1
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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; 23:2518-2531. [PMID: 38810119 PMCID: PMC11232104 DOI: 10.1021/acs.jproteome.4c00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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Li R, Yao J, Ming Y, Guo J, Deng J, Liu D, Li Z, Cheng Y. Integrated proteomic analysis reveals interactions between phosphorylation and ubiquitination in rose response to Botrytis infection. HORTICULTURE RESEARCH 2024; 11:uhad238. [PMID: 38222823 PMCID: PMC10782497 DOI: 10.1093/hr/uhad238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/06/2023] [Indexed: 01/16/2024]
Abstract
As two of the most abundant post-translational modifications, phosphorylation and ubiquitination play a significant role in modulating plant-pathogen interactions and increasing evidence indicates their crosstalk in plant immunity. Rose (Rosa sp.) is one of the most important ornamental plants and can be seriously infected by Botrytis cinerea. Here, integrated proteomics analysis was performed to detect global proteome, phosphorylation, and ubiquitination changes in rose upon B. cinerea infection and investigate the possible phosphorylation and ubiquitination crosstalk. A total of 6165 proteins, 11 774 phosphorylation and 10 582 ubiquitination sites, and 77 phosphorylation and 13 ubiquitination motifs were identified. Botrytis cinerea infection resulted in 169 up-regulated and 122 down-regulated proteins, 291 up-regulated and 404 down-regulated phosphorylation sites, and 250 up-regulated and 634 down-regulated ubiquitination sites. There were 12 up-regulated PR10 proteins and half of them also showed reduced ubiquitination. A lot of kinases probably involved in plant pattern-triggered immunity signaling were up-regulated phosphoproteins. Noticeably, numerous kinases and ubiquitination-related proteins also showed a significant change in ubiquitination and phosphorylation, respectively. A cross-comparison of phosphoproteome and ubiquitylome indicated that both of two post-translational modifications of 104 proteins were dynamically regulated, and many putative pattern-triggered immunity signaling components in the plant plasma membrane were co-regulated. Moreover, five selected proteins, including four PR10 proteins and a plasma membrane aquaporin, were proven to be involved in rose resistance to B. cinerea. Our study provides insights into the molecular mechanisms underlying rose resistance to B. cinerea and also increases the database of phosphorylation and ubiquitination sites in plants.
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Affiliation(s)
- Rui Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Juanni Yao
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Yue Ming
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Jia Guo
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Jingjing Deng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Daofeng Liu
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Yulin Cheng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
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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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Chen L, Yang J, Hu H, Jiang Y, Feng L, Liu J, Zhong K, Liu P, Ma Y, Chen M, Yang J. Large-scale phosphoproteome analysis in wheat seedling leaves provides evidence for extensive phosphorylation of regulatory proteins during CWMV infection. BMC PLANT BIOLOGY 2023; 23:532. [PMID: 37914991 PMCID: PMC10621099 DOI: 10.1186/s12870-023-04559-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 10/25/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Chinese wheat mosaic virus (CWMV) often causes severe damage to wheat (Triticum aestivum L.) growth and yield. It is well known that a successful infection in plants depends on a complex interaction between the host plant and the pathogen. Post-translational modification (PTM) of proteins is considered to be one of the main processes that decides the outcome of the plant-pathogen arms race during this interaction. Although numerous studies have investigated PTM in various organisms, there has been no large-scale phosphoproteomic analysis of virus-infected wheat plants. We therefore aimed to investigate the CWMV infection-induced phosphoproteomics changes in wheat by high-resolution liquid chromatography-tandem mass spectroscopy (LC-MS/MS) using affinity-enriched peptides followed by comprehensive bioinformatics analysis. RESULTS Through this study, a total of 4095 phosphorylation sites have been identified in 1968 proteins, and 11.6% of the phosphorylated proteins exhibited significant changes (PSPCs) in their phosphorylation levels upon CWMV infection. The result of Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that most of the PSPCs were associated with photosynthesis, plant-pathogen interactions, and MAPK signaling pathways. The protein-protein interaction (PPI) network analysis result showed that these PSPCs were mainly participated in the regulation of biosynthesis and metabolism, protein kinase activities, and transcription factors. Furthermore, the phosphorylation levels of TaChi1 and TaP5CS, two plant immunity-related enzymes, were significantly changed upon CWMV infection, resulting in a significant decrease in CWMV accumulation in the infected plants. CONCLUSIONS Our results indicate that phosphorylation modification of protein plays a critical role in wheat resistance to CWMV infection. Upon CWMV infection, wheat plants will regulate the levels of extra- and intra-cellular signals and modifications of enzyme activities via protein phosphorylation. This novel information about the strategies used by wheat to resist CWMV infection will help researchers to breed new CWMV-resistant cultivars and to better understand the arms race between wheat and CWMV.
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Affiliation(s)
- Lu Chen
- Institute of Crop Sciences, State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jin Yang
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Haichao Hu
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yaoyao Jiang
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Lixiao Feng
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jiaqian Liu
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Kaili Zhong
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Peng Liu
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Youzhi Ma
- Institute of Crop Sciences, State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Ming Chen
- Institute of Crop Sciences, State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Jian Yang
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
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Li Q, Li M, Ma H, Xue M, Chen T, Ding X, Zhang S, Xiao J. Quantitative Phosphoproteomic Analysis Provides Insights into the Sodium Bicarbonate Responsiveness of Glycine max. Biomolecules 2023; 13:1520. [PMID: 37892202 PMCID: PMC10605096 DOI: 10.3390/biom13101520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/24/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Sodium bicarbonate stress caused by NaHCO3 is one of the most severe abiotic stresses affecting agricultural production worldwide. However, little attention has been given to the molecular mechanisms underlying plant responses to sodium bicarbonate stress. To understand phosphorylation events in signaling pathways triggered by sodium bicarbonate stress, TMT-labeling-based quantitative phosphoproteomic analyses were performed on soybean leaf and root tissues under 50 mM NaHCO3 treatment. In the present study, a total of 7856 phosphopeptides were identified from cultivated soybeans (Glycine max L. Merr.), representing 3468 phosphoprotein groups, in which 2427 phosphoprotein groups were newly identified. These phosphoprotein groups contained 6326 unique high-probability phosphosites (UHPs), of which 77.2% were newly identified, increasing the current soybean phosphosite database size by 43.4%. Among the phosphopeptides found in this study, we determined 67 phosphopeptides (representing 63 phosphoprotein groups) from leaf tissue and 554 phosphopeptides (representing 487 phosphoprotein groups) from root tissue that showed significant changes in phosphorylation levels under sodium bicarbonate stress (fold change >1.2 or <0.83, respectively; p < 0.05). Localization prediction showed that most phosphoproteins localized in the nucleus for both leaf and root tissues. GO and KEGG enrichment analyses showed quite different enriched functional terms between leaf and root tissues, and more pathways were enriched in the root tissue than in the leaf tissue. Moreover, a total of 53 different protein kinases and 7 protein phosphatases were identified from the differentially expressed phosphoproteins (DEPs). A protein kinase/phosphatase interactor analysis showed that the interacting proteins were mainly involved in/with transporters/membrane trafficking, transcriptional level regulation, protein level regulation, signaling/stress response, and miscellaneous functions. The results presented in this study reveal insights into the function of post-translational modification in plant responses to sodium bicarbonate stress.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (Q.L.)
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China
| | - Minglong Li
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China
| | - Huiying Ma
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China
| | - Man Xue
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China
| | - Tong Chen
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China
| | - Xiaodong Ding
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (Q.L.)
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China
| | - Shuzhen Zhang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (Q.L.)
| | - Jialei Xiao
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (Q.L.)
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China
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Peng W, Wang Y, Zeng X, Li W, Song N, Liu J, Wang B, Dai L. Integrative transcriptomic, proteomic, and phosphoproteomic analysis on the defense response to Magnaporthe oryzae reveals different expression patterns at the molecular level of durably resistant rice cultivar Mowanggu. FRONTIERS IN PLANT SCIENCE 2023; 14:1212510. [PMID: 37521912 PMCID: PMC10373791 DOI: 10.3389/fpls.2023.1212510] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/30/2023] [Indexed: 08/01/2023]
Abstract
Rice blast, caused by Magnaporthe oryzae is one of the most destructive diseases of rice (Oryza sativa L.) in most rice-cultivated areas worldwide. Mowanggu (MWG) is a traditional landrace rice variety in Yunnan with broad-spectrum and durable blast resistance against rice blast fungus. However, the underlying disease-resistance mechanisms remain unknown. An integrative transcriptomic, proteomic, and phosphoproteomic analysis of MWG was performed after inoculation with M. oryzae in this study. The transcriptomic and proteomic results revealed that MWG was moderately correlated at the transcriptional and protein levels. Differentially expressed genes and proteins were up-regulated and significantly enriched in protein phosphorylation, peroxisome, plant-pathogen interactions, phenylpropanoid metabolism and phenylalanine biosynthesis pathways. The phosphoproteomic profile and phosphorylated-protein-interaction network revealed that the altered phosphoproteins were primarily associated with reactive oxygen species (ROS), glycolysis, MAPK signaling pathways, and amino acid biosynthesis. In addition, a series of physiological and biochemical parameters, including ROS, soluble sugars, soluble protein and callus accumulation and defense-related enzyme activities, were used to validate the possible blast resistance mechanisms of MWG. The integrative transcriptomic, proteomic, and phosphoproteomic analysis revealed the different expression patterns at the molecular level of the durably resistant rice cultivar MWG after inoculation with M. oryzae, which provides insight into the molecular mechanisms of rice blast resistance.
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Affiliation(s)
- Weiye Peng
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan, China
| | - Yunsheng Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Xuanning Zeng
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Wei Li
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Na Song
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Jing Liu
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Bing Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Liangying Dai
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
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7
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Feng C, Roitinger E, Hudecz O, Cuacos M, Lorenz J, Schubert V, Wang B, Wang R, Mechtler K, Heckmann S. TurboID-based proteomic profiling of meiotic chromosome axes in Arabidopsis thaliana. NATURE PLANTS 2023; 9:616-630. [PMID: 36914898 PMCID: PMC7614470 DOI: 10.1038/s41477-023-01371-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
During meiotic prophase I, sister chromatids are arranged in a loop-base array along a proteinaceous structure, called the meiotic chromosome axis. This structure is essential for synapsis and meiotic recombination progression and hence formation of genetically diverse gametes. Proteomic studies in plants aiming to unravel the composition and regulation of meiotic axes are constrained by limited meiotic cells embedded in floral organs. Here we report TurboID (TbID)-based proximity labelling (PL) in meiotic cells of Arabidopsis thaliana. TbID fusion to the two meiotic chromosome axis proteins ASY1 and ASY3 enabled the identification of their proximate 'interactomes' based on affinity purification coupled with mass spectrometry. We identified 39 ASY1 and/or ASY3 proximate candidates covering most known chromosome axis-related proteins. Functional studies of selected candidates demonstrate that not only known meiotic candidates but also new meiotic proteins were uncovered. Hence, TbID-based PL in meiotic cells enables the identification of chromosome axis proximate proteins in A. thaliana.
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Affiliation(s)
- Chao Feng
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Seeland, Germany
| | - Elisabeth Roitinger
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Vienna, Austria
| | - Otto Hudecz
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Vienna, Austria
| | - Maria Cuacos
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Seeland, Germany
| | - Jana Lorenz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Seeland, Germany
| | - Baicui Wang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Seeland, Germany
| | - Rui Wang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Seeland, Germany
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Vienna, Austria
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Seeland, Germany.
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8
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Wang N, Shi Y, Jiang Q, Li H, Fan W, Feng Y, Li L, Liu B, Lin F, Jing W, Zhang W, Shen L. A 14-3-3 protein positively regulates rice salt tolerance by stabilizing phospholipase C1. PLANT, CELL & ENVIRONMENT 2023; 46:1232-1248. [PMID: 36539986 DOI: 10.1111/pce.14520] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/06/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
The phosphatidylinositol-specific phospholipase Cs (PI-PLCs) catalyze the hydrolysis of phosphatidylinositols, which play crucial roles in signaling transduction during plant development and stress response. However, the regulation of PI-PLC is still poorly understood. A previous study showed that a rice PI-PLC, OsPLC1, was essential to rice salt tolerance. Here, we identified a 14-3-3 protein, OsGF14b, as an interaction partner of OsPLC1. Similar to OsPLC1, OsGF14b also positively regulates rice salt tolerance, and their interaction can be promoted by NaCl stress. OsGF14b also positively regulated the hydrolysis activity of OsPLC1, and is essential to NaCl-induced activation of rice PI-PLCs. We further discovered that OsPLC1 was degraded via ubiquitin-proteasome pathway, and OsGF14b could inhibit the ubiquitination of OsPLC1 to protect OsPLC1 from degradation. Under salt stress, the OsPLC1 protein level in osgf14b was lower than the corresponding value of WT, whereas overexpression of OsGF14b results in a significant increase of OsPLC1 stability. Taken together, we propose that OsGF14b can interact with OsPLC1 and promote its activity and stability, thereby improving rice salt tolerance. This study provides novel insights into the important roles of 14-3-3 proteins in regulating protein stability and function in response to salt stress.
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Affiliation(s)
- Ningna Wang
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yiyuan Shi
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Qun Jiang
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Huan Li
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Wenxia Fan
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yu Feng
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Li Li
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Bin Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Feng Lin
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Wen Jing
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Wenhua Zhang
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Like Shen
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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Ma L, Hao Y, Liu X, Shao L, Wang H, Zhou H, Zhang D, Zhu T, Ding Q, Ma L. Proteomic and Phosphoproteomic Analyses Reveal a Complex Network Regulating Pollen Abortion and Potential Candidate Proteins in TCMS Wheat. Int J Mol Sci 2022; 23:6428. [PMID: 35742874 PMCID: PMC9224247 DOI: 10.3390/ijms23126428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 02/04/2023] Open
Abstract
Thermosensitive sterile lines are natural materials for exploring the effects of anther development on male fertility. To study the possible molecular mechanisms regulating protein activity during the induction of male sterility, proteomic and phosphoproteomic analyses with tandem mass tags (TMTs) were used to study the binucleate anther of the thermosensitive sterile wheat line YS3038. A total of 9072 proteins, including 5019 phosphoproteins, were identified. Enrichment analyses of differentially abundant proteins (DAPs) and phosphoproteins (DAPPs) in metabolic pathways showed that both were mainly related to energy metabolism. Soluble sugar and ATP content were significantly decreased, free fatty acid content was significantly increased, and ROS was abnormally accumulated in male sterile YS3038-A. In addition, 233 kinase-substrate pairs involved in potential phosphorylation control networks were predicted to regulate fertility. Candidate proteins were identified, and a quantitative real-time polymerase chain reaction (qRT-PCR) analysis was used to validate the TMT results. TaPDCD5 is likely to be involved in fertility conversion of YS3038 by barley stripe mosaic virus-induced gene silencing (BSMV-VIGS). Our data provide new insights into the mechanism of TCMS, which has value for identifying potential candidate proteins associated with the formation or abortion of pollen and promotion of wheat heterosis utilization.
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Affiliation(s)
- Liting Ma
- College of Agronomy, Northwest A&F University, Yangling 712100, China; (L.M.); (Y.H.); (X.L.); (L.S.); (H.W.); (H.Z.); (D.Z.); (T.Z.)
| | - Yuran Hao
- College of Agronomy, Northwest A&F University, Yangling 712100, China; (L.M.); (Y.H.); (X.L.); (L.S.); (H.W.); (H.Z.); (D.Z.); (T.Z.)
| | - Xiaorong Liu
- College of Agronomy, Northwest A&F University, Yangling 712100, China; (L.M.); (Y.H.); (X.L.); (L.S.); (H.W.); (H.Z.); (D.Z.); (T.Z.)
| | - Leilei Shao
- College of Agronomy, Northwest A&F University, Yangling 712100, China; (L.M.); (Y.H.); (X.L.); (L.S.); (H.W.); (H.Z.); (D.Z.); (T.Z.)
| | - Hairong Wang
- College of Agronomy, Northwest A&F University, Yangling 712100, China; (L.M.); (Y.H.); (X.L.); (L.S.); (H.W.); (H.Z.); (D.Z.); (T.Z.)
| | - Hao Zhou
- College of Agronomy, Northwest A&F University, Yangling 712100, China; (L.M.); (Y.H.); (X.L.); (L.S.); (H.W.); (H.Z.); (D.Z.); (T.Z.)
| | - Dazhong Zhang
- College of Agronomy, Northwest A&F University, Yangling 712100, China; (L.M.); (Y.H.); (X.L.); (L.S.); (H.W.); (H.Z.); (D.Z.); (T.Z.)
| | - Ting Zhu
- College of Agronomy, Northwest A&F University, Yangling 712100, China; (L.M.); (Y.H.); (X.L.); (L.S.); (H.W.); (H.Z.); (D.Z.); (T.Z.)
| | - Qin Ding
- College of Horticulture, Northwest A&F University, Yangling 712100, China;
| | - Lingjian Ma
- College of Agronomy, Northwest A&F University, Yangling 712100, China; (L.M.); (Y.H.); (X.L.); (L.S.); (H.W.); (H.Z.); (D.Z.); (T.Z.)
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10
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Li Q, Sun Q, Wang D, Liu Y, Zhang P, Lu H, Zhang Y, Zhang S, Wang A, Ding X, Xiao J. Quantitative phosphoproteomics reveals the role of wild soybean GsSnRK1 as a metabolic regulator under drought and alkali stresses. J Proteomics 2022; 258:104528. [PMID: 35182787 DOI: 10.1016/j.jprot.2022.104528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/04/2022] [Accepted: 02/04/2022] [Indexed: 11/25/2022]
Abstract
Drought and alkali stresses cause detrimental effects on plant growth and development. SnRK1 protein kinases act as key energy and stress sensors by phosphorylation-mediated signaling in the regulation of plant defense reactions against adverse environments. To understand SnRK1-dependent phosphorylation events in signaling pathways triggered by abiotic factors, we employed quantitative phosphoproteomics to compare the global changes in phosphopeptides and phosphoproteins in 2kinm mutant Arabidopsis (SnRK1.1 T-DNA knockout and SnRK1.2 knockdown by β-estradiol-induced RNAi) complemented with wild soybean GsSnRK1(wt) or dominant negative mutant GsSnRK1(K49M) in response to drought and alkali stresses. Among 4014 phosphopeptides (representing 2380 phosphoproteins) identified in this study, we finalized 74 phosphopeptides (representing 61 phosphoproteins), and 75 phosphopeptides (representing 57 phosphoproteins) showing significant changes in phosphorylation levels under drought and alkali treatments respectively. Function enrichment and protein-protein interaction analyses indicated that the differentially-expressed phosphoproteins (DPs) under drought and alkali stresses were mainly involved in signaling transduction, stress response, carbohydrate and energy metabolism, transport and membrane trafficking, RNA splicing and processing, DNA binding and gene expression, and protein synthesis/folding/degradation. These results provide assistance to identify bona fide and novel SnRK1 phosphorylation substrates and shed new light on the biological functions of SnRK1 kinase in responses to abiotic stresses. SIGNIFICANCE: These results provide assistance to identify novel SnRK1 phosphorylation substrates and regulatory proteins, and shed new light on investigating the potential roles of reversible phosphorylation in plant responses to abiotic stresses.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China
| | - Qi Sun
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China
| | - Di Wang
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China
| | - Yuanming Liu
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China
| | - Pengmin Zhang
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China
| | - Haoran Lu
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China
| | - Yao Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Shuzhen Zhang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China
| | - Aoxue Wang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
| | - Xiaodong Ding
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China.
| | - Jialei Xiao
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China.
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11
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Lewandowska D, Orr J, Schreiber M, Colas I, Ramsay L, Zhang R, Waugh R. The proteome of developing barley anthers during meiotic prophase I. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1464-1482. [PMID: 34758083 PMCID: PMC8890616 DOI: 10.1093/jxb/erab494] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/08/2021] [Indexed: 05/11/2023]
Abstract
Flowering plants reproduce sexually by combining a haploid male and female gametophyte during fertilization. Male gametophytes are localized in the anthers, each containing reproductive (meiocyte) and non-reproductive tissue necessary for anther development and maturation. Meiosis, where chromosomes pair and exchange their genetic material during a process called recombination, is one of the most important and sensitive stages in breeding, ensuring genetic diversity. Most anther development studies have focused on transcript variation, but very few have been correlated with protein abundance. Taking advantage of a recently published barley anther transcriptomic (BAnTr) dataset and a newly developed sensitive mass spectrometry-based approach to analyse the barley anther proteome, we conducted high-resolution mass spectrometry analysis of barley anthers, collected at six time points and representing their development from pre-meiosis to metaphase. Each time point was carefully staged using immunocytology, providing a robust and accurate staging mirroring our previous BAnTr dataset. We identified >6100 non-redundant proteins including 82 known and putative meiotic proteins. Although the protein abundance was relatively stable throughout prophase I, we were able to quantify the dynamic variation of 336 proteins. We present the first quantitative comparative proteomics study of barley anther development during meiotic prophase I when the important process of homologous recombination is taking place.
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Affiliation(s)
- Dominika Lewandowska
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Jamie Orr
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Miriam Schreiber
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Isabelle Colas
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Luke Ramsay
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- Division of Plant Sciences, University of Dundee, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Waite Research Precinct, Glen Osmond, SA 5064, Australia
- Correspondence:
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12
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Sun L, Mo A, Lu P. Proteomic-, Phosphoproteomic-, and Acetylomic-Based Mass Spectrometry to Identify Tissue-Specific Protein Complexes and Phosphorylation in Plant Gametogenesis. Methods Mol Biol 2022; 2484:13-22. [PMID: 35461441 DOI: 10.1007/978-1-0716-2253-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Using proteomics to analyze phosphorylation, acetylation, and other posttranslational modifications has been a very important method in biological research. Here we take the rice meiotic anther as an example to introduce the experimentally verified proteomic analysis methods of plant tissue-specific phosphorylation and acetylation, including total protein extraction, trypsin digestion, phosphopeptide enrichment by TiO2 microcolumn, affinity enrichment of lysine-acetylated peptides, desalting, Nano UHPLC-MS/MS analysis, database search and data analysis, and bioinformatic analysis.
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Affiliation(s)
- Lu Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Aowei Mo
- School of Life Sciences, Fudan University, Shanghai, China
| | - Pingli Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China.
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13
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Identification of proteins associated with bast fiber growth of ramie by differential proteomic analysis. BMC Genomics 2021; 22:865. [PMID: 34856929 PMCID: PMC8638140 DOI: 10.1186/s12864-021-08195-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/22/2021] [Indexed: 11/24/2022] Open
Abstract
Background Ramie is an important fiber-producing crop in China, and its fibers are widely used as textile materials. Fibers contain specialized secondary cellular walls that are mainly composed of cellulose, hemicelluloses, and lignin. Understanding the mechanism underlying the secondary wall biosynthesis of fibers will benefit the improvement of fiber yield and quality in ramie. Results Here, we performed a proteomic analysis of the bark from the top and middle parts of the stem, where fiber growth is at different stages. We identified 6971 non-redundant proteins from bast bark. Proteomic comparison revealed 983 proteins with differential expression between the two bark types. Of these 983 proteins, 46 were identified as the homolog of known secondary wall biosynthetic proteins of Arabidopsis, indicating that they were potentially associated with fiber growth. Then, we proposed a molecular model for the secondary wall biosynthesis of ramie fiber. Furthermore, interaction analysis of 46 candidate proteins revealed two interacting networks that consisted of eight cellulose biosynthetic enzymes and seven lignin biosynthetic proteins, respectively. Conclusion This study sheds light on the proteomic basis underlying bast fiber growth in ramie, and the identification of many candidates associated with fiber growth provides important basis for understanding the fiber growth in this crop. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08195-9.
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14
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A Decade of Pollen Phosphoproteomics. Int J Mol Sci 2021; 22:ijms222212212. [PMID: 34830092 PMCID: PMC8619407 DOI: 10.3390/ijms222212212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/01/2021] [Accepted: 11/08/2021] [Indexed: 12/15/2022] Open
Abstract
Angiosperm mature pollen represents a quiescent stage with a desiccated cytoplasm surrounded by a tough cell wall, which is resistant to the suboptimal environmental conditions and carries the genetic information in an intact stage to the female gametophyte. Post pollination, pollen grains are rehydrated, activated, and a rapid pollen tube growth starts, which is accompanied by a notable metabolic activity, synthesis of novel proteins, and a mutual communication with female reproductive tissues. Several angiosperm species (Arabidopsis thaliana, tobacco, maize, and kiwifruit) were subjected to phosphoproteomic studies of their male gametophyte developmental stages, mostly mature pollen grains. The aim of this review is to compare the available phosphoproteomic studies and to highlight the common phosphoproteins and regulatory trends in the studied species. Moreover, the pollen phosphoproteome was compared with root hair phosphoproteome to pinpoint the common proteins taking part in their tip growth, which share the same cellular mechanisms.
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Novel Translational and Phosphorylation Modification Regulation Mechanisms of Tomato ( Solanum lycopersicum) Fruit Ripening Revealed by Integrative Proteomics and Phosphoproteomics. Int J Mol Sci 2021; 22:ijms222111782. [PMID: 34769214 PMCID: PMC8584006 DOI: 10.3390/ijms222111782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 11/26/2022] Open
Abstract
The tomato is a research model for fruit-ripening, however, its fruit-ripening mechanism still needs more extensive and in-depth exploration. Here, using TMT and LC-MS, the proteome and phosphoproteome of AC++ (wild type) and rin (ripening-inhibitor) mutant fruits were studied to investigate the translation and post-translational regulation mechanisms of tomato fruit-ripening. A total of 6141 proteins and 4011 phosphorylation sites contained quantitative information. One-hundred proteins were identified in both omics’ profiles, which were mainly found in ethylene biosynthesis and signal transduction, photosynthesis regulation, carotenoid and flavonoid biosynthesis, chlorophyll degradation, ribosomal subunit expression changes, MAPK pathway, transcription factors and kinases. The affected protein levels were correlated with their corresponding gene transcript levels, such as NAC-NOR, MADS-RIN, IMA, TAGL1, MADS-MC and TDR4. Changes in the phosphorylation levels of NAC-NOR and IMA were involved in the regulation of tomato fruit-ripening. Although photosynthesis was inhibited, there were diverse primary and secondary metabolic pathways, such as glycolysis, fatty acid metabolism, vitamin metabolism and isoprenoid biosynthesis, regulated by phosphorylation. These data constitute a map of protein—protein phosphorylation in the regulation of tomato fruit-ripening, which lays the foundation for future in-depth study of the sophisticated molecular mechanisms of fruit-ripening and provide guidance for molecular breeding.
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16
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Zeng Z, Li F, Huang R, Wang Y, Liu T. Phosphoproteome analysis reveals an extensive phosphorylation of proteins associated with bast fiber growth in ramie. BMC PLANT BIOLOGY 2021; 21:473. [PMID: 34656094 PMCID: PMC8520194 DOI: 10.1186/s12870-021-03252-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Phosphorylation modification, one of the most common post-translational modifications of proteins, widely participates in the regulation of plant growth and development. Fibers extracted from the stem bark of ramie are important natural textile fibers; however, the role of phosphorylation modification in the growth of ramie fibers is largely unknown. RESULTS Here, we report a phosphoproteome analysis for the barks from the top and middle section of ramie stems, in which the fiber grows at different stages. A total of 10,320 phosphorylation sites from 9,170 unique phosphopeptides that were assigned to 3,506 proteins was identified, and 458 differentially phosphorylated sites from 323 proteins were detected in the fiber developmental barks. Twelve differentially phosphorylated proteins were the homologs of Arabidopsis fiber growth-related proteins. We further focused on the function of the differentially phosphorylated KNOX protein whole_GLEAN_10029667, and found that this protein dramatically repressed the fiber formation in Arabidopsis. Additionally, using a yeast two-hybridization assay, we identified a kinase and a phosphatase that interact with whole_GLEAN_10029667, indicating that they potentially target this KNOX protein to regulate its phosphorylation level. CONCLUSION The finding of this study provided insights into the involvement of phosphorylation modification in ramie fiber growth, and our functional characterization of whole_GLEAN_10029667 provide the first evidence to indicate the involvement of phosphorylation modification in the regulation of KNOX protein function in plants.
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Affiliation(s)
- Zheng Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Fu Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Renyan Huang
- Hunan Institute of Plant protection, Changsha, 410205, China
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.
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He Q, Zeng Z, Li F, Huang R, Wang Y, Liu T. Ubiquitylome analysis reveals the involvement of ubiquitination in the bast fiber growth of ramie. PLANTA 2021; 254:1. [PMID: 34081200 DOI: 10.1007/s00425-021-03652-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/29/2021] [Indexed: 06/12/2023]
Abstract
A total of 249 sites from 197 proteins showed a differential ubiquitination level in the fiber development of ramie barks. The function of two differentially ubiquitinated proteins for fiber growth was demonstrated. Ubiquitination is one of the most common post-translational modifications of proteins, and it plays essential roles in plant growth and development. However, the involvement of ubiquitination in the growth of plant fibers remains largely unknown. We compared the ubiquitylome of the top and middle stems of ramie bark, with different fiber growth stages. We identified 249 differentially ubiquitinated sites in 197 proteins in fiber-developing barks in the stems and found that seven were homologs of Arabidopsis proteins associated with fiber growth. Overexpression of the differentially ubiquitinated proteins, RWA3 homolog whole_GLEAN_10024150 and MYB protein whole_GLEAN_10015497, significantly promoted fiber growth in transgenic Arabidopsis, indicating their involvement in this process. We also found that the abundance of these proteins decreased when their ubiquitination levels increased and vice versa in the fiber-developing bark. These results indicated that the abundance of these two proteins was adjusted through ubiquitin-dependent degradation. Collectively, our findings provide important insights into the involvement of ubiquitination in the growth of ramie fibers.
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Affiliation(s)
- Qiaoyun He
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Zheng Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Fu Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Renyan Huang
- Hunan Institute of Plant Protection, Changsha, 410125, China
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.
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Tappiban P, Ying Y, Xu F, Bao J. Proteomics and Post-Translational Modifications of Starch Biosynthesis-Related Proteins in Developing Seeds of Rice. Int J Mol Sci 2021; 22:5901. [PMID: 34072759 PMCID: PMC8199009 DOI: 10.3390/ijms22115901] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/25/2022] Open
Abstract
Rice (Oryza sativa L.) is a foremost staple food for approximately half the world's population. The components of rice starch, amylose, and amylopectin are synthesized by a series of enzymes, which are responsible for rice starch properties and functionality, and then affect rice cooking and eating quality. Recently, proteomics technology has been applied to the establishment of the differentially expressed starch biosynthesis-related proteins and the identification of posttranslational modifications (PTMs) target starch biosynthesis proteins as well. It is necessary to summarize the recent studies in proteomics and PTMs in rice endosperm to deepen our understanding of starch biosynthesis protein expression and regulation, which will provide useful information to rice breeding programs and industrial starch applications. The review provides a comprehensive summary of proteins and PTMs involved in starch biosynthesis based on proteomic studies of rice developing seeds. Starch biosynthesis proteins in rice seeds were differentially expressed in the developing seeds at different developmental stages. All the proteins involving in starch biosynthesis were identified using proteomics methods. Most starch biosynthesis-related proteins are basically increased at 6-20 days after flowering (DAF) and decreased upon the high-temperature conditions. A total of 10, 14, 2, 17, and 7 starch biosynthesis related proteins were identified to be targeted by phosphorylation, lysine acetylation, succinylation, lysine 2-hydroxyisobutyrylation, and malonylation, respectively. The phosphoglucomutase is commonly targeted by five PTMs types. Research on the function of phosphorylation in multiple enzyme complex formation in endosperm starch biosynthesis is underway, while the functions of other PTMs in starch biosynthesis are necessary to be conducted in the near future.
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Affiliation(s)
- Piengtawan Tappiban
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Yining Ying
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Feifei Xu
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Jinsong Bao
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China
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Arefian M, Bhagya N, Prasad TSK. Phosphorylation-mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops. Biol Rev Camb Philos Soc 2021; 96:2164-2191. [PMID: 34047006 DOI: 10.1111/brv.12748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/18/2022]
Abstract
Protein phosphorylation is a major post-translational modification, regulating protein function, stability, and subcellular localization. To date, annotated phosphorylation data are available mainly for model organisms and humans, despite the economic importance of crop species and their large kinomes. Our understanding of the phospho-regulation of flowering in relation to the biology and interaction between the pollen and pistil is still significantly lagging, limiting our knowledge on kinase signalling and its potential applications to crop production. To address this gap, we bring together relevant literature that were previously disconnected to present an overview of the roles of phosphoproteomic signalling pathways in modulating molecular and cellular regulation within specific tissues at different morphological stages of flowering. This review is intended to stimulate research, with the potential to increase crop productivity by providing a platform for novel molecular tools.
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Affiliation(s)
- Mohammad Arefian
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - N Bhagya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
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20
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Orr JN, Waugh R, Colas I. Ubiquitination in Plant Meiosis: Recent Advances and High Throughput Methods. FRONTIERS IN PLANT SCIENCE 2021; 12:667314. [PMID: 33897750 PMCID: PMC8058418 DOI: 10.3389/fpls.2021.667314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/15/2021] [Indexed: 06/06/2023]
Abstract
Meiosis is a specialized cell division which is essential to sexual reproduction. The success of this highly ordered process involves the timely activation, interaction, movement, and removal of many proteins. Ubiquitination is an extraordinarily diverse post-translational modification with a regulatory role in almost all cellular processes. During meiosis, ubiquitin localizes to chromatin and the expression of genes related to ubiquitination appears to be enhanced. This may be due to extensive protein turnover mediated by proteasomal degradation. However, degradation is not the only substrate fate conferred by ubiquitination which may also mediate, for example, the activation of key transcription factors. In plant meiosis, the specific roles of several components of the ubiquitination cascade-particularly SCF complex proteins, the APC/C, and HEI10-have been partially characterized indicating diverse roles in chromosome segregation, recombination, and synapsis. Nonetheless, these components remain comparatively poorly understood to their counterparts in other processes and in other eukaryotes. In this review, we present an overview of our understanding of the role of ubiquitination in plant meiosis, highlighting recent advances, remaining challenges, and high throughput methods which may be used to overcome them.
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Affiliation(s)
- Jamie N. Orr
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- School of Agriculture and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Isabelle Colas
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
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Dukowic-Schulze S, van der Linde K. Oxygen, secreted proteins and small RNAs: mobile elements that govern anther development. PLANT REPRODUCTION 2021; 34:1-19. [PMID: 33492519 PMCID: PMC7902584 DOI: 10.1007/s00497-020-00401-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/24/2020] [Indexed: 05/24/2023]
Abstract
Correct anther development is essential for male fertility and subsequently agricultural yield. Defects in anther development range from the early stage of stamen formation until the late stage of tapetum degeneration. In particular, the specification of the four distinct somatic layers and the inner sporogenous cells need perfect orchestration relying on precise cell-cell communication. Up to now, several signals, which coordinate the anther´s developmental program, have been identified. Among the known signals are phytohormones, environmental conditions sensed via glutaredoxins, several receptor-like kinases triggered by ligands like MAC1, and small RNAs such as miRNAs and the monocot-prevalent reproductive phasiRNAs. Rather than giving a full review on anther development, here we discuss anther development with an emphasis on mobile elements like ROS/oxygen, secreted proteins and small RNAs (only briefly touching on phytohormones), how they might act and interact, and what the future of this research area might reveal.
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Affiliation(s)
- Stefanie Dukowic-Schulze
- Department of Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany.
| | - Karina van der Linde
- Department of Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany.
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22
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Zhang Y, Song Q, Zhang L, Li Z, Wang C, Zhang G. Comparative Proteomic Analysis of Developmental Changes in P-Type Cytoplasmic Male Sterile and Maintainer Anthers in Wheat. Int J Mol Sci 2021; 22:ijms22042012. [PMID: 33670552 PMCID: PMC7922732 DOI: 10.3390/ijms22042012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/10/2021] [Accepted: 02/16/2021] [Indexed: 11/16/2022] Open
Abstract
Cytoplasmic male sterility (CMS) plays an important role in the application of heterosis in wheat (Triticum aestivum L.). However, the molecular mechanism underlying CMS remains unknown. This study provides a comprehensive morphological and proteomic analysis of the anthers of a P-type CMS wheat line (P) and its maintainer line, Yanshi 9 hao (Y). Cytological observations indicated that the P-type CMS line shows binucleate microspore abortion. In this line, the tapetum degraded early, leading to anther cuticle defects, which could not provide the nutrition needed for microspore development in a timely manner, thus preventing the development of the microspore to the normal binucleate stage. Proteomic analysis revealed novel proteins involved in P-type CMS. Up to 2576 differentially expressed proteins (DEPs) were quantified in all anthers, and these proteins were significantly enriched in oxidative phosphorylation, glycolysis/gluconeogenesis, citrate cycle (TCA cycle), starch and sucrose metabolism, phenylpropanoid biosynthesis, and pyruvate metabolism pathways. These proteins may comprise a network that regulates male sterility in wheat. Based on the function analysis of DEPs involved in the complex network, we concluded that the P-type CMS line may be due to cellular dysfunction caused by disturbed carbohydrate metabolism, inadequate energy supply, and disturbed protein synthesis. These results provide insights into the molecular mechanism underlying male sterility and serve as a valuable resource for researchers in plant biology, in general, and plant sexual reproduction, in particular.
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Affiliation(s)
- Yamin Zhang
- National Yangling Agricultural Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Qilu Song
- National Yangling Agricultural Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Lili Zhang
- National Yangling Agricultural Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Zheng Li
- National Yangling Agricultural Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Chengshe Wang
- National Yangling Agricultural Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Gaisheng Zhang
- National Yangling Agricultural Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, College of Agronomy, Northwest A&F University, Yangling 712100, China
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23
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Luo L, Wan Q, Zhang K, Zhang X, Guo R, Wang C, Zheng C, Liu F, Ding Z, Wan Y. AhABI4s Negatively Regulate Salt-Stress Response in Peanut. FRONTIERS IN PLANT SCIENCE 2021; 12:741641. [PMID: 34721468 PMCID: PMC8551806 DOI: 10.3389/fpls.2021.741641] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/13/2021] [Indexed: 05/04/2023]
Abstract
Soil salinity is one of the major factors that limit the area of cultivable land and yield potential of crops. The ability of salt tolerance varies with plant species. Peanut (Arachis hypogaea L.) is a moderately salt-sensitive and economically important crop, however, their biological processes involved in salt-stress response remain unclear. In this study, we investigated the role of A. hypogaea L. ABSCISIC ACID INSENSITIVE 4s (AhABI4s) in salt tolerance and elucidated its mode of action in peanuts. The results showed that the downregulation of AhABI4s via whole plant virus-induced gene silencing has enhanced the survival rate, biomass accumulation, and root/shoot ratio of peanut seedlings in response to salt-stress. Transcriptomics, quantitative proteomics, and phosphoproteomic analyses were performed using AhABI4s-silenced and Mock plants. The expression pattern of 15,247 genes, 1,900 proteins, and 2,620 phosphorylation sites were affected by silencing of AhABI4s in peanut leaf and root after sodium chloride (NaCl) treatment. Among them, 63 potential downstream target genes of ABI4 changed consistently at both transcription and translation levels, and the protein/phosphorylation levels of 31 ion transporters/channels were also affected. Electrophoretic mobility shift assays (EMSA) showed that ABI4 was able to bind to the promoters of HSP70, fructokinase (FRK), and pyruvate kinase (PK) coding genes in vitro. In addition, we also detected a binding preference of AhABI4 for CACT(G/T)GCA motif in the promoters of down-regulated genes in peanut leaf. Collectively, the potential downstream targets which were regulated at the levels of transcription and translation, binding preference, and in vivo phosphorylation sites that had been revealed in this study will provide new insight into the AhABI4s-mediated salt tolerance regulation mechanism in peanuts.
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Affiliation(s)
- Lu Luo
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, College of Life Sciences, Shandong University, Qingdao, China
| | - Qian Wan
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Kun Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Xiurong Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Ruijie Guo
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Cai Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Chengchao Zheng
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Fengzhen Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
- *Correspondence: Fengzhen Liu
| | - Zhaojun Ding
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, College of Life Sciences, Shandong University, Qingdao, China
- Zhaojun Ding
| | - Yongshan Wan
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
- Yongshan Wan
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24
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Zhou Q, Meng Q, Tan X, Ding W, Ma K, Xu Z, Huang X, Gao H. Protein Phosphorylation Changes During Systemic Acquired Resistance in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:748287. [PMID: 34858456 PMCID: PMC8632492 DOI: 10.3389/fpls.2021.748287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/08/2021] [Indexed: 05/03/2023]
Abstract
Systemic acquired resistance (SAR) in plants is a defense response that provides resistance against a wide range of pathogens at the whole-plant level following primary infection. Although the molecular mechanisms of SAR have been extensively studied in recent years, the role of phosphorylation that occurs in systemic leaves of SAR-induced plants is poorly understood. We used a data-independent acquisition (DIA) phosphoproteomics platform based on high-resolution mass spectrometry in an Arabidopsis thaliana model to identify phosphoproteins related to SAR establishment. A total of 8011 phosphorylation sites from 3234 proteins were identified in systemic leaves of Pseudomonas syringae pv. maculicola ES4326 (Psm ES4326) and mock locally inoculated plants. A total of 859 significantly changed phosphoproteins from 1119 significantly changed phosphopeptides were detected in systemic leaves of Psm ES4326 locally inoculated plants, including numerous transcription factors and kinases. A variety of defense response-related proteins were found to be differentially phosphorylated in systemic leaves of Psm ES4326 locally inoculated leaves, suggesting that these proteins may be functionally involved in SAR through phosphorylation or dephosphorylation. Significantly changed phosphoproteins were enriched mainly in categories related to response to abscisic acid, regulation of stomatal movement, plant-pathogen interaction, MAPK signaling pathway, purine metabolism, photosynthesis-antenna proteins, and flavonoid biosynthesis. A total of 28 proteins were regulated at both protein and phosphorylation levels during SAR. RT-qPCR analysis revealed that changes in phosphorylation levels of proteins during SAR did not result from changes in transcript abundance. This study provides comprehensive details of key phosphoproteins associated with SAR, which will facilitate further research on the molecular mechanisms of SAR.
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Affiliation(s)
- Qingfeng Zhou
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Qi Meng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi’an, China
| | - Xiaomin Tan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi’an, China
| | - Wei Ding
- Shanghai Omicsspace Biotechnology Co., Ltd., Shanghai, China
| | - Kang Ma
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Ziqin Xu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi’an, China
| | - Xuan Huang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi’an, China
- *Correspondence: Xuan Huang,
| | - Hang Gao
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
- Hang Gao,
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25
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Lee YS, Maple R, Dürr J, Dawson A, Tamim S, Del Genio C, Papareddy R, Luo A, Lamb JC, Amantia S, Sylvester AW, Birchler JA, Meyers BC, Nodine MD, Rouster J, Gutierrez-Marcos J. A transposon surveillance mechanism that safeguards plant male fertility during stress. NATURE PLANTS 2021; 7:34-41. [PMID: 33398155 DOI: 10.1038/s41477-020-00818-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
Although plants are able to withstand a range of environmental conditions, spikes in ambient temperature can impact plant fertility causing reductions in seed yield and notable economic losses1,2. Therefore, understanding the precise molecular mechanisms that underpin plant fertility under environmental constraints is critical to safeguarding future food production3. Here, we identified two Argonaute-like proteins whose activities are required to sustain male fertility in maize plants under high temperatures. We found that MALE-ASSOCIATED ARGONAUTE-1 and -2 associate with temperature-induced phased secondary small RNAs in pre-meiotic anthers and are essential to controlling the activity of retrotransposons in male meiocyte initials. Biochemical and structural analyses revealed how male-associated Argonaute activity and its interaction with retrotransposon RNA targets is modulated through the dynamic phosphorylation of a set of highly conserved, surface-located serine residues. Our results demonstrate that an Argonaute-dependent, RNA-guided surveillance mechanism is critical in plants to sustain male fertility under environmentally constrained conditions, by controlling the mutagenic activity of transposons in male germ cells.
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Affiliation(s)
- Yang-Seok Lee
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Robert Maple
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Julius Dürr
- School of Life Sciences, University of Warwick, Coventry, UK
| | | | - Saleh Tamim
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Charo Del Genio
- Centre for Fluid and Complex Systems, School of Computing, Electronics and Mathematics, Coventry University, Coventry, UK
| | - Ranjith Papareddy
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Anding Luo
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | - Jonathan C Lamb
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
- BayerCrop Science Division, St. Louis, MO, USA
| | - Stefano Amantia
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Anne W Sylvester
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Blake C Meyers
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Michael D Nodine
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
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26
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Zhu L, Cheng H, Peng G, Wang S, Zhang Z, Ni E, Fu X, Zhuang C, Liu Z, Zhou H. Ubiquitinome Profiling Reveals the Landscape of Ubiquitination Regulation in Rice Young Panicles. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:305-320. [PMID: 33147495 PMCID: PMC7801245 DOI: 10.1016/j.gpb.2019.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 12/06/2018] [Accepted: 01/11/2019] [Indexed: 02/04/2023]
Abstract
Ubiquitination, an essential post-transcriptional modification (PTM), plays a vital role in nearly every biological process, including development and growth. Despite its functions in plant reproductive development, its targets in rice panicles remain unclear. In this study, we used proteome-wide profiling of lysine ubiquitination in rice (O. sativa ssp. indica) young panicles. We created the largest ubiquitinome dataset in rice to date, identifying 1638 lysine ubiquitination sites on 916 unique proteins. We detected three conserved ubiquitination motifs, noting that acidic glutamic acid (E) and aspartic acid (D) were most frequently present around ubiquitinated lysine. Enrichment analysis of Gene Ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of these ubiquitinated proteins revealed that ubiquitination plays an important role in fundamental cellular processes in rice young panicles. Interestingly, enrichment analysis of protein domains indicated that ubiquitination was enriched on a variety of receptor-like kinases and cytoplasmic tyrosine and serine-threonine kinases. Furthermore, we analyzed the crosstalk between ubiquitination, acetylation, and succinylation, and constructed a potential protein interaction network within our rice ubiquitinome. Moreover, we identified ubiquitinated proteins related to pollen and grain development, indicating that ubiquitination may play a critical role in the physiological functions in young panicles. Taken together, we reported the most comprehensive lysine ubiquitinome in rice so far, and used it to reveal the functional role of lysine ubiquitination in rice young panicles.
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Affiliation(s)
- Liya Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Han Cheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China; School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Guoqing Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Shuansuo Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, National Centre for Plant Gene Research, Beijing 100101, China
| | - Zhiguo Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Erdong Ni
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiangdong Fu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, National Centre for Plant Gene Research, Beijing 100101, China
| | - Chuxiong Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zexian Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China; College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Hai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
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27
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Vessal S, Arefian M, Siddique KHM. Proteomic responses to progressive dehydration stress in leaves of chickpea seedlings. BMC Genomics 2020; 21:523. [PMID: 32727351 PMCID: PMC7392671 DOI: 10.1186/s12864-020-06930-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/20/2020] [Indexed: 12/14/2022] Open
Abstract
Background Chickpea is an important food legume crop with high protein levels that is widely grown in rainfed areas prone to drought stress. Using an integrated approach, we describe the relative changes in some physiological parameters and the proteome of a drought-tolerant (MCC537, T) and drought-sensitive (MCC806, S) chickpea genotype. Results Under progressive dehydration stress, the T genotype relied on a higher relative leaf water content after 3 and 5 d (69.7 and 49.3%) than the S genotype (59.7 and 40.3%) to maintain photosynthetic activities and improve endurance under stress. This may have been facilitated by greater proline accumulation in the T genotype than the S genotype (14.3 and 11.1 μmol g− 1 FW at 5 d, respectively). Moreover, the T genotype had less electrolyte leakage and lower malondialdehyde contents than the S genotype under dehydration stress, indicating greater membrane stability and thus greater dehydration tolerance. The proteomic analysis further confirmed that, in response to dehydration, the T genotype activated more proteins related to photosynthesis, stress response, protein synthesis and degradation, and gene transcription and signaling than the S genotype. Of the time-point dependent proteins, the largest difference in protein abundance occurred at 5 d, with 29 spots increasing in the T genotype and 30 spots decreasing in the S genotype. Some of the identified proteins—including RuBisCo, ATP synthase, carbonic anhydrase, psbP domain-containing protein, L-ascorbate peroxidase, 6-phosphogluconate dehydrogenase, elongation factor Tu, zinc metalloprotease FTSH 2, ribonucleoproteins and auxin-binding protein—may play a functional role in drought tolerance in chickpea. Conclusions This study highlights the significance of genotype- and time-specific proteins associated with dehydration stress and identifies potential resources for molecular drought tolerance improvement in chickpea.
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Affiliation(s)
- Saeedreza Vessal
- Research Center for Plant Sciences, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Mohammad Arefian
- Plant Biotechnology and Breeding Department, College of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia
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28
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Wang X, Cheng C, Li Q, Zhang K, Lou Q, Li J, Chen J. Multi-omics analysis revealed that MAPK signaling and flavonoid metabolic pathway contributed to resistance against Meloidogyne incognita in the introgression line cucumber. J Proteomics 2020; 220:103675. [PMID: 32004728 DOI: 10.1016/j.jprot.2020.103675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/07/2020] [Accepted: 01/28/2020] [Indexed: 01/04/2023]
Abstract
Inhibiting giant cells (GCs) development is an important characteristic of introgression line cucumber IL10-1 against Meloidogyne incognita proved by our previous study, but the systematic regulatory pathways were unknown. To reveal the regulation pathways more comprehensively, in the current study, we performed a joint analysis of RNA-Seq and lable-free quantitative proteomics between the IL10-1 (resistant) and the CC3 (susceptible cucumber) after inoculation with M. incognita. The results indicated that flavonoid biosynthesis pathway was specifically enriched in IL10-1. And protein species of Csa5P590220 and Csa5P589940 associated with flavonoid biosynthesis were highly translated in IL10-1 compared with these in CC3 at 3 days post inoculation (dpi), which would resulted in the excess of flavonoids in IL10-1 roots. In addition, phosphoproteomic analysis found that phosphorylated protein species involved in MAPK signaling cascade were enhanced in IL10-1, while they were inhibited in CC3 at 3 dpi. Accordingly, we speculate that the enhanced MAPK cascade signaling plays an important role in signal transduction for IL10-1 regulating the flavonoid biosynthesis. Knowledge from the study provide important regulatory pathways and protein species of introgression line cucumber against M. incognita, which will help in efforts to improve the recognition of the resistance mechanism of plants against nematode. SIGNIFICANCE: The current approach of joint analysis in transcription level, protein level and protein phosphorylation level more comprehensively revealed the different expression patterns at the molecular level of resistant and susceptible cucumber after inoculation with M. incognita. Based on the different expression patterns, we explore the pathway of resistance regulation of resistant cucumber IL10-1. Moreover, our results are helpful for the discovery of key genes and then apply them to M. incognita-resistance breeding.
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Affiliation(s)
- Xing Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Chunyan Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Qingrong Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Kaijing Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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29
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Zhang C, Feng X, Hu M, Zhang Z. How to Study the Proteomes and Phosphoproteomes of Anther and Pollen. Methods Mol Biol 2020; 2061:259-265. [PMID: 31583665 DOI: 10.1007/978-1-4939-9818-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Proteomics analysis was a powerful technology for characterizing proteins and protein posttranslational modification (PTMs). Recently, many anther and pollen-related proteomic analyses have been reported, which have expanded our understanding of anther and pollen development and regulation. In this chapter, we describe a detailed, optimized protocol for the separation, digestion, tagging, and subsequent mass spectrometry-based identification and quantification of proteins and phosphoproteins from anther and pollen.
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Affiliation(s)
- Chi Zhang
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Xiaobing Feng
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Menghui Hu
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Zaibao Zhang
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China.
- Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan, China.
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30
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Chang Z, Xu C, Huang X, Yan W, Qiu S, Yuan S, Ni H, Chen S, Xie G, Chen Z, Wu J, Tang X. The plant-specific ABERRANT GAMETOGENESIS 1 gene is essential for meiosis in rice. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:204-218. [PMID: 31587067 DOI: 10.1093/jxb/erz441] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
Meiotic recombination plays a central role in maintaining genome stability and increasing genetic diversity. Although meiotic progression and core components are widely conserved across kingdoms, significant differences remain among species. Here we identify a rice gene ABERRANT GAMETOGENESIS 1 (AGG1) that controls both male and female gametogenesis. Cytological and immunostaining analysis showed that in the osagg1 mutant the early recombination processes and synapsis occurred normally, but the chiasma number was dramatically reduced. Moreover, OsAGG1 was found to interact with ZMM proteins OsHEI10, OsZIP4, and OsMSH5. These results suggested that OsAGG1 plays an important role in crossover formation. Phylogenetic analysis showed that OsAGG1 is a plant-specific protein with a highly conserved N-terminal region. Further genetic and protein interaction analyses revealed that the conserved N-terminus was essential for the function of the OsAGG1 protein. Overall, our work demonstrates that OsAGG1 is a novel and critical component in rice meiotic crossover formation, expanding our understanding of meiotic progression. This study identified a plant-specific gene ABERRANT GAMETOGENESIS 1 that is required for meiotic crossover formation in rice. The conserved N-terminus of the AGG1 protein was found to be essential for its function.
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Affiliation(s)
- Zhenyi Chang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, China
| | - Chunjue Xu
- Shenzhen Institute of Molecular Crop Design, Shenzhen, China
| | - Xiaoyan Huang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Wei Yan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, China
| | - Shijun Qiu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Shuting Yuan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Haoling Ni
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Shujing Chen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Gang Xie
- Shenzhen Institute of Molecular Crop Design, Shenzhen, China
| | - Zhufeng Chen
- Shenzhen Institute of Molecular Crop Design, Shenzhen, China
| | - Jianxin Wu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoyan Tang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, China
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31
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Yang J, Xie MY, Yang XL, Liu BH, Lin HH. Phosphoproteomic Profiling Reveals the Importance of CK2, MAPKs and CDPKs in Response to Phosphate Starvation in Rice. PLANT & CELL PHYSIOLOGY 2019; 60:2785-2796. [PMID: 31424513 DOI: 10.1093/pcp/pcz167] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 08/14/2019] [Indexed: 05/21/2023]
Abstract
Phosphorus is one of the most important macronutrients required for plant growth and development. The importance of phosphorylation modification in regulating phosphate (Pi) homeostasis in plants is emerging. We performed phosphoproteomic profiling to characterize proteins whose degree of phosphorylation is altered in response to Pi starvation in rice root. A subset of 554 proteins, including 546 down-phosphorylated and eight up-phosphorylated proteins, exhibited differential phosphorylation in response to Pi starvation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis with the differentially phosphorylated proteins indicated that RNA processing, transport, splicing and translation and carbon metabolism played critical roles in response to Pi starvation in rice. Levels of phosphorylation of four mitogen-activated protein kinases (MAPKs), including OsMAPK6, five calcium-dependent protein kinases (CDPKs) and OsCK2β3 decreased in response to Pi starvation. The decreased phosphorylation level of OsMAPK6 was confirmed by Western blotting. Mutation of OsMAPK6 led to Pi accumulation under Pi-sufficient conditions. Motif analysis indicated that the putative MAPK, casein kinase 2 (CK2) and CDPK substrates represented about 54.4%, 21.5% and 4.7%, respectively, of the proteins exhibiting differential phosphorylation. Based on the motif analysis, 191, 151 and 46 candidate substrates for MAPK, CK2 and CDPK were identified. These results indicate that modification of phosphorylation profiles provides complementary information on Pi-starvation-induced processes, with CK2, MAPK and CDPK protein kinase families playing key roles in these processes in rice.
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Affiliation(s)
- Jian Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Sichuan, Chengdu 610065, China
| | - Meng-Yang Xie
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Sichuan, Chengdu 610065, China
| | - Xiao-Li Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Sichuan, Chengdu 610065, China
| | - Bao-Hui Liu
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Hong-Hui Lin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Sichuan, Chengdu 610065, China
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32
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Akagi T, Pilkington SM, Varkonyi-Gasic E, Henry IM, Sugano SS, Sonoda M, Firl A, McNeilage MA, Douglas MJ, Wang T, Rebstock R, Voogd C, Datson P, Allan AC, Beppu K, Kataoka I, Tao R. Two Y-chromosome-encoded genes determine sex in kiwifruit. NATURE PLANTS 2019; 5:801-809. [PMID: 31383971 DOI: 10.1038/s41477-019-0489-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/02/2019] [Indexed: 05/20/2023]
Abstract
Dioecy, the presence of male and female individuals, has evolved independently in multiple flowering plant lineages1-3. Although theoretical models for the evolution of dioecy, such as the 'two-mutations' model, are well established4,5, little is known about the specific genes determining sex and their evolutionary history3. Kiwifruit, a major tree crop consumed worldwide, is a dioecious species. In kiwifruit we previously identified a Y-encoded sex-determinant candidate gene acting as the suppressor of feminization (SuF), named Shy Girl (SyGI)6. Here, we identify a second Y-encoded sex-determinant that we named Friendly Boy (FrBy), which exhibits strong expression in tapetal cells. Gene-editing and complementation analyses in Arabidopsis thaliana and Nicotiana tabacum indicated that FrBy acts for the maintenance of male (M) functions, independently of SyGI, and that these functions are conserved across angiosperm species. We further characterized the genomic architecture of the small (<1 megabase pairs (Mb)) male-specific region of the Y chromosome (MSY), which harbours only two genes expressed extensively in developing gynoecia and androecia, respectively: SyGI and FrBy. Re-sequencing of the genome of a natural hermaphrodite kiwifruit revealed that this individual is genetically male but carries deletion(s) of parts of the Y chromosome, including SyGI. Additionally, expression of FrBy in female kiwifruit resulted in hermaphrodite plants. These results clearly indicate that Y-encoded SyGI and FrBy act independently as the SuF and M factors in kiwifruit, respectively, and provide insight into not only the evolutionary path leading to a two-factor sex-determination system, but also a new breeding approach for dioecious species.
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Affiliation(s)
- Takashi Akagi
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
- JST, PRESTO, Kawaguchi-shi, Saitama, Japan.
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
| | - Sarah M Pilkington
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, USA
| | - Shigeo S Sugano
- JST, PRESTO, Kawaguchi-shi, Saitama, Japan
- R-GIRO, Ritsumeikan University, Shiga, Japan
| | - Minori Sonoda
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Alana Firl
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, USA
| | - Mark A McNeilage
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Mikaela J Douglas
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Tianchi Wang
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Ria Rebstock
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Charlotte Voogd
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Paul Datson
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Andrew C Allan
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Kenji Beppu
- Faculty of Agriculture, Kagawa University, Miki, Kagawa, Japan
| | - Ikuo Kataoka
- Faculty of Agriculture, Kagawa University, Miki, Kagawa, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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Yang Y, Wei F, Braynen J, Wei X, Tian B, Shi G, Cao G, Yuan J, Zhang X. Cytological and proteomic analyses of floral buds reveal an altered atlas of meiosis in autopolyploid Brassica rapa. Cell Biosci 2019; 9:49. [PMID: 31236208 PMCID: PMC6580506 DOI: 10.1186/s13578-019-0313-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/14/2019] [Indexed: 12/21/2022] Open
Abstract
Background Polyploidy is considered as a basic event in plant speciation and evolution in nature, and the cytological and proteomic profilings of floral buds at meiosis (FAM) would definitely contribute to a better understanding of the polyploid-associated effects during plant reproduction cycle. Results Herein, the cytological investigations demonstrated that chromosome behaviors such as univalent and multivalent at prophase I, chaotic alignments at metaphase, aberrant segregation at telophase, were frequently observed during meiosis in autotetraploid Brassica rapa. The proteomic analysis showed a total of 562 differentially expressed proteins (DEPs) were identified in FAM between autotetraploid and diploid B. rapa. Notably, PARP2 and LIG1 related to base excision repair and BARD1 involved in recombination were significantly down-regulated in autotetraploid B. rapa, which indicated DNA repair pathway were more likely affected during meiosis in autotetraploid B. rapa. The functional analysis showed that DEPs assigned to “chromatin structure and dynamics”, “cell cycle control, cell division, chromosome partitioning” and “cytoskeleton” were preferentially up-regulated, which suggested a robust regulation of cell division in autotetraploid B. rapa. In combination with the floral RNA-seq data released, a number of DEPs were found positively correlated with their transcript abundance, but posttranslational modification of proteins might also play a role in regulating meiosis course after polyploidization. Conclusions In general, this study provides a detailed cytology and proteome landscape of FAM between diploid and autotetraploid B. rapa, which definitely affords us a better understanding of uniformity and discrepancy of meiosis at the plant reproductive stage before and after polyploidization. Electronic supplementary material The online version of this article (10.1186/s13578-019-0313-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yan Yang
- 1School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China.,2School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Fang Wei
- 1School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China.,2School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Janeen Braynen
- 2School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China.,3Institute of Horticultural Research, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan People's Republic of China
| | - Xiaochun Wei
- 3Institute of Horticultural Research, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan People's Republic of China
| | - Baoming Tian
- 1School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Gongyao Shi
- 1School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Gangqiang Cao
- 1School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Jiachen Yuan
- 2School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Xiaowei Zhang
- 3Institute of Horticultural Research, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan People's Republic of China
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Zhang Z, Ke D, Hu M, Zhang C, Deng L, Li Y, Li J, Zhao H, Cheng L, Wang L, Yuan H. Quantitative phosphoproteomic analyses provide evidence for extensive phosphorylation of regulatory proteins in the rhizobia-legume symbiosis. PLANT MOLECULAR BIOLOGY 2019; 100:265-283. [PMID: 30989446 DOI: 10.1007/s11103-019-00857-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Symbiotic nitrogen fixation in root nodules of grain legumes is essential for high yielding. Protein phosphorylation/dephosphorylation plays important role in root nodule development. Differences in the phosphoproteomes may either be developmental specific and related to nitrogen fixation activity. An iTRAQ-based quantitative phosphoproteomic analyses during nodule development enables identification of specific phosphorylation signaling in the Lotus-rhizobia symbiosis. During evolution, legumes (Fabaceae) have evolved a symbiotic relationship with rhizobia, which fix atmospheric nitrogen and produce ammonia that host plants can then absorb. Root nodule development depends on the activation of protein phosphorylation-mediated signal transduction cascades. To investigate possible molecular mechanisms of protein modulation during nodule development, we used iTRAQ-based quantitative proteomic analyses to identify root phosphoproteins during rhizobial colonization and infection of Lotus japonicus. 1154 phosphoproteins with 2957 high-confidence phosphorylation sites were identified. Gene ontology enrichment analysis of functional groups of these genes revealed that the biological processes mediated by these proteins included cellular processes, signal transduction, and transporter activity. Quantitative data highlighted the dynamics of protein phosphorylation during nodule development and, based on regulatory trends, seven groups were identified. RNA splicing and brassinosteroid (BR) signaling pathways were extensively affected by phosphorylation, and most Ser/Arg-rich (SR) proteins were multiply phosphorylated. In addition, many proposed kinase-substrate pairs were predicted, and in these MAPK6 substrates were found to be highly enriched. This study offers insights into the regulatory processes underlying nodule development, provides an accessible resource cataloging the phosphorylation status of thousands of Lotus proteins during nodule development, and develops our understanding of post-translational regulatory mechanisms in the Lotus-rhizobia symbiosis.
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Affiliation(s)
- Zaibao Zhang
- Henan Key Laboratory of Tea Plant Biology, Xinyang Normal University, Xinyang, Henan, China
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Danxia Ke
- Henan Key Laboratory of Tea Plant Biology, Xinyang Normal University, Xinyang, Henan, China
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Menghui Hu
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Chi Zhang
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Lijun Deng
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Yuting Li
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Jiuli Li
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Hai Zhao
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Lin Cheng
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Lei Wang
- Henan Key Laboratory of Tea Plant Biology, Xinyang Normal University, Xinyang, Henan, China.
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China.
| | - Hongyu Yuan
- Henan Key Laboratory of Tea Plant Biology, Xinyang Normal University, Xinyang, Henan, China.
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China.
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35
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Liao PF, Ouyang JX, Zhang JJ, Yang L, Wang X, Peng XJ, Wang D, Zhu YL, Li SB. OsDCL3b affects grain yield and quality in rice. PLANT MOLECULAR BIOLOGY 2019; 99:193-204. [PMID: 30652247 DOI: 10.1007/s11103-018-0806-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
We reported that knockdown of OsDCL3b decreased grain yield but increased grain quality in rice, which is helpful for molecular breeding in crops. Multiple DICER-LIKE (DCL) genes usually exist and show diverse biochemical and phenotypic functions in land plants. In rice, the biochemical function of OsDCL3b is known to process 24-nucleotide panicle phased small RNAs, however, its phenotypic functions are unclear. Here we reported that knockdown of OsDCL3b led to reduced pollen fertility, seed setting rate, and decreased grain yield but increased grain quality in rice. To reveal the molecular mechanism of the above phenomena, extracted RNAs from rice panicles of the wild type (WT) and OsDCL3b-RNAi line S6-1 were analyzed by deep sequencing. It showed that knockdown of OsDCL3b affected the biogenesis of both 21- and 24-nucleotide small RNAs including miRNAs and phased small RNAs. Using RNA-seq, 644 up- and 530 down-regulated mRNA genes were identified in panicles of line S6-1, and 550 and 273 differentially spliced genes with various alternative splicing (AS) events were observed in panicles of line S6-1 and WT, respectively, suggesting that OsDCL3b involved in influencing the transcript levels of mRNA genes and the AS events in rice panicles. Thus, our results show that knockdown of OsDCL3b will affect the biogenesis of small RNAs, which is involved in regulating the transcription of mRNA genes, and consequently influence the grain yield and quality in rice.
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Affiliation(s)
- Peng-Fei Liao
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Jie-Xiu Ouyang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Jian-Jun Zhang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Lan Yang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Xin Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Xiao-Jue Peng
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - You-Lin Zhu
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, 330031, China.
| | - Shao-Bo Li
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, 330031, China.
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36
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Lewandowska D, Zhang R, Colas I, Uzrek N, Waugh R. Application of a Sensitive and Reproducible Label-Free Proteomic Approach to Explore the Proteome of Individual Meiotic-Phase Barley Anthers. FRONTIERS IN PLANT SCIENCE 2019; 10:393. [PMID: 31001307 PMCID: PMC6454111 DOI: 10.3389/fpls.2019.00393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 03/14/2019] [Indexed: 05/02/2023]
Abstract
Meiosis is a highly dynamic and precisely regulated process of cell division, leading to the production of haploid gametes from one diploid parental cell. In the crop plant barley (Hordeum vulgare), male meiosis occurs in anthers, in specialized cells called meiocytes. Barley meiotic tissue is scarce and not easily accessible, making meiosis study a challenging task. We describe here a new micro-proteomics workflow that allows sensitive and reproducible genome-wide label-free proteomic analysis of individual staged barley anthers. This micro-proteomic approach detects more than 4,000 proteins from such small amounts of material as two individual anthers, covering a dynamic range of protein relative abundance levels across five orders of magnitude. We applied our micro-proteomics workflow to investigate the proteome of the developing barley anther containing pollen mother cells in the early stages of meiosis and we successfully identified 57 known and putative meiosis-related proteins. Meiotic proteins identified in our study were found to be key players of many steps and processes in early prophase such as: chromosome condensation, synapsis, DNA double-strand breaks or crossover formation. Considering the small amount of starting material, this work demonstrates an important technological advance in plant proteomics and can be applied for proteomic examination of many size-limited plant specimens. Moreover, it is the first insight into the proteome of individual barley anther at early meiosis. The proteomic data have been deposited to the ProteomeXchange with the accession number PXD010887.
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Affiliation(s)
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Isabelle Colas
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Nicola Uzrek
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- *Correspondence: Robbie Waugh,
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37
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G protein subunit phosphorylation as a regulatory mechanism in heterotrimeric G protein signaling in mammals, yeast, and plants. Biochem J 2018; 475:3331-3357. [PMID: 30413679 DOI: 10.1042/bcj20160819] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/28/2018] [Accepted: 10/02/2018] [Indexed: 12/15/2022]
Abstract
Heterotrimeric G proteins composed of Gα, Gβ, and Gγ subunits are vital eukaryotic signaling elements that convey information from ligand-regulated G protein-coupled receptors (GPCRs) to cellular effectors. Heterotrimeric G protein-based signaling pathways are fundamental to human health [Biochimica et Biophysica Acta (2007) 1768, 994-1005] and are the target of >30% of pharmaceuticals in clinical use [Biotechnology Advances (2013) 31, 1676-1694; Nature Reviews Drug Discovery (2017) 16, 829-842]. This review focuses on phosphorylation of G protein subunits as a regulatory mechanism in mammals, budding yeast, and plants. This is a re-emerging field, as evidence for phosphoregulation of mammalian G protein subunits from biochemical studies in the early 1990s can now be complemented with contemporary phosphoproteomics and genetic approaches applied to a diversity of model systems. In addition, new evidence implicates a family of plant kinases, the receptor-like kinases, which are monophyletic with the interleukin-1 receptor-associated kinase/Pelle kinases of metazoans, as possible GPCRs that signal via subunit phosphorylation. We describe early and modern observations on G protein subunit phosphorylation and its functional consequences in these three classes of organisms, and suggest future research directions.
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38
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Chen P, Li R, Zhou R. Comparative phosphoproteomic analysis reveals differentially phosphorylated proteins regulate anther and pollen development in kenaf cytoplasmic male sterility line. Amino Acids 2018; 50:841-862. [DOI: 10.1007/s00726-018-2564-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/29/2018] [Indexed: 12/28/2022]
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39
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Pang Y, Zhou X, Chen Y, Bao J. Comparative Phosphoproteomic Analysis of the Developing Seeds in Two Indica Rice ( Oryza sativa L.) Cultivars with Different Starch Quality. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:3030-3037. [PMID: 29486119 DOI: 10.1021/acs.jafc.8b00074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Protein phosphorylation plays important roles in regulation of various molecular events such as plant growth and seed development. However, its involvement in starch biosynthesis is less understood. Here, a comparative phosphoproteomic analysis of two indica rice cultivars during grain development was performed. A total of 2079 and 2434 phosphopeptides from 1273 and 1442 phosphoproteins were identified, covering 2441 and 2808 phosphosites in indica rice 9311 and Guangluai4 (GLA4), respectively. Comparative analysis identified 303 differentially phosphorylated peptides, and 120 and 258 specifically phosphorylated peptides in 9311 and GLA4, respectively. Phosphopeptides in starch biosynthesis related enzymes such as AGPase, SSIIa, SSIIIa, BEI, BEIIb, PUL, and Pho1were identified. GLA4 and 9311 had different amylose content, pasting viscosities, and gelatinization temperature, suggesting subtle difference in starch biosynthesis and regulation between GLA4 and 9311. Our study will give added impetus to further understanding the regulatory mechanism of starch biosynthesis at the phosphorylation level.
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Affiliation(s)
- Yuehan Pang
- Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology , Zhejiang University , Huajiachi Campus, Hangzhou , 310029 , China
| | - Xin Zhou
- Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology , Zhejiang University , Huajiachi Campus, Hangzhou , 310029 , China
| | - Yaling Chen
- College of Life Sciences , Jiangxi Normal University , Nanchang , 330022 , China
| | - Jinsong Bao
- Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology , Zhejiang University , Huajiachi Campus, Hangzhou , 310029 , China
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40
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Cai W, Zhang D. The role of receptor-like kinases in regulating plant male reproduction. PLANT REPRODUCTION 2018; 31:77-87. [PMID: 29508076 DOI: 10.1007/s00497-018-0332-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/19/2018] [Indexed: 05/21/2023]
Abstract
RLKs in anther development. The cell-to-cell communication is essential for specifying different cell types during plant growth, development and adaption to the ever-changing environment. Plant male reproduction, in particular, requires the exquisitely synchronized development of different cell layers within the male tissue, the anther. Receptor-like kinases (RLKs) belong to a large group of kinases localized on the cell surfaces, perceiving extracellular signals and thereafter regulating intracellular processes. Here we update the role of RLKs in early anther development by defining the cell fate and anther patterning, responding to the changing environment and controlling anther carbohydrate metabolism. We provide speculation of the poorly characterized ligands and substrates of these RLKs. The conserved and diversified aspects underlying the function of RLKs in anther development are discussed.
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Affiliation(s)
- Wenguo Cai
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, 5064, Australia.
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41
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Zhang Z, Hu M, Feng X, Gong A, Cheng L, Yuan H. Proteomes and Phosphoproteomes of Anther and Pollen: Availability and Progress. Proteomics 2018; 17. [PMID: 28665021 DOI: 10.1002/pmic.201600458] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 06/02/2017] [Indexed: 12/24/2022]
Abstract
In flowering plants, anther development plays crucial role in sexual reproduction. Within the anther, microspore mother cells meiosis produces microspores, which further develop into pollen grains that play decisive role in plant reproduction. Previous studies on anther biology mainly focused on single gene functions relying on genetic and molecular methods. Recently, anther development has been expanded from multiple OMICS approaches like transcriptomics, proteomics/phosphoproteomics, and metabolomics. The development of proteomics techniques allowing increased proteome coverage and quantitative measurements of proteins which can characterize proteomes and their modulation during normal development, biotic and abiotic stresses in anther development. In this review, we summarize the achievements of proteomics and phosphoproteomics with anther and pollen organs from model plant and crop species (i.e. Arabidopsis, rice, tobacco). The increased proteomic information facilitated translation of information from the models to crops and thus aid in agricultural improvement.
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Affiliation(s)
- Zaibao Zhang
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, P. R. China.,College of Life Science, Xinyang Normal College, Xinyang, Henan, P. R. China
| | - Menghui Hu
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, P. R. China.,College of Life Science, Xinyang Normal College, Xinyang, Henan, P. R. China
| | - Xiaobing Feng
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, P. R. China.,College of Life Science, Xinyang Normal College, Xinyang, Henan, P. R. China
| | - Andong Gong
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, P. R. China.,College of Life Science, Xinyang Normal College, Xinyang, Henan, P. R. China
| | - Lin Cheng
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, P. R. China.,College of Life Science, Xinyang Normal College, Xinyang, Henan, P. R. China
| | - Hongyu Yuan
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, P. R. China.,College of Life Science, Xinyang Normal College, Xinyang, Henan, P. R. China
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Osman K, Yang J, Roitinger E, Lambing C, Heckmann S, Howell E, Cuacos M, Imre R, Dürnberger G, Mechtler K, Armstrong S, Franklin FCH. Affinity proteomics reveals extensive phosphorylation of the Brassica chromosome axis protein ASY1 and a network of associated proteins at prophase I of meiosis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:17-33. [PMID: 29078019 PMCID: PMC5767750 DOI: 10.1111/tpj.13752] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 10/10/2017] [Accepted: 10/17/2017] [Indexed: 05/18/2023]
Abstract
During meiosis, the formation of crossovers (COs) generates genetic variation and provides physical links that are essential for accurate chromosome segregation. COs occur in the context of a proteinaceous chromosome axis. The transcriptomes and proteomes of anthers and meiocytes comprise several thousand genes and proteins, but because of the level of complexity relatively few have been functionally characterized. Our understanding of the physical and functional interactions between meiotic proteins is also limited. Here we use affinity proteomics to analyse the proteins that are associated with the meiotic chromosome axis protein, ASY1, in Brassica oleracea anthers and meiocytes. We show that during prophase I ASY1 and its interacting partner, ASY3, are extensively phosphorylated, and we precisely assign phosphorylation sites. We identify 589 proteins that co-immunoprecipitate with ASY1. These correspond to 492 Arabidopsis orthologues, over 90% of which form a coherent protein-protein interaction (PPI) network containing known and candidate meiotic proteins, including proteins more usually associated with other cellular processes such as DNA replication and proteolysis. Mutant analysis confirms that affinity proteomics is a viable strategy for revealing previously unknown meiotic proteins, and we show how the PPI network can be used to prioritise candidates for analysis. Finally, we identify another axis-associated protein with a role in meiotic recombination. Data are available via ProteomeXchange with identifier PXD006042.
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Affiliation(s)
- Kim Osman
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Jianhua Yang
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- Present address:
Faculty of Engineering and ComputingCoventry UniversityCoventryCV1 5FBUK
| | | | - Christophe Lambing
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- Present address:
Department of Plant SciencesUniversity of CambridgeDowning StreetCambridgeCB2 3EAUK
| | - Stefan Heckmann
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- Present address:
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)OT Gatersleben, Corrensstrasse 3D‐06466Stadt SeelandGermany
| | - Elaine Howell
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Maria Cuacos
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- Present address:
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)OT Gatersleben, Corrensstrasse 3D‐06466Stadt SeelandGermany
| | | | - Gerhard Dürnberger
- IMP‐IMBA1030ViennaAustria
- Gregor Mendel Institute of Molecular Plant BiologyDr. Bohr‐Gasse 31030ViennaAustria
| | | | - Susan Armstrong
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
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43
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Li X, Ye J, Ma H, Lu P. Proteomic analysis of lysine acetylation provides strong evidence for involvement of acetylated proteins in plant meiosis and tapetum function. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:142-154. [PMID: 29124795 DOI: 10.1111/tpj.13766] [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: 08/19/2017] [Revised: 10/20/2017] [Accepted: 10/25/2017] [Indexed: 05/18/2023]
Abstract
Protein lysine acetylation (KAC) is a dynamic and reversible post-translational modification that has important biological roles in many organisms. Although KAC has been shown to affect reproductive development and meiosis in yeast and animals, similar studies are largely lacking in flowering plants, especially proteome-scale investigations for particular reproductive stages. Here, we report results from a proteomic investigation to detect the KAC status of the developing rice anthers near the time of meiosis (RAM), providing strong biochemical evidence for roles of many KAC-affected proteins during anther development and meiosis in rice. We identified a total of 1354 KAC sites in 676 proteins. Among these, 421 acetylated proteins with 629 KAC sites are novel, greatly enriching our knowledge on KAC in flowering plants. Gene Ontology enrichment analysis showed chromatin silencing, protein folding, fatty acid biosynthetic process and response to stress to be over-represented. In addition, certain potentially specific KAC motifs in RAM were detected. Importantly, 357 rice meiocyte proteins were acetylated; and four proteins genetically identified to be important for rice tapetum and pollen development were acetylated on 14 KAC sites in total. Furthermore, 47 putative secretory proteins were detected to exhibit acetylated status in RAM. Moreover, by comparing our lysine acetylome with the RAM phosphoproteome we obtained previously, we proposed a correlation between KAC and phosphorylation as a potential modulatory mechanism in rice RAM. This study provides the first global survey of KAC in plant reproductive development, making a promising starting point for further functional analysis of KAC during rice anther development and meiosis.
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Affiliation(s)
- Xiaojing Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Juanying Ye
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Pingli Lu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
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Lambing C, Heckmann S. Tackling Plant Meiosis: From Model Research to Crop Improvement. FRONTIERS IN PLANT SCIENCE 2018; 9:829. [PMID: 29971082 PMCID: PMC6018109 DOI: 10.3389/fpls.2018.00829] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/28/2018] [Indexed: 05/04/2023]
Abstract
Genetic engineering and traditional plant breeding, which harnesses the natural genetic variation that arises during meiosis, will have key roles to improve crop varieties and thus deliver Food Security in the future. Meiosis, a specialized cell division producing haploid gametes to maintain somatic diploidy following their fusion, assures genetic variation by regulated genetic exchange through homologous recombination. However, meiotic recombination events are restricted in their total number and their distribution along chromosomes limiting allelic variations in breeding programs. Thus, modifying the number and distribution of meiotic recombination events has great potential to improve and accelerate plant breeding. In recent years much progress has been made in understanding meiotic progression and recombination in plants. Many genes and factors involved in these processes have been identified primarily in Arabidopsis thaliana but also more recently in crops such as Brassica, rice, barley, maize, or wheat. These advances put researchers in the position to translate acquired knowledge to various crops likely improving and accelerating breeding programs. However, although fundamental aspects of meiotic progression and recombination are conserved between species, differences in genome size and organization (due to repetitive DNA content and ploidy level) exist, particularly among plants, that likely account for differences in meiotic progression and recombination patterns found between species. Thus, tools and approaches are needed to better understand differences and similarities in meiotic progression and recombination among plants, to study fundamental aspects of meiosis in a variety of plants including crops and non-model species, and to transfer knowledge into crop species. In this article, we provide an overview of tools and approaches available to study plant meiosis, highlight new techniques, give examples of areas of future research and review distinct aspects of meiosis in non-model species.
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Affiliation(s)
- Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Christophe Lambing, Stefan Heckmann,
| | - Stefan Heckmann
- Independent Research Group Meiosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- *Correspondence: Christophe Lambing, Stefan Heckmann,
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iTRAQ-Based Quantitative Proteomics Analysis on Rice Anther Responding to High Temperature. Int J Mol Sci 2017; 18:ijms18091811. [PMID: 28832496 PMCID: PMC5618475 DOI: 10.3390/ijms18091811] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 02/08/2023] Open
Abstract
As one of the most important crops, rice provides the major food for more than half of the world population. However, its production is limited by many environmental factors, among which high temperature stress (HS) frequently occurs during anthesis and reduces its spikelet fertility. To explore the mechanism of HS tolerance in rice, we conducted a comparative proteomics analysis on the anthers between HS resistant and sensitive cultivars under different levels of high temperature. Under the same HS treatment, the resistant cultivar showed much higher spikelet fertility than the sensitive cultivar. Proteomic data showed that HS lead to the degradation of ribosomal proteins in the sensitive cultivar but not in the resistant one, which might result in the injury of protein biosynthetic machinery. In contrast, HS induced the increase of sHSP, β-expansins and lipid transfer proteins in the resistant cultivar, which might contribute to its ability to tolerate HS. The results provide some new insights into the mechanism of rice HS response.
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46
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Wang Y, Tong X, Qiu J, Li Z, Zhao J, Hou Y, Tang L, Zhang J. A phosphoproteomic landscape of rice (Oryza sativa) tissues. PHYSIOLOGIA PLANTARUM 2017; 160:458-475. [PMID: 28382632 DOI: 10.1111/ppl.12574] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 02/24/2017] [Indexed: 06/07/2023]
Abstract
Protein phosphorylation is an important posttranslational modification that regulates various plant developmental processes. Here, we report a comprehensive, quantitative phosphoproteomic profile of six rice tissues, including callus, leaf, root, shoot meristem, young panicle and mature panicle from Nipponbare by employing a mass spectrometry (MS)-based, label-free approach. A total of 7171 unique phosphorylation sites in 4792 phosphopeptides from 2657 phosphoproteins were identified, of which 4613 peptides were differentially phosphorylated (DP) among the tissues. Motif-X analysis revealed eight significantly enriched motifs, such as [sP], [Rxxs] and [tP] from the rice phosphosites. Hierarchical clustering analysis divided the DP peptides into 63 subgroups, which showed divergent spatial-phosphorylation patterns among tissues. These clustered proteins are functionally related to nutrition uptake in roots, photosynthesis in leaves and tissue differentiation in panicles. Phosphorylations were specific in the tissues where the target proteins execute their functions, suggesting that phosphorylation might be a key mechanism to regulate the protein activity in different tissues. This study greatly expands the rice phosphoproteomic dataset, and also offers insight into the regulatory roles of phosphorylation in tissue development and functions.
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Affiliation(s)
- Yifeng Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Xiaohong Tong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Jiehua Qiu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhiyong Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Juan Zhao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yuxuan Hou
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Liqun Tang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Jian Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
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47
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Ranjan R, Khurana R, Malik N, Badoni S, Parida SK, Kapoor S, Tyagi AK. bHLH142 regulates various metabolic pathway-related genes to affect pollen development and anther dehiscence in rice. Sci Rep 2017; 7:43397. [PMID: 28262713 PMCID: PMC5338287 DOI: 10.1038/srep43397] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 01/20/2017] [Indexed: 01/14/2023] Open
Abstract
Apposite development of anther and its dehiscence are important for the reproductive success of the flowering plants. Recently, bHLH142, a bHLH transcription factor encoding gene of rice has been found to show anther-specific expression and mutant analyses suggest its functions in regulating tapetum differentiation and degeneration during anther development. However, our study on protein level expression and gain-of-function phenotype revealed novel aspects of its regulation and function during anther development. Temporally dissimilar pattern of bHLH142 transcript and polypeptide accumulation suggested regulation of its expression beyond transcriptional level. Overexpression of bHLH142 in transgenic rice resulted in indehiscent anthers and aborted pollen grains. Defects in septum and stomium rupture caused anther indehiscence while pollen abortion phenotype attributed to abnormal degeneration of the tapetum. Furthermore, RNA-Seq-based transcriptome analysis of tetrad and mature pollen stage anthers of wild type and bHLH142OEplants suggested that it might regulate carbohydrate and lipid metabolism, cell wall modification, reactive oxygen species (ROS) homeostasis and cell death-related genes during rice anther development. Thus, bHLH142 is an anther-specific gene whose expression is regulated at transcriptional and post-transcriptional/translational levels. It plays a role in pollen maturation and anther dehiscence by regulating expression of various metabolic pathways-related genes.
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Affiliation(s)
- Rajeev Ranjan
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Reema Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Marg, New Delhi 110021, India
| | - Naveen Malik
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swarup K. Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sanjay Kapoor
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Marg, New Delhi 110021, India
| | - Akhilesh K. Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Marg, New Delhi 110021, India
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48
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Ferguson AC, Pearce S, Band LR, Yang C, Ferjentsikova I, King J, Yuan Z, Zhang D, Wilson ZA. Biphasic regulation of the transcription factor ABORTED MICROSPORES (AMS) is essential for tapetum and pollen development in Arabidopsis. THE NEW PHYTOLOGIST 2017; 213:778-790. [PMID: 27787905 PMCID: PMC5215365 DOI: 10.1111/nph.14200] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 08/03/2016] [Indexed: 05/19/2023]
Abstract
Viable pollen is essential for plant reproduction and crop yield. Its production requires coordinated expression at specific stages during anther development, involving early meiosis-associated events and late pollen wall formation. The ABORTED MICROSPORES (AMS) transcription factor is a master regulator of sporopollenin biosynthesis, secretion and pollen wall formation in Arabidopsis. Here we show that it has complex regulation and additional essential roles earlier in pollen formation. An inducible-AMS reporter was created for functional rescue, protein expression pattern analysis, and to distinguish between direct and indirect targets. Mathematical modelling was used to create regulatory networks based on wild-type RNA and protein expression. Dual activity of AMS was defined by biphasic protein expression in anther tapetal cells, with an initial peak around pollen meiosis and then later during pollen wall development. Direct AMS-regulated targets exhibit temporal regulation, indicating that additional factors are associated with their regulation. We demonstrate that AMS biphasic expression is essential for pollen development, and defines distinct functional activities during early and late pollen development. Mathematical modelling suggests that AMS may competitively form a protein complex with other tapetum-expressed transcription factors, and that biphasic regulation is due to repression of upstream regulators and promotion of AMS protein degradation.
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Affiliation(s)
- Alison C. Ferguson
- Division of Plant & Crop SciencesSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughborough, LeicestershireLE12 5RDUK
| | - Simon Pearce
- Faculty of BiologyUniversity of ManchesterMichael Smith Building, Oxford RoadManchesterM13 9PLUK
- School of MathematicsUniversity of ManchesterAlan Turing Building, Oxford RoadManchesterM13 9PLUK
| | - Leah R. Band
- Division of Plant & Crop SciencesSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughborough, LeicestershireLE12 5RDUK
- Centre for Plant Integrative BiologyUniversity of NottinghamSutton Bonington CampusLoughborough, LeicestershireLE12 5RDUK
- School of Mathematical SciencesUniversity of NottinghamNottinghamNG7 2RDUK
| | - Caiyun Yang
- Division of Plant & Crop SciencesSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughborough, LeicestershireLE12 5RDUK
| | - Ivana Ferjentsikova
- Division of Plant & Crop SciencesSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughborough, LeicestershireLE12 5RDUK
| | - John King
- Centre for Plant Integrative BiologyUniversity of NottinghamSutton Bonington CampusLoughborough, LeicestershireLE12 5RDUK
- School of Mathematical SciencesUniversity of NottinghamNottinghamNG7 2RDUK
| | - Zheng Yuan
- Joint International Research Laboratory of Metabolic & Developmental SciencesShanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and HealthSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental SciencesShanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and HealthSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - Zoe A. Wilson
- Division of Plant & Crop SciencesSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughborough, LeicestershireLE12 5RDUK
- Centre for Plant Integrative BiologyUniversity of NottinghamSutton Bonington CampusLoughborough, LeicestershireLE12 5RDUK
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49
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Hashiguchi A, Komatsu S. Posttranslational Modifications and Plant-Environment Interaction. Methods Enzymol 2016; 586:97-113. [PMID: 28137579 DOI: 10.1016/bs.mie.2016.09.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Posttranslational modifications (PTMs) of proteins such as phosphorylation and ubiquitination are crucial for controlling protein stability, localization, and conformation. Genetic information encoded in DNA is transcribed, translated, and increases its complexity by multiple PTMs. Conformational change introduced by PTMs affects interacting partners of each proteins and their downstream signaling; therefore, PTMs are the major level of modulations of total outcome of living cells. Plants are living in harsh environment that requires unremitting physiological modulation to survive, and the plant response to various environment stresses is regulated by PTMs of proteins. This review deals with the novel knowledge of PTM-focused proteomic studies on various life conditions. PTMs are focused that mediate plant-environment interaction such as stress perception, protein homeostasis, control of energy shift, and defense by immune system. Integration of diverse signals on a protein via multiple PTMs is discussed as well, considering current situation where signal integration became an emerging area approached by systems biology into account.
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Affiliation(s)
- A Hashiguchi
- Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - S Komatsu
- National Institute of Crop Science, NARO, Tsukuba, Japan.
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50
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Chao Q, Gao ZF, Wang YF, Li Z, Huang XH, Wang YC, Mei YC, Zhao BG, Li L, Jiang YB, Wang BC. The proteome and phosphoproteome of maize pollen uncovers fertility candidate proteins. PLANT MOLECULAR BIOLOGY 2016; 91:287-304. [PMID: 26969016 DOI: 10.1007/s11103-016-0466-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 03/03/2016] [Indexed: 06/05/2023]
Abstract
Maize is unique since it is both monoecious and diclinous (separate male and female flowers on the same plant). We investigated the proteome and phosphoproteome of maize pollen containing modified proteins and here we provide a comprehensive pollen proteome and phosphoproteome which contain 100,990 peptides from 6750 proteins and 5292 phosphorylated sites corresponding to 2257 maize phosphoproteins, respectively. Interestingly, among the total 27 overrepresented phosphosite motifs we identified here, 11 were novel motifs, which suggested different modification mechanisms in plants compared to those of animals. Enrichment analysis of pollen phosphoproteins showed that pathways including DNA synthesis/chromatin structure, regulation of RNA transcription, protein modification, cell organization, signal transduction, cell cycle, vesicle transport, transport of ions and metabolisms, which were involved in pollen development, the following germination and pollen tube growth, were regulated by phosphorylation. In this study, we also found 430 kinases and 105 phosphatases in the maize pollen phosphoproteome, among which calcium dependent protein kinases (CDPKs), leucine rich repeat kinase, SNF1 related protein kinases and MAPK family proteins were heavily enriched and further analyzed. From our research, we also uncovered hundreds of male sterility-associated proteins and phosphoproteins that might influence maize productivity and serve as targets for hybrid maize seed production. At last, a putative complex signaling pathway involving CDPKs, MAPKs, ubiquitin ligases and multiple fertility proteins was constructed. Overall, our data provides new insight for further investigation of protein phosphorylation status in mature maize pollen and construction of maize male sterile mutants in the future.
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Affiliation(s)
- Qing Chao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
| | - Zhi-Fang Gao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
| | - Yue-Feng Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
| | - Zhe Li
- The State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xia-He Huang
- Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ying-Chun Wang
- Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ying-Chang Mei
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
| | - Biligen-Gaowa Zhao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
| | - Liang Li
- Institute of Crop Cultivation and Farming, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Yu-Bo Jiang
- Institute of Crop Cultivation and Farming, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Bai-Chen Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China.
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