iTRAQ-Based Quantitative Proteomic Analysis of Cotton Roots and Leaves Reveals Pathways Associated with Salt Stress

Abstract

Salinity is a major abiotic stress that affects plant growth and development. In this study, we performed a proteomic analysis of cotton roots and leaf tissue following exposure to saline stress. 611 and 1477 proteins were differentially expressed in the roots and leaves, respectively. In the roots, 259 (42%) proteins were up-regulated and 352 (58%) were down-regulated. In the leaves, 748 (51%) proteins were up-regulated and 729 (49%) were down-regulated. On the basis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, we concluded that the phenylalanine metabolism and starch and sucrose metabolism were active for energy homeostasis to cope with salt stress in cotton roots. Moreover, photosynthesis, pyruvate metabolism, glycolysis / gluconeogenesis, carbon fixation in photosynthetic organisms and phenylalanine metabolism were inhabited to reduce energy consumption. Characterization of the signaling pathways will help elucidate the mechanism activated by cotton in response to salt stress.

Fig 1. Identification and analysis of DEPs from roots and leaves in cotton.

(A) Total spectra, spectra, unique spectra, peptides, unique peptide, and proteins identified from iTRAQ proteomic analysis. (B) Identified proteins were grouped according to the protein mass. (C) Number of peptides that match to proteins as indicated by MASCOT 2.3.02.

Fig 2. Number of up- or down-regulated proteins under salt stress in roots and leaves.

Fig 3. Gene Ontology (GO) classification of the DEPs in cotton.

(A) GO classification of the DEPs in roots; (B) GO classification of the DEPs in leaves. The number of each category is displayed based on cellular components, molecular function, or biological process.

Fig 4. Metabolism pathways involved in the response to salt stress in cotton.

Proteins involved in phenylalanine and starch and sucrose metabolism were mostly up-regulated in roots; Proteins involved in photosynthesis, carbon fixation, glycolysis, pyruvate metabolism and phenylalanine were mostly down-regulated in leaves. Red and green numbers represent expression level of up- and down-regulated proteins, respectively. PAL: phenylalanine ammonialyase; 4CL: 4-coumarate—CoA ligase; POD: peroxidase; UDPG: uridine diphosphate glucose; PGAL: glyceraldehyde 3-phosphate; PGA: 3-glyceric acid phosphate.