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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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Apicomplexan M/LDH Clade.Same phylogeny as Figure 3B with aLRT branch supports and clades shown in full detail.DOI:http://dx.doi.org/10.7554/eLife.02304.013
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fig3s3: Apicomplexan M/LDH Clade.Same phylogeny as Figure 3B with aLRT branch supports and clades shown in full detail.DOI:http://dx.doi.org/10.7554/eLife.02304.013

Mentions: Intriguingly, three different groups of LDH proteins cluster with high confidence outside of the canonical LDH clade. A set of trichomonad LDHs found in the cytosolic-like MDH clade are thought to have evolved from a recent gene duplication of an MDH (Wu and Fiser, 1999). The Trichomonads appear to lack a canonical LDH. A prominent eukaryotic group of LDH and MDH proteins from the Apicomplexa nests deep within the bacterial ‘LDH-like’ MDHs, sister to many Rickettsiales sequences, signifying a horizontal gene transfer event from α-proteobacteria to the eukaryotic Apicomplexa. We find no evidence that the Apicomplexa have canonical LDH or conventional eukaryotic-type MDH (either cytosolic- or mitochondrial-like MDHs), despite searching in many available complete apicomplexan genomes (multiple Eimeria, Neospora, Toxoplasma, Plasmodium, and Cryptosporidium species) (Heiges et al., 2006; Gajria et al., 2008; Aurrecoechea et al., 2009). In the Apicomplexa, LDH activity has apparently evolved independently twice (Figure 3B, Figure 3—figure supplement 3), once in a lineage leading to Plasmodium-related species and once in Cryptosporidium. The apicomplexan portion of the LDH/MDH gene phylogeny is consistent with recent apicomplexan species phylogenies constructed from concatenated protein sequences (Templeton et al., 2009).


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)

Apicomplexan M/LDH Clade.Same phylogeny as Figure 3B with aLRT branch supports and clades shown in full detail.DOI:http://dx.doi.org/10.7554/eLife.02304.013
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig3s3: Apicomplexan M/LDH Clade.Same phylogeny as Figure 3B with aLRT branch supports and clades shown in full detail.DOI:http://dx.doi.org/10.7554/eLife.02304.013
Mentions: Intriguingly, three different groups of LDH proteins cluster with high confidence outside of the canonical LDH clade. A set of trichomonad LDHs found in the cytosolic-like MDH clade are thought to have evolved from a recent gene duplication of an MDH (Wu and Fiser, 1999). The Trichomonads appear to lack a canonical LDH. A prominent eukaryotic group of LDH and MDH proteins from the Apicomplexa nests deep within the bacterial ‘LDH-like’ MDHs, sister to many Rickettsiales sequences, signifying a horizontal gene transfer event from α-proteobacteria to the eukaryotic Apicomplexa. We find no evidence that the Apicomplexa have canonical LDH or conventional eukaryotic-type MDH (either cytosolic- or mitochondrial-like MDHs), despite searching in many available complete apicomplexan genomes (multiple Eimeria, Neospora, Toxoplasma, Plasmodium, and Cryptosporidium species) (Heiges et al., 2006; Gajria et al., 2008; Aurrecoechea et al., 2009). In the Apicomplexa, LDH activity has apparently evolved independently twice (Figure 3B, Figure 3—figure supplement 3), once in a lineage leading to Plasmodium-related species and once in Cryptosporidium. The apicomplexan portion of the LDH/MDH gene phylogeny is consistent with recent apicomplexan species phylogenies constructed from concatenated protein sequences (Templeton et al., 2009).

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