As two of the most abundant post-translational modifications, phosphorylation and ubiquitination play a significant role in modulating plant–pathogen interactions and increasing evidence indicates their crosstalk in plant immunity. Rose (Rosa sp.) is one of the most important ornamental plants and can be seriously infected by Botrytis cinerea. Here, integrated proteomics analysis was performed to detect global proteome, phosphorylation, and ubiquitination changes in rose upon B. cinerea infection and investigate the possible phosphorylation and ubiquitination crosstalk. A total of 6165 proteins, 11 774 phosphorylation and 10 582 ubiquitination sites, and 77 phosphorylation and 13 ubiquitination motifs were identified. Botrytis cinerea infection resulted in 169 up-regulated and 122 down-regulated proteins, 291 up-regulated and 404 down-regulated phosphorylation sites, and 250 up-regulated and 634 down-regulated ubiquitination sites. There were 12 up-regulated PR10 proteins and half of them also showed reduced ubiquitination. A lot of kinases probably involved in plant pattern-triggered immunity signaling were up-regulated phosphoproteins. Noticeably, numerous kinases and ubiquitination-related proteins also showed a significant change in ubiquitination and phosphorylation, respectively. A cross-comparison of phosphoproteome and ubiquitylome indicated that both of two post-translational modifications of 104 proteins were dynamically regulated, and many putative pattern-triggered immunity signaling components in the plant plasma membrane were co-regulated. Moreover, five selected proteins, including four PR10 proteins and a plasma membrane aquaporin, were proven to be involved in rose resistance to B. cinerea. Our study provides insights into the molecular mechanisms underlying rose resistance to B. cinerea and also increases the database of phosphorylation and ubiquitination sites in plants.

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