Meirav, E. | Search bioRxiv

bioRxiv2026

Polyketide synthase 12 is an in vivo essential source of novel mycolyl lipids in Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) is a major pathogen worldwide that infects and transmits only among humans, yet nearly all in vivo virulence research occurs in non-human hosts. To overcome this central challenge in tuberculosis research, we leveraged a dataset of more than 50,000 sequenced isolates to identify Mtb genes that that are functionally preserved during natural infection, disease causation, and transmission between humans. This whole-genome ranking identified polyketide synthase 12 (pks12 ) as an exceptionally in vivo essential gene in human tuberculosis, which we validated in zebrafish and mouse models. Though Pks12 produces a mycoketide lipid in only trace amounts, pks12 deletion severely altered the host-facing surface and arabinoglycan architecture of Mtb. This amplified effect was explained through the discovery of mannosyl-{beta}-1-phosphomycoketide monomycolate (MPMMM), which is synthesized from the known Pks12 product at higher abundance by antigen 85 mycolyltransferases. Thus, we used a new host-facing genomic-metabolomic-phenotypic approach to discover the functions of an in vivo essential Mtb gene, which controls the physical structure of the Mtb-host interface.

microbiology↗

bioRxiv2026

Encoded metabolic remodeling amplifies drug resistance in Mycobacterium tuberculosis

Antibiotic pressure causes pathogens to evolve many forms of altered drug susceptibility. In addition to target or activator mutations conferring canonical drug resistance, mutations can serve as steppingstones to or enhancers of resistance. In clinical strains of Mycobacterium tuberculosis (Mtb), we find that idsA2, which encodes an isoprenyl pyrophosphate synthase involved in the synthesis of precursors for essential components of the cell wall and electron transport chain, is undergoing diversifying selection and that these mutations are associated with the acquisition of first-line antibiotic resistance. By engineering isogenic Mtb strains that express clinically prevalent variants of idsA2, we show that clinical variants increase the minimum inhibitory concentration of ethambutol and, to a lesser extent, of isoniazid. Targeted lipid analyses reveal that disrupting IdsA2 function redirects limited resources in the isoprenoid synthesis pathway, leading to increased production of decaprenylphosporyl pentose which can compete with ethambutol for binding to arabinosyltransferases. IdsA2 mutations most often occur after embB mutation and lead to a multiplicative increase in ethambutol resistance. Thus, identification of idsA2 mutations can be utilized to improve the specificity of genotypic ethambutol susceptibility testing. Together, this work defines idsA2 as an ethambutol resistance gene and demonstrates how metabolic remodeling can augment drug resistance. Author SummaryTuberculosis is the deadliest infectious disease in the world and becomes more difficult to treat with the acquisition of drug resistance. Defining the mechanisms and genetic basis of drug resistance will allow for improved screening and drug regimen optimization for treatment success. To identify previously unrecognized mechanisms of altered drug susceptibility, we have combined population genomics and experimental genetics approaches, focusing on Mycobacterium tuberculosis genes evolving in clinical strains. We identified idsA2 as a target of frequent mutations that are associated with drug resistance. Experimental data indicate that idsA2 variants decrease the susceptibility of the bacteria to multiple antibiotics through isoprenoid synthesis remodeling, with the strongest effect on ethambutol resistance. IdsA2 mutations often occur after embB mutations to multiplicatively increase ethambutol resistance. These data suggest that inclusion of idsA2 variants in drug resistance testing could improve the specificity of genotypic detection of ethambutol resistance.

microbiology↗