Proteome and transcriptome profile analysis reveals regulatory and stress-responsive networks in the russet fruit skin of sand pear

Abstract

The epidermal tissues of the cuticular membrane (CM) and periderm membrane (PM) confer first-line protection from environmental stresses in terrestrial plants. Although PM protection is essentially ubiquitous in plants, the protective mechanism, the function of many transcription factors and enzymes, and the genetic control of metabolic signaling pathways are poorly understood. Different microphenotypes and cellular components in russet (PM-covered) and green (CM-covered) fruit skins of pear were revealed by scanning and transmission electron microscopy. The two types of fruit skins showed distinct phytohormone accumulation, and different transcriptomic and proteomic profiles. The enriched pathways were detected by differentially expressed genes and proteins from the two omics analyses. A detailed analysis of the suberin biosynthesis pathways identified the regulatory signaling network, highlighting the general mechanisms required for periderm formation in russet fruit skin. The regulation of aquaporins at the protein level should play an important role in the specialized functions of russet fruit skin and PM-covered plant tissues.

Keywords: Protein-protein interaction networks; Transcriptomics.

Fig. 1. Phenotypes of the russet and green fruit skin of sand pear.

The russet a and green b skin fruit of sand pear grown in an orchard. Scanning electron microscopy analysis of russet c and green d fruit surfaces showed that the skins of the two genotypes are covered by stacked suberized cells and cutin wax, respectively. Transmission electron microscopy analysis of russet e and green f fruit epidermal cells at the russet development stage showed that more tylosis (Ty) accumulated in the russet skin cells. C Cuticle; CL cuticular layer; Ml middle lamella; Pw primary wall; SL suberin layer; Sw secondary wall; V vacuole; Ty tylosis

Fig. 2. RWL of the russet and green skin fruit of sand pear at different storage periods under room conditions after harvest.

After storage under room conditions, the russet fruit skin exhibited obvious shrinkage due to water loss a. The reported value is the mean ± SE b

Fig. 3. Differential accumulations of JA, SA, and ABA between the russet and green fruit skin of sand pear.

Different significant differences from the control at P_0.05 (Tukey’s test). The error bar is too small to be seen for c, d, and e

Fig. 4. Bubble diagrams of the KEGG enrichment of DEGs between russet (A) and green (B) fruit skin at the transcript and protein levels.

The abscissa is the ratio of the number of DEGs in the pathway to that of total genes identified. A larger value indicates the higher concentration of DEGs in the pathway. The color shade of the point represents the change in the P-value determined by a hypergeometric test. A smaller P-value indicates more statistical significance and greater test reliability. The dot size indicates the number of DEGs in certain pathways. A larger size represents more DEGs

Fig. 5. Schematic of the transcriptome and proteome revealing the regulation of the long fatty acid biosynthesis pathway in the russet fruit skin of sand pear.

a A detailed diagram of long fatty acid biosynthesis including the subset of nodes or metabolites and enzymes that are involved in the process. The enzymes with repressed expression in russet fruit skin at the transcript and/or protein levels are shown in green. b Heat map of differentially expressed transcripts or proteins. Transcript c and protein abundance d of russet-related genes involved in long fatty acid biosynthesis

Fig. 6. Schematic of the transcriptome and proteome revealed the regulation of the pathway map00073 for cutin, suberin, and wax biosynthesis in russet fruit skin in sand pear.

a A detailed diagram of cutin, suberin, and wax biosynthesis, including the subset of nodes or metabolites and enzymes involved in the process. Enzymes with repressed or enhanced expression in russet fruit skin at the transcript and/or protein levels are shown in green or red, respectively. b Heat map of the differentially expressed transcripts or proteins. Transcript c and protein abundance d of russet-related genes involved in cutin, suberin, and wax biosynthesis

Fig. 7. Regulation of the phenylpropanoid biosynthesis pathway in the russet fruit skin of sand pear.

a A partial diagram of phenylpropanoid biosynthesis constructed based on the KEGG pathway and gene expression data. Enzymes with enhanced expression in the russet fruit skin at the transcript and protein levels are shown in red. Transcript b and protein abundance c of russet-related genes involved in phenylpropanoid biosynthesis

Fig. 8. Schematic diagram summarizing the metabolism and signaling in the russet fruit skin of sand pear.

The diagram was constructed based on the metabolic pathways summarized in the hypersensitive cell death response in Arabidopsis by Raffaele et al.. Enzymes and partial diagrams marked in red or green indicate strongly enhanced or repressed regulation, respectively, in russet fruit skin at the transcript and/or protein levels. The differential regulation of wax esters in russet skin are indicated in red. We hypothesize that a low content of VLCFAs represses the biosynthesis of signaling molecules that could block or alter the signaling pathway, as indicated by the dotted arrow. PM plasma membrane; CW cell wall

Fig. 9

Enhanced expression of PLP2 genes (Gene ID: 103956635, 103957040, 103957112, and 103959548) and CRK genes (GI: 694350157 and 694428606) at the transcript and/or protein levels in russet fruit skin of sand pear

Fig. 10. Expression characteristics of stress-responsive genes at the transcript and protein levels in the fruit skin of sand pear.

Except for 103927172, all these genes were strongly induced at the protein level in russet fruit skin

Fig. 11. Differential regulation of aquaporin genes at the transcript and protein levels in the russet and green fruit skin of sand pear.

All these genes showed constant transcript levels but were strongly repressed at the protein level in russet fruit skin compared with green fruit skin of sand pear