Ancestral reconstruction of duplicated signaling proteins reveals the evolution of signaling specificity

  1. Isabel Nocedal
  2. Michael T Laub  Is a corresponding author
  1. Massachusetts Institute of Technology, United States
  2. Massachusetts Institute of Technology, Howard Hughes Medical Institute, United States

Abstract

Gene duplication is crucial to generating novel signaling pathways during evolution. However, it remains unclear how the redundant proteins produced by gene duplication ultimately acquire new interaction specificities to establish insulated paralogous signaling pathways. Here, we used ancestral sequence reconstruction to resurrect and characterize a bacterial two-component signaling system that duplicated in a-proteobacteria. We determined the interaction specificities of the signaling proteins that existed before and immediately after this duplication event and then identified key mutations responsible for establishing specificity in the two systems. Just three mutations, in only two of the four interacting proteins, were sufficient to establish specificity of the extant systems. Some of these mutations weakened interactions between paralogous systems to limit crosstalk. However, others strengthened interactions within a system, indicating that the ancestral interaction, although functional, had the potential to be strengthened. Our work suggests that protein-protein interactions with such latent potential may be highly amenable to duplication and divergence.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. All gels are provided as Source Data with a master file indicating which individual file contains each gel that appears in the paper. All data plotted in graphs are provided in Excel files.

Article and author information

Author details

  1. Isabel Nocedal

    Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4706-1113
  2. Michael T Laub

    Department of Biology, Massachusetts Institute of Technology, Howard Hughes Medical Institute, Cambridge, United States
    For correspondence
    laub@mit.edu
    Competing interests
    Michael T Laub, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8288-7607

Funding

National Institute of General Medical Sciences (1F32GM126765)

  • Isabel Nocedal

Howard Hughes Medical Institute

  • Michael T Laub

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Karina B Xavier, Instituto Gulbenkian de Ciência, Portugal

Publication history

  1. Received: January 25, 2022
  2. Preprint posted: February 11, 2022 (view preprint)
  3. Accepted: May 27, 2022
  4. Accepted Manuscript published: June 10, 2022 (version 1)
  5. Version of Record published: June 20, 2022 (version 2)

Copyright

© 2022, Nocedal & Laub

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.

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  1. Isabel Nocedal
  2. Michael T Laub
(2022)
Ancestral reconstruction of duplicated signaling proteins reveals the evolution of signaling specificity
eLife 11:e77346.
https://doi.org/10.7554/eLife.77346
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