Proteome Dynamics Analysis Reveals the Potential Mechanisms of Salinity and Drought Response during Seed Germination and Seedling Growth in Tamarix hispida

Abstract

Understanding the molecular mechanisms of seed germination and seedling growth is vital for mining functional genes for the improvement of plant drought in a desert. Tamarix hispida is extremely resistant to drought and soil salinity perennial shrubs or trees. This study was the first to investigate the protein abundance profile of the transition process during the processes of T. hispida seed germination and seedling growth using label-free proteomics approaches. Our data suggested that asynchronous regulation of transcriptomics and proteomics occurs upon short-term seed germination and seedling growth of T. hispida. Enrichment analysis revealed that the main differentially abundant proteins had significant enrichment in stimulus response, biosynthesis, and metabolism. Two delta-1-pyrroline-5-carboxylate synthetases (P5CS), one Ycf3-interacting protein (Y3IP), one low-temperature-induced 65 kDa protein-like molecule, and four peroxidases (PRX) were involved in both water deprivation and hyperosmotic salinity responses. Through a comparative analysis of transcriptomics and proteomics, we found that proteomics may be better at studying short-term developmental processes. Our results support the existence of several mechanisms that enhance tolerance to salinity and drought stress during seedling growth in T. hispida.

Keywords: Tamarix hispida; drought stress; proteomics; seed germination; seedling growth.

Figure 1

The distribution of proteome data and annotations. (a) Overview of protein identification. (b) Length distribution of identified peptides. (c) Peptide count distribution of identified proteins. (d) Protein functional annotation overview of COG/KOG, Gene Ontology, KEGG pathways, and protein domains.

Figure 2

Comparative analysis between differentially abundant proteins (DAP) and differently expressed unigenes (DEGs). (a) Numbers of upregulated and downregulated DAPs at pairwise stages. (b) Venn plot between DEGs and identified proteins. (c) Numbers of upregulated and downregulated DEGs at pairwise stages. (d) Venn plot between DEGs of stage 4 and stage 3 and DAPs of stage 5 vs. stage 4. Upregulated DAPs and DEGs are shown at the top, and downregulated DAPs and DEGs are shown at the bottom. Asterisks indicate degree of significance (*** p < 0.001).

Figure 3

Functional analysis of differentially abundant proteins (DAP). (a) GO classifications of DAPs between stage 4 and stage 3. (b) GO classifications of DAPs between stage 5 and stage 4. (c) KEGG pathways enrichment of DAPs between stage 4 and stage 3. (d) KEGG pathways enrichment of DAPs between stage 5 and stage 4. (e) Venn plot between DEGs of stage 4 vs. stage 3 and DEGs of stage 5 vs. stage 4.

Figure 4

Analysis of DAPs in the flavonoid biosynthesis pathway. (a) Mapping of enriched DAPs in the flavonoid biosynthesis pathway (ko00941) [44,45,46]. The orange marks represent DAP upregulated in stage 5 vs. stage 4; the green marks represent DAPs downregulated in stage 5 vs. stage 4; the yellow marks represent the upregulated DAPs and downregulated DAPs in stage 5 vs. stage 4. The grey marks represent proteins stable in stage 5 and stage 4. (b) Abundance pattern of DAPs involved in flavonoid biosynthesis pathway at different stages.

Figure 5

Clustering analyses of KEGG and GO enrichment results. (a) Clustering analysis of KEGG enrichment categories of DAPs. (b) Clustering analysis of KEGG enrichment categories of upregulated DAPs and downregulated DAPs. (c) Clustering analysis of Gene Ontology (GO) enrichment entries of DAPs. (d) Clustering analysis of GO enrichment entries of upregulated DAPs and downregulated DAPs. The horizontal side of the heatmap is different comparison groups, and the vertical side is the description of the correlation functions enriched by differentially abundant proteins in the different comparison groups. The color block corresponds to the functional descriptions of enrichment differentially abundant proteins, showing the degree of enrichment. Red means strong enrichment, blue means weak enrichment.

Figure 6

Abundance analysis of DAPs based on proteomics. (a) Heat map of water-deprivation-response-associated DAPs. (b) Heat map of hyperosmotic-salinity-response-associated DAPs. (c) Venn plot between response to water-deprivation-associated DAPs and hyperosmotic-salinity-response-associated DAPs. (d) Analysis of the functional network by STRING 11.0 of DAPs tied to responses to both water deprivation and hyperosmotic salinity. Red indicates significantly upregulated DAPs, and blue indicates significantly downregulated DAPs.