Molecular Evolution and Expression Divergence of the Aconitase (ACO) Gene Family in Land Plants

Abstract

Aconitase (ACO) is a key enzyme that catalyzes the isomerization of citrate to isocitrate in the tricarboxylic acid (TCA) and glyoxylate cycles. The function of ACOs has been well studied in model plants, such as Arabidopsis. In contrast, the evolutionary patterns of the ACO family in land plants are poorly understood. In this study, we systematically examined the molecular evolution and expression divergence of the ACO gene family in 12 land plant species. Thirty-six ACO genes were identified from the 12 land plant species representing the four major land plant lineages: Bryophytes, lycophytes, gymnosperms, and angiosperms. All of these ACOs belong to the cytosolic isoform. Three gene duplication events contributed to the expansion of the ACO family in angiosperms. The ancestor of angiosperms may have contained only one ACO gene. One gene duplication event split angiosperm ACOs into two distinct clades. Two clades showed a divergence in selective pressure and gene expression patterns. The cis-acting elements that function in light responsiveness were most abundant in the promoter region of the ACO genes, indicating that plant ACO genes might participate in light regulatory pathways. Our findings provide comprehensive insights into the ACO gene family in land plants.

Keywords: aconitase; evolution; gene expression; gene family; land plants.

Figure 1

Copy number variations of ACO genes in 12 land plant genomes. The species relationships were redrawn according to Vanneste et al. (2014).

Figure 2

Pairwise protein sequence identity plots for the full-length ACO proteins vs. AcnA_IRP domain (A), full-length ACO proteins vs. AcnA_IRP_Swivel domain (B), and AcnA_IRP domain vs. AcnA_IRP_Swivel domain (C).

Figure 3

Phylogenetic tree of 36 ACOs from 12 land plants. Squares indicate three duplication events, annotated with α, β, and γ, respectively. Only bootstrap values >50% are shown.

Figure 4

Schematic representation of the duplication history of ACO genes in seed plants. The designation of each clade corresponds to the Figure 3.

Figure 5

d_N/d_S plot for the AcnA_IRP domain vs. the AcnA_IRP_Swivel domain for each pair of 36 ACO genes.

Figure 6

Duplicate gene pairs created by segmental duplication in Z. mays, P. trichocarpa, and G. max. Homologous genome blocks are shaded with gray and connected with lines. Duplicate gene pairs are connected with red dotted lines.

Figure 7

Phylogenetic relationships and Gene structure of ACO gene family in land plants. (A) The phylogenetic relationships of ACO genes, clade A1, and clade A2 are shaded in green and red, respectively. Putative pesudogene is marked with an asterisk. (B) Exon number of corresponding ACO genes. (C) Gene structure of ACO genes. AcnA_IRP domain and AcnA_IRP_Swivel domain are highlighted by the purple and blue boxes, respectively; introns are indicated as lines.

Figure 8

The tissue-specific expression patterns of ACO genes. Expression profiles for Z. mays, S. bicolor, O. sativa, B. distachyon, G. max, A. thaliana, P. trichocarpa, and P. patens are shown. Color indicates normalized expression level (the relative percent of the highest expression in each species). SAM is the abbreviation of shoot apical meristem.

Figure 9

Number of variations of cis-acting elements in the promoter region of the ACO gene in land plants. All cis-acting elements were divided into six categories according to their function. N.A. indicates that data are not available.