Phenotypic analysis combined with tandem mass tags (TMT) labeling reveal the heterogeneity of strawberry stolon buds

Drought induces epitranscriptome and proteome changes in stem-differentiating xylem of Populus trichocarpa

Understanding gene expression and regulation requires insights into RNA transcription, processing, modification, and translation. However, the relationship between the epitranscriptome and the proteome under drought stress remains undetermined in poplar (Populus trichocarpa). In this study, we used Nanopore direct RNA sequencing and tandem mass tag-based proteomic analysis to examine epitranscriptomic and proteomic regulation induced by drought treatment in stem-differentiating xylem (SDX). Our results revealed a decreased full-length read ratio under drought treatment and, especially, a decreased association between transcriptome and proteome changes in response to drought. Epitranscriptome analysis of cellulose- and lignin-related genes revealed an increased N6-Methyladenosine (m6A) ratio, which was accompanied by decreased RNA abundance and translation, under drought stress. Interestingly, usage of the distal poly(A) site increased during drought stress. Finally, we found that transcripts of highly expressed genes tend to have shorter poly(A) tail length (PAL), and drought stress increased the percentage of transcripts with long PAL. These findings provide insights into the interplay among m6A, polyadenylation, PAL, and translation under drought stress in P. trichocarpa SDX.

Comparative Proteomic Analysis of Grapevine Rootstock in Response to Waterlogging Stress

Waterlogging severely affects global agricultural production. Clarifying the regulatory mechanism of grapevine in response to waterlogging stress will help to improve the waterlogging tolerance of grapevine. In the present study, the physiological and proteomic responses of SO4 grapevine rootstock to different waterlogging tolerances were comparatively assayed. The results showed that the activities of SOD and POD first increased and then decreased, while the change trend of CAT and APX activities was the opposite. In addition, the MDA and H₂O₂ contents increased after waterlogging treatment, but the chlorophyll a and chlorophyll b contents decreased. A total of 5,578 grapevine proteins were identified by the use of the tandem mass tag (TMT) labeling technique. Among them, 214 (103 and 111 whose expression was upregulated and downregulated, respectively), 314 (129 and 185 whose expression was upregulated and downregulated, respectively), and 529 (248 and 281 whose expression was upregulated and downregulated, respectively) differentially expressed proteins (DEPs) were identified in T0d vs. T10d, T10d vs. T20d, and T0d vs. T20d comparison groups, respectively. Enrichment analysis showed that these DEPs were mainly involved in glutathione metabolism, carbon fixation, amino sugar and nucleotide sugar metabolism, biosynthesis of amino acids, photosynthesis, carbon metabolism, starch, and sucrose metabolism, galactose metabolism, protein processing and ribosomes. To further verify the proteomic data, the expression of corresponding genes that encode eight DEPs was confirmed by quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). The results of this study presented an important step toward understanding the resistance mechanisms of grapevine in response to waterlogging stress at the proteome level.