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An atomic-resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases.

Boucher JI, Jacobowitz JR, Beckett BC, Classen S, Theobald DL - Elife (2014)

Bottom Line: Using ancestral protein resurrection, we find that specificity evolved in apicomplexan LDHs by classic neofunctionalization characterized by long-range epistasis, a promiscuous intermediate, and few gain-of-function mutations of large effect.Residues far from the active site also determine specificity, as shown by the crystal structures of three ancestral proteins bracketing the key duplication event.This work provides an unprecedented atomic-resolution view of evolutionary trajectories creating a nascent enzymatic function.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Brandeis University, Waltham, United States.

ABSTRACT
Malate and lactate dehydrogenases (MDH and LDH) are homologous, core metabolic enzymes that share a fold and catalytic mechanism yet possess strict specificity for their substrates. In the Apicomplexa, convergent evolution of an unusual LDH from MDH produced a difference in specificity exceeding 12 orders of magnitude. The mechanisms responsible for this extraordinary functional shift are currently unknown. Using ancestral protein resurrection, we find that specificity evolved in apicomplexan LDHs by classic neofunctionalization characterized by long-range epistasis, a promiscuous intermediate, and few gain-of-function mutations of large effect. In canonical MDHs and LDHs, a single residue in the active-site loop governs substrate specificity: Arg102 in MDHs and Gln102 in LDHs. During the evolution of the apicomplexan LDH, however, specificity switched via an insertion that shifted the position and identity of this 'specificity residue' to Trp107f. Residues far from the active site also determine specificity, as shown by the crystal structures of three ancestral proteins bracketing the key duplication event. This work provides an unprecedented atomic-resolution view of evolutionary trajectories creating a nascent enzymatic function.

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Sequence identity of ancestral and modern proteins.DOI:http://dx.doi.org/10.7554/eLife.02304.018
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fig5s1: Sequence identity of ancestral and modern proteins.DOI:http://dx.doi.org/10.7554/eLife.02304.018

Mentions: All four ancestral proteins are highly active in steady state kinetic assays, with substrate preferences and catalytic efficiencies that are similar to their modern apicomplexan descendants (Figure 5), despite sharing only 49–71% sequence identity with the modern apicomplexan proteins (Figure 5—figure supplement 1). AncMDH1, AncMDH2, and AncMDH3 are highly specific MDHs with negligible pyruvate activity, having even greater activity towards oxaloacetate than modern Plasmodium and Cryptosporidium MDHs (Figure 5). AncLDH is a highly active and specific LDH, with very low activity towards oxaloacetate (Figure 5).10.7554/eLife.02304.016Figure 5.Evolution of novel LDHs in Apicomplexa.


An atomic-resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases.

Boucher JI, Jacobowitz JR, Beckett BC, Classen S, Theobald DL - Elife (2014)

Sequence identity of ancestral and modern proteins.DOI:http://dx.doi.org/10.7554/eLife.02304.018
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4109310&req=5

fig5s1: Sequence identity of ancestral and modern proteins.DOI:http://dx.doi.org/10.7554/eLife.02304.018
Mentions: All four ancestral proteins are highly active in steady state kinetic assays, with substrate preferences and catalytic efficiencies that are similar to their modern apicomplexan descendants (Figure 5), despite sharing only 49–71% sequence identity with the modern apicomplexan proteins (Figure 5—figure supplement 1). AncMDH1, AncMDH2, and AncMDH3 are highly specific MDHs with negligible pyruvate activity, having even greater activity towards oxaloacetate than modern Plasmodium and Cryptosporidium MDHs (Figure 5). AncLDH is a highly active and specific LDH, with very low activity towards oxaloacetate (Figure 5).10.7554/eLife.02304.016Figure 5.Evolution of novel LDHs in Apicomplexa.

Bottom Line: Using ancestral protein resurrection, we find that specificity evolved in apicomplexan LDHs by classic neofunctionalization characterized by long-range epistasis, a promiscuous intermediate, and few gain-of-function mutations of large effect.Residues far from the active site also determine specificity, as shown by the crystal structures of three ancestral proteins bracketing the key duplication event.This work provides an unprecedented atomic-resolution view of evolutionary trajectories creating a nascent enzymatic function.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Brandeis University, Waltham, United States.

ABSTRACT
Malate and lactate dehydrogenases (MDH and LDH) are homologous, core metabolic enzymes that share a fold and catalytic mechanism yet possess strict specificity for their substrates. In the Apicomplexa, convergent evolution of an unusual LDH from MDH produced a difference in specificity exceeding 12 orders of magnitude. The mechanisms responsible for this extraordinary functional shift are currently unknown. Using ancestral protein resurrection, we find that specificity evolved in apicomplexan LDHs by classic neofunctionalization characterized by long-range epistasis, a promiscuous intermediate, and few gain-of-function mutations of large effect. In canonical MDHs and LDHs, a single residue in the active-site loop governs substrate specificity: Arg102 in MDHs and Gln102 in LDHs. During the evolution of the apicomplexan LDH, however, specificity switched via an insertion that shifted the position and identity of this 'specificity residue' to Trp107f. Residues far from the active site also determine specificity, as shown by the crystal structures of three ancestral proteins bracketing the key duplication event. This work provides an unprecedented atomic-resolution view of evolutionary trajectories creating a nascent enzymatic function.

Show MeSH
Related in: MedlinePlus