Evolution Analysis of the Aux/IAA Gene Family in Plants Shows Dual Origins and Variable Nuclear Localization Signals

Abstract

The plant hormone auxin plays pivotal roles in many aspects of plant growth and development. The auxin/indole-3-acetic acid (Aux/IAA) gene family encodes short-lived nuclear proteins acting on auxin perception and signaling, but the evolutionary history of this gene family remains to be elucidated. In this study, the Aux/IAA gene family in 17 plant species covering all major lineages of plants is identified and analyzed by using multiple bioinformatics methods. A total of 434 Aux/IAA genes was found among these plant species, and the gene copy number ranges from three (Physcomitrella patens) to 63 (Glycine max). The phylogenetic analysis shows that the canonical Aux/IAA proteins can be generally divided into five major clades, and the origin of Aux/IAA proteins could be traced back to the common ancestor of land plants and green algae. Many truncated Aux/IAA proteins were found, and some of these truncated Aux/IAA proteins may be generated from the C-terminal truncation of auxin response factor (ARF) proteins. Our results indicate that tandem and segmental duplications play dominant roles for the expansion of the Aux/IAA gene family mainly under purifying selection. The putative nuclear localization signals (NLSs) in Aux/IAA proteins are conservative, and two kinds of new primordial bipartite NLSs in P. patens and Selaginella moellendorffii were discovered. Our findings not only give insights into the origin and expansion of the Aux/IAA gene family, but also provide a basis for understanding their functions during the course of evolution.

Keywords: Aux/IAA; evolution; gene expansion; nuclear localization signals; phylogeny.

Figure 1

Graphical representation of 11 types of Aux/IAAs and their comparative analysis among the 17 plant species. The chart at the bottom shows the conserve amino acid composition of different motifs on average. The content of conservative amino acids is expressed by the height of characters. The phylogenetic tree at the top is from the Tree of Life Web Project (Available online: http://www.tolweb.org/Green_plants).

Figure 2

Phylogenetic relationship among canonical Aux/IAA genes. The deduced full-length amino acid sequences of canonical Aux/IAA genes were aligned by ClustalX (2.1), and the neighbor-joining (NJ) tree was constructed by Mega7. The bootstrap values with 1000 replicates are placed on the nodes. The Aux/IAAs derived from different categories are shown in different colors.

Figure 3

Evolution relationships between representative Aux/IAAs and ARFs. (A) Multiple sequence alignment of representative Aux/IAAs and ARFs. Conservative domains III and IV are underlined. The height of the bars indicates the number of identical residues at each position. The β-grasp fold in domains III and IV is marked with “β1”, “β2”, “α1”, “β3”, “β4”, “α2”, “β5” and “α3”. The part enclosed by the red line is the conservative motif site “GDDP” in ARFs and “GDVP” in Aux/IAAs. The asterisk (*), colon (:), and dot (.) represent different conservative level from high and low; (B) Putative model for generating Aux/IAAs from truncated ARFs. Some truncated putative Aux/IAA genes were derived from truncated ARF genes, which only compose the Aux/IAA domain (domains III and IV), but lack their typical domains I and II.

Figure 4

Phylogeny of Aux/IAAs and ARFs in Physcomitrella patens, Selaginella moellendorffii, and Picea abies. The deduced full-length amino acid sequences of Aux/IAA genes and ARF genes were aligned by ClustalX (2.1), and the neighbor-joining (NJ) tree was constructed by Mega7. The bootstrap values with 1000 replicates are placed on the nodes. The Aux/IAA and ARF clusters are grouped into two clades, but there exists a group of Aux/IAA genes highlighted with orange that clustered closer to the ARF clade.

Figure 5

Duplication events of Aux/IAAs in the plant kingdom. This phylogenetic tree was decorated with whole-genome duplication events (Available online: http://chibba.pgml.uga.edu/duplication/index/files) and the number of genes derived from segmental duplication, tandem duplication, and both events. The phylogenetic tree of 17 species was from the Tree of Life Web Project (Available online: http://www.tolweb.org/Green_plants). Seg: segmental duplication; Tan: tandem duplication; Seg&Tan: genes belonging both to segmental duplication and tandem duplication; Total: total Aux/IAA gene number in the species.

Figure 6

Molecular evolutionary rate of Aux/IAAs in the plant kingdom. (A) Rates of molecular evolution in segmental duplication of dicot and monocot Aux/IAA genes; (B) Rates of molecular evolution in tandem duplication of dicot and monocot Aux/IAA genes. Two gene pairs are excluded from the plot and exist in the above table; (C) Rates of molecular evolution in segmental duplication and tandem duplication in plants.

Figure 7

Presence of conservative amino acids in the nuclear localization signal (NLS) of Aux/IAAs. The content of conservative amino acids is expressed by the height of characters. The amino acids under the symbol * are conservative NLS sites.