Global analysis of modifications of the human BK virus structural proteins by LC-MS/MS

Fang, Chiung‐Yao; Chen, Hsiang-Ying; Wang, Meilin; Chen, Pei-Lain; Chang, Chien‐Wen; Chen, Lisheng; Shen, Cheng‐Huang; Ou, Wei-Chih; Tsai, Max; Hsu, Pang-Hung; Chang, Deching

doi:10.1016/j.virol.2010.03.029

Cited by 35 publications

(43 citation statements)

References 49 publications

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“…1B). According to our previous results of Western blot (Fang et al, 2010), the additional bands are fragments of capsid proteins. In order to profile the histone PTMs present in BKPyV minichromosomes and in BKPyV's host cells, we employed TAU-PAGE to separate the modified histone species, followed by mass spectrometry analysis to identify the sites and types of the PTMs.…”

Section: Tau-page Analysis Of Histones In Bkpyv Virions and Host Cellsmentioning

confidence: 67%

“…Cell culture and BKPyV propagation were performed as described in our previous report (Fang et al, 2010). Briefly, Vero cells were infected with BKPyV (UT strain, a generous gift from Dr. W. Atwood, Brown University).…”

Section: Bkpyv Propagationmentioning

confidence: 99%

“…The BKPyV purification procedures were similar to that described in our previous report (Fang et al, 2010). Briefly, the BKPyV-infected cell pellet described above was resuspended in Trisbuffered saline and incubated with type V neuraminidase.…”

Section: Bkpyv Purificationmentioning

confidence: 99%

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Global profiling of histone modifications in the polyomavirus BK virion minichromosome

et al. 2015

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During polyomavirus infection, the viral DNA adopts histones from host cells and forms minichromosomes as an important part of the viral life cycle. However, the detailed mechanisms of this histone incorporation remain unclear. Here, we profiled the histone posttranslational modifications (PTMs) in BKPyV minichromosomes and in the chromatin of BKPyV host cells. Through Triton-acetic acid-urea (TAU)-PAGE separation followed by nanoflow liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) analysis, we identified different kinds of PTMs on histones from BKPyV minichromosomes and from host cells. We observed not only the common PTMs on histones such as acetylation, methylation, phosphorylation, ubiquitination, and formylation but also several novel PTM sites. Our results also confirmed that the BKPyV minichromosome is hyperacetylated. Our detailed histone PTM profiles for the BKPyV minichromosome provide insights for future exploration of the underlying mechanisms and biological relevance of these histone PTMs.

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Section: Tau-page Analysis Of Histones In Bkpyv Virions and Host Cellsmentioning

confidence: 67%

Section: Bkpyv Propagationmentioning

confidence: 99%

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Global profiling of histone modifications in the polyomavirus BK virion minichromosome

et al. 2015

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“…The phosphorylation sites were analyzed using high-resolution and high-mass-accuracy nanoflow liquid chromatography-tandem MS (LC-MS/MS) on a linear quadrupole ion trap-Fourier transform (LTQ-FT) ion cyclotron resonance mass spectrometer (Thermo Fisher Scientific) with procedures described previously (8).…”

Section: Mass Spectrometry (Ms) Analysismentioning

confidence: 99%

Intermolecular Binding between TIFA-FHA and TIFA-pT Mediates Tumor Necrosis Factor Alpha Stimulation and NF-κB Activation

Huang

Weng

Wei

et al. 2012

Molecular and Cellular Biology

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T he forkhead-associated (FHA) domain, discovered in 1995 (10) and first suggested to bind phosphoproteins in 1998 (24), is known to specifically recognize phosphothreonine (pT) to exert its function (5,20). Although the sequence homology among different FHA-containing proteins is relatively low, the structural architecture of FHA domains is highly conserved. It contains a six-stranded ␤-sheet and another five-stranded ␤-sheet, forming a ␤-sandwich. The FHA-pT binding has been shown to regulate diverse biological functions, ranging from DNA damage repair to cell cycle checkpoints to signal transduction (18). Furthermore, the mechanism of FHA-phosphoprotein binding varies greatly among different FHA-containing proteins. The structure, specificity, mechanism, and biological functions of FHA domains have been summarized in recent reviews (16,18).TRAF-interacting protein with an FHA domain (TIFA) was first identified as a tumor necrosis factor (TNF) receptor-associated factor 2 (TRAF2) binding protein. Consisting of 184 amino acids, TIFA is the smallest FHA domain-containing protein in humans (Fig. 1A). In the absence of TNF-␣ stimulation, TIFA overexpression in HEK 293T cells can activate NF-B and AP-1 (14), suggesting a direct involvement of TIFA in TNF-mediated immune responses. This involvement of TIFA was further attributed to the binding of TRAF2, which requires the TRAF domain of TRAF2 and almost the entire TIFA protein (residues 1 to 162) (14). TIFA was also reported to bind to TNF-associated factor 6 (TRAF6) (25). The consensus binding site of TIFA for TRAF6 was mapped to be glutamic acid 178 (E178) (11, 25), indicating different binding mechanisms in TIFA-TRAF2 and TIFA-TARF6 interactions. In addition, TIFA overexpression, even in the absence of interleukin-1 (IL-1), was shown to activate NF-B and c-Jun aminoterminal kinase (JNK), possibly through its enhancement of TRAF6 binding to IL-1 receptor-associated kinase 1 (IRAK-1). On the other hand, mutation of E178 abolished the binding of TIFA to TRAF6 and the ensuing activation of NF-B (25). In a follow-up report, TIFA was shown to promote oligomerization and ubiquitination of TRAF6, leading to activation of IB kinase (IKK), based on in vitro studies (6).Although the studies of Takatsuna et al. (25) and Ea et al. (6) have previously established the key function of TIFA in its interaction with TRAF6, several issues still remain inconclusive. For example, TIFA has been suggested to be phosphorylated, and the integrity of the FHA domain of TIFA is essential for its function (6, 25), but little information has been unveiled about the molecular basis of TIFA phosphorylation and its functional consequences.In this work, we report that threonine 9 (T9) is a newly identified phosphorylation site of TIFA and that the phosphorylation level of T9 increases upon TNF-␣ treatment. Based on data collected here, we concluded that TIFA-FHA binds to this pT9 site. Such a TIFA-FHA/pT9 binding directs TIFA self-association and promotes NF-B activation through the oligomerizatio...

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“…Unfortunately, NCCR and full-genome sequencing shed little light on the origin of the contaminating virus, as BKPyV UT appears to be a relatively common variant, having been found in patient samples both in North Norway in 1990 (50) and in the United States in 2005 (51). Of note, this strain has also been used in several research labs (10,46,(72)(73)(74). Although we cannot pinpoint the infection temporally, we can be certain that BKPyV has been present in the cells at least since 2006 based on ATCC records.…”

Section: Discussionmentioning

confidence: 99%

The Human Fetal Glial Cell Line SVG p12 Contains Infectious BK Polyomavirus

Henriksen

Tylden

Dumoulin

et al. 2014

J Virol

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The human fetal glial cell line SVG was generated in 1985 by transfecting primary fetal brain cells with a plasmid containing an origin-defective mutant of simian virus 40 (SV40). The cells, which express SV40 large T-antigen, support the replication of human JC polyomavirus (JCPyV) and have been used for JCPyV studies but also for other studies in which cells of neural origin were desirable. We intended to use the SVG p12 cells from ATCC for antiviral drug studies with JCPyV. However, during initial experiments, immunofluorescence microscopy controls unexpectedly revealed cells expressing the late viral proteins VP1, VP2/ VP3, and agno. This was confirmed by Western blotting. Since our agnoprotein antiserum is specific for BKPyV agnoprotein, infection with BKPyV was suspected. Indeed, specific BKPyV PCR of SVG p12 supernatants revealed a viral load of >1 ؋ 10

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Global analysis of modifications of the human BK virus structural proteins by LC-MS/MS

Cited by 35 publications

References 49 publications

Global profiling of histone modifications in the polyomavirus BK virion minichromosome

Global profiling of histone modifications in the polyomavirus BK virion minichromosome

Intermolecular Binding between TIFA-FHA and TIFA-pT Mediates Tumor Necrosis Factor Alpha Stimulation and NF-κB Activation

The Human Fetal Glial Cell Line SVG p12 Contains Infectious BK Polyomavirus

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