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Nonlytic cellular release of hepatitis A virus requires dual capsid recruitment of the ESCRT-associated Bro1 domain proteins HD-PTP and ALIX

Takayoshi Shirasaki, Hui Feng, Helen M. E. Duyvesteyn, William G. Fusco, Kevin L. McKnight, Ling Xie, Mark Boyce, Sathish Kumar, Rina Barouch-Bentov, Olga González-López, Ryan McNamara, Li Wang, Adriana Hertel-Wulff, Xian Chen, Shirit Einav, Joseph A. Duncan, Maryna Kapustina, Elizabeth E. Fry, David I. Stuart, View ORCID ProfileStanley M. Lemon
doi: https://doi.org/10.1101/2022.04.26.489493
Takayoshi Shirasaki
1Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Hui Feng
1Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Helen M. E. Duyvesteyn
2Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
3Diamond Light Source, Didcot OX11 0DE, UK
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William G. Fusco
4Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Kevin L. McKnight
1Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Ling Xie
1Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
5Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7292, USA
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Mark Boyce
2Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
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Sathish Kumar
6Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
7Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
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Rina Barouch-Bentov
6Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
7Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
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Olga González-López
1Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Ryan McNamara
1Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Li Wang
1Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
5Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7292, USA
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Adriana Hertel-Wulff
1Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Xian Chen
1Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
5Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7292, USA
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Shirit Einav
6Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
7Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
8Chan-Zuckerberg BioHub, San Francisco, CA 94158
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Joseph A. Duncan
1Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
4Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
9Department of Pharmacology, The University of North Carolina at Chapel Hill
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Maryna Kapustina
10Department of Cell Biology & Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Elizabeth E. Fry
2Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
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David I. Stuart
2Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
3Diamond Light Source, Didcot OX11 0DE, UK
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Stanley M. Lemon
1Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
4Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
11Department of Microbiology & Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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  • ORCID record for Stanley M. Lemon
  • For correspondence: smlemon@med.unc.edu
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Abstract

Although picornaviruses are conventionally considered ‘nonenveloped’, members of multiple picornaviral genera are released nonlytically from infected cells in extracellular vesicles. The mechanisms underlying this process are poorly understood. Here, we describe interactions of the hepatitis A virus (HAV) capsid with components of host endosomal sorting complexes required for transport (ESCRT) that play an essential role in release. We show release of quasi-enveloped virus (eHAV) in exosome-like vesicles requires a conserved export signal located within the 8 kDa C-terminal VP1 pX extension that functions in a manner analogous to late domains of canonical enveloped viruses. Fusing pX to a self-assembling engineered protein nanocage (EPN-pX) resulted in its ESCRT-dependent release in extracellular vesicles. Mutational analysis identified a 24 amino acid peptide sequence located within the center of pX that was both necessary and sufficient for nanocage release. Deleting a YxxL motif within this sequence ablated eHAV release, resulting in virus accumulating intracellularly. The pX export signal is conserved in non-human hepatoviruses from a wide range of mammalian species, and functional in pX sequences from bat hepatoviruses when fused to the nanocage protein, suggesting these viruses are released as quasi-enveloped virions. Quantitative proteomics identified multiple ESCRT-related proteins associating with EPN-pX, including ALG2-interacting protein X (ALIX), and its paralog, tyrosine-protein phosphatase non-receptor type 23 (HD-PTP), a second Bro1 domain protein linked to sorting of ubiquitylated cargo into multivesicular endosomes. RNAi-mediated depletion of either Bro1 domain protein impeded eHAV release. Super-resolution fluorescence microscopy demonstrated colocalization of viral capsids with endogenous ALIX and HD-PTP. Co-immunoprecipitation assays using biotin-tagged peptides and recombinant proteins revealed pX interacts directly through the export signal with N-terminal Bro1 domains of both HD-PTP and ALIX. Our study identifies an exceptionally potent viral export signal mediating extracellular release of virus-sized protein assemblies and shows release requires non-redundant activities of both HD-PTP and ALIX.

Authors’ Summary Mechanisms underlying nonlytic release of canonical nonenveloped viruses from infected cells are poorly understood. We show here that release of hepatitis A virus from cells in exosome-like vesicles requires nonredundant activities of two distinct Bro1-domain proteins associated with host cell machinery (ESCRT) for endosomal sorting, HD-PTP and ALIX. We demonstrate both Bro1 domain proteins are recruited to the viral capsid by the pX segment of the 1D capsid protein, and that they act in a non-redundant manner to mediate virus release. Fusing pX to a self-assembling nanocage protein resulted in ESCRT-dependent release mediated by a short pX peptide sequence conserved in hepatoviruses from bats to humans. Mutations within the pX sequence ablate release and result in noncytolytic virus accumulating intracellularly. Our study identifies an exceptionally potent viral export signal mediating extracellular release of virus-sized protein assemblies and shows nonlytic release of quasi-enveloped virus is an ancient evolutionary trait of hepatoviruses.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted April 26, 2022.
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Nonlytic cellular release of hepatitis A virus requires dual capsid recruitment of the ESCRT-associated Bro1 domain proteins HD-PTP and ALIX
Takayoshi Shirasaki, Hui Feng, Helen M. E. Duyvesteyn, William G. Fusco, Kevin L. McKnight, Ling Xie, Mark Boyce, Sathish Kumar, Rina Barouch-Bentov, Olga González-López, Ryan McNamara, Li Wang, Adriana Hertel-Wulff, Xian Chen, Shirit Einav, Joseph A. Duncan, Maryna Kapustina, Elizabeth E. Fry, David I. Stuart, Stanley M. Lemon
bioRxiv 2022.04.26.489493; doi: https://doi.org/10.1101/2022.04.26.489493
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Nonlytic cellular release of hepatitis A virus requires dual capsid recruitment of the ESCRT-associated Bro1 domain proteins HD-PTP and ALIX
Takayoshi Shirasaki, Hui Feng, Helen M. E. Duyvesteyn, William G. Fusco, Kevin L. McKnight, Ling Xie, Mark Boyce, Sathish Kumar, Rina Barouch-Bentov, Olga González-López, Ryan McNamara, Li Wang, Adriana Hertel-Wulff, Xian Chen, Shirit Einav, Joseph A. Duncan, Maryna Kapustina, Elizabeth E. Fry, David I. Stuart, Stanley M. Lemon
bioRxiv 2022.04.26.489493; doi: https://doi.org/10.1101/2022.04.26.489493

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