Bacterial DNA uptake sequences can accumulate by molecular drive alone.

Genetics
Heather MaughanRosemary J Redfield

Abstract

Uptake signal sequences are DNA motifs that promote DNA uptake by competent bacteria in the family Pasteurellaceae and the genus Neisseria. The genomes of these bacteria contain many copies of their canonical uptake sequence (often >100-fold overrepresentation), so the bias of the uptake machinery causes cells to prefer DNA derived from close relatives over DNA from other sources. However, the molecular and evolutionary forces responsible for the abundance of uptake sequences in these genomes are not well understood, and their presence is not easily explained by any of the current models of the evolution of competence. Here we describe use of a computer simulation model to thoroughly evaluate the simplest explanation for uptake sequences, that they accumulate in genomes by a form of molecular drive generated by biased DNA uptake and evolutionarily neutral (i.e., unselected) recombination. In parallel we used an unbiased search algorithm to characterize genomic uptake sequences and DNA uptake assays to refine the Haemophilus influenzae uptake specificity. These analyses showed that biased uptake and neutral recombination are sufficient to drive uptake sequences to high densities, with the spacings, stabilities, and strong consen...Continue Reading

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Citations

Jul 4, 2012·Nucleic Acids Research·Joshua Chang MellRosemary J Redfield
May 15, 2012·Applied and Environmental Microbiology·Bodil M KristensenRosemary J Redfield
Jan 29, 2011·BMC Genomics·Jeremiah J DavieAnthony A Campagnari
May 3, 2013·PLoS Genetics·Stephan A FryeOle Herman Ambur
Jun 30, 2016·Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology·R Jeremy Johnson
Feb 4, 2014·Journal of Bacteriology·Joshua Chang Mell, Rosemary J Redfield
Feb 28, 2019·Frontiers in Genetics·Bhaskar Chandra Mohan Ramisetty, Pavithra Anantharaman Sudhakari
Sep 9, 2019·Trends in Microbiology·Michiel VosBram Kuijper

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