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

M. J. Shepherd; J. S. Horton; T. B. Taylor

doi:10.1093/molbev/msac132

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

M. J. Shepherd, J. S. Horton, T. B. Taylor

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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 utilizing genomic features to predict and identify hotspot positions capable of enforcing near-deterministic evolution.

Original language	English
Article number	msac132
Journal	Molecular Biology and Evolution
Volume	39
Issue number	6
Early online date	16 Jun 2022
DOIs	https://doi.org/10.1093/molbev/msac132
Publication status	Published - 30 Jun 2022

Bibliographical note

We thank Prof. Laurence Hurst and Prof. Heath Murray for comments on earlier versions of this manuscript. This work was funded by a Royal Society Research Fellows Grant (RG160491; awarded to TBT) supporting MJS; a University of Bath University Research Studentship Account (awarded to TBT) and a BBSRC NI grant (BB/T012994/1; awarded to TBT) supporting JSH; a Royal Society Dorothy Hodgkin Research Fellowship (DH150169; awarded to and supporting TBT). Figure 1A and B were created using BioRender.com. Bioinformatics analyses for the letter was carried out using the Medical Research Council’s (MRC) Cloud Infrastructure for Microbial Bioinformatics (CLIMB), and Illumina Whole-Genome Sequencing conducted by MiGs, Pittsburgh, PA, USA.

Data Availability
All raw data for this study is available on the Open Science Framework (OSF), and can be accessed at https://osf.io/twcvd/.

Keywords

Mutation bias
mutation hotspot
predicting evolution

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Molecular Biology
Genetics

Access to Document

10.1093/molbev/msac132Licence: CC BY

MBE_22_0307_JSHorton_AdvanceAccessAccepted author manuscript, 906 KBLicence: CC BY

Cite this

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title = "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 utilizing genomic features to predict and identify hotspot positions capable of enforcing near-deterministic evolution. ",

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note = "We thank Prof. Laurence Hurst and Prof. Heath Murray for comments on earlier versions of this manuscript. This work was funded by a Royal Society Research Fellows Grant (RG160491; awarded to TBT) supporting MJS; a University of Bath University Research Studentship Account (awarded to TBT) and a BBSRC NI grant (BB/T012994/1; awarded to TBT) supporting JSH; a Royal Society Dorothy Hodgkin Research Fellowship (DH150169; awarded to and supporting TBT). Figure 1A and B were created using BioRender.com. Bioinformatics analyses for the letter was carried out using the Medical Research Council{\textquoteright}s (MRC) Cloud Infrastructure for Microbial Bioinformatics (CLIMB), and Illumina Whole-Genome Sequencing conducted by MiGs, Pittsburgh, PA, USA. Data Availability All raw data for this study is available on the Open Science Framework (OSF), and can be accessed at https://osf.io/twcvd/.",

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

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

Access to Document

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Predicting evolution: using comparative experimental evolution to test the role of mutation, selection and genetic background on repeatable evolution

Cite this

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

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Projects

Predicting evolution: using comparative experimental evolution to test the role of mutation, selection and genetic background on repeatable evolution

Cite this