title: Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation.
abstract: The sequence logo for DNA binding sites of the bacteriophage P1 replication protein RepA shows unusually high sequence conservation ( approximately 2 bits) at a minor groove that faces RepA. However, B-form DNA can support only 1 bit of sequence conservation via contacts into the minor groove. The high conservation in RepA sites therefore implies a distorted DNA helix with direct or indirect contacts to the protein. Here I show that a high minor groove conservation signature also appears in sequence logos of sites for other replication origin binding proteins (Rts1, DnaA, P4 alpha, EBNA1, ORC) and promoter binding proteins (sigma(70), sigma(D) factors). This finding implies that DNA binding proteins generally use non-B-form DNA distortion such as base flipping to initiate replication and transcription.
authors.affiliation: National Cancer Institute at Frederick, Laboratory of Experimental and Computational Biology, Building 469, PO Box B, Frederick, MD 21702-1201, USA. toms@ncifcrf.gov
authors.forename: T D
authors.initials: TD
authors.lastname: Schneider
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004265:DNA Helicases / Q000378:metabolism; D004261:DNA Replication; D004268:DNA-Binding Proteins / Q000378:metabolism*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D019309:Epstein-Barr Virus Nuclear Antigens / Q000378:metabolism; D009690:Nucleic Acid Conformation; D051738:Origin Recognition Complex; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012316:RNA Nucleotidyltransferases / Q000378:metabolism; D018741:Replication Origin; D012808:Sigma Factor / Q000378:metabolism; D024363:Transcription Initiation Site; D014158:Transcription, Genetic; D014764:Viral Proteins
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; C066312:DnaA protein, Bacteria; D019309:Epstein-Barr Virus Nuclear Antigens; D051738:Origin Recognition Complex; D012808:Sigma Factor; D014764:Viral Proteins; C095083:alpha protein, Bacteriophage P4; D004247:DNA; D012316:RNA Nucleotidyltransferases; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases; D004265:DNA Helicases; C417029:EBV-encoded nuclear antigen 1