Khrustalev Vladislav Victorovich, Barkovsky Eugene Victorovich
Department of General Chemistry, Belarussian State Medical University, 83 Dzerzinskogo Prospect, Minsk 220000, Belarus.
Comput Biol Chem. 2009 Aug;33(4):295-302. doi: 10.1016/j.compbiolchem.2009.06.005. Epub 2009 Jun 27.
Total GC-content (G+C), GC-content in codon positions and 0-fold, 2-fold and 4-fold degenerated sites in all coding districts from 10 completely sequenced genomes of simplex and varicello viruses have been calculated by the original "Coding Genome Scanner" algorithm. The low coefficient of correlation (R<0.5) between 3GC and G+C in all coding districts from unique regions (UL and US) of alphaherpesvirus genome is a new criterion of the strong mutational pressure that is the process of increasing the rates of nonsynonymous mutations because of the extreme saturation (GC-pressure) or desaturation (AT-pressure) of third (liberal) codon positions with G and C. Unique regions of HSV1, HSV2, CeHV1, CeHV2, CeHV16 and BoHV5 are under the influence of strong GC-pressure caused mostly by AT to GC transversions. Unique regions of EqHV1 are under the influence of weak GC-pressure. In unique regions of CeHV9 AT-pressure is strong; in EqHV4 and VZV unique regions AT-pressure is weak. Mutational AT-pressure in CeHV9 and VZV is caused mostly by transitions, while in EqHV4 it is caused mostly by transversions. The level of 3GC in coding districts situated in long terminal inverted repeats (LTR) of all these viruses is much higher than in coding districts from UL and US. Higher GC-content does not seem to depend on the gene itself, but it does depend on its location. V67 gene of EqHV1 is situated in LTR (3GC=0.853), while V67 gene of EqHV4 is situated in US (3GC=0.397). Higher rates of AT to GC transversions in coding districts situated in LTR should be due to the "anatomy" of long terminal inverted repeats. The process of AT to GC transversions is thought to take place only in doublestranded DNA. Indeed, in the potential secondary structure formed by singlestranded genomic DNA of alphaherpesviruses only joined inverted repeats should be doublestranded.
利用原始的“编码基因组扫描器”算法，计算了单纯疱疹病毒和水痘病毒10个全序列基因组所有编码区的总GC含量（G+C）、密码子位置的GC含量以及0倍、2倍和4倍简并位点的GC含量。α疱疹病毒基因组独特区域（UL和US）所有编码区中3GC与G+C之间的低相关系数（R<0.5）是强突变压力的一个新标准，强突变压力是由于第三（宽松）密码子位置被G和C极度饱和（GC压力）或去饱和（AT压力）而导致非同义突变率增加的过程。HSV1、HSV2、CeHV1、CeHV2、CeHV16和BoHV5的独特区域受到主要由AT到GC颠换引起的强GC压力的影响。EqHV1的独特区域受到弱GC压力的影响。在CeHV9的独特区域，AT压力很强；在EqHV4和VZV的独特区域，AT压力较弱。CeHV9和VZV中的突变AT压力主要由转换引起，而在EqHV4中主要由颠换引起。所有这些病毒位于长末端反向重复序列（LTR）中的编码区的3GC水平远高于UL和US编码区。较高的GC含量似乎不取决于基因本身，而是取决于其位置。EqHV1的V67基因位于LTR中（3GC=0.853），而EqHV4的V67基因位于US中（3GC=0.397）。位于LTR中的编码区中AT到GC颠换率较高应该归因于长末端反向重复序列的“结构”。AT到GC颠换的过程被认为仅发生在双链DNA中。确实，在α疱疹病毒单链基因组DNA形成的潜在二级结构中，只有连接的反向重复序列应该是双链的。
