title: Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression.
abstract: BACKGROUND
  Transcription slippage occurs on certain patterns of repeat mononucleotides, resulting in synthesis of a heterogeneous population of mRNAs. Individual mRNA molecules within this population differ in the number of nucleotides they contain that are not specified by the template. When transcriptional slippage occurs in a coding sequence, translation of the resulting mRNAs yields more than one protein product. Except where the products of the resulting mRNAs have distinct functions, transcription slippage occurring in a coding region is expected to be disadvantageous. This probably leads to selection against most slippage-prone sequences in coding regions.
  
  
  RESULTS
  To find a length at which such selection is evident, we analyzed the distribution of repetitive runs of A and T of different lengths in 108 bacterial genomes. This length varies significantly among different bacteria, but in a large proportion of available genomes corresponds to nine nucleotides. Comparative sequence analysis of these genomes was used to identify occurrences of 9A and 9T transcriptional slippage-prone sequences used for gene expression.
  
  
  CONCLUSIONS
  IS element genes are the largest group found to exploit this phenomenon. A number of genes with disrupted open reading frames (ORFs) have slippage-prone sequences at which transcriptional slippage would result in uninterrupted ORF restoration at the mRNA level. The ability of such genes to encode functional full-length protein products brings into question their annotation as pseudogenes and in these cases is pertinent to the significance of the term 'authentic frameshift' frequently assigned to such genes.
authors.affiliation: Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA. baranov@genetics.utah.edu
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Baranov
authors.forename: Andrew W
authors.initials: AW
authors.lastname: Hammer
authors.forename: Jiadong
authors.initials: J
authors.lastname: Zhou
authors.forename: Raymond F
authors.initials: RF
authors.lastname: Gesteland
authors.forename: John F
authors.initials: JF
authors.lastname: Atkins
mesh_terms: D000241:Adenosine / Q000032:analysis; D001419:Bacteria / Q000235:genetics*; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D004251:DNA Transposable Elements / Q000235:genetics*; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D023281:Genomics; D008954:Models, Biological; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D012329:RNA, Bacterial / Q000096:biosynthesis*; D012641:Selection, Genetic; D016415:Sequence Alignment; D013936:Thymidine / Q000032:analysis; D014158:Transcription, Genetic / Q000502:physiology*
chemical_list: D004251:DNA Transposable Elements; D012329:RNA, Bacterial; D000241:Adenosine; D013936:Thymidine