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Angeleri M, Muth-Pawlak D, Aro EM, Battchikova N. Study of O-Phosphorylation Sites in Proteins Involved in Photosynthesis-Related Processes in Synechocystis sp. Strain PCC 6803: Application of the SRM Approach. J Proteome Res 2016; 15:4638-4652. [DOI: 10.1021/acs.jproteome.6b00732] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Martina Angeleri
- Molecular Plant Biology,
Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Dorota Muth-Pawlak
- Molecular Plant Biology,
Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Eva-Mari Aro
- Molecular Plant Biology,
Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Natalia Battchikova
- Molecular Plant Biology,
Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
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52
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Quantitative proteomics and phosphoproteomics of sugar beet monosomic addition line M14 in response to salt stress. J Proteomics 2016; 143:286-297. [PMID: 27233743 DOI: 10.1016/j.jprot.2016.04.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/21/2016] [Accepted: 04/11/2016] [Indexed: 12/18/2022]
Abstract
UNLABELLED Salinity is a major abiotic stress affecting plant growth, development and agriculture productivity. Understanding the molecular mechanisms of salt stress tolerance will provide valuable information for effective crop engineering and breeding. Sugar beet monosomic addition line M14 obtained from the intercross between Beta vulgaris L. and Beta corolliflora Zoss exhibits tolerance to salt stress. In this study, the changes in the M14 proteome and phosphoproteome induced by salt stress were analyzed. We report the characteristics of the M14 plants under 0, 200, and 400mM NaCl using label-free quantitative proteomics approaches. Protein samples were subjected to total proteome profiling using LC-MS/MS and phosphopeptide enrichment to identify phosphopeptides and phosphoproteins. A total of 2182 proteins were identified and 114 proteins showed differential levels under salt stress. Interestingly, 189 phosphoproteins exhibited significant changes at the phosphorylation level under salt stress. Several signaling components associated with salt stress were found, e.g. 14-3-3 and mitogen-activated protein kinases (MAPK). Fifteen differential phosphoproteins and proteins involved in signal transduction were tested at the transcriptional level. The results revealed the short-term salt responsive mechanisms of the special sugar beet M14 line using label-free quantitative phosphoproteomics. BIOLOGICAL SIGNIFICANCE Sugar beet monosomic addition line M14 is a special germplasm with salt stress tolerance. Analysis of the M14 proteome and phosphoproteome under salt stress has provided insight into specific response mechanisms underlying salt stress tolerance. Reversible protein phosphorylation regulates a wide range of cellular processes such as transmembrane signaling, intracellular amplification of signals, and cell-cycle control. This study has identified significantly changed proteins and phosphoproteins, and determined their potential relevance to salt stress response. The knowledge gained can be potentially applied to improving crop salt tolerance.
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Kim SY, Bender KW, Walker BJ, Zielinski RE, Spalding MH, Ort DR, Huber SC. The Plastid Casein Kinase 2 Phosphorylates Rubisco Activase at the Thr-78 Site but Is Not Essential for Regulation of Rubisco Activation State. FRONTIERS IN PLANT SCIENCE 2016; 7:404. [PMID: 27064346 PMCID: PMC4814456 DOI: 10.3389/fpls.2016.00404] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/16/2016] [Indexed: 05/05/2023]
Abstract
Rubisco activase (RCA) is essential for the activation of Rubisco, the carboxylating enzyme of photosynthesis. In Arabidopsis, RCA is composed of a large RCAα and small RCAβ isoform that are formed by alternative splicing of a single gene (At2g39730). The activity of Rubisco is controlled in response to changes in irradiance by regulation of RCA activity, which is known to involve a redox-sensitive disulfide bond located in the carboxy-terminal extension of the RCAα subunit. Additionally, phosphorylation of RCA threonine-78 (Thr-78) has been reported to occur in the dark suggesting that phosphorylation may also be associated with dark-inactivation of RCA and deactivation of Rubisco. In the present study, we developed site-specific antibodies to monitor phosphorylation of RCA at the Thr-78 site and used non-reducing SDS-PAGE to monitor the redox status of the RCAα subunit. By immunoblotting, phosphorylation of both RCA isoforms occurred at low light and in the dark and feeding peroxide or DTT to leaf segments indicated that redox status of the chloroplast stroma was a critical factor controlling RCA phosphorylation. Use of a knockout mutant identified the plastid-targeted casein kinase 2 (cpCK2α) as the major protein kinase involved in RCA phosphorylation. Studies with recombinant cpCK2α and synthetic peptide substrates identified acidic residues at the -1, +2, and +3 positions surrounding Thr-78 as strong positive recognition elements. The cpck2 knockout mutant had strongly reduced phosphorylation at the Thr-78 site but was similar to wild type plants in terms of induction kinetics of photosynthesis following transfer from darkness or low light to high light, suggesting that if phosphorylation of RCA Thr-78 plays a direct role it would be redundant to redox regulation for control of Rubisco activation state under normal conditions.
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Affiliation(s)
- Sang Y. Kim
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture – Agricultural Research Service, UrbanaIL, USA
- Plant Biology, University of Illinois at Champaign–Urbana, UrbanaIL, USA
| | - Kyle W. Bender
- Plant Biology, University of Illinois at Champaign–Urbana, UrbanaIL, USA
| | - Berkley J. Walker
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture – Agricultural Research Service, UrbanaIL, USA
- Carl R. Woese Institute for Genomic Biology, UrbanaIL, USA
| | | | - Martin H. Spalding
- Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
| | - Donald R. Ort
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture – Agricultural Research Service, UrbanaIL, USA
- Plant Biology, University of Illinois at Champaign–Urbana, UrbanaIL, USA
- Carl R. Woese Institute for Genomic Biology, UrbanaIL, USA
| | - Steven C. Huber
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture – Agricultural Research Service, UrbanaIL, USA
- Plant Biology, University of Illinois at Champaign–Urbana, UrbanaIL, USA
- *Correspondence: Steven C. Huber,
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54
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Mattei B, Spinelli F, Pontiggia D, De Lorenzo G. Comprehensive Analysis of the Membrane Phosphoproteome Regulated by Oligogalacturonides in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2016; 7:1107. [PMID: 27532006 PMCID: PMC4969306 DOI: 10.3389/fpls.2016.01107] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 07/12/2016] [Indexed: 05/03/2023]
Abstract
Early changes in the Arabidopsis thaliana membrane phosphoproteome in response to oligogalacturonides (OGs), a class of plant damage-associated molecular patterns (DAMPs), were analyzed by two complementary proteomic approaches. Differentially phosphorylated sites were determined through phosphopeptide enrichment followed by LC-MS/MS using label-free quantification; differentially phosphorylated proteins were identified by 2D-DIGE combined with phospho-specific fluorescent staining (phospho-DIGE). This large-scale phosphoproteome analysis of early OG-signaling enabled us to determine 100 regulated phosphosites using LC-MS/MS and 46 differential spots corresponding to 34 pdhosphoproteins using phospho-DIGE. Functional classification showed that the OG-responsive phosphoproteins include kinases, phosphatases and receptor-like kinases, heat shock proteins (HSPs), reactive oxygen species (ROS) scavenging enzymes, proteins related to cellular trafficking, transport, defense and signaling as well as novel candidates for a role in immunity, for which elicitor-induced phosphorylation changes have not been shown before. A comparison with previously identified elicitor-regulated phosphosites shows only a very limited overlap, uncovering the immune-related regulation of 70 phosphorylation sites and revealing novel potential players in the regulation of elicitor-dependent immunity.
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55
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Kwon OK, Kim SJ, Lee YM, Lee YH, Bae YS, Kim JY, Peng X, Cheng Z, Zhao Y, Lee S. Global analysis of phosphoproteome dynamics in embryonic development of zebrafish (Danio rerio). Proteomics 2015; 16:136-49. [DOI: 10.1002/pmic.201500017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 09/04/2015] [Accepted: 10/01/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Oh Kwang Kwon
- College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu South Korea
| | - Sun Ju Kim
- College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu South Korea
| | - You-Mie Lee
- College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu South Korea
| | - Young-Hoon Lee
- School of Life Sciences, KNU Creative BioResearch Group (BK21 plus program); Kyungpook National University; Daegu Korea
| | - Young-Seuk Bae
- School of Life Sciences, KNU Creative BioResearch Group (BK21 plus program); Kyungpook National University; Daegu Korea
| | - Jin Young Kim
- Mass Spectrometry Research Center; Korea Basic Science Institute; Ochang Chungbuk Republic of Korea
| | - Xiaojun Peng
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd; Hangzhou P. R. China
| | - Zhongyi Cheng
- Advanced Institute of Translational Medicine; Tongji University; Shanghai P. R. China
| | - Yingming Zhao
- Ben May Department for Cancer Research; University of Chicago; Chicago IL USA
| | - Sangkyu Lee
- College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu South Korea
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56
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Kwon OK, Sim J, Kim SJ, Sung E, Kim JY, Jeong TC, Lee S. Comprehensive Analysis of in Vivo Phosphoproteome of Mouse Liver Microsomes. J Proteome Res 2015; 14:5215-24. [PMID: 26487105 DOI: 10.1021/acs.jproteome.5b00812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Protein phosphorylation at serine, threonine, and tyrosine residues are some of the most widespread reversible post-translational modifications. Microsomes are vesicle-like bodies, not ordinarily present within living cells, which form from pieces of the endoplasmic reticulum (ER), plasma membrane, mitochondria, or Golgi apparatus of broken eukaryotic cells. Here we investigated the total phosphoproteome of mouse liver microsomes (MLMs) using TiO2 enrichment of phosphopeptides coupled to on-line 2D-LC-MS/MS. In total, 699 phosphorylation sites in 527 proteins were identified in MLMs. When compared with the current phosphoSitePlus database, 155 novel phosphoproteins were identified in MLM. The distributions of phosphosites were 89.4, 8.0, and 2.6% for phosphoserine, phosphotheronine, and phosphotyrosine, respectively. By Motif-X analysis, eight Ser motifs and one Thr motif were found, and five acidic, two basophilic-, and two proline-directed motifs were assigned. The potential functions of phosphoproteins in MLM were assigned by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. In GO annotation, phosphorylated microsomal proteins were involved in mRNA processing, mRNA metabolic processes, and RNA splicing. In the KEGG pathway analysis, phosphorylated microsomal proteins were highly enriched in ribosome protein processing in ER and ribosomes and in RNA transport. Furthermore, we determined that 52 and 23 phosphoproteins were potential substrates of cAMP-dependent protein kinase A and casein kinase II, respectively, many of which are 40S/60S ribosomal proteins. Overall, our results provide an overview of features of protein phosphorylation in MLMs that should be a valuable resource for the future understanding of protein synthesis or translation involving phosphorylation.
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Affiliation(s)
- Oh Kwang Kwon
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University , Daegu 41566, Republic of Korea
| | - JuHee Sim
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University , Daegu 41566, Republic of Korea
| | - Sun Ju Kim
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University , Daegu 41566, Republic of Korea
| | - Eunji Sung
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University , Daegu 41566, Republic of Korea
| | - Jin Young Kim
- Mass Spectrometry Research Center, Korea Basic Science Institute , Ochang, Chungbuk 28115, Republic of Korea
| | - Tae Cheon Jeong
- College of Pharmacy, Yeungnam University , Gyeongsan 38541, Republic of Korea
| | - Sangkyu Lee
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University , Daegu 41566, Republic of Korea
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57
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Battchikova N, Angeleri M, Aro EM. Proteomic approaches in research of cyanobacterial photosynthesis. PHOTOSYNTHESIS RESEARCH 2015; 126:47-70. [PMID: 25359503 DOI: 10.1007/s11120-014-0050-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 10/18/2014] [Indexed: 05/03/2023]
Abstract
Oxygenic photosynthesis in cyanobacteria, algae, and plants is carried out by a fabulous pigment-protein machinery that is amazingly complicated in structure and function. Many different approaches have been undertaken to characterize the most important aspects of photosynthesis, and proteomics has become the essential component in this research. Here we describe various methods which have been used in proteomic research of cyanobacteria, and demonstrate how proteomics is implemented into on-going studies of photosynthesis in cyanobacterial cells.
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Affiliation(s)
- Natalia Battchikova
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland.
| | - Martina Angeleri
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland
| | - Eva-Mari Aro
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland
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58
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Lin LL, Hsu CL, Hu CW, Ko SY, Hsieh HL, Huang HC, Juan HF. Integrating Phosphoproteomics and Bioinformatics to Study Brassinosteroid-Regulated Phosphorylation Dynamics in Arabidopsis. BMC Genomics 2015; 16:533. [PMID: 26187819 PMCID: PMC4506601 DOI: 10.1186/s12864-015-1753-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 07/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Protein phosphorylation regulated by plant hormone is involved in the coordination of fundamental plant development. Brassinosteroids (BRs), a group of phytohormones, regulated phosphorylation dynamics remains to be delineated in plants. In this study, we performed a mass spectrometry (MS)-based phosphoproteomics to conduct a global and dynamic phosphoproteome profiling across five time points of BR treatment in the period between 5 min and 12 h. MS coupling with phosphopeptide enrichment techniques has become the powerful tool for profiling protein phosphorylation. However, MS-based methods tend to have data consistency and coverage issues. To address these issues, bioinformatics approaches were used to complement the non-detected proteins and recover the dynamics of phosphorylation events. RESULTS A total of 1104 unique phosphorylated peptides from 739 unique phosphoproteins were identified. The time-dependent gene ontology (GO) analysis shows the transition of biological processes from signaling transduction to morphogenesis and stress response. The protein-protein interaction analysis found that most of identified phosphoproteins have strongly connections with known BR signaling components. The analysis by using Motif-X was performed to identify 15 enriched motifs, 11 of which correspond to 6 known kinase families. To uncover the dynamic activities of kinases, the enriched motifs were combined with phosphorylation profiles and revealed that the substrates of casein kinase 2 and mitogen-activated protein kinase were significantly phosphorylated and dephosphorylated at initial time of BR treatment, respectively. The time-dependent kinase-substrate interaction networks were constructed and showed many substrates are the downstream of other signals, such as auxin and ABA signaling. While comparing BR responsive phosphoproteome and gene expression data, we found most of phosphorylation changes were not led by gene expression changes. Our results suggested many downstream proteins of BR signaling are induced by phosphorylation via various kinases, not through transcriptional regulation. CONCLUSIONS Through a large-scale dynamic profile of phosphoproteome coupled with bioinformatics, a complicated kinase-centered network related to BR-regulated growth was deciphered. The phosphoproteins and phosphosites identified in our study provide a useful dataset for revealing signaling networks of BR regulation, and also expanded our knowledge of protein phosphorylation modification in plants as well as further deal to solve the plant growth problems.
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Affiliation(s)
- Li-Ling Lin
- Department of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
| | - Chia-Lang Hsu
- Department of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
| | - Chia-Wei Hu
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
| | - Shiao-Yun Ko
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
| | - Hsu-Liang Hsieh
- Institute of Plant Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, No.155, Sec.2, Linong Street, Taipei, 112, Taiwan.
| | - Hsueh-Fen Juan
- Department of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan. .,Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan. .,Graduate Institute of Biomedical Electronic and Bioinformatics, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
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59
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Aryal UK, Ross ARS, Krochko JE. Enrichment and Analysis of Intact Phosphoproteins in Arabidopsis Seedlings. PLoS One 2015; 10:e0130763. [PMID: 26158488 PMCID: PMC4497735 DOI: 10.1371/journal.pone.0130763] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 05/23/2015] [Indexed: 12/19/2022] Open
Abstract
Protein phosphorylation regulates diverse cellular functions and plays a key role in the early development of plants. To complement and expand upon previous investigations of protein phosphorylation in Arabidopsis seedlings we used an alternative approach that combines protein extraction under non-denaturing conditions with immobilized metal-ion affinity chromatography (IMAC) enrichment of intact phosphoproteins in Rubisco-depleted extracts, followed by identification using two-dimensional gel electrophoresis (2-DE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). In-gel trypsin digestion and analysis of selected gel spots identified 144 phosphorylated peptides and residues, of which only18 phosphopeptides and 8 phosphosites were found in the PhosPhAt 4.0 and P3DB Arabidopsis thaliana phosphorylation site databases. More than half of the 82 identified phosphoproteins were involved in carbohydrate metabolism, photosynthesis/respiration or oxidative stress response mechanisms. Enrichment of intact phosphoproteins prior to 2-DE and LC-MS/MS appears to enhance detection of phosphorylated threonine and tyrosine residues compared with methods that utilize peptide-level enrichment, suggesting that the two approaches are somewhat complementary in terms of phosphorylation site coverage. Comparing results for young seedlings with those obtained previously for mature Arabidopsis leaves identified five proteins that are differentially phosphorylated in these tissues, demonstrating the potential of this technique for investigating the dynamics of protein phosphorylation during plant development.
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Affiliation(s)
- Uma K. Aryal
- National Research Council of Canada, Saskatoon, SK, S7N 0W9, Canada
| | - Andrew R. S. Ross
- National Research Council of Canada, Saskatoon, SK, S7N 0W9, Canada
- * E-mail:
| | - Joan E. Krochko
- National Research Council of Canada, Saskatoon, SK, S7N 0W9, Canada
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60
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Franck WL, Gokce E, Randall SM, Oh Y, Eyre A, Muddiman DC, Dean RA. Phosphoproteome Analysis Links Protein Phosphorylation to Cellular Remodeling and Metabolic Adaptation during Magnaporthe oryzae Appressorium Development. J Proteome Res 2015; 14:2408-24. [PMID: 25926025 PMCID: PMC4838196 DOI: 10.1021/pr501064q] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The rice pathogen, Magnaporthe oryzae, undergoes a complex developmental process leading to formation of an appressorium prior to plant infection. In an effort to better understand phosphoregulation during appressorium development, a mass spectrometry based phosphoproteomics study was undertaken. A total of 2924 class I phosphosites were identified from 1514 phosphoproteins from mycelia, conidia, germlings, and appressoria of the wild type and a protein kinase A (PKA) mutant. Phosphoregulation during appressorium development was observed for 448 phosphosites on 320 phosphoproteins. In addition, a set of candidate PKA targets was identified encompassing 253 phosphosites on 227 phosphoproteins. Network analysis incorporating regulation from transcriptomic, proteomic, and phosphoproteomic data revealed new insights into the regulation of the metabolism of conidial storage reserves and phospholipids, autophagy, actin dynamics, and cell wall metabolism during appressorium formation. In particular, protein phosphorylation appears to play a central role in the regulation of autophagic recycling and actin dynamics during appressorium formation. Changes in phosphorylation were observed in multiple components of the cell wall integrity pathway providing evidence that this pathway is highly active during appressorium development. Several transcription factors were phosphoregulated during appressorium formation including the bHLH domain transcription factor MGG_05709. Functional analysis of MGG_05709 provided further evidence for the role of protein phosphorylation in regulation of glycerol metabolism and the metabolic reprogramming characteristic of appressorium formation. The data presented here represent a comprehensive investigation of the M. oryzae phosphoproteome and provide key insights on the role of protein phosphorylation during infection-related development.
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Affiliation(s)
- William L. Franck
- Center for Integrated Fungal Research, North Carolina State University, Raleigh, North Carolina, 27606
| | - Emine Gokce
- W.M. Keck Fourier Transform-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27606
| | - Shan M. Randall
- W.M. Keck Fourier Transform-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27606
| | - Yeonyee Oh
- Center for Integrated Fungal Research, North Carolina State University, Raleigh, North Carolina, 27606
| | - Alex Eyre
- Center for Integrated Fungal Research, North Carolina State University, Raleigh, North Carolina, 27606
| | - David C. Muddiman
- W.M. Keck Fourier Transform-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27606
| | - Ralph A. Dean
- Center for Integrated Fungal Research, North Carolina State University, Raleigh, North Carolina, 27606
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61
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Bergner SV, Scholz M, Trompelt K, Barth J, Gäbelein P, Steinbeck J, Xue H, Clowez S, Fucile G, Goldschmidt-Clermont M, Fufezan C, Hippler M. STATE TRANSITION7-Dependent Phosphorylation Is Modulated by Changing Environmental Conditions, and Its Absence Triggers Remodeling of Photosynthetic Protein Complexes. PLANT PHYSIOLOGY 2015; 168:615-34. [PMID: 25858915 PMCID: PMC4453777 DOI: 10.1104/pp.15.00072] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/04/2015] [Indexed: 05/18/2023]
Abstract
In plants and algae, the serine/threonine kinase STN7/STT7, orthologous protein kinases in Chlamydomonas reinhardtii and Arabidopsis (Arabidopsis thaliana), respectively, is an important regulator in acclimation to changing light environments. In this work, we assessed STT7-dependent protein phosphorylation under high light in C. reinhardtii, known to fully induce the expression of light-harvesting complex stress-related protein3 (LHCSR3) and a nonphotochemical quenching mechanism, in relationship to anoxia where the activity of cyclic electron flow is stimulated. Our quantitative proteomics data revealed numerous unique STT7 protein substrates and STT7-dependent protein phosphorylation variations that were reliant on the environmental condition. These results indicate that STT7-dependent phosphorylation is modulated by the environment and point to an intricate chloroplast phosphorylation network responding in a highly sensitive and dynamic manner to environmental cues and alterations in kinase function. Functionally, the absence of the STT7 kinase triggered changes in protein expression and photoinhibition of photosystem I (PSI) and resulted in the remodeling of photosynthetic complexes. This remodeling initiated a pronounced association of LHCSR3 with PSI-light harvesting complex I (LHCI)-ferredoxin-NADPH oxidoreductase supercomplexes. Lack of STT7 kinase strongly diminished PSII-LHCII supercomplexes, while PSII core complex phosphorylation and accumulation were significantly enhanced. In conclusion, our study provides strong evidence that the regulation of protein phosphorylation is critical for driving successful acclimation to high light and anoxic growth environments and gives new insights into acclimation strategies to these environmental conditions.
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Affiliation(s)
- Sonja Verena Bergner
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Munster, Germany (S.V.B., M.S., K.T., J.B., P.G., J.S., H.X., C.F., M.H.);Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141 Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, 75005 Paris, France (S.C.); andDepartment of Botany and Plant Biology and Institute of Genetics and Genomics in Geneva, University of Geneva, CH-1211 Geneva 4, Switzerland (G.F., M.G.-C.)
| | - Martin Scholz
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Munster, Germany (S.V.B., M.S., K.T., J.B., P.G., J.S., H.X., C.F., M.H.);Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141 Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, 75005 Paris, France (S.C.); andDepartment of Botany and Plant Biology and Institute of Genetics and Genomics in Geneva, University of Geneva, CH-1211 Geneva 4, Switzerland (G.F., M.G.-C.)
| | - Kerstin Trompelt
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Munster, Germany (S.V.B., M.S., K.T., J.B., P.G., J.S., H.X., C.F., M.H.);Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141 Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, 75005 Paris, France (S.C.); andDepartment of Botany and Plant Biology and Institute of Genetics and Genomics in Geneva, University of Geneva, CH-1211 Geneva 4, Switzerland (G.F., M.G.-C.)
| | - Johannes Barth
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Munster, Germany (S.V.B., M.S., K.T., J.B., P.G., J.S., H.X., C.F., M.H.);Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141 Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, 75005 Paris, France (S.C.); andDepartment of Botany and Plant Biology and Institute of Genetics and Genomics in Geneva, University of Geneva, CH-1211 Geneva 4, Switzerland (G.F., M.G.-C.)
| | - Philipp Gäbelein
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Munster, Germany (S.V.B., M.S., K.T., J.B., P.G., J.S., H.X., C.F., M.H.);Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141 Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, 75005 Paris, France (S.C.); andDepartment of Botany and Plant Biology and Institute of Genetics and Genomics in Geneva, University of Geneva, CH-1211 Geneva 4, Switzerland (G.F., M.G.-C.)
| | - Janina Steinbeck
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Munster, Germany (S.V.B., M.S., K.T., J.B., P.G., J.S., H.X., C.F., M.H.);Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141 Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, 75005 Paris, France (S.C.); andDepartment of Botany and Plant Biology and Institute of Genetics and Genomics in Geneva, University of Geneva, CH-1211 Geneva 4, Switzerland (G.F., M.G.-C.)
| | - Huidan Xue
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Munster, Germany (S.V.B., M.S., K.T., J.B., P.G., J.S., H.X., C.F., M.H.);Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141 Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, 75005 Paris, France (S.C.); andDepartment of Botany and Plant Biology and Institute of Genetics and Genomics in Geneva, University of Geneva, CH-1211 Geneva 4, Switzerland (G.F., M.G.-C.)
| | - Sophie Clowez
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Munster, Germany (S.V.B., M.S., K.T., J.B., P.G., J.S., H.X., C.F., M.H.);Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141 Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, 75005 Paris, France (S.C.); andDepartment of Botany and Plant Biology and Institute of Genetics and Genomics in Geneva, University of Geneva, CH-1211 Geneva 4, Switzerland (G.F., M.G.-C.)
| | - Geoffrey Fucile
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Munster, Germany (S.V.B., M.S., K.T., J.B., P.G., J.S., H.X., C.F., M.H.);Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141 Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, 75005 Paris, France (S.C.); andDepartment of Botany and Plant Biology and Institute of Genetics and Genomics in Geneva, University of Geneva, CH-1211 Geneva 4, Switzerland (G.F., M.G.-C.)
| | - Michel Goldschmidt-Clermont
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Munster, Germany (S.V.B., M.S., K.T., J.B., P.G., J.S., H.X., C.F., M.H.);Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141 Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, 75005 Paris, France (S.C.); andDepartment of Botany and Plant Biology and Institute of Genetics and Genomics in Geneva, University of Geneva, CH-1211 Geneva 4, Switzerland (G.F., M.G.-C.)
| | - Christian Fufezan
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Munster, Germany (S.V.B., M.S., K.T., J.B., P.G., J.S., H.X., C.F., M.H.);Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141 Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, 75005 Paris, France (S.C.); andDepartment of Botany and Plant Biology and Institute of Genetics and Genomics in Geneva, University of Geneva, CH-1211 Geneva 4, Switzerland (G.F., M.G.-C.)
| | - Michael Hippler
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Munster, Germany (S.V.B., M.S., K.T., J.B., P.G., J.S., H.X., C.F., M.H.);Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141 Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, 75005 Paris, France (S.C.); andDepartment of Botany and Plant Biology and Institute of Genetics and Genomics in Geneva, University of Geneva, CH-1211 Geneva 4, Switzerland (G.F., M.G.-C.)
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Phosphoproteomic analysis of the highly-metastatic hepatocellular carcinoma cell line, MHCC97-H. Int J Mol Sci 2015; 16:4209-25. [PMID: 25690035 PMCID: PMC4346953 DOI: 10.3390/ijms16024209] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/03/2015] [Accepted: 02/03/2015] [Indexed: 11/29/2022] Open
Abstract
Invasion and metastasis of hepatocellular carcinoma (HCC) is a major cause for lethal liver cancer. Signaling pathways associated with cancer progression are frequently reconfigured by aberrant phosphorylation of key proteins. To capture the key phosphorylation events in HCC metastasis, we established a methodology by an off-line high-pH HPLC separation strategy combined with multi-step IMAC and LC–MS/MS to study the phosphoproteome of a metastatic HCC cell line, MHCC97-H (high metastasis). In total, 6593 phosphopeptides with 6420 phosphorylation sites (p-sites) of 2930 phosphoproteins were identified. Statistical analysis of gene ontology (GO) categories for the identified phosphoproteins showed that several of the biological processes, such as transcriptional regulation, mRNA processing and RNA splicing, were over-represented. Further analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations demonstrated that phosphoproteins in multiple pathways, such as spliceosome, the insulin signaling pathway and the cell cycle, were significantly enriched. In particular, we compared our dataset with a previously published phosphoproteome in a normal liver sample, and the results revealed that a number of proteins in the spliceosome pathway, such as U2 small nuclear RNA Auxiliary Factor 2 (U2AF2), Eukaryotic Initiation Factor 4A-III (EIF4A3), Cell Division Cycle 5-Like (CDC5L) and Survival Motor Neuron Domain Containing 1 (SMNDC1), were exclusively identified as phosphoproteins only in the MHCC97-H cell line. These results indicated that the phosphorylation of spliceosome proteins may participate in the metastasis of HCC by regulating mRNA processing and RNA splicing.
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Li J, Silva-Sanchez C, Zhang T, Chen S, Li H. Phosphoproteomics technologies and applications in plant biology research. FRONTIERS IN PLANT SCIENCE 2015; 6:430. [PMID: 26136758 PMCID: PMC4468387 DOI: 10.3389/fpls.2015.00430] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/27/2015] [Indexed: 05/20/2023]
Abstract
Protein phosphorylation has long been recognized as an essential mechanism to regulate many important processes of plant life. However, studies on phosphorylation mediated signaling events in plants are challenged with low stoichiometry and dynamic nature of phosphorylated proteins. Significant advances in mass spectrometry based phosphoproteomics have taken place in recent decade, including phosphoprotein/phosphopeptide enrichment, detection and quantification, and phosphorylation site localization. This review describes a variety of separation and enrichment methods for phosphoproteins and phosphopeptides, the applications of technological innovations in plant phosphoproteomics, and highlights significant achievement of phosphoproteomics in the areas of plant signal transduction, growth and development.
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Affiliation(s)
- Jinna Li
- College of Life Sciences, Heilongjiang UniversityHarbin, China
| | - Cecilia Silva-Sanchez
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of FloridaGainesville, FL, USA
| | - Tong Zhang
- Plant Molecular and Cellular Biology Program, Department of Biology, UF Genetics Institute, University of FloridaGainesville, FL, USA
| | - Sixue Chen
- College of Life Sciences, Heilongjiang UniversityHarbin, China
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of FloridaGainesville, FL, USA
- Plant Molecular and Cellular Biology Program, Department of Biology, UF Genetics Institute, University of FloridaGainesville, FL, USA
| | - Haiying Li
- College of Life Sciences, Heilongjiang UniversityHarbin, China
- *Correspondence: Haiying Li, College of Life Sciences, Heilongjiang University, 74 Xuefu Rd, Harbin 150080, China
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Abstract
Mitochondria are highly dynamic organelles that are continuously shaped by the antagonistic fission and fusion processes. The major machineries of mitochondrial fission and fusion, as well as mechanisms that regulate the function of key players in these processes have been analyzed in different experimental systems. In plants however, the mitochondrial fusion machinery is still largely unknown, and the regulatory mechanisms of the fission machinery are just beginning to be elucidated. This review focuses on the molecular mechanisms underlying plant mitochondrial dynamics and regulation of some of the key factors, especially the roles of membrane lipids such as cardiolipin.
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Affiliation(s)
- Ronghui Pan
- Department of Energy Plant Research Laboratory; Michigan State University; East Lansing, MI USA
- Department of Biochemistry and Molecular Biology; Michigan State University; East Lansing, MI USA
| | - Jianping Hu
- Department of Energy Plant Research Laboratory; Michigan State University; East Lansing, MI USA
- Department of Plant Biology; Michigan State University; East Lansing, MI USA
- Correspondence to: Jianping Hu;
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Cheng H, Deng W, Wang Y, Ren J, Liu Z, Xue Y. dbPPT: a comprehensive database of protein phosphorylation in plants. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau121. [PMID: 25534750 PMCID: PMC4273206 DOI: 10.1093/database/bau121] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
As one of the most important protein post-translational modifications, the reversible phosphorylation is critical for plants in regulating a variety of biological processes such as cellular metabolism, signal transduction and responses to environmental stress. Numerous efforts especially large-scale phosphoproteome profiling studies have been contributed to dissect the phosphorylation signaling in various plants, while a large number of phosphorylation events were identified. To provide an integrated data resource for further investigations, here we present a comprehensive database of dbPPT (database of Phosphorylation site in PlanTs, at http://dbppt.biocuckoo.org), which contains experimentally identified phosphorylation sites in proteins from plants. The phosphorylation sites in dbPPT were manually curated from the literatures, whereas datasets in other public databases were also integrated. In total, there were 82 175 phosphorylation sites in 31 012 proteins from 20 plant organisms in dbPPT, presenting a larger quantity of phosphorylation sites and a higher coverage of plant species in comparison with other databases. The proportions of residue types including serine, threonine and tyrosine were 77.99, 17.81 and 4.20%, respectively. All the phosphoproteins and phosphorylation sites in the database were critically annotated. Since the phosphorylation signaling in plants attracted great attention recently, such a comprehensive resource of plant protein phosphorylation can be useful for the research community. Database URL:http://dbppt.biocuckoo.org
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Affiliation(s)
- Han Cheng
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Wankun Deng
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Yongbo Wang
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Jian Ren
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Zexian Liu
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Yu Xue
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
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Gao J, van Kleeff PJM, Oecking C, Li KW, Erban A, Kopka J, Hincha DK, de Boer AH. Light modulated activity of root alkaline/neutral invertase involves the interaction with 14-3-3 proteins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:785-96. [PMID: 25256212 DOI: 10.1111/tpj.12677] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/04/2014] [Accepted: 09/10/2014] [Indexed: 05/17/2023]
Abstract
Alkaline/neutral invertases (A/N-Invs) are now recognized as essential proteins in plant life. They catalyze the irreversible breakdown of sucrose into glucose and fructose and thus supply the cells with energy as well as signaling molecules. In this study we report on a mechanism that affects the activity of the cytosolic invertase AtCINV1 (At-A/N-InvG or AT1G35580). We demonstrate that Ser547 at the extreme C-terminus of the AtCINV1 protein is a substrate of calcium-dependent kinases (CPK3 and 21) and that phosphorylation creates a high-affinity binding site for 14-3-3 proteins. The invertase as such has basal activity, but we provide evidence that interaction with 14-3-3 proteins enhances its activity. The analysis of three quadruple 14-3-3 mutants generated from six T-DNA insertion mutants of the non-epsilon family shows both specificity as well as redundancy for this function of 14-3-3 proteins. The strong reduction in hexose levels in the roots of one 14-3-3 quadruple mutant plant is in line with the activating function of 14-3-3 proteins. The physiological relevance of this mechanism that affects A/N-invertase activity is underscored by the light-induced activation and is another example of the central role of 14-3-3 proteins in mediating dark/light signaling. The nature of the light-induced signal that travels from the shoot to root and the question whether this signal is transmitted via cytosolic Ca(++) changes that activate calcium-dependent kinases, await further study.
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Affiliation(s)
- Jing Gao
- Department of Structural Biology, Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
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Wang K, Zhao Y, Li M, Gao F, Yang MK, Wang X, Li S, Yang P. Analysis of phosphoproteome in rice pistil. Proteomics 2014; 14:2319-34. [PMID: 25074045 DOI: 10.1002/pmic.201400004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 06/19/2014] [Accepted: 07/28/2014] [Indexed: 11/07/2022]
Abstract
As the female reproductive part of a flower, the pistil consists of the ovary, style, and stigma, and is a critical organ for the process from pollen recognition to fertilization and seed formation. Previous studies on pollen-pistil interaction mainly focused on gene expression changes with comparative transcriptomics or proteomics method. However, studies on protein PTMs are still lacking. Here we report a phosphoproteomic study on mature pistil of rice. Using IMAC enrichment, hydrophilic interaction chromatography fraction and high-accuracy MS instrument (TripleTOF 5600), 2347 of high-confidence (Ascore ≥ 19, p ≤ 0.01), phosphorylation sites corresponding to 1588 phosphoproteins were identified. Among them, 1369 phosphorylation sites within 654 phosphoproteins were newly identified; 41 serine phosphorylation motifs, which belong to three groups: proline-directed, basophilic, and acidic motifs were identified after analysis by motif-X. Two hundred and one genes whose phosphopeptides were identified here showed tissue-specific expression in pistil based on information mining of previous microarray data. All MS data have been deposited in the ProteomeXchange with identifier PXD000923 (http://proteomecentral.proteomexchange.org/dataset/PXD000923). This study will help us to understand pistil development and pollination on the posttranslational level.
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Affiliation(s)
- Kun Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan, P. R. China
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Zhang M, Ma CY, Lv DW, Zhen SM, Li XH, Yan YM. Comparative phosphoproteome analysis of the developing grains in bread wheat (Triticum aestivum L.) under well-watered and water-deficit conditions. J Proteome Res 2014; 13:4281-97. [PMID: 25145454 DOI: 10.1021/pr500400t] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Wheat (Triticum aestivum), one of the most important cereal crops, is often threatened by drought. In this study, water deficit significantly reduced the height of plants and yield of grains. To explore further the effect of drought stress on the development and yield of grains, we first performed a large scale phosphoproteome analysis of developing grains in wheat. A total of 590 unique phosphopeptides, representing 471 phosphoproteins, were identified under well-watered conditions. Motif-X analysis showed that four motifs were enriched, including [sP], [Rxxs], [sDxE], and [sxD]. Through comparative phosphoproteome analysis between well-watered and water-deficit conditions, we found that 63 unique phosphopeptides, corresponding to 61 phosphoproteins, showed significant changes in phosphorylation level (≥2-fold intensities). Functional analysis suggested that some of these proteins may be involved in signal transduction, embryo and endosperm development of grains, and drought response and defense under water-deficit conditions. Moreover, we also found that some chaperones may play important roles in protein refolding or degradation when the plant is subjected to water stress. These results provide a detailed insight into the stress response and defense mechanisms of developmental grains at the phosphoproteome level. They also suggested some potential candidates for further study of transgenosis and drought stress as well as incorporation into molecular breeding for drought resistance.
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Affiliation(s)
- Ming Zhang
- College of Life Science, Capital Normal University , 100048 Beijing, China
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Veley KM, Maksaev G, Frick EM, January E, Kloepper SC, Haswell ES. Arabidopsis MSL10 has a regulated cell death signaling activity that is separable from its mechanosensitive ion channel activity. THE PLANT CELL 2014; 26:3115-31. [PMID: 25052715 PMCID: PMC4145136 DOI: 10.1105/tpc.114.128082] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 06/19/2014] [Accepted: 06/27/2014] [Indexed: 05/08/2023]
Abstract
Members of the MscS superfamily of mechanosensitive ion channels function as osmotic safety valves, releasing osmolytes under increased membrane tension. MscS homologs exhibit diverse topology and domain structure, and it has been proposed that the more complex members of the family might have novel regulatory mechanisms or molecular functions. Here, we present a study of MscS-Like (MSL)10 from Arabidopsis thaliana that supports these ideas. High-level expression of MSL10-GFP in Arabidopsis induced small stature, hydrogen peroxide accumulation, ectopic cell death, and reactive oxygen species- and cell death-associated gene expression. Phosphomimetic mutations in the MSL10 N-terminal domain prevented these phenotypes. The phosphorylation state of MSL10 also regulated its ability to induce cell death when transiently expressed in Nicotiana benthamiana leaves but did not affect subcellular localization, assembly, or channel behavior. Finally, the N-terminal domain of MSL10 was sufficient to induce cell death in tobacco, independent of phosphorylation state. We conclude that the plant-specific N-terminal domain of MSL10 is capable of inducing cell death, this activity is regulated by phosphorylation, and MSL10 has two separable activities-one as an ion channel and one as an inducer of cell death. These findings further our understanding of the evolution and significance of mechanosensitive ion channels.
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Affiliation(s)
- Kira M Veley
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Grigory Maksaev
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Elizabeth M Frick
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Emma January
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Sarah C Kloepper
- Department of Biology, Washington University, St. Louis, Missouri 63130
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Chen FC, Chuang TJ, Lin HY, Hsu MK. The evolution of the coding exome of the Arabidopsis species--the influences of DNA methylation, relative exon position, and exon length. BMC Evol Biol 2014; 14:145. [PMID: 24965500 PMCID: PMC4079183 DOI: 10.1186/1471-2148-14-145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 06/19/2014] [Indexed: 11/10/2022] Open
Abstract
Background The evolution of the coding exome is a major driving force of functional divergence both between species and between protein isoforms. Exons at different positions in the transcript or in different transcript isoforms may (1) mutate at different rates due to variations in DNA methylation level; and (2) serve distinct biological roles, and thus be differentially targeted by natural selection. Furthermore, intrinsic exonic features, such as exon length, may also affect the evolution of individual exons. Importantly, the evolutionary effects of these intrinsic/extrinsic features may differ significantly between animals and plants. Such inter-lineage differences, however, have not been systematically examined. Results Here we examine how DNA methylation at CpG dinucleotides (CpG methylation), in the context of intrinsic exonic features (exon length and relative exon position in the transcript), influences the evolution of coding exons of Arabidopsis thaliana. We observed fairly different evolutionary patterns in A. thaliana as compared with those reported for animals. Firstly, the mutagenic effect of CpG methylation is the strongest for internal exons and the weakest for first exons despite the stringent selective constraints on the former group. Secondly, the mutagenic effect of CpG methylation increases significantly with length in first exons but not in the other two exon groups. Thirdly, CpG methylation level is correlated with evolutionary rates (dS, dN, and the dN/dS ratio) with markedly different patterns among the three exon groups. The correlations are generally positive, negative, and mixed for first, last, and internal exons, respectively. Fourthly, exon length is a CpG methylation-independent indicator of evolutionary rates, particularly for dN and the dN/dS ratio in last and internal exons. Finally, the evolutionary patterns of coding exons with regard to CpG methylation differ significantly between Arabidopsis species and mammals. Conclusions Our results suggest that intrinsic features, including relative exonic position in the transcript and exon length, play an important role in the evolution of A. thaliana coding exons. Furthermore, CpG methylation is correlated with exonic evolutionary rates differentially between A. thaliana and animals, and may have served different biological roles in the two lineages.
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Affiliation(s)
- Feng-Chi Chen
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, Taiwan.
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Pan R, Kaur N, Hu J. The Arabidopsis mitochondrial membrane-bound ubiquitin protease UBP27 contributes to mitochondrial morphogenesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:1047-59. [PMID: 24707813 DOI: 10.1111/tpj.12532] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 03/28/2014] [Accepted: 04/01/2014] [Indexed: 05/13/2023]
Abstract
Mitochondria are essential organelles with dynamic morphology and function. Post-translational modifications (PTMs), which include protein ubiquitination, are critically involved in animal and yeast mitochondrial dynamics. How PTMs contribute to plant mitochondrial dynamics is just beginning to be elucidated, and mitochondrial enzymes involved in ubiquitination have not been reported from plants. In this study, we identified an Arabidopsis mitochondrial localized ubiquitin protease, UBP27, through a screen that combined bioinformatics and fluorescent fusion protein targeting analysis. We characterized UBP27 with respect to its membrane topology and enzymatic activities, and analysed the mitochondrial morphological changes in UBP27T-DNA insertion mutants and overexpression lines. We have shown that UBP27 is embedded in the mitochondrial outer membrane with an Nin -Cout orientation and possesses ubiquitin protease activities in vitro. UBP27 demonstrates similar sub-cellular localization, domain structure, membrane topology and enzymatic activities with two mitochondrial deubiquitinases, yeast ScUBP16 and human HsUSP30, which indicated that these proteins are functional orthologues in eukaryotes. Although loss-of-function mutants of UBP27 do not show obvious phenotypes in plant growth and mitochondrial morphology, UBP27 overexpression can change mitochondrial morphology from rod to spherical shape and reduce the mitochondrial association of dynamin-related protein 3 (DRP3) proteins, large GTPases that serve as the main mitochondrial fission factors. Thus, our study has uncovered a plant ubiquitin protease that plays a role in mitochondrial morphogenesis possibly through modulation of the function of organelle division proteins.
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Affiliation(s)
- Ronghui Pan
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
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Lv DW, Li X, Zhang M, Gu AQ, Zhen SM, Wang C, Li XH, Yan YM. Large-scale phosphoproteome analysis in seedling leaves of Brachypodium distachyon L. BMC Genomics 2014; 15:375. [PMID: 24885693 PMCID: PMC4079959 DOI: 10.1186/1471-2164-15-375] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 05/06/2014] [Indexed: 01/03/2023] Open
Abstract
Background Protein phosphorylation is one of the most important post-translational modifications involved in the regulation of plant growth and development as well as diverse stress response. As a member of the Poaceae, Brachypodium distachyon L. is a new model plant for wheat and barley as well as several potential biofuel grasses such as switchgrass. Vegetative growth is vital for biomass accumulation of plants, but knowledge regarding the role of protein phosphorylation modification during vegetative growth, especially in biofuel plants, is far from comprehensive. Results In this study, we carried out the first large-scale phosphoproteome analysis of seedling leaves in Brachypodium accession Bd21 using TiO2 microcolumns combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) and MaxQuant software. A total of 1470 phosphorylation sites in 950 phosphoproteins were identified, and these phosphoproteins were implicated in various molecular functions and basic cellular processes by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Among the 950 phosphoproteins identified, 127 contained 3 to 8 phosphorylation sites. Conservation analysis showed that 93.4% of the 950 phosphoproteins had phosphorylation orthologs in other plant species. Motif-X analysis of the phosphorylation sites identified 13 significantly enriched phosphorylation motifs, of which 3 were novel phosphorylation motifs. Meanwhile, there were 91 phosphoproteins with both multiple phosphorylation sites and multiple phosphorylation motifs. In addition, we identified 58 phosphorylated transcription factors across 21 families and found out 6 significantly over-represented transcription factor families (C3H, Trihelix, CAMTA, TALE, MYB_related and CPP). Eighty-four protein kinases (PKs), 8 protein phosphatases (PPs) and 6 CESAs were recognized as phosphoproteins. Conclusions Through a large-scale bioinformatics analysis of the phosphorylation data in seedling leaves, a complicated PKs- and PPs- centered network related to rapid vegetative growth was deciphered in B. distachyon. We revealed a MAPK cascade network that might play the crucial roles during the phosphorylation signal transduction in leaf growth and development. The phosphoproteins and phosphosites identified from our study expanded our knowledge of protein phosphorylation modification in plants, especially in monocots. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-375) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Yue-Ming Yan
- College of Life Science, Capital Normal University, Beijing 100048, China.
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Boex-Fontvieille E, Daventure M, Jossier M, Hodges M, Zivy M, Tcherkez G. Phosphorylation pattern of Rubisco activase in Arabidopsis leaves. PLANT BIOLOGY (STUTTGART, GERMANY) 2014; 16:550-7. [PMID: 24119201 DOI: 10.1111/plb.12100] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 07/20/2013] [Indexed: 05/09/2023]
Abstract
Rubisco activase (RCA) is an ancillary photosynthetic protein essential for Rubisco activity. Some data suggest that post-translational modifications (such as reduction of disulphide bridges) are involved in the regulation of RCA activity. However, despite the key role of protein phosphorylation in general metabolic regulation, RCA phosphorylation has not been well characterised. We took advantage of phosphoproteomics and gas exchange analyses with instant sampling adapted to Arabidopsis rosettes to examine the occurrence and variations of phosphopeptides associated with RCA in different photosynthetic contexts (CO2 mole fraction, light and dark). We detected two phosphopeptides from RCA corresponding to residues Thr 78 and Ser 172, and show that the former is considerably more phosphorylated in the dark than in the light, while the latter show no light/dark pattern. The CO2 mole fraction did not influence phosphorylation of either residue. Phosphorylation thus appears to be a potential mechanism associated with RCA dark inactivation, when Rubisco-catalysed carboxylation is arrested. Since Thr 78 and Ser 172 are located in the N and Walker domains of the protein, respectively, the involvement of phosphorylation in protein-protein interaction and catalysis is likely.
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Affiliation(s)
- E Boex-Fontvieille
- Institut de biologie des plantes, CNRS UMR 8618, Université Paris-Sud, Orsay, France
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75
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Fan S, Meng Y, Song M, Pang C, Wei H, Liu J, Zhan X, Lan J, Feng C, Zhang S, Yu S. Quantitative phosphoproteomics analysis of nitric oxide-responsive phosphoproteins in cotton leaf. PLoS One 2014; 9:e94261. [PMID: 24714030 PMCID: PMC3979775 DOI: 10.1371/journal.pone.0094261] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 03/14/2014] [Indexed: 11/24/2022] Open
Abstract
Knowledge of phosphorylation events and their regulation is crucial to understanding the functional biology of plant proteins, but very little is currently known about nitric oxide-responsive phosphorylation in plants. Here, we report the first large-scale, quantitative phosphoproteome analysis of cotton (Gossypium hirsutum) treated with sodium nitroprusside (nitric oxide donor) by utilizing the isobaric tag for relative and absolute quantitation (iTRAQ) method. A total of 1315 unique phosphopeptides, spanning 1528 non-redundant phosphorylation sites, were detected from 1020 cotton phosphoproteins. Among them, 183 phosphopeptides corresponding to 167 phosphoproteins were found to be differentially phosphorylated in response to sodium nitroprusside. Several of the phosphorylation sites that we identified, including RQxS, DSxE, TxxxxSP and SPxT, have not, to our knowledge, been reported to be protein kinase sites in other species. The phosphoproteins identified are involved in a wide range of cellular processes, including signal transduction, RNA metabolism, intracellular transport and so on. This study reveals unique features of the cotton phosphoproteome and provides new insight into the biochemical pathways that are regulated by nitric oxide.
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Affiliation(s)
- Shuli Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan Province, China
| | - Yanyan Meng
- Key Laboratory of Cotton Biology and Breeding in the Middle Reaches of the Changjing River, Institute of Economic Crop, Hubei Academy of Agricultural Science, Wuhan, Hubei Province, China
| | - Meizhen Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan Province, China
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan Province, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan Province, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan Province, China
- College of Agronomy, Northwest A & F University, Yangling, Shaanxi Province, China
| | - Xianjin Zhan
- Key Laboratory of Cotton Biology and Breeding in the Middle Reaches of the Changjing River, Institute of Economic Crop, Hubei Academy of Agricultural Science, Wuhan, Hubei Province, China
| | - Jiayang Lan
- Key Laboratory of Cotton Biology and Breeding in the Middle Reaches of the Changjing River, Institute of Economic Crop, Hubei Academy of Agricultural Science, Wuhan, Hubei Province, China
| | - Changhui Feng
- Key Laboratory of Cotton Biology and Breeding in the Middle Reaches of the Changjing River, Institute of Economic Crop, Hubei Academy of Agricultural Science, Wuhan, Hubei Province, China
| | - Shengxi Zhang
- Key Laboratory of Cotton Biology and Breeding in the Middle Reaches of the Changjing River, Institute of Economic Crop, Hubei Academy of Agricultural Science, Wuhan, Hubei Province, China
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan Province, China
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76
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Grienenberger E, Douglas CJ. Arabidopsis VASCULAR-RELATED UNKNOWN PROTEIN1 regulates xylem development and growth by a conserved mechanism that modulates hormone signaling. PLANT PHYSIOLOGY 2014; 164:1991-2010. [PMID: 24567189 PMCID: PMC3982757 DOI: 10.1104/pp.114.236406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 02/22/2014] [Indexed: 05/17/2023]
Abstract
Despite a strict conservation of the vascular tissues in vascular plants (tracheophytes), our understanding of the genetic basis underlying the differentiation of secondary cell wall-containing cells in the xylem of tracheophytes is still far from complete. Using coexpression analysis and phylogenetic conservation across sequenced tracheophyte genomes, we identified a number of Arabidopsis (Arabidopsis thaliana) genes of unknown function whose expression is correlated with secondary cell wall deposition. Among these, the Arabidopsis VASCULAR-RELATED UNKNOWN PROTEIN1 (VUP1) gene encodes a predicted protein of 24 kD with no annotated functional domains but containing domains that are highly conserved in tracheophytes. Here, we show that the VUP1 expression pattern, determined by promoter-β-glucuronidase reporter gene expression, is associated with vascular tissues, while vup1 loss-of-function mutants exhibit collapsed morphology of xylem vessel cells. Constitutive overexpression of VUP1 caused dramatic and pleiotropic developmental defects, including severe dwarfism, dark green leaves, reduced apical dominance, and altered photomorphogenesis, resembling brassinosteroid-deficient mutants. Constitutive overexpression of VUP homologs from multiple tracheophyte species induced similar defects. Whole-genome transcriptome analysis revealed that overexpression of VUP1 represses the expression of many brassinosteroid- and auxin-responsive genes. Additionally, deletion constructs and site-directed mutagenesis were used to identify critical domains and amino acids required for VUP1 function. Altogether, our data suggest a conserved role for VUP1 in regulating secondary wall formation during vascular development by tissue- or cell-specific modulation of hormone signaling pathways.
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77
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Lv DW, Ge P, Zhang M, Cheng ZW, Li XH, Yan YM. Integrative network analysis of the signaling cascades in seedling leaves of bread wheat by large-scale phosphoproteomic profiling. J Proteome Res 2014; 13:2381-95. [PMID: 24679076 DOI: 10.1021/pr401184v] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Here, we conducted the first large-scale leaf phosphoproteome analysis of two bread wheat cultivars by liquid chromatography-tandem mass spectrometry. Altogether, 1802 unambiguous phosphorylation sites representing 1175 phosphoproteins implicated in various molecular functions and cellular processes were identified by gene ontology enrichment analysis. Among the 1175 phosphoproteins, 141 contained 3-10 phosphorylation sites. The phosphorylation sites were located more frequently in the N- and C-terminal regions than in internal regions, and ∼70% were located outside the conserved regions. Conservation analysis showed that 90.5% of the phosphoproteins had phosphorylated orthologs in other plant species. Eighteen significantly enriched phosphorylation motifs, of which six were new wheat phosphorylation motifs, were identified. In particular, 52 phosphorylated transcription factors (TFs), 85 protein kinases (PKs), and 16 protein phosphatases (PPs) were classified and analyzed in depth. All the Tyr phosphorylation sites were in PKs such as mitogen-activated PKs (MAPKs) and SHAGGY-like kinases. A complicated cross-talk phosphorylation regulatory network based on PKs such as Snf1-related kinases (SnRKs), calcium-dependent PKs (CDPKs), and glycogen synthase kinase 3 (GSK3) and PPs including PP2C, PP2A, and BRI1 suppressor 1 (BSU1)-like protein (BSL) was constructed and was found to be potentially involved in rapid leaf growth. Our results provide a series of phosphoproteins and phosphorylation sites in addition to a potential network of phosphorylation signaling cascades in wheat seedling leaves.
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Affiliation(s)
- Dong-Wen Lv
- College of Life Science, Capital Normal University , 100048 Beijing, China
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78
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Vialaret J, Di Pietro M, Hem S, Maurel C, Rossignol M, Santoni V. Phosphorylation dynamics of membrane proteins fromArabidopsisroots submitted to salt stress. Proteomics 2014; 14:1058-70. [DOI: 10.1002/pmic.201300443] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 12/19/2013] [Accepted: 01/20/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Jérôme Vialaret
- Laboratoire de Protéomique Fonctionnelle; Institut National de la Recherche Agronomique, Unité de Recherche 1199; Montpellier France
| | - Magali Di Pietro
- Biochimie et Physiologie Moléculaire des Plantes; Unité Mixte de Recherche 5004; Centre National de la Recherche Scientifique/Unité Mixte de Recherche 0386; Institut National de la Recherche Agronomique/Montpellier SupAgro/Université Montpellier II; Montpellier France
| | - Sonia Hem
- Laboratoire de Protéomique Fonctionnelle; Institut National de la Recherche Agronomique, Unité de Recherche 1199; Montpellier France
| | - Christophe Maurel
- Biochimie et Physiologie Moléculaire des Plantes; Unité Mixte de Recherche 5004; Centre National de la Recherche Scientifique/Unité Mixte de Recherche 0386; Institut National de la Recherche Agronomique/Montpellier SupAgro/Université Montpellier II; Montpellier France
| | - Michel Rossignol
- Laboratoire de Protéomique Fonctionnelle; Institut National de la Recherche Agronomique, Unité de Recherche 1199; Montpellier France
| | - Véronique Santoni
- Biochimie et Physiologie Moléculaire des Plantes; Unité Mixte de Recherche 5004; Centre National de la Recherche Scientifique/Unité Mixte de Recherche 0386; Institut National de la Recherche Agronomique/Montpellier SupAgro/Université Montpellier II; Montpellier France
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79
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Quan S, Yang P, Cassin-Ross G, Kaur N, Switzenberg R, Aung K, Li J, Hu J. Proteome analysis of peroxisomes from etiolated Arabidopsis seedlings identifies a peroxisomal protease involved in β-oxidation and development. PLANT PHYSIOLOGY 2013; 163:1518-38. [PMID: 24130194 PMCID: PMC3850190 DOI: 10.1104/pp.113.223453] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plant peroxisomes are highly dynamic organelles that mediate a suite of metabolic processes crucial to development. Peroxisomes in seeds/dark-grown seedlings and in photosynthetic tissues constitute two major subtypes of plant peroxisomes, which had been postulated to contain distinct primary biochemical properties. Multiple in-depth proteomic analyses had been performed on leaf peroxisomes, yet the major makeup of peroxisomes in seeds or dark-grown seedlings remained unclear. To compare the metabolic pathways of the two dominant plant peroxisomal subtypes and discover new peroxisomal proteins that function specifically during seed germination, we performed proteomic analysis of peroxisomes from etiolated Arabidopsis (Arabidopsis thaliana) seedlings. The detection of 77 peroxisomal proteins allowed us to perform comparative analysis with the peroxisomal proteome of green leaves, which revealed a large overlap between these two primary peroxisomal variants. Subcellular targeting analysis by fluorescence microscopy validated around 10 new peroxisomal proteins in Arabidopsis. Mutant analysis suggested the role of the cysteine protease RESPONSE TO DROUGHT21A-LIKE1 in β-oxidation, seed germination, and growth. This work provides a much-needed road map of a major type of plant peroxisome and has established a basis for future investigations of peroxisomal proteolytic processes to understand their roles in development and in plant interaction with the environment.
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80
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An atypical tubulin kinase mediates stress-induced microtubule depolymerization in Arabidopsis. Curr Biol 2013; 23:1969-78. [PMID: 24120637 DOI: 10.1016/j.cub.2013.08.006] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/02/2013] [Accepted: 08/05/2013] [Indexed: 12/29/2022]
Abstract
BACKGROUND As sessile organisms, plants adapt to adverse environmental conditions by quickly adjusting cell physiology and metabolism. Transient depolymerization of interphase microtubules is triggered by various acute stresses and biotic interactions with pathogenic organisms. Although rapid remodeling of plant microtubule arrays in response to external stresses is an intriguing phenomenon, the underlying molecular mechanisms and the advantages of this response to plant performance are poorly understood. RESULTS A domain with weak homology to the slime mold actin-fragmin kinase in the Arabidopsis mitogen-activated protein kinase phosphatase PROPYZAMIDE-HYPERSENSITIVE 1 (PHS1) is a Mn2+-dependent kinase. This atypical kinase domain phosphorylates Thr349 of α-tubulin at the longitudinal interdimer interface, thereby generating a polymerization-incompetent isoform, and effectively depolymerizes microtubule arrays when ectopically expressed in plant or animal cells. The intrinsic tubulin kinase activity is normally suppressed by the phosphatase activity of PHS1 but is unmasked immediately after osmotic stress. In the phs1 null mutant, stress-induced microtubule depolymerization does not occur. CONCLUSIONS The rapid and reversible modification of tubulin subunits by PHS1-mediated phosphorylation enables dynamic remodeling of the plant microtubule cytoskeleton in response to external stimuli. Suppression of the potent tubulin kinase activity by the juxtaposed phosphatase domain tightly controls this stress-activated microtubule regulator.
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