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SARS-CoV-2 QTQTN motif mutant PTM-peptide mapping

ABSTRACT: 3 strains of SARS-CoV-2 were created to the function of the QTQTN motif adjacent to the Furin cleavage site on Spike protein: WT (QTQTN), Mutant 1 (QTQVN), Mutant 2 (QVQVN).

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Cercopithecus Aethiops (green Monkey) (grivet)

TISSUE(S): Cell Culture, Fibroblast

DISEASE(S): Severe Acute Respiratory Syndrome

SUBMITTER: Aaron Bailey

LAB HEAD: Vineet D. Menachery

PROVIDER: PXD034332 | Pride | 2022-07-20

REPOSITORIES: Pride

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			Action	DRS
	QTmt1-chymo_Vineet_120k15k_120min_pepM_aob_110421_018.raw	Raw
	QTmt1-chymo_Vineet_EThcD_120k15k_120min_pepM_aob_110421_031.raw	Raw
	QTmt1-tryp_Vineet_120k15k_120min_pepM_aob_110421_017.raw	Raw
	QTmt1-tryp_Vineet_EThcD_120k15k_120min_pepM_aob_110421_030.raw	Raw
	QTmt2-chymo_Vineet_120k15k_120min_pepM_aob_110421_020.raw	Raw

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Characterisation of the transcriptome and proteome of SARS-CoV-2 using direct RNA sequencing and tandem mass spectrometry reveals evidence for a cell passage induced in-frame deletion in the spike glycoprotein that removes the furin-like cleavage site.

Project description:Direct RNA sequencing using an Oxford Nanopore MinION characterised the transcriptome of SARS-CoV-2 grown in Vero E6 cells. This cell line is being widely used to propagate the novel coronavirus. The viral transcriptome was analysed using a recently developed ORF-centric pipeline. This revealed the pattern of viral transcripts, (i.e. subgenomic mRNAs), generally fitted the predicted replication and transcription model for coronaviruses. A 24 nt in-frame deletion was detected in subgenomic mRNAs encoding the spike (S) glycoprotein. This feature was identified in over half of the mapped transcripts and was predicted to remove a proposed furin cleavage site from the S glycoprotein. This motif directs cleavage of the S glycoprotein into functional subunits during virus entry or exit. Cleavage of the S glycoprotein can be a barrier to zoonotic coronavirus transmission and affect viral pathogenicity. Allied to this transcriptome analysis, tandem mass spectrometry was used to identify over 500 viral peptides and 44 phosphopeptides, covering almost all of the proteins predicted to be encoded by the SARS-CoV-2 genome, including peptides unique to the deleted variant of the S glycoprotein. Detection of an apparently viable deletion in the furin cleavage site of the S glycoprotein reinforces the point that this and other regions of SARS-CoV-2 proteins may readily mutate. This is of clear significance given the interest in the S glycoprotein as a potential vaccine target and the observation that the furin cleavage site likely contributes strongly to the pathogenesis and zoonosis of this virus. The viral genome sequence should be carefully monitored during the growth of viral stocks for research, animal challenge models and, potentially, in clinical samples. Such variations may result in different levels of virulence, morbidity and mortality.

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Transcription profiling of mouse naive T cells isolated from CD4+ CD62L+ CD44- T cells were isolated from Fur flox/flox and CD4 cre Fur flox/flox mice reveals T cell-expressed proprotein convertase furin is essential for maintenance of peripheral tolerance

Project description:Furin is a proprotein convertase induced in activated T cells, reported to processes the anti-inflammatory cytokine TGFb-1. Herein, we show that conditional deletion of furin in T cells allowed for normal T cell development but impaired the function of regulatory T cells and effector cells, which produced less TGFb-1. Furin-deficient Treg cells, were less protective in a T cell transfer colitis model and failed to induce Foxp3 in normal T cells. Furin-deficient effector cells were inherently overly active and were resistant to suppressive activity of wild-type Tregs. Thus, our results indicate that furin is indispensable in maintaining peripheral tolerance, which is due, at least in part, to its nonredundant, essential function in regulating TGFb-1 production. Targeting furin has emerged as a strategy in malignant and infectious disease. The current work suggests that inhibiting furin might activate immune responses, but may result in a breakdown in peripheral tolerance. Experiment Overall Design: Naive CD4+ CD62L+ CD44- T cells were isolated from Fur flox/flox and CD4 cre Fur flox/flox mice. Replicated samples were achieved for wild type and knockout conditions.

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