The intervening domain is required for DNA-binding and functional identity of plant MADS transcription factors

Xuelei Lai,Jose M Muino,Cezary Smaczniak,Rosario Vega-Léon,Richard Immink,François Parcy,Catarina S Silva,Agnès Jourdain,Romain Blanc-Mathieu,Chloe Zubieta,Max H Nanao,Jérémy Lucas,Veronique Hugouvieux,Froukje Van Der Wal,Kerstin Kaufmann

doi:10.1038/s41467-021-24978-w

Abstract

The MADS transcription factors (TF) are an ancient eukaryotic protein family. In plants, the family is divided into two main lineages. Here, we demonstrate that DNA binding in both lineages absolutely requires a short amino acid sequence C-terminal to the MADS domain (M domain) called the Intervening domain (I domain) that was previously defined only in type II lineage MADS. Structural elucidation of the MI domains from the floral regulator, SEPALLATA3 (SEP3), shows a conserved fold with the I domain acting to stabilise the M domain. Using the floral organ identity MADS TFs, SEP3, APETALA1 (AP1) and AGAMOUS (AG), domain swapping demonstrate that the I domain alters genome-wide DNA-binding specificity and dimerisation specificity. Introducing AG carrying the I domain of AP1 in the Arabidopsis ap1 mutant resulted in strong complementation and restoration of first and second whorl organs. Taken together, these data demonstrate that the I domain acts as an integral part of the DNA-binding domain and significantly contributes to the functional identity of the MADS TF.

Highlights

The MADS transcription factors (TF) are an ancient eukaryotic protein family
Each monomer adopts the same secondary and tertiary structure with an N-terminal alpha helix (α1; aa 18–40) and two antiparallel beta strands (β1; aa 44–48 and β2; aa 55–58). These elements make up the core MADS DBD and are conserved in the MEF2 and SRF-like MADS TFs (Fig. 1a, b)
How the MADS TF family is able to regulate diverse developmental processes and different target genes with such a highly conserved DBD has been a fundamental question leading to the speculation that regions distal to the DBD may play a role in DNA-binding specificity either via the formation of higher-order complexes, the recruitment of ternary factors or via allosteric alterations in DNA-binding specificity of the MADS-box domain

Summary

Introduction

The MADS transcription factors (TF) are an ancient eukaryotic protein family. In plants, the family is divided into two main lineages. In addition to changes in amino acids important for direct base readout, the region C-terminally adjacent to the MADS-box domain varies based on sequence alignments and available structural data for mammalian and fungal SRF-like and MEF2-like MADS transcription factors (TFs). These carboxyl-terminal sequences have been shown to be important for dimerisation and DNA binding they do not directly contact the DNA4,7,11. The type II MADS play well established roles in many developmental processes including meristem identity, flowering time, fruit and seed development and floral organ identity[26]

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Results

Conclusion