Asymmetric cytosine deamination revealed by spontaneous mutational specificity in an Ung− strain of Escherichia coli

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Abstract
A collection of 164 spontaneous lacI − mutations were recovered from a uracil-DNA glycosylase deficient (Ung−) strain of Escherichia coli and analyzed by DNA sequencing. As predicted by genetic studies, G:C→A:T transitions predominated among base substitution events. However, DNA sequence analysis indicated that these events did not occur at random. Of the 31 G:C→A:T transitions recovered, 24 involved cytosine residues located in the nontranscribed strand of the gene and 15 of the 31 transitions occurred at cytosines located on the 3′ side of 3 or more A:T base pairs. These differentials likely reflect the more single-stranded character of the non-transcribed strand of the gene and of regions rich in A:T base pairs. In addition, mutation at the frameshift hotspot was altered in the Ung− strain, suggesting a role for DNA repair in the formation of structural intermediates that potentiate these events. Also, the analysis of non-hotspot frameshifts, deletions and duplication showed that many involved local DNA sequence. Specifically, several of the frameshift, deletion and duplication mutations occurred near the sequence 5′-CTGG-3′. Thus, DNA sequence analysis of mutational specificity in an Ung− strain has provided evidence that gene expression, DNA repair and DNA context can all potentially influence the classes and frequencies of spontaneous mutation.