ESCPE-1 mediates retrograde endosomal sorting of the SARS-CoV-2 host factor Neuropilin-1

Boris Simonetti; James Daly; Katja Klein; Carlos Anton Plagaro; Lorna R Hodgson; Kate J Heesom; Deborah K Shoemark; Andrew D Davidson; Yohei Yamauchi; Pete J Cullen; al et

doi:10.1073/pnas.2201980119

ESCPE-1 mediates retrograde endosomal sorting of the SARS-CoV-2 host factor Neuropilin-1

Boris Simonetti^*, James Daly, Katja Klein, Carlos Anton Plagaro, Lorna R Hodgson, Kate J Heesom, Deborah K Shoemark, Andrew D Davidson, Yohei Yamauchi, Pete J Cullen ^*, al et

^*Corresponding author for this work

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Abstract

Endosomal sorting maintains cellular homeostasis by recycling transmembrane proteins and associated proteins and lipids (termed “cargoes”) from the endosomal network to multiple subcellular destinations, including retrograde traffic to the trans-Golgi network (TGN). Viral and bacterial pathogens subvert retrograde trafficking machinery to facilitate infectivity. Here, we develop a proteomic screen to identify retrograde cargo proteins of the endosomal SNX-BAR sorting complex promoting exit 1 (ESCPE-1). Using this methodology, we identify Neuropilin-1 (NRP1), a recently characterized host factor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, as a cargo directly bound and trafficked by ESCPE-1. ESCPE-1 mediates retrograde trafficking of engineered nanoparticles functionalized with the NRP1-interacting peptide of the SARS-CoV-2 spike (S) protein. CRISPR-Cas9 deletion of ESCPE-1 subunits reduces SARS-CoV-2 infection levels in cell culture. ESCPE-1 sorting of NRP1 may therefore play a role in the intracellular membrane trafficking of NRP1-interacting viruses such as SARS-CoV-2.

Original language	English
Article number	2201980119
Number of pages	11
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	119
Issue number	25
Early online date	13 Jun 2022
DOIs	https://doi.org/10.1073/pnas.2201980119
Publication status	Published - 21 Jun 2022

Bibliographical note

Funding Information:
ACKNOWLEDGMENTS. We thank Guido Serini (Candiolo Cancer Institute, Fondazione del Piemonte per l’Oncologia, (IRCCS), Candiolo, Torino, Italy) and Donatella Valdembri (Department of Oncology, University of Torino School of Medicine) for their gift of the GFP-tagged Nrp1 construct and invaluable discussion. We thank Kevin A. Wilkinson (School of Biochemistry, University of Bristol, Bristol, UK) for the gift of the Scramble shRNA puro-GFP lentiviral plasmid. We thank the Wolfson Bioimaging Facility and the Proteomics Facility at the University of Bristol for their support. We thank the University of Bristol Advanced Computing Research Centre for the provision of high performance computing. P.J.C. is supported by the Wellcome Trust (104568/Z/14/Z and 220260/Z/20/Z), the Medical Research Council (MRC) (MR/L007363/1 and MR/P018807/1), the Lister Institute of Preventive Medicine, and the award of a Royal Society Noreen Murray Research Professorship (RSRP/R1/211004). J.L.D. is supported by a Wellcome Trust studentship from the Dynamic Molecular Cell Biology PhD program (203959/Z/16/Z). C.A.-P. is supported by Beca Fundación Ramón Areces Estudios Postdoctorales en el Extranjero. D.K.S. is supported by a BrisSynBio Biotechnology and Biological Sciences Research Council (BBSRC) research grant (BB/ L01386X/1). B.M.C. is supported by a Senior Research Fellowship and Project Grant from the National Health and MRC (APP1136021 and APP1156493). Y.Y. is supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (No. 856581–CHUbVi). A.D.D. is supported by UK Research and Innovation/MRC (MR/W005611/1). T.T. is supported by the European Regional Development Fund (Project No. 2014-2020.4.01.15-0012), by the Estonian Research Council (grants PRG230 and EAG79), and European Research Association (ERA)-NET EuroNanoMed III project iNanogun.

Publisher Copyright:
© 2022 the Author(s).

Keywords

endosome
Neuropilin-1
SARS-CoV-2
COVID-19
sorting nexin

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Simonetti, B., Daly, J., Klein, K., Anton Plagaro, C., Hodgson, L. R., Heesom, K. J., Shoemark, D. K., Davidson, A. D., Yamauchi, Y., Cullen , P. J., & et, A. (2022). ESCPE-1 mediates retrograde endosomal sorting of the SARS-CoV-2 host factor Neuropilin-1. Proceedings of the National Academy of Sciences of the United States of America, 119(25), Article 2201980119. https://doi.org/10.1073/pnas.2201980119

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abstract = "Endosomal sorting maintains cellular homeostasis by recycling transmembrane proteins and associated proteins and lipids (termed “cargoes”) from the endosomal network to multiple subcellular destinations, including retrograde traffic to the trans-Golgi network (TGN). Viral and bacterial pathogens subvert retrograde trafficking machinery to facilitate infectivity. Here, we develop a proteomic screen to identify retrograde cargo proteins of the endosomal SNX-BAR sorting complex promoting exit 1 (ESCPE-1). Using this methodology, we identify Neuropilin-1 (NRP1), a recently characterized host factor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, as a cargo directly bound and trafficked by ESCPE-1. ESCPE-1 mediates retrograde trafficking of engineered nanoparticles functionalized with the NRP1-interacting peptide of the SARS-CoV-2 spike (S) protein. CRISPR-Cas9 deletion of ESCPE-1 subunits reduces SARS-CoV-2 infection levels in cell culture. ESCPE-1 sorting of NRP1 may therefore play a role in the intracellular membrane trafficking of NRP1-interacting viruses such as SARS-CoV-2.",

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note = "Funding Information: ACKNOWLEDGMENTS. We thank Guido Serini (Candiolo Cancer Institute, Fondazione del Piemonte per l{\textquoteright}Oncologia, (IRCCS), Candiolo, Torino, Italy) and Donatella Valdembri (Department of Oncology, University of Torino School of Medicine) for their gift of the GFP-tagged Nrp1 construct and invaluable discussion. We thank Kevin A. Wilkinson (School of Biochemistry, University of Bristol, Bristol, UK) for the gift of the Scramble shRNA puro-GFP lentiviral plasmid. We thank the Wolfson Bioimaging Facility and the Proteomics Facility at the University of Bristol for their support. We thank the University of Bristol Advanced Computing Research Centre for the provision of high performance computing. P.J.C. is supported by the Wellcome Trust (104568/Z/14/Z and 220260/Z/20/Z), the Medical Research Council (MRC) (MR/L007363/1 and MR/P018807/1), the Lister Institute of Preventive Medicine, and the award of a Royal Society Noreen Murray Research Professorship (RSRP/R1/211004). J.L.D. is supported by a Wellcome Trust studentship from the Dynamic Molecular Cell Biology PhD program (203959/Z/16/Z). C.A.-P. is supported by Beca Fundaci{\'o}n Ram{\'o}n Areces Estudios Postdoctorales en el Extranjero. D.K.S. is supported by a BrisSynBio Biotechnology and Biological Sciences Research Council (BBSRC) research grant (BB/ L01386X/1). B.M.C. is supported by a Senior Research Fellowship and Project Grant from the National Health and MRC (APP1136021 and APP1156493). Y.Y. is supported by the European Research Council under the European Union{\textquoteright}s Horizon 2020 research and innovation program (No. 856581–CHUbVi). A.D.D. is supported by UK Research and Innovation/MRC (MR/W005611/1). T.T. is supported by the European Regional Development Fund (Project No. 2014-2020.4.01.15-0012), by the Estonian Research Council (grants PRG230 and EAG79), and European Research Association (ERA)-NET EuroNanoMed III project iNanogun. Publisher Copyright: {\textcopyright} 2022 the Author(s).",

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Simonetti, B, Daly, J, Klein, K , Anton Plagaro, C, Hodgson, LR, Heesom, KJ , Shoemark, DK , Davidson, AD, Yamauchi, Y, Cullen , PJ & et, A 2022, 'ESCPE-1 mediates retrograde endosomal sorting of the SARS-CoV-2 host factor Neuropilin-1', Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 25, 2201980119. https://doi.org/10.1073/pnas.2201980119

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T1 - ESCPE-1 mediates retrograde endosomal sorting of the SARS-CoV-2 host factor Neuropilin-1

AU - Simonetti, Boris

AU - Daly, James

AU - Klein, Katja

AU - Anton Plagaro, Carlos

AU - Hodgson, Lorna R

AU - Heesom, Kate J

AU - Shoemark, Deborah K

AU - Davidson, Andrew D

AU - Yamauchi, Yohei

AU - Cullen , Pete J

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N1 - Funding Information: ACKNOWLEDGMENTS. We thank Guido Serini (Candiolo Cancer Institute, Fondazione del Piemonte per l’Oncologia, (IRCCS), Candiolo, Torino, Italy) and Donatella Valdembri (Department of Oncology, University of Torino School of Medicine) for their gift of the GFP-tagged Nrp1 construct and invaluable discussion. We thank Kevin A. Wilkinson (School of Biochemistry, University of Bristol, Bristol, UK) for the gift of the Scramble shRNA puro-GFP lentiviral plasmid. We thank the Wolfson Bioimaging Facility and the Proteomics Facility at the University of Bristol for their support. We thank the University of Bristol Advanced Computing Research Centre for the provision of high performance computing. P.J.C. is supported by the Wellcome Trust (104568/Z/14/Z and 220260/Z/20/Z), the Medical Research Council (MRC) (MR/L007363/1 and MR/P018807/1), the Lister Institute of Preventive Medicine, and the award of a Royal Society Noreen Murray Research Professorship (RSRP/R1/211004). J.L.D. is supported by a Wellcome Trust studentship from the Dynamic Molecular Cell Biology PhD program (203959/Z/16/Z). C.A.-P. is supported by Beca Fundación Ramón Areces Estudios Postdoctorales en el Extranjero. D.K.S. is supported by a BrisSynBio Biotechnology and Biological Sciences Research Council (BBSRC) research grant (BB/ L01386X/1). B.M.C. is supported by a Senior Research Fellowship and Project Grant from the National Health and MRC (APP1136021 and APP1156493). Y.Y. is supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (No. 856581–CHUbVi). A.D.D. is supported by UK Research and Innovation/MRC (MR/W005611/1). T.T. is supported by the European Regional Development Fund (Project No. 2014-2020.4.01.15-0012), by the Estonian Research Council (grants PRG230 and EAG79), and European Research Association (ERA)-NET EuroNanoMed III project iNanogun. Publisher Copyright: © 2022 the Author(s).

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N2 - Endosomal sorting maintains cellular homeostasis by recycling transmembrane proteins and associated proteins and lipids (termed “cargoes”) from the endosomal network to multiple subcellular destinations, including retrograde traffic to the trans-Golgi network (TGN). Viral and bacterial pathogens subvert retrograde trafficking machinery to facilitate infectivity. Here, we develop a proteomic screen to identify retrograde cargo proteins of the endosomal SNX-BAR sorting complex promoting exit 1 (ESCPE-1). Using this methodology, we identify Neuropilin-1 (NRP1), a recently characterized host factor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, as a cargo directly bound and trafficked by ESCPE-1. ESCPE-1 mediates retrograde trafficking of engineered nanoparticles functionalized with the NRP1-interacting peptide of the SARS-CoV-2 spike (S) protein. CRISPR-Cas9 deletion of ESCPE-1 subunits reduces SARS-CoV-2 infection levels in cell culture. ESCPE-1 sorting of NRP1 may therefore play a role in the intracellular membrane trafficking of NRP1-interacting viruses such as SARS-CoV-2.

AB - Endosomal sorting maintains cellular homeostasis by recycling transmembrane proteins and associated proteins and lipids (termed “cargoes”) from the endosomal network to multiple subcellular destinations, including retrograde traffic to the trans-Golgi network (TGN). Viral and bacterial pathogens subvert retrograde trafficking machinery to facilitate infectivity. Here, we develop a proteomic screen to identify retrograde cargo proteins of the endosomal SNX-BAR sorting complex promoting exit 1 (ESCPE-1). Using this methodology, we identify Neuropilin-1 (NRP1), a recently characterized host factor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, as a cargo directly bound and trafficked by ESCPE-1. ESCPE-1 mediates retrograde trafficking of engineered nanoparticles functionalized with the NRP1-interacting peptide of the SARS-CoV-2 spike (S) protein. CRISPR-Cas9 deletion of ESCPE-1 subunits reduces SARS-CoV-2 infection levels in cell culture. ESCPE-1 sorting of NRP1 may therefore play a role in the intracellular membrane trafficking of NRP1-interacting viruses such as SARS-CoV-2.

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KW - SARS-CoV-2

KW - COVID-19

KW - sorting nexin

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DO - 10.1073/pnas.2201980119

M3 - Article (Academic Journal)

C2 - 35696571

SN - 0027-8424

VL - 119

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

IS - 25

M1 - 2201980119

ER -

ESCPE-1 mediates retrograde endosomal sorting of the SARS-CoV-2 host factor Neuropilin-1

Abstract

Bibliographical note

Keywords

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