Regulation of gene expression in a type II restriction-modification system

Nagornykh, Maxim; Bogdanova, Ekaterina; Protsenko, A. S.; Zakharova, Marina; Solonin, Alexander S.; Severinov, Konstantin

doi:10.1134/s1022795408050037

Cited by 18 publications

(22 citation statements)

References 51 publications

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“…In certain RM systems, methylation of sites in the promoter region of the genes has been shown to impact expression of the RM genes (35). However, no BfuI recognition sites were found upstream of ORF 2755 or anywhere else in the ECII-specific cassette harboring the putative RM system.…”

Section: Resultsmentioning

confidence: 88%

A Novel Restriction-Modification System Is Responsible for Temperature-Dependent Phage Resistance in Listeria monocytogenes ECII

Kim

Dutta

Elhanafi

et al. 2012

Appl Environ Microbiol

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Listeria monocytogenes epidemic clone II (ECII) strains are unusual in being completely resistant to phage when grown at low temperatures (<30°C). In the current study we constructed and characterized a mariner-based mutant (J46C) of the ECII strain H7550-Cd S that lacked temperature-dependent resistance to phage. The transposon was localized in LMOh7858_2753 (open reading frame [ORF] 2753), a member of a 12-ORF genomic island unique to ECII strains. ORF 2753 and ORF 2754 exhibited homologies to restriction endonucleases and methyltransferases associated with type II restriction-modification (RM) systems. In silico-based predictions of the recognition site for this putative RM system were supported by resistance of DNA from ECII strains to digestion by BfuI, a type II restriction enzyme specific for GTATCC (N6/5). Similarly to J46C, a mutant harboring an in-frame deletion of ORF 2753 was susceptible to phage regardless of temperature of growth (25°C or 37°C). Genetic complementation restored phage resistance in 25°C-grown cells of ORF 2753 mutants. Reverse transcription (RT) and quantitative realtime PCR data suggested enhanced transcription of ORF 2753 at low temperatures (<25°C) compared to 37°C. In contrast, available transcriptional data suggested that the putative methyltransferase (ORF 2754) was constitutively expressed at all tested temperatures (4 to 37°C). Thus, temperature-dependent resistance of L. monocytogenes ECII to phage is mediated by temperature-dependent expression of the restriction endonuclease associated with a novel RM system (LmoH7) unique to this epidemic clone.L isteria monocytogenes remains a major food-borne pathogen for at-risk populations, including pregnant women and their fetuses, the elderly, and patients with compromised immunity. Even though listeriosis is relatively infrequent, it is accompanied with high mortality and severe symptoms, such as septicemia, meningitis, and stillbirths (38,45).A number of genotypic tools have revealed that strains from different outbreaks can be closely related, constituting epidemic clones (6,8,9,10,22,42,50). Epidemic clone I (ECI) and epidemic clone II (ECII) have been most extensively characterized. ECI strains have been responsible for numerous outbreaks of listeriosis in North America and Europe, with the first documented outbreak being the coleslaw-associated outbreak in the Maritime Provinces, Canada (8, 9, 22, 42). In contrast, ECII was not recognized until the 1998-1999 multistate outbreak of listeriosis in the United States, which was attributed to contaminated hot dogs. ECII was subsequently implicated in another multistate outbreak in 2002 that involved contaminated turkey deli meats, as well as in an outbreak in Belgium (4, 5, 23, 52; M. Yde, personal communication).A special phenotypic characteristic of ECII strains is their temperature-dependent resistance to phage. In contrast to all other screened Listeria strains, ECII strains failed to form plaques when the bacteria were grown at temperatures below 30°C but did so following gr...

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Section: Resultsmentioning

confidence: 88%

A Novel Restriction-Modification System Is Responsible for Temperature-Dependent Phage Resistance in Listeria monocytogenes ECII

Kim

Dutta

Elhanafi

et al. 2012

Appl Environ Microbiol

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“…RM recognition sites in the vicinity of the promoter region play an important role in transcription control of some RM systems by reducing transcription when the sites are methylated (26). The sole LmoJ2 recognition site (GCAGC) in LmoJ2 was located within the methyltransferase gene (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The deduced product of lmoJ3R (designated R.LmoJ3P) belonged to a protein family represented by the restriction endonuclease NgoFVII (recognition sequence GCSGC, where S ϭ C or G) (pfam09565) (33). The deduced product of the third ORF, lmoJ3C (designated C.LmoJ3P), harbored a helix-turn-helix motif (pfam01381), suggesting that it is a DNAbinding protein that may function as a control (C) protein in the regulation of the RM cassette (26).…”

Section: Resultsmentioning

confidence: 99%

Two Novel Type II Restriction-Modification Systems Occupying Genomically Equivalent Locations on the Chromosomes of Listeria monocytogenes Strains

Lee

Ward

Siletzky

et al. 2012

Appl Environ Microbiol

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ABSTRACTListeria monocytogenesis responsible for the potentially life-threatening food-borne disease listeriosis. One epidemic-associated clonal group ofL. monocytogenes, epidemic clone I (ECI), harbors a Sau3AI-like restriction-modification (RM) system also present in the same genomic region in certain strains of other lineages. In this study, we identified and characterized two other, novel type II RM systems, LmoJ2 and LmoJ3, at this same locus. LmoJ2 and LmoJ3 appeared to recognize GCWGC (W = A or T) and GCNGC, respectively. Both RM systems consisted of genes with GC content below the genome average and were in the same genomic region in strains of different serotypes and lineages, suggesting site-specific horizontal gene transfer. Genomic DNA from the LmoJ2 and LmoJ3 strains grown at various temperatures (4 to 42°C) was resistant to digestion with restriction enzymes recognizing GCWGC or GCNGC, indicating that the methyltransferases were expressed under these conditions. Phages propagated in an LmoJ2-harboring strain exhibited moderately increased infectivity for this strain at 4 and 8°C but not at higher temperatures, while phages propagated in an LmoJ3 strain had dramatically increased infectivity for this strain at all temperatures. Among the sequencedListeriaphages, lytic phages possessed significantly fewer recognition sites for these RM systems than lysogenic phages, suggesting that in lytic phages sequence content evolved toward reduced susceptibility to such RM systems. The ability of LmoJ2 and LmoJ3 to protect against phages may affect the efficiency of phages as biocontrol agents forL. monocytogenesstrains harboring these RM systems.

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“…To minimize the possibility of such an outcome, R-M systems evolved mechanisms helping to ensure that endonuclease expression is activated only after the host DNA is completely modified by the methylase. Several distinct mechanisms that ensure delayed appearance of the restriction endonuclease activity have been described (2). Numerous R-M systems encode an additional protein, the product of a C (control) gene, which orchestrates cooperative time-delayed switching from methylase gene transcription to endonuclease gene transcription (3–6).…”

Section: Introductionmentioning

confidence: 99%

Regulation of gene expression in restriction-modification system Eco29kI

Nagornykh

Zakharova

Protsenko

et al. 2011

Nucleic Acids Research

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The Eco29kI restriction-modification (R-M) system consists of two partially overlapping genes, eco29kIR, encoding a restriction endonuclease and eco29kIM, encoding methyltransferase. The two genes are thought to form an operon with the eco29kIR gene preceding the eco29kIM gene. Such an organization is expected to complicate establishment of plasmids containing this R-M system in naive hosts, since common logic dictates that methyltransferase should be synthesized first to protect the DNA from cleavage by the endonuclease. Here, we characterize the Eco29kI gene transcription. We show that a separate promoter located within the eco29kIR gene is sufficient to synthesize enough methyltransferase to completely modify host DNA. We further show that transcription from two intragenic antisense promoters strongly decreases the levels of eco29kIR gene transcripts. The antisense transcripts act by preventing translation initiation from the bicistronic eco29kIR–eco29kIM mRNA and causing its degradation. Both eco29kIM and antisense promoters are necessary for Eco29kI genes establishment and/or stable maintenance, indicating that they jointly contribute to coordinated expression of Eco29kI genes.

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Regulation of gene expression in a type II restriction-modification system

Cited by 18 publications

References 51 publications

A Novel Restriction-Modification System Is Responsible for Temperature-Dependent Phage Resistance in Listeria monocytogenes ECII

A Novel Restriction-Modification System Is Responsible for Temperature-Dependent Phage Resistance in Listeria monocytogenes ECII

Two Novel Type II Restriction-Modification Systems Occupying Genomically Equivalent Locations on the Chromosomes of Listeria monocytogenes Strains

Regulation of gene expression in restriction-modification system Eco29kI

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