title: Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use.
abstract: Genetic decoding is not 'frozen' as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational 'correction' of problem or 'savior' indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5' or 3' of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3' from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression.
authors.affiliation: School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland School of Microbiology, University College Cork, Cork, Ireland Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA j.atkins@ucc.ie.
authors.forename: John F
authors.initials: JF
authors.lastname: Atkins
authors.affiliation: School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
authors.forename: Gary
authors.initials: G
authors.lastname: Loughran
authors.affiliation: School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
authors.forename: Pramod R
authors.initials: PR
authors.lastname: Bhatt
authors.affiliation: Division of Virology, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK.
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Firth
authors.affiliation: School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Baranov
mesh_terms: D000818:Animals; D057486:Carbon Cycle; D002875:Chromosomes / Q000235:genetics; D003062:Codon / Q000235:genetics; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D018965:Frameshifting, Ribosomal / Q000235:genetics*; D006801:Humans; D008928:Mitochondria / Q000378:metabolism; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames / Q000235:genetics; D011073:Polyamines / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics; D012335:RNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D012194:RNA-Directed DNA Polymerase / Q000378:metabolism; D018626:Retroelements / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D019098:Telomerase / Q000378:metabolism; D014158:Transcription, Genetic / Q000235:genetics*; D014780:Viruses / Q000235:genetics
chemical_list: D003062:Codon; D011073:Polyamines; D012333:RNA, Messenger; D012335:RNA, Ribosomal; D018626:Retroelements; D012194:RNA-Directed DNA Polymerase; D019098:Telomerase; D012321:DNA-Directed RNA Polymerases; D004259:DNA-Directed DNA Polymerase