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Chandrasekharan G, Unnikrishnan M. High throughput methods to study protein-protein interactions during host-pathogen interactions. Eur J Cell Biol 2024; 103:151393. [PMID: 38306772 DOI: 10.1016/j.ejcb.2024.151393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 02/04/2024] Open
Abstract
The ability of a pathogen to survive and cause an infection is often determined by specific interactions between the host and pathogen proteins. Such interactions can be both intra- and extracellular and may define the outcome of an infection. There are a range of innovative biochemical, biophysical and bioinformatic techniques currently available to identify protein-protein interactions (PPI) between the host and the pathogen. However, the complexity and the diversity of host-pathogen PPIs has led to the development of several high throughput (HT) techniques that enable the study of multiple interactions at once and/or screen multiple samples at the same time, in an unbiased manner. We review here the major HT laboratory-based technologies employed for host-bacterial interaction studies.
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Affiliation(s)
| | - Meera Unnikrishnan
- Division of Biomedical Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom.
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2
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Gomaa AE, El Mounadi K, Parperides E, Garcia-Ruiz H. Cell Fractionation and the Identification of Host Proteins Involved in Plant-Virus Interactions. Pathogens 2024; 13:53. [PMID: 38251360 PMCID: PMC10819628 DOI: 10.3390/pathogens13010053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/23/2024] Open
Abstract
Plant viruses depend on host cellular factors for their replication and movement. There are cellular proteins that change their localization and/or expression and have a proviral role or antiviral activity and interact with or target viral proteins. Identification of those proteins and their roles during infection is crucial for understanding plant-virus interactions and to design antiviral resistance in crops. Important host proteins have been identified using approaches such as tag-dependent immunoprecipitation or yeast two hybridization that require cloning individual proteins or the entire virus. However, the number of possible interactions between host and viral proteins is immense. Therefore, an alternative method is needed for proteome-wide identification of host proteins involved in host-virus interactions. Here, we present cell fractionation coupled with mass spectrometry as an option to identify protein-protein interactions between viruses and their hosts. This approach involves separating subcellular organelles using differential and/or gradient centrifugation from virus-free and virus-infected cells (1) followed by comparative analysis of the proteomic profiles obtained for each subcellular organelle via mass spectrometry (2). After biological validation, prospect host proteins with proviral or antiviral roles can be subject to fundamental studies in the context of basic biology to shed light on both virus replication and cellular processes. They can also be targeted via gene editing to develop virus-resistant crops.
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Affiliation(s)
- Amany E. Gomaa
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA (E.P.)
- Department of Botany, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
| | - Kaoutar El Mounadi
- Department of Biology, Kutztown University of Pennsylvania, Kutztown, PA 19530, USA
| | - Eric Parperides
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA (E.P.)
| | - Hernan Garcia-Ruiz
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA (E.P.)
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3
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Selvaraj C, Shri GR, Vijayakumar R, Alothaim AS, Ramya S, Singh SK. Viral hijacking mechanism in humans through protein-protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 131:261-276. [PMID: 35871893 DOI: 10.1016/bs.apcsb.2022.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Numerous viruses have evolved mechanisms to inhibit or alter the host cell's apoptotic response as part of their coevolution with their hosts. The analysis of virus-host protein interactions require an in-depth understanding of both the viral and host protein structures and repertoires, as well as evolutionary mechanisms and pertinent biological facts. Throughout the course of a viral infection, there is constant battle for binding between virus and cellular proteins. Exogenous interfaces facilitating viral-host interactions are well known for constantly targeting and suppressing endogenous interfaces mediating intraspecific interactions, such as viral-viral and host-host connections. In these interactions, the protein-protein interactions (PPIs), are mostly shown as networks (protein interaction networks, PINs), with proteins represented as nodes and their interactions represented as edges. Host proteins with a higher degree of connectivity are more likely to interact with viral proteins. Due to technical advancements, three-dimensional interactions may now be visualized computationally utilizing molecular modeling and cryo-EM approaches. The uniqueness of viral domain repertoires, their evolution, and their activities during viral infection make viruses fascinating models for research. This chapter aims to provide readers a complete picture of the viral hijacking mechanism in protein-protein interactions.
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Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
| | - Gurunathan Rubha Shri
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Rajendran Vijayakumar
- Department of Biology, College of Science in Zulfi, Majmaah University, Majmaah, Saudi Arabia
| | - Abdulaziz S Alothaim
- Department of Biology, College of Science in Zulfi, Majmaah University, Majmaah, Saudi Arabia
| | - Saravanan Ramya
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
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Du X, Zhou D, Zhou J, Xue J, Cheng Z. Marek's Disease Virus and Reticuloendotheliosis Virus Coinfection Enhances Viral Replication and Alters Cellular Protein Profiles. Front Vet Sci 2022; 9:854007. [PMID: 35392111 PMCID: PMC8981388 DOI: 10.3389/fvets.2022.854007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/08/2022] [Indexed: 12/12/2022] Open
Abstract
Coinfection with Marek's disease virus (MDV) and reticuloendotheliosis virus (REV) causes synergistic pathogenic effects and serious losses to the poultry industry. However, whether there is a synergism between the two viruses in viral replication and the roles of host factors in regulating MDV and REV coinfection remains elusive. In this study, we found that MDV and REV coinfection increased viral replication in coinfected cells as compared to a single infection in a limited period. Further, we explore the host cell responses to MDV and REV coinfection using tandem mass tag (TMT) peptide labeling coupled with liquid chromatography–tandem mass spectrometry (LC-MS/MS). Compared with MDV/REV-infected cells, 38 proteins increased (fold change > 1.2) and 60 decreased (fold change < 0.83) their abundance in MDV and REV coinfected cells. Differentially accumulated proteins (DAPs) were involved in important biological processes involved in the immune system process, cell adhesion and migration, cellular processes, and multicellular organismal systems. STRING analysis found that IRF7, MX1, TIMP3, and AKT1 may be associated with MDV and REV synergistic replication in chicken embryo fibroblasts (CEFs). Western blotting analysis showed that the selected DAPs were identical to the quantitative proteomics data. Taken together, we verified that MDV and REV can synergistically replicate in coinfected cells and revealed the host molecules involved in it. However, the synergistic pathogenesis of MDV and REV needs to be further studied.
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Abstract
Coinfections involving viruses are being recognized to influence the disease pattern that occurs relative to that with single infection. Classically, we usually think of a clinical syndrome as the consequence of infection by a single virus that is isolated from clinical specimens. However, this biased laboratory approach omits detection of additional agents that could be contributing to the clinical outcome, including novel agents not usually considered pathogens. The presence of an additional agent may also interfere with the targeted isolation of a known virus. Viral interference, a phenomenon where one virus competitively suppresses replication of other coinfecting viruses, is the most common outcome of viral coinfections. In addition, coinfections can modulate virus virulence and cell death, thereby altering disease severity and epidemiology. Immunity to primary virus infection can also modulate immune responses to subsequent secondary infections. In this review, various virological mechanisms that determine viral persistence/exclusion during coinfections are discussed, and insights into the isolation/detection of multiple viruses are provided. We also discuss features of heterologous infections that impact the pattern of immune responsiveness that develops.
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He X, Jiang HW, Chen H, Zhang HN, Liu Y, Xu ZW, Wu FL, Guo SJ, Hou JL, Yang MK, Yan W, Deng JY, Bi LJ, Zhang XE, Tao SC. Systematic Identification of Mycobacterium tuberculosis Effectors Reveals that BfrB Suppresses Innate Immunity. Mol Cell Proteomics 2017; 16:2243-2253. [PMID: 29018126 DOI: 10.1074/mcp.ra117.000296] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Indexed: 12/14/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) has evolved multiple strategies to counter the human immune system. The effectors of Mtb play important roles in the interactions with the host. However, because of the lack of highly efficient strategies, there are only a handful of known Mtb effectors, thus hampering our understanding of Mtb pathogenesis. In this study, we probed Mtb proteome microarray with biotinylated whole-cell lysates of human macrophages, identifying 26 Mtb membrane proteins and secreted proteins that bind to macrophage proteins. Combining GST pull-down with mass spectroscopy then enabled the specific identification of all binders. We refer to this proteome microarray-based strategy as SOPHIE (Systematic unlOcking of Pathogen and Host Interacting Effectors). Detailed investigation of a novel effector identified here, the iron storage protein BfrB (Rv3841), revealed that BfrB inhibits NF-κB-dependent transcription through binding and reducing the nuclear abundance of the ribosomal protein S3 (RPS3), which is a functional subunit of NF- κB. The importance of this interaction was evidenced by the promotion of survival in macrophages of the mycobacteria, Mycobacterium smegmatis, by overexpression of BfrB. Thus, beyond demonstrating the power of SOPHIE in the discovery of novel effectors of human pathogens, we expect that the set of Mtb effectors identified in this work will greatly facilitate the understanding of the pathogenesis of Mtb, possibly leading to additional potential molecular targets in the battle against tuberculosis.
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Affiliation(s)
- Xiang He
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China.,§School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - He-Wei Jiang
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong Chen
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Nan Zhang
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yin Liu
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhao-Wei Xu
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fan-Lin Wu
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shu-Juan Guo
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing-Li Hou
- ¶Instrumental Analysis Center of Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ming-Kun Yang
- ‖Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wei Yan
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiao-Yu Deng
- **State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Li-Jun Bi
- ‡‡National Key Laboratory of Biomacromolecules, Key Laboratory of Non-Coding; RNA and Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,§§School of Stomatology and Medicine, Foshan University, Foshan 528000, Guangdong Province, China
| | - Xian-En Zhang
- ‡‡National Key Laboratory of Biomacromolecules, Key Laboratory of Non-Coding; RNA and Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sheng-Ce Tao
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China; .,§School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.,¶¶State Key Laboratory of Oncogenes and Related Genes, Shanghai 200240, China
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Uddin R, Tariq SS, Azam SS, Wadood A, Moin ST. Identification of Histone Deacetylase (HDAC) as a drug target against MRSA via interolog method of protein-protein interaction prediction. Eur J Pharm Sci 2017; 106:198-211. [PMID: 28591562 DOI: 10.1016/j.ejps.2017.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 05/15/2017] [Accepted: 06/02/2017] [Indexed: 12/27/2022]
Abstract
Patently, Protein-Protein Interactions (PPIs) lie at the core of significant biological functions and make the foundation of host-pathogen relationships. Hence, the current study is aimed to use computational biology techniques to predict host-pathogen Protein-Protein Interactions (HP-PPIs) between MRSA and Humans as potential drug targets ultimately proposing new possible inhibitors against them. As a matter of fact this study is based on the Interolog method which implies that homologous proteins retain their ability to interact. A distant homolog approach based on Interolog method was employed to speculate MRSA protein homologs in Humans using PSI-BLAST. In addition the protein interaction partners of these homologs as listed in Database of Interacting Proteins (DIP) were predicted to interact with MRSA as well. Moreover, a direct approach using BLAST was also applied so as to attain further confidence in the strategy. Consequently, the common HP-PPIs predicted by both approaches are suggested as potential drug targets (22%) whereas, the unique HP-PPIs estimated only through distant homolog approach are presented as novel drug targets (12%). Furthermore, the most repeated entry in our results was found to be MRSA Histone Deacetylase (HDAC) which was then modeled using SWISS-MODEL. Eventually, small molecules from ZINC, selected randomly, were docked against HDAC using Auto Dock and are suggested as potential binders (inhibitors) based on their energetic profiles. Thus the current study provides basis for further in-depth analysis of such data which not only include MRSA but other deadly pathogens as well.
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Affiliation(s)
- Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan.
| | - Syeda Sumayya Tariq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan
| | - Syed Sikander Azam
- National Centre for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Syed Tarique Moin
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan
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8
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Human enterovirus 71 protein interaction network prompts antiviral drug repositioning. Sci Rep 2017; 7:43143. [PMID: 28220872 PMCID: PMC5318855 DOI: 10.1038/srep43143] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 01/19/2017] [Indexed: 12/28/2022] Open
Abstract
As a predominant cause of human hand, foot, and mouth disease, enterovirus 71 (EV71) infection may lead to serious diseases and result in severe consequences that threaten public health and cause widespread panic. Although the systematic identification of physical interactions between viral proteins and host proteins provides initial information for the recognition of the cellular mechanism involved in viral infection and the development of new therapies, EV71-host protein interactions have not been explored. Here, we identified interactions between EV71 proteins and host cellular proteins and confirmed the functional relationships of EV71-interacting proteins (EIPs) with virus proliferation and infection by integrating a human protein interaction network and by functional annotation. We found that most EIPs had known interactions with other viruses. We also predicted ATP6V0C as a broad-spectrum essential host factor and validated its essentiality for EV71 infection in vitro. EIPs and their interacting proteins were more likely to be targets of anti-inflammatory and neurological drugs, indicating their potential to serve as host-oriented antiviral targets. Thus, we used a connectivity map to find drugs that inhibited EIP expression. We predicted tanespimycin as a candidate and demonstrated its antiviral efficiency in vitro. These findings provide the first systematic identification of EV71-host protein interactions, an analysis of EIP protein characteristics and a demonstration of their value in developing host-oriented antiviral therapies.
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9
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In Silico Designing and Analysis of Inhibitors against Target Protein Identified through Host-Pathogen Protein Interactions in Malaria. INTERNATIONAL JOURNAL OF MEDICINAL CHEMISTRY 2016; 2016:2741038. [PMID: 27057354 PMCID: PMC4739458 DOI: 10.1155/2016/2741038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/13/2015] [Accepted: 11/17/2015] [Indexed: 01/20/2023]
Abstract
Malaria, a life-threatening blood disease, has been a major concern in the field of healthcare. One of the severe forms of malaria is caused by the parasite Plasmodium falciparum which is initiated through protein interactions of pathogen with the host proteins. It is essential to analyse the protein-protein interactions among the host and pathogen for better understanding of the process and characterizing specific molecular mechanisms involved in pathogen persistence and survival. In this study, a complete protein-protein interaction network of human host and Plasmodium falciparum has been generated by integration of the experimental data and computationally predicting interactions using the interolog method. The interacting proteins were filtered according to their biological significance and functional roles. α-tubulin was identified as a potential protein target and inhibitors were designed against it by modification of amiprophos methyl. Docking and binding affinity analysis showed two modified inhibitors exhibiting better docking scores of −10.5 kcal/mol and −10.43 kcal/mol and an improved binding affinity of −83.80 kJ/mol and −98.16 kJ/mol with the target. These inhibitors can further be tested and validated in vivo for their properties as an antimalarial drug.
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10
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Yang R, Motin VL. Yersinia pestis in the Age of Big Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 918:257-272. [PMID: 27722866 DOI: 10.1007/978-94-024-0890-4_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
Abstract
As omics-driven technologies developed rapidly, genomics, transcriptomics, proteomics, metabolomics and other omics-based data have been accumulated in unprecedented speed. Omics-driven big data in biology have changed our way of research. "Big science" has promoted our understanding of biology in a holistic overview that is impossibly achieved by traditional hypothesis-driven research. In this chapter, we gave an overview of omics-driven research on Y. pestis, provided a way of thinking on Yersinia pestis research in the age of big data, and made some suggestions to integrate omics-based data for systems understanding of Y. pestis.
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Affiliation(s)
- Ruifu Yang
- Beijing Institute of Microbiology and Epidemiology, No. Dongdajie, Fengtai, Beijing, 100071, China.
| | - Vladimir L Motin
- Departments of Pathology and Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
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Calderone A, Licata L, Cesareni G. VirusMentha: a new resource for virus-host protein interactions. Nucleic Acids Res 2014; 43:D588-92. [PMID: 25217587 PMCID: PMC4384001 DOI: 10.1093/nar/gku830] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Viral infections often cause diseases by perturbing several cellular processes in the infected host. Viral proteins target host proteins and either form new complexes or modulate the formation of functional host complexes. Describing and understanding the perturbation of the host interactome following viral infection is essential for basic virology and for the development of antiviral therapies. In order to provide a general overview of such interactions, a few years ago we developed VirusMINT. We have now extended the scope and coverage of VirusMINT and established VirusMentha, a new virus-virus and virus-host interaction resource build on the detailed curation protocols of the IMEx consortium and on the integration strategies developed for mentha. VirusMentha is regularly and automatically updated every week by capturing, via the PSICQUIC protocol, interactions curated by five different databases that are part of the IMEx consortium. VirusMentha can be freely browsed at http://virusmentha.uniroma2.it/ and its complete data set is available for download.
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Affiliation(s)
| | - Luana Licata
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Gianni Cesareni
- Department of Biology, University of Rome Tor Vergata, Rome, Italy Fondazione Santa Lucia Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
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Bailer SM, Lieber D. A high-throughput yeast two-hybrid protocol to determine virus-host protein interactions. Methods Mol Biol 2014; 1064:1-15. [PMID: 23996246 PMCID: PMC7122120 DOI: 10.1007/978-1-62703-601-6_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The yeast two-hybrid (Y2H) system is a powerful method to identify and analyze binary protein interactions. In the field of virology, the Y2H system has significantly increased our knowledge of structure and function of viral proteins by systematically assessing intraviral protein interactions. Several comprehensive approaches to determine virus-host interactions have provided insight into viral strategies to manipulate the host for efficient replication and to escape host-derived countermeasures. To expand our knowledge of intraviral and virus-host protein interactions, we here present a Y2H protocol that is well suited for high-throughput screening. Yeast mating followed by liquid handling in a 96-well format as well as fluorescent readout of the reporter system provides a highly standardized and fully automated screening situation. The protocol can either be applied to screen complex host cDNA libraries or protein pairs arrayed for cross-testing. The ease of use, the cost-effectiveness as well as the robotic handling allows for extensive and multiple rounds of screening providing high coverage of protein-protein interactions. Thus, this protocol represents an improved "deep" screening method for high-throughput Y2H assays.
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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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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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14
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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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15
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Braun P, Aubourg S, Van Leene J, De Jaeger G, Lurin C. Plant protein interactomes. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:161-87. [PMID: 23330791 DOI: 10.1146/annurev-arplant-050312-120140] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Protein-protein interactions are a critical element of biological systems, and the analysis of interaction partners can provide valuable hints about unknown functions of a protein. In recent years, several large-scale protein interaction studies have begun to unravel the complex networks through which plant proteins exert their functions. Two major classes of experimental approaches are used for protein interaction mapping: analysis of direct interactions using binary methods such as yeast two-hybrid or split ubiquitin, and analysis of protein complexes through affinity purification followed by mass spectrometry. In addition, bioinformatics predictions can suggest interactions that have evaded detection by other methods or those of proteins that have not been investigated. Here we review the major approaches to construct, analyze, use, and carry out quality control on plant protein interactome networks. We present experimental and computational approaches for large-scale mapping, methods for validation or smaller-scale functional studies, important bioinformatics resources, and findings from recently published large-scale plant interactome network maps.
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Affiliation(s)
- Pascal Braun
- Department of Plant Systems Biology, Center for Life and Food Sciences Weihenstephan, Technische Universität München (TUM), 85354 Freising-Weihenstephan, Germany.
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Braun P. Interactome mapping for analysis of complex phenotypes: insights from benchmarking binary interaction assays. Proteomics 2012; 12:1499-518. [PMID: 22589225 DOI: 10.1002/pmic.201100598] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Protein interactions mediate essentially all biological processes and analysis of protein-protein interactions using both large-scale and small-scale approaches has contributed fundamental insights to the understanding of biological systems. In recent years, interactome network maps have emerged as an important tool for analyzing and interpreting genetic data of complex phenotypes. Complementary experimental approaches to test for binary, direct interactions, and for membership in protein complexes are used to explore the interactome. The two approaches are not redundant but yield orthogonal perspectives onto the complex network of physical interactions by which proteins mediate biological processes. In recent years, several publications have demonstrated that interactions from high-throughput experiments can be equally reliable as the high quality subset of interactions identified in small-scale studies. Critical for this insight was the introduction of standardized experimental benchmarking of interaction and validation assays using reference sets. The data obtained in these benchmarking experiments have resulted in greater appreciation of the limitations and the complementary strengths of different assays. Moreover, benchmarking is a central element of a conceptual framework to estimate interactome sizes and thereby measure progress toward near complete network maps. These estimates have revealed that current large-scale data sets, although often of high quality, cover only a small fraction of a given interactome. Here, I review the findings of assay benchmarking and discuss implications for quality control, and for strategies toward obtaining a near-complete map of the interactome of an organism.
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Affiliation(s)
- Pascal Braun
- Department of Plant Systems Biology, Center of Life and Food Sciences, Technische Universität München, Freising, Germany.
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Leptospiral outer membrane protein microarray, a novel approach to identification of host ligand-binding proteins. J Bacteriol 2012; 194:6074-87. [PMID: 22961849 DOI: 10.1128/jb.01119-12] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Leptospirosis is a zoonosis with worldwide distribution caused by pathogenic spirochetes belonging to the genus Leptospira. The leptospiral life cycle involves transmission via freshwater and colonization of the renal tubules of their reservoir hosts. Infection requires adherence to cell surfaces and extracellular matrix components of host tissues. These host-pathogen interactions involve outer membrane proteins (OMPs) expressed on the bacterial surface. In this study, we developed an Leptospira interrogans serovar Copenhageni strain Fiocruz L1-130 OMP microarray containing all predicted lipoproteins and transmembrane OMPs. A total of 401 leptospiral genes or their fragments were transcribed and translated in vitro and printed on nitrocellulose-coated glass slides. We investigated the potential of this protein microarray to screen for interactions between leptospiral OMPs and fibronectin (Fn). This approach resulted in the identification of the recently described fibronectin-binding protein, LIC10258 (MFn8, Lsa66), and 14 novel Fn-binding proteins, denoted Microarray Fn-binding proteins (MFns). We confirmed Fn binding of purified recombinant LIC11612 (MFn1), LIC10714 (MFn2), LIC11051 (MFn6), LIC11436 (MFn7), LIC10258 (MFn8, Lsa66), and LIC10537 (MFn9) by far-Western blot assays. Moreover, we obtained specific antibodies to MFn1, MFn7, MFn8 (Lsa66), and MFn9 and demonstrated that MFn1, MFn7, and MFn9 are expressed and surface exposed under in vitro growth conditions. Further, we demonstrated that MFn1, MFn4 (LIC12631, Sph2), and MFn7 enable leptospires to bind fibronectin when expressed in the saprophyte, Leptospira biflexa. Protein microarrays are valuable tools for high-throughput identification of novel host ligand-binding proteins that have the potential to play key roles in the virulence mechanisms of pathogens.
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Mapping of Chikungunya virus interactions with host proteins identified nsP2 as a highly connected viral component. J Virol 2012; 86:3121-34. [PMID: 22258240 DOI: 10.1128/jvi.06390-11] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that has been responsible for an epidemic outbreak of unprecedented magnitude in recent years. Since then, significant efforts have been made to better understand the biology of this virus, but we still have poor knowledge of CHIKV interactions with host cell components at the molecular level. Here we describe the extensive use of high-throughput yeast two-hybrid (HT-Y2H) assays to characterize interactions between CHIKV and human proteins. A total of 22 high-confidence interactions, which essentially involved the viral nonstructural protein nsP2, were identified and further validated in protein complementation assay (PCA). These results were integrated to a larger network obtained by extensive mining of the literature for reports on alphavirus-host interactions. To investigate the role of cellular proteins interacting with nsP2, gene silencing experiments were performed in cells infected by a recombinant CHIKV expressing Renilla luciferase as a reporter. Collected data showed that heterogeneous nuclear ribonucleoprotein K (hnRNP-K) and ubiquilin 4 (UBQLN4) participate in CHIKV replication in vitro. In addition, we showed that CHIKV nsP2 induces a cellular shutoff, as previously reported for other Old World alphaviruses, and determined that among binding partners identified by yeast two-hybrid methods, the tetratricopeptide repeat protein 7B (TTC7B) plays a significant role in this activity. Altogether, this report provides the first interaction map between CHIKV and human proteins and describes new host cell proteins involved in the replication cycle of this virus.
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Wang X, Gulbahce N, Yu H. Network-based methods for human disease gene prediction. Brief Funct Genomics 2011; 10:280-93. [PMID: 21764832 DOI: 10.1093/bfgp/elr024] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Despite the considerable progress in disease gene discovery, we are far from uncovering the underlying cellular mechanisms of diseases since complex traits, even many Mendelian diseases, cannot be explained by simple genotype-phenotype relationships. More recently, an increasingly accepted view is that human diseases result from perturbations of cellular systems, especially molecular networks. Genes associated with the same or similar diseases commonly reside in the same neighborhood of molecular networks. Such observations have built the basis for a large collection of computational approaches to find previously unknown genes associated with certain diseases. The majority of the methods are based on protein interactome networks, with integration of other large-scale genomic data or disease phenotype information, to infer how likely it is that a gene is associated with a disease. Here, we review recent, state of the art, network-based methods used for prioritizing disease genes as well as unraveling the molecular basis of human diseases.
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Affiliation(s)
- Xiujuan Wang
- Department of Biological Statistics and Computational Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850, USA
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20
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Zhou S, Liu R, Zhao X, Huang C, Wei Y. Viral proteomics: the emerging cutting-edge of virus research. SCIENCE CHINA-LIFE SCIENCES 2011; 54:502-12. [PMID: 21706410 PMCID: PMC7089374 DOI: 10.1007/s11427-011-4177-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Accepted: 12/03/2010] [Indexed: 11/21/2022]
Abstract
Viruses replicate and proliferate in host cells while continuously adjusting to and modulating the host environment. They encode a wide spectrum of multifunctional proteins, which interplay with and modify proteins in host cells. Viral genomes were chronologically the first to be sequenced. However, the corresponding viral proteomes, the alterations of host proteomes upon viral infection, and the dynamic nature of proteins, such as post-translational modifications, enzymatic cleavage, and activation or destruction by proteolysis, remain largely unknown. Emerging high-throughput techniques, in particular quantitative or semi-quantitative mass spectrometry-based proteomics analysis of viral and cellular proteomes, have been applied to define viruses and their interactions with their hosts. Here, we review the major areas of viral proteomics, including virion proteomics, structural proteomics, viral protein interactomics, and changes to the host cell proteome upon viral infection.
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Affiliation(s)
- ShengTao Zhou
- Department of Gynecology and Obstetrics, West China Second Hospital, Sichuan University, Chengdu, China
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Vidal M, Cusick ME, Barabási AL. Interactome networks and human disease. Cell 2011; 144:986-98. [PMID: 21414488 DOI: 10.1016/j.cell.2011.02.016] [Citation(s) in RCA: 1117] [Impact Index Per Article: 85.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 02/07/2011] [Accepted: 02/09/2011] [Indexed: 02/06/2023]
Abstract
Complex biological systems and cellular networks may underlie most genotype to phenotype relationships. Here, we review basic concepts in network biology, discussing different types of interactome networks and the insights that can come from analyzing them. We elaborate on why interactome networks are important to consider in biology, how they can be mapped and integrated with each other, what global properties are starting to emerge from interactome network models, and how these properties may relate to human disease.
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Affiliation(s)
- Marc Vidal
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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22
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Detecting protein-protein interactions in vesicular stomatitis virus using a cytoplasmic yeast two hybrid system. J Virol Methods 2011; 173:203-12. [PMID: 21320532 DOI: 10.1016/j.jviromet.2011.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 02/03/2011] [Accepted: 02/07/2011] [Indexed: 12/18/2022]
Abstract
Protein-protein interactions play an important role in many virus-encoded functions and in virus-host interactions. While a "classical" yeast two-hybrid system (Y2H) is one of the most common techniques to detect such interactions, it has a number of limitations, including a requirement for the proteins of interest to be relocated to the nucleus. Modified Y2H, such as the Sos recruitment system (SRS), which detect interactions occurring in the cytoplasm rather than the nucleus, allow proteins from viruses replicating in the cytoplasm to be tested in a more natural context. In this study, a SRS was used to detect interactions involving proteins from vesicular stomatitis virus (VSV), a prototypic non-segmented negative strand RNA (NNS) virus. All five full-length VSV proteins, as well as several truncated proteins, were screened against each other. Using the SRS, most interactions demonstrated previously involving VSV phosphoprotein, nucleocapsid (N) and large polymerase proteins were confirmed independently, while difficulties were encountered using the membrane associated matrix and glycoproteins. A human cDNA library was also screened against VSV N protein and one cellular protein, SFRS18, was identified which interacted with N in this context. The system presented can be redesigned easily for studies in other less tractable NNS viruses.
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Min BE, Martin K, Wang R, Tafelmeyer P, Bridges M, Goodin M. A host-factor interaction and localization map for a plant-adapted rhabdovirus implicates cytoplasm-tethered transcription activators in cell-to-cell movement. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2010; 23:1420-32. [PMID: 20923350 DOI: 10.1094/mpmi-04-10-0097] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
To identify host factors that play critical roles in processes, including cell-to-cell movement of plant-adapted rhabdoviruses, we constructed and validated a high-resolution Nicotiana benthamiana yeast two-hybrid library. The library was screened with the putative movement protein (sc4), nucleocapsid (N), and matrix (M) proteins of Sonchus yellow net virus (SYNV). This resulted in identification of 31 potential host factors. Steady-state localization studies using autofluorescent protein fusions to full-length clones of interactors were conducted in transgenic N. benthamiana marker lines. Bimolecular fluorescence complementation assays were used to validate two-hybrid interactions. The sc4 interactor, sc4i21, localized to microtubules. The N interactor, Ni67, localized to punctuate loci on the endoplasmic reticulum. These two proteins are 84% identical homologues of the Arabidopsis phloem-associated transcription activator AtVOZ1, and contain functional nuclear localization signals. Sc4i17 is a microtubule-associated motor protein. The M interactor, Mi7, is a nuclear-localized transcription factor. Combined with a binary interaction map for SYNV proteins, our data support a model in which the SYNV nucleocapsids are exported from the nucleus and moved cell-to-cell by transcription activators tethered in the cytoplasm.
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Affiliation(s)
- Byoung-Eun Min
- Department of Plant Pathology, University of Kentucky, Lexington 40546, USA
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Werner T. Next generation sequencing in functional genomics. Brief Bioinform 2010; 11:499-511. [PMID: 20501549 DOI: 10.1093/bib/bbq018] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Genome-wide sequencing has enabled modern biomedical research to relate more and more events in healthy as well as disease-affected cells and tissues to the genomic sequence. Now next generation sequencing (NGS) extends that reach into multiple almost complete genomes of the same species, revealing more and more details about how individual genomes as well as individual aspects of their regulation differ from each other. The inclusion of NGS-based transcriptome sequencing, chromatin-immunoprecipitation (ChIP) of transcription factor binding and epigenetic analyses (usually based on DNA methylation or histone modification ChIP) completes the picture with unprecedented resolution enabling the detection of even subtle differences such as alternative splicing of individual exons. Functional genomics aims at the elucidation of the molecular basis of biological functions and requires analyses that go far beyond the primary analysis of the reads such as mapping to a genome template sequence. The various and complex interactions between the genome, gene products and metabolites define biological function, which necessitates inclusion of results other than sequence tags in quite elaborative approaches. However, the extra efforts pay off in revealing mechanisms as well as providing the foundation for new strategies in systems biology and personalized medicine. This review emphasizes the particular contribution NGS-based technologies make to functional genomics research with a special focus on gene regulation by transcription factor binding sites.
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Früh K, Finlay B, McFadden G. On the road to systems biology of host-pathogen interactions. Future Microbiol 2010; 5:131-3. [PMID: 20143936 DOI: 10.2217/fmb.09.130] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Klaus Früh
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Ave., Beaverton, OR 97006, USA.
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Stellberger T, Häuser R, Baiker A, Pothineni VR, Haas J, Uetz P. Improving the yeast two-hybrid system with permutated fusions proteins: the Varicella Zoster Virus interactome. Proteome Sci 2010; 8:8. [PMID: 20205919 PMCID: PMC2832230 DOI: 10.1186/1477-5956-8-8] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2009] [Accepted: 02/15/2010] [Indexed: 11/24/2022] Open
Abstract
Background Yeast two-hybrid (Y2H) screens have been among the most powerful methods to detect and analyze protein-protein interactions. However, they suffer from a significant degree of false negatives, i.e. true interactions that are not detected, and to a certain degree from false positives, i.e. interactions that appear to take place only in the context of the Y2H assay. While the fraction of false positives remains difficult to estimate, the fraction of false negatives in typical Y2H screens is on the order of 70-90%. Here we present novel Y2H vectors that significantly decrease the number of false negatives and help to mitigate the false positive problem. Results We have constructed two new vectors (pGBKCg and pGADCg) that allow us to make both C-terminal fusion proteins of DNA-binding and activation domains. Both vectors can be combined with existing vectors for N-terminal fusions and thus allow four different bait-prey combinations: NN, CC, NC, and CN. We have tested all ~4,900 pairwise combinations of the 70 Varicella-Zoster-Virus (VZV) proteins for interactions, using all possible combinations. About ~20,000 individual Y2H tests resulted in 182 NN, 89 NC, 149 CN, and 144 CC interactions. Overlap between screens ranged from 17% (NC-CN) to 43% (CN-CC). Performing four screens (i.e. permutations) instead of one resulted in about twice as many interactions and thus much fewer false negatives. In addition, interactions that are found in multiple combinations confirm each other and thus provide a quality score. This study is the first systematic analysis of such N- and C-terminal Y2H vectors. Conclusions Permutations of C- and N-terminal Y2H vectors dramatically increase the coverage of interactome studies and thus significantly reduce the number of false negatives. We suggest that future interaction screens should use such vector combinations on a routine basis, not the least because they provide a built-in quality score for Y2H interactions that can provide a measure of reproducibility without additional assays.
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Affiliation(s)
- Thorsten Stellberger
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, PO Box 3640, D-76021 Karlsruhe, Germany.
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