Data-Independent Acquisition-Based Proteome and Phosphoproteome Profiling Reveals Early Protein Phosphorylation and Dephosphorylation Events in <i>Arabidopsis</i> Seedlings upon Cold Exposure
Protein phosphorylation plays an important role in mediating signal transduction in cold response in plants. To better understand how plants sense and respond to the early temperature drop, we performed data-independent acquisition (DIA) method-based mass spectrometry analysis to profile the proteom...
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| Format: | Article |
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MDPI AG
2021-11-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/23/12856 |
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| author | Jinjuan Tan Zhongjing Zhou Hanqian Feng Jiayun Xing Yujie Niu Zhiping Deng |
| author_facet | Jinjuan Tan Zhongjing Zhou Hanqian Feng Jiayun Xing Yujie Niu Zhiping Deng |
| author_sort | Jinjuan Tan |
| collection | DOAJ |
| description | Protein phosphorylation plays an important role in mediating signal transduction in cold response in plants. To better understand how plants sense and respond to the early temperature drop, we performed data-independent acquisition (DIA) method-based mass spectrometry analysis to profile the proteome and phosphoproteome of <i>Arabidopsis</i> seedlings upon cold stress in a time-course manner (10, 30 and 120 min of cold treatments). Our results showed the rapid and extensive changes at the phosphopeptide levels, but not at the protein abundance levels, indicating cold-mediated protein phosphorylation and dephosphorylation events. Alteration of over 1200 proteins at phosphopeptide levels were observed within 2 h of cold treatment, including over 140 kinases, over 40 transcriptional factors and over 40 E3 ligases, revealing the complexity of regulation of cold adaption. We summarized cold responsive phosphoproteins involved in phospholipid signaling, cytoskeleton reorganization, calcium signaling, and MAPK cascades. Cold-altered levels of 73 phosphopeptides (mostly novel cold-responsive) representing 62 proteins were validated by parallel reaction monitoring (PRM). In summary, this study furthers our understanding of the molecular mechanisms of cold adaption in plants and strongly supports that DIA coupled with PRM are valuable tools in uncovering early signaling events in plants. |
| first_indexed | 2024-03-10T04:53:41Z |
| format | Article |
| id | doaj.art-cba05350515d4251949fb4ecaabedaff |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T04:53:41Z |
| publishDate | 2021-11-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-cba05350515d4251949fb4ecaabedaff2023-11-23T02:29:11ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-11-0122231285610.3390/ijms222312856Data-Independent Acquisition-Based Proteome and Phosphoproteome Profiling Reveals Early Protein Phosphorylation and Dephosphorylation Events in <i>Arabidopsis</i> Seedlings upon Cold ExposureJinjuan Tan0Zhongjing Zhou1Hanqian Feng2Jiayun Xing3Yujie Niu4Zhiping Deng5State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaCollege of Agronomy, Hunan Agricultural University, Changsha 410128, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaProtein phosphorylation plays an important role in mediating signal transduction in cold response in plants. To better understand how plants sense and respond to the early temperature drop, we performed data-independent acquisition (DIA) method-based mass spectrometry analysis to profile the proteome and phosphoproteome of <i>Arabidopsis</i> seedlings upon cold stress in a time-course manner (10, 30 and 120 min of cold treatments). Our results showed the rapid and extensive changes at the phosphopeptide levels, but not at the protein abundance levels, indicating cold-mediated protein phosphorylation and dephosphorylation events. Alteration of over 1200 proteins at phosphopeptide levels were observed within 2 h of cold treatment, including over 140 kinases, over 40 transcriptional factors and over 40 E3 ligases, revealing the complexity of regulation of cold adaption. We summarized cold responsive phosphoproteins involved in phospholipid signaling, cytoskeleton reorganization, calcium signaling, and MAPK cascades. Cold-altered levels of 73 phosphopeptides (mostly novel cold-responsive) representing 62 proteins were validated by parallel reaction monitoring (PRM). In summary, this study furthers our understanding of the molecular mechanisms of cold adaption in plants and strongly supports that DIA coupled with PRM are valuable tools in uncovering early signaling events in plants.https://www.mdpi.com/1422-0067/22/23/12856data-independent acquisition (DIA)proteomephosphoproteomecold stressparallel reaction monitoring (PRM)MAP kinase |
| spellingShingle | Jinjuan Tan Zhongjing Zhou Hanqian Feng Jiayun Xing Yujie Niu Zhiping Deng Data-Independent Acquisition-Based Proteome and Phosphoproteome Profiling Reveals Early Protein Phosphorylation and Dephosphorylation Events in <i>Arabidopsis</i> Seedlings upon Cold Exposure International Journal of Molecular Sciences data-independent acquisition (DIA) proteome phosphoproteome cold stress parallel reaction monitoring (PRM) MAP kinase |
| title | Data-Independent Acquisition-Based Proteome and Phosphoproteome Profiling Reveals Early Protein Phosphorylation and Dephosphorylation Events in <i>Arabidopsis</i> Seedlings upon Cold Exposure |
| title_full | Data-Independent Acquisition-Based Proteome and Phosphoproteome Profiling Reveals Early Protein Phosphorylation and Dephosphorylation Events in <i>Arabidopsis</i> Seedlings upon Cold Exposure |
| title_fullStr | Data-Independent Acquisition-Based Proteome and Phosphoproteome Profiling Reveals Early Protein Phosphorylation and Dephosphorylation Events in <i>Arabidopsis</i> Seedlings upon Cold Exposure |
| title_full_unstemmed | Data-Independent Acquisition-Based Proteome and Phosphoproteome Profiling Reveals Early Protein Phosphorylation and Dephosphorylation Events in <i>Arabidopsis</i> Seedlings upon Cold Exposure |
| title_short | Data-Independent Acquisition-Based Proteome and Phosphoproteome Profiling Reveals Early Protein Phosphorylation and Dephosphorylation Events in <i>Arabidopsis</i> Seedlings upon Cold Exposure |
| title_sort | data independent acquisition based proteome and phosphoproteome profiling reveals early protein phosphorylation and dephosphorylation events in i arabidopsis i seedlings upon cold exposure |
| topic | data-independent acquisition (DIA) proteome phosphoproteome cold stress parallel reaction monitoring (PRM) MAP kinase |
| url | https://www.mdpi.com/1422-0067/22/23/12856 |
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