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Halehalli RR, Nagarajaram HA. Molecular principles of human virus protein-protein interactions. ACTA ACUST UNITED AC 2014; 31:1025-33. [PMID: 25417202 DOI: 10.1093/bioinformatics/btu763] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 11/12/2014] [Indexed: 01/01/2023]
Abstract
MOTIVATION Viruses, from the human protein-protein interaction network perspective, target hubs, bottlenecks and interconnected nodes enriched in certain biological pathways. However, not much is known about the general characteristic features of the human proteins interacting with viral proteins (referred to as hVIPs) as well as the motifs and domains utilized by human-virus protein-protein interactions (referred to as Hu-Vir PPIs). RESULTS Our study has revealed that hVIPs are mostly disordered proteins, whereas viral proteins are mostly ordered proteins. Protein disorder in viral proteins and hVIPs varies from one subcellular location to another. In any given viral-human PPI pair, at least one of the two proteins is structurally disordered suggesting that disorder associated conformational flexibility as one of the characteristic features of virus-host interaction. Further analyses reveal that hVIPs are (i) slowly evolving proteins, (ii) associated with high centrality scores in human-PPI network, (iii) involved in multiple pathways, (iv) enriched in eukaryotic linear motifs (ELMs) associated with protein modification, degradation and regulatory processes, (v) associated with high number of splice variants and (vi) expressed abundantly across multiple tissues. These aforementioned findings suggest that conformational flexibility, spatial diversity, abundance and slow evolution are the characteristic features of the human proteins targeted by viral proteins. Hu-Vir PPIs are mostly mediated via domain-motif interactions (DMIs) where viral proteins employ motifs that mimic host ELMs to bind to domains in human proteins. DMIs are shared among viruses belonging to different families indicating a possible convergent evolution of these motifs to help viruses to adopt common strategies to subvert host cellular pathways. AVAILABILITY AND IMPLEMENTATION Hu-Vir PPI data, DDI and DMI data for human-virus PPI can be downloaded from http://cdfd.org.in/labpages/computational_biology_datasets.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rachita Ramachandra Halehalli
- Laboratory of Computational Biology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500001, India and Graduate School, Manipal University, Manipal, 576104, Karnataka, India Laboratory of Computational Biology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500001, India and Graduate School, Manipal University, Manipal, 576104, Karnataka, India
| | - Hampapathalu Adimurthy Nagarajaram
- Laboratory of Computational Biology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500001, India and Graduate School, Manipal University, Manipal, 576104, Karnataka, India
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Morris JH, Knudsen GM, Verschueren E, Johnson JR, Cimermancic P, Greninger AL, Pico AR. Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc 2014; 9:2539-54. [PMID: 25275790 PMCID: PMC4332878 DOI: 10.1038/nprot.2014.164] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
By determining protein-protein interactions in normal, diseased and infected cells, we can improve our understanding of cellular systems and their reaction to various perturbations. In this protocol, we discuss how to use data obtained in affinity purification-mass spectrometry (AP-MS) experiments to generate meaningful interaction networks and effective figures. We begin with an overview of common epitope tagging, expression and AP practices, followed by liquid chromatography-MS (LC-MS) data collection. We then provide a detailed procedure covering a pipeline approach to (i) pre-processing the data by filtering against contaminant lists such as the Contaminant Repository for Affinity Purification (CRAPome) and normalization using the spectral index (SIN) or normalized spectral abundance factor (NSAF); (ii) scoring via methods such as MiST, SAInt and CompPASS; and (iii) testing the resulting scores. Data formats familiar to MS practitioners are then transformed to those most useful for network-based analyses. The protocol also explores methods available in Cytoscape to visualize and analyze these types of interaction data. The scoring pipeline can take anywhere from 1 d to 1 week, depending on one's familiarity with the tools and data peculiarities. Similarly, the network analysis and visualization protocol in Cytoscape takes 2-4 h to complete with the provided sample data, but we recommend taking days or even weeks to explore one's data and find the right questions.
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Affiliation(s)
- John H Morris
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Giselle M Knudsen
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Erik Verschueren
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA
| | - Jeffrey R Johnson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA
| | - Peter Cimermancic
- 1] Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA. [2] Graduate Group in Bioinformatics, University of California, San Francisco, San Francisco, California, USA
| | - Alexander L Greninger
- School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Alexander R Pico
- Gladstone Institutes, University of California, San Francisco, San Francisco, California, USA
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O’Connor JE, Herrera G, Martínez-Romero A, de Oyanguren FS, Díaz L, Gomes A, Balaguer S, Callaghan RC. Systems Biology and immune aging. Immunol Lett 2014; 162:334-45. [DOI: 10.1016/j.imlet.2014.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 09/12/2014] [Indexed: 10/24/2022]
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Killick KE, Magee DA, Park SDE, Taraktsoglou M, Browne JA, Conlon KM, Nalpas NC, Gormley E, Gordon SV, MacHugh DE, Hokamp K. Key Hub and Bottleneck Genes Differentiate the Macrophage Response to Virulent and Attenuated Mycobacterium bovis. Front Immunol 2014; 5:422. [PMID: 25324841 PMCID: PMC4181336 DOI: 10.3389/fimmu.2014.00422] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 08/19/2014] [Indexed: 01/07/2023] Open
Abstract
Mycobacterium bovis is an intracellular pathogen that causes tuberculosis in cattle. Following infection, the pathogen resides and persists inside host macrophages by subverting host immune responses via a diverse range of mechanisms. Here, a high-density bovine microarray platform was used to examine the bovine monocyte-derived macrophage transcriptome response to M. bovis infection relative to infection with the attenuated vaccine strain, M. bovis Bacille Calmette-Guérin. Differentially expressed genes were identified (adjusted P-value ≤0.01) and interaction networks generated across an infection time course of 2, 6, and 24 h. The largest number of biological interactions was observed in the 24-h network, which exhibited scale-free network properties. The 24-h network featured a small number of key hub and bottleneck gene nodes, including IKBKE, MYC, NFKB1, and EGR1 that differentiated the macrophage response to virulent and attenuated M. bovis strains, possibly via the modulation of host cell death mechanisms. These hub and bottleneck genes represent possible targets for immuno-modulation of host macrophages by virulent mycobacterial species that enable their survival within a hostile environment.
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Affiliation(s)
- Kate E Killick
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland ; Systems Biology Ireland, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin , Ireland
| | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - Stephen D E Park
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland ; IdentiGEN Ltd. , Dublin , Ireland
| | - Maria Taraktsoglou
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland ; Biological Agents Unit, Health and Safety Executive , Leeds , UK
| | - John A Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - Kevin M Conlon
- UCD School of Veterinary Medicine, University College Dublin , Dublin , Ireland ; Science Foundation Ireland (SFI) , Dublin , Ireland
| | - Nicolas C Nalpas
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - Eamonn Gormley
- Tuberculosis Diagnostics and Immunology Research Centre, UCD School of Veterinary Medicine, University College Dublin , Dublin , Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin , Dublin , Ireland ; UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin , Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland ; UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin , Ireland
| | - Karsten Hokamp
- Smurfit Institute of Genetics, Trinity College , Dublin , Ireland
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O'Connor JE, Herrera G, Martínez-Romero A, Oyanguren FSD, Díaz L, Gomes A, Balaguer S, Callaghan RC. WITHDRAWN: Systems Biology and Immune Aging. Immunol Lett 2014:S0165-2478(14)00197-7. [PMID: 25251659 DOI: 10.1016/j.imlet.2014.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 09/12/2014] [Indexed: 10/24/2022]
Abstract
The Publisher regrets that this article is an accidental duplication of anarticle that has already been published, http://dx.doi.org/10.1016/j.imlet.2014.09.009. The duplicate article has therefore been withdrawn.
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Affiliation(s)
- José-Enrique O'Connor
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain.
| | - Guadalupe Herrera
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Alicia Martínez-Romero
- Cytometry Technological Service, Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Francisco Sala-de Oyanguren
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Laura Díaz
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Angela Gomes
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Susana Balaguer
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Robert C Callaghan
- Department of Pathology, Faculty of Medicine, The University of Valencia, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
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Identification of molecular sub-networks associated with cell survival in a chronically SIVmac-infected human CD4+ T cell line. Virol J 2014; 11:152. [PMID: 25163480 PMCID: PMC4163169 DOI: 10.1186/1743-422x-11-152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 08/15/2014] [Indexed: 12/31/2022] Open
Abstract
Background The deciphering of cellular networks to determine susceptibility to infection by HIV or the related simian immunodeficiency virus (SIV) is a major challenge in infection biology. Results Here, we have compared gene expression profiles of a human CD4+ T cell line at 24 h after infection with a cell line of the same origin permanently releasing SIVmac. A new knowledge-based-network approach (Inter-Chain-Finder, ICF) has been used to identify sub-networks associated with cell survival of a chronically SIV-infected T cell line. Notably, the method can identify not only differentially expressed key hub genes but also non-differentially expressed, critical, ‘hidden’ regulators. Six out of the 13 predicted major hidden key regulators were among the landscape of proteins known to interact with HIV. Several sub-networks were dysregulated upon chronic infection with SIV. Most prominently, factors reported to be engaged in early stages of acute viral infection were affected, e.g. entry, integration and provirus transcription and other cellular responses such as apoptosis and proliferation were modulated. For experimental validation of the gene expression analyses and computational predictions, individual pathways/sub-networks and significantly altered key regulators were investigated further. We showed that the expression of caveolin-1 (Cav-1), the top hub in the affected protein-protein interaction network, was significantly upregulated in chronically SIV-infected CD4+ T cells. Cav-1 is the main determinant of caveolae and a central component of several signal transduction pathways. Furthermore, CD4 downregulation and modulation of the expression of alternate and co-receptors as well as pathways associated with viral integration into the genome were also observed in these cells. Putatively, these modifications interfere with re-infection and the early replication cycle and inhibit cell death provoked by syncytia formation and bystander apoptosis. Conclusions Thus, by using the novel approach for network analysis, ICF, we predict that in the T cell line chronically infected with SIV, cellular processes that are known to be crucial for early phases of HIV/SIV replication are altered and cellular responses that result in cell death are modulated. These modifications presumably contribute to cell survival despite chronic infection. Electronic supplementary material The online version of this article (doi:10.1186/1743-422X-11-152) contains supplementary material, which is available to authorized users.
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107
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Mine A, Sato M, Tsuda K. Toward a systems understanding of plant-microbe interactions. FRONTIERS IN PLANT SCIENCE 2014; 5:423. [PMID: 25202320 PMCID: PMC4142988 DOI: 10.3389/fpls.2014.00423] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 08/07/2014] [Indexed: 05/25/2023]
Abstract
Plants are closely associated with microorganisms including pathogens and mutualists that influence plant fitness. Molecular genetic approaches have uncovered a number of signaling components from both plants and microbes and their mode of actions. However, signaling pathways are highly interconnected and influenced by diverse sets of environmental factors. Therefore, it is important to have systems views in order to understand the true nature of plant-microbe interactions. Indeed, systems biology approaches have revealed previously overlooked or misinterpreted properties of the plant immune signaling network. Experimental reconstruction of biological networks using exhaustive combinatorial perturbations is particularly powerful to elucidate network structure and properties and relationships among network components. Recent advances in metagenomics of microbial communities associated with plants further point to the importance of systems approaches and open a research area of microbial community reconstruction. In this review, we highlight the importance of a systems understanding of plant-microbe interactions, with a special emphasis on reconstruction strategies.
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Affiliation(s)
- Akira Mine
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Masanao Sato
- Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural SciencesOkazaki, Japan
| | - Kenichi Tsuda
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding ResearchCologne, Germany
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108
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The domain landscape of virus-host interactomes. BIOMED RESEARCH INTERNATIONAL 2014; 2014:867235. [PMID: 24991570 PMCID: PMC4065681 DOI: 10.1155/2014/867235] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 03/19/2014] [Indexed: 12/31/2022]
Abstract
Viral infections result in millions of deaths in the world today. A thorough analysis of virus-host interactomes may reveal insights into viral infection and pathogenic strategies. In this study, we presented a landscape of virus-host interactomes based on protein domain interaction. Compared to the analysis at protein level, this domain-domain interactome provided a unique abstraction of protein-protein interactome. Through comparisons among DNA, RNA, and retrotranscribing viruses, we identified a core of human domains, that viruses used to hijack the cellular machinery and evade the immune system, which might be promising antiviral drug targets. We showed that viruses preferentially interacted with host hub and bottleneck domains, and the degree and betweenness centrality among three categories of viruses are significantly different. Further analysis at functional level highlighted that different viruses perturbed the host cellular molecular network by common and unique strategies. Most importantly, we creatively proposed a viral disease network among viral domains, human domains and the corresponding diseases, which uncovered several unknown virus-disease relationships that needed further verification. Overall, it is expected that the findings will help to deeply understand the viral infection and contribute to the development of antiviral therapy.
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109
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Hagai T, Azia A, Babu MM, Andino R. Use of host-like peptide motifs in viral proteins is a prevalent strategy in host-virus interactions. Cell Rep 2014; 7:1729-1739. [PMID: 24882001 DOI: 10.1016/j.celrep.2014.04.052] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 03/25/2014] [Accepted: 04/24/2014] [Indexed: 12/31/2022] Open
Abstract
Viruses interact extensively with host proteins, but the mechanisms controlling these interactions are not well understood. We present a comprehensive analysis of eukaryotic linear motifs (ELMs) in 2,208 viral genomes and reveal that viruses exploit molecular mimicry of host-like ELMs to possibly assist in host-virus interactions. Using a statistical genomics approach, we identify a large number of potentially functional ELMs and observe that the occurrence of ELMs is often evolutionarily conserved but not uniform across virus families. Some viral proteins contain multiple types of ELMs, in striking similarity to complex regulatory modules in host proteins, suggesting that ELMs may act combinatorially to assist viral replication. Furthermore, a simple evolutionary model suggests that the inherent structural simplicity of ELMs often enables them to tolerate mutations and evolve quickly. Our findings suggest that ELMs may allow fast rewiring of host-virus interactions, which likely assists rapid viral evolution and adaptation to diverse environments.
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Affiliation(s)
- Tzachi Hagai
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16(th) Street, GH-S572, UCSF Box 2280, San Francisco, CA 94143-2280, USA
| | - Ariel Azia
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - M Madan Babu
- The Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16(th) Street, GH-S572, UCSF Box 2280, San Francisco, CA 94143-2280, USA.
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110
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Puniya BL, Kulshreshtha D, Verma SP, Kumar S, Ramachandran S. Integrated gene co-expression network analysis in the growth phase of Mycobacterium tuberculosis reveals new potential drug targets. MOLECULAR BIOSYSTEMS 2014; 9:2798-815. [PMID: 24056838 DOI: 10.1039/c3mb70278b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We have carried out weighted gene co-expression network analysis of Mycobacterium tuberculosis to gain insights into gene expression architecture during log phase growth. The differentially expressed genes between at least one pair of 11 different M. tuberculosis strains as source of biological variability were used for co-expression network analysis. This data included genes with highest coefficient of variation in expression. Five distinct modules were identified using topological overlap based clustering. All the modules together showed significant enrichment in biological processes: fatty acid biosynthesis, cell membrane, intracellular membrane bound organelle, DNA replication, Quinone biosynthesis, cell shape and peptidoglycan biosynthesis, ribosome and structural constituents of ribosome and transposition. We then extracted the co-expressed connections which were supported either by transcriptional regulatory network or STRING database or high edge weight of topological overlap. The genes trpC, nadC, pitA, Rv3404c, atpA, pknA, Rv0996, purB, Rv2106 and Rv0796 emerged as top hub genes. After overlaying this network on the iNJ661 metabolic network, the reactions catalyzed by 15 highly connected metabolic genes were knocked down in silico and evaluated by Flux Balance Analysis. The results showed that in 12 out of 15 cases, in 11 more than 50% of reactions catalyzed by genes connected through co-expressed connections also had altered fluxes. The modules 'Turquoise', 'Blue' and 'Red' also showed enrichment in essential genes. We could map 152 of the previously known or proposed drug targets in these modules and identified 15 new potential drug targets based on their high degree of co-expressed connections and strong correlation with module eigengenes.
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Affiliation(s)
- Bhanwar Lal Puniya
- G N Ramachandran Knowledge Centre for Genome Informatics, CSIR - Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India.
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Abstract
MOTIVATION Because susceptibility to diseases increases with age, studying aging gains importance. Analyses of gene expression or sequence data, which have been indispensable for investigating aging, have been limited to studying genes and their protein products in isolation, ignoring their connectivities. However, proteins function by interacting with other proteins, and this is exactly what biological networks (BNs) model. Thus, analyzing the proteins' BN topologies could contribute to the understanding of aging. Current methods for analyzing systems-level BNs deal with their static representations, even though cells are dynamic. For this reason, and because different data types can give complementary biological insights, we integrate current static BNs with aging-related gene expression data to construct dynamic age-specific BNs. Then, we apply sensitive measures of topology to the dynamic BNs to study cellular changes with age. RESULTS While global BN topologies do not significantly change with age, local topologies of a number of genes do. We predict such genes to be aging-related. We demonstrate credibility of our predictions by (i) observing significant overlap between our predicted aging-related genes and 'ground truth' aging-related genes; (ii) observing significant overlap between functions and diseases that are enriched in our aging-related predictions and those that are enriched in 'ground truth' aging-related data; (iii) providing evidence that diseases which are enriched in our aging-related predictions are linked to human aging; and (iv) validating our high-scoring novel predictions in the literature. AVAILABILITY AND IMPLEMENTATION Software executables are available upon request.
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Affiliation(s)
- Fazle E Faisal
- Department of Computer Science and Engineering, ECK Institute for Global Health and Interdisciplinary Center for Network Science and Applications, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Tijana Milenković
- Department of Computer Science and Engineering, ECK Institute for Global Health and Interdisciplinary Center for Network Science and Applications, University of Notre Dame, Notre Dame, IN 46556, USA
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Bhaduri A, Misra R, Maji A, Bhetaria PJ, Mishra S, Arora G, Singh LK, Dhasmana N, Dubey N, Virdi JS, Singh Y. Mycobacterium tuberculosis cyclophilin A uses novel signal sequence for secretion and mimics eukaryotic cyclophilins for interaction with host protein repertoire. PLoS One 2014; 9:e88090. [PMID: 24505389 PMCID: PMC3913756 DOI: 10.1371/journal.pone.0088090] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 01/03/2014] [Indexed: 11/19/2022] Open
Abstract
Cyclophilins are prolyl isomerases with multitude of functions in different cellular processes and pathological conditions. Cyclophilin A (PpiA) of Mycobacterium tuberculosis is secreted during infection in intraphagosomal niche. However, our understanding about the evolutionary origin, secretory mechanism or the interactome of M. tuberculosis PpiA is limited. This study demonstrates through phylogenetic and structural analyses that PpiA has more proximity to human cyclophilins than the prokaryotic counterparts. We report a unique N-terminal sequence (MADCDSVTNSP) present in pathogenic mycobacterial PpiA and absent in non-pathogenic strains. This sequence stretch was shown to be essential for PpiA secretion. The overexpression of full-length PpiA from M. tuberculosis in non-pathogenic Mycobacterium smegmatis resulted in PpiA secretion while truncation of the N-terminal stretch obstructed the secretion. In addition, presence of an ESX pathway substrate motif in M. tuberculosis PpiA suggested possible involvement of Type VII secretion system. Site-directed mutagenesis of key residues in this motif in full-length PpiA also hindered the secretion in M. smegmatis. Bacterial two-hybrid screens with human lung cDNA library as target were utilized to identify interaction partners of PpiA from host repertoire, and a number of substrates with functional representation in iron storage, signal transduction and immune responses were detected. The extensive host interactome coupled with the sequence and structural similarity to human cyclophilins is strongly suggestive of PpiA being deployed by M. tuberculosis as an effector mimic against the host cyclophilins.
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Affiliation(s)
- Asani Bhaduri
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Department of Microbiology, University of Delhi, Delhi, India
| | - Richa Misra
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Abhijit Maji
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | | | - Sonakshi Mishra
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Gunjan Arora
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | | | - Neha Dhasmana
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Neha Dubey
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | | | - Yogendra Singh
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- * E-mail: mail:
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113
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Rachita HR, Nagarajaram HA. Viral proteins that bridge unconnected proteins and components in the human PPI network. ACTA ACUST UNITED AC 2014; 10:2448-58. [DOI: 10.1039/c4mb00219a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Viral proteins bridging unconnected components of the Hu-PPI network play a crucial role in viral replication and hence form attractive targets for therapeutic interventions.
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Affiliation(s)
- H. R. Rachita
- Centre for DNA Fingerprinting and Diagnostics
- Gruhakalpa
- Hyderabad 500001, India
| | - H. A. Nagarajaram
- Centre for DNA Fingerprinting and Diagnostics
- Gruhakalpa
- Hyderabad 500001, India
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114
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Kshirsagar M, Carbonell J, Klein-Seetharaman J. Multitask learning for host-pathogen protein interactions. Bioinformatics 2013; 29:i217-26. [PMID: 23812987 PMCID: PMC3694681 DOI: 10.1093/bioinformatics/btt245] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Motivation: An important aspect of infectious disease research involves understanding the differences and commonalities in the infection mechanisms underlying various diseases. Systems biology-based approaches study infectious diseases by analyzing the interactions between the host species and the pathogen organisms. This work aims to combine the knowledge from experimental studies of host–pathogen interactions in several diseases to build stronger predictive models. Our approach is based on a formalism from machine learning called ‘multitask learning’, which considers the problem of building models across tasks that are related to each other. A ‘task’ in our scenario is the set of host–pathogen protein interactions involved in one disease. To integrate interactions from several tasks (i.e. diseases), our method exploits the similarity in the infection process across the diseases. In particular, we use the biological hypothesis that similar pathogens target the same critical biological processes in the host, in defining a common structure across the tasks. Results: Our current work on host–pathogen protein interaction prediction focuses on human as the host, and four bacterial species as pathogens. The multitask learning technique we develop uses a task-based regularization approach. We find that the resulting optimization problem is a difference of convex (DC) functions. To optimize, we implement a Convex–Concave procedure-based algorithm. We compare our integrative approach to baseline methods that build models on a single host–pathogen protein interaction dataset. Our results show that our approach outperforms the baselines on the training data. We further analyze the protein interaction predictions generated by the models, and find some interesting insights. Availability: The predictions and code are available at: http://www.cs.cmu.edu/∼mkshirsa/ismb2013_paper320.html Contact:j.klein-seetharaman@warwick.ac.uk Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Meghana Kshirsagar
- Language Technologies Institute, School of Computer Science, Carnegie Mellon University, 5000 Forbes Ave, PA 15213, USA
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Garamszegi S, Franzosa EA, Xia Y. Signatures of pleiotropy, economy and convergent evolution in a domain-resolved map of human-virus protein-protein interaction networks. PLoS Pathog 2013; 9:e1003778. [PMID: 24339775 PMCID: PMC3855575 DOI: 10.1371/journal.ppat.1003778] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 10/06/2013] [Indexed: 01/09/2023] Open
Abstract
A central challenge in host-pathogen systems biology is the elucidation of general, systems-level principles that distinguish host-pathogen interactions from within-host interactions. Current analyses of host-pathogen and within-host protein-protein interaction networks are largely limited by their resolution, treating proteins as nodes and interactions as edges. Here, we construct a domain-resolved map of human-virus and within-human protein-protein interaction networks by annotating protein interactions with high-coverage, high-accuracy, domain-centric interaction mechanisms: (1) domain-domain interactions, in which a domain in one protein binds to a domain in a second protein, and (2) domain-motif interactions, in which a domain in one protein binds to a short, linear peptide motif in a second protein. Analysis of these domain-resolved networks reveals, for the first time, significant mechanistic differences between virus-human and within-human interactions at the resolution of single domains. While human proteins tend to compete with each other for domain binding sites by means of sequence similarity, viral proteins tend to compete with human proteins for domain binding sites in the absence of sequence similarity. Independent of their previously established preference for targeting human protein hubs, viral proteins also preferentially target human proteins containing linear motif-binding domains. Compared to human proteins, viral proteins participate in more domain-motif interactions, target more unique linear motif-binding domains per residue, and contain more unique linear motifs per residue. Together, these results suggest that viruses surmount genome size constraints by convergently evolving multiple short linear motifs in order to effectively mimic, hijack, and manipulate complex host processes for their survival. Our domain-resolved analyses reveal unique signatures of pleiotropy, economy, and convergent evolution in viral-host interactions that are otherwise hidden in the traditional binary network, highlighting the power and necessity of high-resolution approaches in host-pathogen systems biology.
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Affiliation(s)
- Sara Garamszegi
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
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116
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Blasche S, Wuchty S, Rajagopala SV, Uetz P. The protein interaction network of bacteriophage lambda with its host, Escherichia coli. J Virol 2013; 87:12745-55. [PMID: 24049175 PMCID: PMC3838138 DOI: 10.1128/jvi.02495-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 09/10/2013] [Indexed: 11/20/2022] Open
Abstract
Although most of the 73 open reading frames (ORFs) in bacteriophage λ have been investigated intensively, the function of many genes in host-phage interactions remains poorly understood. Using yeast two-hybrid screens of all lambda ORFs for interactions with its host Escherichia coli, we determined a raw data set of 631 host-phage interactions resulting in a set of 62 high-confidence interactions after multiple rounds of retesting. These links suggest novel regulatory interactions between the E. coli transcriptional network and lambda proteins. Targeted host proteins and genes required for lambda infection are enriched among highly connected proteins, suggesting that bacteriophages resemble interaction patterns of human viruses. Lambda tail proteins interact with both bacterial fimbrial proteins and E. coli proteins homologous to other phage proteins. Lambda appears to dramatically differ from other phages, such as T7, because of its unusually large number of modified and processed proteins, which reduces the number of host-virus interactions detectable by yeast two-hybrid screens.
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Affiliation(s)
- Sonja Blasche
- Genomics and Proteomics Core Facilities, German Cancer Research Center, Heidelberg, Germany
| | - Stefan Wuchty
- National Center of Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Peter Uetz
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, USA
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117
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Noval MG, Gallo M, Perrone S, Salvay AG, Chemes LB, de Prat-Gay G. Conformational dissection of a viral intrinsically disordered domain involved in cellular transformation. PLoS One 2013; 8:e72760. [PMID: 24086265 PMCID: PMC3785498 DOI: 10.1371/journal.pone.0072760] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 07/14/2013] [Indexed: 12/25/2022] Open
Abstract
Intrinsic disorder is abundant in viral genomes and provides conformational plasticity to its protein products. In order to gain insight into its structure-function relationships, we carried out a comprehensive analysis of structural propensities within the intrinsically disordered N-terminal domain from the human papillomavirus type-16 E7 oncoprotein (E7N). Two E7N segments located within the conserved CR1 and CR2 regions present transient α-helix structure. The helix in the CR1 region spans residues L8 to L13 and overlaps with the E2F mimic linear motif. The second helix, located within the highly acidic CR2 region, presents a pH-dependent structural transition. At neutral pH the helix spans residues P17 to N29, which include the retinoblastoma tumor suppressor LxCxE binding motif (residues 21-29), while the acidic CKII-PEST region spanning residues E33 to I38 populates polyproline type II (PII) structure. At pH 5.0, the CR2 helix propagates up to residue I38 at the expense of loss of PII due to charge neutralization of acidic residues. Using truncated forms of HPV-16 E7, we confirmed that pH-induced changes in α-helix content are governed by the intrinsically disordered E7N domain. Interestingly, while at both pH the region encompassing the LxCxE motif adopts α-helical structure, the isolated 21-29 fragment including this stretch is unable to populate an α-helix even at high TFE concentrations. Thus, the E7N domain can populate dynamic but discrete structural ensembles by sampling α-helix-coil-PII-ß-sheet structures. This high plasticity may modulate the exposure of linear binding motifs responsible for its multi-target binding properties, leading to interference with key cell signaling pathways and eventually to cellular transformation by the virus.
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Affiliation(s)
- María G. Noval
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA- CONICET, Buenos Aires, Argentina
| | - Mariana Gallo
- NMR Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Sebastián Perrone
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA- CONICET, Buenos Aires, Argentina
| | - Andres G. Salvay
- Institute of Physics of Liquids and Biological Systems, Universidad Nacional de La Plata, La Plata, Argentina
- Department of Science and Technology, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Lucía B. Chemes
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA- CONICET, Buenos Aires, Argentina
| | - Gonzalo de Prat-Gay
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA- CONICET, Buenos Aires, Argentina
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118
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Functional characterization of human genes from exon expression and RNA interference results. Methods Mol Biol 2013; 910:33-53. [PMID: 22821591 DOI: 10.1007/978-1-61779-965-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Complex biological systems comprise a large number of interacting molecules. The identification and detailed characterization of the functions of the involved genes and proteins are crucial for modeling and understanding such systems. To interrogate the various cellular processes, high-throughput techniques such as the Affymetrix Exon Array or RNA interference (RNAi) screens are powerful experimental approaches for functional genomics. However, they typically yield long gene lists that require computational methods to further analyze and functionally annotate the experimental results and to gain more insight into important molecular interactions. Here, we focus on bioinformatics software tools for the functional interpretation of exon expression data to discover alternative splicing events and their impact on gene and protein architecture, molecular networks, and pathways. We additionally demonstrate how to explore large lists of candidate genes as they also result from RNAi screens. In particular, our exemplary application studies show how to analyze the function of human genes that play a major role in human stem cells or viral infections.
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119
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Integration of chemical and RNAi multiparametric profiles identifies triggers of intracellular mycobacterial killing. Cell Host Microbe 2013; 13:129-42. [PMID: 23414754 DOI: 10.1016/j.chom.2013.01.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 11/02/2012] [Accepted: 01/03/2013] [Indexed: 01/22/2023]
Abstract
Pharmacological modulators of host-microbial interactions can in principle be identified using high-content screens. However, a severe limitation of this approach is the lack of insights into the mode of action of compounds selected during the primary screen. To overcome this problem, we developed a combined experimental and computational approach. We designed a quantitative multiparametric image-based assay to measure intracellular mycobacteria in primary human macrophages, screened a chemical library containing FDA-approved drugs, and validated three compounds for intracellular killing of M. tuberculosis. By integrating the multiparametric profiles of the chemicals with those of siRNAs from a genome-wide survey on endocytosis, we predicted and experimentally verified that two compounds modulate autophagy, whereas the third accelerates endosomal progression. Our findings demonstrate the value of integrating small molecules and genetic screens for identifying cellular mechanisms modulated by chemicals. Furthermore, selective pharmacological modulation of host trafficking pathways can be applied to intracellular pathogens beyond mycobacteria.
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120
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Zoraghi R, Reiner NE. Protein interaction networks as starting points to identify novel antimicrobial drug targets. Curr Opin Microbiol 2013; 16:566-72. [PMID: 23938265 DOI: 10.1016/j.mib.2013.07.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 07/12/2013] [Accepted: 07/16/2013] [Indexed: 01/17/2023]
Abstract
Novel classes of antimicrobials are needed to address the challenge of multidrug-resistant bacteria. Current bacterial drug targets mainly consist of specific proteins or subsets of proteins without regard for either how these targets are integrated in cellular networks or how they may interact with host proteins. However, proteins rarely act in isolation, and the majority of biological processes are dependent on interactions with other proteins. Consequently, protein-protein interaction (PPI) networks offer a realm of unexplored potential for next-generation drug targets. In this review, we argue that the architecture of bacterial or host-pathogen protein interactomes can provide invaluable insights for the identification of novel antibacterial drug targets.
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Affiliation(s)
- Roya Zoraghi
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, Canada
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121
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Segura-Cabrera A, García-Pérez CA, Guo X, Rodríguez-Pérez MA. A viral-human interactome based on structural motif-domain interactions captures the human infectome. PLoS One 2013; 8:e71526. [PMID: 23951184 PMCID: PMC3738538 DOI: 10.1371/journal.pone.0071526] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 06/28/2013] [Indexed: 11/23/2022] Open
Abstract
Protein interactions between a pathogen and its host are fundamental in the establishment of the pathogen and underline the infection mechanism. In the present work, we developed a single predictive model for building a host-viral interactome based on the identification of structural descriptors from motif-domain interactions of protein complexes deposited in the Protein Data Bank (PDB). The structural descriptors were used for searching, in a database of protein sequences of human and five clinically important viruses; therefore, viral and human proteins sharing a descriptor were predicted as interacting proteins. The analysis of the host-viral interactome allowed to identify a set of new interactions that further explain molecular mechanism associated with viral infections and showed that it was able to capture human proteins already associated to viral infections (human infectome) and non-infectious diseases (human diseasome). The analysis of human proteins targeted by viral proteins in the context of a human interactome showed that their neighbors are enriched in proteins reported with differential expression under infection and disease conditions. It is expected that the findings of this work will contribute to the development of systems biology for infectious diseases, and help guide the rational identification and prioritization of novel drug targets.
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Affiliation(s)
- Aldo Segura-Cabrera
- Laboratorio de Bioinformática, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, México.
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122
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Li Z, Cui X, Li F, Li P, Ni M, Wang S, Bo X. Exploring the role of human miRNAs in virus-host interactions using systematic overlap analysis. ACTA ACUST UNITED AC 2013; 29:2375-9. [PMID: 23926228 DOI: 10.1093/bioinformatics/btt391] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
MOTIVATION Human miRNAs have recently been found to have important roles in viral replication. Understanding the patterns and details of human miRNA interactions during virus-host interactions may help uncover novel antiviral therapies. Based on the abundance of knowledge available regarding protein-protein interactions (PPI), virus-host protein interactions, experimentally validated human miRNA-target pairs and transcriptional regulation of human miRNAs, it is possible to explore the complex regulatory network that exists between viral proteins and human miRNAs at the system level. RESULTS By integrating current data regarding the virus-human interactome and human miRNA-target pairs, the overlap between targets of viral proteins and human miRNAs was identified and found to represent topologically important proteins (e.g. hubs or bottlenecks) at the global center of the human PPI network. Viral proteins and human miRNAs were also found to significantly target human PPI pairs. Furthermore, an overlap analysis of virus targets and transcription factors (TFs) of human miRNAs revealed that viral proteins preferentially target human miRNA TFs, representing a new pattern of virus-host interactions. Potential feedback loops formed by viruses, human miRNAs and miRNA TFs were also identified, and these may be exploited by viruses resulting in greater virulence and more effective replication strategies.
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Affiliation(s)
- Zhenpeng Li
- Beijing Institute of Radiation Medicine, Beijing 100850, China
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123
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Wu L, Wang S, Chen X, Wang X, Wu L, Zu X, Chen Y. Proteomic and phytohormone analysis of the response of maize (Zea mays L.) seedlings to sugarcane mosaic virus. PLoS One 2013; 8:e70295. [PMID: 23894637 PMCID: PMC3720893 DOI: 10.1371/journal.pone.0070295] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Accepted: 06/22/2013] [Indexed: 12/27/2022] Open
Abstract
Background Sugarcane mosaic virus (SCMV) is an important virus pathogen in crop production, causing serious losses in grain and forage yields in susceptible cultivars. Control strategies have been developed, but only marginal successes have been achieved. For the efficient control of this virus, a better understanding of its interactions and associated resistance mechanisms at the molecular level is required. Methodology/Principal Findings The responses of resistant and susceptible genotypes of maize to SCMV and the molecular basis of the resistance were studied using a proteomic approach based on two-dimensional polyacrylamide gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS/MS) analysis. Ninety-six protein spots showed statistically significant differences in intensity after SCMV inoculation. The classification of differentially expressed proteins showed that SCMV-responsive proteins were mainly involved in energy and metabolism, stress and defense responses, and photosynthesis. Most of the proteins identified were located in chloroplasts, chloroplast membranes, and the cytoplasm. Analysis of changes in phytohormone levels after virus inoculation suggested that salicylic acid, abscisic acid, jasmonic acid, and azelaic acid may played important roles in the maize response to SCMV infection. Conclusions/Significance Among these identified proteins, 19 have not been identified previously as virus-responsive proteins, and seven were new and did not have assigned functions. These proteins may be candidate proteins for future investigation, and they may present new biological functions and play important roles in plant-virus interactions. The behavioural patterns of the identified proteins suggest the existence of defense mechanisms operating during the early stages of infection that differed in two genotypes. In addition, there are overlapping and specific phytohormone responses to SCMV infection between resistant and susceptible maize genotypes. This study may provide important insights into the molecular events during plant responses to virus infection.
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Affiliation(s)
- Liuji Wu
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, China
- Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Zhengzhou, China
| | - Shunxi Wang
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, China
| | - Xiao Chen
- Henan Province Seed Control Station, Zhengzhou, China
| | - Xintao Wang
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, China
| | - Liancheng Wu
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, China
- Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Zhengzhou, China
| | - Xiaofeng Zu
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, China
| | - Yanhui Chen
- Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, China
- Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Zhengzhou, China
- * E-mail:
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124
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Muller M, Cassonnet P, Favre M, Jacob Y, Demeret C. A comparative approach to characterize the landscape of host-pathogen protein-protein interactions. J Vis Exp 2013:e50404. [PMID: 23893119 DOI: 10.3791/50404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Significant efforts were gathered to generate large-scale comprehensive protein-protein interaction network maps. This is instrumental to understand the pathogen-host relationships and was essentially performed by genetic screenings in yeast two-hybrid systems. The recent improvement of protein-protein interaction detection by a Gaussia luciferase-based fragment complementation assay now offers the opportunity to develop integrative comparative interactomic approaches necessary to rigorously compare interaction profiles of proteins from different pathogen strain variants against a common set of cellular factors. This paper specifically focuses on the utility of combining two orthogonal methods to generate protein-protein interaction datasets: yeast two-hybrid (Y2H) and a new assay, high-throughput Gaussia princeps protein complementation assay (HT-GPCA) performed in mammalian cells. A large-scale identification of cellular partners of a pathogen protein is performed by mating-based yeast two-hybrid screenings of cDNA libraries using multiple pathogen strain variants. A subset of interacting partners selected on a high-confidence statistical scoring is further validated in mammalian cells for pair-wise interactions with the whole set of pathogen variants proteins using HT-GPCA. This combination of two complementary methods improves the robustness of the interaction dataset, and allows the performance of a stringent comparative interaction analysis. Such comparative interactomics constitute a reliable and powerful strategy to decipher any pathogen-host interplays.
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Affiliation(s)
- Mandy Muller
- Unité de Génétique, Papillomavirus et Cancer Humain (GPCH), Institut Pasteur
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125
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de Chassey B, Aublin-Gex A, Ruggieri A, Meyniel-Schicklin L, Pradezynski F, Davoust N, Chantier T, Tafforeau L, Mangeot PE, Ciancia C, Perrin-Cocon L, Bartenschlager R, André P, Lotteau V. The interactomes of influenza virus NS1 and NS2 proteins identify new host factors and provide insights for ADAR1 playing a supportive role in virus replication. PLoS Pathog 2013; 9:e1003440. [PMID: 23853584 PMCID: PMC3701712 DOI: 10.1371/journal.ppat.1003440] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 05/06/2013] [Indexed: 12/24/2022] Open
Abstract
Influenza A NS1 and NS2 proteins are encoded by the RNA segment 8 of the viral genome. NS1 is a multifunctional protein and a virulence factor while NS2 is involved in nuclear export of viral ribonucleoprotein complexes. A yeast two-hybrid screening strategy was used to identify host factors supporting NS1 and NS2 functions. More than 560 interactions between 79 cellular proteins and NS1 and NS2 proteins from 9 different influenza virus strains have been identified. These interacting proteins are potentially involved in each step of the infectious process and their contribution to viral replication was tested by RNA interference. Validation of the relevance of these host cell proteins for the viral replication cycle revealed that 7 of the 79 NS1 and/or NS2-interacting proteins positively or negatively controlled virus replication. One of the main factors targeted by NS1 of all virus strains was double-stranded RNA binding domain protein family. In particular, adenosine deaminase acting on RNA 1 (ADAR1) appeared as a pro-viral host factor whose expression is necessary for optimal viral protein synthesis and replication. Surprisingly, ADAR1 also appeared as a pro-viral host factor for dengue virus replication and directly interacted with the viral NS3 protein. ADAR1 editing activity was enhanced by both viruses through dengue virus NS3 and influenza virus NS1 proteins, suggesting a similar virus-host co-evolution. Viruses are obligate intracellular parasites that rely on cellular functions for efficient replication. As most biological processes are sustained by protein-protein interactions, the identification of interactions between viral and host proteins can provide a global overview about the cellular functions engaged during viral replication. Influenza viruses express 13 viral proteins, including NS1 and NS2, which are translated from an alternatively spliced RNA derived from the same genome segment. We present here a comprehensive overview of possible interactions of cellular proteins with NS1 and NS2 from 9 viral strains. Seventy nine cellular proteins were identified to interact with NS1, NS2 or both NS1 and NS2. These interacting host cell proteins are potentially involved in many steps of the virus life cycle and 7 can directly control the viral replication. Most of the cellular targets are shared by the majority of the virus strains, especially the double-stranded RNA binding domain protein family that is strikingly targeted by NS1. One of its members, ADAR1, is essential for influenza virus replication. ADAR1 colocalizes with NS1 in nuclear structures and its editing activity is enhanced by NS1 expressed on its own and during virus infection. A similar phenomenon is observed for dengue virus whose NS3 protein also interacts with ADAR1, suggesting a parallel virus-host co-evolution.
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Affiliation(s)
- Benoît de Chassey
- Hospices Civils de Lyon, Hôpital de la Croix Rousse, Laboratory of Virology, Lyon, France
| | - Anne Aublin-Gex
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Alessia Ruggieri
- Department for Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Laurène Meyniel-Schicklin
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Fabrine Pradezynski
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Nathalie Davoust
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Thibault Chantier
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Lionel Tafforeau
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Philippe-Emmanuel Mangeot
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Claire Ciancia
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Laure Perrin-Cocon
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Ralf Bartenschlager
- Department for Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Patrice André
- Hospices Civils de Lyon, Hôpital de la Croix Rousse, Laboratory of Virology, Lyon, France
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Vincent Lotteau
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
- * E-mail:
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Recruitment of EB1, a master regulator of microtubule dynamics, to the surface of the Theileria annulata schizont. PLoS Pathog 2013; 9:e1003346. [PMID: 23675298 PMCID: PMC3649978 DOI: 10.1371/journal.ppat.1003346] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 03/22/2013] [Indexed: 12/13/2022] Open
Abstract
The apicomplexan parasite Theileria annulata transforms infected host cells, inducing uncontrolled proliferation and clonal expansion of the parasitized cell population. Shortly after sporozoite entry into the target cell, the surrounding host cell membrane is dissolved and an array of host cell microtubules (MTs) surrounds the parasite, which develops into the transforming schizont. The latter does not egress to invade and transform other cells. Instead, it remains tethered to host cell MTs and, during mitosis and cytokinesis, engages the cell's astral and central spindle MTs to secure its distribution between the two daughter cells. The molecular mechanism by which the schizont recruits and stabilizes host cell MTs is not known. MT minus ends are mostly anchored in the MT organizing center, while the plus ends explore the cellular space, switching constantly between phases of growth and shrinkage (called dynamic instability). Assuming the plus ends of growing MTs provide the first point of contact with the parasite, we focused on the complex protein machinery associated with these structures. We now report how the schizont recruits end-binding protein 1 (EB1), a central component of the MT plus end protein interaction network and key regulator of host cell MT dynamics. Using a range of in vitro experiments, we demonstrate that T. annulata p104, a polymorphic antigen expressed on the schizont surface, functions as a genuine EB1-binding protein and can recruit EB1 in the absence of any other parasite proteins. Binding strictly depends on a consensus SxIP motif located in a highly disordered C-terminal region of p104. We further show that parasite interaction with host cell EB1 is cell cycle regulated. This is the first description of a pathogen-encoded protein to interact with EB1 via a bona-fide SxIP motif. Our findings provide important new insight into the mode of interaction between Theileria and the host cell cytoskeleton. The apicomplexan parasite Theileria can reprogram the cell it infects, inducing uncontrolled proliferation and clonal expansion. This is brought about by the schizont, which resides free in the host cell cytoplasm. As the schizont never leaves the cell to infect other cells, it can only persist provided it is distributed over the two daughter cells each time the host cell divides. This is achieved by interacting dynamically with microtubules (MTs) that form part of the host cell mitotic apparatus. How MTs are recruited to the schizont surface is not known. MTs are highly dynamic, undergoing continuous cycles of growth and shrinkage that is regulated to a large extent by an array of proteins, called +TIPs, that associate with the free plus-ends of MTs. End-binding protein 1 (EB1) is a master regulator and central adaptor that mediates MT plus-end tracking of potentially all other +TIPs. We established that a schizont surface protein, p104, provides a docking site for EB1, which critically depends on a consensus SxIP motif, present in p104. These finding provides important new insight into the complex interaction of the transforming schizont with host cell MTs. To our knowledge, p104 is the first pathogen-derived protein identified so far to join the SxIP family of EB1-binding proteins.
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Park JH, Park S, Yang JS, Kwon OS, Kim S, Jang SK. Discovery of cellular proteins required for the early steps of HCV infection using integrative genomics. PLoS One 2013; 8:e60333. [PMID: 23593195 PMCID: PMC3625227 DOI: 10.1371/journal.pone.0060333] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Accepted: 02/25/2013] [Indexed: 02/06/2023] Open
Abstract
Successful viral infection requires intimate communication between virus and host cell, a process that absolutely requires various host proteins. However, current efforts to discover novel host proteins as therapeutic targets for viral infection are difficult. Here, we developed an integrative-genomics approach to predict human genes involved in the early steps of hepatitis C virus (HCV) infection. By integrating HCV and human protein associations, co-expression data, and tight junction-tetraspanin web specific networks, we identified host proteins required for the early steps in HCV infection. Moreover, we validated the roles of newly identified proteins in HCV infection by knocking down their expression using small interfering RNAs. Specifically, a novel host factor CD63 was shown to directly interact with HCV E2 protein. We further demonstrated that an antibody against CD63 blocked HCV infection, indicating that CD63 may serve as a new therapeutic target for HCV-related diseases. The candidate gene list provides a source for identification of new therapeutic targets.
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Affiliation(s)
- Ji Hoon Park
- Division of Molecular and Life Science, Pohang University of Science and Technology, Pohang, Korea
| | - Solip Park
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Korea
| | - Jae-Seong Yang
- Division of Molecular and Life Science, Pohang University of Science and Technology, Pohang, Korea
| | - Oh Sung Kwon
- Division of Molecular and Life Science, Pohang University of Science and Technology, Pohang, Korea
| | - Sanguk Kim
- Division of Molecular and Life Science, Pohang University of Science and Technology, Pohang, Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Korea
- Division of IT Convergence Engineering, Pohang University of Science and Technology, Pohang, Korea
- * E-mail: (SK); (SKJ)
| | - Sung Key Jang
- Division of Molecular and Life Science, Pohang University of Science and Technology, Pohang, Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Korea
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Korea
- Biotechnology Research Center, Pohang University of Science and Technology, Pohang, Korea
- * E-mail: (SK); (SKJ)
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128
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Durmuş Tekir S, Çakır T, Ardıç E, Sayılırbaş AS, Konuk G, Konuk M, Sarıyer H, Uğurlu A, Karadeniz İ, Özgür A, Sevilgen FE, Ülgen KÖ. PHISTO: pathogen–host interaction search tool. Bioinformatics 2013; 29:1357-8. [DOI: 10.1093/bioinformatics/btt137] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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129
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Schleker S, Trilling M. Data-warehousing of protein-protein interactions indicates that pathogens preferentially target hub and bottleneck proteins. Front Microbiol 2013; 4:51. [PMID: 23483866 PMCID: PMC3593624 DOI: 10.3389/fmicb.2013.00051] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 02/21/2013] [Indexed: 01/08/2023] Open
Affiliation(s)
- Sylvia Schleker
- Institute of Complex Systems, Molecular Biophysics (ICS-5), Forschungszentrum Juelich GmbH Juelich, Germany
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130
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Dong C, Zhao G, Zhong M, Yue Y, Wu L, Xiong S. RNA sequencing and transcriptomal analysis of human monocyte to macrophage differentiation. Gene 2013; 519:279-87. [PMID: 23458880 DOI: 10.1016/j.gene.2013.02.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Revised: 01/02/2013] [Accepted: 02/07/2013] [Indexed: 12/24/2022]
Abstract
Monocytes can be differentiated into macrophages in vivo and these cells play an important role in innate and adaptive immune responses. To reveal the global gene transcription change that occurs during monocyte to macrophage differentiation, we performed genome-wide RNA sequencing and analyses in human primary monocytes and monocyte-derived macrophages. We show that 1208 genes (with >twofold differences) were differentially expressed in macrophages compared with monocytes, including 800 upregulated and 408 downregulated genes. Gene ontology, pathway, and protein-protein interaction analyses indicated that the upregulated genes were related to macrophage functions in phagocytosis, metabolic processes, and cell cycle. The majority of downregulated genes comprised genes involved in the inflammatory response and locomotion. Genes encoding transcription regulatory factors, such as FOXO1, RUNX3, NF-κB1, and C/EBP δ, were highly expressed in monocytes and appeared to function in significant transcriptional repression, resulting in slight metabolic activity. Our transcriptome comparison between human monocytes and monocyte-derived macrophages using RNA sequencing revealed novel molecules and pathways associated with the differentiation process. These molecules and pathways may represent candidate targets involved in the pathophysiology of these important immune cells.
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Affiliation(s)
- Chunsheng Dong
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Science, Soochow University, Suzhou 215123, PR China.
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131
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Ma-Lauer Y, Lei J, Hilgenfeld R, von Brunn A. Virus-host interactomes--antiviral drug discovery. Curr Opin Virol 2013; 2:614-21. [PMID: 23057872 PMCID: PMC7102765 DOI: 10.1016/j.coviro.2012.09.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 09/05/2012] [Accepted: 09/06/2012] [Indexed: 12/21/2022]
Abstract
One of the key questions in virology is how viruses, encoding relatively few genes, gain temporary or constant control over their hosts. To understand pathogenicity of a virus it is important to gain knowledge on the function of the individual viral proteins in the host cell, on their interactions with viral and cellular proteins and on the consequences of these interactions on cellular signaling pathways. A combination of transcriptomics, proteomics, high-throughput technologies and the bioinformatical analysis of the respective data help to elucidate specific cellular antiviral drug target candidates. In addition, viral and human interactome analyses indicate that different viruses target common, central human proteins for entering cellular signaling pathways and machineries which might constitute powerful broad-spectrum antiviral targets.
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Affiliation(s)
- Yue Ma-Lauer
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-University (LMU) Munich, Pettenkoferstrasse 9a, 80336 München, Germany
| | - Jian Lei
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
- German Center for Infection Research (DZIF), University of Lübeck, Germany
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
- German Center for Infection Research (DZIF), University of Lübeck, Germany
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Rd., Shanghai 201203, China
| | - Albrecht von Brunn
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-University (LMU) Munich, Pettenkoferstrasse 9a, 80336 München, Germany
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132
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Abrusán G, Szilágyi A, Zhang Y, Papp B. Turning gold into 'junk': transposable elements utilize central proteins of cellular networks. Nucleic Acids Res 2013; 41:3190-200. [PMID: 23341038 PMCID: PMC3597677 DOI: 10.1093/nar/gkt011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The numerous discovered cases of domesticated transposable element (TE) proteins led to the recognition that TEs are a significant source of evolutionary innovation. However, much less is known about the reverse process, whether and to what degree the evolution of TEs is influenced by the genome of their hosts. We addressed this issue by searching for cases of incorporation of host genes into the sequence of TEs and examined the systems-level properties of these genes using the Saccharomyces cerevisiae and Drosophila melanogaster genomes. We identified 51 cases where the evolutionary scenario was the incorporation of a host gene fragment into a TE consensus sequence, and we show that both the yeast and fly homologues of the incorporated protein sequences have central positions in the cellular networks. An analysis of selective pressure (Ka/Ks ratio) detected significant selection in 37% of the cases. Recent research on retrovirus-host interactions shows that virus proteins preferentially target hubs of the host interaction networks enabling them to take over the host cell using only a few proteins. We propose that TEs face a similar evolutionary pressure to evolve proteins with high interacting capacities and take some of the necessary protein domains directly from their hosts.
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Affiliation(s)
- György Abrusán
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Temesváry krt. 62. Szeged H-6701, Hungary.
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133
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Arvey A, Tempera I, Tsai K, Chen HS, Tikhmyanova N, Klichinsky M, Leslie C, Lieberman PM. An atlas of the Epstein-Barr virus transcriptome and epigenome reveals host-virus regulatory interactions. Cell Host Microbe 2013; 12:233-45. [PMID: 22901543 DOI: 10.1016/j.chom.2012.06.008] [Citation(s) in RCA: 190] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 04/13/2012] [Accepted: 06/01/2012] [Indexed: 02/06/2023]
Abstract
Epstein-Barr virus (EBV), which is associated with multiple human tumors, persists as a minichromosome in the nucleus of B lymphocytes and induces malignancies through incompletely understood mechanisms. Here, we present a large-scale functional genomic analysis of EBV. Our experimentally generated nucleosome positioning maps and viral protein binding data were integrated with over 700 publicly available high-throughput sequencing data sets for human lymphoblastoid cell lines mapped to the EBV genome. We found that viral lytic genes are coexpressed with cellular cancer-associated pathways, suggesting that the lytic cycle may play an unexpected role in virus-mediated oncogenesis. Host regulators of viral oncogene expression and chromosome structure were identified and validated, revealing a role for the B cell-specific protein Pax5 in viral gene regulation and the cohesin complex in regulating higher order chromatin structure. Our findings provide a deeper understanding of latent viral persistence in oncogenesis and establish a valuable viral genomics resource for future exploration.
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Affiliation(s)
- Aaron Arvey
- Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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134
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Mairiang D, Zhang H, Sodja A, Murali T, Suriyaphol P, Malasit P, Limjindaporn T, Finley RL. Identification of new protein interactions between dengue fever virus and its hosts, human and mosquito. PLoS One 2013; 8:e53535. [PMID: 23326450 PMCID: PMC3543448 DOI: 10.1371/journal.pone.0053535] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 12/03/2012] [Indexed: 11/26/2022] Open
Abstract
The four divergent serotypes of dengue virus are the causative agents of dengue fever, dengue hemorrhagic fever and dengue shock syndrome. About two-fifths of the world's population live in areas where dengue is prevalent, and thousands of deaths are caused by the viruses every year. Dengue virus is transmitted from one person to another primarily by the yellow fever mosquito, Aedes aegypti. Recent studies have begun to define how the dengue viral proteins interact with host proteins to mediate viral replication and pathogenesis. A combined analysis of these studies, however, suggests that many virus-host protein interactions remain to be identified, especially for the mosquito host. In this study, we used high-throughput yeast two-hybrid screening to identify mosquito and human proteins that physically interact with dengue proteins. We tested each identified host protein against the proteins from all four serotypes of dengue to identify interactions that are conserved across serotypes. We further confirmed many of the interactions using co-affinity purification assays. As in other large-scale screens, we identified some previously detected interactions and many new ones, moving us closer to a complete host - dengue protein interactome. To help summarize and prioritize the data for further study, we combined our interactions with other published data and identified a subset of the host-dengue interactions that are now supported by multiple forms of evidence. These data should be useful for understanding the interplay between dengue and its hosts and may provide candidates for drug targets and vector control strategies.
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Affiliation(s)
- Dumrong Mairiang
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Huamei Zhang
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Ann Sodja
- Department of Biology, Wayne State University, Detroit, Michigan, United States of America
| | - Thilakam Murali
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Prapat Suriyaphol
- Bioinformatics and Data Management for Research Unit, Faculty of Medicine Siriraj Hospital, and Center for Emerging and Neglected Infectious Diseases, Mahidol University, Bangkok, Thailand
| | - Prida Malasit
- Dengue Hemorrhagic Fever Research Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok, Thailand
| | - Thawornchai Limjindaporn
- Department of Anatomy, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Russell L. Finley
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
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135
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Durmuş Tekir SD, Ülgen KÖ. Systems biology of pathogen-host interaction: networks of protein-protein interaction within pathogens and pathogen-human interactions in the post-genomic era. Biotechnol J 2013; 8:85-96. [PMID: 23193100 PMCID: PMC7161785 DOI: 10.1002/biot.201200110] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 09/17/2012] [Accepted: 10/11/2012] [Indexed: 12/13/2022]
Abstract
Infectious diseases comprise some of the leading causes of death and disability worldwide. Interactions between pathogen and host proteins underlie the process of infection. Improved understanding of pathogen-host molecular interactions will increase our knowledge of the mechanisms involved in infection, and allow novel therapeutic solutions to be devised. Complete genome sequences for a number of pathogenic microorganisms, as well as the human host, has led to the revelation of their protein-protein interaction (PPI) networks. In this post-genomic era, pathogen-host interactions (PHIs) operating during infection can also be mapped. Detailed systematic analyses of PPI and PHI data together are required for a complete understanding of pathogenesis of infections. Here we review the striking results recently obtained during the construction and investigation of these networks. Emphasis is placed on studies producing large-scale interaction data by high-throughput experimental techniques.
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Affiliation(s)
| | - Kutlu Ö. Ülgen
- Department of Chemical Engineering, Boǧaziçi University, Istanbul, Turkey
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136
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Abstract
High-throughput methods for screening of physical and functional interactions now provide the means to study virus-host interactions on a genome scale. The limited coverage of these methods and the large size and uncertain quality of the identified interaction sets, however, require sophisticated computational approaches to obtain novel insights and hypotheses on virus infection processes from these interactions. Here, we describe the central steps of bioinformatics methods applied most commonly for this task and highlight important aspects that need to be considered and potential pitfalls that should be avoided.
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Affiliation(s)
- Susanne M. Bailer
- University of Stuttgart Institute of Interfacial Process, Stuttgart, Germany
| | - Diana Lieber
- Ulm University Medical Center Institute of Virology, Ulm, Germany
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137
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Franzosa EA, Garamszegi S, Xia Y. Toward a three-dimensional view of protein networks between species. Front Microbiol 2012; 3:428. [PMID: 23267356 PMCID: PMC3528071 DOI: 10.3389/fmicb.2012.00428] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Accepted: 12/06/2012] [Indexed: 01/27/2023] Open
Abstract
General principles governing biomolecular interactions between species are expected to differ significantly from known principles governing the interactions within species, yet these principles remain poorly understood at the systems level. A key reason for this knowledge gap is the lack of a detailed three-dimensional (3D), atomistic view of biomolecular interaction networks between species. Recent progress in structural biology, systems biology, and computational biology has enabled accurate and large-scale construction of 3D structural models of nodes and edges for protein–protein interaction networks within and between species. The resulting within- and between-species structural interaction networks have provided new biophysical, functional, and evolutionary insights into species interactions and infectious disease. Here, we review the nascent field of between-species structural systems biology, focusing on interactions between host and pathogens such as viruses.
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138
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Yang R, Du Z, Han Y, Zhou L, Song Y, Zhou D, Cui Y. Omics strategies for revealing Yersinia pestis virulence. Front Cell Infect Microbiol 2012; 2:157. [PMID: 23248778 PMCID: PMC3521224 DOI: 10.3389/fcimb.2012.00157] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 11/27/2012] [Indexed: 01/12/2023] Open
Abstract
Omics has remarkably changed the way we investigate and understand life. Omics differs from traditional hypothesis-driven research because it is a discovery-driven approach. Mass datasets produced from omics-based studies require experts from different fields to reveal the salient features behind these data. In this review, we summarize omics-driven studies to reveal the virulence features of Yersinia pestis through genomics, trascriptomics, proteomics, interactomics, etc. These studies serve as foundations for further hypothesis-driven research and help us gain insight into Y. pestis pathogenesis.
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Affiliation(s)
- Ruifu Yang
- Beijing Institute of Microbiology and Epidemiology Beijing, China.
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139
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Droniou-Bonzom ME, Cannon PM. A systems biology starter kit for arenaviruses. Viruses 2012; 4:3625-46. [PMID: 23342371 PMCID: PMC3528283 DOI: 10.3390/v4123625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 11/28/2012] [Accepted: 12/05/2012] [Indexed: 12/05/2022] Open
Abstract
Systems biology approaches in virology aim to integrate viral and host biological networks, and thus model the infection process. The growing availability of high-throughput “-omics” techniques and datasets, as well as the ever-increasing sophistication of in silico modeling tools, has resulted in a corresponding rise in the complexity of the analyses that can be performed. The present study seeks to review and organize published evidence regarding virus-host interactions for the arenaviruses, from alterations in the host proteome during infection, to reported protein-protein interactions. In this way, we hope to provide an overview of the interplay between arenaviruses and the host cell, and lay the foundations for complementing current arenavirus research with a systems-level approach.
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Affiliation(s)
- Magali E Droniou-Bonzom
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, Los Angeles, CA 90033, USA.
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140
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Zhou H, Jin J, Wong L. Progress in computational studies of host-pathogen interactions. J Bioinform Comput Biol 2012; 11:1230001. [PMID: 23600809 DOI: 10.1142/s0219720012300018] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Host-pathogen interactions are important for understanding infection mechanism and developing better treatment and prevention of infectious diseases. Many computational studies on host-pathogen interactions have been published. Here, we review recent progress and results in this field and provide a systematic summary, comparison and discussion of computational studies on host-pathogen interactions, including prediction and analysis of host-pathogen protein-protein interactions; basic principles revealed from host-pathogen interactions; and database and software tools for host-pathogen interaction data collection, integration and analysis.
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Affiliation(s)
- Hufeng Zhou
- NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, Singapore 117456, Singapore.
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141
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New horizons for antiviral drug discovery from virus–host protein interaction networks. Curr Opin Virol 2012; 2:606-13. [DOI: 10.1016/j.coviro.2012.09.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/05/2012] [Accepted: 09/05/2012] [Indexed: 12/21/2022]
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142
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Towards an integrated molecular model of plant-virus interactions. Curr Opin Virol 2012; 2:719-24. [PMID: 23017245 DOI: 10.1016/j.coviro.2012.09.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Accepted: 09/07/2012] [Indexed: 11/22/2022]
Abstract
The application in recent years of network theory methods to the study of host-virus interactions is providing a new perspective to the way viruses manipulate the host to promote their own replication. An integrated molecular model of such pathosystems require three detailed maps describing, firstly, the interactions between viral elements, secondly, the interactions between host elements, and thirdly, the cross-interactions between viral and host elements. Here, we compile available information for Potyvirus infecting Arabidopsis thaliana. With an integrated model, it is possible to analyze the mode of virus action and how the perturbation of the virus targets propagates along the network. These studies suggest that viral pathogenicity results not only from the alteration of individual elements but it is a systemic property.
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143
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Solava RW, Michaels RP, Milenkovic T. Graphlet-based edge clustering reveals pathogen-interacting proteins. Bioinformatics 2012; 28:i480-i486. [PMID: 22962470 PMCID: PMC3436803 DOI: 10.1093/bioinformatics/bts376] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
MOTIVATION Prediction of protein function from protein interaction networks has received attention in the post-genomic era. A popular strategy has been to cluster the network into functionally coherent groups of proteins and assign the entire cluster with a function based on functions of its annotated members. Traditionally, network research has focused on clustering of nodes. However, clustering of edges may be preferred: nodes belong to multiple functional groups, but clustering of nodes typically cannot capture the group overlap, while clustering of edges can. Clustering of adjacent edges that share many neighbors was proposed recently, outperforming different node clustering methods. However, since some biological processes can have characteristic 'signatures' throughout the network, not just locally, it may be of interest to consider edges that are not necessarily adjacent. RESULTS We design a sensitive measure of the 'topological similarity' of edges that can deal with edges that are not necessarily adjacent. We cluster edges that are similar according to our measure in different baker's yeast protein interaction networks, outperforming existing node and edge clustering approaches. We apply our approach to the human network to predict new pathogen-interacting proteins. This is important, since these proteins represent drug target candidates. AVAILABILITY Software executables are freely available upon request. CONTACT tmilenko@nd.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- R W Solava
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
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144
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Arnold R, Boonen K, Sun MG, Kim PM. Computational analysis of interactomes: current and future perspectives for bioinformatics approaches to model the host-pathogen interaction space. Methods 2012; 57:508-18. [PMID: 22750305 PMCID: PMC7128575 DOI: 10.1016/j.ymeth.2012.06.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 06/20/2012] [Accepted: 06/21/2012] [Indexed: 11/05/2022] Open
Abstract
Bacterial and viral pathogens affect their eukaryotic host partly by interacting with proteins of the host cell. Hence, to investigate infection from a systems' perspective we need to construct complete and accurate host-pathogen protein-protein interaction networks. Because of the paucity of available data and the cost associated with experimental approaches, any construction and analysis of such a network in the near future has to rely on computational predictions. Specifically, this challenge consists of a number of sub-problems: First, prediction of possible pathogen interactors (e.g. effector proteins) is necessary for bacteria and protozoa. Second, the prospective host binding partners have to be determined and finally, the impact on the host cell analyzed. This review gives an overview of current bioinformatics approaches to obtain and understand host-pathogen interactions. As an application example of the methods covered, we predict host-pathogen interactions of Salmonella and discuss the value of these predictions as a prospective for further research.
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Affiliation(s)
- Roland Arnold
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada M5S 3E1
| | - Kurt Boonen
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada M5S 3E1
| | - Mark G.F. Sun
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada M5S 3E1
| | - Philip M. Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada M5S 3E1
- Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada M5S 3E1
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 3E1
- Department of Computer Science, University of Toronto, Toronto, ON, Canada M5S 3E1
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145
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Rodrigo G, Carrera J, Ruiz-Ferrer V, del Toro FJ, Llave C, Voinnet O, Elena SF. A meta-analysis reveals the commonalities and differences in Arabidopsis thaliana response to different viral pathogens. PLoS One 2012; 7:e40526. [PMID: 22808182 PMCID: PMC3395709 DOI: 10.1371/journal.pone.0040526] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 06/12/2012] [Indexed: 11/19/2022] Open
Abstract
Understanding the mechanisms by which plants trigger host defenses in response to viruses has been a challenging problem owing to the multiplicity of factors and complexity of interactions involved. The advent of genomic techniques, however, has opened the possibility to grasp a global picture of the interaction. Here, we used Arabidopsis thaliana to identify and compare genes that are differentially regulated upon infection with seven distinct (+)ssRNA and one ssDNA plant viruses. In the first approach, we established lists of genes differentially affected by each virus and compared their involvement in biological functions and metabolic processes. We found that phylogenetically related viruses significantly alter the expression of similar genes and that viruses naturally infecting Brassicaceae display a greater overlap in the plant response. In the second approach, virus-regulated genes were contextualized using models of transcriptional and protein-protein interaction networks of A. thaliana. Our results confirm that host cells undergo significant reprogramming of their transcriptome during infection, which is possibly a central requirement for the mounting of host defenses. We uncovered a general mode of action in which perturbations preferentially affect genes that are highly connected, central and organized in modules.
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Affiliation(s)
- Guillermo Rodrigo
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia, València, Spain
| | - Javier Carrera
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia, València, Spain
- Instituto ITACA, Universidad Politécnica de Valencia, València, Spain
| | | | | | - César Llave
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Olivier Voinnet
- Institut de Biologie Moléculaire des Plantes, CNRS, Strasbourg, France
| | - Santiago F. Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia, València, Spain
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- * E-mail:
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146
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Diamond DL, Krasnoselsky AL, Burnum KE, Monroe ME, Webb-Robertson BJ, McDermott JE, Yeh MM, Dzib JFG, Susnow N, Strom S, Proll SC, Belisle SE, Purdy DE, Rasmussen AL, Walters KA, Jacobs JM, Gritsenko MA, Camp DG, Bhattacharya R, Perkins JD, Carithers RL, Liou IW, Larson AM, Benecke A, Waters KM, Smith RD, Katze MG. Proteome and computational analyses reveal new insights into the mechanisms of hepatitis C virus-mediated liver disease posttransplantation. Hepatology 2012; 56:28-38. [PMID: 22331615 PMCID: PMC3387320 DOI: 10.1002/hep.25649] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 01/25/2012] [Indexed: 12/23/2022]
Abstract
UNLABELLED Liver transplant tissues offer the unique opportunity to model the longitudinal protein abundance changes occurring during hepatitis C virus (HCV)-associated liver disease progression in vivo. In this study, our goal was to identify molecular signatures, and potential key regulatory proteins, representative of the processes influencing early progression to fibrosis. We performed global protein profiling analyses on 24 liver biopsy specimens obtained from 15 HCV(+) liver transplant recipients at 6 and/or 12 months posttransplantation. Differentially regulated proteins associated with early progression to fibrosis were identified by analysis of the area under the receiver operating characteristic curve. Analysis of serum metabolites was performed on samples obtained from an independent cohort of 60 HCV(+) liver transplant patients. Computational modeling approaches were applied to identify potential key regulatory proteins of liver fibrogenesis. Among 4,324 proteins identified, 250 exhibited significant differential regulation in patients with rapidly progressive fibrosis. Patients with rapid fibrosis progression exhibited enrichment in differentially regulated proteins associated with various immune, hepatoprotective, and fibrogenic processes. The observed increase in proinflammatory activity and impairment in antioxidant defenses suggests that patients who develop significant liver injury experience elevated oxidative stresses. This was supported by an independent study demonstrating the altered abundance of oxidative stress-associated serum metabolites in patients who develop severe liver injury. Computational modeling approaches further highlight a potentially important link between HCV-associated oxidative stress and epigenetic regulatory mechanisms impacting on liver fibrogenesis. CONCLUSION Our proteome and metabolome analyses provide new insights into the role for increased oxidative stress in the rapid fibrosis progression observed in HCV(+) liver transplant recipients. These findings may prove useful in prognostic applications for predicting early progression to fibrosis.
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Affiliation(s)
- Deborah L. Diamond
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | | | - Kristin E. Burnum
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Matthew E. Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | | | - Jason E. McDermott
- Computational Biology & Bioinformatics, Pacific Northwest National Laboratory, Richland, WA
| | - Matthew M. Yeh
- Dept. of Pathology, University of Washington School of Medicine, Seattle, WA
| | | | - Nathan Susnow
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA
| | - Susan Strom
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA
| | - Sean C. Proll
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - Sarah E. Belisle
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - David E. Purdy
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - Angela L. Rasmussen
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - Kathie-Anne Walters
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - Jon M. Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Marina A. Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - David G. Camp
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Renuka Bhattacharya
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA
| | - James D. Perkins
- Dept. of Surgery, University of Washington School of Medicine, Seattle, WA
| | - Robert L. Carithers
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA
| | - Iris W. Liou
- Institut des Hautes Etudes Scientifiques, CNRS, Bures-sur-Yvette, France
| | - Anne M. Larson
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA
| | - Arndt Benecke
- Institut des Hautes Etudes Scientifiques, CNRS, Bures-sur-Yvette, France
| | - Katrina M. Waters
- Computational Biology & Bioinformatics, Pacific Northwest National Laboratory, Richland, WA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Michael G. Katze
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA,Washington National Primate Research Center, University of Washington, Seattle, WA
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147
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Muller M, Jacob Y, Jones L, Weiss A, Brino L, Chantier T, Lotteau V, Favre M, Demeret C. Large scale genotype comparison of human papillomavirus E2-host interaction networks provides new insights for e2 molecular functions. PLoS Pathog 2012; 8:e1002761. [PMID: 22761572 PMCID: PMC3386243 DOI: 10.1371/journal.ppat.1002761] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 05/04/2012] [Indexed: 11/30/2022] Open
Abstract
Human Papillomaviruses (HPV) cause widespread infections in humans, resulting in latent infections or diseases ranging from benign hyperplasia to cancers. HPV-induced pathologies result from complex interplays between viral proteins and the host proteome. Given the major public health concern due to HPV-associated cancers, most studies have focused on the early proteins expressed by HPV genotypes with high oncogenic potential (designated high-risk HPV or HR-HPV). To advance the global understanding of HPV pathogenesis, we mapped the virus/host interaction networks of the E2 regulatory protein from 12 genotypes representative of the range of HPV pathogenicity. Large-scale identification of E2-interaction partners was performed by yeast two-hybrid screenings of a HaCaT cDNA library. Based on a high-confidence scoring scheme, a subset of these partners was then validated for pair-wise interaction in mammalian cells with the whole range of the 12 E2 proteins, allowing a comparative interaction analysis. Hierarchical clustering of E2-host interaction profiles mostly recapitulated HPV phylogeny and provides clues to the involvement of E2 in HPV infection. A set of cellular proteins could thus be identified discriminating, among the mucosal HPV, E2 proteins of HR-HPV 16 or 18 from the non-oncogenic genital HPV. The study of the interaction networks revealed a preferential hijacking of highly connected cellular proteins and the targeting of several functional families. These include transcription regulation, regulation of apoptosis, RNA processing, ubiquitination and intracellular trafficking. The present work provides an overview of E2 biological functions across multiple HPV genotypes. Over 100 types of human papillomaviruses are responsible for widespread infections in humans. They cause a wide range of pathologies, ranging from inapparent infections to benign lesions, hyperplasia or cancers. Such heterogeneity results from variable interplay among viral and host cell proteins. Aiming to identify specific features that distinguish different pathological genotypes, we mapped the virus-host interaction networks of the regulatory E2 proteins from a set of 12 genotypes representative of HPV diversity. The E2-host interaction profiles recapitulate HPV phylogeny, thus providing a valuable framework for understanding the role of E2 in HPV infection of different pathological traits. The E2 proteins tend to bind to highly connected cellular proteins, indicating a profound effect on the host cell. These interactions predominantly impact on a subset of cellular processes, like transcriptional regulation, apoptosis, RNA metabolism, ubiquitination or intracellular transport. This work improves the global understanding of HPV-associated pathologies, and provides a framework to select interactions that can be used as targets for the development of new therapeutics.
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Affiliation(s)
- Mandy Muller
- Unité de Génétique, Papillomavirus et Cancer Humain (GPCH), Institut Pasteur, Paris, France
- University Paris Diderot, Sorbonne Paris cite, Cellule Pasteur, Paris, France
| | - Yves Jacob
- Unité de Génétique, Papillomavirus et Cancer Humain (GPCH), Institut Pasteur, Paris, France
| | - Louis Jones
- Groupe Logiciels et banques de données, Institut Pasteur, Paris, France
| | | | | | | | | | - Michel Favre
- Unité de Génétique, Papillomavirus et Cancer Humain (GPCH), Institut Pasteur, Paris, France
| | - Caroline Demeret
- Unité de Génétique, Papillomavirus et Cancer Humain (GPCH), Institut Pasteur, Paris, France
- * E-mail:
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148
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Chen TW, Gan RRC, Wu TH, Lin WC, Tang P. VIP DB--a viral protein domain usage and distribution database. Genomics 2012; 100:149-56. [PMID: 22735743 DOI: 10.1016/j.ygeno.2012.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Revised: 06/13/2012] [Accepted: 06/15/2012] [Indexed: 11/19/2022]
Abstract
During the viral infection and replication processes, viral proteins are highly regulated and may interact with host proteins. However, the functions and interaction partners of many viral proteins have yet to be explored. Here, we compiled a VIral Protein domain DataBase (VIP DB) to associate viral proteins with putative functions and interaction partners. We systematically assign domains and infer the functions of proteins and their protein interaction partners from their domain annotations. A total of 2,322 unique domains that were identified from 2,404 viruses are used as a starting point to correlate GO classification, KEGG metabolic pathway annotation and domain-domain interactions. Of the unique domains, 42.7% have GO records, 39.6% have at least one domain-domain interaction record and 26.3% can also be found in either mammals or plants. This database provides a resource to help virologists identify potential roles for viral protein. All of the information is available at http://vipdb.cgu.edu.tw.
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Affiliation(s)
- Ting-Wen Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.
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149
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Abstract
The decoding of the Tritryp reference genomes nearly 7 years ago provided a first peek into the biology of pathogenic trypanosomatids and a blueprint that has paved the way for genome-wide studies. Although 60-70% of the predicted protein coding genes in Trypanosoma brucei, Trypanosoma cruzi and Leishmania major remain unannotated, the functional genomics landscape is rapidly changing. Facilitated by the advent of next-generation sequencing technologies, improved structural and functional annotation and genes and their products are emerging. Information is also growing for the interactions between cellular components as transcriptomes, regulatory networks and metabolomes are characterized, ushering in a new era of systems biology. Simultaneously, the launch of comparative sequencing of multiple strains of kinetoplastids will finally lead to the investigation of a vast, yet to be explored, evolutionary and pathogenomic space.
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Affiliation(s)
- J Choi
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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150
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Schleker S, Garcia-Garcia J, Klein-Seetharaman J, Oliva B. Prediction and comparison of Salmonella-human and Salmonella-Arabidopsis interactomes. Chem Biodivers 2012; 9:991-1018. [PMID: 22589098 PMCID: PMC3407687 DOI: 10.1002/cbdv.201100392] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Salmonellosis caused by Salmonella bacteria is a food-borne disease and a worldwide health threat causing millions of infections and thousands of deaths every year. This pathogen infects an unusually broad range of host organisms including human and plants. A better understanding of the mechanisms of communication between Salmonella and its hosts requires identifying the interactions between Salmonella and host proteins. Protein-protein interactions (PPIs) are the fundamental building blocks of communication. Here, we utilize the prediction platform BIANA to obtain the putative Salmonella-human and Salmonella-Arabidopsis interactomes based on sequence and domain similarity to known PPIs. A gold standard list of Salmonella-host PPIs served to validate the quality of the human model. 24,726 and 10,926 PPIs comprising interactions between 38 and 33 Salmonella effectors and virulence factors with 9,740 human and 4,676 Arabidopsis proteins, respectively, were predicted. Putative hub proteins could be identified, and parallels between the two interactomes were discovered. This approach can provide insight into possible biological functions of so far uncharacterized proteins. The predicted interactions are available via a web interface which allows filtering of the database according to parameters provided by the user to narrow down the list of suspected interactions. The interactions are available via a web interface at http://sbi.imim.es/web/SHIPREC.php.
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Affiliation(s)
- Sylvia Schleker
- Forschungszentrum Jülich, Institute of Complex Systems (ICS-5), 52425 Jülich, Germany
| | - Javier Garcia-Garcia
- Structural Bioinformatics Group (GRIB-IMIM). Universitat Pompeu Fabra. Barcelona Research Park of Biomedicine (PRBB), Barcelona 08003, Catalonia, Spain (phone: +34 933 160 509; fax: +34 933 160 550
| | - Judith Klein-Seetharaman
- Forschungszentrum Jülich, Institute of Complex Systems (ICS-5), 52425 Jülich, Germany
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA (phone: +1 412 383 7325; fax: +1 412 648 8998
| | - Baldo Oliva
- Structural Bioinformatics Group (GRIB-IMIM). Universitat Pompeu Fabra. Barcelona Research Park of Biomedicine (PRBB), Barcelona 08003, Catalonia, Spain (phone: +34 933 160 509; fax: +34 933 160 550
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