Modeling-dependent protein characterization of the rice aldehyde dehydrogenase (ALDH) superfamily reveals distinct functional and structural features.

Simeon O Kotchoni,Manfredo J Seufferheld,Jose C Jimenez-Lopez,Dongying Gao,Emma W Gachomo,Vincent Edwards,Venu M Margam

doi:10.1371/journal.pone.0011516

Abstract

The completion of the rice genome sequence has made it possible to identify and characterize new genes and to perform comparative genomics studies across taxa. The aldehyde dehydrogenase (ALDH) gene superfamily encoding for NAD(P)+-dependent enzymes is found in all major plant and animal taxa. However, the characterization of plant ALDHs has lagged behind their animal- and prokaryotic-ALDH homologs. In plants, ALDHs are involved in abiotic stress tolerance, male sterility restoration, embryo development and seed viability and maturation. However, there is still no structural property-dependent functional characterization of ALDH protein superfamily in plants. In this paper, we identify members of the rice ALDH gene superfamily and use the evolutionary nesting events of retrotransposons and protein-modeling–based structural reconstitution to report the genetic and molecular and structural features of each member of the rice ALDH superfamily in abiotic/biotic stress responses and developmental processes. Our results indicate that rice-ALDHs are the most expanded plant ALDHs ever characterized. This work represents the first report of specific structural features mediating functionality of the whole families of ALDHs in an organism ever characterized.

Highlights

Aldehydes are intermediates in several fundamental metabolic pathways, including the syntheses of carbohydrates, vitamins, steroids, amino acids and lipids [1,2]
Active aldehyde dehydrogenase (ALDH) represent an important mechanism for detoxification of reactive aldehyde molecules generated in various developmental growth processes and under environmental stress conditions [5]
The more abundant plant ALDH gene families were highly divergent from each other but were located at the most distant portions in three out of the four clades of the phylogenetic tree (Figure 1). This pattern implies that functional constraints have somehow evolved over time, which might be responsible for the rapid evolution and sequence divergence of these ALDH genes

Summary

Introduction

Aldehydes are intermediates in several fundamental metabolic pathways, including the syntheses of carbohydrates, vitamins, steroids, amino acids and lipids [1,2]. Aldehyde dehydrogenases are an evolutionarily conserved group of enzymes that catalyze the irreversible oxidation of a wide range of endogenous reactive aldehyde molecules to their corresponding carboxylic acids [4,5,8]. These include the substrate-specific; the non-substrate specific ALDHs; the betaine dehydrogenases; the non-phosphorylating glyceraldehyde 3-phosphate dehydrogenases; the phenylacetaldehyde dehydrogenases; the lactaldehyde dehydrogenases and the ALDH-like proteins [8]. They are functionally well characterized in bacteria, humans, fungi, and metazoa [8]. Functional and structural characterizations of plant ALDHs and gene duplication events underlying their diversification have lagged behind that of their mammalian and bacterial counterparts

Methods

Results

Conclusion