Comprehensive Characterization of Transcriptional Activity during Influenza A Virus Infection Reveals Biases in Cap-Snatching of Host RNA Sequences.

Macrophages in the lung detect and respond to influenza A virus (IAV), determining the nature of the immune response. Using terminal-depth cap analysis of gene expression (CAGE), we quantified transcriptional activity of both host and pathogen over a 24-h time course of IAV infection in primary human monocyte-derived macrophages (MDMs). This method allowed us to observe heterogenous host sequences incorporated into IAV mRNA, "snatched" 5' RNA caps, and corresponding RNA sequences from host RNAs. In order to determine whether cap-snatching is random or exhibits a bias, we systematically compared host sequences incorporated into viral mRNA ("snatched") against a complete survey of all background host RNA in the same cells, at the same time. Using a computational strategy designed to eliminate sources of bias due to read length, sequencing depth, and multimapping, we were able to quantify overrepresentation of host RNA features among the sequences that were snatched by IAV. We demonstrate biased snatching of numerous host RNAs, particularly small nuclear RNAs (snRNAs), and avoidance of host transcripts encoding host ribosomal proteins, which are required by IAV for replication. We then used a systems approach to describe the transcriptional landscape of the host response to IAV, observing many new features, including a failure of IAV-treated MDMs to induce feedback inhibitors of inflammation, seen in response to other treatments.IMPORTANCE Infection with influenza A virus (IAV) infection is responsible for an estimated 500,000 deaths and up to 5 million cases of severe respiratory illness each year. In this study, we looked at human primary immune cells (macrophages) infected with IAV. Our method allows us to look at both the host and the virus in parallel. We used these data to explore a process known as "cap-snatching," where IAV snatches a short nucleotide sequence from capped host RNA. This process was believed to be random. We demonstrate biased snatching of numerous host RNAs, including those associated with snRNA transcription, and avoidance of host transcripts encoding host ribosomal proteins, which are required by IAV for replication. We then describe the transcriptional landscape of the host response to IAV, observing new features, including a failure of IAV-treated MDMs to induce feedback inhibitors of inflammation, seen in response to other treatments.

Recruitment of RED-SMU1 complex by Influenza A Virus RNA polymerase to control Viral mRNA splicing.

Influenza A viruses are major pathogens in humans and in animals, whose genome consists of eight single-stranded RNA segments of negative polarity. Viral mRNAs are synthesized by the viral RNA-dependent RNA polymerase in the nucleus of infected cells, in close association with the cellular transcriptional machinery. Two proteins essential for viral multiplication, the exportin NS2/NEP and the ion channel protein M2, are produced by splicing of the NS1 and M1 mRNAs, respectively. Here we identify two human spliceosomal factors, RED and SMU1, that control the expression of NS2/NEP and are required for efficient viral multiplication. We provide several lines of evidence that in infected cells, the hetero-trimeric viral polymerase recruits a complex formed by RED and SMU1 through interaction with its PB2 and PB1 subunits. We demonstrate that the splicing of the NS1 viral mRNA is specifically affected in cells depleted of RED or SMU1, leading to a decreased production of the spliced mRNA species NS2, and to a reduced NS2/NS1 protein ratio. In agreement with the exportin function of NS2, these defects impair the transport of newly synthesized viral ribonucleoproteins from the nucleus to the cytoplasm, and strongly reduce the production of infectious influenza virions. Overall, our results unravel a new mechanism of viral subversion of the cellular splicing machinery, by establishing that the human splicing factors RED and SMU1 act jointly as key regulators of influenza virus gene expression. In addition, our data point to a central role of the viral RNA polymerase in coupling transcription and alternative splicing of the viral mRNAs.

A gene expression atlas of the domestic pig.

BACKGROUND: This work describes the first genome-wide analysis of the transcriptional landscape of the pig. A new porcine Affymetrix expression array was designed in order to provide comprehensive coverage of the known pig transcriptome. The new array was used to generate a genome-wide expression atlas of pig tissues derived from 62 tissue/cell types. These data were subjected to network correlation analysis and clustering. RESULTS: The analysis presented here provides a detailed functional clustering of the pig transcriptome where transcripts are grouped according to their expression pattern, so one can infer the function of an uncharacterized gene from the company it keeps and the locations in which it is expressed. We describe the overall transcriptional signatures present in the tissue atlas, where possible assigning those signatures to specific cell populations or pathways. In particular, we discuss the expression signatures associated with the gastrointestinal tract, an organ that was sampled at 15 sites along its length and whose biology in the pig is similar to human. We identify sets of genes that define specialized cellular compartments and region-specific digestive functions. Finally, we performed a network analysis of the transcription factors expressed in the gastrointestinal tract and demonstrate how they sub-divide into functional groups that may control cellular gastrointestinal development. CONCLUSIONS: As an important livestock animal with a physiology that is more similar than mouse to man, we provide a major new resource for understanding gene expression with respect to the known physiology of mammalian tissues and cells. The data and analyses are available on the websites http://biogps.org and http://www.macrophages.com/pig-atlas.

Avian Influenza A virus polymerase association with nucleoprotein, but not polymerase assembly, is impaired in human cells during the course of infection.

Strong determinants of the host range of influenza A viruses have been identified on the polymerase complex formed by the PB1, PB2, and PA subunits and on the nucleoprotein (NP). In the present study, molecular mechanisms that may involve these four core proteins and contribute to the restriction of avian influenza virus multiplication in human cells have been investigated. The efficiencies with which the polymerase complexes of a human and an avian influenza virus isolate assemble and interact with the viral NP and cellular RNA polymerase II proteins were compared in mammalian and in avian infected cells. To this end, recombinant influenza viruses expressing either human or avian-derived core proteins with a PB2 protein fused to the One-Strep purification tag at the N or C terminus were generated. Copurification experiments performed on infected cell extracts indicate that the avian-derived polymerase is assembled and interacts physically with the cellular RNA polymerase II at least as efficiently as does the human-derived polymerase in human as well as in avian cells. Restricted growth of the avian isolate in human cells correlates with low levels of the core proteins in infected cell extracts and with poor association of the NP with the polymerase compared to what is observed for the human isolate. The NP-polymerase association is restored by a Glu-to-Lys substitution at residue 627 of PB2. Overall, our data point to viral and cellular factors regulating the NP-polymerase interaction as key determinants of influenza A virus host range. Recombinant viruses expressing a tagged polymerase should prove useful for further studies of the molecular interactions between viral polymerase and host factors during the infection cycle.

Epitope mapping of a monoclonal antibody specific for human herpesvirus 6 variant A immediate-early 2 protein.

BACKGROUND: Human herpesvirus 6 (HHV-6) variants A and B are distinct viruses that differ in their biological properties and association to disease. Diagnostic tools able to discriminate between these two variants and between active or latent HHV-6 infection are much needed. In our effort to develop variant-specific antibodies against HHV-6 immediate-early (IE) proteins, we had previously generated P6H8, a monoclonal antibody (mAb) reacting specifically with the immediate-early 2 (IE2) proteins from HHV-6A. OBJECTIVES: To characterize the P6H8 HHV-6 variant specific mAb and evaluate its potential as part of a variant-specific diagnostic tool for HHV-6A infection. Consequently, our objective was to map the epitope recognized by P6H8. STUDY DESIGN: In order to map P6H8 reactivity by Western blotting, we generated deletion mutants of IE2 protein as well as various GST-IE2 fusion proteins. HHV-6A infected cells were used to demonstrate P6H8 reactivity against native IE2. A synthetic peptide corresponding to the P6H8 epitope was used to confirm our results and block P6H8 reactivity. RESULTS: We mapped the P6H8 epitope to amino acids 1078-1089 of HHV-6A IE2. A peptide (FTPFYYQSSRTR) recreating this epitope was effective in blocking the recognition of both native and recombinant IE2 by P6H8. CONCLUSIONS: Our work provides a precise characterization of the P6H8 mAb and its specificity toward the IE2 protein of HHV-6 variant A which could prove useful for the differential diagnostic of active infection by HHV-6.

Do membrane rafts contribute to human immunosenescence?

Aging is associated with an alteration of the immune response called immunosenescence. It is now well accepted that all parts of the immune system, the adaptive as well as the innate, undergo immunosenescence. However, the adaptive immune response and especially T cell functions are the most affected by aging. Aging is associated with profound changes in lymphocytes subpopulations, however, the functional changes within these subsets are more important to elucidate. Indeed, T cells present functional modifications resulting in a decreased clonal expansion and interleukin-2 (IL-2) production. So there should be an alteration in the activation process of T cells with aging involving the T cell receptor (TCR) and CD28 receptor signaling cascades. The alterations in membrane rafts composition and function can underline this altered activation of T cells with aging and then contribute to human immunosenescence. The experimental data in favor of this hypothesis will be reviewed.

Host restriction of avian influenza viruses at the level of the ribonucleoproteins.

Although transmission of avian influenza viruses to mammals, particularly humans, has been repeatedly documented, adaptation and sustained transmission in the new host is a rare event that in the case of humans may result in pandemics. Host restriction involves multiple genetic determinants. Among the known determinants of host range, key determinants have been identified on the genes coding for the nucleoprotein and polymerase proteins that, together with the viral RNA segments, form the ribonucleoproteins (RNPs). The RNP genes form host-specific lineages and harbor host-associated genetic signatures. The functional significance of these determinants has been studied by reassortment and reverse genetics experiments, underlining the influence of the global genetic context. In some instances the molecular mechanisms have been approached, pointing to the importance of the polymerase activity and interaction with cellular host factors. Better knowledge of determinants of host restriction will allow monitoring of the pandemic potential of avian influenza viruses.

Mapping of human herpesvirus 6 immediate-early 2 protein transactivation domains.

The immediate-early 2 (IE2) protein of human herpesvirus 6 (HHV-6) is a potent transactivator of multiple cellular and viral promoters. Deletion mutants of HHV-6 variant A IE2 allowed us to map functional transactivation domains acting on complex and minimal promoter sequences. This mapping showed that both the N-terminal and C-terminal domains of IE2 are required for efficient transactivation, and that deletion of the C-terminal (1397-1466) tail of IE2 drastically reduces both transactivation and the intranuclear distribution of IE2. Moreover, we determined that the ATF/CRE binding site within the HHV-6A polymerase promoter is not required for efficient transactivation by IE2, whereas the R3 repeat region of the putative immediate-early promoter of HHV-6A is responsive to and positively regulated by IE2. These results contrast sharply to that of human cytomegalovirus (HCMV) IE2, which down-regulates its promoter. Our characterization of HHV-6 IE2 transactivating activity provides a better understanding of the complex interactions of this protein with the viral and cellular transcription machinery and highlights significant differences with the IE2 protein of HCMV.

Functional interaction between human herpesvirus 6 immediate-early 2 protein and ubiquitin-conjugating enzyme 9 in the absence of sumoylation.

The immediate-early 2 (IE2) protein of human herpesvirus 6 is a potent transactivator of cellular and viral promoters. To better understand the biology of IE2, we generated a LexA-IE2 fusion protein and screened, using the yeast two-hybrid system, a Jurkat T-cell cDNA library for proteins that could interact with IE2. The most frequently isolated IE2-interacting protein was the human ubiquitin-conjugating enzyme 9 (Ubc9), a protein involved in the small ubiquitin-like modifier (SUMO) conjugation pathway. Using deletion mutants of IE2, we mapped the IE2-Ubc9-interacting region to residues 989 to 1037 of IE2. The interaction was found to be of functional significance to IE2, as Ubc9 overexpression significantly repressed promoter activation by IE2. The C93S Ubc9 mutant exhibited a similar effect on IE2, indicating that the E2 SUMO-conjugating function of Ubc9 is not required for its repressive action on IE2. No consensus sumoylation sites or evidence of IE2 conjugation to SUMO could be demonstrated under in vivo or in vitro conditions. Moreover, expression levels and nuclear localization of IE2 were not altered by Ubc9 overexpression, suggesting that Ubc9's repressive function likely occurs at the transcriptional complex level. Overall, our results indicate that Ubc9 influences IE2's function and provide new information on the complex interactions that occur between herpesviruses and the sumoylation pathway.

Characterization of the immediate-early 2 protein of human herpesvirus 6, a promiscuous transcriptional activator.

In the present work we report the cloning of a full-length cDNA encoding the immediate-early (IE) 2 protein from human herpesvirus 6 (HHV-6) variant A (GS strain). The transcript is 4690 nucleotides long and composed of 5 exons. Translation initiation occurs within the third exon and proceeds to the end of U86. Kinetic studies indicate that the 5.5-kb IE2 mRNA is expressed under IE condition, within 2-4 h of infection. IE2 transcripts from both variants A and B are expressed under similar kinetics with IE2 transcripts accumulating up to 96 h postinfection. Although several large transcripts (>5.5 kb) hybridized with the IE2 probe, suggesting multiple transcription initiation sites, a single form of the IE2 protein, in excess of 200 kDa, was detected by Western blot. Within cells, the IE2 protein was detected (8-48 h) as intranuclear granules while at later time points (72-120 h), the IE2 protein coalesced into a few large immunoreactive patches. Transfection of cells with an IE2 expression vector (pBK-IE2A) failed to reproduce the patch-like distribution, suggesting that other viral proteins are necessary for this process to occur. Last, IE2 was found to behave as a promiscuous transcriptional activator. Cotransfection experiments in T cells indicate that IE2 can induce the transcription of a complex promoter, such as the HIV-LTR, as well as simpler promoters, whose expression is driven by a unique set of responsive elements (CRE, NFAT, NF-kB). Moreover, minimal promoters having a single TATA box or no defined eukaryotic regulatory elements were significantly activated by IE2, suggesting that IE2 is likely to play an important role in initiating the expression of several HHV-6 genes. In all, the work presented represents the first report on the successful cloning, expression, and functional characterization of the major regulatory IE2 gene/protein of HHV-6.