Putatively Noncoding Transcripts Show Extensive Association with Ribosomes

Abstract

There have been recent surprising reports that whole genes can evolve de novo from noncoding sequences. This would be extraordinary if the noncoding sequences were random with respect to amino acid identity. However, if the noncoding sequences were previously translated at low rates, with the most strongly deleterious cryptic polypeptides purged by selection, then de novo gene origination would be more plausible. Here we analyze Saccharomyces cerevisiae data on noncoding transcripts found in association with ribosomes. We find many such transcripts. Although their average ribosomal densities are lower than those of protein-coding genes, a significant proportion of noncoding transcripts nevertheless have ribosomal densities comparable to those of coding genes. Most show increased ribosomal association in response to starvation, as has been previously reported for other noncoding sequences such as untranslated regions and introns. In rich media, ribosomal association is correlated with start codons but is not usually consistent and contiguous beyond that, suggesting that translation occurs only at low rates. One transcript contains a 28-codon open reading frame, which we name RDT1, which shows evidence of translation, and may be a new protein-coding gene that originated de novo from noncoding sequence. But the bulk of the ribosomal association cannot be attributed to unannotated protein-coding genes. Our primary finding of extensive ribosome association shows that a necessary precondition for selective purging is met, making de novo gene evolution more plausible. Our analysis is also proof of principle of the utility of ribosomal profiling data for the purpose of gene annotation.

Integration of New Genes into Cellular Networks, and Their Structural Maturation

“…Real proteins are not random structures; i.e., they can be characterized with distinct biophysical properties like stability or aggregation propensity (DePristo et al 2005;Monsellier and Chiti 2007), although, quite surprisingly, some of their basic features, like the presence of secondary structural elements (a-helices and b-strands), are already formed in random sequences (Schaefer et al 2010). Genome-wide studies of transcription in several species indicate that a large fraction of genome, including the noncoding part, is transcribed in most species (Kapranov et al 2007;Nagalakshmi et al 2008;Xu et al 2009), and some of the noncoding transcripts are associated with ribosomes and occasionally translated (Wilson and Masel 2011).…”

Methods for distinguishing between protein-coding and long noncoding RNAs and the elusive biological purpose of translation of long noncoding RNAs

“…8 Such metrics can classify by read density similar to the density in coding regions [65], the match of the RPF to the reading frame [55], and nucleotide composition and conservation [66].…”

“…A different and interesting way to view pervasive translation of lncRNAs is that these genes can serve as a platform for de novo protein evolution [65,90]. Characteristics of a majority of lncRNAs, in particular, their relative novelty and lineage specificity, suggest that these lncRNAs could be strong candidates as precursors for new proteins.…”

Cellular mRNAs access second ORFs using a novel amino acid sequence-dependent coupled translation termination–reinitiation mechanism

“…If the sequence surrounding the first AUG is not favorable the ribosome may use leaky scanning to initiate translation at the next AUG to generate additional proteins (Kozak 1997). Ribosomes can be detected translating alternative reading frames (Wilson and Masel 2011;Michel et al 2012). Additional translational initiation mechanisms include the use of internal ribosome entry sites (IRES), ribosomal shunting, and coupled translation (Ahmadian et al 2000;Rogers et al 2004;Spriggs et al 2008).…”