Quantitative proteomics and transcriptomics reveal key metabolic processes associated with cotton fiber initiation

Wang, Xuchu; Li, Qin; Jin, Xiang; Xiao, Gao; Liu, Gaojun; Liu, Nin-Jing; Qin, Yong-Mei

doi:10.1016/j.jprot.2014.10.022

Cited by 41 publications

(36 citation statements)

References 52 publications

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“…GO terms for fatty acid elongation, sulfur amino acid metabolic processes and post-replication repair were enriched in ovule-specific proteins. Notably, for GO:0030497, fatty acid elongation was enriched in ovule-specific proteins, which is consistent with our previous work Wang et al, 2015). Additionally, several previously reported biological processes, such as root hair elongation, galactose metabolic process, and D-xylose metabolic process were attributed to the fiber-specific proteins ( Figure S1-S3 in Supporting Information).…”

Section: Annotation Of Tissue-specific Proteins Yielded Differential supporting

confidence: 90%

“…However, scarce information was available about the largest portion of 2DE-detectable protein spots, usually more than 1,000 protein spots, beyond differentially expressed proteins. Gel-free high-throughput MS approaches have been rapidly developed in recent years and have identified 1,000-5,000 or more proteins in cotton tissues (Hu et al, 2013;Meng et al, 2011;Wang et al, 2015). However, these data were still lacking global proteome information in some aspects that could be provided by 2DE maps, such as protein spot visualization, reliable evidence for existing protein isoforms and the abundances of individual protein spots.…”

Section: Discussionmentioning

confidence: 99%

“…Most of the results were reasonable and consistent with previous findings. Lipid metabolic processes have been reported to be important during fiber initiation Wang et al, 2015), and we found that 119 commonly expressed proteins were classified with GO terms of carbohydrate metabolic, cellular amino acid metabolic and lipid metabolic processes ( Figure 2B). The biosynthesis of pectic precursors has been reported to play important roles during fiber elongation (Pang et al, 2010), and we also found that galactose metabolic and D-xylose metabolic processes were enriched in fiber-specific proteins.…”

Section: Annotation and Network Analyses Of Tissue-specific Proteins mentioning

confidence: 93%

“…However, studies on the cotton proteome have not been as abundant as those of the transcriptome, partly due to a lack of information about cotton genome sequences (Du et al, 2013;Liu et al, 2012;Yang et al, 2008;Zheng et al, 2012). 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).…”

Section: Introductionmentioning

confidence: 99%

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Two-dimensional gel electrophoresis-based analysis provides global insights into the cotton ovule and fiber proteomes

Jin

Wang

et al. 2016

Sci. China Life Sci.

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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. cotton, 2DE, MALDI-TOF/TOF, GO enrichment, protein-protein interaction networks Citation:Jin, X., Wang, L., He, L., Feng, W., and Wang, X. (2016). Two-dimensional gel electrophoresis-based analysis provides global insights into the cotton ovule and fiber proteomes. Sci China Life Sci 59, 154 -163.

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Section: Annotation Of Tissue-specific Proteins Yielded Differential supporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Section: Annotation and Network Analyses Of Tissue-specific Proteins mentioning

confidence: 93%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Two-dimensional gel electrophoresis-based analysis provides global insights into the cotton ovule and fiber proteomes

Jin

Wang

et al. 2016

Sci. China Life Sci.

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“…This result is understandable because energy supplement is prerequisite for rapid fiber cell elongation [2, 4], whereas fast cell growth, such as the cotton fiber elongation process, needs an intracellular oxidation-reduction equilibrium [19] and a fast protein turnover rate [2, 8]. In addition, protein synthesis, amino acid and flavonoid metabolism also contained more than three DDPs, suggesting their possible important roles in cotton fiber elongation process [12, 14]. Moreover, different DDPs of each functional groups have unique protein abundance variance (Fig.…”

Section: Resultsmentioning

confidence: 99%

Comparative proteomic analyses of Asian cotton ovules with attached fibers in the early stages of fiber elongation process

Zhang

et al. 2016

Proteome Sci

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BackgroundPlenty of proteomic studies were performed to characterize the allotetraploid upland cotton fiber elongation process, whereas little is known about the elongating diploid cotton fiber proteome.MethodsIn this study, we used a two-dimensional electrophoresis-based comparative proteomic approach to profile dynamic proteomes of diploid Asian cotton ovules with attached fibers in the early stages of fiber elongation process. One-way ANOVA and Student-Newman-Keuls test were used to find the differentially displayed protein (DDP) spots.ResultsA total of 55 protein spots were found having different abundance ranging from 1 to 9 days post-anthesis (DPA) in a two-day interval. These 55 DDP spots were all successfully identified using high-resolution mass spectrometric analyses. Gene ontology analyses revealed that proteoforms involved in energy/carbohydrate metabolism, redox homeostasis, and protein metabolism are the most abundant. In addition, orthologues of the 13 DDP spots were also found in differential proteome of allotetraploid elongating cotton fibers, suggesting their possible essential roles in fiber elongation process.ConclusionsOur results not only revealed the dynamic proteome change of diploid Asian cotton fiber and ovule during early stages of fiber elongation process but also provided valuable resource for future studies on the molecular mechanism how the polyploidization improves the trait of fiber length.Electronic supplementary materialThe online version of this article (doi:10.1186/s12953-016-0101-1) contains supplementary material, which is available to authorized users.

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Quantitative proteomic analysis of upland cotton stem terminal buds reveals phytohormone-related pathways associated with dwarfism

Tu¹,

Li²,

Wang³

et al. 2017

Biol. plant.

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Quantitative proteomics and transcriptomics reveal key metabolic processes associated with cotton fiber initiation

Cited by 41 publications

References 52 publications

Two-dimensional gel electrophoresis-based analysis provides global insights into the cotton ovule and fiber proteomes

Two-dimensional gel electrophoresis-based analysis provides global insights into the cotton ovule and fiber proteomes

Comparative proteomic analyses of Asian cotton ovules with attached fibers in the early stages of fiber elongation process

Quantitative proteomic analysis of upland cotton stem terminal buds reveals phytohormone-related pathways associated with dwarfism

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