Structure-aware mycobacterium tuberculosis functional annotation uncloaks resistance, metabolic, and virulence genes

• Main Authors: Baughn, A.D (Author), Chan, C.K (Author), Dhillon, N. (Author), Dillon, N.A (Author), Elghraoui, A. (Author), Gunasekaran, D. (Author), Kuo, N. (Author), Modlin, S.J (Author), Robinhold, C. (Author), Valafar, F. (Author), Zlotnicki, A.M (Author)
• Format: Article
• Language: English
• Published: American Society for Microbiology 2021
• Subjects: antibiotic agent; antibiotic resistance; Article; bacterial enzyme; bacterial gene; bacterial genome; bacterial protein; bacterial virulence; bacterium mutant; carrier protein; coenzyme A; controlled study; drug efficacy; drug metabolism; Mycobacterium tuberculosis; nonhuman; Protein Data Bank; protein structure; pyrazinamide; transposon; tuberculosis; type strain; virulence factor
• Online Access: View Fulltext in Publisher

 Accurate and timely functional genome annotation is essential for translating basic pathogen research into clinically impactful advances. Here, through literature curation and structure-function inference, we systematically update the functional genome annotation of Mycobacterium tuberculosis virulent type strain H37Rv. First, we systematically curated annotations for 589 genes from 662 publications, including 282 gene products absent from leading databases. Second, we modeled 1,711 underannotated proteins and developed a semiautomated pipeline that captured shared function between 400 protein models and structural matches of known function on Protein Data Bank, including drug efflux proteins, metabolic enzymes, and virulence factors. In aggregate, these structure- and literature-derived annotations update 940/1,725 underannotated H37Rv genes and generate hundreds of functional hypotheses. Retrospectively applying the annotation to a recent whole-genome transposon mutant screen provided missing function for 48% (13/27) of underannotated genes altering antibiotic efficacy and 33% (23/69) required for persistence during mouse tuberculosis (TB) infection. Prospective application of the protein models enabled us to functionally interpret novel laboratory generated pyrazinamide (PZA)-resistant mutants of unknown function, which implicated the emerging coenzyme A depletion model of PZA action in the mutants’ PZA resistance. Our findings demonstrate the functional insight gained by integrating structural modeling and systematic literature curation, even for widely studied microorganisms. Functional annotations and protein structure models are available at https://tuberculosis.sdsu.edu/H37Rv in human- and machine-readable formats. Copyright © 2021 Modlin et al.