Random barcode transposon-site sequencing in Mycobacterium tuberculosis reveals the functions of uncharacterized genes

Mycobacterium tuberculosis (Mtb) is a human bacterial pathogen that establishes chronic infection in the lung. Although the genome of Mtb was sequenced nearly 25 years ago, the genetic basis of Mtb’s success as a human pathogen remains to be fully elucidated. Large-scale genetic approaches to understanding gene function are hindered by the limited throughput of traditional transposon sequencing strategies used in mycobacteria. To create a resource for determining the function of genes, we generated a pooled random barcode transposon-site sequencing (RB-TnSeq) library in Mycobacterium tuberculosis (Mtb). A unique twenty-nucleotide barcode in the transposon allows for rapid, high-throughput genetic screening without the laborious protocol of standard bacterial TnSeq screens. We performed 95 RB-TnSeq screens on an array of carbon sources, nitrogen sources, stressors, and antibiotics. Using the resulting dataset, we examined phenotypes of PE/PPE genes, a mycobacterial gene family whose function has long been elusive, uncovering 187 novel phenotypes across 37 genes in this family. We propose a pathway for lactate utilization in which the ESX-5 type VII secretion system exports PPE3, facilitating the import of D- and L-lactate into the bacterial cell. Notably, we identify a candidate D-lactate dehydrogenase that may mediate this metabolic capability. Additionally, we find that the proton-pumping NADH dehydrogenase Nuo is required for utilization of propionate, highlighting the metabolic flexibility of Mtb. Lastly, we characterize a novel mutant that confers resistance to the new tuberculosis antibiotic pretomanid. Results from these genetic screens will facilitate the development of additional new hypotheses about the function of uncharacterized genes and will expand our knowledge of Mtb metabolism and resistance to stress.