Quantitative temporal viromics: an approach to investigate host-pathogen interaction.
Bottom Line: QTV predicted natural killer and T cell ligands, as well as 29 viral proteins present at the cell surface, potential therapeutic targets.Temporal profiles of >80% of HCMV canonical genes and 14 noncanonical HCMV open reading frames were defined.QTV is a powerful method that can yield important insights into viral infection and is applicable to any virus with a robust in vitro model.
Affiliation: Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA; Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK. Electronic address: email@example.com.Show MeSH
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Mentions: We were unable to confidently resolve the profile of UL122 (IE2). UL122 and UL123 are expressed by alternative splicing of a single major immediate-early transcript. Exons 1, 2, 3, and 4 encode UL123 and exons 1, 2, 3, and 5 encode UL122; however, additional transcripts have also been detected from the region of exon 5 (Stenberg et al., 1989; Stern-Ginossar et al., 2012). We examined each peptide quantified from every exon (Figure S5A). The profiles of all peptides from exon 4 peaked at 18–24 hr, corresponding to the predicted expression of UL123 protein. The profiles of ten exon 5 peptides corresponding to the late-expressed internal ORF, ORFL265C.iORF1 (Stern-Ginossar et al., 2012) peaked at 96 hr. A single peptide N-terminal to this ORF that is likely to originate from UL122 had a distinct profile with expression from 6 hr that peaked at 48 hr, similar to UL122 mRNA (Stern-Ginossar et al., 2012). This suggests the existence of at least two proteins arising wholly or in part from exon 5 and corresponds to the detection of an abundant late 40 kDa protein, previously detected from the same internal exon 5 ORF of AD169 strain (Stenberg et al., 1989). It is likely that ORFL265C.iORF1 protein is more abundant than UL122, effectively masking the earlier signal from most UL122 exon 5 peptides. Our quantitation of DNA polymerase processivity subunit UL44 may similarly have been complicated due to multiple transcription start sites (Data S1).
Affiliation: Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA; Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK. Electronic address: firstname.lastname@example.org.