The nucleotide sequence recognised by the Escherichia coli D type I restriction and modification enzyme

Nagaraja, Valakunja; Stieger, Martin; Nager, Christoph; Hadi, S. M.; Bickle, Thomas A.

doi:10.1093/nar/13.2.389

Cited by 20 publications

(8 citation statements)

References 26 publications

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“…3C). In fact, B and D differ only at position 18 and the carboxyl terminus, although the tetranucleotide elements of their target sequences are very different (7,8): TGCT for B and GTCY for D. Gough and Murray (4) concluded that there was insufficient variability here for the different specificities of interaction. The inclusion of the sequences for the Salmonella polypeptides increases the diversity, but three of the differences are common to both Salmonella specificities.…”

Section: Resultsmentioning

confidence: 99%

“…The DNA sequences recognized by type I restriction enzymes comprise specific trinucleotide and tetranucleotide (or pentanucleotide) segments separated by a spacer of defined length but of nonspecific sequence (7)(8)(9). One interpretation of the heteroduplex analyses correlates the two variable regions of the hsdS gene, and hence of the S polypeptide, with the two specific segments of the DNA target sequence (4).…”

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confidence: 99%

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Two DNA recognition domains of the specificity polypeptides of a family of type I restriction enzymes.

Fuller-Pace¹,

Murray²

1986

Proc. Natl. Acad. Sci. U.S.A.

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The hsd genes of Salmonella typhimurium and Salmonella potsdam encode related type I restriction and modification systems designated SB and SP, respectively; the polypeptide encoded by the hsdS gene dictates the DNA sequence recognized. The hsdS genes of the SB and SP systems have a conserved sequence of around 100 base pairs flanked by two nonhomologous (variable) regions of around 500 base pairs. Recombination between the hsdS genes of SB and SP generated a system (SQ) with a different recognition specificity.We have localized the position of the crossover in the central conserved region by analysis of nucleotide sequences. Concomitant with the generation of a new combination of flanking variable regions is the recombination of minor differences in the central conserved region. A polypeptide domain encoded on the 5' side of the crossover dictates recognition of the trinucleotide component of the target sequence, and a second domain, encoded on the 3' side of the crossover, similarly governs recognition of the tetra-or penta-nucleotide component. Our analysis implicates at least parts of the variable regions in the determination of the specificity of interaction between protein and DNA. Furthermore, the trinucleotide components of the recognition sequences of S. typhimurium and Escherichia coli K-12 are identical, and the 5' segments of their hsdS genes are strikingly homologous rather than variable.Some strains of Escherichia coli and Salmonella spp have type I restriction systems that are related to that of E. coli K-12 (K system). The concept of a family of enzymes, members of which carry out essentially the same reactions following the recognition of different DNA sequences, poses questions concerning both the specific interaction of the enzyme with its target sequence and the evolution ofdifferent specificities of interaction. Type I restriction endonucleases are encoded by three chromosomal genes: hsdR, hsdM, and hsdS. Genetic experiments show that the corresponding polypeptides (R, M, and S) can be interchanged between related systems and identify the S subunit as the determinant of the specificity of recognition (1-3). The various S polypeptides interact with related polypeptides to produce modification enzymes and with M and R subunits in the formation of restriction endonucleases. Related S subunits must retain a basic similarity for their interactions with other M and R polypeptides but have diverged to enable recognition of different nucleotide sequences.The hsdS genes of related E. coli systems (K, B, and D) have only localized DNA sequence homology (4). The genes vary in length from 1335 to 1425 base pairs (bp), and the regions of homology are -100 bp in the middle and 250 bp at the 3' end. Although these two regions are highly conserved, the remainder of each hsdS gene shares little or no homology with either of the other two.The K family includes the SB system found in Salmonella typhimurium and the SP system of Salmonella potsdam. When the SP hsd genes were transferred by phage P1 trans...

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Two DNA recognition domains of the specificity polypeptides of a family of type I restriction enzymes.

Fuller-Pace¹,

Murray²

1986

Proc. Natl. Acad. Sci. U.S.A.

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“…DNAs from laboratory and natural isolates of E. coli were screened, as well as a small sample of DNAs of other enteric bacteria. Related specificity systems were detected, some of which have been described elsewhere (19,23,29), and both the K and A families were represented in more than one genus. Nevertheless, as judged by our failure to detect homologous sequences, most E. coli strains lacked either Kor A-related hsd genes.…”

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confidence: 82%

Distribution and diversity of hsd genes in Escherichia coli and other enteric bacteria

et al. 1988

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isolates of Escherichia coli for DNA sequences homologous to those encoding each of two unrelated type I restriction and modification systems (EcoK and EcoA). Both K-and A-related hsd genes were identified, but never both in the same strain. S. typhimurium encodes three restriction and modification systems, but its DNA hybridized only to the K-specific probe which we know to identify the StySB system. No homology to either probe was detected in the majority of E. coli strains, but in C. freundii, we identified homology to the A-specific probe. We cloned this region of the C. freundii genome and showed that it encoded a functional, A-related restriction system whose specificity differs from those of known type I enzymes. Sequences immediately flanking the hsd K genes of E. coli K-12 and the hsd A genes of E. coli I1T-were shown to be homologous, indicating similar or even identical positions in their respective chromosomes. E. coli C has no known restriction system, and the organization of its chromosome is consistent with deletion of the three hsd genes and their neighbor, mcrB.The fundamental attribute of a restriction endonuclease is its ability to recognize and selectively attack foreign DNA. This DNA is usually identified by the absence of a sequencespecific modification (methylation). Although modification is always sequence specific, restriction endonucleases do not necessarily cut within the DNA target sequence identified by methylation. Most enzymes classified as type II do, while others, classified as either type I or III, do not (for reviews, see references 6 and 43).This paper is concerned with type I restriction systems. These, in every way, are the most complex; they comprise three subunits, have complex cofactor requirements, and cut DNA nonspecifically some thousands of base pairs from the target sequence for modification. The genes encoding these restriction endonucleases are designated hsd for host specificity of DNA. The specificity polypeptide, encoded by hsdS, associates with that encoded by hsdM to form a modification methylase and with those encoded by hsdM and hsdR to produce a restriction endonuclease.It is generally accepted that restriction endonucleases function to prevent the acquisition and expression of foreign DNA (2). One consequence would be a degree of protection against infection by bacteriophages, an advantageous feature for the initial establishment of populations of bacteria in new habitats (25) Two commonly used laboratory strains, Escherichia coli K-12 and E. coli B, each have a single, chromosomally encoded, type I system, while E. coli 15T-has both a chromosomally encoded type I system, designated A, and a plasmid-encoded type III system, designated P15 (4). Plasmids encoding restriction systems represeptative of all three types have been isolated from E. coli strains, but to date the chromosomally encoded systems are all type I. No E. coli strain has been shown to have more than one chromosomally encoded restriction system, but the chromosomal genes of Salmonella typhim...

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“…The sequences of recognition sites are asymmetric but not palindromic. Examples include 5′-AACN 6 GTGC-3′ and 5′-GCACN 6 GTT-3′ for EcoKI, 5′-TGAN 8 TGCT-3′ and 5′-AG-CAN 8 TCA-3′ for EcoBI, and 5′-TTAN 7 GTCY-3′ and 5′-RGACN 7 TAA-3′ for EcoDI (methylated adenine is underlined; R: A/G, Y: C/T, N: A/C/G/T) [29,30].…”

Section: Type I Rm Systemsmentioning

confidence: 99%

“…Recent epigenetic studies have developed many methods to analyze DNA methylation [29,30,[69][70][71][72][73][74][75][76]. Although most of these studies aimed to analyze 5-methylation of cytosine at spe-cific sites, or differential DNA methylation in chromosomes, there are a few methods that exhaustively determine methylated consensus sites in chromosomes as follows.…”

Section: Methylation Site Analysismentioning

confidence: 99%

Host-Mimicking Strategies in DNA Methylation for Improved Bacterial Transformation

Suzuki¹

2012

Methylation - From DNA, RNA and Histones to Diseases and Treatment

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The nucleotide sequence recognised by the Escherichia coli D type I restriction and modification enzyme

Cited by 20 publications

References 26 publications

Two DNA recognition domains of the specificity polypeptides of a family of type I restriction enzymes.

Two DNA recognition domains of the specificity polypeptides of a family of type I restriction enzymes.

Distribution and diversity of hsd genes in Escherichia coli and other enteric bacteria

Host-Mimicking Strategies in DNA Methylation for Improved Bacterial Transformation

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