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Quantitative temporal viromics: an approach to investigate host-pathogen interaction.

Weekes MP, Tomasec P, Huttlin EL, Fielding CA, Nusinow D, Stanton RJ, Wang EC, Aicheler R, Murrell I, Wilkinson GW, Lehner PJ, Gygi SP - Cell (2014)

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.

View Article: PubMed Central - PubMed

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: mpw1001@cam.ac.uk.

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HCMV Proteins Quantified at the Surface of Infected Fibroblasts(A) Histogram of peptide ratios for all GO-annotated proteins quantified in experiments PM1 or PM2. “PM only,” not detected in experiments WCL1 or WCL2. “PM annotation”: “plasma membrane”, “cell surface,” “extracellular,” or “short GO.”(B) Temporal profiles of all high-confidence PM proteins (Table S6). Virion envelope glycoproteins were generally detected significantly earlier in whole-cell lysates than in plasma membrane samples. Arrows, quantitation of fusion or binding of the virion envelope and the plasma membrane.See also Figure S6 and Table S7.
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fig6: HCMV Proteins Quantified at the Surface of Infected Fibroblasts(A) Histogram of peptide ratios for all GO-annotated proteins quantified in experiments PM1 or PM2. “PM only,” not detected in experiments WCL1 or WCL2. “PM annotation”: “plasma membrane”, “cell surface,” “extracellular,” or “short GO.”(B) Temporal profiles of all high-confidence PM proteins (Table S6). Virion envelope glycoproteins were generally detected significantly earlier in whole-cell lysates than in plasma membrane samples. Arrows, quantitation of fusion or binding of the virion envelope and the plasma membrane.See also Figure S6 and Table S7.

Mentions: We detected a total of 67 viral proteins in experiments PM1 and PM2. Plasma membrane profiling provides a very substantial enrichment for PM glycoproteins (up to 90% of proteins from unfractionated samples, and approximately 60% of proteins from fractionated samples have indicative Gene Ontology (GO) terms (Figure S1A) (Weekes et al., 2012). Subcellular localization of viral proteins is, however, poorly annotated, making it difficult to determine which might be non-PM contaminants, such as abundant viral tegument and nuclear proteins. We therefore developed a filtering strategy: for every GO-annotated human protein quantified in experiment PM1 or PM2 (Figure S1A), we calculated the ratio of peptides (experiments PM1 + PM2)/(experiments WCL1+WCL2). Ninety-two percent of proteins that were GO-defined non-PM had a ratio of <1.4; 88% of human proteins scoring above 1.4 were annotated as PM proteins, demonstrating the predictive value of this metric (Figure 6A). Applying this filter, we defined 29 high-confidence viral PM proteins, which included the majority of viral proteins previously identified at the surface of either infected or transduced cells, and excluded all proteins unlikely to be present at the cell surface based on their known function (Table S7).


Quantitative temporal viromics: an approach to investigate host-pathogen interaction.

Weekes MP, Tomasec P, Huttlin EL, Fielding CA, Nusinow D, Stanton RJ, Wang EC, Aicheler R, Murrell I, Wilkinson GW, Lehner PJ, Gygi SP - Cell (2014)

HCMV Proteins Quantified at the Surface of Infected Fibroblasts(A) Histogram of peptide ratios for all GO-annotated proteins quantified in experiments PM1 or PM2. “PM only,” not detected in experiments WCL1 or WCL2. “PM annotation”: “plasma membrane”, “cell surface,” “extracellular,” or “short GO.”(B) Temporal profiles of all high-confidence PM proteins (Table S6). Virion envelope glycoproteins were generally detected significantly earlier in whole-cell lysates than in plasma membrane samples. Arrows, quantitation of fusion or binding of the virion envelope and the plasma membrane.See also Figure S6 and Table S7.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4048463&req=5

fig6: HCMV Proteins Quantified at the Surface of Infected Fibroblasts(A) Histogram of peptide ratios for all GO-annotated proteins quantified in experiments PM1 or PM2. “PM only,” not detected in experiments WCL1 or WCL2. “PM annotation”: “plasma membrane”, “cell surface,” “extracellular,” or “short GO.”(B) Temporal profiles of all high-confidence PM proteins (Table S6). Virion envelope glycoproteins were generally detected significantly earlier in whole-cell lysates than in plasma membrane samples. Arrows, quantitation of fusion or binding of the virion envelope and the plasma membrane.See also Figure S6 and Table S7.
Mentions: We detected a total of 67 viral proteins in experiments PM1 and PM2. Plasma membrane profiling provides a very substantial enrichment for PM glycoproteins (up to 90% of proteins from unfractionated samples, and approximately 60% of proteins from fractionated samples have indicative Gene Ontology (GO) terms (Figure S1A) (Weekes et al., 2012). Subcellular localization of viral proteins is, however, poorly annotated, making it difficult to determine which might be non-PM contaminants, such as abundant viral tegument and nuclear proteins. We therefore developed a filtering strategy: for every GO-annotated human protein quantified in experiment PM1 or PM2 (Figure S1A), we calculated the ratio of peptides (experiments PM1 + PM2)/(experiments WCL1+WCL2). Ninety-two percent of proteins that were GO-defined non-PM had a ratio of <1.4; 88% of human proteins scoring above 1.4 were annotated as PM proteins, demonstrating the predictive value of this metric (Figure 6A). Applying this filter, we defined 29 high-confidence viral PM proteins, which included the majority of viral proteins previously identified at the surface of either infected or transduced cells, and excluded all proteins unlikely to be present at the cell surface based on their known function (Table S7).

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.

View Article: PubMed Central - PubMed

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: mpw1001@cam.ac.uk.

Show MeSH
Related in: MedlinePlus