Data from: Evolution of the ARF gene family in land plants: old domains, new tricks

Auxin Response Factors (ARF) are key players in plant development. They
mediate the cellular response to the plant hormone auxin by activating or
repressing the expression of downstream developmental genes. The pivotal
activation function of ARF proteins is enabled by their four-domain
architecture, which includes both DNA-binding and protein dimerization
motifs. To determine the evolutionary origin of this characteristic
architecture, we built a comprehensive dataset of 224 ARF-related protein
sequences that represents all major living divisions of land plants,
except hornworts. We found that ARFs are split into three subfamilies that
could be traced back to the origin of the land plants. We also show that
repeated events of extensive gene duplication contributed to the expansion
of those three original subfamilies. Further examination of our dataset
uncovered a broad diversity in the structure of ARF transcripts and
allowed us to identify an additional conserved motif in ARF proteins. We
found that additional structural diversity in ARF proteins is mainly
generated by two mechanisms: genomic truncation and alternative splicing.
We propose that the loss of domains from the canonical, four-domain ARF
structure has promoted functional shifts within the ARF family by
disrupting either dimerization or DNA binding capabilities. For instance,
the loss of dimerization domains in some ARFs from moss and spikemoss
genomes leads to proteins which are reminiscent of Aux/IAA proteins,
possibly providing a clue on the evolution of these modulators of ARF
function. We also assessed the functional impact of alternative splicing
in the case of ARF4, for which we have identified a novel isoform in
Arabidopsis thaliana. Genetic analysis showed that these two transcripts
exhibit markedly different developmental roles in A. thaliana. Gene
duplications, domain rearrangement and post-transcriptional regulation
have thus enabled a subtle control of auxin signaling through ARF proteins
that may have contributed to the critical importance of these regulators
in plant development and evolution.