title: Quantitative proteomics and transcriptomics reveal key metabolic processes associated with cotton fiber initiation.
abstract: An iTRAQ-based proteomics of ovules from the upland cotton species Gossypium hirsutum and its fuzzless-lintless mutant was performed, and finally 2729 proteins that preferentially accumulated at anthesis in wild-type ovules were identified. We confirmed that the gene expression levels of 2005 among these proteins also increased by performing an RNA sequencing transcriptomics. Expression of proteins involved in carboxylic acid metabolism, small-molecule metabolic processes, hormone regulation, and lipid metabolism was significantly enhanced in wild-type ovules. Quantitative real-time PCR verified the increased expression of 26 genes involved in these processes. Cotton 3-hydroxyacyl-CoA dehydratase (GhPAS2) catalyzing the third reaction of very long-chain fatty acid (VLCFA) biosynthesis, accumulated at anthesis in wild-type ovules. Heterogeneous expression of GhPAS2 restored viability to the Saccharomyces cerevisiae haploid psh1-deletion strain deficient in PAS2 activity. Application of VLCFA biosynthesis inhibitor acetochlor (2-chloro-N-[ethoxymethyl]-N-[2-ethyl-6-methyl-phenyl]-acetamide; ACE) and gibberellic acid to the unfertilized cotton ovules significantly suppressed fiber cell protrusion. In this study, the profiling of gene expression at both transcriptome and proteome levels provides new insights into cotton fiber cell initiation.
  
  
  CONCLUSIONS
  Cotton fiber initiation determines the ultimate number of fibers per ovule, thereby determining fiber yield. In total, 2729 proteins were preferentially accumulated in wild-type ovules at anthesis. The most up-regulated proteins were assigned to carboxylic acid metabolism, small-molecule metabolic processes, hormone regulation, and lipid metabolism. In consistence with these findings, we characterized GhPAS2 gene coding for the enzyme that catalyzes VLCFA production. VLCFA biosynthesis inhibitor, acetochlor, was shown to significantly suppress fiber initiation. This study provides a genome-scale transcriptomic and proteomic characterization of fiber initial cells, laying a solid basis for further investigation of the molecular processes governing fiber cell development.
authors.affiliation: The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China; Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.
authors.forename: Xu-Chu
authors.initials: XC
authors.lastname: Wang
authors.affiliation: The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
authors.forename: Qin
authors.initials: Q
authors.lastname: Li
authors.affiliation: Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.
authors.forename: Xiang
authors.initials: X
authors.lastname: Jin
authors.affiliation: The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
authors.forename: Guang-Hui
authors.initials: GH
authors.lastname: Xiao
authors.affiliation: The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
authors.forename: Gao-Jun
authors.initials: GJ
authors.lastname: Liu
authors.affiliation: The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
authors.forename: Nin-Jing
authors.initials: NJ
authors.lastname: Liu
authors.affiliation: The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China. Electronic address: qinym@pku.edu.cn.
authors.forename: Yong-Mei
authors.initials: YM
authors.lastname: Qin
mesh_terms: D032561:Cotton Fiber; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D003368:Gossypium / Q000235:genetics* / Q000378:metabolism*; D053858:Metabolic Networks and Pathways / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D020543:Proteome
keywords: Cotton fiber initiation; Gossypium hirsutum; Hydroxyacyl-CoA dehydratase; RNA-sequencing; Very long-chain fatty acid; iTRAQ