TY - JOUR
T1 - Electric charge divergence in proteins
T2 - insights into the evolution of their three-dimensional properties
AU - Sato, Yukuto
AU - Nishida, Mutsumi
N1 - Funding Information:
The manuscript benefited from the comments of two anonymous reviewers. The Tetraodon , Fugu , stickleback, medaka, and zebrafish sequence data were produced by Genoscope and the Broad Institute, the International Fugu Genome Consortium, the Broad Institute, and the National Institute of Genetics, Japan, and the Sanger Institute respectively. The frog and chicken sequence data were produced by the Joint Genome Institute and the Genome Sequencing Center at Washington University, St Louis, respectively. The human, mouse, dog, cow, and platypus sequence data were produced by the International Human Genome Sequencing Consortium, the Mouse Genome Sequencing Consortium, the Broad Institute of MIT/Harvard, the Human Genome Sequencing Center at Baylor College of Medicine, and the National Human Genome Research Institute (NHGRI) and National Institutes of Health (NIH), respectively. This work was partially supported by Grants-in-Aid from the Japan Society for the Promotion of Science to MN.
PY - 2009/7/15
Y1 - 2009/7/15
N2 - Previous studies of protein evolution have identified important mutations in various proteins that affect a small number of residues, but dramatically alter protein function. However, the evolutionary process underlying the three-dimensional protein properties, which are determined by a much larger number of residues, remains unclear. Based on a comparative evolutionary analysis of teleost phosphoglucose isomerases (PGIs; EC 5.3.1.9), we previously demonstrated that the relatively weak selection on many amino acid sites has played an important role in the evolution of protein electric charge as a model of three-dimensional protein properties. To ascertain the generality of this finding, we sought further evidence of this type of protein evolution. For this purpose, we analyzed the vertebrate isoforms of fructose-1,6-bisphosphate aldolase (ALD; EC 4.1.2.13), for which electric charges are known to have diverged after gene duplication. The results showed that the divergence in electric charge between the ALD isoforms was also driven by weak selection on many amino acid sites, as in PGI, confirming the generality of earlier findings. To obtain further insights, ALD and PGI were compared to the proteins pancreatic ribonuclease (EC 3.1.27.5) and triose-phosphate isomerase (EC 5.3.1.1), for which electric charges likely evolved through a well-defined mode of molecular evolution; namely, strong selection on specific amino acid sites. Comparison of the number and composition of amino acids on the protein surface suggested that the absolute number of evolutionarily changeable amino acids in a protein affects the strength of selection pressure acting on individual amino acid sites.
AB - Previous studies of protein evolution have identified important mutations in various proteins that affect a small number of residues, but dramatically alter protein function. However, the evolutionary process underlying the three-dimensional protein properties, which are determined by a much larger number of residues, remains unclear. Based on a comparative evolutionary analysis of teleost phosphoglucose isomerases (PGIs; EC 5.3.1.9), we previously demonstrated that the relatively weak selection on many amino acid sites has played an important role in the evolution of protein electric charge as a model of three-dimensional protein properties. To ascertain the generality of this finding, we sought further evidence of this type of protein evolution. For this purpose, we analyzed the vertebrate isoforms of fructose-1,6-bisphosphate aldolase (ALD; EC 4.1.2.13), for which electric charges are known to have diverged after gene duplication. The results showed that the divergence in electric charge between the ALD isoforms was also driven by weak selection on many amino acid sites, as in PGI, confirming the generality of earlier findings. To obtain further insights, ALD and PGI were compared to the proteins pancreatic ribonuclease (EC 3.1.27.5) and triose-phosphate isomerase (EC 5.3.1.1), for which electric charges likely evolved through a well-defined mode of molecular evolution; namely, strong selection on specific amino acid sites. Comparison of the number and composition of amino acids on the protein surface suggested that the absolute number of evolutionarily changeable amino acids in a protein affects the strength of selection pressure acting on individual amino acid sites.
KW - Amino acid sites
KW - Protein evolution
KW - Selection
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U2 - 10.1016/j.gene.2008.06.026
DO - 10.1016/j.gene.2008.06.026
M3 - Article
C2 - 18652881
AN - SCOPUS:67349114539
VL - 441
SP - 3
EP - 11
JO - Gene
JF - Gene
SN - 0378-1119
IS - 1-2
ER -