The negative regulator of splicing element of Rous sarcoma virus promotes polyadenylation

Diverse roles of heterogeneous nuclear ribonucleoproteins in viral life cycle

Understanding the host-virus interactions helps to decipher the viral replication strategies and pathogenesis. Viruses have limited genetic content and rely significantly on their host cell to establish a successful infection. Viruses depend on the host for a broad spectrum of cellular RNA-binding proteins (RBPs) throughout their life cycle. One of the major RBP families is the heterogeneous nuclear ribonucleoproteins (hnRNPs) family. hnRNPs are typically localized in the nucleus, where they are forming complexes with pre-mRNAs and contribute to many aspects of nucleic acid metabolism. hnRNPs contain RNA binding motifs and frequently function as RNA chaperones involved in pre-mRNA processing, RNA splicing, and export. Many hnRNPs shuttle between the nucleus and the cytoplasm and influence cytoplasmic processes such as mRNA stability, localization, and translation. The interactions between the hnRNPs and viral components are well-known. They are critical for processing viral nucleic acids and proteins and, therefore, impact the success of the viral infection. This review discusses the molecular mechanisms by which hnRNPs interact with and regulate each stage of the viral life cycle, such as replication, splicing, translation, and assembly of virus progeny. In addition, we expand on the role of hnRNPs in the antiviral response and as potential targets for antiviral drug research and development.

Retroviral RNA Processing

This review is an accompaniment to a Special Issue on “Retroviral RNA Processing”. It discusses post-transcriptional regulation of retroviruses, ranging from the ancient foamy viruses to more modern viruses, such as HIV-1, HTLV-1, Rous sarcoma virus, murine leukemia virus, mouse mammary tumor virus, and Mason-Pfizer monkey virus. This review is not comprehensive. However, it tries to address some of the major questions in the field with examples of how different retroviruses express their genes. It is amazing that a single primary RNA transcript can have so many possible fates: genomic RNA, unspliced mRNA, and up to 50 different alternatively spliced mRNAs. This review will discuss the sorting of RNAs for packaging or translation, RNA nuclear export mechanisms, splicing, translation, RNA modifications, and avoidance of nonsense-mediated RNA decay.

Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development

Stress proteins (SPs) including heat-shock proteins (HSPs), RNA chaperones, and ER associated stress proteins are molecular chaperones essential for cellular homeostasis. The major functions of HSPs include chaperoning misfolded or unfolded polypeptides, protecting cells from toxic stress, and presenting immune and inflammatory cytokines. Regarded as a double-edged sword, HSPs also cooperate with numerous viruses and cancer cells to promote their survival. RNA chaperones are a group of heterogeneous nuclear ribonucleoproteins (hnRNPs), which are essential factors for manipulating both the functions and metabolisms of pre-mRNAs/hnRNAs transcribed by RNA polymerase II. hnRNPs involve in a large number of cellular processes, including chromatin remodelling, transcription regulation, RNP assembly and stabilization, RNA export, virus replication, histone-like nucleoid structuring, and even intracellular immunity. Dysregulation of stress proteins is associated with many human diseases including human cancer, cardiovascular diseases, neurodegenerative diseases (e.g., Parkinson’s diseases, Alzheimer disease), stroke and infectious diseases. In this review, we summarized the biologic function of stress proteins, and current progress on their mechanisms related to virus reproduction and diseases caused by virus infections. As SPs also attract a great interest as potential antiviral targets (e.g., COVID-19), we also discuss the present progress and challenges in this area of HSP-based drug development, as well as with compounds already under clinical evaluation.

Evidence that a threshold of serine/arginine-rich (SR) proteins recruits CFIm to promote rous sarcoma virus mRNA 3' end formation

The weak polyadenylation site (PAS) of Rous sarcoma virus (RSV) is activated by the juxtaposition of SR protein binding sites within the spatially separate negative regulator of splicing (NRS) element and the env RNA splicing enhancer (Env enhancer), which are far upstream of the PAS. Juxtaposition occurs by formation of the NRS - 3' ss splicing regulatory complex and is thought to provide a threshold of SR proteins that facilitate long-range stimulation of the PAS. We provide evidence for the threshold model by showing that greater than three synthetic SR protein binding sites are needed to substitute for the Env enhancer, that either the NRS or Env enhancer alone promotes polyadenylation when the distance to the PAS is decreased, and that SR protein binding sites promote binding of the polyadenylation factor cleavage factor I (CFIm) to the weak PAS. These observations may be relevant for cellular PASs.

Common Viral Integration Sites Identified in Avian Leukosis Virus-Induced B-Cell Lymphomas

Avian leukosis virus (ALV) induces B-cell lymphoma and other neoplasms in chickens by integrating within or near cancer genes and perturbing their expression. Four genes—MYC, MYB, Mir-155, and TERT—have previously been identified as common integration sites in these virus-induced lymphomas and are thought to play a causal role in tumorigenesis. In this study, we employ high-throughput sequencing to identify additional genes driving tumorigenesis in ALV-induced B-cell lymphomas. In addition to the four genes implicated previously, we identify other genes as common integration sites, including TNFRSF1A, MEF2C, CTDSPL, TAB2, RUNX1, MLL5, CXorf57, and BACH2. We also analyze the genome-wide ALV integration landscape in vivo and find increased frequency of ALV integration near transcriptional start sites and within transcripts. Previous work has shown ALV prefers a weak consensus sequence for integration in cultured human cells. We confirm this consensus sequence for ALV integration in vivo in the chicken genome.

Avian leukosis virus induces B-cell lymphomas in chickens. Earlier studies showed that ALV can induce tumors through insertional mutagenesis, and several genes have been implicated in the development of these tumors. In this study, we use high-throughput sequencing to reveal the genome-wide ALV integration landscape in ALV-induced B-cell lymphomas. We find elevated levels of ALV integration near transcription start sites and use common integration site analysis to greatly expand the number of genes implicated in the development of these tumors. Interestingly, we identify several genes targeted by viral insertions that have not been previously shown to be involved in cancer.

Polyadenylation of Friend murine leukemia virus env-mRNA is affected by its splicing

As splicing was previously found to be important for increasing Friend murine leukemia virus env-mRNA stability and translation, we investigated whether splicing of env-mRNA affected the poly(A) tail length using env expression vectors that yielded unspliced or spliced env-mRNA. Incomplete polyadenylation was detected in a fraction of the unspliced env-mRNA products in an env gene-dependent manner, showing that splicing of Friend murine leukemia virus plays an important role in the efficiency of complete polyadenylation of env-mRNA. These results suggested that the promotion of complete polyadenylation of env-mRNA by splicing might partially explain up-regulation of Env protein expression as a result of splicing.

Posttranscriptional regulation of retroviral gene expression: primary RNA transcripts play three roles as pre-mRNA, mRNA, and genomic RNA

After reverse transcription of the retroviral RNA genome and integration of the DNA provirus into the host genome, host machinery is used for viral gene expression along with viral proteins and RNA regulatory elements. Here, we discuss co-transcriptional and posttranscriptional regulation of retroviral gene expression, comparing simple and complex retroviruses. Cellular RNA polymerase II synthesizes full-length viral primary RNA transcripts that are capped and polyadenylated. All retroviruses generate a singly spliced env mRNA from this primary transcript, which encodes the viral glycoproteins. In addition, complex viral RNAs are alternatively spliced to generate accessory proteins, such as Rev, which is involved in posttranscriptional regulation of HIV-1 RNA. Importantly, the splicing of all retroviruses is incomplete; they must maintain and export a fraction of their primary RNA transcripts. This unspliced RNA functions both as the major mRNA for Gag and Pol proteins and as the packaged genomic RNA. Different retroviruses export their unspliced viral RNA from the nucleus to the cytoplasm by either Tap-dependent or Rev/CRM1-dependent routes. Translation of the unspliced mRNA involves frame-shifting or termination codon suppression so that the Gag proteins, which make up the capsid, are expressed more abundantly than the Pol proteins, which are the viral enzymes. After the viral polyproteins assemble into viral particles and bud from the cell membrane, a viral encoded protease cleaves them. Some retroviruses have evolved mechanisms to protect their unspliced RNA from decay by nonsense-mediated RNA decay and to prevent genome editing by the cellular APOBEC deaminases.

Regulation of retroviral polyadenylation

Cellular and viral preRNAs are extensively cotranscriptionally modified. These modifications include the processing of the 3' end. Most preRNAs are polyadenylated, which is required for nuclear export, RNA stability, and efficient translation. Integrated retroviral genomes are flanked by 3' and 5' long terminal repeats (LTRs). Both LTRs are identical on the nucleotide level, but 3' processing has to be limited to the 3'LTR. Otherwise, polyadenylation at the 5'LTR would result in prematurely terminated, noncoding viral RNAs. Retroviruses have developed a variety of different mechanisms to restrict polyadenylation to the 3'LTR, although the overall structure of the LTRs is similar among all retroviruses. In general, these mechanisms can be divided into three main groups: (1) activation of polyadenylation only at the 3' end by encoding the essential polyadenylation signal in the unique 3 region; (2) suppression of polyadenylation at the 5'LTR by downstream elements such as the major splice donor; and (3) the usage of weak polyadenylation sites, which results in some premature polyadenylated noncoding RNAs and in read-through transcripts at the 3'LTR. All these mechanisms exhibit intrinsic problems, and retroviruses have evolved additional regulatory elements to promote polyadenylation at the 3'LTR only. In this review, we describe the molecular regulation of retroviral polyadenylation and highlight the different mechanisms used for polyadenylation control.

Long-distance regulation of Add2 pre-mRNA3'end processing

Accurate 3′end processing depends on the correct recognition of polyadenylation regulatory elements by specific protein complexes. In addition to the well-known hexanucleotide motif and downstream sequence element (DSE), less-defined auxiliary elements are usually found to modulate cleavage and polyadenylation. They are generally located in close proximity to the core polyadenylation elements but, in most of the cases, the molecular mechanisms involved are not well defined. We concentrated our studies on the regulation of the mouse β adducin (Add2) pre-mRNA cleavage and polyadenylation. It contains two proximal erythroid-specific (PAS1 and PAS2-3) and one distal brain-specific (PAS4) polyadenylation sites along the 3′UTR. Using an in vivo approach based in the transfection of minigenes containing the Add2 polyadenylation signals, we previously identified the core regulatory elements responsible for PAS4 activity. Here, we have identified two novel non-canonical cis-acting elements regulating 3′end processing at PAS4, which show long-distance activities. The first of these elements, which spans for 257 nucleotides and is located at more than 5 kb upstream the PAS4, was essential to enable processing at the Add2 PAS4. The second element, located at about 4.5 kb upstream of the PAS4, reduces PAS4 processing. Both elements display long-distance activities and, to our knowledge, long-distance upstream polyadenylation regulatory elements have not been previously described in non-viral eukaryotic transcripts. These results highlight the complexity of the regulatory mechanisms directing Add2 pre-mRNA 3′end processing, and suggests that pre-mRNA 3′ end processing of other genes may also be unexpectedly regulated by non-canonical auxiliary elements.

Juxtaposition of two distant, serine-arginine-rich protein-binding elements is required for optimal polyadenylation in Rous sarcoma virus

The Rous sarcoma virus (RSV) polyadenylation site (PAS) is very poorly used in vitro due to suboptimal upstream and downstream elements, and yet ∼85% of viral transcripts are polyadenylated in vivo. The mechanisms that orchestrate polyadenylation at the weak PAS are not completely understood. It was previously shown that serine-arginine (SR)-rich proteins stimulate RSV PAS use in vitro and in vivo. It has been proposed that viral RNA polyadenylation is stimulated through a nonproductive splice complex that forms between a pseudo 5' splice site (5'ss) within the negative regulator of splicing (NRS) and a downstream 3'ss, which repositions NRS-bound SR proteins closer to the viral PAS. This repositioning is thought to be important for long-distance poly(A) stimulation by the NRS. We report here that a 308-nucleotide deletion downstream of the env 3'ss decreased polyadenylation efficiency, suggesting the presence of an additional element required for optimal RSV polyadenylation. Mapping studies localized the poly(A) stimulating element to a region coincident with the Env splicing enhancer, which binds SR proteins, and inactivation of the enhancer and SR protein binding decreased polyadenylation efficiency. The positive effect of the Env enhancer on polyadenylation could be uncoupled from its role in splicing. As with the NRS, the Env enhancer also stimulated use of the viral PAS in vitro. These results suggest that a critical threshold of SR proteins, achieved by juxtaposition of SR protein binding sites within the NRS and Env enhancer, is required for long-range polyadenylation stimulation.

Nucleophosmin deposition during mRNA 3' end processing influences poly(A) tail length

During polyadenylation, the multi-functional protein nucleophosmin (NPM1) is deposited onto all cellular mRNAs analysed to date. Premature termination of poly(A) tail synthesis in the presence of cordycepin abrogates deposition of the protein onto the mRNA, indicating natural termination of poly(A) addition is required for NPM1 binding. NPM1 appears to be a bona fide member of the complex involved in 3' end processing as it is associated with the AAUAAA-binding CPSF factor and can be co-immunoprecipitated with other polyadenylation factors. Furthermore, reduction in the levels of NPM1 results in hyperadenylation of mRNAs, consistent with alterations in poly(A) tail chain termination. Finally, knockdown of NPM1 results in retention of poly(A)(+) RNAs in the cell nucleus, indicating that NPM1 influences mRNA export. Collectively, these data suggest that NPM1 has an important role in poly(A) tail length determination and may help network 3' end processing with other aspects of nuclear mRNA maturation.

An LYPSL late domain in the gag protein contributes to the efficient release and replication of Rous sarcoma virus

The efficient release of newly assembled retrovirus particles from the plasma membrane requires the recruitment of a network of cellular proteins (ESCRT machinery) normally involved in the biogenesis of multivesicular bodies and in cytokinesis. Retroviruses and other enveloped viruses recruit the ESCRT machinery through three classes of short amino acid consensus sequences termed late domains: PT/SAP, PPXY, and LYPX(n)L. The major late domain of Rous sarcoma virus (RSV) has been mapped to a PPPY motif in Gag that binds members of the Nedd4 family of ubiquitin ligases. RSV Gag also contains a second putative late domain motif, LYPSL, positioned 5 amino acids downstream of PPPY. LYPX(n)L motifs have been shown to support budding in other retroviruses by binding the ESCRT adaptor protein Alix. To investigate a possible role of the LYPSL motif in RSV budding, we constructed PPPY and LYPSL mutants in the context of an infectious virus and then analyzed the budding rates, spreading profiles, and budding morphology. The data imply that the LYPSL motif acts as a secondary late domain and that its role in budding is amplified in the absence of a fully functional PPPY motif. The LYPXL motif proved to be a stronger late domain when an aspartic acid was substituted for the native serine, recapitulating the properties of the LYPDL late domain of equine infectious anemia virus. The overexpression of human Alix in the absence of a fully functional PPPY late domain partially rescued both the viral budding rate and viral replication, supporting a model in which the RSV LYPSL motif mediates budding through an interaction with the ESCRT adaptor protein Alix.

Molecular mechanisms of eukaryotic pre-mRNA 3' end processing regulation

Messenger RNA (mRNA) 3′ end formation is a nuclear process through which all eukaryotic primary transcripts are endonucleolytically cleaved and most of them acquire a poly(A) tail. This process, which consists in the recognition of defined poly(A) signals of the pre-mRNAs by a large cleavage/polyadenylation machinery, plays a critical role in gene expression. Indeed, the poly(A) tail of a mature mRNA is essential for its functions, including stability, translocation to the cytoplasm and translation. In addition, this process serves as a bridge in the network connecting the different transcription, capping, splicing and export machineries. It also participates in the quantitative and qualitative regulation of gene expression in a variety of biological processes through the selection of single or alternative poly(A) signals in transcription units. A large number of protein factors associates with this machinery to regulate the efficiency and specificity of this process and to mediate its interaction with other nuclear events. Here, we review the eukaryotic 3′ end processing machineries as well as the comprehensive set of regulatory factors and discuss the different molecular mechanisms of 3′ end processing regulation by proposing several overlapping models of regulation.

The signal peptide of a simple retrovirus envelope functions as a posttranscriptional regulator of viral gene expression

Retroviruses use different strategies to regulate transcription and translation and exploit the cellular machinery involved in these processes. This study shows that the signal peptide of the envelope glycoprotein (Env) of Jaagsiekte sheep retrovirus (JSRV) plays a major role in posttranscriptional viral gene expression. Expression of the JSRV Env in trans increases viral particle production by mechanisms dependent on (i) its leader sequence, (ii) an intact signal peptide cleavage site, (iii) a cis-acting RNA-responsive element located in the viral genome, (iv) Crm1, and (v) B23. The signal peptide of the JSRV Env (JSE-SP) is 80 amino acid residues in length and contains putative nuclear localization and export signals, in addition to an arginine-rich RNA binding motif. JSE-SP localizes both in the endoplasmic reticulum and in the nucleus, where it colocalizes with nucleolar markers. JSE-SP is a multifunctional protein, as it moderately enhances nuclear export of unspliced viral mRNA and considerably increases viral particle release by favoring a posttranslational step of the replication cycle.

Characterization of Rous sarcoma virus polyadenylation site use in vitro

Polyadenylation of Rous sarcoma virus (RSV) RNA is inefficient, as approximately 15% of RSV RNAs represent read-through transcripts that use a downstream cellular polyadenylation site (poly(A) site). Read-through transcription has implications for the virus and the host since it is associated with oncogene capture and tumor induction. To explore the basis of inefficient RSV RNA 3'-end formation, we characterized RSV polyadenylation in vitro using HeLa cell nuclear extracts and HEK293 whole cell extracts. RSV polyadenylation substrates composed of the natural 3' end of viral RNA and various lengths of upstream sequence showed little or no polyadenylation, indicating that the RSV poly(A) site is suboptimal. Efficiently used poly(A) sites often have identifiable upstream and downstream elements (USEs and DSEs) in close proximity to the conserved AAUAAA signal. The sequences upstream and downstream of the RSV poly(A) site deviate from those found in efficiently used poly(A) sites, which may explain inefficient RSV polyadenylation. To assess the quality of the RSV USEs and DSEs, the well-characterized SV40 late USEs and/or DSEs were substituted for the RSV elements and vice versa, which showed that the USEs and DSEs from RSV are suboptimal but functional. CstF interacted poorly with the RSV polyadenylation substrate, and the inactivity of the RSV poly(A) site was at least in part due to poor CstF binding since tethering CstF to the RSV substrate activated polyadenylation. Our data are consistent with poor polyadenylation factor binding sites in both the USE and DSE as the basis for inefficient use of the RSV poly(A) site and point to the importance of additional elements within RSV RNA in promoting 3' end formation.

RNA processing control in avian retroviruses

Upon integration into the host chromosome, retroviral gene expression requires transcription by the host RNA polymerase II, and viral messages are subject RNA processing events including 5'-end capping, pre-mRNA splicing, and polyadenylation. At a minimum, RNA splicing is required to generate the env mRNA, but viral replication requires substantial amounts of unspliced RNA to serve as mRNA and for incorporation into progeny virions as genomic RNA. Therefore, splicing has to be controlled to preserve the large unspliced RNA pool. Considering the current view that splicing and polyadenylation are coupled, the question arises as to how genome-length viral RNA is efficiently polyadenylated in the absence of splicing. Polyadenylation of many retroviral mRNAs is inefficient; in avian retroviruses, approximately 15 percent of viral transcripts extend into and are polyadenylated at downstream host genes, which often has profound biological consequences. Retroviruses have served as important models to study RNA processing and this review summarizes a body of work using avian retroviruses that has led to the discovery of novel RNA splicing and polyadenylation control mechanisms.

Functional interplay between viral and cellular SR proteins in control of post-transcriptional gene regulation

Viruses take advantage of cellular machineries to facilitate their gene expression in the host. SR proteins, a superfamily of cellular precursor mRNA splicing factors, contain a domain consisting of repetitive arginine/serine dipeptides, termed the RS domain. The authentic RS domain or variants can also be found in some virus‐encoded proteins. Viral proteins may act through their own RS domain or through interaction with cellular SR proteins to facilitate viral gene expression. Numerous lines of evidence indicate that cellular SR proteins are important for regulation of viral RNA splicing and participate in other steps of post‐transcriptional viral gene expression control. Moreover, viral infection may alter the expression levels or modify the phosphorylation status of cellular SR proteins and thus perturb cellular precursor mRNA splicing. We review our current understanding of the interplay between virus and host in post‐transcriptional regulation of gene expression via RS domain‐containing proteins.

Polyadenylation site choice in yeast is affected by competition between Npl3 and polyadenylation factor CFI

Multiple steps in mRNA processing and transcription are coupled. Notably, the processing of mRNA 3' ends is linked to transcription termination by RNA polymerase II. Previously, we found that the yeast hnRNP protein Npl3 can negatively regulate 3' end mRNA formation and termination at the GAL1 gene. Here we show that overexpression of the Hrp1 or Rna14 subunits of the CF IA polyadenylation factor increases recognition of a weakened polyadenylation site. Genetic interactions of mutant alleles of NPL3 or HRP1 with RNA15 also indicate antagonism between these factors. Npl3 competes with Rna15 for binding to a polyadenylation precursor and inhibits cleavage and polyadenylation in vitro. These results suggest that an important function of hnRNP proteins is to ensure the fidelity of mRNA processing. Our results support a model in which balanced competition of Npl3 with mRNA processing factors may promote recognition of proper polyadenylation sites while suppressing cryptic sites.

Serine/arginine-rich proteins contribute to negative regulator of splicing element-stimulated polyadenylation in rous sarcoma virus

Rous sarcoma virus (RSV) requires large amounts of unspliced RNA for replication. Splicing and polyadenylation are coupled in the cells they infect, which raises the question of how viral RNA is efficiently polyadenylated in the absence of splicing. Optimal RSV polyadenylation requires a far-upstream splicing control element, the negative regulator of splicing (NRS), that binds SR proteins and U1/U11 snRNPs and functions as a pseudo-5' splice site that interacts with and sequesters 3' splice sites. We investigated a link between NRS-mediated splicing inhibition and efficient polyadenylation. In vitro, the NRS alone activated a model RSV polyadenylation substrate, and while the effect did not require the snRNP-binding sites or a downstream 3' splice site, SR proteins were sufficient to stimulate polyadenylation. Consistent with this, SELEX-binding sites for the SR proteins ASF/SF2, 9G8, and SRp20 were able to stimulate polyadenylation when placed upstream of the RSV poly(A) site. In vivo, however, the SELEX sites improved polyadenylation in proviral clones only when the NRS-3' splice site complex could form. Deletions that positioned the SR protein-binding sites closer to the poly(A) site eliminated the requirement for the NRS-3' splice site interaction. This indicates a novel role for SR proteins in promoting RSV polyadenylation in the context of the NRS-3' splice site complex, which is thought to bridge the long distance between the NRS and poly(A) site. The results further suggest a more general role for SR proteins in polyadenylation of cellular mRNAs.