The recent SARS CoV-2 outbreak has been an example of how fast viral infections can be globally spread in a minimal fraction of time, and how extremely vulnerable to the action of virus we are. The virus has a high mutation rate, this helps the virus to cope with antivirals and to gain resistance against them. Finding host cells’ molecules that interact with the virus and targeting that interaction with new drugs could diminish the probability of antiviral resistance. In this work, we evaluate the role of human cytoplasmic dynein-1 (dynein) in the replication cycle of the Zika virus (ZIKV) and obtained clear evidence that indicates that those two proteins interact in vitro as well as in infected cells. First, we investigated whether this interaction could be present in infected cells, by infecting Vero cells, fixing samples at 12, 24, and 48 h post-infection. We revised the immunolocalization of the ZIKV and the naturally occurring dynein HC (Fig.
1), the maximum colocalization was at 24 h, this is consistent with the reported initiation of viral protein synthesis in this cell lane [
17]. The colocalization of the protein-antibody complex in confocal microscopy could have interactions around 400–600 nm due to the limited resolution of the optical system. To increase the resolution of our method, we used the proximity ligation assay, which has a theoretical maximum limit of 40 nm. There are some limitations or false interpretations of this technique [
18]. The loss of the interaction after 18 h, could mean that the ZIKV is being processed inside vesicles, so there is no need for a direct interaction of dynein with the virus. The kinetics seems consistent with what was observed in our colocalization experiments, and with the colocalization showed by Shrivastava et al. These results suggest that in an early stage of the infection, dynein would have the task of transporting ZIKV by interacting directly with the E protein. Also, we observed an increase in the expression of dynein HC in infected cells at 12 h (Fig.
3) On the other hand, during the transport of the virus towards the perinuclear zone, the virus is transported in the endosome. For this, the necessary machinery is GTPase Rab 5 or 7, which regulates transport to early or late endosomes, respectively [
19]. These membrane proteins of the endosome interact with the cargo adaptor on one end, and on the other end, it interacts with the dynein–dynactin complex [
20]. The endosome membrane proteins, and the coiled-coil cargo adaptor whose length we have calculated to be approximately 66 nm [
21], would not allow us to obtain a signal in the PLA (< 40 nm). In addition, during immunoprecipitation, the RIPA buffer solubilizes the lipids from the native membranes, since ZIKV is inside the vesicle, in case the interaction that we are capturing could be with the ZIKV inside a membrane vesicle, the virus would be released of the vesicle, and it will not interact with dynein HC. Since we are still detecting dynein-ZIKV interaction with the immunoprecipitation experiments, it means that we are capturing a complex with direct interaction (Fig.
4). We have also performed kinetics of the infection, with a maximum of PLA signal at 18 h.p.i. and after this time, we observed a decrease of the PLA dots (Fig.
2). We increased the MOI from 1 to 5 in order to check some insights of direct interaction at the beginning of the replication cycle with no positive PLA at 12 h or less, nor after 24 h (data not shown). We propose that after 18 h, the viruses are being processed inside vesicles, so the direct interaction between ZIKV and dynein is not detectable. Taken together, our data led us to propose the next addition on the ZIKV replication cycle; since the ZIKV release of the first new virions is approximately 24 h post-infection, and we are losing both, colocalization and PLA signals after 18 h, we believe that ZIKV’s replication cycle step on which dynein participates should be when newly synthesized viral proteins in the cytoplasm [
11]. The co-localization assay and PLA could only determine closeness and no interaction in vitro, which led us to analyze the interaction through the immunoprecipitation of the complex, this assay in infected Vero cells guarantees that this interaction occurs naturally during the viral replication cycle. We propose three possible scenarios; first, we suggest that the ZIKV polyprotein starts translating on the cytosol, where it hijacks the infection-dependent highly expressed dynein (12–18 h) that transports the full or partially non-processed polyprotein to the viral factories (not direct dynein-ZIKV interaction), where the virions will be processed, assembled and then, transported into the Golgi apparatus to its final maturation step before it is released to the extracellular space (24 h). There is evidence in the literature of a non-processed polyprotein composed of C-prM-E-NS1 proteins of the YFV flavivirus, synthesized with the in vitro translation system in rabbit reticulocyte lysates [
13]. This translation system in rabbit reticulocyte lysates has no microsomal membranes. The second scenario is that the dynein-ZIKV complex could be formed due to the translocation of factors from the ER lumen to the cell surface that could facilitate in yet unknown ways apoptotic signaling cascade [
8]. It has been observed that, under stress conditions, the permeability of the ER allows luminal proteins to be released or translocate to the cytoplasmic side of the ER [
22]. This would also require the transport of E protein by the dynein to the viral replication factories. The third and final scenario we are proposing is a dual polyprotein topology an unknown process of post-translational translocation leading to the non-uniform topology, where there is an equilibrium of envelope protein copies in luminal or in cytosolic compartments [
8]. In hepatitis B virus (HBV) has been observed that all envelope proteins synthesized in transfected cells or in a cell-free system adopt more than one transmembrane orientation [
23]. In this way, vesicles with E protein from ZIKV facing cytosol could bind to dynein and the whole vesicle will be transported by the molecular motor in order to reach the viral factories. Thus, we have shown strong evidence of the first non-coiled-coil protein that interacts with dynein without a cargo adaptor or dynactin. In order to prove this strong interaction with the complete Zika virion, we attached the His6NTDyn into an affinity Nickel column and then, we bound an enriched extract of virions from infected Vero cells to this column and elute the samples. We show that NTDyn was able to bind Zika virions since both molecules co-elute with imidazole. Once we eliminate the helical-bundles 1, 2 and 3 (residues 202–504) of the NTDyn by using the NDD (Fig.
5B and F), we carry out the same experiment where we observe the same result the obtained with the NTDyn, this delimits the interaction to the first 201 amino acids of the amino-terminal fraction of the heavy chain of dynein. This could be the answer to why the ZIKV binds to dynein without dynactin or cargo adaptor; dynactin and the cargo adaptors BICDR, BICD2 and HOOK3 bind to the helical bundles 1, 2 and 3, the interaction we are proposing is in the ‘opposite face’ of dynein. Although we do not know the mechanism of this interaction and whether ZIKV binding promotes dynein processivity we suggest that it is a retrograde transport function.