1
|
Zhang L, Ma C, Kang X, Pei ZQ, Bai X, Wang J, Zheng S, Zhang TG. Identification and expression analysis of MAPK cascade gene family in foxtail millet ( Setaria italica). PLANT SIGNALING & BEHAVIOR 2023; 18:2246228. [PMID: 37585594 PMCID: PMC10435010 DOI: 10.1080/15592324.2023.2246228] [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: 05/19/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/18/2023]
Abstract
The mitogen-activated protein kinase (MAPK) cascade pathway is a highly conserved plant cell signaling pathway that plays an important role in plant growth and development and stress response. Currently, MAPK cascade genes have been identified and reported in a variety of plants including Arabidopsis thaliana, Oryza sativa, and Triticum aestivum, but have not been identified in foxtail millet (Setaria italica). In this study, a total of 93 MAPK cascade genes, including 15 SiMAPKs, 10 SiMAPKKs and 68 SiMAPKKKs genes, were identified by genome-wide analysis of foxtail millet, and these genes were distributed on nine chromosomes of foxtail millet. Using phylogenetic analysis, we divided the SiMAPKs and SiMAPKKs into four subgroups, respectively, and the SiMAPKKKs into three subgroups (Raf, ZIK, and MEKK). Whole-genome duplication analysis revealed that there are 14 duplication pairs in the MAPK cascade family in foxtail millet, and they are expanded by segmental replication events. Results from quantitative real-time PCR (qRT-PCR) revealed that the expression levels of most SiMAPKs and SiMAPKKs were changed under both exogenous hormone and abiotic stress treatments, with SiMAPK3 and SiMAPKK4-2 being induced under almost all treatments, while the expression of SiMAPKK5 was repressed. In a nutshell, this study will shed some light on the evolution of MAPK cascade genes and the functional mechanisms underlying MAPK cascade genes in response to hormonal and abiotic stress signaling pathways in foxtail millet (Setaria italica).
Collapse
Affiliation(s)
- Lu Zhang
- Laboratory of plant molecular physiology, College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Cheng Ma
- Laboratory of plant molecular physiology, College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Xin Kang
- Laboratory of plant molecular physiology, College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Zi-Qi Pei
- Laboratory of plant molecular physiology, College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Xue Bai
- Laboratory of plant molecular physiology, College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Juan Wang
- Laboratory of plant molecular physiology, College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Sheng Zheng
- Laboratory of plant molecular physiology, College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Teng-Guo Zhang
- Laboratory of plant molecular physiology, College of Life Sciences, Northwest Normal University, Lanzhou, China
| |
Collapse
|
2
|
Aono AH, Pimenta RJG, Dambroz CMDS, Costa FCL, Kuroshu RM, de Souza AP, Pereira WA. Genome-wide characterization of the common bean kinome: Catalog and insights into expression patterns and genetic organization. Gene 2023; 855:147127. [PMID: 36563714 DOI: 10.1016/j.gene.2022.147127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/06/2022] [Accepted: 12/16/2022] [Indexed: 12/25/2022]
Abstract
The protein kinase (PK) superfamily is one of the largest superfamilies in plants and is the core regulator of cellular signaling. Even considering this substantial importance, the kinome of common bean (Phaseolus vulgaris) has not been profiled yet. Here, we identified and characterised the complete set of kinases of common bean, performing an in-depth investigation with phylogenetic analyses and measurements of gene distribution, structural organization, protein properties, and expression patterns over a large set of RNA-Sequencing data. Being composed of 1,203 PKs distributed across all P. vulgaris chromosomes, this set represents 3.25% of all predicted proteins for the species. These PKs could be classified into 20 groups and 119 subfamilies, with a more pronounced abundance of subfamilies belonging to the receptor-like kinase (RLK)-Pelle group. In addition to provide a vast and rich reservoir of data, our study supplied insights into the compositional similarities between PK subfamilies, their evolutionary divergences, highly variable functional profile, structural diversity, and expression patterns, modeled with coexpression networks for investigating putative interactions associated with stress response.
Collapse
Affiliation(s)
- Alexandre Hild Aono
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil.
| | | | | | | | - Reginaldo Massanobu Kuroshu
- Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo (UNIFESP), São José dos Campos, Brazil.
| | - Anete Pereira de Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil; Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, Brazil.
| | | |
Collapse
|
3
|
Majeed Y, Zhu X, Zhang N, ul-Ain N, Raza A, Haider FU, Si H. Harnessing the role of mitogen-activated protein kinases against abiotic stresses in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:932923. [PMID: 36909407 PMCID: PMC10000299 DOI: 10.3389/fpls.2023.932923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Crop plants are vulnerable to various biotic and abiotic stresses, whereas plants tend to retain their physiological mechanisms by evolving cellular regulation. To mitigate the adverse effects of abiotic stresses, many defense mechanisms are induced in plants. One of these mechanisms is the mitogen-activated protein kinase (MAPK) cascade, a signaling pathway used in the transduction of extracellular stimuli into intercellular responses. This stress signaling pathway is activated by a series of responses involving MAPKKKs→MAPKKs→MAPKs, consisting of interacting proteins, and their functions depend on the collaboration and activation of one another by phosphorylation. These proteins are key regulators of MAPK in various crop plants under abiotic stress conditions and also related to hormonal responses. It is revealed that in response to stress signaling, MAPKs are characterized as multigenic families and elaborate the specific stimuli transformation as well as the antioxidant regulation system. This pathway is directed by the framework of proteins and stopping domains confer the related associates with unique structure and functions. Early studies of plant MAPKs focused on their functions in model plants. Based on the results of whole-genome sequencing, many MAPKs have been identified in plants, such as Arbodiposis, tomato, potato, alfalfa, poplar, rice, wheat, maize, and apple. In this review, we summarized the recent work on MAPK response to abiotic stress and the classification of MAPK cascade in crop plants. Moreover, we highlighted the modern research methodologies such as transcriptomics, proteomics, CRISPR/Cas technology, and epigenetic studies, which proposed, identified, and characterized the novel genes associated with MAPKs and their role in plants under abiotic stress conditions. In-silico-based identification of novel MAPK genes also facilitates future research on MAPK cascade identification and function in crop plants under various stress conditions.
Collapse
Affiliation(s)
- Yasir Majeed
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Xi Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Noor ul-Ain
- Fujian Agricultural and Forestry University (FAFU) and University of Illinois Urbana-Champaign-School of Integrative Biology (UIUC-SIB) Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ali Raza
- College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, China
| | - Fasih Ullah Haider
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| |
Collapse
|
4
|
Regulatory Mechanisms of Mitogen-Activated Protein Kinase Cascades in Plants: More than Sequential Phosphorylation. Int J Mol Sci 2022; 23:ijms23073572. [PMID: 35408932 PMCID: PMC8998894 DOI: 10.3390/ijms23073572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/20/2022] [Accepted: 03/24/2022] [Indexed: 02/02/2023] Open
Abstract
Mitogen-activated protein kinase (MAPK) cascades play crucial roles in almost all biological processes in plants. They transduce extracellular cues into cells, typically through linear and sequential phosphorylation and activation of members of the signaling cascades. However, accumulating data suggest various regulatory mechanisms of plant MAPK cascades in addition to the traditional phosphorylation pathway, in concert with their large numbers and coordinated roles in plant responses to complex ectocytic signals. Here, we highlight recent studies that describe the uncanonical mechanism of regulation of MAPK cascades, regarding the activation of each tier of the signaling cascades. More particularly, we discuss the unusual role for MAPK kinase kinases (MAPKKKs) in the regulation of MAPK cascades, as accumulating data suggest the non-MAPKKK function of many MAPKKKs. In addition, future work on the biochemical activation of MAPK members that needs attention will be discussed.
Collapse
|
5
|
Mitogen-Activated Protein Kinase and Substrate Identification in Plant Growth and Development. Int J Mol Sci 2022; 23:ijms23052744. [PMID: 35269886 PMCID: PMC8911294 DOI: 10.3390/ijms23052744] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/17/2022] [Accepted: 02/28/2022] [Indexed: 02/01/2023] Open
Abstract
Mitogen-activated protein kinases (MAPKs) form tightly controlled signaling cascades that play essential roles in plant growth, development, and defense response. However, the molecular mechanisms underlying MAPK cascades are still very elusive, largely because of our poor understanding of how they relay the signals. The MAPK cascade is composed of MAPK, MAPKK, and MAPKKK. They transfer signals through the phosphorylation of MAPKKK, MAPKK, and MAPK in turn. MAPKs are organized into a complex network for efficient transmission of specific stimuli. This review summarizes the research progress in recent years on the classification and functions of MAPK cascades under various conditions in plants, especially the research status and general methods available for identifying MAPK substrates, and provides suggestions for future research directions.
Collapse
|
6
|
Xi L, Zhang Z, Herold S, Kassem S, Wu XN, Schulze WX. Phosphorylation Site Motifs in Plant Protein Kinases and Their Substrates. Methods Mol Biol 2021; 2358:1-16. [PMID: 34270043 DOI: 10.1007/978-1-0716-1625-3_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Protein phosphorylation is an important cellular regulatory mechanism affecting the activity, localization, conformation, and interaction of proteins. Protein phosphorylation is catalyzed by kinases, and thus kinases are the enzymes regulating cellular signaling cascades. In the model plant Arabidopsis, 940 genes encode for kinases. The substrate proteins of kinases are phosphorylated at defined sites, which consist of common patterns around the phosphorylation site, known as phosphorylation motifs. The discovery of kinase specificity with a preference of phosphorylation of certain motifs and application of such motifs in deducing signaling cascades helped to reveal underlying regulation mechanisms, and facilitated the prediction of kinase-target pairs. In this mini-review, we took advantage of retrieved data as examples to present the functions of kinase families along with their commonly found phosphorylation motifs from their substrates.
Collapse
Affiliation(s)
- Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany.
| | - Zhaoxia Zhang
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sandra Herold
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sarah Kassem
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Xu Na Wu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| |
Collapse
|
7
|
Yin Z, Zhu W, Zhang X, Chen X, Wang W, Lin H, Wang J, Ye W. Molecular characterization, expression and interaction of MAPK, MAPKK and MAPKKK genes in upland cotton. Genomics 2020; 113:1071-1086. [PMID: 33181247 DOI: 10.1016/j.ygeno.2020.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 09/28/2020] [Accepted: 11/02/2020] [Indexed: 01/17/2023]
Abstract
Mitogen-activated protein kinase (MAPK) signaling cascades, consisting of three types of sequentially phosphorylated kinases (MAPKKK, MAPKK, and MAPK), play vital roles in various processes including plant development and stress response. In this study, 52 GhMAPKs, 23 GhMAPKKs, and 166 GhMAPKKKs were identified in upland cotton. Chromosomal locations, gene duplication and structure, motifs, cis-regulatory elements, and protein subcellular localization were further analyzed. With the identified MAPK cascade genes in G. arboretum and G. raimondii, a syntenic diagram of three cotton species was constructed. The interactions of seven GhMAPK cascade genes were investigated. Two complete signaling modules were defined: The GhMEKK24/GhMEKK31-GhMAPKK9-GhMAPK10 and GhMEKK3/GhMEKK24/GhMEKK31-GhMAPKK16-GhMAPK10/GhMAPK11 cascades. Moreover, interaction networks and the interaction pairs were combined with their expression patterns and demonstrated that the network mediated by the MAPK signaling cascade participates in abiotic stress signaling. Our research provides a foundation for studying the molecular mechanism of the MAPK signaling pathway under abiotic stress.
Collapse
Affiliation(s)
- Zujun Yin
- Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Henan, PR China.
| | - Weidong Zhu
- Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Henan, PR China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, PR China
| | - Xiaopei Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Shandong, PR China
| | - Xiugui Chen
- Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Henan, PR China
| | - Wei Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Shandong, PR China
| | - Huan Lin
- Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Henan, PR China
| | - Junjuan Wang
- Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Henan, PR China
| | - Wuwei Ye
- Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Henan, PR China.
| |
Collapse
|
8
|
Zhu D, Chang Y, Pei T, Zhang X, Liu L, Li Y, Zhuang J, Yang H, Qin F, Song C, Ren D. MAPK-like protein 1 positively regulates maize seedling drought sensitivity by suppressing ABA biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:747-760. [PMID: 31863495 DOI: 10.1111/tpj.14660] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 12/11/2019] [Indexed: 05/18/2023]
Abstract
Mitogen-activated protein kinase (MAPK) cascades play vital roles in regulating plant growth, development, and stress responses. MAPK-like (MPKL) proteins are a group of kinases containing the MAPK signature TxY motif and showing sequence similarity to MAPKs. However, the functions of plant MPKL proteins are currently unknown. The maize (Zea mays) genome contains four genes encoding MPKL proteins, here named ZmMPKL1 to ZmMPKL4. In this study, we show that ZmMPKL1 possesses kinase activity and that drought-induced ZmMPKL1 expression, ZmMPKL1 overexpression and knockout maize seedlings exhibited no visible morphological difference from wild-type B73 seedlings when grown under normal conditions. By contrast, under drought conditions, ZmMPKL1-overexpressing seedlings showed increased stomatal aperture, water loss, and leaf wilting and knockout seedlings showed the opposite phenotypes. Moreover, these drought-sensitive phenotypes in ZmMPKL1-overexpressing seedlings were restored by exogenous abscisic acid (ABA). ZmMPKL1 overexpression reduced drought-induced ABA production in seedlings and the knockout showed enhanced ABA production. Drought-induced transcription of ABA biosynthetic genes were suppressed and ABA catabolic genes were enhanced in ZmMPKL1-overexpressing seedlings, while their transcription were reversely regulated in knockout seedlings. These results suggest that ZmMPKL1 positively regulates seedlings drought sensitivity by altering the transcription of ABA biosynthetic and catabolic genes, and ABA homeostasis.
Collapse
Affiliation(s)
- Dan Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ying Chang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Collaborative Innovation Center of Crop Stress Biology, Henan Province, Institute of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475001, China
| | - Ting Pei
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiuyan Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Lan Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuan Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Junhong Zhuang
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Hailian Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Feng Qin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Chunpeng Song
- Collaborative Innovation Center of Crop Stress Biology, Henan Province, Institute of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475001, China
| | - Dongtao Ren
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
9
|
Rodríguez-Rojas F, Celis-Plá PSM, Méndez L, Moenne F, Muñoz PT, Lobos MG, Díaz P, Sánchez-Lizaso JL, Brown MT, Moenne A, Sáez CA. MAPK Pathway under Chronic Copper Excess in Green Macroalgae (Chlorophyta): Involvement in the Regulation of Detoxification Mechanisms. Int J Mol Sci 2019; 20:ijms20184546. [PMID: 31540290 PMCID: PMC6771120 DOI: 10.3390/ijms20184546] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/01/2019] [Accepted: 09/01/2019] [Indexed: 12/16/2022] Open
Abstract
Following the physiological complementary/parallel Celis-Plá et al., by inhibiting extracellular signal regulated kinases (ERK), c-Jun N-terminal kinases (JNK), and cytokinin specific binding protein (p38), we assessed the role of the mitogen-activated protein kinases (MAPK) pathway in detoxification responses mediated by chronic copper (10 µM) in U. compressa. Parameters were taken at 6, 24, and 48 h, and 6 days (d). H2O2 and lipid peroxidation under copper and inhibition of ERK, JNK, or p38 alone increased but recovered by the sixth day. By blocking two or more MAPKs under copper, H2O2 and lipid peroxidation decayed even below controls. Inhibition of more than one MAPK (at 6 d) caused a decrease in total glutathione (reduced glutathione (GSH) + oxidised glutathione (GSSG)) and ascorbate (reduced ascorbate (ASC) + dehydroascorbate (DHA)), although in the latter it did not occur when the whole MAPK was blocked. Catalase (CAT), superoxide dismutase (SOD), thioredoxin (TRX) ascorbate peroxidase (APX), dehydroascorbate reductase (DHAR), and glutathione synthase (GS), were downregulated when blocking more than one MAPK pathway. When one MAPK pathway was blocked under copper, a recovery and even enhancement of detoxification mechanisms was observed, likely due to crosstalk within the MAPKs and/or other signalling processes. In contrast, when more than one MAPK pathway were blocked under copper, impairment of detoxification defences occurred, demonstrating that MAPKs were key signalling mechanisms for detoxification in macroalgae.
Collapse
Affiliation(s)
- Fernanda Rodríguez-Rojas
- Laboratory of Aquatic Environmental Research, Centro de Estudios Avanzados, Universidad de Playa Ancha, Viña del Mar 2520000, Chile
- HUB-AMBIENTAL UPLA, Universidad de Playa Ancha, Valparaíso 2340000, Chile
| | - Paula S M Celis-Plá
- Laboratory of Aquatic Environmental Research, Centro de Estudios Avanzados, Universidad de Playa Ancha, Viña del Mar 2520000, Chile
- HUB-AMBIENTAL UPLA, Universidad de Playa Ancha, Valparaíso 2340000, Chile
| | - Lorena Méndez
- Laboratory of Aquatic Environmental Research, Centro de Estudios Avanzados, Universidad de Playa Ancha, Viña del Mar 2520000, Chile
| | - Fabiola Moenne
- Laboratory of Aquatic Environmental Research, Centro de Estudios Avanzados, Universidad de Playa Ancha, Viña del Mar 2520000, Chile
- HUB-AMBIENTAL UPLA, Universidad de Playa Ancha, Valparaíso 2340000, Chile
| | - Pamela T Muñoz
- Laboratory of Aquatic Environmental Research, Centro de Estudios Avanzados, Universidad de Playa Ancha, Viña del Mar 2520000, Chile
- Doctorado Interdisciplinario en Ciencias Ambientales, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso 2340000, Chile
- Doctorado en Ciencias del Mar y Biología Aplicada, Departamento de Ciencias del Mar y Biología Aplicada, Universidad de Alicante, 03080 Alicante, Spain
| | - M Gabriela Lobos
- Laboratory of Environmental and Analytical Chemistry, Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 234000, Chile
| | - Patricia Díaz
- Laboratory of Environmental and Analytical Chemistry, Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 234000, Chile
| | - José Luis Sánchez-Lizaso
- Departamento de Ciencias del Mar y Biología Aplicada, Universidad de Alicante, 03080 Alicante, Spain
| | - Murray T Brown
- School of Biological and Marine Sciences, University of Plymouth, PL4 8AA Plymouth, UK
| | - Alejandra Moenne
- Laboratory of Marine Biotechnology, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 9170020, Chile
| | - Claudio A Sáez
- Laboratory of Aquatic Environmental Research, Centro de Estudios Avanzados, Universidad de Playa Ancha, Viña del Mar 2520000, Chile.
- HUB-AMBIENTAL UPLA, Universidad de Playa Ancha, Valparaíso 2340000, Chile.
| |
Collapse
|
10
|
Neupane S, Schweitzer SE, Neupane A, Andersen EJ, Fennell A, Zhou R, Nepal MP. Identification and Characterization of Mitogen-Activated Protein Kinase (MAPK) Genes in Sunflower ( Helianthus annuus L.). PLANTS (BASEL, SWITZERLAND) 2019; 8:E28. [PMID: 30678298 PMCID: PMC6409774 DOI: 10.3390/plants8020028] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/07/2019] [Accepted: 01/16/2019] [Indexed: 12/12/2022]
Abstract
Mitogen-Activated Protein Kinase (MAPK) genes encode proteins that regulate biotic and abiotic stresses in plants through signaling cascades comprised of three major subfamilies: MAP Kinase (MPK), MAPK Kinase (MKK), and MAPKK Kinase (MKKK). The main objectives of this research were to conduct genome-wide identification of MAPK genes in Helianthus annuus and examine functional divergence of these genes in relation to those in nine other plant species (Amborella trichopoda, Aquilegia coerulea, Arabidopsis thaliana, Daucus carota, Glycine max, Oryza sativa, Solanum lycopersicum, Sphagnum fallax, and Vitis vinifera), representing diverse taxonomic groups of the Plant Kingdom. A Hidden Markov Model (HMM) profile of the MAPK genes utilized reference sequences from A. thaliana and G. max, yielding a total of 96 MPKs and 37 MKKs in the genomes of A. trichopoda, A. coerulea, C. reinhardtii, D. carota, H. annuus, S. lycopersicum, and S. fallax. Among them, 28 MPKs and eight MKKs were confirmed in H. annuus. Phylogenetic analyses revealed four clades within each subfamily. Transcriptomic analyses showed that at least 19 HaMPK and seven HaMKK genes were induced in response to salicylic acid (SA), sodium chloride (NaCl), and polyethylene glycol (Peg) in leaves and roots. Of the seven published sunflower microRNAs, five microRNA families are involved in targeting eight MPKs. Additionally, we discussed the need for using MAP Kinase nomenclature guidelines across plant species. Our identification and characterization of MAP Kinase genes would have implications in sunflower crop improvement, and in advancing our knowledge of the diversity and evolution of MAPK genes in the Plant Kingdom.
Collapse
Affiliation(s)
- Surendra Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Sarah E Schweitzer
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Achal Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Ethan J Andersen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Anne Fennell
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, USA.
| | - Ruanbao Zhou
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| |
Collapse
|
11
|
Jiang M, Chu Z. Comparative analysis of plant MKK gene family reveals novel expansion mechanism of the members and sheds new light on functional conservation. BMC Genomics 2018; 19:407. [PMID: 29843611 PMCID: PMC5975520 DOI: 10.1186/s12864-018-4793-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 05/14/2018] [Indexed: 12/15/2022] Open
Abstract
Background Mitogen-activated protein kinase (MAPK) cascades play critical functions in almost every aspect of plant growth and development, which regulates many physiological and biochemical processes. As a middle nodal point of the MAPK cascades, although evolutionary analysis of MKK from individual plant families had some reports, their evolutionary history in entire plants is still not clear. Results To better understand the evolution and function of plant MKKs, we performed systematical molecular evolutionary analysis of the MAPKK gene family and also surveyed their gene organizations, sequence features and expression patterns in different subfamilies. Phylogenetic analysis showed that plant MAPKK fall into five different groups (Group A–E). Majority orthology groups seemed to be a single or low-copy genes in all plant species analyzed in Group B, C and D, whereas group A MKKs undergo several duplication events, generating multiple gene copies. Further analysis showed that these duplication events were on account of whole genome duplications (WGDs) in plants and the duplicate genes maybe have undergone functional divergence. We also found that group E MKKs had mutation with one change of serine or theronine might lead to inactivity originated through the ancient tandem duplicates in monocots. Moreover, we also identified MKK3 integrated NTF2 domain that might have gradually lost the cytoplasmic-nuclear trafficking activity, which suggests that they may involve with the gene function more and more sophistication in the evolutionary process. Moreover, expression analyses indicated that plant MKK genes play probable roles in UV-B signaling. Conclusion In general, ancient gene and genome duplications are significantly conducive to the expansion of the plant MKK gene family. Our study reveals two distinct evolutionary patterns for plant MKK proteins and sheds new light on the functional evolution of this gene family. Electronic supplementary material The online version of this article (10.1186/s12864-018-4793-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Min Jiang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.,Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Zhaoqing Chu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China. .,Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China.
| |
Collapse
|
12
|
Goyal RK, Tulpan D, Chomistek N, González-Peña Fundora D, West C, Ellis BE, Frick M, Laroche A, Foroud NA. Analysis of MAPK and MAPKK gene families in wheat and related Triticeae species. BMC Genomics 2018; 19:178. [PMID: 29506469 PMCID: PMC5838963 DOI: 10.1186/s12864-018-4545-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 02/13/2018] [Indexed: 12/16/2022] Open
Abstract
Background The mitogen-activated protein kinase (MAPK) family is involved in signal transduction networks that underpin many different biological processes in plants, ranging from development to biotic and abiotic stress responses. To date this class of enzymes has received little attention in Triticeae species, which include important cereal crops (wheat, barley, rye and triticale) that represent over 20% of the total protein food-source worldwide. Results The work presented here focuses on two subfamilies of Triticeae MAPKs, the MAP kinases (MPKs), and the MAPK kinases (MKKs) whose members phosphorylate the MPKs. In silico analysis of multiple Triticeae sequence databases led to the identification of 152 MAPKs belonging to these two sub-families. Some previously identified MAPKs were renamed to reflect the literature consensus on MAPK nomenclature. Two novel MPKs, MPK24 and MPK25, have been identified, including the first example of a plant MPK carrying the TGY activation loop sequence common to mammalian p38 MPKs. An EF-hand calcium-binding domain was found in members of the Triticeae MPK17 clade, a feature that appears to be specific to Triticeae species. New insights into the novel MEY activation loop identified in MPK11s are offered. When the exon-intron patterns for some MPKs and MKKs of wheat, barley and ancestors of wheat were assembled based on transcript data in GenBank, they showed deviations from the same sequence predicted in Ensembl. The functional relevance of MAPKs as derived from patterns of gene expression, MPK activation and MKK-MPK interaction is discussed. Conclusions A comprehensive resource of accurately annotated and curated Triticeae MPK and MKK sequences has been created for wheat, barley, rye, triticale, and two ancestral wheat species, goat grass and red wild einkorn. The work we present here offers a central information resource that will resolve existing confusion in the literature and sustain expansion of MAPK research in the crucial Triticeae grains. Electronic supplementary material The online version of this article (10.1186/s12864-018-4545-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ravinder K Goyal
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 - 1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Dan Tulpan
- Information and Communication Technologies, National Research Council of Canada, 100 des Aboiteaux Street, Moncton, New Brunswick, E1A 7R1, Canada
| | - Nora Chomistek
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 - 1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Dianevys González-Peña Fundora
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 - 1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Connor West
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 - 1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Brian E Ellis
- Michael Smith Laboratories, University of British Columbia, #301 - 2185 East Mall, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Michele Frick
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 - 1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - André Laroche
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 - 1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Nora A Foroud
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 - 1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada.
| |
Collapse
|
13
|
Singh A, Nath O, Singh S, Kumar S, Singh IK. Genome-wide identification of the MAPK gene family in chickpea and expression analysis during development and stress response. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.plgene.2017.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
14
|
Dahlke RI, Fraas S, Ullrich KK, Heinemann K, Romeiks M, Rickmeyer T, Klebe G, Palme K, Lüthen H, Steffens B. Protoplast Swelling and Hypocotyl Growth Depend on Different Auxin Signaling Pathways. PLANT PHYSIOLOGY 2017; 175:982-994. [PMID: 28860155 PMCID: PMC5619902 DOI: 10.1104/pp.17.00733] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/29/2017] [Indexed: 05/10/2023]
Abstract
Members of the TRANSPORT INHIBITOR RESPONSE1/AUXIN SIGNALING F-BOX PROTEIN (TIR1/AFB) family are known auxin receptors. To analyze the possible receptor function of AUXIN BINDING PROTEIN1 (ABP1), an auxin receptor currently under debate, we performed different approaches. We performed a pharmacological approach using α-(2,4-dimethylphenylethyl-2-oxo)-indole-3-acetic acid (auxinole), α-(phenylethyl-2-oxo)-indole-3-acetic acid (PEO-IAA), and 5-fluoroindole-3-acetic acid (5-F-IAA) to discriminate between ABP1- and TIR1/AFB-mediated processes in Arabidopsis (Arabidopsis thaliana). We used a peptide of the carboxyl-terminal region of AtABP1 as a tool. We performed mutant analysis with the null alleles of ABP1, abp1-c1 and abp1-TD1, and the TILLING mutant abp1-5 We employed Coimbra, an accession that exhibits an amino acid exchange in the auxin-binding domain of ABP1. We measured either volume changes of single hypocotyl protoplasts or hypocotyl growth, both at high temporal resolution. 5-F-IAA selectively activated the TIR1/AFB pathway but did not induce protoplast swelling; instead, it showed auxin activity in the hypocotyl growth test. In contrast, PEO-IAA induced an auxin-like swelling response but no hypocotyl growth. The carboxyl-terminal peptide of AtABP1 induced an auxin-like swelling response. In the ABP1-related mutants and Coimbra, no auxin-induced protoplast swelling occurred. ABP1 seems to be involved in mediating rapid auxin-induced protoplast swelling, but it is not involved in the control of rapid auxin-induced growth.
Collapse
Affiliation(s)
- Renate I Dahlke
- Plant Physiology, Faculty of Biology, University of Marburg, 35043 Marburg, Germany
| | - Simon Fraas
- Molecular Plant Physiology, Department of Biology, University of Hamburg, 22609 Hamburg, Germany
| | - Kristian K Ullrich
- Plant Cell Biology, Philipps University, Faculty of Biology, University of Marburg, 35043 Marburg, Germany
| | - Kirka Heinemann
- Molecular Plant Physiology, Department of Biology, University of Hamburg, 22609 Hamburg, Germany
| | - Maren Romeiks
- Molecular Plant Physiology, Department of Biology, University of Hamburg, 22609 Hamburg, Germany
| | - Thomas Rickmeyer
- Pharmaceutical Chemistry, University of Marburg, 35032 Marburg, Germany
| | - Gerhard Klebe
- Pharmaceutical Chemistry, University of Marburg, 35032 Marburg, Germany
| | - Klaus Palme
- Institute of Biology II, BIOSS Centre for Biological Signaling Studies, Institute for Advanced Sciences and Centre for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany
| | - Hartwig Lüthen
- Molecular Plant Physiology, Department of Biology, University of Hamburg, 22609 Hamburg, Germany
| | - Bianka Steffens
- Plant Physiology, Faculty of Biology, University of Marburg, 35043 Marburg, Germany
| |
Collapse
|
15
|
Wei W, Chai Z, Xie Y, Gao K, Cui M, Jiang Y, Feng J. Bioinformatics identification and transcript profile analysis of the mitogen-activated protein kinase gene family in the diploid woodland strawberry Fragaria vesca. PLoS One 2017; 12:e0178596. [PMID: 28562633 PMCID: PMC5451138 DOI: 10.1371/journal.pone.0178596] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 05/16/2017] [Indexed: 11/21/2022] Open
Abstract
Mitogen-activated protein kinases (MAPKs) play essential roles in mediating biotic and abiotic stress responses in plants. However, the MAPK gene family in strawberry has not been systematically characterized. Here, we performed a genome-wide survey and identified 12 MAPK genes in the Fragaria vesca genome. Protein domain analysis indicated that all FvMAPKs have typical protein kinase domains. Sequence alignments and phylogenetic analysis classified the FvMAPK genes into four different groups. Conserved motif and exon-intron organization supported the evolutionary relationships inferred from the phylogenetic analysis. Analysis of the stress-related cis-regulatory element in the promoters and subcellular localization predictions of FvMAPKs were also performed. Gene transcript profile analysis showed that the majority of the FvMAPK genes were ubiquitously transcribed in strawberry leaves after Podosphaera aphanis inoculation and after treatment with cold, heat, drought, salt and the exogenous hormones abscisic acid, ethephon, methyl jasmonate, and salicylic acid. RT-qPCR showed that six selected FvMAPK genes comprehensively responded to various stimuli. Additionally, interaction networks revealed that the crucial signaling transduction controlled by FvMAPKs may be involved in the biotic and abiotic stress responses. Our results may provide useful information for future research on the function of the MAPK gene family and the genetic improvement of strawberry resistance to environmental stresses.
Collapse
Affiliation(s)
- Wei Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, China
| | - Zhuangzhuang Chai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, China
| | - Yinge Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, China
| | - Kuan Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, China
| | - Mengyuan Cui
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, China
| | - Ying Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, China
| | - Jiayue Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, China
- * E-mail:
| |
Collapse
|
16
|
Fei X, Yu J, Li Y, Deng X. CrMAPK3 regulates the expression of iron-deficiency-responsive genes in Chlamydomonas reinhardtii. BMC BIOCHEMISTRY 2017; 18:6. [PMID: 28511672 PMCID: PMC5434638 DOI: 10.1186/s12858-017-0081-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 04/28/2017] [Indexed: 01/06/2023]
Abstract
BACKGROUND Under iron-deficient conditions, Chlamydomonas exhibits high affinity for iron absorption. Nevertheless, the response, transmission, and regulation of downstream gene expression in algae cells have not to be investigated. Considering that the MAPK pathway is essential for abiotic stress responses, we determined whether this pathway is involved in iron deficiency signal transduction in Chlamydomonas. RESULTS Arabidopsis MAPK gene sequences were used as entry data to search for homologous genes in Chlamydomonas reinhardtii genome database to investigate the functions of mitogen-activated protein kinase (MAPK) gene family in C. reinhardtii under iron-free conditions. Results revealed 16 C. reinhardtii MAPK genes labeled CrMAPK2-CrMAPK17 with TXY conserved domains and low homology to MAPK in yeast, Arabidopsis, and humans. The expression levels of these genes were then analyzed through qRT-PCR and exposure to high salt (150 mM NaCl), low nitrogen, or iron-free conditions. The expression levels of these genes were also subjected to adverse stress conditions. The mRNA levels of CrMAPK2, CrMAPK3, CrMAPK4, CrMAPK5, CrMAPK6, CrMAPK8, CrMAPK9, and CrMAPK11 were remarkably upregulated under iron-deficient stress. The increase in CrMAPK3 expression was 43-fold greater than that in the control. An RNA interference vector was constructed and transformed into C. reinhardtii 2A38, an algal strain with an exogenous FOX1:ARS chimeric gene, to silence CrMAPK3. After this gene was silenced, the mRNA levels and ARS activities of FOX1:ARS chimeric gene and endogenous CrFOX1 were decreased. The mRNA levels of iron-responsive genes, such as CrNRAMP2, CrATX1, CrFTR1, and CrFEA1, were also remarkably reduced. CONCLUSION CrMAPK3 regulates the expression of iron-deficiency-responsive genes in C. reinhardtii.
Collapse
Affiliation(s)
- Xiaowen Fei
- School of Science, Hainan Medical College, Haikou, 571101, China
| | - Junmei Yu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Haikou, 571101, China
| | - Yajun Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Haikou, 571101, China
| | - Xiaodong Deng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Haikou, 571101, China.
| |
Collapse
|
17
|
Bioinformatics Analysis of MAPKKK Family Genes in Medicago truncatula. Genes (Basel) 2016; 7:genes7040013. [PMID: 27049397 PMCID: PMC4846843 DOI: 10.3390/genes7040013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 03/25/2016] [Accepted: 03/29/2016] [Indexed: 01/24/2023] Open
Abstract
Mitogen-activated protein kinase kinase kinase (MAPKKK) is a component of the MAPK cascade pathway that plays an important role in plant growth, development, and response to abiotic stress, the functions of which have been well characterized in several plant species, such as Arabidopsis, rice, and maize. In this study, we performed genome-wide and systemic bioinformatics analysis of MAPKKK family genes in Medicago truncatula. In total, there were 73 MAPKKK family members identified by search of homologs, and they were classified into three subfamilies, MEKK, ZIK, and RAF. Based on the genomic duplication function, 72 MtMAPKKK genes were located throughout all chromosomes, but they cluster in different chromosomes. Using microarray data and high-throughput sequencing-data, we assessed their expression profiles in growth and development processes; these results provided evidence for exploring their important functions in developmental regulation, especially in the nodulation process. Furthermore, we investigated their expression in abiotic stresses by RNA-seq, which confirmed their critical roles in signal transduction and regulation processes under stress. In summary, our genome-wide, systemic characterization and expressional analysis of MtMAPKKK genes will provide insights that will be useful for characterizing the molecular functions of these genes in M. truncatula.
Collapse
|
18
|
Feng K, Liu F, Zou J, Xing G, Deng P, Song W, Tong W, Nie X. Genome-Wide Identification, Evolution, and Co-expression Network Analysis of Mitogen-Activated Protein Kinase Kinase Kinases in Brachypodium distachyon. FRONTIERS IN PLANT SCIENCE 2016; 7:1400. [PMID: 27695474 PMCID: PMC5025453 DOI: 10.3389/fpls.2016.01400] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/02/2016] [Indexed: 05/22/2023]
Abstract
Mitogen-activated protein kinase (MAPK) cascades are the conserved and universal signal transduction modules in all eukaryotes, which play the vital roles in plant growth, development, and in response to multiple stresses. In this study, we used bioinformatics methods to identify 86 MAPKKK protein encoded by 73 MAPKKK genes in Brachypodium. Phylogenetic analysis of MAPKKK family from Arabidopsis, rice, and Brachypodium has classified them into three subfamilies, of which 28 belonged to MEKK, 52 to Raf, and 6 to ZIK subfamily, respectively. Conserved protein motif, exon-intron organization, and splicing intron phase in kinase domains supported the evolutionary relationships inferred from the phylogenetic analysis. And gene duplication analysis suggested the chromosomal segment duplication happened before the divergence of the rice and Brachypodium, while all of three tandem duplicated gene pairs happened after their divergence. We further demonstrated that the MAPKKKs have evolved under strong purifying selection, implying the conservation of them. The splicing transcripts expression analysis showed that the splicesome translating longest protein tended to be adopted. Furthermore, the expression analysis of BdMAPKKKs in different organs and development stages as well as heat, virus and drought stresses revealed that the MAPKKK genes were involved in various signaling pathways. And the circadian analysis suggested there were 41 MAPKKK genes in Brachypodium showing cycled expression in at least one condition, of which seven MAPKKK genes expressed in all conditions and the promoter analysis indicated these genes possessed many cis-acting regulatory elements involved in circadian and light response. Finally, the co-expression network of MAPK, MAPKK, and MAPKKK in Brachypodium was constructed using 144 microarray and RNA-seq datasets, and ten potential MAPK cascades pathway were predicted. To conclude, our study provided the important information for evolutionary and functional characterization of MAPKKK family in Brachypodium, which will facilitate the functional analysis of BdMAPKKK genes, and also will facilitate better understanding the MAPK signal pathway in Brachypodium and beyond.
Collapse
Affiliation(s)
- Kewei Feng
- College of Agronomy, Northwest A&F UniversityYangling, China
| | - Fuyan Liu
- College of Agronomy, Northwest A&F UniversityYangling, China
| | - Jinwei Zou
- College of Agronomy, Northwest A&F UniversityYangling, China
| | - Guangwei Xing
- College of Agronomy, Northwest A&F UniversityYangling, China
| | - Pingchuan Deng
- College of Agronomy, Northwest A&F UniversityYangling, China
| | - Weining Song
- College of Agronomy, Northwest A&F UniversityYangling, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F UniversityYangling, China
- Australia-China Joint Research Centre for Abiotic and Biotic Stress Management in Agriculture, Horticulture and Forestry, Northwest A&F UniversityYangling, China
| | - Wei Tong
- College of Agronomy, Northwest A&F UniversityYangling, China
- Wei Tong
| | - Xiaojun Nie
- College of Agronomy, Northwest A&F UniversityYangling, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F UniversityYangling, China
- *Correspondence: Xiaojun Nie
| |
Collapse
|
19
|
Song Q, Li D, Dai Y, Liu S, Huang L, Hong Y, Zhang H, Song F. Characterization, expression patterns and functional analysis of the MAPK and MAPKK genes in watermelon (Citrullus lanatus). BMC PLANT BIOLOGY 2015; 15:298. [PMID: 26700161 PMCID: PMC5477810 DOI: 10.1186/s12870-015-0681-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 12/13/2015] [Indexed: 05/23/2023]
Abstract
BACKGROUND Mitogen-activated protein kinase (MAPK) cascades, which consist of three functionally associated protein kinases, namely MEKKs, MKKs and MPKs, are universal signaling modules in all eukaryotes and have been shown to play critical roles in many physiological and biochemical processes in plants. However, little or nothing is known about the MPK and MKK families in watermelon. RESULTS In the present study, we performed a systematic characterization of the ClMPK and ClMKK families including the identification and nomenclature, chromosomal localization, phylogenetic relationships, ClMPK-ClMKK interactions, expression patterns in different tissues and in response to abiotic and biotic stress and transient expression-based functional analysis for their roles in disease resistance. Genome-wide survey identified fifteen ClMPK and six ClMKK genes in watermelon genome and phylogenetic analysis revealed that both of the ClMPK and ClMKK families can be classified into four distinct groups. Yeast two-hybrid assays demonstrated significant interactions between members of the ClMPK and ClMKK families, defining putative ClMKK2-1/ClMKK6-ClMPK4-1/ClMPK4-2/ClMPK13 and ClMKK5-ClMPK6 cascades. Most of the members in the ClMPK and ClMKK families showed differential expression patterns in different tissues and in response to abiotic (e.g. drought, salt, cold and heat treatments) and biotic (e.g. infection of Fusarium oxysporum f. sp. niveum) stresses. Transient expression of ClMPK1, ClMPK4-2 and ClMPK7 in Nicotiana benthamiana resulted in enhanced resistance to Botrytis cinerea and upregulated expression of defense genes while transient expression of ClMPK6 and ClMKK2-2 led to increased susceptibility to B. cinerea. Furthermore, transient expression of ClMPK7 also led to hypersensitive response (HR)-like cell death and significant accumulation of H2O2 in N. benthamiana. CONCLUSION We identified fifteen ClMPK and six ClMKK genes from watermelon and analyzed their phylogenetic relationships, expression patterns and protein-protein interactions and functions in disease resistance. Our results demonstrate that ClMPK1, ClMPK4-2 and ClMPK7 positively but ClMPK6 and ClMKK2-2 negatively regulate the resistance to B. cinerea when transiently expressed in N. benthamiana and that ClMPK7 functions as a regulator of HR-like cell death through modulating the generation of H2O2.
Collapse
Affiliation(s)
- Qiuming Song
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 P. R. China
| | - Dayong Li
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 P. R. China
| | - Yi Dai
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 P. R. China
| | - Shixia Liu
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 P. R. China
| | - Lei Huang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 P. R. China
| | - Yongbo Hong
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 P. R. China
| | - Huijuan Zhang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 P. R. China
- College of Life Science, Taizhou University, Taizhou, Zhejiang 318001 P. R. China
| | - Fengming Song
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 P. R. China
| |
Collapse
|
20
|
Mohanta TK, Arora PK, Mohanta N, Parida P, Bae H. Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel activation loop variants. BMC Genomics 2015; 16:58. [PMID: 25888265 PMCID: PMC4363184 DOI: 10.1186/s12864-015-1244-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 01/15/2015] [Indexed: 11/30/2022] Open
Abstract
Background Mitogen Activated Protein Kinase (MAPK) signaling is of critical importance in plants and other eukaryotic organisms. The MAPK cascade plays an indispensible role in the growth and development of plants, as well as in biotic and abiotic stress responses. The MAPKs are constitute the most downstream module of the three tier MAPK cascade and are phosphorylated by upstream MAP kinase kinases (MAPKK), which are in turn are phosphorylated by MAP kinase kinase kinase (MAPKKK). The MAPKs play pivotal roles in regulation of many cytoplasmic and nuclear substrates, thus regulating several biological processes. Results A total of 589 MAPKs genes were identified from the genome wide analysis of 40 species. The sequence analysis has revealed the presence of several N- and C-terminal conserved domains. The MAPKs were previously believed to be characterized by the presence of TEY/TDY activation loop motifs. The present study showed that, in addition to presence of activation loop TEY/TDY motifs, MAPKs are also contain MEY, TEM, TQM, TRM, TVY, TSY, TEC and TQY activation loop motifs. Phylogenetic analysis of all predicted MAPKs were clustered into six different groups (group A, B, C, D, E and F), and all predicted MAPKs were assigned with specific names based on their orthology based evolutionary relationships with Arabidopsis or Oryza MAPKs. Conclusion We conducted global analysis of the MAPK gene family of plants from lower eukaryotes to higher eukaryotes and analyzed their genomic and evolutionary aspects. Our study showed the presence of several new activation loop motifs and diverse conserved domains in MAPKs. Advance study of newly identified activation loop motifs can provide further information regarding the downstream signaling cascade activated in response to a wide array of stress conditions, as well as plant growth and development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1244-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Tapan Kumar Mohanta
- School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook, 712749, Republic of Korea.
| | - Pankaj Kumar Arora
- School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook, 712749, Republic of Korea.
| | - Nibedita Mohanta
- Department of Biotechnology, North Orissa University, Sri Ramchandra Vihar, Takatpur, Baripada, Mayurbhanj, Orissa, 757003, India.
| | - Pratap Parida
- Center for Studies in Biotechnology, Dibrugarh University, Dibrugarh, Assam, 786004, India.
| | - Hanhong Bae
- School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook, 712749, Republic of Korea.
| |
Collapse
|
21
|
Liu Z, Shi L, Liu Y, Tang Q, Shen L, Yang S, Cai J, Yu H, Wang R, Wen J, Lin Y, Hu J, Liu C, Zhang Y, Mou S, He S. Genome-wide identification and transcriptional expression analysis of mitogen-activated protein kinase and mitogen-activated protein kinase kinase genes in Capsicum annuum. FRONTIERS IN PLANT SCIENCE 2015; 6:780. [PMID: 26442088 PMCID: PMC4585111 DOI: 10.3389/fpls.2015.00780] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 09/10/2015] [Indexed: 05/18/2023]
Abstract
The tripartite mitogen-activated protein kinase (MAPK) signaling cascades have been implicated in plant growth, development, and environment adaptation, but a comprehensive understanding of MAPK signaling at genome-wide level is limited in Capsicum annuum. Herein, genome-wide identification and transcriptional expression analysis of MAPK and MAPK kinase (MAPKK) were performed in pepper. A total of 19 pepper MAPK (CaMAPKs) genes and five MAPKK (CaMAPKKs) genes were identified. Phylogenetic analysis indicated that CaMAPKs and CaMAPKKs could be classified into four groups and each group contains similar exon-intron structures. However, significant divergences were also found. Notably, five members of the pepper MAPKK family were much less conserved than those found in Arabidopsis, and 9 Arabidopsis MAPKs did not have orthologs in pepper. Additionally, 7 MAPKs in Arabidopsis had either two or three orthologs in the pepper genome, and six pepper MAPKs and one MAPKK differing in sequence were found in three pepper varieties. Quantitative real-time RT-PCR analysis showed that the majority of MAPK and MAPKK genes were ubiquitously expressed and transcriptionally modified in pepper leaves after treatments with heat, salt, and Ralstonia solanacearum inoculation as well as exogenously applied salicylic acid, methyl jasmonate, ethephon, and abscisic acid. The MAPKK-MAPK interactome was tested by yeast two-hybrid assay, the results showed that one MAPKK might interact with multiple MAPKs, one MAPK might also interact with more than one MAPKKs, constituting MAPK signaling networks which may collaborate in transmitting upstream signals into appropriate downstream cellular responses and processes. These results will facilitate future functional characterization of MAPK cascades in pepper.
Collapse
Affiliation(s)
- Zhiqin Liu
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Lanping Shi
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Yanyan Liu
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Qian Tang
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Lei Shen
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Sheng Yang
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Jinsen Cai
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Life Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Huanxin Yu
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Rongzhang Wang
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Jiayu Wen
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Youquan Lin
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Jiong Hu
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Cailing Liu
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Yangwen Zhang
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Shaoliang Mou
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Life Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Shuilin He
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
- *Correspondence: Shuilin He, College of Crop Science, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou, China
| |
Collapse
|
22
|
Zhang X, Wang L, Xu X, Cai C, Guo W. Genome-wide identification of mitogen-activated protein kinase gene family in Gossypium raimondii and the function of their corresponding orthologs in tetraploid cultivated cotton. BMC PLANT BIOLOGY 2014; 14:345. [PMID: 25492847 PMCID: PMC4270029 DOI: 10.1186/s12870-014-0345-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 11/20/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Mitogen-activated protein kinase (MAPK) cascades play a crucial role in plant growth and development as well as biotic and abiotic stress responses. Knowledge about the MAPK gene family in cotton is limited, and systematic investigation of MAPK family proteins has not been reported. RESULTS By performing a bioinformatics homology search, we identified 28 putative MAPK genes in the Gossypium raimondii genome. These MAPK members were anchored onto 11 chromosomes in G. raimondii, with uneven distribution. Phylogenetic analysis showed that the MAPK candidates could be classified into the four known A, B, C and D groups, with more MAPKs containing the TEY phosphorylation site (18 members) than the TDY motif (10 members). Furthermore, 21 cDNA sequences of MAPKs with complete open reading frames (ORFs) were identified in G. hirsutum via PCR-based approaches, including 13 novel MAPKs and eight with homologs reported previously in tetraploid cotton. The expression patterns of 23 MAPK genes reveal their important roles in diverse functions in cotton, in both various developmental stages of vegetative and reproductive growth and in the stress response. Using a reverse genetics approach based on tobacco rattle virus-induced gene silencing (TRV-VIGS), we further verified that MPK9, MPK13 and MPK25 confer resistance to defoliating isolates of Verticillium dahliae in cotton. Silencing of MPK9, MPK13 and MPK25 can significantly enhance cotton susceptibility to this pathogen. CONCLUSIONS This study presents a comprehensive identification of 28 mitogen-activated protein kinase genes in G. raimondii. Their phylogenetic relationships, transcript expression patterns and responses to various stressors were verified. This study provides the first systematic analysis of MAPKs in cotton, improving our understanding of defense responses in general and laying the foundation for future crop improvement using MAPKs.
Collapse
Affiliation(s)
- Xueying Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, P. R. China.
| | - Liman Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, P. R. China.
| | - Xiaoyang Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, P. R. China.
| | - Caiping Cai
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, P. R. China.
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, P. R. China.
| |
Collapse
|
23
|
Ovečka M, Takáč T, Komis G, Vadovič P, Bekešová S, Doskočilová A, Šamajová V, Luptovčiak I, Samajová O, Schweighofer A, Meskiene I, Jonak C, Křenek P, Lichtscheidl I, Škultéty L, Hirt H, Šamaj J. Salt-induced subcellular kinase relocation and seedling susceptibility caused by overexpression of Medicago SIMKK in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2335-50. [PMID: 24648569 PMCID: PMC4036504 DOI: 10.1093/jxb/eru115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Dual-specificity mitogen-activated protein kinases kinases (MAPKKs) are the immediate upstream activators of MAPKs. They simultaneously phosphorylate the TXY motif within the activation loop of MAPKs, allowing them to interact with and regulate multiple substrates. Often, the activation of MAPKs triggers their nuclear translocation. However, the spatiotemporal dynamics and the physiological consequences of the activation of MAPKs, particularly in plants, are still poorly understood. Here, we studied the activation and localization of the Medicago sativa stress-induced MAPKK (SIMKK)-SIMK module after salt stress. In the inactive state, SIMKK and SIMK co-localized in the cytoplasm and in the nucleus. Upon salt stress, however, a substantial part of the nuclear pool of both SIMKK and SIMK relocated to cytoplasmic compartments. The course of nucleocytoplasmic shuttling of SIMK correlated temporally with the dual phosphorylation of the pTEpY motif. SIMKK function was further studied in Arabidopsis plants overexpressing SIMKK-yellow fluorescent protein (YFP) fusions. SIMKK-YFP plants showed enhanced activation of Arabidopsis MPK3 and MPK6 kinases upon salt treatment and exhibited high sensitivity against salt stress at the seedling stage, although they were salt insensitive during seed germination. Proteomic analysis of SIMKK-YFP overexpressors indicated the differential regulation of proteins directly or indirectly involved in salt stress responses. These proteins included catalase, peroxiredoxin, glutathione S-transferase, nucleoside diphosphate kinase 1, endoplasmic reticulum luminal-binding protein 2, and finally plasma membrane aquaporins. In conclusion, Arabidopsis seedlings overexpressing SIMKK-YFP exhibited higher salt sensitivity consistent with their proteome composition and with the presumptive MPK3/MPK6 hijacking of the salt response pathway.
Collapse
Affiliation(s)
- Miroslav Ovečka
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71 Olomouc, Czech Republic
| | - Tomáš Takáč
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71 Olomouc, Czech Republic
| | - George Komis
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71 Olomouc, Czech Republic
| | - Pavol Vadovič
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71 Olomouc, Czech Republic
| | - Slávka Bekešová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71 Olomouc, Czech Republic
| | - Anna Doskočilová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71 Olomouc, Czech Republic
| | - Veronika Šamajová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71 Olomouc, Czech Republic
| | - Ivan Luptovčiak
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71 Olomouc, Czech Republic
| | - Olga Samajová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71 Olomouc, Czech Republic
| | - Alois Schweighofer
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Dr Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Irute Meskiene
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Dr Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Claudia Jonak
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Dr Bohr-Gasse 3, A-1030 Vienna, Austria
| | - Pavel Křenek
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71 Olomouc, Czech Republic
| | - Irene Lichtscheidl
- Institution of Cell Imaging and Ultrastructure Research, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
| | - L'udovít Škultéty
- Department of Rickettsiology, Institute of Virology, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava, 845 05, Slovakia
| | - Heribert Hirt
- Unité de Recherche en Genomique Végétale, Université d'Evry-Val-d'essone, 2, rue Gaston Crémieux, F-91057 Evry, France
| | - Jozef Šamaj
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71 Olomouc, Czech Republic
| |
Collapse
|
24
|
Asif MH, Lakhwani D, Pathak S, Bhambhani S, Bag SK, Trivedi PK. Genome-wide identification and expression analysis of the mitogen-activated protein kinase gene family from banana suggest involvement of specific members in different stages of fruit ripening. Funct Integr Genomics 2013; 14:161-75. [PMID: 24275941 DOI: 10.1007/s10142-013-0349-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 11/01/2013] [Accepted: 11/04/2013] [Indexed: 10/26/2022]
Abstract
Mitogen-activated protein kinases (MAPKs) are important components of the tripartite mitogen-activated protein kinase signaling cascade and play an important role in plant growth and development. Although members of the MAPK gene family have been identified in model plants, little information is available regarding this gene family in fruit crops. In this study, we carried out a computational analysis using the Musa Genome database to identify members of the MAPK gene family in banana, an economically important crop and the most popular fruit worldwide. Our analysis identified 25 members of the MAP kinase (MAPK or MPK) gene family. Phylogenetic analyses of MPKs in Arabidopsis, Oryza, and Populus have classified these MPKs into four subgroups. The presence of conserved domains in the deduced amino acid sequences, phylogeny, and genomic organization strongly support their identity as members of the MPK gene family. Expression analysis during ethylene-induced banana fruit ripening suggests the involvement of several MPKs in the ethylene signal transduction pathway that are necessary for banana fruit ripening. Analysis of the cis-regulatory elements in the promoter regions and the involvement of the identified MPKs in various cellular processes, as analyzed using Pathway Studio, suggest a role for the banana MPK gene family in diverse functions related to growth, development, and the stress response. This report is the first concerning the identification of members of a gene family and the elucidation of their role in various processes using the Musa Genome database.
Collapse
Affiliation(s)
- Mehar Hasan Asif
- National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
| | | | | | | | | | | |
Collapse
|
25
|
Solovieva AD, Frolova OY, Solovyev AG, Morozov SY, Zamyatnin AA. Effect of mitochondria-targeted antioxidant SkQ1 on programmed cell death induced by viral proteins in tobacco plants. BIOCHEMISTRY. BIOKHIMIIA 2013; 78:1006-12. [PMID: 24228922 DOI: 10.1134/s000629791309006x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Programmed cell death (PCD) is the main defense mechanism in plants to fight various pathogens including viruses. The best-studied example of virus-induced PCD in plants is Tobacco mosaic virus (TMV)-elicited hypersensitive response in tobacco plants containing the N resistance gene. It was previously reported that the animal mitochondrial protein Bcl-xL, which lacks a homolog in plants, effectively suppresses plant PCD induced by TMV p50 - the elicitor of hypersensitive response in Nicotiana tabacum carrying the N gene. Our studies show that the mitochondria-targeted antioxidant SkQ1 effectively suppresses p50-induced PCD in tobacco plants. On the other hand, SkQ1 did not affect Poa semilatent virus TGB3-induced endoplasmic reticulum stress, which is followed by PCD, in Nicotiana benthamiana epidermal cells. These data suggest that mitochondria-targeted antioxidant SkQ1 can be used to study molecular mechanisms of PCD suppression in plants.
Collapse
Affiliation(s)
- A D Solovieva
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | | | | | | | | |
Collapse
|
26
|
Liang W, Yang B, Yu BJ, Zhou Z, Li C, Jia M, Sun Y, Zhang Y, Wu F, Zhang H, Wang B, Deyholos MK, Jiang YQ. Identification and analysis of MKK and MPK gene families in canola (Brassica napus L.). BMC Genomics 2013; 14:392. [PMID: 23758924 PMCID: PMC3701561 DOI: 10.1186/1471-2164-14-392] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 05/21/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Eukaryotic mitogen-activated protein kinase (MAPK/MPK) signaling cascades transduce and amplify environmental signals via three types of reversibly phosphorylated kinases to activate defense gene expression. Canola (oilseed rape, Brassica napus) is a major crop in temperate regions. Identification and characterization of MAPK and MAPK kinases (MAPKK/MKK) of canola will help to elucidate their role in responses to abiotic and biotic stresses. RESULTS We describe the identification and analysis of seven MKK (BnaMKK) and 12 MPK (BnaMPK) members from canola. Sequence alignments and phylogenetic analyses of the predicted amino acid sequences of BnaMKKs and BnaMPKs classified them into four different groups. We also examined the subcellular localization of four and two members of BnaMKK and BnaMPK gene families, respectively, using green fluorescent protein (GFP) and, found GFP signals in both nuclei and cytoplasm. Furthermore, we identified several interesting interaction pairs through yeast two-hybrid (Y2H) analysis of interactions between BnaMKKs and BnaMPKs, as well as BnaMPK and BnaWRKYs. We defined contiguous signaling modules including BnaMKK9-BnaMPK1/2-BnaWRKY53, BnaMKK2/4/5-BnaMPK3/6-BnaWRKY20/26 and BnaMKK9-BnaMPK5/9/19/20. Of these, several interactions had not been previously described in any species. Selected interactions were validated in vivo by a bimolecular fluorescence complementation (BiFC) assay. Transcriptional responses of a subset of canola MKK and MPK genes to stimuli including fungal pathogens, hormones and abiotic stress treatments were analyzed through real-time RT-PCR and we identified a few of BnaMKKs and BnaMPKs responding to salicylic acid (SA), oxalic acid (OA), Sclerotinia sclerotiorum or other stress conditions. Comparisons of expression patterns of putative orthologs in canola and Arabidopsis showed that transcript expression patterns were generally conserved, with some differences suggestive of sub-functionalization. CONCLUSIONS We identified seven MKK and 12 MPK genes from canola and examined their phylogenetic relationships, transcript expression patterns, subcellular localization, and protein-protein interactions. Not all expression patterns and interactions were conserved between canola and Arabidopsis, highlighting the limitations of drawing inferences about crops from model species. The data presented here provide the first systematic description of MKK-MPK-WRKY signaling modules in canola and will further improve our understanding of defense responses in general and provide a basis for future crop improvement.
Collapse
Affiliation(s)
- Wanwan Liang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A & F University, Yangling, Shaanxi 712100, China
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Candelori A, Luporini P, Alimenti C, Vallesi A. Characterization and expression of the gene encoding En-MAPK1, an intestinal cell kinase (ICK)-like kinase activated by the autocrine pheromone-signaling loop in the Polar Ciliate, Euplotes nobilii. Int J Mol Sci 2013; 14:7457-67. [PMID: 23552830 PMCID: PMC3645696 DOI: 10.3390/ijms14047457] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 03/21/2013] [Accepted: 03/21/2013] [Indexed: 11/16/2022] Open
Abstract
In the protozoan ciliate Euplotes, a transduction pathway resulting in a mitogenic cell growth response is activated by autocrine receptor binding of cell type-specific, water-borne signaling protein pheromones. In Euplotes raikovi, a marine species of temperate waters, this transduction pathway was previously shown to involve the phosphorylation of a nuclear protein kinase structurally similar to the intestinal-cell and male germ cell-associated kinases described in mammals. In E. nobilii, which is phylogenetically closely related to E. raikovi but inhabits Antarctic and Arctic waters, we have now characterized a gene encoding a structurally homologous kinase. The expression of this gene requires +1 translational frameshifting and a process of intron splicing for the production of the active protein, designated En-MAPK1, which contains amino acid substitutions of potential significance for cold-adaptation.
Collapse
Affiliation(s)
- Annalisa Candelori
- Laboratory of Eukaryotic Microbiology and Animal Biology, Department of Environmental and Natural Sciences, University of Camerino, Camerino 62032, Italy.
| | | | | | | |
Collapse
|