A Cell Fractionation and Quantitative Proteomics Pipeline to Enable Functional Analyses of Cotton Fiber Development

Overview

Journal Plant J

Specialties Biology
Cell Biology
Molecular Biology

Date 2025 Feb 19

PMID 39970036

Authors

Youngwoo Lee

Heena Rani

Eileen L Mallery

Daniel B Szymanski

Affiliations

Soon will be listed here.

Abstract

Cotton fibers are aerial trichoblasts that employ a highly polarized diffuse growth mechanism to emerge from the developing ovule epidermis. After executing a complicated morphogenetic program, the cells reach lengths over 2 cm and serve as the foundation of a multi-billion-dollar textile industry. Important traits such as fiber diameter, length, and strength are defined by the growth patterns and cell wall properties of individual cells. At present, the ability to engineer fiber traits is limited by our lack of understanding regarding the primary controls governing the rate, duration, and patterns of cell growth. To gain insights into the compartmentalized functions of proteins in cotton fiber cells, we developed a label-free liquid chromatography mass spectrometry method for systems-level analyses of fiber proteome. Purified fibers from a single locule were used to fractionate the fiber proteome into apoplast (APO), membrane-associated (p200), and crude cytosolic (s200) fractions. Subsequently, proteins were identified, and their localizations and potential functions were analyzed using combinations of size exclusion chromatography, statistical and bioinformatic analyses. This method had good coverage of the p200 and APO fractions, the latter of which was dominated by proteins associated with particulate membrane-enclosed compartments. The apoplastic proteome was diverse, the proteins were not degraded, and some displayed distinct multimerization states compared to their cytosolic pool. This quantitative proteomic pipeline can be used to improve coverage and functional analyses of the cotton fiber proteome as a function of developmental time or differing genotypes.

References

Soltis D, Misra B, Shan S, Chen S, Soltis P . Polyploidy and the proteome. Biochim Biophys Acta. 2016; 1864(8):896-907. DOI: 10.1016/j.bbapap.2016.03.010. View

Gu Y, Rasmussen C . Cell biology of primary cell wall synthesis in plants. Plant Cell. 2021; 34(1):103-128. PMC: 8774047. DOI: 10.1093/plcell/koab249. View

Tyanova S, Temu T, Sinitcyn P, Carlson A, Hein M, Geiger T . The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat Methods. 2016; 13(9):731-40. DOI: 10.1038/nmeth.3901. View

Zhang D, Chen C, Wang H, Niu E, Zhao P, Fang S . Cotton Fiber Development Requires the Pentatricopeptide Repeat Protein GhIm for Splicing of Mitochondrial nad7 mRNA. Genetics. 2021; 217(1):1-17. PMC: 8045684. DOI: 10.1093/genetics/iyaa017. View

Boudart G, Jamet E, Rossignol M, Lafitte C, Borderies G, Jauneau A . Cell wall proteins in apoplastic fluids of Arabidopsis thaliana rosettes: identification by mass spectrometry and bioinformatics. Proteomics. 2004; 5(1):212-21. DOI: 10.1002/pmic.200400882. View

Bao Y, Hu G, Flagel L, Salmon A, Bezanilla M, Paterson A . Parallel up-regulation of the profilin gene family following independent domestication of diploid and allopolyploid cotton (Gossypium). Proc Natl Acad Sci U S A. 2011; 108(52):21152-7. PMC: 3248529. DOI: 10.1073/pnas.1115926109. View

Yang Y, Bian S, Yao Y, Liu J . Comparative proteomic analysis provides new insights into the fiber elongating process in cotton. J Proteome Res. 2008; 7(11):4623-37. DOI: 10.1021/pr800550q. View

Yatsu L, Espelie K, Kolattukudy P . Ultrastructural and chemical evidence that the cell wall of green cotton fiber is suberized. Plant Physiol. 1983; 73(2):521-4. PMC: 1066496. DOI: 10.1104/pp.73.2.521. View

Barabas A, Aryal U, Gaskill B . Proteome characterization of used nesting material and potential protein sources from group housed male mice, Mus musculus. Sci Rep. 2019; 9(1):17524. PMC: 6879570. DOI: 10.1038/s41598-019-53903-x. View

10.

Havugimana P, Hart G, Nepusz T, Yang H, Turinsky A, Li Z . A census of human soluble protein complexes. Cell. 2012; 150(5):1068-81. PMC: 3477804. DOI: 10.1016/j.cell.2012.08.011. View

11.

Wang L, Liu C, Liu Y, Luo M . Fumonisin B1-Induced Changes in Cotton Fiber Elongation Revealed by Sphingolipidomics and Proteomics. Biomolecules. 2020; 10(9). PMC: 7564794. DOI: 10.3390/biom10091258. View

12.

Singh B, Avci U, Eichler Inwood S, Grimson M, Landgraf J, Mohnen D . A specialized outer layer of the primary cell wall joins elongating cotton fibers into tissue-like bundles. Plant Physiol. 2009; 150(2):684-99. PMC: 2689960. DOI: 10.1104/pp.109.135459. View

13.

Han L, Li Y, Wang H, Wu X, Li C, Luo M . The dual functions of WLIM1a in cell elongation and secondary wall formation in developing cotton fibers. Plant Cell. 2013; 25(11):4421-38. PMC: 3875727. DOI: 10.1105/tpc.113.116970. View

14.

McWhite C, Papoulas O, Drew K, Cox R, June V, Dong O . A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies. Cell. 2020; 181(2):460-474.e14. PMC: 7297045. DOI: 10.1016/j.cell.2020.02.049. View

15.

Morris J, Caldo K, Liang S, Facchini P . PR10/Bet v1-like Proteins as Novel Contributors to Plant Biochemical Diversity. Chembiochem. 2020; 22(2):264-287. DOI: 10.1002/cbic.202000354. View

16.

Wang J, Wang H, Zhao P, Han L, Jiao G, Zheng Y . Overexpression of a profilin (GhPFN2) promotes the progression of developmental phases in cotton fibers. Plant Cell Physiol. 2010; 51(8):1276-90. DOI: 10.1093/pcp/pcq086. View

17.

Rudolph J, Cox J . A Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis. J Proteome Res. 2019; 18(5):2052-2064. PMC: 6578358. DOI: 10.1021/acs.jproteome.8b00927. View

18.

Avci U, Pattathil S, Singh B, Brown V, Hahn M, Haigler C . Cotton fiber cell walls of Gossypium hirsutum and Gossypium barbadense have differences related to loosely-bound xyloglucan. PLoS One. 2013; 8(2):e56315. PMC: 3572956. DOI: 10.1371/journal.pone.0056315. View

19.

Yu Y, Wu S, Nowak J, Wang G, Han L, Feng Z . Live-cell imaging of the cytoskeleton in elongating cotton fibres. Nat Plants. 2019; 5(5):498-504. DOI: 10.1038/s41477-019-0418-8. View

20.

Borniego M, Innes R . Extracellular RNA: mechanisms of secretion and potential functions. J Exp Bot. 2023; 74(7):2389-2404. PMC: 10082932. DOI: 10.1093/jxb/erac512. View