Mutation rate plasticity in rifampicin resistance depends on Escherichia coli cell–cell interactions

Variation of mutation rate at a particular site in a particular genotype, in other words mutation rate plasticity (MRP), can be caused by stress or ageing. However, mutation rate control by other factors is less well characterized. Here we show that in wild-type Escherichia coli (K-12 and B strains), the mutation rate to rifampicin resistance is plastic and inversely related to population density: lowering density can increase mutation rates at least threefold. This MRP is genetically switchable, dependent on the quorum-sensing gene luxS—specifically its role in the activated methyl cycle—and is socially mediated via cell–cell interactions. Although we identify an inverse association of mutation rate with fitness under some circumstances, we find no functional link with stress-induced mutagenesis. Our experimental manipulation of mutation rates via the social environment raises the possibility that such manipulation occurs in nature and could be exploited medically.

[1]  R. MacLean,et al.  Evaluating evolutionary models of stress-induced mutagenesis in bacteria , 2013, Nature Reviews Genetics.

[2]  Philip J. Farabaugh,et al.  Molecular basis of base substitution hotspots in Escherichia coli , 1978, Nature.

[3]  Mitchel van Loon,et al.  Mixed effects models , 2013 .

[4]  D. Cox,et al.  An Analysis of Transformations , 1964 .

[5]  Analysis of the Luria-Delbrück distribution using discrete convolution powers , 1992 .

[6]  M. Surette,et al.  Quorum sensing in Escherichia coli and Salmonella typhimurium. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Jeffrey E. Barrick,et al.  Genome evolution and adaptation in a long-term experiment with Escherichia coli , 2009, Nature.

[8]  Jeffrey H. Miller,et al.  Polymerases Leave Fingerprints: Analysis of the Mutational Spectrum in Escherichia coli rpoB To Assess the Role of Polymerase IV in Spontaneous Mutation , 2004, Journal of bacteriology.

[9]  K. Winzer,et al.  Quantitative liquid chromatography-tandem mass spectrometry profiling of activated methyl cycle metabolites involved in LuxS-dependent quorum sensing in Escherichia coli. , 2010, Analytical biochemistry.

[10]  P. Foster,et al.  Methods for determining spontaneous mutation rates. , 2006, Methods in enzymology.

[11]  M. Winkler,et al.  Depletion of the cellular amounts of the MutS and MutH methyl-directed mismatch repair proteins in stationary-phase Escherichia coli K-12 cells , 1996, Journal of bacteriology.

[12]  Sally Freeman,et al.  Synthesis and bioluminescence-inducing properties of autoinducer (S)-4,5-dihydroxypentane-2,3-dione and its enantiomer. , 2010, Bioorganic & medicinal chemistry letters.

[13]  Ivan Matic,et al.  Causes and Consequences of DNA Repair Activity Modulation During Stationary Phase in Escherichia coli , 2007, Critical reviews in biochemistry and molecular biology.

[14]  A. Agrawal,et al.  Evidence for elevated mutation rates in low-quality genotypes , 2012, Proceedings of the National Academy of Sciences.

[15]  B. Wanner,et al.  One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[16]  J. Drake,et al.  Rates of spontaneous mutation. , 1998, Genetics.

[17]  Chang-Xing Ma,et al.  Fluctuation AnaLysis CalculatOR: a web tool for the determination of mutation rate using Luria-Delbrück fluctuation analysis , 2009, Bioinform..

[18]  A. Clatworthy,et al.  Targeting virulence: a new paradigm for antimicrobial therapy , 2007, Nature Chemical Biology.

[19]  Zbigniew Michalewicz,et al.  Parameter Control in Evolutionary Algorithms , 2007, Parameter Setting in Evolutionary Algorithms.

[20]  R. Kaplan Evolutionary adjustment of spontaneous mutation rates , 2004, Humangenetik.

[21]  S. Lederberg,et al.  Methylated Bases in the Host-Modified Deoxyribonucleic Acid of Escherichia coli and Bacteriophage λ , 1966, Journal of bacteriology.

[22]  Panos M. Pardalos,et al.  Springer Proceedings in Mathematics & Statistics , 2013 .

[23]  J. Bayona,et al.  Multidrug-resistant and extensively drug-resistant tuberculosis: a threat to global control of tuberculosis , 2010, The Lancet.

[24]  A. Agrawal,et al.  Genetic loads under fitness‐dependent mutation rates , 2002 .

[25]  S. Rosenberg,et al.  Mutation as a Stress Response and the Regulation of Evolvability , 2007, Critical reviews in biochemistry and molecular biology.

[26]  B. Bassler,et al.  Regulation of Uptake and Processing of the Quorum-Sensing Autoinducer AI-2 in Escherichia coli , 2005, Journal of bacteriology.

[27]  P. Foster,et al.  Determining mutation rates in bacterial populations. , 2000, Methods.

[28]  H. A. Orr,et al.  Fitness and its role in evolutionary genetics , 2009, Nature Reviews Genetics.

[29]  Alan Hodgkinson,et al.  Variation in the mutation rate across mammalian genomes , 2011, Nature Reviews Genetics.

[30]  Lilach Hadany,et al.  THE EVOLUTION OF STRESS‐INDUCED HYPERMUTATION IN ASEXUAL POPULATIONS , 2012, Evolution; international journal of organic evolution.

[31]  G. Hommel A stagewise rejective multiple test procedure based on a modified Bonferroni test , 1988 .

[32]  F. Taddei,et al.  Highly variable mutation rates in commensal and pathogenic Escherichia coli. , 1997, Science.

[33]  F. M. Stewart Fluctuation tests: how reliable are the estimates of mutation rates? , 1994, Genetics.

[34]  R. Lenski,et al.  Long-Term Experimental Evolution in Escherichia coli. I. Adaptation and Divergence During 2,000 Generations , 1991, The American Naturalist.

[35]  E. Rocha,et al.  Natural Genome Diversity of AI-2 Quorum Sensing in Escherichia coli: Conserved Signal Production but Labile Signal Reception , 2012, Genome biology and evolution.

[36]  Valeria Souza,et al.  Stress-Induced Mutagenesis in Bacteria , 2003, Science.

[37]  D. Bates,et al.  Mixed-Effects Models in S and S-PLUS , 2001 .

[38]  S. Gillespie,et al.  A Practical Guide to Measuring Mutation Rates in Antibiotic Resistance , 2008, Antimicrobial Agents and Chemotherapy.

[39]  Andrew W. Murray,et al.  Estimating the Per-Base-Pair Mutation Rate in the Yeast Saccharomyces cerevisiae , 2008, Genetics.

[40]  A. Sturtevant Essays on Evolution. I. On the Effects of Selection on Mutation Rate , 1937, The Quarterly Review of Biology.

[41]  E. Boedeker,et al.  The possible influence of LuxS in the in vivo virulence of rabbit enteropathogenic Escherichia coli. , 2007, Veterinary microbiology.

[42]  Michael Herrmann,et al.  Advances in Artificial Life, ECAL 2011 , 2011 .

[43]  Thomas Egli,et al.  Specific growth rate and not cell density controls the general stress response in Escherichia coli. , 2004, Microbiology.

[44]  R. Lenski,et al.  The population genetics of ecological specialization in evolving Escherichia coli populations , 2000, Nature.

[45]  Haixu Tang,et al.  Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing , 2012, Proceedings of the National Academy of Sciences.

[46]  Lurias,et al.  MUTATIONS OF BACTERIA FROM VIRUS SENSITIVITY TO VIRUS RESISTANCE’-’ , 2003 .

[47]  Kathleen Marchal,et al.  COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia , 2013, Nucleic Acids Res..

[48]  K. Xavier,et al.  AI-2-mediated signalling in bacteria. , 2013, FEMS microbiology reviews.

[49]  Thomas G. Doak,et al.  Drift-barrier hypothesis and mutation-rate evolution , 2012, Proceedings of the National Academy of Sciences.

[50]  P. Modrich,et al.  Recognition sequence of the dam methylase of Escherichia coli K12 and mode of cleavage of Dpn I endonuclease. , 1979, The Journal of biological chemistry.

[51]  R. MacLean,et al.  The Fitness Cost of Rifampicin Resistance in Pseudomonas aeruginosa Depends on Demand for RNA Polymerase , 2011, Genetics.

[52]  Tom Lenaerts,et al.  Advances in Artificial Life, ECAL 2011: Proceedings of the Eleventh European Conference on the Synthesis and Simulation of Living Systems , 2011 .

[53]  Marcelo P. Sircili,et al.  AI-3 Synthesis Is Not Dependent on luxS in Escherichia coli , 2006, Journal of bacteriology.

[54]  Hilla Peretz,et al.  Ju n 20 03 Schrödinger ’ s Cat : The rules of engagement , 2003 .

[55]  S. Sarkar,et al.  On fluctuation analysis: a new, simple and efficient method for computing the expected number of mutants , 2004, Genetica.