Systems biology of pathogen‐host interaction: Networks of protein‐protein interaction within pathogens and pathogen‐human interactions in the post‐genomic era

Tekir, Saliha Durmuş; Ülgen, Kutlu Ö.

doi:10.1002/biot.201200110

Cited by 40 publications

(23 citation statements)

References 121 publications

(218 reference statements)

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“…As most tick proteins are not annotatable using standard computational tools, the use of in silico method to predict PPIs will may of limited use and we may have to rely on classical techniques such as two‐hybrid, pull down assays, antitag‐mediated co‐immunoprecipitation, peptide arrays, large‐scale co‐immunoprecipitation studies and mass spectrometry to initiate the field. For predicting pathogen–host interactions, in silico methods may prove valuable, as supporting large data sets are available to be used as scaffolds .…”

Section: Insight From Tick Protein Evolution: Targeting Of Binding Spmentioning

confidence: 99%

Strategies for new and improved vaccines against ticks and tick‐borne diseases

Fuente

Kopáček

Lew-Tabor

et al. 2016

Parasite Immunology

117

105

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SUMMARYTicks infest a variety of animal species and transmit pathogens causing disease in both humans and animals worldwide. Tick-host-pathogen interactions have evolved through dynamic processes that accommodated the genetic traits of the hosts, pathogens transmitted and the vector tick species that mediate their development and survival. New approaches for tick control are dependent on defining molecular interactions between hosts, ticks and pathogens to allow for discovery of key molecules that could be tested in vaccines or new generation therapeutics for intervention of tick-pathogen cycles. Currently, tick vaccines constitute an effective and environmentally sound approach for the control of ticks and the transmission of the associated tick-borne diseases. New candidate protective antigens will most likely be identified by focusing on proteins with relevant biological function in the feeding, reproduction, development, immune response, subversion of host immunity of the tick vector and/ or molecules vital for pathogen infection and transmission. This review addresses different approaches and strategies used for the discovery of protective antigens, including focusing on relevant tick biological functions and proteins, reverse genetics, vaccinomics and tick protein evolution and interactomics. New and improved tick vaccines will most likely contain multiple antigens to control tick infestations and pathogen infection and transmission.

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Section: Insight From Tick Protein Evolution: Targeting Of Binding Spmentioning

confidence: 99%

Strategies for new and improved vaccines against ticks and tick‐borne diseases

Fuente

Kopáček

Lew-Tabor

et al. 2016

Parasite Immunology

117

105

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“…Although these single-species studies have provided insights into the pathogenic and defensive mechanisms for host-pathogen interactions, they did not give clues about interspecies functional associations between host and pathogen. Detailed knowledge of host-pathogen protein interactions may enable us to comprehend the mechanisms of infection and to identify better strategies to prevent or cure infection [47]. Accordingly, in this study, we developed a computational framework to efficiently construct the interspecies PPI network focusing on the characterization of interspecies interactions between host and pathogen.…”

Section: Discussionmentioning

confidence: 99%

Interspecies protein-protein interaction network construction for characterization of host-pathogen interactions: a Candida albicans-zebrafish interaction study

et al. 2013

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BackgroundDespite clinical research and development in the last decades, infectious diseases remain a top global problem in public health today, being responsible for millions of morbidities and mortalities each year. Therefore, many studies have sought to investigate host-pathogen interactions from various viewpoints in attempts to understand pathogenic and defensive mechanisms, which could help control pathogenic infections. However, most of these efforts have focused predominately on the host or the pathogen individually rather than on a simultaneous analysis of both interaction partners.ResultsIn this study, with the help of simultaneously quantified time-course Candida albicans-zebrafish interaction transcriptomics and other omics data, a computational framework was developed to construct the interspecies protein-protein interaction (PPI) network for C. albicans-zebrafish interactions based on the inference of ortholog-based PPIs and the dynamic modeling of regulatory responses. The identified C. albicans-zebrafish interspecies PPI network highlights the association between C. albicans pathogenesis and the zebrafish redox process, indicating that redox status is critical in the battle between the host and pathogen.ConclusionsAdvancing from the single-species network construction method, the interspecies network construction approach allows further characterization and elucidation of the host-pathogen interactions. With continued accumulation of interspecies transcriptomics data, the proposed method could be used to explore progressive network rewiring over time, which could benefit the development of network medicine for infectious diseases.

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“…Even among highly connected proteins (degree k>5) in the human interactome, the degree of virus targets was twice as large as those of nontargeted proteins. Independent analyses found that viral proteins preferably target human host proteins that are involved in a large number of interactions [14,49,50,[54][55][56][57][58][59][60]. As the number of interactions is a local measure of centrality, other more global measures of centrality were considered as well.…”

Section: What Are the Protein Targets Of Human Viruses?mentioning

confidence: 99%

“…Indeed, various viruses target human host proteins with high betweenness centrality. As a corollary, such central proteins also have significantly shorter paths to other proteins [14,49,50,[54][55][56][57][58][59][60], as well as participate in a higher number of pathways and protein complexes [61]. Furthermore, topological analyses of revealed that human host proteins that were targeted by viruses are strongly connected among each other [61].…”

Section: What Are the Protein Targets Of Human Viruses?mentioning

confidence: 99%

Protein-protein interactions of human viruses

Goodacre

Devkota

Bae

et al. 2020

Seminars in Cell & Developmental Biology

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Viruses infect their human hosts by a series of interactions between viral and host proteins, indicating that detailed knowledge of such virus-host interaction interfaces are critical for our understanding of viral infection mechanisms, disease etiology and the development of new drugs. In this review, we primarily survey human host-virus interaction data that are available from public databases following the standardized PSI-MS format. Notably, available host-virus protein interaction information is strongly biased toward a small number of virus families including herpesviridae, papillomaviridae, orthomyxoviridae and retroviridae. While we explore the reliability and relevance of these protein interactions we also survey the current knowledge about viruses functional and topological targets. Furthermore, we assess emerging frontiers of host-virus protein interaction research, focusing on protein interaction interfaces of hosts that are infected by different viruses and viruses that infect multiple hosts. Finally, we cover the current status of research that investigates the relationships of virus-targeted host proteins to other comorbidities as well as the influence of host-virus protein interactions on human metabolism.

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Systems biology of pathogen‐host interaction: Networks of protein‐protein interaction within pathogens and pathogen‐human interactions in the post‐genomic era

Cited by 40 publications

References 121 publications

Strategies for new and improved vaccines against ticks and tick‐borne diseases

Strategies for new and improved vaccines against ticks and tick‐borne diseases

Interspecies protein-protein interaction network construction for characterization of host-pathogen interactions: a Candida albicans-zebrafish interaction study

Protein-protein interactions of human viruses

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