Convergent Evolution of a 2-Methylbutyryl-CoA Dehydrogenase from Isovaleryl-CoA Dehydrogenase in Solanum tuberosum

Abstract

The potato cDNAs Solanum tuberosum isovaleryl-CoA dehydrogenases 1 and 2 (St-IVD1 and St-IVD2) encode proteins that are 84% identical to each other and 65 and 64% identical to human IVD, respectively. St-IVD2 protein was previously partially purified from potato tubers and confirmed to be an IVD. The function of St-IVD1 is unknown. In these experiments, both proteins were expressed in Escherichia coli and purified as intact homotetramers. The substrate preference profile of the St-IVD2 protein was similar to that of human IVD. However, recombinant St-IVD1 had maximal activity with 2-methylbutyryl-CoA, which in humans is dehydrogenated by short/branched-chain acyl-CoA dehydrogenase (SBCAD). Whereas molecular modeling predicts that the 2-methylbutyryl-CoA dehydrogenase (2MBCD) and IVD substrate binding pockets are nearly identical, 2MBCD has amino acid substitutions at five residues that are invariant among all of the known and putative IVDs. Site-directed mutagenesis was used to match the human IVD active site with that of potato 2MBCD. The resulting mutant IVD had detectable activity with 2-methylbutyryl-CoA and no activity with isovalerylCoA. The 2MBCD active site was compared with that of human SBCAD using molecular modeling. Residues Met-361 and Ala-365 of 2MBCD appear to partially substitute for the function of Tyr-380 in human SBCAD, binding the methyl branch linked to C 2 of 2-methylbutyryl-CoA, whereas residues Val-88, Val-92, and Val-96 appear to bind the distal C 4 methyl group. The presence of a 2MBCD in potato that is highly homologous to IVD is an example of convergent evolution within the acyl-CoA dehydrogenase family, leading to the independent occurrence of two enzymes (SBCAD and 2MBCD) specific for 2-methylbutyryl-CoA.

Branched-Chain Amino Acid Metabolism inArabidopsis thaliana

“…In contrast to Arabidopsis thaliana, where only a single IVD gene is present, two genes (StIVD1 and StIVD2) have been found in potato (Faivre-Nitschke et al, 2001;Goetzman et al, 2005). StIVD2 exhibits the same substrate specifi city as the Arabidopsis thaliana protein, while StIVD1 shows strongest activity with 2-methylbutyryl-CoA.…”

“…This is a degradation intermediate of Ile and StIVD1 was accordingly designated 2-methylbutyryl-CoA dehydrogenase. However, potato might be a special case among plants since no homologue of this gene has been found in other plant species (Goetzman et al, 2005).…”

Acyl-CoA Dehydrogenases: Dynamic History of Protein Family Evolution

“…Two functionally diverged IVD paralogs that share 84% residues were previously found in S. tuberosum (Faivre-Nitschke et al 2001). While one of the two IVD paralogs was found to function as an IVD, the other paralog had maximum activity with 2-methylbutyryl-CoA as substrate, corresponding to human SBCAD (Goetzman et al 2005). Since plants do not contain SBCAD homologs, this is an example of functional substitution for a lost enzyme.…”

Broad connections in the Arabidopsis seed metabolic network revealed by metabolite profiling of an amino acid catabolism mutant

“…Based upon published results, it is not clear whether IVD enzyme participates in Ile degradation, or influences Ile accumulation less directly. In fact, the Solanum tuberosum (potato) homologue to A. thaliana IVD1 (St-IVD2) showed only 5% as much activity with the Ile breakdown product 2-methylbutyryl-CoA compared with isovaleryl-CoA (Goetzman et al, 2005), suggesting that another enzyme is involved in plant Ile metabolism. We propose two possible mechanisms for increased Ile in ivd1 mutants.…”