1. Structural Biology and Molecular Biophysics
  2. Evolutionary Biology
Download icon

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
Research Article
  • Cited 41
  • Views 3,277
  • Annotations
Cite this article as: eLife 2014;3:e02304 doi: 10.7554/eLife.02304
Voice your concerns about research culture and research communication: Have your say in our 7th annual survey.

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

  • 3,277
    Page views
  • 417
    Downloads
  • 41
    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)

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

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

Further reading

    1. Neuroscience
    2. Structural Biology and Molecular Biophysics
    Monica L Fernández-Quintero et al.
    Research Article Updated

    Voltage-gated calcium channels control key functions of excitable cells, like synaptic transmission in neurons and the contraction of heart and skeletal muscles. To accomplish such diverse functions, different calcium channels activate at different voltages and with distinct kinetics. To identify the molecular mechanisms governing specific voltage sensing properties, we combined structure modeling, mutagenesis, and electrophysiology to analyze the structures, free energy, and transition kinetics of the activated and resting states of two functionally distinct voltage sensing domains (VSDs) of the eukaryotic calcium channel CaV1.1. Both VSDs displayed the typical features of the sliding helix model; however, they greatly differed in ion-pair formation of the outer gating charges. Specifically, stabilization of the activated state enhanced the voltage dependence of activation, while stabilization of resting states slowed the kinetics. This mechanism provides a mechanistic model explaining how specific ion-pair formation in separate VSDs can realize the characteristic gating properties of voltage-gated cation channels.

    1. Cell Biology
    2. Structural Biology and Molecular Biophysics
    Agata Szuba et al.
    Research Article Updated

    Septins are conserved cytoskeletal proteins that regulate cell cortex mechanics. The mechanisms of their interactions with the plasma membrane remain poorly understood. Here, we show by cell-free reconstitution that binding to flat lipid membranes requires electrostatic interactions of septins with anionic lipids and promotes the ordered self-assembly of fly septins into filamentous meshworks. Transmission electron microscopy reveals that both fly and mammalian septin hexamers form arrays of single and paired filaments. Atomic force microscopy and quartz crystal microbalance demonstrate that the fly filaments form mechanically rigid, 12- to 18-nm thick, double layers of septins. By contrast, C-terminally truncated septin mutants form 4-nm thin monolayers, indicating that stacking requires the C-terminal coiled coils on DSep2 and Pnut subunits. Our work shows that membrane binding is required for fly septins to form ordered arrays of single and paired filaments and provides new insights into the mechanisms by which septins may regulate cell surface mechanics.