Pervasive translation in Mycobacterium tuberculosis
- New York State Department of Health, United States
- University of Notre Dame, United States
Abstract
Most bacterial ORFs are identified by automated prediction algorithms. However, these algorithms often fail to identify ORFs lacking canonical features such as a length of >50 codons or the presence of an upstream Shine-Dalgarno sequence. Here, we use ribosome profiling approaches to identify actively translated ORFs in Mycobacterium tuberculosis. Most of the ORFs we identify have not been previously described, indicating that the M. tuberculosis transcriptome is pervasively translated. The newly described ORFs are predominantly short, with many encoding proteins of ≤50 amino acids. Codon usage of the newly discovered ORFs suggests that most have not been subject to purifying selection, and hence are unlikely to contribute to cell fitness. Nevertheless, we identify 90 new ORFs (median length of 52 codons) that bear the hallmarks of purifying selection. Thus, our data suggest that pervasive translation of short ORFs in Mycobacterium tuberculosis serves as a rich source for the evolution of new functional proteins.
Data availability
Raw Illumina sequencing data are available from the ArrayExpress and European Nucleotide Archive repositories with accession numbers E-MTAB-8039 and E-MTAB-10695. Raw mass spectrometry data are available through MassIVE, with exchange #MSV000087541. Reviewers can access the raw mass spectrometry data at ftp://MSV000087541@massive.ucsd.edu, password: sproteinTBPython code is available at https://github.com/wade-lab/Mtb_Ribo-RET.
-
Pervasive Translation in Mycobacterium tuberculosisEBI ArrayExpress E-MTAB-8039.
-
Pervasive Translation in Mycobacterium tuberculosisEBI ArrayExpress E-MTAB-10695.
Article and author information
Author details
Funding
National Institute of Allergy and Infectious Diseases (R21AI117158)
- Keith M Derbyshire
- Todd A Gray
- Joseph T Wade
National Institute of Allergy and Infectious Diseases (R21AI119427)
- Keith M Derbyshire
- Todd A Gray
- Joseph T Wade
National Institute of General Medical Sciences (R01GM139277)
- Matthew M Champion
- Keith M Derbyshire
- Todd A Gray
- Joseph T Wade
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Bavesh D Kana, University of the Witwatersrand, South Africa
Version history
- Preprint posted: June 10, 2019 (view preprint)
- Received: September 17, 2021
- Accepted: March 25, 2022
- Accepted Manuscript published: March 28, 2022 (version 1)
- Version of Record published: May 11, 2022 (version 2)
- Version of Record updated: May 23, 2022 (version 3)
Copyright
This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
Metrics
-
- 2,496
- views
-
- 447
- downloads
-
- 29
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Pervasive translation in Mycobacterium tuberculosis
eLife 11:e73980.
https://doi.org/10.7554/eLife.73980
Further reading
-
- Microbiology and Infectious Disease
- Structural Biology and Molecular Biophysics
Genetic diversity is a hallmark of RNA viruses and the basis for their evolutionary success. Taking advantage of the uniquely large genomic database of SARS-CoV-2, we examine the impact of mutations across the spectrum of viable amino acid sequences on the biophysical phenotypes of the highly expressed and multifunctional nucleocapsid protein. We find variation in the physicochemical parameters of its extended intrinsically disordered regions (IDRs) sufficient to allow local plasticity, but also observe functional constraints that similarly occur in related coronaviruses. In biophysical experiments with several N-protein species carrying mutations associated with major variants, we find that point mutations in the IDRs can have nonlocal impact and modulate thermodynamic stability, secondary structure, protein oligomeric state, particle formation, and liquid-liquid phase separation. In the Omicron variant, distant mutations in different IDRs have compensatory effects in shifting a delicate balance of interactions controlling protein assembly properties, and include the creation of a new protein-protein interaction interface in the N-terminal IDR through the defining P13L mutation. A picture emerges where genetic diversity is accompanied by significant variation in biophysical characteristics of functional N-protein species, in particular in the IDRs.
-
- Microbiology and Infectious Disease
- Structural Biology and Molecular Biophysics
A new study reveals how naturally occurring mutations affect the biophysical properties of nucleocapsid proteins in SARS-CoV-2.
