Nucleotide sequence of the EcoRII restriction endonuclease gene

Kossykh, Valery; Repyk, Alexander V.; Kaliman, A V; Buryanov, Yа. I.

doi:10.1016/0167-4781(89)90117-6

Cited by 18 publications

(9 citation statements)

References 5 publications

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“…E. coli strains produce a variety of restriction endonucleases, including those of type I and III R-M systems. Type I and III systems are located on the chromosome; in contrast, most of the structural genes of type II R-M systems are located on a plasmid (5,20,27,38,39), and quite a few are located on chromosomal DNA (16, 21). Escherichia coli TH38, isolated from a pig, produces a type II restriction endonuclease, R.EcoT38I, that recognizes and cleaves the nucleotide sequence 5Ј-G(A/G)GC(C/T) 2C-3Ј (23).…”

Section: Restriction (R)-modification (M) Systems (R-m Systems)mentioning

confidence: 99%

Evidence for Horizontal Transfer of the Eco T38I Restriction- Modification Gene to Chromosomal DNA by the P2 Phage and Diversity of Defective P2 Prophages in Escherichia coli TH38 Strains

2003

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A DNA fragment carrying the genes coding for a novel EcoT38I restriction endonuclease (R.EcoT38I) and EcoT38I methyltransferase (M.EcoT38I), which recognize G(A/G)GC(C/T)C, was cloned from the chromosomal DNA of Escherichia coli TH38. The endonuclease and methyltransferase genes were in a head-to-head orientation and were separated by a 330-nucleotide intergenic region. A third gene, the C.EcoT38I gene, was found in the intergenic region, partially overlapping the R.EcoT38I gene. The gene product, C.EcoT38I, acted as both a positive regulator of R.EcoT38I gene expression and a negative regulator of M.EcoT38I gene expression. M.EcoT38I purified from recombinant E. coli cells was shown to be a monomeric protein and to methylate the inner cytosines in the recognition sequence. R.EcoT38I was purified from E. coli HB101 expressing M.EcoT38I and formed a homodimer. The EcoT38I restriction (R)-modification (M) system (R-M system) was found to be inserted between the A and Q genes of defective bacteriophage P2, which was lysogenized in the chromosome at locI, one of the P2 phage attachment sites observed in both E. coli K-12 MG1655 and TH38 chromosomal DNAs. Ten strains of E. coli TH38 were examined for the presence of the EcoT38I R-M gene on the P2 prophage. Conventional PCR analysis and assaying of R activity demonstrated that all strains carried a single copy of the EcoT38I R-M gene and expressed R activity but that diversity of excision in the ogr, D, H, I, and J genes in the defective P2 prophage had arisen. Restriction (R)-modification (M) systems (R-M systems)serve as bacterial immune systems that destroy foreign DNA entering a cell. Typically, type II R-M systems consist of two enzymes: an endonuclease that recognizes and cleaves a specific DNA sequence and a methyltransferase that modifies the same sequence to protect the host chromosome from cleavage. More than 3,000 restriction endonucleases and methyltransferases have been isolated from many species of bacteria and have been subjected to biochemical and genetic studies (30). E. coli strains produce a variety of restriction endonucleases, including those of type I and III R-M systems. Type I and III systems are located on the chromosome; in contrast, most of the structural genes of type II R-M systems are located on a plasmid (5,20,27,38,39), and quite a few are located on chromosomal DNA (16, 21). Escherichia coli TH38, isolated from a pig, produces a type II restriction endonuclease, R.EcoT38I, that recognizes and cleaves the nucleotide sequence 5Ј-G(A/G)GC(C/T) 2C-3Ј (23). The occurrence of Hsd (host specificity for DNA) plasmids in E. coli TH38 has been investigated; one large plasmid was isolated from E. coli TH38, but Hsd ϩ transformants were not detected by use of a plasmid (38). These findings strongly suggest the possibility of chromosomal localization of the EcoT38I R-M system. Restriction endonucleases that show the same specificity as R.EcoT38I, such as R.BanII (14), have been isolated from a variety of bacteria, but none of the gene structures ha...

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Section: Restriction (R)-modification (M) Systems (R-m Systems)mentioning

confidence: 99%

Evidence for Horizontal Transfer of the Eco T38I Restriction- Modification Gene to Chromosomal DNA by the P2 Phage and Diversity of Defective P2 Prophages in Escherichia coli TH38 Strains

2003

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“…Our interest in studying this enzyme is due to its sequence similarity to Eco-RII, a type IIE enzyme (reviewed in Ref. 19), which being somewhat larger than SsoII is a dimer of identical subunits each consisting of 404 amino acid residues (20,21). As a type IIE enzyme EcoRII has two DNA-binding sites, one associated with the catalytic center and the other serving as an effector site (22) (which has led to the acronym type IIE) (23)(24)(25), similar to that shown for NaeI (26 -29).…”

mentioning

confidence: 99%

Evolutionary Relationship between Different Subgroups of Restriction Endonucleases

Pingoud¹,

Кубарева²,

Stengel³

et al. 2002

Journal of Biological Chemistry

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The type II restriction endonuclease SsoII shows sequence similarity with 10 other restriction endonucleases, among them the type IIE restriction endonuclease EcoRII, which requires binding to an effector site for efficient DNA cleavage, and the type IIF restriction endonuclease NgoMIV, which is active as a homotetramer and cleaves DNA with two recognition sites in a concerted reaction. We show here that SsoII is an orthodox type II enzyme, which is active as a homodimer and does not require activation by binding to an effector site. Nevertheless, it shares with EcoRII and NgoMIV a very similar DNA-binding site and catalytic center as shown here by a mutational analysis, indicative of an evolutionary relationship between these three enzymes. We suggest that a similar relationship exists between other orthodox type II, type IIE, and type IIF restriction endonucleases. This may explain why similarities may be more pronounced between members of different subtypes of restriction enzymes than among the members of a given subtype.More than 3000 different type II restriction endonucleases are known and characterized with respect to their cleavage specificities (1). This group of enzymes probably constitutes one of the largest families of enzymes with the same basic function. This makes type II restriction endonucleases (like DNA methyltransferases) ideal objects to study evolutionary relationships. Moreover, in principle, the family relationships should eventually allow predicting structural and functional features of an individual restriction endonuclease, solely on the basis of sequence comparisons. This was not obvious for a long time since only 10 years ago restriction endonucleases, because of their little sequence conservation, were not considered to be related in evolution (2, 3). But this changed due to the progress made in the analysis of sequence similarities (4 -6) and, in particular, due to the increasing number of crystal structures of restriction enzymes (reviewed in Refs. 7 and 8), which made it obvious that these enzymes have very similar structural cores. Nevertheless, it has been shown recently that some genuine restriction enzymes belong to distinct nuclease superfamilies (Nuc, HNH, and GIY-YIG), which are unrelated and structurally dissimilar to each other and to the "archetypal" (P)D . . . (D/E)XK superfamily (9 -11). These findings make comparative studies using sequences of restriction enzymes even more challenging.We have begun to study the restriction endonuclease SsoII recently (12-15). It is a type II enzyme (reviewed in Refs. 8 and 16) composed of identical subunits each consisting of 305 amino acid residues (17). It cleaves the palindromic sequence 2CC-NGG in the presence of Mg 2ϩ as indicated (18). Our interest in studying this enzyme is due to its sequence similarity to Eco-RII, a type IIE enzyme (reviewed in Ref. 19), which being somewhat larger than SsoII is a dimer of identical subunits each consisting of 404 amino acid residues (20, 21). As a type IIE enzyme EcoRII has two DNA-binding...

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“…Genes coding for the EcoRII REase and MTase were cloned and their nucleotide sequence was determined. The two genes are convergently transcribed from separate promoters on opposite DNA strands (Kosykh et al 1980;Som et al 1987;Kosykh et al 1989, Bhagwat et al 1990Reuter et al 1999). The open reading frame of the EcoRII REase codes for a protein with a molecular mass of 44 and 45.6 kDa, respectively (Kosykh et al 1982;Bhagwat et al 1990),and that of the MTase gene codes for a protein of about 54.6 kDa (Som et al 1987).…”

mentioning

confidence: 97%

Structure and Function of Type IIE Restriction Endonucleases — or: From a Plasmid That Restricts Phage Replication to A New Molecular DNA Recognition Mechanism

Reuter

Mücke

Krüger

2004

Restriction Endonucleases

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Nucleotide sequence of the EcoRII restriction endonuclease gene

Cited by 18 publications

References 5 publications

Evidence for Horizontal Transfer of the Eco T38I Restriction- Modification Gene to Chromosomal DNA by the P2 Phage and Diversity of Defective P2 Prophages in Escherichia coli TH38 Strains

Evidence for Horizontal Transfer of the Eco T38I Restriction- Modification Gene to Chromosomal DNA by the P2 Phage and Diversity of Defective P2 Prophages in Escherichia coli TH38 Strains

Evolutionary Relationship between Different Subgroups of Restriction Endonucleases

Structure and Function of Type IIE Restriction Endonucleases — or: From a Plasmid That Restricts Phage Replication to A New Molecular DNA Recognition Mechanism

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