Time-resolved Global and Chromatin Proteomics during Herpes Simplex Virus Type 1 (HSV-1) Infection.
Herpes simplex virus (HSV-1) lytic infection results in global changes to the host cell proteome and the proteins associated with host chromatin. We present a system level characterization of proteome dynamics during infection by performing a multi-dimensional analysis during HSV-1 lytic infection of human foreskin fibroblast (HFF) cells. Our study includes identification and quantification of the host and viral proteomes, phosphoproteomes, chromatin bound proteomes and post-translational modifications (PTMs) on cellular histones during infection. We analyzed proteomes across six time points of virus infection (0, 3, 6, 9, 12 and 15 h post-infection) and clustered trends in abundance using fuzzy c-means. Globally, we accurately quantified more than 4000 proteins, 200 differently modified histone peptides and 9000 phosphorylation sites on cellular proteins. In addition, we identified 67 viral proteins and quantified 571 phosphorylation events (465 with high confidence site localization) on viral proteins, which is currently the most comprehensive map of HSV-1 phosphoproteome. We investigated chromatin bound proteins by proteomic analysis of the high-salt chromatin fraction and identified 510 proteins that were significantly different in abundance during infection. We found 53 histone marks significantly regulated during virus infection, including a steady increase of histone H3 acetylation (H3K9ac and H3K14ac). Our data provide a resource of unprecedented depth for human and viral proteome dynamics during infection. Collectively, our results indicate that the proteome composition of the chromatin of HFF cells is highly affected during HSV-1 infection, and that phosphorylation events are abundant on viral proteins. We propose that our epi-proteomics approach will prove to be important in the characterization of other model infectious systems that involve changes to chromatin composition.
From the ‡Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.|§Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
Katarzyna
K
Kulej
From the ‡Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.|§Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
Daphne C
DC
Avgousti
¶Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.|‖Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Simone
S
Sidoli
§Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.|**Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Christin
C
Herrmann
§Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
Ashley N
AN
Della Fera
From the ‡Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.|§Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
Eui Tae
ET
Kim
¶Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania; weitzmanm@email.chop.edu bgarci@mail.med.upenn.edu.|‖Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Benjamin A
BA
Garcia
From the ‡Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania; weitzmanm@email.chop.edu bgarci@mail.med.upenn.edu.|§Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
Matthew D
MD
Weitzman
D002478:Cells, Cultured; D002843:Chromatin / Q000378:metabolism / Q000821:virology*; D002868:Chromosomal Proteins, Non-Histone / Q000378:metabolism; D005347:Fibroblasts / Q000166:cytology / Q000378:metabolism / Q000821:virology; D052816:Foreskin / Q000166:cytology / Q000378:metabolism / Q000821:virology*; D017143:Fuzzy Logic; D015967:Gene Expression Regulation, Viral; D006367:HeLa Cells; D006561:Herpes Simplex / Q000378:metabolism*; D018259:Herpesvirus 1, Human / Q000378:metabolism*; D006657:Histones / Q000378:metabolism; D006801:Humans; D008297:Male; D010766:Phosphorylation; D011499:Protein Processing, Post-Translational; D040901:Proteomics / Q000379:methods*; D014764:Viral Proteins / Q000378:metabolism*
D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D006657:Histones; D014764:Viral Proteins