1
|
Zhou Y, Zhao M, Shen Q, Zhang M, Wang C, Zhang Y, Yang Q, Bo Y, Hu Z, Yang J, Zhang M, Lyu X. Genetic mapping reveals a candidate gene CmoFL1 controlling fruit length in pumpkin. FRONTIERS IN PLANT SCIENCE 2024; 15:1408602. [PMID: 38867882 PMCID: PMC11168575 DOI: 10.3389/fpls.2024.1408602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/06/2024] [Indexed: 06/14/2024]
Abstract
Fruit length (FL) is an important economical trait that affects fruit yield and appearance. Pumpkin (Cucurbita moschata Duch) contains a wealth genetic variation in fruit length. However, the natural variation underlying differences in pumpkin fruit length remains unclear. In this study, we constructed a F2 segregate population using KG1 producing long fruit and MBF producing short fruit as parents to identify the candidate gene for fruit length. By bulked segregant analysis (BSA-seq) and Kompetitive Allele-Specific PCR (KASP) approach of fine mapping, we obtained a 50.77 kb candidate region on chromosome 14 associated with the fruit length. Then, based on sequence variation, gene expression and promoter activity analyses, we identified a candidate gene (CmoFL1) encoding E3 ubiquitin ligase in this region may account for the variation of fruit length. One SNP variation in promoter of CmoFL1 changed the GT1CONSENSUS, and DUAL-LUC assay revealed that this variation significantly affected the promoter activity of CmoFL1. RNA-seq analysis indicated that CmoFL1 might associated with the cell division process and negatively regulate fruit length. Collectively, our work identifies an important allelic affecting fruit length, and provides a target gene manipulating fruit length in future pumpkin breeding.
Collapse
Affiliation(s)
- Yimei Zhou
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Meng Zhao
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qinghui Shen
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Mengyi Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Chenhao Wang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yutong Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qinrong Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | | | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
- Key laboratory of Horticultural Plant growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
- Key laboratory of Horticultural Plant growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
- Key laboratory of Horticultural Plant growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China
| | - Xiaolong Lyu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| |
Collapse
|
2
|
Zaragoza JZ, Klap K, Heidstra R, Zhou W, Scheres B. The dual role of the RETINOBLASTOMA-RELATED protein in the DNA damage response is coordinated by the interaction with LXCXE-containing proteins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1194-1206. [PMID: 38321589 DOI: 10.1111/tpj.16665] [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: 02/08/2022] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 02/08/2024]
Abstract
Living organisms possess mechanisms to safeguard genome integrity. To avoid spreading mutations, DNA lesions are detected and cell division is temporarily arrested to allow repair mechanisms. Afterward, cells either resume division or respond to unsuccessful repair by undergoing programmed cell death (PCD). How the success rate of DNA repair connects to later cell fate decisions remains incompletely known, particularly in plants. The Arabidopsis thaliana RETINOBLASTOMA-RELATED1 (RBR) protein and its partner E2FA, play both structural and transcriptional functions in the DNA damage response (DDR). Here we provide evidence that distinct RBR protein interactions with LXCXE motif-containing proteins guide these processes. Using the N849F substitution in the RBR B-pocket domain, which specifically disrupts binding to the LXCXE motif, we show that these interactions are dispensable in unchallenging conditions. However, N849F substitution abolishes RBR nuclear foci and promotes PCD and growth arrest upon genotoxic stress. NAC044, which promotes growth arrest and PCD, accumulates after the initial recruitment of RBR to foci and can bind non-focalized RBR through the LXCXE motif in a phosphorylation-independent manner, allowing interaction at different cell cycle phases. Disrupting NAC044-RBR interaction impairs PCD, but their genetic interaction points to opposite independent roles in the regulation of PCD. The LXCXE-binding dependency of the roles of RBR in the DDR suggests a coordinating mechanism to translate DNA repair success to cell survival. We propose that RBR and NAC044 act in two distinct DDR pathways, but interact to integrate input from both DDR pathways to decide upon an irreversible cell fate decision.
Collapse
Affiliation(s)
- Jorge Zamora Zaragoza
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Department of Biotechnology, Rijk Zwaan Breeding B.V., Eerste Kruisweg 9, 4793 RS, Fijnaart, The Netherlands
| | - Katinka Klap
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Renze Heidstra
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Wenkun Zhou
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ben Scheres
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Department of Biotechnology, Rijk Zwaan Breeding B.V., Eerste Kruisweg 9, 4793 RS, Fijnaart, The Netherlands
| |
Collapse
|
3
|
Mineta K, Hirota J, Yamada K, Itoh T, Chen P, Iwakawa H, Takatsuka H, Nomoto Y, Ito M. MYB3R-mediated and cell cycle-dependent transcriptional regulation of a tobacco ortholog of SCARECROW-LIKE28 in synchronized cultures of BY-2 cells. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:353-359. [PMID: 38434109 PMCID: PMC10905365 DOI: 10.5511/plantbiotechnology.23.0515a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/15/2023] [Indexed: 03/05/2024]
Abstract
Although it is well known that hierarchical transcriptional networks are essential for various aspects of plant development and environmental response, little has been investigated about whether and how they also regulate the plant cell cycle. Recent studies on cell cycle regulation in Arabidopsis thaliana identified SCARECROW-LIKE28 (SCL28), a GRAS-type transcription factor, that constitutes a hierarchical transcriptional pathway comprised of MYB3R, SCL28 and SIAMESE-RELATED (SMR). In this pathway, MYB3R family proteins regulate the G2/M-specific transcription of the SCL28 gene, of which products, in turn, positively regulate the transcription of SMR genes encoding a group of plant-specific inhibitor proteins of cyclin-dependent kinases. However, this pathway with a role in cell cycle inhibition is solely demonstrated in A. thaliana, thus leaving open the question of whether and to what extent this pathway is evolutionarily conserved in plants. In this study, we conducted differential display RT-PCR on synchronized Nicotiana tabacum (tobacco) BY-2 cells and identified several M-phase-specific cDNA clones, one of which turned out to be a tobacco ortholog of SCL28 and was designated NtSCL28. We showed that NtSCL28 is expressed specifically during G2/M and early G1 in the synchronized cultures of BY-2 cells. NtSCL28 contains MYB3R-binding promoter elements, so-called mitosis-specific activator elements, and is upregulated by a hyperactive form of NtmybA2, one of the MYB3R proteins from tobacco. Our study indicated that a part of the hierarchical pathway identified in A. thaliana is equally operating in tobacco cells, suggesting the conservation of this pathway across different families in evolution of angiosperm.
Collapse
Affiliation(s)
- Keito Mineta
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Junya Hirota
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Kesuke Yamada
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Takashi Itoh
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Poyu Chen
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Hidekazu Iwakawa
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Hirotomo Takatsuka
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Yuji Nomoto
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Masaki Ito
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| |
Collapse
|
4
|
Williamson D, Tasker-Brown W, Murray JAH, Jones AR, Band LR. Modelling how plant cell-cycle progression leads to cell size regulation. PLoS Comput Biol 2023; 19:e1011503. [PMID: 37862377 PMCID: PMC10653611 DOI: 10.1371/journal.pcbi.1011503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 11/16/2023] [Accepted: 09/07/2023] [Indexed: 10/22/2023] Open
Abstract
Populations of cells typically maintain a consistent size, despite cell division rarely being precisely symmetrical. Therefore, cells must possess a mechanism of "size control", whereby the cell volume at birth affects cell-cycle progression. While size control mechanisms have been elucidated in a number of other organisms, it is not yet clear how this mechanism functions in plants. Here, we present a mathematical model of the key interactions in the plant cell cycle. Model simulations reveal that the network of interactions exhibits limit-cycle solutions, with biological switches underpinning both the G1/S and G2/M cell-cycle transitions. Embedding this network model within growing cells, we test hypotheses as to how cell-cycle progression can depend on cell size. We investigate two different mechanisms at both the G1/S and G2/M transitions: (i) differential expression of cell-cycle activator and inhibitor proteins (with synthesis of inhibitor proteins being independent of cell size), and (ii) equal inheritance of inhibitor proteins after cell division. The model demonstrates that both these mechanisms can lead to larger daughter cells progressing through the cell cycle more rapidly, and can thus contribute to cell-size control. To test how these features enable size homeostasis over multiple generations, we then simulated these mechanisms in a cell-population model with multiple rounds of cell division. These simulations suggested that integration of size-control mechanisms at both G1/S and G2/M provides long-term cell-size homeostasis. We concluded that while both size independence and equal inheritance of inhibitor proteins can reduce variations in cell size across individual cell-cycle phases, combining size-control mechanisms at both G1/S and G2/M is essential to maintain size homeostasis over multiple generations. Thus, our study reveals how features of the cell-cycle network enable cell-cycle progression to depend on cell size, and provides a mechanistic understanding of how plant cell populations maintain consistent size over generations.
Collapse
Affiliation(s)
- Daniel Williamson
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - William Tasker-Brown
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, United Kingdom
| | - James A. H. Murray
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, United Kingdom
| | - Angharad R. Jones
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, United Kingdom
| | - Leah R. Band
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| |
Collapse
|
5
|
Distinct roles of Arabidopsis ORC1 proteins in DNA replication and heterochromatic H3K27me1 deposition. Nat Commun 2023; 14:1270. [PMID: 36882445 PMCID: PMC9992703 DOI: 10.1038/s41467-023-37024-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 02/24/2023] [Indexed: 03/09/2023] Open
Abstract
Most cellular proteins involved in genome replication are conserved in all eukaryotic lineages including yeast, plants and animals. However, the mechanisms controlling their availability during the cell cycle are less well defined. Here we show that the Arabidopsis genome encodes for two ORC1 proteins highly similar in amino acid sequence and that have partially overlapping expression domains but with distinct functions. The ancestral ORC1b gene, present before the partial duplication of the Arabidopsis genome, has retained the canonical function in DNA replication. ORC1b is expressed in both proliferating and endoreplicating cells, accumulates during G1 and is rapidly degraded upon S-phase entry through the ubiquitin-proteasome pathway. In contrast, the duplicated ORC1a gene has acquired a specialized function in heterochromatin biology. ORC1a is required for efficient deposition of the heterochromatic H3K27me1 mark by the ATXR5/6 histone methyltransferases. The distinct roles of the two ORC1 proteins may be a feature common to other organisms with duplicated ORC1 genes and a major difference with animal cells.
Collapse
|
6
|
Szurman-Zubrzycka M, Jędrzejek P, Szarejko I. How Do Plants Cope with DNA Damage? A Concise Review on the DDR Pathway in Plants. Int J Mol Sci 2023; 24:ijms24032404. [PMID: 36768727 PMCID: PMC9916837 DOI: 10.3390/ijms24032404] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
DNA damage is induced by many factors, some of which naturally occur in the environment. Because of their sessile nature, plants are especially exposed to unfavorable conditions causing DNA damage. In response to this damage, the DDR (DNA damage response) pathway is activated. This pathway is highly conserved between eukaryotes; however, there are some plant-specific DDR elements, such as SOG1-a transcription factor that is a central DDR regulator in plants. In general, DDR signaling activates transcriptional and epigenetic regulators that orchestrate the cell cycle arrest and DNA repair mechanisms upon DNA damage. The cell cycle halts to give the cell time to repair damaged DNA before replication. If the repair is successful, the cell cycle is reactivated. However, if the DNA repair mechanisms fail and DNA lesions accumulate, the cell enters the apoptotic pathway. Thereby the proper maintenance of DDR is crucial for plants to survive. It is particularly important for agronomically important species because exposure to environmental stresses causing DNA damage leads to growth inhibition and yield reduction. Thereby, gaining knowledge regarding the DDR pathway in crops may have a huge agronomic impact-it may be useful in breeding new cultivars more tolerant to such stresses. In this review, we characterize different genotoxic agents and their mode of action, describe DDR activation and signaling and summarize DNA repair mechanisms in plants.
Collapse
|
7
|
Dysin AP, Shcherbakov YS, Nikolaeva OA, Terletskii VP, Tyshchenko VI, Dementieva NV. Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics. Genes (Basel) 2022; 13:genes13122221. [PMID: 36553488 PMCID: PMC9778375 DOI: 10.3390/genes13122221] [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: 09/12/2022] [Revised: 10/19/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.
Collapse
Affiliation(s)
- Artem P. Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
- Correspondence:
| | - Yuri S. Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Olga A. Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Valerii P. Terletskii
- All-Russian Research Veterinary Institute of Poultry Science-Branch of the Federal Scientific Center, All-Russian Research and Technological Poultry Institute (ARRVIPS), Lomonosov, 198412 St. Petersburg, Russia
| | - Valentina I. Tyshchenko
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| |
Collapse
|
8
|
Lin X, Xiao Y, Song Y, Gan C, Deng X, Wang P, Liu J, Jiang Z, Peng L, Zhou D, He X, Bian J, Zhu C, Liu B, He H, Xu J. Rice microtubule-associated protein OsMAP65-3.1, but not OsMAP65-3.2, plays a critical role in phragmoplast microtubule organization in cytokinesis. FRONTIERS IN PLANT SCIENCE 2022; 13:1030247. [PMID: 36388546 PMCID: PMC9643714 DOI: 10.3389/fpls.2022.1030247] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/10/2022] [Indexed: 06/10/2023]
Abstract
In plants, MAP65 preferentially cross-links the anti-parallel microtubules (MTs) and plays an important role for cytokinesis. However, the functions of MAP65 isoforms in rice (Oryza sativa. L) are largely unknown. Here, we identified two MAP65-3 homologs in rice, OsMAP65-3.1 and OsMAP65-3.2. We found that both OsMAP65-3.1 and OsMAP65-3.2 were similar in dimerization and location to AtMAP65-3, and the expression of either rice genes driven by the AtMAP65-3 promoter suppressed the cytokinesis failure and growth defect of atmap65-3. However, OsMAP65-3.1 with native promoter also recovered the atmap65-3, but OsMAP65-3.2 with its own promoter had no effects. OsMAP65-3.1 but not OsMAP65-3.2 was actively expressed in tissues enriched with dividing cells. R1R2R3-Myb (MYB3R) transcription factors directly bound to the OsMAP65-3.1 promoter but not that of OsMAP65-3.2. Furthermore, osmap65-3.2 had no obvious phenotype, while either osmap65-3.1 or osmap65-3.1(+/-) was lethal. The eminent MTs around the daughter nuclei and cytokinesis defects were frequently observed in OsMAP65-3.1-defective plants. Taken together, our findings suggest that OsMAP65-3.1, rather than OsMAP65-3.2, plays essential roles in rice cytokinesis resulting from their differential expression which were passably directly regulated by OsMYB3Rs.
Collapse
Affiliation(s)
- Xiaoli Lin
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding of the Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yu Xiao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, China
| | - Yongping Song
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding of the Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Cong Gan
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding of the Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Xingguang Deng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, China
| | - Peng Wang
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding of the Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Jialong Liu
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding of the Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Zhishu Jiang
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding of the Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Limei Peng
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding of the Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Dahu Zhou
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding of the Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Xiaopeng He
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding of the Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Jianmin Bian
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding of the Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Changlan Zhu
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding of the Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Bo Liu
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, Davis, CA, United States
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding of the Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Jie Xu
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding of the Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| |
Collapse
|
9
|
Nomoto Y, Takatsuka H, Yamada K, Suzuki T, Suzuki T, Huang Y, Latrasse D, An J, Gombos M, Breuer C, Ishida T, Maeo K, Imamura M, Yamashino T, Sugimoto K, Magyar Z, Bögre L, Raynaud C, Benhamed M, Ito M. A hierarchical transcriptional network activates specific CDK inhibitors that regulate G2 to control cell size and number in Arabidopsis. Nat Commun 2022; 13:1660. [PMID: 35351906 PMCID: PMC8964727 DOI: 10.1038/s41467-022-29316-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 03/07/2022] [Indexed: 12/13/2022] Open
Abstract
AbstractHow cell size and number are determined during organ development remains a fundamental question in cell biology. Here, we identified a GRAS family transcription factor, called SCARECROW-LIKE28 (SCL28), with a critical role in determining cell size in Arabidopsis. SCL28 is part of a transcriptional regulatory network downstream of the central MYB3Rs that regulate G2 to M phase cell cycle transition. We show that SCL28 forms a dimer with the AP2-type transcription factor, AtSMOS1, which defines the specificity for promoter binding and directly activates transcription of a specific set of SIAMESE-RELATED (SMR) family genes, encoding plant-specific inhibitors of cyclin-dependent kinases and thus inhibiting cell cycle progression at G2 and promoting the onset of endoreplication. Through this dose-dependent regulation of SMR transcription, SCL28 quantitatively sets the balance between cell size and number without dramatically changing final organ size. We propose that this hierarchical transcriptional network constitutes a cell cycle regulatory mechanism that allows to adjust cell size and number to attain robust organ growth.
Collapse
|
10
|
Li J, Liang W, Liu Y, Ren Z, Ci D, Chang J, Qian W. The Arabidopsis ATR-SOG1 signaling module regulates pleiotropic developmental adjustments in response to 3'-blocked DNA repair intermediates. THE PLANT CELL 2022; 34:852-866. [PMID: 34791445 PMCID: PMC8824664 DOI: 10.1093/plcell/koab282] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/08/2021] [Indexed: 06/01/2023]
Abstract
Base excision repair and active DNA demethylation produce repair intermediates with DNA molecules blocked at the 3'-OH end by an aldehyde or phosphate group. However, both the physiological consequences of these accumulated single-strand DNAs break with 3'-blocked ends (DNA 3'-blocks) and the signaling pathways responding to unrepaired DNA 3'-blocks remain unclear in plants. Here, we investigated the effects of DNA 3'-blocks on plant development using the zinc finger DNA 3'-phosphoesterase (zdp) AP endonuclease2 (ape2) double mutant, in which 3'-blocking residues are poorly repaired. The accumulation of DNA 3'-blocked triggered diverse developmental defects that were dependent on the ATM and RAD3-related (ATR)-suppressor of gamma response 1 (SOG1) signaling module. SOG1 mutation rescued the developmental defects of zdp ape2 leaves by preventing cell endoreplication and promoting cell proliferation. However, SOG1 mutation caused intensive meristematic cell death in the radicle of zdp ape2 following germination, resulting in rapid termination of radicle growth. Notably, mutating FORMAMIDOPYRIMIDINE DNA GLYCOSYLASE (FPG) in zdp ape2 sog1 partially recovered its radicle growth, demonstrating that DNA 3'-blocks generated by FPG caused the meristematic defects. Surprisingly, despite lacking a functional radicle, zdp ape2 sog1 mutants compensated the lack of root growth by generating anchor roots having low levels of DNA damage response. Our results reveal dual roles of SOG1 in regulating root establishment when seeds germinate with excess DNA 3'-blocks.
Collapse
Affiliation(s)
- Jinchao Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Wenjie Liang
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Yi Liu
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhitong Ren
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Dong Ci
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Jinjie Chang
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- School of Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
11
|
Pedroza-Garcia JA, Xiang Y, De Veylder L. Cell cycle checkpoint control in response to DNA damage by environmental stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:490-507. [PMID: 34741364 DOI: 10.1111/tpj.15567] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/26/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Being sessile organisms, plants are ubiquitously exposed to stresses that can affect the DNA replication process or cause DNA damage. To cope with these problems, plants utilize DNA damage response (DDR) pathways, consisting of both highly conserved and plant-specific elements. As a part of this DDR, cell cycle checkpoint control mechanisms either pause the cell cycle, to allow DNA repair, or lead cells into differentiation or programmed cell death, to prevent the transmission of DNA errors in the organism through mitosis or to its offspring via meiosis. The two major DDR cell cycle checkpoints control either the replication process or the G2/M transition. The latter is largely overseen by the plant-specific SOG1 transcription factor, which drives the activity of cyclin-dependent kinase inhibitors and MYB3R proteins, which are rate limiting for the G2/M transition. By contrast, the replication checkpoint is controlled by different players, including the conserved kinase WEE1 and likely the transcriptional repressor RBR1. These checkpoint mechanisms are called upon during developmental processes, in retrograde signaling pathways, and in response to biotic and abiotic stresses, including metal toxicity, cold, salinity, and phosphate deficiency. Additionally, the recent expansion of research from Arabidopsis to other model plants has revealed species-specific aspects of the DDR. Overall, it is becoming evidently clear that the DNA damage checkpoint mechanisms represent an important aspect of the adaptation of plants to a changing environment, hence gaining more knowledge about this topic might be helpful to increase the resilience of plants to climate change.
Collapse
Affiliation(s)
- José 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
| | - Yanli Xiang
- 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
| |
Collapse
|
12
|
Li WF, Kang Y, Zhang Y, Zang QL, Qi LW. Concerted control of the LaRAV1-LaCDKB1;3 module by temperature during dormancy release and reactivation of larch. TREE PHYSIOLOGY 2021; 41:1918-1937. [PMID: 33847364 PMCID: PMC8498939 DOI: 10.1093/treephys/tpab052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 04/07/2021] [Indexed: 05/03/2023]
Abstract
Dormancy release and reactivation of temperate-zone trees involve the temperature-modulated expression of cell-cycle genes. However, information on the detailed regulatory mechanism is limited. Here, we compared the transcriptomes of the stems of active and dormant larch trees, emphasizing the expression patterns of cell-cycle genes and transcription factors and assessed their relationships and responses to temperatures. Twelve cell-cycle genes and 31 transcription factors were strongly expressed in the active stage. Promoter analysis suggested that these 12 genes might be regulated by transcription factors from 10 families. Altogether, 73 cases of regulation between 16 transcription factors and 12 cell-cycle genes were predicted, while the regulatory interactions between LaMYB20 and LaCYCB1;1, and LaRAV1 and LaCDKB1;3 were confirmed by yeast one-hybrid and dual-luciferase assays. Last, we found that LaRAV1 and LaCDKB1;3 had almost the same expression patterns during dormancy release and reactivation induced naturally or artificially by temperature, indicating that the LaRAV1-LaCDKB1;3 module functions in the temperature-modulated dormancy release and reactivation of larch trees. These results provide new insights into the link between temperature and cell-cycle gene expression, helping to understand the temperature control of tree growth and development in the context of climate change.
Collapse
Affiliation(s)
- Wan-Feng Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1, Dongxiaofu, Xiangshan Road, Haidian District, Beijing 100091, People's Republic of China
| | - Yanhui Kang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1, Dongxiaofu, Xiangshan Road, Haidian District, Beijing 100091, People's Republic of China
| | - Yao Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, No. 1, Dongxiaofu, Xiangshan Road, Haidian District, Beijing 100091, People's Republic of China
| | - Qiao-Lu Zang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1, Dongxiaofu, Xiangshan Road, Haidian District, Beijing 100091, People's Republic of China
| | - Li-Wang Qi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1, Dongxiaofu, Xiangshan Road, Haidian District, Beijing 100091, People's Republic of China
| |
Collapse
|
13
|
Gentric N, Genschik P, Noir S. Connections between the Cell Cycle and the DNA Damage Response in Plants. Int J Mol Sci 2021; 22:ijms22179558. [PMID: 34502465 PMCID: PMC8431409 DOI: 10.3390/ijms22179558] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 12/02/2022] Open
Abstract
Due to their sessile lifestyle, plants are especially exposed to various stresses, including genotoxic stress, which results in altered genome integrity. Upon the detection of DNA damage, distinct cellular responses lead to cell cycle arrest and the induction of DNA repair mechanisms. Interestingly, it has been shown that some cell cycle regulators are not only required for meristem activity and plant development but are also key to cope with the occurrence of DNA lesions. In this review, we first summarize some important regulatory steps of the plant cell cycle and present a brief overview of the DNA damage response (DDR) mechanisms. Then, the role played by some cell cycle regulators at the interface between the cell cycle and DNA damage responses is discussed more specifically.
Collapse
|
14
|
Qian Q, Ma Q, Wang B, Qian Q, Zhao C, Feng F, Dong X. MicroRNA-205-5p targets E2F1 to promote autophagy and inhibit pulmonary fibrosis in silicosis through impairing SKP2-mediated Beclin1 ubiquitination. J Cell Mol Med 2021; 25:9214-9227. [PMID: 34428336 PMCID: PMC8500965 DOI: 10.1111/jcmm.16825] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 05/20/2021] [Accepted: 07/16/2021] [Indexed: 12/11/2022] Open
Abstract
Silicosis is an occupational disease characterized by extensive pulmonary fibrosis, and the underlying pathological process remains uncertain. Herein, we explored the molecular mechanism by which microRNA‐205‐5p (miR‐205‐5p) affects the autophagy of alveolar macrophages (AMs) and pulmonary fibrosis in mice with silicosis through the E2F transcription factor 1 (E2F1)/S‐phase kinase‐associated protein 2 (SKP2)/Beclin1 axis. Alveolar macrophages (MH‐S cells) were exposed to crystalline silica (CS) to develop an in vitro model, and mice were treated with CS to establish an in vivo model. Decreased Beclin1 and increased SKP2 and E2F1 were identified in mice with silicosis. We silenced or overexpressed miR‐205‐5p, E2F1, SKP2 and Beclin1 to investigate their potential roles in pulmonary fibrosis in vivo and autophagy in vitro. Recombinant adenovirus mRFP‐GFP‐LC3 was transduced into the MH‐S cells to assay autophagic flow. Knocking down Beclin1 promoted pulmonary fibrosis and suppressed the autophagy. Co‐immunoprecipitation and ubiquitination assays suggested that SKP2 induced K48‐linked ubiquitination of Beclin1. Furthermore, chromatin immunoprecipitation‐PCR revealed the site where E2F1 bound to the SKP2 promoter between 1638 bp and 1645 bp. As shown by dual‐luciferase reporter gene assay, the transfection with miR‐205‐5p mimic inhibited the luciferase activity of the wild‐type E2F1 3′untranslated region, suggesting that miR‐205‐5p targeted E2F1. Additionally, miR‐205‐5p overexpression increased autophagy and reduced the pulmonary fibrosis, while overexpression of E2F1 or SKP2 or inhibition of Beclin1 could annul this effect. The current study elucidated that miR‐205‐5p targeted E2F1, thereby inhibiting SKP2‐mediated Beclin1 ubiquitination to promote macrophage autophagy and inhibit pulmonary fibrosis in mice with silicosis.
Collapse
Affiliation(s)
- Qingzeng Qian
- School of Public Health, North China University of Science and Technology, Tangshan, China
| | - Qinghua Ma
- Department of Preventive Health, The Third People's Hospital of Xiangcheng District in Suzhou, Suzhou, China
| | - Bin Wang
- Department of Pediatrics, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Qingqiang Qian
- Department of Neurology, Tangshan Gongren Hospital, Tangshan, China
| | - Changsong Zhao
- Department of Emergency, Tangshan Hospital of Traditional Chinese Medicine, Tangshan, China
| | - Fumin Feng
- School of Public Health, North China University of Science and Technology, Tangshan, China
| | - Xiaona Dong
- Department of Respiratory Medicine, Tangshan People's Hospital, Tangshan, China
| |
Collapse
|
15
|
Takatsuka H, Nomoto Y, Araki S, Machida Y, Ito M. Identification of two tobacco genes encoding MYB3R proteins with repressor function and showing cell cycle-regulated transcript accumulation. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:269-275. [PMID: 34393606 PMCID: PMC8329274 DOI: 10.5511/plantbiotechnology.21.0224a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 02/24/2021] [Indexed: 05/09/2023]
Abstract
MYB3R family transcription factors play a central role in the regulation of G2/M-specific gene transcription in Arabidopsis thaliana. Among the members of this family, MYB3R3 and MYB3R5 are structurally closely related and are involved in the transcriptional repression of target genes in both proliferating and quiescent cells. This type of MYB3R repressor is widespread in plants; however, apart from the studies on MYB3Rs in Arabidopsis thaliana, little information about them is available. Here we isolated tobacco cDNA clones encoding two closely related MYB3R proteins designated as NtmybC1 and NtmybC2 and determined the nucleotide sequences of the entire coding regions. Phylogenetic analysis suggested that NtmybC1 and NtmybC2 can be grouped into a conserved subfamily of plant MYB3Rs that also contains MYB3R3 and MYB3R5. When transiently expressed in protoplasts prepared from tobacco BY-2 cells, NtmybC1 and NtmybC2 repressed the activity of target promoters and blocked promoter activation mediated by NtmybA2, a MYB3R activator from tobacco. Unlike MYB3R3 and MYB3R5, NtmybC1 and NtmybC2 showed cell cycle-regulated transcript accumulation. In synchronized cultures of BY-2 cells, mRNAs for both NtmybC1 and NtmybC2 were preferentially expressed during the G2 and M phases, coinciding with the expression of NtmybA2 and G2/M-specific target genes. These results not only broadly confirm our fundamental view that this type of MYB3R protein acts as transcriptional repressor of G2/M-specific genes but also suggest a possible divergence of MYB3R repressors in terms of the mechanisms of their action and regulation.
Collapse
Affiliation(s)
- Hirotomo Takatsuka
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Yuji Nomoto
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Satoshi Araki
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Masaki Ito
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- E-mail: Tel & Fax: +81-76-264-6207
| |
Collapse
|
16
|
The Arabidopsis GRAS-type SCL28 transcription factor controls the mitotic cell cycle and division plane orientation. Proc Natl Acad Sci U S A 2021; 118:2005256118. [PMID: 33526654 DOI: 10.1073/pnas.2005256118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Gene expression is reconfigured rapidly during the cell cycle to execute the cellular functions specific to each phase. Studies conducted with synchronized plant cell suspension cultures have identified hundreds of genes with periodic expression patterns across the phases of the cell cycle, but these results may differ from expression occurring in the context of intact organs. Here, we describe the use of fluorescence-activated cell sorting to analyze the gene expression profile of G2/M cells in the growing root. To this end, we isolated cells expressing the early mitosis cell cycle marker CYCLINB1;1-GFP from Arabidopsis root tips. Transcriptome analysis of these cells allowed identification of hundreds of genes whose expression is reduced or enriched in G2/M cells, including many not previously reported from cell suspension cultures. From this dataset, we identified SCL28, a transcription factor belonging to the GRAS family, whose messenger RNA accumulates to the highest levels in G2/M and is regulated by MYB3R transcription factors. Functional analysis indicates that SCL28 promotes progression through G2/M and modulates the selection of cell division planes.
Collapse
|
17
|
Gualtieri C, Gianella M, Pagano A, Cadeddu T, Araújo S, Balestrazzi A, Macovei A. Exploring microRNA Signatures of DNA Damage Response Using an Innovative System of Genotoxic Stress in Medicago truncatula Seedlings. FRONTIERS IN PLANT SCIENCE 2021; 12:645323. [PMID: 33767724 PMCID: PMC7985446 DOI: 10.3389/fpls.2021.645323] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/15/2021] [Indexed: 05/08/2023]
Abstract
One of the challenges that living organisms face is to promptly respond to genotoxic stress to avoid DNA damage. To this purpose, all organisms, including plants, developed complex DNA damage response (DDR) mechanisms. These mechanisms are highly conserved among organisms and need to be finely regulated. In this scenario, microRNAs (miRNAs) are emerging as active players, thus attracting the attention of the research community. The involvement of miRNAs in DDR has been investigated prominently in human cells whereas studies in plants are still scarce. To experimentally investigate the involvement of plant miRNAs in the regulation of DDR-associated pathways, an ad hoc system was developed, using the model legume Medicago truncatula. Specific treatments with camptothecin (CPT) and/or NSC120686 (NSC), targeting distinct components of DDR, namely topoisomerase I (TopI) and tyrosyl-DNA phosphodiesterase 1 (TDP1), were used. Phenotypic (germination percentage and speed, seedling growth) and molecular (cell death, DNA damage, and gene expression profiles) analyses demonstrated that the imposed treatments impact DDR. Our results show that these treatments do not influence the germination process but rather inhibit seedling development, causing an increase in cell death and accumulation of DNA damage. Moreover, treatment-specific changes in the expression of suppressor of gamma response 1 (SOG1), master-regulator of plant DDR, were observed. Additionally, the expression of multiple genes playing important roles in different DNA repair pathways and cell cycle regulation were differentially expressed in a treatment-specific manner. Subsequently, specific miRNAs identified from our previous bioinformatics approaches as putatively targeting genes involved in DDR processes were investigated alongside their targets. The obtained results indicate that under most conditions when a miRNA is upregulated the corresponding candidate target gene is downregulated, providing an indirect evidence of miRNAs action over these targets. Hence, the present study extends the present knowledge on the information available regarding the roles played by miRNAs in the post-transcriptional regulation of DDR in plants.
Collapse
Affiliation(s)
- Carla Gualtieri
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Maraeva Gianella
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Andrea Pagano
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Tiziano Cadeddu
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Susana Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Association BLC3, Technology and Innovation Campus, Centre BIO- R&D Unit, Lagares da Beira, Portugal
| | - Alma Balestrazzi
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Anca Macovei
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| |
Collapse
|
18
|
Cabral LM, Masuda HP, Ballesteros HF, de Almeida-Engler J, Alves-Ferreira M, De Toni KLG, Bizotto FM, Ferreira PCG, Hemerly AS. ABAP1 Plays a Role in the Differentiation of Male and Female Gametes in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:642758. [PMID: 33643370 PMCID: PMC7903899 DOI: 10.3389/fpls.2021.642758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/22/2021] [Indexed: 05/07/2023]
Abstract
The correct development of a diploid sporophyte body and a haploid gametophyte relies on a strict coordination between cell divisions in space and time. During plant reproduction, these divisions have to be temporally and spatially coordinated with cell differentiation processes, to ensure a successful fertilization. Armadillo BTB Arabidopsis protein 1 (ABAP1) is a plant exclusive protein that has been previously reported to control proliferative cell divisions during leaf growth in Arabidopsis. Here, we show that ABAP1 binds to different transcription factors that regulate male and female gametophyte differentiation, repressing their target genes expression. During male gametogenesis, the ABAP1-TCP16 complex represses CDT1b transcription, and consequently regulates microspore first asymmetric mitosis. In the female gametogenesis, the ABAP1-ADAP complex represses EDA24-like transcription, regulating polar nuclei fusion to form the central cell. Therefore, besides its function during vegetative development, this work shows that ABAP1 is also involved in differentiation processes during plant reproduction, by having a dual role in regulating both the first asymmetric cell division of male gametophyte and the cell differentiation (or cell fusion) of female gametophyte.
Collapse
Affiliation(s)
- Luiz M. Cabral
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Biologia Celular e Molecular, Instituto de Biologia, Universidade Federal Fluminense, Niterói, Brazil
| | - Hana P. Masuda
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, Brazil
| | - Helkin F. Ballesteros
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Janice de Almeida-Engler
- Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Institut Sophia Agrobiotech, Université Côte d’Azur, Sophia Antipolis, France
| | - Márcio Alves-Ferreira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Karen L. G. De Toni
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernanda M. Bizotto
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, Brazil
| | - Paulo C. G. Ferreira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adriana S. Hemerly
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- *Correspondence: Adriana S. Hemerly, ;
| |
Collapse
|
19
|
Wu ZG, Jiang W, Tao ZM, Pan XJ, Yu WH, Huang HL. Morphological and stage-specific transcriptome analyses reveal distinct regulatory programs underlying yam (Dioscorea alata L.) bulbil growth. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1899-1914. [PMID: 31832647 PMCID: PMC7242083 DOI: 10.1093/jxb/erz552] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/12/2019] [Indexed: 06/09/2023]
Abstract
In yam (Dioscorea spp) species, bulbils at leaf axils are the most striking species-specific axillary structure and exhibit important ecological niches. Genetic regulation underlying bulbil growth remains largely unclear so far. Here, we characterize yam (Dioscorea alata L.) bulbil development using histological analysis, and perform full transcriptional profiling on key developmental stages together with phytohormone analyses. Using the stage-specific scoring algorithm, we have identified 3451 stage-specifically expressed genes that exhibit a tight link between major transcriptional changes and stages. Co-expressed gene clusters revealed an obvious over-representation of genes associated with cell division and expansion at the initiation stage of bulbils (T1). Transcriptional changes of hormone-related genes highly coincided with hormone levels, indicating that bulbil initiation and growth are coordinately controlled by multiple phytohormones. In particular, localized auxin is transiently required to trigger bulbil initiation, and be further depleted or exported from bulbils to promote growth by up-regulation of genes involved in auxinconjugation and efflux. The sharp increase in supply of sucrose and an enhanced trehalose-6-phophate pathway at T1 were observed, suggesting that sucrose probably functions as a key signal and promotes bulbil initiation. Analysis of the expression of transcription factors (TFs) predicated 149 TFs as stage-specifically expressed; several T1-specific TFs (from Aux/IAA, E2F, MYB, and bHLH families) have been shown to play key roles in triggering bulbil formation. Together, our work provides a crucial angle for in-depth understanding of the molecular programs underlying yam's unique bulbil development processes. Stage-specific gene sets can be queried to obtain key candidates regulating bulbil growth, serving as valuable resources for further functional research.
Collapse
Affiliation(s)
- Zhi-Gang Wu
- Key Laboratory for Plant Genetic Improvement, Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Wu Jiang
- Key Laboratory for Plant Genetic Improvement, Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Zheng-Ming Tao
- Key Laboratory for Plant Genetic Improvement, Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Xiao-Jun Pan
- School of Pharmacy, Wenzhou Medical University, Wenzhou, China
| | - Wen-Hui Yu
- Quzhou Academy of Agricultural Sciences, Quzhou, China
| | - Hui-Lian Huang
- Key Laboratory of Modern Preparation of Traditional Chinese Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| |
Collapse
|
20
|
Raynaud C, Nisa M. A conserved role for γ-tubulin as a regulator of E2F transcription factors. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1199-1202. [PMID: 32076727 DOI: 10.1093/jxb/erz557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This article comments on:
Kállai BM, Kourová H, Chumová J, Papdi C, Trögelová L, Kofroňová O, Hozák P, Filimonenko V, Mészáros T, Magyar Z, Bögre L, Binarová P. 2020. γ-Tubulin interacts with E2F transcription factors to regulate proliferation and endocycling in Arabidopsis. Journal of Experimental Botany 71, 1265–1277.
Collapse
Affiliation(s)
- Cécile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Maherun Nisa
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| |
Collapse
|
21
|
Vercruysse J, Van Bel M, Osuna‐Cruz CM, Kulkarni SR, Storme V, Nelissen H, Gonzalez N, Inzé D, Vandepoele K. Comparative transcriptomics enables the identification of functional orthologous genes involved in early leaf growth. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:553-567. [PMID: 31361386 PMCID: PMC6953196 DOI: 10.1111/pbi.13223] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/10/2019] [Accepted: 07/25/2019] [Indexed: 05/20/2023]
Abstract
Leaf growth is a complex trait for which many similarities exist in different plant species, suggesting functional conservation of the underlying pathways. However, a global view of orthologous genes involved in leaf growth showing conserved expression in dicots and monocots is currently missing. Here, we present a genome-wide comparative transcriptome analysis between Arabidopsis and maize, identifying conserved biological processes and gene functions active during leaf growth. Despite the orthology complexity between these distantly related plants, 926 orthologous gene groups including 2829 Arabidopsis and 2974 maize genes with similar expression during leaf growth were found, indicating conservation of the underlying molecular networks. We found 65% of these genes to be involved in one-to-one orthology, whereas only 28.7% of the groups with divergent expression had one-to-one orthology. Within the pool of genes with conserved expression, 19 transcription factor families were identified, demonstrating expression conservation of regulators active during leaf growth. Additionally, 25 Arabidopsis and 25 maize putative targets of the TCP transcription factors with conserved expression were determined based on the presence of enriched transcription factor binding sites. Based on large-scale phenotypic data, we observed that genes with conserved expression have a higher probability to be involved in leaf growth and that leaf-related phenotypes are more frequently present for genes having orthologues between dicots and monocots than clade-specific genes. This study shows the power of integrating transcriptomic with orthology data to identify or select candidates for functional studies during leaf development in flowering plants.
Collapse
Affiliation(s)
- Jasmien Vercruysse
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Michiel Van Bel
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Cristina M. Osuna‐Cruz
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Shubhada R. Kulkarni
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Véronique Storme
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Nathalie Gonzalez
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
- INRAUMR1332 Biologie du fruit et PathologieINRA Bordeaux AquitaineVillenave d'Ornon CedexFrance
| | - Dirk Inzé
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| |
Collapse
|
22
|
Ćosić T, Raspor M, Savić J, Cingel A, Matekalo D, Zdravković-Korać S, Ninković S. Expression profiles of organogenesis-related genes over the time course of one-step de novo shoot organogenesis from intact seedlings of kohlrabi. JOURNAL OF PLANT PHYSIOLOGY 2019; 232:257-269. [PMID: 30537612 DOI: 10.1016/j.jplph.2018.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/30/2018] [Accepted: 11/02/2018] [Indexed: 06/09/2023]
Abstract
Kohlrabi (Brassica oleracea var. gongylodes) is an important vegetable crop that is able to undergo shoot regeneration in culture from intact seedlings in a single-step regeneration process, using cytokinin as the only plant growth regulator. In this work, we present the expression profiles of seven organogenesis-related genes over the time course of shoot regeneration from intact seedlings of kohlrabi cv. Vienna Purple on shoot regeneration media containing trans-zeatin, cis-zeatin, benzyl adenine or thidiazuron. Two auxin transporter genes - PIN3 and PIN4, a cytokinin response regulator - ARR5, two shoot apical meristem-related transcription factors - CUC1 and RGD3, and two cell cycle-related genes - CDKB2;1 and CYCB2;4 - displayed bimodal expression patterns on most cytokinin-containing media when their expression levels were normalized against control plants grown on hormone-free media. The first expression peak corresponded to direct upregulation by cytokinin from the growth media, and the second one reflected transcriptional events related to callus formation and/or acquisition of organogenic competence, corresponding to the shoot regeneration phases that have already been characterized in Arabidopsis thaliana. We demonstrate that the genes involved in the two-step shoot regeneration of Arabidopsis display their expected expression profiles during the single-step shoot regeneration of its close phylogenetic relative kohlrabi confirming the universality of their roles in the distinct phases of the regeneration process in Brassicaceae. The results presented here represent a first step towards genetic characterization of the morphogenetic processes in this important crop species.
Collapse
Affiliation(s)
- Tatjana Ćosić
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia.
| | - Martin Raspor
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia
| | - Jelena Savić
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia
| | - Aleksandar Cingel
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia
| | - Dragana Matekalo
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia
| | - Snežana Zdravković-Korać
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia
| | - Slavica Ninković
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia
| |
Collapse
|
23
|
Nisa MU, Huang Y, Benhamed M, Raynaud C. The Plant DNA Damage Response: Signaling Pathways Leading to Growth Inhibition and Putative Role in Response to Stress Conditions. FRONTIERS IN PLANT SCIENCE 2019; 10:653. [PMID: 31164899 PMCID: PMC6534066 DOI: 10.3389/fpls.2019.00653] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/30/2019] [Indexed: 05/02/2023]
Abstract
Maintenance of genome integrity is a key issue for all living organisms. Cells are constantly exposed to DNA damage due to replication or transcription, cellular metabolic activities leading to the production of Reactive Oxygen Species (ROS) or even exposure to DNA damaging agents such as UV light. However, genomes remain extremely stable, thanks to the permanent repair of DNA lesions. One key mechanism contributing to genome stability is the DNA Damage Response (DDR) that activates DNA repair pathways, and in the case of proliferating cells, stops cell division until DNA repair is complete. The signaling mechanisms of the DDR are quite well conserved between organisms including in plants where they have been investigated into detail over the past 20 years. In this review we summarize the acquired knowledge and recent advances regarding the DDR control of cell cycle progression. Studying the plant DDR is particularly interesting because of their mode of development and lifestyle. Indeed, plants develop largely post-embryonically, and form new organs through the activity of meristems in which cells retain the ability to proliferate. In addition, they are sessile organisms that are permanently exposed to adverse conditions that could potentially induce DNA damage in all cell types including meristems. In the second part of the review we discuss the recent findings connecting the plant DDR to responses to biotic and abiotic stresses.
Collapse
|
24
|
Umen JG. Sizing up the cell cycle: systems and quantitative approaches in Chlamydomonas. CURRENT OPINION IN PLANT BIOLOGY 2018; 46:96-103. [PMID: 30212737 PMCID: PMC6269190 DOI: 10.1016/j.pbi.2018.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/14/2018] [Accepted: 08/16/2018] [Indexed: 05/06/2023]
Abstract
The unicellular green alga Chlamydomonas provides a simplified model for defining core cell cycle functions conserved in the green lineage and for understanding multiple fission, a common cell cycle variation found in many algae. Systems-level approaches including a recent groundbreaking screen for conditional lethal cell cycle mutants and genome-wide transcriptome analyses are revealing the complex relationships among cell cycle regulators and helping define roles for CDKA/CDK1 and CDKB, the latter of which is unique to the green lineage and plays a central role in mitotic regulation. Genetic screens and quantitative single-cell analyses have provided insight into cell-size control during multiple fission including the identification of a candidate `sizer' protein. Quantitative single-cell tracking and modeling are promising approaches for gaining additional insight into regulation of cellular and subcellular scaling during the Chlamydomonas cell cycle.
Collapse
Affiliation(s)
- James G Umen
- Donald Danforth Plant Science Center, 975 N. Warson Rd., St. Louis, MO 63132, USA.
| |
Collapse
|
25
|
Wang W, Su X, Tian Z, Liu Y, Zhou Y, He M. Transcriptome profiling provides insights into dormancy release during cold storage of Lilium pumilum. BMC Genomics 2018; 19:196. [PMID: 29703130 PMCID: PMC6389108 DOI: 10.1186/s12864-018-4536-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 02/06/2018] [Indexed: 12/31/2022] Open
Abstract
Background Bulbs of the ornamental flower Lilium pumilum enter a period of dormancy after flowering in spring, and require exposure to cold for a period of time in order to release dormancy. Previous studies focused mainly on anatomical, physiological and biochemical changes during dormancy release. There are no dormancy studies of the northern cold-hardy wild species of Lilium at the molecular level. This study observed bulb cell and starch granule ultrastructures during cold storage; and analysed the transcriptome using sequencing. The combination of morphological and transcriptomic methods provides valuable insights into dormancy release during cold storage of Lilium pumilum. Results Ultrastructural changes reflected dormancy release during cold storage of the bulbs. We compared gene expression levels among samples at 0 (S1 stage), 30 (S2 stage), 60 (S3 stage) and 90 (S4 stage) d of cold storage, with 0 d as the control. The data showed that some regulatory pathways such as carbohydrate metabolism and plant hormone signal transduction were activated to break dormancy. Some differentially expressed genes (DEGs) related to antioxidant activity, epigenetic modification and transcription factors were induced to respond to low temperature conditions. These genes constituted a complex regulatory mechanism of dormancy release. Conclusions Cytological data related to dormancy regulation was obtained through histomorphological observation; transcriptome sequencing provided comprehensive sequences and digital gene expression tag profiling (DGE) data, and bulb cell ultrastructural changes were closely related to DEGs. The novel Lilium pumilum genetic information from this study provides a reference for the regulation of dormancy by genetic engineering using molecular biology tools. Electronic supplementary material The online version of this article (10.1186/s12864-018-4536-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Wang Wang
- Northeast Forestry University, Harbin, China
| | - Xiaoxia Su
- Northeast Forestry University, Harbin, China
| | | | - Yu Liu
- Northeast Forestry University, Harbin, China
| | - Yunwei Zhou
- Northeast Forestry University, Harbin, China.
| | - Miao He
- Northeast Forestry University, Harbin, China.
| |
Collapse
|
26
|
Gao S, Gao Y, Xiong C, Yu G, Chang J, Yang Q, Yang C, Ye Z. The tomato B-type cyclin gene, SlCycB2, plays key roles in reproductive organ development, trichome initiation, terpenoids biosynthesis and Prodenia litura defense. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 262:103-114. [PMID: 28716406 DOI: 10.1016/j.plantsci.2017.05.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 05/08/2017] [Accepted: 05/11/2017] [Indexed: 05/10/2023]
Abstract
Cyclins exist extensively in various plant species. Among them, B-type cyclins play important roles in the transition of G2-to-M. However, few B-type cyclins have been reported to participate in reproductive organ development and trichome formation. In this study, transgene analysis showed that SlCycB2 overexpression caused abnormal flower with the unclosed stamen, shortened style and aberrant pollen. In addition, nearly all non-glandular trichomes, as well as the glandular ones were disappeared. On the contrary, suppression of SlCycB2 could promote type III and type V trichomes formation. Detection of secondary metabolites indicated that the production of monoterpene and sesquiterpene were significantly decreased in SlCycB2-OE plants, which thus resulted in the reduction of the defense against Prodenia litura. Transcriptome profile demonstrated that the differentially expressed genes mainly participate in the biosynthesis of terpenes, cutin, suberine and wax. Furthermore, we identified several homologs of SlCycB2, SlCycB3, NtCycB2, AtCycB2, which have similar regulatory functions in trichome formation. These results indicate that SlCycB2 plays a critical role in reproductive organ development, multicellular trichome initiation, secondary metabolite biosynthesis and Prodenia litura defense in tomato. The similar roles of its homologs in multicellular trichome formation suggest that Solanaceous species may share common regulatory pathway.
Collapse
Affiliation(s)
- Shenghua Gao
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yanna Gao
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Cheng Xiong
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Gang Yu
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Jiang Chang
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Qihong Yang
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Changxian Yang
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| |
Collapse
|
27
|
Wildermuth MC, Steinwand MA, McRae AG, Jaenisch J, Chandran D. Adapted Biotroph Manipulation of Plant Cell Ploidy. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:537-564. [PMID: 28617655 DOI: 10.1146/annurev-phyto-080516-035458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Diverse plant biotrophs that establish a sustained site of nutrient acquisition induce localized host endoreduplication. Endoreduplication is a process by which cells successively replicate their genomes without mitosis, resulting in an increase in nuclear DNA ploidy. Elevated ploidy is associated with enhanced cell size, metabolic capacity, and the capacity to differentiate. Localized host endoreduplication induced by adapted plant biotrophs promotes biotroph colonization, development, and/or proliferation. When induced host endoreduplication is limited, biotroph growth and/or development are compromised. Herein, we examine a diverse set of plant-biotroph interactions to identify (a) common host components manipulated to promote induced host endoreduplication and (b) biotroph effectors that facilitate this induced host process. Shared mechanisms to promote host endoreduplication and development of nutrient exchange/feeding sites include manipulation centered on endocycle entry at the G2-M transition as well as yet undefined roles for differentiation regulators (e.g., CLE peptides) and pectin/cell wall modification.
Collapse
Affiliation(s)
- Mary C Wildermuth
- Department of Plant & Microbial Biology, University of California, Berkeley, California 94720;
| | - Michael A Steinwand
- Department of Plant & Microbial Biology, University of California, Berkeley, California 94720;
| | - Amanda G McRae
- Department of Plant & Microbial Biology, University of California, Berkeley, California 94720;
| | - Johan Jaenisch
- Department of Plant & Microbial Biology, University of California, Berkeley, California 94720;
| | - Divya Chandran
- Regional Center for Biotechnology, NCR Biotech Science Cluster, Faridabad, India 121001
| |
Collapse
|
28
|
Maniga A, Ghisaura S, Perrotta L, Marche MG, Cella R, Albani D. Distinctive features and differential regulation of the DRTS genes of Arabidopsis thaliana. PLoS One 2017; 12:e0179338. [PMID: 28594957 PMCID: PMC5464667 DOI: 10.1371/journal.pone.0179338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/26/2017] [Indexed: 01/16/2023] Open
Abstract
In plants and protists, dihydrofolate reductase (DHFR) and thymidylate synthase (TS) are part of a bifunctional enzyme (DRTS) that allows efficient recycling of the dihydrofolate resulting from TS activity. Arabidopsis thaliana possesses three DRTS genes, called AtDRTS1, AtDRTS2 and AtDRTS3, that are located downstream of three members of the sec14-like SFH gene family. In this study, a characterization of the AtDRTS genes identified alternatively spliced transcripts coding for AtDRTS isoforms which may account for monofunctional DHFR enzymes supporting pathways unrelated to DNA synthesis. Moreover, we discovered a complex differential regulation of the AtDRTS genes that confirms the expected involvement of the AtDRTS genes in cell proliferation and endoreduplication, but indicates also functions related to other cellular activities. AtDRTS1 is widely expressed in both meristematic and differentiated tissues, whereas AtDRTS2 expression is almost exclusively limited to the apical meristems and AtDRTS3 is preferentially expressed in the shoot apex, in stipules and in root cap cells. The differential regulation of the AtDRTS genes is associated to distinctive promoter architectures and the expression of AtDRTS1 in the apical meristems is strictly dependent on the presence of an intragenic region that includes the second intron of the gene. Upon activation of cell proliferation in germinating seeds, the activity of the AtDRTS1 and AtDRTS2 promoters in meristematic cells appears to be maximal at the G1/S phase of the cell cycle. In addition, the promoters of AtDRTS2 and AtDRTS3 are negatively regulated through E2F cis-acting elements and both genes, but not AtDRTS1, are downregulated in plants overexpressing the AtE2Fa factor. Our study provides new information concerning the function and the regulation of plant DRTS genes and opens the way to further investigations addressing the importance of folate synthesis with respect to specific cellular activities.
Collapse
Affiliation(s)
- Antonio Maniga
- Department of Agriculture, University of Sassari, Sassari, Italy
| | - Stefania Ghisaura
- Department of Science for Nature and Environmental Resources, University of Sassari, Sassari, Italy
| | - Lara Perrotta
- Department of Agriculture, University of Sassari, Sassari, Italy
- Department of Science for Nature and Environmental Resources, University of Sassari, Sassari, Italy
| | | | - Rino Cella
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Diego Albani
- Department of Agriculture, University of Sassari, Sassari, Italy
- Center of Excellence for Biotechnology Development and Biodiversity Research, University of Sassari, Sassari, Italy
- * E-mail:
| |
Collapse
|
29
|
Yu J, Xiong H, Zhu X, Zhang H, Li H, Miao J, Wang W, Tang Z, Zhang Z, Yao G, Zhang Q, Pan Y, Wang X, Rashid MAR, Li J, Gao Y, Li Z, Yang W, Fu X, Li Z. OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap. BMC Biol 2017; 15:28. [PMID: 28385155 PMCID: PMC5383996 DOI: 10.1186/s12915-017-0365-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/10/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Most agronomic traits in rice are complex and polygenic. The identification of quantitative trait loci (QTL) for grain length is an important objective of rice genetic research and breeding programs. RESULTS Herein, we identified 99 QTL for grain length by GWAS based on approximately 10 million single nucleotide polymorphisms from 504 cultivated rice accessions (Oryza sativa L.), 13 of which were validated by four linkage populations and 92 were new loci for grain length. We scanned the Ho (observed heterozygosity per locus) index of coupled-parents of crosses mapping the same QTL, based on linkage and association mapping, and identified two new genes for grain length. We named this approach as Ho-LAMap. A simulation study of six known genes showed that Ho-LAMap could mine genes rapidly across a wide range of experimental variables using deep-sequencing data. We used Ho-LAMap to clone a new gene, OsLG3, as a positive regulator of grain length, which could improve rice yield without influencing grain quality. Sequencing of the promoter region in 283 rice accessions from a wide geographic range identified four haplotypes that seem to be associated with grain length. Further analysis showed that OsLG3 alleles in the indica and japonica evolved independently from distinct ancestors and low nucleotide diversity of OsLG3 in indica indicated artificial selection. Phylogenetic analysis showed that OsLG3 might have much potential value for improvement of grain length in japonica breeding. CONCLUSIONS The results demonstrated that Ho-LAMap is a potential approach for gene discovery and OsLG3 is a promising gene to be utilized in genomic assisted breeding for rice cultivar improvement.
Collapse
Affiliation(s)
- Jianping Yu
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Haiyan Xiong
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xiaoyang Zhu
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Hongliang Zhang
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Huihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinli Miao
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Wensheng Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zuoshun Tang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhanying Zhang
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Guoxin Yao
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qiang Zhang
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yinghua Pan
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Xin Wang
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - M A R Rashid
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jinjie Li
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yongming Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weicai Yang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiangdong Fu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zichao Li
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
30
|
Van Hoeck A, Horemans N, Nauts R, Van Hees M, Vandenhove H, Blust R. Lemna minor plants chronically exposed to ionising radiation: RNA-seq analysis indicates a dose rate dependent shift from acclimation to survival strategies. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 257:84-95. [PMID: 28224921 DOI: 10.1016/j.plantsci.2017.01.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/21/2016] [Accepted: 01/17/2017] [Indexed: 05/22/2023]
Abstract
Ecotoxicological research provides knowledge on ionising radiation-induced responses in different plant species. However, the sparse data currently available are mainly extracted from acute exposure treatments. To provide a better understanding of environmental exposure scenarios, the response to stress in plants must be followed in more natural relevant chronic conditions. We previously showed morphological and biochemical responses in Lemna minor plants continuously exposed for 7days in a dose-rate dependent manner. In this study responses on molecular (gene expression) and physiological (photosynthetic) level are evaluated in L. minor plants exposed to ionising radiation. To enable this, we examined the gene expression profiles of irradiated L. minor plants by using an RNA-seq approach. The gene expression data reveal indications that L. minor plants exposed at lower dose rates, can tolerate the exposure by triggering acclimation responses. In contrast, at the highest dose rate tested, a high number of genes related to antioxidative defense systems, DNA repair and cell cycle were differentially expressed suggesting that only high dose rates of ionising radiation drive L. minor plants into survival strategies. Notably, the photosynthetic process seems to be unaffected in L. minor plants among the tested dose rates. This study, supported by our earlier work, clearly indicates that plants shift from acclimation responses towards survival responses at increasing dose rates of ionising radiation.
Collapse
Affiliation(s)
- Arne Van Hoeck
- SCK●CEN, Boeretang, 200 2400, Mol, Belgium; Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium.
| | - Nele Horemans
- SCK●CEN, Boeretang, 200 2400, Mol, Belgium; Centre for Environmental Research, University of Hasselt, Universiteitslaan 1, 3590 Diepenbeek, Belgium.
| | | | | | | | - Ronny Blust
- Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium.
| |
Collapse
|
31
|
Magyar Z, Bögre L, Ito M. DREAMs make plant cells to cycle or to become quiescent. CURRENT OPINION IN PLANT BIOLOGY 2016; 34:100-106. [PMID: 27816815 DOI: 10.1016/j.pbi.2016.10.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/23/2016] [Accepted: 10/07/2016] [Indexed: 05/03/2023]
Abstract
Cell cycle phase specific oscillation of gene transcription has long been recognized as an underlying principle for ordered processes during cell proliferation. The G1/S-specific and G2/M-specific cohorts of genes in plants are regulated by the E2F and the MYB3R transcription factors. Mutant analysis suggests that activator E2F functions might not be fully required for cell cycle entry. In contrast, the two activator-type MYB3Rs are part of positive feedback loops to drive the burst of mitotic gene expression, which is necessary at least to accomplish cytokinesis. Repressor MYB3Rs act outside the mitotic time window during cell cycle progression, and are important for the shutdown of mitotic genes to impose quiescence in mature organs. The two distinct classes of E2Fs and MYB3Rs together with the RETINOBLATOMA RELATED are part of multiprotein complexes that may be evolutionary related to what is known as DREAM complex in animals. In plants, there are multiple such complexes with distinct compositions and functions that may be involved in the coordinated cell cycle and developmental regulation of E2F targets and mitotic genes.
Collapse
Affiliation(s)
- Zoltán Magyar
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - László Bögre
- Royal Holloway, University of London, School of Biological Sciences, Egham, Surrey TW20 0EX, UK
| | - Masaki Ito
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan; JST, CREST, Chikusa, Nagoya 464-8601, Japan.
| |
Collapse
|
32
|
Kobayashi K, Suzuki T, Iwata E, Magyar Z, Bögre L, Ito M. MYB3Rs, plant homologs of Myb oncoproteins, control cell cycle-regulated transcription and form DREAM-like complexes. Transcription 2016; 6:106-11. [PMID: 26556011 DOI: 10.1080/21541264.2015.1109746] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Plant MYB3R transcription factors, homologous to Myb oncoproteins, regulate the genes expressed at G2 and M phases in the cell cycle. Recent studies showed that MYB3Rs constitute multiprotein complexes that may correspond to animal complexes known as DREAM or dREAM. Discovery of the putative homologous complex in plants uncovered their significant varieties in structure, function, dynamics, and heterogeneity, providing insight into conserved and diversified aspects of cell cycle-regulated gene transcription.
Collapse
Affiliation(s)
- Kosuke Kobayashi
- a Graduate School of Bioagricultural Sciences; Nagoya University ; Chikusa , Nagoya , Japan
| | - Toshiya Suzuki
- a Graduate School of Bioagricultural Sciences; Nagoya University ; Chikusa , Nagoya , Japan.,b JST; CREST ; Chikusa , Nagoya , Japan
| | - Eriko Iwata
- a Graduate School of Bioagricultural Sciences; Nagoya University ; Chikusa , Nagoya , Japan
| | - Zoltán Magyar
- c Institute of Plant Biology; Biological Research Centre ; Szeged , Hungary.,d Royal Holloway; University of London; School of Biological Sciences ; Egham , Surrey , UK
| | - László Bögre
- d Royal Holloway; University of London; School of Biological Sciences ; Egham , Surrey , UK
| | - Masaki Ito
- a Graduate School of Bioagricultural Sciences; Nagoya University ; Chikusa , Nagoya , Japan.,b JST; CREST ; Chikusa , Nagoya , Japan
| |
Collapse
|
33
|
A phloem-limited fijivirus induces the formation of neoplastic phloem tissues that house virus multiplication in the host plant. Sci Rep 2016; 6:29848. [PMID: 27432466 PMCID: PMC4949464 DOI: 10.1038/srep29848] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 06/24/2016] [Indexed: 11/26/2022] Open
Abstract
A number of phloem-limited viruses induce the development of tumours (enations) in the veins of host plants, but the relevance of tumour induction to the life cycle of those viruses is unclear. In this study, we performed molecular and structural analyses of tumours induced by rice black-streaked dwarf virus (RBSDV, genus Fijivirus) infection in maize plants. The transcript level of the maize cdc2 gene, which regulates the cell cycle, was highly elevated in tumour tissues. Two-dimensional electrophoresis identified 25 cellular proteins with altered accumulation in the tumour tissues. These proteins are involved in various metabolic pathways, including photosynthesis, redox, energy pathways and amino acid synthesis. Histological analysis indicated that the tumours predominantly originated from hyperplastic growth of phloem, but those neoplastic tissues have irregular structures and cell arrangements. Immunodetection assays and electron microscopy observations indicated that in the shoots, RBSDV is confined to phloem and tumour regions and that virus multiplication actively occurs in the tumour tissue, as indicated by the high accumulation of non-structural proteins and formation of viroplasms in the tumour cells. Thus, the induction of tumours by RBSDV infection provides a larger environment that is favourable for virus propagation in the host plant.
Collapse
|
34
|
Ercoli MF, Rojas AML, Debernardi JM, Palatnik JF, Rodriguez RE. Control of cell proliferation and elongation by miR396. PLANT SIGNALING & BEHAVIOR 2016; 11:e1184809. [PMID: 27172373 PMCID: PMC4973763 DOI: 10.1080/15592324.2016.1184809] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The combinatory effects of cell proliferation and cell elongation determines the rate at which organs growth. In the root meristematic zone cells both divide and expand, while post-mitotic cells in the elongation zone only expands until they reach their final size. The transcription factors of the GROWTH-REGULATING FACTOR (GRF) class promote cell proliferation in various plant organs. Their expression is restricted to cells with a high proliferative capacity, yet strong downregulation of the GRF activity compromise the plant survival. Part of expression pattern of the GRFs is ensured by the post-transcriptional repression mediated by the conserved microRNA miR396. Here we show the quantitative effects in root growth caused by GRF depletion in a series of transgenic lines with different miR396 levels. We show that high miRNA levels affect cell elongation and proliferation in roots. Detailed analysis suggests that cell proliferation is restricted due to a reduction in cell cycle speed that might result from defects in the accumulation of mitotic cyclins. The results provide insights into the participation of the miRNA-GRF regulatory network in root development.
Collapse
Affiliation(s)
- María Florencia Ercoli
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Arantxa M. L. Rojas
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Juan Manuel Debernardi
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Javier F. Palatnik
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Ramiro E. Rodriguez
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- CONTACT Ramiro E. Rodriguez,
| |
Collapse
|
35
|
Haim Y, Blüher M, Slutsky N, Goldstein N, Klöting N, Harman-Boehm I, Kirshtein B, Ginsberg D, Gericke M, Guiu Jurado E, Kovsan J, Tarnovscki T, Kachko L, Bashan N, Gepner Y, Shai I, Rudich A. Elevated autophagy gene expression in adipose tissue of obese humans: A potential non-cell-cycle-dependent function of E2F1. Autophagy 2015; 11:2074-2088. [PMID: 26391754 PMCID: PMC4824599 DOI: 10.1080/15548627.2015.1094597] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Autophagy genes' expression is upregulated in visceral fat in human obesity, associating with obesity-related cardio-metabolic risk. E2F1 (E2F transcription factor 1) was shown in cancer cells to transcriptionally regulate autophagy. We hypothesize that E2F1 regulates adipocyte autophagy in obesity, associating with endocrine/metabolic dysfunction, thereby, representing non-cell-cycle function of this transcription factor. E2F1 protein (N=69) and mRNA (N=437) were elevated in visceral fat of obese humans, correlating with increased expression of ATG5 (autophagy-related 5), MAP1LC3B/LC3B (microtubule-associated protein 1 light chain 3 β), but not with proliferation/cell-cycle markers. Elevated E2F1 mainly characterized the adipocyte fraction, whereas MKI67 (marker of proliferation Ki-67) was elevated in the stromal-vascular fraction of adipose tissue. In human visceral fat explants, chromatin-immunoprecipitation revealed body mass index (BMI)-correlated increase in E2F1 binding to the promoter of MAP1LC3B, but not to the classical cell cycle E2F1 target, CCND1 (cyclin D1). Clinically, omental fat E2F1 expression correlated with insulin resistance, circulating free-fatty-acids (FFA), and with decreased circulating ADIPOQ/adiponectin, associations attenuated by adjustment for autophagy genes. Overexpression of E2F1 in HEK293 cells enhanced promoter activity of several autophagy genes and autophagic flux, and sensitized to further activation of autophagy by TNF. Conversely, mouse embryonic fibroblast (MEF)-derived adipocytes from e2f1 knockout mice (e2f1−/−) exhibited lower autophagy gene expression and flux, were more insulin sensitive, and secreted more ADIPOQ. Furthermore, e2f1−/− MEF-derived adipocytes, and autophagy-deficient (by Atg7 siRNA) adipocytes were resistant to cytokines-induced decrease in ADIPOQ secretion. Jointly, upregulated E2F1 sensitizes adipose tissue autophagy to inflammatory stimuli, linking visceral obesity to adipose and systemic metabolic-endocrine dysfunction.
Collapse
Affiliation(s)
- Yulia Haim
- a Department of Clinical Biochemistry and Pharmacology ; Faculty of Health Sciences; Ben-Gurion University of the Negev ; Beer-Sheva , Israel
| | - Matthias Blüher
- b Department of Medicine ; University of Leipzig ; Leipzig , Germany
| | - Noa Slutsky
- a Department of Clinical Biochemistry and Pharmacology ; Faculty of Health Sciences; Ben-Gurion University of the Negev ; Beer-Sheva , Israel
| | - Nir Goldstein
- a Department of Clinical Biochemistry and Pharmacology ; Faculty of Health Sciences; Ben-Gurion University of the Negev ; Beer-Sheva , Israel
| | - Nora Klöting
- b Department of Medicine ; University of Leipzig ; Leipzig , Germany
| | - Ilana Harman-Boehm
- c Soroka Academic Medical Center and Faculty of Health Sciences; Ben-Gurion University of the Negev ; Beer-Sheva , Israel
| | - Boris Kirshtein
- c Soroka Academic Medical Center and Faculty of Health Sciences; Ben-Gurion University of the Negev ; Beer-Sheva , Israel
| | - Doron Ginsberg
- d The Mina and Everard Goodman Faculty of Life Science; Bar-Ilan University ; Ramat Gan , Israel
| | - Martin Gericke
- e Institute of Anatomy; University of Leipzig ; Leipzig , Germany
| | | | - Julia Kovsan
- a Department of Clinical Biochemistry and Pharmacology ; Faculty of Health Sciences; Ben-Gurion University of the Negev ; Beer-Sheva , Israel
| | - Tanya Tarnovscki
- a Department of Clinical Biochemistry and Pharmacology ; Faculty of Health Sciences; Ben-Gurion University of the Negev ; Beer-Sheva , Israel
| | - Leonid Kachko
- c Soroka Academic Medical Center and Faculty of Health Sciences; Ben-Gurion University of the Negev ; Beer-Sheva , Israel
| | - Nava Bashan
- a Department of Clinical Biochemistry and Pharmacology ; Faculty of Health Sciences; Ben-Gurion University of the Negev ; Beer-Sheva , Israel
| | - Yiftach Gepner
- f Department of Epidemiology ; Ben-Gurion University of the Negev ; Beer-Sheva , Israel
| | - Iris Shai
- f Department of Epidemiology ; Ben-Gurion University of the Negev ; Beer-Sheva , Israel
| | - Assaf Rudich
- a Department of Clinical Biochemistry and Pharmacology ; Faculty of Health Sciences; Ben-Gurion University of the Negev ; Beer-Sheva , Israel.,g National Institute of Biotechnology in the Negev; Ben-Gurion University of the Negev ; Beer-Sheva , Israel
| |
Collapse
|
36
|
Analysis of the DNA-Binding Activities of the Arabidopsis R2R3-MYB Transcription Factor Family by One-Hybrid Experiments in Yeast. PLoS One 2015; 10:e0141044. [PMID: 26484765 PMCID: PMC4613820 DOI: 10.1371/journal.pone.0141044] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/02/2015] [Indexed: 12/20/2022] Open
Abstract
The control of growth and development of all living organisms is a complex and dynamic process that requires the harmonious expression of numerous genes. Gene expression is mainly controlled by the activity of sequence-specific DNA binding proteins called transcription factors (TFs). Amongst the various classes of eukaryotic TFs, the MYB superfamily is one of the largest and most diverse, and it has considerably expanded in the plant kingdom. R2R3-MYBs have been extensively studied over the last 15 years. However, DNA-binding specificity has been characterized for only a small subset of these proteins. Therefore, one of the remaining challenges is the exhaustive characterization of the DNA-binding specificity of all R2R3-MYB proteins. In this study, we have developed a library of Arabidopsis thaliana R2R3-MYB open reading frames, whose DNA-binding activities were assayed in vivo (yeast one-hybrid experiments) with a pool of selected cis-regulatory elements. Altogether 1904 interactions were assayed leading to the discovery of specific patterns of interactions between the various R2R3-MYB subgroups and their DNA target sequences and to the identification of key features that govern these interactions. The present work provides a comprehensive in vivo analysis of R2R3-MYB binding activities that should help in predicting new DNA motifs and identifying new putative target genes for each member of this very large family of TFs. In a broader perspective, the generated data will help to better understand how TF interact with their target DNA sequences.
Collapse
|
37
|
Ortiz-Gutiérrez E, García-Cruz K, Azpeitia E, Castillo A, Sánchez MDLP, Álvarez-Buylla ER. A Dynamic Gene Regulatory Network Model That Recovers the Cyclic Behavior of Arabidopsis thaliana Cell Cycle. PLoS Comput Biol 2015; 11:e1004486. [PMID: 26340681 PMCID: PMC4560428 DOI: 10.1371/journal.pcbi.1004486] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 08/03/2015] [Indexed: 01/02/2023] Open
Abstract
Cell cycle control is fundamental in eukaryotic development. Several modeling efforts have been used to integrate the complex network of interacting molecular components involved in cell cycle dynamics. In this paper, we aimed at recovering the regulatory logic upstream of previously known components of cell cycle control, with the aim of understanding the mechanisms underlying the emergence of the cyclic behavior of such components. We focus on Arabidopsis thaliana, but given that many components of cell cycle regulation are conserved among eukaryotes, when experimental data for this system was not available, we considered experimental results from yeast and animal systems. We are proposing a Boolean gene regulatory network (GRN) that converges into only one robust limit cycle attractor that closely resembles the cyclic behavior of the key cell-cycle molecular components and other regulators considered here. We validate the model by comparing our in silico configurations with data from loss- and gain-of-function mutants, where the endocyclic behavior also was recovered. Additionally, we approximate a continuous model and recovered the temporal periodic expression profiles of the cell-cycle molecular components involved, thus suggesting that the single limit cycle attractor recovered with the Boolean model is not an artifact of its discrete and synchronous nature, but rather an emergent consequence of the inherent characteristics of the regulatory logic proposed here. This dynamical model, hence provides a novel theoretical framework to address cell cycle regulation in plants, and it can also be used to propose novel predictions regarding cell cycle regulation in other eukaryotes. In multicellular organisms, cells undergo a cyclic behavior of DNA duplication and delivery of a copy to daughter cells during cell division. In each of the main cell-cycle (CC) stages different sets of proteins are active and genes are expressed. Understanding how such cycling cellular behavior emerges and is robustly maintained in the face of changing developmental and environmental conditions, remains a fundamental challenge of biology. The molecular components that cycle through DNA duplication and citokinesis are interconnected in a complex regulatory network. Several models of such network have been proposed, although the regulatory network that robustly recovers a limit-cycle steady state that resembles the behavior of CC molecular components has been recovered only in a few cases, and no comprehensive model exists for plants. In this paper we used the plant Arabidopsis thaliana, as a study system to propose a core regulatory network to recover a cyclic attractor that mimics the oscillatory behavior of the key CC components. Our analyses show that the proposed GRN model is robust to transient alterations, and is validated with the loss- and gain-of-function mutants of the CC components. The interactions proposed for Arabidopsis thaliana CC can inspire predictions for further uncovering regulatory motifs in the CC of other organisms including human.
Collapse
Affiliation(s)
- Elizabeth Ortiz-Gutiérrez
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Junto a Jardín Botánico Exterior, México, D.F. CP 04510, México; Centro de Ciencias de la Complejidad-C3, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70-275, México, D.F. 04510, México
| | - Karla García-Cruz
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Junto a Jardín Botánico Exterior, México, D.F. CP 04510, México
| | - Eugenio Azpeitia
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Junto a Jardín Botánico Exterior, México, D.F. CP 04510, México; Centro de Ciencias de la Complejidad-C3, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70-275, México, D.F. 04510, México
| | - Aaron Castillo
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Junto a Jardín Botánico Exterior, México, D.F. CP 04510, México; Centro de Ciencias de la Complejidad-C3, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70-275, México, D.F. 04510, México
| | - María de la Paz Sánchez
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Junto a Jardín Botánico Exterior, México, D.F. CP 04510, México
| | - Elena R Álvarez-Buylla
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Junto a Jardín Botánico Exterior, México, D.F. CP 04510, México; Centro de Ciencias de la Complejidad-C3, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70-275, México, D.F. 04510, México
| |
Collapse
|
38
|
Spatial Regulation of Root Growth: Placing the Plant TOR Pathway in a Developmental Perspective. Int J Mol Sci 2015; 16:19671-97. [PMID: 26295391 PMCID: PMC4581319 DOI: 10.3390/ijms160819671] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 07/11/2015] [Accepted: 08/11/2015] [Indexed: 12/30/2022] Open
Abstract
Plant cells contain specialized structures, such as a cell wall and a large vacuole, which play a major role in cell growth. Roots follow an organized pattern of development, making them the organs of choice for studying the spatio-temporal regulation of cell proliferation and growth in plants. During root growth, cells originate from the initials surrounding the quiescent center, proliferate in the division zone of the meristem, and then increase in length in the elongation zone, reaching their final size and differentiation stage in the mature zone. Phytohormones, especially auxins and cytokinins, control the dynamic balance between cell division and differentiation and therefore organ size. Plant growth is also regulated by metabolites and nutrients, such as the sugars produced by photosynthesis or nitrate assimilated from the soil. Recent literature has shown that the conserved eukaryotic TOR (target of rapamycin) kinase pathway plays an important role in orchestrating plant growth. We will summarize how the regulation of cell proliferation and cell expansion by phytohormones are at the heart of root growth and then discuss recent data indicating that the TOR pathway integrates hormonal and nutritive signals to orchestrate root growth.
Collapse
|
39
|
Kobayashi K, Suzuki T, Iwata E, Nakamichi N, Suzuki T, Chen P, Ohtani M, Ishida T, Hosoya H, Müller S, Leviczky T, Pettkó-Szandtner A, Darula Z, Iwamoto A, Nomoto M, Tada Y, Higashiyama T, Demura T, Doonan JH, Hauser MT, Sugimoto K, Umeda M, Magyar Z, Bögre L, Ito M. Transcriptional repression by MYB3R proteins regulates plant organ growth. EMBO J 2015; 34:1992-2007. [PMID: 26069325 DOI: 10.15252/embj.201490899] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 05/12/2015] [Indexed: 11/09/2022] Open
Abstract
In multicellular organisms, temporal and spatial regulation of cell proliferation is central for generating organs with defined sizes and morphologies. For establishing and maintaining the post-mitotic quiescent state during cell differentiation, it is important to repress genes with mitotic functions. We found that three of the Arabidopsis MYB3R transcription factors synergistically maintain G2/M-specific genes repressed in post-mitotic cells and restrict the time window of mitotic gene expression in proliferating cells. The combined mutants of the three repressor-type MYB3R genes displayed long roots, enlarged leaves, embryos, and seeds. Genome-wide chromatin immunoprecipitation revealed that MYB3R3 binds to the promoters of G2/M-specific genes and to E2F target genes. MYB3R3 associates with the repressor-type E2F, E2FC, and the RETINOBLASTOMA RELATED proteins. In contrast, the activator MYB3R4 was in complex with E2FB in proliferating cells. With mass spectrometry and pairwise interaction assays, we identified some of the other conserved components of the multiprotein complexes, known as DREAM/dREAM in human and flies. In plants, these repressor complexes are important for periodic expression during cell cycle and to establish a post-mitotic quiescent state determining organ size.
Collapse
Affiliation(s)
- Kosuke Kobayashi
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan
| | - Toshiya Suzuki
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan JST, CREST, Chikusa, Nagoya, Japan
| | - Eriko Iwata
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan
| | - Norihito Nakamichi
- WPI Institute of Transformative Bio-Molecules, Nagoya University, Chikusa, Nagoya, Japan Graduate School of Sciences, Nagoya University, Chikusa, Nagoya, Japan
| | - Takamasa Suzuki
- Graduate School of Sciences, Nagoya University, Chikusa, Nagoya, Japan JST ERATO Higashiyama Live-Holonics Project, Nagoya University, Chikusa, Nagoya, Japan
| | - Poyu Chen
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Misato Ohtani
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Takashi Ishida
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Hanako Hosoya
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Sabine Müller
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Tünde Leviczky
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | | | - Zsuzsanna Darula
- Laboratory of Proteomic Research, Biological Research Centre, Szeged, Hungary
| | - Akitoshi Iwamoto
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Mika Nomoto
- Graduate School of Sciences, Nagoya University, Chikusa, Nagoya, Japan
| | - Yasuomi Tada
- Center for Gene Research, Division of Biological Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Tetsuya Higashiyama
- WPI Institute of Transformative Bio-Molecules, Nagoya University, Chikusa, Nagoya, Japan Graduate School of Sciences, Nagoya University, Chikusa, Nagoya, Japan JST ERATO Higashiyama Live-Holonics Project, Nagoya University, Chikusa, Nagoya, Japan
| | - Taku Demura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - John H Doonan
- The National Plant Phenomics Centre, Aberystwyth University, Aberystwyth, UK
| | - Marie-Theres Hauser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Masaaki Umeda
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan JST, CREST, Ikoma, Nara, Japan
| | - Zoltán Magyar
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary Royal Holloway, School of Biological Sciences, University of London, Egham, Surrey, UK
| | - László Bögre
- Royal Holloway, School of Biological Sciences, University of London, Egham, Surrey, UK
| | - Masaki Ito
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan JST, CREST, Chikusa, Nagoya, Japan
| |
Collapse
|
40
|
Hermann K, Klahre U, Venail J, Brandenburg A, Kuhlemeier C. The genetics of reproductive organ morphology in two Petunia species with contrasting pollination syndromes. PLANTA 2015; 241:1241-1254. [PMID: 25656052 DOI: 10.1007/s00425-015-2251-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 01/19/2015] [Indexed: 05/29/2023]
Abstract
Switches between pollination syndromes have happened frequently during angiosperm evolution. Using QTL mapping and reciprocal introgressions, we show that changes in reproductive organ morphology have a simple genetic basis. In animal-pollinated plants, flowers have evolved to optimize pollination efficiency by different pollinator guilds and hence reproductive success. The two Petunia species, P. axillaris and P. exserta, display pollination syndromes adapted to moth or hummingbird pollination. For the floral traits color and scent, genetic loci of large phenotypic effect have been well documented. However, such large-effect loci may be typical for shifts in simple biochemical traits, whereas the evolution of morphological traits may involve multiple mutations of small phenotypic effect. Here, we performed a quantitative trait locus (QTL) analysis of floral morphology, followed by an in-depth study of pistil and stamen morphology and the introgression of individual QTL into reciprocal parental backgrounds. Two QTLs, on chromosomes II and V, are sufficient to explain the interspecific difference in pistil and stamen length. Since most of the difference in organ length is caused by differences in cell number, genes underlying these QTLs are likely to be involved in cell cycle regulation. Interestingly, conservation of the locus on chromosome II in a different P. axillaris subspecies suggests that the evolution of organ elongation was initiated on chromosome II in adaptation to different pollinators. We recently showed that QTLs for pistil and stamen length on chromosome II are tightly linked to QTLs for petal color and volatile emission. Linkage of multiple traits will enable major phenotypic change within a few generations in hybridizing populations. Thus, the genomic architecture of pollination syndromes in Petunia allows for rapid responses to changing pollinator availability.
Collapse
Affiliation(s)
- Katrin Hermann
- Institute of Plant Sciences, Altenbergrain 21, 3013, Bern, Switzerland
| | | | | | | | | |
Collapse
|
41
|
Guo J, Liu H, He Y, Cui X, Du X, Zhu J. Origination of asexual plantlets in three species of Crassulaceae. PROTOPLASMA 2015; 252:591-603. [PMID: 25252887 DOI: 10.1007/s00709-014-0704-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 09/12/2014] [Indexed: 05/20/2023]
Abstract
During asexual plant reproduction, cells from different organs can be reprogrammed to produce new individuals, a process that requires the coordination of cell cycle reactivation with the acquisition of other cellular morphological characteristics. However, the factors that influence the variety of asexual reproduction have not yet been determined. Here, we report on plantlet formation in Kalanchoe daigremontiana, Graptopetalum paraguayense, and Crassula portulacea (Crassulaceae) and analyse the effect of initiating cells on asexual reproduction in these three species. Additionally, the roles of WUSCHEL (WUS) and CUP-SHAPED COTYLEDON 1 (CUC1) in the asexual reproduction of these species were analysed through qRT-PCR. Our results indicated that pre-existing stem cell-like cells at the sites of asexual reproduction were responsible for the formation of plantlets. These cells were arrested in different phases of the cell cycle and showed different cell morphological characteristics and cell counts. The accumulation of auxin and cytokinin at the sites of asexual plantlet formation indicated their important functions, particularly for cell cycle reactivation. These differences may influence the pattern and complexity of asexual reproduction in these Crassulaceae species. Additionally, the dynamic expression levels of CUC1 and WUS may indicate that CUC1 functions in the formation of callus and shoot meristems; whereas, WUS was only associated with shoot induction.
Collapse
Affiliation(s)
- Jiansheng Guo
- Department of Molecular and Cell Biology, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | | | | | | | | | | |
Collapse
|
42
|
Chandran D, Rickert J, Huang Y, Steinwand MA, Marr SK, Wildermuth MC. Atypical E2F transcriptional repressor DEL1 acts at the intersection of plant growth and immunity by controlling the hormone salicylic acid. Cell Host Microbe 2015; 15:506-13. [PMID: 24721578 DOI: 10.1016/j.chom.2014.03.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 11/27/2013] [Accepted: 03/10/2014] [Indexed: 12/11/2022]
Abstract
In plants, the activation of immunity is often inversely correlated with growth. Mechanisms that control plant growth in the context of pathogen challenge and immunity are unclear. Investigating Arabidopsis infection with the powdery mildew fungus, we find that the Arabidopsis atypical E2F DEL1, a transcriptional repressor known to promote cell proliferation, represses accumulation of the hormone salicylic acid (SA), an established regulator of plant immunity. DEL1-deficient plants are more resistant to pathogens and slightly smaller than wild-type. The resistance and size phenotypes of DEL1-deficient plants are due to the induction of SA and activation of immunity in the absence of pathogen challenge. Moreover, Enhanced Disease Susceptibility 5 (EDS5), a SA transporter required for elevated SA and immunity, is a direct repressed target of DEL1. Together, these findings indicate that DEL1 control of SA levels contributes to regulating the balance between growth and immunity in developing leaves.
Collapse
Affiliation(s)
- Divya Chandran
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
| | - Joshua Rickert
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
| | - Yingxiang Huang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
| | - Michael A Steinwand
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
| | - Sharon K Marr
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
| | - Mary C Wildermuth
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA.
| |
Collapse
|
43
|
Cai H, Tian S, Dong H, Guo C. Pleiotropic effects of TaMYB3R1 on plant development and response to osmotic stress in transgenic Arabidopsis. Gene 2015; 558:227-34. [PMID: 25560188 DOI: 10.1016/j.gene.2014.12.066] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 11/02/2014] [Accepted: 12/29/2014] [Indexed: 11/25/2022]
Abstract
In a previous study, we isolated and characterized TaMYB3R1, a MYB3R gene, from wheat (Triticum aestivum L.). In vitro assays showed that the TaMYB3R1 protein is localized to the nucleus, and functions as an MSA-binding transcriptional activator. Expression of TaMYB3R1 is induced by exogenous abscisic acid (ABA) and abiotic stress, which encouraged us to further investigate its function in planta. In the present study, we generated transgenic Arabidopsis plants overexpressing TaMYB3R1. Compared with wild-type plants, the transgenic lines produced more rosette leaves, and thus more inflorescences, but the plants showed delayed development at the reproductive stage. The TaMYB3R1 protein also functions in the osmotic stress response. Transgenic Arabidopsis plants showed enhanced tolerance to drought and salt stresses, and the tolerance phenotype was conveyed by limiting transpiration through increasing stomatal closure as well as reducing water loss. In addition, TaMYB3R1 influenced the expression of both ABA-dependent and ABA-independent responsive genes, implicating TaMYB3R1 in diverse osmotic stress-response mechanisms in Arabidopsis. Our study sheds light on novel functions of a plant MYB3R protein.
Collapse
Affiliation(s)
- Hongsheng Cai
- Key Laboratory of Molecular and Cytogenetics of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Shan Tian
- Ministry of Agriculture of PR China Key Laboratory of Monitoring and Management of Crop Pathogens and Insect Pests, Nanjing Agricultural University, Nanjing 210095, China
| | - Hansong Dong
- Ministry of Agriculture of PR China Key Laboratory of Monitoring and Management of Crop Pathogens and Insect Pests, Nanjing Agricultural University, Nanjing 210095, China.
| | - Changhong Guo
- Key Laboratory of Molecular and Cytogenetics of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China.
| |
Collapse
|
44
|
Kyo M, Nagano A, Yamaji N, Hashimoto Y. Timing of the G1/S transition in tobacco pollen vegetative cells as a primary step towards androgenesis in vitro. PLANT CELL REPORTS 2014; 33:1595-606. [PMID: 24917172 DOI: 10.1007/s00299-014-1640-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 05/27/2014] [Indexed: 06/03/2023]
Abstract
KEY MESSAGE Mid-bicellular pollen vegetative cells in tobacco escape from G1 arrest and proceed to the G1/S transition towards androgenesis within 1 day under glutamine starvation conditions in vitro. In the Nicotiana tabacum pollen culture system, immature pollen grains at the mid-bicellular stage can mature in the presence of glutamine; however, if glutamine is absent, they deviate from their native cell fate in a few days. The glutamine-starved pollen grains cannot undergo maturation, even when supplied with glutamine later. Instead, they undergo cell division towards androgenesis slowly within 10 days in a medium containing appropriate nutrients. During the culture period, they ought to escape from G1 arrest to proceed into S phase as the primary step towards androgenesis. However, this event has not been experimentally confirmed. Here, we demonstrated that the pollen vegetative cells proceeded to the G1/S transition within approximately 15-36 h after the start of culture. These results were obtained by analyzing transgenic pollen possessing a fusion gene encoding nuclear-localizing GFP under the control of an E2F motif-containing promoter isolated from a gene encoding one of DNA replication licensing factors. Observations using a 5-ethynyl-2'-deoxyuridine DNA labeling and detection technique uncovered that the G1/S transition was soon followed by S phase. These hallmarks of vegetative cells undergoing dedifferentiation give us new insights into upstream events causing the G1/S transition and also provide a novel strategy to increase the frequency of the androgenic response in tobacco and other species, including recalcitrants.
Collapse
Affiliation(s)
- Masaharu Kyo
- Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki, Kagawa, 761-0795, Japan,
| | | | | | | |
Collapse
|
45
|
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.
Collapse
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.)
| |
Collapse
|
46
|
A quiescent path to plant longevity. Trends Cell Biol 2014; 24:443-8. [DOI: 10.1016/j.tcb.2014.03.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 03/06/2014] [Accepted: 03/07/2014] [Indexed: 01/17/2023]
|
47
|
The ASH1-RELATED3 SET-domain protein controls cell division competence of the meristem and the quiescent center of the Arabidopsis primary root. PLANT PHYSIOLOGY 2014; 166:632-43. [PMID: 25034019 DOI: 10.1104/pp.114.244798] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The stem cell niche of the Arabidopsis (Arabidopsis thaliana) primary root apical meristem is composed of the quiescent (or organizing) center surrounded by stem (initial) cells for the different tissues. Initial cells generate a population of transit-amplifying cells that undergo a limited number of cell divisions before elongating and differentiating. It is unclear whether these divisions occur stochastically or in an orderly manner. Using the thymidine analog 5-ethynyl-2'-deoxyuridine to monitor DNA replication of cells of Arabidopsis root meristems, we identified a pattern of two, four, and eight neighboring cells with synchronized replication along the cortical, epidermal, and endodermal cell files, suggested to be daughters, granddaughters, and great-granddaughters of the direct progeny of each stem cell. Markers of mitosis and cytokinesis were not present in the region closest to the transition zone where the cells start to elongate, suggesting that great-granddaughter cells switch synchronously from the mitotic cell cycle to endoreduplication. Mutations in the stem cell niche-expressed ASH1-RELATED3 (ASHR3) gene, encoding a SET-domain protein conferring histone H3 lysine-36 methylation, disrupted this pattern of coordinated DNA replication and cell division and increased the cell division rate in the quiescent center. E2Fa/E2Fb transcription factors controlling the G1-to-S-phase transition regulate ASHR3 expression and bind to the ASHR3 promoter, substantiating a role for ASHR3 in cell division control. The reduced length of the root apical meristem and primary root of the mutant ashr3-1 indicate that synchronization of replication and cell divisions is required for normal root growth and development.
Collapse
|
48
|
Desvoyes B, Fernández-Marcos M, Sequeira-Mendes J, Otero S, Vergara Z, Gutierrez C. Looking at plant cell cycle from the chromatin window. FRONTIERS IN PLANT SCIENCE 2014; 5:369. [PMID: 25120553 PMCID: PMC4110626 DOI: 10.3389/fpls.2014.00369] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/11/2014] [Indexed: 05/03/2023]
Abstract
The cell cycle is defined by a series of complex events, finely coordinated through hormonal, developmental and environmental signals, which occur in a unidirectional manner and end up in producing two daughter cells. Accumulating evidence reveals that chromatin is not a static entity throughout the cell cycle. In fact, there are many changes that include nucleosome remodeling, histone modifications, deposition and exchange, among others. Interestingly, it is possible to correlate the occurrence of several of these chromatin-related events with specific processes necessary for cell cycle progression, e.g., licensing of DNA replication origins, the E2F-dependent transcriptional wave in G1, the activation of replication origins in S-phase, the G2-specific transcription of genes required for mitosis or the chromatin packaging occurring in mitosis. Therefore, an emerging view is that chromatin dynamics must be considered as an intrinsic part of cell cycle regulation. In this article, we review the main features of several key chromatin events that occur at defined times throughout the cell cycle and discuss whether they are actually controlling the transit through specific cell cycle stages.
Collapse
Affiliation(s)
| | | | | | | | | | - Crisanto Gutierrez
- *Correspondence: Crisanto Gutierrez, Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas, Universidad Autónoma de Madrid, Nicolas Cabrera 1, Cantoblanco, Madrid 28049, Spain e-mail:
| |
Collapse
|
49
|
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: 155] [Impact Index Per Article: 15.5] [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.
Collapse
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
| |
Collapse
|
50
|
Dehghan Nayeri F. Identification of transcription factors linked to cell cycle regulation in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2014; 9:e972864. [PMID: 25482767 PMCID: PMC4622563 DOI: 10.4161/15592316.2014.972864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 07/24/2014] [Accepted: 07/25/2014] [Indexed: 06/04/2023]
Abstract
Cell cycle is an essential process in growth and development of living organisms consists of the replication and mitotic phases separated by 2 gap phases; G1 and G2. It is tightly controlled at the molecular level and especially at the level of transcription. Precise regulation of the cell cycle is of central significance for plant growth and development and transcription factors are global regulators of gene expression playing essential roles in cell cycle regulation. This study has uncovered TFs that are involved in the control of cell cycle progression. With the aid of multi-parallel quantitative RT-PCR, the expression changes of 1880 TFs represented in the Arabidopsis TF platform was monitored in Arabidopsis synchronous MM2d cells during a 19 h period representing different time points corresponding to the 4 cell cycle phases after treatment of MM2d cells with Aphidicolin. Comparative TF expression analyses performed on synchronous cells resulted in the identification of 239 TFs differentially expressed during the cell cycle, while about one third of TFs were constitutively expressed through all time points. Phase-specific TFs were also identified.
Collapse
Affiliation(s)
- Fatemeh Dehghan Nayeri
- Max-Planck Institute of Molecular Plant Physiology; Am Mühlenberg 1; Potsdam-Golm, Germany
- Department of Agricultural Biotechnology; Faculty of Engineering and Technology; Imam Khomeini International University; Qazvin, Iran
| |
Collapse
|