Sequence specificity of the P1 modification methylase (M·Eco P1) and the DNA methylase (M·Eco dam) controlled by the Escherichia coli dam gene

Hattman, Stanley; Brooks, Joan E.; Masurekar, Malthi

doi:10.1016/0022-2836(78)90046-3

Cited by 184 publications

(84 citation statements)

References 26 publications

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“…Only one (PE) appeared to bind a clearly liver specific factor in vitro (APF/HNF1 [4]). At this point, we noticed that this element contains an MboI restriction site (-53 GATC -50), where the adenine on each strand is methylated by DAM (19) in the standard E. coli K-12 strains used for the preparation of plasmids. At least one of the two methylated adenines (A/-51) on the coding strand has been shown by methylation interference to be a major contact point for APF in vitro (4).…”

Section: Resultsmentioning

confidence: 99%

“…Large-scale preparations of the different constructions were obtained from E. coli K-12 DH5-1-transformed bacteria. A dam mutant strain (GM113 dam3) was used for the preparation of plasmid DNA unmethylated at DAM methylation sites (5'-GATC-3') (19). We have controlled for the absence of DAM methylation by restriction analysis with the MboI enzyme, which recognizes GATC and cleaves only unmethylated DNA.…”

Section: Methodsmentioning

confidence: 99%

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The rat albumin promoter: cooperation with upstream elements is required when binding of APF/HNF1 to the proximal element is partially impaired by mutation or bacterial methylation.

et al. 1989

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Mol. Cell. Biol. 9:4750-4758, 1989) [29]). Third, additional sequences sometimes prove to be required in order to obtain the correct expression pattern in transgenic mice (18). This is the case for the albumin gene (31): in transgenic mice, abundant and liver-specific albumin gene transcription requires the presence of a region located between -8.5 and -10.4 kilobases in addition to the promoter.We have previously shown that the 150 base pairs upstream of the rat albumin gene constitutes a fully functional promoter in the differentiated hepatoma cell line H4II (32), where it is as active as the sinian virus 40 early promoter (20). In striking contrast, in dedifferentiated H5 hepatoma cells (12) or in fibroblasts, this promoter is 100-fold less active. The homologous region of the mouse albumin gene was shown to be required for tissue-specific transcription in vitro, using nuclear extracts from liver or other organs (15). We have shown that the tissue-specific promoter activity obtained after transfection relies on six independent positive elements, four of which bind a characterized trans-acting factor in vitro. Distal element II (DEII), at nucleotide -120, binds NF1/CTF, DEI at -90 binds C/EBP20 (1, 5, 27), a CCAAT box at -83 binds ACFINFY (33), and a proximal element (PE) at -60 binds the APF factor (4), also designated HNF-1, LF-B1, or HP1 in other contexts. Present only in hepatocytes and differentiated hepatoma cells, this last factor also participates in the transcriptional control of several other liver-specific genes, including al-antitrypsin (28), pyruvate kinase (S. Vaulont, personal communication), AFP (14,17), and transthyretin (8) genes.The strict tissue distribution of the APF/HNF1 factor, combined with the presence of its target sequence in a 4759

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The rat albumin promoter: cooperation with upstream elements is required when binding of APF/HNF1 to the proximal element is partially impaired by mutation or bacterial methylation.

et al. 1989

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“…2b), invariant residues that have been implicated in specific EcoRV-DNA interactions 29 . A P126S mutation generates the so-called Dam h form of T4Dam and T2Dam 30 ; which is prone to methylate noncognate sites such as the internal adenine in AGACC resulting in resistance to cleavage by the R.EcoP1 restriction endonuclease 2 . In vivo Dam h causes virion DNA hypermethylation 31 .…”

Section: Conserved Residues and The Effects Of Mutationsmentioning

confidence: 99%

Structure of the bacteriophage T4 DNA adenine methyltransferase

Yang

Horton

Zhou

et al. 2003

Nat Struct Mol Biol

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DNA-adenine methylation at certain GATC sites plays a pivotal role in bacterial and phage gene expression as well as bacterial virulence. We report here the crystal structures of the bacteriophage T4Dam DNA adenine methyltransferase (MTase) in a binary complex with the methyl-donor product S-adenosyl-L-homocysteine (AdoHcy) and in a ternary complex with a synthetic 12-bp DNA duplex and AdoHcy. T4Dam contains two domains: a seven-stranded catalytic domain that harbors the binding site for AdoHcy and a DNA binding domain consisting of a five-helix bundle and a β-hairpin that is conserved in the family of GATC-related MTase orthologs. Unexpectedly, the sequence-specific T4Dam bound to DNA in a nonspecific mode that contained two Dam monomers per synthetic duplex, even though the DNA contains a single GATC site. The ternary structure provides a rare snapshot of an enzyme poised for linear diffusion along the DNA.DNA MTases catalyze methyl group transfer from donor S-adenosyl-L-methionine (AdoMet), producing S-adenosyl-L-homocysteine (AdoHcy) and methylated DNA. Although most prokaryote DNA MTases are components of restriction-modification systems, some MTases are not associated with cognate restriction enzymes, such as the Escherichia coli DNA adenine MTase (Dam). This enzyme methylates an exocyclic amino nitrogen (N6) of the adenine in GATC 1,2 . Dam MTase gene orthologs are widespread among enteric bacteria and their bacteriophages (see Fig. 1 legend). Dam methylation is not essential for the viability of E. coli, unless it is combined with certain other mutations 3 ; however, Dam is an essential gene in Vibrio cholerae and Yersinia pesudotuberculosis, at least under the tested growth conditions 4 . Dam methylation is essential for the virulence of Salmonella serovar typhimurium in a murine model of typhoid fever [5][6][7] . These observations COMPETING INTERESTS STATEMENTThe authors declare that they have no competing financial interests. NIH Public Access RESULTS Overall structure of DamThe monomeric Dam structure contains 9 β-strands and 11 α-helices (Fig. 1). The Nterminal region (residues 1-52) and C-terminal region (residues 149-259) come together, forming the catalytic domain (green in Figs. 1 and 2a) with a seven-stranded β-sheet, a characteristic feature of the class-I AdoMet-dependent MTases 28 . The N-terminal helices αZ and αA are located on one side of the β-sheet, and helices αC, αD1 and αD2 and αE are on the other side. Between strands β2 and β3 is a separate domain, which we designate as the target-recognition domain (TRD). TRD is composed of a five-helix bundle (αB1-αB5) (yellow in Figs. 1 and 2a) and a 25-residue segment containing a β-hairpin (β8 and β9) inserted between helices αB4 and αB5 (red). The overall dimensions of the molecule are 55 × 34 × 28 Å, with an open cleft located between the catalytic domain (green) and the TRD (yellow and red). Conserved residues and the effects of mutationsBased on the linear arrangement of conserved motifs in DNA MTases, T4Dam is classified in the...

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“…Methylation at GATC sites by the dam methylase (Marinus & Morris, 1975;Hattman et al, 1978) directs a mismatch repair system in E. coli. This may reduce mutant yield by directing mismatch repair towards the methylated template strand (Radman et al, 1980;Glickman, 1982;Kramer et al, 1984a).…”

Section: Mutagenesis Using Mismatched Oligonucleotidesmentioning

confidence: 99%