Complementary specificity of restriction endonucleases of Diplococcus pneumoniae with respect to DNA methylation

“…the Escherichia coli DNA adenine MTase (EcoDam), which methylates the exocyclic amino nitrogen (N 6 ) of the Ade in GATC (1,2). DNAadenine methylation at specific GATC sites plays a pivotal role in the regulation of bacterial gene expression and DNA replication, mismatch repair, and is essential for bacterial virulence for many Gram-negative bacteria (3).…”

Section: ) and Insertion Of The Flipped Target Base Into The Active mentioning

confidence: 99%

Two Alternative Conformations of S-Adenosyl-L-homocysteine Bound to Escherichia coli DNA Adenine Methyltransferase and the Implication of Conformational Changes in Regulating the Catalytic Cycle

Liebert

Horton

Chahar

et al. 2007

Journal of Biological Chemistry

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“…The observations presented above contribute to only a handful of reported cases where the presence of a methyl group on DNA is required in a positive way for an effective DNA-protein interaction. One of the most striking cases is restriction enzyme Dpn I, which cleaves the sequence 5' GATC 3' only when the adenines in the recognition site carry N6 methyl groups (16). The Dpn I-DNA interaction has not yet been analyzed in structural detail.…”

Section: Discussionmentioning

confidence: 99%

Efficient Tn10 transposition into a DNA insertion hot spot in vivo requires the 5-methyl groups of symmetrically disposed thymines within the hot-spot consensus sequence.

Lee

Butler

Kleckner

1987

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

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Transposon Tn1O inserts preferentially at particular insertion "hot spots" that share a symmetrical 6-base-pair consensus sequence: 5' GCTNAGC 3'. The protein that recognizes this sequence is not known but is likely to be the TnlO-encoded transposase protein. We present evidence that the 5-methyl groups of the two thymines in this sequence are essential for efficient transposon insertion; in their absence the sequence is still recognized, but at lower efficiency. We have reached this conclusion by examination of a specific hot spot whose sequence is 5' GCCAGGC 3'. The innermost cytosines ofthis sequence happen to be substrates for methylation at their 5 positions by the bacterial dcm-encoded methylase. We find that TnWO transposes into this site 15 times more frequently in a Dcm' host than in a Dcm-host; in the Dcm-host, insertions still occur, but at a low frequency. Thus, at this site, the absence of pyrimidine 5-methyl groups at the third positions of the consensus sequence is sufficient to convert a strong insertion hot spot into a weaker but still recognizable hot spot. This observation supports the general proposition, suggested previously by comparisons among consensus sequences, that the presence or absence of these 5-methyl groups is one major feature that can make the difference between a strong and a weak TnlO insertion hot spot.Transposon TnJO can insert into many different sites in the bacterial genome. However, it inserts preferentially into particular specific DNA sites or "hot spots" (1). DNA sequencing of many different TnJO insertion hot spots has revealed the presence of a symmetrical 6-base-pair (bp) consensus sequence that plays a major role in determining TnWO insertion-site selection (2). This sequence is necessary but not sufficient to determine insertion specificity; other base pairs in the immediate vicinity and/or long-range structural features of the DNA also influence the distribution of insertions among different sites (2).Insertion of TnJO always results in the direct duplication of a 9-bp target-site sequence and integration of the transposon in between the duplicated copies ( Fig. 1; refs. 3-5). The existence of such "9-bp repeats" is interpreted to mean that the target DNA duplex is cleaved by a pair of appropriately spaced single-strand nicks during insertion (3, 6, 7). The symmetrical 6-bp TnWO insertion hot-spot consensus sequence is itself symmetrically disposed within the 9-bp repeat sequence in the target DNA. As shown in Fig. 1 TnJO results in duplication of a 9-bp target DNA sequence; the element is inserted between the duplicated copies. Transposition is presumed to involve staggered single-strand cleavages of the target DNA; the actual strand polarity of these cleavages is not known. The TnlO insertion-specificity consensus sequence is symmetrically located within the 9-bp target sequence.TnJO-encoded transposase protein, but no direct evidence to this effect is yet available.The consensus TnlO insertion-specificity sequence is 5' GCTNAGC 3' (where N represents...

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Complementary specificity of restriction endonucleases of Diplococcus pneumoniae with respect to DNA methylation

Cited by 364 publications

References 28 publications

Can partial methylation explain the complex fragment patterns observed when plant mitochondrial DNA is cleaved with restriction endonucleases?

Can partial methylation explain the complex fragment patterns observed when plant mitochondrial DNA is cleaved with restriction endonucleases?

Two Alternative Conformations of S-Adenosyl-L-homocysteine Bound to Escherichia coli DNA Adenine Methyltransferase and the Implication of Conformational Changes in Regulating the Catalytic Cycle

Efficient Tn10 transposition into a DNA insertion hot spot in vivo requires the 5-methyl groups of symmetrically disposed thymines within the hot-spot consensus sequence.

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