Functional Divergence of APETALA1 and FRUITFULL is due to Changes in both Regulation and Coding Sequence

Abstract

Gene duplications are prevalent in plants, and functional divergence subsequent to duplication may be linked with the occurrence of novel phenotypes in plant evolution. Here, we examine the functional divergence of Arabidopsis thaliana APETALA1 (AP1) and FRUITFULL (FUL), which arose via a duplication correlated with the origin of the core eudicots. Both AP1 and FUL play a role in floral meristem identity, but AP1 is required for the formation of sepals and petals whereas FUL is involved in cauline leaf and fruit development. AP1 and FUL are expressed in mutually exclusive domains but also differ in sequence, with unique conserved motifs in the C-terminal domains of the proteins that suggest functional differentiation. To determine whether the functional divergence of AP1 and FUL is due to changes in regulation or changes in coding sequence, we performed promoter swap experiments, in which FUL was expressed in the AP1 domain in the ap1 mutant and vice versa. Our results show that FUL can partially substitute for AP1, and AP1 can partially substitute for FUL; thus, the functional divergence between AP1 and FUL is due to changes in both regulation and coding sequence. We also mutated AP1 and FUL conserved motifs to determine if they are required for protein function and tested the ability of these mutated proteins to interact in yeast with known partners. We found that these motifs appear to play at best a minor role in protein function and dimerization capability, despite being strongly conserved. Our results suggest that the functional differentiation of these two paralogous key transcriptional regulators involves both differences in regulation and in sequence; however, sequence changes in the form of unique conserved motifs do not explain the differences observed.

Identification and analysis of glutathione S-transferase gene family in sweet potato reveal divergent GST-mediated networks in aboveground and underground tissues in response to abiotic stresses

“…Makova et al (2003) uncovered that nonsynonymous (Ka) and synonymous (Ks) substitution rates were significantly correlated with gene expression divergences of human duplicate genes at early stages after duplication [ 50 ]. McCarthy et al (2015) reported that the functional divergence between two Arabidopsis paralogous genes is attributable to both regulation and changes in coding sequence [ 52 ]. In our study, we examined whether two genes with high similarity in coding sequences shared high similarity in gene expression patterns across different tissues.…”

Divergent Functional Diversification Patterns in the SEP/AGL6/AP1 MADS-Box Transcription Factor Superclade

“…Petunia AP1/SQUA Family Members Function in a Largely Redundant Fashion and Are Required for IM Identity Different members of the AP1/SQUA subfamily in Arabidopsis have evolved unique roles during development as exemplified by the distinct phenotypes of the single ap1 and ful mutants. Swapping experiments suggest that functional divergence between AP1 and FUL is due to changes in both expression pattern and coding sequence (McCarthy et al, 2015). At the same time, AP1, CAL, and FUL have retained a redundant function in inflorescence architecture (Ferrándiz et al, 2000), whereas CAL shares a cryptic role in petal development redundantly with AP1 (Castillejo et al, 2005).…”

Evolution of Gene Duplication in Plants

“…There is a large body of experimental evidence demonstrating how biological process functions differ between two plant duplicates. For example, paralogous MADS domain transcription factors control different aspects of plant development, and this functional divergence is due to changes in both promoter and coding regions (McCarthy et al, 2015). To summarize how the biological processes involving duplicates differ from those involving singleton genes, one approach is to examine annotated gene functions.…”