A Functional –1 Ribosomal Frameshift Signal in the Human Paraneoplastic Ma3 Gene

Abstract

A bioinformatics approach to finding new cases of ؊1 frameshifting in the expression of human genes revealed a classical retroviruslike heptanucleotide shift site followed by a potential structural stimulator in the paraneoplastic antigen Ma3 and Ma5 genes. Analysis of the sequence 3 of the shift site demonstrated that an RNA pseudoknot in Ma3 is important for promoting efficient ؊1 frameshifting. Ma3 is a member of a family of six genes in humans whose protein products contain homology to retroviral Gag proteins. The ؊1 frameshift site and pseudoknot structure are conserved in other mammals, but there are some sequence differences. Although the functions of the Ma genes are unknown, the serious neurological effects of ectopic expression in tumor cells indicate their importance in the brain.Although nonoverlapping triplet reading of mRNA codons is the essence of genetic decoding, dynamic nonstandard events at specific sites can permit product diversity and provide regulatory options. One of these recoding events involves shifting to an alternative reading frame by a proportion of ribosomes, thereby changing the linearity of readout. Such utilized frameshifting commonly features both a "shifty site" in the mRNA and an appropriately positioned structural feature in the mRNA that acts to enhance the level of frameshifting, i.e. it is programmed. Although the shift involved can be to either alternative frame, a shift to the Ϫ1 frame often involves tRNAs in both the A and P sites detaching from their codons and re-pairing to mRNA at the two overlapping Ϫ1 frame codons (1, 2). This tandem detachment and re-pairing usually occurs on a "slippery" heptanucleotide sequence that follows the general pattern of X XXY YYZ where the A and P site tRNAs detach from the zero frame codons XXY YYZ and re-pair after shifting 1 nucleotide to XXX YYY. The spacer region between the shift site and the 3Ј structural element is commonly 6 -8 nt 2 (3). The most common 3Ј recoding signals for Ϫ1 frameshifting are pseudoknots (4, 5) with distinct features (6, 7). A less common type of pseudoknot is the kissing stem-loop found in the human coronavirus, HCV229E (8), but bioinformatic studies suggest that it may be involved for transmissible gastroenteritis virus frameshifting also (9).Examples of genes that require Ϫ1 frameshifting for expression are well known in viral genomes. There is only one demonstrated case of Ϫ1 frameshifting in a mammalian cellular gene (10, 11), but it does not display the phylogenetic breadth of the ϩ1 frameshifting utilized in decoding antizyme mRNA, conserved from mammals to yeasts (12). Frameshifting near the end of a coding sequence often allows a proportion of ribosomes to access an ORF that extends beyond the zero frame terminator so that the transframe (coupled ORF) protein is longer than that of standard decoding. The easiest class of Ϫ1 programmed frameshift events to search for is one that has conserved architecture of two ORFs that partially overlap and contains a defined shift site. In these cases conser...

Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning

“…105) and PNMA3 (REF. 106). Although it is likely that many cases of productive PRF are still undiscovered, it is also likely that productive PRF is very rare among non-mobile chromosomal genes in most organisms (see below for a noticeable exception involving pervasive frameshifting in Euplotes spp.).…”

Mammalian Gene PEG10 Expresses Two Reading Frames by High Efficiency –1 Frameshifting in Embryonic-associated Tissues

“…The human paraneoplastic antigen gene Ma3 has a functional frameshift element, shown to be active between two reporter genes at ϳ20% efficiency in vitro and ϳ18% in cell culture (46). The Ma3 ORF1 contains homology to retroviral Gag proteins in rodents and other primates, but the poorly conserved putative ORF2 protein does not contain a Pol-like sequence and shows no homology to any proteins in the data base (46).…”

Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes

“…Only one Ma protein has conserved the CCHC zinc finger domain present in the ancestral Gag protein, and two genes use a retroviral-like À1 ribosomal frameshift. (79) Ma1/Map-1 is able to interact with the pro-apoptotic Bax protein and to mediate caspase-dependent apoptosis. (82) The Fv1 (Friend virus susceptibility 1) gene, another gagderived sequence, restricts murine leukemia virus replication.…”

“…(69) A second unrelated family of gag-derived genes called Ma has been identified in human and other mammalian genomes. (79,80) These genes encode neuronal proteins that are target of the autoimmune response associated with paraneoplastic neurological disorders. (80,81) Six genes have been described in human, three of them being located on the X chromosome.…”