Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape.

PLoS Genet
Authors
Keywords
Abstract

RNA-seq technologies have provided significant insight into the transcription networks of mycobacteria. However, such studies provide no definitive information on the translational landscape. Here, we use a combination of high-throughput transcriptome and proteome-profiling approaches to more rigorously understand protein expression in two mycobacterial species. RNA-seq and ribosome profiling in Mycobacterium smegmatis, and transcription start site (TSS) mapping and N-terminal peptide mass spectrometry in Mycobacterium tuberculosis, provide complementary, empirical datasets to examine the congruence of transcription and translation in the Mycobacterium genus. We find that nearly one-quarter of mycobacterial transcripts are leaderless, lacking a 5' untranslated region (UTR) and Shine-Dalgarno ribosome-binding site. Our data indicate that leaderless translation is a major feature of mycobacterial genomes and is comparably robust to leadered initiation. Using translational reporters to systematically probe the cis-sequence requirements of leaderless translation initiation in mycobacteria, we find that an ATG or GTG at the mRNA 5' end is both necessary and sufficient. This criterion, together with our ribosome occupancy data, suggests that mycobacteria encode hundreds of small, unannotated proteins at the 5' ends of transcripts. The conservation of small proteins in both mycobacterial species tested suggests that some play important roles in mycobacterial physiology. Our translational-reporter system further indicates that mycobacterial leadered translation initiation requires a Shine Dalgarno site in the 5' UTR and that ATG, GTG, TTG, and ATT codons can robustly initiate translation. Our combined approaches provide the first comprehensive view of mycobacterial gene structures and their non-canonical mechanisms of protein expression.

Year of Publication
2015
Journal
PLoS Genet
Volume
11
Issue
11
Pages
e1005641
Date Published
2015 Nov
ISSN
1553-7404
URL
DOI
10.1371/journal.pgen.1005641
PubMed ID
26536359
PubMed Central ID
PMC4633059
Links
Grant list
2T32AI049928 / AI / NIAID NIH HHS / United States
F32 AI085911 / AI / NIAID NIH HHS / United States
5T32AI007535-15 / AI / NIAID NIH HHS / United States
AI097191-01A1 / AI / NIAID NIH HHS / United States
1DP2OD001378-01 / OD / NIH HHS / United States
U19 AI107774 / AI / NIAID NIH HHS / United States
DP2 OD001378 / OD / NIH HHS / United States
R01 AI097191 / AI / NIAID NIH HHS / United States
5F32AI085911-02 / AI / NIAID NIH HHS / United States