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Modeling Metabolism and Finding New Antibiotics. Bioinformatics 2023. [DOI: 10.1007/978-3-662-65036-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
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Influence of breast cancer risk factors on proliferation and DNA damage in human breast glandular tissues: role of intracellular estrogen levels, oxidative stress and estrogen biotransformation. Arch Toxicol 2021; 96:673-687. [PMID: 34921608 PMCID: PMC8837527 DOI: 10.1007/s00204-021-03198-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/09/2021] [Indexed: 12/03/2022]
Abstract
Breast cancer etiology is associated with both proliferation and DNA damage induced by estrogens. Breast cancer risk factors (BCRF) such as body mass index (BMI), smoking, and intake of estrogen-active drugs were recently shown to influence intratissue estrogen levels. Thus, the aim of the present study was to investigate the influence of BCRF on estrogen-induced proliferation and DNA damage in 41 well-characterized breast glandular tissues derived from women without breast cancer. Influence of intramammary estrogen levels and BCRF on estrogen receptor (ESR) activation, ESR-related proliferation (indicated by levels of marker transcripts), oxidative stress (indicated by levels of GCLC transcript and oxidative derivatives of cholesterol), and levels of transcripts encoding enzymes involved in estrogen biotransformation was identified by multiple linear regression models. Metabolic fluxes to adducts of estrogens with DNA (E-DNA) were assessed by a metabolic network model (MNM) which was validated by comparison of calculated fluxes with data on methoxylated and glucuronidated estrogens determined by GC– and UHPLC–MS/MS. Intratissue estrogen levels significantly influenced ESR activation and fluxes to E-DNA within the MNM. Likewise, all BCRF directly and/or indirectly influenced ESR activation, proliferation, and key flux constraints influencing E-DNA (i.e., levels of estrogens, CYP1B1, SULT1A1, SULT1A2, and GSTP1). However, no unambiguous total effect of BCRF on proliferation became apparent. Furthermore, BMI was the only BCRF to indeed influence fluxes to E-DNA (via congruent adverse influence on levels of estrogens, CYP1B1 and SULT1A2).
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Liang C, Rios-Miguel AB, Jarick M, Neurgaonkar P, Girard M, François P, Schrenzel J, Ibrahim ES, Ohlsen K, Dandekar T. Staphylococcusaureus Transcriptome Data and Metabolic Modelling Investigate the Interplay of Ser/Thr Kinase PknB, Its Phosphatase Stp, the glmR/yvcK Regulon and the cdaA Operon for Metabolic Adaptation. Microorganisms 2021; 9:microorganisms9102148. [PMID: 34683468 PMCID: PMC8537086 DOI: 10.3390/microorganisms9102148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 01/17/2023] Open
Abstract
Serine/threonine kinase PknB and its corresponding phosphatase Stp are important regulators of many cell functions in the pathogen S. aureus. Genome-scale gene expression data of S. aureus strain NewHG (sigB+) elucidated their effect on physiological functions. Moreover, metabolic modelling from these data inferred metabolic adaptations. We compared wild-type to deletion strains lacking pknB, stp or both. Ser/Thr phosphorylation of target proteins by PknB switched amino acid catabolism off and gluconeogenesis on to provide the cell with sufficient components. We revealed a significant impact of PknB and Stp on peptidoglycan, nucleotide and aromatic amino acid synthesis, as well as catabolism involving aspartate transaminase. Moreover, pyrimidine synthesis was dramatically impaired by stp deletion but only slightly by functional loss of PknB. In double knockouts, higher activity concerned genes involved in peptidoglycan, purine and aromatic amino acid synthesis from glucose but lower activity of pyrimidine synthesis from glucose compared to the wild type. A second transcriptome dataset from S. aureus NCTC 8325 (sigB−) validated the predictions. For this metabolic adaptation, PknB was found to interact with CdaA and the yvcK/glmR regulon. The involved GlmR structure and the GlmS riboswitch were modelled. Furthermore, PknB phosphorylation lowered the expression of many virulence factors, and the study shed light on S. aureus infection processes.
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Affiliation(s)
- Chunguang Liang
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany; (C.L.); (A.B.R.-M.); (P.N.)
| | - Ana B. Rios-Miguel
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany; (C.L.); (A.B.R.-M.); (P.N.)
- Department of Environmental Microbiology, Institute of Water and Wetland Research, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Marcel Jarick
- Institute for Molecular Infection Biology, Josef-Schneider-Straße 2/D15, University of Würzburg, 97080 Würzburg, Germany; (M.J.); (E.S.I.)
| | - Priya Neurgaonkar
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany; (C.L.); (A.B.R.-M.); (P.N.)
| | - Myriam Girard
- Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, CH-1211 Geneva 14, Switzerland; (M.G.); (P.F.); (J.S.)
| | - Patrice François
- Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, CH-1211 Geneva 14, Switzerland; (M.G.); (P.F.); (J.S.)
| | - Jacques Schrenzel
- Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, CH-1211 Geneva 14, Switzerland; (M.G.); (P.F.); (J.S.)
| | - Eslam S. Ibrahim
- Institute for Molecular Infection Biology, Josef-Schneider-Straße 2/D15, University of Würzburg, 97080 Würzburg, Germany; (M.J.); (E.S.I.)
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Knut Ohlsen
- Institute for Molecular Infection Biology, Josef-Schneider-Straße 2/D15, University of Würzburg, 97080 Würzburg, Germany; (M.J.); (E.S.I.)
- Correspondence: (K.O.); (T.D.); Tel.: +49-931-31-82155 (K.O.); +49-931-31-84551 (T.D.)
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany; (C.L.); (A.B.R.-M.); (P.N.)
- Correspondence: (K.O.); (T.D.); Tel.: +49-931-31-82155 (K.O.); +49-931-31-84551 (T.D.)
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Insuasty A, Carrara S, Tang L, Forsyth C, Hogan CF, McNeill CR, Langford SJ. A Family of Heterocyclic Naphthalene Diimide (NDI) Analogues: Comparing Parent Isoquinoline Diimides and Phthalazine Diimides with NDI. Chempluschem 2019; 84:1638-1642. [DOI: 10.1002/cplu.201900596] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/17/2019] [Indexed: 02/03/2023]
Affiliation(s)
- Alberto Insuasty
- Department of Chemistry and Biotechnology Swinburne University of Technology Hawthorn, VIC 3122 Australia
| | - Serena Carrara
- La Trobe Institute for Molecular Science La Trobe University Melbourne, VIC 3086 Australia
| | - Linjing Tang
- Department of Materials Science and Engineering Monash University Clayton, Victoria 3800 Australia
| | - Craig Forsyth
- School of Chemistry Monash University Clayton, VIC 3800 Australia
| | - Conor F. Hogan
- La Trobe Institute for Molecular Science La Trobe University Melbourne, VIC 3086 Australia
| | - Christopher R. McNeill
- Department of Materials Science and Engineering Monash University Clayton, Victoria 3800 Australia
| | - Steven J. Langford
- Department of Chemistry and Biotechnology Swinburne University of Technology Hawthorn, VIC 3122 Australia
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Srivastava M, Bencurova E, Gupta SK, Weiss E, Löffler J, Dandekar T. Aspergillus fumigatus Challenged by Human Dendritic Cells: Metabolic and Regulatory Pathway Responses Testify a Tight Battle. Front Cell Infect Microbiol 2019; 9:168. [PMID: 31192161 PMCID: PMC6540932 DOI: 10.3389/fcimb.2019.00168] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/06/2019] [Indexed: 12/18/2022] Open
Abstract
Dendritic cells (DCs) are antigen presenting cells which serve as a passage between the innate and the acquired immunity. Aspergillosis is a major lethal condition in immunocompromised patients caused by the adaptable saprophytic fungus Aspergillus fumigatus. The healthy human immune system is capable to ward off A. fumigatus infections however immune-deficient patients are highly vulnerable to invasive aspergillosis. A. fumigatus can persist during infection due to its ability to survive the immune response of human DCs. Therefore, the study of the metabolism specific to the context of infection may allow us to gain insight into the adaptation strategies of both the pathogen and the immune cells. We established a metabolic model of A. fumigatus central metabolism during infection of DCs and calculated the metabolic pathway (elementary modes; EMs). Transcriptome data were used to identify pathways activated when A. fumigatus is challenged with DCs. In particular, amino acid metabolic pathways, alternative carbon metabolic pathways and stress regulating enzymes were found to be active. Metabolic flux modeling identified further active enzymes such as alcohol dehydrogenase, inositol oxygenase and GTP cyclohydrolase participating in different stress responses in A. fumigatus. These were further validated by qRT-PCR from RNA extracted under these different conditions. For DCs, we outlined the activation of metabolic pathways in response to the confrontation with A. fumigatus. We found the fatty acid metabolism plays a crucial role, along with other metabolic changes. The gene expression data and their analysis illuminate additional regulatory pathways activated in the DCs apart from interleukin regulation. In particular, Toll-like receptor signaling, NOD-like receptor signaling and RIG-I-like receptor signaling were active pathways. Moreover, we identified subnetworks and several novel key regulators such as UBC, EGFR, and CUL3 of DCs to be activated in response to A. fumigatus. In conclusion, we analyze the metabolic and regulatory responses of A. fumigatus and DCs when confronted with each other.
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Affiliation(s)
- Mugdha Srivastava
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Elena Bencurova
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Shishir K Gupta
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Esther Weiss
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Jürgen Löffler
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.,EMBL Heidelberg, Structural and Computational Biology, Heidelberg, Germany
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Balasubramanian S, Skaf J, Holzgrabe U, Bharti R, Förstner KU, Ziebuhr W, Humeida UH, Abdelmohsen UR, Oelschlaeger TA. A New Bioactive Compound From the Marine Sponge-Derived Streptomyces sp. SBT348 Inhibits Staphylococcal Growth and Biofilm Formation. Front Microbiol 2018; 9:1473. [PMID: 30050506 PMCID: PMC6050364 DOI: 10.3389/fmicb.2018.01473] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/13/2018] [Indexed: 01/09/2023] Open
Abstract
Staphylococcus epidermidis, the common inhabitant of human skin and mucosal surfaces has emerged as an important pathogen in patients carrying surgical implants and medical devices. Entering the body via surgical sites and colonizing the medical devices through formation of multi-layered biofilms leads to refractory and persistent device-related infections (DRIs). Staphylococci organized in biofilms are more tolerant to antibiotics and immune responses, and thus are difficult-to-treat. The consequent morbidity and mortality, and economic losses in health care systems has strongly necessitated the need for development of new anti-bacterial and anti-biofilm-based therapeutics. In this study, we describe the biological activity of a marine sponge-derived Streptomyces sp. SBT348 extract in restraining staphylococcal growth and biofilm formation on polystyrene, glass, medically relevant titan metal, and silicone surfaces. A bioassay-guided fractionation was performed to isolate the active compound (SKC3) from the crude SBT348 extract. Our results demonstrated that SKC3 effectively inhibits the growth (MIC: 31.25 μg/ml) and biofilm formation (sub-MIC range: 1.95–<31.25 μg/ml) of S. epidermidis RP62A in vitro. Chemical characterization of SKC3 by heat and enzyme treatments, and mass spectrometry (HRMS) revealed its heat-stable and non-proteinaceous nature, and high molecular weight (1258.3 Da). Cytotoxicity profiling of SKC3 in vitro on mouse fibroblast (NIH/3T3) and macrophage (J774.1) cell lines, and in vivo on the greater wax moth larvae Galleria mellonella revealed its non-toxic nature at the effective dose. Transcriptome analysis of SKC3 treated S. epidermidis RP62A has further unmasked its negative effect on central metabolism such as carbon flux as well as, amino acid, lipid, and energy metabolism. Taken together, these findings suggest a potential of SKC3 as a putative drug to prevent staphylococcal DRIs.
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Affiliation(s)
| | - Joseph Skaf
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Würzburg, Germany
| | - Ulrike Holzgrabe
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Würzburg, Germany
| | - Richa Bharti
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Konrad U Förstner
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Wilma Ziebuhr
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Ute H Humeida
- GEOMAR Helmholtz Centre for Ocean Research, RD3 Marine Microbiology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Usama R Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Tobias A Oelschlaeger
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
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Identification of Antifungal Targets Based on Computer Modeling. J Fungi (Basel) 2018; 4:jof4030081. [PMID: 29973534 PMCID: PMC6162656 DOI: 10.3390/jof4030081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/24/2018] [Accepted: 06/29/2018] [Indexed: 01/07/2023] Open
Abstract
Aspergillus fumigatus is a saprophytic, cosmopolitan fungus that attacks patients with a weak immune system. A rational solution against fungal infection aims to manipulate fungal metabolism or to block enzymes essential for Aspergillus survival. Here we discuss and compare different bioinformatics approaches to analyze possible targeting strategies on fungal-unique pathways. For instance, phylogenetic analysis reveals fungal targets, while domain analysis allows us to spot minor differences in protein composition between the host and fungi. Moreover, protein networks between host and fungi can be systematically compared by looking at orthologs and exploiting information from host⁻pathogen interaction databases. Further data—such as knowledge of a three-dimensional structure, gene expression data, or information from calculated metabolic fluxes—refine the search and rapidly put a focus on the best targets for antimycotics. We analyzed several of the best targets for application to structure-based drug design. Finally, we discuss general advantages and limitations in identification of unique fungal pathways and protein targets when applying bioinformatics tools.
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Lipid Biosynthesis as an Antifungal Target. J Fungi (Basel) 2018; 4:jof4020050. [PMID: 29677130 PMCID: PMC6023442 DOI: 10.3390/jof4020050] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 12/15/2022] Open
Abstract
Lipids, commonly including phospholipids, sphingolipids, fatty acids, sterols, and triacylglycerols (TAGs), are important biomolecules for the viability of all cells. Phospholipids, sphingolipids, and sterols are important constituents of biological membranes. Many lipids play important roles in the regulation of cell metabolism by acting as signaling molecules. Neutral lipids, including TAGs and sterol esters (STEs), are important storage lipids in cells. In view of the importance of lipid molecules, this review briefly summarizes the metabolic pathways for sterols, phospholipids, sphingolipids, fatty acids, and neutral lipids in fungi and illustrates the differences between fungal and human (or other mammalian) cells, especially in relation to lipid biosynthetic pathways. These differences might provide valuable clues for us to find target proteins for novel antifungal drugs. In addition, the development of lipidomics technology in recent years has supplied us with a shortcut for finding new antifungal drug targets; this ability is important for guiding our research on pathogenic fungi.
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Complete Genome Sequence and Annotation of the Staphylococcus aureus Strain HG001. GENOME ANNOUNCEMENTS 2017; 5:5/32/e00783-17. [PMID: 28798184 PMCID: PMC5552993 DOI: 10.1128/genomea.00783-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Staphylococcus aureus is an opportunistic Gram-positive pathogen responsible for a wide range of infections from minor skin abscesses to life-threatening diseases. Here, we report the draft genome assembly and current annotation of the HG001 strain, a derivative of the RN1 (NCT8325) strain with restored rbsU (a positive activator of SigB).
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Czakai K, Dittrich M, Kaltdorf M, Müller T, Krappmann S, Schedler A, Bonin M, Dühring S, Schuster S, Speth C, Rambach G, Einsele H, Dandekar T, Löffler J. Influence of Platelet-rich Plasma on the immune response of human monocyte-derived dendritic cells and macrophages stimulated with Aspergillus fumigatus. Int J Med Microbiol 2016; 307:95-107. [PMID: 27965080 DOI: 10.1016/j.ijmm.2016.11.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 11/22/2016] [Accepted: 11/27/2016] [Indexed: 12/19/2022] Open
Abstract
Dendritic cells (DCs) and macrophages (MΦ) are critical for protection against pathogenic fungi including Aspergillus fumigatus. To analyze the role of platelets in the innate immune response, human DCs and MΦs were challenged with A. fumigatus in presence or absence of human platelet rich plasma (PRP). Gene expression analyses and functional investigations were performed. A systems biological approach was used for initial modelling of the DC - A. fumigatus interaction. DCs in a quiescent state together with different corresponding activation states were validated using gene expression data from DCs and MΦ stimulated with A. fumigatus. To characterize the influence of platelets on the immune response of DCs and MΦ to A. fumigatus, we experimentally quantified their cytokine secretion, phagocytic capacity, maturation, and metabolic activity with or without platelets. PRP in combination with A. fumigatus treatment resulted in the highest expression of the maturation markers CD80, CD83 and CD86 in DCs. Furthermore, PRP enhanced the capacity of macrophages and DCs to phagocytose A. fumigatus conidia. In parallel, PRP in combination with the innate immune cells significantly reduced the metabolic activity of the fungus. Interestingly, A. fumigatus and PRP stimulated MΦ showed a significantly reduced gene expression and secretion of IL6 while PRP only reduced the IL-6 secretion of A. fumigatus stimulated DCs. The in silico systems biological model correlated well with these experimental data. Different modules centrally involved in DC function became clearly apparent, including DC maturation, cytokine response and apoptosis pathways. Taken together, the ability of PRP to suppress IL-6 release of human DCs might prevent local excessive inflammatory hemorrhage, tissue infarction and necrosis in the human lung.
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Affiliation(s)
- Kristin Czakai
- Department of Internal Medicine, University Hospital of Würzburg, Würzburg, Germany
| | - Marcus Dittrich
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Martin Kaltdorf
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Tobias Müller
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Sven Krappmann
- Microbiology Institute-Clinical Microbiology, Immunology and Hygiene, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Anette Schedler
- Department of Internal Medicine, University Hospital of Würzburg, Würzburg, Germany
| | | | - Sybille Dühring
- Deparment of Bioinformatics, Friedrich-Schiller-University Jena, Jena, Germany
| | - Stefan Schuster
- Deparment of Bioinformatics, Friedrich-Schiller-University Jena, Jena, Germany
| | - Cornelia Speth
- Hygiene und Medizinische Mikrobiologie, Medizinische Universität Innsbruck, Innsbruck, Austria
| | - Günter Rambach
- Hygiene und Medizinische Mikrobiologie, Medizinische Universität Innsbruck, Innsbruck, Austria
| | - Hermann Einsele
- Department of Internal Medicine, University Hospital of Würzburg, Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Jürgen Löffler
- Department of Internal Medicine, University Hospital of Würzburg, Würzburg, Germany.
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Kaltdorf M, Srivastava M, Gupta SK, Liang C, Binder J, Dietl AM, Meir Z, Haas H, Osherov N, Krappmann S, Dandekar T. Systematic Identification of Anti-Fungal Drug Targets by a Metabolic Network Approach. Front Mol Biosci 2016; 3:22. [PMID: 27379244 PMCID: PMC4911368 DOI: 10.3389/fmolb.2016.00022] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 05/24/2016] [Indexed: 11/13/2022] Open
Abstract
New antimycotic drugs are challenging to find, as potential target proteins may have close human orthologs. We here focus on identifying metabolic targets that are critical for fungal growth and have minimal similarity to targets among human proteins. We compare and combine here: (I) direct metabolic network modeling using elementary mode analysis and flux estimates approximations using expression data, (II) targeting metabolic genes by transcriptome analysis of condition-specific highly expressed enzymes, and (III) analysis of enzyme structure, enzyme interconnectedness ("hubs"), and identification of pathogen-specific enzymes using orthology relations. We have identified 64 targets including metabolic enzymes involved in vitamin synthesis, lipid, and amino acid biosynthesis including 18 targets validated from the literature, two validated and five currently examined in own genetic experiments, and 38 further promising novel target proteins which are non-orthologous to human proteins, involved in metabolism and are highly ranked drug targets from these pipelines.
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Affiliation(s)
- Martin Kaltdorf
- Department of Bioinformatics, Biocenter, University of Würzburg Würzburg, Germany
| | - Mugdha Srivastava
- Department of Bioinformatics, Biocenter, University of Würzburg Würzburg, Germany
| | - Shishir K Gupta
- Department of Bioinformatics, Biocenter, University of Würzburg Würzburg, Germany
| | - Chunguang Liang
- Department of Bioinformatics, Biocenter, University of Würzburg Würzburg, Germany
| | - Jasmin Binder
- Microbiology Institute - Clinical Microbiology, Immunology and Hygiene, Friedrich-Alexander University Erlangen-Nürnberg, University Hospital of Erlangen Erlangen, Germany
| | - Anna-Maria Dietl
- Division of Molecular Biology/Biocenter, Medical University Innsbruck Innsbruck, Austria
| | - Zohar Meir
- Aspergillus and Antifungal Research Laboratory, Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University Tel-Aviv, Israel
| | - Hubertus Haas
- Division of Molecular Biology/Biocenter, Medical University Innsbruck Innsbruck, Austria
| | - Nir Osherov
- Aspergillus and Antifungal Research Laboratory, Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University Tel-Aviv, Israel
| | - Sven Krappmann
- Microbiology Institute - Clinical Microbiology, Immunology and Hygiene, Friedrich-Alexander University Erlangen-Nürnberg, University Hospital of Erlangen Erlangen, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg Würzburg, Germany
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12
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A Staphylococcus aureus Proteome Overview: Shared and Specific Proteins and Protein Complexes from Representative Strains of All Three Clades. Proteomes 2016; 4:proteomes4010008. [PMID: 28248218 PMCID: PMC5217359 DOI: 10.3390/proteomes4010008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 01/31/2016] [Accepted: 02/05/2016] [Indexed: 12/23/2022] Open
Abstract
Staphylococcus aureus is an important model organism and pathogen. This S. aureus proteome overview details shared and specific proteins and selected virulence-relevant protein complexes from representative strains of all three major clades. To determine the strain distribution and major clades we used a refined strain comparison combining ribosomal RNA, MLST markers, and looking at highly-conserved regions shared between strains. This analysis shows three sub-clades (A–C) for S. aureus. As calculations are complex and strain annotation is quite time consuming we compare here key representatives of each clade with each other: model strains COL, USA300, Newman, and HG001 (clade A), model strain N315 and Mu50 (clade B) and ED133 and MRSA252 (clade C). We look at these individual proteomes and compare them to a background of 64 S. aureus strains. There are overall 13,284 S. aureus proteins not part of the core proteome which are involved in different strain-specific or more general complexes requiring detailed annotation and new experimental data to be accurately delineated. By comparison of the eight representative strains, we identify strain-specific proteins (e.g., 18 in COL, 105 in N315 and 44 in Newman) that characterize each strain and analyze pathogenicity islands if they contain such strain-specific proteins. We identify strain-specific protein repertoires involved in virulence, in cell wall metabolism, and phosphorylation. Finally we compare and analyze protein complexes conserved and well-characterized among S. aureus (a total of 103 complexes), as well as predict and analyze several individual protein complexes, including structure modeling in the three clades.
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Abstract
A large proportion of hospital-related infections are acquired and spread due to the direct contacts between patients and healthcare workers. Accordingly, proper infection prevention measures, and especially hand hygiene, are key to limit the spread of infections in nosocomial settings. However, healthcare workers frequently experience difficulties in complying strictly to hand disinfection protocols. This study was therefore aimed at the development of a hand rub with antimicrobial activity that forms a protective film on the hand, a so-called microglove, in order to enhance hand hygiene. For this purpose, various co-polymer formulations consisting of different ratios of Polyvinylpyrrolidone (PVP) and a branched C20 derivatized maleate (M20) in combination with the known biocide benzalkonium chloride (BKC) were tested for their combined film-forming and antimicrobial activities. The results of a series of novel contamination and transmission assays show that a formulation of 80% PVP and 20% M20 co-polymer with 0.9% BKC fulfils the elementary requirements for an antimicrobial microglove.
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