Discovering the cellular RNA-binding proteins controlling virus infection

Our new research published in Molecular Cell has discovered that virus infection rewires cellular RNA-binding proteins on a global level. This reflects two antagonistic processes: the virus hijacking key cellular resources and the antiviral defence mechanisms of the cell. This work provides a comprehensive snapshot of the virus-host cell battlefield and opens new avenues for the development of antiviral therapies.

RNA-binding proteins are a critical component of the cellular machinery that dictate the fate of RNA molecules. As RNA virus genomes are small, they rely on host RNA-binding proteins to control the life of the viral RNA. However, which of these host proteins are required for virus infection remains largely unknown. Alfredo’s group developed a novel technique called ‘comparative RNA interactome capture’ to interrogate which RNA-binding proteins are involved in the infection of a model virus called Sindbis (SINV). This work uncovered that SINV infection alters the activity of more than 200 cellular RNA-binding proteins, thus rewiring cellular RNA metabolism (Figure 1A).

“The infection alters the activity of more than two hundred RNA-binding proteins – says Marko Noerenberg -. This is likely reflecting the battle between the virus and the host cell for the control of the cellular resources.”

SINV turns off RNA-binding proteins participating in the nuclear life of the RNA, while activates key regulators of protein synthesis, RNA degradation and storage and in innate immunity. Removal of the proteins with enhanced activity from the cell SINV infection was severely affected, highlighting their key role at controlling viral replication. The intimate connection between these host proteins and the virus was confirmed by microscopy, showing that they accumulate at the places in the cell where the SINV replicates co-localising with the viral RNA (Figure 1B).

 “Sindbis virus synthesises massive amounts of viral RNA – explained Manuel Garcia-Moreno -, and these RNA molecules act as spider webs that capture the proteins that the virus needs in the places where they are needed.”  “Sindbis virus synthesises massive amounts of viral RNA – explained Manuel Garcia-Moreno -, and these RNA molecules act as spider webs that capture the proteins that the virus needs in the places where they are needed.”

The researchers also reported a dramatic degradation of cellular RNAs while viral RNA accumulates. They discovered that cells lacking the exonuclease XRN1, mediator cellular RNA clearance, become resistant to SINV infection. Therefore, cellular RNA degradation emerges as a key process supporting viral infection. Moreover, their study revealed that the cellular protein GEMIN5 binds to the viral RNAs and inhibits their translation, which represents a new antiviral mechanism to control virus infection.

“We discovered many RNA-binding proteins that are central for virus infection – added Alfredo Castello, who led this work-. These results open new avenues for the discovery of new therapies against viruses”. 

Original article

System-wide profiling of RNA-binding proteins uncovers key regulators of virus infection. Garcia-Moreno M*,  Noerenberg M*, Ni S*,  Järvelin AI, González-Almela E, Lenz CE, Bach-Pages M, Cox V, Avolio R, Davis T, Hester S, Sohier TJM, Li B, Heikel G, Michlewski G,  Sanz MA, Carrasco L, Ricci EP, Pelechano V, Davis I, Fischer B, Mohammed S and Castello A. Molecular Cell. DOI: https://doi.org/10.1016/j.molcel.2019.01.017
https://www.cell.com/molecular-cell/fulltext/S1097-2765(19)30037-1

Riboregulation: when RNA controls protein function

It is established that interactions of proteins with RNA play a crucial role at regulating RNA fate. However, a recent work led by the Hentze lab at EMBL has discovered that the reverse relationship is also possible. In other words, proteins can be regulated by RNA. We refer to this phenomenon as ‘riboregulation’.

This study shows that the RNA vault 1-1 (vtRNA1-1) interacts and regulates the protein p62, which is a key component of the autophagy machinery. As its name suggests, autophagy is a process by which a cell ‘eats itself’ to recycle its unnecessary or dysfunctional components. Interaction of vtRNA1-1 with p62 inhibits autophagy and this regulatory circuit exists in both human and mouse cells.

Importantly, the amount of vtRNA1-1 inside a cell varies according to the cell’s nutritional status. When is deprived of amino acids, vtRNA1-1 is reduced to enhance autophagy that will refill the pool of amino acids from unnecessary proteins to cover the cell needs.

This study raises the question of how common ‘riboregulation’ is and which processes are controlled by RNA. We hope to find the answer to these important questions in the years to come.

Original publication

The Small Non-coding Vault RNA1-1 Acts as a Riboregulator of Autophagy.

Horos R, Büscher M, Kleinendorst R, Alleaume AM, Tarafder AK, Schwarzl T, Dziuba D, Tischer C, Zielonka EM, Adak A, Castello A, Huber W, Sachse C, Hentze MW. Cell. 2019 Feb 21;176(5):1054-1067.e12. doi: 10.1016/j.cell.2019.01.030. Epub 2019 Feb 14.PMID: 30773316

A brave new world of RNA-binding proteins

Our last review was recently published in Nature Reviews – Molecular and Cell Biology. We discuss about the recurrent identification of unorthodox RBPs by proteome-wide methods to identify proteins bound to RNA, and discuss about the potential biological meaning of this exciting discovery.


What can we expect from the discovery of so many new RBPs? Some might side with Miranda from Shakespeare’s The Tempest and marvel at these novel and goodly RBPs that populate the RNA interactome. Others might think of Huxley’s brave new world and fear dystopia, considering the newly discovered RBPs as nonconformist misfits lacking biological function. Which roles do these new RBPs play?


A brave new world of RNA-binding proteins.

Hentze MW, Castello A, Schwarzl T, Preiss T.
2018 Jan 17. doi: 10.1038/nrm.2017.130.

 

Protocol to identify the RNA-binding domains of RBPs in a global scale

RBDmap employs UV crosslinking, oligo(dT) selection, partial proteolysis and quantitative proteomics to identify the protein regions engaged in RNA binding in a system-wide scale. Applied to HeLa cells it reported 1,174 RNA-binding sites mapping to 529 RBPs, many of which lacking known RNA-binding domains. A detail RBDmap protocol has now been released for the community in Nature protocols


The use of RBDmap can now be extended to other cell lines or organisms and can be used to profile in a global scale the behaviour of RNA-binding domains in response to different physiological conditions and stresses.”


Identification of RNA-binding domains of RNA-binding proteins in cultured cells on a system-wide scale with RBDmap. Castello A, Frese CK, Fischer B, Järvelin AI, Horos R, Alleaume AM, Foehr S, Curk T, Krijgsveld J, Hentze MW. Nat Protoc. 2017 Dec;12(12):2447-2464. doi: 10.1038/nprot.2017.106. Epub 2017 Nov 2. PMID:  29095441

The activity of TRIM25 is controlled by RNA

The E3 ubiquitin ligase TRIM25 is an antiviral factor recently discovered to bind RNA by the RNA interactome studies (Castello et al., 2012 and Kwon et al., 2013). In a recent work led by our collaborator Gracjan Michlewsky (Wellcome Centre for Cell Biology, University of Edinburgh), we dissected how this protein binds to RNA and what are the consequences of this interaction in TRIM25 function. We discovered that TRIM25 binds RNA via its PRY/SPRY domain and that the interaction with RNA enhances TRIM25 E3 ligase activity, which is necessary for its antiviral role. Using CLIP analyses we showed that TRIM25 binds G-rich sequences present in hundreds of cellular RNAs. Moreover, We discovered that TRIM25 controls the levels of a key component in the interferon response pathway, ZAP (also known as PARP13 and ZC3HAV1).


In conclusion, the E3 ligase activity of TRIM25 is controlled by RNA, breaking once more the view that proteins act on RNA and not the opposite.


Original publication:
RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination
Nila Roy Choudhury, Gregory Heikel, Maryia Trubitsyna, Peter Kubik, Jakub S. Nowak, Shaun Webb, Sander Granneman, Christos Spanos, Juri Rappsilber, Alfredo Castello and Gracjan Michlewski
BMC biology