scholarly journals High allelic diversity in the methyltransferase gene of a phase variable type III restriction-modification system has implications for the fitness of Haemophilus influenzae

2006 ◽  
Vol 34 (14) ◽  
pp. 4046-4059 ◽  
Author(s):  
Christopher D. Bayliss ◽  
Martin J. Callaghan ◽  
E. Richard Moxon
Keyword(s):  
Haemophilus Influenzae ◽  
Allelic Diversity ◽  
Phase Variable ◽  
Modification System ◽  
Type Iii ◽  
Variable Type ◽  
Restriction Modification System ◽  
Methyltransferase Gene ◽  
High Allelic Diversity ◽  
Restriction Modification

scholarly journals A Type III restriction–modification system in Mycoplasma mycoides subsp. capri

Open Biology ◽  
2012 ◽  
Vol 2 (10) ◽  
pp. 120115 ◽  
Author(s):  
Mikkel A. Algire ◽  
Michael G. Montague ◽  
Sanjay Vashee ◽  
Carole Lartigue ◽  
Chuck Merryman
Keyword(s):  
Phase Variable ◽  
Coding Region ◽  
Dinucleotide Repeats ◽  
Modification System ◽  
Type Iii ◽  
Restriction Modification System ◽  
Mycoplasma Mycoides ◽  
Methyltransferase Gene ◽  
Translational Termination ◽  
Restriction Modification

The sequenced genome of Mycoplasma mycoides subsp. capri revealed the presence of a Type III restriction–modification system (MmyCI). The methyltransferase (modification) subunit of MmyCI (M.MmyCI) was shown to recognize the sequence 5′-TGAG-3′ and methylate the adenine. The coding region of the methyltransferase gene contains 12 consecutive AG dinucleotide repeats that result in a translational termination at a TAA codon immediately beyond the repeat region. This strain does not have MmyCI activity. A clone was found with 10 AG repeats such that the gene is in frame, and this strain has MmyCI activity, suggesting that the expression of the MmyCI methyltransferase may be phase variable.

scholarly journals Transcriptional Phase Variation of a Type III Restriction-Modification System in Helicobacter pylori

2002 ◽  
Vol 184 (23) ◽  
pp. 6615-6623 ◽  
Author(s):  
Nicolette de Vries ◽  
Dirk Duinsbergen ◽  
Ernst J. Kuipers ◽  
Raymond G. J. Pot ◽  
Patricia Wiesenekker ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Phase Variation ◽  
Transcriptional Level ◽  
Length Variation ◽  
Phase Variable ◽  
Modification System ◽  
Type Iii ◽  
Restriction Modification System ◽  
H Pylori ◽  
Restriction Modification

ABSTRACT Phase variation is important in bacterial pathogenesis, since it generates antigenic variation for the evasion of immune responses and provides a strategy for quick adaptation to environmental changes. In this study, a Helicobacter pylori clone, designated MOD525, was identified that displayed phase-variable lacZ expression. The clone contained a transcriptional lacZ fusion in a putative type III DNA methyltransferase gene (mod, a homolog of the gene JHP1296 of strain J99), organized in an operon-like structure with a putative type III restriction endonuclease gene (res, a homolog of the gene JHP1297), located directly upstream of it. This putative type III restriction-modification system was common in H. pylori, as it was present in 15 out of 16 clinical isolates. Phase variation of the mod gene occurred at the transcriptional level both in clone MOD525 and in the parental H. pylori strain 1061. Further analysis showed that the res gene also displayed transcriptional phase variation and that it was cotranscribed with the mod gene. A homopolymeric cytosine tract (C tract) was present in the 5′ coding region of the res gene. Length variation of this C tract caused the res open reading frame (ORF) to shift in and out of frame, switching the res gene on and off at the translational level. Surprisingly, the presence of an intact res ORF was positively correlated with active transcription of the downstream mod gene. Moreover, the C tract was required for the occurrence of transcriptional phase variation. Our finding that translation and transcription are linked during phase variation through slipped-strand mispairing is new for H. pylori.

Phase variation in a type III restriction-modification system of Helicobacter pylori

2000 ◽  
Vol 118 (4) ◽  
pp. A736 ◽  
Author(s):  
Nicolette Vries de ◽  
Dirk Duinsbergen ◽  
Ernst J. Kuipers ◽  
Patricia Wiesenekker ◽  
Christina M. Vandenbroucke-Grauls ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Phase Variation ◽  
Modification System ◽  
Type Iii ◽  
Restriction Modification System ◽  
Restriction Modification

scholarly journals Analysis of a phase-variable restriction modification system of the human gut symbiont Bacteroides fragilis

2020 ◽  
Vol 48 (19) ◽  
pp. 11040-11053
Author(s):  
Nadav Ben-Assa ◽  
Michael J Coyne ◽  
Alexey Fomenkov ◽  
Jonathan Livny ◽  
William P Robins ◽  
...  
Keyword(s):  
Bacteroides Fragilis ◽  
Surface Proteins ◽  
Type I ◽  
Phase Variable ◽  
Modification System ◽  
Restriction Modification System ◽  
Recognition Sites ◽  
Specificity Protein ◽  
Restriction Modification

Abstract The genomes of gut Bacteroidales contain numerous invertible regions, many of which contain promoters that dictate phase-variable synthesis of surface molecules such as polysaccharides, fimbriae, and outer surface proteins. Here, we characterize a different type of phase-variable system of Bacteroides fragilis, a Type I restriction modification system (R-M). We show that reversible DNA inversions within this R-M locus leads to the generation of eight specificity proteins with distinct recognition sites. In vitro grown bacteria have a different proportion of specificity gene combinations at the expression locus than bacteria isolated from the mammalian gut. By creating mutants, each able to produce only one specificity protein from this region, we identified the R-M recognition sites of four of these S-proteins using SMRT sequencing. Transcriptome analysis revealed that the locked specificity mutants, whether grown in vitro or isolated from the mammalian gut, have distinct transcriptional profiles, likely creating different phenotypes, one of which was confirmed. Genomic analyses of diverse strains of Bacteroidetes from both host-associated and environmental sources reveal the ubiquity of phase-variable R-M systems in this phylum.

scholarly journals NmeSI Restriction-Modification System Identified by Representational Difference Analysis of a HypervirulentNeisseria meningitidis Strain

2001 ◽  
Vol 69 (3) ◽  
pp. 1816-1820 ◽  
Author(s):  
Aldert Bart ◽  
Yvonne Pannekoek ◽  
Jacob Dankert ◽  
Arie van der Ende
Keyword(s):  
Open Reading Frames ◽  
Representational Difference Analysis ◽  
Chromosomal Dna ◽  
Modification System ◽  
Difference Analysis ◽  
Restriction Modification System ◽  
Methyltransferase Gene ◽  
Specific Restriction ◽  
Restriction Modification ◽  
Reading Frames

ABSTRACT Neisseria meningitidis is a gram-negative bacterium that may cause meningitis, sepsis, or both. The increase in the incidence of meningococcal disease in various countries in the past 2 decades is mainly due the genotypically related lineage III meningococci. The chromosomal DNA differences between lineage III strains and non-lineage III strains were identified using representational difference analysis. Thus, a 1.8-kb locus that is specific for lineage III meningococci was identified. The locus contains three open reading frames encoding the NmeSI restriction-modification system. The methyltransferase gene was cloned and expressed in Escherichia coli. Site AGTACT was found to be modified by the enzyme. In conclusion, lineage III strains differ from endemic strains by the presence of a specific restriction-modification system. This restriction-modification system may contribute to the clonal and hypervirulent character of lineage III strains by influencing horizontal gene transfer and transcription.

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