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Ramsbottom KA, Prakash A, Perez-Riverol Y, Camacho OM, Sun Z, Kundu DJ, Bowler-Barnett E, Martin M, Fan J, Chebotarov D, McNally KL, Deutsch EW, Vizcaíno JA, Jones AR. Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome. J Proteome Res 2024. [PMID: 38810119 DOI: 10.1021/acs.jproteome.4c00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Phosphorylation is the most studied post-translational modification, and has multiple biological functions. In this study, we have reanalyzed publicly available mass spectrometry proteomics data sets enriched for phosphopeptides from Asian rice (Oryza sativa). In total we identified 15,565 phosphosites on serine, threonine, and tyrosine residues on rice proteins. We identified sequence motifs for phosphosites, and link motifs to enrichment of different biological processes, indicating different downstream regulation likely caused by different kinase groups. We cross-referenced phosphosites against the rice 3,000 genomes, to identify single amino acid variations (SAAVs) within or proximal to phosphosites that could cause loss of a site in a given rice variety and clustered the data to identify groups of sites with similar patterns across rice family groups. The data has been loaded into UniProt Knowledge-Base─enabling researchers to visualize sites alongside other data on rice proteins, e.g., structural models from AlphaFold2, PeptideAtlas, and the PRIDE database─enabling visualization of source evidence, including scores and supporting mass spectra.
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Affiliation(s)
- Kerry A Ramsbottom
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, United Kingdom
| | - Ananth Prakash
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Oscar Martin Camacho
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, United Kingdom
| | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Deepti J Kundu
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Emily Bowler-Barnett
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Maria Martin
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Jun Fan
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Dmytro Chebotarov
- International Rice Research Institute, DAPO Box 7777, Manila 1301, Philippines
| | - Kenneth L McNally
- International Rice Research Institute, DAPO Box 7777, Manila 1301, Philippines
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Andrew R Jones
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, United Kingdom
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2
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Ramsbottom KA, Prakash A, Riverol YP, Camacho OM, Sun Z, Kundu DJ, Bowler-Barnett E, Martin M, Fan J, Chebotarov D, McNally KL, Deutsch EW, Vizcaíno JA, Jones AR. A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.17.567512. [PMID: 38014076 PMCID: PMC10680829 DOI: 10.1101/2023.11.17.567512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Phosphorylation is the most studied post-translational modification, and has multiple biological functions. In this study, we have re-analysed publicly available mass spectrometry proteomics datasets enriched for phosphopeptides from Asian rice (Oryza sativa). In total we identified 15,522 phosphosites on serine, threonine and tyrosine residues on rice proteins. We identified sequence motifs for phosphosites, and link motifs to enrichment of different biological processes, indicating different downstream regulation likely caused by different kinase groups. We cross-referenced phosphosites against the rice 3,000 genomes, to identify single amino acid variations (SAAVs) within or proximal to phosphosites that could cause loss of a site in a given rice variety. The data was clustered to identify groups of sites with similar patterns across rice family groups, for example those highly conserved in Japonica, but mostly absent in Aus type rice varieties - known to have different responses to drought. These resources can assist rice researchers to discover alleles with significantly different functional effects across rice varieties. The data has been loaded into UniProt Knowledge-Base - enabling researchers to visualise sites alongside other data on rice proteins e.g. structural models from AlphaFold2, PeptideAtlas and the PRIDE database - enabling visualisation of source evidence, including scores and supporting mass spectra.
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Affiliation(s)
- Kerry A Ramsbottom
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7BE, United Kingdom
| | - Ananth Prakash
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Yasset Perez Riverol
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Oscar Martin Camacho
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7BE, United Kingdom
| | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Deepti J. Kundu
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Emily Bowler-Barnett
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Maria Martin
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Jun Fan
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Dmytro Chebotarov
- International Rice Research Institute, DAPO 7777, Manila 1301, Philippines
| | - Kenneth L McNally
- International Rice Research Institute, DAPO 7777, Manila 1301, Philippines
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Andrew R Jones
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7BE, United Kingdom
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Wang G, Gao G, Yang X, Yang X, Ma P. Casein kinase CK2 structure and activities in plants. JOURNAL OF PLANT PHYSIOLOGY 2022; 276:153767. [PMID: 35841742 DOI: 10.1016/j.jplph.2022.153767] [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: 04/26/2022] [Revised: 07/10/2022] [Accepted: 07/10/2022] [Indexed: 06/15/2023]
Abstract
Casein kinase CK2 is a highly conserved serine/threonine protein kinase and exists in all eukaryotes. It has been demonstrated to be widely involved in the biological processes of plants. The CK2 holoenzyme is a heterotetramer consisting of two catalytic subunits (α and/or α') and two regulatory subunits (β). CK2 in plants is generally encoded by multiple genes, with monomeric and oligomeric forms present in the tissue. Various subunit genes of CK2 have been cloned and characterized from Arabidopsis thaliana, tobacco, maize, wheat, tomato, and other plants. This paper reviews the structural features of CK2, provides a clear classification of its physiological functions and mechanisms of action, and elaborates on the regulation of CK2 activity to provide a knowledge base for subsequent studies of CK2 in plants.
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Affiliation(s)
- Guanfeng Wang
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Geling Gao
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Xiangna Yang
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Xiangdong Yang
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
| | - Pengda Ma
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China.
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4
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Jonwal S, Verma N, Sinha AK. Regulation of photosynthetic light reaction proteins via reversible phosphorylation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 321:111312. [PMID: 35696912 DOI: 10.1016/j.plantsci.2022.111312] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/10/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
The regulation of photosynthesis occurs at different levels including the control of nuclear and plastid genes transcription, RNA processing and translation, protein translocation, assemblies and their post translational modifications. Out of all these, post translational modification enables rapid response of plants towards changing environmental conditions. Among all post-translational modifications, reversible phosphorylation is known to play a crucial role in the regulation of light reaction of photosynthesis. Although, phosphorylation of PS II subunits has been extensively studied but not much attention is given to other photosynthetic complexes such as PS I, Cytochrome b6f complex and ATP synthase. Phosphorylation reaction is known to protect photosynthetic apparatus in challenging environment conditions such as high light, elevated temperature, high salinity and drought. Recent studies have explored the role of photosynthetic protein phosphorylation in conferring plant immunity against the rice blast disease. The evolution of phosphorylation of different subunits of photosynthetic proteins occurred along with the evolution of plant lineage for their better adaptation to the changing environment conditions. In this review, we summarize the progress made in the research field of phosphorylation of photosynthetic proteins and highlights the missing links that need immediate attention.
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Affiliation(s)
- Sarvesh Jonwal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Neetu Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Alok Krishna Sinha
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Xie X, Yan Y, Liu T, Chen J, Huang M, Wang L, Chen M, Li X. Data-independent acquisition proteomic analysis of biochemical factors in rice seedlings following treatment with chitosan oligosaccharides. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 170:104681. [PMID: 32980063 DOI: 10.1016/j.pestbp.2020.104681] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 08/01/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
Chitosan oligosaccharides (COS) can elicit plant immunity and defence responses in rice plants, but exactly how this promotes plant growth remains largely unknown. Herein, we explored the effects of 0.5 mg/L COS on plant growth promotion in rice seedlings by measuring root and stem length, investigating biochemical factors in whole plants via proteomic analysis, and confirming upregulated and downregulated genes by real-time quantitative PCR. Pathway enrichment results showed that COS promoted root and stem growth, and stimulated metabolic (biosynthetic and catabolic processes) and photosynthesis in rice plants during the seedling stage. Expression levels of genes related to chlorophyll a-b binding, RNA binding, catabolic processes and calcium ion binding were upregulated following COS treatment. Furthermore, comparative analysis indicated that numerous proteins involved in the biosynthesis, metabolic (catabolic) processes and photosynthesis pathways were upregulated. The findings indicate that COS may upregulate calcium ion binding, photosynthesis, RNA binding, and catabolism proteins associated with plant growth during the rice seedling stage.
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Affiliation(s)
- Xin Xie
- College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Yunlong Yan
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China; College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Tao Liu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Jun Chen
- College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Maoxi Huang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Li Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China; College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Meiqing Chen
- College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Xiangyang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China; College of Agriculture, Guizhou University, Guiyang 550025, PR China.
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6
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Song W, Tang F, Cai W, Zhang Q, Zhou F, Ning M, Tian H, Shan C. iTRAQ-based quantitative proteomics analysis of cantaloupe (Cucumis melo var. saccharinus) after cold storage. BMC Genomics 2020; 21:390. [PMID: 32493266 PMCID: PMC7268308 DOI: 10.1186/s12864-020-06797-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/26/2020] [Indexed: 12/25/2022] Open
Abstract
Background Cantaloupe is susceptible to cold stress when it is stored at low temperatures, resulting in the loss of edible and commercial quality. To ascertain the molecular mechanisms of low temperatures resistance in cantaloupe, a cold-sensitive cultivar, Golden Empress-308 (GE) and a cold-tolerant cultivar, Jia Shi-310 (JS), were selected in parallel for iTRAQ quantitative proteomic analysis. Results The two kinds of commercial cultivars were exposed to a temperature of 0.5 °C for 0, 12 and 24 days. We found that the cold-sensitive cultivar (GE) suffered more severe damage as the length of the cold treatment increased. Proteomic analysis of both cultivars indicated that the number of differentially expressed proteins (DEPs) changed remarkably during the chilly treatment. JS expressed cold-responsive proteins more rapidly and mobilized more groups of proteins than GE. Furthermore, metabolic analysis revealed that more amino acids were up-regulated in JS during the early phases of low temperatures stress. The DEPs we found were mainly related to carbohydrate and energy metabolism, structural proteins, reactive oxygen species scavenging, amino acids metabolism and signal transduction. The consequences of phenotype assays, metabolic analysis and q-PCR validation confirm the findings of the iTRAQ analysis. Conclusion We found that the prompt response and mobilization of proteins in JS allowed it to maintain a higher level of cold tolerance than GE, and that the slower cold responses in GE may be a vital reason for the severe chilling injury commonly found in this cultivar. The candidate proteins we identified will form the basis of future studies and may improve our understanding of the mechanisms of cold tolerance in cantaloupe.
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Affiliation(s)
- Wen Song
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Fengxian Tang
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Wenchao Cai
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Qin Zhang
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Fake Zhou
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Ming Ning
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Huan Tian
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Chunhui Shan
- College of Food, Shihezi University, Xinjiang, 832000, China.
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A Systematic View Exploring the Role of Chloroplasts in Plant Abiotic Stress Responses. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6534745. [PMID: 31396532 PMCID: PMC6668530 DOI: 10.1155/2019/6534745] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 11/18/2022]
Abstract
Chloroplasts are intracellular semiautonomous organelles central to photosynthesis and are essential for plant growth and yield. The significance of the function of chloroplast-related genes in response to climate change has not been well studied in crops. In the present study, the initial focus was on genes that were predicted to be located in the chloroplast genome in rice, a model crop plant, with genes either preferentially expressed in the leaf or ubiquitously expressed in all organs. The characteristics were analyzed by Gene Ontology (GO) enrichment and MapMan functional classification tools. It was then identified that 110 GO terms (45 for leaf expression and 65 for ubiquitous expression) and 1,695 genes mapped to MapMan overviews were strongly associated with chloroplasts. In particular, the MapMan cellular response overview revealed a close association between heat stress response and chloroplast-related genes in rice. Moreover, features of these genes in response to abiotic stress were analyzed using a large-scale publicly available transcript dataset. Consequently, the expression of 215 genes was found to be upregulated in response to high temperature stress. Conversely, genes that responded to other stresses were extremely limited. In other words, chloroplast-related genes were found to affect abiotic stress response mainly through high temperature response, with little effect on response to drought and salinity stress. These results suggest that genes involved in diurnal rhythm in the leaves participate in the reaction to recognize temperature changes in the environment. Furthermore, the predicted protein–protein interaction network analysis associated with high temperature stress is expected to provide a very important basis for the study of molecular mechanisms by which chloroplasts will respond to future climate changes.
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Yu QB, Zhao TT, Ye LS, Cheng L, Wu YQ, Huang C, Yang ZN. pTAC10, an S1-domain-containing component of the transcriptionally active chromosome complex, is essential for plastid gene expression in Arabidopsis thaliana and is phosphorylated by chloroplast-targeted casein kinase II. PHOTOSYNTHESIS RESEARCH 2018; 137:69-83. [PMID: 29330702 DOI: 10.1007/s11120-018-0479-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 12/28/2017] [Indexed: 06/07/2023]
Abstract
In higher plant chloroplasts, the plastid-encoded RNA polymerase (PEP) consists of four catalytic subunits and numerous nuclear-encoded accessory proteins, including pTAC10, an S1-domain-containing protein. In this study, pTAC10 knockout lines were characterized. Two ptac10 mutants had an albino phenotype and severely impaired chloroplast development. The pTAC10 genomic sequence fused to a four-tandem MYC tag driven by its own promoter functionally complemented the ptac10-1 mutant phenotype. pTAC10 was present in both the chloroplast stroma and thylakoids. Two-dimensional blue native polyacrylamide gel electrophoresis (BN-PAGE), and immunoblotting assays showed that pTAC10:MYC co-migrates with one of the PEP core subunits, RpoB. A comprehensive investigation of the plastid gene expression profiles by quantitative RT-PCR revealed that, compared with wild-type plants, the abundance of PEP-dependent plastid transcripts is severely decreased in the ptac10-1 mutant, while the amount of plastid transcripts exclusively transcribed by NEP either barely changes or even increases. RNA blot analysis confirmed that PEP-dependent chloroplast transcripts, including psaB, psbA and rbcL, substantially decrease in the ptac10-1 mutant. Immunoblotting showed reduced accumulation of most chloroplast proteins in the ptac10 mutants. These data indicate the essential role of pTAC10 in plastid gene expression and plastid development. pTAC10 interacts with chloroplast-targeted casein kinase 2 (cpCK2) in vitro and in vivo and can be phosphorylated by Arabidopsis cpCK2 in vitro at sites Ser95, Ser396 and Ser434. RNA-EMSA assays showed that pTAC10 is able to bind to the psbA, atpE and accD transcripts, suggesting a non-specific RNA-binding activity of pTAC10. The RNA affinity of pTAC10 was enhanced by phosphorylation and decreased by the amino acid substitution Ser434-Ala of pTAC10. These data show that pTAC10 is essential for plastid gene expression in Arabidopsis and that it can be phosphorylated by cpCK2.
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Affiliation(s)
- Qing-Bo Yu
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Tuan-Tuan Zhao
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Lin-Shan Ye
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Ling Cheng
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Ying-Qian Wu
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Chao Huang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhong-Nan Yang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China.
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9
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White-Gloria C, Johnson JJ, Marritt K, Kataya A, Vahab A, Moorhead GB. Protein Kinases and Phosphatases of the Plastid and Their Potential Role in Starch Metabolism. FRONTIERS IN PLANT SCIENCE 2018; 9:1032. [PMID: 30065742 PMCID: PMC6056723 DOI: 10.3389/fpls.2018.01032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/25/2018] [Indexed: 05/03/2023]
Abstract
Phospho-proteomic studies have confirmed that phosphorylation is a common mechanism to regulate protein function in the chloroplast, including the enzymes of starch metabolism. In addition to the photosynthetic machinery protein kinases (STN7 and STN8) and their cognate protein phosphatases PPH1 (TAP38) and PBCP, multiple other protein kinases and phosphatases have now been localized to the chloroplast. Here, we build a framework for understanding protein kinases and phosphatases, their regulation, and potential roles in starch metabolism. We also catalog mapped phosphorylation sites on proteins of chloroplast starch metabolism to illustrate the potential and mostly unknown roles of protein phosphorylation in the regulation of starch biology.
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Affiliation(s)
- Chris White-Gloria
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Jayde J. Johnson
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Kayla Marritt
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Amr Kataya
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
- Department of Chemistry and Biosciences, University of Stavanger, Stavanger, Norway
| | - Ahmad Vahab
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Greg B. Moorhead
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
- *Correspondence: Greg B. Moorhead,
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Grieco M, Jain A, Ebersberger I, Teige M. An evolutionary view on thylakoid protein phosphorylation uncovers novel phosphorylation hotspots with potential functional implications. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3883-96. [PMID: 27117338 DOI: 10.1093/jxb/erw164] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The regulation of photosynthetic light reactions by reversible protein phosphorylation is well established today, but functional studies have so far mostly been restricted to processes affecting light-harvesting complex II and the core proteins of photosystem II. Virtually no functional data are available on regulatory effects at the other photosynthetic complexes despite the identification of multiple phosphorylation sites. Therefore we summarize the available data from 50 published phospho-proteomics studies covering the main complexes involved in photosynthetic light reactions in the 'green lineage' (i.e. green algae and land plants) as well as its cyanobacterial counterparts. In addition, we performed an extensive orthologue search for the major photosynthetic thylakoid proteins in 41 sequenced genomes and generated sequence alignments to survey the phylogenetic distribution of phosphorylation sites and their evolutionary conservation from green algae to higher plants. We observed a number of uncharacterized phosphorylation hotspots at photosystem I and the ATP synthase with potential functional relevance as well as an unexpected divergence of phosphosites. Although technical limitations might account for a number of those differences, we think that many of these phosphosites have important functions. This is particularly important for mono- and dicot plants, where these sites might be involved in regulatory processes such as stress acclimation.
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Affiliation(s)
- Michele Grieco
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, A-1090 Vienna, Austria
| | - Arpit Jain
- Department for Applied Bioinformatics, Institute for Cell Biology and Neuroscience, Goethe University, Max-von-Laue Str. 13, D-60438 Frankfurt, Germany
| | - Ingo Ebersberger
- Department for Applied Bioinformatics, Institute for Cell Biology and Neuroscience, Goethe University, Max-von-Laue Str. 13, D-60438 Frankfurt, Germany Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Anlage 25, D-60325 Frankfurt, Germany
| | - Markus Teige
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, A-1090 Vienna, Austria
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11
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Lohscheider JN, Friso G, van Wijk KJ. Phosphorylation of plastoglobular proteins in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3975-84. [PMID: 26962209 PMCID: PMC4915526 DOI: 10.1093/jxb/erw091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plastoglobules (PGs) are plastid lipid-protein particles with a small specialized proteome and metabolome. Among the 30 core PG proteins are six proteins of the ancient ABC1 atypical kinase (ABC1K) family and their locations in an Arabidopsis mRNA-based co-expression network suggested central regulatory roles. To identify candidate ABC1K targets and a possible ABC1K hierarchical phosphorylation network within the chloroplast PG proteome, we searched Arabidopsis phosphoproteomics data from publicly available sources. Evaluation of underlying spectra and/or associated information was challenging for a variety of reasons, but supported pSer sites and a few pThr sites in nine PG proteins, including five FIBRILLINS. PG phosphorylation motifs are discussed in the context of possible responsible kinases. The challenges of collection and evaluation of published Arabidopsis phosphorylation data are discussed, illustrating the importance of deposition of all mass spectrometry data in well-organized repositories such as PRIDE and ProteomeXchange. This study provides a starting point for experimental testing of phosho-sites in PG proteins and also suggests that phosphoproteomics studies specifically designed toward the PG proteome and its ABC1K are needed to understand phosphorylation networks in these specialized particles.
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Affiliation(s)
- Jens N Lohscheider
- Section of Plant Biology, School of Integrated Plant Science (SIPS), Cornell University, Ithaca, NY 14853, USA
| | - Giulia Friso
- Section of Plant Biology, School of Integrated Plant Science (SIPS), Cornell University, Ithaca, NY 14853, USA
| | - Klaas J van Wijk
- Section of Plant Biology, School of Integrated Plant Science (SIPS), Cornell University, Ithaca, NY 14853, USA
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12
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Richter AS, Gartmann H, Fechler M, Rödiger A, Baginsky S, Grimm B. Identification of four plastid-localized protein kinases. FEBS Lett 2016; 590:1749-56. [PMID: 27214872 DOI: 10.1002/1873-3468.12223] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 12/16/2023]
Abstract
In chloroplasts, protein phosphorylation regulates important processes, including metabolism, photosynthesis, gene expression, and signaling. Because the hitherto known plastid protein kinases represent only a fraction of existing kinases, we aimed at the identification of novel plastid-localized protein kinases that potentially phosphorylate enzymes of the tetrapyrrole biosynthesis (TBS) pathway. We screened publicly available databases for proteins annotated as putative protein kinase family proteins with predicted chloroplast localization. Additionally, we analyzed chloroplast fractions which were separated by sucrose density gradient centrifugation by mass spectrometry. We identified four new candidates for protein kinases, which were confirmed to be plastid localized by expression of GFP-fusion proteins in tobacco leaves. A phosphorylation assay with the purified kinases confirmed the protein kinase activity for two of them.
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Affiliation(s)
- Andreas S Richter
- Humboldt Universität zu Berlin, Institute of Biology/Plant Physiology, Berlin, Germany
| | - Hans Gartmann
- Humboldt Universität zu Berlin, Institute of Biology/Plant Physiology, Berlin, Germany
| | - Mona Fechler
- Humboldt Universität zu Berlin, Institute of Biology/Plant Physiology, Berlin, Germany
| | - Anja Rödiger
- Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Sacha Baginsky
- Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Bernhard Grimm
- Humboldt Universität zu Berlin, Institute of Biology/Plant Physiology, Berlin, Germany
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13
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Baginsky S. Protein phosphorylation in chloroplasts - a survey of phosphorylation targets. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3873-82. [PMID: 26969742 DOI: 10.1093/jxb/erw098] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The development of new software tools, improved mass spectrometry equipment, a suite of optimized scan types, and better-quality phosphopeptide affinity capture have paved the way for an explosion of mass spectrometry data on phosphopeptides. Because phosphoproteomics achieves good sensitivity, most studies use complete cell extracts for phosphopeptide enrichment and identification without prior enrichment of proteins or subcellular compartments. As a consequence, the phosphoproteome of cell organelles often comes as a by-product from large-scale studies and is commonly assembled from these in meta-analyses. This review aims at providing some guidance on the limitations of meta-analyses that combine data from analyses with different scopes, reports on the current status of knowledge on chloroplast phosphorylation targets, provides initial insights into phosphorylation site conservation in different plant species, and highlights emerging information on the integration of gene expression with metabolism and photosynthesis by means of protein phosphorylation.
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Affiliation(s)
- Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany
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14
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Vélez-Bermúdez IC, Carretero-Paulet L, Legnaioli T, Ludevid D, Pagès M, Riera M. Novel CK2α and CK2β subunits in maize reveal functional diversification in subcellular localization and interaction capacity. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 235:58-69. [PMID: 25900566 DOI: 10.1016/j.plantsci.2015.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/06/2015] [Accepted: 03/07/2015] [Indexed: 05/17/2023]
Abstract
In plants, CK2α/β subunits are encoded by multigenic families. They assemble as heterotetrameric holoenzymes or remain as individual subunits and are usually located in distinct cell compartments. Here we revise the number of maize CK2α/β genes, bringing them up to a total of eight (four CK2α catalytic and four CK2β regulatory subunits). We characterize CK2β4, which presents nuclear localization and interacts with CK2α1, CK2α3, CK2β1, and CK2β3. We also describe two CK2α isoforms (CK2α2 and CK2α4) containing N-terminal extensions that correspond to putative cTPs (chloroplast transit peptides). These cTPs are functional and responsible for the subcellular localization of CK2α2 and CK2α4 in chloroplasts. Phylogenetic analysis of the CK2α gene family, further supported by the gene structure and architecture of conserved protein domains, reveals the evolutionary expansion and diversification of this family. The subcellular localization of all four CK2α isoforms was found to be altered when were co-expressed with CK2β, thereby pointing to the latter as regulators of CK2α localization.
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Affiliation(s)
- I C Vélez-Bermúdez
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Campus UAB - Edifici CRAG, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - L Carretero-Paulet
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Campus UAB - Edifici CRAG, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - T Legnaioli
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Campus UAB - Edifici CRAG, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - D Ludevid
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Campus UAB - Edifici CRAG, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - M Pagès
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Campus UAB - Edifici CRAG, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - M Riera
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Campus UAB - Edifici CRAG, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain.
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