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Shao X, Zhang Z, Yang F, Yu Y, Guo J, Li J, Xu T, Pan X. Chilling stress response in tobacco seedlings: insights from transcriptome, proteome, and phosphoproteome analyses. FRONTIERS IN PLANT SCIENCE 2024; 15:1390993. [PMID: 38872895 PMCID: PMC11170286 DOI: 10.3389/fpls.2024.1390993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 05/06/2024] [Indexed: 06/15/2024]
Abstract
Tobacco (Nicotiana tabacum L.) is an important industrial crop, which is sensitive to chilling stress. Tobacco seedlings that have been subjected to chilling stress readily flower early, which seriously affects the yield and quality of their leaves. Currently, there has been progress in elucidating the molecular mechanisms by which tobacco responds to chilling stress. However, little is known about the phosphorylation that is mediated by chilling. In this study, the transcriptome, proteome and phosphoproteome were analyzed to elucidate the mechanisms of the responses of tobacco shoot and root to chilling stress (4 °C for 24 h). A total of 6,113 differentially expressed genes (DEGs), 153 differentially expressed proteins (DEPs) and 345 differential phosphopeptides were identified in the shoot, and the corresponding numbers in the root were 6,394, 212 and 404, respectively. This study showed that the tobacco seedlings to 24 h of chilling stress primarily responded to this phenomenon by altering their levels of phosphopeptide abundance. Kyoto Encyclopedia of Genes and Genomes analyses revealed that starch and sucrose metabolism and endocytosis were the common pathways in the shoot and root at these levels. In addition, the differential phosphopeptide corresponding proteins were also significantly enriched in the pathways of photosynthesis-antenna proteins and carbon fixation in photosynthetic organisms in the shoot and arginine and proline metabolism, peroxisome and RNA transport in the root. These results suggest that phosphoproteins in these pathways play important roles in the response to chilling stress. Moreover, kinases and transcription factors (TFs) that respond to chilling at the levels of phosphorylation are also crucial for resistance to chilling in tobacco seedlings. The phosphorylation or dephosphorylation of kinases, such as CDPKs and RLKs; and TFs, including VIP1-like, ABI5-like protein 2, TCP7-like, WRKY 6-like, MYC2-like and CAMTA7 among others, may play essential roles in the transduction of tobacco chilling signal and the transcriptional regulation of the genes that respond to chilling stress. Taken together, these findings provide new insights into the molecular mechanisms and regulatory networks of the responses of tobacco to chilling stress.
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Affiliation(s)
- Xiuhong Shao
- Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangdong Provincial Engineering & Technology Research Center for Tobacco Breeding and Comprehensive Utilization, Guangzhou, China
| | - Zhenchen Zhang
- Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangdong Provincial Engineering & Technology Research Center for Tobacco Breeding and Comprehensive Utilization, Guangzhou, China
| | - Faheng Yang
- China National Tobacco Corporation, Guangdong Company, Guangzhou, China
| | - Yongchao Yu
- China National Tobacco Corporation, Guangdong Company, Guangzhou, China
| | - Junjie Guo
- China National Tobacco Corporation, Guangdong Company, Guangzhou, China
| | - Jiqin Li
- Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangdong Provincial Engineering & Technology Research Center for Tobacco Breeding and Comprehensive Utilization, Guangzhou, China
| | - Tingyu Xu
- Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangdong Provincial Engineering & Technology Research Center for Tobacco Breeding and Comprehensive Utilization, Guangzhou, China
| | - Xiaoying Pan
- Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangdong Provincial Engineering & Technology Research Center for Tobacco Breeding and Comprehensive Utilization, Guangzhou, China
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Fan Z, Zhao B, Lai R, Wu H, Jia L, Zhao X, Luo J, Huang Y, Chen Y, Lin Y, Lai Z. Genome-Wide Identification of the MPK Gene Family and Expression Analysis under Low-Temperature Stress in the Banana. PLANTS (BASEL, SWITZERLAND) 2023; 12:2926. [PMID: 37631138 PMCID: PMC10460080 DOI: 10.3390/plants12162926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/04/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023]
Abstract
Mitogen-activated protein kinases (MAPKs and MPKs) are important in the process of resisting plant stress. In this study, 21, 12, 18, 16, and 10 MPKs were identified from Musa acuminata, Musa balbisiana, Musa itinerans, Musa schizocarpa, and Musa textilis, respectively. These MPKs were divided into Group A, B, C, and D. Phylogenetic analysis revealed that this difference in number was due to the gene shrinkage of the Group B subfamily of Musa balbisiana and Musa textilis. KEGG annotations revealed that K14512, which is involved in plant hormone signal transduction and the plant-pathogen interaction, was the most conserved pathway of the MPKs. The results of promoter cis-acting element prediction and focTR4 (Fusarium oxysporum f. sp. cubense tropical race 4) transcriptome expression analysis preliminarily confirmed that MPKs were relevant to plant hormone and biotic stress, respectively. The expression of MPKs in Group A was significantly upregulated at 4 °C, and dramatically, the MPKs in the root were affected by low temperature. miR172, miR319, miR395, miR398, and miR399 may be the miRNAs that regulate MPKs during low-temperature stress, with miR172 being the most critical. miRNA prediction and qRT-PCR results indicated that miR172 may negatively regulate MPKs. Therefore, we deduced that MPKs might coordinate with miR172 to participate in the process of the resistance to low-temperature stress in the roots of the banana. This study will provide a theoretical basis for further analysis of the mechanism of MPKs under low-temperature stress of bananas, and this study could be applied to molecular breeding of bananas in the future.
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Affiliation(s)
- Zhengyang Fan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.F.); (B.Z.); (R.L.); (H.W.); (L.J.); (X.Z.); (J.L.); (Y.H.); (Y.C.); (Y.L.)
| | - Bianbian Zhao
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.F.); (B.Z.); (R.L.); (H.W.); (L.J.); (X.Z.); (J.L.); (Y.H.); (Y.C.); (Y.L.)
| | - Ruilian Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.F.); (B.Z.); (R.L.); (H.W.); (L.J.); (X.Z.); (J.L.); (Y.H.); (Y.C.); (Y.L.)
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Huan Wu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.F.); (B.Z.); (R.L.); (H.W.); (L.J.); (X.Z.); (J.L.); (Y.H.); (Y.C.); (Y.L.)
| | - Liang Jia
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.F.); (B.Z.); (R.L.); (H.W.); (L.J.); (X.Z.); (J.L.); (Y.H.); (Y.C.); (Y.L.)
| | - Xiaobing Zhao
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.F.); (B.Z.); (R.L.); (H.W.); (L.J.); (X.Z.); (J.L.); (Y.H.); (Y.C.); (Y.L.)
| | - Jie Luo
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.F.); (B.Z.); (R.L.); (H.W.); (L.J.); (X.Z.); (J.L.); (Y.H.); (Y.C.); (Y.L.)
| | - Yuji Huang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.F.); (B.Z.); (R.L.); (H.W.); (L.J.); (X.Z.); (J.L.); (Y.H.); (Y.C.); (Y.L.)
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.F.); (B.Z.); (R.L.); (H.W.); (L.J.); (X.Z.); (J.L.); (Y.H.); (Y.C.); (Y.L.)
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.F.); (B.Z.); (R.L.); (H.W.); (L.J.); (X.Z.); (J.L.); (Y.H.); (Y.C.); (Y.L.)
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.F.); (B.Z.); (R.L.); (H.W.); (L.J.); (X.Z.); (J.L.); (Y.H.); (Y.C.); (Y.L.)
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Zhou M, Li Y, Yan Y, Gao L, He C, Wang J, Yuan Q, Miao L, Li S, Di Q, Yu X, Sun M. Proteome and phosphoproteome analysis of 2,4-epibrassinolide-mediated cold stress response in cucumber seedlings. FRONTIERS IN PLANT SCIENCE 2023; 14:1104036. [PMID: 36895878 PMCID: PMC9989176 DOI: 10.3389/fpls.2023.1104036] [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: 11/21/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
The 2, 4-epibrassinolide (EBR) significantly increased plants cold tolerance. However, mechanisms of EBR in regulating cold tolerance in phosphoproteome and proteome levels have not been reported. The mechanism of EBR regulating cold response in cucumber was studied by multiple omics analysis. In this study, phosphoproteome analysis showed that cucumber responded to cold stress through multi-site serine phosphorylation, while EBR further upregulated single-site phosphorylation for most of cold-responsive phosphoproteins. Association analysis of the proteome and phosphoproteome revealed that EBR reprogrammed proteins in response to cold stress by negatively regulating protein phosphorylation and protein content, and phosphorylation negatively regulated protein content in cucumber. Further functional enrichment analysis of proteome and phosphoproteome showed that cucumber mainly upregulated phosphoproteins related to spliceosome, nucleotide binding and photosynthetic pathways in response to cold stress. However, different from the EBR regulation in omics level, hypergeometric analysis showed that EBR further upregulated 16 cold-up-responsive phosphoproteins participated photosynthetic and nucleotide binding pathways in response to cold stress, suggested their important function in cold tolerance. Analysis of cold-responsive transcription factors (TFs) by correlation between proteome and phosphoproteome showed that cucumber regulated eight class TFs may through protein phosphorylation under cold stress. Further combined with cold-related transcriptome found that cucumber phosphorylated eight class TFs, and mainly through targeting major hormone signal genes by bZIP TFs in response to cold stress, while EBR further increased these bZIP TFs (CsABI5.2 and CsABI5.5) phosphorylation level. In conclusion, the EBR mediated schematic of molecule response mechanisms in cucumber under cold stress was proposed.
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Affiliation(s)
- Mengdi Zhou
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Tablecrops, China Agricultural University, Beijing, China
| | - Yansu Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Yan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihong Gao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Tablecrops, China Agricultural University, Beijing, China
| | - Chaoxing He
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Quan Yuan
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Li Miao
- College of Horticulture, Zhejiang A & F University, Hangzhou, China
| | - Shuzhen Li
- College of Life Science, Gannan Normal University, Ganzhou, China
| | - Qinghua Di
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianchang Yu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mintao Sun
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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Chong L, Hsu CC, Zhu Y. Advances in mass spectrometry-based phosphoproteomics for elucidating abscisic acid signaling and plant responses to abiotic stress. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6547-6557. [PMID: 35959917 DOI: 10.1093/jxb/erac324] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
Abiotic stresses have significant impacts on crop yield and quality. Even though significant efforts during the past decade have been devoted to uncovering the core signaling pathways associated with the phytohormone abscisic acid (ABA) and abiotic stress in plants, abiotic stress signaling mechanisms in most crops remain largely unclear. The core components of the ABA signaling pathway, including early events in the osmotic stress-induced phosphorylation network, have recently been elucidated in Arabidopsis with the aid of phosphoproteomics technologies. We now know that SNF1-related kinases 2 (SnRK2s) are not only inhibited by the clade A type 2C protein phosphatases (PP2Cs) through dephosphorylation, but also phosphorylated and activated by upstream mitogen-activated protein kinase kinase kinases (MAP3Ks). Through describing the course of studies to elucidate abiotic stress and ABA signaling, we will discuss how we can take advantage of the latest innovations in mass-spectrometry-based phosphoproteomics and structural proteomics to boost our investigation of plant regulation and responses to ABA and abiotic stress.
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Affiliation(s)
- Leelyn Chong
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Chuan-Chih Hsu
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Sanya Institute of Henan University, Sanya, Hainan, China
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Wang J, Sun Z, Chen C, Xu M. The MKK2a Gene Involved in the MAPK Signaling Cascades Enhances Populus Salt Tolerance. Int J Mol Sci 2022; 23:ijms231710185. [PMID: 36077589 PMCID: PMC9456161 DOI: 10.3390/ijms231710185] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Mitogen-activated protein kinase (MAPK) cascades are highly conserved signal transduction modules, which transmit environmental signals in plant cells through stepwise phosphorylation and play indispensable roles in a wide range of physiological and biochemical processes. Here, we isolated and characterized a gene encoding MKK2 protein from poplar through the rapid amplification of cDNA ends (RACE). The full-length PeMKK2a gene was 1571 bp, including a 1068 bp open reading frame (ORF) encoding 355 amino acids, and the putative PeMKK2a protein belongs to the PKc_like (protein kinase domain) family (70–336 amino acids) in the PKc_MAPKK_plant subfamily and contains 62 sites of possible phosphorylation and two conserved domains, DLK and S/T-xxxxx-S/T. Detailed information about its gene structure, sequence similarities, subcellular localization, and transcript profiles under salt-stress conditions was revealed. Transgenic poplar lines overexpressing PeMKK2a exhibited higher activities of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) than non-transgenic poplar under salt stress conditions. These results will provide insight into the roles of MAPK signaling cascades in poplar response to salt stress.
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Affiliation(s)
| | | | | | - Meng Xu
- Correspondence: ; Tel.: +86-150-9430-7586
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Yan S, Bhawal R, Yin Z, Thannhauser TW, Zhang S. Recent advances in proteomics and metabolomics in plants. MOLECULAR HORTICULTURE 2022; 2:17. [PMID: 37789425 PMCID: PMC10514990 DOI: 10.1186/s43897-022-00038-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/20/2022] [Indexed: 10/05/2023]
Abstract
Over the past decade, systems biology and plant-omics have increasingly become the main stream in plant biology research. New developments in mass spectrometry and bioinformatics tools, and methodological schema to integrate multi-omics data have leveraged recent advances in proteomics and metabolomics. These progresses are driving a rapid evolution in the field of plant research, greatly facilitating our understanding of the mechanistic aspects of plant metabolisms and the interactions of plants with their external environment. Here, we review the recent progresses in MS-based proteomics and metabolomics tools and workflows with a special focus on their applications to plant biology research using several case studies related to mechanistic understanding of stress response, gene/protein function characterization, metabolic and signaling pathways exploration, and natural product discovery. We also present a projection concerning future perspectives in MS-based proteomics and metabolomics development including their applications to and challenges for system biology. This review is intended to provide readers with an overview of how advanced MS technology, and integrated application of proteomics and metabolomics can be used to advance plant system biology research.
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Affiliation(s)
- Shijuan Yan
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ruchika Bhawal
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 139 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853, USA
| | - Zhibin Yin
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | | | - Sheng Zhang
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 139 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853, USA.
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Wang F, Das P, Pal N, Bhawal R, Zhang S, Bhattacharyya MK. A Phosphoproteomics Study of the Soybean root necrosis 1 Mutant Revealed Type II Metacaspases Involved in Cell Death Pathway. FRONTIERS IN PLANT SCIENCE 2022; 13:882561. [PMID: 35928708 PMCID: PMC9344878 DOI: 10.3389/fpls.2022.882561] [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: 02/23/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
The soybean root necrosis 1 (rn1) mutation causes progressive browning of the roots soon after germination and provides increased tolerance to the soil-borne oomycete pathogen Phytophthora sojae in soybean. Toward understanding the molecular basis of the rn1 mutant phenotypes, we conducted tandem mass tag (TMT)-labeling proteomics and phosphoproteomics analyses of the root tissues of the rn1 mutant and progenitor T322 line to identify potential proteins involved in manifestation of the mutant phenotype. We identified 3,160 proteins. When the p-value was set at ≤0.05 and the fold change of protein accumulation between rn1 and T322 at ≥1.5 or ≤0.67, we detected 118 proteins that showed increased levels and 32 proteins decreased levels in rn1 as compared to that in T322. The differentially accumulated proteins (DAPs) are involved in several pathways including cellular processes for processing environmental and genetic information, metabolism and organismal systems. Five pathogenesis-related proteins were accumulated to higher levels in the mutant as compared to that in T322. Several of the DAPs are involved in hormone signaling, redox reaction, signal transduction, and cell wall modification processes activated in plant-pathogen interactions. The phosphoproteomics analysis identified 22 phosphopeptides, the levels of phosphorylation of which were significantly different between rn1 and T322 lines. The phosphorylation levels of two type II metacaspases were reduced in rn1 as compared to T322. Type II metacaspase has been shown to be a negative regulator of hypersensitive cell death. In absence of the functional Rn1 protein, two type II metacaspases exhibited reduced phosphorylation levels and failed to show negative regulatory cell death function in the soybean rn1 mutant. We hypothesize that Rn1 directly or indirectly phosphorylates type II metacaspases to negatively regulate the cell death process in soybean roots.
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Affiliation(s)
- Feifei Wang
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Priyanka Das
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Narinder Pal
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Ruchika Bhawal
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, United States
| | - Sheng Zhang
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, United States
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Movahedi A, Wei H, Zhou X, Fountain JC, Chen ZH, Mu Z, Sun W, Zhang J, Li D, Guo B, Varshney RK, Yang L, Zhuge Q. Precise exogenous insertion and sequence replacements in poplar by simultaneous HDR overexpression and NHEJ suppression using CRISPR-Cas9. HORTICULTURE RESEARCH 2022; 9:uhac154. [PMID: 36133672 PMCID: PMC9478684 DOI: 10.1093/hr/uhac154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 07/22/2022] [Accepted: 06/27/2022] [Indexed: 05/21/2023]
Abstract
CRISPR-mediated genome editing has become a powerful tool for the genetic modification of biological traits. However, developing an efficient, site-specific, gene knock-in system based on homology-directed DNA repair (HDR) remains a significant challenge in plants, especially in woody species like poplar. Here, we show that simultaneous inhibition of non-homologous end joining (NHEJ) recombination cofactor XRCC4 and overexpression of HDR enhancer factors CtIP and MRE11 can improve HDR efficiency for gene knock-in. Using this approach, the BleoR gene was integrated onto the 3' end of the MKK2 MAP kinase gene to generate a BleoR-MKK2 fusion protein. Based on fully edited nucleotides evaluated by TaqMan real-time PCR, the HDR-mediated knock-in efficiency was up to 48% when using XRCC4 silencing incorporated with a combination of CtIP and MRE11 overexpression compared with no HDR enhancement or NHEJ silencing. Furthermore, this combination of HDR enhancer overexpression and NHEJ repression also increased genome targeting efficiency and gave 7-fold fewer CRISPR-induced insertions and deletions (InDels), resulting in no functional effects on MKK2-based salt stress responses in poplar. Therefore, this approach may be useful not only in poplar and plants or crops but also in mammals for improving CRISPR-mediated gene knock-in efficiency.
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Affiliation(s)
| | - Hui Wei
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | | | | | - Zhong-Hua Chen
- School of Science, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Zhiying Mu
- College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Weibo Sun
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Jiaxin Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Dawei Li
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Baozhu Guo
- USDA-ARS, Crop Genetics and Breeding Research Unit, Tifton, GA 31793, USA
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Gao Z, Sun B, Chen Z, Zhai H, Yao Y, Du Y. Phosphoproteomic analysis of ozone stress-responsive mechanisms in grapevine identifies KEG required for stress regulation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 311:111008. [PMID: 34482911 DOI: 10.1016/j.plantsci.2021.111008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 07/13/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
The environmental damage caused by ozone is of increasing concern globally. The phosphoproteomics approach was used to explore the mechanisms underlying grapevine tolerance to ozone stress and identify phosphoproteins altered by ozone treatment. Results revealed that 194 of 2275 quantitatively analyzed phosphoproteins were significantly regulated after ozone treatment. Biological pathways related to transport were significantly enriched by the differentially regulated phosphoproteins. Among these phosphoproteins, the phosphorylation of RING E3 ligase in grape (V. vinifera KEEP ON GOING, VvKEG) decreased after ozone treatment. Over-expression of VvKEG in Arabidopsis decreased abscisic acid (ABA) sensitivity and enhanced ozone tolerance. Furthermore, VvKEG interacted with the ABA-responsive transcription factor ABSCISIC ACID-INSENSITIVE3 (ABI3). The exogenous application of ABA on grapevine leaves significantly influenced chlorophyll fluorescence, chlorophyll, and malondialdehyde (MDA) contents under ozone treatment; however, treatment with 150 μmol ABA aggravated ozone stress. These results indicate that phosphorylation modification provides information on ozone-induced processes and that VvKEG plays a critical role in these processes via regulation of the ABA signaling pathway in grape.
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Affiliation(s)
- Zhen Gao
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Baozhen Sun
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Zhengwen Chen
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Heng Zhai
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yuxin Yao
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yuanpeng Du
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
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10
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Praat M, De Smet I, van Zanten M. Protein kinase and phosphatase control of plant temperature responses. JOURNAL OF EXPERIMENTAL BOTANY 2021:erab345. [PMID: 34283227 DOI: 10.1093/jxb/erab345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Indexed: 06/13/2023]
Abstract
Plants must cope with ever-changing temperature conditions in their environment. Suboptimal high and low temperatures, and stressful extreme temperatures, induce adaptive mechanisms that allow optimal performance and survival, respectively. These processes have been extensively studied at the physiological, transcriptional and (epi)genetic level. Cellular temperature signalling cascades and tolerance mechanisms also involve post-translational modifications (PTMs), particularly protein phosphorylation. Many protein kinases are known to be involved in cold acclimation and heat stress responsiveness but research on the role and importance of kinases and phosphatases in triggering responses to mild changes in temperature such as thermomorphogenesis is inadequately understood. In this review, we summarize the current knowledge on the roles of kinases and phosphatases in plant temperature responses. We discuss how kinases can function over a range of temperatures in different signalling pathways and provide an outlook to the application of PTM-modifying factors for the development of thermotolerant crops.
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Affiliation(s)
- Myrthe Praat
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University. Padualaan 8, 3584CH Utrecht, the Netherlands
| | - Ive De Smet
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Martijn van Zanten
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University. Padualaan 8, 3584CH Utrecht, the Netherlands
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11
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The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators. Cells 2021; 10:cells10071665. [PMID: 34359847 PMCID: PMC8303113 DOI: 10.3390/cells10071665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/15/2021] [Accepted: 06/28/2021] [Indexed: 12/20/2022] Open
Abstract
Auxin plays a dual role in growth regulation and, depending on the tissue and concentration of the hormone, it can either promote or inhibit division and expansion processes in plants. Recent studies have revealed that, beyond transcriptional reprogramming, alternative auxin-controlled mechanisms regulate root growth. Here, we explored the impact of different concentrations of the synthetic auxin NAA that establish growth-promoting and -repressing conditions on the root tip proteome and phosphoproteome, generating a unique resource. From the phosphoproteome data, we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results, together with previously published studies, suggest that auxin, H+-ATPases, cell wall modifications and cell wall sensing receptor-like kinases are tightly embedded in a pathway regulating cell elongation. Furthermore, our study assigned a novel role to MKK2 as a regulator of primary root growth and a (potential) regulator of auxin biosynthesis and signalling, and suggests the importance of the MKK2 Thr31 phosphorylation site for growth regulation in the Arabidopsis root tip.
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12
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Gao J, Dou T, He W, Sheng O, Bi F, Deng G, Gao H, Dong T, Li C, Zhang S, Yi G, Hu C, Yang Q. MaMAPK3-MaICE1-MaPOD P7 pathway, a positive regulator of cold tolerance in banana. BMC PLANT BIOLOGY 2021; 21:97. [PMID: 33596830 PMCID: PMC7890976 DOI: 10.1186/s12870-021-02868-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 02/01/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND Banana is a tropical fruit with a high economic impact worldwide. Cold stress greatly affects the development and production of banana. RESULTS In the present study, we investigated the functions of MaMAPK3 and MaICE1 involved in cold tolerance of banana. The effect of RNAi of MaMAPK3 on Dajiao (Musa spp. 'Dajiao'; ABB Group) cold tolerance was evaluated. The leaves of the MaMAPK3 RNAi transgenic plants showed wilting and severe necrotic symptoms, while the wide-type (WT) plants remained normal after cold exposure. RNAi of MaMAPK3 significantly changed the expressions of the cold-responsive genes, and the oxidoreductase activity was significantly changed in WT plants, while no changes in transgenic plants were observed. MaICE1 interacted with MaMAPK3, and the expression level of MaICE1 was significantly decreased in MaMAPK3 RNAi transgenic plants. Over-expression of MaICE1 in Cavendish banana (Musa spp. AAA group) indicated that the cold resistance of transgenic plants was superior to that of the WT plants. The POD P7 gene was significantly up-regulated in MaICE1-overexpressing transgenic plants compared with WT plants, and the POD P7 was proved to interact with MaICE1. CONCLUSIONS Taken together, our work provided new and solid evidence that MaMAPK3-MaICE1-MaPOD P7 pathway positively improved the cold tolerance in monocotyledon banana, shedding light on molecular breeding for the cold-tolerant banana or other agricultural species.
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Affiliation(s)
- Jie Gao
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Tongxin Dou
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China
| | - Weidi He
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China
| | - Ou Sheng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China
| | - Fangcheng Bi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China
| | - Guiming Deng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China
| | - Huijun Gao
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China
| | - Tao Dong
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China
| | - Chunyu Li
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China
| | - Sheng Zhang
- Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Ganjun Yi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China
| | - Chunhua Hu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China.
| | - Qiaosong Yang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China.
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PhosPhAt 4.0: An Updated Arabidopsis Database for Searching Phosphorylation Sites and Kinase-Target Interactions. Methods Mol Biol 2021; 2358:189-202. [PMID: 34270056 DOI: 10.1007/978-1-0716-1625-3_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The PhosPhAt 4.0 database contains information on Arabidopsis phosphorylation sites identified by mass spectrometry in large-scale experiments from different research groups. So far PhosPhAt 4.0 has been one of the most significant large-scale data resources for plant phosphorylation studies. Functionalities of the web application, besides display of phosphorylation sites, include phosphorylation site prediction and kinase-target relationships retrieval. Here, we present an overview and user instructions for the PhosPhAt 4.0 database, with strong emphasis on recent renewals regarding protein annotation by SUBA4.0 and Mapman4, and additional phosphorylation site information imported from other databases, such as UniProt. Here, we provide a user guide for the retrieval of phosphorylation motifs from the kinase-target database and how to visualize these results. The improvements incorporated into the PhosPhAt 4.0 database have produced much more functionality and user flexibility for phosphoproteomic analysis.
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Zhang X, Zhuang L, Liu Y, Yang Z, Huang B. Protein phosphorylation associated with drought priming-enhanced heat tolerance in a temperate grass species. HORTICULTURE RESEARCH 2020; 7:207. [PMID: 33328446 PMCID: PMC7705721 DOI: 10.1038/s41438-020-00440-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/12/2020] [Accepted: 10/20/2020] [Indexed: 05/24/2023]
Abstract
Protein phosphorylation is known to play crucial roles in plant tolerance to individual stresses, but how protein phosphorylation is associated with cross-stress tolerance, particularly drought priming-enhanced heat tolerance is largely unknown. The objectives of the present study were to identify phosphorylated proteins and phosphorylation sites that were responsive to drought priming and to determine whether drought priming-enhanced heat tolerance in temperate grass species involves changes in protein phosphorylation. Comparative analysis of phosphoproteomic profiles was performed on leaves of tall fescue (Festuca arundinacea) exposed to heat stress (38/33 °C, day/night) with or without drought priming. A total of 569 differentially regulated phosphoproteins (DRPs) with 1098 phosphorylation sites were identified in response to drought priming or heat stress individually or sequentially. Most DRPs were nuclear-localized and cytosolic proteins. Motif analysis detected [GS], [DSD], and [S..E] as major phosphorylation sites in casein kinase-II and mitogen-activated protein kinases regulated by drought priming and heat stress. Functional annotation and gene ontology analysis demonstrated that DRPs in response to drought priming and in drought-primed plants subsequently exposed to heat stress were mostly enriched in four major biological processes, including RNA splicing, transcription control, stress protection/defense, and stress perception/signaling. These results suggest the involvement of post-translational regulation of the aforementioned biological processes and signaling pathways in drought priming memory and cross-tolerance with heat stress in a temperate grass species.
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Affiliation(s)
- Xiaxiang Zhang
- College of Agro-grassland Science, Nanjing Agricultural University, 210095, Nanjing, China
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Lili Zhuang
- College of Agro-grassland Science, Nanjing Agricultural University, 210095, Nanjing, China
| | - Yu Liu
- College of Agro-grassland Science, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhimin Yang
- College of Agro-grassland Science, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Bingru Huang
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA.
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15
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Kamal MM, Ishikawa S, Takahashi F, Suzuki K, Kamo M, Umezawa T, Shinozaki K, Kawamura Y, Uemura M. Large-Scale Phosphoproteomic Study of Arabidopsis Membrane Proteins Reveals Early Signaling Events in Response to Cold. Int J Mol Sci 2020; 21:E8631. [PMID: 33207747 PMCID: PMC7696906 DOI: 10.3390/ijms21228631] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/22/2022] Open
Abstract
Cold stress is one of the major factors limiting global crop production. For survival at low temperatures, plants need to sense temperature changes in the surrounding environment. How plants sense and respond to the earliest drop in temperature is still not clearly understood. The plasma membrane and its adjacent extracellular and cytoplasmic sites are the first checkpoints for sensing temperature changes and the subsequent events, such as signal generation and solute transport. To understand how plants respond to early cold exposure, we used a mass spectrometry-based phosphoproteomic method to study the temporal changes in protein phosphorylation events in Arabidopsis membranes during 5 to 60 min of cold exposure. The results revealed that brief cold exposures led to rapid phosphorylation changes in the proteins involved in cellular ion homeostasis, solute and protein transport, cytoskeleton organization, vesical trafficking, protein modification, and signal transduction processes. The phosphorylation motif and kinase-substrate network analysis also revealed that multiple protein kinases, including RLKs, MAPKs, CDPKs, and their substrates, could be involved in early cold signaling. Taken together, our results provide a first look at the cold-responsive phosphoproteome changes of Arabidopsis membrane proteins that can be a significant resource to understand how plants respond to an early temperature drop.
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Affiliation(s)
- Md Mostafa Kamal
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (M.M.K.); (Y.K.)
| | - Shinnosuke Ishikawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei 184-8588, Japan; (S.I.); (T.U.)
| | - Fuminori Takahashi
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 3-1-1 Koyadai, Tsukuba 305-0074, Japan; (F.T.); (K.S.)
| | - Ko Suzuki
- Department of Biochemistry, Iwate Medical University, Yahaba 028-3694, Japan; (K.S.); (M.K.)
| | - Masaharu Kamo
- Department of Biochemistry, Iwate Medical University, Yahaba 028-3694, Japan; (K.S.); (M.K.)
| | - Taishi Umezawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei 184-8588, Japan; (S.I.); (T.U.)
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 3-1-1 Koyadai, Tsukuba 305-0074, Japan; (F.T.); (K.S.)
| | - Yukio Kawamura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (M.M.K.); (Y.K.)
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (M.M.K.); (Y.K.)
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
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16
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Yan J, Long Y, Zhou T, Ren J, Li Q, Song G, Cui Z. Dynamic Phosphoproteome Profiling of Zebrafish Embryonic Fibroblasts during Cold Acclimation. Proteomics 2020; 20:e1900257. [PMID: 31826332 DOI: 10.1002/pmic.201900257] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/24/2019] [Indexed: 11/09/2022]
Abstract
Temperature affects almost all aspects of the fish life. To cope with low temperature, fish have evolved the ability of cold acclimation for survival. However, intracellular signaling events underlying cold acclimation in fish remain largely unknown. Here, the formation of cold acclimation in zebrafish embryonic fibroblasts (ZF4) is monitored and the phosphorylation events during the process are investigated through a large-scale quantitative phosphoproteomic approach. In total, 11 474 phosphorylation sites are identified on 4066 proteins and quantified 5772 phosphosites on 2519 proteins. Serine, threonine, and tyrosine (Ser/Thr/Tyr) phosphorylation accounted for 85.5%, 13.3%, and 1.2% of total phosphosites, respectively. Among all phosphosites, 702 phosphosites on 510 proteins show differential regulation during cold acclimation of ZF4 cells. These phosphosites are divided into six clusters according to their dynamic changes during cold exposure. Kinase-substrate prediction reveals that mitogen-activated protein kinase (MAPK) among the kinase groups is predominantly responsible for phosphorylation of these phosphosites. The differentially regulated phosphoproteins are functionally associated with various cellular processes such as regulation of actin cytoskeleton and MAPK signaling pathway. These data enrich the database of protein phosphorylation sites in zebrafish and provide key clues for the elucidation of intracellular signaling networks during cold acclimation of fish.
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Affiliation(s)
- Junjun Yan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Long
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan, 430072, China
| | - Tong Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Ren
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan, 430072, China
| | - Guili Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan, 430072, China
| | - Zongbin Cui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan, 430072, China.,The Innovative Academy of Seed Design, Chinese Academy of Sciences, Hubei, Wuhan, 430072, China
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17
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Liu S, Li J, Zhang Y, Liu N, Viljoen A, Mostert D, Zuo C, Hu C, Bi F, Gao H, Sheng O, Deng G, Yang Q, Dong T, Dou T, Yi G, Ma L, Li C. Fusaric acid instigates the invasion of banana by Fusarium oxysporum f. sp. cubense TR4. THE NEW PHYTOLOGIST 2020; 225:913-929. [PMID: 31513293 PMCID: PMC6973005 DOI: 10.1111/nph.16193] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 09/05/2019] [Indexed: 05/04/2023]
Abstract
Fusaric acid (FSA) is a phytotoxin produced by several Fusarium species and has been associated with plant disease development, although its role is still not well understood. Mutation of key genes in the FSA biosynthetic gene (FUB) cluster in Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) reduced the FSA production, and resulted in decreased disease symptoms and reduced fungal biomass in the host banana plants. When pretreated with FSA, both banana leaves and pseudostems exhibited increased sensitivity to Foc TR4 invasion. Banana embryogenic cell suspensions (ECSs) treated with FSA exhibited a lower rate of O2 uptake, loss of mitochondrial membrane potential, increased reactive oxygen species (ROS) accumulation, and greater nuclear condensation and cell death. Consistently, transcriptomic analysis of FSA-treated ECSs showed that FSA may induce plant cell death through regulating the expression of genes involved in mitochondrial functions. The results herein demonstrated that the FSA from Foc TR4 functions as a positive virulence factor and acts at the early stage of the disease development before the appearance of the fungal hyphae in the infected tissues.
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Affiliation(s)
- Siwen Liu
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource UtilizationMinistry of AgricultureKey laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong ProvinceInstitution of Fruit Tree ResearchGuangdong Academy of Agricultural SciencesGuangzhou510640Guangdong ProvinceChina
| | - Jian Li
- College of HorticultureShenyang Agricultural UniversityShenyang110866Liaoning ProvinceChina
| | - Yong Zhang
- Institute of BiotechnologyZhejiang UniversityHangzhou310058China
| | - Na Liu
- School of Life SciencesSun Yat‐sen UniversityGuangzhou510275China
| | - Altus Viljoen
- Department of Biochemistry and Molecular BiologyUniversity of MassachusettsAmherstMA01003USA
| | - Diane Mostert
- Department of Biochemistry and Molecular BiologyUniversity of MassachusettsAmherstMA01003USA
| | - Cunwu Zuo
- Department of Plant PathologyUniversity of StellenboschPrivate Bag X1Matieland7602South Africa
| | - Chunhua Hu
- Department of Plant PathologyUniversity of StellenboschPrivate Bag X1Matieland7602South Africa
| | - Fangcheng Bi
- Department of Plant PathologyUniversity of StellenboschPrivate Bag X1Matieland7602South Africa
| | - Huijun Gao
- Department of Plant PathologyUniversity of StellenboschPrivate Bag X1Matieland7602South Africa
| | - Ou Sheng
- Department of Plant PathologyUniversity of StellenboschPrivate Bag X1Matieland7602South Africa
| | - Guiming Deng
- Department of Plant PathologyUniversity of StellenboschPrivate Bag X1Matieland7602South Africa
| | - Qiaosong Yang
- Department of Plant PathologyUniversity of StellenboschPrivate Bag X1Matieland7602South Africa
| | - Tao Dong
- Department of Plant PathologyUniversity of StellenboschPrivate Bag X1Matieland7602South Africa
| | - Tongxin Dou
- Department of Plant PathologyUniversity of StellenboschPrivate Bag X1Matieland7602South Africa
| | - Ganjun Yi
- Department of Plant PathologyUniversity of StellenboschPrivate Bag X1Matieland7602South Africa
| | - Li‐Jun Ma
- Institute of BiotechnologyZhejiang UniversityHangzhou310058China
| | - Chunyu Li
- Department of Plant PathologyUniversity of StellenboschPrivate Bag X1Matieland7602South Africa
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18
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Integrated proteomic and metabolomic analysis suggests high rates of glycolysis are likely required to support high carotenoid accumulation in banana pulp. Food Chem 2019; 297:125016. [DOI: 10.1016/j.foodchem.2019.125016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 06/10/2019] [Accepted: 06/14/2019] [Indexed: 11/20/2022]
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19
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Hsu CC, Zhu Y, Arrington JV, Paez JS, Wang P, Zhu P, Chen IH, Zhu JK, Tao WA. Universal Plant Phosphoproteomics Workflow and Its Application to Tomato Signaling in Response to Cold Stress. Mol Cell Proteomics 2018; 17:2068-2080. [PMID: 30006488 DOI: 10.1074/mcp.tir118.000702] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 06/21/2018] [Indexed: 01/08/2023] Open
Abstract
Phosphorylation-mediated signaling transduction plays a crucial role in the regulation of plant defense mechanisms against environmental stresses. To address the high complexity and dynamic range of plant proteomes and phosphoproteomes, we present a universal sample preparation procedure that facilitates plant phosphoproteomic profiling. This advanced workflow significantly improves phosphopeptide identifications, enabling deep insight into plant phosphoproteomes. We then applied the workflow to study the phosphorylation events involved in tomato cold tolerance mechanisms. Phosphoproteomic changes of two tomato species (N135 Green Gage and Atacames) with distinct cold tolerance phenotypes were profiled under cold stress. In total, we identified more than 30,000 unique phosphopeptides from tomato leaves, representing about 5500 phosphoproteins, thereby creating the largest tomato phosphoproteomic resource to date. The data, along with the validation through in vitro kinase reactions, allowed us to identify kinases involved in cold tolerant signaling and discover distinctive kinase-substrate events in two tomato species in response to a cold environment. The activation of SnRK2s and their direct substrates may assist N135 Green Gage tomatoes in surviving long-term cold stress. Taken together, the streamlined approach and the resulting deep phosphoproteomic analyses revealed a global view of tomato cold-induced signaling mechanisms.
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Affiliation(s)
- Chuan-Chih Hsu
- From the ‡Department of Biochemistry, Purdue University, West Lafayette, IN 47907
| | - Yingfang Zhu
- §Department of Horticulture and Landscape, Purdue University, West Lafayette, IN 47907.,¶Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.,‖Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | | | - Juan Sebastian Paez
- From the ‡Department of Biochemistry, Purdue University, West Lafayette, IN 47907
| | - Pengcheng Wang
- ‖Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China.,¶Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Peipei Zhu
- **Department of Chemistry, Purdue University, West Lafayette, IN 47907
| | - I-Hsuan Chen
- From the ‡Department of Biochemistry, Purdue University, West Lafayette, IN 47907
| | - Jian-Kang Zhu
- From the ‡Department of Biochemistry, Purdue University, West Lafayette, IN 47907.,‖Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China.,¶Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - W Andy Tao
- From the ‡Department of Biochemistry, Purdue University, West Lafayette, IN 47907; .,**Department of Chemistry, Purdue University, West Lafayette, IN 47907
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20
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Genome-wide identification and characterization of mRNAs and lncRNAs involved in cold stress in the wild banana (Musa itinerans). PLoS One 2018; 13:e0200002. [PMID: 29985922 PMCID: PMC6037364 DOI: 10.1371/journal.pone.0200002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 06/18/2018] [Indexed: 12/19/2022] Open
Abstract
Cold stress seriously affects banana growth, yield and fruit quality. Long noncoding RNAs (lncRNAs) have been demonstrated as key regulators of biotic and abiotic stress in plants, but the identification and prediction of cold responsive mRNAs and lncRNAs in wild banana remains unexplored. In present study, a cold resistant wild banana line from China was used to profile the cold-responsive mRNAs and lncRNAs by RNA-seq under cold stress conditions, i.e. 13°C (critical growth temperature), 4°C (chilling temperature), 0°C (freezing temperature) and normal growing condition, i.e. 28°C (control group). A total of 12,462 lncRNAs were identified in cold-stressed wild banana. In mRNA, much more alternative splicing events occurred in wild banana under the cold stress conditions compared with that in the normal growing condition. The GO analysis of differential expression genes (DEGs) showed the biochemical processes and membrane related genes responded positively to the cold stress. The KEGG pathway enrichment analysis of the DEGs showed that the pathways of photosynthesis, photosynthesis–antenna proteins, circadian rhythm–plant, glutathione metabolism, starch and sucrose metabolism, cutin/suberine/biosynthesis were altered or affected by the cold stress conditions. Our analyses of the generated transcriptome and lncRNAs provide new insights into regulating expression of genes and lncRNAs that respond to cold stress in the wild banana.
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21
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OsMAPK3 Phosphorylates OsbHLH002/OsICE1 and Inhibits Its Ubiquitination to Activate OsTPP1 and Enhances Rice Chilling Tolerance. Dev Cell 2018; 43:731-743.e5. [PMID: 29257952 DOI: 10.1016/j.devcel.2017.11.016] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/17/2017] [Accepted: 11/19/2017] [Indexed: 11/20/2022]
Abstract
Improvement of chilling tolerance is a major target in rice breeding. The signaling pathways regulating chilling consist of complex networks, including key transcription factors and their targets. However, it remains largely unknown how transcription factors are activated by chilling stress. Here, we report that the transcription factor OsbHLH002/OsICE1 is phosphorylated by OsMAPK3 under chilling stress. The osbhlh002-1 knockout mutant and antisense transgenic plants showed chilling hypersensitivity, whereas OsbHLH002-overexpressing plants exhibited enhanced chilling tolerance. OsbHLH002 can directly target OsTPP1, which encodes a key enzyme for trehalose biosynthesis. OsMAPK3 interacts with OsbHLH002 to prevent its ubiquitination by the E3 ligase OsHOS1. Under chilling stress, active OsMAPK3 phosphorylates OsbHLH002, leading to accumulation of phospho-OsbHLH002, which promotes OsTPP1 expression and increases trehalose content and resistance to chilling damage. Taken together, these results indicate that OsbHLH002 is phosphorylated by OsMAPK3, which enhances OsbHLH002 activation to its target OsTPP1 during chilling stress.
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He WD, Gao J, Dou TX, Shao XH, Bi FC, Sheng O, Deng GM, Li CY, Hu CH, Liu JH, Zhang S, Yang QS, Yi GJ. Early Cold-Induced Peroxidases and Aquaporins Are Associated With High Cold Tolerance in Dajiao ( Musa spp. 'Dajiao'). FRONTIERS IN PLANT SCIENCE 2018; 9:282. [PMID: 29568304 PMCID: PMC5852111 DOI: 10.3389/fpls.2018.00282] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/19/2018] [Indexed: 05/20/2023]
Abstract
Banana is an important tropical fruit with high economic value. One of the main cultivars ('Cavendish') is susceptible to low temperatures, while another closely related specie ('Dajiao') has considerably higher cold tolerance. We previously reported that some membrane proteins appear to be involved in the cold tolerance of Dajiao bananas via an antioxidation mechanism. To investigate the early cold stress response of Dajiao, here we applied comparative membrane proteomics analysis for both cold-sensitive Cavendish and cold-tolerant Dajiao bananas subjected to cold stress at 10°C for 0, 3, and 6 h. A total of 2,333 and 1,834 proteins were identified in Cavendish and Dajiao, respectively. Subsequent bioinformatics analyses showed that 692 Cavendish proteins and 524 Dajiao proteins were predicted to be membrane proteins, of which 82 and 137 differentially abundant membrane proteins (DAMPs) were found in Cavendish and Dajiao, respectively. Interestingly, the number of DAMPs with increased abundance following 3 h of cold treatment in Dajiao (80) was seven times more than that in Cavendish (11). Gene ontology molecular function analysis of DAMPs for Cavendish and Dajiao indicated that they belong to eight categories including hydrolase activity, binding, transporter activity, antioxidant activity, etc., but the number in Dajiao is twice that in Cavendish. Strikingly, we found peroxidases (PODs) and aquaporins among the protein groups whose abundance was significantly increased after 3 h of cold treatment in Dajiao. Some of the PODs and aquaporins were verified by reverse-transcription PCR, multiple reaction monitoring, and green fluorescent protein-based subcellular localization analysis, demonstrating that the global membrane proteomics data are reliable. By combining the physiological and biochemical data, we found that membrane-bound Peroxidase 52 and Peroxidase P7, and aquaporins (MaPIP1;1, MaPIP1;2, MaPIP2;4, MaPIP2;6, MaTIP1;3) are mainly involved in decreased lipid peroxidation and maintaining leaf cell water potential, which appear to be the key cellular adaptations contributing to the cold tolerance of Dajiao. This membrane proteomics study provides new insights into cold stress tolerance mechanisms of banana, toward potential applications for ultimate genetic improvement of cold tolerance in banana.
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Affiliation(s)
- Wei-Di He
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization of the Ministry of Agriculture/Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jie Gao
- Institute of Environmental Horticulture Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Tong-Xin Dou
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization of the Ministry of Agriculture/Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiu-Hong Shao
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization of the Ministry of Agriculture/Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, China
| | - Fang-Cheng Bi
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization of the Ministry of Agriculture/Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ou Sheng
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization of the Ministry of Agriculture/Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Gui-Ming Deng
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization of the Ministry of Agriculture/Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chun-Yu Li
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization of the Ministry of Agriculture/Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chun-Hua Hu
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization of the Ministry of Agriculture/Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ji-Hong Liu
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Sheng Zhang
- Institute of Biotechnology, Cornell University, Ithaca, NY, United States
| | - Qiao-Song Yang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization of the Ministry of Agriculture/Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- *Correspondence: Gan-Jun Yi, Qiao-Song Yang,
| | - Gan-Jun Yi
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization of the Ministry of Agriculture/Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- *Correspondence: Gan-Jun Yi, Qiao-Song Yang,
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