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

Developing a successful part II project

Jess and Morgan have worked in their part II projects for near six months in the Castello lab. They have studied different aspects of HIV biology by using cutting edge RNA biology, virology, molecular biology and microscopy techniques. Morgan has developed a new approach to elucidate the composition of the HIV ribonucleoproteins. Jess has assessed whether cellular RNA-binding proteins are incorporated into HIV particles. We hope they enjoyed working in the lab and wish them all the best for the coming scientific challenges.

Princeton student visit the Castello lab

Leslie worked in the Castello lab for five months as part of her degree in Princeton. She was interested in the understanding the role of a family of tumour suppressors recently classified as RNA-binding proteins by RNA interactome studies.

“Applying for this semester-long research opportunity at Oxford is one of the best decisions I have made at Princeton!  I am constantly intellectually stimulated and challenged by my research project and my PI’s thoughtful feedback – said Leslie-.  In my lab’s supportive environment,  I have come to really appreciate microscopy, beautiful silver staining/Western blot gels, the satisfying popping sound in the homogenizing process of my RNA interactome capture whole cell lysates, and so much more!  Would definitely consider coming back for grad school!”