A small stem-loop structure of the Ebola virus trailer is essential for replication and interacts with heat-shock protein A8.

Ebola virus (EBOV) is a single-stranded negative-sense RNA virus belonging to the Filoviridae family. The leader and trailer non-coding regions of the EBOV genome likely regulate its transcription, replication, and progeny genome packaging. We investigated the cis-acting RNA signals involved in RNA-RNA and RNA-protein interactions that regulate replication of eGFP-encoding EBOV minigenomic RNA and identified heat shock cognate protein family A (HSC70) member 8 (HSPA8) as an EBOV trailer-interacting host protein. Mutational analysis of the trailer HSPA8 binding motif revealed that this interaction is essential for EBOV minigenome replication. Selective 2'-hydroxyl acylation analyzed by primer extension analysis of the secondary structure of the EBOV minigenomic RNA indicates formation of a small stem-loop composed of the HSPA8 motif, a 3' stem-loop (nucleotides 1868-1890) that is similar to a previously identified structure in the replicative intermediate (RI) RNA and a panhandle domain involving a trailer-to-leader interaction. Results of minigenome assays and an EBOV reverse genetic system rescue support a role for both the panhandle domain and HSPA8 motif 1 in virus replication.

Association of the cellular coactivator HCF-1 with the Golgi apparatus in sensory neurons.

HCF-1 is a cellular transcriptional coactivator that is critical for mediating the regulated expression of the immediate-early genes of the alphaherpesviruses herpes simplex virus type 1 and varicella-zoster virus. HCF-1 functions, at least in part, by modulating the modification of nucleosomes at these viral promoters to reverse cell-mediated repressive marks and promote activating marks. Strikingly, HCF-1 is specifically sequestered in the cytoplasm of sensory neurons where these viruses establish latency and is rapidly relocalized to the nucleus upon stimuli that result in viral reactivation. However, the analysis of HCF-1 in latently infected neurons and the protein's specific subcellular location have not been determined. Therefore, in this study, the localization of HCF-1 in unstimulated and induced latently infected sensory neurons was investigated and was found to be similar to that observed in uninfected mice, with a time course of induced nuclear accumulation that correlated with viral reactivation. Using a primary neuronal cell culture system, HCF-1 was localized to the Golgi apparatus in unstimulated neurons, a unique location for a transcriptional coactivator. Upon disruption of the Golgi body, HCF-1 was rapidly relocalized to the nucleus in contrast to other Golgi apparatus-associated proteins. The location of HCF-1 is distinct from that of CREB3, an endoplasmic reticulum-resident HCF-1 interaction partner that has been proposed to sequester HCF-1. The results support the model that HCF-1 is an important component of the viral latency-reactivation cycle and that it is regulated by association with a component that is distinct from the identified HCF-1 interaction factors.

Endogenous expression of an anti-TAR aptamer reduces HIV-1 replication.

An anti-TAR RNA aptamer called R06, which binds tightly and specifically to the trans-activation responsive (TAR) element of the human immunodeficiency virus type 1 (HIV-1) through loop-loop interactions has been previously selected.(1) We used HIV-based retroviral vectors to express the R06 aptamer. Its synthesis was driven by the U16 snoRNA. We investigated the ability of this cassette to interfere with TAR-mediated transcription using HeLa P4 cells stably expressing the beta-galactosidase gene under the control of the HIV-1 5'LTR. We demonstrated that, upon HIV-1 infection, the beta-galactosidase activity was reduced in cells expressing the nucleolar U16-R06 transcript. The replication of HIV-1 in these cells was also reduced as shown by quantification of the HIV-1 protease gene 24 h post-infection. This effect was specific and related to the formation of R06 TAR complex as an aptamer with a mutated loop, which was no longer able to bind to TAR, did not show any effect. The nucleolus is likely a compartment of interest for targeting the TAR-protein complex responsible for the trans-activation of transcription of the HIV-1 genome.

Selection by phage display of peptides targeting the HIV-1 TAR element.

As transcription regulatory element, the HIV-1 TAR RNA element is a promising target to inhibit viral replication; indeed, ligands of TAR RNA could prevent the transcription trans-activation process. Phage display in vitro selection was undertaken to select peptidic ligands of TAR RNA. In preliminary experiments, the selection was performed in a magnesium rich buffer (3 mM), but only phages targeted to plastic wells or streptavidin emerged; in addition, a "super-infectious" phage present in the New England Biolabs library (SVSVGMKPSPRP) selected by others with different targets was cloned, due to a high amplification potential. In contrast, the absence of magnesium or an increasing magnesium concentration (0 to 0.5 mM) led to phage selection with 57 amino acid peptides. K(D)s of 420-550 nM were measured by filter binding assays; a significant specificity was obtained when TAR target was compared with unrelated RNA targets. Surprisingly, the binding of selected peptides does not depend on the magnesium concentration.

Hexitol nucleic acid-containing aptamers are efficient ligands of HIV-1 TAR RNA.

The transactivation responsive element (TAR) plays a crucial role in the transcription of the HIV-1 genome upon specific binding of the viral protein Tat and cellular proteins. We have previously identified a RNA hairpin aptamer forming a stable and specific kissing complex with TAR RNA (Ducongé, F., and Toulmé, J. J. (1999) RNA 5, 1605-1614). We chemically modified this aptamer with hexitol nucleic acid (HNA) residues. We demonstrate that a fully HNA-modified aptamer is a poor ligand but, in contrast, mixmers containing both HNA and unmodified RNA nucleotides display interesting properties. Two HNA-RNA mixmers bind to TAR with an equilibrium dissociation constant in the low-nanomolar range and show a reduced nuclease sensitivity. In addition, they show a moderate dependence on magnesium ions for binding to TAR. These HNA-RNA mixmers are able to inhibit transactivation of transcription in an in vitro assay.

Modulating viral gene expression by aptamers to RNA structures.

Oligonucleotides exhibiting a strong affinity and a high specificity for RNA hairpins were obtained by in vitro selection. Such oligomers give rise to loop-loop complexes with the target hairpins: the trans-activation responsive (TAR) element of the Human Immunodeficiency virus-1 (HIV-1) or subdomains of the Hepatitis C virus (HCV) mRNA. Chemically modified derivatives of an antiTAR aptamer were shown to compete out the binding of the viral protein Tat and to selectively inhibit the in vitro TAR-dependent transcription of a reporter gene. In addition, antisense oligomers derived from sequences selected against the domain IIId of the HCV internal ribosome entry site were shown to specifically block translation both in a cell-free assay and in cultured cells.