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Lee S, Kim J, Kim MS, Min CW, Kim ST, Choi SB, Lee JH, Choi D. The Phytophthora nucleolar effector Pi23226 targets host ribosome biogenesis to induce necrotrophic cell death. PLANT COMMUNICATIONS 2023; 4:100606. [PMID: 37087572 PMCID: PMC10504586 DOI: 10.1016/j.xplc.2023.100606] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 03/15/2023] [Accepted: 04/19/2023] [Indexed: 05/03/2023]
Abstract
Pathogen effectors target diverse subcellular organelles to manipulate the plant immune system. Although the nucleolus has emerged as a stress marker and several effectors are localized in the nucleolus, the roles of nucleolar-targeted effectors remain elusive. In this study, we showed that Phytophthora infestans infection of Nicotiana benthamiana results in nucleolar inflation during the transition from the biotrophic to the necrotrophic phase. Multiple P. infestans effectors were localized in the nucleolus: Pi23226 induced cell death in N. benthamiana and nucleolar inflation similar to that observed in the necrotrophic stage of infection, whereas its homolog Pi23015 and a deletion mutant (Pi23226ΔC) did not induce cell death or affect nucleolar size. RNA immunoprecipitation and individual-nucleotide-resolution UV crosslinking and immunoprecipitation sequencing analysis indicated that Pi23226 bound to the 3' end of 25S rRNA precursors, resulting in accumulation of unprocessed 27S pre-rRNAs. The nucleolar stress marker NAC082 was strongly upregulated under Pi23226-expressing conditions. Pi23226 subsequently inhibited global protein translation in host cells by interacting with ribosomes. Pi23226 enhanced P. infestans pathogenicity, indicating that Pi23226-induced ribosome malfunction and cell death were beneficial for pathogenesis in the host. Our results provide evidence for the molecular mechanism underlying RNA-binding effector activity in host ribosome biogenesis and lead to new insights into the nucleolar action of effectors in pathogenesis.
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Affiliation(s)
- Soeui Lee
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of Korea; Plant Genomics and Breeding Institute, Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Jaehwan Kim
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of Korea; Plant Genomics and Breeding Institute, Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Myung-Shin Kim
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of Korea; Interdisciplinary Programs in Agricultural Genomics, College of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea; Division of Bioscience and Bioinformatics, Myongji University, Yongin 449-728, Republic of Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Sang-Bong Choi
- Division of Bioscience and Bioinformatics, Myongji University, Yongin 449-728, Republic of Korea
| | - Joo Hyun Lee
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of Korea.
| | - Doil Choi
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of Korea; Plant Genomics and Breeding Institute, Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea.
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2
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Ding F, Huang D, Wang M, Peng J. An 86 amino acids motif in CAPN3 is essential for formation of the nucleolus-localized Def-CAPN3 complex. Biochem Biophys Res Commun 2022; 623:66-73. [PMID: 35878425 DOI: 10.1016/j.bbrc.2022.06.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022]
Abstract
Digestive-organ expansion factor (Def) is a nucleolar protein that recruits cysteine proteinase Calpain3 (CAPN3) into the nucleolus to form the Def-CAPN3 complex in both human and zebrafish. This complex mediates the degradation of the tumor suppressor p53 and ribosome biogenesis factor mitotic phosphorylated protein 10 (Mpp10) in nucleolus, demonstrating the importance of this complex in regulating cell cycle and ribosome biogenesis. However, the Def and CAPN3 interacting motifs have yet been identified. In this report, by using a series of truncated or internally deleted human CAPN3 (hCAPN3) derivatives we identify that an essential motif of 86 amino acids (86-aa) (430-515aa) in hCAPN3 for its interaction with human Def (hDef), and this 86-aa motif is highly conserved in zebrafish Capn3b (zCapn3b) and is also required for the interaction between zebrafish Def (zDef) and zCapn3b. We further identify the 2/3 C-terminus of hDef is responsible for mediating the hDef-hCAPN3 interaction, and the corresponding region is conserved for the zDef and zCapn3b interaction. Our results lay the ground to resolve the structure of the Def-CAPN3 complex in the future.
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Affiliation(s)
- Feng Ding
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Delai Huang
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Mingyun Wang
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
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3
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Zhao S, Huang D, Peng J. Nucleolus-localized Def-CAPN3 protein degradation pathway and its role in cell cycle control and ribosome biogenesis. J Genet Genomics 2021; 48:955-960. [PMID: 34452850 DOI: 10.1016/j.jgg.2021.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 12/25/2022]
Abstract
The nucleolus, as the 'nucleus of the nucleus', is a prominent subcellular organelle in a eukaryocyte. The nucleolus serves as the centre for ribosome biogenesis, as well as an important site for cell-cycle regulation, cellular senescence, and stress response. The protein composition of the nucleolus changes dynamically through protein turnover to meet the needs of cellular activities or stress responses. Recent studies have identified a nucleolus-localized protein degradation pathway in zebrafish and humans, namely the Def-CAPN3 pathway, which is essential to ribosome production and cell-cycle progression, by controlling the turnover of multiple substrates (e.g., ribosomal small-subunit [SSU] processome component Mpp10, transcription factor p53, check-point proteins Chk1 and Wee1). This pathway relies on the Ca2+-dependent cysteine proteinase CAPN3 and is independent of the ubiquitin-mediated proteasome pathway. CAPN3 is recruited by nucleolar protein Def from cytoplasm to nucleolus, where it proteolyzes its substrates which harbor a CAPN3 recognition-motif. Def depletion leads to the exclusion of CAPN3 and accumulation of p53, Wee1, Chk1, and Mpp10 in the nucleolus that result in cell-cycle arrest and rRNA processing abnormality. Here, we summarize the discovery of the Def-CAPN3 pathway and propose its biological role in cell-cycle control and ribosome biogenesis.
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Affiliation(s)
- Shuyi Zhao
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Delai Huang
- Department of Biology, University of Virginia, Charlottesville, VA 22904, United States
| | - Jinrong Peng
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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Hsu PJ, Tan MC, Shen HL, Chen YH, Wang YY, Hwang SG, Chiang MH, Le QV, Kuo WS, Chou YC, Lin SY, Jauh GY, Cheng WH. The nucleolar protein SAHY1 is involved in pre-rRNA processing and normal plant growth. PLANT PHYSIOLOGY 2021; 185:1039-1058. [PMID: 33793900 PMCID: PMC8133687 DOI: 10.1093/plphys/kiaa085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/01/2020] [Indexed: 05/29/2023]
Abstract
Although the nucleolus is involved in ribosome biogenesis, the functions of numerous nucleolus-localized proteins remain unclear. In this study, we genetically isolated Arabidopsis thaliana salt hypersensitive mutant 1 (sahy1), which exhibits slow growth, short roots, pointed leaves, and sterility. SAHY1 encodes an uncharacterized protein that is predominantly expressed in root tips, early developing seeds, and mature pollen grains and is mainly restricted to the nucleolus. Dysfunction of SAHY1 primarily causes the accumulation of 32S, 18S-A3, and 27SB pre-rRNA intermediates. Coimmunoprecipitation experiments further revealed the interaction of SAHY1 with ribosome proteins and ribosome biogenesis factors. Moreover, sahy1 mutants are less sensitive to protein translation inhibitors and show altered expression of structural constituents of ribosomal genes and ribosome subunit profiles, reflecting the involvement of SAHY1 in ribosome composition and ribosome biogenesis. Analyses of ploidy, S-phase cell cycle progression, and auxin transport and signaling indicated the impairment of mitotic activity, translation of auxin transport carrier proteins, and expression of the auxin-responsive marker DR5::GFP in the root tips or embryos of sahy1 plants. Collectively, these data demonstrate that SAHY1, a nucleolar protein involved in ribosome biogenesis, plays critical roles in normal plant growth in association with auxin transport and signaling.
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Affiliation(s)
- Pei-jung Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Mei-Chen Tan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Hwei-Ling Shen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ya-Huei Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Ya-Ying Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - San-Gwang Hwang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ming-Hau Chiang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Quang-Vuong Le
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wen-Shuo Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ying-Chan Chou
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Neipu, Pingtung County,Taiwan
| | - Shih-Yun Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Guang-Yuh Jauh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wan-Hsing Cheng
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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5
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Wang W, Ryu KH, Bruex A, Barron C, Schiefelbein J. Molecular Basis for a Cell Fate Switch in Response to Impaired Ribosome Biogenesis in the Arabidopsis Root Epidermis. THE PLANT CELL 2020; 32:2402-2423. [PMID: 32371546 PMCID: PMC7346552 DOI: 10.1105/tpc.19.00773] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/30/2020] [Accepted: 04/29/2020] [Indexed: 05/12/2023]
Abstract
The Arabidopsis (Arabidopsis thaliana) root epidermis consists of a position-dependent pattern of root hair cells and non-hair cells. Underlying this cell type patterning is a network of transcription factors including a central MYB-basic helix-loop-helix-WD40 complex containing WEREWOLF (WER), GLABRA3 (GL3)/ENHANCER OF GLABRA3, and TRANSPARENT TESTA GLABRA1. In this study, we used a genetic enhancer screen to identify apum23-4, a mutant allele of the ribosome biogenesis factor (RBF) gene ARABIDOPSIS PUMILIO23 (APUM23), which caused prospective root hair cells to instead adopt the non-hair cell fate. We discovered that this cell fate switch relied on MYB23, a MYB protein encoded by a WER target gene and acting redundantly with WER. In the apum23-4 mutant, MYB23 exhibited ectopic expression that was WER independent and instead required ANAC082, a recently identified ribosomal stress response mediator. We examined additional RBF mutants that produced ectopic non-hair cells and determined that this cell fate switch is generally linked to defects in ribosome biogenesis. Furthermore, the flagellin peptide flg22 triggers the ANAC082-MYB23-GL2 pathway. Taken together, our study provides a molecular explanation for root epidermal cell fate switch in response to ribosomal defects and, more generally, it demonstrates a novel regulatory connection between stress conditions and cell fate control in plants.
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Affiliation(s)
- Wenjia Wang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
- Joint BioEnergy Institute, Emeryville, California 94608
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Kook Hui Ryu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Angela Bruex
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Christa Barron
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
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6
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Huang W, Chen F, Ma Q, Xin J, Li J, Chen J, Zhou B, Chen M, Li J, Peng J. Ribosome biogenesis gene DEF/UTP25 is essential for liver homeostasis and regeneration. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1651-1664. [PMID: 32303961 DOI: 10.1007/s11427-019-1635-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/17/2020] [Indexed: 12/19/2022]
Abstract
Hepatocytes are responsible for diverse metabolic activities in a liver. Proper ribosome biogenesis is essential to sustain the function of hepatocytes. There are approximately 200 factors involved in ribosome biogenesis; however, few studies have focused on the role of these factors in maintaining liver homeostasis. The digestive organ expansion factor (def) gene encodes a nucleolar protein Def that participates in ribosome biogenesis. In addition, Def forms a complex with cysteine protease Calpain3 (Capn3) and recruits Capn3 to the nucleolus to cleave protein targets. However, the function of Def has not been characterized in the mammalian digestive organs. In this report, we show that conditional knockout of the mouse def gene in hepatocytes causes cell morphology abnormality and constant infiltration of inflammatory cells in the liver. As age increases, the def conditional knockout liver displays multiple tissue damage foci and biliary hyperplasia. Moreover, partial hepatectomy leads to sudden acute death to the def conditional knockout mice and this phenotype is rescued by intragastric injection of the anti-inflammation drug dexamethasone one day before hepatectomy. Our results demonstrate that Def is essential for maintaining the liver homeostasis and liver regeneration capacity in mammals.
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Affiliation(s)
- Weidong Huang
- MOE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Feng Chen
- MOE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Quanxin Ma
- Academy of Chinese Medicine/Institute of Comparative Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jiaojiao Xin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Jiaqi Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Bin Zhou
- The State Key Laboratory of Cell Biology, CAS Center for Excellence on Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Minli Chen
- Academy of Chinese Medicine/Institute of Comparative Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
| | - Jun Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.
| | - Jinrong Peng
- MOE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
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7
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Zhao S, Chen Y, Chen F, Huang D, Shi H, Lo LJ, Chen J, Peng J. Sas10 controls ribosome biogenesis by stabilizing Mpp10 and delivering the Mpp10-Imp3-Imp4 complex to nucleolus. Nucleic Acids Res 2019; 47:2996-3012. [PMID: 30773582 PMCID: PMC6451133 DOI: 10.1093/nar/gkz105] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 01/29/2019] [Accepted: 02/09/2019] [Indexed: 01/19/2023] Open
Abstract
Mpp10 forms a complex with Imp3 and Imp4 that serves as a core component of the ribosomal small subunit (SSU) processome. Mpp10 also interacts with the nucleolar protein Sas10/Utp3. However, it remains unknown how the Mpp10-Imp3-Imp4 complex is delivered to the nucleolus and what biological function the Mpp10-Sas10 complex plays. Here, we report that the zebrafish Mpp10 and Sas10 are conserved nucleolar proteins essential for the development of the digestive organs. Mpp10, but not Sas10/Utp3, is a target of the nucleolus-localized Def-Capn3 protein degradation pathway. Sas10 protects Mpp10 from Capn3-mediated cleavage by masking the Capn3-recognition site on Mpp10. Def interacts with Sas10 to form the Def-Sas10-Mpp10 complex to facilitate the Capn3-mediated cleavage of Mpp10. Importantly, we found that Sas10 determines the nucleolar localization of the Mpp10-Imp3-Imp4 complex. In conclusion, Sas10 is essential not only for delivering the Mpp10-Imp3-Imp4 complex to the nucleolus for assembling the SSU processome but also for fine-tuning Mpp10 turnover in the nucleolus during organogenesis.
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Affiliation(s)
- Shuyi Zhao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yayue Chen
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Feng Chen
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Delai Huang
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hui Shi
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Li Jan Lo
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
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8
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Sáez-Vásquez J, Delseny M. Ribosome Biogenesis in Plants: From Functional 45S Ribosomal DNA Organization to Ribosome Assembly Factors. THE PLANT CELL 2019; 31:1945-1967. [PMID: 31239391 PMCID: PMC6751116 DOI: 10.1105/tpc.18.00874] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 05/28/2019] [Accepted: 06/25/2019] [Indexed: 05/11/2023]
Abstract
The transcription of 18S, 5.8S, and 18S rRNA genes (45S rDNA), cotranscriptional processing of pre-rRNA, and assembly of mature rRNA with ribosomal proteins are the linchpins of ribosome biogenesis. In yeast (Saccharomyces cerevisiae) and animal cells, hundreds of pre-rRNA processing factors have been identified and their involvement in ribosome assembly determined. These studies, together with structural analyses, have yielded comprehensive models of the pre-40S and pre-60S ribosome subunits as well as the largest cotranscriptionally assembled preribosome particle: the 90S/small subunit processome. Here, we present the current knowledge of the functional organization of 45S rDNA, pre-rRNA transcription, rRNA processing activities, and ribosome assembly factors in plants, focusing on data from Arabidopsis (Arabidopsis thaliana). Based on yeast and mammalian cell studies, we describe the ribonucleoprotein complexes and RNA-associated activities and discuss how they might specifically affect the production of 40S and 60S subunits. Finally, we review recent findings concerning pre-rRNA processing pathways and a novel mechanism involved in a ribosome stress response in plants.
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Affiliation(s)
- Julio Sáez-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France, and Universite Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Michel Delseny
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France, and Universite Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
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Ohbayashi I, Sugiyama M. Plant Nucleolar Stress Response, a New Face in the NAC-Dependent Cellular Stress Responses. FRONTIERS IN PLANT SCIENCE 2018; 8:2247. [PMID: 29375613 PMCID: PMC5767325 DOI: 10.3389/fpls.2017.02247] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 12/21/2017] [Indexed: 05/24/2023]
Abstract
The nucleolus is the most prominent nuclear domain, where the core processes of ribosome biogenesis occur vigorously. All these processes are finely orchestrated by many nucleolar factors to build precisely ribosome particles. In animal cells, perturbations of ribosome biogenesis, mostly accompanied by structural disorders of the nucleolus, cause a kind of cellular stress to induce cell cycle arrest, senescence, or apoptosis, which is called nucleolar stress response. The best-characterized pathway of this stress response involves p53 and MDM2 as key players. p53 is a crucial transcription factor that functions in response to not only nucleolar stress but also other cellular stresses such as DNA damage stress. These cellular stresses release p53 from the inhibition by MDM2, an E3 ubiquitin ligase targeting p53, in various ways, which leads to p53-dependent activation of a set of genes. In plants, genetic impairments of ribosome biogenesis factors or ribosome components have been shown to cause characteristic phenotypes, including a narrow and pointed leaf shape, implying a common signaling pathway connecting ribosomal perturbations and certain aspects of growth and development. Unlike animals, however, plants have neither p53 nor MDM2 family proteins. Then the question arises whether plant cells have a nucleolar stress response pathway. In recent years, it has been reported that several members of the plant-specific transcription factor family NAC play critical roles in the pathways responsive to various cellular stresses. In this mini review, we outline the plant cellular stress response pathways involving NAC transcription factors with reference to the p53-MDM2-dependent pathways of animal cells, and discuss the possible involvement of a plant-unique, NAC-mediated pathway in the nucleolar stress response in plants.
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Affiliation(s)
- Iwai Ohbayashi
- FAFU-UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Munetaka Sugiyama
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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10
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Shanmugam T, Abbasi N, Kim HS, Kim HB, Park NI, Park GT, Oh SA, Park SK, Muench DG, Choi Y, Park YI, Choi SB. An Arabidopsis divergent pumilio protein, APUM24, is essential for embryogenesis and required for faithful pre-rRNA processing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:1092-1105. [PMID: 29031033 DOI: 10.1111/tpj.13745] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 09/28/2017] [Accepted: 10/03/2017] [Indexed: 05/06/2023]
Abstract
Pumilio RNA-binding proteins are largely involved in mRNA degradation and translation repression. However, a few evolutionarily divergent Pumilios are also responsible for proper pre-rRNA processing in human and yeast. Here, we describe an essential Arabidopsis nucleolar Pumilio, APUM24, that is expressed in tissues undergoing rapid proliferation and cell division. A T-DNA insertion for APUM24 did not affect the male and female gametogenesis, but instead resulted in a negative female gametophytic effect on zygotic cell division immediately after fertilization. Additionally, the mutant embryos displayed defects in cell patterning from pro-embryo through globular stages. The mutant embryos were marked by altered auxin maxima, which were substantiated by the mislocalization of PIN1 and PIN7 transporters in the defective embryos. Homozygous apum24 callus accumulates rRNA processing intermediates, including uridylated and adenylated 5.8S and 25S rRNA precursors. An RNA-protein interaction assay showed that the histidine-tagged recombinant APUM24 binds RNAin vitro with no apparent specificity. Overall, our results demonstrated that APUM24 is required for rRNA processing and early embryogenesis in Arabidopsis.
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Affiliation(s)
- Thiruvenkadam Shanmugam
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Nazia Abbasi
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Hyung-Sae Kim
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Ho Bang Kim
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Nam-Il Park
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Guen Tae Park
- School of Biological Sciences, Seoul National University, Seoul, 151-747, South Korea
| | - Sung Aeong Oh
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, South Korea
| | - Soon Ki Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, South Korea
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Yeonhee Choi
- School of Biological Sciences, Seoul National University, Seoul, 151-747, South Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 305-764, South Korea
| | - Sang-Bong Choi
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
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11
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Aryal NK, Wasylishen AR, Pant V, Riley-Croce M, Lozano G. Loss of digestive organ expansion factor ( Diexf) reveals an essential role during murine embryonic development that is independent of p53. Oncotarget 2017; 8:103996-104006. [PMID: 29262616 PMCID: PMC5732782 DOI: 10.18632/oncotarget.22087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/10/2017] [Indexed: 01/01/2023] Open
Abstract
Increased levels of inhibitors of the p53 tumor suppressor such as Mdm2 and Mdm4 drive tumor development and thus serve as targets for therapeutic intervention. Recently, digestive organ expansion factor (Diexf) has been identified as a novel inhibitor of p53 in zebrafish. Here, we address the potential role of Diexf as a regulator of the p53 pathway in mammals by generating Diexf knockout mice. We demonstrate that, similar to Mdm2 and Mdm4, homozygous deletion of Diexf is embryonic lethal. However, unlike in Mdm2 and Mdm4 mice, loss of p53 does not rescue this phenotype. Moreover, Diexf heterozygous animals are not sensitive to sub-lethal ionizing radiation. Thus, we conclude that Diexf is an essential developmental gene in the mouse, but is not a significant regulator of the p53 pathway during development or in response to ionizing radiation.
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Affiliation(s)
- Neeraj K Aryal
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Genes and Development Program, The University of Texas MD Anderson Cancer Center, UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Amanda R Wasylishen
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vinod Pant
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maurisa Riley-Croce
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guillermina Lozano
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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12
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Hao L, Wei X, Zhu J, Shi J, Liu J, Gu H, Tsuge T, Qu LJ. SNAIL1 is essential for female gametogenesis in Arabidopsis thaliana. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:629-641. [PMID: 28776932 DOI: 10.1111/jipb.12572] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/02/2017] [Indexed: 06/07/2023]
Abstract
Two yeast Brix family members Ssf1 and Ssf2, involved in large ribosomal subunit synthesis, are essential for yeast cell viability and mating efficiency. Their putative homologs exist in the Arabidopsis genome; however, their role in plant development is unknown. Here, we show that Arabidopsis thaliana SNAIL1 (AtSNAIL1), a protein sharing high sequence identity with yeast Ssf1 and Ssf2, is critical to mitosis progression of female gametophyte development. The snail1 homozygous mutant was nonviable and its heterozygous mutant was semi-sterile with shorter siliques. The mutation in SNAIL1 led to absence of female transmission and reduced male transmission. Further phenotypic analysis showed that the synchronic development of female gametophyte in the snail1 heterozygous mutant was greatly impaired and the snail1 pollen tube growth, in vivo, was also compromised. Furthermore, SNAIL1 was a nucleolar-localized protein with a putative role in protein synthesis. Our data suggest that SNAIL1 may function in ribosome biogenesis like Ssf1 and Ssf2 and plays an important role during megagametogenesis in Arabidopsis.
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Affiliation(s)
- Lihong Hao
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaolin Wei
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jiulei Zhu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jiao Shi
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jingjing Liu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
- National Plant Gene Research Center (Beijing), Beijing 100101, China
| | - Hongya Gu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
- National Plant Gene Research Center (Beijing), Beijing 100101, China
| | - Tomohiko Tsuge
- Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611-0011, Japan
| | - Li-Jia Qu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
- National Plant Gene Research Center (Beijing), Beijing 100101, China
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13
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Tao T, Sondalle SB, Shi H, Zhu S, Perez-Atayde AR, Peng J, Baserga SJ, Look AT. The pre-rRNA processing factor DEF is rate limiting for the pathogenesis of MYCN-driven neuroblastoma. Oncogene 2017; 36:3852-3867. [PMID: 28263972 PMCID: PMC5501763 DOI: 10.1038/onc.2016.527] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/08/2016] [Accepted: 12/22/2016] [Indexed: 02/07/2023]
Abstract
The nucleolar factor, digestive organ expansion factor (DEF), has a key role in ribosome biogenesis, functioning in pre-ribosomal RNA (pre-rRNA) processing as a component of the small ribosomal subunit (SSU) processome. Here we show that the peripheral sympathetic nervous system (PSNS) is very underdeveloped in def-deficient zebrafish, and that def haploinsufficiency significantly decreases disease penetrance and tumor growth rate in a MYCN-driven transgenic zebrafish model of neuroblastoma that arises in the PSNS. Consistent with these findings, DEF is highly expressed in human neuroblastoma, and its depletion in human neuroblastoma cell lines induces apoptosis. Interestingly, overexpression of MYCN in zebrafish and in human neuroblastoma cells results in the appearance of intermediate pre-rRNAs species that reflect the processing of pre-rRNAs through Pathway 2, a pathway that processes pre-rRNAs in a different temporal order than the more often used Pathway 1. Our results indicate that DEF and possibly other components of the SSU processome provide a novel site of vulnerability in neuroblastoma cells that could be exploited for targeted therapy.
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Affiliation(s)
- T Tao
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - S B Sondalle
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - H Shi
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - S Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center and Mayo Clinic Center for Individualized Medicine, Rochester, MN, USA.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center and Mayo Clinic Center for Individualized Medicine, Rochester, MN, USA
| | - A R Perez-Atayde
- Department of Pathology, Children's Hospital Boston, Harvard Medical School, Boston, MA, USA
| | - J Peng
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - S J Baserga
- Departments of Molecular Biophysics &Biochemistry, Genetics and Therapeutic Radiology, Yale University and Yale University School of Medicine, New Haven, CT, USA
| | - A T Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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14
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Zhu DZ, Zhao XF, Liu CZ, Ma FF, Wang F, Gao XQ, Zhang XS. Interaction between RNA helicase ROOT INITIATION DEFECTIVE 1 and GAMETOPHYTIC FACTOR 1 is involved in female gametophyte development in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5757-5768. [PMID: 27683728 PMCID: PMC5066494 DOI: 10.1093/jxb/erw341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
ROOT INITIATION DEFECTIVE 1 (RID1) is an Arabidopsis DEAH/RHA RNA helicase. It functions in hypocotyl de-differentiation, de novo meristem formation, and cell specification of the mature female gametophyte (FG). However, it is unclear how RID1 regulates FG development. In this study, we observed that mutations to RID1 disrupted the developmental synchrony and retarded the progression of FG development. RID1 exhibited RNA helicase activity, with a preference for unwinding double-stranded RNA in the 3' to 5' direction. Furthermore, we found that RID1 interacts with GAMETOPHYTIC FACTOR 1 (GFA1), which is an integral protein of the spliceosome component U5 small nuclear ribonucleoprotein (snRNP) particle. Substitution of specific RID1 amino acids (Y266F and T267I) inhibited the interaction with GFA1. In addition, the mutated RID1 could not complement the seed-abortion phenotype of the rid1 mutant. The rid1 and gfa1 mutants exhibited similar abnormalities in pre-mRNA splicing and down-regulated expression of some genes involved in FG development. Our results suggest that an interaction between RID1 and the U5 snRNP complex regulates essential pre-mRNA splicing of the genes required for FG development. This study provides new information regarding the mechanism underlying the FG developmental process.
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Affiliation(s)
- Dong Zi Zhu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Xue Fang Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Chang Zhen Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Fang Fang Ma
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Fang Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Xin-Qi Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
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15
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Guan Y, Huang D, Chen F, Gao C, Tao T, Shi H, Zhao S, Liao Z, Lo LJ, Wang Y, Chen J, Peng J. Phosphorylation of Def Regulates Nucleolar p53 Turnover and Cell Cycle Progression through Def Recruitment of Calpain3. PLoS Biol 2016; 14:e1002555. [PMID: 27657329 PMCID: PMC5033581 DOI: 10.1371/journal.pbio.1002555] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 08/19/2016] [Indexed: 01/15/2023] Open
Abstract
Digestive organ expansion factor (Def) is a nucleolar protein that plays dual functions: it serves as a component of the ribosomal small subunit processome for the biogenesis of ribosomes and also mediates p53 degradation through the cysteine proteinase calpain-3 (CAPN3). However, nothing is known about the exact relationship between Def and CAPN3 or the regulation of the Def function. In this report, we show that CAPN3 degrades p53 and its mutant proteins p53A138V, p53M237I, p53R248W, and p53R273P but not the p53R175H mutant protein. Importantly, we show that Def directly interacts with CAPN3 in the nucleoli and determines the nucleolar localisation of CAPN3, which is a prerequisite for the degradation of p53 in the nucleolus. Furthermore, we find that Def is modified by phosphorylation at five serine residues: S50, S58, S62, S87, and S92. We further show that simultaneous phosphorylations at S87 and S92 facilitate the nucleolar localisation of Capn3 that is not only essential for the degradation of p53 but is also important for regulating cell cycle progression. Hence, we propose that the Def-CAPN3 pathway serves as a nucleolar checkpoint for cell proliferation by selective inactivation of cell cycle-related substrates during organogenesis.
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Affiliation(s)
- Yihong Guan
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Delai Huang
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Feng Chen
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Ce Gao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Ting Tao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Hui Shi
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Shuyi Zhao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Zuyuan Liao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Li Jan Lo
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, China
- * E-mail: (JC); (JRP)
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China
- * E-mail: (JC); (JRP)
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16
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Carvalho SD, Chatterjee M, Coleman L, Clancy MA, Folta KM. Analysis of Block of cell proliferation 1 (BOP1) activity in strawberry and Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 245:84-93. [PMID: 26940494 DOI: 10.1016/j.plantsci.2016.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 12/30/2015] [Accepted: 01/08/2016] [Indexed: 06/05/2023]
Abstract
Block of cell proliferation (BOP) proteins are conserved among eukaryotes, and studies in mammals and yeast have described their role in ribosome biogenesis and cell cycle regulation. A BOP1 orthologue was identified in plants, and loss-of-function analyses in tobacco cells confirmed similar activities. This report characterizes a role for BOP1 activity in planta. Two transgenic plant species were used: the diploid strawberry (Fragaria vesca) and Arabidopsis thaliana. FvBOP1 silencing showed changes in pre-rRNA processing, and demonstrated FvBOP1's role in growth and physiology throughout different stages of plant development. In the strawberry, repression of FvBOP1 activity decreased plant fitness prior to flowering, followed by plant death after the reproductive transition, indicating that BOP1 activity is required for transition back to vegetative growth after flowering. A T-DNA null allele of the AtBOP1 gene is lethal, and a 50% decrease in transcript accumulation is sufficient to cause severe developmental defects linked to defective cell division. The conserved protein BOP1 is essential for viability. Lower transcript levels result in defects in rRNA processing and developmental abnormalities that are consistent with its predicted role in ribosome biogenesis.
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Affiliation(s)
- Sofia D Carvalho
- Horticultural Sciences Department, University of Florida, Gainesville, FL,USA
| | - Mithu Chatterjee
- Horticultural Sciences Department, University of Florida, Gainesville, FL,USA
| | - Lauren Coleman
- Horticultural Sciences Department, University of Florida, Gainesville, FL,USA
| | - Maureen A Clancy
- Horticultural Sciences Department, University of Florida, Gainesville, FL,USA
| | - Kevin M Folta
- Horticultural Sciences Department, University of Florida, Gainesville, FL,USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, USA.
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17
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Weis BL, Kovacevic J, Missbach S, Schleiff E. Plant-Specific Features of Ribosome Biogenesis. TRENDS IN PLANT SCIENCE 2015; 20:729-740. [PMID: 26459664 DOI: 10.1016/j.tplants.2015.07.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 06/19/2015] [Accepted: 07/15/2015] [Indexed: 05/03/2023]
Abstract
The biogenesis of eukaryotic ribosomes is a fundamental process involving hundreds of ribosome biogenesis factors (RBFs) in three compartments of the cell, namely the nucleolus, nucleus, and cytoplasm. Many RBFs are involved in the processing of the primary ribosomal (r)RNA transcript, in which three of the four rRNAs are imbedded. While pre-rRNA processing is well described for yeast and mammals, a detailed processing scheme for plants is lacking. Here, we discuss the emerging scheme of pre-rRNA processing in Arabidopsis thaliana in comparison to other eukaryotes, with a focus on plant characteristics. In addition, we highlight the impact of the ribosome and its biogenesis on developmental processes because common phenotypes can be observed for ribosomal protein and RBF mutants.
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Affiliation(s)
- Benjamin L Weis
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Jelena Kovacevic
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Sandra Missbach
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Current address: Sanofi-Aventis GmbH, Industriepark Höchst, K703, 65926 Frankfurt am Main, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Cluster of Excellence Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Buchman Institute for Molecular Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.
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18
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An equation to estimate the difference between theoretically predicted and SDS PAGE-displayed molecular weights for an acidic peptide. Sci Rep 2015; 5:13370. [PMID: 26311515 PMCID: PMC4550835 DOI: 10.1038/srep13370] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 07/23/2015] [Indexed: 12/11/2022] Open
Abstract
The molecular weight (MW) of a protein can be predicted based on its amino acids (AA) composition. However, in many cases a non-chemically modified protein shows an SDS PAGE-displayed MW larger than its predicted size. Some reports linked this fact to high content of acidic AA in the protein. However, the exact relationship between the acidic AA composition and the SDS PAGE-displayed MW is not established. Zebrafish nucleolar protein Def is composed of 753 AA and shows an SDS PAGE-displayed MW approximately 13 kDa larger than its predicted MW. The first 188 AA in Def is defined by a glutamate-rich region containing ~35.6% of acidic AA. In this report, we analyzed the relationship between the SDS PAGE-displayed MW of thirteen peptides derived from Def and the AA composition in each peptide. We found that the difference between the predicted and SDS PAGE-displayed MW showed a linear correlation with the percentage of acidic AA that fits the equation y = 276.5x − 31.33 (x represents the percentage of acidic AA, 11.4% ≤ x ≤ 51.1%; y represents the average ΔMW per AA). We demonstrated that this equation could be applied to predict the SDS PAGE-displayed MW for thirteen different natural acidic proteins.
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19
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Sánchez-García AB, Aguilera V, Micol-Ponce R, Jover-Gil S, Ponce MR. Arabidopsis MAS2, an Essential Gene That Encodes a Homolog of Animal NF-κ B Activating Protein, Is Involved in 45S Ribosomal DNA Silencing. THE PLANT CELL 2015; 27:1999-2015. [PMID: 26139346 PMCID: PMC4531349 DOI: 10.1105/tpc.15.00135] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/02/2015] [Accepted: 06/12/2015] [Indexed: 05/24/2023]
Abstract
Ribosome biogenesis requires stoichiometric amounts of ribosomal proteins and rRNAs. Synthesis of rRNAs consumes most of the transcriptional activity of eukaryotic cells, but its regulation remains largely unclear in plants. We conducted a screen for ethyl methanesulfonate-induced suppressors of Arabidopsis thaliana ago1-52, a hypomorphic allele of AGO1 (ARGONAUTE1), a key gene in microRNA pathways. We identified nine extragenic suppressors as alleles of MAS2 (MORPHOLOGY OF AGO1-52 SUPPRESSED2). Positional cloning showed that MAS2 encodes the putative ortholog of NKAP (NF-κ B activating protein), a conserved eukaryotic protein involved in transcriptional repression and splicing in animals. The mas2 point mutations behave as informational suppressors of ago1 alleles that cause missplicing. MAS2 is a single-copy gene whose insertional alleles are embryonic lethal. In yeast two-hybrid assays, MAS2 interacted with splicing and ribosome biogenesis proteins, and fluorescence in situ hybridization showed that MAS2 colocalizes with the 45S rDNA at the nucleolar organizer regions (NORs). The artificial microRNA amiR-MAS2 partially repressed MAS2 and caused hypomethylation of 45S rDNA promoters as well as partial NOR decondensation, indicating that MAS2 negatively regulates 45S rDNA expression. Our results thus reveal a key player in the regulation of rRNA synthesis in plants.
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Affiliation(s)
| | - Verónica Aguilera
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
| | - Rosa Micol-Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
| | - Sara Jover-Gil
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
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20
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Bensussan M, Lefebvre V, Ducamp A, Trouverie J, Gineau E, Fortabat MN, Guillebaux A, Baldy A, Naquin D, Herbette S, Lapierre C, Mouille G, Horlow C, Durand-Tardif M. Suppression of Dwarf and irregular xylem Phenotypes Generates Low-Acetylated Biomass Lines in Arabidopsis. PLANT PHYSIOLOGY 2015; 168:452-63. [PMID: 25888614 PMCID: PMC4453781 DOI: 10.1104/pp.15.00122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 04/15/2015] [Indexed: 05/17/2023]
Abstract
eskimo1-5 (esk1-5) is a dwarf Arabidopsis (Arabidopsis thaliana) mutant that has a constitutive drought syndrome and collapsed xylem vessels, along with low acetylation levels in xylan and mannan. ESK1 has xylan O-acetyltransferase activity in vitro. We used a suppressor strategy on esk1-5 to screen for variants with wild-type growth and low acetylation levels, a favorable combination for ethanol production. We found a recessive mutation in the KAKTUS (KAK) gene that suppressed dwarfism and the collapsed xylem character, the cause of decreased hydraulic conductivity in the esk1-5 mutant. Backcrosses between esk1-5 and two independent knockout kak mutants confirmed suppression of the esk1-5 effect. kak single mutants showed larger stem diameters than the wild type. The KAK promoter fused with a reporter gene showed activity in the vascular cambium, phloem, and primary xylem in the stem and hypocotyl. However, suppression of the collapsed xylem phenotype in esk1 kak double mutants was not associated with the recovery of cell wall O-acetylation or any major cell wall modifications. Therefore, our results indicate that, in addition to its described activity as a repressor of endoreduplication, KAK may play a role in vascular development. Furthermore, orthologous esk1 kak double mutants may hold promise for ethanol production in crop plants.
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Affiliation(s)
- Matthieu Bensussan
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Valérie Lefebvre
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Aloïse Ducamp
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Jacques Trouverie
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Emilie Gineau
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Marie-Noëlle Fortabat
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Alexia Guillebaux
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Aurélie Baldy
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Delphine Naquin
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Stéphane Herbette
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Catherine Lapierre
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Gregory Mouille
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Christine Horlow
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
| | - Mylène Durand-Tardif
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Equipe de Recherche Labellisée Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, F-78026 Versailles, France (M.B., V.L., A.D., J.T., E.G., M.-N.F., A.G., A.B., C.L., G.M., C.H., M.D.-T.);Centre de Génétique Moléculaire, Unité Propre de Recherche 3404, Centre National de la Recherche Scientifique, Fédération de Recherche Centre National de la Recherche Scientifique 3115, F-91198 Gif-sur-Yvette, France (D.N.); andClermont Université, Université Blaise Pascal, and Institut National de la Recherche Agronomique, Unité Mixte de Recherche 547 Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier, F-63000 Clermont-Ferrand, France (S.H.)
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21
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Weis BL, Missbach S, Marzi J, Bohnsack MT, Schleiff E. The 60S associated ribosome biogenesis factor LSG1-2 is required for 40S maturation in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:1043-1056. [PMID: 25319368 DOI: 10.1111/tpj.12703] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 10/01/2014] [Accepted: 10/06/2014] [Indexed: 06/04/2023]
Abstract
Ribosome biogenesis involves a large ensemble of trans-acting factors, which catalyse rRNA processing, ribosomal protein association and ribosomal subunit assembly. The circularly permuted GTPase Lsg1 is such a ribosome biogenesis factor, which is involved in maturation of the pre-60S ribosomal subunit in yeast. We identified two orthologues of Lsg1 in Arabidopsis thaliana. Both proteins differ in their C-terminus, which is highly charged in atLSG1-2 but missing in atLSG1-1. This C-terminus of atLSG1-2 contains a functional nuclear localization signal in a part of the protein that also targets atLSG1-2 to the nucleolus. Furthermore, only atLSG1-2 is physically associated with ribosomes suggesting its function in ribosome biogenesis. Homozygous T-DNA insertion lines are viable for both LSG1 orthologues. In plants lacking atLSG1-2 18S rRNA precursors accumulate and a 20S pre-rRNA is detected, while the amount of pre-rRNAs that lead to the 25S and 5.8S rRNA is not changed. Thus, our results suggest that pre-60S subunit maturation is important for the final steps of pre-40S maturation in plants. In addition, the lsg1-2 mutants show severe developmental defects, including triple cotyledons and upward curled leaves, which link ribosome biogenesis to early plant and leaf development.
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Affiliation(s)
- Benjamin L Weis
- Department of Biosciences, Goethe University, Molecular Cell Biology of Plants and Cluster of Excellence, Max von Laue Str. 9, 60438 Frankfurt/Main, Frankfurt, Germany
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22
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Zsögön A, Szakonyi D, Shi X, Byrne ME. Ribosomal Protein RPL27a Promotes Female Gametophyte Development in a Dose-Dependent Manner. PLANT PHYSIOLOGY 2014; 165:1133-1143. [PMID: 24872379 PMCID: PMC4081327 DOI: 10.1104/pp.114.241778] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Ribosomal protein mutations in Arabidopsis (Arabidopsis thaliana) result in a range of specific developmental phenotypes. Why ribosomal protein mutants have specific phenotypes is not fully known, but such defects potentially result from ribosome insufficiency, ribosome heterogeneity, or extraribosomal functions of ribosomal proteins. Here, we report that ovule development is sensitive to the level of Ribosomal Protein L27a (RPL27a) and is disrupted by mutations in the two paralogs RPL27aC and RPL27aB. Mutations in RPL27aC result in high levels of female sterility, whereas mutations in RPL27aB have a significant but lesser effect on fertility. Progressive reduction in RPL27a function results in increasing sterility, indicating a dose-dependent relationship between RPL27a and female fertility. RPL27a levels in both the sporophyte and gametophyte affect female gametogenesis, with different developmental outcomes determined by the dose of RPL27a. These results demonstrate that RPL27aC and RPL27aB act redundantly and reveal a function for RPL27a in coordinating complex interactions between sporophyte and gametophyte during ovule development.
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Affiliation(s)
- Agustin Zsögön
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Dóra Szakonyi
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Xiuling Shi
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Mary E Byrne
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
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23
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Zhu Z, Chen J, Xiong JW, Peng J. Haploinsufficiency of Def activates p53-dependent TGFβ signalling and causes scar formation after partial hepatectomy. PLoS One 2014; 9:e96576. [PMID: 24801718 PMCID: PMC4011785 DOI: 10.1371/journal.pone.0096576] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 04/09/2014] [Indexed: 01/07/2023] Open
Abstract
The metazoan liver exhibits a remarkable capacity to regenerate lost liver mass without leaving a scar following partial hepatectomy (PH). Whilst previous studies have identified components of several different signaling pathways that are essential for activation of hepatocyte proliferation during liver regeneration, the mechanisms that enable such regeneration to occur without accompanying scar formation remain poorly understood. Here we use the adult zebrafish liver, which can regenerate within two weeks following PH, as a new genetic model to address this important question. We focus on the role of Digestive-organ-expansion-factor (Def), a nucleolar protein which has recently been shown to complex with calpain3 (Capn3) to mediate p53 degradation specifically in the nucleolus, in liver regeneration. Firstly, we show that Def expression is up-regulated in the wild-type liver following amputation, and that the defhi429/+ heteroozygous mutant (def+/−) suffers from haploinsufficiency of Def in the liver. We then show that the expression of pro-inflammatory cytokines is up-regulated in the def+/− liver, which leads to distortion of the migration and the clearance of leukocytes after PH. Transforming growth factor β (TGFβ) signalling is thus activated in the wound epidermis in def+/− due to a prolonged inflammatory response, which leads to fibrosis at the amputation site. Fibrotic scar formation in def+/− is blocked by the over-expression of Def, by the loss-of-function of p53, and by treatment with anti-inflammation drug dexamethasone or TGFβ-signalling inhibitor SB431542. We finally show that the Def- p53 pathway suppresses fibrotic scar formation, at least in part, through the regulation of the expression of the pro-inflammatory factor, high-mobility group box 1. We conclude that the novel Def- p53 nucleolar pathway functions specifically to prevent a scar formation at the amputation site in a normal amputated liver.
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Affiliation(s)
- Zhihui Zhu
- Key Laboratory for Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jing-Wei Xiong
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jinrong Peng
- Key Laboratory for Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, China
- * E-mail:
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24
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Reňák D, Gibalová A, Solcová K, Honys D. A new link between stress response and nucleolar function during pollen development in Arabidopsis mediated by AtREN1 protein. PLANT, CELL & ENVIRONMENT 2014; 37:670-83. [PMID: 23961845 DOI: 10.1111/pce.12186] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Heat shock transcription factors (Hsfs) are involved in multiple aspects of stress response and plant growth. However, their role during male gametophyte development is largely unknown, although the generative phase is the most sensitive and critical period in the plant life cycle. Based on a wide screen of T-DNA mutant lines, we identified the atren1 mutation (restricted to nucleolus1) in early male gametophytic gene At1g77570, which has the closest homology to HSFA5 gene, the member of a heat shock transcription factor (HSF) gene family. The mutation causes multiple defects in male gametophyte development in both structure and function. Because the mutation disrupts an early acting (AtREN1) gene, these pollen phenotype abnormalities appear from bicellular pollen stage to pollen maturation. Moreover, the consequent progamic phase is compromised as well as documented by pollen germination defects and limited transmission via male gametophyte. In addition, atren1/- plants are defective in heat stress (HS) response and produce notably higher proportion of aberrant pollen grains. AtREN1 protein is targeted specifically to the nucleolus that, together with the increased size of the nucleolus in atren1 pollen, suggests that it is likely to be involved in ribosomal RNA biogenesis or other nucleolar functions.
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Affiliation(s)
- David Reňák
- Laboratory of Pollen Biology, Institute of Experimental Botany v.v.i. ASCR, Rozvojová 263, Prague 6, 165 02, Czech Republic
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25
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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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26
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Villa-Hernández JM, Dinkova TD, Aguilar-Caballero R, Rivera-Cabrera F, Sánchez de Jiménez E, Pérez-Flores LJ. Regulation of ribosome biogenesis in maize embryonic axes during germination. Biochimie 2013; 95:1871-9. [PMID: 23806421 DOI: 10.1016/j.biochi.2013.06.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 06/14/2013] [Indexed: 11/28/2022]
Abstract
Ribosome biogenesis is a pre-requisite for cell growth and proliferation; it is however, a highly regulated process that consumes a great quantity of energy. It requires the coordinated production of rRNA, ribosomal proteins and non-ribosomal factors which participate in the processing and mobilization of the new ribosomes. Ribosome biogenesis has been studied in yeast and animals; however, there is little information about this process in plants. The objective of the present work was to study ribosome biogenesis in maize seeds during germination, a stage characterized for its fast growth, and the effect of insulin in this process. Insulin has been reported to accelerate germination and to induce seedling growth. It was observed that among the first events reactivated just after 3 h of imbibition are the rDNA transcription and the pre-rRNA processing and that insulin stimulates both of them (40-230%). The transcript of nucleolin, a protein which regulates rDNA transcription and pre-rRNA processing, is among the messages stored in quiescent dry seeds and it is mobilized into the polysomal fraction during the first hours of imbibition (6 h). In contrast, de novo ribosomal protein synthesis was low during the first hours of imbibition (3 and 6 h) increasing by 60 times in later stages (24 h). Insulin increased this synthesis (75%) at 24 h of imbibition; however, not all ribosomal proteins were similarly regulated. In this regard, an increase in RPS6 and RPL7 protein levels was observed, whereas RPL3 protein levels did not change even though its transcription was induced. Results show that ribosome biogenesis in the first stages of imbibition is carried out with newly synthesized rRNA and ribosomal proteins translated from stored mRNA.
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Affiliation(s)
- J M Villa-Hernández
- Departamento de Ciencias de la Salud, Universidad Autónoma Metropolitana, Av. San Rafael Atlixco 186, Col. Vicentina, CP 09340 D. F. México, Mexico
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27
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Tao T, Shi H, Huang D, Peng J. Def functions as a cell autonomous factor in organogenesis of digestive organs in zebrafish. PLoS One 2013; 8:e58858. [PMID: 23593122 PMCID: PMC3625206 DOI: 10.1371/journal.pone.0058858] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 02/08/2013] [Indexed: 01/29/2023] Open
Abstract
Digestive organs originate from the endoderm. Morphogenesis of the digestive system is precisely controlled by multiple factors that dictate the cell fate and behavior so that the specific digestive organs are timely formed in the right place and develop into right size and structure. We showed previously that digestive organ expansion factor (def) is a gene whose expression is enriched in the liver, pancreas and intestine. Loss-of-function of def in the defhi429 mutant confers hypoplastic digestive organs partly due to alteration of expression of genes related to the p53 pathway. However, the molecular mechanism for the involvement of Def in the organogenesis of digestive organs is still largely unknown. For example, it is not known whether Def regulates specific pathways in a specific organ. To address this question, we generated four independent Tg(fabp10a:def) transgenic fish lines which over-expressed Def specifically in the liver. We characterized Tg-I, one of the transgenic lines, in detail with genetic, molecular and histological approaches. We found that Tg-I restored the liver but not exocrine pancreas and intestine development in the defhi429 mutant. However, Tg-I adult fish in the wild type (WT) background exhibits reduced liver-to-body ratio and all four transgenic lines conferred abnormal intrahepatic structure. Microarray data analysis showed that certain specific functional pathways were affected in the liver of Tg-I. These results demonstrate that Def functions in a cell autonomous manner during early liver development and aberrant Def protein expression might lead to disruption of the structural integrity of a normal adult liver.
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Affiliation(s)
- Ting Tao
- Key Laboratory for Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Hui Shi
- Key Laboratory for Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Delai Huang
- Key Laboratory for Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Jinrong Peng
- Key Laboratory for Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
- * E-mail:
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28
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Missbach S, Weis BL, Martin R, Simm S, Bohnsack MT, Schleiff E. 40S ribosome biogenesis co-factors are essential for gametophyte and embryo development. PLoS One 2013; 8:e54084. [PMID: 23382868 PMCID: PMC3559688 DOI: 10.1371/journal.pone.0054084] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 12/05/2012] [Indexed: 12/13/2022] Open
Abstract
Ribosome biogenesis is well described in Saccharomyces cerevisiae. In contrast only very little information is available on this pathway in plants. This study presents the characterization of five putative protein co-factors of ribosome biogenesis in Arabidopsis thaliana, namely Rrp5, Pwp2, Nob1, Enp1 and Noc4. The characterization of the proteins in respect to localization, enzymatic activity and association with pre-ribosomal complexes is shown. Additionally, analyses of T-DNA insertion mutants aimed to reveal an involvement of the plant co-factors in ribosome biogenesis. The investigated proteins localize mainly to the nucleolus or the nucleus, and atEnp1 and atNob1 co-migrate with 40S pre-ribosomal complexes. The analysis of T-DNA insertion lines revealed that all proteins are essential in Arabidopsis thaliana and mutant plants show alterations of rRNA intermediate abundance already in the heterozygous state. The most significant alteration was observed in the NOB1 T-DNA insertion line where the P-A3 fragment, a 23S-like rRNA precursor, accumulated. The transmission of the T-DNA through the male and female gametophyte was strongly inhibited indicating a high importance of ribosome co-factor genes in the haploid stages of plant development. Additionally impaired embryogenesis was observed in some mutant plant lines. All results support an involvement of the analyzed proteins in ribosome biogenesis but differences in rRNA processing, gametophyte and embryo development suggested an alternative regulation in plants.
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Affiliation(s)
- Sandra Missbach
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany
| | - Benjamin L. Weis
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany
| | - Roman Martin
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany
| | - Stefan Simm
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany
| | - Markus T. Bohnsack
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany
- Cluster of Excellence Frankfurt; Goethe University, Frankfurt/Main, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany
- Cluster of Excellence Frankfurt; Goethe University, Frankfurt/Main, Germany
- Center of Membrane Proteomics, Goethe University, Frankfurt/Main, Germany
- * E-mail:
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Def defines a conserved nucleolar pathway that leads p53 to proteasome-independent degradation. Cell Res 2013; 23:620-34. [PMID: 23357851 PMCID: PMC3641591 DOI: 10.1038/cr.2013.16] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
p53 protein turnover through the ubiquitination pathway is a vital mechanism in the regulation of its transcriptional activity; however, little is known about p53 turnover through proteasome-independent pathway(s). The digestive organ expansion factor (Def) protein is essential for the development of digestive organs. In zebrafish, loss of function of def selectively upregulates the expression of p53 response genes, which raises a question as to what is the relationship between Def and p53. We report here that Def is a nucleolar protein and that loss of function of def leads to the upregulation of p53 protein, which surprisingly accumulates in the nucleoli. Our extensive studies have demonstrated that Def can mediate the degradation of p53 protein and that this process is independent of the proteasome pathway, but dependent on the activity of Calpain3, a cysteine protease. Our findings define a novel nucleolar pathway that regulates the turnover function of p53, which will advance our understanding of p53's role in organogenesis and tumorigenesis.
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Wang SQ, Shi DQ, Long YP, Liu J, Yang WC. GAMETOPHYTE DEFECTIVE 1, a putative subunit of RNases P/MRP, is essential for female gametogenesis and male competence in Arabidopsis. PLoS One 2012; 7:e33595. [PMID: 22509260 PMCID: PMC3324470 DOI: 10.1371/journal.pone.0033595] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 02/13/2012] [Indexed: 01/15/2023] Open
Abstract
RNA biogenesis, including biosynthesis and maturation of rRNA, tRNA and mRNA, is a fundamental process that is critical for cell growth, division and differentiation. Previous studies showed that mutations in components involved in RNA biogenesis resulted in abnormalities in gametophyte and leaf development in Arabidopsis. In eukaryotes, RNases P/MRP (RNase mitochondrial RNA processing) are important ribonucleases that are responsible for processing of tRNA, and transcription of small non-coding RNAs. Here we report that Gametophyte Defective 1 (GAF1), a gene encoding a predicted protein subunit of RNases P/MRP, AtRPP30, plays a role in female gametophyte development and male competence. Embryo sacs were arrested at stages ranging from FG1 to FG7 in gaf1 mutant, suggesting that the progression of the gametophytic division during female gametogenesis was impaired in gaf1 mutant. In contrast, pollen development was not affected in gaf1. However, the fitness of the mutant pollen tube was weaker than that of the wild-type, leading to reduced transmission through the male gametes. GAF1 is featured as a typical RPP30 domain protein and interacts physically with AtPOP5, a homologue of RNases P/MRP subunit POP5 of yeast. Together, our data suggest that components of the RNases P/MRP family, such as RPP30, play important roles in gametophyte development and function in plants.
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Affiliation(s)
- Si-Qi Wang
- State Key Laboratory of Molecular Developmental Biology, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Dong-Qiao Shi
- State Key Laboratory of Molecular Developmental Biology, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (DQS); (WCY)
| | - Yan-Ping Long
- State Key Laboratory of Molecular Developmental Biology, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jie Liu
- State Key Laboratory of Molecular Developmental Biology, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wei-Cai Yang
- State Key Laboratory of Molecular Developmental Biology, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (DQS); (WCY)
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Berger N, Dubreucq B, Roudier F, Dubos C, Lepiniec L. Transcriptional regulation of Arabidopsis LEAFY COTYLEDON2 involves RLE, a cis-element that regulates trimethylation of histone H3 at lysine-27. THE PLANT CELL 2011; 23:4065-78. [PMID: 22080598 PMCID: PMC3246333 DOI: 10.1105/tpc.111.087866] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 10/11/2011] [Accepted: 10/30/2011] [Indexed: 05/17/2023]
Abstract
LEAFY COTYLEDON2 (LEC2) is a master regulator of seed development in Arabidopsis thaliana. In vegetative organs, LEC2 expression is negatively regulated by Polycomb Repressive Complex2 (PRC2) that catalyzes histone H3 Lys 27 trimethylation (H3K27me3) and plays a crucial role in developmental phase transitions. To characterize the cis-regulatory elements involved in the transcriptional regulation of LEC2, molecular dissections and functional analyses of the promoter region were performed in vitro, both in yeast and in planta. Two cis-activating elements and a cis-repressing element (RLE) that is required for H3K27me3 marking were characterized. Remarkably, insertion of the RLE cis-element into pF3H, an unrelated promoter, is sufficient for repressing its transcriptional activity in different tissues. Besides improving our understanding of LEC2 regulation, this study provides important new insights into the mechanisms underlying H3K27me3 deposition and PRC2 recruitment at a specific locus in plants.
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Affiliation(s)
- Nathalie Berger
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique–Agro-ParisTech, Saclay Plant Sciences, 78026 Versailles cedex, France
| | - Bertrand Dubreucq
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique–Agro-ParisTech, Saclay Plant Sciences, 78026 Versailles cedex, France
| | - François Roudier
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8197–Institut National de la Santé et de la Recherche Médicale U1024, 75230 Paris cedex 05, France
| | - Christian Dubos
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique–Agro-ParisTech, Saclay Plant Sciences, 78026 Versailles cedex, France
| | - Loïc Lepiniec
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique–Agro-ParisTech, Saclay Plant Sciences, 78026 Versailles cedex, France
- Address correspondence to
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