Viral Messenger RNA: Transcription, Processing, Splicing and Molecular Structure

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Transcription, Processing, Splicing and Molecular Structure

Structural and biochemical data suggests that interaction of D12 with the guanine-N7 MTase domain induces conformational changes necessary for efficient catalysis Multifunctional RNA capping enzymes. The enzyme composes of two subunits D1 and D D12 subunit is colored in green. B Bluetongue virus capping enzyme VP4 structure. The guanine-N7 MTase domain is composed of two discontinuous sequences which are colored in light brown and beige. The putative TPase catalytic residue Cys is colored in bright green.

Bluetongue virus capping enzyme VP4 consolidates all 4 enzymatic activities to generate the cap 1 structure — The protein adopts an elongated shape with the N-terminal and C-terminal domains responsible for homodimerization, which is required for the assembly of VP4 into the viral core-like particle Biochemical studies have located the lysine responsible for the lysyl-phosphoguanosine intermediate near the C-terminal of the protein However, no conserved GTase fold can be found in the VP4 structures.

RNA splicing - Wikipedia

Despite the many questions these crystal structures answered, more interesting questions arise. Does the enzyme undergo a dramatic conformational change or oligomerize to efficiently carry out guanine-N7 MTase activity on the newly capped RNA? More biochemical evidence and RNA-bound structures will be needed to shed light on these puzzles.

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Interestingly, a significant portion of the snatched sequences derived from the less understood promoter-associated small RNA PASRs , which has recently been shown to be capped by the cytoplasmic capping machinery 28 see Cytoplasmic RNA re -capping above. The S. The similarity of the snatching process to the canonical GTase activity suggests an evolutionary link between totivirus cap snatching and the eukaryotic capping mechanism , As discussed in the previous sections, the cap 0 structure is required for efficient translation of the mRNA in vivo.

The new developments in fluorescently-labeled GTP compatible with the translation machinery has enabled in vitro synthesis of fluorescent-labeled RNA As the template for protein synthesis, introduction of mRNA into cells is the most intuitive way to drive the expression of target proteins in the cell. Although the transfection of RNA into cells had been reported in the s, RNA-driven gene expression had not been explored in detail largely because of the uncertainty in the stability, efficiency and immunogenicity of exogenous RNA.

With better understanding of the biological roles of base and ribose modifications, cellular degradation pathways, combined with technological advances in enzymatic synthesis and modification of RNA and cellular delivery vehicles, the administration of exogenous mRNA has become a viable option to drive protein expression in situ Stem cell reprogramming — , vaccination — and expression of therapeutic proteins — are only a few of the ever growing examples of exogenous mRNA technologies , As a means of driving target protein expression in situ , administration of RNA offers a number of advantages over DNA.

Second, while DNA vectors need to enter the nucleus to be transcribed into mRNA, which is then exported to the cytoplasm for translation, direct delivery of mRNA into cytoplasm bypasses these hurdles. In addition, it has been shown that the kinetics of protein expression after RNA administration peaks and decays within days, much more rapidly than with DNA-driven protein expression that exhibits a slow decay in weeks , making RNA a better option for applications such as vaccination where transient expression is desired.

The use of mRNA also allows for simultaneous expression of multiple proteins in situ. As with DNA vectors, mRNA-based therapy or vaccination regimes benefit from the potential for rapid manufacture and dispatch that can be critical in response to disease outbreaks. To avoid carryover of animal or viral material, it is desirable to manufacture therapeutic RNAs enzymatically using animal-free materials in vitro.

The poly A tail can be generated co-transcriptionally by incorporating a poly T tract in the template DNA or separately by using a poly A polymerase. The transcript may be capped co-transcriptionally by using a cap analog or separately using a capping enzyme. Co-transcriptional capping using a cap analog has the advantage of being a simple workflow.

Vaccination via mRNA administration has many positive attributes compared to traditional live attenuated whole organisms. Not only it does not induce anti-vector immunity, mRNA vaccines are a short-lived and often self-limiting source of in situ production of antigen. It has the potential to be regulated and tuned over the RNA function and gene expression. Manufacturing is simple and can response quickly once the genome sequence of the disease causing agent is available Unlike DNA vaccines, the response time of antigen production is faster and more efficient, as mRNA vaccines can be translated directly in the cytosol.

There is also no concern of potential genome integration In situ g eneration of tumor-specific proteins antigen, rapid induction of T and activation of natural killer cells, infiltration of immune cells into tumor mass have been documented The mRNA may be delivered by viral vectors or synthetic carriers. Recent advances in the formulation of synthetic carriers has allowed efficient mRNA vaccine delivery , , , , therefore avoiding the use of viral vectors and the risk of contamination with animal materials during manufacturing.

Taking advantage of the RNA transcription-capping apparatus of alphavirus, a self-amplifying mRNA technology has been developed as an in situ gene expression vehicle for vaccination. By replacing the capsid proteins genes with the gene of interest, capped and polyadenylated self-amplifying RNA constructs were shown to be more potent in eliciting immune response than vaccination through standard mRNA , and efficacious in animal models , , , For an in-depth account of the current state of research, pre-clinical trials and manufacturing of mRNA and self-amplifying mRNA, we refer the reader to the following reports , The desthiobiotinylated capped RNA species can then be enriched and deep-sequenced.

Cappable-seq achieved a fold enrichment of primary transcripts and identified previously unreported transcription start sites TSS genome-wide at single base resolution in Escherichia coli The method had also been applied to identify the microbiome transcriptome from mouse cecum samples and for the first time identified TSS in a microbiome. Cappable-seq therefore effectively reduces the complexity of the transcriptome and the cost of sequencing.

While mRNA cap structures were discovered in the s, their biological roles have only been more deeply understood as the result of recent work. In addition to its role in mRNA export, mRNA maturation and protein synthesis, new understanding of the role of the RNA cap in innate immunity has helped advance the field of synthetic mRNA and their in vivo and therapeutic applications. Research on these viral systems have revealed a surprisingly diverse means and molecular machineries to generate capped RNA.

It also resulted in applications such as efficient in vitro RNA capping systems and self-amplifying mRNA technology, facilitating large scale production of functional mRNA for in vitro and therapeutic applications. Novel application of RNA capping enzymes has also enabled sequencing and quantification of microbiome transcriptomes. There are, as always, new questions to be asked as we learn more.

Does the enzyme complex go through extensive remodeling or does it form higher order oligomer? On a different front, the discovery of cytoplasmic re- capping machinery is exciting and invites further interesting questions. What processes are these re-capped RNAs involved in? What is the interplay between cytoplasmic re- capping and P-body RNA storage and degradation?

Perhaps more surprisingly, RNA caps are more wide-spread and diverse than the m7G cap. Are they also present in archaea and eukaryotes? These are only some of the exciting questions waiting to be answered. Conflict of interest statement. Robb and S.

Chan are current emloyees of New England Biolabs that markets molecular biology reagents. Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide. Sign In or Create an Account. Sign In. Advanced Search. Article Navigation. Close mobile search navigation Article Navigation. Volume Article Contents. New England Biolabs, Inc.

Gene Expression and Regulation

Oxford Academic. Google Scholar. Brett Robb. Siu-Hong Chan. Cite Citation.

Gene expression

Permissions Icon Permissions. Open in new tab Download slide. Table 1. Open in new tab. Search ADS. The cytoplasmic capping complex assembles on adapter protein Nck1 bound to the Proline-rich C-terminus of mammalian capping enzyme. Characterization of human, Schizosaccharomyces pombe , and Candida albicans mRNA cap methyltransferases and complete replacement of the yeast capping apparatus by mammalian enzymes.

Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures. Movement of Eukaryotic mRNAs between polysomes and cytoplasmic processing bodies. Supernatants were collected at 48 hours post-infection and were titrated by plaque assay. No such significant differences were observed upon infection with VSV Indiana strain, a negative-stranded RNA virus which replicates in the cytoplasm Figure 5C , triangle symbols , nor with Adenovirus 5 which replicates in the nucleus and is dependent on the cellular splicing machinery Figure 5C , square symbols.

The positions of primers and probes are indicated by black and white arrowheads, respectively, that are oriented according to the sense or antisense orientation of the oligonucleotides. The signals were quantified and normalized with respect to tubulin. The ratio of NS2 over NS1 proteins was reduced at 6 and 9 hpi 5- and 3-fold, respectively, in RED-silenced cells; 3- and 2-fold, respectively, in SMU1-silenced cells , whereas the ratio of M2 over M1 protein remained stable except for a 2-fold reduction in RED-silenced cells at 6 hpi.

The membranes were scanned with a G-box Syngene and the signals were quantified using GeneTools software Syngene and normalized with respect to tubulin. For each viral protein at each time point, the levels in RED- and SMU1-silenced cells relative to control cells set at an arbitrary value of 1 are indicated.

One essential function of the NS2 protein is to mediate the export of neosynthetized vRNPs from the nucleus to the cytoplasm, which allows them to be transported to the cellular plasmic membrane and incorporated into virions. At 5 hpi, the intracellular localisation of the NP protein was detected by indirect immunofluorescence. Scoring of NP localisation on a mean of cells per experimental condition indicated that RED depletion decreased the proportion of cells in which NP was exclusively cytoplasmic, and increased the proportion of cells in which NP was exclusively nuclear Figure 8B.

At 5 hpi, cells were fixed, permeabilized, and stained with an antibody specific for the NP protein and with Hoechst Representative images of NP localization. Percentage of cells with different NP localization. The results of two independent experiments is shown, in which and 94 cells exp a , and and cells exp b , were scored for the NT and RED siRNA experimental condition, respectively. Highly conserved homologues of RED and SMU1 were identified in Caenorhabditis elegans and Arabidopsis thaliana , and were also found to interact with each other in vitro and in vivo [19] , [21].

They are consistent with cross-effects of RED and SMU1 silencing observed by us and by others [19] , [21] , which suggest that the two proteins are stabilizing each other and that a significant proportion is present as functional RED-SMU1 complexes. The RED protein that co-purifies with PB2-Strep in infected cell lysates is most likely associated to the viral trimeric polymerase. This hypothesis is in line with a recent publication showing that trans -activating polymerases are required for activation of resident polymerases which carry out vRNA synthesis [43].

It was recently demonstrated that the presence of such a weak splice site and the resulting slow accumulation of the splice product, the NS2 protein, are beneficial for the virus as they ensure a proper timing of viral replication [9]. The viral polymerase thus seems to play a central role in coupling transcription and alternative splicing of the viral mRNAs.

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This is in line with the current view that cellular mRNA synthesis, processing and splicing are closely linked [44] , [45]. Our study is stressing the fact that different cellular factors and mechanisms are involved in the splicing regulation of influenza virus NS1 and M1 mRNAs. In contrast, both proteins show motifs that promote the assembly of multi-protein complexes, i.

A comprehensive mapping of protein-protein interactions among human spliceosomal proteins suggested that RED and SMU1, together with MFAP1, may contribute to protein recruitment during B complex formation at an early stage of splicing [31]. In agreement with the well-documented function of NS2 as an exportin, the nuclear export of neo-synthetized vRNPs was strongly impaired, which very likely contributed to the reduced production of infectious progeny virions.

The NS2 protein was recently found to be involved in other aspects of the viral cycle for a review, see [6] , including the regulation of viral RNA transcription and replication [47]. In addition, distinct, non-NS2-mediated effects of RED depletion on the viral cycle can be envisioned. Indeed, beyond its function as a splicing factor, the RED protein was reported to associate to the spindle poles and to be required for mitotic progression [37]. It would thus be interesting to explore whether the viral polymerase-RED interaction is linked to the prevention of cell cycle entry into S phase [48].

The investigation of cellular pathways that are essential for influenza A virus replication, and the identification of the underlying interactions between viral and cellular components, might open the way to new antiviral strategies. The resulting plasmids allowed the expression of Gluc2, Gluc1 or mCherry fusion proteins.

All constructs were verified by Sanger sequencing. The sequences of the oligonucleotides used for amplification and sequencing can be provided upon request. The protein complementation assay was performed as described in [27]. The NLR cut-off value that reduces false positive background below 2. Six hours post-infection, cells were lysed in 0. After three washes with 1 ml of lysis buffer, protein complexes were eluted from StrepTactin beads with desthiobiotin IBA. Purification samples were either diluted in Laemmli sample buffer and analyzed by western-blot, or diluted in Renilla lysis buffer Promega and submitted to Gaussia princeps luciferase enzymatic activity measurement, using the Renilla luciferase assay reagent Promega and a Berthold Centro XS luminometer.

For multicycle growth assays and single cycle infection assays, cells were infected at 36 h post-transfection at a low and a high moi, respectively. Total cell lysates prepared at different time points by direct lysis in Laemmli buffer were analyzed by western blotting. Western blots were performed as described earlier [54]. Negatives controls, i. The corresponding sequences are indicated in Methods S1.

The cycle thresholds Ct were determined by second derivative quantification using the analytical LightCycler Software, release 1. These calibration curves were also used to assess the specificity of each set of primers and probe. At 41 hours post-transfection, cells were fixed, permeabilized, and stained with Hoechst and with an antibody specific for the RED upper panels or SMU1 protein lower panels. Cells were fixed at 6 hpi and they were stained with Hoechst Supporting information is provided on the yeast two-hybrid-plus-one assay, indirect immunofluorescence assays and reverse transcription-quantitative PCR assays.

Viral-human protein-protein interactions detected in the yeast two-hybrid-plus-one and the yeast two-hybrid assays. We are very grateful to J. Ortin and S. Landera-Buenos for helpful discussions, and for providing advice and materials for the AdV5 experiment. We thank J. Bureau for assistance with statistical analysis, A. Komarova for advice on purification experiments, U. Steltz, P. Fortes, G. Brownlee, F. Baudin, D. Marc, and O. Delmas for providing materials, P. Cassonnet and C.

Diot for assistance with some experiments, C. Diot and C. Barbezange for critical reading of the manuscript, and S. Wrote the paper: GF NN. Abstract Influenza A viruses are major pathogens in humans and in animals, whose genome consists of eight single-stranded RNA segments of negative polarity. Author Summary Influenza A viruses are major pathogens which pose continuous animal and public health challenges. Introduction Viruses are dependent on host cell functions for their replication.

Results Identification of RED as an interactor of influenza virus polymerase in a yeast two-hybrid screen Structural data indicate that the PB1, PB2 and PA subunits of influenza virus polymerase are tightly associated [22] , [23] , suggesting that some interactions of the viral polymerase with host factors are either mediated by more than one viral polymerase subunit, or dependent on conformational transition upon polymerase complex formation. Extreme cases also include the decreased regulation or hijacking of endogenous mRNA export complexes by viruses, which enables specific viral genes to hybridize with the mRNA transcript and be expressed in the organism.

But with the vast knowledge of the mRNA export process, these malfunctions can be better understood and more easily preventable, and it may be possible to address many issues of diseases and gain a complete understanding of the way cellular function is generated at the simplest level: molecularly. In prokaryotes, because the mRNA does not need to be modified or transported, it can be translated by the ribosomes right after transcription. In eukaryotes, however, mRNA can only be translated after it has been modified and transported to the cytoplasm the mature mRNAs. Translation starts by the ribosomes binding to a site on the 5' side.

When this binding occurs, the ribosome is joined by an initiator tRNA that carries a formylmethionine fMet group that recognizes the start codon. Next, an aminoacyl-tRNA that can base pair with the next codon appears and joins the ribosome complex. The initiator tRNA is then released and the ribosome shifts one codon toward the 3' end. The newly bound amino acids are the translated mRNA into a protein. The ribosomal complex containing the tRNA splits back up into its separate parts, re-assembling when new mRNA needs to be translated into protein.

The elongation process "terminates" when a stop codon reaches the A site of the ribosome. Incoming tRNA, which carries the subsequent amino acid, will not be accepted by the ribosome at the A site. The A site will then be specific to a protein called the release factor.

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  5. The release factor will hydrolyze the bond of the tRNA to the polypeptide in the P site, thus releasing the polypeptide chain. The two ribosomal subunits, release factor, and mRNA then come apart to signify the end of the termination process. An mRNA can be changed its nucleotide composition in some instances. This process is called editing. In human, the apolipoprotein mRNA is one of the cases.

    This editing mRNA takes place in some tissues, but not all of them. In this edition, the mRNA's codon is given an early stop, therefore, it will produce a shorter protein when going to the translation process. Several proteins have been identified as being similar to C-to-U mRNA editing enzymes based on their structural domains and the occurrence of a catalytic domain characteristic of cytidine deaminases.

    Viral Messenger RNA

    In light of the hypothesis that these proteins might represent novel mRNA editing systems that could affect proteome diversity, we consider their structure, expression and relevance to biomedically significant processes or pathologies. The message transported through mRNA after a certain amount of time will be degraded and be deleted. This process is called degradation. The cell can easily and quickly changed the protein production in case of any changing needs due to the lifetime of the mRNA.

    The lifetime of different types of mRNA can be different. The life span of mRNA molecules in the cytoplasm is an important key in determining the pattern of protein synthesis within a cell. Prokaryotic mRNA molecules often are degraded by enzymes within a few minutes of their synthesis and this is one reason as to why prokaryotes can vary their patterns of protein synthesis so quickly in response to changes in their environment.

    Eukaryotic mRNA, on the other hand, typically survives for hours, days, or for some instances, weeks. One example of multicellular mRNA is hemoglobin polypeptides which, in the process of developing red blood cells which are unusually stable, these long-lived mRNAs are translated repeatedly in the cell. Once the cap is removed, nuclease enzymes can then move in and rapidly chew up the mRNA. This process of mRNA degradation relies on deadenylation. The shortening of poly-A tail is initiated by deadenylase and afterward, mRNA is either fully degraded or stored in the case of certain cells.

    They are formed from longer RNA precursors that fold back on themselves, forming a long, double-stranded hairpin structure held together by hydrogen bonds. These small singled stranded RNA molecules can bind to complementary sequences in mRNA molecules and an enzyme, called the Dicer, can then cut the double-stranded RNA molecules into short fragments.

    One of the two strands is degraded and then the other stand, often the miRNA associates with a large protein complex and which allows the complex to bind to any mRNA molecule with a complementary sequence to either degrade or block translation of mRNAs. Scientists also observed that gene expression inhibited by RNA molecules was possible. This was observed when they noticed that injecting double stranded RNA molecules into a cell somehow turned off a gene with the same sequence. Researched showed that the cellular machinery for making siRNAs was the same mechanism for creating miRNAs in the cell.

    The mechanisms by which these small RNAs function are also the same.

    Viral Messenger RNA: Transcription, Processing, Splicing and Molecular Structure Viral Messenger RNA: Transcription, Processing, Splicing and Molecular Structure
    Viral Messenger RNA: Transcription, Processing, Splicing and Molecular Structure Viral Messenger RNA: Transcription, Processing, Splicing and Molecular Structure
    Viral Messenger RNA: Transcription, Processing, Splicing and Molecular Structure Viral Messenger RNA: Transcription, Processing, Splicing and Molecular Structure
    Viral Messenger RNA: Transcription, Processing, Splicing and Molecular Structure Viral Messenger RNA: Transcription, Processing, Splicing and Molecular Structure
    Viral Messenger RNA: Transcription, Processing, Splicing and Molecular Structure Viral Messenger RNA: Transcription, Processing, Splicing and Molecular Structure
    Viral Messenger RNA: Transcription, Processing, Splicing and Molecular Structure Viral Messenger RNA: Transcription, Processing, Splicing and Molecular Structure

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