Comparative genomics of the Pasteurella multocida toxin

Heat Labile ◽

Pasteurella multocida is a zoonotic pathogen whose genetic heterogeneity is well known. Five serogroups and 16 serotypes of P. multocida have been recognized thus far based on capsular polysaccharide typing and lipopolysaccharide typing, respectively. Progressive atrophic rhinitis in domestic pigs is caused by P. multocida strains containing toxA, which encodes a heat-labile toxin. In this study, by comparative analyses of the genomes of many strains, it has been shown that toxA is sparsely distributed in P. multocida. Furthermore, full-length homologs of P. multocida toxA were found only in two other bacterial species. It has also been shown that toxA is usually associated with a prophage. Among the toxA-containing prophages that were compared, an operon putatively encoding a type II restriction-modification system was present only in strains LFB3, HN01, and HN06. These results indicate that the selection and maintenance of the heat-labile toxin and the type II restriction-modification system are evolutionarily less favorable among P. multocida strains. Phylogenetic analysis using the alignment- and parameter-free method CVTree3 showed that deduced proteome sequences can be used as effectively as whole/core genome single nucleotide polymorphisms to group P. multocida strains in relation to their serotypes and/or genotypes.

Type II DNA restriction-modification system and an endonuclease from the ruminal bacterium Fibrobacter succinogenes S85.

Journal of Bacteriology ◽

10.1128/jb.174.16.5275-5283.1992 ◽

1992 ◽

Vol 174 (16) ◽

pp. 5275-5283 ◽

Cited By ~ 17

Author(s):

S F Lee ◽

C W Forsberg ◽

A M Gibbins

Keyword(s):

Fibrobacter Succinogenes ◽

Type Ii ◽

Ruminal Bacterium ◽

Modification System ◽

Dna Restriction ◽

Characterization of the archaeal, plasmid-encoded type II restriction-modification system MthTI from Methanobacterium thermoformicicum THF: homology to the bacterial NgoPII system from Neisseria gonorrhoeae.

Journal of Bacteriology ◽

10.1128/jb.174.17.5719-5726.1992 ◽

1992 ◽

Vol 174 (17) ◽

pp. 5719-5726 ◽

Cited By ~ 27

Author(s):

J Nölling ◽

W M de Vos

Keyword(s):

Neisseria Gonorrhoeae ◽

Type Ii ◽

Modification System ◽

Low-level expression of the Type II restriction–modification system confers potent bacteriophage resistance in Escherichia coli

DNA Research ◽

10.1093/dnares/dsaa003 ◽

2020 ◽

Vol 27 (1) ◽

Author(s):

Karolina Wilkowska ◽

Iwona Mruk ◽

Beata Furmanek-Blaszk ◽

Marian Sektas

Keyword(s):

Dna Methyltransferase ◽

Host Bacterium ◽

Type Ii ◽

Potential Conflict ◽

Modification System ◽

Biological Assays ◽

Highly Sensitive ◽

System Maintenance ◽

Abstract Restriction–modification systems (R–M) are one of the antiviral defense tools used by bacteria, and those of the Type II family are composed of a restriction endonuclease (REase) and a DNA methyltransferase (MTase). Most entering DNA molecules are usually cleaved by the REase before they can be methylated by MTase, although the observed level of fragmented DNA may vary significantly. Using a model EcoRI R–M system, we report that the balance between DNA methylation and cleavage may be severely affected by transcriptional signals coming from outside the R–M operon. By modulating the activity of the promoter, we obtained a broad range of restriction phenotypes for the EcoRI R–M system that differed by up to 4 orders of magnitude in our biological assays. Surprisingly, we found that high expression levels of the R–M proteins were associated with reduced restriction of invading bacteriophage DNA. Our results suggested that the regulatory balance of cleavage and methylation was highly sensitive to fluctuations in transcriptional signals both up- and downstream of the R–M operon. Our data provided further insights into Type II R–M system maintenance and the potential conflict within the host bacterium.

Species-Specific Type II Restriction-Modification System of Xylella fastidiosa Temecula1

Applied and Environmental Microbiology ◽

10.1128/aem.03034-09 ◽

2010 ◽

Vol 76 (12) ◽

pp. 4092-4095 ◽

Cited By ~ 17

Author(s):

Ayumi Matsumoto ◽

Michele M. Igo

Keyword(s):

Escherichia Coli ◽

Transformation Efficiency ◽

Xylella Fastidiosa ◽

Type Ii ◽

Modification System ◽

Species Specific ◽

ABSTRACT The transformation efficiency of Xylella fastidiosa can be increased by interfering with restriction by the strain-specific type II system encoded by the PD1607 and PD1608 genes. Here, we report results for two strategies: in vitro methylation using M.SssI and isolation of DNA from an Escherichia coli strain expressing the methylase PD1607.

MmeI: a minimal Type II restriction-modification system that only modifies one DNA strand for host protection

Nucleic Acids Research ◽

10.1093/nar/gkn711 ◽

2008 ◽

Vol 36 (20) ◽

pp. 6558-6570 ◽

Cited By ~ 40

Author(s):

Richard D. Morgan ◽

Tanya K. Bhatia ◽

Lindsay Lovasco ◽

Theodore B. Davis

Keyword(s):

Type Ii ◽

Modification System ◽

Host Protection ◽

Minimal Type ◽

Dna Strand ◽

Characterization of pECL18 and pKPN2: a proposed pathway for the evolution of two plasmids that carry identical genes for a Type II restriction-modification system

Molecular Genetics and Genomics ◽

10.1007/s00438-002-0644-y ◽

2002 ◽

Vol 267 (2) ◽

pp. 171-178 ◽

Cited By ~ 12

Author(s):

M. Zakharova ◽

I. Beletskaya ◽

M. Denjmukhametov ◽

T. Yurkova ◽

L. Semenova ◽

...

Keyword(s):

Type Ii ◽

Modification System ◽

Genome sequence of Pseudomonas aeruginosa PAO1161, a PAO1 derivative with the ICEPae1161 integrative and conjugative element

BMC Genomics ◽

10.1186/s12864-019-6378-6 ◽

2020 ◽

Vol 21 (1) ◽

Cited By ~ 2

Author(s):

Adam Kawalek ◽

Karolina Kotecka ◽

Magdalena Modrzejewska ◽

Jan Gawor ◽

Grazyna Jagura-Burdzy ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Genome Sequence ◽

Dna Methyltransferase ◽

Laboratory Strain ◽

Mercury Resistance ◽

Nucleotide Polymorphisms ◽

Modification System ◽

Integrative Conjugative Element ◽

Abstract Background Pseudomonas aeruginosa is a cause of nosocomial infections, especially in patients with cystic fibrosis and burn wounds. PAO1 strain and its derivatives are widely used to study the biology of this bacterium, however recent studies demonstrated differences in the genomes and phenotypes of derivatives from different laboratories. Results Here we report the genome sequence of P. aeruginosa PAO1161 laboratory strain, a leu-, RifR, restriction-modification defective PAO1 derivative, described as the host of IncP-8 plasmid FP2, conferring the resistance to mercury. Comparison of PAO1161 genome with PAO1-UW sequence revealed lack of an inversion of a large genome segment between rRNA operons and 100 nucleotide polymorphisms, short insertions and deletions. These included a change in leuA, resulting in E108K substitution, which caused leucine auxotrophy and a mutation in rpoB, likely responsible for the rifampicin resistance. Nonsense mutations were detected in PA2735 and PA1939 encoding a DNA methyltransferase and a putative OLD family endonuclease, respectively. Analysis of revertants in these two genes showed that PA2735 is a component of a restriction-modification system, independent of PA1939. Moreover, a 12 kb RPG42 prophage and a novel 108 kb PAPI-1 like integrative conjugative element (ICE) encompassing a mercury resistance operon were identified. The ICEPae1161 was transferred to Pseudomonas putida cells, where it integrated in the genome and conferred the mercury resistance. Conclusions The high-quality P. aeruginosa PAO1161 genome sequence provides a reference for further research including e.g. investigation of horizontal gene transfer or comparative genomics. The strain was found to carry ICEPae1161, a functional PAPI-1 family integrative conjugative element, containing loci conferring mercury resistance, in the past attributed to the FP2 plasmid of IncP-8 incompatibility group. This indicates that the only known member of IncP-8 is in fact an ICE.

Transcription regulation of the type II restriction-modification system AhdI

Nucleic Acids Research ◽

10.1093/nar/gkm1116 ◽

2008 ◽

Vol 36 (5) ◽

pp. 1429-1442 ◽

Cited By ~ 36

Author(s):

Ekaterina Bogdanova ◽

Marko Djordjevic ◽

Ioanna Papapanagiotou ◽

Tomasz Heyduk ◽

Geoff Kneale ◽

...

Keyword(s):

Transcription Regulation ◽

Type Ii ◽

Modification System ◽

Genetic Isolation of Meningococci of the Electrophoretic Type 37 Complex

Journal of Bacteriology ◽

10.1128/jb.183.8.2570-2575.2001 ◽

2001 ◽

Vol 183 (8) ◽

pp. 2570-2575 ◽

Cited By ~ 22

Author(s):

H. Claus ◽

J. Stoevesandt ◽

M. Frosch ◽

U. Vogel

Keyword(s):

Genetic Diversity ◽

Genomic Dna ◽

Bacterial Species ◽

Chromosomal Integration ◽

Genetic Isolation ◽

Differential Distribution ◽

Modification System ◽

Dna Coding ◽

ABSTRACT Neisseria meningitidis (the meningococcus) is a naturally competent bacterial species in which intra- and interspecific horizontal gene transfer is a major source of genetic diversity. In strains of the electrophoretic type 37 (ET-37) complex and of the A4 cluster, we identified genomic DNA coding for a novel restriction-modification system and for the tail of a previously unidentified prophage. Furthermore, a novel 7.2-kb DNA segment restricted to clones of the ET-37 complex and the A4 cluster was isolated and shown to occur both as a plasmid (pJS-B) and as a chromosomal integration. Neither the genomic loci nor pJS-B was present in ET-5 complex, lineage 3, or serogroup A meningococci. The differential distribution of the DNA segments described herein, as well as of opcA, porB, nmeAI, nmeBI, and nmeDIdescribed previously, supports the concept of genetic isolation of hypervirulent lineages responsible for most cases of serogroup C disease worldwide.