title: Genome-Wide Identification and Functional Classification of Tomato (Solanum lycopersicum) Aldehyde Dehydrogenase (ALDH) Gene Superfamily.
abstract: Aldehyde dehydrogenases (ALDHs) is a protein superfamily that catalyzes the oxidation of aldehyde molecules into their corresponding non-toxic carboxylic acids, and responding to different environmental stresses, offering promising genetic approaches for improving plant adaptation. The aim of the current study is the functional analysis for systematic identification of S. lycopersicum ALDH gene superfamily. We performed genome-based ALDH genes identification and functional classification, phylogenetic relationship, structure and catalytic domains analysis, and microarray based gene expression. Twenty nine unique tomato ALDH sequences encoding 11 ALDH families were identified, including a unique member of the family 19 ALDH. Phylogenetic analysis revealed 13 groups, with a conserved relationship among ALDH families. Functional structure analysis of ALDH2 showed a catalytic mechanism involving Cys-Glu couple. However, the analysis of ALDH3 showed no functional gene duplication or potential neo-functionalities. Gene expression analysis reveals that particular ALDH genes might respond to wounding stress increasing the expression as ALDH2B7. Overall, this study reveals the complexity of S. lycopersicum ALDH gene superfamily and offers new insights into the structure-functional features and evolution of ALDH gene families in vascular plants. The functional characterization of ALDHs is valuable and promoting molecular breeding in tomato for the improvement of stress tolerance and signaling.
authors.affiliation: Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), 1 Profesor Albareda, Granada, E-18008, Spain.|The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia.
authors.forename: Jose C
authors.identifier: http://orcid.org/0000-0002-1470-360X
authors.initials: JC
authors.lastname: Jimenez-Lopez
authors.affiliation: Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), 1 Profesor Albareda, Granada, E-18008, Spain.
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Lopez-Valverde
authors.affiliation: Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), 1 Profesor Albareda, Granada, E-18008, Spain.
authors.forename: Paula
authors.initials: P
authors.lastname: Robles-Bolivar
authors.affiliation: Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), 1 Profesor Albareda, Granada, E-18008, Spain.
authors.forename: Elena
authors.initials: E
authors.lastname: Lima-Cabello
authors.affiliation: Department of Biology, Rutgers University, 315 Penn St, Camden, New Jersey, 08102, United States of America.
authors.forename: Emma W
authors.initials: EW
authors.lastname: Gachomo
authors.affiliation: Department of Biology, Rutgers University, 315 Penn St, Camden, New Jersey, 08102, United States of America.|Center for Computational and Integrative Biology (CCIB), Rutgers University, 315 Penn St, Camden, New Jersey, 08102, United States of America.
authors.forename: Simeon O
authors.initials: SO
authors.lastname: Kotchoni
mesh_terms: D000444:Aldehyde Dehydrogenase / Q000737:chemistry / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D001665:Binding Sites; D055162:Biocatalysis; D003067:Coenzymes / Q000737:chemistry / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D006860:Hydrogen Bonding; D008024:Ligands; D018551:Solanum lycopersicum / Q000235:genetics* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D017434:Protein Structure, Tertiary; D013312:Stress, Physiological
chemical_list: D003067:Coenzymes; D008024:Ligands; D010940:Plant Proteins; D000444:Aldehyde Dehydrogenase