The origin of floral quartet formation - Ancient exon duplications shaped the evolution of MIKC-type MADS-domain transcription factor interactions

Abstract

During development of flowering plants, some MIKC-type MADS-domain transcription factors (MTFs) exert their regulatory function as heterotetrameric complexes bound to two sites on the DNA of target genes. This way they constitute 'floral quartets' or related 'floral quartet-like complexes' (FQCs), involving a unique multimeric system of paralogous protein interactions. Tetramerisation of MTFs is brought about mainly by interactions of keratin-like (K) domains. The K-domain associated with the more ancient DNA-binding MADS-domain during evolution in the stem group of extant streptophytes (charophyte green algae + land plants). However, whether this was sufficient for MTF tetramerisation and FQC formation to occur, remains unknown. Here, we provide biophysical and bioinformatic data indicating that the ancestral MTFs were not able to form FQCs. According to our data, FQC formation originated in the stem group of land plants in a sublineage of MIKC-type genes termed MIKCC-type genes. In the stem group of this gene lineage, the duplication of the most downstream exon encoding the K-domain led to a C-terminal elongation of the second K-domain helix, thus generating the tetramerisation interface found in extant MIKCC-type proteins. In the stem group of the sister lineage of the MIKCC-type genes, termed MIKC*-type genes, the duplication of two other exons of the K-domain occurred, extending the K-domain at its N-terminal end. Our data indicate that this structural change prevents heterodimerisation between MIKCC-type and MIKC*-type proteins. This way, two largely independent gene regulatory networks could be established, featuring MIKCC-type or MIKC*-type proteins, respectively, that control different aspects of plant development.

Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution

“…In transcriptomic data (One Thousand Plant Transcriptomes Initiative, 2019, Sayers et al, 2021), however, we found MADS-box genes encoding a K domain in other Zygnematophyceae including a Zygnema species, which form a separate clade. This suggests the presence of two MADS-box gene in the Zygnematophyceae ancestor: (i) an ancestral Type II that did not acquire the K-domain yet and is thus very likely unable to form FQCs, and (ii) the MIKC-type, for which in one case FQC formation has already experimentally been demonstrated in vitro (Rümpler et al, 2022). The clade of the K-domain encoding genes was apparently lost in the Zygnema species sequenced here ( Figure S16 ).…”

Deep evolution of MADS-box genes in Archaeplastida

“…Tetramerization of MIKC C proteins is conferred by the C-terminal part of the K domain (Puranik, et al 2014). Recently, however, it has been shown that MIKC proteins from some streptophyte algae do only have a weak or no ability to form tetrameric complexes, this way corroborating the view that the K domain may initially have been mainly involved in strengthening protein dimerization (Kaufmann, et al 2005;Rümpler, et al 2022). Nevertheless, the acquisition of the K box by a MADS-box gene in an ancestor of streptophytes may represent some kind of pre-adaptation that, after an elongation of the part encoding the C-terminal region of the K domain (Rümpler, et al 2022), gained the ability of tetramerization.…”

“…Most remarkably, the group not encoding the K domain was lost at the base of land plants (Figure 3). Also in the stem group of land plants, MIKC-type genes were duplicated to give rise to the two clades of MIKC C and MIKC* genes (Rümpler, et al 2022), followed by a great expansion mainly of the MIKC C genes and the evolution of a diversity of functions that the encoded proteins are so well known for in flowering plants, ranging from root to flower and fruit development (Gramzow and Theissen 2010; Smaczniak, et al 2012).…”

Cracking the floral quartet code: How do multimers of MIKCC-type MADS-domain transcription factors recognize their target genes?

“…The ancestral MIKC-type gene present in charophytes was duplicated in the stem group of extant embryophytes (land plants), resulting in the lineages of MIKC C -type and MIKC*-type genes [15,[27][28][29].…”

“…FQC formation depends on some remarkable structural features of the K-domain [24], but not all MIKC-type proteins can do the trick. Recent data suggest that some MIKC-type proteins of charophyte algae are capable of FQC-formation, but that an exon duplication that led to an elongation of the K-domain in the stem group of extant MIKC C -type genes strongly favored it [29]. In contrast, MIKC*-type proteins appear to bind to DNA only as dimers, not as tetramers [29].…”