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The role of neisserial Opa proteins in interactions with host cells.

Pathogenic Neisseria spp. possess a repertoire of phase-variable Opa proteins that mediate various pathogen--host cell interactions, including bacterial engulfment by epithelial cells and opsonin-independent phagocytosis by professional phagocytes. Recent studies have identified cellular targets recognized by defined Opa proteins and have begun to reveal host signalling events involved in mediating these Opa-dependent cellular processes.

Animals↗

Prediction of functional regions of the maize streak virus replication-associated proteins by protein-protein interaction analysis.

The replication of the geminiviruses depends on the viral encoded early (complementary-sense) proteins and on host genome encoded factors. Additionally, some of the early proteins (the AL2 protein of subgroup III, and the RepA (formerly known as C1) or Rep (C1:C2) proteins of subgroup I geminiviruses) can function as transcriptional activators of virion- (V-)sense gene expression. The yeast two-hybrid system has allowed us to predict some of the functionally important regions of the maize streak virus (MSV) early proteins RepA and Rep. Defined domains of these proteins were shown to act as transactivators in yeast cells. We detected the association of the RepA and Rep proteins, and their subfragments, with the maize retinoblastoma protein (ZmRb1) which is likely to be one of the interacting host proteins. We showed the self-association capability of the MSV proteins and suggest that homo- or hetero-oligomerization may play an important role in virus replication. These results provide new insights into the role of different regions of the MSV proteins in relation to transcriptional activation and regulation of viral DNA replication.

Amino Acid Sequence↗

Structure-resolved virus-host interactomics by cross-linking mass spectrometry.

Viruses depend on host protein networks to replicate, assemble progeny, and spread between cells and organisms. Defining these virus-host protein interactions is challenging because they are highly dependent on infection stage, cell type, species, and because mechanistic interpretation requires information about structural interfaces and conformational states. Cross-linking mass spectrometry (XL-MS) addresses these challenges by adding a spatial and structural dimension to virus-host interactomics in native systems. In this review, we discuss how XL-MS has advanced from targeted analysis of viral protein complexes to structure-resolved mapping of virion architecture and infected-cell virus-host interactomes. We highlight how XL-MS complements AP-MS, cryo-EM/cryo-ET, quantitative proteomics, genetic perturbation, and structure prediction to connect physical proximity with molecular mechanisms. Finally, we discuss current limitations in sensitivity, chemical coverage, temporal resolution, and model interpretation, and outline how future quantitative and integrative XL-MS workflows may enable systems-level structural virology.

Mass Spectrometry↗

Simian virus 40 large T antigen stably complexes with a 185-kilodalton host protein.

Stable interactions between simian virus 40 large T antigen and host proteins are believed to play a major role in the ability of the viral protein to transform cells in culture and induce tumors in vivo. Two of these host proteins, the retinoblastoma susceptibility protein (pRB) and p53, are products of tumor suppressor genes, suggesting that T antigen exerts at least a portion of its transforming activity by complexing with and inactivating the function of these proteins. While analyzing T antigen-host protein complexes in mouse cells, we noted a protein of 185 kDa (p185) which specifically coimmunoprecipitates with T antigen. Coimmunoprecipitation results from the formation of stable complexes between T antigen and p185. Complex formation is independent of the interactions of T antigen with pRB, p120, and p53. Furthermore, analysis of T-antigen mutants suggests that T antigen-p185 complex formation may be important in transformation by simian virus 40.

3T3 Cells↗

Hepatitis C virus-host interactions: the NS5A protein and the interferon/chemokine systems.

The interactions that occur between viral proteins and host factors, such as cellular proteins and signal transduction machinery, have a significant influence on the replication, persistence, and pathogenesis of all viruses. This is exemplified by hepatitis C virus (HCV), which infects an estimated 3% of the world's population and is a significant cause of liver disease. HCV-host interactions also affect the outcome of interferon (IFN) antiviral therapy, which is effective only in certain patients. In this review, we focus on the HCV nonstructural 5A (NS5A) protein, a model for diverse virus-host interactions, and highlight the interaction of viruses, including HCV, with the chemokine system.

Antiviral Agents↗

A functional atlas of transposon-encoded products and their integration into host networks.

Transposable elements (TEs) are pervasive genomic components that propagate via self-encoded factors, yet the nature, regulation, and function of these factors remain largely unresolved. Here, we integrated extensive long- and short-read transcriptome data, regulatory network analyses, deep proteomics, and structural predictions to construct a comprehensive atlas of TE products in Arabidopsis. We show that TE expression is embedded within host regulatory circuits, with DNA methylation and transcription factors jointly shaping TE transcriptional activity. Proteomic analyses confirm the production of over a hundred of high-confidence TE-encoded proteins, and structure-guided analyses of the transcript-informed TE proteome predict previously uncharacterized structural folds, multimerization capacity, and host protein interaction potential. Structural alignments further uncover cryptic homologies between TE-encoded proteins and host factors, including cases of domestications and co-options. Together, our study reveals the functional integration of TEs into cellular pathways and underscores the role of TEs as active drivers of genome function and innovation.

Arabidopsis↗

Prediction of DtxR regulon: identification of binding sites and operons controlled by Diphtheria toxin repressor in Corynebacterium diphtheriae.

BACKGROUND: The diphtheria toxin repressor, DtxR, of Corynebacterium diphtheriae has been shown to be an iron-activated transcription regulator that controls not only the expression of diphtheria toxin but also of iron uptake genes. This study aims to identify putative binding sites and operons controlled by DtxR to understand the role of DtxR in patho-physiology of Corynebacterium diphtheriae. RESULT: Positional Shannon relative entropy method was used to build the DtxR-binding site recognition profile and the later was used to identify putative regulatory sites of DtxR within C. diphtheriae genome. In addition, DtxR-regulated operons were also identified taking into account the predicted DtxR regulatory sites and genome annotation. Few of the predicted motifs were experimentally validated by electrophoretic mobility shift assay. The analysis identifies motifs upstream to the novel iron-regulated genes that code for Formamidopyrimidine-DNA glycosylase (FpG), an enzyme involved in DNA-repair and starvation inducible DNA-binding protein (Dps) which is involved in iron storage and oxidative stress defense. In addition, we have found the DtxR motifs upstream to the genes that code for sortase which catalyzes anchoring of host-interacting proteins to the cell wall of pathogenic bacteria and the proteins of secretory system which could be involved in translocation of various iron-regulated virulence factors including diphtheria toxin. CONCLUSIONS: We have used an in silico approach to identify the putative binding sites and genes controlled by DtxR in Corynebacterium diphtheriae. Our analysis shows that DtxR could provide a molecular link between Fe+2-induced Fenton's reaction and protection of DNA from oxidative damage. DtxR-regulated Dps prevents lethal combination of Fe+2 and H2O2 and also protects DNA by nonspecific DNA-binding. In addition DtxR could play an important role in host interaction and virulence by regulating the levels of sortase, a potential vaccine candidate and proteins of secretory system.

Bacterial Proteins↗

The complete genomic sequence of the modified vaccinia Ankara strain: comparison with other orthopoxviruses.

The complete genomic DNA sequence of the highly attenuated vaccinia strain modified vaccinia Ankara (MVA) was determined. The genome of MVA is 178 kb in length, significantly smaller than that of the vaccinia Copenhagen genome, which is 192 kb. The 193 open reading frames (ORFs) mapped in the MVA genome probably correspond to 177 genes, 25 of which are split and/or have suffered mutations resulting in truncated proteins. The left terminal genomic region of MVA contains four large deletions and one large insertion relative to the Copenhagen strain. In addition, many ORFs in this region are fragmented, leaving only eight genes structurally intact and therefore presumably functional. The inserted DNA codes for a cluster of genes that is also found in the vaccinia WR strain and in cowpox virus and includes a highly fragmented gene homologous to the cowpox virus host range gene, providing further evidence that a cowpox-like virus was the ancestor of vaccinia. Surprisingly, the central conserved region of the genome also contains some fragmented genes, including ORF F5L, encoding a major membrane protein, and ORFs F11L and O1L, encoding proteins of 39.7 and 77.6 kDa, respectively. The right terminal genomic region carries three large deletions all classical poxviral immune evasion genes and all ankyrin-like genes located in this region are fragmented except for those encoding the interleukin-1 beta receptor and the 68-kDa ankyrin-like protein B18R. Thus, the attenuated phenotype of MVA is the result of numerous mutations, particularly affecting the host interactive proteins, including the ankyrin-like genes, but also involving some structural proteins.

Ankyrins↗

A chloroplast protein binds a viroid RNA in vivo and facilitates its hammerhead-mediated self-cleavage.

Viroids, small single-stranded circular RNAs (246-401 nucleotides), do not have mRNA capacity and must recruit host proteins to assist in the steps of their biological cycle. The nature of these cellular factors is poorly understood due to a lack of reliable experimental approaches. Here, to screen for host proteins interacting with viroid RNAs in vivo, we UV-irradiated avocado leaves infected with avocado sunblotch viroid (ASBVd), the type member of chloroplast viroids containing hammerhead ribozymes. This resulted in the detection of several ASBVd-host protein adducts. Tandem mass spectrometry analysis of the most abundant cross-linked species identified the protein component as two closely related chloroplast RNA-binding proteins (PARBP33 and PARBP35) of a family whose members previously have been shown to be involved in stabilization, maturation and editing of chloroplast transcripts. PARBP33 behaves as an RNA chaperone that stimulates in vitro the hammerhead-mediated self-cleavage of the multimeric ASBVd transcripts that result from rolling circle replication, indicating that this reaction, despite its RNA-based mechanism, is facilitated by proteins. The structural and functional parallelism between PARBP33 and PARBP35, and some proteins involved in viral RNA replication, indicates that viroids and RNA viruses recruit similar host proteins for their replication.

Amino Acid Sequence↗

Growth hormone interacts with the Marek's disease virus SORF2 protein and is associated with disease resistance in chicken.

Marek's disease (MD) is a lymphoproliferative disease of chickens induced by a herpesvirus, the MD virus (MDV). Because MD is a significant economic problem to the poultry industry, there is great interest in enhancing genetic resistance, which is controlled by multiple genes. The influence of the MHC has been clearly demonstrated, and several relevant quantitative trait loci have been mapped; however, no single gene influencing MD resistance has been identified. Transcription of SORF2 is perturbed in the MDV recombinant clone RM1 due to a solo insertion of the reticuloendotheliosis virus long terminal repeat, which may explain the loss of oncogenicity for this strain. Hypothesizing that SORF2-interacting host proteins are involved in MD resistance, we screened a chicken splenic cDNA library by the yeast two-hybrid assay using SORF2 as bait. The chicken growth hormone (GH) structural peptide was identified, and the specific interaction was verified by coimmunoprecipitation. Immunohistochemical staining and indirect immunofluorescence assay indicated that GH and SORF2 can be coexpressed in MDV-infected cells both in vitro and in vivo. Furthermore, polymorphism in the GH gene (GH1) is associated with the number of tissues with tumors in commercial White Leghorn chickens with the MHC B*2/B*15 genotype. We conclude that GH1 may well be a MD resistance gene.

Animals↗

A comprehensive screen for chicken proteins that interact with proteins unique to virulent strains of Marek's disease virus.

Genetic resistance to Marek's disease (MD) has been proposed as a method to augment current vaccinal control of MD. Although it is possible to identify QTL and candidate genes that are associated with MD resistance, it is necessary to integrate functional screens with linkage analysis to confirm the identity of true MD resistance genes. To help achieve this objective, a comprehensive 2-hybrid screen was conducted using genes unique to virulent Marek's disease virus (MDV) strains. Potential MDV-host protein interactions were tested by an in vitro binding assay to confirm the initial two-hybrid results. As a result, 7 new MDV-chicken protein interactions were identified and included the chicken proteins MHC class II beta (BLB) and invariant (Ii) chain (CD74), growth-related translationally controlled tumor protein (TPT1), complement component Clq-binding protein (C1QBP), retinoblastoma-binding protein 4 (RBBP4), and alpha-enolase (ENO1). Mapping of the encoding chicken genes suggests that BLB, the gene for MHC class II beta chain, is a positional candidate gene. In addition, the known functions of the chicken proteins suggest mechanisms that MDV might use to evade the chicken immune system and alter host gene regulation. Taken together, our results indicate that integrated genomic methods provide a powerful strategy to gain insights on complex biological processes and yield a manageable number of genes and pathways for further characterization.

Animals↗

Hepatitis B virus X protein: structure, function and biology.

The X gene is conserved among mammalian hepadnaviruses and the X protein, pX, is essential for viral propagation at least in the woodchuck. During the last decade, efforts have centered on elucidating the oncogenic role of pX in hepatitis B virus infection. The accumulating knowledge on pX indicates that it is a multifunctional regulatory protein which modulates many host functions by communicating directly or indirectly with a variety of host targets as is the case for many viral regulatory proteins, such as T antigens, E1A, and human T cell lymphotropic virus tax. pX, which modulates the transcription machinery and/or modulation protein kinase signaling cascades, transactivates many host genes involved in cell proliferation, cytokine networks, acute immune response, and house-keeping functions. Distinct from the transactivation, pX also modulates DNA repair processes by interacting with p53 and/or repair enzymes which may accumulate mutations and sensitize cells to genotoxic stimuli. Several X-interaction host proteins remain to be characterized as targets of pX. The biological roles of pX have been addressed in various systems in addition to the role of pX on viral reproduction. pX may affect cell cycle progress, response to apoptotic stimuli, cell transformation, and carcinogenesis in the presence or absence of additional oncogenic factors. These biological roles of pX have not been described in terms of pX functions and targets and remain subjects of future research using improved experimental systems and technologies. Such efforts will identify important function(s) of pX for hepatocarcinogenesis.

Amino Acid Sequence↗

What surgeons should know about viral hepatitis and hepatocellular carcinoma.

Most patients with hepatocellular carcinoma (HCC) have viral hepatitis, either hepatitis C (HCV) or hepatitis B (HBV). HCV is an RNA virus that does not integrate into the host genome but likely induces HCC through viral protein: for example, host protein interactions or via the inflammatory response to the virus. Eradication of HCV with interferon plus riboviron therapy may help prevent cancer recurrence in selected patients. In contrast to HCV, HBV is an DNA virus that integrates into the host genome, and this integration is believed, in part, to be carcinogenic. HBV is usually classified as replicative (DNA-positive in the serum) or nonreplicative (DNA-negative in the serum). Treatment with nucleoside analogs is indicated in most patients with cirrhotic-stage replicating HBV. Nonreplicative stages of this virus do not merit therapy with these agents.

Carcinoma, Hepatocellular↗

The role of Steinernema feltiae body-surface lipids in host-parasite immunological interactions.

Interactions between entomopathogenic nematodes (Steinernema feltiae) and insect host (Galleria mellonella) immune system were investigated. We focused on the immunosuppressive properties of the parasite cuticle and on its interaction with hemolymph humoral components. Effects of parasite cuticle against host proPO system enzymatic cascade were evaluated a short time after infection. The presence of parasite cuticles decreased both normal and LPS-elicited proPO system activity, suggesting that S. feltiae body surface plays a key role in the early parasitation phase, probably interfering with host proPO activation pathways. The data obtained showed that cuticle lipidic compounds are able to interact with host humoral components, removing them from the hemolymph. The depletion of these molecules, arbitrarily named host-interacting proteins (HIPs), seems to be responsible of the drastic decrease in proPO system activity. Moreover, hemolymph HIPs showed LPS-binding properties and parasite cuticle cross-reacted with anti-LPS antibodies. Finally, we also assessed the involvement of parasite body surface on immunoevasion strategies of S. feltiae against host cell-mediated encapsulation processes. We conclude that S. feltiae body surface is responsible for short-term immunosuppression and immunoevasion processes; since it is able to sequester host hemolymph compounds involved in proPO system activation and this process could be responsible for a molecular disguise strategy against cellular encapsulation.

Animals↗

Down-regulation of antibacterial peptide synthesis in an insect model induced by the body-surface of an entomoparasite (Steinernema feltiae).

This study focuses on the interaction between an entomopathogenic nematode and an insect model to further investigate the role of parasite body-surface and its compounds (particularly epicuticular lipids) in the immunosuppression of host defences. Our goal was to ascertain the potential interference of the parasite epicuticular lipids with the antimicrobial response mounted by Gram-negative bacteria-challenged hosts. Since the parasite model used in this study (Steinernema feltiae) releases symbiontic bacteria in the host hemocoel during the late phase of infection, the inhibition of the antimicrobial response could be needed to avoid the activity of host factors potentially harmful for the microorganisms. After bacterial challenge, when insect hosts were infected with purified parasite cuticles, we always observed lack of bacterial clearance concurrently with the absence of hemolymph low molecular weight components. The observed effects seem to be related to the interaction of parasite cuticular lipids (PCLs) with specific components of the host hemolymph; these host interacting proteins (HIP17, HIP26 and HIP35) were removed by the parasite, and their absence (or reduction) apparently prevented antimicrobial peptide synthesis. The inhibitory properties were lost when cuticles were pre-treated with compounds (such as lipase or methanol-chloroform) affecting their lipidic moiety. Moreover, the key role of epicuticular lipids was also confirmed by the inhibitory properties of methanol-chloroform extracted lipids, which were comparable to those of parasite whole cuticles. Finally, the involvement of HIPs was assessed by their partial purification followed by injection into the host. When HIPs were co-injected with bacteria into cuticle-inhibited larvae, the antimicrobial activity was completely restored.

Animals↗

Isolation and characterization of an oligomerization-negative mutant of HIV-1 integrase.

The yeast two-hybrid method was used to screen mutagenized DNAs to isolate a variant of the human immunodeficiency virus type 1 integrase (IN) that does not interact with the wild-type IN. The responsible mutation, leading to a single amino acid change (V260E) in the C-terminal domain of IN, blocks IN-IN multimerization but has only small effect on binding to a host interacting protein, INI1 (hSNF5). Binding studies in vitro confirmed the defect in multimerization of the mutant IN. Biochemical analyses of the mutant IN enzyme expressed in bacteria detected only subtle changes in its properties, suggesting that the yeast system is a sensitive reporter of correct IN conformation. Mutant virus carrying the V260E substitution was blocked in replication at the time of DNA integration, consistent with IN multimerization being important for its activity in vivo.

Amino Acid Sequence↗

The vaccinia virus B1R kinase induces p53 downregulation by an Mdm2-dependent mechanism.

Poxvirus infection has a strong effect on cellular functions. To understand viral pathogenesis, it is necessary to know how viral proteins interact with host proteins. The B1R kinase is an early viral gene required for vaccinia virus DNA synthesis and replication, but no cellular substrate is known for this viral kinase. B1R is able to hyperphosphorylate p53 in several residues in the N-terminal transactivation domain, including Ser15 and Thr18. B1R does not phosphorylate Mdm2. B1R promotes an increase in p53 ubiquitination and a reduction of p53 acetylation by p300. The over-expressed B1R protein induces the degradation of p53 in a concentration-dependent manner and is lost when Ser15 and Th18 are changed to alanine or when the B1R kinase is inactivated by introducing the K149Q substitution. The B1R-induced downregulation of p53 requires Mdm2. The hyperphosphorylated p53 is transcriptionally active, and this activity also falls as B1R increases. The BAX gene promoter is more sensitive to this reduction of transcription than p21 or 14-3-3 gene promoters. This effect of B1R on p53 can be one of the mechanisms by which vaccinia virus exerts its role in infected cells.

Alanine↗

Convergent evolution among immunoglobulin G-binding bacterial proteins.

Protein G, a bacterial cell-wall protein with high affinity for the constant region of IgG (IgGFc) antibodies, contains homologous repeats responsible for the interaction with IgGFc. A synthetic peptide corresponding to an 11-amino acid-long sequence in the COOH-terminal region of the repeats was found to bind to IgGFc and block the interaction with protein G. Moreover, two other IgGFc-binding bacterial proteins (proteins A and H), which do not contain any sequences homologous to the peptide, were also inhibited in their interactions with IgGFc by the peptide. Finally, a decapeptide based on a sequence in IgGFc blocked the binding of all three proteins to IgGFc. This unusually clear example of convergent evolution emphasizes the complexity of protein-protein interactions and suggests that bacterial surface-protein interaction with host protein adds selective advantages to the microorganism.

Amino Acid Sequence↗