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.

Fig 1. Comparative phylogenetic analysis of tomato ALDHs.

Phylogenetic analysis was made using 97 ALDH proteins from Solanum lycopersicum (Sl), Arabidopsis thaliana (At), Zea mays (Zm), Physcomitrella patens (Pp), and Chlamydomonas reinhardtii (Cr).

Fig 2. Structural analysis of S. lycopersicum ALDH2 superfamily.

Three-dimensional structure of tomato SlALDH2 corresponding to the families (A) 2B1, (B) 2B3, (C) 2B4, (D) 2B7, and (E) 2C4. Structures were depicted as a cartoon diagram. α-helices, β-sheets and coils are depicted in red, yellow and green, respectively. Two views rotated 180 around the x-axis are provided for SlALDH2 superfamily of the electrostatic potential representation on the SlALDH2 protein surfaces. The surface colors are clamped at red (-10) or blue (+10). F) Detailed view of the SlALDH2 chain and the active (catalytic) site, and the spatial distribution of the coenzyme. Residues are depicted as stick and colored according with atoms.

Fig 3. Coenzyme and ligand-binding domain analysis of ALDH2 superfamily.

(A) Hydrogen-bonding interactions in the SlALDH2B1 coenzyme and ligand-binding domain and its interaction with NADH. Hydrogen bonds are shown in broken lines. Critical catalytic amino acids (C223 and E189) are highlighted in blue background. (B) Distribution of the NADH cofactor (red color) and the spatial distribution of the residues that integrate the cofactor-substrate binding cleft. Residues are depicted as stick and orange colored and green/blue colors the catalytic residues. (C) Detailed representation of the amino acids interacting with NADH and stabilizing the cofactor in the catalytic domain. Additional table shows the key amino acids involving the coenzyme-substrate binding domain. Catalytic crucial residues as grey color shadowed.

Fig 4. Tomato ALDH3H1 protein structure, coenzyme and ligand-binding domain analysis.

(A) Three-dimensional structure of tomato SlALDH3H1. Structures were depicted as a cartoon diagram. α-helices, β-sheets and coils are depicted in red, yellow and green, respectively. Two views rotated 180 around the x-axis are provided for SlALDH3H1 superfamily of the electrostatic potential representation on the SlALDH3H1 protein surfaces. The surface colors are clamped at red (-10) or blue (+10). (B) Detailed view of the SlALDH3H1 chain and the active (catalytic) site, and the spatial distribution of the coenzyme the amino acids involved in holding NAD+. Residues are depicted as stick and colored according with atoms. (C) Hydrogen-bonding interactions in the SlALDH3H1 coenzyme domain and its interaction with NAD+. Hydrogen bonds are shown in broken lines. (D) Detailed view of the catalytic-binding domain showing residues configuring this domain, and critical catalytic amino acids (C244 and N114) highlighted in pink and purple color in proper position related to the substrate (red dot).

Fig 5. Tomato ALDH3F1 (b and d variants) proteins structure, coenzyme and ligand-binding domain analysis.

Three-dimensional structure of tomato (A) SlALDH3F1b missing the complete oligomerization domain and partially the coenzyme domain; (B) SlALDH3F1d. Structures were depicted as a cartoon diagram. α-helices, β-sheets and coils are depicted in red, yellow and green, respectively. Two views rotated 180 around the x-axis are provided for both SlALDH3F1 protein variants of the electrostatic potential representation on the SlALDH3F1 proteins surfaces. The surface colors are clamped at red (-10) or blue (+10); (C) Superimposition of SlALDH3F1b and SlALDH3F1d showing the three main domains (coenzyme, oligomerization and catalytic), and highlighting with black arrows all the 2D-structural elements missing in SlALDH3F1b; (D) Detailed view of the superimposition showing the co-enzyme/catalytic cleft accommodating the NAD+ and substrate holding amino acids; (E) Detailed view of the catalytic-binding domain showing residues integrating this domain, and critical catalytic amino acids (C132 and N116) highlighted in green and blue colors in proper position related to the substrate (fatty aldehyde).