Sequence motifs characteristic of DNA[cytosine-N4]methyltransferases: similarity to adenine and cytosine-C5 DNA-methylases

Klimašauskas, Saulius; Timinskas, Albertas; Saulius, Menkevicius; Butkienè, Danguolè; Butkus, Viktoras; Janulaitis, A.

doi:10.1093/nar/17.23.9823

Cited by 154 publications

(117 citation statements)

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“…Two amino acid sequence motifs in DNA methyltransferases have been pointed out previously (26). One of them, -GlSu-X-Phe-X-Gly-X-Gly-, where X stands for any amino acid, was suggested to be the S-adenosylmethionine binding site, and indeed, at amino acids 216 to 222, the trmA gene product has the sequence -Uj-Leu-Tyr-Cys-_1y-Asn-ily-.…”

Section: Resultsmentioning

confidence: 95%

The trmA promoter has regulatory features and sequence elements in common with the rRNA P1 promoter family of Escherichia coli

et al. 1991

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The tRNA(m5U54)methyltransferase, whose structural gene is designated trmA, catalyzes the formation of 5-methyluridine in position 54 of all tRNA species in Escherichia coli. The synthesis of this enzyme has previously been shown to be both growth rate dependent and stringently regulated, suggesting regulatory features similar to those of rRNA. We have determined the complete nucleotide sequence of the trmA operon in E. coli and the sequence of the trmA promoter region in SalmoneUa typhimurium and also analyzed the transcriptional regulation of the gene. The trmA and the btuB (encoding the vitamin B12 outer membrane receptor protein) promoters are divergent promoters separated by 102 bp between the transcriptional start sites. The trmA promoters of both E. coli and S. typhimurium share promoter elements with the rRNA P1 promoter. The sequence downstream from the -10 region of the trmA promoter is homologous to the discriminatory region found in stringently regulated promoters. Next to and upstream from the -10 region is a sequence, TCCC, in the trmA promoter that is present in all of the seven rRNA P1 promoters and in some tRNA promoters but not in any other Co70 promoter. However, a similar motif is also found in promoters transcribed by the heat shock sigma factor CJ32. The trmA gene is transcribed as a monocistronic operon, and the 3' end of the transcript is shown to be located downstream from a dyad symmetry region not followed by a poly(U) stretch. Using a trmA-cat operon fusion, we show that the growth rate-dependent regulation of trmA resembles that of rRNA and operates at the level of transcription.

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Section: Resultsmentioning

confidence: 95%

The trmA promoter has regulatory features and sequence elements in common with the rRNA P1 promoter family of Escherichia coli

et al. 1991

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“…We have searched the H. pylori DNA sequence looking for the following: a potential DNA MTase (M) gene containing conserved MTase sequence motifs (20,21) and an adjacent putative restriction endonuclease (R) gene, which either shares sequence similarity with the existing Type II endonuclease or shares no similarity with any known gene in the GenBank. Fourteen potential Type II R-M systems were found by using these criteria and are summarized in Table 1.…”

Section: Resultsmentioning

confidence: 99%

Comparative genomics of the restriction-modification systems in Helicobacter pylori

Lin

Pósfai

Roberts

et al. 2001

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

153

164

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Helicobacter pylori is a Gram-negative bacterial pathogen with a small genome of 1.64 -1.67 Mb. More than 20 putative DNA restrictionmodification (R-M) systems, comprising more than 4% of the total genome, have been identified in the two completely sequenced H. pylori strains, 26695 and J99, based on sequence similarities. In this study, we have investigated the biochemical activities of 14 Type II R-M systems in H. pylori 26695. Less than 30% of the Type II R-M systems in 26695 are fully functional, similar to the results obtained from strain J99. Although nearly 90% of the R-M genes are shared by the two H. pylori strains, different sets of these R-M genes are functionally active in each strain. Interestingly, all strain-specific R-M genes are active, whereas most shared genes are inactive. This agrees with the notion that strain-specific genes have been acquired more recently through horizontal transfer from other bacteria and selected for function. Thus, they are less likely to be impaired by random mutations. Our results also show that H. pylori has extremely diversified R-M systems in different strains, and that the diversity may be maintained by constantly acquiring new R-M systems and by inactivating and deleting the old ones.H elicobacter pylori is one of the most common bacterial pathogens that colonizes the gastric mucosa of humans. H. pylori is implicated in a wide range of gastroduodenal diseases (1, 2). H. pylori is commonly believed to be a very diverse species. It is believed that, in addition to genetic recombination, de novo mutation could have a role in generating the high level of genetic variation in H. pylori (3). MutH and MutL homologues cannot be found in H. pylori genomes, which suggests H. pylori may not have a functional mismatch repair system (4, 5). Recent analysis of the complete genomic sequences of two unrelated H. pylori isolates reveals that although intraspecies variation does exist, the overall genomic organization, gene order, and predicted proteins of the two strains are quite similar (5, 6). Approximately 6-7% of the genes are specific to each strain (5). The 26695 and J99 strains have a relatively small genome size of 1.67 and 1.64 megabase pairs (4, 5). However, more than twenty DNA restriction-modification (R-M) systems can be identified in each strain based on sequence similarities. The biological significance of this large complement of R-M systems is not clear. The majority of the H. pylori R-M systems are of Type II, which consist of two separate enzymes: the restriction endonucleases, which are responsible for degrading unmodified foreign DNA, and the modification DNA methyltransferases (methylase or M), which protect endogenous DNA from endonucleolytic digestion by methylating them at the endonuclease recognition sites (7).Interesting observations have been reported regarding H. pylori R-M genes. A novel H. pylori gene, iceA (induced when the bacteria contact the host epithelium), was identified recently (8). DNA sequences have revealed two alleles of the iceA locu...

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“…An FXGXG motif, also present in cytosine-C 5-MTases, and a DPPY motif (consensus sequence, (S/N/D)PP(Y/F/W)) are moderately conserved (17)(18)(19)(20), and the homologies of seven additional motifs are weak. Consequently, these additional motifs only recently could be identified in structure-guided alignments (21).…”

mentioning

confidence: 99%

Functional Roles of Conserved Amino Acid Residues in DNA Methyltransferases Investigated by Site-directed Mutagenesis of theEcoRV Adenine-N6-methyltransferase

Roth

Helm-Kruse

Friedrich

et al. 1998

Journal of Biological Chemistry

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Sequence motifs characteristic of DNA[cytosine-N4]methyltransferases: similarity to adenine and cytosine-C5 DNA-methylases

Cited by 154 publications

References 46 publications

The trmA promoter has regulatory features and sequence elements in common with the rRNA P1 promoter family of Escherichia coli

The trmA promoter has regulatory features and sequence elements in common with the rRNA P1 promoter family of Escherichia coli

Comparative genomics of the restriction-modification systems in Helicobacter pylori

Functional Roles of Conserved Amino Acid Residues in DNA Methyltransferases Investigated by Site-directed Mutagenesis of theEcoRV Adenine-N6-methyltransferase

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