Abstract
Proteomic analysis of upland cotton was performed to profile the global detectable proteomes of ovules and fibers using two-dimensional electrophoresis (2DE). A total of 1,203 independent protein spots were collected from representative 2DE gels, which were digested with trypsin and identified by matrix-assisted laser desorption and ionization-time-offlight/ time-of-flight (MALDI-TOF/TOF) mass spectrometry. The mass spectrometry or tandem mass spectrometry (MS or MS/MS) data were then searched against a local database constructed from Gossypium hirsutum genome sequences, resulting in successful identification of 975 protein spots (411 for ovules and 564 for fibers). Functional annotation analysis of the 975 identified proteins revealed that ovule-specific proteins were mainly enriched in functions related to fatty acid elongation, sulfur amino acid metabolism and post-replication repair, while fiber-specific proteins were enriched in functions related to root hair elongation, galactose metabolism and D-xylose metabolic processes. Further annotation analysis of the most abundant protein spots showed that 28.96% of the total proteins in the ovule were mainly located in the Golgi apparatus, endoplasmic reticulum, mitochondrion and ribosome, whereas in fibers, 27.02% of the total proteins were located in the cytoskeleton, nuclear envelope and cell wall. Quantitative real-time polymerase chain reaction (qRT-PCR) analyses of the ovule-specific protein spots P61, P93 and P198 and fiber-specific protein spots 230, 477 and 511 were performed to validate the proteomics data. Protein-protein interaction network analyses revealed very different network cluster patterns between ovules and fibers. This work provides the largest protein identification dataset of 2DE-detectable proteins in cotton ovules and fibers and indicates potentially important roles of tissue-specific proteins, thus providing insights into the cotton ovule and fiber proteomes on a global scale.
Highlights
Cotton fiber is the most prevalent natural material used in the textile industry, and upland cotton (Gossypium hirsutum, Gh) is the most widely cultivated cotton species
Two-dimensional electrophoresis (2DE) of 0 day post-anthesis (DPA) ovules and 10 DPA fibers were performed to investigate the global proteomes of these tissues
A total of 1,203 independent protein spots were excised from 2DE gels and subjected to MALDITOF/TOF analysis after in-gel trypsin digestion
Summary
Cotton fiber is the most prevalent natural material used in the textile industry, and upland cotton (Gossypium hirsutum, Gh) is the most widely cultivated cotton species. Over the past 10 years, numerous studies have reported important functional genes and biological processes for cotton fiber development, including ethylene signaling, very long-chain fatty acids, biosynthesis of pectic precursors, ascorbate peroxidase, sucrose synthase gene family, calcium-dependent protein kinase, DNA methylation and miRNAs (Huang et al, 2008; Jin et al, 2013b; Li et al, 2007; Li et al, 2012; Pang et al, 2010; Pei, 2015; Qin. Jin, X., et al Sci China Life Sci February (2016) Vol.. Expressed sequence tags (EST) and next-generation sequencing data of the transcriptome collected in the last few years have been used to construct a database to identify the mass spectrometric (MS) data of proteins (Jin et al, 2013a; Wang et al, 2015)
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