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Title: Resurrection of ancestral effector caspases identifies novel networks for evolution of substrate specificity

Abstract

Apoptotic caspases evolved with metazoans more than 950 million years ago (MYA), and a series of gene duplications resulted in two subfamilies consisting of initiator and effector caspases. The effector caspase genes (caspases-3, -6, and -7) were subsequently fixed into the Chordata phylum more than 650 MYA when the gene for a common ancestor (CA) duplicated, and the three effector caspases have persisted throughout mammalian evolution. All caspases prefer an aspartate residue at the P1 position of substrates, so each caspase evolved discrete cellular roles through changes in substrate recognition at the P4 position combined with allosteric regulation. We examined the evolution of substrate specificity in caspase-6, which prefers valine at the P4 residue, compared with caspases-3 and -7, which prefer aspartate, by reconstructing the CA of effector caspases (AncCP-Ef1) and the CA of caspase-6 (AncCP-6An). We show that AncCP-Ef1 is a promiscuous enzyme with little distinction between Asp, Val, or Leu at P4. The specificity of caspase-6 was defined early in its evolution, where AncCP-6An demonstrates a preference for Val over Asp at P4. Structures of AncCP-Ef1 and of AncCP-6An show a network of charged amino acids near the S4 pocket that, when combined with repositioning a flexible activemore » site loop, resulted in a more hydrophobic binding pocket in AncCP-6An. The ancestral protein reconstructions show that the caspase-hemoglobinase fold has been conserved for over 650 million years and that only three substitutions in the scaffold are necessary to shift substrate selection toward Val over Asp.« less

Authors:
 [1];  [2];  [2];  [3];  [4]; ORCiD logo [2]
  1. Department of Biology, University of Texas at Arlington, Arlington, TX 76019, U.S.A; Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, U.S.A
  2. Department of Biology, University of Texas at Arlington, Arlington, TX 76019, U.S.A
  3. Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, U.S.A
  4. Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, U.S.A
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institutes of Health (NIH)
OSTI Identifier:
1577159
Resource Type:
Journal Article
Journal Name:
Biochemical Journal
Additional Journal Information:
Journal Volume: 476; Journal Issue: 22; Journal ID: ISSN 0264-6021
Publisher:
Biochemical Society
Country of Publication:
United States
Language:
ENGLISH

Citation Formats

Grinshpon, Robert D., Shrestha, Suman, Titus-McQuillan, James, Hamilton, Paul T., Swartz, Paul D., and Clark, A. Clay. Resurrection of ancestral effector caspases identifies novel networks for evolution of substrate specificity. United States: N. p., 2019. Web. doi:10.1042/BCJ20190625.
Grinshpon, Robert D., Shrestha, Suman, Titus-McQuillan, James, Hamilton, Paul T., Swartz, Paul D., & Clark, A. Clay. Resurrection of ancestral effector caspases identifies novel networks for evolution of substrate specificity. United States. doi:10.1042/BCJ20190625.
Grinshpon, Robert D., Shrestha, Suman, Titus-McQuillan, James, Hamilton, Paul T., Swartz, Paul D., and Clark, A. Clay. Thu . "Resurrection of ancestral effector caspases identifies novel networks for evolution of substrate specificity". United States. doi:10.1042/BCJ20190625.
@article{osti_1577159,
title = {Resurrection of ancestral effector caspases identifies novel networks for evolution of substrate specificity},
author = {Grinshpon, Robert D. and Shrestha, Suman and Titus-McQuillan, James and Hamilton, Paul T. and Swartz, Paul D. and Clark, A. Clay},
abstractNote = {Apoptotic caspases evolved with metazoans more than 950 million years ago (MYA), and a series of gene duplications resulted in two subfamilies consisting of initiator and effector caspases. The effector caspase genes (caspases-3, -6, and -7) were subsequently fixed into the Chordata phylum more than 650 MYA when the gene for a common ancestor (CA) duplicated, and the three effector caspases have persisted throughout mammalian evolution. All caspases prefer an aspartate residue at the P1 position of substrates, so each caspase evolved discrete cellular roles through changes in substrate recognition at the P4 position combined with allosteric regulation. We examined the evolution of substrate specificity in caspase-6, which prefers valine at the P4 residue, compared with caspases-3 and -7, which prefer aspartate, by reconstructing the CA of effector caspases (AncCP-Ef1) and the CA of caspase-6 (AncCP-6An). We show that AncCP-Ef1 is a promiscuous enzyme with little distinction between Asp, Val, or Leu at P4. The specificity of caspase-6 was defined early in its evolution, where AncCP-6An demonstrates a preference for Val over Asp at P4. Structures of AncCP-Ef1 and of AncCP-6An show a network of charged amino acids near the S4 pocket that, when combined with repositioning a flexible active site loop, resulted in a more hydrophobic binding pocket in AncCP-6An. The ancestral protein reconstructions show that the caspase-hemoglobinase fold has been conserved for over 650 million years and that only three substitutions in the scaffold are necessary to shift substrate selection toward Val over Asp.},
doi = {10.1042/BCJ20190625},
journal = {Biochemical Journal},
issn = {0264-6021},
number = 22,
volume = 476,
place = {United States},
year = {2019},
month = {11}
}

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