Biology subjects

Boradia, V.

Publications and source records attributed to Boradia, V..

4 recordsLinked to original sources

bioRxiv2026

Inorganic sulfate transport by the Mycobacterium tuberculosis PE22/PPE36 complex

Mycobacterium tuberculosis (Mtb) encodes two multigene families with 169 members that are exclusive to mycobacteria, the pe and ppe genes. These genes have unusual sequences including low-complexity repeat regions, but their functions--and whether they share a common function--have long been unclear. Recently, several members of the pe/ppe family were shown to transport nutrients across the outer Mtb membrane, a role for which no other proteins have yet been identified. Whether nutrient transport is a family-wide function and the range of nutrients transported by the PE/PPEs remains unclear. Sulfur is an essential nutrient for Mtb physiology and pathogenesis. To test whether PE/PPE transporters contribute to sulfur acquisition, we analyzed the transcriptional response of Mtb to sulfate by RNA sequencing. The pe22/ppe36 genes were induced in sulfate-limiting conditions. Deletion of pe22/ppe36 impaired growth in low-sulfate media and reduced intracellular sulfate levels, effects that were reversed by heterologous expression of the Mycobacterium smegmatis porin MspA. The response of sulfur-responsive genes to sulfur was muted in the pe22/ppe36 deletion strain, and mass spectrometry showed lower sulfolipid and sulfur metabolite levels in the deletion strain. These findings identify PE22/PPE36 as a specific sulfate uptake system and supports the emerging idea of PE/PPE proteins as nutrient uptake systems across the Mtb outer membrane. Significance statementThe mechanism of nutrient transport across the porin-less mycobacterial outer membrane and the function of the large pe/ppe gene family have been longstanding questions in mycobacterial biology. This study shows that the Mycobacterium tuberculosis PE22/PPE36 complex serves as a selective conduit for inorganic sulfate. Deletion of this complex disrupts intracellular sulfur homeostasis and triggers a metabolic seesaw that depletes cell-surface sulfolipids. Our findings expand the PE/PPE transport paradigm and suggest a direct link between nutrient acquisition and TB transmission.

microbiology↗

bioRxiv2025

PE/PPE proteins contribute to Mycobacterium tuberculosis drug resistance

The outer membrane (OM) of mycobacteria is a formidable permeability barrier that confers drug tolerance, and whether drugs traverse the OM by mechanisms beyond passive diffusion remains unclear. The proline-glutamic acid (PE) and proline-proline-glutamic acid (PPE) proteins of pathogenic mycobacteria include several OM transporters. Here, we tested the role of PE/PPE proteins in Mycobacterium tuberculosis (Mtb) drug transport and resistance. Mutations in multiple pe/ppe genes were strongly associated with drug resistance in a genetic association study, and mutations in ppe42 and ppe51 also conferred increased resistance in vitro. Deletion of a pe/ppe pair transcriptionally responsive to drug exposure, pe25/ppe41, led to elevated resistance to isoniazid (INH) across all major Mtb lineages and accelerated INH resistance emergence in vitro. These data identify a role for Mtb PE/PPE proteins in drug resistance consistent with the PE/PPE transporter paradigm, suggest a broader contribution of this large protein family, and a new factor of Mtb clinical drug resistance.

microbiology↗

bioRxiv2022

Calcium transport by the Mycobacterium tuberculosis PE15/PPE20 proteins

Many aspects of eukaryotic physiology are regulated by calcium ions (Ca2+). Whether bacteria have similar Ca2+ systems for transport, storage, binding, and response to Ca2+ is not well understood. To identify components of Ca2+ signaling in Mycobacterium tuberculosis, we determined its transcriptional response to Ca2+. Overall, only few genes changed expression, suggesting a limited role of Ca2+ as a transcriptional regulator. However, two of the most strongly downregulated genes were the pe15 and ppe20 genes that code for members of a large family of proteins that localizes to the outer membrane. PE15 and PPE20 formed a complex and PPE20 directly bound Ca2+. Ca2+-associated phenotypes such as an increase in ATP consumption and increase in biofilm formation were reversed in a pe15/ppe20 knockout strain, suggesting a direct role in Ca2+ homeostasis. To test whether the complex has a role in Ca2+ transport across the outer membrane, we created a fluorescence resonance energy transfer (FRET)-based Ca2+ reporter strain. A pe15/ppe20 knockout in the FRET background showed a specific and selective loss of Ca2+ influx that was dependent on the presence of an intact outer cell wall. These data show that PE15/PPE20 form a Ca2+-binding protein complex that selectively imports Ca2+ and support the emerging idea of a general family-wide role of PE/PPE proteins in transport across the outer membrane.

microbiology↗

bioRxiv2022

The Mycobacterium tuberculosis protein O-phosphorylation landscape

Bacterial phosphosignaling has long been synonymous with the histidine kinases of the two component systems, but many bacteria, including Mycobacterium tuberculosis (Mtb), also code for Ser/Thr protein kinases (STPKs). STPKs are the main phosphosignaling enzymes in eukaryotes, but the full extent of phosphorylation on protein Ser/Thr and Tyr (O-phosphorylation) in bacteria remains unclear. Here, we explored the global signaling capacity of the STPKs in Mtb. We generated STPK loss-and gain-of-function strains and measured the resulting O-phosphorylation and transcriptional changes. This deep phosphoproteome shows that O-phosphorylation in Mtb is an underexplored protein modification that affects >70% of the proteome. The substrate-STPK interactions show an extensive interface with the transcriptional machinery, resulting in regulation of gene expression of [~]30% of Mtb genes. Mtb O-phosphorylation gives rise to an expansive, distributed, and cooperative network of a complexity that has previously only been associated with eukaryotic phosphosignaling networks.

microbiology↗