Evolution of the ARF Gene Family in Land Plants: Old Domains, New Tricks

Abstract

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 data set 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 data set 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 that 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.

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

“…As the ARF family traces its origins back to the first land plants, we investigated whether the maize and Arabidopsis ARF binding properties have diverged in the 140-150 million years since their last common ancestor (Finet et al, 2013). Testing a maize co-ortholog of ARF5 (ZmARF29; Galli et al, 2015) on maize gDNA (Zm-gDNA) by DAP-seq, we observed similar, but not identical, motif spacing preferences with two dominant spacing groups in maize compared to the eight more distributed groups in Arabidopsis ( Figure 6C).…”

The PB1 Domain in Auxin Response Factor and Aux/IAA Proteins: A Versatile Protein Interaction Module in the Auxin Response

“…Furthermore, the Auxin_resp domain is not found in ARFs before plants emerged from an aquatic to land environment. Freshwater algae ancestors of land plants, the charophytes, are reported to contain precursor ARF-like proteins with a B3 domain and domain III/IV, but lack the Auxin_resp domain Finet et al, 2013). The charophyte Klebsormidium flaccidum has an ARF-like protein with an AP2/ERF-related DBD, a B3 domain, and a C-terminal domain III/IV containing the conserved lysine and OPCA motifs found in PB1 domains, but no sequence related to the DD or BRWD found in typical ARF proteins (annotated gene sequence kf100094_0070 in 40528 Klebsormidium flaccidum genome V1.0; Hori et al, 2014).…”

Recapitulation of the forward nuclear auxin response pathway in yeast

“…A lumped internal state, which combines multiple reactions including the binding of auxin to the AFB receptor and related molecular machinery, is represented by x. IAA protein levels are represented by y. The model has eight parameters (k [1][2][3][4][5][6][7][8] ) that intuitively correspond to the biological processes listed in Table 1. We tested the validity of this interpretation numerically by evaluating fits of the data using different assumptions about which parameters change when different ARFs or IAAs are used in the circuit (SI Appendix).…”

“…Limited expression studies available The variable x represents a lumped internal state, which combines multiple reactions including the binding of auxin to the AFB receptor, and the variable y represents IAA protein levels. The model has eight parameters (k [1][2][3][4][5][6][7][8] ) that intuitively correspond to the biological processes listed in Table 1. We focused on three parameters with strong effect on ARC dynamics: IAA expression level (k 3 for IAA and ARF family members indicate that multiple family members are often coexpressed in plant cells, raising the question of how specificity or ordering is encoded (14,15).…”

“…The small molecule auxin is linked to signaling modules that allowed plants to move to land, develop new organs, and respond to the environment (1,2). Despite the wide range of auxin responses, the core auxin signal transduction pathway is quite simple, involving a small number of components from perception through transcription (Fig.…”