Controller protein of restriction-modification system Kpn2I affects transcription of its gene by acting as a transcription elongation roadblock

• Published in: Nucleic acids research 2018-11, Vol.46 (20), p.10810-10826
• Main Authors: Klimuk, Evgeny, Bogdanova, Ekaterina, Nagornykh, Max, Rodic, Andjela, Djordjevic, Marko, Medvedeva, Sofia, Pavlova, Olga, Severinov, Konstantin
• Format: Article
• Language: English
• Subjects: Molecular Biology
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gky880

Abstract C-proteins control restriction-modification (R-M) systems' genes transcription to ensure sufficient levels of restriction endonuclease to allow protection from foreign DNA while avoiding its modification by excess methyltransferase. Here, we characterize transcription regulation in C-protein dependent R-M system Kpn2I. The Kpn2I restriction endonuclease gene is transcribed from a constitutive, weak promoter, which, atypically, is C-protein independent. Kpn2I C-protein (C.Kpn2I) binds upstream of the strong methyltransferase gene promoter and inhibits it, likely by preventing the interaction of the RNA polymerase sigma subunit with the -35 consensus element. Diminished transcription from the methyltransferase promoter increases transcription from overlapping divergent C-protein gene promoters. All known C-proteins affect transcription initiation from R-M genes promoters. Uniquely, the C.Kpn2I binding site is located within the coding region of its gene. C.Kpn2I acts as a roadblock stalling elongating RNA polymerase and decreasing production of full-length C.Kpn2I mRNA. Mathematical modeling shows that this unusual mode of regulation leads to the same dynamics of accumulation of R-M gene transcripts as observed in systems where C-proteins act at transcription initiation stage only. Bioinformatics analyses suggest that transcription regulation through binding of C.Kpn2I-like proteins within the coding regions of their genes may be widespread.