S-adenosyl-l-methionine is required for DNA cleavage by type III restriction enzymes

Bist, Pradeep; Sistla, Srivani; Krishnamurthy, Vinita; Acharya, Asha; Chandrakala, B.; Rao, Desirazu N.

doi:10.1006/jmbi.2001.4744

Cited by 28 publications

(29 citation statements)

References 39 publications

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“…3,7,[15][16][17] Moreover, it was unclear whether the surrounding sequence context of 5′-CAGCAG affects the decision on which of the two reactive DNA sites is cleaved. A systematic study of how the bases in the vicinity of the EcoP15I recognition site and the enzyme concentration affect EcoP15I cleavage efficiency has not been performed.…”

Section: Introductionmentioning

confidence: 99%

Functional Characterization and Modulation of the DNA Cleavage Efficiency of Type III Restriction Endonuclease EcoP15I in Its Interaction with Two Sites in the DNA Target

Möncke‐Buchner

Rothenberg

Reich

et al. 2009

Journal of Molecular Biology

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Section: Introductionmentioning

confidence: 99%

Functional Characterization and Modulation of the DNA Cleavage Efficiency of Type III Restriction Endonuclease EcoP15I in Its Interaction with Two Sites in the DNA Target

Möncke‐Buchner

Rothenberg

Reich

et al. 2009

Journal of Molecular Biology

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“…We think that in a fraction of purified protein AdoMet may be bound. This was also observed for EcoP15I, which required additional treatment after isolation to remove bound AdoMet [6]. Unfortunately, the method to remove bound AdoMet from the enzyme described in the cited paper was not suitable for MmeI, which is extremely unstable and difficult to isolate.…”

Section: The Effect Of Adomet/sin On the Structural Stability Of Mmeimentioning

confidence: 98%

“…Similarly, in the case of type I R-M enzymes AdoMet stimulates specific binding of the enzyme to DNA and promotes discrimination between specific and non-specific substrates. It was also shown that EcoP1I and EcoP15I representing type III R-M enzymes require AdoMet for their restriction activity and that AdoMet acts as a positive allosteric effector in this reaction [6].…”

Section: Introductionmentioning

confidence: 99%

Binding of MmeI Restriction–modification Enzyme to its Specific Recognition Sequence is Stimulated by S-adenosyl-l-methionine

et al. 2007

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Restriction endonucleases serve as a very good model for studying specific protein-DNA interaction. MmeI is a very interesting restriction endonuclease, but although it is useful in Serial Analysis of Gene Expression, still very little is known about the mechanism of its interaction with DNA. MmeI is a unique enzyme as besides cleaving DNA it also methylates specific sequence. For endonucleolytic activity MmeI requires Mg(II) and S-adenosyl-l-methionine (AdoMet). AdoMet is a methyl donor in the methylation reaction, but its requirement for DNA cleavage remains unclear. In the present article we investigated MmeI interaction with DNA with the use of numerous methods. Our electrophoretic mobility shift assay revealed formation of two types of specific protein-DNA complexes. We speculate that faster migrating complex consists of one protein molecule and one DNA fragment whereas, slower migrating complex, which appears in the presence of AdoMet, may be a dimer or multimer form of MmeI interacting with specific DNA. Additionally, using spectrophotometric measurements we showed that in the presence of AdoMet, MmeI protein undergoes conformational changes. We think that such change in the enzyme structure, upon addition of AdoMet, may enhance its specific binding to DNA. In the absence of AdoMet MmeI binds DNA to the much lower extent.

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“…The POGs with PQs of Ն2 add to this list several functions related to virulence, such as holins and lysis proteins, that also appear in their cellular hosts, although in far lower abundance than in phages. In contrast, enzymes of cellular metabolism tend to belong to POGs with low PQs, such as GTP cyclohydrolase I with a PQ of Ϫ4.5 (indicating its appearance in 4 to 5 orders of magnitude fewer phage genomes than microbial ones), although exceptions do occur, such as S-adenosyl-L-methionine hydrolase with a PQ of infinity, presumably used by the phage in restriction-modification warfare with the host to ensure the unmodified status of its own DNA, which would be useful, for example, when the phage encodes its own methylation-dependent restriction enzymes (9).…”

Section: Vol 193 2011 Phage Orthologous Groups 1809mentioning

confidence: 99%

Evolutionarily Conserved Orthologous Families in Phages Are Relatively Rare in Their Prokaryotic Hosts

Kristensen

Cai

Mushegian

2011

Journal of Bacteriology

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We have identified conserved orthologs in completely sequenced genomes of double-strand DNA phages and arranged them into evolutionary families (phage orthologous groups [POGs]). Using this resource to analyze the collection of known phage genomes, we find that most orthologs are unique in their genomes (having no diverged duplicates [paralogs]), and while many proteins contain multiple domains, the evolutionary recombination of these domains does not appear to be a major factor in evolution of these orthologous families. The number of POGs has been rapidly increasing over the past decade, the percentage of genes in phage genomes that have orthologs in other phages has also been increasing, and the percentage of unknown "ORFans" is decreasing as more proteins find homologs and establish a family. Other properties of phage genomes have remained relatively stable over time, most notably the high fraction of genes that are never or only rarely observed in their cellular hosts. This suggests that despite the renowned ability of phages to transduce cellular genes, these cellular "hitchhiker" genes do not dominate the phage genomic landscape, and a large fraction of the genes in phage genomes maintain an evolutionary trajectory that is distinct from that of the host genes.

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S-adenosyl-l-methionine is required for DNA cleavage by type III restriction enzymes

Cited by 28 publications

References 39 publications

Functional Characterization and Modulation of the DNA Cleavage Efficiency of Type III Restriction Endonuclease EcoP15I in Its Interaction with Two Sites in the DNA Target

Functional Characterization and Modulation of the DNA Cleavage Efficiency of Type III Restriction Endonuclease EcoP15I in Its Interaction with Two Sites in the DNA Target

Binding of MmeI Restriction–modification Enzyme to its Specific Recognition Sequence is Stimulated by S-adenosyl-l-methionine

Evolutionarily Conserved Orthologous Families in Phages Are Relatively Rare in Their Prokaryotic Hosts

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