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.
Highlights
The completion of maize genome sequencing has resulted in the identification of a large number of uncharacterized genes
To better understand the roles of RF2A/ALDH2B2, we explore in detail the structural features of the maize RF2A/ALDH2B2 tunnel like cavity and discuss here it functional relevance compared to other members of maize aldehyde dehydrogenase (ALDH) families
The maize ALDH gene superfamily: revised nomenclature and phylogenetic analysis The release of maize genome sequence provides a powerful tool for identification and functional characterization of genes
Summary
The completion of maize genome sequencing has resulted in the identification of a large number of uncharacterized genes. Endogenous aldehyde molecules are intermediates/byproducts of several fundamental metabolic pathways [1], and are produced in response to environmental stresses including salinity, dehydration, desiccation, cold, and heat shock [2,3]. Indispensable to biological processes, they are toxic in excessive physiological concentrations [4]. The damaging effects of aldehydes and derivatives of aldehyde molecules, which include cytotoxicity, mutagenicity, and carcinogenicity, have been well studied in human, bacteria and fungi [4,5]. Cellular levels of aldehydes must be regulated to ensure normal developmental growth processes. Aldehyde dehydrogenases (ALDHs) constitute a large family of NAD(P)+-dependent enzymes that catalyze the irreversible oxidation of a wide range of reactive aldehydes to their corresponding carboxylic acids [2].
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