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Juranić M, Tucker MR, Schultz CJ, Shirley NJ, Taylor JM, Spriggs A, Johnson SD, Bulone V, Koltunow AM. Asexual Female Gametogenesis Involves Contact with a Sexually-Fated Megaspore in Apomictic Hieracium. PLANT PHYSIOLOGY 2018; 177:1027-1049. [PMID: 29844228 PMCID: PMC6052994 DOI: 10.1104/pp.18.00342] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/16/2018] [Indexed: 05/03/2023]
Abstract
Apomixis results in asexual seed formation where progeny are identical to the maternal plant. In ovules of apomictic species of the Hieracium subgenus Pilosella, meiosis of the megaspore mother cell generates four megaspores. Aposporous initial (AI) cells form during meiosis in most ovules. The sexual pathway terminates during functional megaspore (FM) differentiation, when an enlarged AI undergoes mitosis to form an aposporous female gametophyte. Then, the mitotically programmed FM dies along with the three other megaspores by unknown mechanisms. Transcriptomes of laser-dissected AIs, ovule cells, and ovaries from apomicts and AI-deficient mutants were analyzed to understand the pathways involved. The steps leading to AI mitosis and sexual pathway termination were determined using antibodies against arabinogalactan protein epitopes found to mark both sexual and aposporous female gametophyte lineages at inception. At most, four AIs differentiated near developing megaspores. The first expanding AI cell to contact the FM formed a functional AI that underwent mitosis soon after megaspore degeneration. Transcriptome analyses indicated that the enlarged, laser-captured AIs were arrested in the S/G2 phase of the cell cycle and were metabolically active. Further comparisons with AI-deficient mutants showed that AIs were enriched in transcripts encoding homologs of genes involved in, and potentially antagonistic to, known FM specification pathways. We propose that AI and FM cell contact provides cues required for AI mitosis and megaspore degeneration. Specific candidates to further interrogate AI-FM interactions were identified here and include Hieracium arabinogalactan protein family genes.
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Affiliation(s)
- Martina Juranić
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Urrbrae, South Australia 5064, Australia
| | - Matthew R Tucker
- School of Agriculture, Food, and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia
| | - Carolyn J Schultz
- School of Agriculture, Food, and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia
| | - Neil J Shirley
- School of Agriculture, Food, and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia
- Australian Research Council Centre of Excellence in Plant Cell Walls, Wine Innovation Central, University of Adelaide, Urrbrae, South Australia 5064, Australia
| | - Jennifer M Taylor
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Black Mountain Laboratories, Black Mountain, Australian Capital Territory 2601, Australia
| | - Andrew Spriggs
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Black Mountain Laboratories, Black Mountain, Australian Capital Territory 2601, Australia
| | - Susan D Johnson
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Urrbrae, South Australia 5064, Australia
| | - Vincent Bulone
- School of Agriculture, Food, and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia
- Australian Research Council Centre of Excellence in Plant Cell Walls, Wine Innovation Central, University of Adelaide, Urrbrae, South Australia 5064, Australia
| | - Anna M Koltunow
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Urrbrae, South Australia 5064, Australia
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Lin HY, Chen JC, Fang SC. A Protoplast Transient Expression System to Enable Molecular, Cellular, and Functional Studies in Phalaenopsis orchids. FRONTIERS IN PLANT SCIENCE 2018; 9:843. [PMID: 29988409 PMCID: PMC6024019 DOI: 10.3389/fpls.2018.00843] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/30/2018] [Indexed: 05/24/2023]
Abstract
The enigmatic nature of the specialized developmental programs of orchids has fascinated plant biologists for centuries. The recent releases of orchid genomes indicate that orchids possess new gene families and family expansions and contractions to regulate a diverse suite of developmental processes. However, the extremely long orchid life cycle and lack of molecular toolkit have hampered the advancement of orchid biology research. To overcome the technical difficulties and establish a platform for rapid gene regulation studies, in this study, we developed an efficient protoplast isolation and transient expression system for Phalaenopsis aphrodite. This protocol was successfully applied to protein subcellular localization and protein-protein interaction studies. Moreover, it was confirmed to be useful in delineating the PaE2F/PaDP-dependent cell cycle pathway and studying auxin response. In summary, the established orchid protoplast transient expression system provides a means to functionally characterize orchid genes at the molecular level allowing assessment of transcriptome responses to transgene expression and widening the scope of molecular studies in orchids.
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Affiliation(s)
- Hsiang-Yin Lin
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Jhun-Chen Chen
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Su-Chiung Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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53
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Negative regulator of E2F transcription factors links cell cycle checkpoint and DNA damage repair. Proc Natl Acad Sci U S A 2018; 115:E3837-E3845. [PMID: 29610335 DOI: 10.1073/pnas.1720094115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DNA damage poses a serious threat to genome integrity and greatly affects growth and development. To maintain genome stability, all organisms have evolved elaborate DNA damage response mechanisms including activation of cell cycle checkpoints and DNA repair. Here, we show that the DNA repair protein SNI1, a subunit of the evolutionally conserved SMC5/6 complex, directly links these two processes in Arabidopsis SNI1 binds to the activation domains of E2F transcription factors, the key regulators of cell cycle progression, and represses their transcriptional activities. In turn, E2Fs activate the expression of SNI1, suggesting that E2Fs and SNI1 form a negative feedback loop. Genetically, overexpression of SNI1 suppresses the phenotypes of E2F-overexpressing plants, and loss of E2F function fully suppresses the sni1 mutant, indicating that SNI1 is necessary and sufficient to inhibit E2Fs. Altogether, our study revealed that SNI1 is a negative regulator of E2Fs and plays dual roles in DNA damage responses by linking cell cycle checkpoint and DNA repair.
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54
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Yu H, Jiao B, Lu L, Wang P, Chen S, Liang C, Liu W. NetMiner-an ensemble pipeline for building genome-wide and high-quality gene co-expression network using massive-scale RNA-seq samples. PLoS One 2018; 13:e0192613. [PMID: 29425247 PMCID: PMC5806890 DOI: 10.1371/journal.pone.0192613] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/27/2018] [Indexed: 01/10/2023] Open
Abstract
Accurately reconstructing gene co-expression network is of great importance for uncovering the genetic architecture underlying complex and various phenotypes. The recent availability of high-throughput RNA-seq sequencing has made genome-wide detecting and quantifying of the novel, rare and low-abundance transcripts practical. However, its potential merits in reconstructing gene co-expression network have still not been well explored. Using massive-scale RNA-seq samples, we have designed an ensemble pipeline, called NetMiner, for building genome-scale and high-quality Gene Co-expression Network (GCN) by integrating three frequently used inference algorithms. We constructed a RNA-seq-based GCN in one species of monocot rice. The quality of network obtained by our method was verified and evaluated by the curated gene functional association data sets, which obviously outperformed each single method. In addition, the powerful capability of network for associating genes with functions and agronomic traits was shown by enrichment analysis and case studies. In particular, we demonstrated the potential value of our proposed method to predict the biological roles of unknown protein-coding genes, long non-coding RNA (lncRNA) genes and circular RNA (circRNA) genes. Our results provided a valuable and highly reliable data source to select key candidate genes for subsequent experimental validation. To facilitate identification of novel genes regulating important biological processes and phenotypes in other plants or animals, we have published the source code of NetMiner, making it freely available at https://github.com/czllab/NetMiner.
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Affiliation(s)
- Hua Yu
- Nantong Medical College and School of Pharmacy, Nantong University, Nantong, China
- State Key Laboratory of Plant Genomics, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail: , , (HY); (CL); (WL)
| | - Bingke Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lu Lu
- Nantong Polytechnic College, Nantong, China
| | - Pengfei Wang
- Nantong Medical College and School of Pharmacy, Nantong University, Nantong, China
| | - Shuangcheng Chen
- Nantong Medical College and School of Pharmacy, Nantong University, Nantong, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail: , , (HY); (CL); (WL)
| | - Wei Liu
- Nantong Medical College and School of Pharmacy, Nantong University, Nantong, China
- * E-mail: , , (HY); (CL); (WL)
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55
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Nelissen H, Sun X, Rymen B, Jikumaru Y, Kojima M, Takebayashi Y, Abbeloos R, Demuynck K, Storme V, Vuylsteke M, De Block J, Herman D, Coppens F, Maere S, Kamiya Y, Sakakibara H, Beemster GT, Inzé D. The reduction in maize leaf growth under mild drought affects the transition between cell division and cell expansion and cannot be restored by elevated gibberellic acid levels. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:615-627. [PMID: 28730636 PMCID: PMC5787831 DOI: 10.1111/pbi.12801] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/07/2017] [Accepted: 07/12/2017] [Indexed: 05/05/2023]
Abstract
Growth is characterized by the interplay between cell division and cell expansion, two processes that occur separated along the growth zone at the maize leaf. To gain further insight into the transition between cell division and cell expansion, conditions were investigated in which the position of this transition zone was positively or negatively affected. High levels of gibberellic acid (GA) in plants overexpressing the GA biosynthesis gene GA20-OXIDASE (GA20OX-1OE ) shifted the transition zone more distally, whereas mild drought, which is associated with lowered GA biosynthesis, resulted in a more basal positioning. However, the increased levels of GA in the GA20OX-1OE line were insufficient to convey tolerance to the mild drought treatment, indicating that another mechanism in addition to lowered GA levels is restricting growth during drought. Transcriptome analysis with high spatial resolution indicated that mild drought specifically induces a reprogramming of transcriptional regulation in the division zone. 'Leaf Growth Viewer' was developed as an online searchable tool containing the high-resolution data.
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Affiliation(s)
- Hilde Nelissen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Xiao‐Huan Sun
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Bart Rymen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Yusuke Jikumaru
- Growth Regulation Research GroupPlant Science CenterRIKENYokohamaJapan
| | - Mikko Kojima
- Plant Productivity Systems Research GroupPlant Science CenterRIKENYokohamaJapan
| | - Yumiko Takebayashi
- Plant Productivity Systems Research GroupPlant Science CenterRIKENYokohamaJapan
| | - Rafael Abbeloos
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Kirin Demuynck
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Veronique Storme
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Marnik Vuylsteke
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Jolien De Block
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Dorota Herman
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Frederik Coppens
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Steven Maere
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
| | - Yuji Kamiya
- Growth Regulation Research GroupPlant Science CenterRIKENYokohamaJapan
| | - Hitoshi Sakakibara
- Plant Productivity Systems Research GroupPlant Science CenterRIKENYokohamaJapan
| | - Gerrit T.S. Beemster
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
- Department of BiologyUniversity of AntwerpAntwerpBelgium
| | - Dirk Inzé
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- Center for Plant Systems BiologyVIBGentBelgium
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Sharma N, Dang TM, Singh N, Ruzicic S, Mueller-Roeber B, Baumann U, Heuer S. Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice. RICE (NEW YORK, N.Y.) 2018; 11:2. [PMID: 29313187 PMCID: PMC5758481 DOI: 10.1186/s12284-017-0192-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/12/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Flooding during seasonal monsoons affects millions of hectares of rice-cultivated areas across Asia. Submerged rice plants die within a week due to lack of oxygen, light and excessive elongation growth to escape the water. Submergence tolerance was first reported in an aus-type rice landrace, FR13A, and the ethylene-responsive transcription factor (TF) gene SUB1A-1 was identified as the major tolerance gene. Intolerant rice varieties generally lack the SUB1A gene but some intermediate tolerant varieties, such as IR64, carry the allelic variant SUB1A-2. Differential effects of the two alleles have so far not been addressed. As a first step, we have therefore quantified and compared the expression of nearly 2500 rice TF genes between IR64 and its derived tolerant near isogenic line IR64-Sub1, which carries the SUB1A-1 allele. Gene expression was studied in internodes, where the main difference in expression between the two alleles was previously shown. RESULTS Nineteen and twenty-six TF genes were identified that responded to submergence in IR64 and IR64-Sub1, respectively. Only one gene was found to be submergence-responsive in both, suggesting different regulatory pathways under submergence in the two genotypes. These differentially expressed genes (DEGs) mainly included MYB, NAC, TIFY and Zn-finger TFs, and most genes were downregulated upon submergence. In IR64, but not in IR64-Sub1, SUB1B and SUB1C, which are also present in the Sub1 locus, were identified as submergence responsive. Four TFs were not submergence responsive but exhibited constitutive, genotype-specific differential expression. Most of the identified submergence responsive DEGs are associated with regulatory hormonal pathways, i.e. gibberellins (GA), abscisic acid (ABA), and jasmonic acid (JA), apart from ethylene. An in-silico promoter analysis of the two genotypes revealed the presence of allele-specific single nucleotide polymorphisms, giving rise to ABRE, DRE/CRT, CARE and Site II cis-elements, which can partly explain the observed differential TF gene expression. CONCLUSION This study identified new gene targets with the potential to further enhance submergence tolerance in rice and provides insights into novel aspects of SUB1A-mediated tolerance.
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Affiliation(s)
- Niharika Sharma
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Plant Genomics Centre, Hartley Grove, Urrbrae, Adelaide, South Australia, 5064, Australia
| | - Trang Minh Dang
- International Rice Research Institute (IRRI), Los Banos, Philippines
- Intrexon Corp, California, USA
| | - Namrata Singh
- International Rice Research Institute (IRRI), Los Banos, Philippines
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | | | | | - Ute Baumann
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Plant Genomics Centre, Hartley Grove, Urrbrae, Adelaide, South Australia, 5064, Australia
| | - Sigrid Heuer
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Plant Genomics Centre, Hartley Grove, Urrbrae, Adelaide, South Australia, 5064, Australia.
- International Rice Research Institute (IRRI), Los Banos, Philippines.
- Rothamsted Research, Plant Science Department, Hertfordshire, Harpenden, AL5 2JQ, UK.
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Yao X, Yang H, Zhu Y, Xue J, Wang T, Song T, Yang Z, Wang S. The Canonical E2Fs Are Required for Germline Development in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:638. [PMID: 29868091 PMCID: PMC5962754 DOI: 10.3389/fpls.2018.00638] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/25/2018] [Indexed: 05/03/2023]
Abstract
A number of cell fate determinations, including cell division, cell differentiation, and programmed cell death, intensely occur during plant germline development. How these cell fate determinations are regulated remains largely unclear. The transcription factor E2F is a core cell cycle regulator. Here we show that the Arabidopsis canonical E2Fs, including E2Fa, E2Fb, and E2Fc, play a redundant role in plant germline development. The e2fa e2fb e2fc (e2fabc) triple mutant is sterile, although its vegetative development appears normal. On the one hand, the e2fabc microspores undergo cell death during pollen mitosis. Microspores start to die at the bicellular stage. By the tricellular stage, the majority of the e2fabc microspores are degenerated. On the other hand, a wild type ovule often has one megaspore mother cell (MMC), whereas the majority of e2fabc ovules have two to three MMCs. The subsequent female gametogenesis of e2fabc mutant is aborted and the vacuole is severely impaired in the embryo sac. Analysis of transmission efficiency showed that the canonical E2Fs from both male and female gametophyte are essential for plant gametogenesis. Our study reveals that the canonical E2Fs are required for plant germline development, especially the pollen mitosis and the archesporial cell (AC)-MMC transition.
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58
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Liu H, Zhang H, Dong YX, Hao YJ, Zhang XS. DNA METHYLTRANSFERASE1-mediated shoot regeneration is regulated by cytokinin-induced cell cycle in Arabidopsis. THE NEW PHYTOLOGIST 2018; 217:219-232. [PMID: 28960381 DOI: 10.1111/nph.14814] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/19/2017] [Indexed: 05/22/2023]
Abstract
DNA methylation plays a critical role in diverse biological processes of plants. Arabidopsis DNA METHYLTRANSFERASE1 (MET1) represses shoot regeneration by inhibiting WUSCHEL (WUS) expression, which is essential for shoot initiation. However, the upstream signals regulating MET1 expression during this process are unclear. We analyzed the signals regulating MET1 expression using a number of established strategies, such as genetic analysis, confocal microscopy, quantitative real-time PCR and chromatin immunoprecipitation. MET1 expression patterns underwent dynamic changes with the initiation of WUS during shoot regeneration. The cell cycle regulator E2FA was characterized as an upstream factor directly promoting MET1 expression. Moreover, cytokinin promoted MET1 expression partially by enhancing CYCD3 expression. Our findings reveal that MET1-mediated shoot regeneration is regulated by the cytokinin-induced cell cycle, and provide new insights into the regulation of DNA methylation in shoot regeneration.
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Affiliation(s)
- Hui Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Hui Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Yu Xiu Dong
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Yu Jin Hao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
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Hou J, Li T, Wang Y, Hao C, Liu H, Zhang X. ADP-glucose pyrophosphorylase genes, associated with kernel weight, underwent selection during wheat domestication and breeding. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1533-1543. [PMID: 28371241 PMCID: PMC5698054 DOI: 10.1111/pbi.12735] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/23/2017] [Accepted: 03/26/2017] [Indexed: 05/04/2023]
Abstract
ADP-glucose pyrophosphorylase, comprising two small subunits and two large subunits, is considered a key enzyme in the endosperm starch synthesis pathway in wheat (Triticum aestivum L.). Two genes, TaAGP-S1-7A and TaAGP-L-1B, were investigated in this study. Haplotypes of these genes were associated with thousand kernel weight (TKW) in different populations. Mean TKWs of favoured haplotypes were significantly higher than those of nonfavoured ones. Two molecular markers developed to distinguish these haplotypes could be used in molecular breeding. Frequencies of favoured haplotypes were dramatically increased in cultivars released in China after the 1940s. These favoured haplotypes were also positively selected in six major wheat production regions globally. Selection of AGP-S1 and AGP-L-1B in wheat mainly occurred during and after hexaploidization. Strong additive effects of the favoured haplotypes of with other genes for starch synthesis were also detected in different populations.
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Affiliation(s)
- Jian Hou
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Tian Li
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yamei Wang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Chenyang Hao
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Hongxia Liu
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xueyong Zhang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
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60
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Garg R, Singh VK, Rajkumar MS, Kumar V, Jain M. Global transcriptome and coexpression network analyses reveal cultivar-specific molecular signatures associated with seed development and seed size/weight determination in chickpea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:1088-1107. [PMID: 28640939 DOI: 10.1111/tpj.13621] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 06/02/2017] [Accepted: 06/09/2017] [Indexed: 05/22/2023]
Abstract
Seed development is an intricate process regulated via a complex transcriptional regulatory network. To understand the molecular mechanisms governing seed development and seed size/weight in chickpea, we performed a comprehensive analysis of transcriptome dynamics during seed development in two cultivars with contrasting seed size/weight (small-seeded, Himchana 1 and large-seeded, JGK 3). Our analysis identified stage-specific expression for a significant proportion (>13%) of the genes in each cultivar. About one half of the total genes exhibited significant differential expression in JGK 3 as compared with Himchana 1. We found that different seed development stages can be delineated by modules of coexpressed genes. A comparative analysis revealed differential developmental stage specificity of some modules between the two cultivars. Furthermore, we constructed transcriptional regulatory networks and identified key components determining seed size/weight. The results suggested that extended period of cell division during embryogenesis and higher level of endoreduplication along with more accumulation of storage compounds during maturation determine large seed size/weight. Further, we identified quantitative trait loci-associated candidate genes harboring single nucleotide polymorphisms in the promoter sequences that differentiate small- and large-seeded chickpea cultivars. The results provide a valuable resource to dissect the role of candidate genes governing seed development and seed size/weight in chickpea.
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Affiliation(s)
- Rohini Garg
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
| | - Vikash K Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mohan Singh Rajkumar
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vinay Kumar
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mukesh Jain
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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Wong DCJ, Lopez Gutierrez R, Gambetta GA, Castellarin SD. Genome-wide analysis of cis-regulatory element structure and discovery of motif-driven gene co-expression networks in grapevine. DNA Res 2017; 24:311-326. [PMID: 28119334 PMCID: PMC5499852 DOI: 10.1093/dnares/dsw061] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/13/2016] [Indexed: 11/29/2022] Open
Abstract
Coordinated transcriptional and metabolic reprogramming ensures a plant’s continued growth and survival under adverse environmental conditions. Transcription factors (TFs) act to modulate gene expression through complex cis-regulatory element (CRE) interactions. Genome-wide analysis of known plant CREs was performed for all currently predicted protein-coding gene promoters in grapevine (Vitis vinifera L.). Many CREs such as abscisic acid (ABA)-responsive, drought-responsive, auxin-responsive, and evening elements, exhibit bona fide CRE properties such as strong position bias towards the transcription start site (TSS) and over-representation when compared with random promoters. Genes containing these CREs are enriched in a large repertoire of plant biological pathways. Large-scale transcriptome analyses also show that these CREs are highly implicated in grapevine development and stress response. Numerous CRE-driven modules in condition-specific gene co-expression networks (GCNs) were identified and many of these modules were highly enriched for plant biological functions. Several modules corroborate known roles of CREs in drought response, pathogen defense, cell wall metabolism, and fruit ripening, whereas others reveal novel functions in plants. Comparisons with Arabidopsis suggest a general conservation in promoter architecture, gene expression dynamics, and GCN structure across species. Systems analyses of CREs provide insights into the grapevine cis-regulatory code and establish a foundation for future genomic studies in grapevine.
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Affiliation(s)
| | | | - Gregory Alan Gambetta
- Ecophysiologie et Génomique Fonctionnelle de la Vigne, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 33140 Villenave d'Ornon, France
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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.
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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:
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Lv Y, Xiao J, Liu J, Xing F. E2F8 is a Potential Therapeutic Target for Hepatocellular Carcinoma. J Cancer 2017; 8:1205-1213. [PMID: 28607595 PMCID: PMC5463435 DOI: 10.7150/jca.18255] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/11/2017] [Indexed: 12/15/2022] Open
Abstract
E2F transcriptional factors are widely expressed in a number of tissues and organs, possessing many regulatory functions related to cellular proliferation, differentiation, DNA repair, cell-cycle and cell apoptosis. E2F8 is a recently identified member of the E2F family with a duplicated DNA-binding domain feature discriminated from E2F1-6, controlling gene expression in a dimerization partner-independent manner. It is indispensable for angiogenesis, lymphangiogenesis and embryonic development. Although E2F8 and E2F7 perform complementary and overlapping functions in many cell metabolisms, E2F8, but not E2F7, overexpresses remarkably in hepatocellular carcinoma (HCC) to facilitate the HCC occurrence and development via activating a E2F1/ Cyclin D1 signaling pathway to regulate the G1- to S-phase transition of cell cycle progression or transcriptionally suppressing CDK1 to induce hepatocyte polyploidization. It also involves closely a variety of cellular physiological functions and pathological processes, which may bring a new breakthrough for the treatment of certain diseases, especially the HCC. Here, we summarize the latest progress of E2F8 on its relevant functions and mechanisms as well as potential application.
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Affiliation(s)
- Yi Lv
- Department of Immunobiology, Institute of Tissue Transplantation and Immunology, Jinan University, Guangzhou, China.,Key Laboratory of Functional Protein Research of Guangdong, Higher Education Institutes, Jinan University, Guangzhou, China
| | - Jia Xiao
- Department of Immunobiology, Institute of Tissue Transplantation and Immunology, Jinan University, Guangzhou, China
| | - Jing Liu
- Department of Stomatology, Jinan University, Guangzhou, China
| | - Feiyue Xing
- Department of Immunobiology, Institute of Tissue Transplantation and Immunology, Jinan University, Guangzhou, China.,Key Laboratory of Functional Protein Research of Guangdong, Higher Education Institutes, Jinan University, Guangzhou, China
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64
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Li D, Liu J, Liu W, Li G, Yang Z, Qin P, Xu L. The ISWI remodeler in plants: protein complexes, biochemical functions, and developmental roles. Chromosoma 2017; 126:365-373. [PMID: 28213686 DOI: 10.1007/s00412-017-0626-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/15/2017] [Accepted: 01/26/2017] [Indexed: 12/01/2022]
Abstract
Imitation Switch (ISWI) is a member of the ATP-dependent chromatin remodeling factor family, whose members move or restructure nucleosomes using energy derived from ATP hydrolysis. ISWI proteins are conserved in eukaryotes and usually form complexes with DDT (DNA-binding homeobox and different transcription factors)-domain proteins. Here, we review recent research on ISWI in the model plant Arabidopsis thaliana (AtISWI). AtISWI forms complexes with AtDDT-domain proteins, many of which have domain structures that differ from those of DDT-domain proteins in yeast and animals. This might suggest that plant ISWI complexes have unique roles. In vivo studies have shown that AtISWI is involved in the formation of the evenly spaced pattern of nucleosome arrangement in gene bodies-this pattern is associated with high transcriptional levels of genes. In addition, AtISWI and the AtDDT-domain protein RINGLET (RLT) are involved in many developmental processes in A. thaliana, including meristem fate transition and organ formation. Studies on the functions of AtISWI may shed light on how chromatin remodeling functions in plants and also provide new information about the evolution of ISWI remodeling complexes in eukaryotes.
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Affiliation(s)
- Dongjie Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.,College of Life and Environment Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jie Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Guang Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.,Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Zhongnan Yang
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Peng Qin
- Department of Instrumentation Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.
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65
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Zaidi MA, O'Leary SJB, Wu S, Chabot D, Gleddie S, Laroche A, Eudes F, Robert LS. Investigating Triticeae anther gene promoter activity in transgenic Brachypodium distachyon. PLANTA 2017; 245:385-396. [PMID: 27787603 DOI: 10.1007/s00425-016-2612-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 10/18/2016] [Indexed: 06/06/2023]
Abstract
In this report, we demonstrate that Brachypodium distachyon could serve as a relatively high throughput in planta functional assay system for Triticeae anther-specific gene promoters. There remains a vast gap in our knowledge of the promoter cis-acting elements responsible for the transcriptional regulation of Triticeae anther-specific genes. In an attempt to identify conserved cis-elements, 14 pollen-specific and 8 tapetum-specific Triticeae putative promoter sequences were analyzed using different promoter sequence analysis tools. Several cis-elements were found to be enriched in these sequences and their possible role in gene expression regulation in the anther is discussed. Despite the fact that potential cis-acting elements can be identified within putative promoter sequence datasets, determining whether particular promoter sequences can in fact direct proper tissue-specific and developmental gene expression still needs to be confirmed via functional assays preferably performed in closely related plants. Transgenic functional assays with Triticeae species remain challenging and Brachypodium distachyon may represent a suitable alternative. The promoters of the triticale pollen-specific genes group 3 pollen allergen (PAL3) and group 4 pollen allergen (PAL4), as well as the tapetum-specific genes chalcone synthase-like 1 (CHSL1), from wheat and cysteine-rich protein 1 (CRP1) from triticale were fused to the green fluorescent protein gene (GFP) and analyzed in transgenic Brachypodium. This report demonstrates that this model species could serve to accelerate the functional analysis of Triticeae anther-specific gene promoters.
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Affiliation(s)
- Mohsin A Zaidi
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Stephen J B O'Leary
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
- National Research Council of Canada, Aquatic and Crop Resource Development, 1411 Oxford Street, Halifax, NS, B3H 3Z1, Canada
| | - Shaobo Wu
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
- Beijing YouAn Hospital, Capital Medical University, Beijing Institute of Hepatology, No. 8 Xi Tou Tiao, You An Men Wai, Fengtai District, Beijing, 100069, People's Republic of China
| | - Denise Chabot
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Steve Gleddie
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - André Laroche
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, T1J 4B1, Canada
| | - François Eudes
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, T1J 4B1, Canada
| | - Laurian S Robert
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.
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67
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Zhang J, Tian M, Yan GX, Shodhan A, Miao W. E2fl1 is a meiosis-specific transcription factor in the protist Tetrahymena thermophila. Cell Cycle 2016; 16:123-135. [PMID: 27892792 DOI: 10.1080/15384101.2016.1259779] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Members of the E2F family of transcription factors have been reported to regulate the expression of genes involved in cell cycle control, DNA replication, and DNA repair in multicellular eukaryotes. Here, E2FL1, a meiosis-specific E2F transcription factor gene, was identified in the model ciliate Tetrahymena thermophila. Loss of this gene resulted in meiotic arrest prior to anaphase I. The cytological experiments revealed that the meiotic homologous pairing was not affected in the absence of E2FL1, but the paired homologous chromosomes did not separate and assumed a peculiar tandem arrangement. This is the first time that an E2F family member has been shown to regulate meiotic events. Moreover, BrdU incorporation showed that DSB processing during meiosis was abnormal upon the deletion of E2FL1. Transcriptome sequencing analysis revealed that E2FL1 knockout decreased the expression of genes involved in DNA replication and DNA repair in T. thermophila, suggesting that the function of E2F is highly conserved in eukaryotes. In addition, E2FL1 deletion inhibited the expression of related homologous chromosome segregation genes in T. thermophila. The result may explain the meiotic arrest phenotype at anaphase I. Finally, by searching for E2F DNA-binding motifs in the entire T. thermophila genome, we identified 714 genes containing at least one E2F DNA-binding motif; of these, 235 downregulated represent putative E2FL1 target genes.
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Affiliation(s)
- Jing Zhang
- a Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , People's Republic of China.,b University of Chinese Academy of Sciences , Beijing , People's Republic of China
| | - Miao Tian
- a Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , People's Republic of China.,c Department of Chromosome Biology and Max F. Perutz Laboratories, Center for Molecular Biology, University of Vienna , Vienna , Austria
| | - Guan-Xiong Yan
- a Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , People's Republic of China.,b University of Chinese Academy of Sciences , Beijing , People's Republic of China
| | - Anura Shodhan
- c Department of Chromosome Biology and Max F. Perutz Laboratories, Center for Molecular Biology, University of Vienna , Vienna , Austria
| | - Wei Miao
- a Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , People's Republic of China
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Yang Y, Mo Y, Yang X, Zhang H, Wang Y, Li H, Wei C, Zhang X. Transcriptome Profiling of Watermelon Root in Response to Short-Term Osmotic Stress. PLoS One 2016; 11:e0166314. [PMID: 27861528 PMCID: PMC5115733 DOI: 10.1371/journal.pone.0166314] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/26/2016] [Indexed: 11/18/2022] Open
Abstract
Osmotic stress adversely affects the growth, fruit quality and yield of watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai). Increasing the tolerance of watermelon to osmotic stress caused by factors such as high salt and water deficit is an effective way to improve crop survival in osmotic stress environments. Roots are important organs in water absorption and are involved in the initial response to osmosis stress; however, few studies have examined the underlying mechanism of tolerance to osmotic stress in watermelon roots. For better understanding of this mechanism, the inbred watermelon accession M08, which exhibits relatively high tolerance to water deficits, was treated with 20% polyethylene glycol (PEG) 6000. The root samples were harvested at 6 h after PEG treatment and untreated samples were used as controls. Transcriptome analyses were carried out by Illumina RNA sequencing. A total of 5246 differentially expressed genes were identified. Gene ontology enrichment and biochemical pathway analyses of these 5246 genes showed that short-term osmotic stress affected osmotic adjustment, signal transduction, hormone responses, cell division, cell cycle and ribosome, and M08 may repress root growth to adapt osmotic stress. The results of this study describe the watermelon root transcriptome under osmotic stress and propose new insight into watermelon root responses to osmotic stress at the transcriptome level. Accordingly, these results allow us to better understand the molecular mechanisms of watermelon in response to drought stress and will facilitate watermelon breeding projects to improve drought tolerance.
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Affiliation(s)
- Yongchao Yang
- College of Horticulture, Northwest A&F University, Yangling, China
- Wenshan Academy of Agricultural Sciences, Wenshan, China
| | - Yanling Mo
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Xiaozheng Yang
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Haifei Zhang
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Yongqi Wang
- College of Horticulture, Northwest A&F University, Yangling, China
- Hanzhong City Agro-technology Extension Center, Hanzhong, China
| | - Hao Li
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Chunhua Wei
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Xian Zhang
- College of Horticulture, Northwest A&F University, Yangling, China
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69
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Wu XY, Hu WJ, Luo H, Xia Y, Zhao Y, Wang LD, Zhang LM, Luo JC, Jing HC. Transcriptome profiling of developmental leaf senescence in sorghum (Sorghum bicolor). PLANT MOLECULAR BIOLOGY 2016; 92:555-580. [PMID: 27586543 DOI: 10.1007/s11103-016-0532-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 08/19/2016] [Indexed: 05/04/2023]
Abstract
This piece of the submission is being sent via mail. Leaf senescence is essential for the nutrient economy of crops and is executed by so-called senescence-associated genes (SAGs). Here we explored the monocot C4 model crop Sorghum bicolor for a holistic picture of SAG profiles by RNA-seq. Leaf samples were collected at four stages during developmental senescence, and in total, 3396 SAGs were identified, predominantly enriched in GO categories of metabolic processes and catalytic activities. These genes were enriched in 13 KEGG pathways, wherein flavonoid and phenylpropanoid biosynthesis and phenylalanine metabolism were overrepresented. Seven regions on Chromosomes 1, 4, 5 and 7 contained SAG 'hotspots' of duplicated genes or members of cupin superfamily involved in manganese ion binding and nutrient reservoir activity. Forty-eight expression clusters were identified, and the candidate orthologues of the known important senescence transcription factors such as ORE1, EIN3 and WRKY53 showed "SAG" expression patterns, implicating their possible roles in regulating sorghum leaf senescence. Comparison of developmental senescence with salt- and dark- induced senescence allowed for the identification of 507 common SAGs, 1996 developmental specific SAGs as well as 176 potential markers for monitoring senescence in sorghum. Taken together, these data provide valuable resources for comparative genomics analyses of leaf senescence and potential targets for the manipulation of genetic improvement of Sorghum bicolor.
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Affiliation(s)
- Xiao-Yuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- Inner Mongolia Research Centre for Practaculture, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Wei-Juan Hu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Hong Luo
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- Inner Mongolia Research Centre for Practaculture, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
| | - Yan Xia
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- Inner Mongolia Research Centre for Practaculture, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
| | - Yi Zhao
- College of Life Sciences and State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, People's Republic of China
| | - Li-Dong Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- Inner Mongolia Research Centre for Practaculture, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
| | - Li-Min Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- Inner Mongolia Research Centre for Practaculture, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
| | - Jing-Chu Luo
- College of Life Sciences and State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, People's Republic of China.
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.
- Inner Mongolia Research Centre for Practaculture, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.
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70
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Kobayashi K, Suzuki T, Iwata E, Magyar Z, Bögre L, Ito M. MYB3Rs, plant homologs of Myb oncoproteins, control cell cycle-regulated transcription and form DREAM-like complexes. Transcription 2016; 6:106-11. [PMID: 26556011 DOI: 10.1080/21541264.2015.1109746] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Plant MYB3R transcription factors, homologous to Myb oncoproteins, regulate the genes expressed at G2 and M phases in the cell cycle. Recent studies showed that MYB3Rs constitute multiprotein complexes that may correspond to animal complexes known as DREAM or dREAM. Discovery of the putative homologous complex in plants uncovered their significant varieties in structure, function, dynamics, and heterogeneity, providing insight into conserved and diversified aspects of cell cycle-regulated gene transcription.
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Affiliation(s)
- Kosuke Kobayashi
- a Graduate School of Bioagricultural Sciences; Nagoya University ; Chikusa , Nagoya , Japan
| | - Toshiya Suzuki
- a Graduate School of Bioagricultural Sciences; Nagoya University ; Chikusa , Nagoya , Japan.,b JST; CREST ; Chikusa , Nagoya , Japan
| | - Eriko Iwata
- a Graduate School of Bioagricultural Sciences; Nagoya University ; Chikusa , Nagoya , Japan
| | - Zoltán Magyar
- c Institute of Plant Biology; Biological Research Centre ; Szeged , Hungary.,d Royal Holloway; University of London; School of Biological Sciences ; Egham , Surrey , UK
| | - László Bögre
- d Royal Holloway; University of London; School of Biological Sciences ; Egham , Surrey , UK
| | - Masaki Ito
- a Graduate School of Bioagricultural Sciences; Nagoya University ; Chikusa , Nagoya , Japan.,b JST; CREST ; Chikusa , Nagoya , Japan
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Liu Y, Lai J, Yu M, Wang F, Zhang J, Jiang J, Hu H, Wu Q, Lu G, Xu P, Yang C. The Arabidopsis SUMO E3 Ligase AtMMS21 Dissociates the E2Fa/DPa Complex in Cell Cycle Regulation. THE PLANT CELL 2016; 28:2225-2237. [PMID: 27492969 PMCID: PMC5059808 DOI: 10.1105/tpc.16.00439] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/22/2016] [Accepted: 08/01/2016] [Indexed: 05/03/2023]
Abstract
Development requires the proper execution and regulation of the cell cycle via precise, conserved mechanisms. Critically, the E2F/DP complex controls the expression of essential genes during cell cycle transitions. Here, we discovered the molecular function of the Arabidopsis thaliana SUMO E3 ligase METHYL METHANESULFONATE SENSITIVITY GENE21 (AtMMS21) in regulating the cell cycle via the E2Fa/DPa pathway. DPa was identified as an AtMMS21-interacting protein and AtMMS21 competes with E2Fa for interaction with DPa. Moreover, DPa is a substrate for SUMOylation mediated by AtMMS21, and this SUMOylation enhances the dissociation of the E2Fa/DPa complex. AtMMS21 also affects the subcellular localization of E2Fa/DPa. The E2Fa/DPa target genes are upregulated in the root of mms21-1 and mms21-1 mutants showed increased endoreplication. Overexpression of DPa affected the root development of mms21-1, and overexpression of AtMMS21 completely recovered the abnormal phenotypes of 35S:E2Fa-DPa plants. Our results suggest that AtMMS21 dissociates the E2Fa/DPa complex via competition and SUMOylation in the regulation of plant cell cycle.
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Affiliation(s)
- Yiyang Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Mengyuan Yu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Feige Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Juanjuan Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jieming Jiang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Huan Hu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Qian Wu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Guohui Lu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Panglian Xu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
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Pfeiffer A, Janocha D, Dong Y, Medzihradszky A, Schöne S, Daum G, Suzaki T, Forner J, Langenecker T, Rempel E, Schmid M, Wirtz M, Hell R, Lohmann JU. Integration of light and metabolic signals for stem cell activation at the shoot apical meristem. eLife 2016; 5. [PMID: 27400267 PMCID: PMC4969040 DOI: 10.7554/elife.17023] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 07/09/2016] [Indexed: 12/12/2022] Open
Abstract
A major feature of embryogenesis is the specification of stem cell systems, but in contrast to the situation in most animals, plant stem cells remain quiescent until the postembryonic phase of development. Here, we dissect how light and metabolic signals are integrated to overcome stem cell dormancy at the shoot apical meristem. We show on the one hand that light is able to activate expression of the stem cell inducer WUSCHEL independently of photosynthesis and that this likely involves inter-regional cytokinin signaling. Metabolic signals, on the other hand, are transduced to the meristem through activation of the TARGET OF RAPAMYCIN (TOR) kinase. Surprisingly, TOR is also required for light signal dependent stem cell activation. Thus, the TOR kinase acts as a central integrator of light and metabolic signals and a key regulator of stem cell activation at the shoot apex. DOI:http://dx.doi.org/10.7554/eLife.17023.001 Plants are able to grow and develop throughout their lives thanks to groups of stem cells at the tips of their shoots and roots, which can constantly divide to produce new cells. Energy captured from sunlight during a process called photosynthesis is the main source of energy for most plants. Therefore, the amount and quality of light in the environment has a big influence on how plants grow and develop. An enzyme called TOR kinase can sense energy levels in animal cells and regulate many processes including growth and cell division. Plants also have a TOR kinase, but it is less clear if it plays the same role in plants, and whether it can respond to light. Plant stem cells only start to divide after the seed germinates. In shoots, a protein called WUSCHEL is required to maintain stem cells in an active state. Here, Pfeiffer et al. studied how shoot stem cells are activated in response to environmental signals in a plant known as Arabidopsis. The experiments show that light is able to activate the production of WUSCHEL independently of photosynthesis via a signal pathway that depends on TOR kinase. The stem cells do not directly sense light; instead other cells detect the light and relay the information to the stem cells with the help of a hormone called cytokinin. Further experiments show that information about energy levels in cells is relayed via another signal pathway that also involves the TOR kinase. Therefore, Pfeiffer et al.’s findings suggest that the activation of TOR by light allows plant cells to anticipate how much energy will be available and efficiently tune their growth and development to cope with the environmental conditions. Future challenges are to understand how TOR kinase is regulated by light signals and how this enzyme is able to act on WUSCHEL to trigger stem cell division. DOI:http://dx.doi.org/10.7554/eLife.17023.002
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Affiliation(s)
- Anne Pfeiffer
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Denis Janocha
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Yihan Dong
- Department of Molecular Plant Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Anna Medzihradszky
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Stefanie Schöne
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Gabor Daum
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Takuya Suzaki
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Joachim Forner
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Tobias Langenecker
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eugen Rempel
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Markus Schmid
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Markus Wirtz
- Department of Molecular Plant Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Rüdiger Hell
- Department of Molecular Plant Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Jan U Lohmann
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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73
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Computational analysis of atpB gene promoter from different Pakistani apple varieties. Comput Biol Chem 2016; 64:1-8. [PMID: 27213556 DOI: 10.1016/j.compbiolchem.2016.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 04/27/2016] [Accepted: 05/05/2016] [Indexed: 11/20/2022]
Abstract
Apple is the fourth most important fruit crop grown in temperate areas of the world belongs to the family Rosaceae. In the present study, the promoter (∼1000bp) region of atpB gene was used to evaluate the genetic diversity and phylogeny of six local apple varieties. atpB gene is one of the large chloroplastic region which encodes β-subunit of ATP synthase and previously it had been used largely in phylogenetic studies. During the present study, atpB promoter was amplified, sequenced and analyzed using various bioinformatics tools including Place Signal Scan, MEGA6 and BLASTn. During the phylogenetic analysis, obtained phylogram divided the studied varieties into two clusters revealing the monophyletic origin of studied apple varieties. Pairwise distance revealed moderate genetic diversity that ranges from 0.047-0.170 with an average of 0.101. While identifying different cis-acting elements present in the atpB promoter region, results exhibited the occurrence of 56 common and 20 unique cis-regulatory elements among studied varieties. The identified cis-acting regulatory elements were mapped as well. It was observed that Kala Kulu has the highest unique features with reference to the availability of cis-acting elements. Moreover, the possible functions of all regulatory elements present on the promoter sequence of atpB gene were predicted based on already reported information regarding their in vivo role.
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74
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The evolutionary history of the E2F and DEL genes in Viridiplantae. Mol Phylogenet Evol 2016; 99:225-234. [PMID: 27033948 DOI: 10.1016/j.ympev.2016.03.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 03/18/2016] [Accepted: 03/21/2016] [Indexed: 10/22/2022]
Abstract
The E2 promoter binding factor (E2F) proteins are present in almost all eukaryotic organisms and are essential to control several processes, such as the cell cycle progression, cell division, DNA replication, and apoptosis. The E2F family comprises two different types of proteins: the typical E2Fs and atypical E2Fs, which differ structurally and have specific functions. The E2F gene family was described for the first time in plants in 1999, and since then several studies have focused on the functional aspects, but the evolutionary history of this gene family is still unknown. Here, we investigated the evolutionary history of the E2F gene family in plants. Our findings suggest that E2F proteins arose early after the emergence of the eukaryotic species, while DEL proteins appear to have arisen before the metazoan and plants origin probably through a partial duplication of an ancient E2F protein. Our data also suggest that E2Fs activators and repressors appeared twice during evolution, once in the metazoan lineage and again in the embryophyte lineage.
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75
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Larsen PE, Sreedasyam A, Trivedi G, Desai S, Dai Y, Cseke LJ, Collart FR. Multi-Omics Approach Identifies Molecular Mechanisms of Plant-Fungus Mycorrhizal Interaction. FRONTIERS IN PLANT SCIENCE 2016; 6:1061. [PMID: 26834754 PMCID: PMC4717292 DOI: 10.3389/fpls.2015.01061] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/16/2015] [Indexed: 05/29/2023]
Abstract
In mycorrhizal symbiosis, plant roots form close, mutually beneficial interactions with soil fungi. Before this mycorrhizal interaction can be established however, plant roots must be capable of detecting potential beneficial fungal partners and initiating the gene expression patterns necessary to begin symbiosis. To predict a plant root-mycorrhizal fungi sensor systems, we analyzed in vitro experiments of Populus tremuloides (aspen tree) and Laccaria bicolor (mycorrhizal fungi) interaction and leveraged over 200 previously published transcriptomic experimental data sets, 159 experimentally validated plant transcription factor binding motifs, and more than 120-thousand experimentally validated protein-protein interactions to generate models of pre-mycorrhizal sensor systems in aspen root. These sensor mechanisms link extracellular signaling molecules with gene regulation through a network comprised of membrane receptors, signal cascade proteins, transcription factors, and transcription factor biding DNA motifs. Modeling predicted four pre-mycorrhizal sensor complexes in aspen that interact with 15 transcription factors to regulate the expression of 1184 genes in response to extracellular signals synthesized by Laccaria. Predicted extracellular signaling molecules include common signaling molecules such as phenylpropanoids, salicylate, and jasmonic acid. This multi-omic computational modeling approach for predicting the complex sensory networks yielded specific, testable biological hypotheses for mycorrhizal interaction signaling compounds, sensor complexes, and mechanisms of gene regulation.
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Affiliation(s)
- Peter E. Larsen
- Argonne National Laboratory, Biosciences DivisionLemont, IL, USA
- Department of Bioengineering, University of Illinois at ChicagoChicago IL, USA
| | - Avinash Sreedasyam
- Department of Biological Sciences, University of Alabama in HuntsvilleHuntsville, AL, USA
| | - Geetika Trivedi
- Department of Biological Sciences, University of Alabama in HuntsvilleHuntsville, AL, USA
| | - Shalaka Desai
- Argonne National Laboratory, Biosciences DivisionLemont, IL, USA
| | - Yang Dai
- Department of Bioengineering, University of Illinois at ChicagoChicago IL, USA
| | - Leland J. Cseke
- Department of Biological Sciences, University of Alabama in HuntsvilleHuntsville, AL, USA
| | - Frank R. Collart
- Argonne National Laboratory, Biosciences DivisionLemont, IL, USA
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76
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Schwarz EM, Roeder AHK. Transcriptomic Effects of the Cell Cycle Regulator LGO in Arabidopsis Sepals. FRONTIERS IN PLANT SCIENCE 2016; 7:1744. [PMID: 27920789 PMCID: PMC5118908 DOI: 10.3389/fpls.2016.01744] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 11/04/2016] [Indexed: 05/03/2023]
Abstract
Endoreduplication is a specialized cell cycle in which DNA replication occurs, but mitosis is skipped creating enlarged polyploid cells. Endoreduplication is associated with the differentiation of many specialized cell types. In the Arabidopsis thaliana sepal epidermis endoreduplicated giant cells form interspersed between smaller cells. Both the transcription factor Arabidopsis thaliana MERISTEM LAYER1 (ATML1) and the plant-specific cyclin dependent kinase inhibitor LOSS OF GIANT CELLS FROM ORGANS (LGO)/SIAMESE RELATED1 (SMR1) are required for the formation of giant cells. Overexpression of LGO is sufficient to produce sepals covered in highly endoreduplicated giant cells. Here we ask whether overexpression of LGO changes the transcriptome of these mature sepals. We show that overexpression of LGO in the epidermis (LGOoe) drives giant cell formation even in atml1 mutant sepals. Using RNA-seq we show that LGOoe has significant effects on the mature sepal transcriptome that are primarily ATML1-independent changes of gene activity. Genes activated by LGOoe, directly or indirectly, predominantly encode proteins involved in defense responses, including responses to wounding, insects (a predator of Arabidopsis), and fungus. They also encode components of the glucosinolate biosynthesis pathway, a key biochemical pathway in defense against herbivores. LGOoe-activated genes include previously known marker genes of systemic acquired resistance such as PR1 through PR5. The defensive functions promoted by LGOoe in sepals overlap with functions recently shown to be transcriptionally activated by hyperimmune cpr5 mutants in a LGO-dependent manner. Our findings show that the cell cycle regulator LGO can directly or indirectly drive specific states of gene expression; in particular, they are consistent with recent findings showing LGO to be necessary for transcriptional activation of many defense genes in Arabidopsis.
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Affiliation(s)
- Erich M. Schwarz
- Department of Molecular Biology and Genetics, Cornell University, IthacaNY, USA
| | - Adrienne H. K. Roeder
- Weill Institute for Cell and Molecular Biology and Section of Plant Biology, School of Integrative Plant Sciences, Cornell University, IthacaNY, USA
- *Correspondence: Adrienne H. K. Roeder,
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77
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Xu J, Zhang L, Yang DL, Li Q, He Z. Thymidine kinases share a conserved function for nucleotide salvage and play an essential role in Arabidopsis thaliana growth and development. THE NEW PHYTOLOGIST 2015; 208:1089-1103. [PMID: 26139575 DOI: 10.1111/nph.13530] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 05/23/2015] [Indexed: 06/04/2023]
Abstract
Thymidine kinases (TKs) are important components in the nucleotide salvage pathway. However, knowledge about plant TKs is quite limited. In this study, the molecular function of TKs in Arabidopsis thaliana was investigated. Two TKs were identified and named AtTK1 and AtTK2. Expression of both genes was ubiquitous, but AtTK1 was strongly expressed in high-proliferation tissues. AtTK1 was localized to the cytosol, whereas AtTK2 was localized to the mitochondria. Mutant analysis indicated that the two genes function coordinately to sustain normal plant development. Enzymatic assays showed that the two TK proteins shared similar catalytic specificity for pyrimidine nucleosides. They were able to complement an Escherichia coli strain lacking TK activity. 5'-Fluorodeoxyuridine (FdU) resistance and 5-ethynyl 2'-deoxyuridine (EdU) incorporation assays confirmed their activity in vivo. Furthermore, the tk mutant phenotype could be alleviated by nucleotide feeding, establishing that the biosynthesis of pyrimidine nucleotides was disrupted by the TK deficiency. Finally, both human and rice (Oryza sativa) TKs were able to rescue the tk mutants, demonstrating the functional conservation of TKs across organisms. Taken together, our findings clarify the specialized function of two TKs in A. thaliana and establish that the salvage pathway mediated by the kinases is essential for plant growth and development.
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Affiliation(s)
- Jing Xu
- National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Lin Zhang
- National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Dong-Lei Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qun Li
- National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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78
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Pettkó-Szandtner A, Cserháti M, Barrôco RM, Hariharan S, Dudits D, Beemster GTS. Core cell cycle regulatory genes in rice and their expression profiles across the growth zone of the leaf. JOURNAL OF PLANT RESEARCH 2015; 128:953-74. [PMID: 26459328 DOI: 10.1007/s10265-015-0754-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 07/12/2015] [Indexed: 05/22/2023]
Abstract
Rice (Oryza sativa L.) as a model and crop plant with a sequenced genome offers an outstanding experimental system for discovering and functionally analyzing the major cell cycle control elements in a cereal species. In this study, we identified the core cell cycle genes in the rice genome through a hidden Markov model search and multiple alignments supported with the use of short protein sequence probes. In total we present 55 rice putative cell cycle genes with locus identity, chromosomal location, approximate chromosome position and EST accession number. These cell cycle genes include nine cyclin dependent-kinase (CDK) genes, 27 cyclin genes, one CKS gene, two RBR genes, nine E2F/DP/DEL genes, six KRP genes, and one WEE gene. We also provide characteristic protein sequence signatures encoded by CDK and cyclin gene variants. Promoter analysis by the FootPrinter program discovered several motifs in the regulatory region of the core cell cycle genes. As a first step towards functional characterization we performed transcript analysis by RT-PCR to determine gene specific variation in transcript levels along the rice leaves. The meristematic zone of the leaves where cells are actively dividing was identified based on kinematic analysis and flow cytometry. As expected, expression of the majority of cell cycle genes was exclusively associated with the meristematic region. However genes such as different D-type cyclins, DEL1, KRP1/3, and RBR2 were also expressed in leaf segments representing the transition zone in which cells start differentiation.
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Affiliation(s)
- A Pettkó-Szandtner
- Biological Research Center, HAS, Temesvári krt 62, Szeged, 6726, Hungary.
- Plant Systems Biology, VIB, Technologiepark 927, 9052, Zwijnaarde, Belgium.
| | - M Cserháti
- Biological Research Center, HAS, Temesvári krt 62, Szeged, 6726, Hungary
- Nebraska Medical Center, Omaha, NE, 68198-5145, USA
- Plant Systems Biology, VIB, Technologiepark 927, 9052, Zwijnaarde, Belgium
| | - R M Barrôco
- Plant Systems Biology, VIB, Technologiepark 927, 9052, Zwijnaarde, Belgium
- CropDesign N.V./BASF, Technologiepark 921C, 9052, Ghent, Zwijnaarde, Belgium
| | - S Hariharan
- Plant Systems Biology, VIB, Technologiepark 927, 9052, Zwijnaarde, Belgium
| | - D Dudits
- Biological Research Center, HAS, Temesvári krt 62, Szeged, 6726, Hungary
| | - G T S Beemster
- Plant Systems Biology, VIB, Technologiepark 927, 9052, Zwijnaarde, Belgium
- Department of Biology, University of Antwerp, Antwerp, Belgium
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79
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Avramova V, AbdElgawad H, Zhang Z, Fotschki B, Casadevall R, Vergauwen L, Knapen D, Taleisnik E, Guisez Y, Asard H, Beemster GTS. Drought Induces Distinct Growth Response, Protection, and Recovery Mechanisms in the Maize Leaf Growth Zone. PLANT PHYSIOLOGY 2015; 169:1382-96. [PMID: 26297138 PMCID: PMC4587441 DOI: 10.1104/pp.15.00276] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 08/20/2015] [Indexed: 05/08/2023]
Abstract
Drought is the most important crop yield-limiting factor, and detailed knowledge of its impact on plant growth regulation is crucial. The maize (Zea mays) leaf growth zone offers unique possibilities for studying the spatiotemporal regulation of developmental processes by transcriptional analyses and methods that require more material, such as metabolite and enzyme activity measurements. By means of a kinematic analysis, we show that drought inhibits maize leaf growth by inhibiting cell division in the meristem and cell expansion in the elongation zone. Through a microarray study, we observed the down-regulation of 32 of the 54 cell cycle genes, providing a basis for the inhibited cell division. We also found evidence for an up-regulation of the photosynthetic machinery and the antioxidant and redox systems. This was confirmed by increased chlorophyll content in mature cells and increased activity of antioxidant enzymes and metabolite levels across the growth zone, respectively. We demonstrate the functional significance of the identified transcriptional reprogramming by showing that increasing the antioxidant capacity in the proliferation zone, by overexpression of the Arabidopsis (Arabidopsis thaliana) iron-superoxide dismutase gene, increases leaf growth rate by stimulating cell division. We also show that the increased photosynthetic capacity leads to enhanced photosynthesis upon rewatering, facilitating the often-observed growth compensation.
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Affiliation(s)
- Viktoriya Avramova
- Department of Biology, University of Antwerp, 2020 Antwerp, Belgium (V.A., H.Ab., L.V., Y.G., H.As., G.T.S.B.);Department of Botany, Faculty of Science, University of Beni-Suef, Beni-Suef 62511, Egypt (H.Ab.);Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China (Z.Z.);Institute of Animal Reproduction and Food Research, 10-748 Olsztyn, Poland (B.F.);Centro de Estudios Fotosintéticos y Bioquímicos, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario, S2002 LRK Rosario, Argentina (R.C.);Department of Veterinary Sciences, University of Antwerp, Campus Drie Eiken, 2610 Wilrijk, Belgium (D.K.); andConsejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), X5020ICA Cordoba, Argentina (E.T.)
| | - Hamada AbdElgawad
- Department of Biology, University of Antwerp, 2020 Antwerp, Belgium (V.A., H.Ab., L.V., Y.G., H.As., G.T.S.B.);Department of Botany, Faculty of Science, University of Beni-Suef, Beni-Suef 62511, Egypt (H.Ab.);Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China (Z.Z.);Institute of Animal Reproduction and Food Research, 10-748 Olsztyn, Poland (B.F.);Centro de Estudios Fotosintéticos y Bioquímicos, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario, S2002 LRK Rosario, Argentina (R.C.);Department of Veterinary Sciences, University of Antwerp, Campus Drie Eiken, 2610 Wilrijk, Belgium (D.K.); andConsejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), X5020ICA Cordoba, Argentina (E.T.)
| | - Zhengfeng Zhang
- Department of Biology, University of Antwerp, 2020 Antwerp, Belgium (V.A., H.Ab., L.V., Y.G., H.As., G.T.S.B.);Department of Botany, Faculty of Science, University of Beni-Suef, Beni-Suef 62511, Egypt (H.Ab.);Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China (Z.Z.);Institute of Animal Reproduction and Food Research, 10-748 Olsztyn, Poland (B.F.);Centro de Estudios Fotosintéticos y Bioquímicos, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario, S2002 LRK Rosario, Argentina (R.C.);Department of Veterinary Sciences, University of Antwerp, Campus Drie Eiken, 2610 Wilrijk, Belgium (D.K.); andConsejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), X5020ICA Cordoba, Argentina (E.T.)
| | - Bartosz Fotschki
- Department of Biology, University of Antwerp, 2020 Antwerp, Belgium (V.A., H.Ab., L.V., Y.G., H.As., G.T.S.B.);Department of Botany, Faculty of Science, University of Beni-Suef, Beni-Suef 62511, Egypt (H.Ab.);Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China (Z.Z.);Institute of Animal Reproduction and Food Research, 10-748 Olsztyn, Poland (B.F.);Centro de Estudios Fotosintéticos y Bioquímicos, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario, S2002 LRK Rosario, Argentina (R.C.);Department of Veterinary Sciences, University of Antwerp, Campus Drie Eiken, 2610 Wilrijk, Belgium (D.K.); andConsejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), X5020ICA Cordoba, Argentina (E.T.)
| | - Romina Casadevall
- Department of Biology, University of Antwerp, 2020 Antwerp, Belgium (V.A., H.Ab., L.V., Y.G., H.As., G.T.S.B.);Department of Botany, Faculty of Science, University of Beni-Suef, Beni-Suef 62511, Egypt (H.Ab.);Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China (Z.Z.);Institute of Animal Reproduction and Food Research, 10-748 Olsztyn, Poland (B.F.);Centro de Estudios Fotosintéticos y Bioquímicos, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario, S2002 LRK Rosario, Argentina (R.C.);Department of Veterinary Sciences, University of Antwerp, Campus Drie Eiken, 2610 Wilrijk, Belgium (D.K.); andConsejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), X5020ICA Cordoba, Argentina (E.T.)
| | - Lucia Vergauwen
- Department of Biology, University of Antwerp, 2020 Antwerp, Belgium (V.A., H.Ab., L.V., Y.G., H.As., G.T.S.B.);Department of Botany, Faculty of Science, University of Beni-Suef, Beni-Suef 62511, Egypt (H.Ab.);Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China (Z.Z.);Institute of Animal Reproduction and Food Research, 10-748 Olsztyn, Poland (B.F.);Centro de Estudios Fotosintéticos y Bioquímicos, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario, S2002 LRK Rosario, Argentina (R.C.);Department of Veterinary Sciences, University of Antwerp, Campus Drie Eiken, 2610 Wilrijk, Belgium (D.K.); andConsejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), X5020ICA Cordoba, Argentina (E.T.)
| | - Dries Knapen
- Department of Biology, University of Antwerp, 2020 Antwerp, Belgium (V.A., H.Ab., L.V., Y.G., H.As., G.T.S.B.);Department of Botany, Faculty of Science, University of Beni-Suef, Beni-Suef 62511, Egypt (H.Ab.);Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China (Z.Z.);Institute of Animal Reproduction and Food Research, 10-748 Olsztyn, Poland (B.F.);Centro de Estudios Fotosintéticos y Bioquímicos, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario, S2002 LRK Rosario, Argentina (R.C.);Department of Veterinary Sciences, University of Antwerp, Campus Drie Eiken, 2610 Wilrijk, Belgium (D.K.); andConsejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), X5020ICA Cordoba, Argentina (E.T.)
| | - Edith Taleisnik
- Department of Biology, University of Antwerp, 2020 Antwerp, Belgium (V.A., H.Ab., L.V., Y.G., H.As., G.T.S.B.);Department of Botany, Faculty of Science, University of Beni-Suef, Beni-Suef 62511, Egypt (H.Ab.);Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China (Z.Z.);Institute of Animal Reproduction and Food Research, 10-748 Olsztyn, Poland (B.F.);Centro de Estudios Fotosintéticos y Bioquímicos, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario, S2002 LRK Rosario, Argentina (R.C.);Department of Veterinary Sciences, University of Antwerp, Campus Drie Eiken, 2610 Wilrijk, Belgium (D.K.); andConsejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), X5020ICA Cordoba, Argentina (E.T.)
| | - Yves Guisez
- Department of Biology, University of Antwerp, 2020 Antwerp, Belgium (V.A., H.Ab., L.V., Y.G., H.As., G.T.S.B.);Department of Botany, Faculty of Science, University of Beni-Suef, Beni-Suef 62511, Egypt (H.Ab.);Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China (Z.Z.);Institute of Animal Reproduction and Food Research, 10-748 Olsztyn, Poland (B.F.);Centro de Estudios Fotosintéticos y Bioquímicos, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario, S2002 LRK Rosario, Argentina (R.C.);Department of Veterinary Sciences, University of Antwerp, Campus Drie Eiken, 2610 Wilrijk, Belgium (D.K.); andConsejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), X5020ICA Cordoba, Argentina (E.T.)
| | - Han Asard
- Department of Biology, University of Antwerp, 2020 Antwerp, Belgium (V.A., H.Ab., L.V., Y.G., H.As., G.T.S.B.);Department of Botany, Faculty of Science, University of Beni-Suef, Beni-Suef 62511, Egypt (H.Ab.);Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China (Z.Z.);Institute of Animal Reproduction and Food Research, 10-748 Olsztyn, Poland (B.F.);Centro de Estudios Fotosintéticos y Bioquímicos, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario, S2002 LRK Rosario, Argentina (R.C.);Department of Veterinary Sciences, University of Antwerp, Campus Drie Eiken, 2610 Wilrijk, Belgium (D.K.); andConsejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), X5020ICA Cordoba, Argentina (E.T.)
| | - Gerrit T S Beemster
- Department of Biology, University of Antwerp, 2020 Antwerp, Belgium (V.A., H.Ab., L.V., Y.G., H.As., G.T.S.B.);Department of Botany, Faculty of Science, University of Beni-Suef, Beni-Suef 62511, Egypt (H.Ab.);Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China (Z.Z.);Institute of Animal Reproduction and Food Research, 10-748 Olsztyn, Poland (B.F.);Centro de Estudios Fotosintéticos y Bioquímicos, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario, S2002 LRK Rosario, Argentina (R.C.);Department of Veterinary Sciences, University of Antwerp, Campus Drie Eiken, 2610 Wilrijk, Belgium (D.K.); andConsejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), X5020ICA Cordoba, Argentina (E.T.)
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80
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Tang G, Xu P, Liu W, Liu Z, Shan L. Cloning and Characterization of 5' Flanking Regulatory Sequences of AhLEC1B Gene from Arachis Hypogaea L. PLoS One 2015; 10:e0139213. [PMID: 26426444 PMCID: PMC4591277 DOI: 10.1371/journal.pone.0139213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 09/09/2015] [Indexed: 11/19/2022] Open
Abstract
LEAFY COTYLEDON1 (LEC1) is a B subunit of Nuclear Factor Y (NF-YB) transcription factor that mainly accumulates during embryo development. We cloned the 5' flanking regulatory sequence of AhLEC1B gene, a homolog of Arabidopsis LEC1, and analyzed its regulatory elements using online software. To identify the crucial regulatory region, we generated a series of GUS expression frameworks driven by different length promoters with 5' terminal and/or 3' terminal deletion. We further characterized the GUS expression patterns in the transgenic Arabidopsis lines. Our results show that both the 65 bp proximal promoter region and the 52 bp 5' UTR of AhLEC1B contain the key motifs required for the essential promoting activity. Moreover, AhLEC1B is preferentially expressed in the embryo and is co-regulated by binding of its upstream genes with both positive and negative corresponding cis-regulatory elements.
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Affiliation(s)
- Guiying Tang
- Bio-Tech Research Centre, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
| | - Pingli Xu
- Bio-Tech Research Centre, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
| | - Wei Liu
- College of Agriculture, Shandong University, Jinan, 250100, China
| | - Zhanji Liu
- Bio-Tech Research Centre, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
| | - Lei Shan
- Bio-Tech Research Centre, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Agriculture, Shandong University, Jinan, 250100, China
- * E-mail:
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81
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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.
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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
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82
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Curto M, Krajinski F, Schlereth A, Rubiales D. Transcriptional profiling of Medicago truncatula during Erysiphe pisi infection. FRONTIERS IN PLANT SCIENCE 2015; 6:517. [PMID: 26217367 PMCID: PMC4496563 DOI: 10.3389/fpls.2015.00517] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/26/2015] [Indexed: 05/21/2023]
Abstract
Resistance to powdery mildew has been studied in a number of plant species, yet the molecular mechanisms remain largely unknown. Transcription factors (TFs) play a critical role in the plant defense response by regulating the transcriptional machinery which coordinates the expression of a large group of genes involved in plant defense. Using high-throughput quantitative real-time PCR (qPCR) technology more than 1000 Medicago truncatula TFs were screened in a pair of susceptible and resistant genotypes of M. truncatula after 4 h of Erysiphe pisi infection. Seventy nine TF genes, belonging to 33 families showed a significant transcriptional change in response to E. pisi infection. Forty eight TF genes were differentially expressed in the resistant genotypes compared to the susceptible one in response to E. pisi infection, including pathogenesis-related transcriptional factors, AP2/EREBP (APETALA2/ETHYLENE-RESPONSIVE ELEMENT BINDING FACTORS), WRKY (highly conserved WRKYGQK amino-acid sequence), MYB (Myeloblastoma), homeodomain (HD) and zinc finger C2C2 (CYS2-CYS2), C2H2, (CYS2-HIS2), LIM (Lin-11, Isl-1, Mec-3) gene families, which are involved in known defense responses. Our results suggest that these TF genes are among the E. pisi responsive genes in resistant M. truncatula that may constitute a regulatory network which controls the transcriptional changes in defense genes involved in resistance to E. pisi.
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Affiliation(s)
- Miguel Curto
- Department of Plant Breeding, Institute for Sustainable Agriculture, Spanish National Research CouncilCórdoba, Spain
| | - Franziska Krajinski
- Department of Plant-Microbe Interactions, Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Armin Schlereth
- Department of Plant-Microbe Interactions, Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Diego Rubiales
- Department of Plant Breeding, Institute for Sustainable Agriculture, Spanish National Research CouncilCórdoba, Spain
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83
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Lermontova I, Sandmann M, Mascher M, Schmit AC, Chabouté ME. Centromeric chromatin and its dynamics in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:4-17. [PMID: 25976696 DOI: 10.1111/tpj.12875] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/27/2015] [Accepted: 04/29/2015] [Indexed: 05/22/2023]
Abstract
Centromeres are chromatin structures that are required for proper separation of chromosomes during mitosis and meiosis. The centromere is composed of centromeric DNA, often enriched in satellite repeats, and kinetochore complex proteins. To date, over 100 kinetochore components have been identified in various eukaryotes. Kinetochore assembly begins with incorporation of centromeric histone H3 variant CENH3 into centromeric nucleosomes. Protein components of the kinetochore are either present at centromeres throughout the cell cycle or localize to centromeres transiently, prior to attachment of microtubules to each kinetochore in prometaphase of mitotic cells. This is the case for the spindle assembly checkpoint (SAC) proteins in animal cells. The SAC complex ensures equal separation of chromosomes between daughter nuclei by preventing anaphase onset before metaphase is complete, i.e. the sister kinetochores of all chromosomes are attached to spindle fibers from opposite poles. In this review, we focus on the organization of centromeric DNA and the kinetochore assembly in plants. We summarize recent advances regarding loading of CENH3 into the centromere, and the subcellular localization and protein-protein interactions of Arabidopsis thaliana proteins involved in kinetochore assembly and function. We describe the transcriptional activity of corresponding genes based on in silico analysis of their promoters and cell cycle-dependent expression. Additionally, barley homologs of all selected A. thaliana proteins have been identified in silico, and their sequences and domain structures are presented.
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Affiliation(s)
- Inna Lermontova
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Corrensstraße 3, D-06466, Stadt Seeland, Germany
| | - Michael Sandmann
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Corrensstraße 3, D-06466, Stadt Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Corrensstraße 3, D-06466, Stadt Seeland, Germany
| | - Anne-Catherine Schmit
- Institut de Biologie Moléculaire des Plantes, CNRS-UPR 2357, associée à l'Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg, France
| | - Marie-Edith Chabouté
- Institut de Biologie Moléculaire des Plantes, CNRS-UPR 2357, associée à l'Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg, France
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84
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Fina JP, Casati P. HAG3, a Histone Acetyltransferase, Affects UV-B Responses by Negatively Regulating the Expression of DNA Repair Enzymes and Sunscreen Content in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2015; 56:1388-400. [PMID: 25907565 DOI: 10.1093/pcp/pcv054] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/02/2015] [Indexed: 05/23/2023]
Abstract
Histone acetylation is regulated by histone acetyltransferases and deacetylases. In Arabidopsis, there are 12 histone acetyltransferases and 18 deacetylases. Histone acetyltransferases are organized in four families: the GNAT/HAG, the MYST, the p300/CBP and the TAFII250 families. Previously, we demonstrated that Arabidopsis mutants in the two members of the MYST acetyltransferase family show increased DNA damage after UV-B irradiation. To investigate further the role of other histone acetyltransferases in UV-B responses, a putative role for enzymes of the GNAT family, HAG1, HAG2 and HAG3, was analyzed. HAG transcripts are not UV-B regulated; however, hag3 RNA interference (RNAi) transgenic plants show a lower inhibition of leaf and root growth by UV-B, higher levels of UV-B-absorbing compounds and less UV-B-induced DNA damage than Wassilewskija (Ws) plants, while hag1 RNAi transgenic plants and hag2 mutants do not show significant differences from wild-type plants. Transcripts for UV-B-regulated genes are highly expressed under control conditions in the absence of UV-B in hag3 RNAi transgenic plants, suggesting that the higher UV-B tolerance may be due to increased levels of proteins that participate in UV-B responses. Together, our data provide evidence that HAG3, directly or indirectly, participates in UV-B-induced DNA damage repair and signaling.
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Affiliation(s)
- Julieta P Fina
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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85
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Hu X, Ren J, Ren X, Huang S, Sabiel SAI, Luo M, Nevo E, Fu C, Peng J, Sun D. Association of Agronomic Traits with SNP Markers in Durum Wheat (Triticum turgidum L. durum (Desf.)). PLoS One 2015; 10:e0130854. [PMID: 26110423 PMCID: PMC4482485 DOI: 10.1371/journal.pone.0130854] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/25/2015] [Indexed: 01/11/2023] Open
Abstract
Association mapping is a powerful approach to detect associations between traits of interest and genetic markers based on linkage disequilibrium (LD) in molecular plant breeding. In this study, 150 accessions of worldwide originated durum wheat germplasm (Triticum turgidum spp. durum) were genotyped using 1,366 SNP markers. The extent of LD on each chromosome was evaluated. Association of single nucleotide polymorphisms (SNP) markers with ten agronomic traits measured in four consecutive years was analyzed under a mix linear model (MLM). Two hundred and one significant association pairs were detected in the four years. Several markers were associated with one trait, and also some markers were associated with multiple traits. Some of the associated markers were in agreement with previous quantitative trait loci (QTL) analyses. The function and homology analyses of the corresponding ESTs of some SNP markers could explain many of the associations for plant height, length of main spike, number of spikelets on main spike, grain number per plant, and 1000-grain weight, etc. The SNP associations for the observed traits are generally clustered in specific chromosome regions of the wheat genome, mainly in 2A, 5A, 6A, 7A, 1B, and 6B chromosomes. This study demonstrates that association mapping can complement and enhance previous QTL analyses and provide additional information for marker-assisted selection.
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Affiliation(s)
- Xin Hu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan Hubei, 430070, China
| | - Jing Ren
- Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University, Dezhou, Shandong, 253023, China
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan Hubei, 430070, China
| | - Sisi Huang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan Hubei, 430070, China
| | - Salih A. I. Sabiel
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan Hubei, 430070, China
| | - Mingcheng Luo
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, United States of America
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, 31905, Israel
| | - Chunjie Fu
- Science and Technology Center, China National Seed Group Co., Ltd, Wuhan, Hubei, 430206, China
| | - Junhua Peng
- Science and Technology Center, China National Seed Group Co., Ltd, Wuhan, Hubei, 430206, China
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan Hubei, 430070, China
- Hubei Collaborative Innovation Center for Grain Industry, Jingzhou, Hubei, 434025, China
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86
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Takatsuka H, Umeda-Hara C, Umeda M. Cyclin-dependent kinase-activating kinases CDKD;1 and CDKD;3 are essential for preserving mitotic activity in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:1004-1017. [PMID: 25942995 DOI: 10.1111/tpj.12872] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 04/14/2015] [Accepted: 04/24/2015] [Indexed: 05/23/2023]
Abstract
For the full activation of cyclin-dependent kinases (CDKs), not only cyclin binding but also CDK phosphorylation is required. This activating phosphorylation is mediated by CDK-activating kinases (CAKs). Arabidopsis has four genes showing similarity to vertebrate-type CAKs, three CDKDs (CDKD;1-CDKD;3) and one CDKF (CDKF;1). We previously found that the cdkf;1 mutant is defective in post-embryonic development, even though the kinase activities of core CDKs remain unchanged relative to the wild type. This raised a question about the involvement of CDKDs in CDK activation in planta. Here we report that the cdkd;1 cdkd;3 double mutant showed gametophytic lethality. Most cdkd;1-1 cdkd;3-1 pollen grains were defective in pollen mitosis I and II, producing one-cell or two-cell pollen grains that lacked fertilization ability. We also found that the double knock-out of CDKD;1 and CDKD;3 caused arrest and/or delay in the progression of female gametogenesis at multiple steps. Our genetic analyses revealed that the functions of CDKF;1 and CDKD;1 or CDKD;3 do not overlap, either during gametophyte and embryo development or in post-embryonic development. Consistent with these analyses, CDKF;1 expression in the cdkd;1-1 cdkd;3-1 mutant could not rescue the gametophytic lethality. These results suggest that, in Arabidopsis, CDKD;1 and CDKD;3 function as CAKs controlling mitosis, whereas CDKF;1 plays a distinct role, mainly in post-embryonic development. We propose that CDKD;1 and CDKD;3 phosphorylate and activate all core CDKs, CDKA, CDKB1 and CDKB2, thereby governing cell cycle progression throughout plant development.
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Affiliation(s)
- Hirotomo Takatsuka
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Chikage Umeda-Hara
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Masaaki Umeda
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
- JST, CREST, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
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87
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Zhang C. Involvement of Iron-Containing Proteins in Genome Integrity in Arabidopsis Thaliana. Genome Integr 2015; 6:2. [PMID: 27330736 PMCID: PMC4911903 DOI: 10.4103/2041-9414.155953] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 03/12/2015] [Indexed: 01/03/2023] Open
Abstract
The Arabidopsis genome encodes numerous iron-containing proteins such as iron-sulfur (Fe-S) cluster proteins and hemoproteins. These proteins generally utilize iron as a cofactor, and they perform critical roles in photosynthesis, genome stability, electron transfer, and oxidation-reduction reactions. Plants have evolved sophisticated mechanisms to maintain iron homeostasis for the assembly of functional iron-containing proteins, thereby ensuring genome stability, cell development, and plant growth. Over the past few years, our understanding of iron-containing proteins and their functions involved in genome stability has expanded enormously. In this review, I provide the current perspectives on iron homeostasis in Arabidopsis, followed by a summary of iron-containing protein functions involved in genome stability maintenance and a discussion of their possible molecular mechanisms.
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Affiliation(s)
- Caiguo Zhang
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, Colorado, USA
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88
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Reitz MU, Gifford ML, Schäfer P. Hormone activities and the cell cycle machinery in immunity-triggered growth inhibition. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2187-97. [PMID: 25821072 PMCID: PMC4986725 DOI: 10.1093/jxb/erv106] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 02/09/2015] [Accepted: 02/19/2015] [Indexed: 05/27/2023]
Abstract
Biotic stress and diseases caused by pathogen attack pose threats in crop production and significantly reduce crop yields. Enhancing immunity against pathogens is therefore of outstanding importance in crop breeding. However, this must be balanced, as immune activation inhibits plant growth. This immunity-coupled growth trade-off does not support resistance but is postulated to reflect the reallocation of resources to drive immunity. There is, however, increasing evidence that growth-immunity trade-offs are based on the reconfiguration of hormone pathways, shared by growth and immunity signalling. Studies in roots revealed the role of hormones in orchestrating growth across different cell types, with some hormones showing a defined cell type-specific activity. This is apparently highly relevant for the regulation of the cell cycle machinery and might be part of the growth-immunity cross-talk. Since plants are constantly exposed to Immuno-activating microbes under agricultural conditions, the transition from a growth to an immunity operating mode can significantly reduce crop yield and can conflict our efforts to generate next-generation crops with improved yield under climate change conditions. By focusing on roots, we outline the current knowledge of hormone signalling on the cell cycle machinery to explain growth trade-offs induced by immunity. By referring to abiotic stress studies, we further introduce how root cell type-specific hormone activities might contribute to growth under immunity and discuss the feasibility of uncoupling the growth-immunity cross-talk.
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Affiliation(s)
- M U Reitz
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - M L Gifford
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - P Schäfer
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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89
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Pedroza-García JA, Nájera-Martínez M, de la Paz Sanchez M, Plasencia J. Arabidopsis thaliana thymidine kinase 1a is ubiquitously expressed during development and contributes to confer tolerance to genotoxic stress. PLANT MOLECULAR BIOLOGY 2015; 87:303-15. [PMID: 25537647 DOI: 10.1007/s11103-014-0277-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/12/2014] [Indexed: 05/23/2023]
Abstract
Thymidine kinase catalyzes the first step in the nucleotide salvage pathway by transferring a phosphate group to a thymidine molecule. In mammals thymidine kinase supplies deoxyribonucleotides for DNA replication and DNA repair, and the expression of the gene is tightly regulated during the cell cycle. Although this gene is phylogenetically conserved in many taxa, its physiological function in plants remains unknown. The genome of the model plant Arabidopsis thaliana has two thymidine kinase genes (AtTK1a and AtTK1b) and microarray data suggest they might have redundant roles. In this study we analyzed the TK1a function by evaluating its expression pattern during development and in response to genotoxic stress. We also studied its role in DNA repair by the characterization of a mutant that contained the T-DNA insertion in the promoter region of the TK1a gene. We found that TK1a is expressed in most tissues during plant development and it was differentially induced by ultraviolet-C radiation because TK1b expression was unaffected. In the mutant, the T-DNA insertion caused a 40 % rise in transcript levels and enzyme activity in Arabidopsis seedlings compared to wild-type plants. This elevation was enough to confer tolerance to ultraviolet-C irradiation in dark conditions, as determined by root growth, and meristem length and structure. TK1a overexpression also provided tolerance to genotoxins that induce double-strand break. Our results suggest that thymidine kinase contributes to several DNA repair pathways by providing deoxythymidine triphosphate that serve as precursors for DNA repair and to balance deoxyribonucleotides pools.
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MESH Headings
- Arabidopsis/enzymology
- Arabidopsis/genetics
- Arabidopsis/radiation effects
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Base Sequence
- DNA Damage
- DNA, Bacterial/genetics
- DNA, Plant/genetics
- Gene Expression Regulation, Developmental/radiation effects
- Gene Expression Regulation, Enzymologic/radiation effects
- Gene Expression Regulation, Plant/radiation effects
- Genes, Plant/radiation effects
- Molecular Sequence Data
- Mutagenesis, Insertional
- Plants, Genetically Modified/enzymology
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/radiation effects
- Promoter Regions, Genetic
- Seedlings/enzymology
- Seedlings/genetics
- Seedlings/radiation effects
- Thymidine Kinase/genetics
- Thymidine Kinase/metabolism
- Ultraviolet Rays/adverse effects
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Affiliation(s)
- José Antonio Pedroza-García
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, 04510, México, D.F., México
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90
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Pena LB, Méndez AAE, Matayoshi CL, Zawoznik MS, Gallego SM. Early response of wheat seminal roots growing under copper excess. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 87:115-123. [PMID: 25576839 DOI: 10.1016/j.plaphy.2014.12.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/30/2014] [Indexed: 06/04/2023]
Abstract
Growth reduction caused by copper excess during plant photoautotrophic metabolism has been widely investigated, but information regarding early responses of root apical meristem (RAM) to toxic concentrations of this metal at the initial heterotrophic stage is certainly scarce. We analysed some determinants of seminal root growth in developing wheat seedlings germinated in the presence of 1, 5 and 10 μM CuCl2, focussing on oxidative damage to cell membrane and to proteins, and investigated the expression patterns of some genes relevant to cell cycle progression and cell expansion. The proliferation zone of the RAM was shorter under 5 and 10 μM CuCl2. Cyclin D and CDKA levels remained unchanged in the root apexes of wheat seedlings grown under these Cu(2+) concentrations, but more carbonylated levels of both proteins and less ubiquitinated-cyclin D was detected under 10 μM CuCl2. Increased levels of ROS were revealed by fluorescent probes at this Cu(2+) dose, and severe cell membrane damage took place at 5 and 10 μM CuCl2. Several genes related to retinoblastome phosphorylation and therefore involved in the transition from G1 to S cell cycle stage were found to be downregulated at 10 μM CuCl2, while most expansin genes here analysed were upregulated, even at a non-toxic concentration of 1 μM. These results together with previous findings suggest that a "common" signal which involves oxidative posttranslational modifications of specific cell cycle proteins may be necessary to induce root growth arrest under Cd(2+) and Cu(2+) stress.
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Affiliation(s)
- Liliana B Pena
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Buenos Aires C1113AAC, Argentina; IQUIFIB-CONICET, Argentina
| | - Andrea A E Méndez
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Buenos Aires C1113AAC, Argentina; IQUIFIB-CONICET, Argentina
| | - Carolina L Matayoshi
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Buenos Aires C1113AAC, Argentina
| | - Myriam S Zawoznik
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Buenos Aires C1113AAC, Argentina
| | - Susana M Gallego
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Buenos Aires C1113AAC, Argentina; IQUIFIB-CONICET, Argentina.
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91
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Hyun Y, Kim J, Cho SW, Choi Y, Kim JS, Coupland G. Site-directed mutagenesis in Arabidopsis thaliana using dividing tissue-targeted RGEN of the CRISPR/Cas system to generate heritable null alleles. PLANTA 2015; 241:271-84. [PMID: 25269397 PMCID: PMC4282705 DOI: 10.1007/s00425-014-2180-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 09/17/2014] [Indexed: 05/18/2023]
Abstract
MAIN CONCLUSION Dividing tissue-targeted site-directed mutagenesis using RGEN of CRISPR/Cas system produces heritable mutations in Arabidopsis thaliana. Site-directed genome engineering in higher plants has great potential for basic research and molecular breeding. Here, we describe a method for site-directed mutagenesis of the Arabidopsis nuclear genome that efficiently generates heritable mutations using the RNA-guided endonuclease (RGEN) derived from bacterial clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 (CRISPR associated) protein system. To induce mutagenesis in proliferating tissues during embryogenesis and throughout the plant life cycle, the single guide RNA (sgRNA) and Cas9 DNA endonuclease were expressed from the U6 snRNA and INCURVATA2 promoters, respectively. After Agrobacterium-mediated introduction of T-DNAs encoding RGENs that targets FLOWERING LOCUS T (FT) and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 4 genes, somatic mutagenesis at the targeted loci was observed in T1 transformants. In the results of FT-RGEN, T1 plants often showed late flowering indicative of the presence of large somatic sectors in which the FT gene is mutated on both chromosomes. DNA sequencing analysis estimated that about 90 % of independent chromosomal DNA fragments carried mutations in the analyzed tissue of a T1 plant showing late flowering. The most frequently detected somatic polymorphism showed a high rate of inheritance in T2 plants, and inheritance of less frequent polymorphisms was also observed. As a result, late-flowering plants homozygous for novel, heritable null alleles of FT including a 1 bp insertion or short deletions were recovered in the following T2 and T3 generations. Our results demonstrate that dividing tissue-targeted mutagenesis using RGEN provides an efficient heritable genome engineering method in A. thaliana.
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Affiliation(s)
- Youbong Hyun
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Jungeun Kim
- National Creative Research Initiatives Center for Genome Engineering, Seoul National University, 151-747 Seoul, Korea
| | - Seung Woo Cho
- National Creative Research Initiatives Center for Genome Engineering, Seoul National University, 151-747 Seoul, Korea
- Department of Chemistry, Seoul National University, 151-747 Seoul, Korea
| | - Yeonhee Choi
- Department of Biological Sciences, Seoul National University, 151-747 Seoul, Korea
| | - Jin-Soo Kim
- National Creative Research Initiatives Center for Genome Engineering, Seoul National University, 151-747 Seoul, Korea
- Department of Chemistry, Seoul National University, 151-747 Seoul, Korea
| | - George Coupland
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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92
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Wang S, Gu Y, Zebell SG, Anderson LK, Wang W, Mohan R, Dong X. A noncanonical role for the CKI-RB-E2F cell-cycle signaling pathway in plant effector-triggered immunity. Cell Host Microbe 2014; 16:787-94. [PMID: 25455564 DOI: 10.1016/j.chom.2014.10.005] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 08/22/2014] [Accepted: 10/03/2014] [Indexed: 11/26/2022]
Abstract
Effector-triggered immunity (ETI), the major host defense mechanism in plants, is often associated with programmed cell death (PCD). Plants lack close homologs of caspases, the key mediators of PCD in animals. So although the NB-LRR receptors involved in ETI are well studied, how they activate PCD and confer disease resistance remains elusive. We show that the Arabidopsis nuclear envelope protein, CPR5, negatively regulates ETI and the associated PCD through a physical interaction with cyclin-dependent kinase inhibitors (CKIs). Upon ETI induction, CKIs are released from CPR5 to cause overactivation of another core cell-cycle regulator, E2F. In cki and e2f mutants, ETI responses induced by both TIR-NB-LRR and CC-NB-LRR classes of immune receptors are compromised. We further show that E2F is deregulated during ETI, probably through CKI-mediated hyperphosphorylation of retinoblastoma-related 1 (RBR1). This study demonstrates that canonical cell-cycle regulators also play important noncanonical roles in plant immunity.
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Affiliation(s)
- Shui Wang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China; Department of Biology, Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, P.O. Box 90338, Duke University, Durham, NC 27708, USA.
| | - Yangnan Gu
- Department of Biology, Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, P.O. Box 90338, Duke University, Durham, NC 27708, USA
| | - Sophia G Zebell
- Department of Biology, Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, P.O. Box 90338, Duke University, Durham, NC 27708, USA
| | - Lisa K Anderson
- Department of Biology, Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, P.O. Box 90338, Duke University, Durham, NC 27708, USA
| | - Wei Wang
- Department of Biology, Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, P.O. Box 90338, Duke University, Durham, NC 27708, USA
| | - Rajinikanth Mohan
- Department of Biology, Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, P.O. Box 90338, Duke University, Durham, NC 27708, USA
| | - Xinnian Dong
- Department of Biology, Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, P.O. Box 90338, Duke University, Durham, NC 27708, USA.
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93
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Sullivan AM, Arsovski AA, Lempe J, Bubb KL, Weirauch MT, Sabo PJ, Sandstrom R, Thurman RE, Neph S, Reynolds AP, Stergachis AB, Vernot B, Johnson AK, Haugen E, Sullivan ST, Thompson A, Neri FV, Weaver M, Diegel M, Mnaimneh S, Yang A, Hughes TR, Nemhauser JL, Queitsch C, Stamatoyannopoulos JA. Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana. Cell Rep 2014; 8:2015-2030. [PMID: 25220462 DOI: 10.1016/j.celrep.2014.08.019] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 05/20/2014] [Accepted: 08/07/2014] [Indexed: 01/23/2023] Open
Abstract
Our understanding of gene regulation in plants is constrained by our limited knowledge of plant cis-regulatory DNA and its dynamics. We mapped DNase I hypersensitive sites (DHSs) in A. thaliana seedlings and used genomic footprinting to delineate ∼ 700,000 sites of in vivo transcription factor (TF) occupancy at nucleotide resolution. We show that variation associated with 72 diverse quantitative phenotypes localizes within DHSs. TF footprints encode an extensive cis-regulatory lexicon subject to recent evolutionary pressures, and widespread TF binding within exons may have shaped codon usage patterns. The architecture of A. thaliana TF regulatory networks is strikingly similar to that of animals in spite of diverged regulatory repertoires. We analyzed regulatory landscape dynamics during heat shock and photomorphogenesis, disclosing thousands of environmentally sensitive elements and enabling mapping of key TF regulatory circuits underlying these fundamental responses. Our results provide an extensive resource for the study of A. thaliana gene regulation and functional biology.
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Affiliation(s)
| | - Andrej A Arsovski
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Janne Lempe
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kerry L Bubb
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology (CAGE) and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Peter J Sabo
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Richard Sandstrom
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Robert E Thurman
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Shane Neph
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Alex P Reynolds
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Andrew B Stergachis
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Benjamin Vernot
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Audra K Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Eric Haugen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Shawn T Sullivan
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Agnieszka Thompson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Fidencio V Neri
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Molly Weaver
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Morgan Diegel
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Sanie Mnaimneh
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto ON M5S 3E1, Canada
| | - Ally Yang
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto ON M5S 3E1, Canada
| | - Timothy R Hughes
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto ON M5S 3E1, Canada; Canadian Institute for Advanced Research (CIFAR) Program in Genetic Networks, Toronto ON M5G 1Z8, Canada
| | | | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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94
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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.
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Affiliation(s)
- Masaharu Kyo
- Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki, Kagawa, 761-0795, Japan,
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95
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Patil RA, Lenka SK, Normanly J, Walker EL, Roberts SC. Methyl jasmonate represses growth and affects cell cycle progression in cultured Taxus cells. PLANT CELL REPORTS 2014; 33:1479-92. [PMID: 24832773 PMCID: PMC4283222 DOI: 10.1007/s00299-014-1632-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 04/18/2014] [Accepted: 04/26/2014] [Indexed: 05/23/2023]
Abstract
Methyl jasmonate elicitation of Taxus cultures enhances paclitaxel accumulation, but represses growth by inhibition of cell cycle progression. Growth repression is evident both at the culture level and transcriptional level. Methyl jasmonate (MeJA) elicitation is an effective strategy to induce and enhance synthesis of the anticancer agent paclitaxel (Taxol(®)) in Taxus cell suspension cultures; however, concurrent decreases in growth are often observed, which is problematic for large-scale bioprocessing. Here, increased accumulation of paclitaxel in Taxus cuspidata suspension cultures with MeJA elicitation was accompanied by a concomitant decrease in cell growth, evident within the first 3 days post-elicitation. Both MeJA-elicited and mock-elicited cultures exhibited similar viability with no apoptosis up to day 16 and day 24 of the cell culture period, respectively, suggesting that growth repression is not attributable to cell death. Flow cytometric analyses demonstrated that MeJA perturbed cell cycle progression of asynchronously dividing Taxus cells. MeJA slowed down cell cycle progression, impaired the G1/S transition as observed by an increase in G0/G1 phase cells, and decreased the number of actively dividing cells. Through a combination of deep sequencing and gene expression analyses, the expression status of Taxus cell cycle-associated genes correlated with observations at the culture level. Results from this study provide valuable insight into the mechanisms governing MeJA perception and subsequent events leading to repression of Taxus cell growth.
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Affiliation(s)
- Rohan A. Patil
- Department of Chemical Engineering, University of Massachusetts, Amherst, MA 01003, USA
| | - Sangram K. Lenka
- Department of Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Jennifer Normanly
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Elsbeth L. Walker
- Department of Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Susan C. Roberts
- Department of Chemical Engineering, University of Massachusetts, Amherst, MA 01003, USA
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96
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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.
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97
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Desvoyes B, de Mendoza A, Ruiz-Trillo I, Gutierrez C. Novel roles of plant RETINOBLASTOMA-RELATED (RBR) protein in cell proliferation and asymmetric cell division. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2657-66. [PMID: 24323507 PMCID: PMC4557542 DOI: 10.1093/jxb/ert411] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The retinoblastoma (Rb) protein was identified as a human tumour suppressor protein that controls various stages of cell proliferation through the interaction with members of the E2F family of transcription factors. It was originally thought to be specific to animals but plants contain homologues of Rb, called RETINOBLASTOMA-RELATED (RBR). In fact, the Rb-E2F module seems to be a very early acquisition of eukaryotes. The activity of RBR depends on phosphorylation of certain amino acid residues, which in most cases are well conserved between plant and animal proteins. In addition to its role in cell-cycle progression, RBR has been shown to participate in various cellular processes such as endoreplication, transcriptional regulation, chromatin remodelling, cell growth, stem cell biology, and differentiation. Here, we discuss the most recent advances to define the role of RBR in cell proliferation and asymmetric cell division. These and other reports clearly support the idea that RBR is used as a landing platform of a plethora of cellular proteins and complexes to control various aspects of cell physiology and plant development.
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Affiliation(s)
- Bénédicte Desvoyes
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, Nicolas Cabrera 1, 28049 Madrid, Spain
| | - Alex de Mendoza
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Catalonia, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Catalonia, Spain
| | - Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, Nicolas Cabrera 1, 28049 Madrid, Spain
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98
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Kuwabara A, Gruissem W. Arabidopsis RETINOBLASTOMA-RELATED and Polycomb group proteins: cooperation during plant cell differentiation and development. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2667-76. [PMID: 24638900 DOI: 10.1093/jxb/eru069] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
RETINOBLASTOMA (RB) is a tumour suppressor gene originally discovered in patients that develop eye tumours. The pRb protein is now well established as a key cell-cycle regulator which suppresses G1-S transition via interaction with E2F-DP complexes. pRb function is also required for a wide range of biological processes, including the regulation of stem-cell maintenance, cell differentiation, permanent cell-cycle exit, DNA repair, and genome stability. Such multifunctionality of pRb is thought to be facilitated through interactions with various binding partners in a context-dependent manner. Although the molecular network in which RB controls various biological processes is not fully understood, it has been found that pRb interacts with transcription factors and chromatin modifiers to either suppress or promote the expression of key genes during the switch from cell proliferation to differentiation. RETINOBLASTOMA-RELATED (RBR) is the plant orthologue of RB and is also known to negatively control the G1-S transition. Similar to its animal counterpart, plant RBR has various roles throughout plant development; however, much of its molecular functions outside of the G1-S transition are still unknown. One of the better-characterized molecular mechanisms is the cooperation of RBR with the Polycomb repressive complex 2 (PRC2) during plant-specific developmental events. This review summarizes the current understanding of this cooperation and focuses on the processes in Arabidopsis in which the RBR-PRC2 cooperation facilitates cell differentiation and developmental transitions.
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Affiliation(s)
- Asuka Kuwabara
- Department of Biology, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Wilhelm Gruissem
- Department of Biology, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland
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99
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Wang H, Liu R, Wang J, Wang P, Shen Y, Liu G. The Arabidopsis kinesin gene AtKin-1 plays a role in the nuclear division process during megagametogenesis. PLANT CELL REPORTS 2014; 33:819-828. [PMID: 24667993 DOI: 10.1007/s00299-014-1594-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 01/15/2014] [Accepted: 02/26/2014] [Indexed: 06/03/2023]
Abstract
Atkin - 1 , the only Kinesin-1 member of Arabidopsis thaliana , plays a role during female gametogenesis through regulation of nuclear division cycles. Kinesins are microtubule-dependent motor proteins found in eukaryotic organisms. They constitute a superfamily that can be further classified into at least 14 families. In the Kinesin-1 family, members from animal and fungi play roles in long-distance transport of organelles and vesicles. Although Kinesin-1-like sequences have been identified in higher plants, little is known about their function in plant cells, other than in a recently identified Kinesin-1-like protein in a rice pollen semi-sterile mutant. In this study, the gene encoding the only Kinesin-1 member in Arabidopsis, AtKin-1 was found to be specifically expressed in ovules and anthers. AtKin-1 loss-of-function mutants showed substantially aborted ovules in siliques, and this finding was supported by complementation testing. Reciprocal crossing between mutant and wild-type plants indicated that a defect in AtKin-1 results in partially aborted megagametophytes, with no observable effects on pollen fertility. Further observation of ovule development in the mutant pistils indicated that the enlargement of the megaspore was blocked and nuclear division arrested at the one-nucleate stage during embryo sac formation. Our data suggest that AtKin-1 plays a role in the nuclear division cycles during megagametogenesis.
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Affiliation(s)
- Haiqing Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, 23 Xinning Road, Xining, 810001, China,
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100
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Sheen J. Master Regulators in Plant Glucose Signaling Networks. JOURNAL OF PLANT BIOLOGY = SINGMUL HAKHOE CHI 2014; 57:67-79. [PMID: 25530701 PMCID: PMC4270195 DOI: 10.1007/s12374-014-0902-7] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The daily life of photosynthetic plants revolves around sugar production, transport, storage and utilization, and the complex sugar metabolic and signaling networks integrate internal regulators and environmental cues to govern and sustain plant growth and survival. Although diverse sugar signals have emerged as pivotal regulators from embryogenesis to senescence, glucose is the most ancient and conserved regulatory signal that controls gene and protein expression, cell-cycle progression, central and secondary metabolism, as well as growth and developmental programs. Glucose signals are perceived and transduced by two principal mechanisms: direct sensing through glucose sensors and indirect sensing via a variety of energy and metabolite sensors. This review focuses on the comparative and functional analyses of three glucose-modulated master regulators in Arabidopsis thaliana, the hexokinase1 (HXK1) glucose sensor, the energy sensor kinases KIN10/KIN11 inactivated by glucose, and the glucose-activated target of rapamycin (TOR) kinase. These regulators are evolutionarily conserved, but have evolved universal and unique regulatory wiring and functions in plants and animals. They form protein complexes with multiple partners as regulators or effectors to serve distinct functions in different subcellular locales and organs, and play integrative and complementary roles from cellular signaling and metabolism to development in the plant glucose signaling networks.
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Affiliation(s)
- Jen Sheen
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
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