1. Rates and kinds of spontaneous mutations were measured in the eubacterial thermophile Thermus thermophilus. This information was combined with that from a previous study of the archaeal thermophile Sulfolobus acidocaldarius to compare with a set of mesophilic prokaryotes. The mutation rate and fraction of base-pair substitutions are markedly lower in thermophiles than in other DNA microbes. This result strongly supports the hypothesis that the average missense mutation is more deleterious at higher temperatures, which in turn drives the evolution of lower rates of base substitution. 2. We reported previously that most mutational spectra contain more mutants with multiple mutations than expected from a random distribution of the mutations. The nonrandom distribution of mutations in tobacco mosaic virus has been modeled as the sum of two sub-populations, a majority with a low mutation frequency and a minority with a high mutation frequency. If this result is general, it will help to model the average mutation rate of riboviruses in combination with their rapid evolution within the host but relative genomic stability over time. Now we are attempting to establish a phage system in which such questions can be more efficiently addressed. 3. DNA polymerase molecules copying a template in vitro can produce nonrandom bursts of mutations, suggesting that a substantial minority of the polymerase molecules have a mutator phenotype. However, a polymerase must be processive to be able to produce cluster of mutations. We therefore closely examined the ability of the mammalian DNA repair polymerase Pol beta to make clusters, as had been suggested in the literature. The putative clusters appear to be artifacts of the measurement systems, confirming that processivity is required for cluster formation. 4. We are now testing whether multiple mutations can arise simultaneously in Escherichia coli at sites separated by hundreds of kilobases, a property that would be required for clusters to promote carcinogenesis in mammalian cells. 5. Because we often use rI mutations in bacteriophage T4 as mutation reporters, we sequence a set of rI-like mutations that did not map at the classical rI locus to determine where they did map. They occupied the gene upstream from rI, or were in the rIII, rIV or rV genes, but not elsewhere. Because the r genes are involved in lysis inhibition, a classical system of interest to students of evolution, this result sets resolves concerns about how many genes are involved. This work is now being prepared for publication. 6. Mutation rates are difficult to measure in riboviruses, the largest class of human pathogens. In particular, the question of whether riboviruses share a common genomic mutation rate has resisted resolution. We have now accumulated sufficient information from the recent literature to estimate the genomic rate at about 0.5k per RNA-genome replication or 1.0k per cell infection and to support the hypothesis that riboviruses have a common mutation rate over a spread of genome sizes of about 40-fold. This study has been submitted for publication.
| Drake, John W (2012) Contrasting mutation rates from specific-locus and long-term mutation-accumulation procedures. G3 (Bethesda) 2:483-5 |
| García-Villada, Libertad; Drake, John W (2012) The three faces of riboviral spontaneous mutation: spectrum, mode of genome replication, and mutation rate. PLoS Genet 8:e1002832 |
| Burch, Lauranell H; Zhang, Leilei; Chao, Frank G et al. (2011) The bacteriophage T4 rapid-lysis genes and their mutational proclivities. J Bacteriol 193:3537-45 |
| García-Villada, Libertad; Drake, John W (2010) Mutational clusters generated by non-processive polymerases: A case study using DNA polymerase betain vitro. DNA Repair (Amst) 9:871-8 |
| Drake, John W (2009) Avoiding dangerous missense: thermophiles display especially low mutation rates. PLoS Genet 5:e1000520 |
| Mackwan, Reena R; Carver, Geraldine T; Kissling, Grace E et al. (2008) The rate and character of spontaneous mutation in Thermus thermophilus. Genetics 180:17-25 |
