Programmed ribosomal frameshifting in the expression of the regulator of intestinal stem cell proliferation, adenomatous polyposis coli (APC)

Abstract

A programmed ribosomal frameshift (PRF) in the decoding of APC (adenomatous polyposis coli) mRNA has been identified and characterized in Caenorhabditis worms, Drosophila and mosquitoes. The frameshift product lacks the C-terminal approximately one-third of the product of standard decoding and instead has a short sequence encoded by the -1 frame which is just 13 residues in C. elegans, but is 125 in D. melanogaster. The frameshift site is A_AA.A_AA.C in Caenorhabditids, fruit flies and the mosquitoes studied while a variant A_AA.A_AA.A is found in some other nematodes. The predicted secondary RNA structure of the downstream stimulators varies considerably in the species studied. In the twelve sequenced Drosophila genomes, it is a long stem with a four-way junction in its loop. In the five sequenced Caenorhabditis species, it is a short RNA pseudoknot with an additional stem in loop 1. The efficiency of frameshifting varies significantly, depending on the particular stimulator within the frameshift cassette, when tested with reporter constructs in rabbit reticulocyte lysates. Phylogenetic analysis of the distribution of APC programmed ribosomal frameshifting cassettes suggests it has an ancient origin and raises questions about a possibility of synthesis of alternative protein products during expression of APC in other organisms such as humans. The origin of APC as a PRF candidate emerged from a prior study of evolutionary signatures derived from comparative analysis of the 12 fly genomes. Three other proposed PRF candidates (Xbp1, CG32736, CG14047) with switches in conservation of reading frames are likely explained by mechanisms other than PRF.

Programmed −1 frameshifting efficiency correlates with RNA pseudoknot conformational plasticity, not resistance to mechanical unfolding

“…Essential aspects of viral function, such as replication of the viral genome and packaging of the genome into a virion, depend critically on the tight regulation of the optimum expression ratio of the frameshifted proteins (5,6). Also, −1 PRF occurs during the expression of cellular genes in a wide range of other organisms (4,(7)(8)(9).…”

Small synthetic molecule-stabilized RNA pseudoknot as an activator for –1 ribosomal frameshifting

“…Many viruses use -1PRF to ensure correct stoichiometry of proteins required for their replication (51)(52)(53). By contrast, the role of -1PRF in eukaryotic system is not fully understood (54)(55)(56)(57)(58)(59)(60)(61)(62). Some -1PRF signals regulate the expression of two distinct polypeptides during embryogenesis (54,55,57), other produce a truncated product that may have functions distinct from the full-length product (58), and some cause premature termination of translation leading to the nonsense-mediated mRNA decay pathway (59,60).…”

“…By contrast, the role of -1PRF in eukaryotic system is not fully understood (54)(55)(56)(57)(58)(59)(60)(61)(62). Some -1PRF signals regulate the expression of two distinct polypeptides during embryogenesis (54,55,57), other produce a truncated product that may have functions distinct from the full-length product (58), and some cause premature termination of translation leading to the nonsense-mediated mRNA decay pathway (59,60). -1PRF is typically triggered by two cisacting mRNA signals, a slippery sequence (63) comprising seven nucleotides (X XXY YYZ; the 0 frame is indicated by spaces) and a downstream secondary structure, which is often an RNA pseudoknot (64)(65)(66).…”

Ribosomal Frameshift Signals in Viral Genomes

“…A possible caveat with this approach is the demonstrated presence of frameshift signals in non-viral, host genomes (Baranov et al, 2011;Belew et al, 2010;Manktelow et al, 2005). Programmed frameshifting on non-viral transcripts has also been linked to the mRNA decay pathway in yeast cells (Plant et al, 2004).…”

“…In addition, frameshift signals have been characterized in several retrotransposons. Recently programmed ribosomal frameshift (PRF) signals were characterized in several invertebrates (Baranov et al, 2011). Currently there is only one characterized example of a frameshift signal in a mammalian genome but it is likely that more will be discovered and described as interest in recoding signals spreads (Manktelow et al, 2005).…”