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Gupta SK, Ponte-Sucre A, Bencurova E, Dandekar T. An Ebola, Neisseria and Trypanosoma human protein interaction census reveals a conserved human protein cluster targeted by various human pathogens. Comput Struct Biotechnol J 2021; 19:5292-5308. [PMID: 34745452 PMCID: PMC8531761 DOI: 10.1016/j.csbj.2021.09.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/28/2022] Open
Abstract
Filovirus ebolavirus (ZE; Zaire ebolavirus, Bundibugyo ebolavirus), Neisseria meningitidis (NM), and Trypanosoma brucei (Tb) are serious infectious pathogens, spanning viruses, bacteria and protists and all may target the blood and central nervous system during their life cycle. NM and Tb are extracellular pathogens while ZE is obligatory intracellular, targetting immune privileged sites. By using interactomics and comparative evolutionary analysis we studied whether conserved human proteins are targeted by these pathogens. We examined 2797 unique pathogen-targeted human proteins. The information derived from orthology searches of experimentally validated protein-protein interactions (PPIs) resulted both in unique and shared PPIs for each pathogen. Comparing and analyzing conserved and pathogen-specific infection pathways for NM, TB and ZE, we identified human proteins predicted to be targeted in at least two of the compared host-pathogen networks. However, four proteins were common to all three host-pathogen interactomes: the elongation factor 1-alpha 1 (EEF1A1), the SWI/SNF complex subunit SMARCC2 (matrix-associated actin-dependent regulator of chromatin subfamily C), the dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (RPN1), and the tubulin beta-5 chain (TUBB). These four human proteins all are also involved in cytoskeleton and its regulation and are often addressed by various human pathogens. Specifically, we found (i) 56 human pathogenic bacteria and viruses that target these four proteins, (ii) the well researched new pandemic pathogen SARS-CoV-2 targets two of these four human proteins and (iii) nine human pathogenic fungi (yet another evolutionary distant organism group) target three of the conserved proteins by 130 high confidence interactions.
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Affiliation(s)
- Shishir K Gupta
- Functional Genomics & Systems Biology Group, Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany
- Evolutionary Genomics Group, Center for Computational and Theoretical Biology, University of Würzburg, 97078 Würzburg, Germany
| | - Alicia Ponte-Sucre
- Laboratorio de Fisiología Molecular, Instituto de Medicina Experimental, Escuela Luis Razetti, Universidad Central de Venezuela, Caracas, Venezuela
- Medical Mission Institute, Hermann-Schell-Str. 7, 97074 Würzburg, Germany
| | - Elena Bencurova
- Functional Genomics & Systems Biology Group, Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany
| | - Thomas Dandekar
- Functional Genomics & Systems Biology Group, Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany
- EMBL Heidelberg, BioComputing Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
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Identification of a Chitooligosaccharide Mechanism against Bacterial Leaf Blight on Rice by In Vitro and In Silico Studies. Int J Mol Sci 2021; 22:ijms22157990. [PMID: 34360756 PMCID: PMC8347687 DOI: 10.3390/ijms22157990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/14/2021] [Accepted: 07/18/2021] [Indexed: 12/12/2022] Open
Abstract
This study focuses on a commercial plant elicitor based on chitooligosaccharides (BIG®), which aids in rice plant growth and disease resistance to bacterial leaf blight (BLB). When the pathogen (Xoo) vigorously attacks rice that has suffered yield losses, it can cause damage in up to 20% of the plant. Furthermore, Xoo is a seed-borne pathogen that can survive in rice seeds for an extended period. In this study, when rice seeds were soaked and sprayed with BIG®, there was a significant increase in shoot and root length, as well as plant biomass. Furthermore, BIG®-treated rice plants showed a significant reduction in BLB severity of more than 33%. Synchrotron radiation-based Fourier transform infrared (SR-FTIR) analysis was used to characterize BIG®’s mechanism in the chemical structure of rice leaves. The SR-FTIR results at 1650, 1735, and 1114 cm−1 indicated changes in biochemical components such as pectins, lignins, proteins, and celluloses. These findings demonstrated that commercial BIG® not only increased rice growth but also induced resistance to BLB. The drug’s target enzyme, Xoo 1075 from Xanthomonas oryzae (PDB ID: 5CY8), was analyzed for its interactions with polymer ingredients, specifically chitooligosaccharides, to gain molecular insights down to the atomic level. The results are intriguing, with a strong binding of the chitooligosaccharide polymer with the drug target, revealing 10 hydrogen bonds between the protein and polymer. Overall, the computational analysis supported the experimentally demonstrated strong binding of chitooligosaccharides to the drug target.
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Thepbandit W, Papathoti NK, Daddam JR, Thumanu K, Siriwong S, Thanh TL, Buensanteai N. Identification of Salicylic Acid Mechanism against Leaf Blight Disease in Oryza sativa by SR-FTIR Microspectroscopic and Docking Studies. Pathogens 2021; 10:652. [PMID: 34074035 PMCID: PMC8225197 DOI: 10.3390/pathogens10060652] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/09/2021] [Accepted: 05/19/2021] [Indexed: 01/05/2023] Open
Abstract
The present study was to investigate the application and mechanism of salicylic acid (SA) as SA-Ricemate for the control of leaf blight disease using a Synchrotron Radiation-based Fourier-Transform Infra-Red (SR-FTIR) microspectroscopy and docking studies. After treating rice plants cv. KDML 105 with SA-Ricemate, the leaves were inoculated with Xanthomonas oryzae pv. oryzae, the causal agent of leaf blight, and disease severity were assessed. The leaves were also used to detect changes in endogenous SA content. The results indicated that SA-Ricemate, as an activated compound, reduced disease severity by 60% at three weeks post-inoculation and increased endogenous content by 50%. The SR-FTIR analysis of changes in the mesophyll of leaves (treated and untreated) showed that the groups of lipids, pectins, and proteins amide I and amide II occurred at higher values, and polysaccharides were shown at lower values in treated compared to untreated. Besides, docking studies were used to model a three-dimensional structure for Pathogenesis-related (PR1b) protein and further identify its interaction with SA. The results showed that ASP28, ARG31, LEU32, GLN97, and ALA93 are important residues that have strong hydrogen bonds with SA. The docking results showed that SA has a good interaction, confirming its role in expression.
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Affiliation(s)
- Wannaporn Thepbandit
- School of Crop Production Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (W.T.); (N.K.P.)
| | - Narendra Kumar Papathoti
- School of Crop Production Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (W.T.); (N.K.P.)
| | - Jayasimha Rayalu Daddam
- Department of Animal Science, Agriculture Research Organization, Volcani Center, Rishon Lezion 7505101, Israel;
| | - Kanjana Thumanu
- Synchrotron Light Research Institute, Nakhon Ratchasima 30000, Thailand; (K.T.); (S.S.)
| | - Supatcharee Siriwong
- Synchrotron Light Research Institute, Nakhon Ratchasima 30000, Thailand; (K.T.); (S.S.)
| | - Toan Le Thanh
- Department of Plant Protection, Can Tho University, Can Tho City 900000, Vietnam;
| | - Natthiya Buensanteai
- School of Crop Production Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (W.T.); (N.K.P.)
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Retanal C, Ball B, Geddes-McAlister J. Post-Translational Modifications Drive Success and Failure of Fungal-Host Interactions. J Fungi (Basel) 2021; 7:jof7020124. [PMID: 33572187 PMCID: PMC7914884 DOI: 10.3390/jof7020124] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/11/2022] Open
Abstract
Post-translational modifications (PTMs) change the structure and function of proteins and regulate a diverse array of biological processes. Fungal pathogens rely on PTMs to modulate protein production and activity during infection, manipulate the host response, and ultimately, promote fungal survival. Given the high mortality rates of fungal infections on a global scale, along with the emergence of antifungal-resistant species, identifying new treatment options is critical. In this review, we focus on the role of PTMs (e.g., phosphorylation, acetylation, ubiquitination, glycosylation, and methylation) among the highly prevalent and medically relevant fungal pathogens, Candida spp., Aspergillus spp., and Cryptococcus spp. We explore the role of PTMs in fungal stress response and host adaptation, the use of PTMs to manipulate host cells and the immune system upon fungal invasion, and the importance of PTMs in conferring antifungal resistance. We also provide a critical view on the current knowledgebase, pose questions key to our understanding of the intricate roles of PTMs within fungal pathogens, and provide research opportunities to uncover new therapeutic strategies.
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Whisnant AW, Jürges CS, Hennig T, Wyler E, Prusty B, Rutkowski AJ, L'hernault A, Djakovic L, Göbel M, Döring K, Menegatti J, Antrobus R, Matheson NJ, Künzig FWH, Mastrobuoni G, Bielow C, Kempa S, Liang C, Dandekar T, Zimmer R, Landthaler M, Grässer F, Lehner PJ, Friedel CC, Erhard F, Dölken L. Integrative functional genomics decodes herpes simplex virus 1. Nat Commun 2020; 11:2038. [PMID: 32341360 PMCID: PMC7184758 DOI: 10.1038/s41467-020-15992-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 04/06/2020] [Indexed: 12/15/2022] Open
Abstract
The predicted 80 open reading frames (ORFs) of herpes simplex virus 1 (HSV-1) have been intensively studied for decades. Here, we unravel the complete viral transcriptome and translatome during lytic infection with base-pair resolution by computational integration of multi-omics data. We identify a total of 201 transcripts and 284 ORFs including all known and 46 novel large ORFs. This includes a so far unknown ORF in the locus deleted in the FDA-approved oncolytic virus Imlygic. Multiple transcript isoforms expressed from individual gene loci explain translation of the vast majority of ORFs as well as N-terminal extensions (NTEs) and truncations. We show that NTEs with non-canonical start codons govern the subcellular protein localization and packaging of key viral regulators and structural proteins. We extend the current nomenclature to include all viral gene products and provide a genome browser that visualizes all the obtained data from whole genome to single-nucleotide resolution.
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Affiliation(s)
- Adam W Whisnant
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Christopher S Jürges
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
| | - Bhupesh Prusty
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Andrzej J Rutkowski
- Department of Medicine, University of Cambridge, Box 157, Addenbrookes Hospital, Hills Road, CB2 0QQ, Cambridge, UK
| | - Anne L'hernault
- Department of Medicine, University of Cambridge, Box 157, Addenbrookes Hospital, Hills Road, CB2 0QQ, Cambridge, UK
| | - Lara Djakovic
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Margarete Göbel
- Core Unit Systems Medicine, Julius-Maximilians-University Würzburg, Josef-Schneider-Str. 2/D15, 97080, Würzburg, Germany
| | - Kristina Döring
- Core Unit Systems Medicine, Julius-Maximilians-University Würzburg, Josef-Schneider-Str. 2/D15, 97080, Würzburg, Germany
| | - Jennifer Menegatti
- Institute of Virology, Building 47, Saarland University Medical School, 66421, Homburg, Saar, Germany
| | - Robin Antrobus
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Florian W H Künzig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Guido Mastrobuoni
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
| | - Chris Bielow
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
| | - Stefan Kempa
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
| | - Chunguang Liang
- Department of Bioinformatics, Biocenter, Am Hubland, Julius-Maximilians-University Würzburg, 97074, Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, Am Hubland, Julius-Maximilians-University Würzburg, 97074, Würzburg, Germany
| | - Ralf Zimmer
- Institute of Informatics, Ludwig-Maximilians-Universität München, Amalienstr. 17, 80333, Munich, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
| | - Friedrich Grässer
- Institute of Virology, Building 47, Saarland University Medical School, 66421, Homburg, Saar, Germany
| | - Paul J Lehner
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Caroline C Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, Amalienstr. 17, 80333, Munich, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany.
| | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany.
- Department of Medicine, University of Cambridge, Box 157, Addenbrookes Hospital, Hills Road, CB2 0QQ, Cambridge, UK.
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), 97080, Würzburg, Germany.
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Gacemi S, Benarous K, Imperial S, Yousfi M. Lepidine B & E as New Target Inhibitors from Lepidium Sativum Seeds Against Four Enzymes of the Pathogen Candida albicans: In Vitro and In Silico Studies. Endocr Metab Immune Disord Drug Targets 2019; 20:127-138. [PMID: 30987578 DOI: 10.2174/1871530319666190415141520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/08/2019] [Accepted: 03/15/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND OBJECTIVE The present paper aims to study the inhibition of Candida albicans growth as candidiasis treatment, using seeds of Lepidium sativum as source. METHODS In vitro assays were carried out on the antifungal activity of three kinds of extracts from L. sativum seeds against four strains of C. albicans, then testing the same phytochemicals on the inhibition of Lipase (LCR). A new in silico study was achieved using molecular docking, with Autodock vina program, to find binding affinity of two important and major lepidine alkaloids (lepidine E and B) towards the four enzymes secreted by C. albicans as target drugs, responsible of vitality and virulence of this yeast cells: Lipase, Serine/threonine phosphatase, Phosphomannose isomerase and Sterol 14-alpha demethylase (CYP51). RESULTS The results of the microdillution assay show that the hexanic and alkaloidal extracts have an antifungal activity with MICs: 2.25 mg/ml and 4.5mg/ml, respectively. However, Candida rugosa lipase assay gives a remarkable IC50 values for the hexanic extract (1.42± 0.04 mg/ml) followed by 1.7± 0.1 and 2.29 ± 0.09 mg/ml of ethyl acetate and alkaloidal extracts respectively. The molecular docking confirms a significant correlation between C. albicans growth and inhibition of crucial enzymes involved in the invasion mechanism and cellular metabolisms, for the first time there were an interesting and new positive results on binding modes of lepidine E and B on the four studied enzymes. CONCLUSION Through this work, we propose Lepidine B & E as potent antifungal drugs.
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Affiliation(s)
- Safia Gacemi
- Department of Biology, Faculty of Sciences, University of Laghouat BP37G 03000, Laghouat, Algeria
| | - Khedidja Benarous
- Department of Biology, Faculty of Sciences, University of Laghouat BP37G 03000, Laghouat, Algeria
| | - Santiago Imperial
- Department of biochemistry, Molecular Biomedicine, Faculty of Biology. University of Barcelona, Avenue de Diagonal, 643 08028 Barcelona, Spain
| | - Mohamed Yousfi
- Department of Biology, Faculty of Sciences, University of Laghouat BP37G 03000, Laghouat, Algeria
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