Barnes, A. B. | Search bioRxiv

bioRxiv2026

SecretTarget: A pipeline for identifying host-interacting effector candidates through secondary localization features

Intracellular parasites cause over 226 million disability-adjusted life years (DALY) globally each year. Current treatment methods fall short of desirable impact due to adverse effects and growing resistance, shifting focus to parasitic effectors for future therapeutic development. Unfortunately, the divergent nature of parasitic proteins has impeded in silico discovery of - and functional inference for - parasitic effectors. Here, we present SecretTarget, a pipeline designed to identify host-interacting effector candidates through secondary localization features. By truncating signal peptides from predicted extracellular proteins ({Delta}SP), we unmask potential underlying localization features that dictate subcellular trafficking within the host. Applying our pipeline to a set of Toxoplasma gondii secreted effectors with known localizations and interactions, we propose a novel host ER-parasite interaction critical for parasite survival, recapitulate published localizations, and provide meaningful biological insights aligning with recent host-parasite interaction discoveries.

bioinformatics↗

bioRxiv2025

Intermolecular β-sheet formation guides the interaction between ubiquitin-like modifier FAT10 and adapter protein NUB1L

Under inflammatory conditions, the ubiquitin-like modifier FAT10 targets proteins for rapid and irreversible degradation by the 26S proteasome. FAT10 is degraded along with its substrates and in this process, the loose folding of FAT10 and adapter protein NUB1L have long been suspected to play crucial roles. We report here the investigation of the N-domain of FAT10 and its interaction with NUB1L by magic-angle spinning (MAS) NMR spectroscopy. A stretch of residues that is intrinsically disordered when the N-domain of FAT10 is in its ubiquitin-like {beta}-grasp fold, becomes part of a regularly structured loop and an intermolecular {beta}-sheet upon binding to NUB1L. The rest of the N-domain is now disordered, with exception of a series of anchor residues and the N-terminus. We propose that, in preparation of degradation by the proteasome, NUB1L stabilizes N-FAT10 in an unfolded state, acting as a holdase. The ability of FAT10 to interact in folded as well as unfolded form is essential for its role in inflammation-linked proteostasis.

biochemistry↗

bioRxiv2019

Pathogen-encoded evasion of CXCL10 and T cell responses

Clearance of intracellular pathogens, such as Leishmania (L.) major, depends on a well-regulated adaptive T cell response. Here we describe a pathogen-encoded mechanism to alter T cell recruitment by suppressing CXCL10, a chemokine that recruits CD4+ and CD8+ T cells by signaling through the CXCR3 receptor. L. major suppresses CXCL10 through the virulence factor and protease, glycoprotein-63 (gp63). GP63 cleaves CXCL10 after amino acid A81, impairing T-cell chemotaxis in vitro. GP63 from either extracellular promastigotes or intracellular amastigotes is capable of cleaving CXCL10. Consistent with CXCL10 cleavage during infection, we observed GP63-mediated impairment of activated CD8+ T-cells in the draining lymph nodes of C57BL/6JWT mice. Correspondingly, in C57BL/6JWT mice, gp63 deletion resulted in slower lesion development and a smaller maximum lesion size. However, infection in C57BL/6Jcxcr3-/- mice revealed the delay to lesion development required CXCR3 signaling. Finally, Salmonella enterica and Chlamydia trachomatis infection also suppress CXCL10, demonstrating convergent evolution of this immune evasion strategy in diverse intracellular pathogens. Understanding mechanisms of CXCL10 evasion may facilitate the development of novel therapeutic strategies to treat intracellular pathogens. Author SummaryLeishmaniasis is an infectious disease that affects over one million people annually. It is caused by intracellular parasites that have evolved to evade the hosts attempts to eliminate the parasite. The most common form of disease, cutaneous leishmaniasis, causes disfiguring skin lesions if the host immune system does not appropriately respond to the infection. A family of molecules called chemokines are critical for the recruitment of specific subsets of immune cells required to eliminate infection. Here, we demonstrate a novel mechanism that the parasite Leishmania (L.) major employs to disrupt the immune response by interfering with chemokine signaling. By this strategy, L. major uses a protease to cleave chemokines known to recruit T-cells required for fighting off infection. We show that L. major cleavage of these immune signals changes the recruitment of CD8+ T-cells and alters disease progression in mice. Finally, we observe that multiple common human intracellular pathogens, including Chlamydia trachomatis and Salmonella enterica, interfere with the same chemokines, suggesting a strong selective pressure to avoid this component of the immune response. Our study provides new insights into how intracellular pathogens interact with the host immune response to enhance pathogen survival and exacerbate disease outcomes.

microbiology↗