Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history.
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.
Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain.
Valeria A
VA
Risso
Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain.
Fadia
F
Manssour-Triedo
Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain.
Asunción
A
Delgado-Delgado
Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain.
Rocio
R
Arco
Unidad de Genómica, Instituto de Parasitología y Biomedicina López Neyra CSIC, PTS Granada, Granada, Spain.
Alicia
A
Barroso-delJesus
Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain.
Alvaro
A
Ingles-Prieto
Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD.
Raquel
R
Godoy-Ruiz
Unidad de Genómica, Instituto de Parasitología y Biomedicina López Neyra CSIC, PTS Granada, Granada, Spain.
Jose A
JA
Gavira
Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD.
Eric A
EA
Gaucher
Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain.
Beatriz
B
Ibarra-Molero
Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain sanchezr@ugr.es.
Jose M
JM
Sanchez-Ruiz
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000235:genetics*; D019143:Evolution, Molecular; D010802:Phylogeny; D017433:Protein Structure, Secondary
D000596:Amino Acids
amino acid replacements; ancestral proteins; molecular evolution