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Taguchi A, Nakashima R, Nishino K. Structural Basis of Nucleotide Selectivity in Pyruvate Kinase. J Mol Biol 2024; 436:168708. [PMID: 39009072 DOI: 10.1016/j.jmb.2024.168708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/17/2024]
Abstract
Nucleoside triphosphates are indispensable in numerous biological processes, with enzymes involved in their biogenesis playing pivotal roles in cell proliferation. Pyruvate kinase (PYK), commonly regarded as the terminal glycolytic enzyme that generates ATP in tandem with pyruvate, is also capable of synthesizing a wide range of nucleoside triphosphates from their diphosphate precursors. Despite their substrate promiscuity, some PYKs show preference towards specific nucleotides, suggesting an underlying mechanism for differentiating nucleotide bases. However, the thorough characterization of this mechanism has been hindered by the paucity of nucleotide-bound PYK structures. Here, we present crystal structures of Streptococcus pneumoniae PYK in complex with four different nucleotides. These structures facilitate direct comparison of the protein-nucleotide interactions and offer structural insights into its pronounced selectivity for GTP synthesis. Notably, this selectivity is dependent on a sequence motif in the nucleotide recognition site that is widely present among prokaryotic PYKs, particularly in Firmicutes species. We show that pneumococcal cell growth is significantly impaired when expressing a PYK variant with compromised GTP and UTP synthesis activity, underscoring the importance of PYK in maintaining nucleotide homeostasis. Our findings collectively advance our understanding of PYK biochemistry and prokaryotic metabolism.
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Affiliation(s)
- Atsushi Taguchi
- SANKEN, Osaka University, Ibaraki, Osaka 567-0047, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan.
| | | | - Kunihiko Nishino
- SANKEN, Osaka University, Ibaraki, Osaka 567-0047, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka 565-0871, Japan.
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2
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Zahra I, DeVine L, Cole R, Malik HA, Wu J, Wen J, Hedfi A, Liaqat A, Ijaz R, Ramzan U, Shakoori AR, Shakoori FR, Betenbaugh MJ. Insights into the differential proteome landscape of a newly isolated Paramecium multimicronucleatum in response to cadmium stress. J Proteomics 2024; 300:105178. [PMID: 38636824 DOI: 10.1016/j.jprot.2024.105178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/01/2024] [Accepted: 04/12/2024] [Indexed: 04/20/2024]
Abstract
Employing microbial systems for the bioremediation of contaminated waters represent a potential option, however, limited understanding of the underlying mechanisms hampers the implication of microbial-mediated bioremediation. The omics tools offer a promising approach to explore the molecular basis of the bioremediation process. Here, a mass spectrometry-based quantitative proteome profiling approach was conducted to explore the differential protein levels in cadmium-treated Paramecium multimicronucleatum. The Proteome Discoverer software was used to identify and quantify differentially abundant proteins. The proteome profiling generated 7,416 peptide spectral matches, yielding 2824 total peptides, corresponding to 989 proteins. The analysis revealed that 29 proteins exhibited significant (p ≤ 0.05) differential levels, including a higher abundance of 6 proteins and reduced levels of 23 proteins in Cd2+ treated samples. These differentially abundant proteins were associated with stress response, energy metabolism, protein degradation, cell growth, and hormone processing. Briefly, a comprehensive proteome profile in response to cadmium stress of a newly isolated Paramecium has been established that will be useful in future studies identifying critical proteins involved in the bioremediation of metals in ciliates. SIGNIFICANCE: Ciliates are considered a good biological indicator of chemical pollution and relatively sensitive to heavy metal contamination. A prominent ciliate, Paramecium is a promising candidate for the bioremediation of polluted water. The proteins related to metal resistance in Paramecium species are still largely unknown and need further exploration. In order to identify and reveal the proteins related to metal resistance in Paramecia, we have reported differential protein abundance in Paramecium multimicronucleatum in response to cadmium stress. The proteins found in our study play essential roles during stress response, hormone processing, protein degradation, energy metabolism, and cell growth. It seems likely that Paramecia are not a simple sponge for metals but they could also transform them into less toxic derivatives or by detoxification by protein binding. This data will be helpful in future studies to identify critical proteins along with their detailed mechanisms involved in the bioremediation and detoxification of metal ions in Paramecium species.
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Affiliation(s)
- Itrat Zahra
- Institute of Zoology, University of the Punjab, New Campus, Lahore 54590, Pakistan.
| | - Lauren DeVine
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Robert Cole
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Hafiza Aroosa Malik
- Bioenergy Research Center, Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan.
| | - Jinke Wu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Junneng Wen
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Amor Hedfi
- Department of Biology, College of Sciences, Taif University, POBox 11099, Taif 21944, Saudi Arabia.
| | - Ayesha Liaqat
- Institute of Zoology, University of the Punjab, New Campus, Lahore 54590, Pakistan.
| | - Roohi Ijaz
- Institute of Zoology, University of the Punjab, New Campus, Lahore 54590, Pakistan.
| | - Uzma Ramzan
- Institute of Zoology, University of the Punjab, New Campus, Lahore 54590, Pakistan.
| | - Abdul Rauf Shakoori
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan.
| | - Farah Rauf Shakoori
- Institute of Zoology, University of the Punjab, New Campus, Lahore 54590, Pakistan.
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
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3
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Trova S, Lin F, Lomada S, Fenton M, Chauhan B, Adams A, Puri A, Di Maio A, Wieland T, Sewell D, Dick K, Wiseman D, Wilks DP, Goodall M, Drayson MT, Khanim FL, Bunce CM. Pathogen and human NDPK-proteins promote AML cell survival via monocyte NLRP3-inflammasome activation. PLoS One 2023; 18:e0288162. [PMID: 37418424 PMCID: PMC10328239 DOI: 10.1371/journal.pone.0288162] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 06/15/2023] [Indexed: 07/09/2023] Open
Abstract
A history of infection has been linked with increased risk of acute myeloid leukaemia (AML) and related myelodysplastic syndromes (MDS). Furthermore, AML and MDS patients suffer frequent infections because of disease-related impaired immunity. However, the role of infections in the development and progression of AML and MDS remains poorly understood. We and others previously demonstrated that the human nucleoside diphosphate kinase (NDPK) NM23-H1 protein promotes AML blast cell survival by inducing secretion of IL-1β from accessory cells. NDPKs are an evolutionary highly conserved protein family and pathogenic bacteria secrete NDPKs that regulate virulence and host-pathogen interactions. Here, we demonstrate the presence of IgM antibodies against a broad range of pathogen NDPKs and more selective IgG antibody activity against pathogen NDPKs in the blood of AML patients and normal donors, demonstrating that in vivo exposure to NDPKs likely occurs. We also show that pathogen derived NDPK-proteins faithfully mimic the catalytically independent pro-survival activity of NM23-H1 against primary AML cells. Flow cytometry identified that pathogen and human NDPKs selectively bind to monocytes in peripheral blood. We therefore used vitamin D3 differentiated monocytes from wild type and genetically modified THP1 cells as a model to demonstrate that NDPK-mediated IL-1β secretion by monocytes is NLRP3-inflammasome and caspase 1 dependent, but independent of TLR4 signaling. Monocyte stimulation by NDPKs also resulted in activation of NF-κB and IRF pathways but did not include the formation of pyroptosomes or result in pyroptotic cell death which are pivotal features of canonical NLRP3 inflammasome activation. In the context of the growing importance of the NLRP3 inflammasome and IL-1β in AML and MDS, our findings now implicate pathogen NDPKs in the pathogenesis of these diseases.
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Affiliation(s)
- Sandro Trova
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Fei Lin
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Santosh Lomada
- Institute of Experimental and Clinical Pharmacology and Toxicology, Heidelberg University, Mannheim, Germany
| | - Matthew Fenton
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Bhavini Chauhan
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Alexandra Adams
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Avani Puri
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Alessandro Di Maio
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Thomas Wieland
- Institute of Experimental and Clinical Pharmacology and Toxicology, Heidelberg University, Mannheim, Germany
| | - Daniel Sewell
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Kirstin Dick
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Daniel Wiseman
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
| | - Deepti P. Wilks
- Cancer Research UK Manchester Institute, Manchester Cancer Research Centre Biobank, The University of Manchester, Manchester, United Kingdom
| | - Margaret Goodall
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Mark T. Drayson
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Farhat L. Khanim
- Clinical Sciences, University of Birmingham, Birmingham, United Kingdom
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4
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Singh S, Yadav PK, Singh AK. In-silico structural characterization and phylogenetic analysis of Nucleoside diphosphate kinase: A novel antiapoptotic protein of Porphyromonas gingivalis. J Cell Biochem 2023; 124:545-556. [PMID: 36815439 DOI: 10.1002/jcb.30389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/24/2023]
Abstract
The Nucleoside diphosphate kinase (NDK) protein of Porphyromonas gingivalis (P. gingivalis) plays a crucial role in immune evasion and inhibition of apoptosis in host cells and has the potential to cause cancer. However, its structure has not yet been characterized. We used an in-silico approach to determine the 3D structure of the P. gingivalis NDK. Furthermore, structural characterization and functional annotation were performed using computational approaches. The 3D structure of NDK was predicted through homology modeling. The structural domains predicted for the model protein belong to the NDK family. Structural alignment of prokaryotic and eukaryotic NDKs with the model protein revealed the conservation of the domain region. Structure-based phylogenetic analysis depicted a significant evolutionary relationship between the model protein and the prokaryotic NDK. Functional annotation of the model confirmed structural homology, exhibiting similar enzymatic functions as NDK, including ATP binding and nucleoside diphosphate kinase activity. Furthermore, molecular dynamic (MD) simulation technique stabilized the model structure and provides a thermo-stable protein structure that can be used as a therapeutic target for further studies.
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Affiliation(s)
- Suchitra Singh
- Department of Bioinformatics, Central University of South Bihar, Gaya, India
| | - Piyush Kumar Yadav
- Department of Bioinformatics, Central University of South Bihar, Gaya, India
| | - Ajay Kumar Singh
- Department of Bioinformatics, Central University of South Bihar, Gaya, India
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Selvapandiyan A, Puri N, Kumar P, Alam A, Ehtesham NZ, Griffin G, Hasnain SE. Zooming in on common immune evasion mechanisms of pathogens in phagolysosomes: potential broad-spectrum therapeutic targets against infectious diseases. FEMS Microbiol Rev 2023; 47:6780197. [PMID: 36309472 DOI: 10.1093/femsre/fuac041] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 10/06/2022] [Accepted: 10/18/2022] [Indexed: 01/19/2023] Open
Abstract
The intracellular viral, bacterial, or parasitic pathogens evade the host immune challenges to propagate and cause fatal diseases. The microbes overpower host immunity at various levels including during entry into host cells, phagosome formation, phagosome maturation, phagosome-lysosome fusion forming phagolysosomes, acidification of phagolysosomes, and at times after escape into the cytosol. Phagolysosome is the final organelle in the phagocyte with sophisticated mechanisms to degrade the pathogens. The immune evasion strategies by the pathogens include the arrest of host cell apoptosis, decrease in reactive oxygen species, the elevation of Th2 anti-inflammatory response, avoidance of autophagy and antigen cross-presentation pathways, and escape from phagolysosomal killing. Since the phagolysosome organelle in relation to infection/cure is seldom discussed in the literature, we summarize here the common host as well as pathogen targets manipulated or utilized by the pathogens established in phagosomes and phagolysosomes, to hijack the host immune system for their benefit. These common molecules or pathways can be broad-spectrum therapeutic targets for drug development for intervention against infectious diseases caused by different intracellular pathogens.
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Affiliation(s)
| | - Niti Puri
- Cellular and Molecular Immunology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Pankaj Kumar
- Department of Biochemistry, Jamia Hamdard, New Delhi, 110062, India.,Centre for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD, 21218, United States
| | - Anwar Alam
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India.,Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology-Delhi, New Delhi, 110016, India
| | - Nasreen Zafar Ehtesham
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
| | - George Griffin
- Department of Cellular and Molecular Medicine, St. George's University of London, London, SW17 0RE, United Kingdom
| | - Seyed Ehtesham Hasnain
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology-Delhi, New Delhi, 110016, India.,Department of Life Science, School of Basic Sciences and Research, Sharda University, Knowledge Park III, Greater Noida, 201310, India
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Guo R, Zhang Z, He T, Li M, Zhuo Y, Yang X, Fan H, Chen X. Isolation and Identification of a New Isolate of Anguillid Herpesvirus 1 from Farmed American Eels ( Anguilla rostrata) in China. Viruses 2022; 14:v14122722. [PMID: 36560731 PMCID: PMC9784739 DOI: 10.3390/v14122722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
Anguillid herpesvirus 1 (AngHV-1) is a pathogen that causes hemorrhagic disease in various farmed and wild freshwater eel species, resulting in significant economic losses. Although AngHV-1 has been detected in the American eel (Anguilla rostrata), its pathogenicity has not been well characterized. In this study, an AngHV-1 isolate, tentatively named AngHV-1-FC, was isolated from diseased American eels with similar symptoms as those observed in AngHV-1-infected European eels and Japanese eels. AngHV-1-FC induced severe cytopathic effects in the European eel spleen cell line (EES), and numerous concentric circular virions were observed in the infected EES cells by transmission electron microscopy. Moreover, AngHV-1-FC caused the same symptoms as the naturally diseased European eels and Japanese eels through experimental infection, resulting in a 100% morbidity rate and 13.3% mortality rate. The whole genome sequence analyses showed that the average nucleotide identity value between AngHV-1-FC and other AngHV-1 isolates ranged from 99.28% to 99.55%. However, phylogenetic analysis revealed that there was a genetic divergence between AngHV-1-FC and other AngHV-1 isolates, suggesting that AngHV-1-FC was a new isolate of AngHV-1. Thus, our results indicated that AngHV-1-FC can infect farmed American eels, with a high pathogenicity, providing new knowledge in regard to the prevalence and prevention of AngHV-1.
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Affiliation(s)
- Rui Guo
- Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fuzhou Ocean and Fisheries Technology Center, Fuzhou 350007, China
| | - Zheng Zhang
- Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tianliang He
- Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Miaomiao Li
- Fujian Provincial Fishery Technical Extension Center, Fuzhou 350002, China
| | - Yuchen Zhuo
- Freshwater Fisheries Research Institute of Fujian Province, Fuzhou 350002, China
| | - Xiaoqiang Yang
- Fuzhou Ocean and Fisheries Technology Center, Fuzhou 350007, China
| | - Haiping Fan
- Freshwater Fisheries Research Institute of Fujian Province, Fuzhou 350002, China
- Correspondence: (X.C.); (H.F.)
| | - Xinhua Chen
- Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
- Correspondence: (X.C.); (H.F.)
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Mishra S, Saito K. Clinically encountered growth phenotypes of tuberculosis-causing bacilli and their in vitro study: A review. Front Cell Infect Microbiol 2022; 12:1029111. [PMID: 36439231 PMCID: PMC9684195 DOI: 10.3389/fcimb.2022.1029111] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/20/2022] [Indexed: 07/11/2024] Open
Abstract
The clinical manifestations of tuberculosis (TB) vary widely in severity, site of infection, and outcomes of treatment-leading to simultaneous efforts to individualize therapy safely and to search for shorter regimens that can be successfully used across the clinical spectrum. In these endeavors, clinicians and researchers alike employ mycobacterial culture in rich media. However, even within the same patient, individual bacilli among the population can exhibit substantial variability in their culturability. Bacilli in vitro also demonstrate substantial heterogeneity in replication rate and cultivation requirements, as well as susceptibility to killing by antimicrobials. Understanding parallels in clinical, ex vivo and in vitro growth phenotype diversity may be key to identifying those phenotypes responsible for treatment failure, relapse, and the reactivation of bacilli that progresses TB infection to disease. This review briefly summarizes the current role of mycobacterial culture in the care of patients with TB and the ex vivo evidence of variability in TB culturability. We then discuss current advances in in vitro models that study heterogenous subpopulations within a genetically identical bulk culture, with an emphasis on the effect of oxidative stress on bacillary cultivation requirements. The review highlights the complexity that heterogeneity in mycobacterial growth brings to the interpretation of culture in clinical settings and research. It also underscores the intricacies present in the interplay between growth phenotypes and antimicrobial susceptibility. Better understanding of population dynamics and growth requirements over time and space promises to aid both the attempts to individualize TB treatment and to find uniformly effective therapies.
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Affiliation(s)
- Saurabh Mishra
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, United States
| | - Kohta Saito
- Department of Medicine, Weill Cornell Medicine, New York, NY, United States
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8
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Advancement of chitin and chitosan as promising biomaterials. JOURNAL OF SAUDI CHEMICAL SOCIETY 2022. [DOI: 10.1016/j.jscs.2022.101561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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9
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Sikarwar J, Singh J, Singh TP, Sharma P, Sharma S. The Mechanism of Action of Lactoferrin - Nucleoside Diphosphate Kinase Complex in Combating Biofilm Formation. Protein Pept Lett 2022; 29:839-850. [PMID: 35975859 DOI: 10.2174/0929866529666220816160517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/16/2022] [Accepted: 06/03/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND The ESKAPE group of pathogens which comprise of multidrug resistant bacteria, namely Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species are the cause of deadly nosocomial infections all over the world. While these pathogens have developed robust strategies to resist most antibiotics, their ability to form biofilms is one of their most combative properties. Hence there is an urgent need to discover new antibacterial agents which could prevent or destroy the biofilms made by these bacteria. Though it has been established that lactoferrin (LF), a potent iron binding antibacterial, antifungal, and antiviral protein displays anti-biofilm properties, its mechanisms of action, in addition to its iron chelation property, still remains unclear. OBJECTIVE The binding and inhibition studies of LF with the enzyme Nucleoside diphosphate Kinase (NDK) and its elastase cleaved truncated 12 kDa fragment (12-NDK). METHODS The characterization studies of NDK and 12-NDK using florescence spectroscopy, dynamic light scattering, size exclusion chromatography and ADP-glo Kinase Assay. Inhibition studies of LF-NDK using ADP-glo kinase assay, Surface Plasmon Resonance and Biofilm inhibition studies. RESULTS NDK and 12-NDK were cloned, expressed and purified from Acinetobacter baumannii and Pseudomonas aeruginosa. The characterization studies revealed NDK and 12-NDK from both species are stable and functional. The inhibition studies of LF-NDK revealed stable binding and inhibition of kinase activity by LF. CONCLUSION The binding and inhibition studies have shown that while LF binds with both the NDK and their truncated forms, it tends to have a higher binding affinity with the truncated 12 kDa fragments, resulting in their decreased kinase activity. This study essentially gives a new direction to the field of inhibition of biofilm formation, as it proves that LF has a novel mechanism of action in other than iron sequestration.
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Affiliation(s)
- Juhi Sikarwar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi - 110029, India
| | - Jiya Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi - 110029, India
| | - Tej P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi - 110029, India
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi - 110029, India
| | - Sujata Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi - 110029, India
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New Complexes of organotin(IV) and organosilicon(IV) with 2-{(3,4-dimethoxybenzylidene)amino}-benzenethiol: Synthesis, spectral, theoretical, antibacterial, docking studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Tarsitano J, Ramis LY, Alonso LG, Russo DM, Zorreguieta A. RapD Is a Multimeric Calcium-Binding Protein That Interacts With the Rhizobium leguminosarum Biofilm Exopolysaccharide, Influencing the Polymer Lengths. Front Microbiol 2022; 13:895526. [PMID: 35875570 PMCID: PMC9298526 DOI: 10.3389/fmicb.2022.895526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/12/2022] [Indexed: 11/15/2022] Open
Abstract
Rhizobium leguminosarum synthesizes an acidic polysaccharide mostly secreted to the extracellular medium, known as exopolysaccharide (EPS) and partially retained on the bacterial surface as a capsular polysaccharide (CPS). Rap proteins, extracellular protein substrates of the PrsDE type I secretion system (TISS), share at least one Ra/CHDL (cadherin-like) domain and are involved in biofilm matrix development either through cleaving the polysaccharide by Ply glycanases or by altering the bacterial adhesive properties. It was shown that the absence or excess of extracellular RapA2 (a monomeric CPS calcium-binding lectin) alters the biofilm matrix’s properties. Here, we show evidence of the role of a new Rap protein, RapD, which comprises an N-terminal Ra/CHDL domain and a C-terminal region of unknown function. RapD was completely released to the extracellular medium and co-secreted with the other Rap proteins in a PrsDE-dependent manner. Furthermore, high levels of RapD secretion were found in biofilms under conditions that favor EPS production. Interestingly, size exclusion chromatography of the EPS produced by the ΔrapA2ΔrapD double mutant showed a profile of EPS molecules of smaller sizes than those of the single mutants and the wild type strain, suggesting that both RapA2 and RapD proteins influence EPS processing on the cell surface. Biophysical studies showed that calcium triggers proper folding and multimerization of recombinant RapD. Besides, further conformational changes were observed in the presence of EPS. Enzyme-Linked ImmunoSorbent Assay (ELISA) and Binding Inhibition Assays (BIA) indicated that RapD specifically binds the EPS and that galactose residues would be involved in this interaction. Taken together, these observations indicate that RapD is a biofilm matrix-associated multimeric protein that influences the properties of the EPS, the main structural component of the rhizobial biofilm.
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Affiliation(s)
- Julián Tarsitano
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Lila Y. Ramis
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Leonardo G. Alonso
- Instituto de Nanobiotecnología (NANOBIOTEC), Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Daniela M. Russo
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- *Correspondence: Daniela M. Russo,
| | - Angeles Zorreguieta
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Angeles Zorreguieta,
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12
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Kushawaha PK, Pati Tripathi CD, Dube A. Leishmania donovani secretory protein nucleoside diphosphate kinase b localizes in its nucleus and prevents ATP mediated cytolysis of macrophages. Microb Pathog 2022; 166:105457. [DOI: 10.1016/j.micpath.2022.105457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 02/22/2022] [Accepted: 02/22/2022] [Indexed: 10/19/2022]
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13
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Gupta A, Sinha KM, Abdin MZ, Puri N, Selvapandiyan A. NDK/NME proteins: a host-pathogen interface perspective towards therapeutics. Curr Genet 2021; 68:15-25. [PMID: 34480234 DOI: 10.1007/s00294-021-01198-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 12/12/2022]
Abstract
No effective vaccine is available for any parasitic disease. The treatment to those is solely dependent on chemotherapy, which is always threatened due to development of drug resistance in bugs. This warrants identification of new drug targets. Here, we discuss Nucleoside diphosphate kinases (NDKs) of pathogens that alter host's intra and extracellular environment, as novel drug targets to simultaneously tackle multiple pathogens. NDKs having diverse functions, are highly conserved among prokaryotes and eukaryotes (the mammal NDKs are called NMEs [non-metastatic enzymes]). However, NDKs and NMEs have been separately analysed in the past for their structure and functions. The role of NDKs of pathogen in modulation of inflammation, phagocytosis, apoptosis, and ROS generation in host is known. Conversely, its combined contribution in host-pathogen interaction has not been studied yet. Through the sequence and domain analysis, we found that NDKs can be classified in two groups. One group comprised NMEs 1-4 and few NDKs of select essential protozoan parasites and the bacterium Mycobacterium tuberculosis. The other group included NME7 and the other NDKs of those parasites, posing challenges in the development of drugs specifically targeting pathogen NDKs, without affecting NME7. However, common drugs targeting group 2 NDKs of pathogens can be designed, as NME7 of group 2 is expressed only in ciliated host cells. This review thus analyses comparatively for the first time the structures and functions of human NMEs and pathogen NDKs and predicts the possibilities of NDKs as drug targets. In addition, pathogen NDKs have been now provided a nomenclature in alignment with the NMEs of humans.
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Affiliation(s)
- Ankit Gupta
- Department of Molecular Medicine, School of Interdisciplinary Sciences and Technology, Jamia Hamdard, New Delhi, 110062, India
| | - Krishna Murari Sinha
- Amity Institute of Biotechnology, Amity University Haryana, Gurgaon, Haryana, 122413, India
| | - Malik Z Abdin
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110062, India
| | - Niti Puri
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Angamuthu Selvapandiyan
- Department of Molecular Medicine, School of Interdisciplinary Sciences and Technology, Jamia Hamdard, New Delhi, 110062, India.
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14
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Medium Optimization and Proteome Analysis of Protease Production by Janthinobacterium sp. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0110-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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15
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Sulheim S, Kumelj T, van Dissel D, Salehzadeh-Yazdi A, Du C, van Wezel GP, Nieselt K, Almaas E, Wentzel A, Kerkhoven EJ. Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production. iScience 2020; 23:101525. [PMID: 32942174 PMCID: PMC7501462 DOI: 10.1016/j.isci.2020.101525] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/19/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023] Open
Abstract
Many biosynthetic gene clusters (BGCs) require heterologous expression to realize their genetic potential, including silent and metagenomic BGCs. Although the engineered Streptomyces coelicolor M1152 is a widely used host for heterologous expression of BGCs, a systemic understanding of how its genetic modifications affect the metabolism is lacking and limiting further development. We performed a comparative analysis of M1152 and its ancestor M145, connecting information from proteomics, transcriptomics, and cultivation data into a comprehensive picture of the metabolic differences between these strains. Instrumental to this comparison was the application of an improved consensus genome-scale metabolic model (GEM) of S. coelicolor. Although many metabolic patterns are retained in M1152, we find that this strain suffers from oxidative stress, possibly caused by increased oxidative metabolism. Furthermore, precursor availability is likely not limiting polyketide production, implying that other strategies could be beneficial for further development of S. coelicolor for heterologous production of novel compounds.
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Affiliation(s)
- Snorre Sulheim
- Department of Biotechnology and Nanomedicine, SINTEF Industry, 7034 Trondheim, Norway
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Tjaša Kumelj
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Dino van Dissel
- Department of Biotechnology and Nanomedicine, SINTEF Industry, 7034 Trondheim, Norway
| | - Ali Salehzadeh-Yazdi
- Department of Systems Biology and Bioinformatics, Faculty of Computer Science and Electrical Engineering, University of Rostock, 18057 Rostock, Germany
| | - Chao Du
- Microbial Biotechnology, Institute of Biology, Leiden University, 2300 Leiden, the Netherlands
| | - Gilles P. van Wezel
- Microbial Biotechnology, Institute of Biology, Leiden University, 2300 Leiden, the Netherlands
| | - Kay Nieselt
- Integrative Transcriptomics, Center for Bioinformatics, University of Tübingen, 72070 Tübingen, Germany
| | - Eivind Almaas
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and General Practice, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Alexander Wentzel
- Department of Biotechnology and Nanomedicine, SINTEF Industry, 7034 Trondheim, Norway
| | - Eduard J. Kerkhoven
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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16
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Ashok N, Bauer CE. Evidence of defined temporal expression patterns that lead a gram-negative cell out of dormancy. PLoS Genet 2020; 16:e1008660. [PMID: 32203501 PMCID: PMC7117780 DOI: 10.1371/journal.pgen.1008660] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 04/02/2020] [Accepted: 02/07/2020] [Indexed: 01/02/2023] Open
Abstract
Many bacterial species are capable of forming long-lived dormant cells. The best characterized are heat and desiccation resistant spores produced by many Gram-positive species. Less characterized are dormant cysts produced by several Gram-negative species that are somewhat tolerant to increased temperature and very resistant to desiccation. While there is progress in understanding regulatory circuits that control spore germination, there is scarce information on how Gram-negative organisms emerges from dormancy. In this study, we show that R. centenum cysts germinate by emerging a pair of motile vegetative cells from a thick cyst cell wall coat ~ 6 hrs post induction of germination. Time-lapse transcriptomic analysis reveals that there is a defined temporal pattern of gene expression changes during R. centenum cyst germination. The first observable changes are increases in expression of genes for protein synthesis, an increase in expression of genes involved in the generation of a membrane potential and the use of this potential for ATP synthesis via ATPase expression. These early events are followed by expression changes that affect the cell wall and membrane composition, followed by expression changes that promote chromosome replication. Midway through germination, expression changes occur that promote the flow of carbon through the TCA cycle to generate reducing power and parallel synthesis of electron transfer components involved in oxidative phosphorylation. Finally, late expression changes promote the synthesis of a photosystem as well as flagellar and chemotaxis components for motility.
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Affiliation(s)
- Nandhini Ashok
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Carl E. Bauer
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, United States of America
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17
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Defining the Environmental Adaptations of Genus Devosia: Insights into its Expansive Short Peptide Transport System and Positively Selected Genes. Sci Rep 2020; 10:1151. [PMID: 31980727 PMCID: PMC6981132 DOI: 10.1038/s41598-020-58163-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/19/2019] [Indexed: 12/21/2022] Open
Abstract
Devosia are well known for their dominance in soil habitats contaminated with various toxins and are best characterized for their bioremediation potential. In this study, we compared the genomes of 27 strains of Devosia with aim to understand their metabolic abilities. The analysis revealed their adaptive gene repertoire which was bared from 52% unique pan-gene content. A striking feature of all genomes was the abundance of oligo- and di-peptide permeases (oppABCDF and dppABCDF) with each genome harboring an average of 60.7 ± 19.1 and 36.5 ± 10.6 operon associated genes respectively. Apart from their primary role in nutrition, these permeases may help Devosia to sense environmental signals and in chemotaxis at stressed habitats. Through sequence similarity network analyses, we identified 29 Opp and 19 Dpp sequences that shared very little homology with any other sequence suggesting an expansive short peptidic transport system within Devosia. The substrate determining components of these permeases viz. OppA and DppA further displayed a large diversity that separated into 12 and 9 homologous clusters respectively in addition to large number of isolated nodes. We also dissected the genome scale positive evolution and found genes associated with growth (exopolyphosphatase, HesB_IscA_SufA family protein), detoxification (moeB, nifU-like domain protein, alpha/beta hydrolase), chemotaxis (cheB, luxR) and stress response (phoQ, uspA, luxR, sufE) were positively selected. The study highlights the genomic plasticity of the Devosia spp. for conferring adaptation, bioremediation and the potential to utilize a wide range of substrates. The widespread toxin-antitoxin loci and ‘open’ state of the pangenome provided evidence of plastic genomes and a much larger genetic repertoire of the genus which is yet uncovered.
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18
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Galdino ACM, de Oliveira MP, Ramalho TC, de Castro AA, Branquinha MH, Santos ALS. Anti-Virulence Strategy against the Multidrug-Resistant Bacterial Pathogen Pseudomonas aeruginosa: Pseudolysin (Elastase B) as a Potential Druggable Target. Curr Protein Pept Sci 2019; 20:471-487. [PMID: 30727891 DOI: 10.2174/1389203720666190207100415] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/26/2019] [Accepted: 01/31/2019] [Indexed: 11/22/2022]
Abstract
Pseudomonas aeruginosa is a non-fermentative, gram-negative bacterium that is one of the most common pathogens responsible for hospital-acquired infections worldwide. The management of the infections caused by P. aeruginosa represents a huge challenge in the healthcare settings due to the increased emergence of resistant isolates, some of them resistant to all the currently available antimicrobials, which results in elevated morbimortality rates. Consequently, the development of new therapeutic strategies against multidrug-resistant P. aeruginosa is urgent and needful. P. aeruginosa is wellrecognized for its extreme genetic versatility and its ability to produce a lush variety of virulence factors. In this context, pseudolysin (or elastase B) outstands as a pivotal virulence attribute during the infectious process, playing multifunctional roles in different aspects of the pathogen-host interaction. This protein is a 33-kDa neutral zinc-dependent metallopeptidase that is the most abundant peptidase found in pseudomonal secretions, which contributes to the invasiveness of P. aeruginosa due to its ability to cleave several extracellular matrix proteins and to disrupt the basolateral intercellular junctions present in the host tissues. Moreover, pseudolysin makes P. aeruginosa able to overcome host defenses by the hydrolysis of many immunologically relevant molecules, including antibodies and complement components. The attenuation of this striking peptidase therefore emerges as an alternative and promising antivirulence strategy to combat antibiotic-refractory infections caused by P. aeruginosa. The anti-virulence approach aims to disarm the P. aeruginosa infective arsenal by inhibiting the expression/activity of bacterial virulence factors in order to reduce the invasiveness of P. aeruginosa, avoiding the emergence of resistance since the proliferation is not affected. This review summarizes the most relevant features of pseudolysin and highlights this enzyme as a promising target for the development of new anti-virulence compounds.
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Affiliation(s)
- Anna Clara M Galdino
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Matheus P de Oliveira
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, United States
| | - Teodorico C Ramalho
- Departamento de Quimica, Universidade Federal de Lavras, Minas Gerais, Brazil
| | | | - Marta H Branquinha
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - André L S Santos
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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19
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Imam N, Alam A, Ali R, Siddiqui MF, Ali S, Malik MZ, Ishrat R. In silico characterization of hypothetical proteins from Orientia tsutsugamushi str. Karp uncovers virulence genes. Heliyon 2019; 5:e02734. [PMID: 31720472 PMCID: PMC6838952 DOI: 10.1016/j.heliyon.2019.e02734] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/29/2019] [Accepted: 10/23/2019] [Indexed: 11/20/2022] Open
Abstract
Scrub typhus also known as bush typhus is a disease with symptoms similar to Chikungunya infection. It is caused by a gram-negative bacterium Orientia tsutsugamushi which resides in its vertebrate host, Mites. The genome of Orientia tsutsugamushi str. Karp encodes for 1,563 proteins, of which 344 are characterized as hypothetical ones. In the present study, we tried to identify the probable functions of these 344 hypothetical proteins (HPs). All the characterized hypothetical proteins (HPs) belong to the various protein classes like enzymes, transporters, binding proteins, metabolic process and catalytic activity and kinase activity. These hypothetical proteins (HPs) were further analyzed for virulence factors with 62 proteins identified as the most virulent proteins among these hypothetical proteins (HPs). In addition, we studied the protein sequence similarity network for visualizing functional trends across protein superfamilies from the context of sequence similarity and it shows great potential for generating testable hypotheses about protein structure-function relationships. Furthermore, we calculated toplogical properties of the network and found them to obey network power law distributions showing a fractal nature. We also identifed two highly interconnected modules in the main network which contained five hub proteins (KJV55465, KJV56211, KJV57212, KJV57203 and KJV57216) having 1.0 clustering coefficient. The structural modeling (2D and 3D structure) of these five hub proteins was carried out and the catalytic site essential for its functioning was analyzed. The outcome of the present study may facilitate a better understanding of the mechanism of virulence, pathogenesis, adaptability to host and up-to-date annotations will make unknown genes easy to identify and target for experimentation. The information on the functional attributes and virulence characteristic of these hypothetical proteins (HPs) are envisaged to facilitate effective development of novel antibacterial drug targets of Orientia tsutsugamushi.
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Affiliation(s)
- Nikhat Imam
- Institute of Computer Science and Information Technology, Magadh University, Bodhgaya, India
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi, India
| | - Aftab Alam
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi, India
| | - Rafat Ali
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi, India
| | - Mohd Faizan Siddiqui
- International Medical Faculty, Osh State University, Osh City, 723500, Kyrgyz Republic (Kyrgyzstan)
| | - Sher Ali
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi, India
| | - Md. Zubbair Malik
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, Delhi, 110067, India
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi, India
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20
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Koendjbiharie JG, Wevers K, van Kranenburg R. Assessing Cofactor Usage in Pseudoclostridium thermosuccinogenes via Heterologous Expression of Central Metabolic Enzymes. Front Microbiol 2019; 10:1162. [PMID: 31178853 PMCID: PMC6543838 DOI: 10.3389/fmicb.2019.01162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/07/2019] [Indexed: 11/13/2022] Open
Abstract
Pseudoclostridium thermosuccinogenes and Hungateiclostridium thermocellum are being studied for their potential to contribute to a more sustainable bio-based economy. Both species were shown previously to rely on GTP or pyrophosphate instead of ATP as cofactors in specific reactions of central energy metabolism for reasons that are not well understood yet. Since it is often impossible to predict cofactor specificity from the primary protein structure, thirteen enzymes from P. thermosuccinogenes were cloned and heterologous expressed in Escherichia coli to assess the cofactor usage in vitro and paint a more complete picture of the cofactor usage in the central metabolism of P. thermosuccinogenes. The assays were conducted with heat-treated E. coli cell-free extract devoid of background activity to allow the quick assessment of a relatively large number of (thermophilic) enzymes. Selected enzymes were also purified to allow the determination of the enzyme kinetics for competing cofactors. Following the results of the glucokinase (GK), galactokinase, xylulokinase (XK), and ribokinase assays, it seems that phosphorylation of monosaccharides by and large is mainly GTP-dependent. Some possible implications of this relating to the adenylate/guanylate energy charge are discussed here. Besides the highly expressed pyrophosphate-dependent 6-phosphofructokinase, another 6-phosphofructokinase was found to be equally dependent on ATP and GTP, while no 6-phosphofructokinase activity could be demonstrated for a third. Both type I glyceraldehyde 3-phosphate dehydrogenases were found to be NAD+-dependent, and further, acetate kinase, isocitrate dehydrogenase, and three enzymes predicted to be responsible for the interconversion of phosphoenolpyruvate and pyruvate (i.e., pyruvate kinase; pyruvate, phosphate dikinase; phosphoenolpyruvate synthase), were also assessed.
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Affiliation(s)
| | - Kimberly Wevers
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Richard van Kranenburg
- Corbion, Gorinchem, Netherlands
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
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21
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Gupta S, Shukla H, Kumar A, Shukla R, Kumari R, Tripathi T, Singh RK, Anupurba S. Mycobacterium tuberculosis nucleoside diphosphate kinase shows interaction with putative ATP binding cassette (ABC) transporter, Rv1273c. J Biomol Struct Dyn 2019; 38:1083-1093. [PMID: 30898047 DOI: 10.1080/07391102.2019.1595150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Protein-protein interactions are crucial for all biological processes. Compiling this network provides many new insights into protein function and gives directions for the development of new drugs targeted to the pathogen. Mycobacterium tuberculosis Nucleoside diphosphate kinase (Mtb Ndk) has been reported to promote survival of mycobacterium within the macrophage and contribute significantly to mycobacterium virulence. Hence, the present study was aimed to identify and characterize the interacting partner for Ndk. The in vitro experiments, pull down and far western blotting have demonstrated that Mtb Ndk interacts with Rv1273c, a probable drug ABC transporter ATP-binding protein annotated to export drugs across the membrane. This observation was further confirmed by molecular docking and dynamic simulations studies. The homology model of Rv1273c was constructed and docked with Mtb Ndk for protein-protein interaction analysis. The critical residues involved at interface of Rv1273c-Ndk interaction were identified. MDS and Principal Component analysis carried out for conformational feasibility and stability concluded that the complex between the two proteins is more stable as compared to apo proteins. Our findings would be expected to improve the dissection of protein-protein interaction network and significantly advance our understanding of tuberculosis infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Smita Gupta
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Harish Shukla
- Department of Biochemistry, North Eastern Hill University, Shillong, India
| | - Arun Kumar
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Rohit Shukla
- Department of Biochemistry, North Eastern Hill University, Shillong, India
| | - Richa Kumari
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Timir Tripathi
- Department of Biochemistry, North Eastern Hill University, Shillong, India
| | - Rakesh K Singh
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Shampa Anupurba
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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22
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Abou-Dobara MI, Omar NF, Diab MA, El-Sonbati AZ, Morgan SM, El-Mogazy MA. Allyl rhodanine azo dye derivatives: Potential antimicrobials target d-alanyl carrier protein ligase and nucleoside diphosphate kinase. J Cell Biochem 2019; 120:1667-1678. [PMID: 30187946 DOI: 10.1002/jcb.27473] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 07/18/2018] [Indexed: 01/24/2023]
Abstract
3-Allyl-5-(4-arylazo)-2-thioxothiazolidine-4-one (HLn ) ligands (where n = 1 to 3) were hypothesized to have antimicrobial activities mediated through inhibition of new antimicrobial targets. The ligands (HLn ) were synthesized and characterized by infrared (IR) and 1 H nuclear magnetic resonance (1 H NMR) spectra. The ligands (HLn ) were in silico screened to their potential inhibition to models of d-alanyl carrier protein ligase (DltA) (from Bacillus cereus, PDB code 3FCE) and nucleoside diphosphate kinase (NDK) (from Staphylococcus aureus; PDB code 3Q8U). HL3 ligand has the best energy and mode of binding to both NDK and DltA, even though its binding to DltA was stronger than that to NDK. In antimicrobial activity of HL3 ligand, morphological and cytological changes in HL3 -treated bacteria agreed with the in silico results. The HL3 ligand showed significant antimicrobial activity against B. cereus, S. aureus, and Fusarium oxysporium. The HL3 -treated bacterial cells appeared malformed and incompletely separated. Its cell walls appeared electron-lucent and ruptured. They contained more mesosomes than normal cells. It was found that the HL3 ligand represented as a bactericide against B. cereus and S. aureusby blocking target DltA, and may target NDK.
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Affiliation(s)
- Mohamed I Abou-Dobara
- Botany and Microbiology Department, Faculty of Science, Damietta University, Damietta, Egypt
| | - Noha F Omar
- Botany and Microbiology Department, Faculty of Science, Damietta University, Damietta, Egypt
| | - Mostafa A Diab
- Chemistry Department, Faculty of Science, Damietta University, Damietta, Egypt
| | - Adel Z El-Sonbati
- Chemistry Department, Faculty of Science, Damietta University, Damietta, Egypt
| | - Shaimaa M Morgan
- Environmental Monitoring Laboratory, Ministry of Health, Port Said, Egypt
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23
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Gautam LK, Sharma P, Capalash N. Bacterial Polyphosphate Kinases Revisited: Role in Pathogenesis and Therapeutic Potential. Curr Drug Targets 2019; 20:292-301. [DOI: 10.2174/1389450119666180801120231] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/02/2018] [Accepted: 07/31/2018] [Indexed: 11/22/2022]
Abstract
Bacterial infections have always been an unrestrained challenge to the medical community due to the rise of multi-drug tolerant and resistant strains. Pioneering work on Escherichia coli polyphosphate kinase (PPK) by Arthur Kornberg has generated great interest in this polyphosphate (PolyP) synthesizing enzyme. PPK has wide distribution among pathogens and is involved in promoting pathogenesis, stress management and susceptibility to antibiotics. Further, the absence of a PPK orthologue in humans makes it a potential drug target. This review covers the functional and structural aspects of polyphosphate kinases in bacterial pathogens. A description of molecules being designed against PPKs has been provided, challenges associated with PPK inhibitor design are highlighted and the strategies to enable development of efficient drug against this enzyme have also been discussed.
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Affiliation(s)
- Lalit Kumar Gautam
- Department of Biotechnology, Panjab University, BMS Block-I, Sector- 25, Chandigarh, 160014, India
| | - Prince Sharma
- Department of Microbiology, Panjab University, BMS Block-I, Sector- 25, Chandigarh, 160014, India
| | - Neena Capalash
- Department of Biotechnology, Panjab University, BMS Block-I, Sector- 25, Chandigarh, 160014, India
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24
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Wang Z, Ge JQ, Chen H, Cheng X, Yang Y, Li J, Whitworth RJ, Chen MS. An insect nucleoside diphosphate kinase (NDK) functions as an effector protein in wheat - Hessian fly interactions. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 100:30-38. [PMID: 29913225 DOI: 10.1016/j.ibmb.2018.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 06/05/2018] [Accepted: 06/13/2018] [Indexed: 05/08/2023]
Abstract
Like pathogens, galling insects deliver effectors into plant tissues that induce gall formation. The gall midge Mayetiola destructor, also called Hessian fly, can convert a whole wheat seedling into a gall by inducing the formation of nutritive cells at the feeding site, inhibiting wheat growth, and reprogramming metabolic pathways of the attacked plants. Here we demonstrated the identification of a secreted Hessian fly protein, the nucleoside diphosphate kinase (NDK), in infested wheat plants through liquid chromatography-tandem mass spectrometry (LC-MS/MS) and western blots. In association with the NDK presence, enzymatic activity of NDK increased significantly in wheat tissues at the feeding site. In addition, there was a sudden increase in ATP abundance at the feeding site of infested susceptible wheat seedlings 24 h following Hessian fly larval infestation. Even though a direct link between cause and effect remains to be established, our data points to the direction that Hessian fly larvae injected NDK into wheat tissues as an effector protein, which plays a role in manipulating host plants and converting the plants into galls.
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Affiliation(s)
- Zhuhong Wang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jun-Qing Ge
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350003, China
| | - Hang Chen
- Research Institute of Resource Insect, Chinese Academy of Forestry, Kunming, 650224, China
| | - Xiaoyan Cheng
- Department of Entomology, Kansas State University, Manhattan, KS, 66506, USA
| | - Yiqun Yang
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
| | - Jun Li
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
| | - R Jeff Whitworth
- Department of Entomology, Kansas State University, Manhattan, KS, 66506, USA
| | - Ming-Shun Chen
- Department of Entomology, Kansas State University, Manhattan, KS, 66506, USA; Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, 66506, USA.
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25
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Dumais M, Davies DR, Lin T, Staker BL, Myler PJ, Van Voorhis WC. Structure and analysis of nucleoside diphosphate kinase from Borrelia burgdorferi prepared in a transition-state complex with ADP and vanadate moieties. Acta Crystallogr F Struct Biol Commun 2018; 74:373-384. [PMID: 29870023 PMCID: PMC5987747 DOI: 10.1107/s2053230x18007392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/16/2018] [Indexed: 01/13/2023] Open
Abstract
Nucleoside diphosphate kinases (NDKs) are implicated in a wide variety of cellular functions owing to their enzymatic conversion of NDP to NTP. NDK from Borrelia burgdorferi (BbNDK) was selected for functional and structural analysis to determine whether its activity is required for infection and to assess its potential for therapeutic inhibition. The Seattle Structural Genomics Center for Infectious Diseases (SSGCID) expressed recombinant BbNDK protein. The protein was crystallized and structures were solved of both the apoenzyme and a liganded form with ADP and vanadate ligands. This provided two structures and allowed the elucidation of changes between the apo and ligand-bound enzymes. Infectivity studies with ndk transposon mutants demonstrated that NDK function was important for establishing a robust infection in mice, and provided a rationale for therapeutic targeting of BbNDK. The protein structure was compared with other NDK structures found in the Protein Data Bank and was found to have similar primary, secondary, tertiary and quaternary structures, with conserved residues acting as the catalytic pocket, primarily using His132 as the phosphohistidine-transfer residue. Vanadate and ADP complexes model the transition state of this phosphoryl-transfer reaction, demonstrating that the pocket closes when bound to ADP, while allowing the addition or removal of a γ-phosphate. This analysis provides a framework for the design of potential therapeutics targeting BbNDK inhibition.
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Affiliation(s)
- Mitchell Dumais
- Department of Allergy and Infectious Disease, University of Washington, Seattle, Washington, USA
| | | | - Tao Lin
- Department of Pathology and Laboratory Medicine, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Bart L. Staker
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute) , Seattle, Washington, USA
| | - Peter J. Myler
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute) , Seattle, Washington, USA
- Department of Biomedical Informatics and Health Education, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Wesley C. Van Voorhis
- Department of Allergy and Infectious Disease, University of Washington, Seattle, Washington, USA
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Lee J, Roberts JS, Atanasova KR, Chowdhury N, Yilmaz Ö. A novel kinase function of a nucleoside-diphosphate-kinase homologue in Porphyromonas gingivalis is critical in subversion of host cell apoptosis by targeting heat-shock protein 27. Cell Microbiol 2018; 20:e12825. [PMID: 29359393 PMCID: PMC5893355 DOI: 10.1111/cmi.12825] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/13/2022]
Abstract
We have previously shown that a homologue of a conserved nucleoside-diphosphate-kinase (Ndk) family of multifunctional enzymes and secreted molecule in Porphyromonas gingivalis can modulate select host molecular pathways including downregulation of reactive-oxygen-species generation to promote bacterial survival in human gingival epithelial cells (GECs). In this study, we describe a novel kinase function for bacterial effector, P. gingivalis-Ndk, in abrogating epithelial cell death by phosphorylating heat-shock protein 27 (HSP27) in GECs. Infection by P. gingivalis was recently suggested to increase phosphorylation of HSP27 in cancer-epithelial cells; however, the mechanism and biological significance of antiapoptotic phospho-HSP27 during infection has never been characterised. Interestingly, using glutathione S-transferase-rNdk pull-down analysed by mass spectrometry, we identified HSP27 in GECs as a strong binder of P. gingivalis-Ndk and further verified using confocal microscopy and ELISA. Therefore, we hypothesised P. gingivalis-Ndk can phosphorylate HSP27 for inhibition of apoptosis in GECs. We further employed P. gingivalis-Ndk protein constructs and an isogenic P. gingivalis-ndk-deficient-mutant strain for functional examination. P. gingivalis-infected GECs displayed significantly increased phospho-HSP27 compared with ndk-deficient-strain during 24 hr infection. Phospho-HSP27 was significantly increased by transfection of GFP-tagged-Ndk into uninfected-GECs, and in vitro phosphorylation assays revealed direct phosphorylation of HSP27 at serines 78 and 82 by P. gingivalis-Ndk. Depletion of HSP27 via siRNA significantly reversed resistance against staurosporine-mediated-apoptosis during infection. Transfection of recombinant P. gingivalis-Ndk protein into GECs substantially decreased staurosporine-induced-apoptosis. Finally, ndk-deficient-mutant strain was unable to inhibit staurosporine-induced Cytochrome C release/Caspase-9 activation. Thus, we show for the first time the phosphorylation of HSP27 by a bacterial effector-P. gingivalis-Ndk-and a novel function of Ndks that is directly involved in inhibition of host cell apoptosis and the subsequent bacterial survival.
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Affiliation(s)
- Jungnam Lee
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Florida, Florida, USA
| | - JoAnn S Roberts
- Department of Oral Health Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
| | | | - Nityananda Chowdhury
- Department of Oral Health Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Özlem Yilmaz
- Department of Oral Health Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
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Ararso Z, Ma C, Qi Y, Feng M, Han B, Hu H, Meng L, Li J. Proteome Comparisons between Hemolymph of Two Honeybee Strains (Apis mellifera ligustica) Reveal Divergent Molecular Basis in Driving Hemolymph Function and High Royal Jelly Secretion. J Proteome Res 2017; 17:402-419. [DOI: 10.1021/acs.jproteome.7b00621] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Zewdu Ararso
- Institute of Apicultural
Research/Key Laboratory of Pollinating Insect Biology, Ministry of
Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuan Ma
- Institute of Apicultural
Research/Key Laboratory of Pollinating Insect Biology, Ministry of
Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuping Qi
- Institute of Apicultural
Research/Key Laboratory of Pollinating Insect Biology, Ministry of
Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mao Feng
- Institute of Apicultural
Research/Key Laboratory of Pollinating Insect Biology, Ministry of
Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bin Han
- Institute of Apicultural
Research/Key Laboratory of Pollinating Insect Biology, Ministry of
Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Han Hu
- Institute of Apicultural
Research/Key Laboratory of Pollinating Insect Biology, Ministry of
Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lifeng Meng
- Institute of Apicultural
Research/Key Laboratory of Pollinating Insect Biology, Ministry of
Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianke Li
- Institute of Apicultural
Research/Key Laboratory of Pollinating Insect Biology, Ministry of
Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Yu H, Rao X, Zhang K. Nucleoside diphosphate kinase (Ndk): A pleiotropic effector manipulating bacterial virulence and adaptive responses. Microbiol Res 2017; 205:125-134. [PMID: 28942838 DOI: 10.1016/j.micres.2017.09.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/23/2017] [Accepted: 09/02/2017] [Indexed: 12/11/2022]
Abstract
Nucleoside diphosphate kinase (Ndk) is a housekeeping enzyme that balances cellular nucleoside triphosphate (NTP) pools by catalyzing the reversible transfer of γ-phosphate from NTPs to nucleoside diphosphates (NDPs). In addition to its fundamental role in nucleotide metabolism, Ndk has roles in protein histidine phosphorylation, DNA cleavage/repair, and gene regulation. Recent studies have also revealed that Ndk secreted from bacteria is important in modulating virulence-associated phenotypes including quorum sensing regulation, type III secretion system activation, and virulence factor production. Moreover, after infection, Ndks released from bacteria are involved in regulating host defense activities, such as cell apoptosis, phagocytosis, and inflammatory responses. Given that Ndk exerts a pleiotropic effect on bacterial virulence and bacteria-host interactions, the biological significance of the bacterial Ndks during infection is intriguing. This review will provide a synopsis of the current knowledge regarding the biological properties and roles of Ndks in regulating bacterial virulence and adaptation and will discuss in depth the biological significance of Ndk during bacteria-host interactions.
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Affiliation(s)
- Hua Yu
- Central Laboratory, Xinqiao Hospital, Third Military Medical University, Chongqing, China; Department of Microbiology, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Xiancai Rao
- Department of Microbiology, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China.
| | - Kebin Zhang
- Central Laboratory, Xinqiao Hospital, Third Military Medical University, Chongqing, China.
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Discovery of novel inhibitors for Leishmania nucleoside diphosphatase kinase (NDK) based on its structural and functional characterization. J Comput Aided Mol Des 2017; 31:547-562. [DOI: 10.1007/s10822-017-0022-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 05/04/2017] [Indexed: 10/19/2022]
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30
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Liu PF, Liu QH, Wu Y, Huang J. Increased nucleoside diphosphate kinase activity induces white spot syndrome virus infection in Litopenaeus vannamei. PLoS One 2017; 12:e0175741. [PMID: 28505172 PMCID: PMC5432163 DOI: 10.1371/journal.pone.0175741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 03/30/2017] [Indexed: 12/02/2022] Open
Abstract
Nucleoside diphosphate kinase (NDK), which has the same sequence as oncoprotein (OP) in humans, can induce nucleoside triphosphates in DNA replication by maintenance of the deoxynucleotide triphosphate (dNTP’s) and is known to be regulated by viral infection in the shrimp Litopenaeus vannamei. This paper describes the relationship between NDK and white spot syndrome virus (WSSV) infection. The recombinant NDK was produced by a prokaryotic expression system. WSSV copy numbers and mRNA levels of IE1 and VP28 were significantly increased in shrimp injected with recombinant NDK at 72 h after WSSV infection. After synthesizing dsRNA-NDK and confirming the efficacy of NDK silencing, we recorded the cumulative mortality of WSSV-infected shrimp injected with NDK and dsRNA-NDK. A comparison between the results demonstrated that silencing NDK delayed the death of shrimps. These findings indicate that NDK has an important role influencing the replication of WSSV replication in shrimp. Furthermore, NDK may have potential target as a new therapeutic strategy against WSSV infection in shrimp.
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Affiliation(s)
- Peng-fei Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Dalian Ocean University, Dalian, China
| | - Qing-hui Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- National Laboratory for Marine Science and Technology, Qingdao, China
- * E-mail:
| | - Yin Wu
- Dalian Ocean University, Dalian, China
| | - Jie Huang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- National Laboratory for Marine Science and Technology, Qingdao, China
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31
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Doulgeraki AI, Efthimiou G, Paramithiotis S, Pappas KM, Typas MA, Nychas GJ. Effect of Rocket ( Eruca sativa) Extract on MRSA Growth and Proteome: Metabolic Adjustments in Plant-Based Media. Front Microbiol 2017; 8:782. [PMID: 28529502 PMCID: PMC5418331 DOI: 10.3389/fmicb.2017.00782] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 04/18/2017] [Indexed: 12/22/2022] Open
Abstract
The emergence of methicillin-resistant Staphylococcus aureus (MRSA) in food has provoked a great concern about the presence of MRSA in associated foodstuff. Although MRSA is often detected in various retailed meat products, it seems that food handlers are more strongly associated with this type of food contamination. Thus, it can be easily postulated that any food could be contaminated with this pathogen in an industrial environment or in household and cause food poisoning. To this direction, the effect of rocket (Eruca sativa) extract on MRSA growth and proteome was examined in the present study. This goal was achieved with the comparative study of the MRSA strain COL proteome, cultivated in rocket extract versus the standard Luria-Bertani growth medium. The obtained results showed that MRSA was able to grow in rocket extract. In addition, proteome analysis using 2-DE method showed that MRSA strain COL is taking advantage of the sugar-, lipid-, and vitamin-rich substrate in the liquid rocket extract, although its growth was delayed in rocket extract compared to Luria–Bertani medium. This work could initiate further research about bacterial metabolism in plant-based media and defense mechanisms against plant-derived antibacterials.
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Affiliation(s)
- Agapi I Doulgeraki
- Laboratory of Microbiology and Biotechnology of Foods, Department of Food Science and Human Nutrition, Agricultural University of AthensAthens, Greece
| | - Georgios Efthimiou
- Department of Genetics and Biotechnology, Faculty of Biology, School of Science, National and Kapodistrian University of AthensAthens, Greece
| | - Spiros Paramithiotis
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of AthensAthens, Greece
| | - Katherine M Pappas
- Department of Genetics and Biotechnology, Faculty of Biology, School of Science, National and Kapodistrian University of AthensAthens, Greece
| | - Milton A Typas
- Department of Genetics and Biotechnology, Faculty of Biology, School of Science, National and Kapodistrian University of AthensAthens, Greece
| | - George-John Nychas
- Laboratory of Microbiology and Biotechnology of Foods, Department of Food Science and Human Nutrition, Agricultural University of AthensAthens, Greece
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Varas M, Valdivieso C, Mauriaca C, Ortíz-Severín J, Paradela A, Poblete-Castro I, Cabrera R, Chávez FP. Multi-level evaluation of Escherichia coli polyphosphate related mutants using global transcriptomic, proteomic and phenomic analyses. Biochim Biophys Acta Gen Subj 2017; 1861:871-883. [PMID: 28069396 DOI: 10.1016/j.bbagen.2017.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 12/26/2016] [Accepted: 01/05/2017] [Indexed: 12/20/2022]
Abstract
BACKGROUND Polyphosphate (polyP) is a linear biopolymer found in all living cells. In bacteria, mutants lacking polyphosphate kinase 1 (PPK1), the enzyme responsible for synthesis of most polyP, have many structural and functional defects. However, little is known about the causes of these pleiotropic alterations. The link between ppk1 deletion and those numerous phenotypes observed can be the result of complex molecular interactions that can be elucidated via a systems biology approach. METHODS By integrating different omics levels (transcriptome, proteome and phenome), we described the functioning of various metabolic pathways among Escherichia coli polyphosphate mutant strains (Δppk1, Δppx, and ΔpolyP). Bioinformatic analyses reveal the complex metabolic and regulatory bases of the phenotypes unique to polyP mutants. RESULTS Our results suggest that during polyP deficiency (Δppk1 mutant), metabolic pathways needed for energy supply are up-regulated, including fermentation, aerobic and anaerobic respiration. Transcriptomic and q-proteomic contrasting changes between Δppk1 and Δppx mutant strains were observed in those central metabolic pathways and confirmed by using Phenotypic microarrays. In addition, our results suggest a regulatory connection between polyP, second messenger metabolism, alternative Sigma/Anti-Sigma factors and type-II toxin-antitoxin (TA) systems. CONCLUSIONS We suggest a broader role for polyP via regulation of ATP-dependent proteolysis of type II toxin-antitoxin system and alternative Sigma/Anti-Sigma factors, that could explain the multiple structural and functional deficiencies described due to alteration of polyP metabolism. GENERAL SIGNIFICANCE Understanding the interplay of polyP in bacterial metabolism using a systems biology approach can help to improve design of novel antimicrobials toward pathogens.
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Affiliation(s)
- Macarena Varas
- Systems Microbiology Laboratory, Department of Biology, Faculty of Science, University of Chile, Chile.
| | - Camilo Valdivieso
- Systems Microbiology Laboratory, Department of Biology, Faculty of Science, University of Chile, Chile; Department of Ecology, Faculty of Science, University of Chile, Chile.
| | - Cecilia Mauriaca
- Systems Microbiology Laboratory, Department of Biology, Faculty of Science, University of Chile, Chile.
| | - Javiera Ortíz-Severín
- Systems Microbiology Laboratory, Department of Biology, Faculty of Science, University of Chile, Chile.
| | | | - Ignacio Poblete-Castro
- Facultad de Ciencias Biológicas, Center for Bioinformatics and Integrative Biology, Biosystems Engineering Laboratory, Universidad Andrés Bello, Chile.
| | - Ricardo Cabrera
- Department of Biology, Faculty of Sciences, University of Chile, Chile.
| | - Francisco P Chávez
- Systems Microbiology Laboratory, Department of Biology, Faculty of Science, University of Chile, Chile.
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Moreira DS, Murta SMF. Involvement of nucleoside diphosphate kinase b and elongation factor 2 in Leishmania braziliensis antimony resistance phenotype. Parasit Vectors 2016; 9:641. [PMID: 27964761 PMCID: PMC5155413 DOI: 10.1186/s13071-016-1930-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/05/2016] [Indexed: 02/07/2023] Open
Abstract
Background Nucleoside diphosphate kinase b (NDKb) is responsible for nucleoside triphosphates synthesis and it has key role in the purine metabolism in trypanosomatid protozoans. Elongation factor 2 (EF2) is an important factor for protein synthesis. Recently, our phosphoproteomic analysis demonstrated that NDKb and EF2 proteins were phosphorylated and dephosphorylated in antimony (SbIII)-resistant L. braziliensis line compared to its SbIII-susceptible pair, respectively. Methods In this study, the overexpression of NDKb and EF2 genes in L. braziliensis and L. infantum was performed to investigate the contribution of these proteins in the SbIII-resistance phenotype. Furthermore, we examined the role of lamivudine on SbIII susceptibility in clones that overexpress the NDKb gene, and the effect of EF2 kinase (EF2K) inhibitor on the growth of EF2-overexpressing parasites. Results Western blot analysis demonstrated that NDKb and EF2 proteins are more and less expressed, respectively, in SbIII-resistant line of L. braziliensis than its wild-type (WTS) counterpart, corroborating our previous phosphoproteomic data. NDKb or EF2-overexpressing L. braziliensis lines were 1.6 to 2.1-fold more resistant to SbIII than the untransfected WTS line. In contrast, no difference in SbIII susceptibility was observed in L. infantum parasites overexpressing NDKb or EF2. Susceptibility assays showed that NDKb-overexpressing L. braziliensis lines presented elevated resistance to lamivudine, an antiviral agent, but it did not alter the leishmanicidal activity in association with SbIII. EF2-overexpressing L. braziliensis clone was slightly more resistant to EF2K inhibitor than the WTS line. Surprisingly, this inhibitor increased the antileishmanial effect of SbIII, suggesting that this association might be a valuable strategy for leishmaniasis chemotherapy. Conclusion Our findings represent the first study of NDKb and EF2 genes overexpression that demonstrates an increase of SbIII resistance in L. braziliensis which can contribute to develop new strategies for leishmaniasis treatment.
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Affiliation(s)
- Douglas S Moreira
- Centro de Pesquisas René Rachou CPqRR, Fundação Oswaldo Cruz - FIOCRUZ, Avenida Augusto de Lima 1715, Belo Horizonte, MG, Brazil
| | - Silvane M F Murta
- Centro de Pesquisas René Rachou CPqRR, Fundação Oswaldo Cruz - FIOCRUZ, Avenida Augusto de Lima 1715, Belo Horizonte, MG, Brazil.
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Nucleoside-Diphosphate-Kinase of P. gingivalis is Secreted from Epithelial Cells In the Absence of a Leader Sequence Through a Pannexin-1 Interactome. Sci Rep 2016; 6:37643. [PMID: 27883084 PMCID: PMC5121656 DOI: 10.1038/srep37643] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/28/2016] [Indexed: 01/22/2023] Open
Abstract
Nucleoside-diphosphate-kinases (NDKs) are leaderless, multifunctional enzymes. The mode(s) of NDK secretion is currently undefined, while extracellular translocation of bacterial NDKs is critical for avoidance of host pathogen clearance by opportunistic pathogens such as Porphyromonas gingivalis. P. gingivalis-NDK during infection inhibits extracellular-ATP (eATP)/P2X7-receptor mediated cell death in gingival epithelial cells (GECs) via eATP hydrolysis. Furthermore, depletion of pannexin-1-hemichannel (PNX1) coupled with P2X7-receptor blocks the infection-induced eATP release in GECs, and P. gingivalis-NDK impacts this pathway. Ultrastructural and confocal microscopy of P. gingivalis-co-cultured GECs or green-fluorescent-protein (GFP)-P. gingivalis-NDK transfected GECs revealed a perinuclear/cytoplasmic localization of NDK. eATP stimulation induced NDK recruitment to the cell periphery. Depletion of PNX1 by siRNA or inhibition by probenecid resulted in significant blocking of extracellular NDK activity and secretion using ATPase and ELISA assays. Co-immunoprecipitation-coupled Mass-spectrometry method revealed association of P. gingivalis-NDK to the myosin-9 motor molecule. Interestingly, inhibition of myosin-9, actin, and lipid-rafts, shown to be involved in PNX1-hemichannel function, resulted in marked intracellular accumulation of NDK and decreased NDK secretion from infected GECs. These results elucidate for the first time PNX1-hemichannels as potentially main extracellular translocation pathway for NDKs from an intracellular pathogen, suggesting that PNX1-hemichannels may represent a therapeutic target for chronic opportunistic infections.
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Skliros D, Kalatzis PG, Katharios P, Flemetakis E. Comparative Functional Genomic Analysis of Two Vibrio Phages Reveals Complex Metabolic Interactions with the Host Cell. Front Microbiol 2016; 7:1807. [PMID: 27895630 PMCID: PMC5107563 DOI: 10.3389/fmicb.2016.01807] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/27/2016] [Indexed: 01/21/2023] Open
Abstract
Sequencing and annotation was performed for two large double stranded DNA bacteriophages, φGrn1 and φSt2 of the Myoviridae family, considered to be of great interest for phage therapy against Vibrios in aquaculture live feeds. In addition, phage–host metabolic interactions and exploitation was studied by transcript profiling of selected viral and host genes. Comparative genomic analysis with other large Vibrio phages was also performed to establish the presence and location of homing endonucleases highlighting distinct features for both phages. Phylogenetic analysis revealed that they belong to the “schizoT4like” clade. Although many reports of newly sequenced viruses have provided a large set of information, basic research related to the shift of the bacterial metabolism during infection remains stagnant. The function of many viral protein products in the process of infection is still unknown. Genome annotation identified the presence of several viral open reading frames (ORFs) participating in metabolism, including a Sir2/cobB (sirtuin) protein and a number of genes involved in auxiliary NAD+ and nucleotide biosynthesis, necessary for phage DNA replication. Key genes were subsequently selected for detail study of their expression levels during infection. This work suggests a complex metabolic interaction and exploitation of the host metabolic pathways and biochemical processes, including a possible post-translational protein modification, by the virus during infection.
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Affiliation(s)
- Dimitrios Skliros
- Laboratory of Molecular Biology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens Athens, Greece
| | - Panos G Kalatzis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, HeraklionCrete, Greece; Marine Biological Section, University of CopenhagenHelsingør, Denmark
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion Crete, Greece
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens Athens, Greece
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Ma W, Zhang D, Li G, Liu J, He G, Zhang P, Yang L, Zhu H, Xu N, Liang S. Antibacterial mechanism of daptomycin antibiotic against Staphylococcus aureus based on a quantitative bacterial proteome analysis. J Proteomics 2016; 150:242-251. [PMID: 27693894 DOI: 10.1016/j.jprot.2016.09.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 09/06/2016] [Accepted: 09/26/2016] [Indexed: 02/05/2023]
Abstract
Daptomycin (DAP) is a novel lipopeptide antibiotic which exhibits excellent antibacterial activity against most clinically relevant Gram-positive bacteria, but the DAP-targeting protein molecules against host bacterial infection are far from clear. In order to discover bacterial protein response to DAP treatment, an iTRAQ-based quantitative proteomic analysis was applied to identify differential bacterial proteome profiling of Staphylococcus aureus (S. aureus) ATCC 25923 to 0.125μg/ml DAP exposure. Totally 51 bacterial proteins were significantly changed with DAP treatment, among which 34 proteins were obviously up-regulated and 17 proteins were down-regulated. Meanwhile, 139 bacterial cell membrane (CM) proteins were identified, and 7 CM proteins were significantly altered to decrease CM potential to disrupt bacterial cell membrane. Especially the up-regulation of NDK and down-regulation of NT5 in several S. aureus strains are validated to be a universal variation tendency response to DAP treatment. Under DAP exposure, bacterial membrane potential is decreased and cell membrane is disrupted, and bacterial chromosome is aggregated, which contributes to bacterial DNA rapid release and induces bacteria death within 2-5h. In general, multiple bacterial protein expressions are changed in response to DAP antibiotic exposure, which disrupts host bacterial physiology by multiple cellular levels. To our knowledge, this is the first time to exactly identify infectious bacterial proteins in response to DAP antibiotic action. Our findings help better understand DAP antibacterial mechanism and develop novel DAP derivatives against the upcoming antibiotic-resistant bacterial infection. BIOLOGICAL SIGNIFICANCE DAP is a novel lipopeptide antibiotic that it exhibits excellent in vitro activity against most clinically relevant Gram-positive bacteria, and the investigations on its pharmaceutical action mode of DAP have dramatically increased in the past decade due to its unique antimicrobial mechanism. However, the target molecules of DAP acting on the infectious bacteria, are far from clear. The state-of-the-art quantitative proteomic technologies provide new avenues to uncover underlying mechanism of antibiotics. Our research main aims to identify bacterial proteome profiling of host strain S. aureus response to DAP treatment through an iTRAQ-based quantitative proteomic analysis, which contributes to understand DAP efficient antibacterial activity and the microbial-antibiotic interactions.
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Affiliation(s)
- Wen Ma
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China
| | - Dan Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China
| | - Guoshun Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China
| | - Jingjing Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China
| | - Gu He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China
| | - Peng Zhang
- Department of Urinary Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, PR China
| | - Li Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China
| | - Hongxia Zhu
- Laboratory of Cell and Molecular Biology, State Key Laboratory of Molecular Oncology, Cancer Institute & Cancer Hospital, Chinese Academy of Medical Sciences, Beijing 100034, PR China
| | - Ningzhi Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China; Laboratory of Cell and Molecular Biology, State Key Laboratory of Molecular Oncology, Cancer Institute & Cancer Hospital, Chinese Academy of Medical Sciences, Beijing 100034, PR China
| | - Shufang Liang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China.
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Yu H, Xiong J, Zhang R, Hu X, Qiu J, Zhang D, Xu X, Xin R, He X, Xie W, Sheng H, Chen Q, Zhang L, Rao X, Zhang K. Ndk, a novel host-responsive regulator, negatively regulates bacterial virulence through quorum sensing in Pseudomonas aeruginosa. Sci Rep 2016; 6:28684. [PMID: 27345215 PMCID: PMC4921839 DOI: 10.1038/srep28684] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/08/2016] [Indexed: 11/09/2022] Open
Abstract
Pathogenic bacteria could adjust gene expression to enable their survival in the distinct host environment. However, the mechanism by which bacteria adapt to the host environment is not well described. In this study, we demonstrated that nucleoside diphosphate kinase (Ndk) of Pseudomonas aeruginosa is critical for adjusting the bacterial virulence determinants during infection. Ndk expression was down-regulated in the pulmonary alveoli of a mouse model of acute pneumonia. Knockout of ndk up-regulated transcription factor ExsA-mediated T3S regulon expression and decreased exoproduct-related gene expression through the inhibition of the quorum sensing hierarchy. Moreover, in vitro and in vivo studies demonstrated that the ndk mutant exhibits enhanced cytotoxicity and host pathogenicity by increasing T3SS proteins. Taken together, our data reveal that ndk is a critical novel host-responsive gene required for coordinating P. aeruginosa virulence upon acute infection.
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Affiliation(s)
- Hua Yu
- Department of Microbiology, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China.,Central Laboratory, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Junzhi Xiong
- Central Laboratory, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Rong Zhang
- Department of Pharmacy, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Xiaomei Hu
- Department of Microbiology, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Jing Qiu
- Central Laboratory, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Di Zhang
- Central Laboratory, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Xiaohui Xu
- Central Laboratory, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Rong Xin
- Central Laboratory, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Xiaomei He
- Central Laboratory, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Wei Xie
- Central Laboratory, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Halei Sheng
- Central Laboratory, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Qian Chen
- Central Laboratory, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Le Zhang
- Central Laboratory, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Xiancai Rao
- Department of Microbiology, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Kebin Zhang
- Central Laboratory, Xinqiao Hospital, Third Military Medical University, Chongqing, China
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Sultan A, Andersen B, Svensson B, Finnie C. Exploring the Plant–Microbe Interface by Profiling the Surface-Associated Proteins of Barley Grains. J Proteome Res 2016; 15:1151-67. [DOI: 10.1021/acs.jproteome.5b01042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Abida Sultan
- Enzyme
and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Elektrovej, Building 375, DK-2800 Kgs. Lyngby, Denmark
| | - Birgit Andersen
- Agricultural
and Environmental Proteomics, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Birte Svensson
- Enzyme
and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Elektrovej, Building 375, DK-2800 Kgs. Lyngby, Denmark
| | - Christine Finnie
- Agricultural
and Environmental Proteomics, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
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Polyphosphate kinases modulate Campylobacter jejuni outer membrane constituents and alter its capacity to invade and survive in intestinal epithelial cells in vitro. Emerg Microbes Infect 2015; 4:e77. [PMID: 26714783 PMCID: PMC4715166 DOI: 10.1038/emi.2015.77] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/28/2015] [Accepted: 10/01/2015] [Indexed: 12/12/2022]
Abstract
Campylobacter jejuni is the most prevalent cause of bacterial gastroenteritis worldwide. Polyphosphate kinases 1 and 2 (PPK1 and PPK2) regulate several cellular processes, including the biosynthesis of the bacterial cell wall. Despite their importance, whether PPK1 and PPK2 modulate the composition of C. jejuni outer membrane constituents (OMCs) and consequently impact its interaction with host cells remains unknown. Our comparative analysis between C. jejuni wild type, Δppk1, and Δppk2 strains showed qualitative and quantitative differences in the total OMC composition among these strains. Importantly, these OMC variations observed on the C. jejuni polyphosphate kinase mutants are directly related to their capacity to invade, survive, and alter the immune response of intestinal epithelial cells in vitro. Specifically, sub-fractionation of the C. jejuni OMC indicated that OMC proteins are uniquely associated with bacterial invasion, whereas C. jejuni OMC proteins, lipids, and lipoglycans are all associated with C. jejuni intracellular survival. This study provides new insights regarding the function of polyphosphate kinases and their role in C. jejuni infection.
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Akanuma G, Yoshizawa R, Nagakura M, Shiwa Y, Watanabe S, Yoshikawa H, Ushio K, Ishizuka M. EliA is required for inducing the stearyl alcohol-mediated expression of secretory proteins and production of polyester in Ralstonia sp. NT80. MICROBIOLOGY-SGM 2015; 162:408-419. [PMID: 26673629 DOI: 10.1099/mic.0.000225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Addition of stearyl alcohol to the culture medium of Ralstonia sp. NT80 induced expression of a significant amount of secretory lipase. Comparative proteomic analysis of extracellular proteins from NT80 cells grown in the presence or absence of stearyl alcohol revealed that stearyl alcohol induced expression of several secretory proteins including lipase, haemolysin-coregulated protein and nucleoside diphosphate kinase. Expression of these secreted proteins was upregulated at the transcriptional level. Stearyl alcohol also induced the synthesis of polyhydroxyalkanoate. Secretory protein EliA was required for all these responses of NT80 cells to stearyl alcohol. Accordingly, the effects of stearyl alcohol were significantly reduced in the eliA deletion mutant cells of NT80 (ΔeliA). The remaining concentration of stearyl alcohol in the culture supernatant of the wild-type cells, but not that in the culture supernatant of the ΔeliA cells, clearly decreased during the course of growth. These observed phenotypes of the ΔeliA mutant were rescued by gene complementation. The results suggested that EliA is essential for these cells to respond to stearyl alcohol, and that it plays an important role in the recognition and assimilation of stearyl alcohol by NT80 cells.
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Affiliation(s)
- Genki Akanuma
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo, Japan.,Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
| | - Rie Yoshizawa
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo, Japan
| | - Mari Nagakura
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo, Japan
| | - Yuh Shiwa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Hirofumi Yoshikawa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan.,Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Kazutoshi Ushio
- Department of Applied Chemistry and Biotechnology, Niihama National College of Technology, Niihama, Ehime, Japan
| | - Morio Ishizuka
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo, Japan
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In silico approaches for the identification of virulence candidates amongst hypothetical proteins of Mycoplasma pneumoniae 309. Comput Biol Chem 2015; 59 Pt A:67-80. [DOI: 10.1016/j.compbiolchem.2015.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 09/08/2015] [Accepted: 09/14/2015] [Indexed: 01/25/2023]
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Omer H, Alpha-Bazin B, Brunet JL, Armengaud J, Duport C. Proteomics identifies Bacillus cereus EntD as a pivotal protein for the production of numerous virulence factors. Front Microbiol 2015; 6:1004. [PMID: 26500610 PMCID: PMC4595770 DOI: 10.3389/fmicb.2015.01004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 09/07/2015] [Indexed: 11/13/2022] Open
Abstract
Bacillus cereus is a Gram-positive pathogen that causes a wide variety of diseases in humans. It secretes into the extracellular milieu proteins that may contribute directly or indirectly to its virulence. EntD is a novel exoprotein identified by proteogenomics of B. cereus ATCC 14579. We constructed a ΔentD mutant and analyzed the impact of entD disruption on the cellular proteome and exoproteome isolated from early, late, and stationary-phase cultures. We identified 308 and 79 proteins regulated by EntD in the cellular proteome and the exoproteome, respectively. The contribution of these proteins to important virulence-associated functions, including central metabolism, cell structure, antioxidative ability, cell motility, and toxin production, are presented. The proteomic data were correlated with the growth defect, cell morphology change, reduced motility, and reduced cytotoxicity of the ΔentD mutant strain. We conclude that EntD is an important player in B. cereus virulence. The function of EntD and the putative EntD-dependent regulatory network are discussed. To our knowledge, this study is the first characterization of an Ent family protein in a species of the B. cereus group.
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Affiliation(s)
- Hélène Omer
- Université d'Avignon et des Pays de Vaucluse, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France ; INRA, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France ; CEA-Marcoule, DSV/IBITEC-S/SPI/Li2D, Laboratory "Innovative technologies for Detection and Diagnostic" Bagnols-sur-Cèze, France
| | - Béatrice Alpha-Bazin
- CEA-Marcoule, DSV/IBITEC-S/SPI/Li2D, Laboratory "Innovative technologies for Detection and Diagnostic" Bagnols-sur-Cèze, France
| | | | - Jean Armengaud
- CEA-Marcoule, DSV/IBITEC-S/SPI/Li2D, Laboratory "Innovative technologies for Detection and Diagnostic" Bagnols-sur-Cèze, France
| | - Catherine Duport
- Université d'Avignon et des Pays de Vaucluse, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France ; INRA, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France
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Chowdhary N, Selvaraj A, KrishnaKumaar L, Kumar GR. Genome Wide Re-Annotation of Caldicellulosiruptor saccharolyticus with New Insights into Genes Involved in Biomass Degradation and Hydrogen Production. PLoS One 2015. [PMID: 26196387 PMCID: PMC4510573 DOI: 10.1371/journal.pone.0133183] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Caldicellulosiruptor saccharolyticus has proven itself to be an excellent candidate for biological hydrogen (H2) production, but still it has major drawbacks like sensitivity to high osmotic pressure and low volumetric H2 productivity, which should be considered before it can be used industrially. A whole genome re-annotation work has been carried out as an attempt to update the incomplete genome information that causes gap in the knowledge especially in the area of metabolic engineering, to improve the H2 producing capabilities of C. saccharolyticus. Whole genome re-annotation was performed through manual means for 2,682 Coding Sequences (CDSs). Bioinformatics tools based on sequence similarity, motif search, phylogenetic analysis and fold recognition were employed for re-annotation. Our methodology could successfully add functions for 409 hypothetical proteins (HPs), 46 proteins previously annotated as putative and assigned more accurate functions for the known protein sequences. Homology based gene annotation has been used as a standard method for assigning function to novel proteins, but over the past few years many non-homology based methods such as genomic context approaches for protein function prediction have been developed. Using non-homology based functional prediction methods, we were able to assign cellular processes or physical complexes for 249 hypothetical sequences. Our re-annotation pipeline highlights the addition of 231 new CDSs generated from MicroScope Platform, to the original genome with functional prediction for 49 of them. The re-annotation of HPs and new CDSs is stored in the relational database that is available on the MicroScope web-based platform. In parallel, a comparative genome analyses were performed among the members of genus Caldicellulosiruptor to understand the function and evolutionary processes. Further, with results from integrated re-annotation studies (homology and genomic context approach), we strongly suggest that Csac_0437 and Csac_0424 encode for glycoside hydrolases (GH) and are proposed to be involved in the decomposition of recalcitrant plant polysaccharides. Similarly, HPs: Csac_0732, Csac_1862, Csac_1294 and Csac_0668 are suggested to play a significant role in biohydrogen production. Function prediction of these HPs by using our integrated approach will considerably enhance the interpretation of large-scale experiments targeting this industrially important organism.
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Affiliation(s)
- Nupoor Chowdhary
- AU-KBC Research Centre, Anna University, MIT Campus, Chrompet, Chennai, 600044, India
| | - Ashok Selvaraj
- AU-KBC Research Centre, Anna University, MIT Campus, Chrompet, Chennai, 600044, India
| | - Lakshmi KrishnaKumaar
- AU-KBC Research Centre, Anna University, MIT Campus, Chrompet, Chennai, 600044, India
| | - Gopal Ramesh Kumar
- AU-KBC Research Centre, Anna University, MIT Campus, Chrompet, Chennai, 600044, India
- * E-mail:
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44
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Bistability in a metabolic network underpins the de novo evolution of colony switching in Pseudomonas fluorescens. PLoS Biol 2015; 13:e1002109. [PMID: 25763575 PMCID: PMC4357382 DOI: 10.1371/journal.pbio.1002109] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/18/2015] [Indexed: 12/22/2022] Open
Abstract
Phenotype switching is commonly observed in nature. This prevalence has allowed the elucidation of a number of underlying molecular mechanisms. However, little is known about how phenotypic switches arise and function in their early evolutionary stages. The first opportunity to provide empirical insight was delivered by an experiment in which populations of the bacterium Pseudomonas fluorescens SBW25 evolved, de novo, the ability to switch between two colony phenotypes. Here we unravel the molecular mechanism behind colony switching, revealing how a single nucleotide change in a gene enmeshed in central metabolism (carB) generates such a striking phenotype. We show that colony switching is underpinned by ON/OFF expression of capsules consisting of a colanic acid-like polymer. We use molecular genetics, biochemical analyses, and experimental evolution to establish that capsule switching results from perturbation of the pyrimidine biosynthetic pathway. Of central importance is a bifurcation point at which uracil triphosphate is partitioned towards either nucleotide metabolism or polymer production. This bifurcation marks a cell-fate decision point whereby cells with relatively high pyrimidine levels favour nucleotide metabolism (capsule OFF), while cells with lower pyrimidine levels divert resources towards polymer biosynthesis (capsule ON). This decision point is present and functional in the wild-type strain. Finally, we present a simple mathematical model demonstrating that the molecular components of the decision point are capable of producing switching. Despite its simple mutational cause, the connection between genotype and phenotype is complex and multidimensional, offering a rare glimpse of how noise in regulatory networks can provide opportunity for evolution. The molecular basis of an experimentally evolved colony-level phenotype switch is revealed to affect a metabolic bifurcation point where nucleotides can be used for either cell division or capsule polymer synthesis. Phenotype switching—the ability to switch rapidly between phenotypic states—is an evolutionary survival strategy commonly used by organisms in the face of unpredictable environmental conditions. However, little is known about how phenotype switches emerge and function in their early evolutionary stages. A previous study observed the evolutionary emergence of colony morphology switching in Pseudomonas fluorescens populations in response to fluctuating selection. Here we describe the underlying molecular basis of this colony switching, providing the first account of the mechanism behind a real-time evolved phenotype switch. We show that colony switching in this instance is underpinned at the cellular level by high frequency ON/OFF expression of colanic acid-like capsules in response to varying levels of a metabolite. Biochemical assays revealed that capsule switching results from mutations that reduce concentrations of intermediates in a central metabolic pathway—the pyrimidine biosynthetic pathway. Of key importance is the partitioning of these metabolic resources between polymer production (leading to capsulation) and cell division (leading to noncapsulation); this bifurcation marks a decision point whereby cells with low metabolite levels divert resources towards polymer production, increasing the likelihood of switching to the capsulated state. As a greater proportion of cells become capsulated, colony switching emerges. These findings show that, while colony switching evolved with relative ease, the underlying molecular mechanism is surprisingly complex.
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45
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Salaemae W, Yap MY, Wegener KL, Booker GW, Wilce MCJ, Polyak SW. Nucleotide triphosphate promiscuity in Mycobacterium tuberculosis dethiobiotin synthetase. Tuberculosis (Edinb) 2015; 95:259-66. [PMID: 25801336 DOI: 10.1016/j.tube.2015.02.046] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 02/26/2015] [Indexed: 11/29/2022]
Abstract
Dethiobiotin synthetase (DTBS) plays a crucial role in biotin biosynthesis in microorganisms, fungi, and plants. Due to its importance in bacterial pathogenesis, and the absence of a human homologue, DTBS is a promising target for the development of new antibacterials desperately needed to combat antibiotic resistance. Here we report the first X-ray structure of DTBS from Mycobacterium tuberculosis (MtDTBS) bound to a nucleotide triphosphate (CTP). The nucleoside base is stabilized in its pocket through hydrogen-bonding interactions with the protein backbone, rather than amino acid side chains. This resulted in the unexpected finding that MtDTBS could utilise ATP, CTP, GTP, ITP, TTP, or UTP with similar Km and kcat values, although the enzyme had the highest affinity for CTP in competitive binding and surface plasmon resonance assays. This is in contrast to other DTBS homologues that preferentially bind ATP primarily through hydrogen-bonds between the purine base and the carboxamide side chain of a key asparagine. Mutational analysis performed alongside in silico experiments revealed a gate-keeper role for Asn175 in Escherichia coli DTBS that excludes binding of other nucleotide triphosphates. Here we provide evidence to show that MtDTBS has a broad nucleotide specificity due to the absence of the gate-keeper residue.
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Affiliation(s)
- Wanisa Salaemae
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Min Y Yap
- Department of Biochemistry and Molecular Biology, School of Biomedical Science, Monash University, Victoria, 3800, Australia
| | - Kate L Wegener
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Grant W Booker
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Matthew C J Wilce
- Department of Biochemistry and Molecular Biology, School of Biomedical Science, Monash University, Victoria, 3800, Australia
| | - Steven W Polyak
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia.
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46
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Crystal structure and biophysical characterization of the nucleoside diphosphate kinase from Leishmania braziliensis. BMC STRUCTURAL BIOLOGY 2015; 15:2. [PMID: 25643978 PMCID: PMC4322457 DOI: 10.1186/s12900-015-0030-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/15/2015] [Indexed: 01/07/2023]
Abstract
BACKGROUND Nucleoside diphosphate kinase (NDK) is a housekeeping enzyme that plays key roles in nucleotide recycling and homeostasis in trypanosomatids. It is also secreted by the intracellular parasite Leishmania to modulate the host response. These functions make NDK an attractive target for drug design and for studies aiming at a better understanding of the mechanisms mediating host-pathogen interactions. RESULTS We report the crystal structure and biophysical characterization of the NDK from Leishmania braziliensis (LbNDK). The subunit consists of six α-helices along with a core of four β-strands arranged in a β2β3β1β4 antiparallel topology order. In contrast to the NDK from L. major, the LbNDK C-terminal extension is partially unfolded. SAXS data showed that LbNDK forms hexamers in solution in the pH range from 7.0 to 4.0, a hydrodynamic behavior conserved in most eukaryotic NDKs. However, DSF assays show that acidification and alkalization decrease the hexamer stability. CONCLUSIONS Our results support that LbNDK remains hexameric in pH conditions akin to that faced by this enzyme when secreted by Leishmania amastigotes in the parasitophorous vacuoles (pH 4.7 to 5.3). The unusual unfolded conformation of LbNDK C-terminus decreases the surface buried in the trimer interface exposing new regions that might be explored for the development of compounds designed to disturb enzyme oligomerization, which may impair the important nucleotide salvage pathway in these parasites.
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Wang X, Dinler BS, Vignjevic M, Jacobsen S, Wollenweber B. Physiological and proteome studies of responses to heat stress during grain filling in contrasting wheat cultivars. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 230:33-50. [PMID: 25480006 DOI: 10.1016/j.plantsci.2014.10.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 10/22/2014] [Accepted: 10/26/2014] [Indexed: 05/18/2023]
Abstract
Experiments to explore physiological and biochemical differences of the effects of heat stress in ten wheat (Triticum aestivum L.) cultivars have been performed. Based on the response of photosynthesis rates, cell membrane lipid peroxide concentrations and grain yield to heat, six cultivars were clustered as heat-tolerant (cv. '579', cv. '810', cv. '1110', cv. Terice, cv. Taifun and cv. Vinjett) and four as heat-sensitive (cv. '490', cv. '633', cv. '1039' and cv. '1159'). Higher rates of photosynthetic carbon- and light-use were accompanied by lower damage to cell membranes in leaves of tolerant compared to sensitive cultivars under heat stress. The tolerant cv. '810' and the sensitive cv. '1039' were selected for further proteome analysis of leaves. Proteins related to photosynthesis, glycolysis, stress defence, heat shock and ATP production were differently expressed in leaves of the tolerant and sensitive cultivar under heat stress in relation to the corresponding control. The abundance of proteins related to signal transduction, heat shock, photosynthesis, and antioxidants increased, while the abundance of proteins related to nitrogen metabolism decreased in the tolerant cv. '810' under heat stress as compared to the control. Collectively, the results indicate that primarily changes in both the amount and activities of enzymes involved in photosynthesis and antioxidant activities in leaves contributed to higher heat tolerance in the cv. '810' compared to the heat sensitive cv. '1039'.
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Affiliation(s)
- Xiao Wang
- Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/Hi-Tech Key Laboratory of Information Agriculture of Jiangsu Province, Nanjing Agricultural University, Nanjing 210095, China; Aarhus University, Faculty of Science and Technology, Institute of Agroecology, Research Centre Flakkebjerg, DK-4200 Slagelse, Denmark; Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Building 224, DK-2800 Kgs. Lyngby, Denmark.
| | - Burcu Seckin Dinler
- Department of Biology, Faculty of Arts and Sciences, Sinop University, Sinop, Turkey
| | - Marija Vignjevic
- Aarhus University, Faculty of Science and Technology, Institute of Agroecology, Research Centre Flakkebjerg, DK-4200 Slagelse, Denmark
| | - Susanne Jacobsen
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Bernd Wollenweber
- Aarhus University, Faculty of Science and Technology, Institute of Agroecology, Research Centre Flakkebjerg, DK-4200 Slagelse, Denmark
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Circovirus transport proceeds via direct interaction of the cytoplasmic dynein IC1 subunit with the viral capsid protein. J Virol 2014; 89:2777-91. [PMID: 25540360 DOI: 10.1128/jvi.03117-14] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED Microtubule transport of circovirus from the periphery of the cell to the nucleus is essential for viral replication in early infection. How the microtubule is recruited to the viral cargo remains unclear. In this study, we observed that circovirus trafficking is dependent on microtubule polymerization and that incoming circovirus particles colocalize with cytoplasmic dynein and endosomes. However, circovirus binding to dynein was independent of the presence of microtubular α-tubulin and translocation of cytoplasmic dynein into the nucleus. The circovirus capsid (Cap) subunit enhanced microtubular acetylation and directly interacted with intermediate chain 1 (IC1) of dynein. N-terminal residues 42 to 100 of the Cap viral protein were required for efficient binding to the dynein IC1 subunit and for retrograde transport. Knockdown of IC1 decreased virus transport and replication. These results demonstrate that Cap is a direct ligand of the cytoplasmic dynein IC1 subunit and an inducer of microtubule α-tubulin acetylation. Furthermore, Cap recruits the host dynein/microtubule machinery to facilitate transport toward the nucleus by an endosomal mechanism distinct from that used for physiological dynein cargo. IMPORTANCE Incoming viral particles hijack the intracellular trafficking machinery of the host in order to migrate from the cell surface to the replication sites. Better knowledge of the interaction between viruses and virus proteins and the intracellular trafficking machinery may provide new targets for antiviral therapies. Currently, little is known about the molecular mechanisms of circovirus transport. Here, we report that circovirus particles enter early endosomes and utilize the microtubule-associated molecular motor dynein to travel along microtubules. The circovirus capsid subunit enhances microtubular acetylation, and N-terminal residues 42 to 100 directly interact with the dynein IC1 subunit during retrograde transport. These findings highlight a mechanism whereby circoviruses recruit dynein for transport to the nucleus via the dynein/microtubule machinery.
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49
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Komatsu S, Kamal AHM, Hossain Z. Wheat proteomics: proteome modulation and abiotic stress acclimation. FRONTIERS IN PLANT SCIENCE 2014; 5:684. [PMID: 25538718 PMCID: PMC4259124 DOI: 10.3389/fpls.2014.00684] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 11/18/2014] [Indexed: 05/21/2023]
Abstract
Cellular mechanisms of stress sensing and signaling represent the initial plant responses to adverse conditions. The development of high-throughput "Omics" techniques has initiated a new era of the study of plant molecular strategies for adapting to environmental changes. However, the elucidation of stress adaptation mechanisms in plants requires the accurate isolation and characterization of stress-responsive proteins. Because the functional part of the genome, namely the proteins and their post-translational modifications, are critical for plant stress responses, proteomic studies provide comprehensive information about the fine-tuning of cellular pathways that primarily involved in stress mitigation. This review summarizes the major proteomic findings related to alterations in the wheat proteomic profile in response to abiotic stresses. Moreover, the strengths and weaknesses of different sample preparation techniques, including subcellular protein extraction protocols, are discussed in detail. The continued development of proteomic approaches in combination with rapidly evolving bioinformatics tools and interactive databases will facilitate understanding of the plant mechanisms underlying stress tolerance.
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Affiliation(s)
- Setsuko Komatsu
- National Institute of Crop Science, National Agriculture and Food Research OrganizationTsukuba, Japan
| | - Abu H. M. Kamal
- National Institute of Crop Science, National Agriculture and Food Research OrganizationTsukuba, Japan
| | - Zahed Hossain
- Plant Stress Biology Lab, Department of Botany, West Bengal State UniversityKolkata, India
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García-Descalzo L, García-López E, Alcázar A, Baquero F, Cid C. Proteomic analysis of the adaptation to warming in the Antarctic bacteria Shewanella frigidimarina. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2229-40. [PMID: 25149826 DOI: 10.1016/j.bbapap.2014.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 08/06/2014] [Accepted: 08/11/2014] [Indexed: 12/27/2022]
Abstract
Antarctica is subjected to extremely variable conditions, but the importance of the temperature increase in cold adapted bacteria is still unknown. To study the molecular adaptation to warming of Antarctic bacteria, cultures of Shewanella frigidimarina were incubated at temperatures ranging from 0°C to 30°C, emulating the most extreme conditions that this strain could tolerate. A proteomic approach was developed to identify the soluble proteins obtained from cells growing at 4°C, 20°C and 28°C. The most drastic effect when bacteria were grown at 28°C was the accumulation of heat shock proteins as well as other proteins related to stress, redox homeostasis or protein synthesis and degradation, and the decrease of enzymes and components of the cell envelope. Furthermore, two main responses in the adaptation to warm temperature were detected: the presence of diverse isoforms in some differentially expressed proteins, and the composition of chaperone interaction networks at the limits of growth temperature. The abundance changes of proteins suggest that warming induces a stress situation in S. frigidimarina forcing cells to reorganize their molecular networks as an adaptive response to these environmental conditions.
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Affiliation(s)
| | - Eva García-López
- Centro de Astrobiologia (CSIC-INTA), 28850 Torrejón de Ardoz, Spain
| | - Alberto Alcázar
- Department of Investigation, Hospital Ramon y Cajal, 28034 Madrid, Spain
| | - Fernando Baquero
- Centro de Astrobiologia (CSIC-INTA), 28850 Torrejón de Ardoz, Spain; Department of Microbiology, Hospital Ramon y Cajal, 28034 Madrid, Spain
| | - Cristina Cid
- Centro de Astrobiologia (CSIC-INTA), 28850 Torrejón de Ardoz, Spain.
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