A Near-Deterministic Mutational Hotspot in Pseudomonas fluorescens Is Constructed by Multiple Interacting Genomic Features

Abstract

Mutation – whilst stochastic – is frequently biased toward certain loci. When combined with selection this results in highly repeatable and predictable evolutionary outcomes. Immotile variants of the bacterium Pseudomonas fluorescens (SBW25) possess a ‘mutational hotspot’ that facilitates repeated occurrences of an identical de novo single nucleotide polymorphism when re-evolving motility, where ≥95% independent lines fix the mutation ntrB A289C. Identifying hotspots of similar potency in other genes and genomic backgrounds would prove valuable for predictive evolutionary models, but to do so we must understand the genomic features that enable such a hotspot to form. Here we reveal that genomic location, local nucleotide sequence, gene strandedness and presence of mismatch repair proteins operate in combination to facilitate the formation of this mutational hotspot. Our study therefore provides a framework for utilising genomic features to predict and identify hotspot positions capable of enforcing near-deterministic evolution.

Evolutionary innovation through transcription factor promiscuity in microbes is constrained by pre-existing gene regulatory network architecture

“…The more evolvable pathway in gaining promiscuity is the NtrBC system in which the negative repressor GlnK prevents runaway ntrBC autoregulation by inhibiting NtrB 63 . All previously observed NtrBC pathway mutations were single de-novo mutations that act to remove repression through GlnK, both directly or indirectly 34,38,39 . These have a dual effect, both hyperactivating the NtrB kinase, and strongly upregulating ntrBC expression through their positive autoregulatory loop.…”

“…This evolutionary rewiring to rescue flagellar gene expression exclusively occurred through the NtrBC system despite there being 20 other FleQ structural homologs present in the SBW25 genome (a transcription factor family called RpoN -dependent e nhancer b inding p roteins – RpoN-EBPs), many of which are predicted to be more structurally similar to FleQ than NtrC 37 . This evolutionary ‘preference’ for innovation through the NtrBC system over any other FleQ-homologous regulator persists even after disruption of a strong mutational hotspot present in the ntrB gene 38,39 . Across these studies, a total of 387 independent replicates of motility rescue were run including varying nutrient conditions, and in two different strain backgrounds (AR2 and Pf0-2x, an engineered aflagellate Pf0-1 mutant), and in all cases mutations occurred in ntrB , or genes glnK and glnA that form part of the NtrBC system.…”

Report of mutation biases mirroring selection in Arabidopsis thaliana unlikely to be entirely due to variant calling errors

“…MSH2 functions as a dimer with MSH6, which is likely targeted to H3K4me1 via its Tudor domain [10,44]. Additional recent studies that support the core findings of [1] include reports of (i) reduced germline and somatic mutations rates in transcribed genes, in genome regions marked by epigenomic features characteristic for gene activation, and in gene bodies, observed in several algae, plants as well as humans and nematodes [17,21,36,42,[47][48][49][50][51][52]; (ii) relationships between histone modifications -especially those linked to gene activation -, mutation rates and DNA repair across diverse species [51,[53][54][55][56][57][58][59][60]; and 8 (iii) H3K4me1 affecting rates of CRISPR-mediated mutagenesis in plants [61]. That the role of histone modifications in driving DNA repair localization is well-established is also reflected in cancer therapeutics targeting histone states being widely pursued (e.g., [62][63][64][65][66]).…”

Transient mutation bias increases the predictability of evolution on an empirical genotype–phenotype landscape

“…Due to this potent localized mutation bias, uncovering other viable targets that comprise the spectrum of the first-step mutations is challenging. However, in previous work, we have demonstrated that the hotspot can be removed through functionally benign genomic augmentations, such as silent mutations [ 11 ] and gene strandedness [ 20 ]. This has allowed us to capture rare mutational targets that did not have the opportunity to be realized when the 289 hotspot remains intact.…”