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bioRxiv · 10.1101/2025.11.19.689332

Control of antigen presentation on MHC-I by a bacterial secretion system

Leddy, O.·McGinn, R.·Allsup, B.·Leone, M.·Timms, P.·Gutierrez-Gonzalez, M.·Fahad, A. S.·Milligan, R.·Garcia-Beltran, W. F.·DeKosky, B. J.·White, F. M.·Bryson, B. D.
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Abstract

Mycobacterium tuberculosis (Mtb) remains one of the worlds leading infectious killers. Although CD8{square} T cells contribute to immune control of tuberculosis, the pathways through which bacterial antigens access major histocompatibility complex class I (MHC-I) antigen presentation remain incompletely defined. Here, we show that the activity of an Mtb secretion system actively promotes antigen presentation on MHC-I. Using quantitative immunopeptidomics, host and bacterial genetic perturbations, and T cell activation assays, we demonstrate that presentation of Mtb-derived peptides on MHC-I requires the ESX-1 type VII secretion system. Presentation of these peptides proceeds in a manner dependent on the transporter associated with antigen processing (TAP) but independent of host cell mechanisms such as autophagy or MPEG1-mediated pore formation. Chemical induction of phagosomal membrane damage fails to restore antigen presentation in the absence of ESX-1 activity, suggesting that pathogen-encoded secretion, not nonspecific membrane rupture, governs access to MHC-I antigen processing pathways. These findings reveal a secretion system-driven mechanism of antigen presentation, redefining how mycobacteria interface with host MHC-I pathways, potentially informing tuberculosis vaccine design strategies, and highlighting a potential route for synthetic antigen delivery to the cytosol in therapeutics and vaccination. One-sentence summaryPresentation of Mycobacterium tuberculosis antigens on MHC class I through a cytosolic pathway depends on a bacterial secretion system rather than host response and cross-presentation pathways.

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Leddy, O., McGinn, R., Allsup, B., Leone, M., Timms, P., Gutierrez-Gonzalez, M., Fahad, A. S., Milligan, R., Garcia-Beltran, W. F., DeKosky, B. J., White, F. M., Bryson, B. D.. 2025-11-20. Control of antigen presentation on MHC-I by a bacterial secretion system. https://doi.org/10.1101/2025.11.19.689332

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