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Cloning and Characterization of a New Site-Specific Methyl-Directed ElmI Endonuclease Recognizing and Cleaving C5-methylated DNA Sequence 5'-G(5mC)^NG(5mC)-3'.

Chernukhin VA, Gonchar DA, Abdurashitov MA, Belichenko OA, Dedkov VS, Mikhnenkova NA, Lomakovskaya EN, Udal'yeva SG, Degtyarev SKh - Acta Naturae (2016 Jan-Mar)

Bottom Line: Putative open reading frames of MD-endonucleases have been identified in Enterobacteria genomes as a result of the search for amino acid sequences homologous to MD-endonuclease BisI.It was discovered that similarly to BisI this enzyme specifically cleaves the methylated DNA sequence 5'-GCNGC- 3' before the central nucleotide "N" if this sequence contains two 5-methylcytosines.However, unlike BisI, ElmI more efficiently cleaves this sequence if more than two cytosine residues are methylated.

View Article: PubMed Central - PubMed

Affiliation: SibEnzyme, Timakova St., 2/12, 630117, Novosibirsk, Russia.

ABSTRACT
Putative open reading frames of MD-endonucleases have been identified in Enterobacteria genomes as a result of the search for amino acid sequences homologous to MD-endonuclease BisI. A highly conserved DNA primary structure of these open reading frames in different genera of Enterobacteria (Escherichia, Klebsiella and Cronobacter) has allowed researchers to create primers for PCR screening, which was carried out on Enterobacteria DNA collected from natural sources. The DNA fragment, about 440 bp in length, was amplified by use of the genomic DNA of a wild E.coli LM N17 strain as a template and was inserted into the pMTL22 vector. Endonuclease activity was detected in an E.coli ER 2267 strain transformed with the obtained construction. A new enzyme named ElmI was purified by chromatographic techniques from the recombinant strain biomass. It was discovered that similarly to BisI this enzyme specifically cleaves the methylated DNA sequence 5'-GCNGC- 3' before the central nucleotide "N" if this sequence contains two 5-methylcytosines. However, unlike BisI, ElmI more efficiently cleaves this sequence if more than two cytosine residues are methylated.

No MeSH data available.


Related in: MedlinePlus

Alignment of the nucleotide sequence of the putative gene encoding ElmI(elmI gene) with the most homologous DNA sequences. Nucleotidesequences are identified by GenBank accession numbers for the correspondingencoded proteins. Nucleotides identical for most, but not for all, of theanalyzed sequences of 5 genes are shown on a gray background. Nucleotides thatare not found in the majority of the sequences are shown in italics andunderlined. The single nucleotide by which the elmI genediffers from the nearest homologues from Escherichia coliBL21(DE3) and C41(DE3) is indicated by a frame. The sequences on the5’ and 3’ ends corresponding to the primers by which the PCRscreening for isolation of coliform bacteria genomic DNA from natural sourceswas performed are indicated by frames as well.
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Figure 2: Alignment of the nucleotide sequence of the putative gene encoding ElmI(elmI gene) with the most homologous DNA sequences. Nucleotidesequences are identified by GenBank accession numbers for the correspondingencoded proteins. Nucleotides identical for most, but not for all, of theanalyzed sequences of 5 genes are shown on a gray background. Nucleotides thatare not found in the majority of the sequences are shown in italics andunderlined. The single nucleotide by which the elmI genediffers from the nearest homologues from Escherichia coliBL21(DE3) and C41(DE3) is indicated by a frame. The sequences on the5’ and 3’ ends corresponding to the primers by which the PCRscreening for isolation of coliform bacteria genomic DNA from natural sourceswas performed are indicated by frames as well.

Mentions: Multiple alignment of the corresponding enterobacterial genes(Figure 2)revealed that their nucleotide compositions also have a high degreeof identity, even though the host organisms belong to different genera. Thesequence of the elmI gene, established in this work, is addedto the alignment.


Cloning and Characterization of a New Site-Specific Methyl-Directed ElmI Endonuclease Recognizing and Cleaving C5-methylated DNA Sequence 5'-G(5mC)^NG(5mC)-3'.

Chernukhin VA, Gonchar DA, Abdurashitov MA, Belichenko OA, Dedkov VS, Mikhnenkova NA, Lomakovskaya EN, Udal'yeva SG, Degtyarev SKh - Acta Naturae (2016 Jan-Mar)

Alignment of the nucleotide sequence of the putative gene encoding ElmI(elmI gene) with the most homologous DNA sequences. Nucleotidesequences are identified by GenBank accession numbers for the correspondingencoded proteins. Nucleotides identical for most, but not for all, of theanalyzed sequences of 5 genes are shown on a gray background. Nucleotides thatare not found in the majority of the sequences are shown in italics andunderlined. The single nucleotide by which the elmI genediffers from the nearest homologues from Escherichia coliBL21(DE3) and C41(DE3) is indicated by a frame. The sequences on the5’ and 3’ ends corresponding to the primers by which the PCRscreening for isolation of coliform bacteria genomic DNA from natural sourceswas performed are indicated by frames as well.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4837579&req=5

Figure 2: Alignment of the nucleotide sequence of the putative gene encoding ElmI(elmI gene) with the most homologous DNA sequences. Nucleotidesequences are identified by GenBank accession numbers for the correspondingencoded proteins. Nucleotides identical for most, but not for all, of theanalyzed sequences of 5 genes are shown on a gray background. Nucleotides thatare not found in the majority of the sequences are shown in italics andunderlined. The single nucleotide by which the elmI genediffers from the nearest homologues from Escherichia coliBL21(DE3) and C41(DE3) is indicated by a frame. The sequences on the5’ and 3’ ends corresponding to the primers by which the PCRscreening for isolation of coliform bacteria genomic DNA from natural sourceswas performed are indicated by frames as well.
Mentions: Multiple alignment of the corresponding enterobacterial genes(Figure 2)revealed that their nucleotide compositions also have a high degreeof identity, even though the host organisms belong to different genera. Thesequence of the elmI gene, established in this work, is addedto the alignment.

Bottom Line: Putative open reading frames of MD-endonucleases have been identified in Enterobacteria genomes as a result of the search for amino acid sequences homologous to MD-endonuclease BisI.It was discovered that similarly to BisI this enzyme specifically cleaves the methylated DNA sequence 5'-GCNGC- 3' before the central nucleotide "N" if this sequence contains two 5-methylcytosines.However, unlike BisI, ElmI more efficiently cleaves this sequence if more than two cytosine residues are methylated.

View Article: PubMed Central - PubMed

Affiliation: SibEnzyme, Timakova St., 2/12, 630117, Novosibirsk, Russia.

ABSTRACT
Putative open reading frames of MD-endonucleases have been identified in Enterobacteria genomes as a result of the search for amino acid sequences homologous to MD-endonuclease BisI. A highly conserved DNA primary structure of these open reading frames in different genera of Enterobacteria (Escherichia, Klebsiella and Cronobacter) has allowed researchers to create primers for PCR screening, which was carried out on Enterobacteria DNA collected from natural sources. The DNA fragment, about 440 bp in length, was amplified by use of the genomic DNA of a wild E.coli LM N17 strain as a template and was inserted into the pMTL22 vector. Endonuclease activity was detected in an E.coli ER 2267 strain transformed with the obtained construction. A new enzyme named ElmI was purified by chromatographic techniques from the recombinant strain biomass. It was discovered that similarly to BisI this enzyme specifically cleaves the methylated DNA sequence 5'-GCNGC- 3' before the central nucleotide "N" if this sequence contains two 5-methylcytosines. However, unlike BisI, ElmI more efficiently cleaves this sequence if more than two cytosine residues are methylated.

No MeSH data available.


Related in: MedlinePlus