Cited by 341Fungal and yeast genetics researchEvolution and Genetic DynamicsGenomics and Phylogenetic Studies

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Resurrecting ancestral alcohol dehydrogenases from yeast

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Thomson, J Michael, Gaucher, Eric A, Burgan, Michelle F, De Kee, Danny W, Li, Tang, Aris, John P, Benner, Steven A·2005·Nature Genetics

DOI 10.1038/ng1553PMC PMC3618678

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Abstract

Modern yeast living in fleshy fruits rapidly convert sugars into bulk ethanol through pyruvate. Pyruvate loses carbon dioxide to produce acetaldehyde, which is reduced by alcohol dehydrogenase 1 (Adh1) to ethanol, which accumulates. Yeast later consumes the accumulated ethanol, exploiting Adh2, an Adh1 homolog differing by 24 (of 348) amino acids. As many microorganisms cannot grow in ethanol, accumulated ethanol may help yeast defend resources in the fruit. We report here the resurrection of the last common ancestor of Adh1 and Adh2, called Adh(A). The kinetic behavior of Adh(A) suggests that the ancestor was optimized to make (not consume) ethanol. This is consistent with the hypothesis that before the Adh1-Adh2 duplication, yeast did not accumulate ethanol for later consumption but rather used Adh(A) to recycle NADH generated in the glycolytic pathway. Silent nucleotide dating suggests that the Adh1-Adh2 duplication occurred near the time of duplication of several other proteins involved in the accumulation of ethanol, possibly in the Cretaceous age when fleshy fruits arose. These results help to connect the chemical behavior of these enzymes through systems analysis to a time of global ecosystem change, a small but useful step towards a planetary systems biology.

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PAML: a program package for phylogenetic analysis by maximum likelihood
Yang, Z. (1997) · Computer applications in the biosciences · doi:10.1093/bioinformatics/13.5.555 · Cited by 5,377
The Evolutionary Fate and Consequences of Duplicate Genes
Lynch, M., & Conery, J. S. (2000) · Science · doi:10.1126/science.290.5494.1151 · Cited by 4,988
Enzyme structure and mechanism
Fersht, A. (1977) · Medical Entomology and Zoology · Cited by 2,875
Enzyme structure and mechanism
Elmore, D. T. (1978) · Endeavour · doi:10.1016/0160-9327(78)90081-9 · Cited by 2,713
Molecular evidence for an ancient duplication of the entire yeast genome
Wolfe, K. H., & Shields, D. C. (1997) · Nature · doi:10.1038/42711 · Cited by 1,785
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
Kellis, M., Birren, B. W., & Lander, E. S. (2004) · Nature · doi:10.1038/nature02424 · Cited by 1,500
Wine Microbiology and Biotechnology
Fleet, G. H. (1993) · Cited by 1,378
A simple and efficient method for direct gene deletion inSaccharomyces cerevisiae
Baudin‐Baillieu, A., Ozier-Kalogéropoulos, O., DENOUEL, A., Lacroute, F., & Cullin, C. (1993) · Nucleic Acids Research · doi:10.1093/nar/21.14.3329 · Cited by 1,268
Myotonic Dystrophy Type 2 Caused by a CCTG Expansion in Intron 1 of ZNF9
Liquori, C. L., Ricker, K., Moseley, M. L., Jacobsen, J. F., Kreß, W., Naylor, S. L., Day, J., & Ranum, L. P. W. (2001) · Science · doi:10.1126/science.1062125 · Cited by 1,254
Fermented beverages of pre- and proto-historic China
McGovern, P. E., Zhang, J., Tang, J., Zhang, Z., Hall, G. R., Moreau, R. A., Nuñez, A., Butrym, E. D., Richards, M. P., Wang, C.-S., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407921102 · Cited by 1,091

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Research works printed but not linked: 3

Swofford, D.L. PAUP* Phylogenetic Analysis Using Parsimony Version 4 (Sinauer Associates, Sunderland, Massachusetts, 1998).
Thomson, J.M. Interpretive Proteomics: Experimental Paleogenetics as a Tool to Analyze Function and Discover Pathways in Yeast. Ph.D. dissertation. (University of Florida, Gainesville, 2002).
Segel, I.H. Enzyme Kinetics (Wiley, New York, 1975).

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Authors: Thomson, J. M., Gaucher, E. A., Burgan, M. F., De Kee, D. W., Li, T., Aris, J. P., & Benner, S. A.
Affiliations: University of North Carolina at Chapel Hill (US)
Foundation for Applied Molecular Evolution (US)
University of Florida (US)
Corresponding author: Benner, Steven A
ORCID: Thomson, J Michael
Gaucher, Eric A
Li, Tang
Aris, John P
Benner, Steven A
Venue: Nature Genetics
Publisher: Springer Science and Business Media LLC
Published: 2005-05-01
Volume: 37
Issue: 6
Pages: 630-635
ISSN: 1061-4036 (ISSN-L)
1546-1718
DOI: 10.1038/ng1553
PMC: PMC3618678
OpenAlex: W1998447705
Cited by: 341
References: 30
Citations by year: 2026: 8 · 2025: 8 · 2024: 14 · 2023: 22 · 2022: 16 · 2021: 10 · 2020: 13 · 2019: 24 · 2018: 17 · 2017: 17 · 2016: 15 · 2015: 19 · 2014: 21 · 2013: 20 · 2012: 19
FWCI: 4.52
Type: journal article
Language: en
Open access: green
europepmc.org
Licence: www.springer.com/tdm (tdm)
Locations: Nature Genetics (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Funders: National Aeronautics and Space Administration
National Institute on Aging (R21AG023719)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: ancestral protein reconstruction, alcohol dehydrogenase, ADH1, ADH2, Saccharomyces cerevisiae, gene duplication, ethanol accumulation, fleshy fruits, NADH regeneration, enzyme kinetics, Cretaceous
MeSH terms: Alcohol Dehydrogenase, Ethanol, Base Sequence, Biological Evolution, Molecular Sequence Data, Saccharomyces cerevisiae

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Resurrecting ancestral alcohol dehydrogenases from yeast

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