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Hoareau M, Rincheval-Arnold A, Gaumer S, Guénal I. DREAM a little dREAM of DRM: Model organisms and conservation of DREAM-like complexes: Model organisms uncover the mechanisms of DREAM-mediated transcription regulation. Bioessays 2024; 46:e2300125. [PMID: 38059789 DOI: 10.1002/bies.202300125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023]
Abstract
DREAM complexes are transcriptional regulators that control the expression of hundreds to thousands of target genes involved in the cell cycle, quiescence, differentiation, and apoptosis. These complexes contain many subunits that can vary according to the considered target genes. Depending on their composition and the nature of the partners they recruit, DREAM complexes control gene expression through diverse mechanisms, including chromatin remodeling, transcription cofactor and factor recruitment at various genomic binding sites. This complexity is particularly high in mammals. Since the discovery of the first dREAM complex (drosophila Rb, E2F, and Myb) in Drosophila melanogaster, model organisms such as Caenorhabditis elegans, and plants allowed a deeper understanding of the processes regulated by DREAM-like complexes. Here, we review the conservation of these complexes. We discuss the contribution of model organisms to the study of DREAM-mediated transcriptional regulatory mechanisms and their relevance in characterizing novel activities of DREAM complexes.
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Affiliation(s)
- Marion Hoareau
- Université Paris-Saclay, UVSQ, LGBC, Versailles, France
- Université PSL, EPHE, Paris, France
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2
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León-Ruiz JA, Cruz Ramírez A. Predicted landscape of RETINOBLASTOMA-RELATED LxCxE-mediated interactions across the Chloroplastida. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1507-1524. [PMID: 36305297 DOI: 10.1111/tpj.16012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/20/2022] [Accepted: 10/14/2022] [Indexed: 05/16/2023]
Abstract
The colonization of land by a single streptophyte algae lineage some 450 million years ago has been linked to multiple key innovations such as three-dimensional growth, alternation of generations, the presence of stomata, as well as innovations inherent to the birth of major plant lineages, such as the origins of vascular tissues, roots, seeds and flowers. Multicellularity, which evolved multiple times in the Chloroplastida coupled with precise spatiotemporal control of proliferation and differentiation were instrumental for the evolution of these traits. RETINOBLASTOMA-RELATED (RBR), the plant homolog of the metazoan Retinoblastoma protein (pRB), is a highly conserved and multifunctional core cell cycle regulator that has been implicated in the evolution of multicellularity in the green lineage as well as in plant multicellularity-related processes such as proliferation, differentiation, stem cell regulation and asymmetric cell division. RBR fulfills these roles through context-specific protein-protein interactions with proteins containing the Leu-x-Cys-x-Glu (LxCxE) short-linear motif (SLiM); however, how RBR-LxCxE interactions have changed throughout major innovations in the Viridiplantae kingdom is a question that remains unexplored. Here, we employ an in silico evo-devo approach to predict and analyze potential RBR-LxCxE interactions in different representative species of key Chloroplastida lineages, providing a valuable resource for deciphering RBR-LxCxE multiple functions. Furthermore, our analyses suggest that RBR-LxCxE interactions are an important component of RBR functions and that interactions with chromatin modifiers/remodelers, DNA replication and repair machinery are highly conserved throughout the Viridiplantae, while LxCxE interactions with transcriptional regulators likely diversified throughout the water-to-land transition.
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Affiliation(s)
- Jesús A León-Ruiz
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato, 36821, Guanajuato, Mexico
| | - Alfredo Cruz Ramírez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato, 36821, Guanajuato, Mexico
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3
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Okumura T, Nomoto Y, Kobayashi K, Suzuki T, Takatsuka H, Ito M. MYB3R-mediated active repression of cell cycle and growth under salt stress in Arabidopsis thaliana. JOURNAL OF PLANT RESEARCH 2021; 134:261-277. [PMID: 33580347 DOI: 10.1007/s10265-020-01250-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
Under environmental stress, plants are believed to actively repress their growth to save resource and alter its allocation to acquire tolerance against the stress. Although a lot of studies have uncovered precise mechanisms for responding to stress and acquiring tolerance, the mechanisms for regulating growth repression under stress are not as well understood. It is especially unclear which particular genes related to cell cycle control are involved in active growth repression. Here, we showed that decreased growth in plants exposed to moderate salt stress is mediated by MYB3R transcription factors that have been known to positively and negatively regulate the transcription of G2/M-specific genes. Our genome-wide gene expression analysis revealed occurrences of general downregulation of G2/M-specific genes in Arabidopsis under salt stress. Importantly, this downregulation is significantly and universally mitigated by the loss of MYB3R repressors by mutations. Accordingly, the growth performance of Arabidopsis plants under salt stress is significantly recovered in mutants lacking MYB3R repressors. This growth recovery involves improved cell proliferation that is possibly due to prolonging and accelerating cell proliferation, which were partly suggested by enlarged root meristem and increased number of cells positive for CYCB1;1-GUS. Our ploidy analysis further suggested that cell cycle progression at the G2 phase was delayed under salt stress, and this delay was recovered by loss of MYB3R repressors. Under salt stress, the changes in expression of MYB3R activators and repressors at both the mRNA and protein levels were not significant. This observation suggests novel mechanisms underlying MYB3R-mediated growth repression under salt stress that are different from the mechanisms operating under other stress conditions such as DNA damage and high temperature.
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Affiliation(s)
- Toru Okumura
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Chikusa, 464-8601, Japan
| | - Yuji Nomoto
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Kosuke Kobayashi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Chikusa, 464-8601, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Hirotomo Takatsuka
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Masaki Ito
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan.
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Takeuchi T, Lin YT, Fekaris N, Umen J, Sears BB, Benning C. Modulation of CHT7 Complexes during Light/Dark- and Nitrogen-Mediated Life Cycle Transitions of Chlamydomonas. PLANT PHYSIOLOGY 2020; 184:1762-1774. [PMID: 33004613 PMCID: PMC7723089 DOI: 10.1104/pp.20.00864] [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: 07/06/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
The Chlamydomonas reinhardtii Compromised Hydrolysis of Triacylglycerols7 (CHT7) protein has been previously implicated in the regulation of DNA metabolism and cell-cycle-related gene expression during nitrogen (N) deprivation, and its predicted protein interaction domains are necessary for function. Here, we examined impacts of the cht7 mutation during the cell division cycle under nutrient deficiency in light-dark synchronized cultures. We explored the potential mechanisms affecting CHT7 complex activities during the cell cycle and N starvation, with a focus on the possible interaction between CHT7 and the C. reinhardtii retinoblastoma tumor suppressor (RB) protein homolog MAT3. Notably, the absence of CHT7 did not negatively impact the synchrony of cell division and cell cycle progression during diel growth. Although the majority of CHT7 and MAT3/RB proteins were observed in separate complexes by blue native-PAGE, the two proteins coimmunoprecipitated both during synchronized growth and following N deprivation, suggesting the presence of low abundance subcomplexes containing CHT7 and MAT3/RB. Furthermore, we observed several phosphorylated isoforms of CHT7 under these conditions. To test the potential role of phosphorylation on the structure and function of CHT7, we performed site-directed mutagenesis of previously identified phosphorylated amino acids within CHT7. These phosphorylated residues were dispensable for CHT7 function, but phosphorylated variants of CHT7 persisted, indicating that yet-unidentified residues within CHT7 are also likely phosphorylated. Based on the interaction of CHT7 and MAT3/RB, we postulate the presence of a low-abundance or transient regulatory complex in C. reinhardtii that may be similar to DREAM-like complexes in other organisms.
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Affiliation(s)
- Tomomi Takeuchi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Yang-Tsung Lin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Nicholas Fekaris
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - James Umen
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Barbara B Sears
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
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Zluhan-Martínez E, Pérez-Koldenkova V, Ponce-Castañeda MV, Sánchez MDLP, García-Ponce B, Miguel-Hernández S, Álvarez-Buylla ER, Garay-Arroyo A. Beyond What Your Retina Can See: Similarities of Retinoblastoma Function between Plants and Animals, from Developmental Processes to Epigenetic Regulation. Int J Mol Sci 2020; 21:E4925. [PMID: 32664691 PMCID: PMC7404004 DOI: 10.3390/ijms21144925] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/29/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022] Open
Abstract
The Retinoblastoma protein (pRb) is a key cell cycle regulator conserved in a wide variety of organisms. Experimental analysis of pRb's functions in animals and plants has revealed that this protein participates in cell proliferation and differentiation processes. In addition, pRb in animals and its orthologs in plants (RBR), are part of highly conserved protein complexes which suggest the possibility that analogies exist not only between functions carried out by pRb orthologs themselves, but also in the structure and roles of the protein networks where these proteins are involved. Here, we present examples of pRb/RBR participation in cell cycle control, cell differentiation, and in the regulation of epigenetic changes and chromatin remodeling machinery, highlighting the similarities that exist between the composition of such networks in plants and animals.
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Affiliation(s)
- Estephania Zluhan-Martínez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
- Posgrado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Av. Universidad 3000, Coyoacán 04510, Mexico
| | - Vadim Pérez-Koldenkova
- Laboratorio Nacional de Microscopía Avanzada, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc, 330. Col. Doctores, Alc. Cuauhtémoc 06720, Mexico;
| | - Martha Verónica Ponce-Castañeda
- Unidad de Investigación Médica en Enfermedades Infecciosas, Centro Médico Nacional SXXI, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico;
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
| | - Sergio Miguel-Hernández
- Laboratorio de Citopatología Ambiental, Departamento de Morfología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Campus Zacatenco, Calle Wilfrido Massieu Esquina Cda, Manuel Stampa 07738, Mexico;
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
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Niu Y, Wu L, Li Y, Huang H, Qian M, Sun W, Zhu H, Xu Y, Fan Y, Mahmood U, Xu B, Zhang K, Qu C, Li J, Lu K. Deciphering the transcriptional regulatory networks that control size, color, and oil content in Brassica rapa seeds. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:90. [PMID: 32467731 PMCID: PMC7236191 DOI: 10.1186/s13068-020-01728-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/09/2020] [Indexed: 06/02/2023]
Abstract
BACKGROUND Brassica rapa is an important oilseed and vegetable crop species and is the A subgenome donor of two important oilseed Brassica crops, Brassica napus and Brassica juncea. Although seed size (SZ), seed color (SC), and oil content (OC) substantially affect seed yield and quality, the mechanisms regulating these traits in Brassica crops remain unclear. RESULTS We collected seeds from a pair of B. rapa accessions with significantly different SZ, SC, and OC at seven seed developmental stages (every 7 days from 7 to 49 days after pollination), and identified 28,954 differentially expressed genes (DEGs) from seven pairwise comparisons between accessions at each developmental stage. K-means clustering identified a group of cell cycle-related genes closely connected to variation in SZ of B. rapa. A weighted correlation analysis using the WGCNA package in R revealed two important co-expression modules comprising genes whose expression was positively correlated with SZ increase and negatively correlated with seed yellowness, respectively. Upregulated expression of cell cycle-related genes in one module was important for the G2/M cell cycle transition, and the transcription factor Bra.A05TSO1 seemed to positively stimulate the expression of two CYCB1;2 genes to promote seed development. In the second module, a conserved complex regulated by the transcription factor TT8 appear to determine SC through downregulation of TT8 and its target genes TT3, TT18, and ANR. In the third module, WRI1 and FUS3 were conserved to increase the seed OC, and Bra.A03GRF5 was revealed as a key transcription factor on lipid biosynthesis. Further, upregulation of genes involved in triacylglycerol biosynthesis and storage in the seed oil body may increase OC. We further validated the accuracy of the transcriptome data by quantitative real-time PCR of 15 DEGs. Finally, we used our results to construct detailed models to clarify the regulatory mechanisms underlying variations in SZ, SC, and OC in B. rapa. CONCLUSIONS This study provides insight into the regulatory mechanisms underlying the variations of SZ, SC, and OC in plants based on transcriptome comparison. The findings hold great promise for improving seed yield, quality and OC through genetic engineering of critical genes in future molecular breeding.
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Affiliation(s)
- Yue Niu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
| | - Limin Wu
- InnoTech Alberta, Hwy 16A & 75 St., PO Bag 4000, Vegreville, AB Canada
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK Canada
| | - Yanhua Li
- Institute of Characteristic Crop Research, Chongqing Academy of Agricultural Sciences, Chongqing, 402160 China
| | - Hualei Huang
- Institute of Characteristic Crop Research, Chongqing Academy of Agricultural Sciences, Chongqing, 402160 China
| | - Mingchao Qian
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
| | - Wei Sun
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
| | - Hong Zhu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
| | - Yuanfang Xu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
| | - Yonghai Fan
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
| | - Umer Mahmood
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
| | - Benbo Xu
- College of Life Sciences, Yangtze University, Jingzhou, 434025 Hubei China
| | - Kai Zhang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715 China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715 China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715 China
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
- College of Life Sciences, Yangtze University, Jingzhou, 434025 Hubei China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715 China
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Takeuchi T, Sears BB, Lindeboom C, Lin YT, Fekaris N, Zienkiewicz K, Zienkiewicz A, Poliner E, Benning C. Chlamydomonas CHT7 Is Required for an Effective Quiescent State by Regulating Nutrient-Responsive Cell Cycle Gene Expression. THE PLANT CELL 2020; 32:1240-1269. [PMID: 32001503 PMCID: PMC7145468 DOI: 10.1105/tpc.19.00628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/07/2020] [Accepted: 01/27/2020] [Indexed: 06/10/2023]
Abstract
COMPROMISED HYDROLYSIS OF TRIACYLGLYCEROLS7 (CHT7) in Chlamydomonas (Chlamydomonas reinhardtii) was previously shown to affect the transcription of a subset of genes during nitrogen (N)-replete growth and following N refeeding. Here, we show that an extensive derepression of genes involved in DNA metabolism and cell cycle-related processes, as well as downregulation of genes encoding oxidoreductases and nutrient transporters, occurs in the cht7 mutant during N deprivation. Cellular mutant phenotypes are consistent with the observed transcriptome misregulation, as cht7 cells fail to properly arrest growth, nuclear replication, and cell division following N deprivation. Reduction in cht7 colony formation following N refeeding is explained by its compromised viability during N deprivation and by the occurrence of abortive divisions during N refeeding. Surprisingly, the largely unstructured C-terminal half of CHT7 with predicted protein binding domains, but not the canonical CXC DNA binding domain, is essential for the ability of CHT7 to form stable complexes and reverse the cellular phenotypes and transcription levels in the cht7 mutant. Hence, although lacking the presumed DNA binding domain, CHT7 modulates the expression of cell cycle genes in response to N availability, which is essential for establishing an effective quiescent state and the coordinated resumption of growth following N refeeding.
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Affiliation(s)
- Tomomi Takeuchi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Barbara B Sears
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Chase Lindeboom
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Yang-Tsung Lin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Nicholas Fekaris
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Krzysztof Zienkiewicz
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Centre of Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland
| | - Agnieszka Zienkiewicz
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Centre of Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824
| | - Eric Poliner
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824
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Leviczky T, Molnár E, Papdi C, Őszi E, Horváth GV, Vizler C, Nagy V, Pauk J, Bögre L, Magyar Z. E2FA and E2FB transcription factors coordinate cell proliferation with seed maturation. Development 2019; 146:dev.179333. [PMID: 31666236 PMCID: PMC6899031 DOI: 10.1242/dev.179333] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 10/21/2019] [Indexed: 01/31/2023]
Abstract
The E2F transcription factors and the RETINOBLASTOMA-RELATED repressor protein are principal regulators coordinating cell proliferation with differentiation, but their role during seed development is little understood. We show that in fully developed Arabidopsis thaliana embryos, cell number was not affected either in single or double mutants for the activator-type E2FA and E2FB. Accordingly, these E2Fs are only partially required for the expression of cell cycle genes. In contrast, the expression of key seed maturation genes LEAFY COTYLEDON 1/2 (LEC1/2), ABSCISIC ACID INSENSITIVE 3, FUSCA 3 and WRINKLED 1 is upregulated in the e2fab double mutant embryo. In accordance, E2FA directly regulates LEC2, and mutation at the consensus E2F-binding site in the LEC2 promoter de-represses its activity during the proliferative stage of seed development. In addition, the major seed storage reserve proteins, 12S globulin and 2S albumin, became prematurely accumulated at the proliferating phase of seed development in the e2fab double mutant. Our findings reveal a repressor function of the activator E2Fs to restrict the seed maturation programme until the cell proliferation phase is completed. Highlighted Article: During seed and embryo development the E2FA and E2FB transcription factors coordinate cell proliferation with differentiation and accumulation of seed reserves; however, they are not essential for sustaining cell proliferation.
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Affiliation(s)
- Tünde Leviczky
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Eszter Molnár
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Csaba Papdi
- Royal Holloway University of London, Department of Biological Sciences, Centre for Systems and Synthetic Biology, Egham, UK
| | - Erika Őszi
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Gábor V. Horváth
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Csaba Vizler
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Viktór Nagy
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - János Pauk
- Department of Biotechnology, Cereal Research Non-Profit Ltd. Co., Alsó kikötő sor 9, 6726 Szeged, Hungary
| | - László Bögre
- Royal Holloway University of London, Department of Biological Sciences, Centre for Systems and Synthetic Biology, Egham, UK
| | - Zoltán Magyar
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
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9
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Takeuchi T, Benning C. Nitrogen-dependent coordination of cell cycle, quiescence and TAG accumulation in Chlamydomonas. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:292. [PMID: 31890020 PMCID: PMC6927116 DOI: 10.1186/s13068-019-1635-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 12/12/2019] [Indexed: 05/07/2023]
Abstract
Microalgae hold great promises as sustainable cellular factories for the production of alternative fuels, feeds, and biopharmaceuticals for human health. While the biorefinery approach for fuels along with the coproduction of high-value compounds with industrial, therapeutic, or nutraceutical applications have the potential to make algal biofuels more economically viable, a number of challenges continue to hamper algal production systems at all levels. One such hurdle includes the metabolic trade-off often observed between the increased yields of desired products, such as triacylglycerols (TAG), and the growth of an organism. Initial genetic engineering strategies to improve lipid productivity in microalgae, which focused on overproducing the enzymes involved in fatty acid and TAG biosynthesis or inactivating competing carbon (C) metabolism, have seen some successes albeit at the cost of often greatly reduced biomass. Emergent approaches that aim at modifying the dynamics of entire metabolic pathways by engineering of pertinent transcription factors or signaling networks appear to have successfully achieved a balance between growth and neutral lipid accumulation. However, the biological knowledge of key signaling networks and molecular components linking these two processes is still incomplete in photosynthetic eukaryotes, making it difficult to optimize metabolic engineering strategies for microalgae. Here, we focus on nitrogen (N) starvation of the model green microalga, Chlamydomonas reinhardtii, to present the current understanding of the nutrient-dependent switch between proliferation and quiescence, and the drastic reprogramming of metabolism that results in the storage of C compounds following N starvation. We discuss the potential components mediating the transcriptional repression of cell cycle genes and the establishment of quiescence in Chlamydomonas, and highlight the importance of signaling pathways such as those governed by the target of rapamycin (TOR) and sucrose nonfermenting-related (SnRK) kinases in the coordination of metabolic status with cellular growth. A better understanding of how the cell division cycle is regulated in response to nutrient scarcity and of the signaling pathways linking cellular growth to energy and lipid homeostasis, is essential to improve the prospects of biofuels and biomass production in microalgae.
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Affiliation(s)
- Tomomi Takeuchi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 USA
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 USA
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 USA
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
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Arabidopsis TSO1 and MYB3R1 form a regulatory module to coordinate cell proliferation with differentiation in shoot and root. Proc Natl Acad Sci U S A 2018. [PMID: 29535223 DOI: 10.1073/pnas.1715903115] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Fundamental to plant and animal development is the regulated balance between cell proliferation and differentiation, a process intimately tied to cell cycle regulation. In Arabidopsis, mutations in TSO1, whose animal homolog is LIN54, resulted in severe developmental abnormalities both in shoot and root, including shoot meristem fasciation and reduced root meristematic zone. The molecular mechanism that could explain the tso1 mutant phenotype is absent. Through a genetic screen, we identified 32 suppressors that map to the MYB3R1 gene, encoding a conserved cell cycle regulator. Further analysis indicates that TSO1 transcriptionally represses MYB3R1, and the ectopic MYB3R1 activity mediates the tso1 mutant phenotype. Since animal homologs of TSO1 and MYB3R1 are components of a cell cycle regulatory complex, the DREAM complex, we tested and showed that TSO1 and MYB3R1 coimmunoprecipitated in tobacco leaf cells. Our work reveals a conserved cell cycle regulatory module, consisting of TSO1 and MYB3R1, for proper plant development.
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Fischer M, Müller GA. Cell cycle transcription control: DREAM/MuvB and RB-E2F complexes. Crit Rev Biochem Mol Biol 2017; 52:638-662. [PMID: 28799433 DOI: 10.1080/10409238.2017.1360836] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The precise timing of cell cycle gene expression is critical for the control of cell proliferation; de-regulation of this timing promotes the formation of cancer and leads to defects during differentiation and development. Entry into and progression through S phase requires expression of genes coding for proteins that function in DNA replication. Expression of a distinct set of genes is essential to pass through mitosis and cytokinesis. Expression of these groups of cell cycle-dependent genes is regulated by the RB pocket protein family, the E2F transcription factor family, and MuvB complexes together with B-MYB and FOXM1. Distinct combinations of these transcription factors promote the transcription of the two major groups of cell cycle genes that are maximally expressed either in S phase (G1/S) or in mitosis (G2/M). In this review, we discuss recent work that has started to uncover the molecular mechanisms controlling the precisely timed expression of these genes at specific cell cycle phases, as well as the repression of the genes when a cell exits the cell cycle.
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Affiliation(s)
- Martin Fischer
- a Molecular Oncology, Medical School, University of Leipzig , Leipzig , Germany.,b Department of Medical Oncology , Dana-Farber Cancer Institute , Boston , MA , USA.,c Department of Medicine, Brigham and Women's Hospital , Harvard Medical School , Boston , MA , USA
| | - Gerd A Müller
- a Molecular Oncology, Medical School, University of Leipzig , Leipzig , Germany
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Magyar Z, Bögre L, Ito M. DREAMs make plant cells to cycle or to become quiescent. CURRENT OPINION IN PLANT BIOLOGY 2016; 34:100-106. [PMID: 27816815 DOI: 10.1016/j.pbi.2016.10.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/23/2016] [Accepted: 10/07/2016] [Indexed: 05/03/2023]
Abstract
Cell cycle phase specific oscillation of gene transcription has long been recognized as an underlying principle for ordered processes during cell proliferation. The G1/S-specific and G2/M-specific cohorts of genes in plants are regulated by the E2F and the MYB3R transcription factors. Mutant analysis suggests that activator E2F functions might not be fully required for cell cycle entry. In contrast, the two activator-type MYB3Rs are part of positive feedback loops to drive the burst of mitotic gene expression, which is necessary at least to accomplish cytokinesis. Repressor MYB3Rs act outside the mitotic time window during cell cycle progression, and are important for the shutdown of mitotic genes to impose quiescence in mature organs. The two distinct classes of E2Fs and MYB3Rs together with the RETINOBLATOMA RELATED are part of multiprotein complexes that may be evolutionary related to what is known as DREAM complex in animals. In plants, there are multiple such complexes with distinct compositions and functions that may be involved in the coordinated cell cycle and developmental regulation of E2F targets and mitotic genes.
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Affiliation(s)
- Zoltán Magyar
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - László Bögre
- Royal Holloway, University of London, School of Biological Sciences, Egham, Surrey TW20 0EX, UK
| | - Masaki Ito
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan; JST, CREST, Chikusa, Nagoya 464-8601, Japan.
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Kobayashi K, Suzuki T, Iwata E, Magyar Z, Bögre L, Ito M. MYB3Rs, plant homologs of Myb oncoproteins, control cell cycle-regulated transcription and form DREAM-like complexes. Transcription 2016; 6:106-11. [PMID: 26556011 DOI: 10.1080/21541264.2015.1109746] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Plant MYB3R transcription factors, homologous to Myb oncoproteins, regulate the genes expressed at G2 and M phases in the cell cycle. Recent studies showed that MYB3Rs constitute multiprotein complexes that may correspond to animal complexes known as DREAM or dREAM. Discovery of the putative homologous complex in plants uncovered their significant varieties in structure, function, dynamics, and heterogeneity, providing insight into conserved and diversified aspects of cell cycle-regulated gene transcription.
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Affiliation(s)
- Kosuke Kobayashi
- a Graduate School of Bioagricultural Sciences; Nagoya University ; Chikusa , Nagoya , Japan
| | - Toshiya Suzuki
- a Graduate School of Bioagricultural Sciences; Nagoya University ; Chikusa , Nagoya , Japan.,b JST; CREST ; Chikusa , Nagoya , Japan
| | - Eriko Iwata
- a Graduate School of Bioagricultural Sciences; Nagoya University ; Chikusa , Nagoya , Japan
| | - Zoltán Magyar
- c Institute of Plant Biology; Biological Research Centre ; Szeged , Hungary.,d Royal Holloway; University of London; School of Biological Sciences ; Egham , Surrey , UK
| | - László Bögre
- d Royal Holloway; University of London; School of Biological Sciences ; Egham , Surrey , UK
| | - Masaki Ito
- a Graduate School of Bioagricultural Sciences; Nagoya University ; Chikusa , Nagoya , Japan.,b JST; CREST ; Chikusa , Nagoya , Japan
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Chandran D, Wildermuth M. Modulation of Host Endocycle During Plant–Biotroph Interactions. DEVELOPMENTAL SIGNALING IN PLANTS 2016; 40:65-103. [DOI: 10.1016/bs.enz.2016.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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