Discovering host-viral protein interactions in autophagy: A LIR discovery pipeline for identifying LC3-interacting region motifs in highly virulent viruses
6 affiliations
- 1Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- 2Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- 3Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada
- 4Department of Biochemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
- 5Biosciences Division, S.R.I. International, Menlo Park, California, United States of America
- 6Artificial Intelligence Center, S.R.I. International, Menlo Park, California, United States of America
Abstract
Hemorrhagic fever virus (HFV) infections are highly fatal, posing a significant global pandemic threat as they continue to emerge in new locations. HFVs and other highly virulent viruses (HVVs), such as Nipah virus, exploit host cell pathways, including the conserved host autophagy pathway, to promote viral replication. The Atg8/microtubule-associated protein 1 light chain 3 (LC3) proteins are necessary for autophagosome formation and maturation. Proteins interact with Atg8-family proteins through LC3-interacting region (LIR) motifs, which is a short linear motif (SLiM) found in intrinsically disordered regions of proteins. The presence of these motifs in viral components suggests they play a role in hijacking or evading the host autophagy pathway, yet the identification of functional LIR motifs in viral proteins remains limited. To address this gap, we developed the LIR Discovery Pipeline (LIR-DP) which integrates amino acid sequence pattern matching, with protein disorder prediction using IUPred3, and modeling with AlphaFold3. Using LIR-DP, we identified 43 putative LIR motifs in 166 proteins from 22 HVVs and predicted that 18 of these LIRs would be functional. In vitro and in cellulo laboratory experiments demonstrated that LIRs from the Marburg virus nucleoprotein, the Nipah virus phosphoprotein, the Ebola virus VP35, and the Rift Valley fever virus NSs protein bind to Atg8/LC3 family proteins. The aromatic amino acid in the first position of each LIR motif was found to be critical for these interactions. We provide evidence for the utility of the LIR-DP in identifying functional LIRs within HVV proteins which may provide valuable insight into the mechanism by which HVVs modulate the autophagy pathway during infection. Author summary: Hemorrhagic fever viruses (HFVs) are highly lethal pathogens that are rarely studied due to the high biosafety requirements. Viral proteins interact with host proteins to facilitate viral replication, and studying these interactions provide insights into pathways that could be therapeutically targeted. Many protein-protein interactions utilize short linear motifs (SLiMs) found in intrinsically disordered regions of proteins. Our work focused on the LC3-interacting region (LIR) motif, which enables interaction with the host autophagy Atg8/LC3 proteins. We integrated artificial intelligence (AI) with laboratory experiments to develop a novel LIR Discovery Pipeline (LIR-DP) which rapidly identifies potential functional LIRs in viral proteins. We validated potential functional LIRs in the following highly virulent viral proteins; Marburg virus nucleoprotein, Ebola virus VP35, and Nipah virus phosphoprotein; for which there is limited understanding of interactions with host proteins. Our results support the broader significance of the LIR-DP, suggesting its potential to also identify functional SLiMs in a wide range of proteins.
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BibTeX
@article{petraccione2026discovering,
title = {{Discovering host-viral protein interactions in autophagy: A LIR discovery pipeline for identifying LC3-interacting region motifs in highly virulent viruses}},
author = {Kaylee D. Petraccione and Haytham M. Wahba and Mohamed G. H. Ali and Timothy Stocker and Ivan Akhrymuk and Yossira Swese and Danuta Sastre and Andrew Silberfarb and Paul E. O’Maille and James G. Omichinski and Kylene Kehn-Hall},
journal = {PLOS Pathogens},
year = {2026},
month = sep,
doi = {10.1371/journal.ppat.1014607},
url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014607},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Discovering host-viral protein interactions in autophagy: A LIR discovery pipeline for identifying LC3-interacting region motifs in highly virulent viruses
AU - Kaylee D. Petraccione
AU - Haytham M. Wahba
AU - Mohamed G. H. Ali
AU - Timothy Stocker
AU - Ivan Akhrymuk
AU - Yossira Swese
AU - Danuta Sastre
AU - Andrew Silberfarb
AU - Paul E. O’Maille
AU - James G. Omichinski
AU - Kylene Kehn-Hall
PY - 2026
DA - 2026/09/11
JO - PLOS Pathogens
DO - 10.1371/journal.ppat.1014607
UR - https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014607
AB - Hemorrhagic fever virus (HFV) infections are highly fatal, posing a significant global pandemic threat as they continue to emerge in new locations. HFVs and other highly virulent viruses (HVVs), such as Nipah virus, exploit host cell pathways, including the conserved host autophagy pathway, to promote viral replication. The Atg8/microtubule-associated protein 1 light chain 3 (LC3) proteins are necessary for autophagosome formation and maturation. Proteins interact with Atg8-family proteins through LC3-interacting region (LIR) motifs, which is a short linear motif (SLiM) found in intrinsically disordered regions of proteins. The presence of these motifs in viral components suggests they play a role in hijacking or evading the host autophagy pathway, yet the identification of functional LIR motifs in viral proteins remains limited. To address this gap, we developed the LIR Discovery Pipeline (LIR-DP) which integrates amino acid sequence pattern matching, with protein disorder prediction using IUPred3, and modeling with AlphaFold3. Using LIR-DP, we identified 43 putative LIR motifs in 166 proteins from 22 HVVs and predicted that 18 of these LIRs would be functional. In vitro and in cellulo laboratory experiments demonstrated that LIRs from the Marburg virus nucleoprotein, the Nipah virus phosphoprotein, the Ebola virus VP35, and the Rift Valley fever virus NSs protein bind to Atg8/LC3 family proteins. The aromatic amino acid in the first position of each LIR motif was found to be critical for these interactions. We provide evidence for the utility of the LIR-DP in identifying functional LIRs within HVV proteins which may provide valuable insight into the mechanism by which HVVs modulate the autophagy pathway during infection. Author summary: Hemorrhagic fever viruses (HFVs) are highly lethal pathogens that are rarely studied due to the high biosafety requirements. Viral proteins interact with host proteins to facilitate viral replication, and studying these interactions provide insights into pathways that could be therapeutically targeted. Many protein-protein interactions utilize short linear motifs (SLiMs) found in intrinsically disordered regions of proteins. Our work focused on the LC3-interacting region (LIR) motif, which enables interaction with the host autophagy Atg8/LC3 proteins. We integrated artificial intelligence (AI) with laboratory experiments to develop a novel LIR Discovery Pipeline (LIR-DP) which rapidly identifies potential functional LIRs in viral proteins. We validated potential functional LIRs in the following highly virulent viral proteins; Marburg virus nucleoprotein, Ebola virus VP35, and Nipah virus phosphoprotein; for which there is limited understanding of interactions with host proteins. Our results support the broader significance of the LIR-DP, suggesting its potential to also identify functional SLiMs in a wide range of proteins.
SN - 1553-7374
ER -