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

• Published in: PloS one Vol. 5; no. 7; p. e11516
• Main Authors: Kotchoni, Simeon O, Jimenez-Lopez, Jose C, Gao, Dongying, Edwards, Vincent, Gachomo, Emma W, Margam, Venu M, Seufferheld, Manfredo J
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 12.07.2010; Public Library of Science (PLoS)
• Subjects: Aldehyde dehydrogenase; Aldehyde Dehydrogenase - chemistry; Aldehyde Dehydrogenase - classification; Aldehyde Dehydrogenase - genetics; Aldehyde Dehydrogenase - metabolism; Aldehydes; ALDH gene; Analysis; Annotations; Automation; Bioinformatics; Computational Biology; Computational Biology/Comparative Sequence Analysis; Computational Biology/Evolutionary Modeling; Computational Biology/Macromolecular Structure Analysis; Computational Biology/Protein Structure Prediction; Computational Biology/Sequence Motif Analysis; Dehydrogenase; Dehydrogenases; Embryonic development; Enzymes; Genes; Genetic aspects; Genome, Plant - genetics; Genomes; Genomics; Homology; Male sterility; Modelling; Models, Molecular; NAD; Nesting; Nucleotide sequence; Oryza - enzymology; Oryza sativa; Phylogenetics; Phylogeny; Plant Biology; Plant Biology/Plant Biochemistry and Physiology; Plant Biology/Plant-Environment Interactions; Plant Proteins - chemistry; Plant Proteins - classification; Plant Proteins - genetics; Plant Proteins - metabolism; Plants (botany); Protein Structure, Secondary; Proteins; Restoration; Retroelements - genetics; Rice; Salinity; Seeds; Simulation; Structural analysis; Structure-function relationships; Taxa; Transposons; Viability; Indiana; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0011516

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.