Genome Research Econo tag

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
QUICK SEARCH:   [advanced]


     

This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Grishin, N. V.
Right arrow Articles by Koonin, E. V.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Grishin, N. V.
Right arrow Articles by Koonin, E. V.
Right arrowPubmed/NCBI databases
*Substance via MeSH
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Vol. 10, Issue 7, 991-1000, July 2000

LETTER
From Complete Genomes to Measures of Substitution Rate Variability Within and Between Proteins

Nick V. Grishin,2,3 Yuri I. Wolf,1 and Eugene V. Koonin

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894 USA

Accumulation of complete genome sequences of diverse organisms creates new possibilities for evolutionary inferences from whole-genome comparisons. In the present study, we analyze the distributions of substitution rates among proteins encoded in 19 complete genomes (the interprotein rate distribution). To estimate these rates, it is necessary to employ another fundamental distribution, that of the substitution rates among sites in proteins (the intraprotein distribution). Using two independent approaches, we show that intraprotein substitution rate variability appears to be significantly greater than generally accepted. This yields more realistic estimates of evolutionary distances from amino-acid sequences, which is critical for evolutionary-tree construction. We demonstrate that the interprotein rate distributions inferred from the genome-to-genome comparisons are similar to each other and can be approximated by a single distribution with a long exponential shoulder. This suggests that a generalized version of the molecular clock hypothesis may be valid on genome scale. We also use the scaling parameter of the obtained interprotein rate distribution to construct a rooted whole-genome phylogeny. The topology of the resulting tree is largely compatible with those of global rRNA-based trees and trees produced by other approaches to genome-wide comparison.

1 Permanent address: Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk 630090, Russia.

2 Present address: University of Texas Southwestern Medical Center, Dallas, Texas 75235 USA.

3 Corresponding author.

10:991-1000 ©2000 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/00 $5.00
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 Microbiol. Mol. Biol. Rev.Home page
M. Ventura, C. Canchaya, A. Tauch, G. Chandra, G. F. Fitzgerald, K. F. Chater, and D. van Sinderen
Genomics of Actinobacteria: Tracing the Evolutionary History of an Ancient Phylum
Microbiol. Mol. Biol. Rev., September 1, 2007; 71(3): 495 - 548.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
L. Y. Yampolsky, F. A. Kondrashov, and A. S. Kondrashov
Distribution of the strength of selection against amino acid replacements in human proteins
Hum. Mol. Genet., November 1, 2005; 14(21): 3191 - 3201.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
P. S. Novichkov, M. V. Omelchenko, M. S. Gelfand, A. A. Mironov, Y. I. Wolf, and E. V. Koonin
Genome-Wide Molecular Clock and Horizontal Gene Transfer in Bacterial Evolution
J. Bacteriol., October 1, 2004; 186(19): 6575 - 6585.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
Y. I. Wolf, I. B. Rogozin, and E. V. Koonin
Coelomata and Not Ecdysozoa: Evidence From Genome-Wide Phylogenetic Analysis
Genome Res., January 1, 2004; 14(1): 29 - 36.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
D. M. Krylov, Y. I. Wolf, I. B. Rogozin, and E. V. Koonin
Gene Loss, Protein Sequence Divergence, Gene Dispensability, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution
Genome Res., October 1, 2003; 13(10): 2229 - 2235.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
P. Lio
Investigating the Relationship Between Genome Structure, Composition, and Ecology in Prokaryotes
Mol. Biol. Evol., June 1, 2002; 19(6): 789 - 800.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
G. D. P. Clarke, R. G. Beiko, M. A. Ragan, and R. L. Charlebois
Inferring Genome Trees by Using a Filter To Eliminate Phylogenetically Discordant Sequences and a Distance Matrix Based on Mean Normalized BLASTP Scores
J. Bacteriol., April 15, 2002; 184(8): 2072 - 2080.
[Abstract] [Full Text]

Home page
 J. Bacteriol.Home page
J. Nolling, G. Breton, M. V. Omelchenko, K. S. Makarova, Q. Zeng, R. Gibson, H. M. Lee, J. Dubois, D. Qiu, J. Hitti, et al.
Genome Sequence and Comparative Analysis of the Solvent-Producing Bacterium Clostridium acetobutylicum
J. Bacteriol., August 15, 2001; 183(16): 4823 - 4838.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
O. Lecompte, R. Ripp, V. Puzos-Barbe, S. Duprat, R. Heilig, J. Dietrich, J.-C. Thierry, and O. Poch
Genome Evolution at the Genus Level: Comparison of Three Complete Genomes of Hyperthermophilic Archaea
Genome Res., June 1, 2001; 11(6): 981 - 993.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
Y. I. Wolf, I. B. Rogozin, A. S. Kondrashov, and E. V. Koonin
Genome Alignment, Evolution of Prokaryotic Genome Organization, and Prediction of Gene Function Using Genomic Context
Genome Res., March 1, 2001; 11(3): 356 - 372.
[Abstract] [Full Text]

Home page
 Genome Res.Home page
I. K. Jordan, K. S. Makarova, J. L. Spouge, Y. I. Wolf, and E. V. Koonin
Lineage-Specific Gene Expansions in Bacterial and Archaeal Genomes
Genome Res., April 1, 2001; 11(4): 555 - 565.
[Abstract] [Full Text]


Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.