Table 1.
The rice ALDH protein superfamily: revised nomenclature.
Figure 1.
Phylogenetic analysis of well characterized plant ALDHs.
Neighbor-Joining (NJ) method was used to performe a phylogenetic analysis of O. sativa (red), A. thaliana (blue), P. patens (green), and C. reinhardtii (yellow) deduced ALDH protein sequences. Members of respective ALDH families are depicted in a specific background colour.
Table 2.
Comparative identification of the ALDH gene families in various organisms.
Figure 2.
Stress responsive ALDH genes are nested by multiple transposable elements.
(A) Os-ALDH18B2 (Os01g62900) gene contains a helitron (I02744) and a MITE (OS1). (B) Os-ALDH7B6 (Os09g26880) harboured a mutator-like element, Os0089, and a nested MITE block, which includes 2 MITEs. (C) Os-ALDH12B1 (Os12g40440) gene also serves as a partial sequence of the retrotransposon, Retro1. The capital letters mean TSDs of transposons. The “ctag” and “aga” are 5′ and 3′end sequences of I02744 in Os-ALDH18B2, respectively.
Figure 3.
Three-dimensional structure analysis of rice ALDH protein superfamily.
All structures are depicted as a cartoon diagram. Within the represented family, the secondary elements are coloured in red (α-helix), yellow (β-sheet) and green (coils). Superimpositions are coloured as follow: Green (ALDH3H1), Blue (ALDH3H2); red (ALDH3B1), yellow (ALDH3E1), blue (ALDH3E2); yellow (ALDH10A5), blue (ALDH10A8); pink (ALDH2B1), yellow (ALDH2B5); red (ALDH2B2), blue (ALDH2C1), turquoise (ALDH2C4).
Figure 4.
Detailed structural conformation and conservation analysis of selected members of rice ALDH family 3.
(A) General structure (cartoon diagram) shows the superimposition of OsALDH3B1 (red), ALDH3E1 (yellow) and ALDH3E2 (blue) with RMSD calculated for each superimposition. Represented structures were rotated at 45°. (B) Best predicted ALDH3B1 model (2D-structure) was subject to consurf-conservational analysis searching for close homologous sequences with known structures using PSI-BLAST. The protein was finally visualized using FirstGlance in Jmol with the conservation scores being colour-coded. The conserved and variable residues are presented as space-filled models and coloured according to the conservation scores. A detailed view of the cavity holding up the NAD(P)+ cofactor (stick model and van der Walls spheres) is shown in high magnification. (C) The surface conformation of ALDH3B1 (rotated 180°) showing the secondary structure elements inside is depicted. The morphology of the cavity accommodating NAD(P)+ cofactor is represented in high magnification. Detail view organization of the predicted amino acids of the pocket is represented in blue colour. The space-filled representation of van der Waals surface of the cofactor, and the catalytic amino acid residues (Cys 271 in green colour and Glu 361 in red) are opposite positioned. (D) Electrostatic surface potential showing all possible views of ALDH3B1 structure. The surface colours are clamped at red (−1) or blue (+1). Top and bottom views are highlighted with a white line coming from front view.
Figure 5.
Electrostatic surface of rice ALDH superfamily.
Electrostatic potential (isocontour value of ±5 kT/e) surface of all rice ALDHs is depicted in 14 models represent the 21 rice ALDH proteins. In families with more than one member, we considered the isocontour of only one model that has the smaller RMSD value compared to the best theoretical model superimposed.