PMID- 34679169 OWN - NLM STAT- MEDLINE VI - 63 IP - 12 TI - Auxin-Responsive (Phospho)proteome Analysis Reveals Key Biological Processes and Signaling Associated with Shoot-Borne Crown Root Development in Rice. PG - 1968-1979 CI - © The Author(s) 2023. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. LA - eng PT - Journal Article PL - Japan TA - Plant Cell Physiol JT - Plant & cell physiology JID - 9430925 IS - 1471-9053 (Electronic) LID - 10.1093/pcp/pcab155 [doi] FAU - Singh, Harshita AU - Singh H AD - Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India. FAU - Singh, Zeenu AU - Singh Z AD - Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India. FAU - Zhu, Tingting AU - Zhu T AD - Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium. AD - VIB Center for Plant Systems Biology, Ghent 9052, Belgium. FAU - Xu, Xiangyu AU - Xu X AUID- ORCID: 0000-0002-6492-9770 AD - Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium. AD - VIB Center for Plant Systems Biology, Ghent 9052, Belgium. FAU - Waghmode, Bhairavnath AU - Waghmode B AD - Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India. FAU - Garg, Tushar AU - Garg T AD - Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India. FAU - Yadav, Shivani AU - Yadav S AD - Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India. FAU - Sircar, Debabrata AU - Sircar D AD - Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India. FAU - De Smet, Ive AU - De Smet I AD - Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium. AD - VIB Center for Plant Systems Biology, Ghent 9052, Belgium. FAU - Yadav, Shri Ram AU - Yadav SR AUID- ORCID: 0000-0002-4083-7054 AD - Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India. IS - 0032-0781 (Linking) RN - 0 (Indoleacetic Acids) RN - 0 (Proteome) RN - 0 (Plant Proteins) SB - IM MH - Indoleacetic Acids/metabolism MH - Plant Roots/metabolism MH - *Oryza/metabolism MH - Proteome/metabolism MH - Chromatography, Liquid MH - Plant Proteins/genetics/metabolism MH - Tandem Mass Spectrometry MH - *Biological Phenomena MH - Signal Transduction/genetics MH - Gene Expression Regulation, Plant OTO - NOTNLM OT -  Adventitious (crown) root primordial OT -  Auxin OT -  GC–MS OT -  LC–MS OT -  Oryza sativa OT -  Phosphorylation DCOM- 20230201 LR - 20230201 DP - 2023 Jan 30 AB - The rice root system is primarily composed of shoot-borne adventitious/crown roots (ARs/CRs) that develop from the coleoptile base, and therefore, it is an excellent model system for studying shoot-to-root trans-differentiation process. We reveal global changes in protein and metabolite abundance and protein phosphorylation in response to an auxin stimulus during CR development. The liquid chromatography-tandem mass spectrometry (LC-MS/MS) and gas chromatography-mass spectrometry (GC-MS) analyses of developing crown root primordia (CRP) and emerged CRs identified 334 proteins and 12 amino acids, respectively, that were differentially regulated upon auxin treatment. Gene ontology enrichment analysis of global proteome data uncovered the biological processes associated with chromatin conformational change, gene expression and cell cycle that were regulated by auxin signaling. Spatial gene expression pattern analysis of differentially abundant proteins disclosed their stage-specific dynamic expression pattern during CRP development. Further, our tempo-spatial gene expression and functional analyses revealed that auxin creates a regulatory module during CRP development and activates ethylene biosynthesis exclusively during CRP initiation. Further, the phosphoproteome analysis identified 8,220 phosphosites, which could be mapped to 1,594 phosphoproteins and of which 66 phosphosites were differentially phosphorylated upon auxin treatment. Importantly, we observed differential phosphorylation of the cyclin-dependent kinase G-2 (OsCDKG;2) and cell wall proteins, in response to auxin signaling, suggesting that auxin-dependent phosphorylation may be required for cell cycle activation and cell wall synthesis during root organogenesis. Thus, our study provides evidence for the translational and post-translational regulation during CR development downstream of the auxin signaling pathway.