Exploring the evolution of protein function in Archaea.
BACKGROUND
Despite recent progress in studies of the evolution of protein function, the questions what were the first functional protein domains and what were their basic building blocks remain unresolved. Previously, we introduced the concept of elementary functional loops (EFLs), which are the functional units of enzymes that provide elementary reactions in biochemical transformations. They are presumably descendants of primordial catalytic peptides.


RESULTS
We analyzed distant evolutionary connections between protein functions in Archaea based on the EFLs comprising them. We show examples of the involvement of EFLs in new functional domains, as well as reutilization of EFLs and functional domains in building multidomain structures and protein complexes.


CONCLUSIONS
Our analysis of the archaeal superkingdom yields the dominating mechanisms in different periods of protein evolution, which resulted in several levels of the organization of biochemical function. First, functional domains emerged as combinations of prebiotic peptides with the very basic functions, such as nucleotide/phosphate and metal cofactor binding. Second, domain recombination brought to the evolutionary scene the multidomain proteins and complexes. Later, reutilization and de novo design of functional domains and elementary functional loops complemented evolution of protein function.
Computational Biology Unit, Uni Research, University of Bergen, N-5008 Bergen, Norway.
Alexander
A
Goncearenco
Igor N
IN
Berezovsky
D000604:Amino Acyl-tRNA Synthetases / Q000235:genetics; D001105:Archaea / Q000737:chemistry / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism*; D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics*; D019143:Evolution, Molecular; D008697:Methane / Q000096:biosynthesis; D008958:Models, Molecular; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D020543:Proteome / Q000737:chemistry / Q000235:genetics; D013329:Structure-Activity Relationship
D019843:Archaeal Proteins; D020543:Proteome; D000604:Amino Acyl-tRNA Synthetases; D008697:Methane