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

  1. Jeffrey I Boucher
  2. Joseph R Jacobowitz
  3. Brian C Beckett
  4. Scott Classen
  5. Douglas L Theobald  Is a corresponding author
  1. Brandeis University, United States
  2. Lawrence Berkeley National Laboratory, 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 resulted in a difference in substrate preference exceeding 12 orders of magnitude. The molecular and evolutionary mechanisms responsible for this extraordinary functional shift are currently unknown. Using ancestral sequence reconstruction, we find that the evolution of pyruvate specificity in apicomplexan LDHs arose through a classic neofunctionalization mechanism characterized by long-range epistasis, a promiscuous intermediate, and relatively few gain-of-function mutations of large effect. Residues far from the active site determine specificity, as shown by the crystal structures of three ancestral proteins that bracket the key gene duplication event. This work provides an unprecedented atomic-resolution view of evolutionary trajectories resulting in the de novo creation of a nascent enzymatic function.

Article and author information

Author details

  1. Jeffrey I Boucher

    Brandeis University, Waltham, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Joseph R Jacobowitz

    Brandeis University, Waltham, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Brian C Beckett

    Brandeis University, Waltham, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Scott Classen

    Lawrence Berkeley National Laboratory, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Douglas L Theobald

    Brandeis University, Waltham, United States
    For correspondence
    dtheobald@brandeis.edu
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. Michael Levitt, Stanford University, United States

Publication history

  1. Received: January 19, 2014
  2. Accepted: June 23, 2014
  3. Accepted Manuscript published: June 25, 2014 (version 1)
  4. Version of Record published: July 29, 2014 (version 2)

Copyright

© 2014, Boucher et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 3,540
    Page views
  • 484
    Downloads
  • 51
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Jeffrey I Boucher
  2. Joseph R Jacobowitz
  3. Brian C Beckett
  4. Scott Classen
  5. Douglas L Theobald
(2014)
An atomic-resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases
eLife 3:e02304.
https://doi.org/10.7554/eLife.02304

Further reading

    1. Structural Biology and Molecular Biophysics
    Hirohide Takahashi, Toshiki Yamada ... Erkan Karakas
    Research Article Updated

    Volume-regulated anion channels (VRACs) mediate volume regulatory Cl- and organic solute efflux from vertebrate cells. VRACs are heteromeric assemblies of LRRC8A-E proteins with unknown stoichiometries. Homomeric LRRC8A and LRRC8D channels have a small pore, hexameric structure. However, these channels are either non-functional or exhibit abnormal regulation and pharmacology, limiting their utility for structure-function analyses. We circumvented these limitations by developing novel homomeric LRRC8 chimeric channels with functional properties consistent with those of native VRAC/LRRC8 channels. We demonstrate here that the LRRC8C-LRRC8A(IL125) chimera comprising LRRC8C and 25 amino acids unique to the first intracellular loop (IL1) of LRRC8A has a heptameric structure like that of homologous pannexin channels. Unlike homomeric LRRC8A and LRRC8D channels, heptameric LRRC8C-LRRC8A(IL125) channels have a large-diameter pore similar to that estimated for native VRACs, exhibit normal DCPIB pharmacology, and have higher permeability to large organic anions. Lipid-like densities are located between LRRC8C-LRRC8A(IL125) subunits and occlude the channel pore. Our findings provide new insights into VRAC/LRRC8 channel structure and suggest that lipids may play important roles in channel gating and regulation.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Sean M Braet, Theresa SC Buckley ... Ganesh S Anand
    Research Article Updated

    SARS-CoV-2 emergent variants are characterized by increased viral fitness and each shows multiple mutations predominantly localized to the spike (S) protein. Here, amide hydrogen/deuterium exchange mass spectrometry has been applied to track changes in S dynamics from multiple SARS-CoV-2 variants. Our results highlight large differences across variants at two loci with impacts on S dynamics and stability. A significant enhancement in stabilization first occurred with the emergence of D614G S followed by smaller, progressive stabilization in subsequent variants. Stabilization preceded altered dynamics in the N-terminal domain, wherein Omicron BA.1 S showed the largest magnitude increases relative to other preceding variants. Changes in stabilization and dynamics resulting from S mutations detail the evolutionary trajectory of S in emerging variants. These carry major implications for SARS-CoV-2 viral fitness and offer new insights into variant-specific therapeutic development.