Methylation-Induced Hypermutation in Natural Populations of Bacteria.

Abstract:

:Methylation of DNA at the C-5 position of cytosine occurs in diverse organisms. This modification can increase the rate of C→T transitions at the methylated position. In Escherichia coli and related enteric bacteria, the inner C residues of the sequence CCWGG (W is A or T) are methylated by the Dcm enzyme. These sites are hot spots of mutation during rapid growth in the laboratory but not in nondividing cells, in which repair by the Vsr protein is effective. It has been suggested that hypermutation at these sites is a laboratory artifact and does not occur in nature. Many other methyltransferases, with a variety of specificities, can be found in bacteria, usually associated with restriction enzymes and confined to a subset of the population. Their methylation targets are also possible sites of hypermutation. Here, I show using whole-genome sequence data for thousands of isolates that there is indeed considerable hypermutation at Dcm sites in natural populations: their transition rate is approximately eight times the average. I also demonstrate hypermutability of targets of restriction-associated methyltransferases in several distantly related bacteria: methylation increases the transition rate by a factor ranging from 12 to 58. In addition, I demonstrate how patterns of hypermutability inferred from massive sequence data can be used to determine previously unknown methylation patterns and methyltransferase specificities.IMPORTANCE A common type of DNA modification, addition of a methyl group to cytosine (C) at carbon atom C-5, can greatly increase the rate of mutation of the C to a T. In mammals, methylation of CG sequences increases the rate of CG→TG mutations. It is unknown whether cytosine C-5 methylation increases the mutation rate in bacteria under natural conditions. I show that sites methylated by the Dcm enzyme exhibit an 8-fold increase in mutation rate in natural bacterial populations. I also show that modifications at other sites in various bacteria also increase the mutation rate, in some cases by a factor of forty or more. Finally, I demonstrate how this phenomenon can be used to infer sequence specificities of methylation enzymes.

journal_name

J Bacteriol

journal_title

Journal of bacteriology

authors

Cherry JL

doi

10.1128/JB.00371-18

subject

Has Abstract

pub_date

2018-11-26 00:00:00

issue

24

eissn

0021-9193

issn

1098-5530

pii

JB.00371-18

journal_volume

200

pub_type

杂志文章
  • Stabilization of colicin E2 by bovine serum albumin.

    abstract::Colicin E2 was partially purified from Escherichia coli W3110. This preparation was remarkably stabilized by bovine serum albumin in a solution at neutral pH, as shown by dilution experiments and tests on heat stability of colicin. One killing unit of colicin E2 was estimated to correspond to one molecule of colicin E...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.100.2.1136-1137.1969

    authors: Mitsui E,Mizuno D

    更新日期:1969-11-01 00:00:00

  • Functional Overlap of hetP and hetZ in Regulation of Heterocyst Differentiation in Anabaena sp. Strain PCC 7120.

    abstract::HetR plays a key role in regulation of heterocyst differentiation and patterning in Anabaena It directly regulates genes involved in heterocyst differentiation (such as hetP and hetZ), genes involved in pattern formation (patA), and many others. In this study, we investigated the functional relationship of hetP and he...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.00707-17

    authors: Zhang H,Wang S,Wang Y,Xu X

    更新日期:2018-04-09 00:00:00

  • Stability of the Escherichia coli division inhibitor protein MinC requires determinants in the carboxy-terminal region of the protein.

    abstract::Certain mutations in the C-terminal region of the Escherichia coli division inhibitor protein MinC cause loss of function of the division inhibitor by making MinC more sensitive to degradation by Lon protease, implying a possible role for the C-terminal region in regulating the stability and cellular concentration of ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.180.1.175-177.1998

    authors: Sen M,Rothfield LI

    更新日期:1998-01-01 00:00:00

  • Formation of the K30 (group I) capsule in Escherichia coli O9:K30 does not require attachment to lipopolysaccharide lipid A-core.

    abstract::Escherichia coli K antigens (capsular polysaccharides) are divided into two broad classes, designated groups I and II, on the basis of a number of chemical, physical, and genetic criteria. Group I K antigens can be further subdivided on the basis of the absence (group IA) or presence (group IB) of amino sugars in the ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.175.23.7515-7522.1993

    authors: MacLachlan PR,Keenleyside WJ,Dodgson C,Whitfield C

    更新日期:1993-12-01 00:00:00

  • Escherichia coli-Salmonella typhimurium hybrid nusA genes: identification of a short motif required for action of the lambda N transcription antitermination protein.

    abstract::The Escherichia coli nusA gene, nusAEc, encodes an essential protein that influences transcription elongation. Derivatives of E. coli in which the Salmonella typhimurium nusA gene, nusASt, has replaced nusAEc are viable. Thus, NusASt can substitute for NusAEc in supporting essential bacterial activities. However, hybr...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.176.5.1394-1404.1994

    authors: Craven MG,Granston AE,Schauer AT,Zheng C,Gray TA,Friedman DI

    更新日期:1994-03-01 00:00:00

  • Chemical analyses of asporogenic mutants of Bacillus cereus.

    abstract::Lundgren, D. G. (Syracuse University, Syracuse, N.Y.) and J. J. Cooney. Chemical analyses of asporogenic mutants of Bacillus cereus. J. Bacteriol. 83:1287-1293. 1962.-Bacillus cereus ATCC 4342 and three temperature-sensitive asporogenic mutants were compared regarding some basic cellular components and response to met...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.83.6.1287-1293.1962

    authors: LUNDGREN DG,COONEY JJ

    更新日期:1962-06-01 00:00:00

  • Identification, cloning, and characterization of the Ima operon, whose gene products are unique to Listeria monocytogenes.

    abstract::The lmaA gene of Listeria monocytogenes encodes a protein capable of inducing delayed-type hypersensitivity reactions in L. monocytogenes-immune mice (S. Göhmann, M. Leimeister-Wachter, E. Schiltz, W. Goebel, and T. Chakraborty, M. Microbiol. 4:1091-1099, 1990). Here we show that it is the last gene of the lma operon,...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.179.8.2707-2716.1997

    authors: Schäferkordt S,Chakraborty T

    更新日期:1997-04-01 00:00:00

  • Functional analysis of OleY L-oleandrosyl 3-O-methyltransferase of the oleandomycin biosynthetic pathway in Streptomyces antibioticus.

    abstract::Oleandomycin, a macrolide antibiotic produced by Streptomyces antibioticus, contains two sugars attached to the aglycon: L-oleandrose and D-desosamine. oleY codes for a methyltransferase involved in the biosynthesis of L-oleandrose. This gene was overexpressed in Escherichia coli to form inclusion bodies and in Strept...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.183.18.5358-5363.2001

    authors: Rodríguez L,Rodríguez D,Olano C,Braña AF,Méndez C,Salas JA

    更新日期:2001-09-01 00:00:00

  • Inhibition of the development of the spore septum and membranes in Bacillus cereus by beta-phenethyl alcohol.

    abstract::Remsen, C. C. (Syracuse University, Syracuse, N.Y.), D. G. Lundgren, and R. A. Slepecky. Inhibition of the development of the spore septum and membranes in Bacillus cereus by beta-phenethyl alcohol. J. Bacteriol. 91:324-331. 1966.-The effect of phenethyl alcohol (PEA) upon the initial stages of sporulation in Bacillus...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.91.1.324-331.1966

    authors: Remsen CC,Lundgren DG,Slepecky RA

    更新日期:1966-01-01 00:00:00

  • Occurrence of a class II restriction endonuclease in Staphylococcus aureus.

    abstract::The occurrence of class II restriction endonucleases (enzymes that both recognize and cleave a specific nucleotide sequence in deoxyribonucleic acid [DNA] in Staphylococcus aureus has been investigated by analysis of crude extracts obtained from different propagating strains of the International Phage Typing System. O...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.131.2.645-649.1977

    authors: Stobberingh EE,Schiphof R,Sussenbach JS

    更新日期:1977-08-01 00:00:00

  • Transcriptional organization of the czc heavy-metal homeostasis determinant from Alcaligenes eutrophus.

    abstract::The Czc system of Alcaligenes eutrophus mediates resistance to cobalt, zinc, and cadmium through ion efflux catalyzed by the CzcCB2A cation-proton antiporter. DNA sequencing of the region upstream of the czcNICBADRS determinant located on megaplasmid pMOL30 revealed the 5' end of czcN and a gene for a MgtC-like protei...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.181.8.2385-2393.1999

    authors: Grosse C,Grass G,Anton A,Franke S,Santos AN,Lawley B,Brown NL,Nies DH

    更新日期:1999-04-01 00:00:00

  • Specialized transduction with lambda plac5: dependence on recB.

    abstract::Genetically disabled lambda plac5 transducing phage derivatives were used to study the recB dependence of recombination during specialized transduction. The frequency of transduction was normalized to colony-forming units, and the end product of recombination was monitored by scoring for addition and substitution tran...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.150.3.1485-1488.1982

    authors: Porter RD,Welliver RA,Witkowski TA

    更新日期:1982-06-01 00:00:00

  • Regulation of sialic acid metabolism in Escherichia coli: role of N-acylneuraminate pyruvate-lyase.

    abstract::In Escherichia coli, synthesis of sialic acid is not regulated by allosteric inhibition mediated by cytidine 5'-monophospho-N-acetylneuraminic acid (CMP-NeuNAc). Evidence for the lack of metabolic control by feedback inhibition was demonstrated by measuring the intracellular level of sialic acid and CMP-NeuNAc in muta...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.164.2.854-860.1985

    authors: Vimr ER,Troy FA

    更新日期:1985-11-01 00:00:00

  • Cloning, sequence analysis, and characterization of the genes involved in isoprimeverose metabolism in Lactobacillus pentosus.

    abstract::Two genes, xylP and xylQ, from the xylose regulon of Lactobacillus pentosus were cloned and sequenced. Together with the repressor gene of the regulon, xylR, the xylPQ genes form an operon which is inducible by xylose and which is transcribed from a promoter located 145 bp upstream of xylP. A putative xylR binding sit...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.180.9.2312-2320.1998

    authors: Chaillou S,Lokman BC,Leer RJ,Posthuma C,Postma PW,Pouwels PH

    更新日期:1998-05-01 00:00:00

  • A subassembly of R27-encoded transfer proteins is dependent on TrhC nucleoside triphosphate-binding motifs for function but not formation.

    abstract::The transfer of plasmid DNA molecules between bacterial cells is achieved by a large array of conjugative transfer proteins which assemble into both cytoplasmic and membrane-associated complexes. TrhC is a membrane-associated protein that is required for the transfer of the IncHI1 resistance plasmid R27. Homologous pr...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.186.6.1606-1613.2004

    authors: Gilmour MW,Taylor DE

    更新日期:2004-03-01 00:00:00

  • Regulation of the aromatic pathway in the cyanobacterium Synechococcus sp. strain Pcc6301 (Anacystis nidulans).

    abstract::A pattern of allosteric control for aromatic biosynthesis in cyanobacteria relies upon early-pathway regulation as the major control point for the entire branched pathway. In Synechococcus sp. strain PCC6301 (Anacystis nidulans), two enzymes which form precursors for L-phenylalanine biosynthesis are subject to control...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.153.1.423-428.1983

    authors: Hall GC,Flick MB,Jensen RA

    更新日期:1983-01-01 00:00:00

  • Flagellar assembly in Salmonella typhimurium: analysis with temperature-sensitive mutants.

    abstract::The process of flagellar assembly in Salmonella typhimurium was investigated by using temperature-sensitive mutants. The mutants were grown at the restrictive temperature and then at the permissive temperature, with radiolabel supplied in the first phase of the experiment and not the second, or vice versa. Flagellar h...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.172.3.1327-1339.1990

    authors: Jones CJ,Macnab RM

    更新日期:1990-03-01 00:00:00

  • Genomic organization of the acidophilic chemolithoautotrophic bacterium Thiobacillus ferrooxidans ATCC 21834.

    abstract::The genomic organization of the acidophilic chemolithoautotrophic bacterium Thiobacillus ferrooxidans ATCC 21834 has been studied by pulsed-field gel electrophoresis (PFGE). Analysis of its intact DNA, as well as the restriction patterns obtained with several endonucleases, allowed the characterization of one circular...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.179.6.1946-1950.1997

    authors: Irazabal N,Marín I,Amils R

    更新日期:1997-03-01 00:00:00

  • Genome sequence of Lactococcus raffinolactis strain 4877, isolated from natural dairy starter culture.

    abstract::The nonstarter lactic acid bacterium Lactococcus raffinolactis is prevalent in a wide range of environments, such as the dairy environment, but little is known about this species. Here, we present the draft genome of Lactococcus raffinolactis strain 4877, isolated from a natural mesophilic dairy starter culture. ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.01697-12

    authors: Meslier V,Loux V,Renault P

    更新日期:2012-11-01 00:00:00

  • Genome sequence of the Spinosyns-producing bacterium Saccharopolyspora spinosa NRRL 18395.

    abstract::Saccharopolyspora spinosa is a Gram-positive bacterium that produces spinosad, a well-known biodegradable insecticide that is used for agricultural pest control and has an excellent environmental and mammalian toxicological profile. Here, we present the first draft genome sequence of the type strain Saccharopolyspora ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.00344-11

    authors: Pan Y,Yang X,Li J,Zhang R,Hu Y,Zhou Y,Wang J,Zhu B

    更新日期:2011-06-01 00:00:00

  • Ultraviolet microscopy of purines and amino acids in the vacuole of Candida albicans.

    abstract::Ultraviolet (UV) microscopy was used to study the capacity of yeast (ATCC 10231 and 10261) and filamentous (ATCC 10259) strains of Candida albicans to accumulate UV-absorbing materials from a medium supplemented with purines, pyrimidines, amino acids, or related compounds as the main nitrogen source. All strains accum...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.96.1.259-265.1968

    authors: Balish E,Svihla G

    更新日期:1968-07-01 00:00:00

  • Caulobacter crescentus pili: structure and stage-specific expression.

    abstract::Pili are functionally expressed during the predivisional and swarmer stages of the Caulobacter crescentus differentiation cycle. They appear on the developing swarmer pole and at the same cellular location as flagella and the phiCbK receptor sites. Pili disappear when the swarmer cell differentiates into a stalked cel...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.131.1.340-346.1977

    authors: Lagenaur C,Agabian N

    更新日期:1977-07-01 00:00:00

  • Genetic and physical analyses of Methylobacterium organophilum XX genes encoding methanol oxidation.

    abstract::When allyl alcohol was used as a suicide substrate, spontaneous mutants and UV light- and nitrous acid-generated mutants of Methylobacterium organophilum XX were selected which grew on methylamine but not on methanol. There was no detectable methanol dehydrogenase (MDH) activity in crude extracts of these mutants, yet...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.170.1.141-148.1988

    authors: Machlin SM,Tam PE,Bastien CA,Hanson RS

    更新日期:1988-01-01 00:00:00

  • Altered mRNA metabolism in ribonuclease III-deficient strains of Escherichia coli.

    abstract::The metabolism of mRNA from the lactose (lac) operon of Escherichia coli has been studied in ribonuclease (RNase) III-deficient strains (rnc-105). The induction lag for beta-galactosidase from the first gene was twice as long, and enzyme synthesis was reduced 10-fold in one such mutant compared with its isogenic rnc+ ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.135.2.528-541.1978

    authors: Talkad V,Achord D,Kennell D

    更新日期:1978-08-01 00:00:00

  • Structural and mutational analysis of band 7 proteins in the cyanobacterium Synechocystis sp. strain PCC 6803.

    abstract::Band 7 proteins, which encompass members of the stomatin, prohibitin, flotillin, and HflK/C protein families, are integral membrane proteins that play important physiological roles in eukaryotes but are poorly characterized in bacteria. We have studied the band 7 proteins encoded by the cyanobacterium Synechocystis sp...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.00644-09

    authors: Boehm M,Nield J,Zhang P,Aro EM,Komenda J,Nixon PJ

    更新日期:2009-10-01 00:00:00

  • Complete genome sequence of Halalkalicoccus jeotgali B3(T), an extremely halophilic archaeon.

    abstract::Halalkalicoccus jeotgali B3(T), isolated from salt-fermented seafood from South Korea, is an extremely halophilic archaeon belonging to the family Halobacteriaceae. Here, we present the complete genome sequence of the type strain H. jeotgali B3(T) (3,698,650 bp, with a G+C content of 62.5%), which consists of one chro...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.00663-10

    authors: Roh SW,Nam YD,Nam SH,Choi SH,Park HS,Bae JW

    更新日期:2010-09-01 00:00:00

  • Functional expression of plastid allophycocyanin genes in a cyanobacterium.

    abstract::In Cyanophora paradoxa, the allophycocyanin apoprotein subunits, alpha and beta, are encoded in the cyanelle (plastid) genome. These genes were transferred to the cyanobacterium Synechococcus sp. PCC 7002 on a plasmid replicon. Phycobilisomes isolated from transformed cyanobacteria were found to contain C. paradoxa al...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.169.5.1830-1835.1987

    authors: de Lorimier R,Guglielmi G,Bryant DA,Stevens SE Jr

    更新日期:1987-05-01 00:00:00

  • Purification and properties of glycogen isolated from a blue-green alga, Nostoc muscorum.

    abstract::Alpha granules were isolated from a blue-green alga, Nostoc muscorum, in large quantities and high purity by sucrose density gradient centrifugation. Sodium deoxycholate was used to eliminate membrane contamination. Isolated alpha granules from this species have average dimension of 31 nm in width and 65 nm in length....

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.105.1.331-338.1971

    authors: Chao L,Bowen CC

    更新日期:1971-01-01 00:00:00

  • Detoxification of protoanemonin by dienelactone hydrolase.

    abstract::Protoanemonin is a toxic metabolite which may be formed during the degradation of some chloroaromatic compounds, such as polychlorinated biphenyls, by natural microbial consortia. We show here that protoanemonin can be transformed by dienelactone hydrolase of Pseudomonas sp. strain B13 to cis-acetylacrylate. Although ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.180.2.400-402.1998

    authors: Brückmann M,Blasco R,Timmis KN,Pieper DH

    更新日期:1998-01-01 00:00:00

  • Pilus production in Acinetobacter baumannii is growth phase dependent and essential for natural transformation.

    abstract::Acinetobacter baumannii is a severe threat to human health as a frequently multidrug-resistant hospital-acquired pathogen. Part of the danger from this bacterium comes from its genome plasticity and ability to evolve quickly by taking up and recombining external DNA into its own genome in a process called natural comp...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.00034-21

    authors: Vesel N,Blokesch M

    更新日期:2021-01-25 00:00:00