title: Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma.
abstract: BACKGROUND
  The genus Alphavirus includes several potentially lethal human viruses. Additionally, species such as Sindbis virus and Semliki Forest virus are important vectors for gene therapy, vaccination and cancer research, and important models for virion assembly and structural analyses. The genome encodes nine known proteins, including the small '6K' protein. 6K appears to be involved in envelope protein processing, membrane permeabilization, virion assembly and virus budding. In protein gels, 6K migrates as a doublet--a result that, to date, has been attributed to differing degrees of acylation. Nonetheless, despite many years of research, its role is still relatively poorly understood.
  
  
  RESULTS
  We report that ribosomal -1 frameshifting, with an estimated efficiency of approximately 10-18%, occurs at a conserved UUUUUUA motif within the sequence encoding 6K, resulting in the synthesis of an additional protein, termed TF (TransFrame protein; approximately 8 kDa), in which the C-terminal amino acids are encoded by the -1 frame. The presence of TF in the Semliki Forest virion was confirmed by mass spectrometry. The expression patterns of TF and 6K were studied by pulse-chase labelling, immunoprecipitation and immunofluorescence, using both wild-type virus and a TF knockout mutant. We show that it is predominantly TF that is incorporated into the virion, not 6K as previously believed. Investigation of the 3' stimulatory signals responsible for efficient frameshifting at the UUUUUUA motif revealed a remarkable diversity of signals between different alphavirus species.
  
  
  CONCLUSIONS
  Our results provide a surprising new explanation for the 6K doublet, demand a fundamental reinterpretation of existing data on the alphavirus 6K protein, and open the way for future progress in the further characterization of the 6K and TF proteins. The results have implications for alphavirus biology, virion structure, viroporins, ribosomal frameshifting, and bioinformatic identification of novel frameshift-expressed genes, both in viruses and in cellular organisms.
authors.affiliation: BioSciences Institute, University College Cork, Cork, Ireland. A.Firth@ucc.ie
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Firth
authors.forename: Betty Yw
authors.initials: BY
authors.lastname: Chung
authors.forename: Marina N
authors.initials: MN
authors.lastname: Fleeton
authors.forename: John F
authors.initials: JF
authors.lastname: Atkins
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D017124:Conserved Sequence; D006224:Cricetinae; D005455:Fluorescent Antibody Technique; D018965:Frameshifting, Ribosomal; D023061:Gene Order; D047468:Immunoprecipitation; D007553:Isotope Labeling; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry; D012672:Semliki forest virus / Q000235:genetics / Q000502:physiology*; D015678:Viral Structural Proteins / Q000096:biosynthesis* / Q000737:chemistry; D014771:Virion / Q000737:chemistry
chemical_list: D012367:RNA, Viral; D015678:Viral Structural Proteins