The rapidly growing database of completely sequenced genomes of bacteria, archaea and eukaryotes (over 200 genomes available by the end of 2004 and many more in progress) creates both new opportunities and new challenges for genome research. During the last year, we performed several studies that took advantage of the genomic information to establish fundamental principles of genome evolution and function. By comparing sequences of human, mouse and rat orthologous genes, we show that in 5'-untranslated regions (5'-UTRs) of mammalian cDNAs but not in 3'-UTRs or coding sequences, AUG is conserved to a significantly greater extent than any of the other 63 nt triplets. Qualitatively similar results were obtained by comparison of orthologous genes from different species of the yeast genus Saccharomyces. Together with the observation that mammalian and yeast 5'-UTRs are significantly depleted in overall AUG content, these findings suggest that AUG triplets in 5'-UTRs are subject to the pressure of purifying selection in two opposite directions: the uAUGs that have no specific function tend to be deleterious and get eliminated during evolution, whereas those uAUGs that do serve a function are conserved. Most probably, the principal role of the conserved uAUGs is attenuation of translation at the initiation stage, which is often additionally regulated by alternative splicing in the mammalian 5'-UTRs. In another project, we assessed the extent of ancestral paralogy, which dates back to the last common ancestor of all eukaryotes, and examine the origins of the ancestral paralogs and their potential roles in the emergence of the eukaryotic cell complexity. A parsimonious reconstruction of ancestral gene repertoires shows that 4137 orthologous gene sets in the last eukaryotic common ancestor (LECA) map back to 2150 orthologous sets in the hypothetical first eukaryotic common ancestor (FECA) [paralogy quotient (PQ) of 1.92]. Analogous reconstructions show significantly lower levels of paralogy in prokaryotes, 1.19 for archaea and 1.25 for bacteria. The only functional class of eukaryotic proteins with a significant excess of paralogous clusters over the mean includes molecular chaperones and proteins with related functions. Almost all genes in this category underwent multiple duplications during early eukaryotic evolution. In structural terms, the most prominent sets of paralogs are superstructure-forming proteins with repetitive domains, such as WD-40 and TPR. In addition to the ancestral paralogs which evolved via duplication at the onset of eukaryotic evolution, numerous pseudoparalogs were detected, i.e. homologous genes that apparently were acquired by early eukaryotes via different routes, including horizontal gene transfer (HGT) from diverse bacteria. The results of this study demonstrate a major increase in the level of gene paralogy as a hallmark of the early evolution of eukaryotes. We also studied universal trends in the evolution of amino acid composition of proteins. 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 phylogenies to polarize amino acid substitutions. Cys, Met, His, Ser and Phe accrue in at least 14 taxa, whereas Pro, Ala, Glu and Gly are consistently lost. The same nine amino acids are currently accrued or lost in human proteins, as shown by analysis of non-synonymous single-nucleotide polymorphisms. All amino acids with declining frequencies are thought to be among the first incorporated into the genetic code; conversely, all amino acids with increasing frequencies, except Ser, were probably recruited late. Thus, expansion of initially under-represented amino acids, which began over 3,400 million years ago, apparently continues to this day.

National Institute of Health (NIH)
National Library of Medicine (NLM)
Intramural Research (Z01)
Project #
Application #
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
National Library of Medicine
United States
Zip Code
Ivankov, Dmitry N; Payne, Samuel H; Galperin, Michael Y et al. (2013) How many signal peptides are there in bacteria? Environ Microbiol 15:983-90
Rogozin, Igor B; Carmel, Liran; Csuros, Miklos et al. (2012) Origin and evolution of spliceosomal introns. Biol Direct 7:11
Mulkidjanian, Armen Y; Bychkov, Andrew Yu; Dibrova, Daria V et al. (2012) Open questions on the origin of life at anoxic geothermal fields. Orig Life Evol Biosph 42:507-16
Denoeud, France; Henriet, Simon; Mungpakdee, Sutada et al. (2010) Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science 330:1381-5
Lee, Renny C H; Gill, Erin E; Roy, Scott W et al. (2010) Constrained intron structures in a microsporidian. Mol Biol Evol 27:1979-82
Koonin, Eugene V (2009) Towards a postmodern synthesis of evolutionary biology. Cell Cycle 8:799-800
Yutin, Natalya; Wolf, Maxim Y; Wolf, Yuri I et al. (2009) The origins of phagocytosis and eukaryogenesis. Biol Direct 4:9
Wolf, Yuri I; Novichkov, Pavel S; Karev, Georgy P et al. (2009) Inaugural Article: The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages. Proc Natl Acad Sci U S A 106:7273-80
Koonin, Eugene V (2009) On the origin of cells and viruses: primordial virus world scenario. Ann N Y Acad Sci 1178:47-64
Basu, Malay Kumar; Poliakov, Eugenia; Rogozin, Igor B (2009) Domain mobility in proteins: functional and evolutionary implications. Brief Bioinform 10:205-16

Showing the most recent 10 out of 101 publications