Kammoun, M. | bioRxiv Science

bioRxiv2020

Global analysis of protein-RNA interactions in SARS-CoV-2 infected cells reveals key regulators of infection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19. SARS-CoV-2 relies on cellular RNA-binding proteins (RBPs) to replicate and spread, although which RBPs control SARS-CoV-2 infection remains largely unknown. Here, we employ a multi-omic approach to identify systematically and comprehensively which cellular and viral RBPs are involved in SARS-CoV-2 infection. We reveal that the cellular RNA-bound proteome is remodelled upon SARS-CoV-2 infection, having widespread effects on RNA metabolic pathways, non-canonical RBPs and antiviral factors. Moreover, we apply a new method to identify the proteins that directly interact with viral RNA, uncovering dozens of cellular RBPs and six viral proteins. Amongst them, several components of the tRNA ligase complex, which we show regulate SARS-CoV-2 infection. Furthermore, we discover that available drugs targeting host RBPs that interact with SARS-CoV-2 RNA inhibit infection. Collectively, our results uncover a new universe of host-virus interactions with potential for new antiviral therapies against COVID-19.

microbiology↗

bioRxiv2018

RLIM enhances BMP signalling mediated fetal lung development in mice

RLIM, also called RNF12, is an X-linked E3 ubiquitin ligase. It is a pleotropic protein acting as a negative regulator of LIM-homeodomain transcription factors and of SMAD7, an antagonist of the BMP and TGF{beta} pathways. Mutations in RLIM are associated with variable congenital malformations in human. The molecular mechanism causing these malformations is still poorly understood.\n\nIn this study, we used a conventional knockout (KO) mouse model to phenotypically characterize male mutants and to investigate the effect of Rlim mutation on BMP pathway signalling. Only 50% of KO male neonates survive and are significantly smaller. We show that Rlim deletion alters lung branching and maturation resulting in severe respiratory distress and neonatal death. Except for a single case of cardiac interventricular septal defect, no other malformations that mimic the human condition were observed. Western blot analysis shows that RLIM deficiency is associated with an increase of its target SMAD7 levels and a loss of SMAD1/5/9 activation. Interestingly, SMAD5 levels were diminished, suggesting another regulatory loop between RLIM and the BMP pathway.\n\nIn conclusion, RLIM is important for lung development in mice and exerts this function in part through intracellular propagation of BMP signalling.\n\nAuthor summaryRLIM is an X-linked gene encoding an enzyme that regulates a number of proteins including SMAD7, an antagonist of BMP pathway. RLIM mutations are associated with intellectual disability and several congenital malformations in boys. In mice, RLIM is thought to be nonessential for embryos development. Using a mouse model in which Rlim is deleted, we show that 50% of males carrying the deletion display respiratory distress and die short after birth. No congenital malformations mimicking the human phenotype have been observed. Histological analysis of lung samples show that Rlim is critical for late lung development and maturation. The analysis of lung samples by western blot, a technique that quantifies proteins, is consistent with a dysregulation of BMP pathway. These finding confirm the importance of RLIM for murine embryos development and provide a link between human RLIM pathology and BMP pathway.

genetics↗