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Dasmeh P, Zheng J, Erdoğan AN, Tokuriki N, Wagner A. Rapid evolutionary change in trait correlations of single proteins. Nat Commun 2024; 15:3327. [PMID: 38637501 PMCID: PMC11026499 DOI: 10.1038/s41467-024-46658-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 03/06/2024] [Indexed: 04/20/2024] Open
Abstract
Many organismal traits are genetically determined and covary in evolving populations. The resulting trait correlations can either help or hinder evolvability - the ability to bring forth new and adaptive phenotypes. The evolution of evolvability requires that trait correlations themselves must be able to evolve, but we know little about this ability. To learn more about it, we here study two evolvable systems, a yellow fluorescent protein and the antibiotic resistance protein VIM-2 metallo beta-lactamase. We consider two traits in the fluorescent protein, namely the ability to emit yellow and green light, and three traits in our enzyme, namely the resistance against ampicillin, cefotaxime, and meropenem. We show that correlations between these traits can evolve rapidly through both mutation and selection on short evolutionary time scales. In addition, we show that these correlations are driven by a protein's ability to fold, because single mutations that alter foldability can dramatically change trait correlations. Since foldability is important for most proteins and their traits, mutations affecting protein folding may alter trait correlations mediated by many other proteins. Thus, mutations that affect protein foldability may also help shape the correlations of complex traits that are affected by hundreds of proteins.
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Affiliation(s)
- Pouria Dasmeh
- Center for Human Genetics, Marburg University, Marburg, 35043, Germany.
- Institute for Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, 8057, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne, 1015, Switzerland.
| | - Jia Zheng
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, 310030, China
- Westlake Laboratory of Life Sciences and Biomedicine, 310030, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, 310030, Hangzhou, China
| | - Ayşe Nisan Erdoğan
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Andreas Wagner
- Institute for Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, 8057, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne, 1015, Switzerland.
- The Santa Fe Institute, Santa Fe, New Mexico, 87501, US.
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, 7600, South Africa.
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Palenchar PM. The Influence of Codon Usage, Protein Abundance, and Protein Stability on Protein Evolution Vary by Evolutionary Distance and the Type of Protein. Protein J 2022; 41:216-229. [PMID: 35147896 DOI: 10.1007/s10930-022-10045-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2022] [Indexed: 12/01/2022]
Abstract
In general, the evolutionary rate of proteins is not primarily related to protein and amino acid functions, and factors such as protein abundance, codon usage, and the protein's TM are more important. To better understand the factors that affect protein evolution, E. coli MG1655 orthologs were compared to those in closely related bacteria and to more distantly related prokaryotes, eukaryotes, and archaea. Also, the evolution of different types of proteins was studied. The analyses indicate that the amino acid conservation of enzymes that do not use macromolecules (e.g. DNA, RNA, and proteins) as substrates and that carry out metabolic processes involving small molecules (i.e. small molecule enzymes) is different than other enzymes. For example, the small molecule enzymes have a lower percent identity than other enzymes when sequences from closely related bacteria are compared. Analyses indicate the lower percent identity is not a result of the amino acid or codon usage of the small molecule enzymes. The small molecule enzymes also don't have a significantly lower protein abundance indicating that is also not likely an important factor driving differences in amino acid conservation. Analyses indicate different methods to measure the TM of proteins have different relationships between amino acid conservation over different evolutionary distances. In totality, the results demonstrate that the relationship between the factors thought to affect protein evolution (protein abundance, codon usage, and proteins TMs) and protein evolution are complex and depend on the factor, the organisms, and the type of proteins being analyzed.
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Affiliation(s)
- Peter M Palenchar
- Department of Chemistry, Villanova University, 800 E. Lancaster Ave, Villanova, PA, 19805, USA.
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Ben-David M, Soskine M, Dubovetskyi A, Cherukuri KP, Dym O, Sussman JL, Liao Q, Szeler K, Kamerlin SCL, Tawfik DS. Enzyme Evolution: An Epistatic Ratchet versus a Smooth Reversible Transition. Mol Biol Evol 2019; 37:1133-1147. [DOI: 10.1093/molbev/msz298] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
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 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.
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Affiliation(s)
- Moshe Ben-David
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Misha Soskine
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Artem Dubovetskyi
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Orly Dym
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Joel L Sussman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Qinghua Liao
- Department of Chemistry – BMC, Uppsala University, Uppsala, Sweden
| | - Klaudia Szeler
- Department of Chemistry – BMC, Uppsala University, Uppsala, Sweden
| | | | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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