A virus-induced specialised ribosome

Lead Research Organisation: University of Leeds
Department Name: Sch of Molecular & Cellular Biology


Ribosomes are complex molecular machines present in all cellular organisms. They are responsible for producing proteins by converting the instructions found in messenger RNA (mRNA) into the chains of amino-acids that make up proteins. Eukaryotic ribosomes are composed of two subunits, termed 60S and 40S, which are composed of ribosomal RNAs and multiple (~80) ribosomal proteins. The process to make ribosomes in the cell is highly complex and coordinated requiring lots of additional ribosome assembly factors which have specific roles in their production.

It has long been thought that all ribosomes in the cell are the same, playing a critical role in protein production but having little influence on controlling the process. However, emerging evidence suggests that subpopulations of ribosomes may exist, which can control which mRNAs are translated into proteins. These so called specialised ribosomes could have fundamental regulatory functions within the cell. A major question now relates to how a subpopulation of specialised ribosomes could be produced in a cell and one possibility is that the composition of ribosomal proteins which make up the 40S and 60S subunits could be altered, changing the regulatory function or specificity of these ribosomes.

We have exciting preliminary data suggesting that viruses have evolved ways to control the production of ribosomes in the infected cell. This would produce a virus-induced specialised ribosome which could control how viral and perhaps cellular mRNAs are translated in infected cells, enhancing virus replication and virion production. We have demonstrated that during herpesvirus infection, some ribosomal proteins are prevented from being involved in producing 40S and 60S subunits, whilst other ribosomal protein levels are increased. This suggests that the composition of ribosomal proteins may be altered during infection. In addition, we have identified a viral protein and novel mechanism of how this may be achieved in infected cells.

We now aim to further investigate these observations and identify what effect viral manipulation of ribosome biogenesis has upon the composition of specialised ribosomes in infected cells and how these changes affect the translation of cellular and viral mRNAs using a global approach called ribosomal profiling. Moreover, we will investigate what effect altering the composition of ribosomes has upon the replication cycle of the virus. Furthermore, we will assess essential virus-host cell interactions which are required for the production of these viral-induced specialised ribosomes which may provide new strategies for the production of novel antiviral reagents for this important family of pathogens.

Technical Summary

For many years ribosomes were believed to play a critical role in translating the genetic code, but had little influence on gene regulation. However, studies revealing variations between transcriptome expression and proteome levels now suggest that cellular abundance of proteins may be controlled at a translation level. This leads to the intriguing possibility that ribosomes may exert a regulatory function or specificity in translation control. For example, heterogeneity in ribosome composition may result in the formation of specialised ribosomes which have dedicated activities which result in a substantial impact on how the genomic template is translated into functional proteins.

We have exciting preliminary data to suggest Kaposi's sarcoma-associated herpesvirus (KSHV) manipulates ribosome biogenesis. As such, this provides an excellent model to study how ribosomes may exert a regulatory function or specificity in translational control. Our preliminary data shows that KSHV infection may lead to the production of a virus-induced specialised ribosome by affected the nuclear import and expression levels of specific ribosomal proteins. We also show that the virus-induced cytoplasmic retention of specific ribosomal proteins is important for virus replication and identify a single virus-encoded protein which is sufficient for this process.

The aim of this project is to determine how virus-mediated manipulation of ribosome biogenesis dictates how the host cell and genomic template is translated during virus infection. We will determine the temporal composition of host cell ribosomes during the course of virus infection and examine the implications of these on both cellular and viral translational output using ribosome profiling. Moreover, the project will examine novel mechanisms to produce virus-induced specialised ribosomes which may highlight potential therapeutic approaches for the treatment of this important family of viruses.

Planned Impact

The proposal builds upon previous novel work which has focussed on applying quantitative proteomic-based strategies to understanding the interactions between viruses and the host cell. The aim of this current proposal is to test the hypothesis that herpesvirus infection manipulates ribosome biogenesis. In particular, we aim to examine how virus-induced changes in ribosome composition dictate how the viral and cellular genomic template is translated.

Whilst this study is fundamental in nature, the impact of the research will be wide reaching. The virus model provides an excellent tool to determine how specialised ribosomes may exert a regulatory function or specificity in translational control. As such, this may provide a new level of complexity in the regulation of gene expression. This postulated "ribosome code" of translational regulation may have analogy to the "histone code", where transcriptional activity is determined by specific combinations of histone proteins, their post-translational modifications and DNA modifications. If so, novel mechanisms which regulate ribosome heterogeneity may lead to important new insights into translational control mechanisms and regulation of gene expression implicated in human disease. Aberrant translation, nucleocytoplasmic transport mechanisms and nucleolar function are all implicated in a number of human diseases, therefore any clues as to how cellular gene expression quality control checkpoints are bypassed by virus infection generated from this project will be of interest to the pharmaceutical industry. Moreover, an understanding of the pathways which regulate ribosome heterogeneity and the role of specific ribosomal proteins may provide potential leads for new therapies and also provide valuable information for engineering ribosomes with applications in biotechnology and synthetic biology. In addition, a key element of this project is the characterisation of essential virus-host cell interactions which will provide avenues for novel antiviral strategies. As numerous virus-host cell interactions are conserved in herpesviruses, this approach may have generic applications for the treatment of a variety of additional human and animal diseases caused by this large family of viruses. Therefore, these discoveries may foster new collaborations with the pharmaceutical and other commercial industries to exploit these findings for new therapeutic strategies.

In the longer term, exploitation of these findings by the commercial sector may lead to new treatments for a wide range of diseases and virus infections, and this will provide benefits to the quality of life of the general public. Moreover, exploitation of the research findings by the commercial sector is also likely to have a direct impact on the prosperity of the general public of the UK, through increased investment and employment opportunities that will arise from new therapeutic drugs.
Description Ribosomes are the macromolecular machines that decode the genetic code into proteins; as such, they are central to gene expression. Until recently ribosomes were thought to be homogeneous, passively translating mRNA into proteins, without any regulatory role. However, an emerging concept is that heterogeneity of ribosomal composition can exist, which can provide an additional level of control in the translation of specific mRNAs.
This grant has highlight several novel findings:
(i) The oncogenic herpesvirus, KSHV, manipulates host cell ribosome biogenesis during infection. This results in the production of KSHV-induced specialised ribosomes which preferentially translate viral transcripts.
(ii) Virus-induced specialized ribosomes are produced by the enhanced association of ribosomal biogenesis factors BUD23 and NOC4L, and a previously uncharacterised KSHV lytic protein, ORF11, with small ribosomal subunit precursor complexes during infection.
(iii) BUD23 and KSHV ORF11 depletion results in significantly reduced viral gene expression and progression through the lytic cascade, culminating in a dramatic reduction of infectious virion production.
(iv) Ribosome profiling demonstrated that BUD23 is essential for the reduced association of ribosomes with KSHV uORFs in late lytic genes, required for the efficient translation of the main open reading frame.
In summary, it describes a new and exciting advancement in the field, demonstrating that KSHV manipulates host ribosome biogenesis during infection, producing virus-induced specialised ribosomes. Importantly, these findings provide new mechanistic insights into how virus-mediated manipulation of ribosome composition can facilitate efficient translation of viral mRNAs.
Exploitation Route The identification of cellular proteins which are essential to enhance virus replication could provide for therapeutic targets and strategies.
This is part of 2022 sLoLA application currently under review

manuscript just uploaded on https://biorxiv.org/cgi/content/short/2022.03.11.483946v1
Sectors Pharmaceuticals and Medical Biotechnology

Description We are determine how virus can manipulate host cell ribosomes to enhance their own replication - we are identifying new cellular proteins which are essential for virus replication which could be developed into new therapeutic strategies
First Year Of Impact 2018
Sector Pharmaceuticals and Medical Biotechnology
Impact Types Societal

Description Collaboration with Prof Melanie Brinkmann 
Organisation Helmholtz Association of German Research Centres
Department Helmholtz Centre for Infection Research (HZI)
Country Germany 
Sector Academic/University 
PI Contribution Effective partnership to assess how viruses regulate ribosome biogenesis
Collaborator Contribution We have performed ribosome profiling to isolate viral proteins associated with virus infection and ribosomes
Impact Research publication
Start Year 2015
Description International collaboration 
Organisation Rhodes University
Country South Africa 
Sector Academic/University 
PI Contribution Dr Adrienne Edkins, Rhodes University, South Africa
Collaborator Contribution Investigating host cell - virus interactions focussing on molecular chaperones
Impact Kirigin. E., Ruck, D.K., Jackson, Z., Murphy, J., McDonnell, E., Okpara, M.O., Whitehouse, A. & Edkins, A.L. (2020). Regulation of Kaposi's sarcoma-associated herpesvirus biology by host molecular chaperones. Book Chapter.
Start Year 2017
Description Be curious Leeds Festival 
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Results and Impact Be Curious is the University's annual, family-friendly, research open day, an event which is usually held on campus, but in 2020 we went virtual. Over 100 of our brilliant researchers were involved in creating lots of fantastic content - from 2 minute demonstrations to try at home activities, research-related digital jigsaws and cartoon strips - to help you explore just some of the exciting things we get up to at the University of Leeds.
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