Cloning and characterization of the BglII restriction–modification system reveals a possible evolutionary footprint

Anton, Brian P.; Heiter, Daniel F.; Benner, Jack S.; Hess, Emma Jean; Greenough, Lucia; Moran, Laurie S.; Slatko, Barton E.; Brooks, Joan E.

doi:10.1016/s0378-1119(96)00638-5

Cited by 58 publications

(42 citation statements)

References 33 publications

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“…The results of the transcription assays are consistent with those of previous studies that implicate C proteins as stimulators of REase gene expression (5,13,31,36,48,58,59). However, the present study provides the first mechanistic evidence that C ⅐ PvuII is a DNA-binding protein that binds to the C box and that autogenous activation by C ⅐ PvuII of the polycistronic pvuIICR promoter contributes to the temporal regulation of pvuIIR expression.…”

Section: Discussionsupporting

confidence: 92%

“…The C proteins, including C ⅐ PvuII, act in trans to stimulate the expression of REase genes (5,13,31,36,59). This stimulation must be strong because, when pvuIIC is inactivated, pvuIIR expression is so low that pvuIIR ϩ pvuIIM cells are viable (though mutants accumulate) (58).…”

Section: ⅐ Pvuii Mediates Temporal Control Of the Pvuii Genesmentioning

confidence: 99%

“…Furthermore, there is some cross-complementation between the C genes from different restriction-modification systems (31,36). New members of this family continue to be identified (5).…”

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confidence: 99%

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Role and Mechanism of Action of C · Pvu II, a Regulatory Protein Conserved among Restriction-Modification Systems

et al. 2000

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The PvuII restriction-modification system is a type II system, which means that its restriction endonuclease and modification methyltransferase are independently active proteins. The PvuII system is carried on a plasmid, and its movement into a new host cell is expected to be followed initially by expression of the methyltransferase gene alone so that the new host's DNA is protected before endonuclease activity appears. Previous studies have identified a regulatory gene (pvuIIC) between the divergently oriented genes for the restriction endonuclease (pvuIIR) and modification methyltransferase (pvuIIM), with pvuIIC in the same orientation as and partially overlapping pvuIIR. The product of pvuIIC, C ⅐ PvuII, was found to act in trans and to be required for expression of pvuIIR. In this study we demonstrate that premature expression of pvuIIC prevents establishment of the PvuII genes, consistent with the model that requiring C ⅐ PvuII for pvuIIR expression provides a timing delay essential for protection of the new host's DNA. We find that the opposing pvuIIC and pvuIIM transcripts overlap by over 60 nucleotides at their 5 ends, raising the possibility that their hybridization might play a regulatory role. We furthermore characterize the action of C ⅐ PvuII, demonstrating that it is a sequence-specific DNA-binding protein that binds to the pvuIIC promoter and stimulates transcription of both pvuIIC and pvuIIR into a polycistronic mRNA. The apparent location of C ⅐ PvuII binding, overlapping the ؊10 promoter hexamer and the pvuIICR transcriptional starting points, is highly unusual for transcriptional activators.The bacterial type II restriction-modification systems include a DNA modification methyltransferase (MTase) and a restriction endonuclease (REase), both of which act independently on the same DNA sequence (65). The REase cleaves duplex DNA sequences in the absence of sequence-specific DNA modification by the MTase. These systems can defend bacterial cells against viral infection, although other functional roles have also been proposed (45). Restriction-modification systems have provided an important focus for studies of molecular recognition. Biochemical and crystallographic analyses are yielding significant insights into the mechanisms of sequence recognition and catalytic activity of these proteins (3,18,50,66).

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Section: Discussionsupporting

confidence: 92%

Section: ⅐ Pvuii Mediates Temporal Control Of the Pvuii Genesmentioning

confidence: 99%

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Role and Mechanism of Action of C · Pvu II, a Regulatory Protein Conserved among Restriction-Modification Systems

et al. 2000

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“…We routinely search the microbial genome database (www.ncbi.nlm.nih.gov/cgi-bin/Entrez/genom_table_cgi) by using the NCBI BLAST server (2,29) in an attempt to find new members of the C protein family of transcriptional regulators among RM systems (3,11,27,59,68,69,72,73). One such match, in S. enterica serovar Paratyphi A (Genome Sequencing Center, personal communication; genome.wustl.edu /gsc/Projects/bacterial/paratyphi/paratyphi.shtml), was flanked by methyltransferase and restriction endonuclease genes, both of which surprisingly showed very close relationship to another RM system cloned in this laboratory-PvuII (10).…”

Section: Resultsmentioning

confidence: 99%

Mobility of a Restriction-Modification System Revealed by Its Genetic Contexts in Three Hosts

et al. 2002

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The flow of genes among prokaryotes plays a fundamental role in shaping bacterial evolution, and restriction-modification systems can modulate this flow. However, relatively little is known about the distribution and movement of restriction-modification systems themselves. We have isolated and characterized the genes for restriction-modification systems from two species of Salmonella, S. enterica serovar Paratyphi A and S. enterica serovar Bareilly. Both systems are closely related to the PvuII restriction-modification system and share its target specificity. In the case of S. enterica serovar Paratyphi A, the restriction endonuclease is inactive, apparently due to a mutation in the subunit interface region. Unlike the chromosomally located Salmonella systems, the PvuII system is plasmid borne. We have completed the sequence characterization of the PvuII plasmid pPvu1, originally from Proteus vulgaris, making this the first completely sequenced plasmid from the genus Proteus. Despite the pronounced similarity of the three restriction-modification systems, the flanking sequences in Proteus and Salmonella are completely different. The SptAI and SbaI genes lie between an equivalent pair of bacteriophage P4-related open reading frames, one of which is a putative integrase gene, while the PvuII genes are adjacent to a mob operon and a XerCD recombination (cer) site.Restriction-modification (RM) systems are nearly ubiquitous among bacteria (both eubacteria and archaea). To date, the only complete bacterial genome sequences lacking candidate RM systems are from the obligate intracellular parasites Chlamydia and Rickettsia. Chlamydia trachomatis is the only known cellular organism that lacks an S-adenosyl-L-methionine (AdoMet) synthetase (63), and a type II RM system with separately active endonuclease and AdoMet-dependent methyltransferase proteins could be dangerous in this context. The other bacterial genomes have between 1 and 22 predicted RM systems (74,75). Even bacteria with the smallest genomes, Mycoplasma and Ureaplasma, have made room for these systems. RM systems provide a defense against DNA bacteriophages, as revealed both by direct experiment and indirectly by the fact that many bacteriophages take specific countermeasures against RM systems (9). In addition to initiating the destruction of some foreign DNAs, RM systems may also promote recombination (6, 51) and improve the spread of some genes by separating them from linked deleterious alleles (4, 42), thus playing both positive and negative roles in modulating the flow of genes among prokaryotes. In the case of type II RM systems, selfish behavior also contributes to their ubiquity (24,45,46). RM system ubiquity is consistent with the selectable phenotypes just summarized, but these phenotypes only help to explain why the systems are maintained once they have entered a given bacterium. It is less clear how these systems move throughout the microbial biosphere. To this end, it would be useful to track the movement of a given RM system by finding very clos...

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“…Many genes for R-M systems have been found to be located on transferable elements such as plasmids and bacteriophages, or, in some cases, genes encoding proteins involved in DNA mobility, such as transposases, integrases, and invertases, are found in the vicinity of R-M systems (5,7,19,26,38,46,51,54,56). These genetic structures may facilitate the transfer of R-M systems and have led to the speculation that R-M genes could migrate among microorganisms of different genera.…”

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confidence: 99%

Evidence for Horizontal Transfer of Ssu DAT1I Restriction-Modification Genes to the Streptococcus suis Genome

et al. 2001

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Different strains of Streptococcus suis serotypes 1 and 2 isolated from pigs either contained a restrictionmodification (R-M) system or lacked it. The R-M system was an isoschizomer of Streptococcus pneumoniae DpnII, which recognizes nucleotide sequence 5-GATC-3. The nucleotide sequencing of the genes encoding the R-M system in S. suis DAT1, designated SsuDAT1I, showed that the SsuDAT1I gene region contained two methyltransferase genes, designated ssuMA and ssuMB, as does the DpnII system. The deduced amino acid sequences of M.SsuMA and M.SsuMB showed 70 and 90% identity to M.DpnII and M.DpnA, respectively. However, the SsuDAT1I system contained two isoschizomeric restriction endonuclease genes, designated ssuRA and ssuRB. The deduced amino acid sequence of R.SsuRA was 49% identical to that of R.DpnII, and R.SsuRB was 72% identical to R.LlaDCHI of Lactococcus lactis subsp. cremoris DCH-4. The four SsuDAT1I genes overlapped and were bounded by purine biosynthetic gene clusters in the following gene order: purF-purMpurN-purH-ssuMA-ssuMB-ssuRA-ssuRB-purD-purE. The G؉C content of the SsuDAT1I gene region (34.1%) was lower than that of the pur region (48.9%), suggesting horizontal transfer of the SsuDAT1I system. No transposable element or long-repeat sequence was found in the flanking regions. The SsuDAT1I genes were functional by themselves, as they were individually expressed in Escherichia coli. Comparison of the sequences between strains with and without the R-M system showed that only the region from 53 bp upstream of ssuMA to 5 bp downstream of ssuRB was inserted in the intergenic sequence between purH and purD and that the insertion target site was not the recognition site of SsuDAT1I. No notable substitutions or insertions could be found, and the structures were conserved among all the strains. These results suggest that the SsuDAT1I system could have been integrated into the S. suis chromosome by an illegitimate recombination mechanism.More than 3,000 restriction-modification (R-M) systems have been identified in a wide variety of microorganisms, where they are thought to protect the host from invasion by foreign DNA. Only a minority of R-M systems have been sequenced (6,37,56). Among them, some type II R-M systems, which recognize 4-bp palindromic sequence 5Ј-GATC-3Ј, involve a variety of isoschizomers. Three classes can be distinguished by their manners of DNA cleavage and susceptibilities to DNA methylation. The first class of isoschizomers, represented by Sau3AI, which was described for Staphylococcus aureus, is prevented from digesting host DNA by a cognate 5-methylcytosine methyltransferase and is not influenced by the modification of N 6 -methyladenine (48, 56). The second class, represented by DpnI, which was described for Streptococcus pneumoniae, is unique among restriction endonucleases in that it cleaves only at methylated DNA sequence 5Ј-GmeATC-3Ј, and thus the cells producing DpnI do not carry the corresponding methyltransferase gene (22,23). The third class, including MboI, DpnII, and LlaDCHI...

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Cloning and characterization of the BglII restriction–modification system reveals a possible evolutionary footprint

Cited by 58 publications

References 33 publications

Role and Mechanism of Action of C · Pvu II, a Regulatory Protein Conserved among Restriction-Modification Systems

Role and Mechanism of Action of C · Pvu II, a Regulatory Protein Conserved among Restriction-Modification Systems

Mobility of a Restriction-Modification System Revealed by Its Genetic Contexts in Three Hosts

Evidence for Horizontal Transfer of Ssu DAT1I Restriction-Modification Genes to the Streptococcus suis Genome

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