Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase

Abstract

Lactate dehydrogenase (LDH) is present in the amitochondriate parasitic protist Trichomonas vaginalis and some but not all other trichomonad species. The derived amino acid sequence of T. vaginalis LDH (TvLDH) was found to be more closely related to the cytosolic malate dehydrogenase (MDH) of the same species than to any other LDH. A key difference between the two T. vaginalis sequences was that Arg91 of MDH, known to be important in coordinating the C-4 carboxyl of oxalacetate͞malate, was replaced by Leu91 in LDH. The change Leu91Arg by site-directed mutagenesis converted TvLDH into an MDH. The reverse single amino acid change Arg91Leu in TvMDH, however, gave a product with no measurable LDH activity. Phylogenetic reconstructions indicate that TvLDH arose from an MDH relatively recently.

Comparative Protein Structure Modeling Using Modeller

“…For example, comparative models can be helpful in designing mutants to test hypotheses about the protein's function (Wu et al, 1999;Vernal et al, 2002); in identifying active and binding sites (Sheng et al, 1996); in searching for, designing, and improving ligand binding strength for a given binding site (Ring et al, 1993;Li et al, 1996;Selzer et al, 1997;Enyedy et al, 2001;Que et al, 2002); modeling substrate specificity (Xu et al, 1996); in predicting antigenic epitopes ; in simulating protein-protein docking (Vakser, 1995); in inferring function from calculated electrostatic potential around the protein (Matsumoto et al, 1995); in facilitating molecular replacement in X-ray structure determination (Howell et al, 1992); in refining models based on NMR constraints (Modi et al, 1996); in testing and improving a sequence-structure alignment (Wolf et al, 1998); in annotating single nucleotide polymorphisms (Mirkovic et al, 2004;Karchin et al, 2005); in structural characterization of large complexes by docking to low-resolution cryo-electron density maps (Spahn et al, 2001;Gao et al, 2003); and in rationalizing known experimental observations.…”

“…Comparative models were constructed for TvLDH and TvMDH to study the sequences in a structural context and to suggest site-directed mutagenesis experiments to elucidate changes in enzymatic specificity in this apparent case of convergent evolution. The native and mutated enzymes were subsequently expressed and their activities compared (Wu et al, 1999). …”

Predicting Protein Function by Genomic Context: Quantitative Evaluation and Qualitative Inferences

“…Substrate Specificity Substrate specificity is a volatile aspect of predicting enzymatic function, not only because the evolutionary signal can be obscured by sequence divergence, but also because proteins can change substrate specificity over relatively short evolutionary distances (Wu et al 1999). The (conserved) operon context of a gene can suggest different substrate specificity than homology searches.…”

Niche metabolism in parasitic protozoa

“…In the absence of further evidence, one hypothesis perhaps worthy of further consideration is that in the absence of a classical glyoxylate cycle, changes in the substrate specificity of enzymes that catalysed mechanistically similar reactions to isocitrate lyase and malate synthase have resulted in the convergent evolution of an unconventional glyoxylate cycle. The example of the 2-hydroxyacid dehydrogenase in Phytomonas (Uttaro et al 2000) possibly provides an example of how such convergent evolution could arise, as does the phylogenetic evidence that lactose dehydrogenases in T. vaginalis and Cryptosporidium arose following duplication and divergence of malate dehydrogenase genes (Wu et al 1999;Madern et al 2004) and that fumarate reductase in anaerobic helminths evolved from succinate dehydrogenase .…”