Temporal Proteomic Analysis of BK Polyomavirus Infection Reveals Virus-Induced G ₂ Arrest and Highly Effective Evasion of Innate Immune Sensing

Abstract

BK polyomavirus (BKPyV) is a small DNA virus that establishes a life-long persistent infection in the urinary tract of most people. BKPyV is known to cause severe morbidity in renal transplant recipients and can lead to graft rejection. The simple 5.2-kbp double-stranded DNA (dsDNA) genome expresses just seven known proteins; thus, it relies heavily on the host machinery to replicate. How the host proteome changes over the course of infection is key to understanding this host-virus interplay. Here, for the first time quantitative temporal viromics has been used to quantify global changes in >9,000 host proteins in two types of primary human epithelial cells throughout 72 h of BKPyV infection. These data demonstrate the importance of cell cycle progression and pseudo-G2 arrest in effective BKPyV replication, along with a surprising lack of an innate immune response throughout the whole virus replication cycle. BKPyV thus evades pathogen recognition to prevent activation of innate immune responses in a sophisticated manner. IMPORTANCE BK polyomavirus can cause serious problems in immune-suppressed patients, in particular, kidney transplant recipients who can develop polyomavirus-associated kidney disease. In this work, we have used advanced proteomics techniques to determine the changes to protein expression caused by infection of two independent primary cell types of the human urinary tract (kidney and bladder) throughout the replication cycle of this virus. Our findings have uncovered new details of a specific form of cell cycle arrest caused by this virus, and, importantly, we have identified that this virus has a remarkable ability to evade detection by host cell defense systems. In addition, our data provide an important resource for the future study of kidney epithelial cells and their infection by urinary tract pathogens.

Temporal Proteomic Analysis of Herpes Simplex Virus 1 Infection Reveals Cell-Surface Remodeling via pUL56-Mediated GOPC Degradation

“…Quantitative temporal viromics (QTV) is a method to enable highly multiplexed quantitative analysis of temporal changes in host and viral proteins throughout the course of a productive infection ( Weekes et al., 2014 ). QTV employs tandem mass tags (TMTs) and triple-stage mass spectrometry (MS3) to facilitate precise quantitation of each protein, and we have applied this technique to study several viruses including human cytomegalovirus (HCMV), Epstein-Barr virus, vaccinia virus, and BK polyomavirus ( Caller et al., 2019 ; Ersing et al., 2017 ; Soday et al., 2019 ; Weekes et al., 2014 ).…”

Comprehensive cell surface proteomics defines markers of classical, intermediate and non-classical monocytes

“…was performed with modifications as previously described 38,39 . Mass spectrometry data was acquired using an Orbitrap Lumos (Thermo Fisher Scientific, San Jose, CA).…”

Effect of the Large and Small T-Antigens of Human Polyomaviruses on Signaling Pathways

“…An E3 ubiquitin ligase was involved in proteasomal degradation of p53. LT alone was sufficient to reduce MDM2 levels and kept p53 inactive by binding to it [195,196]. p53 repressed JCPyV DNA replication by interacting with LT [192].…”

“…A recent proteomic-based study could not detect changes in protein levels of IFN-stimulated genes in BKPyV-infected RPTE cells after 24, 48, and 72 hours p .i. [195]. It is unclear why some cells trigger expression of IFN-stimulating genes in response to BKPyV or JCPyV infection and others do not, but the induced antiviral state may restrict BKPyV or JCPyV replication in the host and enable the establishment of a long-term infection [100].…”

“…Alternatively, cells may lack the machinery to detect viral infection or viruses may counteract cellular defense responses through immune-evasion activity. Hence, no expression of IFN-stimulating genes occurs after HPyV infection [195,252].…”