Decoding the Auxin Matrix: Auxin Biology Through the Eye of the Computer

Abstract

The plant hormone auxin is certainly the most studied developmental regulator in plants. The many functions of auxin during development, from the embryo to the root and shoot construction, are mediated by an ever-growing collection of molecular regulators, with an overwhelming degree of both ubiquity and complexity that we are still far from fully understanding and that biological experiments alone cannot grasp. In this review, we discuss how bioinformatics and computational modeling approaches have helped in recent years to explore this complexity and to push the frontiers of our understanding of auxin biology. We focus on how analysis of massive amounts of genomic data and construction of computational models to simulate auxin-regulated processes at different scales have complemented wet experiments to increase the understanding of how auxin acts in the nucleus to regulate transcription and how auxin movement between cells regulates development at the tissular scale. Expected final online publication date for the Annual Review of Plant Biology, Volume 74 is May 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Regulation of indole‐3‐acetic acid biosynthesis and consequences of auxin production deficiency in Serratia plymuthica

“…Indole‐3‐acetic acid (IAA) is the most abundant naturally occurring auxin phytohormone and plays a critical role in plant growth, development and responses against a broad range of biotic and abiotic stresses (Martin‐Arevalillo & Vernoux, 2023 ; Waadt et al, 2022 ; Zhao, 2018 ). Remarkably, auxin biosynthesis is not restricted to plants, but is an ubiquitous signal molecule found in all kingdoms of life (Duca & Glick, 2020 ), controlling processes as diverse as inflammatory and carcinogenic processes in humans (Addi et al, 2019 ; Tintelnot et al, 2023 ), microalgal growth (Lin et al, 2022 ) or fungal physiology and sporulation (Nicastro et al, 2021 ).…”

Auxin-mediated regulation of susceptibility to toxic metabolites, c-di-GMP levels, and phage infection in the rhizobacterium Serratia plymuthica

“…IAA is a multi-faceted signal molecule that exerts a variety of regulatory functions in phylogenetically distant species. Next to its pivotal role in plant growth and development ( 23 – 25 ), it regulates fungal physiology ( 67 ), microalgal growth ( 68 ), inflammatory and carcinogenic processes in animals and humans ( 69 , 70 ), and, as shown here, bacterial metabolism and physiology. Among the signals that play a major role in plant environments, IAA is emerging as a key compound, allowing plant-associated microbes to adapt efficiently to their hosts and to establish interactions with other (micro)organisms in plant niches ( 18 – 20 , 29 , 33 ).…”

“…A number of key plant signaling molecules were shown to be of great relevance to establish plant-bacteria interactions, including cytokinins ( 7 , 14 ), ethylene ( 15 ), gibberelins ( 16 , 17 ), salicylic acid ( 1 , 15 ), abscisic acid ( 15 , 18 ), auxins ( 19 , 20 ), ɣ-aminobutyric acid ( 7 , 21 ), and strigolactones ( 15 , 22 ). The auxin indole-3-acetic acid (IAA) is a key phytohormone that coordinates plant growth and development, as well as plant responses to a broad range of biotic and abiotic stresses ( 23 – 25 ). In addition, IAA is an essential signal molecule in the interaction between plants and microbes.…”