New insights into the evolutionary history of plant sorbitol dehydrogenase

Abstract

Background: Sorbitol dehydrogenase (SDH, EC 1.1.1.14) is the key enzyme involved in sorbitol metabolism in higher plants. SDH genes in some Rosaceae species could be divided into two groups. L-idonate-5-dehydrogenase (LIDH, EC 1.1.1.264) is involved in tartaric acid (TA) synthesis in Vitis vinifera and is highly homologous to plant SDHs. Despite efforts to understand the biological functions of plant SDH, the evolutionary history of plant SDH genes and their phylogenetic relationship with the V. vinifera LIDH gene have not been characterized.

Results: A total of 92 SDH genes were identified from 42 angiosperm species. SDH genes have been highly duplicated within the Rosaceae family while monocot, Brassicaceae and most Asterid species exhibit singleton SDH genes. Core Eudicot SDHs have diverged into two phylogenetic lineages, now classified as SDH Class I and SDH Class II. V. vinifera LIDH was identified as a Class II SDH. Tandem duplication played a dominant role in the expansion of plant SDH family and Class II SDH genes were positioned in tandem with Class I SDH genes in several plant genomes. Protein modelling analyses of V. vinifera SDHs revealed 19 putative active site residues, three of which exhibited amino acid substitutions between Class I and Class II SDHs and were influenced by positive natural selection in the SDH Class II lineage. Gene expression analyses also demonstrated a clear transcriptional divergence between Class I and Class II SDH genes in V. vinifera and Citrus sinensis (orange).

Conclusions: Phylogenetic, natural selection and synteny analyses provided strong support for the emergence of SDH Class II by positive natural selection after tandem duplication in the common ancestor of core Eudicot plants. The substitutions of three putative active site residues might be responsible for the unique enzyme activity of V. vinifera LIDH, which belongs to SDH Class II and represents a novel function of SDH in V. vinifera that may be true also of other Class II SDHs. Gene expression analyses also supported the divergence of SDH Class II at the expression level. This study will facilitate future research into understanding the biological functions of plant SDHs.

Figure 1

Distribution of SDH homologous genes in higher plants. Closely related species were specified accordingly. The gene abundance heat map was based on the total copy number of SDH genes in each species. SDHs of P. bretschneideri [39] and E. japonica (loquat) [35] were obtained from literature; additional SDHs may be identified in these two species when complete genome information becomes available. The classification of SDH Class I and SDH Class II was based on the phylogenetic analysis carried out in the present study.

Figure 2

Phylogenetic tree showing the evolutionary history of the angiosperm SDH family. A: A simplified schematic phylogeny of the SDH family inferred by MEGA 6.0 [97] software using the Neighbour Joining method. Values (as percentage, cutoff value 50) of Internal branch test (1000 replicates) supports are indicated above the corresponding branches. B: The Maximum Likelihood phylogeny of the SDH family developed by MEGA 6.0 [97] software using the selected best-fitting substitution model JTT + G [99]. 1000 times Bootstraping supports (cut off at 0.5) are displayed above corresponding branch. Closely related species are annotated accordingly. The V. vinifera LIDH (GSVIVT01010646001) is also marked.

Figure 3

Multiple sequence alignment of plant SDH family. ESPript output was obtained with the sequence alignment of plant SDHs and human SDH. Secondary structures were inferred using human SDH (PDB: 1PL8) as a template, with springs representing helices and arrows representing beta-strands. Sequences were grouped into 1 (1PL8 and core Eudicot SDH Class I), 2 (core Eudicot SDH Class II), 3 (A.coerlea SDH) and 4 (monocot SDH). Amino acid site numbering above the alignment is according to LIDH (Q1PSI9) without the first 20 amino acids. Adjacent similarity amino acid sites were boxed in blue frame. Similarity calculations were based on the complete SDH alignments but only partial sequences for SDH Class I and SDH Class II were displayed. The active site residues identified in this study are marked with red triangles. Conserved domains are indicated above the alignment.

Figure 4

Identification of collinear gene pairs among plant SDH families. A circular plot of SDH gene family collinearity. Collinear SDH genes are linked by red curved lines. SDH genes located at each position in corresponding chromosomes are indicated. Family collinearity is shown in the genomic collinearity background. Only those chromosomes containing SDH genes are included.

Figure 5

Homology models of Vv_LIDH and Vv_SDH and proposed reaction mechanisms. A. Structure superimposition of Vv_LIDH_idonate (green) and Vv_SDH_sorbitol (yellow) in Ribbon forms. B. The proposed reaction mechanism for Vv_LIDH on the oxidation of L-idonate into 5-keto-D-gluconate (5KGA). C. Superimposition of the active site residues of Vv_LIDH (green) and Vv_SDH (yellow). The distances (Å) between corresponding atoms are labelled. Target active site residues are shown in stick forms and labelled correspondingly. D. Hydrophobicity variance at Y42H between Vv_LIDH (green) and Vv_SDH (yellow) with red and white colours representing the highest hydrophobicity and the lowest hydrophobicity respectively. (All amino acid site numbering is according to LIDH (UniProt No: Q1PSI9) without the first 20 amino acids).

Figure 6

Transcript and gene co-expression profiles of SDH in different plants. A. Expression profiles for Class I and Class II SDH genes in various tissues and developmental stages of V. vinifera. Class I and II SDH genes were moderately to highly expressed in most tissues (Log2 intensity > 10; 50th percentile of all gene expression values, see Methods). The heatmap was adjusted to colour ranges between log2 intensity of 5 (blue), 10 (white) and 15 (red) to illustrate low, moderate and high expression when compared to all other genes respectively. B. Expression profiles for Class I and Class II SDH gene in citrus. The heatmap was adjusted to colour ranges between log2 intensity of 4 (blue), 10 (white) and 14 (red) to illustrate low, moderate and high expression when compared to all other genes respectively. C. Heatmap of selected enriched GO terms (−log10 (adj. p-value) for genes co-expressed with SDHs from A. thaliana (At), V. vinifera (Vv), C. sinensis (Cs), P .trichocarpa [84], O. sativa (Os) and associated frequencies in the plants tested. Light and dark orange denote enrichment scores between 1 and 3 respectively. Highly enriched scores (>5) are coloured in red. Grey colour denotes no significant enrichment.