Regulation of RNA Polymerase Promoter Selectivity by Covalent Modification of DNA

Zakharova, Marina; Minakhin, Leonid; Solonin, Alexander S.; Severinov, Konstantin

doi:10.1016/j.jmb.2003.09.081

Cited by 16 publications

(16 citation statements)

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“…We here show that the AhdI methylase attenuates transcription of its own genes by methylating a site that partially overlaps with the -10 element of its promoter. This mechanism of negative autoregulation is similar to that we previously described for CfrBI, a C-protein-independent R-M system whose divergent transcription is controlled by methylation of a CfrBI site overlapping with the -35 element of the methyltransferase promoter (19). The ‘engineering’ solution used in AhdI for attenuation of the synthesis of methyltransferase, is clearly not the only one possible in convergently-transcribed C-protein-dependent systems.…”

Section: Discussionsupporting

confidence: 73%

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Transcription regulation of the type II restriction-modification system AhdI

Bogdanova

Djordjevic

Papapanagiotou

et al. 2008

Nucleic Acids Research

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The Restriction-modification system AhdI contains two convergent transcription units, one with genes encoding methyltransferase subunits M and S and another with genes encoding the controller (C) protein and the restriction endonuclease (R). We show that AhdI transcription is controlled by two independent regulatory loops that are well-optimized to ensure successful establishment in a naïve bacterial host. Transcription from the strong MS promoter is attenuated by methylation of an AhdI site overlapping the -10 element of the promoter. Transcription from the weak CR promoter is regulated by the C protein interaction with two DNA-binding sites. The interaction with the promoter-distal high-affinity site activates transcription, while interaction with the weaker promoter-proximal site represses it. Because of high levels of cooperativity, both C protein-binding sites are always occupied in the absence of RNA polymerase, raising a question how activated transcription is achieved. We develop a mathematical model that is in quantitative agreement with the experiment and indicates that RNA polymerase outcompetes C protein from the promoter-proximal-binding site. Such an unusual mechanism leads to a very inefficient activation of the R gene transcription, which presumably helps control the level of the endonuclease in the cell.

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Section: Discussionsupporting

confidence: 73%

“…Escherichia coli Z85 and HB101 (19), XL1-Blue (Stratagene) were used as host strains to study gene expression restriction of the λvir phage growth. Phage λvir was propagated as described (20).…”

Section: Methodsmentioning

confidence: 99%

Transcription regulation of the type II restriction-modification system AhdI

Bogdanova

Djordjevic

Papapanagiotou

et al. 2008

Nucleic Acids Research

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“…For example, in the CfrBI system of Citrobacter freundii, methylation of a cytosine (underlined) within the 5Ј-CCATGG-3Ј DNA restriction site decreases expression of the CfrBI methylase (CfrBIM) and concomitantly increases expression of the CfrBI restriction enzyme (CfrBIR) (18,294). This appears to occur as a result of the location of the cfrBI site within the Ϫ35 RNA polymerase 70 binding site of the cfrBIM gene.…”

Section: Origins: R-m Systemsmentioning

confidence: 99%

Epigenetic Gene Regulation in the Bacterial World

Casadesús

Low

2006

Microbiol Mol Biol Rev

553

562

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SUMMARY Like many eukaryotes, bacteria make widespread use of postreplicative DNA methylation for the epigenetic control of DNA-protein interactions. Unlike eukaryotes, however, bacteria use DNA adenine methylation (rather than DNA cytosine methylation) as an epigenetic signal. DNA adenine methylation plays roles in the virulence of diverse pathogens of humans and livestock animals, including pathogenic Escherichia coli, Salmonella, Vibrio, Yersinia, Haemophilus, and Brucella. In Alphaproteobacteria, methylation of adenine at GANTC sites by the CcrM methylase regulates the cell cycle and couples gene transcription to DNA replication. In Gammaproteobacteria, adenine methylation at GATC sites by the Dam methylase provides signals for DNA replication, chromosome segregation, mismatch repair, packaging of bacteriophage genomes, transposase activity, and regulation of gene expression. Transcriptional repression by Dam methylation appears to be more common than transcriptional activation. Certain promoters are active only during the hemimethylation interval that follows DNA replication; repression is restored when the newly synthesized DNA strand is methylated. In the E. coli genome, however, methylation of specific GATC sites can be blocked by cognate DNA binding proteins. Blockage of GATC methylation beyond cell division permits transmission of DNA methylation patterns to daughter cells and can give rise to distinct epigenetic states, each propagated by a positive feedback loop. Switching between alternative DNA methylation patterns can split clonal bacterial populations into epigenetic lineages in a manner reminiscent of eukaryotic cell differentiation. Inheritance of self-propagating DNA methylation patterns governs phase variation in the E. coli pap operon, the agn43 gene, and other loci encoding virulence-related cell surface functions.

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“…The presence of two LlaJI recognition sequences, and therefore methylated bases within the LlaJI promoter region initially suggested to us that, as for the CfrBI (Zakharova et al, 2004) and LlaDII (Christensen and Josephsen, 2004) systems, the methylation status of these modified cytosines is responsible for the control of LlaJI transcription. The presence of an N-terminal extension on M1.LlaJI beyond conserved motif I is structurally similar to those described for a number of prokaryotic MTases which exhibit an autoregulatory activity, achieved by direct binding to sequences within their respective promoters (Som and Friedman, 1994;Karyagina et al, 1997;Butler and Fitzgerald, 2001).…”

Section: Discussionmentioning

confidence: 99%