Computational Disorder Analysis in Ethylene Response Factors Uncovers Binding Motifs Critical to Their Diverse Functions

Abstract

APETALA2/ETHYLENE RESPONSE FACTOR transcription factors (AP2/ERFs) play crucial roles in adaptation to stresses such as those caused by pathogens, wounding and cold. Although their name suggests a specific role in ethylene signalling, some ERF members also co-ordinate signals regulated by other key plant stress hormones such as jasmonate, abscisic acid and salicylate. We analysed a set of ERF proteins from three divergent plant species for intrinsically disorder regions containing conserved segments involved in protein–protein interaction known as Molecular Recognition Features (MoRFs). Then we correlated the MoRFs identified with a number of known functional features where these could be identified. Our analyses suggest that MoRFs, with plasticity in their disordered surroundings, are highly functional and may have been shuffled between related protein families driven by selection. A particularly important role may be played by the alpha helical component of the structured DNA binding domain to permit specificity. We also present examples of computationally identified MoRFs that have no known function and provide a valuable conceptual framework to link both disordered and ordered structural features within this family to diverse function.

Cytokinin Signaling Downstream of the His-Asp Phosphorelay Network: Cytokinin-Regulated Genes and Their Functions

“…According to sequence similarity, CRF2 , CRF5 , and CRF6 are the three cytokinin-responsive genes of a group of six identified as the CRF (Cytokinin Response Factor) subset of ERF/AP2 transcription factor genes ( Rashotte et al, 2006 ; Rashotte and Goertzen, 2010 ; Cutcliffe et al, 2011 ; Jeon et al, 2016 ). Among other functions, they play a major role in establishing adjustments to pathogens, wounding and cold ( Müller and Munné-Bosch, 2015 ; Sun X. et al, 2020 ). All three of the encoded proteins contain a highly conserved DNA-binding AP2 domain in the central region.…”

“…All three of the encoded proteins contain a highly conserved DNA-binding AP2 domain in the central region. This domain is around 60 amino acids long ( Weigel, 1995 ; Cutcliffe et al, 2011 ) and directly binds to the GCC-Box, which appears to be the key motif in the promoters of ethylene-responsive genes ( Hao et al, 1998 ; Sakuma et al, 2002 ; Rashotte and Goertzen, 2010 ; Sun X. et al, 2020 ). Additionally, they have a C-terminal MAPK phosphorylation site and an N-terminal CRF domain.…”

EgJUB1 and EgERF113 transcription factors as potential master regulators of defense response in Elaeis guineensis against the hemibiotrophic Ganoderma boninense

“…In addition, bHLH-MYB association was involved in the biosynthesis of flavonoids secondary metabolites under phytohormones signaling, wounding and fungal interaction [ 36 , 37 ]. Interaction to specific DNA sequences (binding motifs) is dependent on the DNA binding domain (DBD) of TFs [ 38 ]. Binding preferences of TF during biotic or abiotic stress such as ERFs have been suggested to correlate with the composition of amino acid sequences in DBD [ 38 , 39 ].…”

“…Interaction to specific DNA sequences (binding motifs) is dependent on the DNA binding domain (DBD) of TFs [ 38 ]. Binding preferences of TF during biotic or abiotic stress such as ERFs have been suggested to correlate with the composition of amino acid sequences in DBD [ 38 , 39 ]. The presence of multiple cis -acting elements in the promoter region contributes to overlapping roles in development and/or defense against multiple stresses of the expressed proteins [ 26 ].…”

Intrinsic Disorder in Plant Transcription Factor Systems: Functional Implications

“…The potentially small binding interface of SLiMs enable participation in transient interactions, many of which are in the low-mid micromolar K d range [ 14 , 17 ]. SLiMs often coincide with molecular recognition features (MoRFs) [ 18 , 19 , 20 ]. MoRFs are structure-prone regions within longer IDRs [ 21 ], which undergo coupled folding and binding [ 21 , 22 ].…”