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

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 posttranslational 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.

Coxsackievirus B3 targets TFEB to disrupt lysosomal function

“…the attenuation of CVB3 titers, supporting recent evidence that TFEB serves as a pro-viral factor to facilitate viral replication [30] and non-lytic egress [32] at early viral infection. Interestingly, we discovered that during late stage of viral infection, TFEB is proteolytically processed and the cleavage fragment further enhances viral propagation.…”

The encephalomyocarditis virus Leader promotes the release of virions inside extracellular vesicles via the induction of secretory autophagy

“…It has been proposed that specific regulators may be recruited to autophagosomes that enable their preferential fusion with the PM or other non-lysosomal compartments, such as GRASP55 and TRIM16 36,48,60,61 . For the picornavirus CVB3, we recently identified a role for the transcription factor EB (TFEB), a known regulator of lysosomal exocytosis, in the activation of secretory autophagy 62 . TFEB depletion limited the ability of CVB3 to induce LC3 release during infection, which correlated with an overall decrease in EV-enclosed virus release.…”

Understanding extracellular vesicles

“…Roberto et al We believe this Special Issue provides a snapshot on the burgeoning field of EV classes and their subpopulations. With the continuing refinement of mass spectrometry-based proteomics [1], especially in the areas of quantitation [2][3][4][5], proteome coverage [6][7][8][9][10], single-cell or subtype analyses [11][12][13] and proteomic profiling with sequential window acquisition of all theoretical fragment ion spectra (SWATH) [4 , 14]: we predict an exciting and diverse future for the EV field, especially in clinical and therapeutic applications.…”