Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity

  1. Conor Howard
  2. Victor Hanson-Smith
  3. Kristopher J Kennedy
  4. Chad J Miller
  5. Hua Jane Lou
  6. Alexander D Johnson
  7. Benjamin Turk
  8. Liam J Holt  Is a corresponding author
  1. University of California Berkeley, United States
  2. University of California, San Francisco, United States
  3. Yale University School of Medicine, United States
  4. University of California San Francisco, United States

Abstract

Protein kinases have evolved diverse specificities to enable cellular information processing. To gain insight into the mechanisms underlying kinase diversification, we studied the CMGC protein kinases using ancestral reconstruction. Within this group, the cyclin dependent kinases (CDKs) and mitogen activated protein kinases (MAPKs), require proline at the +1 position of their substrates, while Ime2 prefers arginine. The resurrected common ancestor of CDKs, MAPKs and Ime2 could phosphorylate substrates with +1 proline or arginine, with preference for proline. This specificity changed to a strong preference for +1 arginine in the lineage leading to Ime2 via an intermediate with equal specificity for proline and arginine. Mutant analysis revealed that a variable residue within the kinase catalytic cleft, DFGx, modulates +1 specificity. Expansion of Ime2 kinase specificity by mutation of this residue did not cause dominant deleterious effects in vivo. Tolerance of cells to new specificities likely enabled the evolutionary divergence of kinases.

Article and author information

Author details

  1. Conor Howard

    University of California Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Victor Hanson-Smith

    University of California, San Francisco, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Kristopher J Kennedy

    University of California Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Chad J Miller

    Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Hua Jane Lou

    Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Alexander D Johnson

    University of California San Francisco, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Benjamin Turk

    Yale University School of Medicine, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Liam J Holt

    University of California Berkeley, Berkeley, United States
    For correspondence
    liamholt@berkeley.edu
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. James Ferrell, Stanford University, United States

Version history

  1. Received: July 23, 2014
  2. Accepted: October 9, 2014
  3. Accepted Manuscript published: October 13, 2014 (version 1)
  4. Accepted Manuscript updated: October 14, 2014 (version 2)
  5. Version of Record published: November 12, 2014 (version 3)
  6. Version of Record updated: April 29, 2016 (version 4)
  7. Version of Record updated: August 5, 2016 (version 5)

Copyright

© 2014, Howard 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

  • 4,954
    Page views
  • 669
    Downloads
  • 42
    Citations

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

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. Conor Howard
  2. Victor Hanson-Smith
  3. Kristopher J Kennedy
  4. Chad J Miller
  5. Hua Jane Lou
  6. Alexander D Johnson
  7. Benjamin Turk
  8. Liam J Holt
(2014)
Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity
eLife 3:e04126.
https://doi.org/10.7554/eLife.04126

Share this article

https://doi.org/10.7554/eLife.04126

Further reading

    1. Biochemistry and Chemical Biology
    2. Cell Biology
    Kristian Davidsen, Jonathan S Marvin ... Lucas B Sullivan
    Research Article

    Intracellular levels of the amino acid aspartate are responsive to changes in metabolism in mammalian cells and can correspondingly alter cell function, highlighting the need for robust tools to measure aspartate abundance. However, comprehensive understanding of aspartate metabolism has been limited by the throughput, cost, and static nature of the mass spectrometry (MS)-based measurements that are typically employed to measure aspartate levels. To address these issues, we have developed a green fluorescent protein (GFP)-based sensor of aspartate (jAspSnFR3), where the fluorescence intensity corresponds to aspartate concentration. As a purified protein, the sensor has a 20-fold increase in fluorescence upon aspartate saturation, with dose-dependent fluorescence changes covering a physiologically relevant aspartate concentration range and no significant off target binding. Expressed in mammalian cell lines, sensor intensity correlated with aspartate levels measured by MS and could resolve temporal changes in intracellular aspartate from genetic, pharmacological, and nutritional manipulations. These data demonstrate the utility of jAspSnFR3 and highlight the opportunities it provides for temporally resolved and high-throughput applications of variables that affect aspartate levels.

    1. Biochemistry and Chemical Biology
    Chi-Ning Chuang, Hou-Cheng Liu ... Ting-Fang Wang
    Research Article

    Serine(S)/threonine(T)-glutamine(Q) cluster domains (SCDs), polyglutamine (polyQ) tracts and polyglutamine/asparagine (polyQ/N) tracts are Q-rich motifs found in many proteins. SCDs often are intrinsically disordered regions that mediate protein phosphorylation and protein-protein interactions. PolyQ and polyQ/N tracts are structurally flexible sequences that trigger protein aggregation. We report that due to their high percentages of STQ or STQN amino acid content, four SCDs and three prion-causing Q/N-rich motifs of yeast proteins possess autonomous protein expression-enhancing activities. Since these Q-rich motifs can endow proteins with structural and functional plasticity, we suggest that they represent useful toolkits for evolutionary novelty. Comparative Gene Ontology (GO) analyses of the near-complete proteomes of 26 representative model eukaryotes reveal that Q-rich motifs prevail in proteins involved in specialized biological processes, including Saccharomyces cerevisiae RNA-mediated transposition and pseudohyphal growth, Candida albicans filamentous growth, ciliate peptidyl-glutamic acid modification and microtubule-based movement, Tetrahymena thermophila xylan catabolism and meiosis, Dictyostelium discoideum development and sexual cycles, Plasmodium falciparum infection, and the nervous systems of Drosophila melanogaster, Mus musculus and Homo sapiens. We also show that Q-rich-motif proteins are expanded massively in 10 ciliates with reassigned TAAQ and TAGQ codons. Notably, the usage frequency of CAGQ is much lower in ciliates with reassigned TAAQ and TAGQ codons than in organisms with expanded and unstable Q runs (e.g. D. melanogaster and H. sapiens), indicating that the use of noncanonical stop codons in ciliates may have coevolved with codon usage biases to avoid triplet repeat disorders mediated by CAG/GTC replication slippage.