Genome-wide co-essentiality analysis in Mycobacterium tuberculosis reveals an itaconate defense enzyme module

Abstract

Genome-wide random mutagenesis screens using transposon sequencing (TnSeq) have been a cornerstone of functional genetics in Mycobacterium tuberculosis (Mtb), helping to define gene essentiality across a wide range of experimental conditions. Here, we harness a recently compiled TnSeq database to identify pairwise correlations of gene essentiality profiles (i.e. co-essentiality analysis) across the Mtb genome and reveal clusters of genes with similar function. We describe selected modules identified by our pipeline, review the literature supporting their associations, and propose hypotheses about novel associations. We focus on a cluster of seven enzymes for experimental validation, characterizing it as an enzymatic arsenal that helps Mtb counter the toxic effects of itaconate, a host-derived antibacterial compound. We extend the use of these correlations to enable prediction of protein complexes by designing a virtual screen that ranks potentially interacting heterodimers from co-essential protein pairs. We envision co-essentiality analysis will help accelerate gene functional discovery in this important human pathogen.