Systematic prediction of control proteins and their DNA binding sites

Сорокин, В. В.; Severinov, Konstantin; Gelfand, Mikhail S.

doi:10.1093/nar/gkn931

Cited by 33 publications

(60 citation statements)

References 30 publications

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“…Kita et al (2002) have previously identified the recognition sequence of C.EcoO109I as a 15 bp sequence comprising two palindromic pentanucleotides separated by a nonbinding pentanucleotide sequence, 5 0 -CTAAG(N 5 )CTTAG-3 0 , located 47 bp upstream of the C gene start codon. This conforms to the sequence motif identified for both C.Csp231I and C.EcoO109I by bioinformatic analysis (Sorokin et al, 2009).…”

Section: Introductionsupporting

confidence: 88%

“…Controller proteins have recently been categorized on the basis of ten distinct DNA-recognition motifs (Sorokin et al, 2009). To date, the structures of three C proteins have been reported (McGeehan et al, 2005(McGeehan et al, , 2008Sawaya et al, 2005); all are highly homologous proteins with similar folds and with similar DNA-recognition sites.…”

Section: Introductionmentioning

confidence: 99%

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Overexpression, purification and preliminary X-ray diffraction analysis of the controller protein C.Csp231I fromCitrobactersp. RFL231

2009

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Restriction-modification controller proteins play an essential role in regulating the temporal expression of restriction-modification genes. The controller protein C.Csp231I represents a new class of controller proteins. The gene was sublconed to allow overexpression in Escherichia coli. The protein was purified to homogeneity and crystallized using the hanging-drop vapour-diffusion method. The crystals diffracted to 2.0 Å resolution and belonged to space group P2 1. An electrophoretic mobility-shift assay provided evidence of strong binding of C.Csp231I to a sequence located upstream of the csp231IC start codon. crystallization communications Acta Cryst. (2009). F65, 898-901 Streeter et al. C.Csp231i 901 Figure 5 Self-rotation function showing NCS. The self-rotation function is shown using a angle of 180 and was calculated using data in the resolution range 20.0-4.0 Å. The radius of integration was 35 Å .

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Section: Introductionsupporting

confidence: 88%

Section: Introductionmentioning

confidence: 99%

Overexpression, purification and preliminary X-ray diffraction analysis of the controller protein C.Csp231I fromCitrobactersp. RFL231

2009

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“…The GC contents of ORF 2753, ORF 2754, and ORF 2755 were 31 to 32%, noticeably lower than the average for the genome of L. monocytogenes H7858 (38%) (36). The size of the deduced C-protein (83 amino acids) is within the range of other C-proteins (48).…”

Section: Resultsmentioning

confidence: 75%

“…The ORF upstream of ORF 2754 (LMOh7858_2755; ORF 2755) belonged to the helix-turn-helix DNA-binding xenobiotic response element family (XRE) of transcriptional regulators (accession number cl09100) and may correspond to the regulatory control (C) protein associated with several RM systems (26,33,43,48,51,54). The GC contents of ORF 2753, ORF 2754, and ORF 2755 were 31 to 32%, noticeably lower than the average for the genome of L. monocytogenes H7858 (38%) (36).…”

Section: Resultsmentioning

confidence: 99%

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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“…However, the degree of sequence homology between species is moderate and the internal symmetry within and between ‘C-boxes’ is also weak in most C/R promoters (16). Moreover, the proposed 3-bp ‘spacers’ within the left and right operator sequences are also largely conserved between species, the consensus sequence being TAT.…”

Section: Introductionmentioning

confidence: 99%

The structural basis of differential DNA sequence recognition by restriction–modification controller proteins

Ball

McGeehan

Streeter

et al. 2012

Nucleic Acids Research

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Controller (C) proteins regulate the expression of restriction–modification (RM) genes in a wide variety of RM systems. However, the RM system Esp1396I is of particular interest as the C protein regulates both the restriction endonuclease (R) gene and the methyltransferase (M) gene. The mechanism of this finely tuned genetic switch depends on differential binding affinities for the promoters controlling the R and M genes, which in turn depends on differential DNA sequence recognition and the ability to recognize dual symmetries. We report here the crystal structure of the C protein bound to the M promoter, and compare the binding affinities for each operator sequence by surface plasmon resonance. Comparison of the structure of the transcriptional repression complex at the M promoter with that of the transcriptional activation complex at the R promoter shows how subtle changes in protein–DNA interactions, underpinned by small conformational changes in the protein, can explain the molecular basis of differential regulation of gene expression.

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Systematic prediction of control proteins and their DNA binding sites

Cited by 33 publications

References 30 publications

Overexpression, purification and preliminary X-ray diffraction analysis of the controller protein C.Csp231I fromCitrobactersp. RFL231

Overexpression, purification and preliminary X-ray diffraction analysis of the controller protein C.Csp231I fromCitrobactersp. RFL231

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

The structural basis of differential DNA sequence recognition by restriction–modification controller proteins

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