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

Kotchoni SO, Jimenez-Lopez JC, Gao D, Edwards V, Gachomo EW, Margam VM, Seufferheld MJ - PLoS ONE (2010)

Bottom Line: The aldehyde dehydrogenase (ALDH) gene superfamily encoding for NAD(P)(+)-dependent enzymes is found in all major plant and animal taxa.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America. skotchon@purdue.edu

ABSTRACT
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.

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Related in: MedlinePlus

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.
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pone-0011516-g004: 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.

Mentions: The ALDH gene superfamily has been characterized in several organisms [8], and the crystallographic structural coordinates of selected ALDHs have been deposited in the Protein Database (PDB) [28]. To our knowledge, structural modeling and conformational feature comparisons of all the members of the ALDH protein superfamily have not been performed in any organism. Using computational modeling, we determined the structural features and uniqueness of the 3D structure of the active sites and the NAD(P)+-ring binding clefts of the members of the entire rice ALDH superfamily. Each sequence was modeled based on the ten best structural templates (Figure 3, Figure 4, Figures S1, S2, S3, S4, S5, S6, S7, S8, S9, S10, S11, S12, and S13) using the structural parameters summarized in Table S2. C-scores were used to estimate the quality of the predicted models based on coverage parameters in the structural simulations and alignment with the template. C-score is a confidence scoring function to assessing the quality of a prediction and estimate the accuracy of the I-TASSER predictions, which is defined based on the quality of the threading alignments and the convergence of I-TASSER's structural assembly refinement simulations. Typically, a good predicted model was obtained from a protein sequence when the estimated level of confidence (C-score) was between −5 and 2. The level of confidence of our predicted models for all the rice ALDHs were in the range of −2.26 to 1.75 (Table S2), indicating that the structures were constructed with high accuracy. Because the native structures have not been crystallized, the structural similarity and accuracy of the models were further checked using the TM-score and root mean square deviation (RMSD) parameters. The correct topology of the models was obtained for all structures with TM-scores >0.5, while TM-score values <0.17 indicated that the predicted structure had low accuracy; which was independent of the protein length [29]. Using these parameters, only ALDH18B1, ALDH18B2 and ALDH12B1 had TM-scores equal to or below 0.5 (0.50, 0.46 and 0.45, respectively) and were within the limit of accuracy but with C-scores higher than −5 (Table S2). The low quality of the modeling might be due to a possible divergence of these ALDH families, being members of two separate branches of the same cluster integrating ALDH family 18 and family 12 (Figure 1). General structural comparisons (Figure 3) and phylogenetic analyses (Figure 1) provided clearer and unexpected insight into the structural divergence of the rice ALDHs. Considering the estimated RMSDs (based on the Cα) of all residues in a pairwise comparison of the predicted models in each cluster, we only show representative models for each family or phylogenetic cluster to reduce the number of structural figures (Figure 3, Figure 4, and Figures S1, S2, S3, S4, S5, S6, S7, S8, S9, S10, S11, S12, and S13). Where necessary, structural superpositions for several members of the same family were constructed (Figure 3, Figure 4A). Our results showed very small deviations in any of the structural comparisons analyzed (>1.3 Å). However, the greatest structural differences were located in the oligomerization region of the ALDHs (Figure 4A,Figures S1A, S2A, S3A, S4A, S5A, S6A, S7A, S8A, S9A, S10A, S11A, S12A, and S13A), but the global topology was quite similar among members of the same family. Based on the catalytic domain, the oligomerization domain and the NAD(P)+ domain [30], we found that OsALDH12B1 and both members of family 18 were the most divergent from the other rice ALDHs (Figure 3).


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

Kotchoni SO, Jimenez-Lopez JC, Gao D, Edwards V, Gachomo EW, Margam VM, Seufferheld MJ - PLoS ONE (2010)

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.
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Related In: Results  -  Collection

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pone-0011516-g004: 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.
Mentions: The ALDH gene superfamily has been characterized in several organisms [8], and the crystallographic structural coordinates of selected ALDHs have been deposited in the Protein Database (PDB) [28]. To our knowledge, structural modeling and conformational feature comparisons of all the members of the ALDH protein superfamily have not been performed in any organism. Using computational modeling, we determined the structural features and uniqueness of the 3D structure of the active sites and the NAD(P)+-ring binding clefts of the members of the entire rice ALDH superfamily. Each sequence was modeled based on the ten best structural templates (Figure 3, Figure 4, Figures S1, S2, S3, S4, S5, S6, S7, S8, S9, S10, S11, S12, and S13) using the structural parameters summarized in Table S2. C-scores were used to estimate the quality of the predicted models based on coverage parameters in the structural simulations and alignment with the template. C-score is a confidence scoring function to assessing the quality of a prediction and estimate the accuracy of the I-TASSER predictions, which is defined based on the quality of the threading alignments and the convergence of I-TASSER's structural assembly refinement simulations. Typically, a good predicted model was obtained from a protein sequence when the estimated level of confidence (C-score) was between −5 and 2. The level of confidence of our predicted models for all the rice ALDHs were in the range of −2.26 to 1.75 (Table S2), indicating that the structures were constructed with high accuracy. Because the native structures have not been crystallized, the structural similarity and accuracy of the models were further checked using the TM-score and root mean square deviation (RMSD) parameters. The correct topology of the models was obtained for all structures with TM-scores >0.5, while TM-score values <0.17 indicated that the predicted structure had low accuracy; which was independent of the protein length [29]. Using these parameters, only ALDH18B1, ALDH18B2 and ALDH12B1 had TM-scores equal to or below 0.5 (0.50, 0.46 and 0.45, respectively) and were within the limit of accuracy but with C-scores higher than −5 (Table S2). The low quality of the modeling might be due to a possible divergence of these ALDH families, being members of two separate branches of the same cluster integrating ALDH family 18 and family 12 (Figure 1). General structural comparisons (Figure 3) and phylogenetic analyses (Figure 1) provided clearer and unexpected insight into the structural divergence of the rice ALDHs. Considering the estimated RMSDs (based on the Cα) of all residues in a pairwise comparison of the predicted models in each cluster, we only show representative models for each family or phylogenetic cluster to reduce the number of structural figures (Figure 3, Figure 4, and Figures S1, S2, S3, S4, S5, S6, S7, S8, S9, S10, S11, S12, and S13). Where necessary, structural superpositions for several members of the same family were constructed (Figure 3, Figure 4A). Our results showed very small deviations in any of the structural comparisons analyzed (>1.3 Å). However, the greatest structural differences were located in the oligomerization region of the ALDHs (Figure 4A,Figures S1A, S2A, S3A, S4A, S5A, S6A, S7A, S8A, S9A, S10A, S11A, S12A, and S13A), but the global topology was quite similar among members of the same family. Based on the catalytic domain, the oligomerization domain and the NAD(P)+ domain [30], we found that OsALDH12B1 and both members of family 18 were the most divergent from the other rice ALDHs (Figure 3).

Bottom Line: The aldehyde dehydrogenase (ALDH) gene superfamily encoding for NAD(P)(+)-dependent enzymes is found in all major plant and animal taxa.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America. skotchon@purdue.edu

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus