Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history

V. Risso, F. Manssour Triedo, A. Delgado Delgado, R. Arco, A. Barroso Deljesús, Á. Inglés Prieto, R. Godoy Ruiz, J. Gavira, E. Gaucher, B. Ibarra Molero, J. Sánchez Ruiz, Molecular Biology and Evolution 32 (2014) 440–455.

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Journal Article | Published | English

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Author
Risso, Valeria; Manssour Triedo, Fadia; Delgado Delgado, Asuncion; Arco, Rocio; Barroso Deljesús, Alicia; Inglés Prieto, ÁlvaroIST Austria ; Godoy Ruiz, Raquel; Gavira, Josè; Gaucher, Eric; Ibarra Molero, Beatriz; Sánchez Ruiz, Jose
Department
Abstract
Local protein interactions ("molecular context" effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations.
Publishing Year
Date Published
2014-11-12
Journal Title
Molecular Biology and Evolution
Volume
32
Issue
2
Page
440 - 455
IST-REx-ID

Cite this

Risso V, Manssour Triedo F, Delgado Delgado A, et al. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. 2014;32(2):440-455. doi:10.1093/molbev/msu312
Risso, V., Manssour Triedo, F., Delgado Delgado, A., Arco, R., Barroso Deljesús, A., Inglés Prieto, Á., … Sánchez Ruiz, J. (2014). Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution, 32(2), 440–455. https://doi.org/10.1093/molbev/msu312
Risso, Valeria, Fadia Manssour Triedo, Asuncion Delgado Delgado, Rocio Arco, Alicia Barroso Deljesús, Álvaro Inglés Prieto, Raquel Godoy Ruiz, et al. “Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History.” Molecular Biology and Evolution 32, no. 2 (2014): 440–55. https://doi.org/10.1093/molbev/msu312.
V. Risso et al., “Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history,” Molecular Biology and Evolution, vol. 32, no. 2, pp. 440–455, 2014.
Risso V, Manssour Triedo F, Delgado Delgado A, Arco R, Barroso Deljesús A, Inglés Prieto Á, Godoy Ruiz R, Gavira J, Gaucher E, Ibarra Molero B, Sánchez Ruiz J. 2014. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. 32(2), 440–455.
Risso, Valeria, et al. “Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History.” Molecular Biology and Evolution, vol. 32, no. 2, Oxford University Press, 2014, pp. 440–55, doi:10.1093/molbev/msu312.
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2018-12-12
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