Charged Amino Acid Frequencies of Proteins over Macroevolutionary Time Scale
- 1 College of Life Sciences, Chongqing Normal University, Chongqing, China
- 2 Art and Sciences Division, Chengdu College University of Electronic Science and Technology of China, Chengdu, China
- 3 College of Life Sciences, Chongqing Normal University, Chongqing, China
- 4 College of Life Sciences, Chongqing Normal University, Chongqing, China
Abstract
Charged amino acids (AAs) are targets for selective forces in protein evolution. To fully explore the trend of charged AA frequencies evolution in macroevolutionary process from prokaryotes to eukaryotes, we extend the analysis of five charged AAs separately and total basic and acidic AAs in protein sequences of 158 prokaryotic and 63 eukaryotic predicted proteomes and 456 clusters of orthologous groups (COGs). Also, we eliminate the biases that may caused by extreme organisms in both predicted proteomes and COGs analyses. More basic AAs, His,Lysand Glu were found in eukaryotic proteins compared with prokaryotic proteins by predicted proteomes analysis. By COGs analysis, we found that basic AAs andLysfrequencies are higher in eukaryotic orthologous proteins than their prokaryotic companions, while the trend of Arg frequency is the opposite. We discussed the agreements and disagreements of two analyses and gained a more credible trend of charged AAs evolution in macroevolutionary time scale.
- H. Hartman, “The Origin of the Eukaryotic Cell,” Speculations Science Technology, Vol. 7, 1984, pp. 77-81.
- L. Margulis and D. Bermudes, “Symbiosis as a Mechanism of Evolution: Status of Cell Symbiosis Theory,” Symbiosis, Vol. 1, 1985, pp. 101-124.
- J. L. Thorne, “Models of Protein Sequence Evolution and Their Applications,” Current Opinion in Genetics & Development, Vol. 10, 2000, pp. 602-605. http://dx.doi.org/10.1016/S0959-437X(00)00142-8
- Y. J. Zhang, H. F. Tian and J. F. Wen, “The Evolution of YidC/Oxa/Alb3 Family in the Three Domains of Life: A Phylogenomic Analysis,” BMC Evolutionary Biology, Vol. 9, 2009, p. 137. http://dx.doi.org/10.1186/1471-2148-9-137
- N. Sinha, S. Mohan, C. A. Lipschultz and S. J. Smith-Gill, “Differences in Electrostatic Properties at Antibody-Antigen Binding Sites: Implications for Specificity and Cross-Reactivity,” Biophysical Journal, Vol. 83, 2002, pp. 2946-2968. http://dx.doi.org/10.1016/S0006-3495(02)75302-2
- J. A. Leunissen, H. W. van den Hooven and W. W. de Jong, “Extreme Differences in Charge Changes during Protein Evolution,” Journal of Molecular Evolution, Vol. 31, 1990, pp. 33-39. http://dx.doi.org/10.1007/BF02101790
- I. K. Jordan, F. A. Kondrashov, I. A. Adzhubei, Y. I. Wolf, E. V. Koonin, A. S. Kondrashov and S. Sunyaev, “A Universal Trend of Amino Acid Gain and Loss in Protein Evolution,” Nature, Vol. 433, 2005, pp. 633-638. http://dx.doi.org/10.1038/nature03306
- S. Paul, S. K. Bag, S. Das, E. T. Harvill and C. Dutta, “Molecular Signature of Hypersaline Adaptation: Insights from Genome and Proteome Composition of Halophilic Prokaryotes,” Genome Biology, Vol. 9, 2008, p. R70. http://dx.doi.org/10.1186/gb-2008-9-4-r70
- W. M. Fitch, “Distinguishing Homologous from Analogous Proteins,” Syst Zool, Vol. 19, 1970, pp. 99-113. http://dx.doi.org/10.2307/2412448
- R. L. Tatusov, E. V. Koonin and D. J. Lipman, “A Genomic Perspective on Protein Families,” Science, Vol. 278, 1997, pp. 631-637. http://dx.doi.org/10.1126/science.278.5338.631