Dynamic remodelling of the human host cell proteome and phosphoproteome upon enterovirus infection

Piero Giansanti, Jeroen R. P. M. Strating, Kyra A. Y. Defourny, Ieva Cesonyte, Alexia M. S. Bottino, Harm Post, Ekaterina G. Viktorova, Vien Quang Tri Ho, Martijn A. Langereis, George A. Belov, Esther N. M. Nolte-‘t Hoen, Albert J. R. Heck () and Frank J. M. van Kuppeveld ()
Additional contact information
Piero Giansanti: Utrecht University
Jeroen R. P. M. Strating: Utrecht University
Kyra A. Y. Defourny: Utrecht University
Ieva Cesonyte: Utrecht University
Alexia M. S. Bottino: Utrecht University
Harm Post: Utrecht University
Ekaterina G. Viktorova: University of Maryland and VA-MD College of Veterinary Medicine
Vien Quang Tri Ho: Utrecht University
Martijn A. Langereis: Utrecht University
George A. Belov: University of Maryland and VA-MD College of Veterinary Medicine
Esther N. M. Nolte-‘t Hoen: Utrecht University
Albert J. R. Heck: Utrecht University
Frank J. M. van Kuppeveld: Utrecht University

Nature Communications, 2020, vol. 11, issue 1, 1-12

Abstract: Abstract The group of enteroviruses contains many important pathogens for humans, including poliovirus, coxsackievirus, rhinovirus, as well as newly emerging global health threats such as EV-A71 and EV-D68. Here, we describe an unbiased, system-wide and time-resolved analysis of the proteome and phosphoproteome of human cells infected with coxsackievirus B3. Of the ~3,200 proteins quantified throughout the time course, a large amount (~25%) shows a significant change, with the majority being downregulated. We find ~85% of the detected phosphosites to be significantly regulated, implying that most changes occur at the post-translational level. Kinase-motif analysis reveals temporal activation patterns of certain protein kinases, with several CDKs/MAPKs immediately active upon the infection, and basophilic kinases, ATM, and ATR engaging later. Through bioinformatics analysis and dedicated experiments, we identify mTORC1 signalling as a major regulation network during enterovirus infection. We demonstrate that inhibition of mTORC1 activates TFEB, which increases expression of lysosomal and autophagosomal genes, and that TFEB activation facilitates the release of virions in extracellular vesicles via secretory autophagy. Our study provides a rich framework for a system-level understanding of enterovirus-induced perturbations at the protein and signalling pathway levels, forming a base for the development of pharmacological inhibitors to treat enterovirus infections.

Date: 2020
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DOI: 10.1038/s41467-020-18168-3

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