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Structural Basis for Plant MADS Transcription Factor Oligomerization


Structural Basis for Plant MADS Transcription Factor Oligomerization

Xuelei Lai et al. Comput Struct Biotechnol J.


MADS transcription factors (TFs) are DNA binding proteins found in almost all eukaryotes that play essential roles in diverse biological processes. While present in animals and fungi as a small TF family, the family has dramatically expanded in plants over the course of evolution, with the model flowering plant, Arabidopsis thaliana, possessing over 100 type I and type II MADS TFs. All MADS TFs contain a core and highly conserved DNA binding domain called the MADS or M domain. Plant MADS TFs have diversified this domain with plant-specific auxiliary domains. Plant type I MADS TFs have a highly diverse and largely unstructured Carboxy-terminal (C domain), whereas type II MADS have added oligomerization domains, called Intervening (I domain) and Keratin-like (K domain), in addition to the C domain. In this mini review, we describe the overall structure of the type II "MIKC" type MADS TFs in plants, with a focus on the K domain, a critical oligomerization module. We summarize the determining factors for oligomerization and provide mechanistic insights on how secondary structural elements are required for oligomerization capability and specificity. Using MADS TFs that are involved in flower organ specification as an example, we provide case studies and homology modeling of MADS TFs complex formation. Finally, we highlight outstanding questions in the field.

Keywords: Arabidopsis; Floral development; MADS transcription factors; Oligomerization.


Fig. 1
Fig. 1
3D model superposition of M domains and I domain extensions of MADS family proteins from yeast and human with plant MI domains modeled. (A) Schematic representation of domain compositions of MIKC type MADS TF using SEP3 amino acid numbering as an example. (B) The coordinates were taken from yeast MCM1 (green, PDB 1MNM; residues 18–91) [47], human SRF (magenta, PDB 1SRS, residues 132–223) [46], human myocyte enhancer factor 2A (MEF2A) (yellow, PDB 3KOV, residues 2–95) [45], human MEF2B (cyan, PDB 1N6J, residues 2–58) [54], human MEF2 chimera (pink, PDB 6BYY, residues MEF2A (1–64 and 91–95) and MEF2B (65–90)) [55]. Two SEP3 models (SEP3-M1 in orange (residues 1–72) and SEP3-M2 in gray (residues 2–89)) were generated from SWISS-MODEL [56], using PDB 1SRS and 6BYY as templates, respectively. (C) Crystal structure of human MEF2B (PDB 6C9L) showing the presence of α-helix, H3 (highlighted in red), on top of H2 helices; Note that H3 in this conformation is only present in one dimer (formed by chain E and F) of the three dimers in the asymmetric unit. (D) Superposition of SEP3 M + I domain models showing different conformation possibilities of the I domain (indicated by a bold arrow). M, M domain; I, I domain; N, N-terminus; C, C-terminus of SEP3-M1; C′, C-terminus of SEP3-M2 (part of I domain is indicated in dash box).
Fig. 2
Fig. 2
K domain sequence alignment of some representative MADS TFs from Arabidopsis and SEP3 K domain structure. (A) K domain sequence alignment of SEP3, SEP1, SEP2, AP1, AG, SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), FLOWERING LOCUS C (FLC), SHORT VEGETATIVE PHASE (SVP), AP3 and PI, using ESPript 3 [65]. TT indicates the kink region that connects α1 and α2. (B) Crystal structure of SEP3 K domain (PDB 4OX0). The residues involved in dimer and tetramer formation are indicated and colored by wheat and magenta, respectively. The insert shows key residues in the kink region colored red.
Fig. 3
Fig. 3
Coiled coil prediction of MADS TFs involved in flower organ specification in Arabidopsis. (A) The coiled coil probability was predicted by MultiCoil [66] using the full-length protein sequence of SEP3, AP1, PI, AG and AP3, respectively, as input. The prediction was set for coiled coil dimer formation with a prediction window of 21 residues. The peak regions correspond to the K domains of the corresponding sequences. (B) Schematic representation of flower quartet model in organ specification. SEP3 labels colored in red indicates strong probability of coiled coil formation, AP1 and PI in green medium, and AP3 and AG in black weak.

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