TY - JOUR
T1 - Lessons from the deep
T2 - mechanisms behind diversification of eukaryotic protein complexes
AU - Prokopchuk, Galina
AU - Butenko, Anzhelika
AU - Dacks, Joel B.
AU - Speijer, Dave
AU - Field, Mark C.
AU - Lukeš, Julius
N1 - Funding Information: We thank Hassan Hashimi, Ondřej Gahura and Alena Zíková (Biology Centre), Evgeny S. Gerasimov (Lomonosov University), and Matúš Valach (University of Montréal) for sequence data and discussions. This work was supported by the Czech Grant Agency (20‐11585S and 23‐06479X) (both to J. L.), ERD funds of the Czech Ministry of Education (16_019/0000759) (to J. L. and M. C. F.) and the Wellcome Trust (204697/Z/16/Z) (to M. C. F.). This article is dedicated to the memory of Oleksandr Kuliukin and junior sergeant Anton Pushkar. Publisher Copyright: © 2023 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.
PY - 2023/12
Y1 - 2023/12
N2 - Genetic variation is the major mechanism behind adaptation and evolutionary change. As most proteins operate through interactions with other proteins, changes in protein complex composition and subunit sequence provide potentially new functions. Comparative genomics can reveal expansions, losses and sequence divergence within protein-coding genes, but in silico analysis cannot detect subunit substitutions or replacements of entire protein complexes. Insights into these fundamental evolutionary processes require broad and extensive comparative analyses, from both in silico and experimental evidence. Here, we combine data from both approaches and consider the gamut of possible protein complex compositional changes that arise during evolution, citing examples of complete conservation to partial and total replacement by functional analogues. We focus in part on complexes in trypanosomes as they represent one of the better studied non-animal/non-fungal lineages, but extend insights across the eukaryotes by extensive comparative genomic analysis. We argue that gene loss plays an important role in diversification of protein complexes and hence enhancement of eukaryotic diversity.
AB - Genetic variation is the major mechanism behind adaptation and evolutionary change. As most proteins operate through interactions with other proteins, changes in protein complex composition and subunit sequence provide potentially new functions. Comparative genomics can reveal expansions, losses and sequence divergence within protein-coding genes, but in silico analysis cannot detect subunit substitutions or replacements of entire protein complexes. Insights into these fundamental evolutionary processes require broad and extensive comparative analyses, from both in silico and experimental evidence. Here, we combine data from both approaches and consider the gamut of possible protein complex compositional changes that arise during evolution, citing examples of complete conservation to partial and total replacement by functional analogues. We focus in part on complexes in trypanosomes as they represent one of the better studied non-animal/non-fungal lineages, but extend insights across the eukaryotes by extensive comparative genomic analysis. We argue that gene loss plays an important role in diversification of protein complexes and hence enhancement of eukaryotic diversity.
KW - constructive neutral evolution
KW - evolutionary divergence
KW - evolutionary mechanisms
KW - gene replacement
KW - molecular evolution
KW - protein complexes
UR - http://www.scopus.com/inward/record.url?scp=85162095919&partnerID=8YFLogxK
U2 - https://doi.org/10.1111/brv.12988
DO - https://doi.org/10.1111/brv.12988
M3 - Article
C2 - 37336550
SN - 1464-7931
VL - 98
SP - 1910
EP - 1927
JO - Biological reviews of the Cambridge Philosophical Society
JF - Biological reviews of the Cambridge Philosophical Society
IS - 6
ER -