1
|
Lang PLM, Erberich JM, Lopez L, Weiß CL, Amador G, Fung HF, Latorre SM, Lasky JR, Burbano HA, Expósito-Alonso M, Bergmann DC. Century-long timelines of herbarium genomes predict plant stomatal response to climate change. Nat Ecol Evol 2024; 8:1641-1653. [PMID: 39117952 PMCID: PMC11383800 DOI: 10.1038/s41559-024-02481-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/21/2024] [Indexed: 08/10/2024]
Abstract
Dissecting plant responses to the environment is key to understanding whether and how plants adapt to anthropogenic climate change. Stomata, plants' pores for gas exchange, are expected to decrease in density following increased CO2 concentrations, a trend already observed in multiple plant species. However, it is unclear whether such responses are based on genetic changes and evolutionary adaptation. Here we make use of extensive knowledge of 43 genes in the stomatal development pathway and newly generated genome information of 191 Arabidopsis thaliana historical herbarium specimens collected over 193 years to directly link genetic variation with climate change. While we find that the essential transcription factors SPCH, MUTE and FAMA, central to stomatal development, are under strong evolutionary constraints, several regulators of stomatal development show signs of local adaptation in contemporary samples from different geographic regions. We then develop a functional score based on known effects of gene knock-out on stomatal development that recovers a classic pattern of stomatal density decrease over the past centuries, suggesting a genetic component contributing to this change. This approach combining historical genomics with functional experimental knowledge could allow further investigations of how different, even in historical samples unmeasurable, cellular plant phenotypes may have already responded to climate change through adaptive evolution.
Collapse
Affiliation(s)
- Patricia L M Lang
- Department of Biology, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
| | - Joel M Erberich
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Lua Lopez
- Department of Biological Sciences, California State University San Bernardino, San Bernardino, CA, USA
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Clemens L Weiß
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Gabriel Amador
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hannah F Fung
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Sergio M Latorre
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Biology, Tübingen, Germany
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Hernán A Burbano
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Biology, Tübingen, Germany
| | - Moisés Expósito-Alonso
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
- Department of Integrative Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Dominique C Bergmann
- Department of Biology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| |
Collapse
|
2
|
Zhou L, Yu S, Liu Y, Wang Y, Wen Y, Zhang Z, Ru Y, He Z, Chen X. Nitric oxide is involved in the regulation of guard mother cell division by inhibiting the synthesis of ACC. PLANT, CELL & ENVIRONMENT 2024; 47:2716-2732. [PMID: 37842726 DOI: 10.1111/pce.14734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/10/2023] [Accepted: 10/03/2023] [Indexed: 10/17/2023]
Abstract
A stoma forms by a series of asymmetric divisions of stomatal lineage precursor cell and the terminal division of a guard mother cell (GMC). GMC division is restricted to once through genetic regulation mechanisms. Here, we show that nitric oxide (NO) is involved in the regulation of the GMC division. NO donor treatment results in the formation of single guard cells (SGCs). SGCs are also produced in plants that accumulate high NO, whereas clustered guard cells (GCs) appear in plants with low NO accumulation. NO treatment promotes the formation of SGCs in the stomatal signalling mutants sdd1, epf1 epf2, tmm1, erl1 erl2 and er erl1 erl2, reduces the cell number per stomatal cluster in the fama-1 and flp1 myb88, but has no effect on stomatal of cdkb1;1 cyca2;234. Aminocyclopropane-1-carboxylic acid (ACC), a positive regulator of GMC division, reduces the NO-induced SGC formation. Further investigation found NO inhibits ACC synthesis by repressing the expression of several ACC SYNTHASE (ACS) genes, and in turn ACC represses NO accumulation by promoting the expression of HEMOGLOBIN 1 (HB1) encoding a NO scavenger. This work shows NO plays a role in the regulation of GMC division by modulating ACC accumulation in the Arabidopsis cotyledon.
Collapse
Affiliation(s)
- Lijuan Zhou
- School of Life Sciences, Yunnan University, Kunming, Yunnan, China
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, China
| | - Shuangshuang Yu
- School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Yue Liu
- School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Yanyan Wang
- International Agricultural Research Institute, Yunnan Academy of Agriculture Sciences, Kunming, Yunnan, China
| | - Yuanyuan Wen
- School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Zijing Zhang
- School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Yanyu Ru
- School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Zhaorong He
- School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Xiaolan Chen
- School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| |
Collapse
|
3
|
Chen L. Regulation of stomatal development by epidermal, subepidermal and long-distance signals. PLANT MOLECULAR BIOLOGY 2024; 114:80. [PMID: 38940934 DOI: 10.1007/s11103-024-01456-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 04/20/2024] [Indexed: 06/29/2024]
Abstract
Plant leaves consist of three layers, including epidermis, mesophyll and vascular tissues. Their development is meticulously orchestrated. Stomata are the specified structures on the epidermis for uptake of carbon dioxide (CO2) while release of water vapour and oxygen (O2), and thus play essential roles in regulation of plant photosynthesis and water use efficiency. To function efficiently, stomatal formation must coordinate with the development of other epidermal cell types, such as pavement cell and trichome, and tissues of other layers, such as mesophyll and leaf vein. This review summarizes the regulation of stomatal development in three dimensions (3D). In the epidermis, specific stomatal transcription factors determine cell fate transitions and also activate a ligand-receptor- MITOGEN-ACTIVATED PROTEIN KINASE (MAPK) signaling for ensuring proper stomatal density and patterning. This forms the core regulation network of stomatal development, which integrates various environmental cues and phytohormone signals to modulate stomatal production. Under the epidermis, mesophyll, endodermis of hypocotyl and inflorescence stem, and veins in grasses secrete mobile signals to influence stomatal formation in the epidermis. In addition, long-distance signals which may include phytohormones, RNAs, peptides and proteins originated from other plant organs modulate stomatal development, enabling plants to systematically adapt to the ever changing environment.
Collapse
Affiliation(s)
- Liang Chen
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China.
| |
Collapse
|
4
|
Zhang X, Cai Q, Li L, Wang L, Hu Y, Chen X, Zhang D, Persson S, Yuan Z. OsMADS6-OsMADS32 and REP1 control palea cellular heterogeneity and morphogenesis in rice. Dev Cell 2024; 59:1379-1395.e5. [PMID: 38593802 DOI: 10.1016/j.devcel.2024.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 01/02/2024] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Precise regulation of cell proliferation and differentiation is vital for organ morphology. Rice palea, serving as sepal, comprises two distinct regions: the marginal region (MRP) and body of palea (BOP), housing heterogeneous cell populations, which makes it an ideal system for studying organ morphogenesis. We report that the transcription factor (TF) REP1 promotes epidermal cell proliferation and differentiation in the BOP, resulting in hard silicified protrusion cells, by regulating the cyclin-dependent kinase gene, OsCDKB1;1. Conversely, TFs OsMADS6 and OsMADS32 are expressed exclusively in the MRP, where they limit cell division rates by inhibiting OsCDKB2;1 expression and promote endoreduplication, yielding elongated epidermal cells. Furthermore, reciprocal inhibition between the OsMADS6-OsMADS32 complex and REP1 fine-tunes the balance between cell division and differentiation during palea morphogenesis. We further show the functional conservation of these organ identity genes in heterogeneous cell growth in Arabidopsis, emphasizing a critical framework for controlling cellular heterogeneity in organ morphogenesis.
Collapse
Affiliation(s)
- Xuelian Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Cai
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Ling Li
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Li Wang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yun Hu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaofei Chen
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya 572024, China
| | - Staffan Persson
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Department of Plant & Environmental Sciences, Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Zheng Yuan
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya 572024, China.
| |
Collapse
|
5
|
Singh D, Banerjee G, Verma N, Sinha AK. MAP kinases may mediate regulation of the cell cycle in rice by E2F2 phosphorylation. FEBS Lett 2023; 597:2993-3009. [PMID: 37843487 DOI: 10.1002/1873-3468.14753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/10/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023]
Abstract
E2F is the key transcription factor that determines the proliferative status of cells by regulating the G1/S phase of the cell cycle. In this study, we show that in rice (Oryza sativa), OsE2F2 is a phosphorylation target of MAP kinases. The MAP kinases OsMPK3, OsMPK4, and OsMPK6 interact with and phosphorylate OsE2F2. Next, we determined the serine and threonine residues that could play a role in the phosphorylation of OsE2F2. Subsequently, our study suggests a possible link between MAP kinase-mediated OsE2F2 phosphorylation and its impact on DNA proliferation in the roots of rice seedlings. Finally, we found positive feedback regulation of OsMPK4 by OsE2F2. Therefore, our study hints at the potential impact of MAP kinase signaling on the cell cycle of rice plants.
Collapse
Affiliation(s)
- Dhanraj Singh
- National Institute of Plant Genome Research, Delhi, New Delhi, India
| | - Gopal Banerjee
- National Institute of Plant Genome Research, Delhi, New Delhi, India
| | - Neetu Verma
- National Institute of Plant Genome Research, Delhi, New Delhi, India
| | | |
Collapse
|
6
|
Wang W, Liu W, Wang B. Identification of CDK gene family and functional analysis of CqCDK15 under drought and salt stress in quinoa. BMC Genomics 2023; 24:461. [PMID: 37592203 PMCID: PMC10433607 DOI: 10.1186/s12864-023-09570-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/09/2023] [Indexed: 08/19/2023] Open
Abstract
as one of the oldest cultivated crops in the world, quinoa has been widely valued for its rich nutritional value and green health. In this study, 22 CDK genes (CqCDK01-CqCDK22) were identified from quinoa genome using bioinformatics method. The number of amino acids was 173-811, the molecular weight was 19,554.89 Da-91,375.70 Da, and the isoelectric point was 4.57-9.77. The phylogenetic tree divided 21 CqCDK genes into six subfamilies, the gene structure showed that 12 (54.5%) CqCDK genes (CqCDK03, CqCDK04, CqCDK05, CqCDK06, CqCDK07, CqCDK11, CqCDK14, CqCDK16, CqCDK18, CqCDK19, CqCDK20 and CqCDK21) had UTR regions at 5' and 3' ends. Each CDK protein had different motifs (3-9 motifs), but the genes with the same motifs were located in the same branch. Promoter analysis revealed 41 cis-regulatory elements related to plant hormones, abiotic stresses, tissue-specific expression and photoresponse. The results of real-time fluorescence quantitative analysis showed that the expression level of some CDK genes was higher under drought and salt stress, which indicated that CDK genes could help plants to resist adverse environmental effects. Subcellular localization showed that CqCDK15 gene was localized to the nucleus and cytoplasm, and transgenic plants overexpressing CqCDK15 gene showed higher drought and salt tolerance compared to the controls. Therefore, CDK genes are closely related to quinoa stress resistance. In this study, the main functions of quinoa CDK gene family and its expression level in different tissues and organs were analyzed in detail, which provided some theoretical support for quinoa stress-resistant breeding. Meanwhile, this study has important implications for further understanding the function of the CDK gene family in quinoa and our understanding of the CDK family in vascular plant.
Collapse
Affiliation(s)
- Wangtian Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of life science and technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Wenyu Liu
- Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Baoqiang Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
- College of life science and technology, Gansu Agricultural University, Lanzhou, 730070, China.
| |
Collapse
|
7
|
Dubois M, Achon I, Brench RA, Polyn S, Tenorio Berrío R, Vercauteren I, Gray JE, Inzé D, De Veylder L. SIAMESE-RELATED1 imposes differentiation of stomatal lineage ground cells into pavement cells. NATURE PLANTS 2023:10.1038/s41477-023-01452-7. [PMID: 37386150 DOI: 10.1038/s41477-023-01452-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 05/30/2023] [Indexed: 07/01/2023]
Abstract
The leaf epidermis represents a multifunctional tissue consisting of trichomes, pavement cells and stomata, the specialized cellular pores of the leaf. Pavement cells and stomata both originate from regulated divisions of stomatal lineage ground cells (SLGCs), but whereas the ontogeny of the stomata is well characterized, the genetic pathways activating pavement cell differentiation remain relatively unexplored. Here, we reveal that the cell cycle inhibitor SIAMESE-RELATED1 (SMR1) is essential for timely differentiation of SLGCs into pavement cells by terminating SLGC self-renewal potency, which depends on CYCLIN A proteins and CYCLIN-DEPENDENT KINASE B1. By controlling SLGC-to-pavement cell differentiation, SMR1 determines the ratio of pavement cells to stomata and adjusts epidermal development to suit environmental conditions. We therefore propose SMR1 as an attractive target for engineering climate-resilient plants.
Collapse
Affiliation(s)
- Marieke Dubois
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Ignacio Achon
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Robert A Brench
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Stefanie Polyn
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Rubén Tenorio Berrío
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Ilse Vercauteren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Julie E Gray
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium.
- Center for Plant Systems Biology, VIB, Gent, Belgium.
| |
Collapse
|
8
|
López-Hernández MN, Vázquez-Ramos JM. Maize CDKA2;1a and CDKB1;1 kinases have different requirements for their activation and participate in substrate recognition. FEBS J 2023; 290:2463-2488. [PMID: 36259272 DOI: 10.1111/febs.16659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/13/2022] [Accepted: 10/18/2022] [Indexed: 05/04/2023]
Abstract
Cyclin-dependent kinases (CDKs), in association with cyclins, control cell cycle progression by phosphorylating a large number of substrates. In animals, activation of CDKs regularly requires both the association with a cyclin and then phosphorylation of a highly conserved threonine residue in the CDK activation loop (the classical mechanism), mediated by a CDK-activating kinase (CAK). In addition to this typical mechanism of activation, some CDKs can also be activated by the association of a cyclin to a monomeric CDK previously phosphorylated by CAK although not all CDKs can be activated by this mechanism. In animals and yeast, cyclin, in addition to being required for CDK activation, provides substrate specificity to the cyclin/CDK complex; however, in plants both the mechanisms of CDKs activation and the relevance of the CDK-associated cyclin for substrate targeting have been poorly studied. In this work, by co-expressing proteins in E. coli, we studied maize CDKA2;1a and CDKB1;1, two of the main types of CDKs that control the cell cycle in plants. These kinases could be activated by the classical mechanism and by the association of CycD2;2a to a phosphorylated intermediate in its activation loop, a previously unproven mechanism for the activation of plant CDKs. Unlike CDKA2;1a, CDKB1;1 did not require CAK for its activation, since it autophosphorylated in its activation loop. Phosphorylation of CDKB1;1 and association of CycD2;2 was not enough for its full activation as association of maize CKS, a scaffolding protein, differentially stimulated substrate phosphorylation. Our results suggest that both CDKs participate in substrate recognition.
Collapse
Affiliation(s)
| | - Jorge M Vázquez-Ramos
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Mexico
| |
Collapse
|
9
|
Chen L. Emerging roles of protein phosphorylation in regulation of stomatal development. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153882. [PMID: 36493667 DOI: 10.1016/j.jplph.2022.153882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Stomata, tiny epidermal spores, control gas exchange between plants and their external environment, thereby playing essential roles in plant development and physiology. Stomatal development requires rapid regulation of components in signaling pathways to respond flexibly to numerous intrinsic and extrinsic signals. In support of this, reversible phosphorylation, which is particularly suitable for rapid signal transduction, has been implicated in this process. This review highlights the current understanding of the essential roles of reversible phosphorylation in the regulation of stomatal development, most of which comes from the dicot Arabidopsis thaliana. Protein phosphorylation tightly controls the activity of SPEECHLESS (SPCH)-SCREAM (SCRM), the stomatal lineage switch, and the activity of several mitogen-activated protein kinases and receptor kinases upstream of SPCH-SCRM, thereby regulating stomatal cell differentiation and patterning. In addition, protein phosphorylation is involved in the establishment of cell polarity during stomatal asymmetric cell division. Finally, cyclin-dependent kinase-mediated protein phosphorylation plays essential roles in cell cycle control during stomatal development.
Collapse
Affiliation(s)
- Liang Chen
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, PR China.
| |
Collapse
|
10
|
Jiang S, Meng B, Zhang Y, Li N, Zhou L, Zhang X, Xu R, Guo S, Song CP, Li Y. An SNW/SKI-INTERACTING PROTEIN influences endoreduplication and cell growth in Arabidopsis. PLANT PHYSIOLOGY 2022; 190:2217-2228. [PMID: 36063458 PMCID: PMC9706482 DOI: 10.1093/plphys/kiac415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Endoreduplication plays an important role in cell growth and differentiation, but the mechanisms regulating endoreduplication are still elusive. We have previously reported that UBIQUITIN-SPECIFIC PROTEASE14 (UBP14) encoded by DA3 interacts with ULTRAVIOLETB INSENSITIVE4 (UVI4) to influence endoreduplication and cell growth in Arabidopsis (Arabidopsis thaliana). The da3-1 mutant possesses larger cotyledons and flowers with higher ploidy levels than the wild-type. Here, we identify the suppressor of da3-1 (SUPPRESSOR OF da3-1 3; SUD3), which encodes SNW/SKI-INTERACTING PROTEIN (SKIP). Biochemical studies demonstrate that SUD3 physically interacts with UBP14/DA3 and UVI4 in vivo and in vitro. Genetic analyses support that SUD3 acts in a common pathway with UBP14/DA3 and UVI4 to control endoreduplication. Our findings reveal an important genetic and molecular mechanism by which SKIP/SUD3 associates with UBP14/DA3 and UVI4 to modulate endoreduplication.
Collapse
Affiliation(s)
- Shan Jiang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bolun Meng
- State Key Laboratory of Crop Stress Adaptation and Improvement, Collaborative Innovation Center of Crop Stress Biology, College of Life Sciences, Henan University, Kaifeng, Henan 475001, China
| | - Yilan Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Collaborative Innovation Center of Crop Stress Biology, College of Life Sciences, Henan University, Kaifeng, Henan 475001, China
| | - Na Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lixun Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuan Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Collaborative Innovation Center of Crop Stress Biology, College of Life Sciences, Henan University, Kaifeng, Henan 475001, China
| | - Ran Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Siyi Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, Collaborative Innovation Center of Crop Stress Biology, College of Life Sciences, Henan University, Kaifeng, Henan 475001, China
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, Collaborative Innovation Center of Crop Stress Biology, College of Life Sciences, Henan University, Kaifeng, Henan 475001, China
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 10039, China
| |
Collapse
|
11
|
Study on the interaction preference between CYCD subclass and CDK family members at the poplar genome level. Sci Rep 2022; 12:16805. [PMID: 36207355 PMCID: PMC9547009 DOI: 10.1038/s41598-022-20800-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/19/2022] [Indexed: 12/31/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) control the progression of the cell cycle. D-type cyclin (CYCD) is generally believed to form a complex with CDK and control the G1/S transition. In plants, CYCD and CDK gene families can be divided into 6 (D1-D7) and 7 (CDKA-CDKG) subclasses, respectively. Different subclasses in the CYCD and CDK families have different numbers, structures and functions. In some heterologous woody plants, the functions of these subclass family members remain unclear. In this study, 43 CYCD and 27 CDK gene family members were identified in the allodiploid Populus tomentosa Carr. Phylogenetic analysis suggested that these CYCDs and CDKs were divided into 6 and 7 subclasses, respectively, which were the same as other species. The analysis of protein properties, gene structure, motifs, domains, cis-acting elements and tissue-specific expression of all members of these CYCDs and CDKs showed that the differences between members of different subclasses varied widely, but members of the same subclass especially in the CDK gene family were very similar. These findings also demonstrated a strong correlation between CYCD and CDK gene family members in response to hormones and specific expression. The collinear analysis of P. tomentosa, Populus trichocarpa and Arabidopsis thaliana showed that the expansion patterns of CYCD and CDK gene families were predominantly whole genome duplications (WGD). The protein interaction prediction results of different subclasses of CYCD and CDKs showed that the interaction between different subclasses of CYCD and CDKs was significantly different. Our previous study found that transgenic PtoCYCD2;1 and PtoCYCD3;3 poplars exhibited opposite phenotypes. Y2H and BIFC results showed that the interaction between PtoCYCD2;1 and PtoCYCD3;3 was significantly different with CDKs. This finding might suggest that the functional differences of different CYCD subclasses in plant growth and development were closely related to the different interactions between CYCD and CDK. Our results provide a good idea and direction for the functional study of CYCD and CDK proteins in woody plants.
Collapse
|
12
|
Peng Y, Zuo W, Zhou H, Miao F, Zhang Y, Qin Y, Liu Y, Long Y, Ma S. EXPLICIT-Kinase: A gene expression predictor for dissecting the functions of the Arabidopsis kinome. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1374-1393. [PMID: 35446465 DOI: 10.1111/jipb.13267] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
Protein kinases regulate virtually all cellular processes, but it remains challenging to determine the functions of all protein kinases, collectively called the "kinome", in any species. We developed a computational approach called EXPLICIT-Kinase to predict the functions of the Arabidopsis kinome. Because the activities of many kinases can be regulated transcriptionally, their gene expression patterns provide clues to their functions. A universal gene expression predictor for Arabidopsis was constructed to predict the expression of 30,172 non-kinase genes based on the expression of 994 kinases. The model reconstituted highly accurate transcriptomes for diverse Arabidopsis samples. It identified the significant kinases as predictor kinases for predicting the expression of Arabidopsis genes and pathways. Strikingly, these predictor kinases were often regulators of related pathways, as exemplified by those involved in cytokinesis, tissue development, and stress responses. Comparative analyses revealed that portions of these predictor kinases are shared and conserved between Arabidopsis and maize. As an example, we identified a conserved predictor kinase, RAF6, from a stomatal movement module. We verified that RAF6 regulates stomatal closure. It can directly interact with SLAC1, a key anion channel for stomatal closure, and modulate its channel activity. Our approach enables a systematic dissection of the functions of the Arabidopsis kinome.
Collapse
Affiliation(s)
- Yuming Peng
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, 230027, China
| | - Wanzhu Zuo
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, 230027, China
| | - Hui Zhou
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Fenfen Miao
- State Key Laboratory for Plant Molecular Genetics, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yu Zhang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, 230027, China
| | - Yue Qin
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, 230027, China
| | - Yi Liu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, 230027, China
| | - Yu Long
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Shisong Ma
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, 230027, China
- School of Data Science, University of Science and Technology of China, Hefei, 230027, China
| |
Collapse
|
13
|
Jiang S, Wei J, Li N, Wang Z, Zhang Y, Xu R, Zhou L, Huang X, Wang L, Guo S, Wang Y, Song CP, Qian W, Li Y. The UBP14-CDKB1;1-CDKG2 cascade controls endoreduplication and cell growth in Arabidopsis. THE PLANT CELL 2022; 34:1308-1325. [PMID: 34999895 PMCID: PMC8972217 DOI: 10.1093/plcell/koac002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/16/2021] [Indexed: 05/31/2023]
Abstract
Endoreduplication, a process in which DNA replication occurs in the absence of mitosis, is found in all eukaryotic kingdoms, especially plants, where it is assumed to be important for cell growth and cell fate maintenance. However, a comprehensive understanding of the mechanism regulating endoreduplication is still lacking. We previously reported that UBIQUITIN-SPECIFIC PROTEASE14 (UBP14), encoded by DA3, acts upstream of CYCLIN-DEPENDENT KINASE B1;1 (CDKB1;1) to influence endoreduplication and cell growth in Arabidopsis thaliana. The da3-1 mutant possesses large cotyledons with enlarged cells due to high ploidy levels. Here, we identified a suppressor of da3-1 (SUPPRESSOR OF da3-1 6; SUD6), encoding CYCLIN-DEPENDENT KINASE G2 (CDKG2), which promotes endoreduplication and cell growth. CDKG2/SUD6 physically associates with CDKB1;1 in vivo and in vitro. CDKB1;1 directly phosphorylates SUD6 and modulates its stability. Genetic analysis indicated that SUD6 acts downstream of DA3 and CDKB1;1 to control ploidy level and cell growth. Thus, our study establishes a regulatory cascade for UBP14/DA3-CDKB1;1-CDKG2/SUD6-mediated control of endoreduplication and cell growth in Arabidopsis.
Collapse
Affiliation(s)
- Shan Jiang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jinwei Wei
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Na Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhibiao Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yilan Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Collaborative Innovation Center of Crop Stress Biology, College of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Ran Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lixun Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Li Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Siyi Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, Collaborative Innovation Center of Crop Stress Biology, College of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, Collaborative Innovation Center of Crop Stress Biology, College of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Wei Qian
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | | |
Collapse
|
14
|
Han SK, Herrmann A, Yang J, Iwasaki R, Sakamoto T, Desvoyes B, Kimura S, Gutierrez C, Kim ED, Torii KU. Deceleration of the cell cycle underpins a switch from proliferative to terminal divisions in plant stomatal lineage. Dev Cell 2022; 57:569-582.e6. [PMID: 35148836 PMCID: PMC8926846 DOI: 10.1016/j.devcel.2022.01.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 11/19/2021] [Accepted: 01/19/2022] [Indexed: 12/25/2022]
Abstract
Differentiation of specialized cell types requires precise cell-cycle control. Plant stomata are generated through asymmetric divisions of a stem-cell-like precursor followed by a single symmetric division that creates paired guard cells surrounding a pore. The stomatal-lineage-specific transcription factor MUTE terminates the asymmetric divisions and commits to differentiation. However, the role of cell-cycle machineries in this transition remains unknown. We discover that the symmetric division is slower than the asymmetric division in Arabidopsis. We identify a plant-specific cyclin-dependent kinase inhibitor, SIAMESE-RELATED4 (SMR4), as a MUTE-induced molecular brake that decelerates the cell cycle. SMR4 physically and functionally associates with CYCD3;1 and extends the G1 phase of asymmetric divisions. By contrast, SMR4 fails to interact with CYCD5;1, a MUTE-induced G1 cyclin, and permits the symmetric division. Our work unravels a molecular framework of the proliferation-to-differentiation switch within the stomatal lineage and suggests that a timely proliferative cell cycle is critical for stomatal-lineage identity. During stomatal differentiation, asymmetric divisions are faster than terminal divisions Upon commitment to differentiation, MUTE induces the cell-cycle inhibitor SMR4 SMR4 decelerates the asymmetric cell division cycle via selective binding to cyclin D Regulating duration of the G1 phase is critical for epidermal cell fate specification
Collapse
Affiliation(s)
- Soon-Ki Han
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Aichi 464-8601, Japan; Institute for Advanced Research (IAR), Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Arvid Herrmann
- Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jiyuan Yang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Rie Iwasaki
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Tomoaki Sakamoto
- Department of Industrial Life Sciences and Center for Plant Sciences, Kyoto Sangyo University, Kyoto-shi, Kyoto 603-8555, Japan
| | - Bénédicte Desvoyes
- Centro de Biologia Molecular Severo Ochoa, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Seisuke Kimura
- Department of Industrial Life Sciences and Center for Plant Sciences, Kyoto Sangyo University, Kyoto-shi, Kyoto 603-8555, Japan
| | - Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Eun-Deok Kim
- Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Keiko U Torii
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Aichi 464-8601, Japan; Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
| |
Collapse
|
15
|
Zuch DT, Doyle SM, Majda M, Smith RS, Robert S, Torii KU. Cell biology of the leaf epidermis: Fate specification, morphogenesis, and coordination. THE PLANT CELL 2022; 34:209-227. [PMID: 34623438 PMCID: PMC8774078 DOI: 10.1093/plcell/koab250] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/18/2021] [Indexed: 05/02/2023]
Abstract
As the outermost layer of plants, the epidermis serves as a critical interface between plants and the environment. During leaf development, the differentiation of specialized epidermal cell types, including stomatal guard cells, pavement cells, and trichomes, occurs simultaneously, each providing unique and pivotal functions for plant growth and survival. Decades of molecular-genetic and physiological studies have unraveled key players and hormone signaling specifying epidermal differentiation. However, most studies focus on only one cell type at a time, and how these distinct cell types coordinate as a unit is far from well-comprehended. Here we provide a review on the current knowledge of regulatory mechanisms underpinning the fate specification, differentiation, morphogenesis, and positioning of these specialized cell types. Emphasis is given to their shared developmental origins, fate flexibility, as well as cell cycle and hormonal controls. Furthermore, we discuss computational modeling approaches to integrate how mechanical properties of individual epidermal cell types and entire tissue/organ properties mutually influence each other. We hope to illuminate the underlying mechanisms coordinating the cell differentiation that ultimately generate a functional leaf epidermis.
Collapse
Affiliation(s)
- Daniel T Zuch
- Department of Molecular Biosciences, Howard Hughes Medical Institute, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Siamsa M Doyle
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå 90183, Sweden
| | - Mateusz Majda
- Department of Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Richard S Smith
- Department of Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Stéphanie Robert
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå 90183, Sweden
| | - Keiko U Torii
- Department of Molecular Biosciences, Howard Hughes Medical Institute, The University of Texas at Austin, Austin, Texas 78712, USA
| |
Collapse
|
16
|
Genome-Wide Identification and Analysis of Cell Cycle Genes in Birch. FORESTS 2022. [DOI: 10.3390/f13010120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Research Highlights: This study identified the cell cycle genes in birch that likely play important roles during the plant’s growth and development. This analysis provides a basis for understanding the regulatory mechanism of various cell cycles in Betula pendula Roth. Background and Objectives: The cell cycle factors not only influence cell cycles progression together, but also regulate accretion, division, and differentiation of cells, and then regulate growth and development of the plant. In this study, we identified the putative cell cycle genes in the B. pendula genome, based on the annotated cell cycle genes in Arabidopsis thaliana (L.) Heynh. It can be used as a basis for further functional research. Materials and Methods: RNA-seq technology was used to determine the transcription abundance of all cell cycle genes in xylem, roots, leaves, and floral tissues. Results: We identified 59 cell cycle gene models in the genome of B. pendula, with 17 highly expression genes among them. These genes were BpCDKA.1, BpCDKB1.1, BpCDKB2.1, BpCKS1.2, BpCYCB1.1, BpCYCB1.2, BpCYCB2.1, BpCYCD3.1, BpCYCD3.5, BpDEL1, BpDpa2, BpE2Fa, BpE2Fb, BpKRP1, BpKRP2, BpRb1, and BpWEE1. Conclusions: By combining phylogenetic analysis and tissue-specific expression data, we identified 17 core cell cycle genes in the Betulapendula genome.
Collapse
|
17
|
Pignon CP, Fernandes SB, Valluru R, Bandillo N, Lozano R, Buckler E, Gore MA, Long SP, Brown PJ, Leakey ADB. Phenotyping stomatal closure by thermal imaging for GWAS and TWAS of water use efficiency-related genes. PLANT PHYSIOLOGY 2021; 187:2544-2562. [PMID: 34618072 PMCID: PMC8644692 DOI: 10.1093/plphys/kiab395] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/26/2021] [Indexed: 05/07/2023]
Abstract
Stomata allow CO2 uptake by leaves for photosynthetic assimilation at the cost of water vapor loss to the atmosphere. The opening and closing of stomata in response to fluctuations in light intensity regulate CO2 and water fluxes and are essential for maintaining water-use efficiency (WUE). However, a little is known about the genetic basis for natural variation in stomatal movement, especially in C4 crops. This is partly because the stomatal response to a change in light intensity is difficult to measure at the scale required for association studies. Here, we used high-throughput thermal imaging to bypass the phenotyping bottleneck and assess 10 traits describing stomatal conductance (gs) before, during and after a stepwise decrease in light intensity for a diversity panel of 659 sorghum (Sorghum bicolor) accessions. Results from thermal imaging significantly correlated with photosynthetic gas exchange measurements. gs traits varied substantially across the population and were moderately heritable (h2 up to 0.72). An integrated genome-wide and transcriptome-wide association study identified candidate genes putatively driving variation in stomatal conductance traits. Of the 239 unique candidate genes identified with the greatest confidence, 77 were putative orthologs of Arabidopsis (Arabidopsis thaliana) genes related to functions implicated in WUE, including stomatal opening/closing (24 genes), stomatal/epidermal cell development (35 genes), leaf/vasculature development (12 genes), or chlorophyll metabolism/photosynthesis (8 genes). These findings demonstrate an approach to finding genotype-to-phenotype relationships for a challenging trait as well as candidate genes for further investigation of the genetic basis of WUE in a model C4 grass for bioenergy, food, and forage production.
Collapse
Affiliation(s)
- Charles P Pignon
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Samuel B Fernandes
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ravi Valluru
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- Lincoln Institute for Agri-Food Technology, University of Lincoln, Lincoln LN1 3QE, UK
| | - Nonoy Bandillo
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58105, USA
| | - Roberto Lozano
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Edward Buckler
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS) R.W. Holley Center for Agriculture and Health, Ithaca, New York 14853, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Stephen P Long
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Lancaster Environment Centre, University of Lancaster, Lancaster LA1 1YX, UK
| | - Patrick J Brown
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Andrew D B Leakey
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- Author for communication:
| |
Collapse
|
18
|
Serna L. The Role of Grass MUTE Orthologs in GMC Progression and GC Morphogenesis. FRONTIERS IN PLANT SCIENCE 2021; 12:678417. [PMID: 34249046 PMCID: PMC8264291 DOI: 10.3389/fpls.2021.678417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/26/2021] [Indexed: 06/13/2023]
Abstract
Stomata arose about 400 million years ago when plants left their aquatic environment. The last step of stomatal development is shared by all plant groups, and it implies a symmetrical cell division from the guard mother cell (GMC) to produce two guard cells (GCs) flanking a pore. In Arabidopsis, the basic helix-loop-helix transcription factor MUTE controls this step, upregulating cell-cycle regulators of the GMC division, and immediately afterward, repressors of theses regulators like FAMA and FOUR LIPS. Recently, three grass MUTE orthologs (BdMUTE from Brachypodium distachyon, OsMUTE from rice, and ZmMUTE from maize) have been identified and characterized. Mutations in these genes disrupt GMC fate, with bdmute also blocking GC morphogenesis. However, because these genes also regulate subsidiary cell recruitment, which takes place before GMC division, their functions regulating GMC division and GC morphogenesis could be an indirect consequence of that inducing the recruitment of subsidiary cells. Comprehensive data evaluation indicates that BdMUTE, and probably grass MUTE orthologs, directly controls GMC fate. Although grass MUTE proteins, whose genes are expressed in the GMC, move between cells, they regulate GMC fate from the cells where they are transcribed. Grass MUTE genes also regulate GC morphogenesis. Specifically, OsMUTE controls GC shape by inducing OsFAMA expression. In addition, while SCs are not required for GMC fate progression, they are for GC maturation.
Collapse
|
19
|
Tripathi DK, Rai P, Guerriero G, Sharma S, Corpas FJ, Singh VP. Silicon induces adventitious root formation in rice under arsenate stress with involvement of nitric oxide and indole-3-acetic acid. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4457-4471. [PMID: 33095869 DOI: 10.1093/jxb/eraa488] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 10/18/2020] [Indexed: 05/04/2023]
Abstract
Arsenic (As) negatively affects plant development. This study evaluates how the application of silicon (Si) can favor the formation of adventitious roots in rice under arsenate stress (AsV) as a mechanism to mitigate its negative effects. The simultaneous application of AsV and Si up-regulated the expression of genes involved in nitric oxide (NO) metabolism, cell cycle progression, auxin (IAA, indole-3-acetic acid) biosynthesis and transport, and Si uptake which accompanied adventitious root formation. Furthermore, Si triggered the expression and activity of enzymes involved in ascorbate recycling. Treatment with L-NAME (NG-nitro L-arginine methyl ester), an inhibitor of NO generation, significantly suppressed adventitious root formation, even in the presence of Si; however, supplying NO in the growth media rescued its effects. Our data suggest that both NO and IAA are essential for Si-mediated adventitious root formation under AsV stress. Interestingly, TIBA (2,3,5-triiodobenzoic acid), a polar auxin transport inhibitor, suppressed adventitious root formation even in the presence of Si and SNP (sodium nitroprusside, an NO donor), suggesting that Si is involved in a mechanism whereby a cellular signal is triggered and that first requires NO formation, followed by IAA biosynthesis.
Collapse
Affiliation(s)
- Durgesh Kumar Tripathi
- Amity Institute of Organic Agriculture (AIOA), Amity University, Noida, Noida, Uttar Pradesh
| | - Padmaja Rai
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, PrayagrajIndia
| | - Gea Guerriero
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, Hautcharage, Luxembourg
| | - Shivesh Sharma
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, PrayagrajIndia
| | - Francisco J Corpas
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry and Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, Granada, Spain
| | - Vijay Pratap Singh
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Allahabad-211002, India
| |
Collapse
|
20
|
Guo X, Park CH, Wang ZY, Nickels BE, Dong J. A spatiotemporal molecular switch governs plant asymmetric cell division. NATURE PLANTS 2021; 7:667-680. [PMID: 33941907 PMCID: PMC9115727 DOI: 10.1038/s41477-021-00906-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/25/2021] [Indexed: 05/18/2023]
Abstract
Asymmetric cell division (ACD) requires protein polarization in the mother cell to produce daughter cells with distinct identities (cell-fate asymmetry). Here, we define a previously undocumented mechanism for establishing cell-fate asymmetry in Arabidopsis stomatal stem cells. In particular, we show that polarization of the protein phosphatase BSL1 promotes stomatal ACD by establishing kinase-based signalling asymmetry in the two daughter cells. BSL1 polarization in the stomatal ACD mother cell is triggered at the onset of mitosis. Polarized BSL1 is inherited by the differentiating daughter cell, where it suppresses cell division and promotes cell-fate determination. Plants lacking BSL proteins exhibit stomatal overproliferation, which demonstrates that the BSL family plays an essential role in stomatal development. Our findings establish that BSL1 polarization provides a spatiotemporal molecular switch that enables cell-fate asymmetry in stomatal ACD daughter cells. We propose that BSL1 polarization is triggered by an ACD checkpoint in the mother cell that monitors the establishment of division-plane asymmetry.
Collapse
Affiliation(s)
- Xiaoyu Guo
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Chan Ho Park
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Zhi-Yong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Bryce E Nickels
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Juan Dong
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.
| |
Collapse
|
21
|
SPEECHLESS and MUTE Mediate Feedback Regulation of Signal Transduction during Stomatal Development. PLANTS 2021; 10:plants10030432. [PMID: 33668323 PMCID: PMC7996297 DOI: 10.3390/plants10030432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/14/2021] [Accepted: 02/21/2021] [Indexed: 01/01/2023]
Abstract
Stomatal density, spacing, and patterning greatly influence the efficiency of gas exchange, photosynthesis, and water economy. They are regulated by a complex of extracellular and intracellular factors through the signaling pathways. After binding the extracellular epidermal patterning factor 1 (EPF1) and 2 (EPF2) as ligands, the receptor-ligand complexes activate by phosphorylation through the MAP-kinase cascades, regulating basic helix-loop-helix (bHLH) transcription factors SPEECHLESS (SPCH), MUTE, and FAMA. In this review, we summarize the molecular mechanisms and signal transduction pathways running within the transition of the protodermal cell into a pair of guard cells with a space (aperture) between them, called a stoma, comprising asymmetric and symmetric cell divisions and draw several functional models. The feedback mechanisms involving the bHLH factors SPCH and MUTE are not fully recognized yet. We show the feedback mechanisms driven by SPCH and MUTE in the regulation of EPF2 and the ERECTA family. Intersections of the molecular mechanisms for fate determination of stomatal lineage cells with the role of core cell cycle-related genes and stabilization of SPCH and MUTE are also reported.
Collapse
|
22
|
Banerjee G, Singh D, Sinha AK. Plant cell cycle regulators: Mitogen-activated protein kinase, a new regulating switch? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110660. [PMID: 33218628 DOI: 10.1016/j.plantsci.2020.110660] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/25/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
Cell cycle is essential for the maintenance of genetic material and continuity of a species. Its regulation involves a complex interplay between multiple proteins with diverse molecular functions such as the kinases, transcription factors, proteases and phosphatases. Every step of this cycle requires a certain combination of these protein regulators which paves the way for the next stage. It is now evident that plants have their own unique features in the context of cell cycle regulation. Cell cycle in plants is not only necessary for maintenance of its physio-morphological parameter but it also regulates traits important for mankind like grain or fruit size. This makes it even more important to understand how plants regulate its cell cycle amidst various a/biotic stresses it is subjected to during its lifetime. The association of MAPK signaling pathways with every major developmental and stress response pathways in plants raises the question of its potential role in cell cycle regulation. There are number of cell cycle regulating proteins with putative sites for MAPK phosphorylation. The MAPK signaling pathway may directly or in a parallel pathway regulate the plant cell cycle. Unraveling the role of MAPK in cell cycle will open up new arenas to explore.
Collapse
Affiliation(s)
- Gopal Banerjee
- National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, 110067, India
| | - Dhanraj Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, 110067, India
| | - Alok Krishna Sinha
- National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, 110067, India.
| |
Collapse
|
23
|
Li S, Zhang J, Liu L, Wang Z, Li Y, Guo L, Li Y, Zhang X, Ren S, Zhao B, Zhang N, Guo YD. SlTLFP8 reduces water loss to improve water-use efficiency by modulating cell size and stomatal density via endoreduplication. PLANT, CELL & ENVIRONMENT 2020; 43:2666-2679. [PMID: 32799324 DOI: 10.1111/pce.13867] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 08/09/2020] [Indexed: 05/23/2023]
Abstract
Improving plant water-use efficiency (WUE) is important to plant survival and crop yield in the context of water limitation. In this study, SlTLFP8 (Tubby-like F-box protein 8) was identified as an osmotic-induced gene in tomato. Transgenic tomato with up-regulated expression of SlTLFP8 showed enhanced water-deficient resistance, whereas knockout mutants generated by CRISPR/Cas9 were more sensitive to water deficit. SlTLFP8 overexpression significantly enhanced WUE by suppressing transpiration under both water-sufficient and water-deficient conditions. Further study showed that overexpressing SlTLFP8 significantly increased leaf epidermal cell size and thereby decreased stomatal density 10-20%, conversely SlTLFP8 knockout resulted in decreased cell size and thereby increased stomatal density 20-50%. SlTLFP8 overexpression and knockout modulated ploidy levels in leaf cells. Changes in expression of cell cycle related genes also indicated that SlTLFP8 affected cell size and stomatal density through endocycle transition. Despite changes in stomata density and transpiration, altering the expression of SlTLFP8 did not change photosynthesis. Additionally, biomass was not altered and there was little difference in fruit yield for transgenic and wild type lines under water-sufficient and water-deficient conditions. Our results demonstrate the effect of SlTLFP8 on endoreduplication and the potential of SlTLFP8 for improvement of WUE. BRIEF SUMMERY: This work found a new mechanism of TLP (Tubby like protein) response to water-deficient stress. SlTLFP8, a member of TLP family, regulates water-deficient resistance by modulating water loss via affecting stomatal density. Expression of SlTLFP8 was induced by osmotic stress. Transgenic tomato lines with SlTLFP8 overexpression or SlTLFP8 knockout showed significantly differences in water-use efficiency (WUE) and water-deficient resistance. The difference of leaf water loss caused by transpiration is the main explanation of the difference in WUE and water-deficient resistance. Additionally, overexpressing SlTLFP8 significantly decreased stomatal density, while SlTLFP8 knockout resulted in increased stomatal density, and SlTLFP8 affected stomatal density through endoreduplication and altered epidermal cell size. Despite changes in stomata density, altering the expression of SlTLFP8 did not result in distinct changes in photosynthesis, biomass and yield of tomato.
Collapse
Affiliation(s)
- Shuangtao Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Jiaojiao Zhang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Lun Liu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Zhirong Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yafei Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Luqin Guo
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yu Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xichun Zhang
- College of Plant Science & Technology, Beijing University of Agriculture, Beijing, China
| | - Shuxin Ren
- School of Agriculture, Virginia State University, Petersburg, Virginia, USA
| | - Bing Zhao
- College of Horticulture, China Agricultural University, Beijing, China
| | - Na Zhang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yang-Dong Guo
- College of Horticulture, China Agricultural University, Beijing, China
| |
Collapse
|
24
|
Wang K, Ndathe RW, Kumar N, Zeringue EA, Kato N, Larkin JC. The CDK Inhibitor SIAMESE Targets Both CDKA;1 and CDKB1 Complexes to Establish Endoreplication in Trichomes. PLANT PHYSIOLOGY 2020; 184:165-175. [PMID: 32694133 PMCID: PMC7479911 DOI: 10.1104/pp.20.00271] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/10/2020] [Indexed: 05/24/2023]
Abstract
Endoreplication, also known as endoreduplication, is a modified cell cycle in which DNA is replicated without subsequent cell division. Endoreplication plays important roles in both normal plant development and in stress responses. The SIAMESE (SIM) gene of Arabidopsis (Arabidopsis thaliana) encodes a cyclin-dependent kinase (CDK) inhibitor that plays a central role in establishing endoreplication, and is the founding member of the SIAMESE-RELATED (SMR) family of plant-specific CDK inhibitor genes. However, there has been conflicting evidence regarding which specific cyclin/CDK complexes are inhibited by SIM in vivo. In this work, we use genetic evidence to show that SIM likely inhibits both CDKA;1- and CDKB1-containing CDK complexes in vivo, thus promoting endoreplication in developing Arabidopsis trichomes. We also show that SIM interacts with CYCA2;3, a binding partner of CDKB1;1, via SIM motif A, which we previously identified as a CDK-binding motif. By contrast, SIM motif C, which has been indicated as a cyclin binding motif in other contexts, appears to be relatively unimportant for interaction between SIM and CYCA2;3. Together with earlier results, our work suggests that SIM and other SMRs likely have a multivalent interaction with CYC/CDK complexes.
Collapse
Affiliation(s)
- Kai Wang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - Ruth W Ndathe
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - Narender Kumar
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - Elizabeth A Zeringue
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - Naohiro Kato
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - John C Larkin
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| |
Collapse
|
25
|
Khan FA, Voß U, Pound MP, French AP. Volumetric Segmentation of Cell Cycle Markers in Confocal Images Using Machine Learning and Deep Learning. FRONTIERS IN PLANT SCIENCE 2020; 11:1275. [PMID: 32983190 PMCID: PMC7483761 DOI: 10.3389/fpls.2020.01275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/05/2020] [Indexed: 06/11/2023]
Abstract
Understanding plant growth processes is important for many aspects of biology and food security. Automating the observations of plant development-a process referred to as plant phenotyping-is increasingly important in the plant sciences, and is often a bottleneck. Automated tools are required to analyze the data in microscopy images depicting plant growth, either locating or counting regions of cellular features in images. In this paper, we present to the plant community an introduction to and exploration of two machine learning approaches to address the problem of marker localization in confocal microscopy. First, a comparative study is conducted on the classification accuracy of common conventional machine learning algorithms, as a means to highlight challenges with these methods. Second, a 3D (volumetric) deep learning approach is developed and presented, including consideration of appropriate loss functions and training data. A qualitative and quantitative analysis of all the results produced is performed. Evaluation of all approaches is performed on an unseen time-series sequence comprising several individual 3D volumes, capturing plant growth. The comparative analysis shows that the deep learning approach produces more accurate and robust results than traditional machine learning. To accompany the paper, we are releasing the 4D point annotation tool used to generate the annotations, in the form of a plugin for the popular ImageJ (FIJI) software. Network models and example datasets will also be available online.
Collapse
Affiliation(s)
- Faraz Ahmad Khan
- Schools of Computer Science and Biosciences, University of Nottingham, Nottingham, United Kingdom
| | | | | | | |
Collapse
|
26
|
Zluhan-Martínez E, Pérez-Koldenkova V, Ponce-Castañeda MV, Sánchez MDLP, García-Ponce B, Miguel-Hernández S, Álvarez-Buylla ER, Garay-Arroyo A. Beyond What Your Retina Can See: Similarities of Retinoblastoma Function between Plants and Animals, from Developmental Processes to Epigenetic Regulation. Int J Mol Sci 2020; 21:E4925. [PMID: 32664691 PMCID: PMC7404004 DOI: 10.3390/ijms21144925] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/29/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022] Open
Abstract
The Retinoblastoma protein (pRb) is a key cell cycle regulator conserved in a wide variety of organisms. Experimental analysis of pRb's functions in animals and plants has revealed that this protein participates in cell proliferation and differentiation processes. In addition, pRb in animals and its orthologs in plants (RBR), are part of highly conserved protein complexes which suggest the possibility that analogies exist not only between functions carried out by pRb orthologs themselves, but also in the structure and roles of the protein networks where these proteins are involved. Here, we present examples of pRb/RBR participation in cell cycle control, cell differentiation, and in the regulation of epigenetic changes and chromatin remodeling machinery, highlighting the similarities that exist between the composition of such networks in plants and animals.
Collapse
Affiliation(s)
- Estephania Zluhan-Martínez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
- Posgrado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Av. Universidad 3000, Coyoacán 04510, Mexico
| | - Vadim Pérez-Koldenkova
- Laboratorio Nacional de Microscopía Avanzada, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc, 330. Col. Doctores, Alc. Cuauhtémoc 06720, Mexico;
| | - Martha Verónica Ponce-Castañeda
- Unidad de Investigación Médica en Enfermedades Infecciosas, Centro Médico Nacional SXXI, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico;
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
| | - Sergio Miguel-Hernández
- Laboratorio de Citopatología Ambiental, Departamento de Morfología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Campus Zacatenco, Calle Wilfrido Massieu Esquina Cda, Manuel Stampa 07738, Mexico;
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
| |
Collapse
|
27
|
Abstract
Stomatal cell fate and patterning, which are regulated by key transcriptional factors and intercellular communications, are critical for plant growth and survival. The known regulators of stomatal development do not appear to have microRNAs (miRNAs) regulating them. Thus, it remains elusive as to whether and how miRNAs are involved in stomatal development. This study identifies stomatal lineage miRNAs including developmental stage-specific miRNAs. Genetic analysis shows that stomatal lineage miRNAs positively or negatively regulate stomatal formation and patterning. Moreover, biological processes modulated by stomatal lineage miRNAs reveal previously unknown regulatory pathways in stomatal development, indicating that miRNAs function as a critical element of stomatal development. These results provide a resource for guiding the study of stomatal development. Stomata in the plant epidermis play a critical role in growth and survival by controlling gas exchange, transpiration, and immunity to pathogens. Plants modulate stomatal cell fate and patterning through key transcriptional factors and signaling pathways. MicroRNAs (miRNAs) are known to contribute to developmental plasticity in multicellular organisms; however, no miRNAs appear to target the known regulators of stomatal development. It remains unclear as to whether miRNAs are involved in stomatal development. Here, we report highly dynamic, developmentally stage-specific miRNA expression profiles from stomatal lineage cells. We demonstrate that stomatal lineage miRNAs positively and negatively regulate stomatal formation and patterning to avoid clustered stomata. Target prediction of stomatal lineage miRNAs implicates potential cellular processes in stomatal development. We show that miR399-mediated PHO2 regulation, involved in phosphate homeostasis, contributes to the control of stomatal development. Our study demonstrates that miRNAs constitute a critical component in the regulatory mechanisms controlling stomatal development.
Collapse
|
28
|
CSN5A Subunit of COP9 Signalosome Temporally Buffers Response to Heat in Arabidopsis. Biomolecules 2019; 9:biom9120805. [PMID: 31795414 PMCID: PMC6995552 DOI: 10.3390/biom9120805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 11/25/2022] Open
Abstract
The COP9 (constitutive photomorphogenesis 9) signalosome (CSN) is an evolutionarily conserved protein complex which regulates various growth and developmental processes. However, the role of CSN during environmental stress is largely unknown. Using Arabidopsis as model organism, we used CSN hypomorphic mutants to study the role of the CSN in plant responses to environmental stress and found that heat stress specifically enhanced the growth of csn5a-1 but not the growth of other hypomorphic photomorphogenesis mutants tested. Following heat stress, csn5a-1 exhibits an increase in cell size, ploidy, photosynthetic activity, and number of lateral roots and an upregulation of genes connected to the auxin response. Immunoblot analysis revealed an increase in deneddylation of CUL1 but not CUL3 following heat stress in csn5a-1, implicating improved CUL1 activity as a basis for the improved growth of csn5a-1 following heat stress. Studies using DR5::N7-VENUS and DII-VENUS reporter constructs confirm that the heat-induced growth is due to an increase in auxin signaling. Our results indicate that CSN5A has a specific role in deneddylation of CUL1 and that CSN5A is required for the recovery of AUX/IAA repressor levels following recurrent heat stress to regulate auxin homeostasis in Arabidopsis.
Collapse
|
29
|
Han SK, Torii KU. Linking cell cycle to stomatal differentiation. CURRENT OPINION IN PLANT BIOLOGY 2019; 51:66-73. [PMID: 31075538 DOI: 10.1016/j.pbi.2019.03.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 05/20/2023]
Abstract
Stomatal differentiation manifests via several rounds of asymmetric cell division and a single symmetric cell division: the former, formative divisions amplify the number of epidermal cells, and the latter is essential for creating a functional guard cell pair. These cell division patterns are coordinated with progressive fate specification and cell-state transitional steps, which rely on the transcriptional regulation by a set of cell type-specific basic helix loop helix (bHLH) transcription factors. It has been proposed that the mechanisms underlying cell-fate decision and cell cycle progression are interconnected in a wide range of developmental processes. This review highlights the recent findings on how cell cycle regulators are transcriptionally regulated and contributing to each step of stomatal lineage progression.
Collapse
Affiliation(s)
- Soon-Ki Han
- Institute of Transformative BioMolecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Keiko U Torii
- Institute of Transformative BioMolecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan; Howard Hughes Medical Institute and Department of Biology, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
30
|
Advances Towards How Meiotic Recombination Is Initiated: A Comparative View and Perspectives for Plant Meiosis Research. Int J Mol Sci 2019; 20:ijms20194718. [PMID: 31547623 PMCID: PMC6801837 DOI: 10.3390/ijms20194718] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 09/19/2019] [Accepted: 09/19/2019] [Indexed: 12/14/2022] Open
Abstract
Meiosis is an essential cell-division process for ensuring genetic diversity across generations. Meiotic recombination ensures the accuracy of genetic interchange between homolous chromosomes and segregation of parental alleles. Programmed DNA double-strand breaks (DSBs), catalyzed by the evolutionarily conserved topoisomerase VIA (a subunit of the archaeal type II DNA topoisomerase)-like enzyme Spo11 and several other factors, is a distinctive feature of meiotic recombination initiation. The meiotic DSB formation and its regulatory mechanisms are similar among species, but certain aspects are distinct. In this review, we introduced the cumulative knowledge of the plant proteins crucial for meiotic DSB formation and technical advances in DSB detection. We also summarized the genome-wide DSB hotspot profiles for different model organisms. Moreover, we highlighted the classical views and recent advances in our knowledge of the regulatory mechanisms that ensure the fidelity of DSB formation, such as multifaceted kinase-mediated phosphorylation and the consequent high-dimensional changes in chromosome structure. We provided an overview of recent findings concerning DSB formation, distribution and regulation, all of which will help us to determine whether meiotic DSB formation is evolutionarily conserved or varies between plants and other organisms.
Collapse
|
31
|
A conserved but plant-specific CDK-mediated regulation of DNA replication protein A2 in the precise control of stomatal terminal division. Proc Natl Acad Sci U S A 2019; 116:18126-18131. [PMID: 31431532 DOI: 10.1073/pnas.1819345116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The R2R3-MYB transcription factor FOUR LIPS (FLP) controls the stomatal terminal division through transcriptional repression of the cell cycle genes CYCLIN-DEPENDENT KINASE (CDK) B1s (CDKB1s), CDKA;1, and CYCLIN A2s (CYCA2s). We mutagenized the weak mutant allele flp-1 seeds with ethylmethane sulfonate and screened out a flp-1 suppressor 1 (fsp1) that suppressed the flp-1 stomatal cluster phenotype. FSP1 encodes RPA2a subunit of Replication Protein A (RPA) complexes that play important roles in DNA replication, recombination, and repair. Here, we show that FSP1/RPA2a functions together with CDKB1s and CYCA2s in restricting stomatal precursor proliferation, ensuring the stomatal terminal division and maintaining a normal guard-cell size and DNA content. Furthermore, we provide direct evidence for the existence of an evolutionarily conserved, but plant-specific, CDK-mediated RPA regulatory pathway. Serine-11 and Serine-21 at the N terminus of RPA2a are CDK phosphorylation target residues. The expression of the phosphorylation-mimic variant RPA2a S11,21/D partially complemented the defective cell division and DNA damage hypersensitivity in cdkb1;1 1;2 mutants. Thus, our study provides a mechanistic understanding of the CDK-mediated phosphorylation of RPA in the precise control of cell cycle and DNA repair in plants.
Collapse
|
32
|
Yin J, Zhang X, Zhang G, Wen Y, Liang G, Chen X. Aminocyclopropane-1-carboxylic acid is a key regulator of guard mother cell terminal division in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:897-908. [PMID: 30462272 PMCID: PMC6363092 DOI: 10.1093/jxb/ery413] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 11/14/2018] [Indexed: 05/05/2023]
Abstract
Stomata have a critical function in the exchange of gases and water vapor between plants and their environment. Stomatal development is under the rigorous control of many regulators. The last step of development is the terminal division of guard mother cells (GMC) into two guard cells (GC). It is still unclear how the symmetric division of GMCs is regulated. Here, we show that the ethylene precursor aminocyclopropane-1-carboxylic acid (ACC) is required for the symmetric division of GMCs into GCs in Arabidopsis. Exogenous application of the ACC biosynthesis inhibitor aminoethoxyvinylglycine (AVG) induced the formation of single guard cells (SGCs). Correspondingly, an acs octuple-mutant with extremely low endogenous ACC also developed SGCs, and exogenous ACC dramatically decreased the number of SGCs in this mutant whereas exogenous ethephon (which is gradually converted into ethylene) had no effect. Furthermore, neither blocking of endogenous ethylene synthesis nor disruption of ethylene signaling transduction could induce the production of SGCs. Further investigation indicated that ACC promoted the division of GMCs in fama-1 and flp-1myb88 mutants whereas AVG inhibited it. Moreover, ACC positively regulated the expression of CDKB1;1 and CYCA2;3 in the fama-1 and flp-1myb88 mutants. The SGC number was not affected by ACC or AVG in cdkb1;11;2 and cyca2;234 mutants. Taken together, the results demonstrate that ACC itself, but not ethylene, positively modulates the symmetric division of GMCs in a manner that is dependent on CDKB1s and CYCA2s.
Collapse
Affiliation(s)
- Jiao Yin
- School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Xiaoqian Zhang
- School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Gensong Zhang
- School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Yuanyuan Wen
- School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Gang Liang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- Correspondence: or
| | - Xiaolan Chen
- School of Life Sciences, Yunnan University, Kunming, Yunnan, China
- Correspondence: or
| |
Collapse
|
33
|
Simmons AR, Davies KA, Wang W, Liu Z, Bergmann DC. SOL1 and SOL2 regulate fate transition and cell divisions in the Arabidopsis stomatal lineage. Development 2019; 146:dev.171066. [PMID: 30665887 DOI: 10.1242/dev.171066] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 01/14/2019] [Indexed: 01/23/2023]
Abstract
In the Arabidopsis stomatal lineage, cells transit through several distinct precursor identities, each characterized by unique cell division behaviors. Flexibility in the duration of these precursor phases enables plants to alter leaf size and stomatal density in response to environmental conditions; however, transitions between phases must be complete and unidirectional to produce functional and correctly patterned stomata. Among direct transcriptional targets of the stomatal initiating factor SPEECHLESS, a pair of genes, SOL1 and SOL2, are required for effective transitions in the lineage. We show that these two genes, which are homologs of the LIN54 DNA-binding components of the mammalian DREAM complex, are expressed in a cell cycle-dependent manner and regulate cell fate and division properties in the self-renewing early lineage. In the terminal division of the stomatal lineage, however, these two proteins appear to act in opposition to their closest paralog, TSO1, revealing complexity in the gene family that may enable customization of cell divisions in coordination with development.
Collapse
Affiliation(s)
- Abigail R Simmons
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
| | - Kelli A Davies
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
| | - Wanpeng Wang
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Dominique C Bergmann
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA .,Howard Hughes Medical Institute (HHMI), Stanford University, Stanford, CA 94305-5020, USA
| |
Collapse
|
34
|
RNA-seq Analysis Reveals Gene Expression Profiling of Female Fertile and Sterile Ovules of PinusTabulaeformis Carr. during Free Nuclear Mitosis of the Female Gametophyte. Int J Mol Sci 2018; 19:ijms19082246. [PMID: 30071597 PMCID: PMC6122031 DOI: 10.3390/ijms19082246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 07/22/2018] [Accepted: 07/26/2018] [Indexed: 01/08/2023] Open
Abstract
The development of the female gametophyte (FG) is one of the key processes of life cycle alteration between the haploid gametophyte and the diploid sporophytes in plants and it is required for successful seed development after fertilization. It is well demonstrated that free nuclear mitosis (FNM) of FG is crucial for the development of the ovule. However, studies of the molecular mechanism of ovule and FG development focused mainly on angiosperms, such as Arabidopsis thaliana and further investigation of gymnosperms remains to be completed. Here, Illumina sequencing of six transcriptomic libraries obtained from developing and abortive ovules at different stages during free nuclear mitosis of magagametophyte (FNMM) was used to acquire transcriptome data and gene expression profiles of Pinus tabulaeformis. Six cDNA libraries generated a total of 71.0 million high-quality clean reads that aligned with 63,449 unigenes and the comparison between developing and abortive ovules identified 7174 differentially expressed genes (DEGs). From the functional annotation results, DEGs involved in the cell cycle and phytohormone regulation were highlighted to reveal their biological importance in ovule development. Furthermore, validation of DEGs from the phytohormone signal transduction pathway was performed using quantitative real-time PCR analysis, revealing the dynamics of transcriptional networks and potential key components in the regulation of FG development in P. tabulaeformis were identified. These findings provide new insights into the regulatory mechanisms of ovule development in woody gymnosperms.
Collapse
|
35
|
Qu X, Yan M, Zou J, Jiang M, Yang K, Le J. A2-type cyclin is required for the asymmetric entry division in rice stomatal development. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3587-3599. [PMID: 29701802 PMCID: PMC6022656 DOI: 10.1093/jxb/ery158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 04/16/2018] [Indexed: 05/19/2023]
Abstract
In rice, and other major cereal grass crops, stomata are arranged in linear files parallel to the long growth axis of leaves. Each stomatal unit comprises two dumbbell-shaped guard cells flanked by two subsidiary cells. These morphological and developmental characteristics enable grass stomata to respond to environmental changes more efficiently. Cyclin-dependent kinases (CDKs) and their cyclin partners co-ordinate cell proliferation and differentiation during the development of multicellular organisms. In contrast to animals, plants have many more types and members of cyclins. In Arabidopsis, four A2-type cyclins (CYCA2s) function redundantly in regulating CDKB1 activity to promote the asymmetric division for stomatal initiation and the symmetric division of guard mother cells (GMCs). In this study, we examine the function of the single A2-type cyclin in rice, OsCYCA2;1, as well the single B1-type CDK, OsCDKB1;1. Cross-species complementation tests demonstrated that OsCYCA2;1 and OsCDKB1;1 could complement the defective stomatal phenotypes of Arabidopsis cyca2 and cdkb1 mutants, but also could suppress DNA endoduplication and cell enlargement. The early asymmetric divisions that establish the stomatal lineages are often missing within the stomatal cell files of OsCYCA2;1-RNAi rice transgenic lines, leading to a significantly reduced stomatal production. However, GMC divisions are not disrupted either in OsCYCA2;1-RNAi or in OsCDKB1;1-RNAi rice transgenic lines as expected. Our results demonstrate a conserved but diverged function and behavior of rice A2-type cyclins, which might be associated with the distinct stomatal development pathways between rice and Arabidopsis.
Collapse
Affiliation(s)
- Xiaoxiao Qu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Yan
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junjie Zou
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Min Jiang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Kezhen Yang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jie Le
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
36
|
Han SK, Qi X, Sugihara K, Dang JH, Endo TA, Miller KL, Kim ED, Miura T, Torii KU. MUTE Directly Orchestrates Cell-State Switch and the Single Symmetric Division to Create Stomata. Dev Cell 2018; 45:303-315.e5. [PMID: 29738710 DOI: 10.1016/j.devcel.2018.04.010] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/20/2018] [Accepted: 04/10/2018] [Indexed: 10/17/2022]
Abstract
Precise cell division control is critical for developmental patterning. For the differentiation of a functional stoma, a cellular valve for efficient gas exchange, the single symmetric division of an immediate precursor is absolutely essential. Yet, the mechanism governing this event remains unclear. Here we report comprehensive inventories of gene expression by the Arabidopsis bHLH protein MUTE, a potent inducer of stomatal differentiation. MUTE switches the gene expression program initiated by SPEECHLESS. MUTE directly induces a suite of cell-cycle genes, including CYCD5;1, in which introduced expression triggers the symmetric divisions of arrested precursor cells in mute, and their transcriptional repressors, FAMA and FOUR LIPS. The regulatory network initiated by MUTE represents an incoherent type 1 feed-forward loop. Our mathematical modeling and experimental perturbations support a notion that MUTE orchestrates a transcriptional cascade leading to a tightly restricted pulse of cell-cycle gene expression, thereby ensuring the single cell division to create functional stomata.
Collapse
Affiliation(s)
- Soon-Ki Han
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA; Department of Biology, University of Washington, Seattle, WA 98195, USA; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Xingyun Qi
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA; Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Kei Sugihara
- Department of Anatomy and Cell Biology, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Jonathan H Dang
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Kristen L Miller
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Eun-Deok Kim
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Takashi Miura
- Department of Anatomy and Cell Biology, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Keiko U Torii
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA; Department of Biology, University of Washington, Seattle, WA 98195, USA; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan.
| |
Collapse
|
37
|
Weimer AK, Matos JL, Sharma N, Patell F, Murray JAH, Dewitte W, Bergmann DC. Lineage- and stage-specific expressed CYCD7;1 coordinates the single symmetric division that creates stomatal guard cells. Development 2018; 145:dev.160671. [PMID: 29467245 DOI: 10.1242/dev.160671] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/13/2018] [Indexed: 11/20/2022]
Abstract
Plants, with cells fixed in place by rigid walls, often utilize spatial and temporally distinct cell division programs to organize and maintain organs. This leads to the question of how developmental regulators interact with the cell cycle machinery to link cell division events with particular developmental trajectories. In Arabidopsis leaves, the development of stomata, two-celled epidermal valves that mediate plant-atmosphere gas exchange, relies on a series of oriented stem cell-like asymmetric divisions followed by a single symmetric division. The stomatal lineage is embedded in a tissue in which other cells transition from proliferation to postmitotic differentiation earlier, necessitating stomatal lineage-specific factors to prolong competence to divide. We show that the D-type cyclin, CYCD7;1, is specifically expressed just prior to the symmetric guard cell-forming division, and that it is limiting for this division. Further, we find that CYCD7;1 is capable of promoting divisions in multiple contexts, likely through RBR1-dependent promotion of the G1/S transition, but that CYCD7;1 is regulated at the transcriptional level by cell type-specific transcription factors that confine its expression to the appropriate developmental window.
Collapse
Affiliation(s)
- Annika K Weimer
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Juliana L Matos
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Nidhi Sharma
- Howard Hughes Medical Institute (HHMI), Stanford University, Stanford, CA 94305, USA
| | - Farah Patell
- Cardiff School of Bioscience, Cardiff University, Cardiff CF10 3AX, UK.,Institute of Biotechnology, University of Cambridge, Cambridge CB2 1QT, UK
| | - James A H Murray
- Cardiff School of Bioscience, Cardiff University, Cardiff CF10 3AX, UK.,Institute of Biotechnology, University of Cambridge, Cambridge CB2 1QT, UK
| | - Walter Dewitte
- Cardiff School of Bioscience, Cardiff University, Cardiff CF10 3AX, UK.,Institute of Biotechnology, University of Cambridge, Cambridge CB2 1QT, UK
| | - Dominique C Bergmann
- Department of Biology, Stanford University, Stanford, CA 94305, USA .,Howard Hughes Medical Institute (HHMI), Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
38
|
Abstract
The eukaryotic nucleus is enclosed by the nuclear envelope, which is perforated by the nuclear pores, the gateways of macromolecular exchange between the nucleoplasm and cytoplasm. The nucleoplasm is organized in a complex three-dimensional fashion that changes over time and in response to stimuli. Within the cell, the nucleus must be viewed as an organelle (albeit a gigantic one) that is a recipient of cytoplasmic forces and capable of morphological and positional dynamics. The most dramatic reorganization of this organelle occurs during mitosis and meiosis. Although many of these aspects are less well understood for the nuclei of plants than for those of animals or fungi, several recent discoveries have begun to place our understanding of plant nuclei firmly into this broader cell-biological context.
Collapse
Affiliation(s)
- Iris Meier
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210;
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom;
| | | | - David E Evans
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom;
| |
Collapse
|
39
|
Tamirisa S, Vudem DR, Khareedu VR. A Cyclin Dependent Kinase Regulatory Subunit (CKS) Gene of Pigeonpea Imparts Abiotic Stress Tolerance and Regulates Plant Growth and Development in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2017; 8:165. [PMID: 28239388 PMCID: PMC5301084 DOI: 10.3389/fpls.2017.00165] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/26/2017] [Indexed: 05/03/2023]
Abstract
Frequent climatic changes in conjunction with other extreme environmental factors are known to affect growth, development and productivity of diverse crop plants. Pigeonpea, a major grain legume of the semiarid tropics, endowed with an excellent deep-root system, is known as one of the important drought tolerant crop plants. Cyclin dependent kinases (CDKs) are core cell cycle regulators and play important role in different aspects of plant growth and development. The cyclin-dependent kinase regulatory subunit gene (CKS) was isolated from the cDNA library of pigeonpea plants subjected to drought stress. Pigeonpea CKS (CcCKS) gene expression was detected in both the root and leaf tissues of pigeonpea and was upregulated by polyethylene glycol (PEG), mannitol, NaCl and abscisic acid (ABA) treatments. The overexpression of CcCKS gene in Arabidopsis significantly enhanced tolerance of transgenics to drought and salt stresses as evidenced by different physiological parameters. Under stress conditions, transgenics showed higher biomass, decreased rate of water loss, decreased MDA levels, higher free proline contents, and glutathione levels. Moreover, under stress conditions transgenics exhibited lower stomatal conductance, lower transpiration, and higher photosynthetic rates. However, under normal conditions, CcCKS-transgenics displayed decreased plant growth rate, increased cell size and decreased stomatal number compared to those of wild-type plants. Real-time polymerase chain reaction revealed that CcCKS could regulate the expression of both ABA-dependent and ABA-independent genes associated with abiotic stress tolerance as well as plant growth and development. As such, the CcCKS seems promising and might serve as a potential candidate gene for enhancing the abiotic stress tolerance of crop plants.
Collapse
|
40
|
Watson-Lazowski A, Lin Y, Miglietta F, Edwards RJ, Chapman MA, Taylor G. Plant adaptation or acclimation to rising CO 2 ? Insight from first multigenerational RNA-Seq transcriptome. GLOBAL CHANGE BIOLOGY 2016; 22:3760-3773. [PMID: 27539677 DOI: 10.1111/gcb.13322] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/17/2016] [Accepted: 03/18/2016] [Indexed: 06/06/2023]
Abstract
Atmospheric carbon dioxide (CO2 ) directly determines the rate of plant photosynthesis and indirectly effects plant productivity and fitness and may therefore act as a selective pressure driving evolution, but evidence to support this contention is sparse. Using Plantago lanceolata L. seed collected from a naturally high CO2 spring and adjacent ambient CO2 control site, we investigated multigenerational response to future, elevated atmospheric CO2 . Plants were grown in either ambient or elevated CO2 (700 μmol mol-1 ), enabling for the first time, characterization of the functional and population genomics of plant acclimation and adaptation to elevated CO2 . This revealed that spring and control plants differed significantly in phenotypic plasticity for traits underpinning fitness including above-ground biomass, leaf size, epidermal cell size and number and stomatal density and index. Gene expression responses to elevated CO2 (acclimation) were modest [33-131 genes differentially expressed (DE)], whilst those between control and spring plants (adaptation) were considerably larger (689-853 DE genes). In contrast, population genomic analysis showed that genetic differentiation between spring and control plants was close to zero, with no fixed differences, suggesting that plants are adapted to their native CO2 environment at the level of gene expression. An unusual phenotype of increased stomatal index in spring but not control plants in elevated CO2 correlated with altered expression of stomatal patterning genes between spring and control plants for three loci (YODA, CDKB1;1 and SCRM2) and between ambient and elevated CO2 for four loci (ER, YODA, MYB88 and BCA1). We propose that the two positive regulators of stomatal number (SCRM2) and CDKB1;1 when upregulated act as key controllers of stomatal adaptation to elevated CO2 . Combined with significant transcriptome reprogramming of photosynthetic and dark respiration and enhanced growth in spring plants, we have identified the potential basis of plant adaptation to high CO2 likely to occur over coming decades.
Collapse
Affiliation(s)
| | - Yunan Lin
- Centre for Biological Sciences, University of Southampton, Life Sciences, Southampton, SO17 1BJ, UK
| | - Franco Miglietta
- Institute of Biometeorology (IBIMET), National Research Council (CNR), Via Caproni 8, Firenze, 50145, Italy
| | - Richard J Edwards
- Centre for Biological Sciences, University of Southampton, Life Sciences, Southampton, SO17 1BJ, UK
| | - Mark A Chapman
- Centre for Biological Sciences, University of Southampton, Life Sciences, Southampton, SO17 1BJ, UK
| | - Gail Taylor
- Centre for Biological Sciences, University of Southampton, Life Sciences, Southampton, SO17 1BJ, UK.
| |
Collapse
|
41
|
Weimer AK, Biedermann S, Harashima H, Roodbarkelari F, Takahashi N, Foreman J, Guan Y, Pochon G, Heese M, Van Damme D, Sugimoto K, Koncz C, Doerner P, Umeda M, Schnittger A. The plant-specific CDKB1-CYCB1 complex mediates homologous recombination repair in Arabidopsis. EMBO J 2016; 35:2068-2086. [PMID: 27497297 PMCID: PMC5048351 DOI: 10.15252/embj.201593083] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 07/14/2016] [Indexed: 01/30/2023] Open
Abstract
Upon DNA damage, cyclin‐dependent kinases (CDKs) are typically inhibited to block cell division. In many organisms, however, it has been found that CDK activity is required for DNA repair, especially for homology‐dependent repair (HR), resulting in the conundrum how mitotic arrest and repair can be reconciled. Here, we show that Arabidopsis thaliana solves this dilemma by a division of labor strategy. We identify the plant‐specific B1‐type CDKs (CDKB1s) and the class of B1‐type cyclins (CYCB1s) as major regulators of HR in plants. We find that RADIATION SENSITIVE 51 (RAD51), a core mediator of HR, is a substrate of CDKB1‐CYCB1 complexes. Conversely, mutants in CDKB1 and CYCB1 fail to recruit RAD51 to damaged DNA. CYCB1;1 is specifically activated after DNA damage and we show that this activation is directly controlled by SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), a transcription factor that acts similarly to p53 in animals. Thus, while the major mitotic cell‐cycle activity is blocked after DNA damage, CDKB1‐CYCB1 complexes are specifically activated to mediate HR.
Collapse
Affiliation(s)
- Annika K Weimer
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS UPR2357, Université de Strasbourg, Strasbourg Cedex, France
| | - Sascha Biedermann
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS UPR2357, Université de Strasbourg, Strasbourg Cedex, France
| | | | | | - Naoki Takahashi
- Plant Growth Regulation Laboratory, Nara Institute of Science and Technology, Graduate School of Biological Sciences, Ikoma, Nara, Japan
| | - Julia Foreman
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Yonsheng Guan
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS UPR2357, Université de Strasbourg, Strasbourg Cedex, France
| | - Gaëtan Pochon
- Department of Developmental Biology, Biozentrum Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Maren Heese
- Department of Developmental Biology, Biozentrum Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Daniël Van Damme
- Department of Plant Systems Biology, VIB, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Japan
| | - Csaba Koncz
- Max-Planck-Institut für Pflanzenzüchtungsforschung, Köln, Germany
| | - Peter Doerner
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Masaaki Umeda
- Plant Growth Regulation Laboratory, Nara Institute of Science and Technology, Graduate School of Biological Sciences, Ikoma, Nara, Japan JST, CREST, Ikoma, Nara, Japan
| | - Arp Schnittger
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS UPR2357, Université de Strasbourg, Strasbourg Cedex, France Department of Developmental Biology, Biozentrum Klein Flottbek, University of Hamburg, Hamburg, Germany Trinationales Institut für Pflanzenforschung, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS, Strasbourg Cedex, France
| |
Collapse
|
42
|
Xu P, Chen H, Ying L, Cai W. AtDOF5.4/OBP4, a DOF Transcription Factor Gene that Negatively Regulates Cell Cycle Progression and Cell Expansion in Arabidopsis thaliana. Sci Rep 2016; 6:27705. [PMID: 27297966 PMCID: PMC4906354 DOI: 10.1038/srep27705] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/24/2016] [Indexed: 01/01/2023] Open
Abstract
In contrast to animals, plant development involves continuous organ formation, which requires strict regulation of cell proliferation. The core cell cycle machinery is conserved across plants and animals, but plants have developed new mechanisms that precisely regulate cell proliferation in response to internal and external stimuli. Here, we report that the DOF transcription factor OBP4 negatively regulates cell proliferation and expansion. OBP4 is a nuclear protein. Constitutive and inducible overexpression of OBP4 reduced the cell size and number, resulting in dwarf plants. Inducible overexpression of OBP4 in Arabidopsis also promoted early endocycle onset and inhibited cell expansion, while inducible overexpression of OBP4 fused to the VP16 activation domain in Arabidopsis delayed endocycle onset and promoted plant growth. Furthermore, gene expression analysis showed that cell cycle regulators and cell wall expansion factors were largely down-regulated in the OBP4 overexpression lines. Short-term inducible analysis coupled with in vivo ChIP assays indicated that OBP4 targets the CyclinB1;1, CDKB1;1 and XTH genes. These results strongly suggest that OBP4 is a negative regulator of cell cycle progression and cell growth. These findings increase our understanding of the transcriptional regulation of the cell cycle in plants.
Collapse
Affiliation(s)
- Peipei Xu
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
| | - Haiying Chen
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
| | - Lu Ying
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
| | - Weiming Cai
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
| |
Collapse
|
43
|
Kumar N, Harashima H, Kalve S, Bramsiepe J, Wang K, Sizani BL, Bertrand LL, Johnson MC, Faulk C, Dale R, Simmons LA, Churchman ML, Sugimoto K, Kato N, Dasanayake M, Beemster G, Schnittger A, Larkin JC. Functional Conservation in the SIAMESE-RELATED Family of Cyclin-Dependent Kinase Inhibitors in Land Plants. THE PLANT CELL 2015; 27:3065-80. [PMID: 26546445 PMCID: PMC4682297 DOI: 10.1105/tpc.15.00489] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/16/2015] [Indexed: 05/03/2023]
Abstract
The best-characterized members of the plant-specific SIAMESE-RELATED (SMR) family of cyclin-dependent kinase inhibitors regulate the transition from the mitotic cell cycle to endoreplication, also known as endoreduplication, an altered version of the cell cycle in which DNA is replicated without cell division. Some other family members are implicated in cell cycle responses to biotic and abiotic stresses. However, the functions of most SMRs remain unknown, and the specific cyclin-dependent kinase complexes inhibited by SMRs are unclear. Here, we demonstrate that a diverse group of SMRs, including an SMR from the bryophyte Physcomitrella patens, can complement an Arabidopsis thaliana siamese (sim) mutant and that both Arabidopsis SIM and P. patens SMR can inhibit CDK activity in vitro. Furthermore, we show that Arabidopsis SIM can bind to and inhibit both CDKA;1 and CDKB1;1. Finally, we show that SMR2 acts to restrict cell proliferation during leaf growth in Arabidopsis and that SIM, SMR1/LGO, and SMR2 play overlapping roles in controlling the transition from cell division to endoreplication during leaf development. These results indicate that differences in SMR function in plant growth and development are primarily due to differences in transcriptional and posttranscriptional regulation, rather than to differences in fundamental biochemical function.
Collapse
Affiliation(s)
- Narender Kumar
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Hirofumi Harashima
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Shweta Kalve
- Department of Biology, Molecular Plant Physiology, and Biotechnology, University of Antwerp, 2020 Antwerp, Belgium
| | - Jonathan Bramsiepe
- Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS-UPR2357, Université de Strasbourg, F-67084 Strasbourg Cedex, France
| | - Kai Wang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Bulelani L Sizani
- Department of Biology, Molecular Plant Physiology, and Biotechnology, University of Antwerp, 2020 Antwerp, Belgium
| | - Laura L Bertrand
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Matthew C Johnson
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Christopher Faulk
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Renee Dale
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - L Alice Simmons
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Michelle L Churchman
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Naohiro Kato
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Maheshi Dasanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Gerrit Beemster
- Department of Biology, Molecular Plant Physiology, and Biotechnology, University of Antwerp, 2020 Antwerp, Belgium
| | - Arp Schnittger
- Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS-UPR2357, Université de Strasbourg, F-67084 Strasbourg Cedex, France
| | - John C Larkin
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| |
Collapse
|
44
|
Ortiz-Gutiérrez E, García-Cruz K, Azpeitia E, Castillo A, Sánchez MDLP, Álvarez-Buylla ER. A Dynamic Gene Regulatory Network Model That Recovers the Cyclic Behavior of Arabidopsis thaliana Cell Cycle. PLoS Comput Biol 2015; 11:e1004486. [PMID: 26340681 PMCID: PMC4560428 DOI: 10.1371/journal.pcbi.1004486] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 08/03/2015] [Indexed: 01/02/2023] Open
Abstract
Cell cycle control is fundamental in eukaryotic development. Several modeling efforts have been used to integrate the complex network of interacting molecular components involved in cell cycle dynamics. In this paper, we aimed at recovering the regulatory logic upstream of previously known components of cell cycle control, with the aim of understanding the mechanisms underlying the emergence of the cyclic behavior of such components. We focus on Arabidopsis thaliana, but given that many components of cell cycle regulation are conserved among eukaryotes, when experimental data for this system was not available, we considered experimental results from yeast and animal systems. We are proposing a Boolean gene regulatory network (GRN) that converges into only one robust limit cycle attractor that closely resembles the cyclic behavior of the key cell-cycle molecular components and other regulators considered here. We validate the model by comparing our in silico configurations with data from loss- and gain-of-function mutants, where the endocyclic behavior also was recovered. Additionally, we approximate a continuous model and recovered the temporal periodic expression profiles of the cell-cycle molecular components involved, thus suggesting that the single limit cycle attractor recovered with the Boolean model is not an artifact of its discrete and synchronous nature, but rather an emergent consequence of the inherent characteristics of the regulatory logic proposed here. This dynamical model, hence provides a novel theoretical framework to address cell cycle regulation in plants, and it can also be used to propose novel predictions regarding cell cycle regulation in other eukaryotes. In multicellular organisms, cells undergo a cyclic behavior of DNA duplication and delivery of a copy to daughter cells during cell division. In each of the main cell-cycle (CC) stages different sets of proteins are active and genes are expressed. Understanding how such cycling cellular behavior emerges and is robustly maintained in the face of changing developmental and environmental conditions, remains a fundamental challenge of biology. The molecular components that cycle through DNA duplication and citokinesis are interconnected in a complex regulatory network. Several models of such network have been proposed, although the regulatory network that robustly recovers a limit-cycle steady state that resembles the behavior of CC molecular components has been recovered only in a few cases, and no comprehensive model exists for plants. In this paper we used the plant Arabidopsis thaliana, as a study system to propose a core regulatory network to recover a cyclic attractor that mimics the oscillatory behavior of the key CC components. Our analyses show that the proposed GRN model is robust to transient alterations, and is validated with the loss- and gain-of-function mutants of the CC components. The interactions proposed for Arabidopsis thaliana CC can inspire predictions for further uncovering regulatory motifs in the CC of other organisms including human.
Collapse
Affiliation(s)
- Elizabeth Ortiz-Gutiérrez
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Junto a Jardín Botánico Exterior, México, D.F. CP 04510, México; Centro de Ciencias de la Complejidad-C3, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70-275, México, D.F. 04510, México
| | - Karla García-Cruz
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Junto a Jardín Botánico Exterior, México, D.F. CP 04510, México
| | - Eugenio Azpeitia
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Junto a Jardín Botánico Exterior, México, D.F. CP 04510, México; Centro de Ciencias de la Complejidad-C3, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70-275, México, D.F. 04510, México
| | - Aaron Castillo
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Junto a Jardín Botánico Exterior, México, D.F. CP 04510, México; Centro de Ciencias de la Complejidad-C3, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70-275, México, D.F. 04510, México
| | - María de la Paz Sánchez
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Junto a Jardín Botánico Exterior, México, D.F. CP 04510, México
| | - Elena R Álvarez-Buylla
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Junto a Jardín Botánico Exterior, México, D.F. CP 04510, México; Centro de Ciencias de la Complejidad-C3, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70-275, México, D.F. 04510, México
| |
Collapse
|
45
|
Yang KZ, Jiang M, Wang M, Xue S, Zhu LL, Wang HZ, Zou JJ, Lee EK, Sack F, Le J. Phosphorylation of Serine 186 of bHLH Transcription Factor SPEECHLESS Promotes Stomatal Development in Arabidopsis. MOLECULAR PLANT 2015; 8:783-95. [PMID: 25680231 DOI: 10.1016/j.molp.2014.12.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 12/05/2014] [Accepted: 12/07/2014] [Indexed: 05/18/2023]
Abstract
The initiation of stomatal lineage and subsequent asymmetric divisions in Arabidopsis require the activity of the basic helix-loop-helix transcription factor SPEECHLESS (SPCH). It has been shown that SPCH controls entry into the stomatal lineage as a substrate either of the MITOGEN-ACTIVATED PROTEIN KINASE (MAPK) cascade or GSK3-like kinase BRASSINOSTEROID INSENSITIVE 2 (BIN2). Here we show that three serine residues of SPCH appear to be the primary phosphorylation targets of Cyclin-Dependent Kinases A;1 (CDKA;1) in vitro, and among them Serine 186 plays a crucial role in stomatal formation. Expression of an SPCH construct harboring a mutation that results in phosphorylation deficiencies on Serine 186 residue failed to rescue stomatal defects in spch null mutants. Expression of a phosphorylation-mimic mutant SPCH(S186D) complemented stomatal production defects in the transgenic lines harboring the targeted expression of dominant-negative CDKA;1.N146. Therefore, in addition to MAPK- and BIN2-mediated phosphorylation on SPCH, phosphorylation at Serine 186 is positively required for SPCH function in regulating stomatal development.
Collapse
Affiliation(s)
- Ke-Zhen Yang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Beijing 100093, China
| | - Min Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Beijing 100093, China
| | - Ming Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Beijing 100093, China
| | - Shan Xue
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Beijing 100093, China
| | - Ling-Ling Zhu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Beijing 100093, China
| | - Hong-Zhe Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Beijing 100093, China
| | - Jun-Jie Zou
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Beijing 100093, China
| | - Eun-Kyoung Lee
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Fred Sack
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Jie Le
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Beijing 100093, China.
| |
Collapse
|
46
|
Huysman MJJ, Tanaka A, Bowler C, Vyverman W, De Veylder L. Functional characterization of the diatom cyclin-dependent kinase A2 as a mitotic regulator reveals plant-like properties in a non-green lineage. BMC PLANT BIOLOGY 2015; 15:86. [PMID: 25887918 PMCID: PMC4392632 DOI: 10.1186/s12870-015-0469-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 02/26/2015] [Indexed: 06/01/2023]
Abstract
BACKGROUND Cyclin-dependent kinases (CDKs) are crucial regulators of cell cycle progression in eukaryotes. The diatom CDKA2 was originally assigned to the classical A-type CDKs, but its cell cycle phase-specific transcription at the G2-to-M phase transition is typical for plant-specific B-type CDKs. RESULTS Here, we report the functional characterization of CDKA2 from the diatom Phaeodactylum tricornutum. Through a yeast two-hybrid library screen, CDKA2 was found to interact with the G2/M-specific CDK scaffolding factor CKS1. Localization of CDKA2 was found to be nuclear in interphase cells, while in cells undergoing cytokinesis, the signal extended to the cell division plane. In addition, overexpression of CDKA2 induced an overall reduction in the cell growth rate. Expression analysis of cell cycle marker genes in the overexpression lines indicates that this growth reduction is primarily due to a prolongation of the mitotic phase. CONCLUSIONS Our study indicates a role for CDKA2 during cell division in diatoms. The functional characterization of a CDK with clear CDKB properties in a non-green organism questions whether the current definition of B-type CDKs being plant-specific might need revision.
Collapse
Affiliation(s)
- Marie J J Huysman
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), 9052, Ghent, Belgium.
- Department of Plant Systems Biology, VIB, and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium.
- Environmental and Evolutionary Genomics Section, Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8186, Institut National de la Santé et de la Recherche Médicale U1024, Ecole Normale Supérieure, 75230, Paris, Cedex 05, France.
| | - Atsuko Tanaka
- Environmental and Evolutionary Genomics Section, Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8186, Institut National de la Santé et de la Recherche Médicale U1024, Ecole Normale Supérieure, 75230, Paris, Cedex 05, France.
- Current address: Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran, Hokkaido, 051-0013, Japan.
| | - Chris Bowler
- Environmental and Evolutionary Genomics Section, Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8186, Institut National de la Santé et de la Recherche Médicale U1024, Ecole Normale Supérieure, 75230, Paris, Cedex 05, France.
| | - Wim Vyverman
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium.
| | - Lieven De Veylder
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), 9052, Ghent, Belgium.
- Department of Plant Systems Biology, VIB, and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
| |
Collapse
|
47
|
Keerthisinghe S, Nadeau JA, Lucas JR, Nakagawa T, Sack FD. The Arabidopsis leucine-rich repeat receptor-like kinase MUSTACHES enforces stomatal bilateral symmetry in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:684-94. [PMID: 25594156 DOI: 10.1111/tpj.12757] [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: 10/09/2014] [Revised: 12/12/2014] [Accepted: 12/22/2014] [Indexed: 05/09/2023]
Abstract
Stomata display a mirror-like symmetry that is adaptive for shoot/atmosphere gas exchange. This symmetry includes the facing guard cells around a lens-shaped and bilaterally symmetric pore, as well as radially arranged microtubule arrays that primarily originate at the pore and then grow outwards. Mutations in MUSTACHES (MUS), which encodes a leucine-rich repeat receptor-like kinase, disrupt this symmetry, resulting in defects ranging from skewed pores and abnormally focused and depolarized radial microtubule arrays, to paired guard cells that face away from each other, or a severe loss of stomatal shape. Translational MUSproMUS:tripleGFP fusions are expressed in cell plates in most cells types in roots and shoots, and cytokinesis and cell plates are mostly normal in mus mutants. However, in guard mother cells, which divide and then form stomata, MUS expression is notably absent from new cell plates, and instead is peripherally located. These results are consistent with a role for MUS in enforcing wall building and cytoskeletal polarity at the centre of the developing stoma via signalling from the vicinity of the guard cell membrane.
Collapse
Affiliation(s)
- Sandra Keerthisinghe
- Botany Department, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | | | | | | | | |
Collapse
|
48
|
Matos JL, Lau OS, Hachez C, Cruz-Ramírez A, Scheres B, Bergmann DC. Irreversible fate commitment in the Arabidopsis stomatal lineage requires a FAMA and RETINOBLASTOMA-RELATED module. eLife 2014; 3. [PMID: 25303364 PMCID: PMC4225492 DOI: 10.7554/elife.03271] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 10/09/2014] [Indexed: 12/17/2022] Open
Abstract
The presumed totipotency of plant cells leads to questions about how specific stem cell lineages and terminal fates could be established. In the Arabidopsis stomatal lineage, a transient self-renewing phase creates precursors that differentiate into one of two epidermal cell types, guard cells or pavement cells. We found that irreversible differentiation of guard cells involves RETINOBLASTOMA-RELATED (RBR) recruitment to regulatory regions of master regulators of stomatal initiation, facilitated through interaction with a terminal stomatal lineage transcription factor, FAMA. Disrupting physical interactions between FAMA and RBR preferentially reveals the role of RBR in enforcing fate commitment over its role in cell-cycle control in this developmental context. Analysis of the phenotypes linked to the modulation of FAMA and RBR sheds new light on the way iterative divisions and terminal differentiation are coordinately regulated in a plant stem-cell lineage. DOI:http://dx.doi.org/10.7554/eLife.03271.001 Stem cells in animals and plants help to make and replenish the tissues of the body by dividing and becoming specialized types of cells. Once specialized for a certain function, it is important that a cell keeps that function. In plant leaves, one type of stem cell makes two different types of specialized cells: pavement cells and stomatal guard cells. Pavement cells lock together to form a waterproof barrier to the outside, while guard cells surround the small pores that open and close to allow the plant to exchange water, oxygen and carbon dioxide with the atmosphere. Once a cell becomes a pavement cell or a guard cell, it does not change its identity again. However, if a single cell is removed from a plant, it can revert to a stem cell and a whole new plant can be grown from it. This poses the question of how, in intact plants, specialized cells like pavement cells and guard cells are prevented from reverting to stem cells. In Arabidopsis thaliana, a small flowering plant that is widely used as a model organism in research, a protein called FAMA is responsible for controlling a set of genes that turn stem cells into guard cells. Matos et al. have now found that FAMA needs to bind to another protein called RBR to control this process. It seems that these two proteins make the transition from stem cell to guard cell permanent by changing the structure of DNA in regions that control stem cell genes. RBR is similar to a human protein called Retinoblastoma that helps prevent tumors and regulate stem cells, but how it actually performs these functions in humans is still debated. Because stem cells and guard cells are displayed on the surface of plant leaves and leave behind clues of their past, Matos et al. were able to watch stem cells grow up to be mature guard cells. When the partnership between FAMA and RBR was broken, it was possible to watch those same guard cells revert backwards into stem cells. Seeing development ‘rewind’ could provide useful insights into the way in which cell identity is controlled in both plants and animals. DOI:http://dx.doi.org/10.7554/eLife.03271.002
Collapse
Affiliation(s)
- Juliana L Matos
- Department of Biology, Stanford University, Stanford, United States
| | - On Sun Lau
- Department of Biology, Stanford University, Stanford, United States
| | - Charles Hachez
- Department of Biology, Stanford University, Stanford, United States
| | | | - Ben Scheres
- Department of Molecular Genetics, Utrecht University, Utrecht, Netherlands
| | | |
Collapse
|
49
|
Le J, Zou J, Yang K, Wang M. Signaling to stomatal initiation and cell division. FRONTIERS IN PLANT SCIENCE 2014; 5:297. [PMID: 25002867 PMCID: PMC4066587 DOI: 10.3389/fpls.2014.00297] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 06/06/2014] [Indexed: 05/06/2023]
Abstract
Stomata are two-celled valves that control epidermal pores whose opening and spacing optimizes shoot-atmosphere gas exchange. Arabidopsis stomatal formation involves at least one asymmetric division and one symmetric division. Stomatal formation and patterning are regulated by the frequency and placement of asymmetric divisions. This model system has already led to significant advances in developmental biology, such as the regulation of cell fate, division, differentiation, and patterning. Over the last 30 years, stomatal development has been found to be controlled by numerous intrinsic genetic and environmental factors. This mini review focuses on the signaling involved in stomatal initiation and in divisions in the cell lineage.
Collapse
Affiliation(s)
- Jie Le
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | | | | | | |
Collapse
|
50
|
Yang K, Wang H, Xue S, Qu X, Zou J, Le J. Requirement for A-type cyclin-dependent kinase and cyclins for the terminal division in the stomatal lineage of Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2449-61. [PMID: 24687979 PMCID: PMC4036514 DOI: 10.1093/jxb/eru139] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The Arabidopsis stoma is a specialized epidermal valve made up of a pair of guard cells around a pore whose aperture controls gas exchange between the shoot and atmosphere. Guard cells (GCs) are produced by a symmetric division of guard mother cells (GMCs). The R2R3-MYB transcription factor FOUR LIPS (FLP) and its paralogue MYB88 restrict the division of a GMC to one. Previously, the upstream regions of several core cell cycle genes were identified as the direct targets of FLP/MYB88, including the B-type cyclin-dependent kinase CDKB1;1 and A2-type cyclin CYCA2;3. Here we show that CDKA;1 is also an immediate direct target of FLP/MYB88 through the binding to cis-regulatory elements in the CDKA;1 promoter region. CDKA;1 activity is required not only for normal GMC divisions but also for the excessive cell overproliferation in flp myb88 mutant GMCs. The impaired defects of GMC division in cdkb1;1 1;2 mutants could be partially rescued by a stage-specific expression of CDKA;1. Although targeted overexpression of CDKA;1 does not affect stomatal development, ectopic expression of the D3-type cyclin CYCD3;2 induces GC subdivision, resulting in a stoma with 3-4 GCs instead of the normal two. Co-overexpression of CDKA;1 with CYCD3;2, but not with CYCA2;3, confers a synergistic effect with respect to GC subdivision. Thus, in addition to a role in stomatal formative asymmetric divisions at early developmental stages, CDKA;1 is needed in triggering GMC symmetric divisions at the late stage of stomatal development. However, timely down-regulation of CDKA;1-CYCD3 activity is required for restriction of GC proliferation.
Collapse
Affiliation(s)
- Kezhen Yang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Beijing 100093, China
| | - Hongzhe Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Beijing 100093, China
| | - Shan Xue
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Beijing 100093, China
| | - Xiaoxiao Qu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Beijing 100093, China
| | - Junjie Zou
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Beijing 100093, China
| | - Jie Le
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Beijing 100093, China
| |
Collapse
|