The floral homeotic protein SEPALLATA3 recognizes target DNA sequences by shape readout involving a conserved arginine residue in the MADS-domain

Abstract

SEPALLATA3 of Arabidopsis thaliana is a MADS-domain transcription factor and acentral player in flower development. MADS-domain proteins bind as dimers to ATrich sequences termed 'CArG-boxes' which share the consensus 5'-CC(A/T) 6 GG-3'.Since only a fraction of the abundant CArG-boxes in the Arabidopsis genome are bound by SEPALLATA3, more elaborate principles have to be discovered to better understand which features turn CArG-box sequences into genuine recognition sites.Here, we investigated to which extent the shape of the DNA contributes to the DNAbinding specificity of SEPALLATA3. We determined in vitro binding affinities of SEPALLATA3 to a variety of DNA probes which all contain the CArG-box motif, but differ in their DNA shape characteristics. We found that binding affinity correlates well with certain DNA shape features associated with 'A-tracts'. Analysis of SEPALLATA3 proteins with single amino acid substitutions in the DNA-binding MADS-domain further revealed that a highly conserved arginine residue, which is expected to contact the DNA minor groove, contributes significantly to the shape readout. Our studies show that the specific recognition of cis-regulatory elements by plant MADSdomain transcription factors heavily depend on shape readout mechanisms and that the absence of a critical arginine residue in the MADS-domain impairs binding specificity. peer-reviewed)

A conserved leucine zipper-like motif accounts for strong tetramerization capabilities of SEPALLATA-like MADS-domain transcription factors

“…Among the four SEP genes, SEP3 has been the best studied ( Favaro et al , 2003 ; Immink et al , 2009 ; Kaufmann et al , 2009 ; Melzer and Theissen, 2009 ; Melzer et al , 2009 ; Smaczniak et al , 2012 ; Jetha et al , 2014 ; Muiño et al , 2016 ; Gusewski et al , 2017 ). Beyond the formation of complexes that determine floral organ identity, SEP3 is also involved in controlling flowering time, floral transition, and ovule development ( Favaro et al , 2003 ; Immink et al , 2009 ; Liu et al , 2009 ; Lopez-Vernaza et al , 2012 ).…”

MADS8 is indispensable for female reproductive development at high ambient temperatures in cereal crops

“…Except for the A-class APETALA 2 ( AP2 ) gene, all ABCDE genes encode MIKC-type MADS-box transcription factors ( Jofuku et al 1994 ). These proteins bind as dimers to DNA sequences named “CArG” boxes and interact to form heterotetrameric complexes that can recognize different CArG targets ( Muiño et al 2014 ; Gusewski et al 2017 ). In rice, there are 2 duplicated D-lineage genes, OsMADS13 and OsMADS21 ; Osmads13 mutants result in the homeotic conversion of ovules into carpels ( Dreni et al 2007 ).…”