Challenges to mapping and defining m6A function in viral RNA.

Viral RNA molecules contain multiple layers of regulatory information. This includes features beyond the primary sequence, such as RNA structures and RNA modifications, including N6-methyladenosine (m6A). Many recent studies have identified the presence and location of m6A in viral RNA and have found diverse regulatory roles for this modification during viral infection. However, to date, viral m6A mapping strategies have limitations that prevent a complete understanding of the function of m6A on individual viral RNA molecules. While m6A sites have been profiled on bulk RNA from many viruses, the resulting m6A maps of viral RNAs described to date present a composite picture of m6A across viral RNA molecules in the infected cell. Thus, for most viruses, it is unknown if unique viral m6A profiles exist throughout infection, nor if they regulate specific viral life cycle stages. Here, we describe several challenges to defining the function of m6A in viral RNA molecules and provide a framework for future studies to help in the understanding of how m6A regulates viral infection.

Programmable protein expression using a genetically encoded m6A sensor.

The N6-methyladenosine (m6A) modification is found in thousands of cellular mRNAs and is a critical regulator of gene expression and cellular physiology. m6A dysregulation contributes to several human diseases, and the m6A methyltransferase machinery has emerged as a promising therapeutic target. However, current methods for studying m6A require RNA isolation and do not provide a real-time readout of mRNA methylation in living cells. Here we present a genetically encoded m6A sensor (GEMS) technology, which couples a fluorescent signal with cellular mRNA methylation. GEMS detects changes in m6A caused by pharmacological inhibition of the m6A methyltransferase, giving it potential utility for drug discovery efforts. Additionally, GEMS can be programmed to achieve m6A-dependent delivery of custom protein payloads in cells. Thus, GEMS is a versatile platform for m6A sensing that provides both a simple readout for m6A methylation and a system for m6A-coupled protein expression.

The Evil DExH/D: Chikungunya virus runs but cannot hide from DDX39A.

In this issue, Tapescu et al.1 identify DDX39A as a novel antiviral protein that acts on conserved features of alphavirus RNA to limit infection in an IFN-independent manner.

CELLULAR RNA INTERACTS WITH MAVS TO PROMOTE ANTIVIRAL SIGNALING.

Immune signaling needs to be well-regulated to promote clearance of pathogens, while preventing aberrant inflammation. Interferons (IFNs) and antiviral genes are activated by the detection of viral RNA by RIG-I-like receptors (RLRs). Signal transduction downstream of RLRs proceeds through a multi-protein complex organized around the central adaptor protein MAVS. Recent work has shown that protein complex function can be modulated by RNA molecules providing allosteric regulation or acting as molecular guides or scaffolds. Thus, we hypothesized that RNA plays a role in organizing MAVS signaling platforms. Here, we show that MAVS, through its central intrinsically disordered domain, directly interacts with the 3' untranslated regions of cellular mRNAs. Importantly, elimination of RNA by RNase treatment disrupts the MAVS signalosome, including newly identified regulators of RLR signaling, and inhibits phosphorylation of the transcription factor IRF3. This supports the hypothesis that RNA molecules scaffold proteins in the MAVS signalosome to induce IFNs. Together, this work uncovers a function for cellular RNA in promoting signaling through MAVS and highlights a generalizable principle of RNA regulatory control of cytoplasmic immune signaling complexes.

How RNA modifications regulate the antiviral response.

Induction of the antiviral innate immune response is highly regulated at the RNA level, particularly by RNA modifications. Recent discoveries have revealed how RNA modifications play key roles in cellular surveillance of nucleic acids and in controlling gene expression in response to viral infection. These modifications have emerged as being essential for a functional antiviral response and maintaining cellular homeostasis. In this review, we will highlight these and other discoveries that describe how the antiviral response is controlled by modifications to both viral and cellular RNA, focusing on how mRNA cap modifications, N6-methyladenosine, and RNA editing all contribute to coordinating an efficient response that properly controls viral infection.

Viral-induced alternative splicing of host genes promotes influenza replication.

Viral infection induces the expression of numerous host genes that impact the outcome of infection. Here, we show that infection of human lung epithelial cells with influenza A virus (IAV) also induces a broad program of alternative splicing of host genes. Although these splicing-regulated genes are not enriched for canonical regulators of viral infection, we find that many of these genes do impact replication of IAV. Moreover, in several cases, specific inhibition of the IAV-induced splicing pattern also attenuates viral infection. We further show that approximately a quarter of the IAV-induced splicing events are regulated by hnRNP K, a host protein required for efficient splicing of the IAV M transcript in nuclear speckles. Finally, we find an increase in hnRNP K in nuclear speckles upon IAV infection, which may alter accessibility of hnRNP K for host transcripts thereby leading to a program of host splicing changes that promote IAV replication.

Functional and Mechanistic Interplay of Host and Viral Alternative Splicing Regulation during Influenza Infection.

Alternative splicing is a pervasive gene regulatory mechanism utilized by both mammalian cells and viruses to expand their genomic coding capacity. The process of splicing and the RNA sequences that guide this process are the same in mammalian and viral transcripts; however, viruses lack the splicing machinery and therefore must usurp both the host spliceosome and many of the associated regulatory proteins in order to correctly process their genes. Here, we use the example of the influenza A virus to both describe how viruses utilize host splicing factors to regulate their own splicing and provide examples of how viral infection can, in turn, alter host splicing. Importantly, we show that at least some of the viral-induced changes in host splicing occur in genes that alter the efficiency of influenza replication. We emphasize the importance of increased understanding of the mechanistic interplay between host and viral splicing, and its functional consequences, in uncovering potential antiviral vulnerabilities.

Structural-functional interactions of NS1-BP protein with the splicing and mRNA export machineries for viral and host gene expression.

The influenza virulence factor NS1 protein interacts with the cellular NS1-BP protein to promote splicing and nuclear export of the viral M mRNAs. The viral M1 mRNA encodes the M1 matrix protein and is alternatively spliced into the M2 mRNA, which is translated into the M2 ion channel. These proteins have key functions in viral trafficking and budding. To uncover the NS1-BP structural and functional activities in splicing and nuclear export, we performed proteomics analysis of nuclear NS1-BP binding partners and showed its interaction with constituents of the splicing and mRNA export machineries. NS1-BP BTB domains form dimers in the crystal. Full-length NS1-BP is a dimer in solution and forms at least a dimer in cells. Mutations suggest that dimerization is important for splicing. The central BACK domain of NS1-BP interacts directly with splicing factors such as hnRNP K and PTBP1 and with the viral NS1 protein. The BACK domain is also the site for interactions with mRNA export factor Aly/REF and is required for viral M mRNA nuclear export. The crystal structure of the C-terminal Kelch domain shows that it forms a ß-propeller fold, which is required for the splicing function of NS1-BP. This domain interacts with the polymerase II C-terminal domain and SART1, which are involved in recruitment of splicing factors and spliceosome assembly, respectively. NS1-BP functions are not only critical for processing a subset of viral mRNAs but also impact levels and nuclear export of a subset of cellular mRNAs encoding factors involved in metastasis and immunity.

Co-regulatory activity of hnRNP K and NS1-BP in influenza and human mRNA splicing.

Three of the eight RNA segments encoded by the influenza A virus (IAV) undergo alternative splicing to generate distinct proteins. Previously, we found that host proteins hnRNP K and NS1-BP regulate IAV M segment splicing, but the mechanistic details were unknown. Here we show NS1-BP and hnRNP K bind M mRNA downstream of the M2 5' splice site (5'ss). NS1-BP binds most proximal to the 5'ss, partially overlapping the U1 snRNP binding site, while hnRNP K binds further downstream and promotes U1 snRNP recruitment. Mutation of either or both the hnRNP K and NS1-BP-binding sites results in M segment mis-splicing and attenuated IAV replication. Additionally, we show that hnRNP K and NS1-BP regulate host splicing events and that viral infection causes mis-splicing of some of these transcripts. Therefore, our proposed mechanism of hnRNP K/NS1-BP mediated IAV M splicing provides potential targets of antiviral intervention and reveals novel host functions for these proteins.

FOXO3, estrogen receptor alpha, and androgen receptor impact tumor growth rate and infiltration of dendritic cell subsets differentially between male and female mice.

Tumors evade immune recognition and destruction in many ways including the creation of an immune-suppressive tumor microenvironment (TME). Dendritic cells (DC) that infiltrate the TME are tolerogenic, and suppress effector T cells and anti-tumor activity. Previous reports demonstrated that a key regulator of tolerance in DC is the transcription factor FOXO3. Gender disparity has been studied in cancer in relation to incidence, aggressiveness, and prognosis. Few studies have touched on the importance in relation to impact on the immune system. In the current study, we show that there are significant differences in tumor growth between males and females. Additionally, frequencies and the function of FOXO3 expressed by DC subsets that infiltrate tumors vary between genders. Our results show for the first time that DC FOXO3 expression and function is altered in females. In vitro results indicate that these differences may be the result of exposure to estrogen. These differences may be critical considerations for the enhancement of immunotherapy for cancer.

Alcohol exposure differentially effects anti-tumor immunity in females by altering dendritic cell function.

Dendritic cells (DCs) are a critical component of anti-tumor immunity due to their ability to induce a robust immune response to antigen (Ag). Alcohol was previously shown to reduce DC ability to present foreign Ag and promote pro-inflammatory responses in situations of infection and trauma. However the impact of alcohol exposure on generation of an anti-tumor response, especially in the context of generation of an immune vaccine has not been examined. In the clinic, DC vaccines are typically generated from autologous blood, therefore prior exposure to substances such as alcohol may be a critical factor to consider regarding the effectiveness in generating an immune response. In this study, we demonstrate for the first time that ethanol differentially affects DC and tumor Ag-specific T cell responses depending on sex. Signaling pathways were found to be differentially regulated in DC in females compared to males and these differences were exacerbated by ethanol treatment. DC from female mice treated with ethanol were unable to activate Ag-specific cytotoxic T cells (CTL) as shown by reduced expression of CD44, CD69, and decreased production of granzyme B and IFNγ. Furthermore, although FOXO3, an immune suppressive mediator of DC function, was found to be upregulated in DC from female mice, ethanol related suppression was independent of FOXO3. These findings demonstrate for the first time differential impacts of alcohol on the immune system of females compared to males and may be a critical consideration for determining the effectiveness of an immune based therapy for cancer in patients that consume alcohol.

FOXO3-NF-κB RelA Protein Complexes Reduce Proinflammatory Cell Signaling and Function.

Tumor-associated myeloid cells, including dendritic cells (DCs) and macrophages, are immune suppressive. This study demonstrates a novel mechanism involving FOXO3 and NF-κB RelA that controls myeloid cell signaling and impacts their immune-suppressive nature. We find that FOXO3 binds NF-κB RelA in the cytosol, impacting both proteins by preventing FOXO3 degradation and preventing NF-κB RelA nuclear translocation. The location of protein-protein interaction was determined to be near the FOXO3 transactivation domain. In turn, NF-κB RelA activation was restored upon deletion of the same sequence in FOXO3 containing the DNA binding domain. We have identified for the first time, to our knowledge, a direct protein-protein interaction between FOXO3 and NF-κB RelA in tumor-associated DCs. These detailed biochemical interactions provide the foundation for future studies to use the FOXO3-NF-κB RelA interaction as a target to enhance tumor-associated DC function to support or enhance antitumor immunity.

TRAP150 interacts with the RNA-binding domain of PSF and antagonizes splicing of numerous PSF-target genes in T cells.

PSF (a.k.a. SFPQ) is a ubiquitously expressed, essential nuclear protein with important roles in DNA damage repair and RNA biogenesis. In stimulated T cells, PSF binds to and suppresses the inclusion of CD45 exon 4 in the final mRNA; however, in resting cells, TRAP150 binds PSF and prevents access to the CD45 RNA, though the mechanism for this inhibition has remained unclear. Here, we show that TRAP150 binds a region encompassing the RNA recognition motifs (RRMs) of PSF using a previously uncharacterized, 70 residue region we have termed the PSF-interacting domain (PID). TRAP150's PID directly inhibits the interaction of PSF RRMs with RNA, which is mediated through RRM2. However, interaction of PSF with TRAP150 does not appear to inhibit the dimerization of PSF with other Drosophila Behavior, Human Splicing (DBHS) proteins, which is also dependent on RRM2. Finally, we use RASL-Seq to identify ∼40 T cell splicing events sensitive to PSF knockdown, and show that for the majority of these, PSF's effect is antagonized by TRAP150. Together these data suggest a model in which TRAP150 interacts with dimeric PSF to block access of RNA to RRM2, thereby regulating the activity of PSF toward a broad set of splicing events in T cells.

Acetone cation chemistry under varying electron density conditions: from unimolecular decomposition to dissociative recombination processes.

The chemistry of ionized acetone:Ar mixtures under varied ionizing electron density conditions has been studied using matrix-isolation techniques. Gaseous acetone diluted in excess argon gas was subjected to electron bombardment with 300 eV electrons at currents between 20 and 200 µA. Linear wire 'pin' and metal 'plate' electron collector geometries were employed, allowing a wide range of electron density conditions to be explored. The products of subsequent reaction processes were matrix isolated and analyzed by Fourier transform infrared absorption spectroscopy. Products included methane, ketene, 1-propen-2-ol (the enol isomer of acetone), CO, HCO, ethane, ethane, acetylene and CCCO. Product absolute and relative yields varied with acetone number density, the choice of anode geometry and the rate of electron bombardment. The overall chemistry observed is rationalized in terms of mechanistic steps involving unimolecular cation decomposition, ion-molecule reactions, radical-radical reactions and dissociative recombination processes.

The polysialyltransferases interact with sequences in two domains of the neural cell adhesion molecule to allow its polysialylation.

The neural cell adhesion molecule (NCAM) is the major substrate for the polysialyltransferases (polySTs), ST8SiaII/STX and ST8SiaIV/PST. The polysialylation of NCAM N-glycans decreases cell adhesion and alters signaling. Previous work demonstrated that the first fibronectin type III repeat (FN1) of NCAM is required for polyST recognition and the polysialylation of the N-glycans on the adjacent Ig5 domain. In this work, we highlight the importance of an FN1 acidic patch in polyST recognition and also reveal that the polySTs are required to interact with sequences in the Ig5 domain for polysialylation to occur. We find that features of the Ig5 domain of the olfactory cell adhesion molecule (OCAM) are responsible for its lack of polysialylation. Specifically, two basic OCAM Ig5 residues (Lys and Arg) found near asparagines equivalent to those carrying the polysialylated N-glycans in NCAM substantially decrease or eliminate polysialylation when used to replace the smaller and more neutral residues (Ser and Asn) in analogous positions in NCAM Ig5. This decrease in polysialylation does not reflect altered glycosylation but instead is correlated with a decrease in polyST-NCAM binding. In addition, inserting non-conserved OCAM sequences into NCAM Ig5, including an "extra" N-glycosylation site, decreases or completely blocks NCAM polysialylation. Taken together, these results indicate that the polySTs not only recognize an acidic patch in the FN1 domain of NCAM but also must contact sequences in the Ig5 domain for polysialylation of Ig5 N-glycans to occur.

Ethane cation decomposition characterization by EBMI spectroscopy: gas-phase dissociative recombination as a source of secondary products.

The decomposition products of the d(6) -ethane cation following charge-transfer ionization with Ar(+) , under conditions of varying ionization electron current, have been isolated in solid argon matrices at 18 K and examined using Fourier transform infrared spectroscopy. Gas samples containing 1 : 1600 d(6) -ethane : Ar were subjected to electron bombardment by using either a high (pin) or a low (plate) ionization density anode configuration with ionization currents between 20 and 150 µA. Under high ionization density conditions, the observed major products were d(4) -ethene (C(2) D(4) ) and d(2) -acetylene (C(2) D(2) ), with smaller yields of C(2) D(5) , C(2) D(3) , and C(2) D. The yield of each dehydrogenation product was enhanced with increased current. Analogous experiments employing the low ionization density plate anode resulted in reduced C(2) D(6) destruction and the formation of only C(2) D(4) and C(2) D(2) . The results suggest the onset of dissociative recombination processes under high ion density conditions. In this context, the results can be interpreted as a dissociative recombination of primary ion products, which gives rise to further dehydrogenation, and appearance of additional neutral radical products.

Fourier transform infrared matrix-isolation analysis of acetaldehyde fragmentation products after charge exchange with Ar•+ under varied ionization density conditions.

The products of the Ar(•+) charge exchange ionization of acetaldehyde have been isolated and compared with related photoionization results and computational work. Acetaldehyde has been used to assess the effect of varied ion density in the ionization region of the electron bombardment matrix isolation apparatus. The amount of acetaldehyde destruction has been measured for constant gas-sample composition and constant ionization current for two anode geometries: a pin anode and a plate anode. For the same ionization current, a pin-shaped anode demonstrates higher precursor molecule destruction efficiency (85%) than the plate-shaped anode (30%), resulting in substantial effect on the yield and quantity of isolated products. When the plate anode is used, the observed infrared products correspond to matrix-isolated carbon monoxide (CO), methane (CH(4)), ketene (CH(2)CO), ethynyloxy radical (HCCO), formyl radical (HCO(•)), acetyl radical (CH(3)CO(•)), vinyl alcohol (H(2)C = CH-OH), and cationic proton-bound dimer, Ar(2)H(+). When the pin anode is used, the same products are observed with different relative proportions and new absorption features corresponding to dicarbon monoxide (CCO) and methyl radical (CH(3)(•)) are observed. The surprising observation of infrared absorptions corresponding to vinyl alcohol along with low yield of products anticipated through the analysis of photoelectron-photoionization coincidence measurements suggests that the initially formed fragmentation products are able to further react within the matrix-isolation environment to influence observed product yields. Related experiments, using the isotopomer CD(3)CHO, suggest that the observed products are formed via radical-radical reactions that occur under the high pressure conditions of the matrix isolation environment.

FTIR matrix-isolation study of the reaction products of vanadium atoms with propene: observation of allylvanadium hydride as a precursor to sacrificial hydrogenation of propene.

Vanadium atoms have been reacted with different partial pressures of propene in Ar under matrix-isolation conditions, and the products have been observed using Fourier transform infrared (FTIR) spectroscopy. Under dilute propene in Ar conditions, new features are observed in the IR spectra corresponding to a C-H insertion product, identified here as H-V-(η(3)-allyl). Use of d(3)-propene (CD(3)-CH═CH(2)) demonstrates that the initial V-atom insertion occurs at the methyl group of the propene molecule, and DFT calculations have been used to support the identity of the initial product. Upon increasing the partial pressure of propene, additional features corresponding to propane (C(3)H(8)) are observed, with the hydrogen-atom source for the observed hydrogenation demonstrated to be additional propene units. Analysis of a systematic increase in the partial pressure of propene in the system demonstrates that the yield of propane correlates with the decrease of the allyl product, demonstrating the H-V(allyl) species as a reactive intermediate in the overall hydrogenation process. An overall mechanism is proposed to rationalize the formation of the insertion product and ultimately the products of hydrogenation, which agrees with previous gas-phase and matrix-isolation work involving propene and the related system, ethene.

Electron-bombardment matrix isolation and PEPICO studies as complementary techniques in ion chemistry: an FTIR study of the decomposition of the vinyl fluoride cation.

FTIR spectra have been obtained for matrices formed following electron bombardment of gas mixtures containing varying amounts of vinyl fluoride (VF) in Ar (1:400 to 1:25,600; VF/Ar). The major matrix-isolated products are a π-complex of HF/C(2)H(2) , fluoroacetylene (HC≡CF) and two isomers of C(2)H(2)F(•). These products correspond well with the products of photoionization of VF near 15.8 eV. These observations support the dominant mechanism of ionization in the EB-MI environment as charge transfer of the substrate molecule to Ar(•+). Some differences are noted between the observed EB-MI products and the results from PEPICO studies, primarily in that the EB-MI products are observed as neutralized forms. The close correlation in EB-MI and photoionization results allows the EB-MI technique to be utilized as an ion structural analysis tool in complement to PEPICO studies, and allows the use of PEPICO studies to help predict and elucidate high-pressure chemistry mechanisms through EB-MI studies. The differences in the EB-MI results and ions observed using the PEPICO technique are rationalized in terms of the differences in the experimental techniques. Using VF as the test system, reagent partial pressure conditions that best complement PEPICO studies are determined. Although the major results are observed for all VF partial pressures, dilute samples give rise to further ionization of the primary products, and more concentrated samples give rise to radical-radical reaction chemistry. As a result, a nominal range of 1:3200 (VF/Ar) is demonstrated to provide the best correlation with the gas-phase PEPICO measurements.

Sequences at the interface of the fifth immunoglobulin domain and first fibronectin type III repeat of the neural cell adhesion molecule are critical for its polysialylation.

Polysialic acid is an anti-adhesive glycan that modifies a select group of mammalian proteins. The primary substrate of the polysialyltransferases (polySTs) is the neural cell adhesion molecule (NCAM). Polysialic acid negatively regulates cell adhesion, is required for proper brain development, and is expressed in specific areas of the adult brain where it promotes on-going cell migration and synaptic plasticity. The first fibronectin type III repeat (FN1) of NCAM is required for polysialylation of the N-glycans on the adjacent immunoglobulin-like domain (Ig5), and acidic residues on the surface of FN1 play a role in polyST recognition. Recent work demonstrated that the FN1 domain from the unpolysialylated olfactory cell adhesion molecule (OCAM) was able to partially replace NCAM FN1 (Foley, D. A., Swartzentruber, K. G., Thompson, M. G., Mendiratta, S. S., and Colley, K. J. (2010) J. Biol. Chem. 285, 35056-35067). Here we demonstrate that individually replacing three identical regions shared by NCAM and OCAM FN1, (500)PSSP(503) (PSSP), (526)GGVPI(530) (GGVPI), and (580)NGKG(583) (NGKG), dramatically reduces NCAM polysialylation. In addition, we show that the polyST, ST8SiaIV/PST, specifically binds NCAM and that this binding requires the FN1 domain. Replacing the FN1 PSSP sequences and the acidic patch residues decreases NCAM-polyST binding, whereas replacing the GGVPI and NGKG sequences has no effect. The location of GGVPI and NGKG in loops that flank the Ig5-FN1 linker and the proximity of PSSP to this linker suggest that GGVPI and NGKG sequences may be critical for stabilizing the Ig5-FN1 linker, whereas PSSP may play a dual role maintaining the Ig5-FN1 interface and a polyST recognition site.