Zika virus remodels and hijacks IGF2BP2 ribonucleoprotein complex to promote viral replication organelle biogenesis

Reviewer #1 (Public Review):

Summary:
This study investigated the co-option of IGF2BP2, an RNA-binding protein by ZIKV proteins. Designed experiments evaluated if IFG2BP2 co-localized to sites of viral RNA replication, interacted with ZIKV proteins, and how ZIKV infection changed the IGF2BP2 interactome.

Strengths:
The authors have used multiple interdisciplinary techniques to address several questions regarding the interaction of ZIKV proteins and IGF2BP2.
The findings could be exciting, specifically regarding how ZIKV infection alters the interactome of IGF2BP2.

Weaknesses:
Significant concerns regarding the current state of the figures, descriptions in the figure legends, and the quality of the immunofluorescence and electron microscopy exist.

Reviewer #2 (Public Review):

Clément Mazeaud et al. identified the insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) as a proviral cellular protein that regulates Zika virus RNA replication by modulating the biogenesis of virus-induced replication organelles.

The absence of IGF2BP2 specifically dampens ZIKV replication without having a major impact on DENV replication. The authors show that ZIKV infection changes IGF2BP2 cellular distribution, which relocates to the perinuclear viral replication compartment. These assays were conducted by infecting cells with an MOI of 10 for 48 hours. Considering the ZIKV life cycle, it is noteworthy that at this time there may be a cytopathic effect. One point of concern arises regarding how the authors can ascertain that the observed change in localization is a consequence of the infection rather than of the cytopathic effect. To address this concern, shorter infection periods (e.g., 24 hours post-infection) or additional controls, such as assessing cellular proteins that do not change their localization or infecting with another flavivirus lacking the IGF2BP2 effect, could be incorporated into their experiments.

By performing co-immunoprecipitation assays on mock and infected cells that express HA-tagged IGF2BP2, the authors propose that the observed change in IGF2BP2 localization results from its recruitment to the replication compartment by the viral NS5 polymerase and associated with the viral RNA. Given that both IGF2BP2 and NS5 are RNA-binding proteins, it is plausible that their interaction is mediated indirectly through the RNA molecule. Notably, the authors do not address the treatment of lysates with RNAse before the IP assay, leaving open the possibility of this indirect interaction between IGF2BP2 and NS5.

In in vitro binding assays, the authors demonstrate that the RNA-recognition motifs of the IGF2BP2 protein specifically bind to the 3' nontranslated region (NTR) of the ZIKV genome, excluding binding to the 5' NTR. However, they cannot rule out the possibility of this host protein associating with other regions of the viral genome. Using a reporter ZIKV subgenomic replicon system in IGF2BP2 knock-down cells, they additionally demonstrate that IGF2BP2 enhances viral genome replication. Despite its proviral function, the authors note that the "overexpression of IGF2BP2 had no impact on total vRNA levels." However, the authors do not delve into a discussion of this latter statement.

In this study, the authors extend their findings by illustrating that ZIKV infection triggers a remodeling of IGF2BP2 ribonucleoprotein complex. They initially evaluate the impact of ZIKV infection on IGF2BP2's interaction with its endogenous mRNA ligands. Their results reveal that viral infection alters the binding of specific mRNA ligands, yet the physiological consequences of this loss of binding in the cell remain unexplored. Additionally, the authors demonstrate that ZIKV infection modifies the IGF2BP2 interactome. Through proteomic assays, they identified 62 altered partners of IGF2BP2 following ZIKV infection, with proteins associated with mRNA splicing and ribosome biogenesis being the most represented. In particular, the authors focused their research on the heightened interaction between IGF2BP2 and Atlastin 2, an ER-shaping protein reported to be involved in flavivirus vesicle packet formation. The validation of this interaction by Western blot assays prompted an analysis of the effect of ZIKV on organelle biogenesis using a newly described replication-independent vesicle packet induction system. Consequently, the authors demonstrate that IGF2BP2 plays a regulatory role in the biogenesis of ZIKV replication organelles.

Based on these findings and previously published data, the authors propose a model outlining the role of IGF2BP2 in ZIKV infectious cycle, detailing the changes in IGF2BP2 interactions with both cellular and viral proteins and RNAs that occur during viral infection.

The conclusions drawn in this paper are generally well substantiated by the data. However, it is worth noting that the majority of infections were conducted at a high MOI for 48 hours, spanning more than one infectious cycle. To enhance the robustness of their findings and mitigate potential cell stress, it would be valuable to observe these effects at shorter time intervals, such as 24 hours post-infection.
Furthermore, the assertion regarding the association of IGF2BP2 with NS5 could be strengthened through additional immunoprecipitation (IP) assays. These assays, performed in the presence of RNAse treatment, would help exclude the possibility of an indirect interaction between IGF2BP2 and NS5 (both RNA-binding proteins) through viral RNA, thus providing more confidence in the observed association.

Reviewer #3 (Public Review):

Summary:
The manuscript by Mazeaud and colleagues pursued a small-scale screen of a targeted RNAi library to identify novel players involved in Zika (ZIKV) and dengue (DENV) virus replication. Loss-of-function of IGF2BP2 resulted in reduced titers for ZIKV of the Asian and African lineages in hepatic Huh7.5 cells, but not for either of the four DENV serotypes nor West Nile virus (WNV). The phenotype was further confirmed in two additional cell lines and using a ZIKV reporter virus. In addition, using immunoprecipitation assays the interaction between IGF2BP2 and ZIKV NS5 protein and RNA genome was detected. The work addressed the role of IGF2BP2 in the infected cell combining confocal microscopy imaging, and proteomic analysis. The approach indicated an altered distribution of IGF2BP2 in infected cells and changes in the protein interactome including disrupted association with partner mRNAs and modulation of the abundance of a specific set of protein partners in IGF2BP2 immunoprecipitated ribonucleoprotein (RNP) complexes. Finally, based on the changes in IGF2BP2 interactome and specifically the increment in the abundance of Atlastin 2, the biogenesis of ZIKV replication organelles (vRO) is investigated using a genetic system that allows virus replication-independent assembly of vRO. Electron microscopy showed that knockdown of IGF2BP2 expression reduced the number of cells with vRO.

Strengths:
The role of IGF2BP2 as a proviral factor for ZIKV replication is novel.

The study follows a logical flow of experiments that altogether support the assembly of a specialized RNP complex containing IGF2BP2 and ZIKV NS5 and RNA genome.

Weaknesses:
The statistical analysis should clearly indicate the number of biological replicates of experiments to support statistical significance.

The claim that IGF2BP2 knockdown impairs de novo viral organelle biogenesis and viral RNA synthesis is built upon data that show a reduction in RNA synthesis <0.5-fold as assessed using a reporter replicon, thus suggesting a limited impact of the knockdown on RNA replication.

Validation of IGF2BP2 partners that are modulated upon ZIKV infection (i.e. virus yield in knocked down cells) can be relevant especially for partners such as Atlastin 2, as the hypothesis of a role for IGF2BP2 RNP in vRO biogenesis is based on the observed increase in the abundance of Atlastin 2 in the RNP complex preciìtated from infected cells.