Grape ASR-Silencing Sways Nuclear Proteome, Histone Marks and Interplay of Intrinsically Disordered Proteins

Abstract

In order to unravel the functions of ASR (Abscisic acid, Stress, Ripening-induced) proteins in the nucleus, we created a new model of genetically transformed grape embryogenic cells by RNAi-knockdown of grape ASR (VvMSA). Nuclear proteomes of wild-type and VvMSA-RNAi grape cell lines were analyzed by quantitative isobaric tagging (iTRAQ 8-plex). The most significantly up- or down-regulated nuclear proteins were involved in epigenetic regulation, DNA replication/repair, transcription, mRNA splicing/stability/editing, rRNA processing/biogenesis, metabolism, cell division/differentiation and stress responses. The spectacular up-regulation in VvMSA-silenced cells was that of the stress response protein VvLEA D-29 (Late Embryogenesis Abundant). Both VvMSA and VvLEA D-29 genes displayed strong and contrasted responsiveness to auxin depletion, repression of VvMSA and induction of VvLEA D-29. In silico analysis of VvMSA and VvLEA D-29 proteins highlighted their intrinsically disordered nature and possible compensatory relationship. Semi-quantitative evaluation by medium-throughput immunoblotting of eighteen post-translational modifications of histones H3 and H4 in VvMSA-knockdown cells showed significant enrichment/depletion of the histone marks H3K4me1, H3K4me3, H3K9me1, H3K9me2, H3K36me2, H3K36me3 and H4K16ac. We demonstrate that grape ASR repression differentially affects members of complex nucleoprotein structures and may not only act as molecular chaperone/transcription factor, but also participates in plant responses to developmental and environmental cues through epigenetic mechanisms.

Polyploidization and genomic selection integration for grapevine breeding: a perspective

“…In addition to genomics, metabolomics, and transcriptomics, derived and innovative omics (such as epigenomics and epitranscriptomics) can also be used for comprehensive understanding of the complex epigenetic modifications in the induced polyploids. Recently, there has been growing recognition of the important roles of epigenetic regulations and memories in the stress response of crops, including grapevines ( Atanassov et al., 2022 ; Dal Santo et al., 2022 ; Jia et al., 2023 ). Epitranscriptomics, which deals with chemical modifications on RNA molecules, is yet to be applied in viticulture.…”

Grape ASR Regulates Glucose Transport, Metabolism and Signaling

“…The description of several ASRs as intrinsically disordered proteins [ 24 , 25 , 26 , 27 , 28 ] perfectly matches with their ability to interact as chaperones with macromolecules, such as nucleic acids and enzymes [ 29 , 30 , 31 ]. ASR proteins can also act as transcription regulators able to recognize and bind to specific promoter sequences [ 32 , 33 , 34 , 35 , 36 ], as well as to form homodimers and heterodimers with other transcription factors [ 37 , 38 , 39 , 40 ].…”

“…All these molecular features in combination with their subcellular distribution, nuclear and cytosolic [ 32 , 33 , 34 , 35 , 41 ], contribute to their physiological functions at the transitions between plant developmental stages [ 18 , 19 , 32 , 42 ] and in the plant responses to abiotic and biotic constraints [ 12 , 15 , 16 , 36 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 ]. Furthermore, the deciphering of ASRs’ plausible involvement in the epigenetic mechanisms throughout their impact on microRNA expression, chromatin modifiers, and histone marks [ 27 , 51 ] may suggest a real biological role in the priming of plant responses to environmental cues.…”