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Contrasting Function of Structured N-Terminal and Unstructured C-Terminal Segments of Mycobacterium tuberculosis PPE37 Protein. mBio 2018; 9:mBio.01712-17. [PMID: 29362230 PMCID: PMC5784249 DOI: 10.1128/mbio.01712-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Pathogens frequently employ eukaryotic linear motif (ELM)-rich intrinsically disordered proteins (IDPs) to perturb and hijack host cell networks for a productive infection. Mycobacterium tuberculosis has a relatively high percentage of IDPs in its proteome, the significance of which is not known. The Mycobacterium-specific PE-PPE protein family has several members with unusually high levels of structural disorder and disorder-promoting Ala/Gly residues. PPE37 protein, a member of this family, carries an N-terminal PPE domain capable of iron binding, two transmembrane domains, and a disordered C-terminal segment harboring ELMs and a eukaryotic nuclear localization signal (NLS). PPE37, expressed as a function of low iron stress, was cleaved by M. tuberculosis protease into N- and C-terminal segments. A recombinant N-terminal segment (P37N) caused proliferation and differentiation of monocytic THP-1 cells, into CD11c, DC-SIGN (dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin)-positive semimature dendritic cells exhibiting high interleukin-10 (IL-10) but negligible IL-12 and also low tumor necrosis factor alpha (TNF-α) secretion—an environment suitable for maintaining tolerogenic immune cells. The C-terminal segment entered the macrophage nucleus and induced caspase-3-dependent apoptosis of host cells. Mice immunized with recombinant PPE37FL and PPE37N evoked strong anti-inflammatory response, validating the in vitro immunostimulatory effect. Analysis of the IgG response of PPE37FL and PPE37N revealed significant immunoreactivities in different categories of TB patients, viz. pulmonary TB (PTB) and extrapulmonary TB (EPTB), vis-a-vis healthy controls. These results support the role of IDPs in performing contrasting activities to modulate the host processes, possibly through molecular mimicry and cross talk in two spatially distinct host environments which may likely aid M. tuberculosis survival and pathogenesis. To hijack the human host cell machinery to enable survival inside macrophages, the pathogen Mycobacterium tuberculosis requires a repertoire of proteins that can mimic host protein function and modulate host cell machinery. Here, we have shown how a single protein can play multiple functions and hijack the host cell for the benefit of the pathogen. Full-length membrane-anchored PPE37 protein is cleaved into N- and C-terminal domains under iron-depleted conditions. The N-terminal domain facilitates the propathogen semimature tolerogenic state of dendritic cells, whereas the C-terminal segment is localized into host cell nucleus and induces apoptosis. The immune implications of these in vitro observations were assessed and validated in mice and also human TB patients. This study presents novel mechanistic insight adopted by M. tuberculosis to survive inside host cells.
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Gouw M, Michael S, Sámano-Sánchez H, Kumar M, Zeke A, Lang B, Bely B, Chemes LB, Davey NE, Deng Z, Diella F, Gürth CM, Huber AK, Kleinsorg S, Schlegel LS, Palopoli N, Roey KV, Altenberg B, Reményi A, Dinkel H, Gibson TJ. The eukaryotic linear motif resource - 2018 update. Nucleic Acids Res 2018; 46:D428-D434. [PMID: 29136216 PMCID: PMC5753338 DOI: 10.1093/nar/gkx1077] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 10/17/2017] [Accepted: 10/23/2017] [Indexed: 11/14/2022] Open
Abstract
Short linear motifs (SLiMs) are protein binding modules that play major roles in almost all cellular processes. SLiMs are short, often highly degenerate, difficult to characterize and hard to detect. The eukaryotic linear motif (ELM) resource (elm.eu.org) is dedicated to SLiMs, consisting of a manually curated database of over 275 motif classes and over 3000 motif instances, and a pipeline to discover candidate SLiMs in protein sequences. For 15 years, ELM has been one of the major resources for motif research. In this database update, we present the latest additions to the database including 32 new motif classes, and new features including Uniprot and Reactome integration. Finally, to help provide cellular context, we present some biological insights about SLiMs in the cell cycle, as targets for bacterial pathogenicity and their functionality in the human kinome.
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Affiliation(s)
- Marc Gouw
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Sushama Michael
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hugo Sámano-Sánchez
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - András Zeke
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Benjamin Lang
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Benoit Bely
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Lucía B Chemes
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires CP 1405, Argentina
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires CP 2160, Argentina
- Instituto de Investigaciones Biotecnoltógicas, Universidad Nacional de General San Martín, IIB-INTECH-CONICET, San Martín, Buenos Aires CP 1650, Argentina
| | - Norman E Davey
- UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ziqi Deng
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Francesca Diella
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | | | | | | | | | - Nicolás Palopoli
- Department of Science and Technology, Universidad Nacional de Quilmes, CONICET, Bernal B1876BXD, Buenos Aires, Argentina
| | - Kim V Roey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Brigitte Altenberg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Attila Reményi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Holger Dinkel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Leibniz-Institute on Aging, Fritz Lipmann Institute (FLI), Jena D-07745, Germany
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
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Som Chaudhury S, Das Mukhopadhyay C. Functional amyloids: interrelationship with other amyloids and therapeutic assessment to treat neurodegenerative diseases. Int J Neurosci 2017; 128:449-463. [PMID: 29076790 DOI: 10.1080/00207454.2017.1398153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Sutapa Som Chaudhury
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, West Bengal, India
| | - Chitrangada Das Mukhopadhyay
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, West Bengal, India
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Donderis J, Bowring J, Maiques E, Ciges-Tomas JR, Alite C, Mehmedov I, Tormo-Mas MA, Penadés JR, Marina A. Convergent evolution involving dimeric and trimeric dUTPases in pathogenicity island mobilization. PLoS Pathog 2017; 13:e1006581. [PMID: 28892519 PMCID: PMC5608427 DOI: 10.1371/journal.ppat.1006581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 09/21/2017] [Accepted: 08/15/2017] [Indexed: 11/18/2022] Open
Abstract
The dUTPase (Dut) enzymes, encoded by almost all free-living organisms and some viruses, prevent the misincorporation of uracil into DNA. We previously proposed that trimeric Duts are regulatory proteins involved in different cellular processes; including the phage-mediated transfer of the Staphylococcus aureus pathogenicity island SaPIbov1. Recently, it has been shown that the structurally unrelated dimeric Dut encoded by phage ϕNM1 is similarly able to mobilize SaPIbov1, suggesting dimeric Duts could also be regulatory proteins. How this is accomplished remains unsolved. Here, using in vivo, biochemical and structural approaches, we provide insights into the signaling mechanism used by the dimeric Duts to induce the SaPIbov1 cycle. As reported for the trimeric Duts, dimeric Duts contain an extremely variable region, here named domain VI, which is involved in the regulatory capacity of these enzymes. Remarkably, our results also show that the dimeric Dut signaling mechanism is modulated by dUTP, as with the trimeric Duts. Overall, our results demonstrate that although unrelated both in sequence and structure, dimeric and trimeric Duts control SaPI transfer by analogous mechanisms, representing a fascinating example of convergent evolution. This conserved mode of action highlights the biological significance of Duts as regulatory molecules.
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Affiliation(s)
- Jorge Donderis
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Janine Bowring
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Elisa Maiques
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - J. Rafael Ciges-Tomas
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Christian Alite
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Iltyar Mehmedov
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - María Angeles Tormo-Mas
- Departamento de Ciencias Biomédicas, Universidad CEU Cardenal Herrera, Moncada, Valencia, Spain
| | - José R. Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail: (AM); (JRP)
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
- * E-mail: (AM); (JRP)
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55
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Zanzoni A, Spinelli L, Braham S, Brun C. Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins. MICROBIOME 2017; 5:89. [PMID: 28793925 PMCID: PMC5551000 DOI: 10.1186/s40168-017-0307-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 07/13/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Fusobacterium nucleatum is a gram-negative anaerobic species residing in the oral cavity and implicated in several inflammatory processes in the human body. Although F. nucleatum abundance is increased in inflammatory bowel disease subjects and is prevalent in colorectal cancer patients, the causal role of the bacterium in gastrointestinal disorders and the mechanistic details of host cell functions subversion are not fully understood. RESULTS We devised a computational strategy to identify putative secreted F. nucleatum proteins (FusoSecretome) and to infer their interactions with human proteins based on the presence of host molecular mimicry elements. FusoSecretome proteins share similar features with known bacterial virulence factors thereby highlighting their pathogenic potential. We show that they interact with human proteins that participate in infection-related cellular processes and localize in established cellular districts of the host-pathogen interface. Our network-based analysis identified 31 functional modules in the human interactome preferentially targeted by 138 FusoSecretome proteins, among which we selected 26 as main candidate virulence proteins, representing both putative and known virulence proteins. Finally, six of the preferentially targeted functional modules are implicated in the onset and progression of inflammatory bowel diseases and colorectal cancer. CONCLUSIONS Overall, our computational analysis identified candidate virulence proteins potentially involved in the F. nucleatum-human cross-talk in the context of gastrointestinal diseases.
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Affiliation(s)
- Andreas Zanzoni
- Aix-Marseille Université, Inserm, TAGC UMR_S1090, Marseille, France.
| | - Lionel Spinelli
- Aix-Marseille Université, Inserm, TAGC UMR_S1090, Marseille, France
| | - Shérazade Braham
- Aix-Marseille Université, Inserm, TAGC UMR_S1090, Marseille, France
| | - Christine Brun
- Aix-Marseille Université, Inserm, TAGC UMR_S1090, Marseille, France
- CNRS, Marseille, France
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56
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Gouw M, Sámano-Sánchez H, Van Roey K, Diella F, Gibson TJ, Dinkel H. Exploring Short Linear Motifs Using the ELM Database and Tools. ACTA ACUST UNITED AC 2017; 58:8.22.1-8.22.35. [PMID: 28654726 DOI: 10.1002/cpbi.26] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Eukaryotic Linear Motif (ELM) resource is dedicated to the characterization and prediction of short linear motifs (SLiMs). SLiMs are compact, degenerate peptide segments found in many proteins and essential to almost all cellular processes. However, despite their abundance, SLiMs remain largely uncharacterized. The ELM database is a collection of manually annotated SLiM instances curated from experimental literature. In this article we illustrate how to browse and search the database for curated SLiM data, and cover the different types of data integrated in the resource. We also cover how to use this resource in order to predict SLiMs in known as well as novel proteins, and how to interpret the results generated by the ELM prediction pipeline. The ELM database is a very rich resource, and in the following protocols we give helpful examples to demonstrate how this knowledge can be used to improve your own research. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Marc Gouw
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Hugo Sámano-Sánchez
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kim Van Roey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Francesca Diella
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Holger Dinkel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Leibniz-Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
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57
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Davey NE, Seo MH, Yadav VK, Jeon J, Nim S, Krystkowiak I, Blikstad C, Dong D, Markova N, Kim PM, Ivarsson Y. Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome. FEBS J 2017; 284:485-498. [PMID: 28002650 DOI: 10.1111/febs.13995] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/04/2016] [Accepted: 12/19/2016] [Indexed: 12/29/2022]
Abstract
The intrinsically disordered regions of eukaryotic proteomes are enriched in short linear motifs (SLiMs), which are of crucial relevance for cellular signaling and protein regulation; many mediate interactions by providing binding sites for peptide-binding domains. The vast majority of SLiMs remain to be discovered highlighting the need for experimental methods for their large-scale identification. We present a novel proteomic peptide phage display (ProP-PD) library that displays peptides representing the disordered regions of the human proteome, allowing direct large-scale interrogation of most potential binding SLiMs in the proteome. The performance of the ProP-PD library was validated through selections against SLiM-binding bait domains with distinct folds and binding preferences. The vast majority of identified binding peptides contained sequences that matched the known SLiM-binding specificities of the bait proteins. For SHANK1 PDZ, we establish a novel consensus TxF motif for its non-C-terminal ligands. The binding peptides mostly represented novel target proteins, however, several previously validated protein-protein interactions (PPIs) were also discovered. We determined the affinities between the VHS domain of GGA1 and three identified ligands to 40-130 μm through isothermal titration calorimetry, and confirmed interactions through coimmunoprecipitation using full-length proteins. Taken together, we outline a general pipeline for the design and construction of ProP-PD libraries and the analysis of ProP-PD-derived, SLiM-based PPIs. We demonstrated the methods potential to identify low affinity motif-mediated interactions for modular domains with distinct binding preferences. The approach is a highly useful complement to the current toolbox of methods for PPI discovery.
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Affiliation(s)
- Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Ireland
| | - Moon-Hyeong Seo
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada
| | | | - Jouhyun Jeon
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada
| | - Satra Nim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada
| | - Izabella Krystkowiak
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Ireland
| | | | - Debbie Dong
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada
| | | | - Philip M Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada.,Department of Molecular Genetics and Department of Computer Science, University of Toronto, Canada
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Sweden
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58
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A bioinformatics pipeline to search functional motifs within whole-proteome data: a case study of poxviruses. Virus Genes 2016; 53:173-178. [PMID: 28000080 PMCID: PMC5357487 DOI: 10.1007/s11262-016-1416-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 12/01/2016] [Indexed: 12/19/2022]
Abstract
Proteins harbor domains or short linear motifs, which facilitate their functions and interactions. Finding functional motifs in protein sequences could predict the putative cellular roles or characteristics of hypothetical proteins. In this study, we present Shetti-Motif, which is an interactive tool to (i) map UniProt and PROSITE flat files, (ii) search for multiple pre-defined consensus patterns or experimentally validated functional motifs in large datasets protein sequences (proteome-wide), (iii) search for motifs containing repeated residues (low-complexity regions, e.g., Leu-, SR-, PEST-rich motifs, etc.). As proof of principle, using this comparative proteomics pipeline, eleven proteomes encoded by member of Poxviridae family were searched against about 100 experimentally validated functional motifs. The closely related viruses and viruses infect the same host cells (e.g. vaccinia and variola viruses) show similar motif-containing proteins profile. The motifs encoded by these viruses are correlated, which explains why poxviruses are able to interact with wide range of host cells. In conclusion, this in silico analysis is useful to establish a dataset(s) or potential proteins for further investigation or compare between species.
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59
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Sen R, Nayak L, De RK. A review on host-pathogen interactions: classification and prediction. Eur J Clin Microbiol Infect Dis 2016; 35:1581-99. [PMID: 27470504 DOI: 10.1007/s10096-016-2716-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/22/2016] [Indexed: 01/01/2023]
Abstract
The research on host-pathogen interactions is an ever-emerging and evolving field. Every other day a new pathogen gets discovered, along with comes the challenge of its prevention and cure. As the intelligent human always vies for prevention, which is better than cure, understanding the mechanisms of host-pathogen interactions gets prior importance. There are many mechanisms involved from the pathogen as well as the host sides while an interaction happens. It is a vis-a-vis fight of the counter genes and proteins from both sides. Who wins depends on whether a host gets an infection or not. Moreover, a higher level of complexity arises when the pathogens evolve and become resistant to a host's defense mechanisms. Such pathogens pose serious challenges for treatment. The entire human population is in danger of such long-lasting persistent infections. Some of these infections even increase the rate of mortality. Hence there is an immediate emergency to understand how the pathogens interact with their host for successful invasion. It may lead to discovery of appropriate preventive measures, and the development of rational therapeutic measures and medication against such infections and diseases. This review, a state-of-the-art updated scenario of host-pathogen interaction research, has been done by keeping in mind this urgency. It covers the biological and computational aspects of host-pathogen interactions, classification of the methods by which the pathogens interact with their hosts, different machine learning techniques for prediction of host-pathogen interactions, and future scopes of this research field.
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Affiliation(s)
- R Sen
- Machine Intelligence Unit, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700108, India
| | - L Nayak
- Machine Intelligence Unit, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700108, India
| | - R K De
- Machine Intelligence Unit, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700108, India.
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60
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Tossavainen H, Aitio O, Hellman M, Saksela K, Permi P. Structural Basis of the High Affinity Interaction between the Alphavirus Nonstructural Protein-3 (nsP3) and the SH3 Domain of Amphiphysin-2. J Biol Chem 2016; 291:16307-17. [PMID: 27268056 DOI: 10.1074/jbc.m116.732412] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Indexed: 12/25/2022] Open
Abstract
We show that a peptide from Chikungunya virus nsP3 protein spanning residues 1728-1744 binds the amphiphysin-2 (BIN1) Src homology-3 (SH3) domain with an unusually high affinity (Kd 24 nm). Our NMR solution complex structure together with isothermal titration calorimetry data on several related viral and cellular peptide ligands reveal that this exceptional affinity originates from interactions between multiple basic residues in the target peptide and the extensive negatively charged binding surface of amphiphysin-2 SH3. Remarkably, these arginines show no fixed conformation in the complex structure, indicating that a transient or fluctuating polyelectrostatic interaction accounts for this affinity. Thus, via optimization of such dynamic electrostatic forces, viral peptides have evolved a superior binding affinity for amphiphysin-2 SH3 compared with typical cellular ligands, such as dynamin, thereby enabling hijacking of amphiphysin-2 SH3-regulated host cell processes by these viruses. Moreover, our data show that the previously described consensus sequence PXRPXR for amphiphysin SH3 ligands is inaccurate and instead define it as an extended Class II binding motif PXXPXRpXR, where additional positive charges between the two constant arginine residues can give rise to extraordinary high SH3 binding affinity.
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Affiliation(s)
- Helena Tossavainen
- From the Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki and
| | - Olli Aitio
- From the Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki and
| | - Maarit Hellman
- From the Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki and
| | - Kalle Saksela
- the Department of Virology, University of Helsinki and Helsinki University Hospital, FI-00014 Helsinki, Finland and
| | - Perttu Permi
- From the Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki and the Departments of Biological and Environmental Science and Chemistry, Nanoscience Center, University of Jyvaskyla, FI-40014 Jyvaskyla, Finland
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61
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Lobb B, Doxey AC. Novel function discovery through sequence and structural data mining. Curr Opin Struct Biol 2016; 38:53-61. [DOI: 10.1016/j.sbi.2016.05.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 05/17/2016] [Accepted: 05/24/2016] [Indexed: 01/30/2023]
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62
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Sobhy H. A Review of Functional Motifs Utilized by Viruses. Proteomes 2016; 4:proteomes4010003. [PMID: 28248213 PMCID: PMC5217368 DOI: 10.3390/proteomes4010003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 01/07/2016] [Accepted: 01/13/2016] [Indexed: 01/05/2023] Open
Abstract
Short linear motifs (SLiM) are short peptides that facilitate protein function and protein-protein interactions. Viruses utilize these motifs to enter into the host, interact with cellular proteins, or egress from host cells. Studying functional motifs may help to predict protein characteristics, interactions, or the putative cellular role of a protein. In virology, it may reveal aspects of the virus tropism and help find antiviral therapeutics. This review highlights the recent understanding of functional motifs utilized by viruses. Special attention was paid to the function of proteins harboring these motifs, and viruses encoding these proteins. The review highlights motifs involved in (i) immune response and post-translational modifications (e.g., ubiquitylation, SUMOylation or ISGylation); (ii) virus-host cell interactions, including virus attachment, entry, fusion, egress and nuclear trafficking; (iii) virulence and antiviral activities; (iv) virion structure; and (v) low-complexity regions (LCRs) or motifs enriched with residues (Xaa-rich motifs).
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Affiliation(s)
- Haitham Sobhy
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden.
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63
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Dinkel H, Van Roey K, Michael S, Kumar M, Uyar B, Altenberg B, Milchevskaya V, Schneider M, Kühn H, Behrendt A, Dahl SL, Damerell V, Diebel S, Kalman S, Klein S, Knudsen AC, Mäder C, Merrill S, Staudt A, Thiel V, Welti L, Davey NE, Diella F, Gibson TJ. ELM 2016--data update and new functionality of the eukaryotic linear motif resource. Nucleic Acids Res 2016; 44:D294-300. [PMID: 26615199 PMCID: PMC4702912 DOI: 10.1093/nar/gkv1291] [Citation(s) in RCA: 224] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 01/18/2023] Open
Abstract
The Eukaryotic Linear Motif (ELM) resource (http://elm.eu.org) is a manually curated database of short linear motifs (SLiMs). In this update, we present the latest additions to this resource, along with more improvements to the web interface. ELM 2016 contains more than 240 different motif classes with over 2700 experimentally validated instances, manually curated from more than 2400 scientific publications. In addition, more data have been made available as individually searchable pages and are downloadable in various formats.
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Affiliation(s)
- Holger Dinkel
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Kim Van Roey
- Health Services Research Unit, Operational Direction Public Health and Surveillance, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Sushama Michael
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Manjeet Kumar
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Bora Uyar
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Brigitte Altenberg
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Vladislava Milchevskaya
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Helen Kühn
- Ruprecht-Karls-Universität, Heidelberg, Germany
| | | | | | | | | | - Sara Kalman
- Ruprecht-Karls-Universität, Heidelberg, Germany
| | | | | | | | | | | | - Vera Thiel
- Ruprecht-Karls-Universität, Heidelberg, Germany
| | - Lukas Welti
- Ruprecht-Karls-Universität, Heidelberg, Germany
| | - Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland
| | - Francesca Diella
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Toby J Gibson
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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Tesina P, Čermáková K, Hořejší M, Procházková K, Fábry M, Sharma S, Christ F, Demeulemeester J, Debyser Z, Rijck JD, Veverka V, Řezáčová P. Multiple cellular proteins interact with LEDGF/p75 through a conserved unstructured consensus motif. Nat Commun 2015; 6:7968. [PMID: 26245978 DOI: 10.1038/ncomms8968] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 07/01/2015] [Indexed: 01/09/2023] Open
Abstract
Lens epithelium-derived growth factor (LEDGF/p75) is an epigenetic reader and attractive therapeutic target involved in HIV integration and the development of mixed lineage leukaemia (MLL1) fusion-driven leukaemia. Besides HIV integrase and the MLL1-menin complex, LEDGF/p75 interacts with various cellular proteins via its integrase binding domain (IBD). Here we present structural characterization of IBD interactions with transcriptional repressor JPO2 and domesticated transposase PogZ, and show that the PogZ interaction is nearly identical to the interaction of LEDGF/p75 with MLL1. The interaction with the IBD is maintained by an intrinsically disordered IBD-binding motif (IBM) common to all known cellular partners of LEDGF/p75. In addition, based on IBM conservation, we identify and validate IWS1 as a novel LEDGF/p75 interaction partner. Our results also reveal how HIV integrase efficiently displaces cellular binding partners from LEDGF/p75. Finally, the similar binding modes of LEDGF/p75 interaction partners represent a new challenge for the development of selective interaction inhibitors.
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Affiliation(s)
- Petr Tesina
- Institute of Organic Chemistry and Biochemistry of the ASCR, v.v.i., Flemingovo nam. 2, 166 10 Prague, Czech Republic.,Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, 128 44 Prague, Czech Republic.,Institute of Molecular Genetics of the ASCR, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic
| | - Kateřina Čermáková
- KU Leuven, Molecular Virology and Gene Therapy, Kapucijnenvoer 33, B-3000 Leuven, Belgium
| | - Magdalena Hořejší
- Institute of Molecular Genetics of the ASCR, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic
| | - Kateřina Procházková
- Institute of Organic Chemistry and Biochemistry of the ASCR, v.v.i., Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics of the ASCR, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic
| | - Subhalakshmi Sharma
- KU Leuven, Molecular Virology and Gene Therapy, Kapucijnenvoer 33, B-3000 Leuven, Belgium
| | - Frauke Christ
- KU Leuven, Molecular Virology and Gene Therapy, Kapucijnenvoer 33, B-3000 Leuven, Belgium
| | - Jonas Demeulemeester
- KU Leuven, Molecular Virology and Gene Therapy, Kapucijnenvoer 33, B-3000 Leuven, Belgium
| | - Zeger Debyser
- KU Leuven, Molecular Virology and Gene Therapy, Kapucijnenvoer 33, B-3000 Leuven, Belgium
| | - Jan De Rijck
- KU Leuven, Molecular Virology and Gene Therapy, Kapucijnenvoer 33, B-3000 Leuven, Belgium
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry of the ASCR, v.v.i., Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry of the ASCR, v.v.i., Flemingovo nam. 2, 166 10 Prague, Czech Republic.,Institute of Molecular Genetics of the ASCR, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic
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65
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Hakimi MA, Bougdour A. Toxoplasma 's ways of manipulating the host transcriptome via secreted effectors. Curr Opin Microbiol 2015; 26:24-31. [DOI: 10.1016/j.mib.2015.04.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 04/06/2015] [Accepted: 04/08/2015] [Indexed: 12/12/2022]
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66
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Convergent evolution and mimicry of protein linear motifs in host–pathogen interactions. Curr Opin Struct Biol 2015; 32:91-101. [DOI: 10.1016/j.sbi.2015.03.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/09/2015] [Accepted: 03/15/2015] [Indexed: 12/21/2022]
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67
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Zhao Y, Dua P, Lukiw WJ. Microbial Sources of Amyloid and Relevance to Amyloidogenesis and Alzheimer's Disease (AD). JOURNAL OF ALZHEIMER'S DISEASE & PARKINSONISM 2015; 5:177. [PMID: 25977840 PMCID: PMC4428612 DOI: 10.4172/2161-0460.1000177] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Since the inception of the human microbiome project (HMP) by the US National Institutes of Health (NIH) in 2007 there has been a keen resurgence in our recognition of the human microbiome and its contribution to development, immunity, neurophysiology, metabolic and nutritive support to central nervous system (CNS) health and disease. What is not generally appreciated is that (i) the ~1014 microbial cells that comprise the human microbiome outnumber human host cells by approximately one hundred-to-one; (ii) together the microbial genes of the microbiome outnumber human host genes by about one hundred-and-fifty to one; (iii) collectively these microbes constitute the largest 'diffuse organ system' in the human body, more metabolically active than the liver; strongly influencing host nutritive-, innate-immune, neuroinflammatory-, neuromodulatory- and neurotransmission-functions; and (iv) that these microbes actively secrete highly complex, immunogenic mixtures of lipopolysaccharide (LPS) and amyloid from their outer membranes into their immediate environment. While secreted LPS and amyloids are generally quite soluble as monomers over time they form into highly insoluble fibrous protein aggregates that are implicated in the progressive degenerative neuropathology of several common, age-related disorders of the human CNS including Alzheimer's disease (AD). This general commentary-perspective paper will highlight some recent findings on microbial-derived secreted LPS and amyloids and the potential contribution of these neurotoxic and proinflammatory microbial exudates to age-related inflammatory amyloidogenesis and neurodegeneration, with specific reference to AD wherever possible.
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Affiliation(s)
- Y Zhao
- LSU Neuroscience Center, Louisiana State University Health Sciences Center, 2020 Gravier Street, New Orleans LA 70112 USA ; Department of Cell Biology and Anatomy, Louisiana State University Health Sciences Center, 1901 Perdido Street, New Orleans LA 70112 USA
| | - P Dua
- Department of Health Information Management, Louisiana State University Ruston LA 71270 USA
| | - W J Lukiw
- LSU Neuroscience Center, Louisiana State University Health Sciences Center, 2020 Gravier Street, New Orleans LA 70112 USA ; Department of Ophthalmology, Louisiana State University Health Sciences Center, 533 Bolivar Street, New Orleans LA 70112 USA ; Department of Neurology, Louisiana State University Health Sciences Center, 1542 Tulane Avenue, New Orleans LA 70112 USA
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68
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Duro N, Miskei M, Fuxreiter M. Fuzziness endows viral motif-mimicry. MOLECULAR BIOSYSTEMS 2015; 11:2821-9. [DOI: 10.1039/c5mb00301f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The local dynamics of host and viral peptide motifs suggests a different scenario for partner recognition. Host peptide motifs serve as molecular recognition elements, while viral motifs preserve the structural heterogeneity and remain fuzzy when bound to the host.
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Affiliation(s)
- Norbert Duro
- MTA-DE Momentum
- Laboratory of Protein Dynamics
- Department of Biochemistry and Molecular Biology
- University of Debrecen
- Hungary
| | - Marton Miskei
- MTA-DE Momentum
- Laboratory of Protein Dynamics
- Department of Biochemistry and Molecular Biology
- University of Debrecen
- Hungary
| | - Monika Fuxreiter
- MTA-DE Momentum
- Laboratory of Protein Dynamics
- Department of Biochemistry and Molecular Biology
- University of Debrecen
- Hungary
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