Transcription as a source of genome instability

N Kim, S **ks-Robertson - Nature Reviews Genetics, 2012 - nature.com
Alterations in genome sequence and structure contribute to somatic disease, affect the
fitness of subsequent generations and drive evolutionary processes. The crucial roles of …

Old trade, new tricks: insights into the spontaneous mutation process from the partnering of classical mutation accumulation experiments with high-throughput …

V Katju, U Bergthorsson - Genome biology and evolution, 2019 - academic.oup.com
Mutations spawn genetic variation which, in turn, fuels evolution. Hence, experimental
investigations into the rate and fitness effects of spontaneous mutations are central to the …

Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing

H Lee, E Popodi, H Tang, PL Foster - … of the National Academy of Sciences, 2012 - pnas.org
Knowledge of the rate and nature of spontaneous mutation is fundamental to understanding
evolutionary and molecular processes. In this report, we analyze spontaneous mutations …

Evidence that mutation is universally biased towards AT in bacteria

R Hershberg, DA Petrov - PLoS genetics, 2010 - journals.plos.org
Mutation is the engine that drives evolution and adaptation forward in that it generates the
variation on which natural selection acts. Mutation is a random process that nevertheless …

Synonymous Codon Usage in Escherichia coli: Selection for Translational Accuracy

N Stoletzki, A Eyre-Walker - Molecular biology and evolution, 2007 - academic.oup.com
In many organisms, selection acts on synonymous codons to improve translation. However,
the precise basis of this selection remains unclear in the majority of species. Selection could …

Whole-genome mutational biases in bacteria

PA Lind, DI Andersson - Proceedings of the National Academy of …, 2008 - pnas.org
A fundamental biological question is what forces shape the guanine plus cytosine (GC)
content of genomes. We studied the specificity and rate of different mutational biases in real …

Transcription-associated mutagenesis

S **ks-Robertson, AS Bhagwat - Annual review of genetics, 2014 - annualreviews.org
Transcription requires unwinding complementary DNA strands, generating torsional stress,
and sensitizing the exposed single strands to chemical reactions and endogenous …

The evolution of genetic regulatory systems in bacteria

HH McAdams, B Srinivasan, AP Arkin - Nature Reviews Genetics, 2004 - nature.com
The genomes of bacterial species show enormous plasticity in the function of individual
genes, in genome organization and in regulatory organization. Over millions of years, both …

Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria

CH Kuo, H Ochman - Biology direct, 2009 - Springer
Background Because bacteria do not have a robust fossil record, attempts to infer the timing
of events in their evolutionary history requires comparisons of molecular sequences. This …

Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis

JL Payne, F Menardo, A Trauner, S Borrell… - PLoS …, 2019 - journals.plos.org
Transition bias, an overabundance of transitions relative to transversions, has been widely
reported among studies of the rates and spectra of spontaneous mutations. However …