1
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Mansoor M, Nauman M, Ur Rehman H, Benso A. Gene Ontology GAN (GOGAN): a novel architecture for protein function prediction. Soft comput 2022. [DOI: 10.1007/s00500-021-06707-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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2
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Unraveling Protein Interactions between the Temperate Virus Bam35 and Its Bacillus Host Using an Integrative Yeast Two Hybrid-High Throughput Sequencing Approach. Int J Mol Sci 2021; 22:ijms222011105. [PMID: 34681765 PMCID: PMC8539640 DOI: 10.3390/ijms222011105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/08/2021] [Accepted: 10/10/2021] [Indexed: 11/20/2022] Open
Abstract
Bacillus virus Bam35 is the model Betatectivirus and member of the family Tectiviridae, which is composed of tailless, icosahedral, and membrane-containing bacteriophages. Interest in these viruses has greatly increased in recent years as they are thought to be an evolutionary link between diverse groups of prokaryotic and eukaryotic viruses. Additionally, betatectiviruses infect bacteria of the Bacillus cereus group, which are known for their applications in industry and notorious since it contains many pathogens. Here, we present the first protein–protein interactions (PPIs) network for a tectivirus–host system by studying the Bam35–Bacillus thuringiensis model using a novel approach that integrates the traditional yeast two-hybrid system and high-throughput sequencing (Y2H-HTS). We generated and thoroughly analyzed a genomic library of Bam35′s host B. thuringiensis HER1410 and screened interactions with all the viral proteins using different combinations of bait–prey couples. Initial analysis of the raw data enabled the identification of over 4000 candidate interactions, which were sequentially filtered to produce 182 high-confidence interactions that were defined as part of the core virus–host interactome. Overall, host metabolism proteins and peptidases were particularly enriched within the detected interactions, distinguishing this host–phage system from the other reported host–phage PPIs. Our approach also suggested biological roles for several Bam35 proteins of unknown function, including the membrane structural protein P25, which may be a viral hub with a role in host membrane modification during viral particle morphogenesis. This work resulted in a better understanding of the Bam35–B. thuringiensis interaction at the molecular level and holds great potential for the generalization of the Y2H-HTS approach for other virus–host models.
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3
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Xu W, Pei G, Liu H, Ju X, Wang J, Ding Q, Li P. Compartmentalization-aided interaction screening reveals extensive high-order complexes within the SARS-CoV-2 proteome. Cell Rep 2021; 36:109482. [PMID: 34297909 PMCID: PMC8285250 DOI: 10.1016/j.celrep.2021.109482] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/21/2021] [Accepted: 07/12/2021] [Indexed: 12/12/2022] Open
Abstract
Bearing a relatively large single-stranded RNA genome in nature, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes sophisticated replication/transcription complexes (RTCs), mainly composed of a network of nonstructural proteins and nucleocapsid protein, to establish efficient infection. In this study, we develop an innovative interaction screening strategy based on phase separation in cellulo, namely compartmentalization of protein-protein interactions in cells (CoPIC). Utilizing CoPIC screening, we map the interaction network among RTC-related viral proteins. We identify a total of 47 binary interactions among 14 proteins governing replication, discontinuous transcription, and translation of coronaviruses. Further exploration via CoPIC leads to the discovery of extensive ternary complexes composed of these components, which infer potential higher-order complexes. Taken together, our results present an efficient and robust interaction screening strategy, and they indicate the existence of a complex interaction network among RTC-related factors, thus opening up opportunities to understand SARS-CoV-2 biology and develop therapeutic interventions for COVID-19.
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Affiliation(s)
- Weifan Xu
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; School of Life Sciences, Tsinghua University, Beijing, China
| | - Gaofeng Pei
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; School of Life Sciences, Tsinghua University, Beijing, China
| | - Hongrui Liu
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaohui Ju
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China; School of Medicine, Tsinghua University, Beijing, China
| | - Jing Wang
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; School of Life Sciences, Tsinghua University, Beijing, China
| | - Qiang Ding
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China; School of Medicine, Tsinghua University, Beijing, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; School of Life Sciences, Tsinghua University, Beijing, China.
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4
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Zhang Y, Liao YT, Salvador A, Lavenburg VM, Wu VCH. Characterization of Two New Shiga Toxin-Producing Escherichia coli O103-Infecting Phages Isolated from an Organic Farm. Microorganisms 2021; 9:microorganisms9071527. [PMID: 34361962 PMCID: PMC8303462 DOI: 10.3390/microorganisms9071527] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 01/21/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) O103 strains have been recently attributed to various foodborne outbreaks in the United States. Due to the emergence of antibiotic-resistant strains, lytic phages are considered as alternative biocontrol agents. This study was to biologically and genomically characterize two STEC O103-infecting bacteriophages, vB_EcoP-Ro103C3lw (or Ro103C3lw) and vB_EcoM-Pr103Blw (or Pr103Blw), isolated from an organic farm. Based on genomic and morphological analyses, phages Ro103C3lw and Pr103Blw belonged to Autographiviridae and Myoviridae families, respectively. Ro103C3lw contained a 39,389-bp double-stranded DNA and encoded a unique tail fiber with depolymerase activity, resulting in huge plaques. Pr103Blw had an 88,421-bp double-stranded DNA with 26 predicted tRNAs associated with the enhancement of the phage fitness. Within each phage genome, no virulence, antibiotic-resistant, and lysogenic genes were detected. Additionally, Ro103C3lw had a short latent period (2 min) and a narrow host range, infecting only STEC O103 strains. By contrast, Pr103Blw had a large burst size (152 PFU/CFU) and a broad host range against STEC O103, O26, O111, O157:H7, and Salmonella Javiana strains. Furthermore, both phages showed strong antimicrobial activities against STEC O103:H2 strains. The findings provide valuable insight into these two phages’ genomic features with the potential antimicrobial activities against STEC O103.
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5
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Chen Z, Kibler RD, Hunt A, Busch F, Pearl J, Jia M, VanAernum ZL, Wicky BIM, Dods G, Liao H, Wilken MS, Ciarlo C, Green S, El-Samad H, Stamatoyannopoulos J, Wysocki VH, Jewett MC, Boyken SE, Baker D. De novo design of protein logic gates. Science 2020; 368:78-84. [PMID: 32241946 DOI: 10.1126/science.aay2790] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 03/05/2020] [Indexed: 12/16/2022]
Abstract
The design of modular protein logic for regulating protein function at the posttranscriptional level is a challenge for synthetic biology. Here, we describe the design of two-input AND, OR, NAND, NOR, XNOR, and NOT gates built from de novo-designed proteins. These gates regulate the association of arbitrary protein units ranging from split enzymes to transcriptional machinery in vitro, in yeast and in primary human T cells, where they control the expression of the TIM3 gene related to T cell exhaustion. Designed binding interaction cooperativity, confirmed by native mass spectrometry, makes the gates largely insensitive to stoichiometric imbalances in the inputs, and the modularity of the approach enables ready extension to three-input OR, AND, and disjunctive normal form gates. The modularity and cooperativity of the control elements, coupled with the ability to de novo design an essentially unlimited number of protein components, should enable the design of sophisticated posttranslational control logic over a wide range of biological functions.
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Affiliation(s)
- Zibo Chen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Ryan D Kibler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Andrew Hunt
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Florian Busch
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Jocelynn Pearl
- Altius Institute for Biomedical Sciences, Seattle, WA 98195, USA
| | - Mengxuan Jia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Zachary L VanAernum
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Basile I M Wicky
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Galen Dods
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hanna Liao
- Altius Institute for Biomedical Sciences, Seattle, WA 98195, USA
| | - Matthew S Wilken
- Altius Institute for Biomedical Sciences, Seattle, WA 98195, USA
| | - Christie Ciarlo
- Altius Institute for Biomedical Sciences, Seattle, WA 98195, USA
| | - Shon Green
- Altius Institute for Biomedical Sciences, Seattle, WA 98195, USA
| | - Hana El-Samad
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.,Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - John Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, WA 98195, USA.,Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Department of Medicine, Division of Oncology, University of Washington, Seattle, WA 98109, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Scott E Boyken
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. .,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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6
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Programmable design of orthogonal protein heterodimers. Nature 2018; 565:106-111. [PMID: 30568301 DOI: 10.1038/s41586-018-0802-y] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/08/2018] [Indexed: 11/09/2022]
Abstract
Specificity of interactions between two DNA strands, or between protein and DNA, is often achieved by varying bases or side chains coming off the DNA or protein backbone-for example, the bases participating in Watson-Crick pairing in the double helix, or the side chains contacting DNA in TALEN-DNA complexes. By contrast, specificity of protein-protein interactions usually involves backbone shape complementarity1, which is less modular and hence harder to generalize. Coiled-coil heterodimers are an exception, but the restricted geometry of interactions across the heterodimer interface (primarily at the heptad a and d positions2) limits the number of orthogonal pairs that can be created simply by varying side-chain interactions3,4. Here we show that protein-protein interaction specificity can be achieved using extensive and modular side-chain hydrogen-bond networks. We used the Crick generating equations5 to produce millions of four-helix backbones with varying degrees of supercoiling around a central axis, identified those accommodating extensive hydrogen-bond networks, and used Rosetta to connect pairs of helices with short loops and to optimize the remainder of the sequence. Of 97 such designs expressed in Escherichia coli, 65 formed constitutive heterodimers, and the crystal structures of four designs were in close agreement with the computational models and confirmed the designed hydrogen-bond networks. In cells, six heterodimers were fully orthogonal, and in vitro-following mixing of 32 chains from 16 heterodimer designs, denaturation in 5 M guanidine hydrochloride and reannealing-almost all of the interactions observed by native mass spectrometry were between the designed cognate pairs. The ability to design orthogonal protein heterodimers should enable sophisticated protein-based control logic for synthetic biology, and illustrates that nature has not fully explored the possibilities for programmable biomolecular interaction modalities.
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7
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Enzymes and Mechanisms Employed by Tailed Bacteriophages to Breach the Bacterial Cell Barriers. Viruses 2018; 10:v10080396. [PMID: 30060520 PMCID: PMC6116005 DOI: 10.3390/v10080396] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/23/2018] [Accepted: 07/26/2018] [Indexed: 01/07/2023] Open
Abstract
Monoderm bacteria possess a cell envelope made of a cytoplasmic membrane and a cell wall, whereas diderm bacteria have and extra lipid layer, the outer membrane, covering the cell wall. Both cell types can also produce extracellular protective coats composed of polymeric substances like, for example, polysaccharidic capsules. Many of these structures form a tight physical barrier impenetrable by phage virus particles. Tailed phages evolved strategies/functions to overcome the different layers of the bacterial cell envelope, first to deliver the genetic material to the host cell cytoplasm for virus multiplication, and then to release the virion offspring at the end of the reproductive cycle. There is however a major difference between these two crucial steps of the phage infection cycle: virus entry cannot compromise cell viability, whereas effective virion progeny release requires host cell lysis. Here we present an overview of the viral structures, key protein players and mechanisms underlying phage DNA entry to bacteria, and then escape of the newly-formed virus particles from infected hosts. Understanding the biological context and mode of action of the phage-derived enzymes that compromise the bacterial cell envelope may provide valuable information for their application as antimicrobials.
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8
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Abstract
Two-hybrid methods remain among the most preferred choices for detecting protein-protein interactions (PPIs) and much of the PPI data in databases have been produced using yeast two-hybrid (Y2H) screens. The Y2H methods are extensively used to detect PPIs because of their scalability and accessibility. Several variants of Y2H methods have been developed and used by different research groups, increasing the accessibility of these methods and their applications in detecting different types of PPIs. However, the availability of variations on the same core methodology emphasizes the need to have a systematic comparison of available Y2H methods in the context of their applicability, coverage and efficiency. In this chapter, we discuss the key parameters of Y2H methods, namely proteins of interest, vectors, libraries, screening strategies, data analysis, and provide a flowchart that should help to decide which Y2H strategy is most appropriate for a protein interaction screen.
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9
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Moosavi B, Mousavi B, Yang WC, Yang GF. Yeast-based assays for detecting protein-protein/drug interactions and their inhibitors. Eur J Cell Biol 2017. [PMID: 28645461 DOI: 10.1016/j.ejcb.2017.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Understanding cellular processes at molecular levels in health and disease requires the knowledge of protein-protein interactions (PPIs). In line with this, identification of PPIs at genome-wide scale is highly valuable to understand how different cellular pathways are interconnected, and it eventually facilitates designing effective drugs against certain PPIs. Furthermore, investigating PPIs at a small laboratory scale for deciphering certain biochemical pathways has been demanded for years. In this regard, yeast two hybrid system (Y2HS) has proven an extremely useful tool to discover novel PPIs, while Y2HS derivatives and novel yeast-based assays are contributing significantly to identification of protein-drug/inhibitor interaction at both large- and small-scale set-ups. These methods have been evolving over time to provide more accurate, reproducible and quantitative results. Here we briefly describe different yeast-based assays for identification of various protein-protein/drug/inhibitor interactions and their specific applications, advantages, shortcomings, and improvements. The broad range of yeast-based assays facilitates application of the most suitable method(s) for each specific need.
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Affiliation(s)
- Behrooz Moosavi
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, PR China.
| | - Bibimaryam Mousavi
- Laboratory of Organometallics, Catalysis and Ordered Materials, State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Wen-Chao Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, PR China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, PR China.
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10
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Boyken SE, Chen Z, Groves B, Langan RA, Oberdorfer G, Ford A, Gilmore JM, Xu C, DiMaio F, Pereira JH, Sankaran B, Seelig G, Zwart PH, Baker D. De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity. Science 2016; 352:680-7. [PMID: 27151862 PMCID: PMC5497568 DOI: 10.1126/science.aad8865] [Citation(s) in RCA: 222] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/23/2016] [Indexed: 12/26/2022]
Abstract
In nature, structural specificity in DNA and proteins is encoded differently: In DNA, specificity arises from modular hydrogen bonds in the core of the double helix, whereas in proteins, specificity arises largely from buried hydrophobic packing complemented by irregular peripheral polar interactions. Here, we describe a general approach for designing a wide range of protein homo-oligomers with specificity determined by modular arrays of central hydrogen-bond networks. We use the approach to design dimers, trimers, and tetramers consisting of two concentric rings of helices, including previously not seen triangular, square, and supercoiled topologies. X-ray crystallography confirms that the structures overall, and the hydrogen-bond networks in particular, are nearly identical to the design models, and the networks confer interaction specificity in vivo. The ability to design extensive hydrogen-bond networks with atomic accuracy enables the programming of protein interaction specificity for a broad range of synthetic biology applications; more generally, our results demonstrate that, even with the tremendous diversity observed in nature, there are fundamentally new modes of interaction to be discovered in proteins.
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Affiliation(s)
- Scott E Boyken
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Zibo Chen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195, USA
| | - Benjamin Groves
- Department of Electrical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Robert A Langan
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Gustav Oberdorfer
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - Alex Ford
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jason M Gilmore
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Chunfu Xu
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jose Henrique Pereira
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/3, 8010-Graz, Austria. Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Banumathi Sankaran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Georg Seelig
- Department of Electrical Engineering, University of Washington, Seattle, WA 98195, USA. Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Peter H Zwart
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. The Center for Advanced Mathematics for Energy Research Applications, Lawrence Berkeley National Laboratories, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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11
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Lum KK, Cristea IM. Proteomic approaches to uncovering virus-host protein interactions during the progression of viral infection. Expert Rev Proteomics 2016; 13:325-40. [PMID: 26817613 PMCID: PMC4919574 DOI: 10.1586/14789450.2016.1147353] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 01/25/2016] [Indexed: 01/10/2023]
Abstract
The integration of proteomic methods to virology has facilitated a significant breadth of biological insight into mechanisms of virus replication, antiviral host responses and viral subversion of host defenses. Throughout the course of infection, these cellular mechanisms rely heavily on the formation of temporally and spatially regulated virus-host protein-protein interactions. Reviewed here are proteomic-based approaches that have been used to characterize this dynamic virus-host interplay. Specifically discussed are the contribution of integrative mass spectrometry, antibody-based affinity purification of protein complexes, cross-linking and protein array techniques for elucidating complex networks of virus-host protein associations during infection with a diverse range of RNA and DNA viruses. The benefits and limitations of applying proteomic methods to virology are explored, and the contribution of these approaches to important biological discoveries and to inspiring new tractable avenues for the design of antiviral therapeutics is highlighted.
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Affiliation(s)
- Krystal K Lum
- Department of Molecular Biology, Princeton
University, Princeton, NJ, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton
University, Princeton, NJ, USA
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12
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The Protein Interactome of Mycobacteriophage Giles Predicts Functions for Unknown Proteins. J Bacteriol 2015; 197:2508-16. [PMID: 25986902 DOI: 10.1128/jb.00164-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/09/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Mycobacteriophages are viruses that infect mycobacterial hosts and are prevalent in the environment. Nearly 700 mycobacteriophage genomes have been completely sequenced, revealing considerable diversity and genetic novelty. Here, we have determined the protein complement of mycobacteriophage Giles by mass spectrometry and mapped its genome-wide protein interactome to help elucidate the roles of its 77 predicted proteins, 50% of which have no known function. About 22,000 individual yeast two-hybrid (Y2H) tests with four different Y2H vectors, followed by filtering and retest screens, resulted in 324 reproducible protein-protein interactions, including 171 (136 nonredundant) high-confidence interactions. The complete set of high-confidence interactions among Giles proteins reveals new mechanistic details and predicts functions for unknown proteins. The Giles interactome is the first for any mycobacteriophage and one of just five known phage interactomes so far. Our results will help in understanding mycobacteriophage biology and aid in development of new genetic and therapeutic tools to understand Mycobacterium tuberculosis. IMPORTANCE Mycobacterium tuberculosis causes over 9 million new cases of tuberculosis each year. Mycobacteriophages, viruses of mycobacterial hosts, hold considerable potential to understand phage diversity, evolution, and mycobacterial biology, aiding in the development of therapeutic tools to control mycobacterial infections. The mycobacteriophage Giles protein-protein interaction network allows us to predict functions for unknown proteins and shed light on major biological processes in phage biology. For example, Giles gp76, a protein of unknown function, is found to associate with phage packaging and maturation. The functions of mycobacteriophage-derived proteins may suggest novel therapeutic approaches for tuberculosis. Our ORFeome clone set of Giles proteins and the interactome data will be useful resources for phage interactomics.
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13
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Abstract
In general, phages cause lysis of the bacterial host to effect release of the progeny virions. Until recently, it was thought that degradation of the peptidoglycan (PG) was necessary and sufficient for osmotic bursting of the cell. Recently, we have shown that in Gram-negative hosts, phage lysis also requires the disruption of the outer membrane (OM). This is accomplished by spanins, which are phage-encoded proteins that connect the cytoplasmic membrane (inner membrane, IM) and the OM. The mechanism by which the spanins destroy the OM is unknown. Here we show that the spanins of the paradigm coliphage lambda mediate efficient membrane fusion. This supports the notion that the last step of lysis is the fusion of the IM and OM. Moreover, data are provided indicating that spanin-mediated fusion is regulated by the meshwork of the PG, thus coupling fusion to murein degradation by the phage endolysin. Because endolysin function requires the formation of μm-scale holes by the phage holin, the lysis pathway is seen to require dramatic dynamics on the part of the OM and IM, as well as destruction of the PG.
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14
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Durmuş S, Çakır T, Özgür A, Guthke R. A review on computational systems biology of pathogen-host interactions. Front Microbiol 2015; 6:235. [PMID: 25914674 PMCID: PMC4391036 DOI: 10.3389/fmicb.2015.00235] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/10/2015] [Indexed: 12/27/2022] Open
Abstract
Pathogens manipulate the cellular mechanisms of host organisms via pathogen-host interactions (PHIs) in order to take advantage of the capabilities of host cells, leading to infections. The crucial role of these interspecies molecular interactions in initiating and sustaining infections necessitates a thorough understanding of the corresponding mechanisms. Unlike the traditional approach of considering the host or pathogen separately, a systems-level approach, considering the PHI system as a whole is indispensable to elucidate the mechanisms of infection. Following the technological advances in the post-genomic era, PHI data have been produced in large-scale within the last decade. Systems biology-based methods for the inference and analysis of PHI regulatory, metabolic, and protein-protein networks to shed light on infection mechanisms are gaining increasing demand thanks to the availability of omics data. The knowledge derived from the PHIs may largely contribute to the identification of new and more efficient therapeutics to prevent or cure infections. There are recent efforts for the detailed documentation of these experimentally verified PHI data through Web-based databases. Despite these advances in data archiving, there are still large amounts of PHI data in the biomedical literature yet to be discovered, and novel text mining methods are in development to unearth such hidden data. Here, we review a collection of recent studies on computational systems biology of PHIs with a special focus on the methods for the inference and analysis of PHI networks, covering also the Web-based databases and text-mining efforts to unravel the data hidden in the literature.
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Affiliation(s)
- Saliha Durmuş
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, KocaeliTurkey
| | - Tunahan Çakır
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, KocaeliTurkey
| | - Arzucan Özgür
- Department of Computer Engineering, Boǧaziçi University, IstanbulTurkey
| | - Reinhard Guthke
- Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knoell-Institute, JenaGermany
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15
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Subramanian N, Torabi-Parizi P, Gottschalk RA, Germain RN, Dutta B. Network representations of immune system complexity. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:13-38. [PMID: 25625853 PMCID: PMC4339634 DOI: 10.1002/wsbm.1288] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 12/09/2014] [Accepted: 12/11/2014] [Indexed: 12/25/2022]
Abstract
The mammalian immune system is a dynamic multiscale system composed of a hierarchically organized set of molecular, cellular, and organismal networks that act in concert to promote effective host defense. These networks range from those involving gene regulatory and protein–protein interactions underlying intracellular signaling pathways and single‐cell responses to increasingly complex networks of in vivo cellular interaction, positioning, and migration that determine the overall immune response of an organism. Immunity is thus not the product of simple signaling events but rather nonlinear behaviors arising from dynamic, feedback‐regulated interactions among many components. One of the major goals of systems immunology is to quantitatively measure these complex multiscale spatial and temporal interactions, permitting development of computational models that can be used to predict responses to perturbation. Recent technological advances permit collection of comprehensive datasets at multiple molecular and cellular levels, while advances in network biology support representation of the relationships of components at each level as physical or functional interaction networks. The latter facilitate effective visualization of patterns and recognition of emergent properties arising from the many interactions of genes, molecules, and cells of the immune system. We illustrate the power of integrating ‘omics’ and network modeling approaches for unbiased reconstruction of signaling and transcriptional networks with a focus on applications involving the innate immune system. We further discuss future possibilities for reconstruction of increasingly complex cellular‐ and organism‐level networks and development of sophisticated computational tools for prediction of emergent immune behavior arising from the concerted action of these networks. WIREs Syst Biol Med 2015, 7:13–38. doi: 10.1002/wsbm.1288 This article is categorized under:
Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Macromolecular Interactions, Methods
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Affiliation(s)
- Naeha Subramanian
- Institute for Systems Biology, Seattle, WA, USA; Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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16
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Solteszova B, Halgasova N, Bukovska G. Interaction between phage BFK20 helicase gp41 and its host Brevibacterium flavum primase DnaG. Virus Res 2015; 196:150-6. [DOI: 10.1016/j.virusres.2014.11.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 11/12/2014] [Accepted: 11/17/2014] [Indexed: 11/24/2022]
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17
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Vidal M, Fields S. The yeast two-hybrid assay: still finding connections after 25 years. Nat Methods 2014; 11:1203-6. [DOI: 10.1038/nmeth.3182] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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18
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Chepelev N, Chepelev L, Alamgir M, Golshani A. Large-Scale Protein-Protein Interaction Detection Approaches: Past, Present and Future. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2008.10817505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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19
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Legrain P, Rain JC. Twenty years of protein interaction studies for biological function deciphering. J Proteomics 2014; 107:93-7. [PMID: 24709640 DOI: 10.1016/j.jprot.2014.03.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 03/25/2014] [Indexed: 12/31/2022]
Abstract
Intensive methodological developments and technology innovation have been devoted to protein-protein interaction studies over 20years. Genetic indirect assays and sophisticated large scale biochemical analyses have jointly contributed to the elucidation of protein-protein interactions, still with a lot of drawbacks despite heavy investment in human resources and technologies. With the most recent developments in mass spectrometry and computational tools for studying protein content of complex samples, the initial goal of deciphering molecular bases of biological functions is now within reach. Here, we described the various steps of this process and gave examples of key milestones in this scientific story line. This article is part of a Special Issue entitled: 20years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini, Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez.
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20
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Young R. Phage lysis: three steps, three choices, one outcome. J Microbiol 2014; 52:243-58. [PMID: 24585055 DOI: 10.1007/s12275-014-4087-z] [Citation(s) in RCA: 246] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 02/15/2014] [Indexed: 11/26/2022]
Abstract
The lysis of bacterial hosts by double-strand DNA bacteriophages, once thought to reflect merely the accumulation of sufficient lysozyme activity during the infection cycle, has been revealed to recently been revealed to be a carefully regulated and temporally scheduled process. For phages of Gramnegative hosts, there are three steps, corresponding to subversion of each of the three layers of the cell envelope: inner membrane, peptidoglycan, and outer membrane. The pathway is controlled at the level of the cytoplasmic membrane. In canonical lysis, a phage encoded protein, the holin, accumulates harmlessly in the cytoplasmic membrane until triggering at an allele-specific time to form micron-scale holes. This allows the soluble endolysin to escape from the cytoplasm to degrade the peptidoglycan. Recently a parallel pathway has been elucidated in which a different type of holin, the pinholin, which, instead of triggering to form large holes, triggers to form small, heptameric channels that serve to depolarize the membrane. Pinholins are associated with SAR endolysins, which accumulate in the periplasm as inactive, membrane-tethered enzymes. Pinholin triggering collapses the proton motive force, allowing the SAR endolysins to refold to an active form and attack the peptidoglycan. Surprisingly, a third step, the disruption of the outer membrane is also required. This is usually achieved by a spanin complex, consisting of a small outer membrane lipoprotein and an integral cytoplasmic membrane protein, designated as o-spanin and i-spanin, respectively. Without spanin function, lysis is blocked and progeny virions are trapped in dead spherical cells, suggesting that the outer membrane has considerable tensile strength. In addition to two-component spanins, there are some single-component spanins, or u-spanins, that have an N-terminal outer-membrane lipoprotein signal and a C-terminal transmembrane domain. A possible mechanism for spanin function to disrupt the outer membrane is to catalyze fusion of the inner and outer membranes.
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Affiliation(s)
- Ryland Young
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843-2128, USA,
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21
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Kuczenski RS, Aggarwal K, Lee KH. Improved understanding of gene expression regulation using systems biology. Expert Rev Proteomics 2014; 2:915-24. [PMID: 16307520 DOI: 10.1586/14789450.2.6.915] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This article reviews the current state of systems biology approaches, including the experimental tools used to generate 'omic' data and computational frameworks to interpret this data. Through illustrative examples, systems biology approaches to understand gene expression and gene expression regulation are discussed. Some of the challenges facing this field and the future opportunities in the systems biology era are highlighted.
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Affiliation(s)
- Robert S Kuczenski
- Cornell University, School of Chemical & Biomolecular Engineering, 120 Olin Hall, Ithaca, NY 14853, USA.
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22
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Sangsuriya P, Huang JY, Chu YF, Phiwsaiya K, Leekitcharoenphon P, Meemetta W, Senapin S, Huang WP, Withyachumnarnkul B, Flegel TW, Lo CF. Construction and application of a protein interaction map for white spot syndrome virus (WSSV). Mol Cell Proteomics 2014; 13:269-82. [PMID: 24217020 PMCID: PMC3879619 DOI: 10.1074/mcp.m113.029199] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 10/21/2013] [Indexed: 01/28/2023] Open
Abstract
White spot syndrome virus (WSSV) is currently the most serious global threat for cultured shrimp production. Although its large, double-stranded DNA genome has been completely characterized, most putative protein functions remain obscure. To provide more informative knowledge about this virus, a proteomic-scale network of WSSV-WSSV protein interactions was carried out using a comprehensive yeast two-hybrid analysis. An array of yeast transformants containing each WSSV open reading frame fused with GAL4 DNA binding domain and GAL4 activation domain was constructed yielding 187 bait and 182 prey constructs, respectively. On screening of ∼28,000 pairwise combinations, 710 interactions were obtained from 143 baits. An independent coimmunoprecipitation assay (co-IP) was performed to validate the selected protein interaction pairs identified from the yeast two-hybrid approach. The program Cytoscape was employed to create a WSSV protein-protein interaction (PPI) network. The topology of the WSSV PPI network was based on the Barabási-Albert model and consisted of a scale-free network that resembled other established viral protein interaction networks. Using the RNA interference approach, knocking down either of two candidate hub proteins gave shrimp more protection against WSSV than knocking down a nonhub gene. The WSSV protein interaction map established in this study provides novel guidance for further studies on shrimp viral pathogenesis, host-viral protein interaction and potential targets for therapeutic and preventative antiviral strategies in shrimp aquaculture.
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Affiliation(s)
- Pakkakul Sangsuriya
- From the ‡Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
- §Department of Biotechnology, Faculty of Science, Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
| | - Jiun-Yan Huang
- ¶Institute of Zoology, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Yu-Fei Chu
- ¶Institute of Zoology, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Kornsunee Phiwsaiya
- From the ‡Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
- ‖National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Pimlapas Leekitcharoenphon
- From the ‡Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
| | - Watcharachai Meemetta
- From the ‡Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
| | - Saengchan Senapin
- From the ‡Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
- ‖National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Wei-Pang Huang
- ¶Institute of Zoology, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Boonsirm Withyachumnarnkul
- From the ‡Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
- **Shrimp Genetic Improvement Center, Surat Thani 84100, Thailand
- ‡‡Department of Anatomy, Faculty of Science, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Timothy W. Flegel
- From the ‡Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
- ‖National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Chu-Fang Lo
- ¶Institute of Zoology, National Taiwan University, Taipei, Taiwan, Republic of China
- ¶¶Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan, Republic of China
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23
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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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24
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Liu Y, Yin Q, Yuan Y, Yang W, Jiang C, Huang C. Infectomics Screening for Novel Antiviral Drug Targets. Drug Dev Res 2012. [PMCID: PMC7163650 DOI: 10.1002/ddr.21027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Copyright 2012 Wiley-Liss, Inc., A Wiley Company Infectomics, a novel way to globally and comprehensively understand the interactions between microbial pathogens and their hosts, has significantly expanded understanding of the microbial infections. The infectomics view of viral–host interactions on the viral perspective principally focuses on gene acquisition, deletion, and point mutation, while traditional antiviral drug discovery concentrates on viral encoding proteins. Recently, high‐throughput technologies, such as mass spectrometry‐based proteomics, activity‐based protein profiling, microarray analysis, yeast two‐hybrid assay, small interfering RNA screening, and micro RNA profiling, have been gradually employed in the research of virus–host interactions. Besides, signaling pathways and cellular processes involved in viral–host interactions provide new insights of infectomics in antiviral drug discovery. In this review, we summarize related infectomics approaches in the studies of virus–host interactions, which shed light on the development of novel antiviral drug targets screening.
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Affiliation(s)
- Yuan Liu
- The State Key Laboratory of Biotherapy; West China Hospital, West China, Sichuan University; Chengdu; 610041; China
| | - Qi Yin
- The State Key Laboratory of Biotherapy; West China Hospital, West China, Sichuan University; Chengdu; 610041; China
| | - Yao Yuan
- The State Key Laboratory of Biotherapy; West China Hospital, West China, Sichuan University; Chengdu; 610041; China
| | - Wenyong Yang
- The State Key Laboratory of Biotherapy; West China Hospital, West China, Sichuan University; Chengdu; 610041; China
| | - Chuangui Jiang
- The State Key Laboratory of Biotherapy; West China Hospital, West China, Sichuan University; Chengdu; 610041; China
| | - Canhua Huang
- The State Key Laboratory of Biotherapy; West China Hospital, West China, Sichuan University; Chengdu; 610041; China
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25
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Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol Mol Biol Rev 2012; 76:331-82. [PMID: 22688816 DOI: 10.1128/mmbr.05021-11] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. Sensitivity and selectivity have improved because of various technical tricks and experimental designs. Here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment complementation assays. These methods have been engineered and employed successfully in microorganisms such as Saccharomyces cerevisiae and Escherichia coli, but also in higher eukaryotes. From single binary pairwise interactions to whole-genome interactome mapping, the self-reassembly concept has been employed widely. Innovative studies report the use of proteins such as ubiquitin, dihydrofolate reductase, and adenylate cyclase as reconstituted reporters. Protein fragment complementation assays have extended the possibilities in protein-protein interaction studies, with technologies that enable spatial and temporal analyses of protein complexes. In addition, one-hybrid and three-hybrid systems have broadened the types of interactions that can be studied and the findings that can be obtained. Applications of these technologies are discussed, together with the advantages and limitations of the available assays.
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26
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Affiliation(s)
- Ian W. Taylor
- Samuel Lunenfeld Research Institute; Mount Sinai Hospital; Toronto Ontario Canada
- Department of Molecular Genetics; University of Toronto; Toronto Ontario Canada
| | - Jeffrey L. Wrana
- Samuel Lunenfeld Research Institute; Mount Sinai Hospital; Toronto Ontario Canada
- Department of Molecular Genetics; University of Toronto; Toronto Ontario Canada
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27
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Braun P, Gingras AC. History of protein-protein interactions: From egg-white to complex networks. Proteomics 2012; 12:1478-98. [DOI: 10.1002/pmic.201100563] [Citation(s) in RCA: 163] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Pascal Braun
- Department of Plant Systems Biology; Center for Life and Food Sciences Weihenstephan; Technical University Munich; Freising Germany
- Research Unit Protein Science; Helmholtz Centre Munich; Munich Germany
| | - Anne-Claude Gingras
- Samuel Lunenfeld Research Institute at Mount Sinai Hospital; Toronto Ontario Canada
- Department of Molecular Genetics; University of Toronto; Toronto Ontario Canada
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28
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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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29
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Golemis EA, Serebriiskii I, Finley RL, Kolonin MG, Gyuris J, Brent R. Interaction trap/two-hybrid system to identify interacting proteins. ACTA ACUST UNITED AC 2012; Chapter 17:17.3.1-17.3.35. [PMID: 22161546 DOI: 10.1002/0471143030.cb1703s53] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The yeast two-hybrid method (or interaction trap) is a powerful technique for detecting protein interactions. The procedure is performed using transcriptional activation of a dual reporter system in yeast to identify interactions between a protein of interest (the bait protein) and the candidate proteins for interaction. The method can be used to screen a protein library for interactions with a bait protein or to test for association between proteins that are expected to interact based on prior evidence. Interaction mating facilitates the screening of a library with multiple bait proteins.
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30
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Koh GCKW, Porras P, Aranda B, Hermjakob H, Orchard SE. Analyzing protein-protein interaction networks. J Proteome Res 2012; 11:2014-31. [PMID: 22385417 DOI: 10.1021/pr201211w] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The advent of the "omics" era in biology research has brought new challenges and requires the development of novel strategies to answer previously intractable questions. Molecular interaction networks provide a framework to visualize cellular processes, but their complexity often makes their interpretation an overwhelming task. The inherently artificial nature of interaction detection methods and the incompleteness of currently available interaction maps call for a careful and well-informed utilization of this valuable data. In this tutorial, we aim to give an overview of the key aspects that any researcher needs to consider when working with molecular interaction data sets and we outline an example for interactome analysis. Using the molecular interaction database IntAct, the software platform Cytoscape, and its plugins BiNGO and clusterMaker, and taking as a starting point a list of proteins identified in a mass spectrometry-based proteomics experiment, we show how to build, visualize, and analyze a protein-protein interaction network.
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Affiliation(s)
- Gavin C K W Koh
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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31
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Golemis EA, Serebriiskii I, Finley RL, Kolonin MG, Gyuris J, Brent R. Interaction trap/two-hybrid system to identify interacting proteins. ACTA ACUST UNITED AC 2012; Chapter 4:Unit 4.4. [PMID: 21462161 DOI: 10.1002/0471142301.ns0404s55] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The yeast two-hybrid method (or interaction trap) is a powerful technique for detecting protein interactions. The procedure is performed using transcriptional activation of a dual reporter system in yeast to identify interactions between a protein of interest (the bait protein) and the candidate proteins for interaction. The method can be used to screen a protein library for interactions with a bait protein or to test for association between proteins that are expected to interact based on prior evidence. Interaction mating facilitates the screening of a library with multiple bait proteins.
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Affiliation(s)
- Erica A Golemis
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA. EA
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32
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Lin TY, Lo YH, Tseng PW, Chang SF, Lin YT, Chen TS. A T3 and T7 recombinant phage acquires efficient adsorption and a broader host range. PLoS One 2012; 7:e30954. [PMID: 22347414 PMCID: PMC3276506 DOI: 10.1371/journal.pone.0030954] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 12/27/2011] [Indexed: 11/19/2022] Open
Abstract
It is usually thought that bacteriophage T7 is female specific, while phage T3 can propagate on male and female Escherichia coli. We found that the growth patterns of phages T7M and T3 do not match the above characteristics, instead showing strain dependent male exclusion. Furthermore, a T3/7 hybrid phage exhibits a broader host range relative to that of T3, T7, as well as T7M, and is able to overcome the male exclusion. The T7M sequence closely resembles that of T3. T3/7 is essentially T3 based, but a DNA fragment containing part of the tail fiber gene 17 is replaced by the T7 sequence. T3 displays inferior adsorption to strains tested herein compared to T7. The T3 and T7 recombinant phage carries altered tail fibers and acquires better adsorption efficiency than T3. How phages T3 and T7 recombine was previously unclear. This study is the first to show that recombination can occur accurately within only 8 base-pair homology, where four-way junction structures are identified. Genomic recombination models based on endonuclease I cleavages at equivalent and nonequivalent sites followed by strand annealing are proposed. Retention of pseudo-palindromes can increase recombination frequency for reviving under stress.
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Affiliation(s)
- Tiao-Yin Lin
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, People's Republic of China.
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33
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Abstract
Molecular interactions are key processes that drive the functions of molecules. Large data sets of protein interaction data are being assembled that will help analyze structural and functional aspects of interactions. This chapter introduces techniques for analyzing both the structural aspects of molecular interactions and methods to use this information to understand and define biological pathways.
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34
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Häuser R, Stellberger T, Rajagopala SV, Uetz P. Matrix-based yeast two-hybrid screen strategies and comparison of systems. Methods Mol Biol 2012; 812:1-20. [PMID: 22218851 DOI: 10.1007/978-1-61779-455-1_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Today, matrix-based screens are used primarily for smaller and medium-size clone collections in combination with automation and cloning techniques that allow for reliable and fast interaction screening. Matrix-based yeast two-hybrid screens are an alternative to library-based screens. However, intermediary forms are possible too and we compare both strategies, including a detailed discussion of matrix-based screens. Recent improvement of matrix screens (also called array screens) uses various pooling strategies as well as novel vectors that increase their efficiency while decreasing false-negative rates and increasing reliability.
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Affiliation(s)
- Roman Häuser
- Karlsruhe Institute of Technology, Karlsruhe, Germany
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35
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Häuser R, Blasche S, Dokland T, Haggård-Ljungquist E, von Brunn A, Salas M, Casjens S, Molineux I, Uetz P. Bacteriophage protein-protein interactions. Adv Virus Res 2012; 83:219-98. [PMID: 22748812 PMCID: PMC3461333 DOI: 10.1016/b978-0-12-394438-2.00006-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Bacteriophages T7, λ, P22, and P2/P4 (from Escherichia coli), as well as ϕ29 (from Bacillus subtilis), are among the best-studied bacterial viruses. This chapter summarizes published protein interaction data of intraviral protein interactions, as well as known phage-host protein interactions of these phages retrieved from the literature. We also review the published results of comprehensive protein interaction analyses of Pneumococcus phages Dp-1 and Cp-1, as well as coliphages λ and T7. For example, the ≈55 proteins encoded by the T7 genome are connected by ≈43 interactions with another ≈15 between the phage and its host. The chapter compiles published interactions for the well-studied phages λ (33 intra-phage/22 phage-host), P22 (38/9), P2/P4 (14/3), and ϕ29 (20/2). We discuss whether different interaction patterns reflect different phage lifestyles or whether they may be artifacts of sampling. Phages that infect the same host can interact with different host target proteins, as exemplified by E. coli phage λ and T7. Despite decades of intensive investigation, only a fraction of these phage interactomes are known. Technical limitations and a lack of depth in many studies explain the gaps in our knowledge. Strategies to complete current interactome maps are described. Although limited space precludes detailed overviews of phage molecular biology, this compilation will allow future studies to put interaction data into the context of phage biology.
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Affiliation(s)
- Roman Häuser
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
- Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Sonja Blasche
- Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Terje Dokland
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Albrecht von Brunn
- Max-von-Pettenkofer-Institut, Lehrstuhl Virologie, Ludwig-Maximilians-Universität, München, Germany
| | - Margarita Salas
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Cantoblanco, Madrid, Spain
| | - Sherwood Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah
| | - Ian Molineux
- Molecular Genetics and Microbiology, Institute for Cell and Molecular Biology, University of Texas–Austin, Austin, Texas, USA
| | - Peter Uetz
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, USA
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DeArmond PD, Xu Y, Strickland EC, Daniels KG, Fitzgerald MC. Thermodynamic analysis of protein-ligand interactions in complex biological mixtures using a shotgun proteomics approach. J Proteome Res 2011; 10:4948-58. [PMID: 21905665 PMCID: PMC3208786 DOI: 10.1021/pr200403c] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Shotgun proteomics protocols are widely used for the identification and/or quantitation of proteins in complex biological samples. Described here is a shotgun proteomics protocol that can be used to identify the protein targets of biologically relevant ligands in complex protein mixtures. The protocol combines a quantitative proteomics platform with a covalent modification strategy, termed Stability of Proteins from Rates of Oxidation (SPROX), which utilizes the denaturant dependence of hydrogen peroxide-mediated oxidation of methionine side chains in proteins to assess the thermodynamic properties of proteins and protein-ligand complexes. The quantitative proteomics platform involves the use of isobaric mass tags and a methionine-containing peptide enhancement strategy. The protocol is evaluated in a ligand binding experiment designed to identify the proteins in a yeast cell lysate that bind the well-known enzyme cofactor, β-nicotinamide adenine dinucleotide (NAD+). The protocol is also used to investigate the protein targets of resveratrol, a biologically active ligand with less well-understood protein targets. A known protein target of resveratrol, cytosolic aldehyde dehydrogenase, was identified in addition to six other potential new proteins targets including four that are associated with the protein translation machinery, which has previously been implicated as a target of resveratrol.
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Affiliation(s)
| | - Ying Xu
- Department of Chemistry, Duke University, Durham, NC 27708
| | | | - Kyle G. Daniels
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27708
| | - Michael C. Fitzgerald
- Department of Chemistry, Duke University, Durham, NC 27708
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27708
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37
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Friedel CC, Haas J. Virus-host interactomes and global models of virus-infected cells. Trends Microbiol 2011; 19:501-8. [PMID: 21855347 DOI: 10.1016/j.tim.2011.07.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 07/12/2011] [Accepted: 07/13/2011] [Indexed: 01/01/2023]
Abstract
Novel high-throughput technologies such as yeast two-hybrid and RNA interference (RNAi) screens provide the tools to study interactions between viral proteins and the host on a genomic scale. In this review, we provide an overview of studies in which these technologies were applied and of computational approaches for the analysis of the identified viral interactors in the context of the host cell. The results of these studies illustrate the advantages of integrative systems biology approaches in the investigation of viral pathogens.
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Affiliation(s)
- Caroline C Friedel
- Institut für Pharmazie und Molekulare Biotechnologie, Universität Heidelberg, 69120 Heidelberg, Germany
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D'haeseleer K, Den Herder G, Laffont C, Plet J, Mortier V, Lelandais-Brière C, De Bodt S, De Keyser A, Crespi M, Holsters M, Frugier F, Goormachtig S. Transcriptional and post-transcriptional regulation of a NAC1 transcription factor in Medicago truncatula roots. THE NEW PHYTOLOGIST 2011; 191:647-661. [PMID: 21770944 DOI: 10.1111/j.1469-8137.2011.03719.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
• Legume roots develop two types of lateral organs, lateral roots and nodules. Nodules develop as a result of a symbiotic interaction with rhizobia and provide a niche for the bacteria to fix atmospheric nitrogen for the plant. • The Arabidopsis NAC1 transcription factor is involved in lateral root formation, and is regulated post-transcriptionally by miRNA164 and by SINAT5-dependent ubiquitination. We analyzed in Medicago truncatula the role of the closest NAC1 homolog in lateral root formation and in nodulation. • MtNAC1 shows a different expression pattern in response to auxin than its Arabidopsis homolog and no changes in lateral root number or nodulation were observed in plants affected in MtNAC1 expression. In addition, no interaction was found with SINA E3 ligases, suggesting that post-translational regulation of MtNAC1 does not occur in M. truncatula. Similar to what was found in Arabidopsis, a conserved miR164 target site was retrieved in MtNAC1, which reduced protein accumulation of a GFP-miR164 sensor. Furthermore, miR164 and MtNAC1 show an overlapping expression pattern in symbiotic nodules, and overexpression of this miRNA led to a reduction in nodule number. • This work suggests that regulatory pathways controlling a conserved transcription factor are complex and divergent between M. truncatula and Arabidopsis.
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Affiliation(s)
- Katrien D'haeseleer
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, 9052 Gent, Belgium
| | - Griet Den Herder
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, 9052 Gent, Belgium
| | - Carole Laffont
- Institut des Sciences du Végétal (ISV), Centre National de la Recherche Scientifique (CNRS), 91198 Gif sur Yvette Cedex, France
| | - Julie Plet
- Institut des Sciences du Végétal (ISV), Centre National de la Recherche Scientifique (CNRS), 91198 Gif sur Yvette Cedex, France
| | - Virginie Mortier
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, 9052 Gent, Belgium
| | - Christine Lelandais-Brière
- Institut des Sciences du Végétal (ISV), Centre National de la Recherche Scientifique (CNRS), 91198 Gif sur Yvette Cedex, France
- Université Paris Diderot Paris 7, 75205 Paris Cedex 13, France
| | - Stefanie De Bodt
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, 9052 Gent, Belgium
| | - Annick De Keyser
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, 9052 Gent, Belgium
| | - Martin Crespi
- Institut des Sciences du Végétal (ISV), Centre National de la Recherche Scientifique (CNRS), 91198 Gif sur Yvette Cedex, France
| | - Marcelle Holsters
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, 9052 Gent, Belgium
| | - Florian Frugier
- Institut des Sciences du Végétal (ISV), Centre National de la Recherche Scientifique (CNRS), 91198 Gif sur Yvette Cedex, France
| | - Sofie Goormachtig
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, 9052 Gent, Belgium
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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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40
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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: 1134] [Impact Index Per Article: 87.2] [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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41
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Abstract
Mass spectrometry analysis of Streptococcus pneumoniae bacteriophage Cp-1 identified a total of 12 proteins, and proteome-wide yeast two-hybrid screens revealed 17 binary interactions mainly among these structural proteins. On the basis of the resulting linkage map, we suggest an improved structural model of the Cp-1 virion.
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42
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Lievens S, Eyckerman S, Lemmens I, Tavernier J. Large-scale protein interactome mapping: strategies and opportunities. Expert Rev Proteomics 2011; 7:679-90. [PMID: 20973641 DOI: 10.1586/epr.10.30] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Interactions between proteins are central to any cellular process, and mapping these into a protein network is informative both for the function of individual proteins and the functional organization of the cell as a whole. Many strategies have been developed that are up to this task, and the last 10 years have seen the high-throughput application of a number of those in large-scale, sometimes proteome-wide, interactome mapping efforts. Although initially the quality of the data produced in these screening campaigns has been questioned, quality standards and empirical validation schemes are now in place to ensure high-quality data generation. Through their integration with other 'omics' data, interactomics datasets have proven highly valuable towards applications in different areas of clinical importance.
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Affiliation(s)
- Sam Lievens
- Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, 9000 Ghent, Belgium
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43
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Berry J, Savva C, Holzenburg A, Young R. The lambda spanin components Rz and Rz1 undergo tertiary and quaternary rearrangements upon complex formation. Protein Sci 2011; 19:1967-77. [PMID: 20734329 DOI: 10.1002/pro.485] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Phage holins and endolysins have long been known to play key roles in lysis of the host cell, disrupting the cytoplasmic membrane and peptidoglycan (PG) layer, respectively. For phages of Gram-negative hosts, a third class of proteins, the spanins, are involved in disrupting the outer membrane (OM). Rz and Rz1, the components of the lambda spanin, are, respectively, a class II inner membrane protein and an OM lipoprotein, are thought to span the entire periplasm by virtue of C-terminal interactions of their soluble domains. Here, the periplasmic domains of Rz and Rz1 have been purified and shown to form dimeric and monomeric species, respectively, in solution. Circular dichroism analysis indicates that Rz has significant alpha-helical character, but much less than predicted, whereas Rz1, which is 25% proline, is unstructured. Mixture of the two proteins leads to complex formation and an increase in secondary structure, especially alpha-helical content. Moreover, transmission electron-microscopy reveals that Rz-Rz1 complexes form large rod-shaped structures which, although heterogeneous, exhibit periodicities that may reflect coiled-coil bundling as well as a long dimension that matches the width of the periplasm. A model is proposed suggesting that the formation of such bundles depends on the removal of the PG and underlies the Rz-Rz1 dependent disruption of the OM.
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Affiliation(s)
- Joel Berry
- Department of Biochemistry and Biophysics, 2128 TAMU, Texas A&M University, College Station, Texas 77843-2128, USA
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44
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Sabri M, Häuser R, Ouellette M, Liu J, Dehbi M, Moeck G, García E, Titz B, Uetz P, Moineau S. Genome annotation and intraviral interactome for the Streptococcus pneumoniae virulent phage Dp-1. J Bacteriol 2011; 193:551-62. [PMID: 21097633 PMCID: PMC3019816 DOI: 10.1128/jb.01117-10] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 11/08/2010] [Indexed: 11/20/2022] Open
Abstract
Streptococcus pneumoniae causes several diseases, including pneumonia, septicemia, and meningitis. Phage Dp-1 is one of the very few isolated virulent S. pneumoniae bacteriophages, but only a partial characterization is currently available. Here, we confirmed that Dp-1 belongs to the family Siphoviridae. Then, we determined its complete genomic sequence of 56,506 bp. It encodes 72 open reading frames, of which 44 have been assigned a function. We have identified putative promoters, Rho-independent terminators, and several genomic clusters. We provide evidence that Dp-1 may be using a novel DNA replication system as well as redirecting host protein synthesis through queuosine-containing tRNAs. Liquid chromatography-mass spectrometry analysis of purified phage Dp-1 particles identified at least eight structural proteins. Finally, using comprehensive yeast two-hybrid screens, we identified 156 phage protein interactions, and this intraviral interactome was used to propose a structural model of Dp-1.
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Affiliation(s)
- Mourad Sabri
- Département de Biochimie, de Microbiologie et Bio-Informatiques, Faculté des Sciences et de Génie, Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec, Canada G1V 0A6, Institute of Toxicology and Genetics, Karlsruhe Institute for Technology, Karlsruhe, Germany, Centre de Recherche en Infectiologie de l'Université Laval, Centre Hospitalier Universitaire de Québec, Québec, Canada G1V 4G2, The Medicines Company, Ville St. Laurent, Quebec, Canada, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain, Crump Institute for Molecular Imaging, Los Angeles, California, J. Craig Venter Institute, Rockville, Maryland
| | - Roman Häuser
- Département de Biochimie, de Microbiologie et Bio-Informatiques, Faculté des Sciences et de Génie, Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec, Canada G1V 0A6, Institute of Toxicology and Genetics, Karlsruhe Institute for Technology, Karlsruhe, Germany, Centre de Recherche en Infectiologie de l'Université Laval, Centre Hospitalier Universitaire de Québec, Québec, Canada G1V 4G2, The Medicines Company, Ville St. Laurent, Quebec, Canada, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain, Crump Institute for Molecular Imaging, Los Angeles, California, J. Craig Venter Institute, Rockville, Maryland
| | - Marc Ouellette
- Département de Biochimie, de Microbiologie et Bio-Informatiques, Faculté des Sciences et de Génie, Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec, Canada G1V 0A6, Institute of Toxicology and Genetics, Karlsruhe Institute for Technology, Karlsruhe, Germany, Centre de Recherche en Infectiologie de l'Université Laval, Centre Hospitalier Universitaire de Québec, Québec, Canada G1V 4G2, The Medicines Company, Ville St. Laurent, Quebec, Canada, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain, Crump Institute for Molecular Imaging, Los Angeles, California, J. Craig Venter Institute, Rockville, Maryland
| | - Jing Liu
- Département de Biochimie, de Microbiologie et Bio-Informatiques, Faculté des Sciences et de Génie, Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec, Canada G1V 0A6, Institute of Toxicology and Genetics, Karlsruhe Institute for Technology, Karlsruhe, Germany, Centre de Recherche en Infectiologie de l'Université Laval, Centre Hospitalier Universitaire de Québec, Québec, Canada G1V 4G2, The Medicines Company, Ville St. Laurent, Quebec, Canada, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain, Crump Institute for Molecular Imaging, Los Angeles, California, J. Craig Venter Institute, Rockville, Maryland
| | - Mohammed Dehbi
- Département de Biochimie, de Microbiologie et Bio-Informatiques, Faculté des Sciences et de Génie, Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec, Canada G1V 0A6, Institute of Toxicology and Genetics, Karlsruhe Institute for Technology, Karlsruhe, Germany, Centre de Recherche en Infectiologie de l'Université Laval, Centre Hospitalier Universitaire de Québec, Québec, Canada G1V 4G2, The Medicines Company, Ville St. Laurent, Quebec, Canada, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain, Crump Institute for Molecular Imaging, Los Angeles, California, J. Craig Venter Institute, Rockville, Maryland
| | - Greg Moeck
- Département de Biochimie, de Microbiologie et Bio-Informatiques, Faculté des Sciences et de Génie, Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec, Canada G1V 0A6, Institute of Toxicology and Genetics, Karlsruhe Institute for Technology, Karlsruhe, Germany, Centre de Recherche en Infectiologie de l'Université Laval, Centre Hospitalier Universitaire de Québec, Québec, Canada G1V 4G2, The Medicines Company, Ville St. Laurent, Quebec, Canada, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain, Crump Institute for Molecular Imaging, Los Angeles, California, J. Craig Venter Institute, Rockville, Maryland
| | - Ernesto García
- Département de Biochimie, de Microbiologie et Bio-Informatiques, Faculté des Sciences et de Génie, Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec, Canada G1V 0A6, Institute of Toxicology and Genetics, Karlsruhe Institute for Technology, Karlsruhe, Germany, Centre de Recherche en Infectiologie de l'Université Laval, Centre Hospitalier Universitaire de Québec, Québec, Canada G1V 4G2, The Medicines Company, Ville St. Laurent, Quebec, Canada, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain, Crump Institute for Molecular Imaging, Los Angeles, California, J. Craig Venter Institute, Rockville, Maryland
| | - Björn Titz
- Département de Biochimie, de Microbiologie et Bio-Informatiques, Faculté des Sciences et de Génie, Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec, Canada G1V 0A6, Institute of Toxicology and Genetics, Karlsruhe Institute for Technology, Karlsruhe, Germany, Centre de Recherche en Infectiologie de l'Université Laval, Centre Hospitalier Universitaire de Québec, Québec, Canada G1V 4G2, The Medicines Company, Ville St. Laurent, Quebec, Canada, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain, Crump Institute for Molecular Imaging, Los Angeles, California, J. Craig Venter Institute, Rockville, Maryland
| | - Peter Uetz
- Département de Biochimie, de Microbiologie et Bio-Informatiques, Faculté des Sciences et de Génie, Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec, Canada G1V 0A6, Institute of Toxicology and Genetics, Karlsruhe Institute for Technology, Karlsruhe, Germany, Centre de Recherche en Infectiologie de l'Université Laval, Centre Hospitalier Universitaire de Québec, Québec, Canada G1V 4G2, The Medicines Company, Ville St. Laurent, Quebec, Canada, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain, Crump Institute for Molecular Imaging, Los Angeles, California, J. Craig Venter Institute, Rockville, Maryland
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie et Bio-Informatiques, Faculté des Sciences et de Génie, Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec, Canada G1V 0A6, Institute of Toxicology and Genetics, Karlsruhe Institute for Technology, Karlsruhe, Germany, Centre de Recherche en Infectiologie de l'Université Laval, Centre Hospitalier Universitaire de Québec, Québec, Canada G1V 4G2, The Medicines Company, Ville St. Laurent, Quebec, Canada, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain, Crump Institute for Molecular Imaging, Los Angeles, California, J. Craig Venter Institute, Rockville, Maryland
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Dyer MD, Neff C, Dufford M, Rivera CG, Shattuck D, Bassaganya-Riera J, Murali TM, Sobral BW. The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis. PLoS One 2010; 5:e12089. [PMID: 20711500 PMCID: PMC2918508 DOI: 10.1371/journal.pone.0012089] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 07/17/2010] [Indexed: 01/01/2023] Open
Abstract
Background Bacillus anthracis, Francisella tularensis, and Yersinia pestis are bacterial pathogens that can cause anthrax, lethal acute pneumonic disease, and bubonic plague, respectively, and are listed as NIAID Category A priority pathogens for possible use as biological weapons. However, the interactions between human proteins and proteins in these bacteria remain poorly characterized leading to an incomplete understanding of their pathogenesis and mechanisms of immune evasion. Methodology In this study, we used a high-throughput yeast two-hybrid assay to identify physical interactions between human proteins and proteins from each of these three pathogens. From more than 250,000 screens performed, we identified 3,073 human-B. anthracis, 1,383 human-F. tularensis, and 4,059 human-Y. pestis protein-protein interactions including interactions involving 304 B. anthracis, 52 F. tularensis, and 330 Y. pestis proteins that are uncharacterized. Computational analysis revealed that pathogen proteins preferentially interact with human proteins that are hubs and bottlenecks in the human PPI network. In addition, we computed modules of human-pathogen PPIs that are conserved amongst the three networks. Functionally, such conserved modules reveal commonalities between how the different pathogens interact with crucial host pathways involved in inflammation and immunity. Significance These data constitute the first extensive protein interaction networks constructed for bacterial pathogens and their human hosts. This study provides novel insights into host-pathogen interactions.
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Affiliation(s)
- Matthew D. Dyer
- Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America
| | - Chris Neff
- Myriad Genetics, Salt Lake City, Utah, United States of America
| | - Max Dufford
- Myriad Genetics, Salt Lake City, Utah, United States of America
| | - Corban G. Rivera
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Donna Shattuck
- Myriad Genetics, Salt Lake City, Utah, United States of America
| | | | - T. M. Murali
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- * E-mail: (TMM); (BWS)
| | - Bruno W. Sobral
- Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America
- * E-mail: (TMM); (BWS)
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46
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Xie C, Gao J, Zhu RZ, Yuan YS, He HL, Huang QS, Han W, Yu Y. Protein-protein interaction map is a key gateway into liver regeneration. World J Gastroenterol 2010; 16:3491-8. [PMID: 20653057 PMCID: PMC2909548 DOI: 10.3748/wjg.v16.i28.3491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Recent studies indicate that the process of liver regeneration involves multiple signaling pathways and a variety of genes, cytokines and growth factors. Protein-protein interactions (PPIs) play a role in nearly all events that take place within the cell and PPI maps should be helpful in further understanding the process of liver regeneration. In this review, we discuss recent progress in understanding the PPIs that occur during liver regeneration especially those in the transforming growth factor β signaling pathways. We believe the use of large-scale PPI maps for integrating the information already known about the liver regeneration is a useful approach in understanding liver regeneration from the standpoint of systems biology.
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Abstract
We present a brief guide to resources on the Internet relating to Protein-Protein
Interactions. These include databases containing experimentally verified and computationally
inferred physical and functional interactions. There are also tools for predicting
interactions and for extracting information on interactions from the literature, and
organism specific databases.
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Affiliation(s)
- J Wixon
- Bioinformatics Division, HGMP-RC Hinxton, Cambridge CB10 1SB, UK
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48
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Mendez-Rios J, Uetz P. Global approaches to study protein-protein interactions among viruses and hosts. Future Microbiol 2010; 5:289-301. [PMID: 20143950 DOI: 10.2217/fmb.10.7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
While high-throughput protein-protein interaction screens were first published approximately 10 years ago, systematic attempts to map interactions among viruses and hosts started only a few years ago. HIV-human interactions dominate host-pathogen interaction databases (with approximately 2000 interactions) despite the fact that probably none of these interactions have been identified in systematic interaction screens. Recently, combinations of protein interaction data with RNAi and other functional genomics data allowed researchers to model more complex interaction networks. The rapid progress in this area promises a flood of new data in the near future, with clinical applications as soon as structural and functional genomics catches up with next-generation sequencing of human variation and structure-based drug design.
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Affiliation(s)
- Jorge Mendez-Rios
- J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.
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49
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Lemmens I, Lievens S, Tavernier J. Strategies towards high-quality binary protein interactome maps. J Proteomics 2010; 73:1415-20. [PMID: 20153845 DOI: 10.1016/j.jprot.2010.02.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Revised: 02/01/2010] [Accepted: 02/05/2010] [Indexed: 01/03/2023]
Abstract
Many processes in a cell depend on protein-protein interactions (PPIs) and perturbations of these interactions can lead to diseases. Comprehensive knowledge of PPI networks will not only give us information on how the cell is organized, but will also provide new drug targets. Current binary PPI networks are mainly generated by high-throughput yeast two-hybrid. Due to the small overlap of these maps, it has long been assumed that these maps are of low quality containing many false positives. However, by using an orthogonal two-hybrid method, MAPPIT (mammalian protein-protein interaction trap), these maps were shown to be of high quality suggesting that the limited overlap is likely due to low sensitivity and not to low specificity.
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Affiliation(s)
- Irma Lemmens
- Department of Medical Protein Research, VIB, Ghent, Belgium
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Golemis EA, Serebriiskii I, Finley RL, Kolonin MG, Gyuris J, Brent R. Interaction trap/two-hybrid system to identify interacting proteins. ACTA ACUST UNITED AC 2009; Chapter 19:19.2.1-19.2.35. [PMID: 19688737 DOI: 10.1002/0471140864.ps1902s57] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The yeast two-hybrid method (or interaction trap) is a powerful technique for detecting protein interactions. The procedure is performed using transcriptional activation of a dual reporter system in yeast to identify interactions between a protein of interest (the bait protein) and the candidate proteins for interaction. The method can be used to screen a protein library for interactions with a bait protein or to test for association between proteins that are expected to interact based on prior evidence. Interaction mating facilitates the screening of a library with multiple bait proteins.
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