Modeling-Dependent Protein Characterization of the Rice Aldehyde Dehydrogenase (ALDH) Superfamily Reveals Distinct Functional and Structural Features

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.

The soybean aldehyde dehydrogenase (ALDH) protein superfamily

“…The soybean genome is so far the largest plant genome with 70% more protein-coding genes than A. thaliana (Schmutz et al, 2010). We are interested in understanding the molecular and genetic bases of drought stress and disease resistance in soybean with a particular emphasis on aldehyde dehydrogenase (ALDH) protein superfamily (Jimenez-Lopez et al, 2010;Kirch et al, 2005;Kotchoni, 2004;Kotchoni et al, 2010a). ALDHs have been studied in various organisms from bacteria to mammals (Jimenez-Lopez et al, 2010;Kotchoni et al, 2010a;Wood and Duff, 2009;Yoshida et al, 1998).…”

“…We are interested in understanding the molecular and genetic bases of drought stress and disease resistance in soybean with a particular emphasis on aldehyde dehydrogenase (ALDH) protein superfamily (Jimenez-Lopez et al, 2010;Kirch et al, 2005;Kotchoni, 2004;Kotchoni et al, 2010a). ALDHs have been studied in various organisms from bacteria to mammals (Jimenez-Lopez et al, 2010;Kotchoni et al, 2010a;Wood and Duff, 2009;Yoshida et al, 1998). ALDHs comprise a protein superfamily of NAD(P) + -dependent enzymes capable of oxidizing a variety of aromatic and aliphatic aldehydes into their corresponding carboxylic acids (Kirch et al, 2004).…”

“…ALDHs comprise a protein superfamily of NAD(P) + -dependent enzymes capable of oxidizing a variety of aromatic and aliphatic aldehydes into their corresponding carboxylic acids (Kirch et al, 2004). Aldehydes are highly reactive molecules ubiquitously produced during different physiological processes in prokaryotes and eukaryotes (Kotchoni et al, 2006;Kotchoni et al, 2010a). They often react with cellular nucleophiles through their carbonyl group causing deleterious effects on organism metabolism under excessive in vivo concentration.…”

“…In addition, we have recently annotated and characterized the entire ALDH gene superfamily of rice and maize (Jimenez-Lopez et al, 2010;Kotchoni et al, 2010a). In this study, we provide a unified annotation and phylogenetic analysis of the soybean ALDH gene superfamily and describe the functional impact of selected members of ALDH gene families in specific metabolic pathways mediating soybean growth development.…”

Effect of thiram on avian growth plate chondrocytes in culture

“…The ALDH inhibitory effect of disulfiram, the ethyl analog of thiram, is the basis of its use in alcohol aversion therapy (Petersen, 1992). The ALDH gene superfamily of enzymes also play important role in protection against cellular stress (Jackson et al, 2011;Kotchoni et al, 2010). In the event of deficiencies of these enzymes induced by toxicants, the cells are likely to experience stress.…”