Evolution of substrate specificity in a retained enzyme driven by gene loss

  1. Ana Lilia Juárez-Vázquez
  2. Janaka E Edirisinghe
  3. Ernesto A Verduzco-Castro
  4. Karolina Michalska
  5. Chenggang Wu
  6. Lianet Noda-García
  7. Gyorgy Babnigg
  8. Michael Endres
  9. Sofía Medina-Ruíz
  10. Julián Santoyo-Flores
  11. Mauricio Carrillo-Tripp
  12. Hung Ton-That
  13. Andrzej Joachimiak
  14. Christopher S Henry
  15. Francisco Barona-Gómez  Is a corresponding author
  1. Evolution of Metabolic Diversity Laboratory, Mexico
  2. Argonne National Laboratory, United States
  3. University of Texas Health Science Cent, United States
  4. Weizmann Institute of Science, Israel
  5. University of California, Berkeley, United States
  6. Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico
  7. Centro de Investigación en Matemáticas, Mexico
  8. University of Texas Health Science Center, United States

Abstract

The connection between gene loss and the functional adaptation of retained proteins is still poorly understood. We apply phylogenomics and metabolic modeling to detect bacterial species that are evolving by gene loss, with the finding that Actinomycetaceae genomes from human cavities are undergoing sizable reductions, including loss of L-histidine and L-tryptophan biosynthesis. We observe that the dual-substrate phosphoribosyl isomerase A or priA gene, at which these pathways converge, appears to coevolve with the occurrence of trp and his genes. Characterization of a dozen PriA homologs shows that these enzymes adapt from bifunctionality in the largest genomes, to a monofunctional, yet not necessarily specialized, inefficient form in genomes undergoing reduction. These functional changes are accomplished via mutations, which result from relaxation of purifying selection, in residues structurally mapped after sequence and X-ray structural analyses. Our results show how gene loss can drive the evolution of substrate specificity from retained enzymes.

Data availability

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Ana Lilia Juárez-Vázquez

    Evolution of Metabolic Diversity Laboratory, Irapuato, Mexico
    Competing interests
    The authors declare that no competing interests exist.
  2. Janaka E Edirisinghe

    Computing, Environment and Life Sciences Directorate, Argonne National Laboratory, Lemont, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Ernesto A Verduzco-Castro

    Evolution of Metabolic Diversity Laboratory, Irapuato, Mexico
    Competing interests
    The authors declare that no competing interests exist.
  4. Karolina Michalska

    Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Lemont, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Chenggang Wu

    Department of Microbiology and Molecular Genetics, University of Texas Health Science Cent, Houston, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Lianet Noda-García

    Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
    Competing interests
    The authors declare that no competing interests exist.
  7. Gyorgy Babnigg

    Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Lemont, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Michael Endres

    Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Lemont, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Sofía Medina-Ruíz

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Julián Santoyo-Flores

    Laboratorio de la Diversidad Biomolecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
    Competing interests
    The authors declare that no competing interests exist.
  11. Mauricio Carrillo-Tripp

    Ciencias de la Computación, Centro de Investigación en Matemáticas, Guanajuato, Mexico
    Competing interests
    The authors declare that no competing interests exist.
  12. Hung Ton-That

    Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Andrzej Joachimiak

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  14. Christopher S Henry

    Computing, Environment and Life Sciences Directorate, Argonne National Laboratory, Lemont, United States
    Competing interests
    The authors declare that no competing interests exist.
  15. Francisco Barona-Gómez

    Evolution of Metabolic Diversity Laboratory, Irapuato, Mexico
    For correspondence
    francisco.barona@cinvestav.mx
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1492-9497

Funding

Consejo Nacional de Ciencia y Tecnología (132376,179290)

  • Ana Lilia Juárez-Vázquez
  • Ernesto A Verduzco-Castro
  • Julián Santoyo-Flores
  • Mauricio Carrillo-Tripp

National Institutes of Health (GM094585)

  • Karolina Michalska
  • Gyorgy Babnigg
  • Michael Endres
  • Andrzej Joachimiak

US Department of Energy (DE-AC02-06CH11357)

  • Andrzej Joachimiak
  • Christopher S Henry

National Science Foundation (1611952)

  • Janaka E Edirisinghe
  • Christopher S Henry

National Institute of Dental and Craniofacial Research (DE017382)

  • Chenggang Wu
  • Hung Ton-That

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

Reviewing Editor

  1. Alfonso Valencia, Barcelona Supercomputing Center - BSC, Spain

Version history

  1. Received: October 25, 2016
  2. Accepted: March 25, 2017
  3. Accepted Manuscript published: March 31, 2017 (version 1)
  4. Version of Record published: April 25, 2017 (version 2)

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Metrics

  • 3,079
    views
  • 538
    downloads
  • 22
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

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. Ana Lilia Juárez-Vázquez
  2. Janaka E Edirisinghe
  3. Ernesto A Verduzco-Castro
  4. Karolina Michalska
  5. Chenggang Wu
  6. Lianet Noda-García
  7. Gyorgy Babnigg
  8. Michael Endres
  9. Sofía Medina-Ruíz
  10. Julián Santoyo-Flores
  11. Mauricio Carrillo-Tripp
  12. Hung Ton-That
  13. Andrzej Joachimiak
  14. Christopher S Henry
  15. Francisco Barona-Gómez
(2017)
Evolution of substrate specificity in a retained enzyme driven by gene loss
eLife 6:e22679.
https://doi.org/10.7554/eLife.22679

Share this article

https://doi.org/10.7554/eLife.22679

Further reading

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Marian Brenner, Christoph Zink ... Antje Gohla
    Research Article

    Vitamin B6 deficiency has been linked to cognitive impairment in human brain disorders for decades. Still, the molecular mechanisms linking vitamin B6 to these pathologies remain poorly understood, and whether vitamin B6 supplementation improves cognition is unclear as well. Pyridoxal 5’-phosphate phosphatase (PDXP), an enzyme that controls levels of pyridoxal 5’-phosphate (PLP), the co-enzymatically active form of vitamin B6, may represent an alternative therapeutic entry point into vitamin B6-associated pathologies. However, pharmacological PDXP inhibitors to test this concept are lacking. We now identify a PDXP and age-dependent decline of PLP levels in the murine hippocampus that provides a rationale for the development of PDXP inhibitors. Using a combination of small-molecule screening, protein crystallography, and biolayer interferometry, we discover, visualize, and analyze 7,8-dihydroxyflavone (7,8-DHF) as a direct and potent PDXP inhibitor. 7,8-DHF binds and reversibly inhibits PDXP with low micromolar affinity and sub-micromolar potency. In mouse hippocampal neurons, 7,8-DHF increases PLP in a PDXP-dependent manner. These findings validate PDXP as a druggable target. Of note, 7,8-DHF is a well-studied molecule in brain disorder models, although its mechanism of action is actively debated. Our discovery of 7,8-DHF as a PDXP inhibitor offers novel mechanistic insights into the controversy surrounding 7,8-DHF-mediated effects in the brain.

    1. Biochemistry and Chemical Biology
    2. Stem Cells and Regenerative Medicine
    Parthasarathy Sampathkumar, Heekyung Jung ... Yang Li
    Research Article

    Molecules that facilitate targeted protein degradation (TPD) offer great promise as novel therapeutics. The human hepatic lectin asialoglycoprotein receptor (ASGR) is selectively expressed on hepatocytes. We have previously engineered an anti-ASGR1 antibody-mutant RSPO2 (RSPO2RA) fusion protein (called SWEETS) to drive tissue-specific degradation of ZNRF3/RNF43 E3 ubiquitin ligases, which achieved hepatocyte-specific enhanced Wnt signaling, proliferation, and restored liver function in mouse models, and an antibody–RSPO2RA fusion molecule is currently in human clinical trials. In the current study, we identified two new ASGR1- and ASGR1/2-specific antibodies, 8M24 and 8G8. High-resolution crystal structures of ASGR1:8M24 and ASGR2:8G8 complexes revealed that these antibodies bind to distinct epitopes on opposing sides of ASGR, away from the substrate-binding site. Both antibodies enhanced Wnt activity when assembled as SWEETS molecules with RSPO2RA through specific effects sequestering E3 ligases. In addition, 8M24-RSPO2RA and 8G8-RSPO2RA efficiently downregulate ASGR1 through TPD mechanisms. These results demonstrate the possibility of combining different therapeutic effects and degradation mechanisms in a single molecule.