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Mass spectrometry-based analysis of kindlin phosphorylation, ubiquitination and interactome

ABSTRACT: Kindlin is an essential activator of integrins and thus indispensable in cell to extracellular matrix (ECM) adhesion. Kindlin abundance and functions are tightly regulated by multiple mechanisms including post-translational modifications (PTMs). Despite the critical roles of kindlin during embryonic development and pathogenesis, the knowledge of kindlin’s PTMs and interactome is far from complete. Here we analyze the phosphorylation, ubiquitination and interacting partners of kindlin in flat, firmly adherent interphase cells and round, weakly attached mitotic cells by immunoprecipitation-based mass spectrometry (IP-MS). The analysis generated potential phosphorylation and ubiquitination sites as well as interactors of kindlin and paved the way to investigate PTMs and binding partners of kindlin.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

SUBMITTER: Nanpeng Chen

LAB HEAD: Reinhard Fässler

PROVIDER: PXD031829 | Pride | 2022-02-22

REPOSITORIES: Pride

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Project description:SARS-CoV-2 emerged in China at the end of 2019 and caused the global pandemic of COVID-19, a disease with high morbidity and mortality. While our understanding of this new virus is rapidly increasing, gaps remain in our understanding of how SARS-CoV-2 can effectively suppress host cell antiviral responses. Recent work on other viruses has demonstrated a novel mechanism through which viral proteins can mimic critical regions of human histone proteins. Histone proteins are responsible for governing genome accessibility and their precise regulation is critical for a cell’s ability to control transcription and respond to viral threats. Here, we show that the protein encoded by ORF8 (Orf8) in SARS-CoV-2 functions as a histone mimic of the ARKS motif in histone 3. Orf8 is associated with chromatin, binds to numerous histone-associated proteins, and is itself acetylated within the histone mimic site. Orf8 expression in cells disrupts multiple critical histone post-translational modifications (PTMs) including H3K9ac, H3K9me3, and H3K27me3 and promotes chromatin compaction while Orf8 lacking the histone mimic motif does not. Further, SARS-CoV-2 infection in human cell lines and postmortem patient lung tissue cause these same disruptions to chromatin. However, deletion of the Orf8 gene from SARS-CoV-2 largely blocks its ability to disrupt host-cell chromatin indicating that Orf8 is responsible for these effects. Finally, deletion of the ORF8 gene affects the host-cell transcriptional response to SARS-CoV-2 infection in multiple cell types and decreases the replication of SARS-CoV-2 in human induced pluripotent stem cell-derived lung alveolar type 2 (iAT2) pulmonary cells. These findings demonstrate a novel function for the poorly understood ORF8-encoded protein and a mechanism through which SARS-CoV-2 disrupts host cell epigenetic regulation. Finally, this work provides a molecular basis for the finding that SARS-CoV-2 lacking ORF8 is associated with decreased severity of COVID-19.

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Mass spectrometry-based analysis of kindlin phosphorylation, ubiquitination and interactome

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