Deciphering the regulatory networks involved in mild and severe salt stress responses in the roots of wild grapevine Vitis vinifera spp. sylvestris

Abstract

Transcriptional regulatory networks are pivotal components of plant's response to salt stress. However, plant adaptation strategies varied as a function of stress intensity, which is mainly modulated by climate change. Here, we determined the gene regulatory networks based on transcription factor (TF) TF_gene co-expression, using two transcriptomic data sets generated from the salt-tolerant "Tebaba" roots either treated with 50 mM NaCl (mild stress) or 150 mM NaCl (severe stress). The analysis of these regulatory networks identified specific TFs as key regulatory hubs as evidenced by their multiple interactions with different target genes related to stress response. Indeed, under mild stress, NAC and bHLH TFs were identified as central hubs regulating nitrogen storage process. Moreover, HSF TFs were revealed as a regulatory hub regulating various aspects of cellular metabolism including flavonoid biosynthesis, protein processing, phenylpropanoid metabolism, galactose metabolism, and heat shock proteins. These processes are essentially linked to short-term acclimatization under mild salt stress. This was further consolidated by the protein-protein interaction (PPI) network analysis showing structural and plant growth adjustment. Conversely, under severe salt stress, dramatic metabolic changes were observed leading to novel TF members including MYB family as regulatory hubs controlling isoflavonoid biosynthesis, oxidative stress response, abscisic acid signaling pathway, and proteolysis. The PPI network analysis also revealed deeper stress defense changes aiming to restore plant metabolic homeostasis when facing severe salt stress. Overall, both the gene co-expression and PPI network provided valuable insights on key transcription factor hubs that can be employed as candidates for future genetic crop engineering programs.

Keywords: Hubs; Regulatory networks; Root-transcriptomics; Salt stress; Transcription factors; Wild grapevines.