Exploitation of a surrogate host, Saccharomyces cerevisiae, to identify cellular targets and develop novel antiviral approaches
Introduction
Plant-infecting RNA viruses are widespread intracellular pathogens with simple genome organization and a limited coding capacity of 4-to-12 genes. These viruses not only rely on the expression of viral replication-associated proteins, coat proteins, plant virus-specific movement proteins and suppressors of host gene silencing from their genomes, but on co-opting numerous cellular factors [1, 2]. Thus, similar to animal viruses, plant viruses inevitably depend on co-opted host factors, which are used to build viral replication compartments or replication organelles inside the infected cells. Many viral processes depend on the interactions between the viral components and cellular proteins, lipids and metabolites that are subverted for viral multiplication. Interestingly, the co-opted host components are sequestered, retargeted and manipulated by viruses to create subcellular environment suitable for virus replication [3•, 4].
Currently, there are only a limited number of plant resistance genes against a limited number of viruses [5, 6]. Although transgenic approaches have been developed against many plant viruses in several crops, the use of transgenic virus-resistant plants is not yet widespread [7]. Moreover, plant viruses evolve, leading to new variants and recombinants as well as new viruses emerge and re-emerge due to global trade and global changes in weather [8, 9, 10•, 11]. These factors make it mandatory for scientists to search for new antiviral targets and develop new antiviral approaches.
This section is divided into two main parts, which describe (i) new antiviral host proteins inhibiting virus replication and (ii) new cellular targets for antiviral intervention, respectively. The central player is tomato bushy stunt virus (TBSV), the type member of the small tombusviruses infecting a wide range of plants. TBSV is highly suitable for these purposes based on the identification of most of the interactions, or networks of interactions, between TBSV and a host cell, namely the model baker yeast (Saccharomyces cerevisiae) [12•, 13]. This short review article cannot cover the dominant and recessive genes-mediated antiviral approaches due to page limit and the readers can find excellent reviews on these topics [5, 14, 15, 16]. Also, plant immunity against viruses at the translational level will not be discussed [17].
Section snippets
A brief introduction to TBSV replication machinery
Many (+)RNA viruses, similar to TBSV, induce ∼70 nm vesicle-like intracellular membrane invaginations (harboring VRCs) with narrow openings toward the cytosol [3•, 18•]. The central role of VRCs is viral RNA synthesis, which generates the new infectious progeny (+)RNAs. This process is driven by the TBSV-coded p92pol replication protein, but co-opted host proteins greatly affect RNA synthesis. Also, the p33 replication protein is the master regulator of the many known steps during VRC assembly [
Yeast as a model system to identify host genes affecting (+)RNA virus replication
The intimate interactions between a given virus and its hosts make it a challenging task to identify all the host components that are either subverted for viral infections or used by the host to combat viruses. Although the number of identified host genes affecting various plant viruses is growing [3•, 19], the list is rather incomplete due to low throughput approaches. With the advent of powerful experimental tools, such as CRISPR, to manipulate the host's genome or proteome [25•], it will be
Exploitation of cell-intrinsic viral restriction factors against TBSV
As pointed out above, a major advance from the systematic genome-wide screens with yeast libraries is the identification of a large group of host factors, which might be possible to exploit for development of new antiviral approaches. Accordingly, many inhibitory host proteins, collectively called cell-intrinsic restriction factors (CIRFs) [46, 47•], could be useful to limit TBSV replication.
Among the most promising CIRFs are cyclophilins and parvulins (Table 1), which are peptidyl-prolyl-
Co-opted pro-viral host factors as new targets for antiviral intervention
The systematic genome-wide screens with TBSV based on yeast libraries have led to the identification of a large group of co-opted pro-viral host factors [13, 19]. Blocking the pro-viral functions of selected host factors might lead to new antiviral approaches, as discussed briefly below. We will also highlight the different approaches used to block the pro-viral functions of host factors.
Chemical inhibitors of host protein functions: One of the outstanding targets is the cellular heat shock
Conclusions
Genome-wide screens with TBSV in yeast surrogate host have revealed the presence of numerous CIRFs, which function either as direct antagonists of viral replication proteins and viral RNA through blocking their essential viral functions, or inhibit the pro-viral functions of other co-opted host proteins. CIRFs, such as cochaperones, might act as guardians of cellular homeostasis by protecting cellular Hsp70 chaperones through inhibiting the virus-mediated subversion of Hsp70 into VRCs [46].
Conflict of interest
The author declares no conflict-of-interest.
References and recommended reading
Papers of particular interest, published within the period of review, have been highlighted as:
• of special interest
•• of outstanding interest
Acknowledgements
This work was supported by the National Science Foundation (MCB-1122039) to PDN.
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2023, Current Opinion in MicrobiologyMultifunctional role of the co-opted Cdc48 AAA+ ATPase in tombusvirus replication
2022, VirologyCitation Excerpt :However, the complete list of co-opted host proteins and lipids and their functions within VROs are not yet known. Tomato bushy stunt virus (TBSV) is intensively studied to dissect host-virus interactions (Nagy, 2016, 2017). TBSV has a single (+)RNA genome of ∼4.8 kb (White and Nagy, 2004).
Co-opted membranes, lipids, and host proteins: what have we learned from tombusviruses?
2022, Current Opinion in VirologyCitation Excerpt :Overall, the biogenesis of TBSV VROs associated with peroxisomes and that of CIRV VROs associated with mitochondria is a rather complex process, but surprisingly similar to each other inspite of the different subcellular environment. Based on previous genome-wide and proteome-wide screens in yeast with TBSV [99,100], which have identified ∼500 host proteins, the contribution of many host proteins to TBSV replication has not been defined yet. It will be interesting to discover how those uncharacterized host proteins will make the interplay between TBSV and the host even more complex.
Key tethering function of Atg11 autophagy scaffold protein in formation of virus-induced membrane contact sites during tombusvirus replication
2022, VirologyCitation Excerpt :TBSV codes for two essential replication proteins, the p92 RdRp and the p33 replication protein, which is the master regulator of VRO assembly and viral (+)RNA recruitment into VRCs (Pogany et al., 2005; Xu and Nagy, 2017). TBSV replicon (rep)RNA replicates in the surrogate host yeast (Saccharomyces cerevisiae) to a high level (Nagy, 2016, 2017; Nagy et al., 2014). Yeast-based genome-wide and proteome-wide studies with TBSV led to the identification of numerous host factors co-opted for viral RNA replication and recombination (Kovalev et al., 2019; Nagy, 2016; Nagy and Pogany, 2012; Prasanth et al., 2016; Xu and Nagy, 2014).
Targeting conserved co-opted host factors to block virus replication: Using allosteric inhibitors of the cytosolic Hsp70s to interfere with tomato bushy stunt virus replication
2021, VirologyCitation Excerpt :Major efforts with several animal viruses using genomic and proteomic approaches have led to the identification of hundreds of pro-viral or antiviral host factors (Acosta et al., 2014; de Wilde et al., 2018; Diamond and Schoggins, 2013; Krishnan et al., 2008; Li et al., 2009a; Neufeldt et al., 2018; Yasunaga et al., 2014). Interestingly, systematic genome-wide screens have also been performed with yeast (Saccharomyces cerevisiae), which can support the replication of plant tomato bushy stunt virus (TBSV) and the unrelated brome mosaic virus and the insect Flock house virus and Nodamura virus (Gancarz et al., 2011; Jiang et al., 2006; Kushner et al., 2003; Nagy, 2016; Nagy, 2017; Panavas et al., 2005b; Pogany et al., 2010; Serviene et al., 2005; Shah Nawaz-Ul-Rehman et al., 2013). Although a large number of host factors is specific for different viruses, the emerging theme from the large-scale studies and from follow-up studies with a number of subverted proteins is that co-opted host factors bear many functional resemblances (Huang et al., 2012; Nagy, 2016, 2017; Nagy and Pogany, 2012; Sanfacon, 2017; Shulla and Randall, 2012; Wang, 2015; Zhang et al., 2019).