title: The evolution of nuclear auxin signalling.
abstract: BACKGROUND
  The plant hormone auxin directs many aspects of plant growth and development. To understand the evolution of auxin signalling, we compared the genes encoding two families of crucial transcriptional regulators, AUXIN RESPONSE FACTOR (ARF) and AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA), among flowering plants and two non-seed plants, Physcomitrella patens and Selaginella moellendorffii.
  
  
  RESULTS
  Comparative analysis of the P. patens, S. moellendorffii and Arabidopsis thaliana genomes suggests that the well-established rapid transcriptional response to auxin of flowering plants, evolved in vascular plants after their divergence from the last common ancestor shared with mosses. An N-terminally truncated ARF transcriptional activator is encoded by the genomes of P. patens and S. moellendorffii, and suggests a supplementary mechanism of nuclear auxin signalling, absent in flowering plants. Site-specific analyses of positive Darwinian selection revealed relatively high rates of synonymous substitution in the A. thaliana ARFs of classes IIa (and their closest orthologous genes in poplar) and Ib, suggesting that neofunctionalization in important functional regions has driven the evolution of auxin signalling in flowering plants. Primary auxin responsive gene families (GH3, SAUR, LBD) show different phylogenetic profiles in P. patens, S. moellendorffii and flowering plants, highlighting genes for further study.
  
  
  CONCLUSIONS
  The genome of P. patens encodes all of the basic components necessary for a rapid auxin response. The spatial separation of the Q-rich activator domain and DNA-binding domain suggests an alternative mechanism of transcriptional control in P. patens distinct from the mechanism seen in flowering plants. Significantly, the genome of S. moellendorffii is predicted to encode proteins suitable for both methods of regulation.
authors.affiliation: Botany, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany. ivan.paponov@biologie.uni-freiburg.de
authors.forename: Ivan A
authors.initials: IA
authors.lastname: Paponov
authors.forename: William
authors.initials: W
authors.lastname: Teale
authors.forename: Daniel
authors.initials: D
authors.lastname: Lang
authors.forename: Martina
authors.initials: M
authors.lastname: Paponov
authors.forename: Ralf
authors.initials: R
authors.lastname: Reski
authors.forename: Stefan A
authors.initials: SA
authors.lastname: Rensing
authors.forename: Klaus
authors.initials: K
authors.lastname: Palme
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D019068:Bryopsida / Q000235:genetics*; D055028:Comparative Genomic Hybridization; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D007210:Indoleacetic Acids / Q000378:metabolism*; D010802:Phylogeny; D010937:Plant Growth Regulators / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics*; D032503:Selaginellaceae / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D015534:Trans-Activators / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D007210:Indoleacetic Acids; D010937:Plant Growth Regulators; D010940:Plant Proteins; D015534:Trans-Activators