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Lee J, Miyagishima SY, Bhattacharya D, Yoon HS. From dusk till dawn: cell cycle progression in the red seaweed Gracilariopsis chorda (Rhodophyta). iScience 2024; 27:110190. [PMID: 38984202 PMCID: PMC11231608 DOI: 10.1016/j.isci.2024.110190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/29/2024] [Accepted: 06/03/2024] [Indexed: 07/11/2024] Open
Abstract
The conserved eukaryotic functions of cell cycle genes have primarily been studied using animal/plant models and unicellular algae. Cell cycle progression and its regulatory components in red (Rhodophyta) seaweeds are poorly understood. We analyzed diurnal gene expression data to investigate the cell cycle in the red seaweed Gracilariopsis chorda. We identified cell cycle progression and transitions in G. chorda which are induced by interactions of key regulators such as E2F/DP, RBR, cyclin-dependent kinases, and cyclins from dusk to dawn. However, several typical CDK inhibitor proteins are absent in red seaweeds. Interestingly, the G1-S transition in G. chorda is controlled by delayed transcription of GINS subunit 3. We propose that the delayed S phase entry in this seaweed may have evolved to minimize DNA damage (e.g., due to UV radiation) during replication. Our results provide important insights into cell cycle-associated physiology and its molecular mechanisms in red seaweeds.
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Affiliation(s)
- JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu 41566, Korea
- Kyungpook Institute of Oceanography, Kyungpook National University, Daegu 41566, Korea
| | - Shin-ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
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2
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Zhang M, Jian H, Shang L, Wang K, Wen S, Li Z, Liu R, Jia L, Huang Z, Lyu D. Transcriptome Analysis Reveals Novel Genes Potentially Involved in Tuberization in Potato. PLANTS (BASEL, SWITZERLAND) 2024; 13:795. [PMID: 38592791 PMCID: PMC10975680 DOI: 10.3390/plants13060795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 04/11/2024]
Abstract
The formation and development of tubers, the primary edible and economic organ of potatoes, directly affect their yield and quality. The regulatory network and mechanism of tuberization have been preliminarily revealed in recent years, but plenty of relevant genes remain to be discovered. A few candidate genes were provided due to the simplicity of sampling and result analysis of previous transcriptomes related to tuberization. We sequenced and thoroughly analyzed the transcriptomes of thirteen tissues from potato plants at the tuber proliferation phase to provide more reference information and gene resources. Among them, eight tissues were stolons and tubers at different developmental stages, which we focused on. Five critical periods of tuberization were selected to perform an analysis of differentially expressed genes (DEGs), according to the results of the tissue correlation. Compared with the unswollen stolons (Sto), 2751, 4897, 6635, and 9700 DEGs were detected in the slightly swollen stolons (Sto1), swollen stolons (Sto2), tubers of proliferation stage 1 (Tu1), and tubers of proliferation stage 4 (Tu4). A total of 854 transcription factors and 164 hormone pathway genes were identified in the DEGs. Furthermore, three co-expression networks associated with Sto-Sto1, Sto2-Tu1, and tubers of proliferation stages two to five (Tu2-Tu5) were built using the weighted gene co-expression network analysis (WGCNA). Thirty hub genes (HGs) and 30 hub transcription factors (HTFs) were screened and focalized in these networks. We found that five HGs were reported to regulate tuberization, and most of the remaining HGs and HTFs co-expressed with them. The orthologs of these HGs and HTFs were reported to regulate processes (e.g., flowering, cell division, hormone synthesis, metabolism and signal transduction, sucrose transport, and starch synthesis) that were also required for tuberization. Such results further support their potential to control tuberization. Our study provides insights and countless candidate genes of the regulatory network of tuberization, laying the foundation for further elucidating the genetic basis of tuber development.
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Affiliation(s)
- Meihua Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Hongju Jian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Southwest University, Chongqing 400715, China
| | - Lina Shang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Ke Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Shiqi Wen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Zihan Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Rongrong Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Lijun Jia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Zhenlin Huang
- Chongqing Agricultural Technical Extension Station, Chongqing 401121, China;
| | - Dianqiu Lyu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Southwest University, Chongqing 400715, China
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3
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Schneider M, Van Bel M, Inzé D, Baekelandt A. Leaf growth - complex regulation of a seemingly simple process. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1018-1051. [PMID: 38012838 DOI: 10.1111/tpj.16558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/08/2023] [Accepted: 11/11/2023] [Indexed: 11/29/2023]
Abstract
Understanding the underlying mechanisms of plant development is crucial to successfully steer or manipulate plant growth in a targeted manner. Leaves, the primary sites of photosynthesis, are vital organs for many plant species, and leaf growth is controlled by a tight temporal and spatial regulatory network. In this review, we focus on the genetic networks governing leaf cell proliferation, one major contributor to final leaf size. First, we provide an overview of six regulator families of leaf growth in Arabidopsis: DA1, PEAPODs, KLU, GRFs, the SWI/SNF complexes, and DELLAs, together with their surrounding genetic networks. Next, we discuss their evolutionary conservation to highlight similarities and differences among species, because knowledge transfer between species remains a big challenge. Finally, we focus on the increase in knowledge of the interconnectedness between these genetic pathways, the function of the cell cycle machinery as their central convergence point, and other internal and environmental cues.
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Affiliation(s)
- Michele Schneider
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Michiel Van Bel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Alexandra Baekelandt
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
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4
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Fábián A, Péntek BK, Soós V, Sági L. Heat stress during male meiosis impairs cytoskeletal organization, spindle assembly and tapetum degeneration in wheat. FRONTIERS IN PLANT SCIENCE 2024; 14:1314021. [PMID: 38259921 PMCID: PMC10800805 DOI: 10.3389/fpls.2023.1314021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024]
Abstract
The significance of heat stress in agriculture is ever-increasing with the progress of global climate changes. Due to a negative effect on the yield of staple crops, including wheat, the impairment of plant reproductive development triggered by high ambient temperature became a restraint in food production. Although the heat sensitivity of male meiosis and the following gamete development in wheat has long been recognized, a detailed structural characterization combined with a comprehensive gene expression analysis has not been done about this phenomenon. We demonstrate here that heat stress severely alters the cytoskeletal configuration, triggers the failure of meiotic division in wheat. Moreover, it changes the expression of genes related to gamete development in male meiocytes and the tapetum layer in a genotype-dependent manner. 'Ellvis', a heat-tolerant winter wheat cultivar, showed high spikelet fertility rate and only scarce structural aberrations upon exposure to high temperature. In addition, heat shock genes and genes involved in scavenging reactive oxygen species were significantly upregulated in 'Ellvis', and the expression of meiosis-specific and major developmental genes showed high stability in this cultivar. In the heat-sensitive 'Mv 17-09', however, genes participating in cytoskeletal fiber nucleation, the spindle assembly checkpoint genes, and tapetum-specific developmental regulators were downregulated. These alterations may be related to the decreased cytoskeleton content, frequent micronuclei formation, and the erroneous persistence of the tapetum layer observed in the sensitive genotype. Our results suggest that understanding the heat-sensitive regulation of these gene functions would be an essential contribution to the development of new, heat-tolerant cultivars.
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Affiliation(s)
- Attila Fábián
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, Hungary
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest, Hungary
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | | | - Vilmos Soós
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, Hungary
| | - László Sági
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Centre for Agricultural Research, Hungarian Research Network, Martonvásár, Hungary
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5
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Wang C, Tang Y, Li Y, Hu C, Li J, Lyu A. Genome-wide identification and bioinformatics analysis of the WD40 transcription factor family and candidate gene screening for anthocyanin biosynthesis in Rhododendron simsii. BMC Genomics 2023; 24:488. [PMID: 37633914 PMCID: PMC10463391 DOI: 10.1186/s12864-023-09604-x] [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: 04/26/2023] [Accepted: 08/19/2023] [Indexed: 08/28/2023] Open
Abstract
WD40 transcription factors (TFs) constitute a large gene family in eukaryotes, playing diverse roles in cellular processes. However, their functions in the major ornamental plant, Rhododendron simsii, remain poorly understood. In this study, we identified 258 WD40 proteins in the R. simsii genome, which exhibited an uneven distribution across chromosomes. Based on domain compositions and phylogenetic analysis, we classified these 258 RsWD40 proteins into 42 subfamilies and 47 clusters. Comparative genomic analysis suggested that the expansion of the WD40 gene family predates the divergence of green algae and higher plants, indicating an ancient origin. Furthermore, by analyzing the duplication patterns of RsWD40 genes, we found that transposed duplication played a major role in their expansion. Notably, the majority of RsWD40 gene duplication pairs underwent purifying selection during evolution. Synteny analysis identified significant orthologous gene pairs between R. simsii and Arabidopsis thaliana, Oryza sativa, Vitis vinifera, and Malus domestica. We also investigated potential candidate genes involved in anthocyanin biosynthesis during different flower development stages in R. simsii using RNA-seq data. Specifically, we identified 10 candidate genes during the bud stage and 7 candidate genes during the full bloom stage. GO enrichment analysis of these candidate genes revealed the potential involvement of the ubiquitination process in anthocyanin biosynthesis. Overall, our findings provide a valuable foundation for further investigation and functional analysis of WD40 genes, as well as research on the molecular mechanisms underlying anthocyanin biosynthesis in Rhododendron species.
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Affiliation(s)
- Cheng Wang
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China
| | - Yafang Tang
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China
| | - Yan Li
- Department of Biology and Chemical Engineering, Weihai Vocational College, Weihai, 264200, China
| | - Chao Hu
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China
| | - Jingyi Li
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China
| | - Ang Lyu
- Institute of Quality Standard and Testing Technology for Agro-Products, Hubei Academy of Agricultural Science, Wuhan, 430064, China.
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6
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Fan H, Quan S, Ye Q, Zhang L, Liu W, Zhu N, Zhang X, Ruan W, Yi K, Crawford NM, Wang Y. A molecular framework underlying low-nitrogen-induced early leaf senescence in Arabidopsis thaliana. MOLECULAR PLANT 2023; 16:756-774. [PMID: 36906802 DOI: 10.1016/j.molp.2023.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 02/09/2023] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
Nitrogen (N) deficiency causes early leaf senescence, resulting in accelerated whole-plant maturation and severely reduced crop yield. However, the molecular mechanisms underlying N-deficiency-induced early leaf senescence remain unclear, even in the model species Arabidopsis thaliana. In this study, we identified Growth, Development and Splicing 1 (GDS1), a previously reported transcription factor, as a new regulator of nitrate (NO3-) signaling by a yeast-one-hybrid screen using a NO3- enhancer fragment from the promoter of NRT2.1. We showed that GDS1 promotes NO3- signaling, absorption and assimilation by affecting the expression of multiple NO3- regulatory genes, including Nitrate Regulatory Gene2 (NRG2). Interestingly, we observed that gds1 mutants show early leaf senescence as well as reduced NO3- content and N uptake under N-deficient conditions. Further analyses indicated that GDS1 binds to the promoters of several senescence-related genes, including Phytochrome-Interacting Transcription Factors 4 and 5 (PIF4 and PIF5) and represses their expression. Interestingly, we found that N deficiency decreases GDS1 protein accumulation, and GDS1 could interact with Anaphase Promoting Complex Subunit 10 (APC10). Genetic and biochemical experiments demonstrated that Anaphase Promoting Complex or Cyclosome (APC/C) promotes the ubiquitination and degradation of GDS1 under N deficiency, resulting in loss of PIF4 and PIF5 repression and consequent early leaf senescence. Furthermore, we discovered that overexpression of GDS1 could delay leaf senescence and improve seed yield and N-use efficiency (NUE) in Arabidopsis. In summary, our study uncovers a molecular framework illustrating a new mechanism underlying low-N-induced early leaf senescence and provides potential targets for genetic improvement of crop varieties with increased yield and NUE.
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Affiliation(s)
- Hongmei Fan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Shuxuan Quan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Qing Ye
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Lei Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Wei Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Ning Zhu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Xiaoqi Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Wenyuan Ruan
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 10081, China
| | - Keke Yi
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 10081, China
| | - Nigel M Crawford
- Section of Cell and Developmental Biology, Division of Biological Science, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China.
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7
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Willems A, Liang Y, Heyman J, Depuydt T, Eekhout T, Canher B, Van den Daele H, Vercauteren I, Vandepoele K, De Veylder L. Plant lineage-specific PIKMIN1 drives APC/CCCS52A2 E3-ligase activity-dependent cell division. PLANT PHYSIOLOGY 2023; 191:1574-1595. [PMID: 36423220 PMCID: PMC10022622 DOI: 10.1093/plphys/kiac528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/18/2022] [Indexed: 06/16/2023]
Abstract
The anaphase-promoting complex/cyclosome (APC/C) marks key cell cycle proteins for proteasomal breakdown, thereby ensuring unidirectional progression through the cell cycle. Its target recognition is temporally regulated by activating subunits, one of which is called CELL CYCLE SWITCH 52 A2 (CCS52A2). We sought to expand the knowledge on the APC/C by using the severe growth phenotypes of CCS52A2-deficient Arabidopsis (Arabidopsis thaliana) plants as a readout in a suppressor mutagenesis screen, resulting in the identification of the previously undescribed gene called PIKMIN1 (PKN1). PKN1 deficiency rescues the disorganized root stem cell phenotype of the ccs52a2-1 mutant, whereas an excess of PKN1 inhibits the growth of ccs52a2-1 plants, indicating the need for control of PKN1 abundance for proper development. Accordingly, the lack of PKN1 in a wild-type background negatively impacts cell division, while its systemic overexpression promotes proliferation. PKN1 shows a cell cycle phase-dependent accumulation pattern, localizing to microtubular structures, including the preprophase band, the mitotic spindle, and the phragmoplast. PKN1 is conserved throughout the plant kingdom, with its function in cell division being evolutionarily conserved in the liverwort Marchantia polymorpha. Our data thus demonstrate that PKN1 represents a novel, plant-specific protein with a role in cell division that is likely proteolytically controlled by the CCS52A2-activated APC/C.
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Affiliation(s)
- Alex Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Yuanke Liang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Jefri Heyman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Thomas Depuydt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Balkan Canher
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Hilde Van den Daele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Ilse Vercauteren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
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8
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Pan T, Gao S, Cui X, Wang L, Yan S. APC/CCDC20 targets SCFFBL17 to activate replication stress responses in Arabidopsis. THE PLANT CELL 2023; 35:910-923. [PMID: 36503931 PMCID: PMC9940874 DOI: 10.1093/plcell/koac360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
DNA replication stress threatens genome stability and affects plant growth and development. How plants resolve replication stress is poorly understood. The protein kinase WEE1-mediated cell cycle arrest is required for replication stress responses. The E3 ubiquitin ligases anaphase-promoting complex/cyclosome (APC/C) and Skp1/Cullin 1/F-box (SCF) are essential regulators of the cell cycle. Here, we show that APC/CCDC20 mediates the degradation of SCFFBL17 during replication stress responses in Arabidopsis thaliana. Biochemically, WEE1 interacts with and phosphorylates the APC/C co-activator APC10, which enhances the interaction between F-BOX-LIKE17 (FBL17) and CELL DIVISION CYCLE 20 (CDC20), an activator of APC/C. Both APC10 and CDC20 are required for the polyubiquitination and degradation of FBL17. Genetically, silencing CDC20 or APC10 confers plant hypersensitivity to replication stress, which is suppressed by loss of FBL17. Collectively, our study suggests that WEE1 activates APC/C to inhibit FBL17, providing insight into replication stress responses in plants.
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Affiliation(s)
- Ting Pan
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Shan Gao
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Xiaoyu Cui
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Lili Wang
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Shunping Yan
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
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9
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The role of non-additive gene action on gene expression variation in plant domestication. EvoDevo 2023; 14:3. [PMID: 36765382 PMCID: PMC9912502 DOI: 10.1186/s13227-022-00206-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/05/2022] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND Plant domestication is a remarkable example of rapid phenotypic transformation of polygenic traits, such as organ size. Evidence from a handful of study cases suggests this transformation is due to gene regulatory changes that result in non-additive phenotypes. Employing data from published genetic crosses, we estimated the role of non-additive gene action in the modulation of transcriptional landscapes in three domesticated plants: maize, sunflower, and chili pepper. Using A. thaliana, we assessed the correlation between gene regulatory network (GRN) connectivity properties, transcript abundance variation, and gene action. Finally, we investigated the propagation of non-additive gene action in GRNs. RESULTS We compared crosses between domesticated plants and their wild relatives to a set of control crosses that included a pair of subspecies evolving under natural selection and a set of inbred lines evolving under domestication. We found abundance differences on a higher portion of transcripts in crosses between domesticated-wild plants relative to the control crosses. These transcripts showed non-additive gene action more often in crosses of domesticated-wild plants than in our control crosses. This pattern was strong for genes associated with cell cycle and cell fate determination, which control organ size. We found weak but significant negative correlations between the number of targets of trans-acting genes (Out-degree) and both the magnitude of transcript abundance difference a well as the absolute degree of dominance. Likewise, we found that the number of regulators that control a gene's expression (In-degree) is weakly but negatively correlated with the magnitude of transcript abundance differences. We observed that dominant-recessive gene action is highly propagable through GRNs. Finally, we found that transgressive gene action is driven by trans-acting regulators showing additive gene action. CONCLUSIONS Our study highlights the role of non-additive gene action on modulating domestication-related traits, such as organ size via regulatory divergence. We propose that GRNs are shaped by regulatory changes at genes with modest connectivity, which reduces the effects of antagonistic pleiotropy. Finally, we provide empirical evidence of the propagation of non-additive gene action in GRNs, which suggests a transcriptional epistatic model for the control of polygenic traits, such as organ size.
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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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Zhang Q, Dai X, Wang H, Wang F, Tang D, Jiang C, Zhang X, Guo W, Lei Y, Ma C, Zhang H, Li P, Zhao Y, Wang Z. Transcriptomic Profiling Provides Molecular Insights Into Hydrogen Peroxide-Enhanced Arabidopsis Growth and Its Salt Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:866063. [PMID: 35463436 PMCID: PMC9019583 DOI: 10.3389/fpls.2022.866063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 02/28/2022] [Indexed: 05/05/2023]
Abstract
Salt stress is an important environmental factor limiting plant growth and crop production. Plant adaptation to salt stress can be improved by chemical pretreatment. This study aims to identify whether hydrogen peroxide (H2O2) pretreatment of seedlings affects the stress tolerance of Arabidopsis thaliana seedlings. The results show that pretreatment with H2O2 at appropriate concentrations enhances the salt tolerance ability of Arabidopsis seedlings, as revealed by lower Na+ levels, greater K+ levels, and improved K+/Na+ ratios in leaves. Furthermore, H2O2 pretreatment improves the membrane properties by reducing the relative membrane permeability (RMP) and malonaldehyde (MDA) content in addition to improving the activities of antioxidant enzymes, including superoxide dismutase, and glutathione peroxidase. Our transcription data show that exogenous H2O2 pretreatment leads to the induced expression of cell cycle, redox regulation, and cell wall organization-related genes in Arabidopsis, which may accelerate cell proliferation, enhance tolerance to osmotic stress, maintain the redox balance, and remodel the cell walls of plants in subsequent high-salt environments.
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Affiliation(s)
- Qikun Zhang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xiuru Dai
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai’an, China
| | - Huanpeng Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Fanhua Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Dongxue Tang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Chunyun Jiang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
- Linyi Center for Disease Control and Prevention, Linyi, China
| | - Xiaoyan Zhang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Wenjing Guo
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Yuanyuan Lei
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Changle Ma
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Hui Zhang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Pinghua Li
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai’an, China
| | - Yanxiu Zhao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Zenglan Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
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Genome Wide Identification and Characterization of Apple WD40 Proteins and Expression Analysis in Response to ABA, Drought, and Low Temperature. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Basic WD40 proteins, which are characterized by a conserved WD40 domain, comprise a superfamily of regulatory proteins in plants and play important roles in plant growth and development. However, WD40 genes have been rarely studied in apple (Malus × domestica Borkh.). In this study, 346 WD40 genes classified in 12 subfamilies, were identified in the apple genome. Evolutionary analysis of WD40 proteins in apple and Arabidopsis revealed that the genes were classifiable into 14 groups, and the exon/intron structure of each group showed a similar structure. Analysis of collinearity showed that the large-scale amplification of WD40 genes in apple was largely attributable to recent whole-genome replication events. Nineteen candidate stress-related genes, selected by GO annotation and comparison with Arabidopsis homologs, showed different expression profiles in six organs at different developmental stages in response to exogenous abscisic acid (ABA), drought, and low temperature. Eight genes (MdWD40-17, 24, 70, 74, 219, 256, 283, and 307) showed a distinct response to one or more treatments (ABA, drought, and low temperature) as indicated by quantitative real-time PCR analysis. Taken together, these data provide rich resources for further study of MdWD40 genes and their potential roles in stress responses in apple.
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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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Transcriptomics and Metabolomics Analyses Provide Novel Insights into Glucose-Induced Trophic Transition of the Marine Diatom Nitzschia laevis. Mar Drugs 2021; 19:md19080426. [PMID: 34436265 PMCID: PMC8401676 DOI: 10.3390/md19080426] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 11/17/2022] Open
Abstract
Diatoms have important ecological roles and are natural sources of bioactive compounds. Nitzschia laevis is a member of marine diatoms that accumulates high-value products including fucoxanthin and eicosapentaenoic acid (EPA). In this study, physiological data showed that comparing to autotrophic growth, mixotrophic cultivation with glucose supplementation led to a decrease of chlorophyll and fucoxanthin content in N. laevis, and an increase of biomass density and EPA yield. To further examine the metabolic barriers for fucoxanthin and EPA biosynthesis, comparative transcriptomic and metabolome analyses were conducted, with a focus on the genes related to carotenoids biosynthesis and fatty acid metabolism. The results indicated that phytoene desaturase (PDS) and zeta-carotene isomerase (ZISO) could be the rate-limiting enzymes in carotenoid biosynthesis. The transcription regulation of 3-ketoacyl-CoA synthase (KCS) and elongation of very long chain fatty acids protein (EVOVL) are important contributors associated with polyunsaturated fatty acids (PUFAs) accumulation. Furthermore, we also investigated the glucose-associated regulatory genes using weighted gene co-expression network analysis, and identified potential hub genes linked with cell cycle, carbohydrate metabolism, purine biosynthesis, and lipid metabolism. This study offers a high-quality transcriptome resource for N. laevis and provides a molecular framework for further metabolic engineering studies on fucoxanthin and EPA production.
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Orr JN, Waugh R, Colas I. Ubiquitination in Plant Meiosis: Recent Advances and High Throughput Methods. FRONTIERS IN PLANT SCIENCE 2021; 12:667314. [PMID: 33897750 PMCID: PMC8058418 DOI: 10.3389/fpls.2021.667314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/15/2021] [Indexed: 06/06/2023]
Abstract
Meiosis is a specialized cell division which is essential to sexual reproduction. The success of this highly ordered process involves the timely activation, interaction, movement, and removal of many proteins. Ubiquitination is an extraordinarily diverse post-translational modification with a regulatory role in almost all cellular processes. During meiosis, ubiquitin localizes to chromatin and the expression of genes related to ubiquitination appears to be enhanced. This may be due to extensive protein turnover mediated by proteasomal degradation. However, degradation is not the only substrate fate conferred by ubiquitination which may also mediate, for example, the activation of key transcription factors. In plant meiosis, the specific roles of several components of the ubiquitination cascade-particularly SCF complex proteins, the APC/C, and HEI10-have been partially characterized indicating diverse roles in chromosome segregation, recombination, and synapsis. Nonetheless, these components remain comparatively poorly understood to their counterparts in other processes and in other eukaryotes. In this review, we present an overview of our understanding of the role of ubiquitination in plant meiosis, highlighting recent advances, remaining challenges, and high throughput methods which may be used to overcome them.
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Affiliation(s)
- Jamie N. Orr
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- School of Agriculture and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Isabelle Colas
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
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Ye X, Huang HY, Wu FL, Cai LY, Lai NW, Deng CL, Guo JX, Yang LT, Chen LS. Molecular mechanisms for magnesium-deficiency-induced leaf vein lignification, enlargement and cracking in Citrus sinensis revealed by RNA-Seq. TREE PHYSIOLOGY 2021; 41:280-301. [PMID: 33104211 DOI: 10.1093/treephys/tpaa128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
Citrus sinensis (L.) Osbeck seedlings were fertigated with nutrient solution containing 2 [magnesium (Mg)-sufficiency] or 0 mM (Mg-deficiency) Mg(NO3)2 for 16 weeks. Thereafter, RNA-Seq was used to investigate Mg-deficiency-responsive genes in the veins of upper and lower leaves in order to understand the molecular mechanisms for Mg-deficiency-induced vein lignification, enlargement and cracking, which appeared only in the lower leaves. In this study, 3065 upregulated and 1220 downregulated, and 1390 upregulated and 375 downregulated genes were identified in Mg-deficiency veins of lower leaves (MDVLL) vs Mg-sufficiency veins of lower leaves (MSVLL) and Mg-deficiency veins of upper leaves (MDVUL) vs Mg-sufficiency veins of upper leaves (MSVUL), respectively. There were 1473 common differentially expressed genes (DEGs) between MDVLL vs MSVLL and MDVUL vs MSVUL, 1463 of which displayed the same expression trend. Magnesium-deficiency-induced lignification, enlargement and cracking in veins of lower leaves might be related to the following factors: (i) numerous transciption factors and genes involved in lignin biosynthesis pathways, regulation of cell cycle and cell wall metabolism were upregulated; and (ii) reactive oxygen species, phytohormone and cell wall integrity signalings were activated. Conjoint analysis of proteome and transcriptome indicated that there were 287 and 56 common elements between DEGs and differentially abundant proteins (DAPs) identified in MDVLL vs MSVLL and MDVUL vs MSVUL, respectively, and that among these common elements, the abundances of 198 and 55 DAPs matched well with the transcript levels of the corresponding DEGs in MDVLL vs MSVLL and MDVUL vs MSVUL, respectively, indicating the existence of concordances between protein and transcript levels.
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Affiliation(s)
- Xin Ye
- Institute of Plant Nutritional Physiology and Molecular Biology, Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University (FAFU), 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China
| | - Hui-Yu Huang
- Institute of Plant Nutritional Physiology and Molecular Biology, Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University (FAFU), 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China
| | - Feng-Lin Wu
- Institute of Plant Nutritional Physiology and Molecular Biology, Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University (FAFU), 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China
| | - Li-Ya Cai
- Institute of Plant Nutritional Physiology and Molecular Biology, Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University (FAFU), 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China
| | - Ning-Wei Lai
- Institute of Plant Nutritional Physiology and Molecular Biology, Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University (FAFU), 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China
| | - Chong-Ling Deng
- Guangxi Key Laboratory of Citrus Biology, Guangxi Academy of Specialty Crops, 40 Putuo Road, Qixing District, Guilin 541004, China
| | - Jiu-Xin Guo
- Institute of Plant Nutritional Physiology and Molecular Biology, Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University (FAFU), 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China
| | - Lin-Tong Yang
- Institute of Plant Nutritional Physiology and Molecular Biology, Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University (FAFU), 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China
| | - Li-Song Chen
- Institute of Plant Nutritional Physiology and Molecular Biology, Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University (FAFU), 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China
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Schwedersky RP, Saleme MDLS, Rocha IA, Montessoro PDF, Hemerly AS, Eloy NB, Ferreira PCG. The Anaphase Promoting Complex/Cyclosome Subunit 11 and Its Role in Organ Size and Plant Development. FRONTIERS IN PLANT SCIENCE 2021; 12:563760. [PMID: 34887878 PMCID: PMC8650582 DOI: 10.3389/fpls.2021.563760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/02/2021] [Indexed: 05/09/2023]
Abstract
The anaphase promoting complex/cyclosome (APC/C), a member of the E3 ubiquitin ligase family, plays an important role in recognizing the substrates to be ubiquitylated. Progression of anaphase, and therefore, of the cell cycle, is coordinated through cyclin degradation cycles dependent on proteolysis triggered by APC/C. The APC/C activity depends on the formation of a pocket comprising the catalytic subunits, APC2, APC11, and APC10. Among these, the role of APC11 outside the cell division cycle is poorly understood. Therefore, the goal of this work was to analyze the function of APC11 during plant development by characterizing apc11 knock-down mutant lines. Accordingly, we observed decreased apc11 expression in the mutant lines, followed by a reduction in meristem root size based on the cortical cell length, and an overall size diminishment throughout the development. Additionally, crosses of apc11-1 and amiR-apc11 with plants carrying a WUSCHEL-RELATED HOMEOBOX5 (WOX5) fluorescent marker showed a weakening of the green fluorescent protein-positive cells in the Quiescent Center. Moreover, plants with apc11-1 show a decreased leaf area, together with a decrease in the cell area when the shoot development was observed by kinematics analysis. Finally, we observed a decreased APC/C activity in the root and shoot meristems in crosses of pCYCB1;1:D-box-GUS with apc11-1 plants. Our results indicate that APC11 is important in the early stages of development, mediating meristematic architecture through APC/C activity affecting the overall plant growth.
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Affiliation(s)
- Rodrigo Porto Schwedersky
- Laboratorio de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marina de Lyra Soriano Saleme
- Department of Biological Sciences, Escola Superior de Agricultura ‘Luiz de Queiroz’, University of São Paulo, Piracicaba, Brazil
| | - Ingrid Andrade Rocha
- Department of Biological Sciences, Escola Superior de Agricultura ‘Luiz de Queiroz’, University of São Paulo, Piracicaba, Brazil
| | - Patricia da Fonseca Montessoro
- Laboratorio de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adriana Silva Hemerly
- Laboratorio de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nubia Barbosa Eloy
- Department of Biological Sciences, Escola Superior de Agricultura ‘Luiz de Queiroz’, University of São Paulo, Piracicaba, Brazil
- *Correspondence: Nubia Barbosa Eloy,
| | - Paulo Cavalcanti Gomes Ferreira
- Laboratorio de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Saleme MDLS, Andrade IR, Eloy NB. The Role of Anaphase-Promoting Complex/Cyclosome (APC/C) in Plant Reproduction. FRONTIERS IN PLANT SCIENCE 2021; 12:642934. [PMID: 33719322 PMCID: PMC7943633 DOI: 10.3389/fpls.2021.642934] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/03/2021] [Indexed: 05/06/2023]
Abstract
Most eukaryotic species propagate through sexual reproduction that requires male and female gametes. In flowering plants, it starts through a single round of DNA replication (S phase) and two consecutive chromosome segregation (meiosis I and II). Subsequently, haploid mitotic divisions occur, which results in a male gametophyte (pollen grain) and a female gametophyte (embryo sac) formation. In order to obtain viable gametophytes, accurate chromosome segregation is crucial to ensure ploidy stability. A precise gametogenesis progression is tightly regulated in plants and is controlled by multiple mechanisms to guarantee a correct evolution through meiotic cell division and sexual differentiation. In the past years, research in the field has shown an important role of the conserved E3-ubiquitin ligase complex, Anaphase-Promoting Complex/Cyclosome (APC/C), in this process. The APC/C is a multi-subunit complex that targets proteins for degradation via proteasome 26S. The functional characterization of APC/C subunits in Arabidopsis, which is one of the main E3 ubiquitin ligase that controls cell cycle, has revealed that all subunits investigated so far are essential for gametophytic development and/or embryogenesis.
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Vidotti AD, Riaño-Pachón DM, Mattiello L, Giraldi LA, Winck FV, Franco TT. Analysis of autotrophic, mixotrophic and heterotrophic phenotypes in the microalgae Chlorella vulgaris using time-resolved proteomics and transcriptomics approaches. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.102060] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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21
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Willems A, Heyman J, Eekhout T, Achon I, Pedroza-Garcia JA, Zhu T, Li L, Vercauteren I, Van den Daele H, van de Cotte B, De Smet I, De Veylder L. The Cyclin CYCA3;4 Is a Postprophase Target of the APC/C CCS52A2 E3-Ligase Controlling Formative Cell Divisions in Arabidopsis. THE PLANT CELL 2020; 32:2979-2996. [PMID: 32690720 PMCID: PMC7474283 DOI: 10.1105/tpc.20.00208] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/12/2020] [Accepted: 07/10/2020] [Indexed: 05/04/2023]
Abstract
The anaphase promoting complex/cyclosome (APC/C) controls unidirectional progression through the cell cycle by marking key cell cycle proteins for proteasomal turnover. Its activity is temporally regulated by the docking of different activating subunits, known in plants as CELL DIVISION PROTEIN20 (CDC20) and CELL CYCLE SWITCH52 (CCS52). Despite the importance of the APC/C during cell proliferation, the number of identified targets in the plant cell cycle is limited. Here, we used the growth and meristem phenotypes of Arabidopsis (Arabidopsis thaliana) CCS52A2-deficient plants in a suppressor mutagenesis screen to identify APC/CCCS52A2 substrates or regulators, resulting in the identification of a mutant cyclin CYCA3;4 allele. CYCA3;4 deficiency partially rescues the ccs52a2-1 phenotypes, whereas increased CYCA3;4 levels enhance the scored ccs52a2-1 phenotypes. Furthermore, whereas the CYCA3;4 protein is promptly broken down after prophase in wild-type plants, it remains present in later stages of mitosis in ccs52a2-1 mutant plants, marking it as a putative APC/CCCS52A2 substrate. Strikingly, increased CYCA3;4 levels result in aberrant root meristem and stomatal divisions, mimicking phenotypes of plants with reduced RETINOBLASTOMA-RELATED PROTEIN1 (RBR1) activity. Correspondingly, RBR1 hyperphosphorylation was observed in CYCA3;4 gain-of-function plants. Our data thus demonstrate that an inability to timely destroy CYCA3;4 contributes to disorganized formative divisions, possibly in part caused by the inactivation of RBR1.
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Affiliation(s)
- Alex Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Jefri Heyman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Ignacio Achon
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Jose Antonio Pedroza-Garcia
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Tingting Zhu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Lei Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Ilse Vercauteren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Hilde Van den Daele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Brigitte van de Cotte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
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22
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Vercruysse J, Baekelandt A, Gonzalez N, Inzé D. Molecular networks regulating cell division during Arabidopsis leaf growth. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2365-2378. [PMID: 31748815 PMCID: PMC7178401 DOI: 10.1093/jxb/erz522] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/21/2019] [Indexed: 05/02/2023]
Abstract
Leaves are the primary organs for photosynthesis, and as such have a pivotal role for plant growth and development. Leaf development is a multifactorial and dynamic process involving many genes that regulate size, shape, and differentiation. The processes that mainly drive leaf development are cell proliferation and cell expansion, and numerous genes have been identified that, when ectopically expressed or down-regulated, increase cell number and/or cell size during leaf growth. Many of the genes regulating cell proliferation are functionally interconnected and can be grouped into regulatory modules. Here, we review our current understanding of six important gene regulatory modules affecting cell proliferation during Arabidopsis leaf growth: ubiquitin receptor DA1-ENHANCER OF DA1 (EOD1), GROWTH REGULATING FACTOR (GRF)-GRF-INTERACTING FACTOR (GIF), SWITCH/SUCROSE NON-FERMENTING (SWI/SNF), gibberellin (GA)-DELLA, KLU, and PEAPOD (PPD). Furthermore, we discuss how post-mitotic cell expansion and these six modules regulating cell proliferation make up the final leaf size.
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Affiliation(s)
- Jasmien Vercruysse
- Center for Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Alexandra Baekelandt
- Center for Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Nathalie Gonzalez
- INRAE, Université de Bordeaux, UMR1332 Biologie du fruit et Pathologie, INRA Bordeaux Aquitaine, Villenave d’Ornon cedex, France
| | - Dirk Inzé
- Center for Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Correspondence:
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23
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Piya S, Liu J, Burch-Smith T, Baum TJ, Hewezi T. A role for Arabidopsis growth-regulating factors 1 and 3 in growth-stress antagonism. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1402-1417. [PMID: 31701146 PMCID: PMC7031083 DOI: 10.1093/jxb/erz502] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/05/2019] [Indexed: 05/21/2023]
Abstract
Growth-regulating factors (GRFs) belong to a small family of transcription factors that are highly conserved in plants. GRFs regulate many developmental processes and plant responses to biotic and abiotic stimuli. Despite the importance of GRFs, a detailed mechanistic understanding of their regulatory functions is still lacking. In this study, we used ChIP sequencing (ChIP-seq) to identify genome-wide binding sites of Arabidopsis GRF1 and GRF3, and correspondingly their direct downstream target genes. RNA-sequencing (RNA-seq) analysis revealed that GRF1 and GRF3 regulate the expression of a significant number of the identified direct targets. The target genes unveiled broad regulatory functions of GRF1 and GRF3 in plant growth and development, phytohormone biosynthesis and signaling, and the cell cycle. Our analyses also revealed that clock core genes and genes with stress- and defense-related functions are most predominant among the GRF1- and GRF3-bound targets, providing insights into a possible role for these transcription factors in mediating growth-defense antagonism and integrating environmental stimuli into developmental programs. Additionally, GRF1 and GRF3 target molecular nodes of growth-defense antagonism and modulate the levels of defense- and development-related hormones in opposite directions. Taken together, our results point to GRF1 and GRF3 as potential key determinants of plant fitness under stress conditions.
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Affiliation(s)
- Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Jinyi Liu
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
- Present address: College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Tessa Burch-Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
- Correspondence:
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24
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Boudichevskaia A, Houben A, Fiebig A, Prochazkova K, Pecinka A, Lermontova I. Depletion of KNL2 Results in Altered Expression of Genes Involved in Regulation of the Cell Cycle, Transcription, and Development in Arabidopsis. Int J Mol Sci 2019; 20:ijms20225726. [PMID: 31731608 PMCID: PMC6888302 DOI: 10.3390/ijms20225726] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/07/2019] [Accepted: 11/11/2019] [Indexed: 11/17/2022] Open
Abstract
Centromeres contain specialized nucleosomes at which histone H3 is partially replaced by the centromeric histone H3 variant cenH3 that is required for the assembly, maintenance, and proper function of kinetochores during mitotic and meiotic divisions. Previously, we identified a KINETOCHORE NULL 2 (KNL2) of Arabidopsis thaliana that is involved in the licensing of centromeres for the cenH3 recruitment. We also demonstrated that a knockout mutant for KNL2 shows mitotic and meiotic defects, slower development, reduced growth rate, and fertility. To analyze an effect of KNL2 mutation on global gene transcription of Arabidopsis, we performed RNA-sequencing experiments using seedling and flower bud tissues of knl2 and wild-type plants. The transcriptome data analysis revealed a high number of differentially expressed genes (DEGs) in knl2 plants. The set was enriched in genes involved in the regulation of the cell cycle, transcription, development, and DNA damage repair. In addition to comprehensive information regarding the effects of KNL2 mutation on the global gene expression, physiological changes in plants are also presented, which provides an integrated understanding of the critical role played by KNL2 in plant growth and development.
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Affiliation(s)
- Anastassia Boudichevskaia
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Seeland, Germany; (A.H.); (A.F.)
- Correspondence: (A.B.); (I.L.); Tel.: +49/39482 5477 (A.B.); +49/39482 5570 (I.L.)
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Seeland, Germany; (A.H.); (A.F.)
| | - Anne Fiebig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Seeland, Germany; (A.H.); (A.F.)
| | - Klara Prochazkova
- Institute of Experimental Botany, Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic; (K.P.); (A.P.)
| | - Ales Pecinka
- Institute of Experimental Botany, Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic; (K.P.); (A.P.)
| | - Inna Lermontova
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466 Seeland, Germany; (A.H.); (A.F.)
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno CZ-62500, Czech Republic
- Correspondence: (A.B.); (I.L.); Tel.: +49/39482 5477 (A.B.); +49/39482 5570 (I.L.)
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25
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Xu R, Xu J, Wang L, Niu B, Copenhaver GP, Ma H, Zheng B, Wang Y. The Arabidopsis anaphase-promoting complex/cyclosome subunit 8 is required for male meiosis. THE NEW PHYTOLOGIST 2019; 224:229-241. [PMID: 31230348 PMCID: PMC6771777 DOI: 10.1111/nph.16014] [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: 12/03/2018] [Accepted: 06/03/2019] [Indexed: 05/07/2023]
Abstract
Faithful chromosome segregation is required for both mitotic and meiotic cell divisions and is regulated by multiple mechanisms including the anaphase-promoting complex/cyclosome (APC/C), which is the largest known E3 ubiquitin-ligase complex and has been implicated in regulating chromosome segregation in both mitosis and meiosis in animals. However, the role of the APC/C during plant meiosis remains largely unknown. Here, we show that Arabidopsis APC8 is required for male meiosis. We used a combination of genetic analyses, cytology and immunolocalisation to define the function of AtAPC8 in male meiosis. Meiocytes from apc8-1 plants exhibit several meiotic defects including improper alignment of bivalents at metaphase I, unequal chromosome segregation during anaphase II, and subsequent formation of polyads. Immunolocalisation using an antitubulin antibody showed that APC8 is required for normal spindle morphology. We also observed mitotic defects in apc8-1, including abnormal sister chromatid segregation and microtubule morphology. Our results demonstrate that Arabidopsis APC/C is required for meiotic chromosome segregation and that APC/C-mediated regulation of meiotic chromosome segregation is a conserved mechanism among eukaryotes.
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Affiliation(s)
- Rong‐Yan Xu
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological EngineeringInstitute of Plant BiologySchool of Life SciencesFudan UniversityShanghai200438China
- Shanghai Chenshan Plant Science Research CenterChinese Academy of SciencesChenshan Botanical GardenShanghai201602China
| | - Jing Xu
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological EngineeringInstitute of Plant BiologySchool of Life SciencesFudan UniversityShanghai200438China
| | - Liudan Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological EngineeringInstitute of Plant BiologySchool of Life SciencesFudan UniversityShanghai200438China
| | - Baixiao Niu
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological EngineeringInstitute of Plant BiologySchool of Life SciencesFudan UniversityShanghai200438China
- Key Laboratory of Plant Functional Genomics of the Ministry of EducationJiangsu Key Laboratory of Crop Genetics and Physiology/Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhou225009China
| | - Gregory P. Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome SciencesUniversity of North Carolina at Chapel HillChapel HillNC27599‐3280USA
- Lineberger Comprehensive Cancer CenterUniversity of North Carolina School of MedicineChapel HillNC27599‐3280USA
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological EngineeringInstitute of Plant BiologySchool of Life SciencesFudan UniversityShanghai200438China
- Center for Evolutionary BiologyInstitutes of Biomedical SciencesSchool of Life SciencesFudan UniversityShanghai200433China
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological EngineeringInstitute of Plant BiologySchool of Life SciencesFudan UniversityShanghai200438China
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological EngineeringInstitute of Plant BiologySchool of Life SciencesFudan UniversityShanghai200438China
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26
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Patronus is the elusive plant securin, preventing chromosome separation by antagonizing separase. Proc Natl Acad Sci U S A 2019; 116:16018-16027. [PMID: 31324745 PMCID: PMC6690013 DOI: 10.1073/pnas.1906237116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Accurate chromosome segregation at mitosis and meiosis is crucial to prevent genome instability, birth defect, and cancer. Accordingly, separase, the protease that triggers chromosome distribution, is tightly regulated by a direct inhibitor, the securin. However, securin has not been identified, neither functionnally nor by sequence similarity, in other clades that fungi and animals. This raised doubts about the conservation of this mechanism in other branches of eukaryotes. Here, we identify and characterize the securin in plants. Despite extreme sequence divergence, the securin kept the same core function and is likely a universal regulator of cell division in eukaryotes. Chromosome distribution at anaphase of mitosis and meiosis is triggered by separase, an evolutionarily conserved protease. Separase must be tightly regulated to prevent the untimely release of chromatid cohesion and disastrous chromosome distribution defects. Securin is the key inhibitor of separase in animals and fungi, but has not been identified in other eukaryotic lineages. Here, we identified PATRONUS1 and PATRONUS2 (PANS1 and PANS2) as the Arabidopsis homologs of securin. Disruption of PANS1 is known to lead to the premature separation of chromosomes at meiosis, and the simultaneous disruption of PANS1 and PANS2 is lethal. Here, we show that PANS1 targeting by the anaphase-promoting complex is required to trigger chromosome separation, mirroring the regulation of securin. We showed that PANS1 acts independently from Shugosins. In a genetic screen for pans1 suppressors, we identified SEPARASE mutants, showing that PANS1 and SEPARASE have antagonistic functions in vivo. Finally, we showed that the PANS1 and PANS2 proteins interact directly with SEPARASE. Altogether, our results show that PANS1 and PANS2 act as a plant securin. Remote sequence similarity was identified between the plant patronus family and animal securins, suggesting that they indeed derive from a common ancestor. Identification of patronus as the elusive plant securin illustrates the extreme sequence divergence of this central regulator of mitosis and meiosis.
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27
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Patrick RM, Lee JCH, Teetsel JRJ, Yang SH, Choy GS, Browning KS. Discovery and characterization of conserved binding of eIF4E 1 (CBE1), a eukaryotic translation initiation factor 4E-binding plant protein. J Biol Chem 2018; 293:17240-17247. [PMID: 30213859 DOI: 10.1074/jbc.ra118.003945] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/08/2018] [Indexed: 12/23/2022] Open
Abstract
In many eukaryotes, translation initiation is regulated by proteins that bind to the mRNA cap-binding protein eukaryotic translation initiation factor 4E (eIF4E). These proteins commonly prevent association of eIF4E with eIF4G or form repressive messenger ribonucleoproteins that exclude the translation machinery. Such gene-regulatory mechanisms in plants, and even the presence of eIF4E-interacting proteins other than eIF4G (and the plant-specific isoform eIFiso4G, which binds eIFiso4E), are unknown. Here, we report the discovery of a plant-specific protein, conserved binding of eIF4E 1 (CBE1). We found that CBE1 has an evolutionarily conserved eIF4E-binding motif in its N-terminal domain and binds eIF4E or eIFiso4E in vitro CBE1 thereby forms cap-binding complexes and is an eIF4E-dependent constituent of these complexes in vivo Of note, plant mutants lacking CBE1 exhibited dysregulation of cell cycle-related transcripts and accumulated higher levels of mRNAs encoding proteins involved in mitosis than did WT plants. Our findings indicate that CBE1 is a plant protein that can form mRNA cap-binding complexes having the potential for regulating gene expression. Because mammalian translation factors are known regulators of cell cycle progression, we propose that CBE1 may represent such first translation factor-associated plant-specific cell cycle regulator.
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Affiliation(s)
- Ryan M Patrick
- From the Department of Molecular Biosciences and Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712
| | - Jessica C H Lee
- From the Department of Molecular Biosciences and Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712
| | - Jade R J Teetsel
- From the Department of Molecular Biosciences and Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712
| | - Soo-Hyun Yang
- From the Department of Molecular Biosciences and Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712
| | - Grace S Choy
- From the Department of Molecular Biosciences and Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712
| | - Karen S Browning
- From the Department of Molecular Biosciences and Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712
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28
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Zhang H, Deng X, Sun B, Lee Van S, Kang Z, Lin H, Lee YRJ, Liu B. Role of the BUB3 protein in phragmoplast microtubule reorganization during cytokinesis. NATURE PLANTS 2018; 4:485-494. [PMID: 29967519 DOI: 10.1038/s41477-018-0192-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 06/04/2018] [Indexed: 05/15/2023]
Abstract
The evolutionarily conserved WD40 protein budding uninhibited by benzimidazole 3 (BUB3) is known for its function in spindle assembly checkpoint control. In the model plant Arabidopsis thaliana, nearly identical BUB3;1 and BUB3;2 proteins decorated the phragmoplast midline through interaction with the microtubule-associated protein MAP65-3 during cytokinesis. BUB3;1 and BUB3;2 interacted with the carboxy-terminal segment of MAP65-3 (but not MAP65-1), which harbours its microtubule-binding domain for its post-mitotic localization. Reciprocally, BUB3;1 and BUB3;2 also regulated MAP65-3 localization in the phragmoplast by enhancing its microtubule association. In the bub3;1 bub3;2 double mutant, MAP65-3 localization was often dissipated away from the phragmoplast midline and abolished upon treatment of low doses of the cytokinesis inhibitory drug caffeine that were tolerated by the control plant. The phragmoplast microtubule array exhibited uncoordinated expansion pattern in the double mutant cells as the phragmoplast edge reached the parental plasma membrane at different times in different areas. Upon caffeine treatment, phragmoplast expansion was halted as if the microtubule array was frozen. As a result, cytokinesis was abolished due to failed cell plate assembly. Our findings have uncovered a novel function of the plant BUB3 in MAP65-3-dependent microtubule reorganization during cytokinesis.
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Affiliation(s)
- Hongchang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA, USA
| | - Xingguang Deng
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA, USA
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Baojuan Sun
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA, USA
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Sonny Lee Van
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA, USA
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Honghui Lin
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yuh-Ru Julie Lee
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA, USA.
| | - Bo Liu
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA, USA.
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29
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Barkla BJ, Rhodes T, Tran KNT, Wijesinghege C, Larkin JC, Dassanayake M. Making Epidermal Bladder Cells Bigger: Developmental- and Salinity-Induced Endopolyploidy in a Model Halophyte. PLANT PHYSIOLOGY 2018; 177:615-632. [PMID: 29724770 PMCID: PMC6001328 DOI: 10.1104/pp.18.00033] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/21/2018] [Indexed: 05/29/2023]
Abstract
Endopolyploidy occurs when DNA replication takes place without subsequent mitotic nuclear division, resulting in cell-specific ploidy levels within tissues. In plants, endopolyploidy plays an important role in sustaining growth and development, but only a few studies have demonstrated a role in abiotic stress response. In this study, we investigated the function of ploidy level and nuclear and cell size in leaf expansion throughout development and tracked cell type-specific ploidy in the halophyte Mesembryanthemum crystallinum In addition to developmental endopolyploidy, we examined the effects of salinity stress on ploidy level. We focused specifically on epidermal bladder cells (EBC), which are modified balloon-like trichomes, due to their large size and role in salt accumulation. Our results demonstrate that ploidy increases as the leaves expand in a similar manner for each leaf type, and ploidy levels up to 512C were recorded for nuclei in EBC of leaves of adult plants. Salt treatment led to a significant increase in ploidy levels in the EBC, and these cells showed spatially related differences in their ploidy and nuclear and cell size depending on the positions on the leaf and stem surface. Transcriptome analysis highlighted salinity-induced changes in genes involved in DNA replication, cell cycle, endoreduplication, and trichome development in EBC. The increase in cell size and ploidy observed in M. crystallinum under salinity stress may contribute to salt tolerance by increasing the storage capacity for sodium sequestration brought about by higher metabolic activity driving rapid cell enlargement in the leaf tissue and EBC.
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Affiliation(s)
- Bronwyn J Barkla
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales 2480, Australia
| | - Timothy Rhodes
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales 2480, Australia
| | - Kieu-Nga T Tran
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Chathura Wijesinghege
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - John C Larkin
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
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30
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Zhang N, Wang Z, Bao Z, Yang L, Wu D, Shu X, Hua J. MOS1 functions closely with TCP transcription factors to modulate immunity and cell cycle in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:66-78. [PMID: 29086441 DOI: 10.1111/tpj.13757] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/03/2017] [Accepted: 10/23/2017] [Indexed: 05/05/2023]
Abstract
Emerging evidence indicates a close connection between cell-cycle progression and the plant immune responses. In Arabidopsis, MODIFIER OF snc1-1 (MOS1) modulates a number of processes including endoreduplication and plant disease resistance, but the molecular mechanism underlying this modulation was not fully understood. Here, we provide biochemical and genetic evidence that TEOSINTE BRANCHED 1, CYCLOIDEA, PCF1 (TCP) transcription factors TCP15 and its homologues are mediators of MOS1 function in the immune response and are likely to be also involved in cell-cycle control. MOS1 and TCP proteins have a direct physical interaction. They both bind to the promoter of the immune receptor gene SUPRESSOR OF npr1-1, CONSTITUTIVE 1 (SNC1) and modulate its expression and consequently immune responses. MOS1 and TCP15 both affect the expression of cell-cycle genes D-type CYCLIN 3;1 (CYCD3;1), which may mediate the MOS1 function in cell-cycle modulation. In addition, CYCD3;1 overexpression upregulates immune responses, and SNC1 expression. This study investigated and revealed a role for MOS1 in transcriptional regulation through TCP15 and its homologues. This finding suggests the coordination of cell-cycle progression and plant immune responses at multiple levels.
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Affiliation(s)
- Ning Zhang
- State Key Laboratory of Rice Biology, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Zhixue Wang
- State Key Laboratory of Rice Biology, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Zhilong Bao
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Leiyun Yang
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Dianxing Wu
- State Key Laboratory of Rice Biology, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
| | - Xiaoli Shu
- State Key Laboratory of Rice Biology, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
| | - Jian Hua
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
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Bolaños-Villegas P, Xu W, Martínez-García M, Pradillo M, Wang Y. Insights Into the Role of Ubiquitination in Meiosis: Fertility, Adaptation and Plant Breeding. THE ARABIDOPSIS BOOK 2018; 16:e0187. [PMID: 31068764 PMCID: PMC6501859 DOI: 10.1199/tab.0187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Ubiquitination is a post-translational modification process that plays a central role in protein degradation in eukaryotic cell cell division, including meiosis. This modification affects different cellular processes on a global scale by its pleiotropic ability to modify numerous proteins. Meiosis is essential for sexual reproduction and involves two rounds of nuclear division following a single round of DNA replication to produce haploid gametes. Unlike mitosis, meiosis has a unique prophase I, which involves homologous chromosome interaction including pairing, synapsis, recombination and segregation. Over the last several decades, molecular genetic studies have identified many proteins that participate in meiotic progression. In this review, we focus on the recent advances regarding the role of ubiquitination during plant meiotic cell cycle progression and recombination, especially the role played by the Anaphase-Promoting Complex and E3 ligases in modulating crossover formation and its impact on evolution and plant breeding.
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Affiliation(s)
- Pablo Bolaños-Villegas
- Fabio Baudrit Agricultural Research Station, University of Costa Rica, Alajuela 20102, Costa Rica
| | - Wanyue Xu
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Marina Martínez-García
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States of America
| | - Mónica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Universidad Complutense, C/José Antonio Novais, 12, Madrid 28040, Spain
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
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The Arabidopsis Auxin Receptor F-Box Proteins AFB4 and AFB5 Are Required for Response to the Synthetic Auxin Picloram. G3-GENES GENOMES GENETICS 2016; 6:1383-90. [PMID: 26976444 PMCID: PMC4856089 DOI: 10.1534/g3.115.025585] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The plant hormone auxin is perceived by a family of F-box proteins called the TIR1/AFBs. Phylogenetic studies reveal that these proteins fall into four clades in flowering plants called TIR1, AFB2, AFB4, and AFB6. Genetic studies indicate that members of the TIR1 and AFB2 groups act as positive regulators of auxin signaling by promoting the degradation of the Aux/IAA transcriptional repressors. In this report, we demonstrate that both AFB4 and AFB5 also function as auxin receptors based on in vitro assays. We also provide genetic evidence that AFB4 and AFB5 are targets of the picloram family of auxinic herbicides in addition to indole-3-acetic acid. In contrast to previous studies we find that null afb4 alleles do not exhibit obvious defects in seedling morphology or auxin hypersensitivity. We conclude that AFB4 and AFB5 act in a similar fashion to other members of the family but exhibit a distinct auxin specificity.
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Juraniec M, Heyman J, Schubert V, Salis P, De Veylder L, Verbruggen N. Arabidopsis COPPER MODIFIED RESISTANCE1/PATRONUS1 is essential for growth adaptation to stress and required for mitotic onset control. THE NEW PHYTOLOGIST 2016; 209:177-91. [PMID: 26261921 DOI: 10.1111/nph.13589] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/01/2015] [Indexed: 05/23/2023]
Abstract
The mitotic checkpoint (MC) guards faithful sister chromatid segregation by monitoring the attachment of spindle microtubules to the kinetochores. When chromosome attachment errors are detected, MC delays the metaphase-to-anaphase transition through the inhibition of the anaphase-promoting complex/cyclosome (APC/C) ubiquitin ligase. In contrast to yeast and mammals, our knowledge on the proteins involved in MC in plants is scarce. Transient synchronization of root tips as well as promoter-reporter gene fusions were performed to analyze temporal and spatial expression of COPPER MODIFIED RESISTANCE1/PATRONUS1 (CMR1/PANS1) in developing Arabidopsis thaliana seedlings. Functional analysis of the gene was carried out, including CYCB1;2 stability in CMR1/PANS1 knockout and overexpressor background as well as metaphase-anaphase chromosome status. CMR1/PANS1 is transcriptionally active during M phase. Its deficiency provokes premature cell cycle exit and in consequence a rapid consumption of the number of meristematic cells in particular under stress conditions that are known to affect spindle microtubules. Root growth impairment is correlated with a failure to delay the onset of anaphase, resulting in anaphase bridges and chromosome missegregation. CMR1/PANS1 overexpression stabilizes the mitotic CYCB1;2 protein. Likely, CMR1/PANS1 coordinates mitotic cell cycle progression by acting as an APC/C inhibitor and plays a key role in growth adaptation to stress.
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Affiliation(s)
- Michal Juraniec
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, B-1050, Brussels, Belgium
| | - Jefri Heyman
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Gent, Belgium
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466, Stadt Seeland, Germany
| | - Pietrino Salis
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, B-1050, Brussels, Belgium
| | - Lieven De Veylder
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Gent, Belgium
| | - Nathalie Verbruggen
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, B-1050, Brussels, Belgium
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Niu B, Wang L, Zhang L, Ren D, Ren R, Copenhaver GP, Ma H, Wang Y. Arabidopsis Cell Division Cycle 20.1 Is Required for Normal Meiotic Spindle Assembly and Chromosome Segregation. THE PLANT CELL 2015; 27:3367-82. [PMID: 26672070 PMCID: PMC4707457 DOI: 10.1105/tpc.15.00834] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/16/2015] [Accepted: 11/22/2015] [Indexed: 05/18/2023]
Abstract
Cell division requires proper spindle assembly; a surveillance pathway, the spindle assembly checkpoint (SAC), monitors whether the spindle is normal and correctly attached to kinetochores. The SAC proteins regulate mitotic chromosome segregation by affecting CDC20 (Cell Division Cycle 20) function. However, it is unclear whether CDC20 regulates meiotic spindle assembly and proper homolog segregation. Here, we show that the Arabidopsis thaliana CDC20.1 gene is indispensable for meiosis and male fertility. We demonstrate that cdc20.1 meiotic chromosomes align asynchronously and segregate unequally and the metaphase I spindle has aberrant morphology. Comparison of the distribution of meiotic stages at different time points between the wild type and cdc20.1 reveals a delay of meiotic progression from diakinesis to anaphase I. Furthermore, cdc20.1 meiocytes exhibit an abnormal distribution of a histone H3 phosphorylation mark mediated by the Aurora kinase, providing evidence that CDC20.1 regulates Aurora localization for meiotic chromosome segregation. Further evidence that CDC20.1 and Aurora are functionally related was provided by meiosis-specific knockdown of At-Aurora1 expression, resulting in meiotic chromosome segregation defects similar to those of cdc20.1. Taken together, these results suggest a critical role for CDC20.1 in SAC-dependent meiotic chromosome segregation.
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Affiliation(s)
- Baixiao Niu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Liudan Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Liangsheng Zhang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ding Ren
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ren Ren
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Gregory P Copenhaver
- Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280 Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-3280
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China Center for Evolutionary Biology, Institutes of Biomedical Sciences School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
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Luo CJ, Wightman R, Meyerowitz E, Smoukov SK. A 3-dimensional fibre scaffold as an investigative tool for studying the morphogenesis of isolated plant pells. BMC PLANT BIOLOGY 2015; 15:211. [PMID: 26310239 PMCID: PMC4550058 DOI: 10.1186/s12870-015-0581-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 07/24/2015] [Indexed: 05/08/2023]
Abstract
BACKGROUND Cell culture methods allow the detailed observations of individual plant cells and their internal processes. Whereas cultured cells are more amenable to microscopy, they have had limited use when studying the complex interactions between cell populations and responses to external signals associated with tissue and whole plant development. Such interactions result in the diverse range of cell shapes observed in planta compared to the simple polygonal or ovoid shapes in vitro. Microfluidic devices can isolate the dynamics of single plant cells but have restricted use for providing a tissue-like and fibrous extracellular environment for cells to interact. A gap exists, therefore, in the understanding of spatiotemporal interactions of single plant cells interacting with their three-dimensional (3D) environment. A model system is needed to bridge this gap. For this purpose we have borrowed a tool, a 3D nano- and microfibre tissue scaffold, recently used in biomedical engineering of animal and human tissue physiology and pathophysiology in vitro. RESULTS We have developed a method of 3D cell culture for plants, which mimics the plant tissue environment, using biocompatible scaffolds similar to those used in mammalian tissue engineering. The scaffolds provide both developmental cues and structural stability to isolated callus-derived cells grown in liquid culture. The protocol is rapid, compared to the growth and preparation of whole plants for microscopy, and provides detailed subcellular information on cells interacting with their local environment. We observe cell shapes never observed for individual cultured cells. Rather than exhibiting only spheroid or ellipsoidal shapes, the cells adapt their shape to fit the local space and are capable of growing past each other, taking on growth and morphological characteristics with greater complexity than observed even in whole plants. Confocal imaging of transgenic Arabidopsis thaliana lines containing fluorescent microtubule and actin reporters enables further study of the effects of interactions and complex morphologies upon cytoskeletal organisation both in 3D and in time (4D). CONCLUSIONS The 3D culture within the fibre scaffolds permits cells to grow freely within a matrix containing both large and small spaces, a technique that is expected to add to current lithographic technologies, where growth is carefully controlled and constricted. The cells, once seeded in the scaffolds, can adopt a variety of morphologies, demonstrating that they do not need to be part of a tightly packed tissue to form complex shapes. This points to a role of the immediate nano- and micro-topography in plant cell morphogenesis. This work defines a new suite of techniques for exploring cell-environment interactions.
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Affiliation(s)
- C J Luo
- Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge, CB3 0FS, UK.
| | - Raymond Wightman
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK.
| | - Elliot Meyerowitz
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK.
- Division of Biology and Biological Engineering, and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Stoyan K Smoukov
- Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge, CB3 0FS, UK.
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Eichmann R, Schäfer P. Growth versus immunity--a redirection of the cell cycle? CURRENT OPINION IN PLANT BIOLOGY 2015; 26:106-12. [PMID: 26190589 DOI: 10.1016/j.pbi.2015.06.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 05/03/2015] [Accepted: 06/07/2015] [Indexed: 05/07/2023]
Abstract
Diseases caused by plant pathogens significantly reduce growth and yield in agricultural crop production. Raising immunity in crops is therefore a major aim in breeding programs. However, efforts to enhance immunity are challenged by the occurrence of growth inhibition triggered by immunity that can be as detrimental as diseases. In this review, we will propose molecular models to explain the inhibitory growth-immunity crosstalk. We will briefly discuss why the resource reallocation model might not represent the driving force for the observed growth-immunity trade-offs. We suggest a model in which immunity redirects and initiates hormone signalling activities that can impair plant growth by antagonising cell cycle regulation and meristem activities.
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Affiliation(s)
- Ruth Eichmann
- School of Life Sciences, University of Warwick, Gibbet Hill, CV4 7AL Coventry, UK
| | - Patrick Schäfer
- School of Life Sciences, University of Warwick, Gibbet Hill, CV4 7AL Coventry, UK; Warwick Integrative Synthetic Biology Centre, University of Warwick, Gibbet Hill, CV4 7AL Coventry, UK.
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Peng Y, Chen L, Lu Y, Wu Y, Dumenil J, Zhu Z, Bevan MW, Li Y. The ubiquitin receptors DA1, DAR1, and DAR2 redundantly regulate endoreduplication by modulating the stability of TCP14/15 in Arabidopsis. THE PLANT CELL 2015; 27:649-62. [PMID: 25757472 PMCID: PMC4558651 DOI: 10.1105/tpc.114.132274] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 02/11/2015] [Accepted: 02/26/2015] [Indexed: 05/18/2023]
Abstract
Organ growth involves the coordination of cell proliferation and cell growth with differentiation. Endoreduplication is correlated with the onset of cell differentiation and with cell and organ size, but little is known about the molecular mechanisms linking cell and organ growth with endoreduplication. We have previously demonstrated that the ubiquitin receptor DA1 influences organ growth by restricting cell proliferation. Here, we show that DA1 and its close family members DAR1 and DAR2 are redundantly required for endoreduplication during leaf development. DA1, DAR1, and DAR2 physically interact with the transcription factors TCP14 and TCP15, which repress endoreduplication by directly regulating the expression of cell-cycle genes. We also show that DA1, DAR1, and DAR2 modulate the stability of TCP14 and TCP15 proteins in Arabidopsis thaliana. Genetic analyses demonstrate that DA1, DAR1, and DAR2 function in a common pathway with TCP14/15 to regulate endoreduplication. Thus, our findings define an important genetic and molecular mechanism involving the ubiquitin receptors DA1, DAR1, and DAR2 and the transcription factors TCP14 and TCP15 that links endoreduplication with cell and organ growth.
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Affiliation(s)
- Yuancheng Peng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Liangliang Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaru Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China College of Biological Science, Hebei Normal University, Shijiazhuang 050024, China
| | - Yingbao Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jack Dumenil
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Zhengge Zhu
- College of Biological Science, Hebei Normal University, Shijiazhuang 050024, China
| | - Michael W Bevan
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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Mercier R, Mézard C, Jenczewski E, Macaisne N, Grelon M. The molecular biology of meiosis in plants. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:297-327. [PMID: 25494464 DOI: 10.1146/annurev-arplant-050213-035923] [Citation(s) in RCA: 327] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Meiosis is the cell division that reshuffles genetic information between generations. Recently, much progress has been made in understanding this process; in particular, the identification and functional analysis of more than 80 plant genes involved in meiosis have dramatically deepened our knowledge of this peculiar cell division. In this review, we provide an overview of advancements in the understanding of all aspects of plant meiosis, including recombination, chromosome synapsis, cell cycle control, chromosome distribution, and the challenge of polyploidy.
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Affiliation(s)
- Raphaël Mercier
- INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France; , , , ,
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Hudik E, Yoshioka Y, Domenichini S, Bourge M, Soubigout-Taconnat L, Mazubert C, Yi D, Bujaldon S, Hayashi H, De Veylder L, Bergounioux C, Benhamed M, Raynaud C. Chloroplast dysfunction causes multiple defects in cell cycle progression in the Arabidopsis crumpled leaf mutant. PLANT PHYSIOLOGY 2014; 166:152-67. [PMID: 25037213 PMCID: PMC4149703 DOI: 10.1104/pp.114.242628] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The majority of research on cell cycle regulation is focused on the nuclear events that govern the replication and segregation of the genome between the two daughter cells. However, eukaryotic cells contain several compartmentalized organelles with specialized functions, and coordination among these organelles is required for proper cell cycle progression, as evidenced by the isolation of several mutants in which both organelle function and overall plant development were affected. To investigate how chloroplast dysfunction affects the cell cycle, we analyzed the crumpled leaf (crl) mutant of Arabidopsis (Arabidopsis thaliana), which is deficient for a chloroplastic protein and displays particularly severe developmental defects. In the crl mutant, we reveal that cell cycle regulation is altered drastically and that meristematic cells prematurely enter differentiation, leading to reduced plant stature and early endoreduplication in the leaves. This response is due to the repression of several key cell cycle regulators as well as constitutive activation of stress-response genes, among them the cell cycle inhibitor SIAMESE-RELATED5. One unique feature of the crl mutant is that it produces aplastidic cells in several organs, including the root tip. By investigating the consequence of the absence of plastids on cell cycle progression, we showed that nuclear DNA replication occurs in aplastidic cells in the root tip, which opens future research prospects regarding the dialogue between plastids and the nucleus during cell cycle regulation in higher plants.
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Affiliation(s)
- Elodie Hudik
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Yasushi Yoshioka
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Séverine Domenichini
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Mickaël Bourge
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Ludivine Soubigout-Taconnat
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Christelle Mazubert
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Dalong Yi
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Sandrine Bujaldon
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Hiroyuki Hayashi
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Lieven De Veylder
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Catherine Bergounioux
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Moussa Benhamed
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Cécile Raynaud
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
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Blomme J, Inzé D, Gonzalez N. The cell-cycle interactome: a source of growth regulators? JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2715-30. [PMID: 24298000 DOI: 10.1093/jxb/ert388] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
When plants develop, cell proliferation and cell expansion are tightly controlled in order to generate organs with a determinate final size such as leaves. Several studies have demonstrated the importance of the cell proliferation phase for leaf growth, illustrating that cell-cycle regulation is crucial for correct leaf development. A large and complex set of interacting proteins that constitute the cell-cycle interactome controls the transition from one cell-cycle phase to another. Here, we review the current knowledge on cell-cycle regulators from this interactome affecting final leaf size when their expression is altered, mainly in Arabidopsis. In addition to the description of mutants of CYCLIN-DEPENDENT KINASES (CDKs), CYCLINS (CYCs), and their transcriptional and post-translational regulators, a phenotypic analysis of gain- and loss-of-function mutants for 27 genes encoding proteins that interact with cell-cycle proteins is presented. This compilation of information shows that when cell-cycle-related genes are mis-expressed, leaf growth is often altered and that, seemingly, three main trends appear to be crucial in the regulation of final organ size by cell-cycle-related genes: (i) cellular compensation; (ii) gene dosage; and (iii) correct transition through the G2/M phase by ANAPHASE PROMOTING COMPLEX/CYCLOSOME (APC/C) activation. In conclusion, this meta-analysis shows that the cell-cycle interactome is enriched in leaf growth regulators, and illustrates the potential to identify new leaf growth regulators among putative new cell-cycle regulators.
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Affiliation(s)
- Jonas Blomme
- Department of Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Nathalie Gonzalez
- Department of Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
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Genschik P, Marrocco K, Bach L, Noir S, Criqui MC. Selective protein degradation: a rheostat to modulate cell-cycle phase transitions. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2603-15. [PMID: 24353246 DOI: 10.1093/jxb/ert426] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Plant growth control has become a major focus due to economic reasons and results from a balance of cell proliferation in meristems and cell elongation that occurs during differentiation. Research on plant cell proliferation over the last two decades has revealed that the basic cell-cycle machinery is conserved between human and plants, although specificities exist. While many regulatory circuits control each step of the cell cycle, the ubiquitin proteasome system (UPS) appears in fungi and metazoans as a major player. In particular, the UPS promotes irreversible proteolysis of a set of regulatory proteins absolutely required for cell-cycle phase transitions. Not unexpectedly, work over the last decade has brought the UPS to the forefront of plant cell-cycle research. In this review, we will summarize our knowledge of the function of the UPS in the mitotic cycle and in endoreduplication, and also in meiosis in higher plants.
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Affiliation(s)
- Pascal Genschik
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357, Conventionné avec l'Université de Strasbourg, 67084 Strasbourg, France Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/SupAgro/UM2, Place Viala, 34060 Montpellier Cedex, France
| | - Katia Marrocco
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/SupAgro/UM2, Place Viala, 34060 Montpellier Cedex, France
| | - Lien Bach
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/SupAgro/UM2, Place Viala, 34060 Montpellier Cedex, France
| | - Sandra Noir
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357, Conventionné avec l'Université de Strasbourg, 67084 Strasbourg, France
| | - Marie-Claire Criqui
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357, Conventionné avec l'Université de Strasbourg, 67084 Strasbourg, France
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Huysman MJ, Martens C, Vyverman W, De Veylder L. Protein degradation during the diatom cell cycle: Annotation and transcriptional analysis of SCF and APC/C ubiquitin ligase genes in Phaeodactylum tricornutum. Mar Genomics 2014; 14:39-46. [DOI: 10.1016/j.margen.2013.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/20/2013] [Accepted: 09/03/2013] [Indexed: 01/10/2023]
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Amiard S, Da Ines O, Gallego ME, White CI. Responses to telomere erosion in plants. PLoS One 2014; 9:e86220. [PMID: 24465970 PMCID: PMC3897657 DOI: 10.1371/journal.pone.0086220] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 12/06/2013] [Indexed: 01/01/2023] Open
Abstract
In striking contrast to animals, plants are able to develop and reproduce in the presence of significant levels of genome damage. This is seen clearly in both the viability of plants carrying knockouts for key recombination and DNA repair genes, which are lethal in vertebrates, and in the impact of telomere dysfunction. Telomerase knockout mice show accelerated ageing and severe developmental phenotypes, with effects on both highly proliferative and on more quiescent tissues, while cell death in Arabidopsis tert mutants is mostly restricted to actively dividing meristematic cells. Through phenotypic and whole-transcriptome RNAseq studies, we present here an analysis of the response of Arabidopsis plants to the continued presence of telomere damage. Comparison of second-generation and seventh-generation tert mutant plants has permitted separation of the effects of the absence of the telomerase enzyme and the ensuing chromosome damage. In addition to identifying a large number of genes affected by telomere damage, many of which are of unknown function, the striking conclusion of this study is the clear difference observed at both cellular and transcriptome levels between the ways in which mammals and plants respond to chronic telomeric damage.
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Affiliation(s)
- Simon Amiard
- Génétique, Reproduction et Développement, Unité Mixte de Recherche 6293, Centre National de la Recherche Scientifique - Clermont Université - Unité 1103, Institut National de la Santé et de la Recherche Médicale, Aubière, France
| | - Olivier Da Ines
- Génétique, Reproduction et Développement, Unité Mixte de Recherche 6293, Centre National de la Recherche Scientifique - Clermont Université - Unité 1103, Institut National de la Santé et de la Recherche Médicale, Aubière, France
| | - Maria Eugenia Gallego
- Génétique, Reproduction et Développement, Unité Mixte de Recherche 6293, Centre National de la Recherche Scientifique - Clermont Université - Unité 1103, Institut National de la Santé et de la Recherche Médicale, Aubière, France
| | - Charles I White
- Génétique, Reproduction et Développement, Unité Mixte de Recherche 6293, Centre National de la Recherche Scientifique - Clermont Université - Unité 1103, Institut National de la Santé et de la Recherche Médicale, Aubière, France
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Kalve S, De Vos D, Beemster GTS. Leaf development: a cellular perspective. FRONTIERS IN PLANT SCIENCE 2014; 5:362. [PMID: 25132838 PMCID: PMC4116805 DOI: 10.3389/fpls.2014.00362] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 07/07/2014] [Indexed: 05/18/2023]
Abstract
Through its photosynthetic capacity the leaf provides the basis for growth of the whole plant. In order to improve crops for higher productivity and resistance for future climate scenarios, it is important to obtain a mechanistic understanding of leaf growth and development and the effect of genetic and environmental factors on the process. Cells are both the basic building blocks of the leaf and the regulatory units that integrate genetic and environmental information into the developmental program. Therefore, to fundamentally understand leaf development, one needs to be able to reconstruct the developmental pathway of individual cells (and their progeny) from the stem cell niche to their final position in the mature leaf. To build the basis for such understanding, we review current knowledge on the spatial and temporal regulation mechanisms operating on cells, contributing to the formation of a leaf. We focus on the molecular networks that control exit from stem cell fate, leaf initiation, polarity, cytoplasmic growth, cell division, endoreduplication, transition between division and expansion, expansion and differentiation and their regulation by intercellular signaling molecules, including plant hormones, sugars, peptides, proteins, and microRNAs. We discuss to what extent the knowledge available in the literature is suitable to be applied in systems biology approaches to model the process of leaf growth, in order to better understand and predict leaf growth starting with the model species Arabidopsis thaliana.
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Affiliation(s)
- Shweta Kalve
- Laboratory for Molecular Plant Physiology and Biotechnology, Department of Biology, University of Antwerp Antwerp, Belgium
| | - Dirk De Vos
- Laboratory for Molecular Plant Physiology and Biotechnology, Department of Biology, University of Antwerp Antwerp, Belgium ; Department of Mathematics and Computer Science, University of Antwerp Antwerp, Belgium
| | - Gerrit T S Beemster
- Laboratory for Molecular Plant Physiology and Biotechnology, Department of Biology, University of Antwerp Antwerp, Belgium
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Choi CM, Gray WM, Mooney S, Hellmann H. Composition, roles, and regulation of cullin-based ubiquitin e3 ligases. THE ARABIDOPSIS BOOK 2014; 12:e0175. [PMID: 25505853 PMCID: PMC4262284 DOI: 10.1199/tab.0175] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Due to their sessile nature, plants depend on flexible regulatory systems that allow them to adequately regulate developmental and physiological processes in context with environmental cues. The ubiquitin proteasome pathway, which targets a great number of proteins for degradation, is cellular tool that provides the necessary flexibility to accomplish this task. Ubiquitin E3 ligases provide the needed specificity to the pathway by selectively binding to particular substrates and facilitating their ubiquitylation. The largest group of E3 ligases known in plants is represented by CULLIN-REALLY INTERESTING NEW GENE (RING) E3 ligases (CRLs). In recent years, a great amount of knowledge has been generated to reveal the critical roles of these enzymes across all aspects of plant life. This review provides an overview of the different classes of CRLs in plants, their specific complex compositions, the variety of biological processes they control, and the regulatory steps that can affect their activities.
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Affiliation(s)
| | | | | | - Hanjo Hellmann
- Washington State University, Pullman, Washington
- Address correspondence to
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Li Q, Zhao P, Li J, Zhang C, Wang L, Ren Z. Genome-wide analysis of the WD-repeat protein family in cucumber and Arabidopsis. Mol Genet Genomics 2013; 289:103-24. [DOI: 10.1007/s00438-013-0789-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 10/19/2013] [Indexed: 12/31/2022]
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Li J, Wei H, Liu T, Zhao PX. GPLEXUS: enabling genome-scale gene association network reconstruction and analysis for very large-scale expression data. Nucleic Acids Res 2013; 42:e32. [PMID: 24178033 PMCID: PMC3950724 DOI: 10.1093/nar/gkt983] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The accurate construction and interpretation of gene association networks (GANs) is challenging, but crucial, to the understanding of gene function, interaction and cellular behavior at the genome level. Most current state-of-the-art computational methods for genome-wide GAN reconstruction require high-performance computational resources. However, even high-performance computing cannot fully address the complexity involved with constructing GANs from very large-scale expression profile datasets, especially for the organisms with medium to large size of genomes, such as those of most plant species. Here, we present a new approach, GPLEXUS (http://plantgrn.noble.org/GPLEXUS/), which integrates a series of novel algorithms in a parallel-computing environment to construct and analyze genome-wide GANs. GPLEXUS adopts an ultra-fast estimation for pairwise mutual information computing that is similar in accuracy and sensitivity to the Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNE) method and runs ∼1000 times faster. GPLEXUS integrates Markov Clustering Algorithm to effectively identify functional subnetworks. Furthermore, GPLEXUS includes a novel ‘condition-removing’ method to identify the major experimental conditions in which each subnetwork operates from very large-scale gene expression datasets across several experimental conditions, which allows users to annotate the various subnetworks with experiment-specific conditions. We demonstrate GPLEXUS’s capabilities by construing global GANs and analyzing subnetworks related to defense against biotic and abiotic stress, cell cycle growth and division in Arabidopsis thaliana.
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Affiliation(s)
- Jun Li
- Plant Biology Division, the Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA and School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
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Centromeric cohesion is protected twice at meiosis, by SHUGOSHINs at anaphase I and by PATRONUS at interkinesis. Curr Biol 2013; 23:2090-9. [PMID: 24206843 DOI: 10.1016/j.cub.2013.08.036] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 08/01/2013] [Accepted: 08/12/2013] [Indexed: 12/30/2022]
Abstract
BACKGROUND At meiosis, two successive rounds of chromosome segregation lead to ploidy halving. This is achieved through a stepwise release of sister chromatid cohesion, along chromosome arms to allow homolog segregation at anaphase I and at centromeres to allow sister chromatid segregation at anaphase II. Cohesins, the protein complex that ensures cohesion, must then be protected at centromeres throughout meiosis, until the onset of anaphase II. Members of the Shugoshin protein family have been shown to protect centromeric cohesins at anaphase I, but much less is known about the protection of cohesion during interkinesis, the stage between meiosis I and meiosis II. RESULTS Here, we (1) show that both Arabidopsis SHUGOSHINs paralogs are required for complete protection of centromeric cohesins during meiosis I, without apparent somatic function, and (2) identified PATRONUS (PANS1), a novel protein required for protection of meiotic centromeric cohesion. Although AtSGO1 and AtSGO2 protect centromeric cohesion during anaphase I, PANS1 is required at a later stage, during interkinesis. Additionally, we identified PANS2, a paralog of PANS1, whose mutation is synthetically lethal with pans1 suggesting that PANS genes are also essential for mitosis. PANS1 interacts directly with the CDC27b and the CDC20.1 subunit of the Anaphase Promoting Complex (APC/C), in a manner suggesting that PANS1 could be both a regulator and a target of the APC/C. CONCLUSIONS This study reveals that centromeric cohesion is actively protected at two successive stages of meiosis, by SHUGOSHINs at anaphase I and by PATRONUS at interkinesis.
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Wijnker E, Schnittger A. Control of the meiotic cell division program in plants. PLANT REPRODUCTION 2013; 26:143-58. [PMID: 23852379 PMCID: PMC3747318 DOI: 10.1007/s00497-013-0223-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 06/23/2013] [Indexed: 05/02/2023]
Abstract
While the question of why organisms reproduce sexually is still a matter of controversy, it is clear that the foundation of sexual reproduction is the formation of gametes with half the genomic DNA content of a somatic cell. This reduction in genomic content is accomplished through meiosis that, in contrast to mitosis, comprises two subsequent chromosome segregation steps without an intervening S phase. In addition, meiosis generates new allele combinations through the compilation of new sets of homologous chromosomes and the reciprocal exchange of chromatid segments between homologues. Progression through meiosis relies on many of the same, or at least homologous, cell cycle regulators that act in mitosis, e.g., cyclin-dependent kinases and the anaphase-promoting complex/cyclosome. However, these mitotic control factors are often differentially regulated in meiosis. In addition, several meiosis-specific cell cycle genes have been identified. We here review the increasing knowledge on meiotic cell cycle control in plants. Interestingly, plants appear to have relaxed cell cycle checkpoints in meiosis in comparison with animals and yeast and many cell cycle mutants are viable. This makes plants powerful models to study meiotic progression and allows unique modifications to their meiotic program to develop new plant-breeding strategies.
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Affiliation(s)
- Erik Wijnker
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg, France
- Trinationales Institut für Pflanzenforschung, Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg, France
| | - Arp Schnittger
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg, France
- Trinationales Institut für Pflanzenforschung, Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg, France
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Baloban M, Vanstraelen M, Tarayre S, Reuzeau C, Cultrone A, Mergaert P, Kondorosi E. Complementary and dose-dependent action of AtCCS52A isoforms in endoreduplication and plant size control. THE NEW PHYTOLOGIST 2013; 198:1049-1059. [PMID: 23528034 DOI: 10.1111/nph.12216] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 02/04/2013] [Indexed: 06/02/2023]
Abstract
· The dimension of organs depends on the number and the size of their component cells. Formation of polyploid cells by endoreduplication cycles is predominantly associated with increases in the cell size and implicated in organ growth. In plants, the CCS52A proteins play a major role in the switch from mitotic to endoreduplication cycles controlling thus the number of mitotic cells and the endoreduplication events in the differentiating cells. · Arabidopsis has two CCS52A isoforms; AtCCS52A1 and AtCCS52A2. Here we focused on their roles in endoreduplication and cell size control during plant development. We demonstrate their complementary and dose-dependent actions that are dependent on their expression patterns. Moreover, the impact of CCS52A overexpression on organ size in transgenic plants was dependent on the expression level; while enhanced expression of the CCS52A genes positively correlated with the ploidy levels, organ sizes were negatively affected by strong overexpression whereas milder overexpression resulted in a significant increase in the organ sizes. · Taken together, these finding support both complementary and dose-dependent actions for the Arabidopsis CCS52A isoforms in plant development and demonstrate that elevated ectopic CCS52A expression positively correlates with organ size, opening a route to higher biomass production.
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Affiliation(s)
- Mikhail Baloban
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, UPR2355, Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France
| | - Marleen Vanstraelen
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, UPR2355, Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France
- VIB Department of Plant Systems Biology, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Sylvie Tarayre
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, UPR2355, Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France
| | - Christophe Reuzeau
- CropDesign N.V., a BASF Plant Science Company, Technologiepark 3, B-9052, Zwijnaarde, Belgium
| | - Antonietta Cultrone
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, UPR2355, Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France
| | - Peter Mergaert
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, UPR2355, Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France
| | - Eva Kondorosi
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, UPR2355, Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France
- Biological Research Centre of the Hungarian Academy of Sciences, Temesvari krt 62, 6726, Szeged, Hungary
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