Deep conservation of response element variants regulating plant hormonal responses

Abstract

8Phytohormones regulate many aspects of plant life by activating transcription factors (TF) that bind 9 sequence-specific response elements (RE) in regulatory regions of target genes. Despite their short 10 length, REs are degenerate with a core of just 3-4bps. This degeneracy is paradoxical, as it reduces 11 specificity, and REs are extremely common in the genome. To study whether RE degeneracy might serve 12 a biological function we developed an algorithm for the detection of regulatory sequence conservation, 13and applied it to phytohormones REs in 45 angiosperms. Surprisingly, we found that specific RE variants 14 are highly conserved in core hormone response genes. Experimental evidence showed that specific 15 variants act to regulate the magnitude and spatial profile of hormonal response in Arabidopsis and 16 tomato. Our results suggest that hormone-regulated TFs bind a spectrum of REs, each coding for a 17 distinct transcriptional response profile. Our approach is applicable for precise editing and rational 18 promoter design. 19

A non-canonical Aux/IAA gene MsIAA32 regulates peltate glandular trichome development in spearmint

“…Two variants of the core AuxRE (TGTC) sites with a 5-bp spacer (TGTCTT—–TGTCCC) were present ( Figure 2A ). ARFs are known to bind as dimers on palindromic AuxREs, which are spaced by 5 to 9 nucleotides ( Michal et al., 2019 ) suggesting a probable regulation of MsIAA32 by ARFs. Additionally, several TFs and light-responsive elements were also present.…”

Genome-Wide Identification of Apple Atypical bHLH Subfamily PRE Members and Functional Characterization of MdPRE4.3 in Response to Abiotic Stress

“…The sequences 2000-bp upstream of each gene ATG were obtained from the GDR database, and cis -acting elements were analyzed by the online database PlantCARE website. The results showed many hormone-responsive elements (TGA-element, ABRE, CGTCA-motif/TGACG-motif, AuxRR-core, P-box, TCA-element) ( Michal et al, 2019 ), stress-responsive elements (WUN-motif, TC-rich repeats ARE, LTR, MBS), and light-responsive elements (G-box, GA-box, GT1-motif, GATA-motif, Box4, TCT-motif) ( Bastian et al, 2010 ; Porto et al, 2014 ; Ning et al, 2017 ). In addition, meristem expression elements (CAT-box) and tissue expression-specific regulatory elements (e.g., O2-site) were contained in some members, indicating that these genes may be influenced by multiple factors ( An et al, 2019 ).…”