Functional analysis and binding affinity of tomato ethylene response factors provide insight on the molecular bases of plant differential responses to ethylene

Abstract

BackgroundThe phytohormone ethylene is involved in a wide range of developmental processes and in mediating plant responses to biotic and abiotic stresses. Ethylene signalling acts via a linear transduction pathway leading to the activation of Ethylene Response Factor genes (ERF) which represent one of the largest gene families of plant transcription factors. How an apparently simple signalling pathway can account for the complex and widely diverse plant responses to ethylene remains yet an unanswered question. Building on the recent release of the complete tomato genome sequence, the present study aims at gaining better insight on distinctive features among ERF proteins.ResultsA set of 28 cDNA clones encoding ERFs in the tomato (Solanum lycopersicon) were isolated and shown to fall into nine distinct subclasses characterised by specific conserved motifs most of which with unknown function. In addition of being able to regulate the transcriptional activity of GCC-box containing promoters, tomato ERFs are also shown to be active on promoters lacking this canonical ethylene-responsive-element. Moreover, the data reveal that ERF affinity to the GCC-box depends on the nucleotide environment surrounding this cis-acting element. Site-directed mutagenesis revealed that the nature of the flanking nucleotides can either enhance or reduce the binding affinity, thus conferring the binding specificity of various ERFs to target promoters.Based on their expression pattern, ERF genes can be clustered in two main clades given their preferential expression in reproductive or vegetative tissues. The regulation of several tomato ERF genes by both ethylene and auxin, suggests their potential contribution to the convergence mechanism between the signalling pathways of the two hormones.ConclusionsThe data reveal that regions flanking the core GCC-box sequence are part of the discrimination mechanism by which ERFs selectively bind to their target promoters. ERF tissue-specific expression combined to their responsiveness to both ethylene and auxin bring some insight on the complexity and fine regulation mechanisms involving these transcriptional mediators. All together the data support the hypothesis that ERFs are the main component enabling ethylene to regulate a wide range of physiological processes in a highly specific and coordinated manner.

Comprehensive Profiling of Ethylene Response Factor Expression Identifies Ripening-Associated ERF Genes and Their Link to Key Regulators of Fruit Ripening in Tomato

“…Taking advantage of the recent release of the complete annotated tomato genome sequence (Tomato Genome Consortium, 2012), 77 tomato ERF genes were identified, but knowledge of their physiological significance has been hampered by the functional redundancy among members of this vast gene family. A number of the ERF genes identified in tomato are ethylene inducible and show a ripeningrelated expression pattern that highlights their putative role in fruit ripening (Sharma et al, 2010;Pirrello et al, 2012;Liu et al, 2014Liu et al, , 2015. Consistent with this hypothesis, tomato LeERF1 was reported to mediate the ethylene response, and its overexpression resulted in a constitutive ethylene response and accelerated fruit ripening and softening (Li et al, 2007).…”

“…Because they are encoded by a large multigene family, ERFs are well suited to mediate the diversity and specificity of ethylene responses through recruiting the desired ethylene-responsive genes (Pirrello et al, 2012). Taking advantage of the recent release of the complete annotated tomato genome sequence (Tomato Genome Consortium, 2012), 77 tomato ERF genes were identified, but knowledge of their physiological significance has been hampered by the functional redundancy among members of this vast gene family.…”

The Hevea brasiliensis AP2/ERF superfamily: from ethylene signalling to latex harvesting and physiological disease response

“…The constitutive expression of several HbERFs led us to consider a post-transcriptional regulation controlling the activity of these proteins. Yet, it has been shown in grapevine, tomato and Arabidopsis as ERF groups (ERF-II, ERF-III, ERF-VII and ERF-IX) were strongly expressed in different tissues (Licausi et al, 2010a;Pirrello et al, 2012;Bailey-Serres et al, 2012). A high abundance transcript in non-stressed condition was potentially a default defence system being present before the stress condition (Cheng et al, 2013b).…”

“…Post-transcriptional regulation of Dehydration Responsive Element Binding Proteins 2 (DREB2) genes by alternative splicing has been reported in Arabidopsis, tomato and wheat (Rehman & Mahmood, 2015;Pirrello et al, 2012;Lata & Prasad, 2011;Lucas et al, 2011;Mizoi et al 2012). In the case of alternative splicing, two types of transcripts may exist.…”

A Co-Opted Hormonal Cascade Activates Dormant Adventitious Root Primordia upon Flooding in Solanum dulcamara

“…Ethylene synthesis and response-related genes were strongly overrepresented among stem-and, to a lesser extent, primordia-up-regulated genes. This included one 1-aminocyclopropane-1-carboxylate (ACC) synthase (ACS), two ACC oxidases (ACO), and orthologs of eight of the 13 ETHYLENE RESPONSE FACTOR-type ERF/AP2 genes from tomato (Solanum lycopersicum) that were shown to be ethylene responsive (Pirrello et al, 2012;Supplemental Data Set S3). Analysis of earlier time points after onset of flooding indicated that induction of three ethylene signaling-associated genes was fast, within 3 h, and peaked earlier in the primordia (after 3 to 6 h) than in the stem (after 12 to 18 h; Supplemental Fig.…”