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Wang J, Zhang T, Tu A, Xie H, Hu H, Chen J, Yang J. Genome-Wide Identification and Analysis of APC E3 Ubiquitin Ligase Genes Family in Triticum aestivum. Genes (Basel) 2024; 15:271. [PMID: 38540330 PMCID: PMC10970508 DOI: 10.3390/genes15030271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 06/15/2024] Open
Abstract
E3 ubiquitin ligases play a pivotal role in ubiquitination, a crucial post-translational modification process. Anaphase-promoting complex (APC), a large cullin-RING E3 ubiquitin ligase, regulates the unidirectional progression of the cell cycle by ubiquitinating specific target proteins and triggering plant immune responses. Several E3 ubiquitin ligases have been identified owing to advancements in sequencing and annotation of the wheat genome. However, the types and functions of APC E3 ubiquitin ligases in wheat have not been reported. This study identified 14 members of the APC gene family in the wheat genome and divided them into three subgroups (CCS52B, CCS52A, and CDC20) to better understand their functions. Promoter sequence analysis revealed the presence of several cis-acting elements related to hormone and stress responses in the APC E3 ubiquitin ligases in wheat. All identified APC E3 ubiquitin ligase family members were highly expressed in the leaves, and the expression of most genes was induced by the application of methyl jasmonate (MeJA). In addition, the APC gene family in wheat may play a role in plant defense mechanisms. This study comprehensively analyzes APC genes in wheat, laying the groundwork for future research on the function of APC genes in response to viral infections and expanding our understanding of wheat immunity mechanisms.
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Affiliation(s)
- Jinnan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.W.); (T.Z.); (A.T.); (H.X.); (H.H.)
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Tianye Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.W.); (T.Z.); (A.T.); (H.X.); (H.H.)
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Aizhu Tu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.W.); (T.Z.); (A.T.); (H.X.); (H.H.)
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Haoxin Xie
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.W.); (T.Z.); (A.T.); (H.X.); (H.H.)
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Haichao Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.W.); (T.Z.); (A.T.); (H.X.); (H.H.)
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.W.); (T.Z.); (A.T.); (H.X.); (H.H.)
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.W.); (T.Z.); (A.T.); (H.X.); (H.H.)
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Wu Q, Yin J, Jiang M, Zhang J, Sui Z. Identification, characterization and expression profiles of E2 and E3 gene superfamilies during the development of tetrasporophytes in Gracilariopsis lemaneiformis (Rhodophyta). BMC Genomics 2023; 24:549. [PMID: 37723489 PMCID: PMC10506303 DOI: 10.1186/s12864-023-09639-0] [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: 04/20/2023] [Accepted: 08/30/2023] [Indexed: 09/20/2023] Open
Abstract
E2 ubiquitin conjugating enzymes and E3 ubiquitin ligases play important roles in the growth and development of plants and animals. To date, the systematic analysis of E2 and E3 genes in Rhodophyta is limited. In this study, 14 E2 genes and 51 E3 genes were identified in Gracilariopsis lemaneiformis, an economically important red alga. E2 genes were classified into four classes according to the structure of the conserved domain, UBC. E3 genes were classified into 12 subfamilies according to individual conserved domains. A phylogenetic tree of seven algae species showed that functional differentiation of RING-type E3s was the highest, and the similarity between orthologous genes was high except in Chlamydomonas reinhardtii and Chara braunii. RNA-seq data analysis showed significant differential expression levels of E2 and E3 genes under the life stages of tetraspore formation and release, especially GlUBCN and GlAPC3. According to GO and KEGG analysis of two transcriptomes, GlUBCN and GlAPC3 were involved in ubiquitin-mediated proteolysis, and other subunits of the anaphase promoting complex or cyclosome (APC/C) and its activators GlCDC20 and GlCDH1 were also enriched into this process. The CDH1 and CDC20 in 981 were down-regulated during tetraspores formation and release, with the down-regulation of CDH1 being particularly significant; CDH1 and CDC20 in WLP-1, ZC, and WT were up-regulated during tetraspores formation and release, with CDC20 being more significantly up-regulated. Therefore, GlCDH1, rather than GlCDC20, in '981' might play the leading role in the activation of the APC/C, and GlCDC20 might play the leading role rather than GlCDH1 in strains WLP-1, ZC and wild type. The low fertility of cultivar 981 might be highly correlated with the inactivity of activators CDH1 and CDC20. This study provided a basic and comprehensive understanding of characteristic of E2 and E3 genes in Gp. lemaneiformis and set a foundation for further understanding of E2 ubiquitin conjugating enzymes and E3 ubiquitin ligase in regulating tetrasporophytes development of Gp. lemaneiformis.
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Affiliation(s)
- Qiong Wu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China), Qingdao, 266003, China
| | - Jingru Yin
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China), Qingdao, 266003, China
| | - Min Jiang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China), Qingdao, 266003, China
| | - Jingyu Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China), Qingdao, 266003, China
| | - Zhenghong Sui
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China), Qingdao, 266003, China.
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Genome-wide identification and expression analysis of anaphase promoting complex/cyclosome (APC/C) in rose. Int J Biol Macromol 2022; 223:1604-1618. [PMID: 36372105 DOI: 10.1016/j.ijbiomac.2022.11.085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/11/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
The anaphase promoting complex/cyclosome (APC/C) is a large multi-subunit complex, regulating plant development and cell cycle. In plants, the APC/C gene family has been identified in Arabidopsis, rice, and maize. The APC/Cs in rose has not yet been reported. In this study, a total of 19 APC/C genes were identified in rose. Furthermore, we also investigated phylogenetic relationships, chromosomal distribution, gene structure, motif analysis, promoter sequence analysis and expression pattern of RhAPC/C genes. Synteny analysis indicated that AtAPC/Cs and RhAPC/Cs show a high degree of conservation. RhAPC/C promoters contains numerous cis-elements involved in plant morphogenesis, hormone response and stress response. Based on the transcription of RhAPC/Cs in different tissues and developmental stages, it appears that RhAPC/Cs may play a variety of roles in rose growth and development. RhAPC/Cs have limitations in the time and space during which they respond to hormones and abiotic stress. RhAPC5, RhAPC11d, RhAPC13a and RhAPC13c may play a role in rose responding to abiotic stress. The expression of RhAPC10 was altered by infection with fungal pathogen. Our study will serve as a basis for determining the functional role of APC/C genes in roses and help future research on woody plants.
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de Oliveira PN, da Silva LFC, Eloy NB. The role of APC/C in cell cycle dynamics, growth and development in cereal crops. FRONTIERS IN PLANT SCIENCE 2022; 13:987919. [PMID: 36247602 PMCID: PMC9558237 DOI: 10.3389/fpls.2022.987919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Cereal crops can be considered the basis of human civilization. Thus, it is not surprising that these crops are grown in larger quantities worldwide than any other food supply and provide more energy to humankind than any other provision. Additionally, attempts to harness biomass consumption continue to increase to meet human energy needs. The high pressures for energy will determine the demand for crop plants as resources for biofuel, heat, and electricity. Thus, the search for plant traits associated with genetic increases in yield is mandatory. In multicellular organisms, including plants, growth and development are driven by cell division. These processes require a sequence of intricated events that are carried out by various protein complexes and molecules that act punctually throughout the cycle. Temporal controlled degradation of key cell division proteins ensures a correct onset of the different cell cycle phases and exit from the cell division program. Considering the cell cycle, the Anaphase-Promoting Complex/Cyclosome (APC/C) is an important conserved multi-subunit ubiquitin ligase, marking targets for degradation by the 26S proteasome. Studies on plant APC/C subunits and activators, mainly in the model plant Arabidopsis, revealed that they play a pivotal role in several developmental processes during growth. However, little is known about the role of APC/C in cereal crops. Here, we discuss the current understanding of the APC/C controlling cereal crop development.
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Cosma MA, Curtis NL, Pain C, Kriechbaumer V, Bolanos-Garcia VM. Biochemical, biophysical, and functional characterisation of the E3 ubiquitin ligase APC/C regulator CDC20 from Arabidopsis thaliana. Front Physiol 2022; 13:938688. [PMID: 35957989 PMCID: PMC9357983 DOI: 10.3389/fphys.2022.938688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/28/2022] [Indexed: 12/03/2022] Open
Abstract
The Anaphase Promoting Complex (APC/C), a large cullin-RING E3-type ubiquitin ligase, constitutes the ultimate target of the Spindle Assembly Checkpoint (SAC), an intricate regulatory circuit that ensures the high fidelity of chromosome segregation in eukaryotic organisms by delaying the onset of anaphase until each chromosome is properly bi-oriented on the mitotic spindle. Cell-division cycle protein 20 homologue (CDC20) is a key regulator of APC/C function in mitosis. The formation of the APC/CCDC20 complex is required for the ubiquitination and degradation of select substrates, which is necessary to maintain the mitotic state. In contrast to the roles of CDC20 in animal species, little is known about CDC20 roles in the regulation of chromosome segregation in plants. Here we address this gap in knowledge and report the expression in insect cells; the biochemical and biophysical characterisation of Arabidopsis thaliana (AtCDC20) WD40 domain; and the nuclear and cytoplasmic distribution of full-length AtCDC20 when transiently expressed in tobacco plants. We also show that most AtCDC20 degrons share a high sequence similarity to other eukaryotes, arguing in favour of conserved degron functions in AtCDC20. However, important exceptions were noted such as the lack of a canonical MAD1 binding motif; a fully conserved RRY-box in all six AtCDC20 isoforms instead of a CRY-box motif, and low conservation of key residues known to be phosphorylated by BUB1 and PLK1 in other species to ensure a robust SAC response. Taken together, our studies provide insights into AtCDC20 structure and function and the evolution of SAC signalling in plants.
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Lin YN, Jiang CK, Cheng ZK, Wang DH, Shen LP, Xu C, Xu ZH, Bai SN. Rice Cell Division Cycle 20s are required for faithful chromosome segregation and cytokinesis during meiosis. PLANT PHYSIOLOGY 2022; 188:1111-1128. [PMID: 34865119 PMCID: PMC8825277 DOI: 10.1093/plphys/kiab543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/25/2021] [Indexed: 05/04/2023]
Abstract
Chromosome segregation must be under strict regulation to maintain chromosome euploidy and stability. Cell Division Cycle 20 (CDC20) is an essential cell cycle regulator that promotes the metaphase-to-anaphase transition and functions in the spindle assembly checkpoint, a surveillance pathway that ensures the fidelity of chromosome segregation. Plant CDC20 genes are present in multiple copies, and whether CDC20s have the same functions in plants as in yeast and animals is unclear, given the potential for divergence or redundancy among the multiple copies. Here, we studied all three CDC20 genes in rice (Oryza sativa) and constructed two triple mutants by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9-mediated genome editing to explore their roles in development. Knocking out all three CDC20 genes led to total sterility but did not affect vegetative development. Loss of the three CDC20 proteins did not alter mitotic division but severely disrupted meiosis as a result of asynchronous and unequal chromosome segregation, chromosome lagging, and premature separation of chromatids. Immunofluorescence of tubulin revealed malformed meiotic spindles in microsporocytes of the triple mutants. Furthermore, cytokinesis of meiosis I was absent or abnormal, and cytokinesis II was completely prevented in all mutant microsporocytes; thus, no tetrads or pollen formed in either cdc20 triple mutant. Finally, the subcellular structures and functions of the tapetum were disturbed by the lack of CDC20 proteins. These findings demonstrate that the three rice CDC20s play redundant roles but are indispensable for faithful meiotic chromosome segregation and cytokinesis, which are required for the production of fertile microspores.
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Affiliation(s)
- Ya-Nan Lin
- State Key Laboratory of Protein and Plant Gene Research, Beijing 100871, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Chen-Kun Jiang
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Zhu-Kuan Cheng
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dong-Hui Wang
- State Key Laboratory of Protein and Plant Gene Research, Beijing 100871, China
- College of Life Sciences, Peking University, Beijing 100871, China
- National Teaching Center for Experimental Biology, Peking University, Beijing 100871, China
| | - Li-Ping Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Cong Xu
- State Key Laboratory of Protein and Plant Gene Research, Beijing 100871, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Zhi-Hong Xu
- State Key Laboratory of Protein and Plant Gene Research, Beijing 100871, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Shu-Nong Bai
- State Key Laboratory of Protein and Plant Gene Research, Beijing 100871, China
- College of Life Sciences, Peking University, Beijing 100871, China
- Author for communication:
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Gong P, Bontinck M, Demuynck K, De Block J, Gevaert K, Eeckhout D, Persiau G, Aesaert S, Coussens G, Van Lijsebettens M, Pauwels L, De Jaeger G, Inzé D, Nelissen H. SAMBA controls cell division rate during maize development. PLANT PHYSIOLOGY 2022; 188:411-424. [PMID: 34791456 PMCID: PMC8774815 DOI: 10.1093/plphys/kiab514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 10/02/2021] [Indexed: 05/10/2023]
Abstract
SAMBA has been identified as a plant-specific regulator of the anaphase-promoting complex/cyclosome (APC/C) that controls unidirectional cell cycle progression in Arabidopsis (Arabidopsis thaliana), but so far its role has not been studied in monocots. Here, we show the association of SAMBA with the APC/C is conserved in maize (Zea mays). Two samba genome edited mutants showed growth defects, such as reduced internode length, shortened upper leaves with erect leaf architecture, and reduced leaf size due to an altered cell division rate and cell expansion, which aggravated with plant age. The two mutants differed in the severity and developmental onset of the phenotypes, because samba-1 represented a knockout allele, while translation re-initiation in samba-3 resulted in a truncated protein that was still able to interact with the APC/C and regulate its function, albeit with altered APC/C activity and efficiency. Our data are consistent with a dosage-dependent role for SAMBA to control developmental processes for which a change in growth rate is pivotal.
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Affiliation(s)
- Pan Gong
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Michiel Bontinck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Kirin Demuynck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jolien De Block
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- VIB Center for Medical Biotechnology, 9000 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Geert Persiau
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Stijn Aesaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Griet Coussens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Mieke Van Lijsebettens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Author for communication:
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Plant CDKs-Driving the Cell Cycle through Climate Change. PLANTS 2021; 10:plants10091804. [PMID: 34579337 PMCID: PMC8468384 DOI: 10.3390/plants10091804] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/03/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023]
Abstract
In a growing population, producing enough food has become a challenge in the face of the dramatic increase in climate change. Plants, during their evolution as sessile organisms, developed countless mechanisms to better adapt to the environment and its fluctuations. One important way is through the plasticity of their body and their forms, which are modulated during plant growth by accurate control of cell divisions. A family of serine/threonine kinases called cyclin-dependent kinases (CDK) is a key regulator of cell divisions by controlling cell cycle progression. In this review, we compile information on the primary response of plants in the regulation of the cell cycle in response to environmental stresses and show how the cell cycle proteins (mainly the cyclin-dependent kinases) involved in this regulation can act as components of environmental response signaling cascades, triggering adaptive responses to drive the cycle through climate fluctuations. Understanding the roles of CDKs and their regulators in the face of adversity may be crucial to meeting the challenge of increasing agricultural productivity in a new climate.
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Gingerich DJ, Hellmann H, Christians MJ, Stone SL. Editorial: Structure, Function, and Evolution of E3 Ligases and Targets. FRONTIERS IN PLANT SCIENCE 2021; 12:767281. [PMID: 34707634 PMCID: PMC8542714 DOI: 10.3389/fpls.2021.767281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 09/13/2021] [Indexed: 05/09/2023]
Affiliation(s)
- Derek J. Gingerich
- Department of Biology, University of Wisconsin-Eau Claire, Eau Claire, WI, United States
- *Correspondence: Derek J. Gingerich
| | - Hanjo Hellmann
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Matthew J. Christians
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, United States
| | - Sophia L. Stone
- Department of Biology, Dalhousie University, Halifax, NS, Canada
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D'Esposito D, Cappetta E, Andolfo G, Ferriello F, Borgonuovo C, Caruso G, De Natale A, Frusciante L, Ercolano MR. Deciphering the biological processes underlying tomato biomass production and composition. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 143:50-60. [PMID: 31479882 DOI: 10.1016/j.plaphy.2019.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/19/2019] [Accepted: 08/13/2019] [Indexed: 05/20/2023]
Abstract
The huge amounts of biomass residues, remaining in the field after tomato fruits harvesting, can be utilized to produce bioenergy. A multiple level approach aimed to characterize two Solanum pennellii introgression lines (ILs), with contrasting phenotypes for plant architecture and biomass was carried out. The study of gene expression dynamics, microscopy cell traits and qualitative and quantitative cell wall chemical compounds variation enabled the discovery of key genes and cell processes involved biomass accumulation and composition. Enhanced biomass production observed in IL2-6 line is due to a more effective coordination of chloroplasts and mitochondria energy fluxes. Microscopy analysis revealed a higher number of cells and chloroplasts in leaf epidermis in the high biomass line whilst chemical measurements on the two lines pointed out striking differences in the cell wall composition and organization. Taken together, our findings shed light on the mechanisms underlying the tomato biomass production and processability.
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Affiliation(s)
- Daniela D'Esposito
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Elisa Cappetta
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Giuseppe Andolfo
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Francesca Ferriello
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Camilla Borgonuovo
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Gianluca Caruso
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Antonino De Natale
- Department of Biology, University of Naples 'Federico II', Via Cinthia, Monte Sant'Angelo, Building 7, 80126, Naples, Italy.
| | - Luigi Frusciante
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Maria Raffaella Ercolano
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
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Lorenzo-Orts L, Witthoeft J, Deforges J, Martinez J, Loubéry S, Placzek A, Poirier Y, Hothorn LA, Jaillais Y, Hothorn M. Concerted expression of a cell cycle regulator and a metabolic enzyme from a bicistronic transcript in plants. NATURE PLANTS 2019; 5:184-193. [PMID: 30737513 DOI: 10.1038/s41477-019-0358-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/04/2019] [Indexed: 05/15/2023]
Abstract
Eukaryotic mRNAs frequently contain upstream open reading frames (uORFs), encoding small peptides that may control translation of the main ORF (mORF). Here, we report the characterization of a distinct bicistronic transcript in Arabidopsis. We analysed loss-of-function phenotypes of the inorganic polyphosphatase TRIPHOSPHATE TUNNEL METALLOENZYME 3 (AtTTM3), and found that catalytically inactive versions of the enzyme could fully complement embryo and growth-related phenotypes. We could rationalize these puzzling findings by characterizing a uORF in the AtTTM3 locus encoding CELL DIVISION CYCLE PROTEIN 26 (CDC26), an orthologue of the cell cycle regulator. We demonstrate that AtCDC26 is part of the plant anaphase promoting complex/cyclosome (APC/C), regulates accumulation of APC/C target proteins and controls cell division, growth and embryo development. AtCDC26 and AtTTM3 are translated from a single transcript conserved across the plant lineage. While there is no apparent biochemical connection between the two gene products, AtTTM3 coordinates AtCDC26 translation by recruiting the transcript into polysomes. Our work highlights that uORFs may encode functional proteins in plant genomes.
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Affiliation(s)
- Laura Lorenzo-Orts
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.
| | - Janika Witthoeft
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Jules Deforges
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Jacobo Martinez
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Sylvain Loubéry
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Aleksandra Placzek
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Yves Poirier
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Ludwig A Hothorn
- Institute of Biostatistics, Leibniz University, Hannover, Germany
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon, France
| | - Michael Hothorn
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany.
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Dedecker M, Van Leene J, De Winne N, Eeckhout D, Persiau G, Van De Slijke E, Cannoot B, Vercruysse L, Dumoulin L, Wojsznis N, Gevaert K, Vandenabeele S, De Jaeger G. Transferring an optimized TAP-toolbox for the isolation of protein complexes to a portfolio of rice tissues. PLANT MOLECULAR BIOLOGY 2016; 91:341-354. [PMID: 27003905 DOI: 10.1007/s11103-016-0471-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 03/10/2016] [Indexed: 06/05/2023]
Abstract
Proteins are the cell's functional entities. Rather than operating independently, they interact with other proteins. Capturing in vivo protein complexes is therefore crucial to gain understanding of the function of a protein in a cellular context. Affinity purification coupled to mass spectrometry has proven to yield a wealth of information about protein complex constitutions for a broad range of organisms. For Oryza sativa, the technique has been initiated in callus and shoots, but has not been optimized ever since. We translated an optimized tandem affinity purification (TAP) approach from Arabidopsis thaliana toward Oryza sativa, and demonstrate its applicability in a variety of rice tissues. A list of non-specific and false positive interactors is presented, based on re-occurrence over more than 170 independent experiments, to filter bona fide interactors. We demonstrate the sensitivity of our approach by isolating the complexes for the rice ANAPHASE PROMOTING COMPLEX SUBUNIT 10 (APC10) and CYCLIN-DEPENDENT KINASE D (CDKD) proteins from the proliferation zone of the emerging fourth leaf. Next to APC10 and CDKD, we tested several additional baits in the different rice tissues and reproducibly retrieved at least one interactor for 81.4 % of the baits screened for in callus tissue and T1 seedlings. By transferring an optimized TAP tag combined with state-of-the-art mass spectrometry, our TAP protocol enables the discovery of interactors for low abundance proteins in rice and opens the possibility to capture complex dynamics by comparing tissues at different stages of a developing rice organ.
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Affiliation(s)
- Maarten Dedecker
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
- CropDesign N.V., Technologiepark 21, 9052, Ghent, Belgium.
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Nancy De Winne
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Geert Persiau
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Bernard Cannoot
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Leen Vercruysse
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Lies Dumoulin
- CropDesign N.V., Technologiepark 21, 9052, Ghent, Belgium
| | | | - Kris Gevaert
- Department of Medical Protein Research and Biochemistry, VIB, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | | | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
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14
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Mohanta TK, Arora PK, Mohanta N, Parida P, Bae H. Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel activation loop variants. BMC Genomics 2015; 16:58. [PMID: 25888265 PMCID: PMC4363184 DOI: 10.1186/s12864-015-1244-7] [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: 11/27/2014] [Accepted: 01/15/2015] [Indexed: 11/30/2022] Open
Abstract
Background Mitogen Activated Protein Kinase (MAPK) signaling is of critical importance in plants and other eukaryotic organisms. The MAPK cascade plays an indispensible role in the growth and development of plants, as well as in biotic and abiotic stress responses. The MAPKs are constitute the most downstream module of the three tier MAPK cascade and are phosphorylated by upstream MAP kinase kinases (MAPKK), which are in turn are phosphorylated by MAP kinase kinase kinase (MAPKKK). The MAPKs play pivotal roles in regulation of many cytoplasmic and nuclear substrates, thus regulating several biological processes. Results A total of 589 MAPKs genes were identified from the genome wide analysis of 40 species. The sequence analysis has revealed the presence of several N- and C-terminal conserved domains. The MAPKs were previously believed to be characterized by the presence of TEY/TDY activation loop motifs. The present study showed that, in addition to presence of activation loop TEY/TDY motifs, MAPKs are also contain MEY, TEM, TQM, TRM, TVY, TSY, TEC and TQY activation loop motifs. Phylogenetic analysis of all predicted MAPKs were clustered into six different groups (group A, B, C, D, E and F), and all predicted MAPKs were assigned with specific names based on their orthology based evolutionary relationships with Arabidopsis or Oryza MAPKs. Conclusion We conducted global analysis of the MAPK gene family of plants from lower eukaryotes to higher eukaryotes and analyzed their genomic and evolutionary aspects. Our study showed the presence of several new activation loop motifs and diverse conserved domains in MAPKs. Advance study of newly identified activation loop motifs can provide further information regarding the downstream signaling cascade activated in response to a wide array of stress conditions, as well as plant growth and development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1244-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tapan Kumar Mohanta
- School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook, 712749, Republic of Korea.
| | - Pankaj Kumar Arora
- School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook, 712749, Republic of Korea.
| | - Nibedita Mohanta
- Department of Biotechnology, North Orissa University, Sri Ramchandra Vihar, Takatpur, Baripada, Mayurbhanj, Orissa, 757003, India.
| | - Pratap Parida
- Center for Studies in Biotechnology, Dibrugarh University, Dibrugarh, Assam, 786004, India.
| | - Hanhong Bae
- School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook, 712749, Republic of Korea.
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15
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Wen F, Zhu H, Li P, Jiang M, Mao W, Ong C, Chu Z. Genome-wide evolutionary characterization and expression analyses of WRKY family genes in Brachypodium distachyon. DNA Res 2014; 21:327-39. [PMID: 24453041 PMCID: PMC4060952 DOI: 10.1093/dnares/dst060] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Members of plant WRKY gene family are ancient transcription factors that function in plant growth and development and respond to biotic and abiotic stresses. In our present study, we have investigated WRKY family genes in Brachypodium distachyon, a new model plant of family Poaceae. We identified a total of 86 WRKY genes from B. distachyon and explored their chromosomal distribution and evolution, domain alignment, promoter cis-elements, and expression profiles. Combining the analysis of phylogenetic tree of BdWRKY genes and the result of expression profiling, results showed that most of clustered gene pairs had higher similarities in the WRKY domain, suggesting that they might be functionally redundant. Neighbour-joining analysis of 301 WRKY domains from Oryza sativa, Arabidopsis thaliana, and B. distachyon suggested that BdWRKY domains are evolutionarily more closely related to O. sativa WRKY domains than those of A. thaliana. Moreover, tissue-specific expression profile of BdWRKY genes and their responses to phytohormones and several biotic or abiotic stresses were analysed by quantitative real-time PCR. The results showed that the expression of BdWRKY genes was rapidly regulated by stresses and phytohormones, and there was a strong correlation between promoter cis-elements and the phytohormones-induced BdWRKY gene expression.
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Affiliation(s)
- Feng Wen
- Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanic Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Hong Zhu
- Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanic Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Peng Li
- Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanic Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Min Jiang
- Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanic Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Wenqing Mao
- Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanic Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Chermaine Ong
- Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanic Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Zhaoqing Chu
- Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanic Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
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16
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de Freitas Lima M, Eloy NB, Bottino MC, Hemerly AS, Ferreira PCG. Overexpression of the anaphase-promoting complex (APC) genes in Nicotiana tabacum promotes increasing biomass accumulation. Mol Biol Rep 2013; 40:7093-102. [PMID: 24178345 DOI: 10.1007/s11033-013-2832-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 10/26/2013] [Indexed: 10/26/2022]
Abstract
The anaphase-promoting complex (APC) plays pivotal roles in cell cycle pathways related to plant development. In this study, we present evidence that overproduction of APC10 from Arabidopsis thaliana in tobacco (Nicotiana tabacum) plants promotes significant increases in biomass. Analyzes of plant's fresh and dried weight, root length, number of days to flower and number of seeds of plants overexpressing AtAPC10 verified an improved agronomic performance of the transgenic plants. Detailed analyzes of the leaf growth at the cellular level, and measurements of leaf cell number, showed that AtAPC10 also produce more cells, showing an enhancement of proliferation in these plants. In addition, crossing of plants overexpressing AtAPC10 and AtCDC27a resulted in a synergistic accumulation of biomass and these transgenic plants exhibited superior characteristics compared to the parental lines. The results of the present study suggest that transgenic plants expressing AtAPC10 and AtAPC10/AtCDC27a concomitantly are promising leads to develop plants with higher biomass.
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Affiliation(s)
- Marcelo de Freitas Lima
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, CCS, Cidade Universitária - Ilha do Fundão, CEP 21941-902, Rio de Janeiro, RJ, Brazil,
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Abstract
E3 ligases comprise a highly diverse and important group of enzymes that act within the 26S ubiquitin proteasome pathway. They facilitate the transfer of ubiquitin moieties to substrate proteins which may be marked for degradation by this step. As such, they serve as central regulators in many cellular and physiological processes in plants. The review provides an update on the multitude of different E3 ligases currently known in plants, and illustrates the central role in plant biology of specific examples.
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Affiliation(s)
- Liyuan Chen
- Plant Stress Physiology, School of Biological Sciences, Abelson 435, PO Box 644236, Washington State University, Pullman, WA 99164-4236, USA
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Heyman J, De Veylder L. The anaphase-promoting complex/cyclosome in control of plant development. MOLECULAR PLANT 2012; 5:1182-94. [PMID: 23034505 DOI: 10.1093/mp/sss094] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Temporal controlled degradation of key cell division proteins ensures a correct onset of the different cell cycle phases and exit from the cell division program. In light of the cell cycle, the Anaphase-Promoting Complex/Cyclosome (APC/C) is an important conserved multi-subunit ubiquitin ligase, marking targets for degradation by the 26S proteasome. However, whereas the APC/C has been studied extensively in yeast and mammals, only in the last decade has the plant APC/C started to unveil its secrets. Research results have shown the importance of the APC/C core complex and its activators during gametogenesis, growth, hormone signaling, symbiotic interactions, and endoreduplication onset. In addition, recently, the first plant APC/C inhibitors have been reported, allowing a fine-tuning of APC/C activity during the cell cycle. Together with the identification of the first APC/C targets, a picture emerges of APC/C activity being essential for many different developmental processes.
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Affiliation(s)
- Jefri Heyman
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
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19
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Vierstra RD. The expanding universe of ubiquitin and ubiquitin-like modifiers. PLANT PHYSIOLOGY 2012; 160:2-14. [PMID: 22693286 PMCID: PMC3440198 DOI: 10.1104/pp.112.200667] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 06/09/2012] [Indexed: 05/18/2023]
Affiliation(s)
- Richard D Vierstra
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA.
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Xu C, Wang Y, Yu Y, Duan J, Liao Z, Xiong G, Meng X, Liu G, Qian Q, Li J. Degradation of MONOCULM 1 by APC/C(TAD1) regulates rice tillering. Nat Commun 2012; 3:750. [PMID: 22434193 PMCID: PMC3316885 DOI: 10.1038/ncomms1743] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 02/10/2012] [Indexed: 12/25/2022] Open
Abstract
A rice tiller is a specialized grain-bearing branch that contributes greatly to grain yield. The MONOCULM 1 (MOC1) gene is the first identified key regulator controlling rice tiller number; however, the underlying mechanism remains to be elucidated. Here we report a novel rice gene, Tillering and Dwarf 1 (TAD1), which encodes a co-activator of the anaphase-promoting complex (APC/C), a multi-subunit E3 ligase. Although the elucidation of co-activators and individual subunits of plant APC/C involved in regulating plant development have emerged recently, the understanding of whether and how this large cell-cycle machinery controls plant development is still very limited. Our study demonstrates that TAD1 interacts with MOC1, forms a complex with OsAPC10 and functions as a co-activator of APC/C to target MOC1 for degradation in a cell-cycle-dependent manner. Our findings uncovered a new mechanism underlying shoot branching and shed light on the understanding of how the cell-cycle machinery regulates plant architecture.
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Affiliation(s)
- Cao Xu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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Vaughn JN, Ellingson SR, Mignone F, von Arnim A. Known and novel post-transcriptional regulatory sequences are conserved across plant families. RNA (NEW YORK, N.Y.) 2012; 18:368-84. [PMID: 22237150 PMCID: PMC3285926 DOI: 10.1261/rna.031179.111] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The sequence elements that mediate post-transcriptional gene regulation often reside in the 5' and 3' untranslated regions (UTRs) of mRNAs. Using six different families of dicotyledonous plants, we developed a comparative transcriptomics pipeline for the identification and annotation of deeply conserved regulatory sequences in the 5' and 3' UTRs. Our approach was robust to confounding effects of poor UTR alignability and rampant paralogy in plants. In the 3' UTR, motifs resembling PUMILIO-binding sites form a prominent group of conserved motifs. Additionally, Expansins, one of the few plant mRNA families known to be localized to specific subcellular sites, possess a core conserved RCCCGC motif. In the 5' UTR, one major subset of motifs consists of purine-rich repeats. A distinct and substantial fraction possesses upstream AUG start codons. Half of the AUG containing motifs reveal hidden protein-coding potential in the 5' UTR, while the other half point to a peptide-independent function related to translation. Among the former, we added four novel peptides to the small catalog of conserved-peptide uORFs. Among the latter, our case studies document patterns of uORF evolution that include gain and loss of uORFs, switches in uORF reading frame, and switches in uORF length and position. In summary, nearly three hundred post-transcriptional elements show evidence of purifying selection across the eudicot branch of flowering plants, indicating a regulatory function spanning at least 70 million years. Some of these sequences have experimental precedent, but many are novel and encourage further exploration.
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Affiliation(s)
- Justin N. Vaughn
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Sally R. Ellingson
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Flavio Mignone
- Dipartimento di Chimica Strutturale e Stereochimica Inorganica, Università degli Studi di Milano, 20133 Milano, Italy
| | - Albrecht von Arnim
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee 37996, USA
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee 37996, USA
- Corresponding author.E-mail .
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Awasthi A, Paul P, Kumar S, Verma SK, Prasad R, Dhaliwal HS. Abnormal endosperm development causes female sterility in rice insertional mutant OsAPC6. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 183:167-174. [PMID: 22195590 DOI: 10.1016/j.plantsci.2011.08.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 08/18/2011] [Accepted: 08/19/2011] [Indexed: 05/28/2023]
Abstract
A T-DNA insertional mutant OsAPC6 of rice, with gibberellic acid insensitivity and reduced height, had up to 45% reduced seed set. The insertion occurred on chromosome 3 of rice in the gene encoding one of the subunits of anaphase promoting complex/Cyclosome APC6. The primary mother cells of the mutant plants had normal meiosis, male gametophyte development and pollen viability. Confocal laser scanning microscopic (CLSM) studies of megagametophyte development showed abnormal mitotic divisions with reduced number or total absence of polar nuclei in about 30-35% megagametophytes of OsAPC6 mutant leading to failure of endosperm and hence embryo and seed development. Abnormal female gametophyte development, high sterility and segregation of tall and gibberellic acid sensitive plants without selectable marker Hpt in the selfed progeny of OsAPC6 mutant plants indicate that the mutant could be maintained in heterozygous condition. The abnormal mitotic divisions during megagametogenesis could be attributed to the inactivation of the APC6/CDC16 of anaphase promoting complex of rice responsible for cell cycle progression during megagametogenesis. Functional validation of the candidate gene through transcriptome profiling and RNAi is in progress.
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Affiliation(s)
- Anjali Awasthi
- Department of Biotechnology, Indian Institute of Technology, Roorkee-247667 India
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23
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Eme L, Trilles A, Moreira D, Brochier-Armanet C. The phylogenomic analysis of the anaphase promoting complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes. BMC Evol Biol 2011; 11:265. [PMID: 21943402 PMCID: PMC3195147 DOI: 10.1186/1471-2148-11-265] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 09/23/2011] [Indexed: 11/10/2022] Open
Abstract
Background The Anaphase Promoting Complex or Cyclosome (APC/C) is the largest member of the ubiquitin ligase [E3] family. It plays a crucial role in the control of the cell cycle and cell proliferation by mediating the proteolysis of key components by the proteasome. APC/C is made of a dozen subunits that assemble into a large complex of ~1.5 MDa, which interacts with various cofactors and targets. Results Using comparative genomic and phylogenetic approaches, we showed that 24 out of 37 known APC/C subunits, adaptors/co-activators and main targets, were already present in the Last Eukaryotic Common Ancestor (LECA) and were well conserved to a few exceptions in all present-day eukaryotic lineages. The phylogenetic analysis of the 24 components inferred to be present in LECA showed that they contain a reliable phylogenetic signal to reconstruct the phylogeny of the domain Eucarya. Conclusions Taken together our analyses indicated that LECA had a complex and highly controlled modern-like cell cycle. Moreover, we showed that, despite what is generally assumed, proteins involved in housekeeping cellular functions may be a good complement to informational genes to study the phylogeny of eukaryotes.
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Affiliation(s)
- Laura Eme
- Aix-Marseille Université, Laboratoire de Chimie Bactérienne, UPR CNRS, Marseille, France
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24
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Kevei Z, Baloban M, Da Ines O, Tiricz H, Kroll A, Regulski K, Mergaert P, Kondorosi E. Conserved CDC20 cell cycle functions are carried out by two of the five isoforms in Arabidopsis thaliana. PLoS One 2011; 6:e20618. [PMID: 21687678 PMCID: PMC3110789 DOI: 10.1371/journal.pone.0020618] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 05/09/2011] [Indexed: 12/21/2022] Open
Abstract
Background The CDC20 and Cdh1/CCS52 proteins are substrate determinants and activators of the Anaphase Promoting Complex/Cyclosome (APC/C) E3 ubiquitin ligase and as such they control the mitotic cell cycle by targeting the degradation of various cell cycle regulators. In yeasts and animals the main CDC20 function is the destruction of securin and mitotic cyclins. Plants have multiple CDC20 gene copies whose functions have not been explored yet. In Arabidopsis thaliana there are five CDC20 isoforms and here we aimed at defining their contribution to cell cycle regulation, substrate selectivity and plant development. Methodology/Principal Findings Studying the gene structure and phylogeny of plant CDC20s, the expression of the five AtCDC20 gene copies and their interactions with the APC/C subunit APC10, the CCS52 proteins, components of the mitotic checkpoint complex (MCC) and mitotic cyclin substrates, conserved CDC20 functions could be assigned for AtCDC20.1 and AtCDC20.2. The other three intron-less genes were silent and specific for Arabidopsis. We show that AtCDC20.1 and AtCDC20.2 are components of the MCC and interact with mitotic cyclins with unexpected specificity. AtCDC20.1 and AtCDC20.2 are expressed in meristems, organ primordia and AtCDC20.1 also in pollen grains and developing seeds. Knocking down both genes simultaneously by RNAi resulted in severe delay in plant development and male sterility. In these lines, the meristem size was reduced while the cell size and ploidy levels were unaffected indicating that the lower cell number and likely slowdown of the cell cycle are the cause of reduced plant growth. Conclusions/Significance The intron-containing CDC20 gene copies provide conserved and redundant functions for cell cycle progression in plants and are required for meristem maintenance, plant growth and male gametophyte formation. The Arabidopsis-specific intron-less genes are possibly “retrogenes” and have hitherto undefined functions or are pseudogenes.
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Affiliation(s)
- Zoltán Kevei
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2355, Gif-sur-Yvette, France
- Institute for Plant Genomics, Human Biotechnology and Bioenergy, Bay Zoltan Foundation for Applied Research, Szeged, Hungary
| | - Mikhail Baloban
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2355, Gif-sur-Yvette, France
| | - Olivier Da Ines
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2355, Gif-sur-Yvette, France
| | - Hilda Tiricz
- Institute for Plant Genomics, Human Biotechnology and Bioenergy, Bay Zoltan Foundation for Applied Research, Szeged, Hungary
| | - Alexandra Kroll
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2355, Gif-sur-Yvette, France
| | - Krzysztof Regulski
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2355, Gif-sur-Yvette, France
| | - Peter Mergaert
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2355, Gif-sur-Yvette, France
| | - Eva Kondorosi
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2355, Gif-sur-Yvette, France
- Institute for Plant Genomics, Human Biotechnology and Bioenergy, Bay Zoltan Foundation for Applied Research, Szeged, Hungary
- * E-mail:
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Zheng B, Chen X, McCormick S. The anaphase-promoting complex is a dual integrator that regulates both MicroRNA-mediated transcriptional regulation of cyclin B1 and degradation of Cyclin B1 during Arabidopsis male gametophyte development. THE PLANT CELL 2011; 23:1033-46. [PMID: 21441434 PMCID: PMC3082252 DOI: 10.1105/tpc.111.083980] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The anaphase-promoting complex/cyclosome (APC/C), an essential ubiquitin protein ligase, regulates mitotic progression and exit by enhancing degradation of cell cycle regulatory proteins, such as CYCB1;1, whose transcripts are upregulated by DUO POLLEN1 (DUO1). DUO1 is required for cell division in male gametophytes and is a target of microRNA 159 (miR159) in Arabidopsis thaliana. Whether APC/C is required for DUO1-dependent CYCB1;1 regulation is unknown. Mutants in both APC8 and APC13 had pleiotrophic phenotypes resembling those of mutants affecting microRNA biogenesis. We show that these apc/c mutants had reduced miR159 levels and increased DUO1 and CYCB1;1 transcript levels and that APC/C is required to recruit RNA polymerase II to MIR159 promoters. Thus, in addition to its role in degrading CYCB1;1, APC/C stimulates production of miR159, which downregulates DUO1 expression, leading to reduced CYCB1;1 transcription. Both MIR159 and APC8-yellow fluorescent protein accumulated in unicellular microspores and bicellular pollen but decreased in tricellular pollen, suggesting that spatial and temporal regulation of miR159 by APC/C ensures mitotic progression. Consistent with this, the percentage of mature pollen with no or single sperm-like cells increased in apc/c mutants and plants overexpressing APC8 partially mimicked the duo1 phenotype. Thus, APC/C is an integrator that regulates both microRNA-mediated transcriptional regulation of CYCB1;1 and degradation of CYCB1;1.
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Affiliation(s)
- Binglian Zheng
- Plant Gene Expression Center, U.S. Department of Agriculture/Agricultural Research Service and Department of Plant and Microbial Biology, University of California-Berkeley, Albany, California 94710
- Department of Botany and Plant Sciences and Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Xuemei Chen
- Department of Botany and Plant Sciences and Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Sheila McCormick
- Plant Gene Expression Center, U.S. Department of Agriculture/Agricultural Research Service and Department of Plant and Microbial Biology, University of California-Berkeley, Albany, California 94710
- Address correspondence to
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