The level of cytosine is usually much higher than the level of guanine in two-fold degenerated sites from third codon positions of genes from Simplex- and Varicelloviruses with G+C higher than 50%.
We studied usage of cytosine and guanine in 914 genes from completely sequenced genomes of five Simplex- and seven Varicelloviruses. In genes with total GC-content higher than 50% usage of cytosine is usually higher than usage of guanine (an average difference for genes with G+C higher than 70% reaches 4.0%). This difference is caused mostly by the elevated usage of cytosine in two-fold degenerated sites situated in third codon positions relatively to the usage of guanine in two-fold degenerated sites situated in third codon positions (an average difference for genes with G+C higher than 70% is equal to 28.2%). The usage of amino acids that are encoded by codons containing cytosine in two-fold degenerated sites situated in third codon positions (AA2TC) is much higher than the usage of amino acids encoded by codons containing guanine in two-fold degenerated sites situated in third codon positions (AA2AG). The usage of AA2AG declines much more steeply with the growth of GC-content than the usage of AA2TC. This effect is the consequence of the nature of genetic code and of the negative selection. In GC-rich genes the usage of cytosine in four-fold degenerated sites is only a little (but significantly) higher than the usage of guanine (in genes with G+C higher than 70% an average difference is equal to 4.3%). This difference may be caused by transcription-associated mutational pressure.
Khrustalev
Vladislav Victorovich
VV
Department of General Chemistry, Belarussian State Medical University, Communisticheskaya 7-24, Dzerzinskogo 83, Minsk 220029, Belarus. vvkhrustalev@mail.ru
Barkovsky
Eugene Victorovich
EV
D000596:Amino Acids / Q000235:genetics; D001482:Base Composition / Q000235:genetics*; D020137:Base Pair Mismatch / Q000235:genetics; D003062:Codon / Q000235:genetics*; D003596:Cytosine / Q000032:analysis*; D004277:DNA, Single-Stranded / Q000235:genetics; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics; D003845:Deoxycytosine Nucleotides / Q000235:genetics; D003849:Deoxyguanosine / Q000031:analogs & derivatives / Q000235:genetics; D005814:Genes, Viral / Q000235:genetics*; D005815:Genetic Code / Q000235:genetics; D006147:Guanine / Q000032:analysis*; D017354:Point Mutation / Q000235:genetics; D012641:Selection, Genetic / Q000235:genetics; D018139:Simplexvirus / Q000235:genetics*; D018140:Varicellovirus / Q000235:genetics*
D000596:Amino Acids; D003062:Codon; D004277:DNA, Single-Stranded; D004279:DNA, Viral; D003845:Deoxycytosine Nucleotides; C037781:deoxycytidylyl-(3'-5')-deoxyguanosine; D006147:Guanine; D003596:Cytosine; D003849:Deoxyguanosine