Sources of spontaneous mutagenesis in bacteria

Abstract

Mutations in an organism's genome can arise spontaneously, that is, in the absence of exogenous stress and prior to selection. Mutations are often neutral or deleterious to individual fitness but can also provide genetic diversity driving evolution. Mutagenesis in bacteria contributes to the already serious and growing problem of antibiotic resistance. However, the negative impacts of spontaneous mutagenesis on human health are not limited to bacterial antibiotic resistance. Spontaneous mutations also underlie tumorigenesis and evolution of drug resistance. To better understand the causes of genetic change and how they may be manipulated in order to curb antibiotic resistance or the development of cancer, we must acquire a mechanistic understanding of the major sources of mutagenesis. Bacterial systems are particularly well-suited to studying mutagenesis because of their fast growth rate and the panoply of available experimental tools, but efforts to understand mutagenic mechanisms can be complicated by the experimental system employed. Here, we review our current understanding of mutagenic mechanisms in bacteria and describe the methods used to study mutagenesis in bacterial systems.

Periodic variation of mutation rates in bacterial genomes associated with replication timing

“…We acknowledge that this model is speculative and requires considerable additional study, although the associations between replication dynamics and RNR activity and dNTP pools and mutation rates are both well supported (53, 56–58). A related possibility is that this periodicity arises from imbalances between rNTP and dNTP pools, which has been demonstrated to be mutagenic (53, 59, 60). At a minimum, this simple model relating ribonucleotide availability with mutation-rate periodicity is empirically testable by additional MA-WGS with defined mutants and altered growth conditions.…”

Half‐Intercalation Stabilizes Slipped Mispairing and Explains Genome Vulnerability to Frameshift Mutagenesis by Endogenous “Molecular Bookmarks”

“…However, the notion of frameshift formation due to asymmetric events during DNA synthesis—the template and the primer strands shifting relative to each other—very soon resurfaced and in fact became extremely popular (ironically, the new idea specifically avoided the involvement of intercalation). Perhaps the resistance to the original asymmetric frameshift mutagenesis idea of Brenner et al was due to the assumption that the slipped‐mispairing intermediate, stabilized by the asymmetric intercalation near the extending 3′‐end (Figure ), would be unstable without an intercalator, while spontaneous frameshift mutations form with relatively high frequencies, similar to base substitutions . The expectation that a strand with an extra nucleotide would not be able to form a local duplex with the complementary strand lacking this nucleotide was in fact already tested and refuted: the two strands still formed a (less stable) duplex, accommodating the unpaired nucleotide(s) in an extrahelical loop…”

“…Yet, no matter how esoteric frameshift mutagenesis may sound today, almost 60 years since it contributed to figuring out the genetic code, the development of a mechanistic model of intercalation‐induced frameshifting is urged by current practical reasons: 1) although originally believed to be rare, spontaneous frameshifts happen at frequencies similar to those of base substitutions; 2) because of its gene‐inactivating nature, spontaneous or induced frameshift mutagenesis is a major contributor to the overall genome instability; 3) obviously, we cannot explore the mechanisms of this important process without formulating its model and testing derived predictions; 4) less obviously, but more importantly, if we do not appreciate the critical contribution of intercalators to frameshift mutagenesis, we remain oblivious to the various classes of endogenous intercalators that are likely contributors to the relatively frequent spontaneous frameshifts; and 5) last but not least, since the phenomenon of intercalation is widely used in the design of modern DNA‐targeting drugs, the risk assessment of the associated frameshift mutagenesis is currently impossible without the knowledge of its mechanism. And exploration of such a mechanism should start with the formulation of a model of the intercalation‐induced frameshifts.…”

“…In contrast to base substitutions, frameshift mutations tend to have severe consequences, inactivating the affected gene by truncating the corresponding protein due to frequent stop codons outside open reading frames . Because of this, one expects the cell to ensure that spontaneous frameshifts are rare relative to base substitutions, but they are not, comprising on average ≈10% of all point mutations across kingdoms . Since frameshifts are efficiently intercepted at two levels: by DNA polymerase proofreading and by mismatch repair, the remaining significant background of these dangerous mutations suggests either the presence of endogenous intercalators in the cell or existence of cellular processes requiring intercalation, or both.…”

Irregularities in genetic variation and mutation rates with environmental stresses

“…For example, mutations empower evolutionary divergence (Maharjan et al, 2012;Leon et al, 2018), antibiotic resistance in bacteria (Blazquez et al, 2012;Blázquez et al, 2018) and cancer in humans (Alexandrov and Stratton, 2014;Petljak and Alexandrov, 2016;Letouze et al, 2017;Phillips, 2018). The supply of mutations needs to be understood to explain such events (Schroeder et al, 2018). This review focuses on new developments with bacterial models addressing how environments influence mutational processes and the ensuing genetic variation.…”