title: Transcription regulation of the type II restriction-modification system AhdI.
abstract: 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.
authors.affiliation: Waksman Institute, Piscataway, NJ 08854, USA.
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Bogdanova
authors.forename: Marko
authors.initials: M
authors.lastname: Djordjevic
authors.forename: Ioanna
authors.initials: I
authors.lastname: Papapanagiotou
authors.forename: Tomasz
authors.initials: T
authors.lastname: Heyduk
authors.forename: Geoff
authors.initials: G
authors.lastname: Kneale
authors.forename: Konstantin
authors.initials: K
authors.lastname: Severinov
mesh_terms: D001665:Binding Sites; D002874:Chromosome Mapping; D018983:DNA Footprinting; D015254:DNA Modification Methylases / Q000096:biosynthesis / Q000235:genetics*; D015252:Deoxyribonucleases, Type II Site-Specific / Q000096:biosynthesis / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D008957:Models, Genetic; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D014157:Transcription Factors; D015254:DNA Modification Methylases; D015252:Deoxyribonucleases, Type II Site-Specific