Abstract
Recent functional, proteomic and ribosome profiling studies in eukaryotes have concurrently demonstrated the translation of alternative open-reading frames (altORFs) in addition to annotated protein coding sequences (CDSs). We show that a large number of small proteins could in fact be coded by these altORFs. The putative alternative proteins translated from altORFs have orthologs in many species and contain functional domains. Evolutionary analyses indicate that altORFs often show more extreme conservation patterns than their CDSs. Thousands of alternative proteins are detected in proteomic datasets by reanalysis using a database containing predicted alternative proteins. This is illustrated with specific examples, including altMiD51, a 70 amino acid mitochondrial fission-promoting protein encoded in MiD51/Mief1/SMCR7L, a gene encoding an annotated protein promoting mitochondrial fission. Our results suggest that many genes are multicoding genes and code for a large protein and one or several small proteins.
Highlights
Current protein databases are cornerstones of modern biology but are based on a number of assumptions
The density of alternative open-reading frames (altORFs) observed in the coding sequences (CDSs), 3’UTRs and ncRNAs (Figure 1f) was markedly higher than in the shuffled transcriptomes, suggesting that these are maintained at frequencies higher than expected by chance, again potentially due to their coding function
We focused on alternative proteins detected with at least two peptide spectrum matches or with high translation initiation site (TIS) reads and selected altMiD51 (IP_294711.1) among the top 2% of alternative proteins detected with the highest number of unique peptides in proteomics studies, and altDDIT3 (IP_211724.1) among the top 2% of altORFs with the most cumulative reads in translation initiation ribosome profiling studies
Summary
Current protein databases are cornerstones of modern biology but are based on a number of assumptions. Minimum size limits are imposed on the length of CDSs, resulting in many RNAs being mistakenly classified as non-coding (ncRNAs) Biochemistry Computational and Systems Biology eLife digest Proteins are often referred to as the workhorses of the cell, and these molecules affect all aspects of human health and disease. Deciphering the entire set of proteins made by an organism is often an important challenge for biologists
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
