Denis A. Kiktev, Ziwei Sheng, Kirill S. Lobachev, and Thomas D. Petes
PNAS July 24, 2018. 115 (30) E7109-E7118
GENETICS
Significance
Chromosomes of most organisms have regions of high GC content interspersed with regions of low GC content. We constructed three variants of the yeast URA3 gene with GC contents of 31%, 43%, and 63%. We found that the high-GC URA3 gene had a substantially elevated rate of mutations, both single-base substitutions and deletions. The elevated base substitutions require an error-prone DNA polymerase, and the high rate of deletions occurs as a consequence of DNA polymerase slippage. The high-GC gene also had substantially elevated rates of mitotic and meiotic recombination. These observations indicate that GC content is an important parameter influencing genome evolution.
Abstract
The chromosomes of many eukaryotes have regions of high GC content interspersed with regions of low GC content. In the yeast Saccharomyces cerevisiae, high-GC regions are often associated with high levels of meiotic recombination. In this study, we constructed URA3 genes that differ substantially in their base composition [URA3-AT (31% GC), URA3-WT (43% GC), and URA3-GC (63% GC)] but encode proteins with the same amino acid sequence. The strain with URA3-GC had an approximately sevenfold elevated rate of ura3 mutations compared with the strains with URA3-WT or URA3-AT. About half of these mutations were single-base substitutions and were dependent on the error-prone DNA polymerase ζ. About 30% were deletions or duplications between short (5–10 base) direct repeats resulting from DNA polymerase slippage. The URA3-GC gene also had elevated rates of meiotic and mitotic recombination relative to the URA3-AT or URA3-WT genes. Thus, base composition has a substantial effect on the basic parameters of genome stability and evolution.
See: http://www.pnas.org/content/115/30/E7109
Figure 1: Rates and types of ura3 mutations in strains with URA3-AT, URA3-WT, and URA3-GC alleles. (A) Rates of ura3 mutations. From measurements of the frequency of 5-FOAR derivatives in multiple cultures, we calculated the rates of mutation in strains with URA3-AT, URA3-WT, and URA3-GC (see Materials and Methods for details). The 95% confidence limits are shown for each measurement. (B) By DNA sequencing, we determined whether the ura3 mutations were single-base substitutions, long (≥5 bp) indels, single-base indels, or complex mutations (more than one mutant substitution). The proportion of each of these classes was multiplied by the rate of ura3 mutations to generate the rates for these classes.
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