title: Nature of the promoter activated by C.PvuII, an unusual regulatory protein conserved among restriction-modification systems.
abstract: A widely distributed family of small regulators, called C proteins, controls a subset of restriction-modification systems. The C proteins studied to date activate transcription of their own genes and that of downstream endonuclease genes; this arrangement appears to delay endonuclease expression relative to that of the protective methyltransferase when the genes enter a new cell. C proteins bind to conserved sequences called C boxes. In the PvuII system, the C boxes have been reported to extend from -23 to +3 relative to the transcription start for the gene for the C protein, an unexpected starting position relative to a bound activator. This study suggests that transcript initiation within the C boxes represents initial, C-independent transcription of pvuIICR. The major C protein-dependent transcript appears to be a leaderless mRNA starting farther downstream, at the initiation codon for the pvuIIC gene. This conclusion is based on nuclease S1 transcript mapping and the effects of a series of nested deletions in the promoter region. Furthermore, replacing the region upstream of the pvuIIC initiation codon with a library of random oligonucleotides, followed by selection for C-dependent transcription, yielded clones having sequences that resemble -10 promoter hexamers. The -35 hexamer of this promoter would lie within the C boxes. However, the spacing between C boxes/-35 and the apparent -10 hexamer can be varied by +/-4 bp with little effect. This suggests that, like some other activator-dependent promoters, PpvuIICR may not require a -35 hexamer. Features of this transcription activation system suggest explanations for its broad host range.
authors.affiliation: Department of Microbiology and Immunology and Program in Bioinformatics and Proteomics/Genomics, Medical College of Ohio, 3055 Arlington Ave., Toledo, OH 43614-5806, USA.
authors.forename: Dieter
authors.initials: D
authors.lastname: Knowle
authors.forename: Robert E
authors.initials: RE
authors.lastname: Lintner
authors.forename: Yara M
authors.initials: YM
authors.lastname: Touma
authors.forename: Robert M
authors.initials: RM
authors.lastname: Blumenthal
mesh_terms: D015280:DNA Restriction-Modification Enzymes / Q000235:genetics / Q000502:physiology; D004268:DNA-Binding Proteins / Q000235:genetics / Q000502:physiology*; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D011514:Proteus vulgaris / Q000201:enzymology* / Q000235:genetics; D017384:Sequence Deletion; D015719:Single-Strand Specific DNA and RNA Endonucleases / Q000378:metabolism; D024363:Transcription Initiation Site; D014158:Transcription, Genetic; D015533:Transcriptional Activation
chemical_list: D015280:DNA Restriction-Modification Enzymes; D004268:DNA-Binding Proteins; C025630:CAGCTG-specific type II deoxyribonucleases; D015252:Deoxyribonucleases, Type II Site-Specific; D015719:Single-Strand Specific DNA and RNA Endonucleases