated to the seed germination gene network. ASG2 is a conserved protein in plants and displays a unique feature that associates WD40 domains and tetratricopeptide repeats. Additionally, we show that ASG2 has a C-terminal CaaX-box that is farnesylated in vitro. Protoplast transfections using CaaX prenyltransferase mutants show that farnesylation provokes ASG2 nucleus exclusion. Moreover, ASG2 interacts with DDB1 (DAMAGE DNA BINDING protein 1), and the subcellular localization of this complex depends on ASG2 farnesylation status. Finally, germination and root elongation experiments reveal that asg2 and the farnesyltransferase mutant era1 (ENHANCED RESPONSE TO ABSCISIC ACID (ABA) 1) behave in similar manners when exposed to ABA or salt stress. To our knowledge, ASG2 is the first farnesylated DWD (DDB1 binding WD40) protein related to ABA response in Arabidopsis that may be linked to era1 phenotypes.
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Affiliation(s)
- Christelle Dutilleul
- EA2106 'Biomolécules et Biotechnologies Végétales', UFR des Sciences et Techniques, Université François Rabelais de Tours, Tours, F-37200, France
| | - Iliana Ribeiro
- EA2106 'Biomolécules et Biotechnologies Végétales', UFR des Sciences et Techniques, Université François Rabelais de Tours, Tours, F-37200, France
| | - Nathalie Blanc
- EA2106 'Biomolécules et Biotechnologies Végétales', UFR des Sciences et Techniques, Université François Rabelais de Tours, Tours, F-37200, France
| | - Cynthia D Nezames
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8104, USA
| | - Xing Wang Deng
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8104, USA
| | - Piotr Zglobicki
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, 30-387, Poland
| | - Ana María Palacio Barrera
- Universidad de Antioquia, Laboratorio de Biotecnología, Sede de Investigación Universitaria, Medellín, Colombia
| | - Lucia Atehortùa
- Universidad de Antioquia, Laboratorio de Biotecnología, Sede de Investigación Universitaria, Medellín, Colombia
| | - Martine Courtois
- EA2106 'Biomolécules et Biotechnologies Végétales', UFR des Sciences et Techniques, Université François Rabelais de Tours, Tours, F-37200, France
| | - Valérie Labas
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, UMR CNRS 7247, UFR, IFC, Plate-forme d'Analyse Intégrative des Biomolécules, Laboratoire de Spectrométrie de Masse, Nouzilly, F-37380, France
| | - Nathalie Giglioli-Guivarc'h
- EA2106 'Biomolécules et Biotechnologies Végétales', UFR des Sciences et Techniques, Université François Rabelais de Tours, Tours, F-37200, France
| | - Eric Ducos
- EA2106 'Biomolécules et Biotechnologies Végétales', UFR des Sciences et Techniques, Université François Rabelais de Tours, Tours, F-37200, France
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15
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Chen H, Zou W, Zhao J. Ribonuclease J is required for chloroplast and embryo development in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2079-91. [PMID: 25871650 PMCID: PMC4378637 DOI: 10.1093/jxb/erv010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/18/2014] [Accepted: 12/19/2014] [Indexed: 05/20/2023]
Abstract
Chloroplasts perform many essential metabolic functions and their proper development is critically important in embryogenesis. However, little is known about how chloroplasts function in embryogenesis and more relevant components need to be characterized. In this study, we show that Arabidopsis Ribonuclease J (RNase J) is required for chloroplast and embryo development. Mutation of AtRNJ led to albino ovules containing aborted embryos; the morphological development of rnj embryos was disturbed after the globular stage. Observation of ultrastructures indicated that these aborted embryos may result from impaired chloroplast development. Furthermore, by analyzing the molecular markers of cell fate decisions (STM, FIL, ML1, SCR, and WOX5) in rnj embryos, we found that this impairment of chloroplast development may lead to aberrant embryo patterning along the apical-basal axis, indicating that AtRNJ is important in initiating and maintaining the organization of shoot apical meristems (SAMs), cotyledons, and hypocotyls. Moreover, the transport and response of auxin in rnj embryos was found to be disrupted, suggesting that AtRNJ may be involved in auxin-mediated pathways during embryogenesis. Therefore, we speculate that RNJ plays a vital role in embryo morphogenesis and apical-basal pattern formation by regulating chloroplast development.
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Affiliation(s)
- Hongyu Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wenxuan Zou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jie Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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16
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Li Q, Zhao P, Li J, Zhang C, Wang L, Ren Z. Genome-wide analysis of the WD-repeat protein family in cucumber and Arabidopsis. Mol Genet Genomics 2013; 289:103-24. [DOI: 10.1007/s00438-013-0789-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 10/19/2013] [Indexed: 12/31/2022]
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17
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Armenta-Medina A, Huanca-Mamani W, Sanchez-León N, Rodríguez-Arévalo I, Vielle-Calzada JP. Functional analysis of sporophytic transcripts repressed by the female gametophyte in the ovule of Arabidopsis thaliana. PLoS One 2013; 8:e76977. [PMID: 24194852 PMCID: PMC3806734 DOI: 10.1371/journal.pone.0076977] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 08/28/2013] [Indexed: 01/07/2023] Open
Abstract
To investigate the genetic and molecular regulation that the female gametophyte could exert over neighboring sporophytic regions of the ovule, we performed a quantitative comparison of global expression in wild-type and nozzle/sporocyteless (spl) ovules of Arabidopsis thaliana (Arabidopsis), using Massively Parallel Signature Sequencing (MPSS). This comparison resulted in 1517 genes showing at least 3-fold increased expression in ovules lacking a female gametophyte, including those encoding 89 transcription factors, 50 kinases, 25 proteins containing a RNA-recognition motif (RRM), and 20 WD40 repeat proteins. We confirmed that eleven of these genes are either preferentially expressed or exclusive of spl ovules lacking a female gametophyte as compared to wild-type, and showed that six are also upregulated in determinant infertile1 (dif1), a meiotic mutant affected in a REC8-like cohesin that is also devoided of female gametophytes. The sporophytic misexpression of IOREMPTE, a WD40/transducin repeat gene that is preferentially expressed in the L1 layer of spl ovules, caused the arrest of female gametogenesis after differentiation of a functional megaspore. Our results show that in Arabidopsis, the sporophytic-gametophytic cross talk includes a negative regulation of the female gametophyte over specific genes that are detrimental for its growth and development, demonstrating its potential to exert a repressive control over neighboring regions in the ovule.
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Affiliation(s)
- Alma Armenta-Medina
- Grupo de Desarrollo Reproductivo y Apomixis, Laboratorio Nacional de Genómica para la Biodiversidad y Departamento de Ingeniería Genética de Plantas, CINVESTAV Irapuato, Irapuato, Mexico
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18
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Bjerkan KN, Grini PE. The Arabidopsis DDB1 interacting protein WDR55 is required for vegetative development. PLANT SIGNALING & BEHAVIOR 2013; 8:25347. [PMID: 23803743 PMCID: PMC4002586 DOI: 10.4161/psb.25347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The CULLIN family of E3 ubiquitin ligases are important regulators of plant development and function. A newly identified class of CULLIN4-RING-E3 ligases (CRL4s) interacts with substrate receptors referred to as DDB1-CUL4 ASSOCIATED FACTORS (DCAFs) via a DDB1 linker protein. We have previously reported that the WD40 protein WDR55 interacts with DDB1A and is thus a putative DCAF. Mutants of WDR55 are embryo lethal, suggesting that a DDB1(WDR55) complex could regulate embryo and endosperm development. Here we report that a weak allele homozygous for wdr55 display pleiotropic phenotypes in the seedling and adult stages, suggesting a novel regulatory role for WDR55 in vegetative development.
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19
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Abstract
E3 ligases comprise a highly diverse and important group of enzymes that act within the 26S ubiquitin proteasome pathway. They facilitate the transfer of ubiquitin moieties to substrate proteins which may be marked for degradation by this step. As such, they serve as central regulators in many cellular and physiological processes in plants. The review provides an update on the multitude of different E3 ligases currently known in plants, and illustrates the central role in plant biology of specific examples.
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Affiliation(s)
- Liyuan Chen
- Plant Stress Physiology, School of Biological Sciences, Abelson 435, PO Box 644236, Washington State University, Pullman, WA 99164-4236, USA
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20
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Gregis V, Andrés F, Sessa A, Guerra RF, Simonini S, Mateos JL, Torti S, Zambelli F, Prazzoli GM, Bjerkan KN, Grini PE, Pavesi G, Colombo L, Coupland G, Kater MM. Identification of pathways directly regulated by SHORT VEGETATIVE PHASE during vegetative and reproductive development in Arabidopsis. Genome Biol 2013; 14:R56. [PMID: 23759218 PMCID: PMC3706845 DOI: 10.1186/gb-2013-14-6-r56] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 04/24/2013] [Accepted: 06/11/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND MADS-domain transcription factors play important roles during plant development. The Arabidopsis MADS-box gene SHORT VEGETATIVE PHASE (SVP) is a key regulator of two developmental phases. It functions as a repressor of the floral transition during the vegetative phase and later it contributes to the specification of floral meristems. How these distinct activities are conferred by a single transcription factor is unclear, but interactions with other MADS domain proteins which specify binding to different genomic regions is likely one mechanism. RESULTS To compare the genome-wide DNA binding profile of SVP during vegetative and reproductive development we performed ChIP-seq analyses. These ChIP-seq data were combined with tiling array expression analysis, induction experiments and qRT-PCR to identify biologically relevant binding sites. In addition, we compared genome-wide target genes of SVP with those published for the MADS domain transcription factors FLC and AP1, which interact with SVP during the vegetative and reproductive phases, respectively. CONCLUSIONS Our analyses resulted in the identification of pathways that are regulated by SVP including those controlling meristem development during vegetative growth and flower development whereas floral transition pathways and hormonal signaling were regulated predominantly during the vegetative phase. Thus, SVP regulates many developmental pathways, some of which are common to both of its developmental roles whereas others are specific to only one of them.
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Affiliation(s)
- Veronica Gregis
- Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Fernando Andrés
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Alice Sessa
- Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Rosalinda F Guerra
- Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Sara Simonini
- Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Julieta L Mateos
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Stefano Torti
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Federico Zambelli
- Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Gian Marco Prazzoli
- Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | | | - Paul E Grini
- Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
| | - Giulio Pavesi
- Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Lucia Colombo
- Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
- Consiglio Nazionale delle Ricerche Istituto di Biofisica, 20133 Milan, Italy
| | - George Coupland
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Martin M Kater
- Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
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21
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Meza TJ, Moen MN, Vågbø CB, Krokan HE, Klungland A, Grini PE, Falnes PØ. The DNA dioxygenase ALKBH2 protects Arabidopsis thaliana against methylation damage. Nucleic Acids Res 2012; 40:6620-31. [PMID: 22532610 PMCID: PMC3413135 DOI: 10.1093/nar/gks327] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The Escherichia coli AlkB protein (EcAlkB) is a DNA repair enzyme which reverses methylation damage such as 1-methyladenine (1-meA) and 3-methylcytosine (3-meC). The mammalian AlkB homologues ALKBH2 and ALKBH3 display EcAlkB-like repair activity in vitro, but their substrate specificities are different, and ALKBH2 is the main DNA repair enzyme for 1-meA in vivo. The genome of the model plant Arabidopsis thaliana encodes several AlkB homologues, including the yet uncharacterized protein AT2G22260, which displays sequence similarity to both ALKBH2 and ALKBH3. We have here characterized protein AT2G22260, by us denoted ALKBH2, as both our functional studies and bioinformatics analysis suggest it to be an orthologue of mammalian ALKBH2. The Arabidopsis ALKBH2 protein displayed in vitro repair activities towards methyl and etheno adducts in DNA, and was able to complement corresponding repair deficiencies of the E. coli alkB mutant. Interestingly, alkbh2 knock-out plants were sensitive to the methylating agent methylmethanesulphonate (MMS), and seedlings from these plants developed abnormally when grown in the presence of MMS. The present study establishes ALKBH2 as an important enzyme for protecting Arabidopsis against methylation damage in DNA, and suggests its homologues in other plants to have a similar function.
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Affiliation(s)
- Trine J Meza
- Department of Molecular Biosciences, University of Oslo, P.O. Box 1041 Blindern, N-0316 Oslo, Norway
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