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 Bacterioljournal_title
Journal of bacteriologyauthors
Cherry JLdoi
10.1128/JB.00371-18subject
Has Abstractpub_date
2018-11-26 00:00:00issue
24eissn
0021-9193issn
1098-5530pii
JB.00371-18journal_volume
200pub_type
杂志文章abstract::Induction of colicin la at a high temperature (42 C) was demonstrated in a wild strain of Shigella sonnei. After transfer of the Col factor, a similar effect was observed in those recipient cells acquiring colicinogeny. The induction is suggested to be due to the presence of a thermosensitive colicin repressor. The wi...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.106.3.720-723.1971
更新日期:1971-06-01 00:00:00
abstract::Bacillus subtilis cells cannot sporulate in the presence of catabolites such as glucose. During the analysis of Tn10-generated mutants, we found that deletion of the C-terminal region of the tnrA gene, which encodes a global regulator that positively regulates a number of genes in response to nitrogen limitation, resu...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.182.17.5009-5012.2000
更新日期:2000-09-01 00:00:00
abstract::Chronic lung infections in cystic fibrosis (CF) could be treated more effectively if the effects of antimicrobials on pathogens in situ were known. Here, we compared changes in the microbial community composition and pathogen growth rates in longitudinal studies of seven pediatric CF patients undergoing intravenous an...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00365-18
更新日期:2018-11-26 00:00:00
abstract::Choline-containing teichoic acid seems to be essential for the adsorption of bacteriophage Dp-1 to pneumococci. This conclusion is based on the following observations: In contrast to pneumococci grown in choline-containing medium, cells grown in medium containing ethanolamine or other submethylated aminoalcohols inste...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.151.3.1581-1590.1982
更新日期:1982-09-01 00:00:00
abstract::The elemental composition of individual cells of rapidly frozen and cryosectioned Escherichia coli B was measured with electron optical microanalytic methods. The Ca content was high (26.2 mmol/kg) in a 10-nm-wide region of the cell envelope. Amounts of cytoplasmic Ca in actively dividing cells were significantly high...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.167.3.935-939.1986
更新日期:1986-09-01 00:00:00
abstract::The genome of Corynebacterium glutamicum type strain ATCC 13032 (accession number BX927147) contains three prophages, CGP1, CGP2, and CGP3. We recently observed that many genes within the CGP3 prophage region have increased mRNA levels in a dtxR deletion mutant that lacks the master regulator of iron homeostasis (J. W...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00310-08
更新日期:2008-07-01 00:00:00
abstract::Phosphorylation of lipopolysaccharide (LPS) from a psychrotrophic bacterium, Pseudomonas syringae, from Antarctica was studied by using sucrose gradient-separated membrane fractions. The bacterium was found to possess an LPS kinase which could phosphorylate more LPS postsynthetically at higher temperatures. The phosph...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.176.14.4243-4249.1994
更新日期:1994-07-01 00:00:00
abstract::Stalk formation is a novel pattern of multicellular organization. Yeast cells which survive UV irradiation form colonies that grow vertically to form very long (0.5 to 3.0 cm) and thin (0.5 to 4 mm in diameter) multicellular structures. We describe the conditions required to obtain these stalk-like structures reproduc...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.180.15.3992-3996.1998
更新日期:1998-08-01 00:00:00
abstract::The complete Bacillus subtilis genome contains two genes with the potential to encode glutamate dehydrogenase (GlutDH) enzymes. Mutations in these genes were constructed and characterized. The rocG gene proved to encode a major GlutDH whose synthesis was induced in media containing arginine or ornithine or, to a lesse...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:
更新日期:1998-12-01 00:00:00
abstract::The draft genome of Methylacidiphilum fumariolicum SolV, a thermoacidophilic methanotroph of the phylum Verrucomicrobia, is presented. Annotation revealed pathways for one-carbon, nitrogen, and hydrogen catabolism and respiration together with central metabolic pathways. The genome encodes three orthologues of particu...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00501-12
更新日期:2012-07-01 00:00:00
abstract::Sphingomonas sp. strain ATCC 31555 can produce an anionic heteropolysaccharide, welan gum, which shows excellent stability and viscosity retention even at high temperatures. Here we present a 4.0-Mb assembly of its genome sequence. We have annotated 10 coding sequences (CDSs) responsible for the welan gum biosynthesis...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.01486-12
更新日期:2012-11-01 00:00:00
abstract::Heat, salinity, or osmotic stress influenced protein synthesis in nitrogen-fixing Anabaena sp. strain L-31. Salinity and osmotic stresses were identical and specifically induced 15 polypeptides. Four polypeptides were unique to heat shock, and four other polypeptides were induced under every stress. The results demons...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.171.9.5187-5189.1989
更新日期:1989-09-01 00:00:00
abstract::MreC and MreD, along with the actin homologue MreB, are required to maintain the shape of rod-shaped bacteria. The depletion of MreCD in rod-shaped bacteria leads to the formation of spherical cells and the accumulation of suppressor mutations. Ovococcus bacteria, such as Streptococcus pneumoniae, lack MreB homologues...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.05245-11
更新日期:2011-08-01 00:00:00
abstract::Grunberg, E. (Hoffman-La Roche, Inc., Nutley, N.J.), and R. Cleeland. Fluorescence and viability of Proteus mirabilis stained directly with fluorescein isothiocyanate. J. Bacteriol. 92:23-27. 1966.-Washed cell suspensions of Proteus mirabilis, under the proper conditions, stained well with fluorescein isothiocyanate w...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.92.1.23-27.1966
更新日期:1966-07-01 00:00:00
abstract::The general stress regulon of Bacillus subtilis comprises approximately 200 genes and is under the control of the alternative sigma factor σ(B). The activation of σ(B) occurs in response to multiple physical stress stimuli as well as energy starvation conditions. The expression of the general stress proteins provides ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00528-12
更新日期:2012-07-01 00:00:00
abstract::A fusion between lacZ and ftsZ of Escherichia coli was constructed to obtain a beta-galactosidase-FtsZ fusion protein. This fusion protein was used to raise antibodies against cell division protein FtsZ. Six monoclonal antibodies were obtained, and they reacted with FtsZ from cytoplasm and membrane fractions. The epit...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.176.7.1886-1893.1994
更新日期:1994-04-01 00:00:00
abstract::An attempt was made to explain the puzzling observation that in bacteria 2,6-diaminopurine can replace guanine for guanineless mutants and for xanthineless mutants (both of which can make adenosine monophosphate de novo) but not for nonexacting purine auxotrophs (which cannot make adenosine monophosphate de novo). The...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.95.2.565-571.1968
更新日期:1968-02-01 00:00:00
abstract::The pbpB gene product penicillin-binding protein 3 (PBP3) of Escherichia coli is one of the major targets of beta-lactam antibiotics. At the permissive temperature, the temperature-sensitive pbpBr1 mutant, which was obtained after selection for increased resistance to cephalexin, shows a dramatic change in shape which...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.170.10.4828-4837.1988
更新日期:1988-10-01 00:00:00
abstract::The extent of change in cytoplasmic proteins which accompanies yeast-to-mycelium morphogenesis of Candida albicans was analyzed by two-dimensional gel electrophoresis. Pure cultures of yeasts and true hyphae (i.e., without concomitant production of pseudohyphae) were grown in a synthetic low-sulfate medium. The two st...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.144.1.258-273.1980
更新日期:1980-10-01 00:00:00
abstract::Tabak, Henry H. (Robert A. Taft Sanitary Engineering Center, Cincinnati, Ohio), Cecil W. Chambers, and Paul W. Kabler. Microbial metabolism of aromatic carbon compounds. I. Decomposition of phenolic compounds and aromatic hydrocarbons by phenol-adapted bacteria. J. Bacteriol. 87:910-919. 1964.-Bacteria from soil and r...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.87.4.910-919.1964
更新日期:1964-04-01 00:00:00
abstract::In both prokaryotes and eukaryotes, hydroxyurea is suggested to inhibit DNA replication by inactivating ribonucleotide reductase and depleting deoxyribonucleoside triphosphate pools. In this study, we show that the inhibition of replication in Escherichia coli is transient even at concentrations of 0.1 M hydroxyurea a...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00713-17
更新日期:2018-02-23 00:00:00
abstract::The cell wall lipopolysaccharides from 17 species belonging to the genus Xanthomonas were extracted from the cells with hot 45% phenol. After purification, the components of the polysaccharide were obtained by acid hydrolysis of the lipopolysaccharide and were quantitatively assayed. Data obtained show that all prepar...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.95.3.980-982.1968
更新日期:1968-03-01 00:00:00
abstract::Lyons, A. J., Jr. (Northern Regional Research Laboratory, Peoria, Ill.) and T. G. Pridham. Proposal to designate strain ATCC 3004 (IMRU 3004) as the neotype strain of Streptomyces albus (Rossi-Doria) Waksman and Henrici. J. Bacteriol. 83:370-380. 1962.-It is proposed that strain ATCC 3004 (IMRU 3004) be designated hen...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.83.2.370-380.1962
更新日期:1962-02-01 00:00:00
abstract::Archaea, constituting the third primary domain of life, harbor a basal transcription apparatus of the eukaryotic type, whereas curiously, a large fraction of the potential transcription regulation factors appear to be of the bacterial type. To date, little information is available on these predicted regulators and on ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.182.13.3661-3672.2000
更新日期:2000-07-01 00:00:00
abstract::In a previous study, we showed that in bacteroids, transcription of the inducible nod genes does not occur and expression of nodD is decreased by 65% (H. R. M. Schlaman, B. Horvath, E. Vijgenboom, R.J.H. Okker, and B. J. J. Lugtenberg, J. Bacteriol. 173:4277-4287, 1991). In the present study, we show, using gel retard...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.174.19.6109-6116.1992
更新日期:1992-10-01 00:00:00
abstract::Sulfate-utilizing revertants of a cysteine auxotroph of Salmonella pullorum have been found that cause an accumulation in growth medium of a sulfur compound more oxidized than sulfide. The sulfur compound was presumptively identified as sulfite by the formation of a colored complex in the presence of basic fuchsin and...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.100.1.365-369.1969
更新日期:1969-10-01 00:00:00
abstract::The two-component system SaeRS of Staphylococcus aureus is closely involved in the regulation of major virulence factors. However, little is known about the signals leading to saeRS activation. A total of four overlapping transcripts (T1 to T4) from three different transcription starting points are expressed in the sa...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.01927-07
更新日期:2008-05-01 00:00:00
abstract::We previously reported that the methicillin resistance gene mecA is carried by a novel type of mobile genetic element, SCCmec (staphylococcal cassette chromosome mec), in the chromosome of methicillin-resistant Staphylococcus aureus (MRSA). These elements are precisely excised from the chromosome and integrated into a...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.185.9.2711-2722.2003
更新日期:2003-05-01 00:00:00
abstract::A periplasmic protein essential for the function of the oligopeptide transport system of Salmonella typhimurium was identified. This protein, encoded by the oppA gene, is one of the most abundant proteins in the periplasm and, with an apparent molecular weight of 52,000, is considerably larger than any other known per...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.155.3.1434-1438.1983
更新日期:1983-09-01 00:00:00
abstract::Many microbes coexist within biofilms, or multispecies communities of cells encased in an extracellular matrix. However, little is known about the microbe-microbe interactions relevant for creating these structures. In this study, we explored a striking dual-species biofilm between Bacillus subtilis and Pantoea agglom...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00670-18
更新日期:2019-08-22 00:00:00