Identification of host factors involved in coronavirus replication by quantitative proteomics analysis

Vogels, Mijke W.; van Balkom, Bas W. M.; Kaloyanova, Dora V.; Batenburg, Joseph J.; Heck, Albert J.; Helms, J. Bernd; Rottier, Peter J. M.; de Haan, Cornelis A. M.

doi:10.1002/pmic.201000309

Cited by 40SARS-CoV-2 and COVID-19 ResearchAdvanced Proteomics Techniques and ApplicationsAnimal Virus Infections Studies

Identification of host factors involved in coronavirus replication by quantitative proteomics analysis

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Vogels, Mijke W., van Balkom, Bas W. M., Kaloyanova, Dora V., Batenburg, Joseph J., Heck, Albert J., Helms, J. Bernd, Rottier, Peter J. M., de Haan, Cornelis A. M.·2011·PROTEOMICS

DOI 10.1002/pmic.201000309PMC PMC7167679

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Abstract

In this study, we applied a quantitative proteomic approach, based on SILAC, to investigate the interactions of coronaviruses with the secretory pathway of the host cell, with the aim to identify host factors involved in coronavirus replication. Comparison of the protein profiles of Golgi‐enriched fractions of cells that were either mock infected or infected with mouse hepatitis virus revealed the significant depletion or enrichment of 116 proteins. Although ribosomal/nucleic acid binding proteins were enriched in the Golgi‐fractions of mouse hepatitis virus‐infected cells, proteins annotated to localize to several organelles of the secretory pathway were overrepresented among the proteins that were depleted from these fractions upon infection. We hypothesized that proteins, of which the abundance or distribution is affected by infection, are likely to be involved in the virus life cycle. Indeed, depletion of a small subset of the affected proteins by using small interfering RNAs identified several host factors involved in coronavirus infection. Transfection of small interfering RNAs targeting either C11orf59 or Golgi apparatus glycoprotein 1 resulted in increased virus replication, whereas depletion of vesicle‐trafficking protein vesicle‐trafficking protein sec22b enhanced the release of infectious progeny virus. Overexpression of these proteins, on the other hand, had a negative effect on virus replication. Overall, our study shows that the SILAC approach is a suitable tool to study host–pathogen interactions and to identify host proteins involved in virus replication.

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Differentially regulated Golgi-resident and vesicle trafficking factors, including SEC22B and LAMTOR1, were shown to affect MHV virion assembly in RNAi and overexpression assays.
“selected differentially regulated Golgi-resident and vesicle trafficking factors, such as SEC22B and the Ragulator complex protein LAMTOR1, were shown to alter MHV virion assembly using RNA interference and overexpression assays.”
From The Impact of Mass Spectrometry–Based Proteomics on Fundamental Discoveries in Virology (2014) · cites this paper as [102]
In mouse hepatitis virus-infected hepatocytes, SILAC measured virus-induced expression changes in Golgi-enriched fractions.
“metabolic labeling using stable isotope labeling in cell culture (SILAC; see Figure 2) was employed to quantify virus-induced expression changes in Golgi-enriched fractions from mouse hepatitis virus (MHV)-infected hepatocytes (102).”
From The Impact of Mass Spectrometry–Based Proteomics on Fundamental Discoveries in Virology (2014) · cites this paper as [102]

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Identification of host proteins involved in host-pathogen interactions. A proteomics approach
Helms, J. B., Rottier, P. J. M., Batenburg, J. J., de Haan, C. A. M., Kaloyanova, D. V., & Vogels, M. W. (2005)
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Determination of host cell proteins constituting the molecular microenvironment of coronavirus replicase complexes by proximity-labeling
V’kovski, P., Gerber, M., Kelly, J. N., Pfänder, S., Ebert, N., Braga, S. M.-P., Simillion, C., Portmann, J., Hanspeter, S., Gaschen, V., et al. (2018) · doi:10.7892/boris.121510

Authors: Vogels, M. W., van Balkom, B. W. M., Kaloyanova, D. V., Batenburg, J. J., Heck, A. J., Helms, J. B., Rottier, P. J. M., & de Haan, C. A. M.
Affiliations: Utrecht University (NL)
ORCID: Heck, Albert J.
Helms, J. Bernd
Venue: PROTEOMICS
Publisher: Wiley
Published: 2010-12-06
Volume: 11
Issue: 1
Pages: 64-80
ISSN: 1615-9853 (ISSN-L)
1615-9861
DOI: 10.1002/pmic.201000309
PMC: PMC7167679
OpenAlex: W2040208749
Cited by: 40
References: 69
Citations by year: 2020: 2 · 2019: 1 · 2018: 1 · 2017: 1 · 2016: 5 · 2015: 4 · 2014: 6 · 2013: 3 · 2012: 10
FWCI: 4.15
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: onlinelibrary.wiley.com/termsAndConditions#vor (vor)
Locations: PROTEOMICS (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Utrecht University Repository (Utrecht University) (submittedVersion)
Funders: Faculty of Veterinary Medicine of Utrecht University, The Netherlands
Topics: Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
Keywords: coronavirus replication, host factors, secretory pathway, Golgi apparatus, mouse hepatitis virus, host-pathogen interaction, Sec22b, vesicle trafficking, protein depletion, siRNA knockdown
MeSH terms: Electrophoresis, Polyacrylamide Gel, HeLa Cells, Murine hepatitis virus, Humans, Sialoglycoproteins, Mass Spectrometry, Virus Replication, Receptors, Fibroblast Growth Factor, Coronavirus, RNA Interference, RNA, Small Interfering, Proteomics, Host-Pathogen Interactions

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Identification of host factors involved in coronavirus replication by quantitative proteomics analysis

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