Enzyme Evolution : An Epistatic Ratchet versus a Smooth Reversible Transition
Ben-David, Moshe ; Soskine, Misha ; Dubovetskyi, Artem ; Cherukuri, Kesava-Phaneendra ; Dym, Orly ; Sussman, Joel L ; Liao, Qinghua ; Szeler, Klaudia ; Kamerlin, Shina Caroline Lynn LU
and Tawfik, Dan S
(2020)
In Molecular biology and evolution
37(4).
p.1133-1147
- Abstract
Evolutionary trajectories are deemed largely irreversible. In a newly diverged protein, reversion of mutations that led to the functional switch typically results in loss of both the new and the ancestral functions. Nonetheless, evolutionary transitions where reversions are viable have also been described. The structural and mechanistic causes of reversion compatibility versus incompatibility therefore remain unclear. We examined two laboratory evolution trajectories of mammalian paraoxonase-1, a lactonase with promiscuous organophosphate hydrolase (OPH) activity. Both trajectories began with the same active-site mutant, His115Trp, which lost the native lactonase activity and acquired higher OPH activity. A neo-functionalization... (More)
Evolutionary trajectories are deemed largely irreversible. In a newly diverged protein, reversion of mutations that led to the functional switch typically results in loss of both the new and the ancestral functions. Nonetheless, evolutionary transitions where reversions are viable have also been described. The structural and mechanistic causes of reversion compatibility versus incompatibility therefore remain unclear. We examined two laboratory evolution trajectories of mammalian paraoxonase-1, a lactonase with promiscuous organophosphate hydrolase (OPH) activity. Both trajectories began with the same active-site mutant, His115Trp, which lost the native lactonase activity and acquired higher OPH activity. A neo-functionalization trajectory amplified the promiscuous OPH activity, whereas the re-functionalization trajectory restored the native activity, thus generating a new lactonase that lacks His115. The His115 revertants of these trajectories indicated opposite trends. Revertants of the neo-functionalization trajectory lost both the evolved OPH and the original lactonase activity. Revertants of the trajectory that restored the original lactonase function were, however, fully active. Crystal structures and molecular simulations show that in the newly diverged OPH, the reverted His115 and other catalytic residues are displaced, thus causing loss of both the original and the new activity. In contrast, in the re-functionalization trajectory, reversion compatibility of the original lactonase activity derives from mechanistic versatility whereby multiple residues can fulfill the same task. This versatility enables unique sequence-reversible compositions that are inaccessible when the active site was repurposed toward a new function.
(Less)
- author
- Ben-David, Moshe
; Soskine, Misha
; Dubovetskyi, Artem
; Cherukuri, Kesava-Phaneendra
; Dym, Orly
; Sussman, Joel L
; Liao, Qinghua
; Szeler, Klaudia
; Kamerlin, Shina Caroline Lynn
LU
and Tawfik, Dan S
- publishing date
- 2020-04-01
- type
- Contribution to journal
- publication status
- published
- keywords
- Aryldialkylphosphatase/genetics, Directed Molecular Evolution, Epistasis, Genetic, Evolution, Molecular, Humans, Phosphoric Monoester Hydrolases/metabolism
- in
- Molecular biology and evolution
- volume
- 37
- issue
- 4
- pages
- 15 pages
- publisher
- Oxford University Press
- external identifiers
-
- scopus:85082147465
- pmid:31873734
- ISSN
- 0737-4038
- DOI
- 10.1093/molbev/msz298
- language
- English
- LU publication?
- no
- additional info
- © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
- id
- 5491377a-2db5-45df-ab93-fd37e0e56ad3
- date added to LUP
- 2025-01-11 20:12:52
- date last changed
- 2025-04-20 11:46:18
@article{5491377a-2db5-45df-ab93-fd37e0e56ad3,
abstract = {{<p>Evolutionary trajectories are deemed largely irreversible. In a newly diverged protein, reversion of mutations that led to the functional switch typically results in loss of both the new and the ancestral functions. Nonetheless, evolutionary transitions where reversions are viable have also been described. The structural and mechanistic causes of reversion compatibility versus incompatibility therefore remain unclear. We examined two laboratory evolution trajectories of mammalian paraoxonase-1, a lactonase with promiscuous organophosphate hydrolase (OPH) activity. Both trajectories began with the same active-site mutant, His115Trp, which lost the native lactonase activity and acquired higher OPH activity. A neo-functionalization trajectory amplified the promiscuous OPH activity, whereas the re-functionalization trajectory restored the native activity, thus generating a new lactonase that lacks His115. The His115 revertants of these trajectories indicated opposite trends. Revertants of the neo-functionalization trajectory lost both the evolved OPH and the original lactonase activity. Revertants of the trajectory that restored the original lactonase function were, however, fully active. Crystal structures and molecular simulations show that in the newly diverged OPH, the reverted His115 and other catalytic residues are displaced, thus causing loss of both the original and the new activity. In contrast, in the re-functionalization trajectory, reversion compatibility of the original lactonase activity derives from mechanistic versatility whereby multiple residues can fulfill the same task. This versatility enables unique sequence-reversible compositions that are inaccessible when the active site was repurposed toward a new function.</p>}},
author = {{Ben-David, Moshe and Soskine, Misha and Dubovetskyi, Artem and Cherukuri, Kesava-Phaneendra and Dym, Orly and Sussman, Joel L and Liao, Qinghua and Szeler, Klaudia and Kamerlin, Shina Caroline Lynn and Tawfik, Dan S}},
issn = {{0737-4038}},
keywords = {{Aryldialkylphosphatase/genetics; Directed Molecular Evolution; Epistasis, Genetic; Evolution, Molecular; Humans; Phosphoric Monoester Hydrolases/metabolism}},
language = {{eng}},
month = {{04}},
number = {{4}},
pages = {{1133--1147}},
publisher = {{Oxford University Press}},
series = {{Molecular biology and evolution}},
title = {{Enzyme Evolution : An Epistatic Ratchet versus a Smooth Reversible Transition}},
url = {{http://dx.doi.org/10.1093/molbev/msz298}},
doi = {{10.1093/molbev/msz298}},
volume = {{37}},
year = {{2020}},
}