Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression.
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.
Baranov
Pavel V
PV
Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA. baranov@genetics.utah.edu
Hammer
Andrew W
AW
Zhou
Jiadong
J
Gesteland
Raymond F
RF
Atkins
John F
JF
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*
D004251:DNA Transposable Elements; D012329:RNA, Bacterial; D000241:Adenosine; D013936:Thymidine