The maize ALDH protein superfamily: linking structural features to functional specificities

Abstract

BackgroundThe completion of maize genome sequencing has resulted in the identification of a large number of uncharacterized genes. Gene annotation and functional characterization of gene products are important to uncover novel protein functionality.ResultsIn this paper, we identify, and annotate members of all the maize aldehyde dehydrogenase (ALDH) gene superfamily according to the revised nomenclature criteria developed by ALDH Gene Nomenclature Committee (AGNC). The maize genome contains 24 unique ALDH sequences encoding members of ten ALDH protein families including the previously identified male fertility restoration RF2A gene, which encodes a member of mitochondrial class 2 ALDHs. Using computational modeling analysis we report here the identification, the physico-chemical properties, and the amino acid residue analysis of a novel tunnel like cavity exclusively found in the maize sterility restorer protein, RF2A/ALDH2B2 by which this protein is suggested to bind variably long chain molecular ligands and/or potentially harmful molecules.ConclusionsOur finding indicates that maize ALDH superfamily is the most expanded of plant ALDHs ever characterized, and the mitochondrial maize RF2A/ALDH2B2 is the only plant ALDH that harbors a newly defined pocket/cavity with suggested functional specificity.

The soybean aldehyde dehydrogenase (ALDH) protein superfamily

“…Based on the AGNC-annotation criteria, deduced amino acid sequences that were more than 40% identical to other previously identified ALDH sequences formed a family, and sequences that were more than 60% identical composed a protein subfamily. Deduced amino acid sequences less than 40% identical would describe a new ALDH protein family as previously reported (Jimenez-Lopez et al, 2010;Kotchoni et al, 2010a).…”

“…In our previous report, we provided for the first time evidence of a crucial role of the maize RF2A/ALDH2B2 tunnel-like cavity in preventing maize infection by Cochliobolus heterostrophus (Jimenez-Lopez et al, 2010). 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 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.…”

“…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).…”