Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005

Universal and Lineage-specific Trends in Protein Evolution

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve. So far, however, no universal trends in ongoing changes of amino acid frequencies have been reported, and it was generally assumed that any such changes would reflect evolution of nucleotide composition of the respective genomes and, consequently, would be unstable over long evolutionary times (1). Another widespread assumption regarding protein evolution is that proteins are in detailed equilibrium, i.e., reciprocal rates of amino acid replacements are equal. The availability of multiple sets of sequenced genomes of relatively close species allows direct testing of these assumptions. We compared sets of orthologous proteins encoded by triplets of closely related genomes from 15 taxa representing all three domains of life (Bacteria, Archaea, and Eukaryota), and used their known phylogenies to polarize amino acid substitutions. The results of this analysis refute both of the above assumptions (2). The content of Cys, Met, His, Ser, and Phe increases in at least 14 taxa, whereas Pro, Ala, Glu, and Gly are consistently lost. This universal trend of protein evolution holds also for the short-term evolution within human populations as shown by analysis of non-synonymous SNPs. All amino acids with decreasing frequencies seem to be among the first incorporated into the genetic code; conversely, all amino acids with increasing frequencies, except Ser, were probably recruited late (3). Thus, expansion of initially under-represented amino acids, which apparently began over 3.5 billion years ago, continues to this day (2). In contrast, the same approach applied to the dynamics of insertions and deletions in proteins revealed lineage-specific trends apparently correlated with the evolution of genome size in the respective taxa.

References and Footnotes
  1. Knight, R. D., Freeland, S. J., and Landweber, L. F. Genome Biol. 2, RESEARCH0010 (2001).
  2. Jordan, I. K., Kondrashov, F. A., Adzhubei, I. A., Wolf, Y. I., Koonin, E. V., Kondrashov, A. S., and Sunyaev, S. Nature 433, 633-638 (2005).
  3. Trifonov, E. N. J Biomol Struct Dyn 22, 1-11 (2004).

E. V. Koonin1,*
I. K. Jordan1
F. A. Kondrashov2
I. A. Adzhubei3
Y. I. Wolf1
A. A. Kondrashov1
S. R. Sunyaev3

1National Center for Biotechnology Information
NIH, Bethesda, Maryland 20894, USA
2Section of Evolution and Ecology
University of California at Davis
Davis, California, 95616, USA
3Division of Genetics
Department of Medicine
Brigham & Women's Hospital
Harvard Medical School
Boston, Massachusetts 02115, USA

*Telephone: 301-435-5913
Fax: 301-435-7794
Email: koonin@ncbi.nlm.nih.gov