---
_id: '1844'
abstract:
- lang: eng
text: '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.'
author:
- first_name: Valeria
full_name: Risso, Valeria
last_name: Risso
- first_name: Fadia
full_name: Manssour Triedo, Fadia
last_name: Manssour Triedo
- first_name: Asuncion
full_name: Delgado Delgado, Asuncion
last_name: Delgado Delgado
- first_name: Rocio
full_name: Arco, Rocio
last_name: Arco
- first_name: Alicia
full_name: Barroso Deljesús, Alicia
last_name: Barroso Deljesús
- first_name: Álvaro
full_name: Inglés Prieto, Álvaro
id: 2A9DB292-F248-11E8-B48F-1D18A9856A87
last_name: Inglés Prieto
orcid: 0000-0002-5409-8571
- first_name: Raquel
full_name: Godoy Ruiz, Raquel
last_name: Godoy Ruiz
- first_name: Josè
full_name: Gavira, Josè
last_name: Gavira
- first_name: Eric
full_name: Gaucher, Eric
last_name: Gaucher
- first_name: Beatriz
full_name: Ibarra Molero, Beatriz
last_name: Ibarra Molero
- first_name: Jose
full_name: Sánchez Ruiz, Jose
last_name: Sánchez Ruiz
citation:
ama: 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
apa: 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. Oxford
University Press. https://doi.org/10.1093/molbev/msu312
chicago: 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. Oxford University Press, 2014. https://doi.org/10.1093/molbev/msu312.
ieee: 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. Oxford University
Press, pp. 440–455, 2014.
ista: 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.
mla: 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.
short: 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.
date_created: 2018-12-11T11:54:19Z
date_published: 2014-11-12T00:00:00Z
date_updated: 2021-01-12T06:53:34Z
day: '12'
ddc:
- '571'
department:
- _id: HaJa
doi: 10.1093/molbev/msu312
file:
- access_level: open_access
checksum: 06215318e66be8f3e0c33abb07e9d3da
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:56Z
date_updated: 2020-07-14T12:45:19Z
file_id: '5247'
file_name: IST-2016-430-v1+1_Mol_Biol_Evol-2015-Risso-440-55.pdf
file_size: 1545246
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 32'
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: 440 - 455
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '5257'
pubrep_id: '430'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mutational studies on resurrected ancestral proteins reveal conservation of
site-specific amino acid preferences throughout evolutionary history
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2014'
...