TAP Family: ARF

Li et al (2016): Auxin is a key regulator of virtually every aspect of plant growth and development from embryogenesis to senescence. Previous studies have indicated that auxin regulates these processes by controlling gene expression via a family of functionally distinct DNA-binding auxin response factors (ARFs). ARFs are likely components that confer specificity to auxin response through selection of target genes as transcription factors. They bind to auxin response DNA elements (AuxRE) in the promoters of auxin-regulated genes and either activate or repress transcription of these genes depending on a specific domain in the middle of the protein. Recent advances have provided information on the regulation of ARF gene expression, the role of ARFs in growth and developmental processes, protein–protein interactions of ARFs and target genes regulated by ARFs in plants. The canonical auxin response pathway evolved at the origin of Streptophyta (Mutte et al., 2018). In land plants, canonical plant ARFs contain an N-terminal B3-type DNA binding domain (Li et al., 2016), and/or an AUX_IAA domain. However, the analysis of TAP complements across brown algae (Denoeud et al., 2024) showed the presence of an auxin_resp domain but the lack of a B3 domain within most examined brown algal species. With the current TAPscan version 4, we cannot say with certainty whether the nature of these proteins is ARF-like. A revised classification of ARF TFs in TAPscan also including sub-family classification of ARFs will be included in the next TAPscan version, taking into account recent work, e.g. Rienstra et al., 2023.

This TAP family belongs to the B3 structural class of the Beta-barrel DNA-binding domains structural superclass, as defined in Plant-TFClass (Blanc-Mathieu et al. 2024)

References:

Denoeud, F., Godfroy, O., Cruaud, C., Heesch, S., Nehr, Z., Tadrent, N., Couloux, A., Brillet-Guéguen, L., Delage, L., Mckeown, D., Motomura, T., Sussfeld, D., Fan, X., Mazéas, L., Terrapon, N., Barrera-Redondo, J., Petroll, R., Reynes, L., Choi, S.-W., … Cock, J. M. (2024). Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems. BioRxiv, 2024.02.19.579948. https://doi.org/10.1101/2024.02.19.579948

Li, S.-B., Xie, Z.-Z., Hu, C.-G., & Zhang, J.-Z. (2016). A Review of Auxin Response Factors (ARFs) in Plants. Frontiers in Plant Science, 7. https://doi.org/10.3389/fpls.2016.00047

Mutte, S. K., Kato, H., Rothfels, C., Melkonian, M., Wong, G. K.-S., & Weijers, D. (2018). Origin and evolution of the nuclear auxin response system. ELife, 7. https://doi.org/10.7554/eLife.33399

Rienstra, J., Hernández-García, J., Weijers, D. (2023) To bind or not to bind: how AUXIN RESPONSE FACTORs select their target genes. J Exp Bot 2023 Dec 1;74(22):6922-6932. doi: 10.1093/jxb/erad259."

Blanc-Mathieu, Romain et al. 2024. Plant-TFClass: a structural classification for plant transcription factors. Trends in Plant Science, Volume 29, Issue 1, 40 - 51