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Ye S, Wang S, Chan R, Cao L, Wang H. Identification of short protein-destabilizing sequences in Arabidopsis cyclin-dependent kinase inhibitors, ICKs. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:772-788. [PMID: 37862584 DOI: 10.1093/jxb/erad411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/18/2023] [Indexed: 10/22/2023]
Abstract
Plants have a family of cyclin-dependent kinase (CDK) inhibitors called interactors/inhibitors of CDK (ICKs) or Kip-related proteins (KRPs). ICK proteins have important functions in cell proliferation, endoreduplication, plant growth, and reproductive development, and their functions depend on the protein levels. However, understanding of how ICK protein levels are regulated is very limited. We fused Arabidopsis ICK sequences to green fluorescent protein (GFP) and determined their effects on the fusion proteins in plants, yeast, and Escherichia coli. The N-terminal regions of ICKs drastically reduced GFP fusion protein levels in Arabidopsis plants. A number of short sequences of 10-20 residues were found to decrease GFP fusion protein levels when fused at the N-terminus or C-terminus. Three of the four short sequences from ICK3 showed a similar function in yeast. Intriguingly, three short sequences from ICK1 and ICK3 caused the degradation of the fusion proteins in E. coli. In addition, computational analyses showed that ICK proteins were mostly disordered and unstructured except for the conserved C-terminal region, suggesting that ICKs are intrinsically disordered proteins. This study has identified a number of short protein-destabilizing sequences, and evidence suggests that some of them may cause protein degradation through structural disorder and instability.
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Affiliation(s)
- Shengjian Ye
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Sheng Wang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Ron Chan
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Ling Cao
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Hong Wang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
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Ajadi AA, Tong X, Wang H, Zhao J, Tang L, Li Z, Liu X, Shu Y, Li S, Wang S, Liu W, Tajo SM, Zhang J, Wang Y. Cyclin-Dependent Kinase Inhibitors KRP1 and KRP2 Are Involved in Grain Filling and Seed Germination in Rice ( Oryza sativa L.). Int J Mol Sci 2019; 21:ijms21010245. [PMID: 31905829 PMCID: PMC6981537 DOI: 10.3390/ijms21010245] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/26/2019] [Accepted: 12/26/2019] [Indexed: 12/19/2022] Open
Abstract
Cyclin-dependent kinase inhibitors known as KRPs (kip-related proteins) control the progression of plant cell cycles and modulate various plant developmental processes. However, the function of KRPs in rice remains largely unknown. In this study, two rice KRPs members, KRP1 and KRP2, were found to be predominantly expressed in developing seeds and were significantly induced by exogenous abscisic acid (ABA) and Brassinosteroid (BR) applications. Sub-cellular localization experiments showed that KRP1 was mainly localized in the nucleus of rice protoplasts. KRP1 overexpression transgenic lines (OxKRP1), krp2 single mutant (crkrp2), and krp1/krp2 double mutant (crkrp1/krp2) all exhibited significantly smaller seed width, seed length, and reduced grain weight, with impaired seed germination and retarded early seedling growth, suggesting that disturbing the normal steady state of KRP1 or KRP2 blocks seed development partly through inhibiting cell proliferation and enlargement during grain filling and seed germination. Furthermore, two cyclin-dependent protein kinases, CDKC;2 and CDKF;3, could interact with KRP1 in a yeast-two-hybrid system, indicating that KRP1 might regulate the mitosis cell cycle and endoreduplication through the two targets. In a word, this study shed novel insights into the regulatory roles of KRPs in rice seed maturation and germination.
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Affiliation(s)
- Abolore Adijat Ajadi
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (A.A.A.); (X.T.); (H.W.); (J.Z.); (L.T.); (Z.L.); (X.L.); (Y.S.); (S.L.); (S.W.); (W.L.); (S.M.T.)
- Biotechnology Unit, National Cereals Research Institute, Badeggi, Bida 912101, Nigeria
| | - Xiaohong Tong
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (A.A.A.); (X.T.); (H.W.); (J.Z.); (L.T.); (Z.L.); (X.L.); (Y.S.); (S.L.); (S.W.); (W.L.); (S.M.T.)
| | - Huimei Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (A.A.A.); (X.T.); (H.W.); (J.Z.); (L.T.); (Z.L.); (X.L.); (Y.S.); (S.L.); (S.W.); (W.L.); (S.M.T.)
| | - Juan Zhao
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (A.A.A.); (X.T.); (H.W.); (J.Z.); (L.T.); (Z.L.); (X.L.); (Y.S.); (S.L.); (S.W.); (W.L.); (S.M.T.)
| | - Liqun Tang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (A.A.A.); (X.T.); (H.W.); (J.Z.); (L.T.); (Z.L.); (X.L.); (Y.S.); (S.L.); (S.W.); (W.L.); (S.M.T.)
| | - Zhiyong Li
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (A.A.A.); (X.T.); (H.W.); (J.Z.); (L.T.); (Z.L.); (X.L.); (Y.S.); (S.L.); (S.W.); (W.L.); (S.M.T.)
| | - Xixi Liu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (A.A.A.); (X.T.); (H.W.); (J.Z.); (L.T.); (Z.L.); (X.L.); (Y.S.); (S.L.); (S.W.); (W.L.); (S.M.T.)
| | - Yazhou Shu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (A.A.A.); (X.T.); (H.W.); (J.Z.); (L.T.); (Z.L.); (X.L.); (Y.S.); (S.L.); (S.W.); (W.L.); (S.M.T.)
| | - Shufan Li
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (A.A.A.); (X.T.); (H.W.); (J.Z.); (L.T.); (Z.L.); (X.L.); (Y.S.); (S.L.); (S.W.); (W.L.); (S.M.T.)
| | - Shuang Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (A.A.A.); (X.T.); (H.W.); (J.Z.); (L.T.); (Z.L.); (X.L.); (Y.S.); (S.L.); (S.W.); (W.L.); (S.M.T.)
- College of Life Science, Yangtze University, Jingzhou 434025, China
| | - Wanning Liu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (A.A.A.); (X.T.); (H.W.); (J.Z.); (L.T.); (Z.L.); (X.L.); (Y.S.); (S.L.); (S.W.); (W.L.); (S.M.T.)
| | - Sani Muhammad Tajo
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (A.A.A.); (X.T.); (H.W.); (J.Z.); (L.T.); (Z.L.); (X.L.); (Y.S.); (S.L.); (S.W.); (W.L.); (S.M.T.)
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (A.A.A.); (X.T.); (H.W.); (J.Z.); (L.T.); (Z.L.); (X.L.); (Y.S.); (S.L.); (S.W.); (W.L.); (S.M.T.)
- Correspondence: (J.Z.); (Y.W.); Tel./Fax: +86-571-6337-0277 (J.Z.); +86-571-6337-0206 (Y.W.)
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (A.A.A.); (X.T.); (H.W.); (J.Z.); (L.T.); (Z.L.); (X.L.); (Y.S.); (S.L.); (S.W.); (W.L.); (S.M.T.)
- Correspondence: (J.Z.); (Y.W.); Tel./Fax: +86-571-6337-0277 (J.Z.); +86-571-6337-0206 (Y.W.)
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Li F, Wang L, Zhang Z, Li T, Feng J, Xu S, Zhang R, Guo D, Xue J. ZmSMR4, a novel cyclin-dependent kinase inhibitor (CKI) gene in maize (Zea mays L.), functions as a key player in plant growth, development and tolerance to abiotic stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 280:120-131. [PMID: 30823990 DOI: 10.1016/j.plantsci.2018.03.007] [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: 10/31/2017] [Revised: 03/06/2018] [Accepted: 03/08/2018] [Indexed: 06/09/2023]
Abstract
Endoreduplication is a key cell cycle variant in the developing maize endosperm and has been associated with cell enlargement and dry matter accumulation. Therefore, identification of the key genes associated with endosperm development and endoreduplication would not only lay the groundwork for understanding the biological process of endoreduplication but also be important for maize breeding. Here, we identified 12 putative endoreduplication-related candidate genes as members of the Zea mays L. SIAMESE-RELATED (ZmSMR) gene family and denoted them ZmSMR1-ZmSMR12. Sequence analysis indicated that all the ZmSMR protein sequences exhibited modest sequence similarity to the SIAMESE gene from Arabidopsis. Further analyses suggested that most ZmSMR genes might be associated with the transition from mitosis to endoreduplication because the expression levels of most ZmSMR genes were upregulated in endosperm cells during the phase of switching to an endoreduplication cell cycle. Additionally, the ZmSMRs responded to various abiotic stresses at the transcriptional level. One member of the ZmSMR gene family, the ZmSMR4 (KY946768) gene, was isolated as the first maize endoreduplication-related gene and has been used to develop transgenic Arabidopsis plants. ZmSMR4 was localized to the nucleus and could interact with ZmCDKA and ZmCDKB. Moreover, ZmSMR4 was able to rescue the multicellular trichome phenotype of Arabidopsis sim mutants and enhanced the endoreduplication levels of transgenic Arabidopsis plants. Arabidopsis plants overexpressing ZmSMR4 not only displayed enhanced leaf margin serrations but also showed several interesting breeding phenotypes, such as early blossoming and fuller seeds. Taken together, our data suggest that the ZmSMR4 gene is plant-specific and functions as a key player in the signalling network that controls plant growth, development and responses to abiotic stress by regulating the transition between the mitotic cycle and endoreduplication.
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Affiliation(s)
- Feifei Li
- Key Laboratory of the Biology and Genetic Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, China; Maize Engineering and Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, 712100, China
| | - Licheng Wang
- Key Laboratory of the Biology and Genetic Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, China; Maize Engineering and Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, 712100, China
| | - Zhengquan Zhang
- Key Laboratory of the Biology and Genetic Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, China; Maize Engineering and Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, 712100, China
| | - Ting Li
- Key Laboratory of the Biology and Genetic Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, China; Maize Engineering and Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, 712100, China
| | - Jiaojiao Feng
- Key Laboratory of the Biology and Genetic Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, China; Maize Engineering and Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, 712100, China
| | - Shutu Xu
- Key Laboratory of the Biology and Genetic Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, China; Maize Engineering and Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, 712100, China
| | - Renhe Zhang
- Key Laboratory of the Biology and Genetic Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, China; Maize Engineering and Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, 712100, China
| | - Dongwei Guo
- Key Laboratory of the Biology and Genetic Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, China; Maize Engineering and Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, 712100, China.
| | - Jiquan Xue
- Key Laboratory of the Biology and Genetic Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, China; Maize Engineering and Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, 712100, China.
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Coelho RR, Vieira P, Antonino de Souza Júnior JD, Martin-Jimenez C, De Veylder L, Cazareth J, Engler G, Grossi-de-Sa MF, de Almeida Engler J. Exploiting cell cycle inhibitor genes of the KRP family to control root-knot nematode induced feeding sites in plants. PLANT, CELL & ENVIRONMENT 2017; 40:1174-1188. [PMID: 28103637 DOI: 10.1111/pce.12912] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 01/06/2017] [Indexed: 05/17/2023]
Abstract
Cell cycle control in galls provoked by root-knot nematodes involves the activity of inhibitor genes like the Arabidopsis ICK/KRP members. Ectopic KRP1, KRP2 and KRP4 expression resulted in decreased gall size by inhibiting mitotic activity, whereas KRP6 induces mitosis in galls. Herein, we investigate the role of KRP3, KRP5 and KRP7 during gall development and compared their role with previously studied members of this class of cell cycle inhibitors. Overexpression of KRP3 and KRP7 culminated in undersized giant cells, with KRP3OE galls presenting peculiar elongated giant cells. Nuclei in KRP3OE and KRP5OE lines presented a convoluted and apparently connected phenotype. This appearance may be associated with the punctuated protein nuclear localization driven by specific common motifs. As well, ectopic expression of KRP3OE and KRP5OE affected nematode development and offspring. Decreased mitotic activity in galls of KRP3OE and KRP7OE lines led to a reduced gall size which presented distinct shapes - from more elongated like in the KRP3OE line to small rounded like in the KRP7OE line. Results presented strongly support the idea that induced expression of cell cycle inhibitors such as KRP3 and KRP7 in galls can be envisaged as a conceivable strategy for nematode feeding site control in crop species attacked by phytopathogenic nematodes.
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Affiliation(s)
- Roberta Ramos Coelho
- INRA, University of Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, PqEB - Av. W5 Norte, Caixa Postal 02372, CEP 70770-917, Brasília, DF, Brazil
| | - Paulo Vieira
- INRA, University of Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
- NemaLab/ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Núcleo da Mitra, Ap., 94,7002-554, Évora, Portugal
| | - José Dijair Antonino de Souza Júnior
- INRA, University of Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, PqEB - Av. W5 Norte, Caixa Postal 02372, CEP 70770-917, Brasília, DF, Brazil
| | - Cristina Martin-Jimenez
- INRA, University of Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Lieven De Veylder
- Department of Plant Systems Biology, VIB, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Gent, Belgium
| | - Julie Cazareth
- Université de Nice Sophia Antipolis, 06103, Nice, France
- Centre National de la Recherche Scientifique (CNRS), Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275, 06560, Valbonne, France
| | - Gilbert Engler
- INRA, University of Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Maria Fatima Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, PqEB - Av. W5 Norte, Caixa Postal 02372, CEP 70770-917, Brasília, DF, Brazil
| | - Janice de Almeida Engler
- INRA, University of Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
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5
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Identification and functional analysis of the ICK gene family in maize. Sci Rep 2017; 7:43818. [PMID: 28262730 PMCID: PMC5338338 DOI: 10.1038/srep43818] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 01/31/2017] [Indexed: 11/29/2022] Open
Abstract
Inhibitors of cyclin-dependent kinases (ICKs) are key regulators of cyclin-dependent kinase activities and cell division. Herein, we identified eight ICKs in maize, which we named Zeama;ICKs (ZmICKs). Primary sequencing and phylogenetic analyses were used to divide the ZmICK family into two classes: group B and group C. Subcellular localization analysis of ZmICK:enhanced green fluorescent protein (eGFP) fusion constructs in tobacco leaf cells indicated that ZmICKs are principally nuclear. Co-localization analysis of the ZmICKs and maize A-type cyclin-dependent kinase (ZmCDKA) was also performed using enhanced green fluorescent protein (eGFP) and red fluorescent protein (RFP) fusion constructs. The ZmICKs and ZmCDKA co-localized in the nucleus. Semi-quantitative RT-PCR analysis of the ZmICKs showed that they were expressed at different levels in all tissues examined and shared similar expression patterns with cell cycle-related genes. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that ZmICK1, ZmICK2, ZmICK3, and ZmICK4 interact with ZmCDKA1 and ZmCDKA3. Interestingly, ZmICK7 interacts with D-type cyclins. Transformed and expressed ZmCDKA1 and ZmICKs together in fission yeast revealed that ZmICK1, ZmICK3, and ZmICK4 can affect ZmCDKA1 function. Moreover, the C-group of ZmICKs could interact with ZmCDKA1 directly and affect ZmCDKA1 function, suggesting that C-group ZmICKs are important for cell division regulation.
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Godínez-Palma SK, Rosas-Bringas FR, Rosas-Bringas OG, García-Ramírez E, Zamora-Zaragoza J, Vázquez-Ramos JM. Two maize Kip-related proteins differentially interact with, inhibit and are phosphorylated by cyclin D-cyclin-dependent kinase complexes. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1585-1597. [PMID: 28369656 PMCID: PMC5444471 DOI: 10.1093/jxb/erx054] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The family of maize Kip-related proteins (KRPs) has been studied and a nomenclature based on the relationship to rice KRP genes is proposed. Expression studies of KRP genes indicate that all are expressed at 24 h of seed germination but expression is differential in the different tissues of maize plantlets. Recombinant KRP1;1 and KRP4;2 proteins, members of different KRP classes, were used to study association to and inhibitory activity on different maize cyclin D (CycD)-cyclin-dependent kinase (CDK) complexes. Kinase activity in CycD2;2-CDK, CycD4;2-CDK, and CycD5;3-CDK complexes was inhibited by both KRPs; however, only KRP1;1 inhibited activity in the CycD6;1-CDK complex, not KRP4;2. Whereas KRP1;1 associated with either CycD2;2 or CycD6;1, and to cyclin-dependent kinase A (CDKA) recombinant proteins, forming ternary complexes, KRP4;2 bound CDKA and CycD2;2 but did not bind CycD6;1, establishing a differential association capacity. All CycD-CDK complexes included here phosphorylated both the retinoblastoma-related (RBR) protein and the two KRPs; interestingly, while KRP4;2 phosphorylated by the CycD2;2-CDK complex increased its inhibitory capacity, when phosphorylated by the CycD6;1-CDK complex the inhibitory capacity was reduced or eliminated. Evidence suggests that the phosphorylated residues in KRP4;2 may be different for every kinase, and this would influence its performance as a cyclin-CDK inhibitor.
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Affiliation(s)
- Silvia K Godínez-Palma
- Facultad de Química, Departamento de Bioquímica, UNAM, Avenida Universidad y Copilco, México DF 04510, México
| | - Fernando R Rosas-Bringas
- Facultad de Química, Departamento de Bioquímica, UNAM, Avenida Universidad y Copilco, México DF 04510, México
- I. Medizinische Klinik and Poliklinik, Universitätsmedizin der Johannes Gutenberg-Universität Mainz Obere Zahlbacherstr. 63 55131 Mainz, Germany
| | - Omar G Rosas-Bringas
- Facultad de Química, Departamento de Bioquímica, UNAM, Avenida Universidad y Copilco, México DF 04510, México
| | - Elpidio García-Ramírez
- Facultad de Química, Departamento de Bioquímica, UNAM, Avenida Universidad y Copilco, México DF 04510, México
| | - Jorge Zamora-Zaragoza
- Facultad de Química, Departamento de Bioquímica, UNAM, Avenida Universidad y Copilco, México DF 04510, México
- Department of Plant Sciences, Plant Developmental Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Jorge M Vázquez-Ramos
- Facultad de Química, Departamento de Bioquímica, UNAM, Avenida Universidad y Copilco, México DF 04510, México
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Vieira P, de Almeida Engler J. Plant Cyclin-Dependent Kinase Inhibitors of the KRP Family: Potent Inhibitors of Root-Knot Nematode Feeding Sites in Plant Roots. FRONTIERS IN PLANT SCIENCE 2017; 8:1514. [PMID: 28943880 PMCID: PMC5596062 DOI: 10.3389/fpls.2017.01514] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/17/2017] [Indexed: 05/14/2023]
Abstract
Root-knot nematodes (RKN), Meloidogyne spp., are distributed worldwide and impose severe economic damage to many agronomically important crops. The plant cell cycle machinery is considered one of the pivotal components for the formation of nematode feeding sites (NFSs) or galls. These feeding sites contain five to nine hypertrophied giant cells (GC) resulting from developmental reprogramming of host root cells by this pathogen. GC undergo synchronous waves of mitotic activity uncoupled from cytokinesis giving rise to large multinucleate cells. As development of the NFS progresses, multiple rounds of DNA synthesis occur in the nuclei of GC, coupled with nuclear and cellular expansion. These cells are highly metabolically active and provide the nematode with nutrients necessary for its development and completion of its life cycle. In Arabidopsis seven cyclin dependent kinase inhibitors (CKIs) belonging to the interactors/inhibitors of the cyclin dependent kinases (ICK) family, also referred as Kip-Related Proteins (KRPs) have been identified. Interactions of KRPs with CDK/Cyclin complexes decrease CDK activity, affecting both cell cycle progression and DNA content in a concentration-dependent manner. We performed the functional analysis of all Arabidopsis KRP gene members during RKN interaction in Arabidopsis to obtain more insight into their role during gall development. We demonstrated that three members of this family (KRP2, KRP5, and KRP6) were highly expressed in galls and were important for cell cycle regulation during NFS development as shown by their different modes of action. We also pointed out that cell cycle inhibition through overexpression of all members of the KRP family can affect NFS development and consequently compromise the nematode's life cycle. In this review we summarized our recent understanding of the KRP family of genes, and their role in controlling cell cycle progression at the RKN feeding site.
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Affiliation(s)
- Paulo Vieira
- Laboratório de Nematologia, Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de ÉvoraÉvora, Portugal
| | - Janice de Almeida Engler
- Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Institut Sophia Agrobiotech, Université Côte d’AzurNice, France
- *Correspondence: Janice de Almeida Engler,
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8
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Vieira P, De Clercq A, Stals H, Van Leene J, Van De Slijke E, Van Isterdael G, Eeckhout D, Persiau G, Van Damme D, Verkest A, Antonino de Souza JD, Júnior, Glab N, Abad P, Engler G, Inzé D, De Veylder L, De Jaeger G, Engler JDA. The Cyclin-Dependent Kinase Inhibitor KRP6 Induces Mitosis and Impairs Cytokinesis in Giant Cells Induced by Plant-Parasitic Nematodes in Arabidopsis. THE PLANT CELL 2014; 26:2633-2647. [PMID: 24963053 PMCID: PMC4114956 DOI: 10.1105/tpc.114.126425] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 04/09/2014] [Accepted: 05/28/2014] [Indexed: 10/25/2023]
Abstract
In Arabidopsis thaliana, seven cyclin-dependent kinase (CDK) inhibitors have been identified, designated interactors of CDKs or Kip-related proteins (KRPs). Here, the function of KRP6 was investigated during cell cycle progression in roots infected by plant-parasitic root-knot nematodes. Contrary to expectations, analysis of Meloidogyne incognita-induced galls of KRP6-overexpressing lines revealed a role for this particular KRP as an activator of the mitotic cell cycle. In accordance, KRP6-overexpressing suspension cultures displayed accelerated entry into mitosis, but delayed mitotic progression. Likewise, phenotypic analysis of cultured cells and nematode-induced giant cells revealed a failure in mitotic exit, with the appearance of multinucleated cells as a consequence. Strong KRP6 expression upon nematode infection and the phenotypic resemblance between KRP6 overexpression cell cultures and root-knot morphology point toward the involvement of KRP6 in the multinucleate and acytokinetic state of giant cells. Along these lines, the parasite might have evolved to manipulate plant KRP6 transcription to the benefit of gall establishment.
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Affiliation(s)
- Paulo Vieira
- Institut National de la Recherche Agronomique, UMR 1355 ISA/Centre National de la Recherche Scientifique, UMR 7254 ISA/Université de Nice-Sophia Antipolis, UMR ISA, 400 route des Chappes, 06903 Sophia-Antipolis, France
| | - Annelies De Clercq
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Hilde Stals
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Jelle Van Leene
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Gert Van Isterdael
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Geert Persiau
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Daniël Van Damme
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Aurine Verkest
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - José Dijair Antonino de Souza
- Institut National de la Recherche Agronomique, UMR 1355 ISA/Centre National de la Recherche Scientifique, UMR 7254 ISA/Université de Nice-Sophia Antipolis, UMR ISA, 400 route des Chappes, 06903 Sophia-Antipolis, France Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, 70770-900 Distrito Federal, Brazil Institut de Biologie des Plantes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8618, Université Paris-Sud, Saclay Plant Sciences, 91405 Orsay Cedex, France
| | - Júnior
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, 70770-900 Distrito Federal, Brazil
| | - Nathalie Glab
- Institut de Biologie des Plantes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8618, Université Paris-Sud, Saclay Plant Sciences, 91405 Orsay Cedex, France
| | - Pierre Abad
- Institut National de la Recherche Agronomique, UMR 1355 ISA/Centre National de la Recherche Scientifique, UMR 7254 ISA/Université de Nice-Sophia Antipolis, UMR ISA, 400 route des Chappes, 06903 Sophia-Antipolis, France
| | - Gilbert Engler
- Institut National de la Recherche Agronomique, UMR 1355 ISA/Centre National de la Recherche Scientifique, UMR 7254 ISA/Université de Nice-Sophia Antipolis, UMR ISA, 400 route des Chappes, 06903 Sophia-Antipolis, France
| | - Dirk Inzé
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Lieven De Veylder
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Janice de Almeida Engler
- Institut National de la Recherche Agronomique, UMR 1355 ISA/Centre National de la Recherche Scientifique, UMR 7254 ISA/Université de Nice-Sophia Antipolis, UMR ISA, 400 route des Chappes, 06903 Sophia-Antipolis, France
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9
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Cheng Y, Cao L, Wang S, Li Y, Shi X, Liu H, Li L, Zhang Z, Fowke LC, Wang H, Zhou Y. Downregulation of multiple CDK inhibitor ICK/KRP genes upregulates the E2F pathway and increases cell proliferation, and organ and seed sizes in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:642-55. [PMID: 23647236 DOI: 10.1111/tpj.12228] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 04/22/2013] [Accepted: 04/30/2013] [Indexed: 05/03/2023]
Abstract
The ICK/KRP cyclin-dependent kinase (CDK) inhibitors are important plant cell cycle factors sharing only limited similarity with the metazoan CIP/KIP family of CDK inhibitors. Little is known about the specific functions of different ICK/KRP genes in planta. In this study, we created double and multiple mutants from five single Arabidopsis ICK/KRP T-DNA mutants, and used a set of 20 lines for the functional investigation of the important gene family. There were gradual increases in CDK activity from single to multiple mutants, indicating that ICK/KRPs act as CDK inhibitors under normal physiological conditions in plants. Whereas lower-order mutants showed no morphological phenotypes, the ick1 ick2 ick6 ick7 and ick1 ick2 ick5 ick6 ick7 mutants had a slightly altered leaf shape. The quintuple mutant had larger cotyledons, leaves, petals and seeds than the wild-type control. At the cellular level, the ICK/KRP mutants had more but smaller cells in all the organs examined. These phenotypic effects became more apparent as more ICK/KRPs were downregulated, suggesting that to a large extent ICK/KRPs function in plants redundantly in a dosage-dependent manner. Analyses also revealed increased expression of E2F-dependent genes, and elevated RBR1 as well as an increased level of phospho-RBB1 protein in the quintuple mutant. Thus, downregulation of multiple ICK/KRP genes increases CDK activity, upregulates the E2F pathway and stimulates cell proliferation, resulting in increased cell numbers, and larger organs and seeds.
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Affiliation(s)
- Yan Cheng
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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10
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Yin T, Pan G, Liu H, Wu J, Li Y, Zhao Z, Fu T, Zhou Y. The chloroplast ribosomal protein L21 gene is essential for plastid development and embryogenesis in Arabidopsis. PLANTA 2012; 235:907-21. [PMID: 22105802 DOI: 10.1007/s00425-011-1547-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 10/31/2011] [Indexed: 05/22/2023]
Abstract
Embryogenesis in higher plants is controlled by a complex gene network. Identification and characterization of genes essential for embryogenesis will provide insights into the early events in embryo development. In this study, a novel mutant with aborted seed development (asd) was identified in Arabidopsis. The asd mutant produced about 25% of albino seeds at the early stage of silique development. The segregation of normal and albino seeds was inherited as a single recessive embryo-lethal trait. The gene disrupted in the asd mutant was isolated through map-based cloning. The mutated gene contains a single base change (A to C) in the coding region of RPL21C (At1g35680) that is predicted to encode the chloroplast 50S ribosomal protein L21. Allele test with other two T-DNA insertion lines in RPL21C and a complementation test demonstrated that the mutation in RPL21C was responsible for the asd phenotype. RPL21C exhibits higher expression in leaves and flowers compared with expression levels in roots and developing seeds. The RPL21C-GFP fusion protein was localized in chloroplasts. Cytological observations showed that the asd embryo development was arrested at the globular stage. There were no plastids with normal thylakoids and as a result no normal chloroplasts formed in mutant cells, indicating an indispensable role of the ASD gene in chloroplasts biogenesis. Our studies suggest that the chloroplast ribosomal protein L21 gene is required for chloroplast development and embryogenesis in Arabidopsis.
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Affiliation(s)
- Tuanzhang Yin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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11
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DePaoli HC, Brito MS, Quiapim AC, Teixeira SP, Goldman GH, Dornelas MC, Goldman MHS. Stigma/style cell cycle inhibitor 1 (SCI1), a tissue-specific cell cycle regulator that controls upper pistil development. THE NEW PHYTOLOGIST 2011; 190:882-895. [PMID: 21388377 DOI: 10.1111/j.1469-8137.2011.03660.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A cDNA encoding a small lysine-rich protein of unknown function was identified in a tobacco (Nicotiana tabacum) stigma/style suppression subtractive hybridization cDNA library. After its characterization, the corresponding gene was designated stigma/style cell cycle inhibitor 1 (SCI1). Fluorescence microscopy with an SCI1-GFP protein fusion demonstrated its nuclear localization, which was confined to the interchromatic region. Real-time RT-PCR and in situ hybridization experiments showed that SCI1 is stigma/style-specific and developmentally regulated. SCI1 RNAi knockdown and overexpression plants had stigmas/styles with remarkably enlarged and reduced areas, respectively, which was attributable to differences in cell numbers. These results indicate that SCI1 is a tissue-specific negative cell cycle regulator. The differences in cell division had an effect on the timing of the differentiation of the stigmatic papillar cells, suggesting that their differentiation is coupled to stigma cell divisions. This is consistent with a role for SCI1 in triggering differentiation through cell proliferation control. Our results revealed that SCI1 is a novel tissue-specific gene that controls cell proliferation/differentiation, probably as a component of a developmental signal transduction pathway.
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Affiliation(s)
- Henrique C DePaoli
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14049-900, Brazil
| | - Michael S Brito
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14049-900, Brazil
| | - Andréa C Quiapim
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil
| | - Simone P Teixeira
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-903, Brazil
| | - Gustavo H Goldman
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-903, Brazil
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Campinas 13083-970, Brazil
| | - Marcelo C Dornelas
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade de Campinas, Campinas 13083-970, Brazil
| | - Maria Helena S Goldman
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil
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12
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Yang R, Tang Q, Wang H, Zhang X, Pan G, Wang H, Tu J. Analyses of two rice (Oryza sativa) cyclin-dependent kinase inhibitors and effects of transgenic expression of OsiICK6 on plant growth and development. ANNALS OF BOTANY 2011; 107:1087-101. [PMID: 21558459 PMCID: PMC3091807 DOI: 10.1093/aob/mcr057] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 12/17/2010] [Accepted: 02/01/2011] [Indexed: 05/07/2023]
Abstract
BACKGROUND AND AIMS Plants have a family of proteins referred to as ICKs (inhibitors of cyclin-dependent kinase, CDK) or KRPs (Kip-related proteins) that function to regulate the activities of CDK. Knowledge of these plant CDK inhibitors has been gained mostly from studies of selected members in dicotyledonous plants, particularly Arabidopsis. Much remains to be learned regarding the differences among various members of the ICK/KRP family, and regarding the function and regulation of these proteins in monocotyledonous plants. METHODS We analysed ICK-related sequences in the rice (Orysa sativa L. subsp. indica) genome and determined that there are six members with the conserved C-terminal signature region for ICK/KRP proteins. They are referred to as OsiICKs and further analyses were performed. The interactions with CDKs and cyclins were determined by a yeast two-hybrid assay, and cellular localization by fusion with the enhanced green fluorescence protein (EGFP). The expression of OsiICK6 in different tissues and in response to several treatments was analysed by reverse transcriptase-mediated polymerase chain reaction (RT-PCR) and real-time PCR. Furthermore, OsiICK6 was over-expressed in transgenic rice plants and significant phenotypes were observed. KEY RESULTS AND CONCLUSIONS Based on putative protein sequences, the six OsiICKs are grouped into two classes, with OsiICK1 and OsiICK6 in each of the two classes, respectively. Results showed that OsiICK1 and OsiICK6 interacted with OsCYCD, but differed in their interactions with CDKA. Both EGFP:OsiICK1 and EGFP:OsiICK6 were localized in the nucleus. Whereas EGFP:OsiICK6 showed a punctuate subnuclear distribution, OsiICK1 had a homogeneous pattern. Over-expression of OsiICK6 resulted in multiple phenotypic effects on plant growth, morphology, pollen viability and seed setting. In OsiICK6-over-expressing plants, leaves rolled toward the abaxial side, suggesting that cell proliferation is critical in maintaining an even growth along the dorsal-ventral plane of leaf blades.
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Affiliation(s)
- Ruifang Yang
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Kaixuan Road 268, Hangzhou 310029, China
| | - Qicai Tang
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Kaixuan Road 268, Hangzhou 310029, China
| | - Huimei Wang
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Kaixuan Road 268, Hangzhou 310029, China
| | - Xiaobo Zhang
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Kaixuan Road 268, Hangzhou 310029, China
| | - Gang Pan
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Kaixuan Road 268, Hangzhou 310029, China
| | - Hong Wang
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Jumin Tu
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Kaixuan Road 268, Hangzhou 310029, China
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13
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Torres Acosta JA, Fowke LC, Wang H. Analyses of phylogeny, evolution, conserved sequences and genome-wide expression of the ICK/KRP family of plant CDK inhibitors. ANNALS OF BOTANY 2011; 107:1141-57. [PMID: 21385782 PMCID: PMC3091803 DOI: 10.1093/aob/mcr034] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 11/23/2010] [Accepted: 01/07/2011] [Indexed: 05/07/2023]
Abstract
BACKGROUND AND AIMS The cell cycle is controlled by cyclin-dependent kinases (CDKs), and CDK inhibitors are major regulators of their activities. The ICK/KRP family of CDK inhibitors has been reported in several plants, with seven members in arabidopsis; however, the phylogenetic relationship among members in different species is unknown. Also, there is a need to understand how these genes and proteins are regulated. Furthermore, little information is available on the functional differences among ICK/KRP family members. METHODS We searched publicly available databases and identified over 120 unique ICK/KRP protein sequences from more than 60 plant species. Phylogenetic analysis was performed using 101 full-length sequences from 40 species and intron-exon organization of ICK/KRP genes in model species. Conserved sequences and motifs were analysed using ICK/KRP protein sequences from arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and poplar (Populus trichocarpa). In addition, gene expression was examined using microarray data from arabidopsis, rice and poplar, and further analysed by RT-PCR for arabidopsis. KEY RESULTS AND CONCLUSIONS Phylogenetic analysis showed that plant ICK/KRP proteins can be grouped into three major classes. Whereas the C-class contains sequences from dicotyledons, monocotyledons and gymnosperms, the A- and B-classes contain only sequences from dicotyledons or monocotyledons, respectively, suggesting that the A- and B-classes might have evolved from the C-class. This classification is also supported by exon-intron organization. Genes in the A- and B- classes have four exons, whereas genes in the C-class have only three exons. Analysis of sequences from arabidopsis, rice and poplar identified conserved sequence motifs, some of which had not been described previously, and putative functional sites. The presence of conserved motifs in different family members is consistent with the classification. In addition, gene expression analysis showed preferential expression of ICK/KRP genes in certain tissues. A model has been proposed for the evolution of this gene family in plants.
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Affiliation(s)
| | | | - Hong Wang
- Department of Biochemistry, University of Saskatchewan, Saskatoon SK, S7N 5E2, Canada
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14
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Van Leene J, Hollunder J, Eeckhout D, Persiau G, Van De Slijke E, Stals H, Van Isterdael G, Verkest A, Neirynck S, Buffel Y, De Bodt S, Maere S, Laukens K, Pharazyn A, Ferreira PCG, Eloy N, Renne C, Meyer C, Faure JD, Steinbrenner J, Beynon J, Larkin JC, Van de Peer Y, Hilson P, Kuiper M, De Veylder L, Van Onckelen H, Inzé D, Witters E, De Jaeger G. Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Mol Syst Biol 2011; 6:397. [PMID: 20706207 PMCID: PMC2950081 DOI: 10.1038/msb.2010.53] [Citation(s) in RCA: 257] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 06/12/2010] [Indexed: 12/27/2022] Open
Abstract
A protein interactome focused towards cell proliferation was mapped comprising 857 interactions among 393 proteins, leading to many new insights in plant cell cycle regulation. A comprehensive view on heterodimeric cyclin-dependent kinase (CDK)/cyclin complexes in plants is obtained, in relation with their regulators. Over 100 new candidate cell cycle proteins were predicted.
The basic underlying mechanisms that govern the cell cycle are conserved among all eukaryotes. Peculiar for plants, however, is that their genome contains a collection of cell cycle regulatory genes that is intriguingly large (Vandepoele et al, 2002; Menges et al, 2005) compared to other eukaryotes. Arabidopsis thaliana (Arabidopsis) encodes 71 genes in five regulatory classes versus only 15 in yeast and 23 in human. Despite the discovery of numerous cell cycle genes, little is known about the protein complex machinery that steers plant cell division. Therefore, we applied tandem affinity purification (TAP) approach coupled with mass spectrometry (MS) on Arabidopsis cell suspension cultures to isolate and analyze protein complexes involved in the cell cycle. This approach allowed us to successfully map a first draft of the basic cell cycle complex machinery of Arabidopsis, providing many new insights into plant cell division. To map the interactome, we relied on a streamlined platform comprising generic Gateway-based vectors with high cloning flexibility, the fast generation of transgenic suspension cultures, TAP adapted for plant cells, and matrix-assisted laser desorption ionization (MALDI) tandem-MS for the identification of purified proteins (Van Leene et al, 2007, 2008Van Leene et al, 2007, 2008). Complexes for 102 cell cycle proteins were analyzed using this approach, leading to a non-redundant data set of 857 interactions among 393 proteins (Figure 1A). Two subspaces were identified in this data set, domain I1, containing interactions confirmed in at least two independent experimental repeats or in the reciprocal purification experiment, and domain I2 consisting of uniquely observed interactions. Several observations underlined the quality of both domains. All tested reverse purifications found the original interaction, and 150 known or predicted interactions were confirmed, meaning that also a huge stack of new interactions was revealed. An in-depth computational analysis revealed enrichment for many cell cycle-related features among the proteins of the network (Figure 1B), and many protein pairs were coregulated at the transcriptional level (Figure 1C). Through integration of known cell cycle-related features, more than 100 new candidate cell cycle proteins were predicted (Figure 1D). Besides common qualities of both interactome domains, their real significance appeared through mutual differences exposing two subspaces in the cell cycle interactome: a central regulatory network of stable complexes that are repeatedly isolated and represent core regulatory units, and a peripheral network comprising transient interactions identified less frequently, which are involved in other aspects of the process, such as crosstalk between core complexes or connections with other pathways. To evaluate the biological relevance of the cell cycle interactome in plants, we validated interactions from both domains by a transient split-luciferase assay in Arabidopsis plants (Marion et al, 2008), further sustaining the hypothesis-generating power of the data set to understand plant growth. With respect to insights into the cell cycle physiology, the interactome was subdivided according to the functional classes of the baits and core protein complexes were extracted, covering cyclin-dependent kinase (CDK)/cyclin core complexes together with their positive and negative regulation networks, DNA replication complexes, the anaphase-promoting complex, and spindle checkpoint complexes. The data imply that mitotic A- and B-type cyclins exclusively form heterodimeric complexes with the plant-specific B-type CDKs and not with CDKA;1, whereas D-type cyclins seem to associate with CDKA;1. Besides the extraction of complexes previously shown in other organisms, our data also suggested many new functional links; for example, the link coupling cell division with the regulation of transcript splicing. The association of negative regulators of CDK/cyclin complexes with transcription factors suggests that their role in reallocation is not solely targeted to CDK/cyclin complexes. New members of the Siamese-related inhibitory proteins were identified, and for the first time potential inhibitors of plant-specific mitotic B-type CDKs have been found in plants. New evidence that the E2F–DP–RBR network is not only active at G1-to-S, but also at the G2-to-M transition is provided and many complexes involved in DNA replication or repair were isolated. For the first time, a plant APC has been isolated biochemically, identifying three potential new plant-specific APC interactors, and finally, complexes involved in the spindle checkpoint were isolated mapping many new but specific interactions. Finally, to get a general view on the complex machinery, modules of interacting cyclins and core cell cycle regulators were ranked along the cell cycle phases according to the transcript expression peak of the cyclins, showing an assorted set of CDK–cyclin complexes with high regulatory differentiation (Figure 4). Even within the same subfamily (e.g. cyclin A3, B1, B2, D3, and D4), cyclins differ not only in their functional time frame but also in the type and number of CDKs, inhibitors, and scaffolding proteins they bind, further indicating their functional diversification. According to our interaction data, at least 92 different variants of CDK–cyclin complexes are found in Arabidopsis. In conclusion, these results reflect how several rounds of gene duplication (Sterck et al, 2007) led to the evolution of a large set of cyclin paralogs and a myriad of regulators, resulting in a significant jump in the complexity of the cell cycle machinery that could accommodate unique plant-specific features such as an indeterminate mode of postembryonic development. Through their extensive regulation and connection with a myriad of up- and downstream pathways, the core cell cycle complexes might offer the plant a flexible toolkit to fine-tune cell proliferation in response to an ever-changing environment. Cell proliferation is the main driving force for plant growth. Although genome sequence analysis revealed a high number of cell cycle genes in plants, little is known about the molecular complexes steering cell division. In a targeted proteomics approach, we mapped the core complex machinery at the heart of the Arabidopsis thaliana cell cycle control. Besides a central regulatory network of core complexes, we distinguished a peripheral network that links the core machinery to up- and downstream pathways. Over 100 new candidate cell cycle proteins were predicted and an in-depth biological interpretation demonstrated the hypothesis-generating power of the interaction data. The data set provided a comprehensive view on heterodimeric cyclin-dependent kinase (CDK)–cyclin complexes in plants. For the first time, inhibitory proteins of plant-specific B-type CDKs were discovered and the anaphase-promoting complex was characterized and extended. Important conclusions were that mitotic A- and B-type cyclins form complexes with the plant-specific B-type CDKs and not with CDKA;1, and that D-type cyclins and S-phase-specific A-type cyclins seem to be associated exclusively with CDKA;1. Furthermore, we could show that plants have evolved a combinatorial toolkit consisting of at least 92 different CDK–cyclin complex variants, which strongly underscores the functional diversification among the large family of cyclins and reflects the pivotal role of cell cycle regulation in the developmental plasticity of plants.
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Nafati M, Frangne N, Hernould M, Chevalier C, Gévaudant F. Functional characterization of the tomato cyclin-dependent kinase inhibitor SlKRP1 domains involved in protein-protein interactions. THE NEW PHYTOLOGIST 2010; 188:136-149. [PMID: 20618916 DOI: 10.1111/j.1469-8137.2010.03364.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
• Cyclin-dependent kinase (CDK) inhibitors (kip-related proteins, KRPs) play a major role in the regulation of plant cell cycle in antagonizing its progression, and are thus regulators of development. The primary sequence of KRPs is characterized by the existence of conserved motifs, for which we have limited information on their functional significance. • We performed a functional analysis of various domains present in KRPs from tomato. A series of deletion mutants of SlKRP1 was generated and used in transient expression assays to define the relevance of conserved protein domains in subcellular and subnuclear localizations. Specific interactions of SlKRP1 and its deletion variants with cell cycle proteins were investigated using two-hybrid assays and bimolecular fluorescent complementation. • Plant KRPs are distributed into two phylogenetic subgroups according to the presence of conserved motifs. Members of subgroup 1 represented by SlKRP1 share 6 conserved motifs whose function in protein localization and protein-protein interactions could be identified. A new interaction motif was localized in the central part of SlKRP1 that targets SlCDKA1 and SlCYCD3;1 to the nucleus. • Our results bring new insights to the functional role of particular domains in KRPs relative to subcellular localization or proteolytic degradation.
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Affiliation(s)
- Mehdi Nafati
- Institut National de la Recherche Agronomique (INRA), Université de Bordeaux, Unité Mixte de Recherche 619 sur la Biologie du Fruit, BP 81, F-33883 Villenave d'Ornon Cedex, France
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Dahan J, Wendehenne D, Ranjeva R, Pugin A, Bourque S. Nuclear protein kinases: still enigmatic components in plant cell signalling. THE NEW PHYTOLOGIST 2010; 185:355-68. [PMID: 19925553 DOI: 10.1111/j.1469-8137.2009.03085.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plants constantly face changing conditions in their environment. Unravelling the transduction mechanisms from signal perception at the plasma membrane level down to gene expression in the nucleus is a fascinating challenge. Protein phosphorylation, catalysed by protein kinases, is one of the major posttranslational modifications involved in the specificity, kinetic(s) and intensity of a signal transduction pathway. Although commonly assumed, the involvement of nuclear protein kinases in signal transduction is often poorly characterized. In particular, both their regulation and mode of action remain to be elucidated and may lead to the unveiling of new original mechanisms. For example, unlike animal cells, plant cells contain only a few strictly nucleus-localized protein kinases, which calls into question the role of this cellular distribution between the cytosol and the nucleus in their activation and functions. The control of their nucleocytoplasmic trafficking appears to play a major role in their regulation, probably through promoting interactions with their substrates under specific cellular conditions. However, recent findings showing that the nucleus can generate complex networks of second messengers (e.g. Ca(2+)or diacyglycerol) suggest that nuclear protein kinases could play an active role in the decoding of such signals.
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Affiliation(s)
- Jennifer Dahan
- UMR INRA 1088/CNRS 5184/Université de Bourgogne Plante-Microbe-Environnement, France
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17
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Wang H, Zhou Y, Bird DA, Fowke LC. Functions, regulation and cellular localization of plant cyclin-dependent kinase inhibitors. J Microsc 2008; 231:234-46. [PMID: 18778421 DOI: 10.1111/j.1365-2818.2008.02039.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cell cycle is regulated by the cyclin-dependent kinase (CDK), and CDK inhibitors can bind to CDKs and inhibit their activities. This review examines plant CDK inhibitors, with particular emphasis on their molecular and cellular functions, regulation and cellular localization. In plants, a family of ICK/KRP CDK inhibitors represented by ICK1 is known and another type of CDK inhibitor represented by the SIMESE (SIM) has recently been reported. Considerable understanding has been gained with the ICK/KRP CDK inhibitors. These plant CDK inhibitors share only limited sequence similarity in the C-terminal region with the KIP/CIP family of mammalian CDK inhibitors. The ICK/KRP CDK inhibitors thus provide good tools to understand the basic machinery as well as the unique aspects of the plant cell cycle. The ICK/KRP CDK inhibitors interact with D-type cyclins or A-type CDKs or both. Several functional regions and motifs have been identified in ICK1 for CDK inhibition, nuclear localization and protein instability. Clear evidence shows that ICK/KRP proteins are important for the cell cycle and endoreduplication. Preliminary evidence suggests that they may also be involved in cell differentiation and cell death. Results so far show that plant CDK inhibitors are exclusively localized in the nucleus. The molecular sequences regulating the localization and functional significance will be discussed.
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Affiliation(s)
- H Wang
- Department of Biochemistry, University of Saskatchewan, Saskatoon SK, S7N 5E5, Canada
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Moes D, Himmelbach A, Korte A, Haberer G, Grill E. Nuclear localization of the mutant protein phosphatase abi1 is required for insensitivity towards ABA responses in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 54:806-819. [PMID: 18298671 DOI: 10.1111/j.1365-313x.2008.03454.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
ABI1, a protein phosphatase 2C, is a key component of ABA signal transduction in Arabidopsis that regulates numerous ABA responses, such as stomatal closure, seed germination and inhibition of vegetative growth. The abi1-1 mutation, so far the only characterized dominant allele for ABI1, impairs ABA responsitivity in both seeds and vegetative tissues. The site of action of ABI1 is unknown. We show that there is an essential requirement for nuclear localization of abi1 to confer insensitivity towards ABA responses. Transient analyses in protoplasts revealed a strict dependence of wild-type ABI1 and mutant abi1 on a functional nuclear localization sequence (NLS) for regulating ABA-dependent gene expression. Arabidopsis lines with ectopic expression of various abi1 forms corroborated the necessity of a functional NLS to control ABA sensitivity. Disruption of the NLS function in abi1 rescued ABA-controlled gene transcription to wild-type levels, but also attenuated abi1-conferred insensitivity towards ABA during seed germination, root growth and stomatal movement. The mutation in the PP2C resulted in a preferential accumulation of the protein in the nucleus. Application of a proteosomal inhibitor led to both a preferential nuclear accumulation of ABI1 and an enhancement of PP2C-dependent inhibitory action on the ABA response. Thus, abi1-1 acts as a hypermorphic allele, and ABI1 reprograms sensitivity towards ABA in the nucleus.
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Affiliation(s)
- Danièle Moes
- Lehrstuhl für Botanik, Technische Universität München, Am Hochanger 4, D-85354 Freising, Germany
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Bird DA, Buruiana MM, Zhou Y, Fowke LC, Wang H. Arabidopsis cyclin-dependent kinase inhibitors are nuclear-localized and show different localization patterns within the nucleoplasm. PLANT CELL REPORTS 2007; 26:861-72. [PMID: 17253089 DOI: 10.1007/s00299-006-0294-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2006] [Revised: 12/08/2006] [Accepted: 12/17/2006] [Indexed: 05/13/2023]
Abstract
The Arabidopsis genome contains seven cyclin-dependent kinase (CDK) inhibitors (ICK for inhibitor/interactor with cyclin-dependent kinase) which share a small conserved C-terminal domain responsible for the CDK-inhibition activity by these proteins. Different ICK/KRPs have been shown to have unique expression patterns within tissues, organs and during the cell cycle. Previous studies have shown that overexpressing one of the ICK/KRPs inhibits CDK activity, cell division, and profoundly affects plant growth and development. In this study, we investigated the subcellular localization of the seven Arabidopsis ICK proteins and domains responsible for this localization. Using transgenic expression in Arabidopsis plants and transient expression in tobacco leaf cells, all ICK/KRPs fused to green fluorescent protein (GFP) were localized to the nucleus, suggesting that the nucleus is the cellular compartment for the plant CDK inhibitors to function. While ICK2/KRP2, ICK4/KRP6, and ICK5/KRP7 were localized to the nucleoplasm in a homogeneous manner, ICK1/KRP1, ICK3/KRP5, ICK6/KRP3, and ICK7/KRP4 showed a punctate pattern of localization. A small motif conserved amongst the latter group of ICK/KRPs is required to confer this subcellular pattern as deletion of this motif from ICK7/KRP4 resulted in a shift from a punctate to a homogeneous pattern of localization. While a single nuclear localization signal (NLS) is responsible for the nuclear localization of ICK2/KRP2, multiple mechanisms for nuclear localization are suggested to exist for the other six ICK/KRPs since deletion mutants lacking predicted NLS motifs and the conserved C-terminal domain are still localized in the nucleus.
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Affiliation(s)
- David A Bird
- Department of Biology, University of Saskatchewan, Saskatoon, Canada SK S7N 5E2
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