Deep conservation of cis-element variants regulating plant hormonal responses

Abstract

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

Architecture of DNA elements mediating ARF transcription factor binding and auxin-responsive gene expression in Arabidopsis

“…The DNA sequence 5′-TGTC-3′ is critical for recruiting ARFs based on in vitro binding assays, as well as the effect of mutations in this element in promoters on the expression of some genes (25,34,40,41). However, the two nucleotides (NN) following the core tetranucleotide play an important role in determining ARF binding affinity in vitro (25,42), and there is strong conservation of several NN variants in auxin-responsive genes in many angiosperms (43). Importantly, protein-binding microarrays revealed large differences in apparent binding affinity to all TGTCNN hexamers (34,35), and a variant with GG as final bases conferred a more potent transcriptional auxin response than a TC variant (38).…”

Genome-wide characterization and expression profiling of B3 superfamily during flower induction stage in pineapple (Ananas comosusL.)

“…Cis-element was short in length with a core of only seveal base-pairs, but could regulate gene expression and related to the functions of downstream genes [54][55]. The results illustrate that 6 phytohormones-related cis-element were existed in AcB3 genes superfamily, include abscisic acid, auxin, ethylene, gibberellin, MeJA and salicylic acid responsiveness elements.…”

Specificity in auxin responses is not explained by the promoter preferences of activator ARFs

“…Variants were specifically embedded at the A1 position, an AuxRE 166 base pairs from the transcriptional start site (TSS) (Pierre-Jerome et al, 2016). This region relative to the TSS has been shown to be enriched for AuxREs within the Arabidopsis genome (Lieberman-Lazarovich et al, 2019).…”

“…AtARF1 and AtARF5 in fact bind most strongly to the AuxRE TGTCGG and its reverse on two AuxREs facing towards each other (Boer et al, 2014). Additionally, DR5 reporters using different AuxRE sequences showed variable activation in a transient expression assay (Lieberman-Lazarovich et al, 2019). We tested how AuxRE sequence impacts activation by AtARF5 and AtARF19 on two AuxREs facing towards each other by comparing activation on the AuxREs TGTCTC/GAGACA and on the AuxREs TGTCGG/CCGACA.…”