Abstract
BackgroundVviERF6Ls are an uncharacterized gene clade in Vitis with only distant Arabidopsis orthologs. Preliminary data indicated these transcription factors may play a role in berry development and extreme abiotic stress responses. To better understand this highly duplicated, conserved clade, additional members of the clade were identified in four Vitis genotypes. A meta-data analysis was performed on publicly available microarray and RNA-Seq data (confirmed and expanded with RT-qPCR), and Vitis VviERF6L1 overexpression lines were established and characterized with phenotyping and RNA-Seq.ResultsA total of 18 PN40024 VviERF6Ls were identified; additional VviERF6Ls were identified in Cabernet Sauvignon, Chardonnay, and Carménère. The amino acid sequences of VviERF6Ls were found to be highly conserved. VviERF6L transcripts were detected in numerous plant organs and were differentially expressed in response to numerous abiotic stresses including water deficit, salinity, and cold as well as biotic stresses such as red blotch virus, N. parvum, and E. necator. VviERF6Ls were differentially expressed across stages of berry development, peaking in the pre-veraison/veraison stage and retaining conserved expression patterns across different vineyards, years, and Vitis cultivars. Co-expression network analysis identified a scarecrow-like transcription factor and a calmodulin-like gene with highly similar expression profiles to the VviERF6L clade. Overexpression of VviERF6L1 in a Seyval Blanc background did not result in detectable morphological phenotypes. Genes differentially expressed in response to VviERF6L1 overexpression were associated with abiotic and biotic stress responses.ConclusionsVviERF6Ls represent a large and distinct clade of ERF transcription factors in grapevine. The high conservation of protein sequence between these 18 transcription factors may indicate these genes originate from a duplication event in Vitis. Despite high sequence similarity and similar expression patterns, VviERF6Ls demonstrate unique levels of expression supported by similar but heterogeneous promoter sequences. VviERF6L gene expression differed between Vitis species, cultivars and organs including roots, leaves and berries. These genes respond to berry development and abiotic and biotic stresses. VviERF6L1 overexpression in Vitis vinifera results in differential expression of genes related to phytohormone and immune system signaling. Further investigation of this interesting gene family is warranted.
Highlights
VviERF6Ls are an uncharacterized gene clade in Vitis with only distant Arabidopsis orthologs
The manually curated VviERF6Ls were confirmed and substantiated as members of this clade from protein motifs identified in Multiple Em for Motif Elicitation (MEME) [22, 23]
To identify additional novel VviERF6Ls that may have been overlooked with the manual annotation, an in-silico detection strategy was devised using the first (Motif 5) and last (Motif 4) spatial amino acid (AA) motifs to query the Vitis proteome
Summary
VviERF6Ls are an uncharacterized gene clade in Vitis with only distant Arabidopsis orthologs Preliminary data indicated these transcription factors may play a role in berry development and extreme abiotic stress responses. ERFs regulate gene expression of targets including transcription factors like RESPONSIVE TO DEHYDRATION 29B (RD29B), LATE EMBRYOGENESIS 4–5 (LEA4–5), HEAT SHOCK PROTEIN 101 (HSP101), and other ERFs, resulting in physiological responses and adaptations that allow a plant to better survive under specific environmental conditions like water deficit and high temperature [8] These transcription factors act as major signaling hubs that integrate cross-talk between ethylene and other phytohormones to mediate gene expression [9,10,11,12,13,14]. This family is divided into 12 sub-families based on regulatory elements and DNA-binding domains
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