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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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Phylogeny of M/LDH superfamily.Same phylogeny as Figure 3A with select branch supports shown (aLRT supports).DOI:http://dx.doi.org/10.7554/eLife.02304.011
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fig3s1: Phylogeny of M/LDH superfamily.Same phylogeny as Figure 3A with select branch supports shown (aLRT supports).DOI:http://dx.doi.org/10.7554/eLife.02304.011

Mentions: A maximum likelihood phylogeny of representatives of all known LDH and MDH proteins provides strong support for five distinct protein clades (Figure 3A, Figure 3—figure supplement 1): canonical LDHs, ‘LDH-like’ MDHs, mitochondrial-like MDHs, cytosolic-like MDHs, and the poorly characterized HicDHs (hydroxyisocaproate-related dehydrogenases), confirming previous phylogenetic analyses (Golding and Dean, 1998; Madern, 2002; Zhu and Keithly, 2002; Madern et al., 2004).


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)

Phylogeny of M/LDH superfamily.Same phylogeny as Figure 3A with select branch supports shown (aLRT supports).DOI:http://dx.doi.org/10.7554/eLife.02304.011
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig3s1: Phylogeny of M/LDH superfamily.Same phylogeny as Figure 3A with select branch supports shown (aLRT supports).DOI:http://dx.doi.org/10.7554/eLife.02304.011
Mentions: A maximum likelihood phylogeny of representatives of all known LDH and MDH proteins provides strong support for five distinct protein clades (Figure 3A, Figure 3—figure supplement 1): canonical LDHs, ‘LDH-like’ MDHs, mitochondrial-like MDHs, cytosolic-like MDHs, and the poorly characterized HicDHs (hydroxyisocaproate-related dehydrogenases), confirming previous phylogenetic analyses (Golding and Dean, 1998; Madern, 2002; Zhu and Keithly, 2002; Madern et al., 2004).

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