1
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Muhi S, Buultjens AH, Porter JL, Marshall JL, Doerflinger M, Pidot SJ, O’Brien DP, Johnson PDR, Lavender CJ, Globan M, McCarthy J, Osowicki J, Stinear TP. Mycobacterium ulcerans challenge strain selection for a Buruli ulcer controlled human infection model. PLoS Negl Trop Dis 2024; 18:e0011979. [PMID: 38701090 PMCID: PMC11095734 DOI: 10.1371/journal.pntd.0011979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/15/2024] [Accepted: 04/21/2024] [Indexed: 05/05/2024] Open
Abstract
Critical scientific questions remain regarding infection with Mycobacterium ulcerans, the organism responsible for the neglected tropical disease, Buruli ulcer (BU). A controlled human infection model has the potential to accelerate our knowledge of the immunological correlates of disease, to test prophylactic interventions and novel therapeutics. Here we present microbiological evidence supporting M. ulcerans JKD8049 as a suitable human challenge strain. This non-genetically modified Australian isolate is susceptible to clinically relevant antibiotics, can be cultured in animal-free and surfactant-free media, can be enumerated for precise dosing, and has stable viability following cryopreservation. Infectious challenge of humans with JKD8049 is anticipated to imitate natural infection, as M. ulcerans JKD8049 is genetically stable following in vitro passage and produces the key virulence factor, mycolactone. Also reported are considerations for the manufacture, storage, and administration of M. ulcerans JKD8049 for controlled human infection.
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Affiliation(s)
- Stephen Muhi
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Service, Royal Melbourne Hospital, Parkville, Victoria, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Andrew H. Buultjens
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jessica L. Porter
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Julia L. Marshall
- Department of Infectious Diseases, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Marcel Doerflinger
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel P. O’Brien
- Victorian Infectious Diseases Service, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Infectious Diseases, Barwon Health, Geelong, Victoria, Australia
| | - Paul D. R. Johnson
- Northeast Public Health Unit, Austin Health, Heidelberg, Victoria, Australia
| | - Caroline J. Lavender
- Victorian Infectious Disease Reference Laboratory (VIDRL), Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Maria Globan
- Victorian Infectious Disease Reference Laboratory (VIDRL), Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - James McCarthy
- Victorian Infectious Diseases Service, Royal Melbourne Hospital, Parkville, Victoria, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Infectious Diseases, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Joshua Osowicki
- Tropical Diseases Research Group, Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, Victoria, Australia
- Infectious Diseases Unit, Department of General Medicine, Royal Children’s Hospital Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
- Victorian Infectious Disease Reference Laboratory (VIDRL), Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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2
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Richter I, Hasan M, Kramer JW, Wein P, Krabbe J, Wojtas KP, Stinear TP, Pidot SJ, Kloss F, Hertweck C, Lackner G. Deazaflavin metabolite produced by endosymbiotic bacteria controls fungal host reproduction. ISME J 2024; 18:wrae074. [PMID: 38691425 PMCID: PMC11104420 DOI: 10.1093/ismejo/wrae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
The endosymbiosis between the pathogenic fungus Rhizopus microsporus and the toxin-producing bacterium Mycetohabitans rhizoxinica represents a unique example of host control by an endosymbiont. Fungal sporulation strictly depends on the presence of endosymbionts as well as bacterially produced secondary metabolites. However, an influence of primary metabolites on host control remained unexplored. Recently, we discovered that M. rhizoxinica produces FO and 3PG-F420, a derivative of the specialized redox cofactor F420. Whether FO/3PG-F420 plays a role in the symbiosis has yet to be investigated. Here, we report that FO, the precursor of 3PG-F420, is essential to the establishment of a stable symbiosis. Bioinformatic analysis revealed that the genetic inventory to produce cofactor 3PG-F420 is conserved in the genomes of eight endofungal Mycetohabitans strains. By developing a CRISPR/Cas-assisted base editing strategy for M. rhizoxinica, we generated mutant strains deficient in 3PG-F420 (M. rhizoxinica ΔcofC) and in both FO and 3PG-F420 (M. rhizoxinica ΔfbiC). Co-culture experiments demonstrated that the sporulating phenotype of apo-symbiotic R. microsporus is maintained upon reinfection with wild-type M. rhizoxinica or M. rhizoxinica ΔcofC. In contrast, R. microsporus is unable to sporulate when co-cultivated with M. rhizoxinica ΔfbiC, even though the fungus was observed by super-resolution fluorescence microscopy to be successfully colonized. Genetic and chemical complementation of the FO deficiency of M. rhizoxinica ΔfbiC led to restoration of fungal sporulation, signifying that FO is indispensable for establishing a functional symbiosis. Even though FO is known for its light-harvesting properties, our data illustrate an important role of FO in inter-kingdom communication.
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Affiliation(s)
- Ingrid Richter
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Thuringia, Germany
| | - Mahmudul Hasan
- Junior Research Group Synthetic Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Thuringia, Germany
| | - Johannes W Kramer
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Thuringia, Germany
| | - Philipp Wein
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Thuringia, Germany
| | - Jana Krabbe
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Thuringia, Germany
| | - K Philip Wojtas
- Transfer Group Anti-Infectives, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Thuringia, Germany
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, 3010 Melbourne, Victoria, Australia
| | - Sacha J Pidot
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, 3010 Melbourne, Victoria, Australia
| | - Florian Kloss
- Transfer Group Anti-Infectives, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Thuringia, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Thuringia, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Thuringia, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Thuringia, Germany
| | - Gerald Lackner
- Junior Research Group Synthetic Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Thuringia, Germany
- Chair of Biochemistry of Microorganisms, Faculty of Life Sciences: Food, Nutrition and Health, University of Bayreuth, 95326 Kulmbach, Bavaria, Germany
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3
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Kaur A, Pickles IB, Sharma M, Madeido Soler N, Scott NE, Pidot SJ, Goddard-Borger ED, Davies GJ, Williams SJ. Widespread Family of NAD +-Dependent Sulfoquinovosidases at the Gateway to Sulfoquinovose Catabolism. J Am Chem Soc 2023; 145:28216-28223. [PMID: 38100472 PMCID: PMC10755693 DOI: 10.1021/jacs.3c11126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
The sulfosugar sulfoquinovose (SQ) is produced by photosynthetic plants, algae, and cyanobacteria on a scale of 10 billion tons per annum. Its degradation, which is essential to allow cycling of its constituent carbon and sulfur, involves specialized glycosidases termed sulfoquinovosidases (SQases), which release SQ from sulfolipid glycoconjugates, so SQ can enter catabolism pathways. However, many SQ catabolic gene clusters lack a gene encoding a classical SQase. Here, we report the discovery of a new family of SQases that use an atypical oxidoreductive mechanism involving NAD+ as a catalytic cofactor. Three-dimensional X-ray structures of complexes with SQ and NAD+ provide insight into the catalytic mechanism, which involves transient oxidation at C3. Bioinformatic survey reveals this new family of NAD+-dependent SQases occurs within sulfoglycolytic and sulfolytic gene clusters that lack classical SQases and is distributed widely including within Roseobacter clade bacteria, suggesting an important contribution to marine sulfur cycling.
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Affiliation(s)
- Arashdeep Kaur
- School
of Chemistry, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Isabelle B. Pickles
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Mahima Sharma
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Niccolay Madeido Soler
- ACRF
Chemical Biology Division, The Walter and
Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
- Department
of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nichollas E. Scott
- Department
of Microbiology and Immunology, University
of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Sacha J. Pidot
- Department
of Microbiology and Immunology, University
of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Ethan D. Goddard-Borger
- ACRF
Chemical Biology Division, The Walter and
Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
- Department
of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Gideon J. Davies
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Spencer J. Williams
- School
of Chemistry, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
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4
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Richter I, Uzum Z, Wein P, Molloy EM, Moebius N, Stinear TP, Pidot SJ, Hertweck C. Transcription activator-like effectors from endosymbiotic bacteria control the reproduction of their fungal host. mBio 2023; 14:e0182423. [PMID: 37971247 PMCID: PMC10746252 DOI: 10.1128/mbio.01824-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/03/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Interactions between fungi and bacteria are critically important in ecology, medicine, and biotechnology. In this study, we shed light on factors that promote the persistence of a toxin-producing, phytopathogenic Rhizopus-Mycetohabitans symbiosis that causes severe crop losses in Asia. We present an unprecedented case where bacterially produced transcription activator-like (TAL) effectors are key to maintaining a stable endosymbiosis. In their absence, fungal sporulation is abrogated, leading to collapse of the phytopathogenic alliance. The Mycetohabitans TAL (MTAL)-mediated mechanism of host control illustrates a unique role of bacterial effector molecules that has broader implications, potentially serving as a model to understand how prokaryotic symbionts interact with their eukaryotic hosts.
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Affiliation(s)
- Ingrid Richter
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Zerrin Uzum
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Philipp Wein
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Evelyn M. Molloy
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Nadine Moebius
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute, Melbourne, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute, Melbourne, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
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5
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Sharkey LKR, Guerillot R, Walsh CJ, Turner AM, Lee JYH, Neville SL, Klatt S, Baines SL, Pidot SJ, Rossello FJ, Seemann T, McWilliam HEG, Cho E, Carter GP, Howden BP, McDevitt CA, Hachani A, Stinear TP, Monk IR. The two-component system WalKR provides an essential link between cell wall homeostasis and DNA replication in Staphylococcus aureus. mBio 2023; 14:e0226223. [PMID: 37850732 PMCID: PMC10746227 DOI: 10.1128/mbio.02262-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 10/19/2023] Open
Abstract
Among the 16 two-component systems in the opportunistic human pathogen Staphylococcus aureus, only WalKR is essential. Like the orthologous systems in other Bacillota, S. aureus WalKR controls autolysins involved in peptidoglycan remodeling and is therefore intimately involved in cell division. However, despite the importance of WalKR in S. aureus, the basis for its essentiality is not understood and the regulon is poorly defined. Here, we defined a consensus WalR DNA-binding motif and the direct WalKR regulon by using functional genomics, including chromatin immunoprecipitation sequencing, with a panel of isogenic walKR mutants that had a spectrum of altered activities. Consistent with prior findings, the direct regulon includes multiple autolysin genes. However, this work also revealed that WalR directly regulates at least five essential genes involved in lipoteichoic acid synthesis (ltaS): translation (rplK), DNA compaction (hup), initiation of DNA replication (dnaA, hup) and purine nucleotide metabolism (prs). Thus, WalKR in S. aureus serves as a polyfunctional regulator that contributes to fundamental control over critical cell processes by coordinately linking cell wall homeostasis with purine biosynthesis, protein biosynthesis, and DNA replication. Our findings further address the essentiality of this locus and highlight the importance of WalKR as a bona fide target for novel anti-staphylococcal therapeutics. IMPORTANCE The opportunistic human pathogen Staphylococcus aureus uses an array of protein sensing systems called two-component systems (TCS) to sense environmental signals and adapt its physiology in response by regulating different genes. This sensory network is key to S. aureus versatility and success as a pathogen. Here, we reveal for the first time the full extent of the regulatory network of WalKR, the only staphylococcal TCS that is indispensable for survival under laboratory conditions. We found that WalKR is a master regulator of cell growth, coordinating the expression of genes from multiple, fundamental S. aureus cellular processes, including those involved in maintaining cell wall metabolism, protein biosynthesis, nucleotide metabolism, and the initiation of DNA replication.
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Affiliation(s)
- Liam K. R. Sharkey
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Romain Guerillot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Calum J. Walsh
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Adrianna M. Turner
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jean Y. H. Lee
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephanie L. Neville
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephan Klatt
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Sarah L. Baines
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Fernando J. Rossello
- University of Melbourne Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Hamish E. G. McWilliam
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Ellie Cho
- Biological Optical Microscopy Platform, University of Melbourne, Melbourne, Victoria, Australia
| | - Glen P. Carter
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Abderrahman Hachani
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Ian R. Monk
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
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6
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Ehinger FJ, Niehs SP, Dose B, Dell M, Krabbe J, Pidot SJ, Stinear TP, Scherlach K, Ross C, Lackner G, Hertweck C. Analysis of Rhizonin Biosynthesis Reveals Origin of Pharmacophoric Furylalanine Moieties in Diverse Cyclopeptides. Angew Chem Int Ed Engl 2023; 62:e202308540. [PMID: 37650335 DOI: 10.1002/anie.202308540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/01/2023]
Abstract
Rhizonin A and B are hepatotoxic cyclopeptides produced by bacterial endosymbionts (Mycetohabitans endofungorum) of the fungus Rhizopus microsporus. Their toxicity critically depends on the presence of 3-furylalanine (Fua) residues, which also occur in pharmaceutically relevant cyclopeptides of the endolide and bingchamide families. The biosynthesis and incorporation of Fua by non-ribosomal peptide synthetases (NRPS), however, has remained elusive. By genome sequencing and gene inactivation we elucidated the gene cluster responsible for rhizonin biosynthesis. A suite of isotope labeling experiments identified tyrosine and l-DOPA as Fua precursors and provided the first mechanistic insight. Bioinformatics, mutational analysis and heterologous reconstitution identified dioxygenase RhzB as necessary and sufficient for Fua formation. RhzB is a novel type of heme-dependent aromatic oxygenases (HDAO) that enabled the discovery of the bingchamide biosynthesis gene cluster through genome mining.
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Affiliation(s)
- Friedrich J Ehinger
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Sarah P Niehs
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Maria Dell
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Jana Krabbe
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Sacha J Pidot
- Department of Microbiology and Immunology, Doherty Institute, 792 Elizabeth Street, Melbourne, 3000, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute, 792 Elizabeth Street, Melbourne, 3000, Australia
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Claudia Ross
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Gerald Lackner
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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7
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Doering T, Tandon K, Topa SH, Pidot SJ, Blackall LL, van Oppen MJH. Genomic exploration of coral-associated bacteria: identifying probiotic candidates to increase coral bleaching resilience in Galaxea fascicularis. Microbiome 2023; 11:185. [PMID: 37596630 PMCID: PMC10439622 DOI: 10.1186/s40168-023-01622-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/14/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND Reef-building corals are acutely threatened by ocean warming, calling for active interventions to reduce coral bleaching and mortality. Corals associate with a wide diversity of bacteria which can influence coral health, but knowledge of specific functions that may be beneficial for corals under thermal stress is scant. Under the oxidative stress theory of coral bleaching, bacteria that scavenge reactive oxygen (ROS) or nitrogen species (RNS) are expected to enhance coral thermal resilience. Further, bacterial carbon export might substitute the carbon supply from algal photosymbionts, enhance thermal resilience and facilitate bleaching recovery. To identify probiotic bacterial candidates, we sequenced the genomes of 82 pure-cultured bacteria that were isolated from the emerging coral model Galaxea fascicularis. RESULTS Genomic analyses showed bacterial isolates were affiliated with 37 genera. Isolates such as Ruegeria, Muricauda and Roseovarius were found to encode genes for the synthesis of the antioxidants mannitol, glutathione, dimethylsulfide, dimethylsulfoniopropionate, zeaxanthin and/or β-carotene. Genes involved in RNS-scavenging were found in many G. fascicularis-associated bacteria, which represents a novel finding for several genera (including Pseudophaeobacter). Transporters that are suggested to export carbon (semiSWEET) were detected in seven isolates, including Pseudovibrio and Roseibium. Further, a range of bacterial strains, including strains of Roseibium and Roseovarius, revealed genomic features that may enhance colonisation and association of bacteria with the coral host, such as secretion systems and eukaryote-like repeat proteins. CONCLUSIONS Our work provides an in-depth genomic analysis of the functional potential of G. fascicularis-associated bacteria and identifies novel combinations of traits that may enhance the coral's ability to withstand coral bleaching. Identifying and characterising bacteria that are beneficial for corals is critical for the development of effective probiotics that boost coral climate resilience. Video Abstract.
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Affiliation(s)
- Talisa Doering
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Kshitij Tandon
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Sanjida H. Topa
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC Australia
| | - Linda L. Blackall
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Madeleine J. H. van Oppen
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
- Australian Institute of Marine Science, Townsville, QLD Australia
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8
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Herisse M, Ishida K, Staiger-Creed J, Judd L, Williams SJ, Howden BP, Stinear TP, Dahse HM, Voigt K, Hertweck C, Pidot SJ. Discovery and Biosynthesis of the Cytotoxic Polyene Terpenomycin in Human Pathogenic Nocardia. ACS Chem Biol 2023; 18:1872-1879. [PMID: 37498707 DOI: 10.1021/acschembio.3c00311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Nocardia are opportunistic human pathogens that can cause a range of debilitating and difficult to treat infections of the lungs, brain, skin, and soft tissues. Despite their close relationship to the well-known secondary metabolite-producing genus, Streptomyces, comparatively few natural products are known from the Nocardia, and even less is known about their involvement in the pathogenesis. Here, we combine chemistry, genomics, and molecular microbiology to reveal the production of terpenomycin, a new cytotoxic and antifungal polyene from a human pathogenic Nocardia terpenica isolate. We unveil the polyketide synthase (PKS) responsible for terpenomycin biosynthesis and show that it combines several unusual features, including "split", skipped, and iteratively used modules, and the use of the unusual extender unit methoxymalonate as a starter unit. To link genes to molecules, we constructed a transposon mutant library in N. terpenica, identifying a terpenomycin-null mutant with an inactivated terpenomycin PKS. Our findings show that the neglected actinomycetes have an unappreciated capacity for the production of bioactive molecules with unique biosynthetic pathways waiting to be uncovered and highlights these organisms as producers of diverse natural products.
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Affiliation(s)
- Marion Herisse
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, Jena 07745, Germany
| | - Jordan Staiger-Creed
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Louise Judd
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Spencer J Williams
- School of Chemistry, University of Melbourne, Melbourne, Victoria 3000, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria3000, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, Jena 07745, Germany
| | - Kerstin Voigt
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstrasse 11a, Jena 07745, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, Jena 07745, Germany
- Natural Product Chemistry, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Sacha J Pidot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
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9
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Awori RM, Waturu CN, Pidot SJ, Amugune NO, Bode HB. Draft genomes, phylogenomic reconstruction and comparative genome analysis of three Xenorhabdus strains isolated from soil-dwelling nematodes in Kenya. Access Microbiol 2023; 5:acmi000531.v4. [PMID: 37323942 PMCID: PMC10267655 DOI: 10.1099/acmi.0.000531.v4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/27/2023] [Indexed: 06/17/2023] Open
Abstract
As a proven source of potent and selective antimicrobials, Xenorhabdus bacteria are important to an age plagued with difficult-to-treat microbial infections. Yet, only 27 species have been described to date. In this study, a novel Xenorhabdus species was discovered through genomic studies on three isolates from Kenyan soils. Soils in Western Kenya were surveyed for steinernematids and Steinernema isolates VH1 and BG5 were recovered from red volcanic loam soils from cultivated land in Vihiga and clay soils from riverine land in Bungoma respectively. From the two nematode isolates, Xenorhabdus sp. BG5 and Xenorhabdus sp. VH1 were isolated. The genomes of these two, plus that of X. griffiniae XN45 - this was previously isolated from Steinernema sp. scarpo that also originated from Kenyan soils - were sequenced and assembled. Nascent genome assemblies of the three isolates were of good quality with over 70 % of their proteome having known functions. These three isolates formed the X. griffiniae clade in a phylogenomic reconstruction of the genus. Their species were delineated using three overall genome relatedness indices: an unnamed species of the genus, Xenorhabdus sp. BG5, X. griffiniae VH1 and X. griffiniae XN45. A pangenome analysis of this clade revealed that over 70 % of species-specific genes encoded unknown functions. Transposases were linked to genomic islands in Xenorhabdus sp. BG5. Thus, overall genome-related indices sufficiently delineated species of two new Xenorhabdus isolates from Kenya, both of which were closely related to X. griffiniae . The functions encoded by most species-specific genes in the X. griffiniae clade remain unknown.
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Affiliation(s)
- Ryan Musumba Awori
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Elakistos Biosciences, PO Box 19301-00100, Nairobi, Kenya
| | - Charles N. Waturu
- Horticulture Research Institute, Kenya Agricultural and Livestock Research Organisation, PO Box 220 Thika
| | - Sacha J. Pidot
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Nelson O. Amugune
- Department of Biology, University of Nairobi, PO Box 30197-00100, Nairobi, Kenya
| | - Helge B. Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Chemical Biology, Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
- Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany
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10
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Büttner H, Pidot SJ, Scherlach K, Hertweck C. Endofungal bacteria boost anthelminthic host protection with the biosurfactant symbiosin. Chem Sci 2022; 14:103-112. [PMID: 36605741 PMCID: PMC9769094 DOI: 10.1039/d2sc04167g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/20/2022] [Indexed: 11/22/2022] Open
Abstract
Effective protection of soil fungi from predators is crucial for their survival in the niche. Thus, fungi have developed efficient defence strategies. We discovered that soil beneficial Mortierella fungi employ a potent cytotoxin (necroxime) against fungivorous nematodes. Interestingly, this anthelminthic agent is produced by bacterial endosymbionts (Candidatus Mycoavidus necroximicus) residing within the fungus. Analysis of the symbiont's genome indicated a rich biosynthetic potential, yet nothing has been known about additional metabolites and their potential synergistic functions. Here we report that two distinct Mortierella endosymbionts produce a novel cyclic lipodepsipeptide (symbiosin), that is clearly of bacterial origin, but has striking similarities to various fungal specialized metabolites. The structure and absolute configuration of symbiosin were fully elucidated. By comparative genomics of symbiosin-positive strains and in silico analyses of the deduced non-ribosomal synthetases, we assigned the (sym) biosynthetic gene cluster and proposed an assembly line model. Bioassays revealed that symbiosin is not only an antibiotic, in particular against mycobacteria, but also exhibits marked synergistic effects with necroxime in anti-nematode tests. By functional analyses and substitution experiments we found that symbiosin is a potent biosurfactant and that this particular property confers a boost in the anthelmintic action, similar to formulations of therapeutics in human medicine. Our findings illustrate that "combination therapies" against parasites already exist in ecological contexts, which may inspire the development of biocontrol agents and therapeutics.
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Affiliation(s)
- Hannah Büttner
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (Leibniz-HKI)Beutenbergstrasse 11a07745 JenaGermany
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute792 Elizabeth StreetMelbourne3000Australia
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (Leibniz-HKI)Beutenbergstrasse 11a07745 JenaGermany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (Leibniz-HKI)Beutenbergstrasse 11a07745 JenaGermany,Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena07743 JenaGermany
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11
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Niehs SP, Scherlach K, Dose B, Uzum Z, Stinear TP, Pidot SJ, Hertweck C. A highly conserved gene locus in endofungal bacteria codes for the biosynthesis of symbiosis-specific cyclopeptides. PNAS Nexus 2022; 1:pgac152. [PMID: 36714835 PMCID: PMC9802438 DOI: 10.1093/pnasnexus/pgac152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/30/2022] [Accepted: 08/03/2022] [Indexed: 02/01/2023]
Abstract
The tight association of the pathogenic fungus Rhizopus microsporus and its toxin-producing, bacterial endosymbionts (Mycetohabitans spp.) is distributed worldwide and has significance for agriculture, food production, and human health. Intriguingly, the endofungal bacteria are essential for the propagation of the fungal host. Yet, little is known about chemical mediators fostering the symbiosis, and universal metabolites that support the mutualistic relationship have remained elusive. Here, we describe the discovery of a complex of specialized metabolites produced by endofungal bacteria under symbiotic conditions. Through full genome sequencing and comparative genomics of eight endofungal symbiont strains from geographically distant regions, we discovered a conserved gene locus (hab) for a nonribosomal peptide synthetase as a unifying trait. Bioinformatics analyses, targeted gene deletions, and chemical profiling uncovered unprecedented depsipeptides (habitasporins) whose structures were fully elucidated. Computational network analysis and labeling experiments granted insight into the biosynthesis of their nonproteinogenic building blocks (pipecolic acid and β-phenylalanine). Deletion of the hab gene locus was shown to impair the ability of the bacteria to enter their fungal host. Our study unveils a common principle of the endosymbiotic lifestyle of Mycetohabitans species and expands the repertoire of characterized chemical mediators of a globally occurring mutualistic association.
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Affiliation(s)
| | | | - Benjamin Dose
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (Leibniz-HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Zerrin Uzum
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (Leibniz-HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, 792 Elizabeth Street, Melbourne, 3000, Australia
| | - Sacha J Pidot
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, 792 Elizabeth Street, Melbourne, 3000, Australia
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12
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Herisse M, Pidot SJ. Mobilization of cryptic antibiotic biosynthesis loci from human-pathogenic Nocardia. Methods Enzymol 2022; 664:173-197. [DOI: 10.1016/bs.mie.2021.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Vandelannoote K, Buultjens AH, Li L, Sharkey LK, Herisse M, Pidot SJ, Hoang T, Howden BP, Monk IR, Seemann T, Lee JYH, Stinear TP. Accessible Platform for High-Throughput COVID-19 Molecular Diagnostics and Genome Sequencing Using a Repurposed 3D Printer for RNA Extraction. ACS Biomater Sci Eng 2021; 7:4669-4676. [PMID: 34437802 PMCID: PMC8424688 DOI: 10.1021/acsbiomaterials.1c00775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The COVID-19 pandemic has exposed the dependence of diagnostic laboratories on a handful of large corporations with market monopolies on the worldwide supply of reagents, consumables, and hardware for molecular diagnostics. Global shortages of key consumables for RT-qPCR detection of SARS-CoV-2 RNA have impaired the ability to run essential, routine diagnostic services. Here, we describe a workflow for rapid detection of SARS-CoV-2 RNA in upper respiratory samples including nasal swabs and saliva, utilizing low-cost equipment and readily accessible reagents. Using repurposed Creality3D Ender-3 three-dimensional (3D) printers, we built a semiautomated paramagnetic bead RNA extraction platform. The hardware for the system was built for $300 USD, and the material cost per reaction was $1 USD. Named the Ender VX500, instrument performance when paired with RT-qPCR for SARS-CoV-2 detection in nasal and saliva specimens was two virus copies per microliter. There was a high-performance agreement (assessed using 458 COVID-19 nasal swab specimens) with the Aptima SARS-CoV-2 assay run on the Hologic Panther, a commercial automated RNA extraction and detection platform. Inter- and intrainstrument precision was excellent (coefficients of variation (CoV) of 1.10 and 0.66-1.32%, respectively) across four instruments. The platform is scalable with throughput ranging from 23 specimens on a single instrument run by one user in 50 min to 364 specimens on four instruments run by four users in 190 min. Step-by-step instructions and protocols for building and running the Ender VX500 have been made available without restriction.
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Affiliation(s)
- Koen Vandelannoote
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth St, Melbourne, Victoria 3000, Australia
| | - Andrew H Buultjens
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth St, Melbourne, Victoria 3000, Australia
| | - Lucy Li
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth St, Melbourne, Victoria 3000, Australia
| | - Liam K Sharkey
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth St, Melbourne, Victoria 3000, Australia
| | - Marion Herisse
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth St, Melbourne, Victoria 3000, Australia
| | - Sacha J Pidot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth St, Melbourne, Victoria 3000, Australia
| | - Tuyet Hoang
- Microbiological Diagnostic Unit Public Health Laboratory, Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth St, Melbourne, Victoria 3000, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth St, Melbourne, Victoria 3000, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth St, Melbourne, Victoria 3000, Australia
- Department of Infectious Diseases, Austin Health, 145 Studley Rd, Heidelberg, Victoria 3084, Australia
| | - Ian R Monk
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth St, Melbourne, Victoria 3000, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth St, Melbourne, Victoria 3000, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth St, Melbourne, Victoria 3000, Australia
| | - Jean Y H Lee
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth St, Melbourne, Victoria 3000, Australia
- Department of Infectious Diseases, Monash Health, 246 Clayton Rd, Clayton, Victoria 3168, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth St, Melbourne, Victoria 3000, Australia
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14
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Mosquera KD, Martinez Villegas LE, Pidot SJ, Sharif C, Klimpel S, Stinear TP, Moreira LA, Tobias NJ, Lorenzo MG. Multi-Omic Analysis of Symbiotic Bacteria Associated With Aedes aegypti Breeding Sites. Front Microbiol 2021; 12:703711. [PMID: 34475861 PMCID: PMC8406634 DOI: 10.3389/fmicb.2021.703711] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/23/2021] [Indexed: 12/31/2022] Open
Abstract
Mosquito breeding sites are complex aquatic environments with wide microbial diversity and physicochemical parameters that can change over time during the development of immature insect stages. Changes in biotic and abiotic conditions in water can alter life-history traits of adult mosquitos but this area remains understudied. Here, using microbial genomic and metabolomics analyses, we explored the metabolites associated with Aedes aegypti breeding sites as well as the potential contribution of Klebsiella sp., symbiotic bacteria highly associated with mosquitoes. We sought to address whether breeding sites have a signature metabolic profile and understand the metabolite contribution of the bacteria in the aquatic niches where Ae. aegypti larvae develop. An analysis of 32 mosquito-associated bacterial genomes, including Klebsiella, allowed us to identify gene clusters involved in primary metabolic pathways. From them, we inferred metabolites that could impact larval development (e.g., spermidine), as well as influence the quality assessment of a breeding site by a gravid female (e.g., putrescine), if produced by bacteria in the water. We also detected significant variance in metabolite presence profiles between water samples representing a decoupled oviposition event (oviposition by single females and manually deposited eggs) versus a control where no mosquito interactions occurred (PERMANOVA: p < 0.05; R2 = 24.64% and R2 = 30.07%). Five Klebsiella metabolites were exclusively linked to water samples where oviposition and development occurred. These data suggest metabolomics can be applied to identify compounds potentially used by female Ae. aegypti to evaluate the quality of a breeding site. Elucidating the physiological mechanisms by which the females could integrate these sensory cues while ovipositing constitutes a growing field of interest, which could benefit from a more depurated list of candidate molecules.
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Affiliation(s)
- Katherine D Mosquera
- Vector Behavior and Pathogen Interaction Group, Instituto René Rachou (FIOCRUZ), Belo Horizonte, Brazil
| | - Luis E Martinez Villegas
- Vector Behavior and Pathogen Interaction Group, Instituto René Rachou (FIOCRUZ), Belo Horizonte, Brazil.,Mosquito Vectors: Endosymbionts and Pathogen-Vector Interactions Group, Instituto Ren Rachou (FIOCRUZ), Belo Horizonte, Brazil
| | - Sacha J Pidot
- Department of Microbiology and Immunology, The Doherty Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Chinhda Sharif
- Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt, Germany
| | - Sven Klimpel
- Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt, Germany.,LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt, Germany.,Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The Doherty Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Luciano A Moreira
- Mosquito Vectors: Endosymbionts and Pathogen-Vector Interactions Group, Instituto Ren Rachou (FIOCRUZ), Belo Horizonte, Brazil
| | - Nicholas J Tobias
- LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt, Germany.,Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany
| | - Marcelo G Lorenzo
- Vector Behavior and Pathogen Interaction Group, Instituto René Rachou (FIOCRUZ), Belo Horizonte, Brazil
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15
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Pidot SJ, Porter JL, Lister T, Stinear TP. In vitro activity of SPR719 against Mycobacterium ulcerans, Mycobacterium marinum and Mycobacterium chimaera. PLoS Negl Trop Dis 2021; 15:e0009636. [PMID: 34310615 PMCID: PMC8341698 DOI: 10.1371/journal.pntd.0009636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 08/05/2021] [Accepted: 07/07/2021] [Indexed: 11/18/2022] Open
Abstract
Nontuberculosis mycobacterial (NTM) infections are increasing in prevalence across the world. In many cases, treatment options for these infections are limited. However, there has been progress in recent years in the development of new antimycobacterial drugs. Here, we investigate the in vitro activity of SPR719, a novel aminobenzimidazole antibiotic and the active form of the clinical-stage compound, SPR720, against several isolates of Mycobacterium ulcerans, Mycobacterium marinum and Mycobacterium chimaera. We show that SPR719 is active against these NTM species with a MIC range of 0.125–4 μg/ml and that this compares favorably with the commonly utilized antimycobacterial antibiotics, rifampicin and clarithromycin. Our findings suggest that SPR720 should be further evaluated for the treatment of NTM infections. Nontuberculosis mycobacteria represent a large group of diverse bacteria that live across a range of environments. Human contact with the habitats in which these organisms live can result in opportunistic infections. Among the NTM, Mycobacterium ulcerans causes necrotic skin ulcers that can lead to significant long term physical impairment; Mycobacterium marinum causes granulomatous skin lesions; and Mycobacterium chimaera has been linked to contaminated heater-cooler units used during cardiac surgery, resulting in prosthetic heart valve infections that are particularly difficult to treat. We performed laboratory experiments to test the susceptibility of these NTM species (M. ulcerans, M. marinum and M. chimaera) to a recently developed antibiotic, SPR719. We found that SPR719 inhibits the growth of these mycobacteria at concentration ranges similar to or better than commonly used anti-mycobacterial antibiotics. As SPR720, the oral prodrug of SPR719, has recently completed a Phase I safety, tolerability and PK study in healthy human volunteers, the potential exists for this product to be explored for the treatment of NTM infections, where new treatment options are urgently needed.
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Affiliation(s)
- Sacha J. Pidot
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Australia
- * E-mail:
| | - Jessica L. Porter
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Troy Lister
- Spero Therapeutics, Cambridge, Massachusetts, United States of America
| | - Timothy P. Stinear
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Australia
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16
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Ishida K, Shabuer G, Schieferdecker S, Pidot SJ, Stinear TP, Knuepfer U, Cyrulies M, Hertweck C. Oak-Associated Negativicute Equipped with Ancestral Aromatic Polyketide Synthase Produces Antimycobacterial Dendrubins. Chemistry 2020; 26:13147-13151. [PMID: 32597507 PMCID: PMC7693217 DOI: 10.1002/chem.202001939] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/26/2020] [Indexed: 11/07/2022]
Abstract
Anaerobic bacteria have only recently been recognized as a source of antibiotics; yet, the metabolic potential of Negativicutes (Gram-negative staining Firmicutes) such as the oak-associated Dendrosporobacter quercicolus has remained unknown. Genome mining of D. quercicolus and phylogenetic analyses revealed a gene cluster for a type II polyketide synthase (PKS) complex that belongs to the most ancestral enzyme systems of this type. Metabolic profiling, NMR analyses, and stable-isotope labeling led to the discovery of a new family of anthraquinone-type polyphenols, the dendrubins, which are diversified by acylation, methylation, and dimerization. Dendrubin A and B were identified as strong antibiotics against a range of clinically relevant, human-pathogenic mycobacteria.
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Affiliation(s)
- Keishi Ishida
- Biomolecular Chemistry, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Gulimila Shabuer
- Biomolecular Chemistry, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Sebastian Schieferdecker
- Biomolecular Chemistry, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Sacha J Pidot
- Department of Microbiology and Immunology, University of Melbourne, 792 Elizabeth Street, 3000, Melbourne, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, University of Melbourne, 792 Elizabeth Street, 3000, Melbourne, Australia
| | - Uwe Knuepfer
- Biopilot Plant, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Michael Cyrulies
- Biopilot Plant, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Biomolecular Chemistry, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany.,Institute for Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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17
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Lee JYH, Best N, McAuley J, Porter JL, Seemann T, Schultz MB, Sait M, Orlando N, Mercoulia K, Ballard SA, Druce J, Tran T, Catton MG, Pryor MJ, Cui HL, Luttick A, McDonald S, Greenhalgh A, Kwong JC, Sherry NL, Graham M, Hoang T, Herisse M, Pidot SJ, Williamson DA, Howden BP, Monk IR, Stinear TP. Validation of a single-step, single-tube reverse transcription loop-mediated isothermal amplification assay for rapid detection of SARS-CoV-2 RNA. J Med Microbiol 2020; 69:1169-1178. [PMID: 32755529 PMCID: PMC7656183 DOI: 10.1099/jmm.0.001238] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/10/2020] [Indexed: 12/21/2022] Open
Abstract
Introduction. The SARS-CoV-2 pandemic of 2020 has resulted in unparalleled requirements for RNA extraction kits and enzymes required for virus detection, leading to global shortages. This has necessitated the exploration of alternative diagnostic options to alleviate supply chain issues.Aim. To establish and validate a reverse transcription loop-mediated isothermal amplification (RT- LAMP) assay for the detection of SARS-CoV-2 from nasopharyngeal swabs.Methodology. We used a commercial RT-LAMP mastermix from OptiGene in combination with a primer set designed to detect the CDC N1 region of the SARS-CoV-2 nucleocapsid (N) gene. A single-tube, single-step fluorescence assay was implemented whereby 1 µl of universal transport medium (UTM) directly from a nasopharyngeal swab could be used as template, bypassing the requirement for RNA purification. Amplification and detection could be conducted in any thermocycler capable of holding 65 °C for 30 min and measure fluorescence in the FAM channel at 1 min intervals.Results. Assay evaluation by assessment of 157 clinical specimens previously screened by E-gene RT-qPCR revealed assay sensitivity and specificity of 87 and 100%, respectively. Results were fast, with an average time-to-positive (Tp) for 93 clinical samples of 14 min (sd±7 min). Using dilutions of SARS-CoV-2 virus spiked into UTM, we also evaluated assay performance against FDA guidelines for implementation of emergency-use diagnostics and established a limit-of-detection of 54 Tissue Culture Infectious Dose 50 per ml (TCID50 ml-1), with satisfactory assay sensitivity and specificity. A comparison of 20 clinical specimens between four laboratories showed excellent interlaboratory concordance; performing equally well on three different, commonly used thermocyclers, pointing to the robustness of the assay.Conclusion. With a simplified workflow, The N1 gene Single Tube Optigene LAMP assay (N1-STOP-LAMP) is a powerful, scalable option for specific and rapid detection of SARS-CoV-2 and an additional resource in the diagnostic armamentarium against COVID-19.
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Affiliation(s)
- Jean Y. H. Lee
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Monash Health, Clayton, Victoria, Australia
| | - Nickala Best
- GenWorks Pty Ltd, Thebarton, South Australia, Australia
| | - Julie McAuley
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jessica L. Porter
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mark B. Schultz
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Michelle Sait
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Nicole Orlando
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Karolina Mercoulia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Susan A. Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Julian Druce
- Victorian Infectious Diseases Reference Laboratory, Melbourne Health at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Thomas Tran
- Victorian Infectious Diseases Reference Laboratory, Melbourne Health at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mike G. Catton
- Victorian Infectious Diseases Reference Laboratory, Melbourne Health at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | | | | | - Sean McDonald
- GenWorks Pty Ltd, Thebarton, South Australia, Australia
| | | | - Jason C. Kwong
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Norelle L. Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Maryza Graham
- Department of Microbiology, Monash Health, Clayton, Victoria, Australia
| | - Tuyet Hoang
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Marion Herisse
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Deborah A. Williamson
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Melbourne Health, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Ian R. Monk
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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18
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Kenshole E, Herisse M, Michael M, Pidot SJ. Natural product discovery through microbial genome mining. Curr Opin Chem Biol 2020; 60:47-54. [PMID: 32853968 DOI: 10.1016/j.cbpa.2020.07.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/17/2020] [Accepted: 07/24/2020] [Indexed: 02/06/2023]
Abstract
The advent of the genomic era has opened up enormous possibilities for the discovery of new natural products. Also known as specialized metabolites, these compounds produced by bacteria, fungi, and plants have long been sought for their bioactive properties. Innovations in both DNA sequencing technologies and bioinformatics now allow the wealth of sequence data to be mined at both the genome and metagenome levels for new specialized metabolites. However, a key problem that remains is rapidly and efficiently linking these identified genes to their corresponding compounds. Within this review, we provide specific examples of studies that have used the power of genomic or metagenomic data to overcome these problems and identify new small molecules and their biosynthetic pathways.
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Affiliation(s)
- Emma Kenshole
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Australia, 3000
| | - Marion Herisse
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Australia, 3000
| | - Michael Michael
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Australia, 3000
| | - Sacha J Pidot
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Australia, 3000.
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19
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Robinson SL, Terlouw BR, Smith MD, Pidot SJ, Stinear TP, Medema MH, Wackett LP. Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia. J Biol Chem 2020; 295:14826-14839. [PMID: 32826316 DOI: 10.1074/jbc.ra120.013528] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 08/07/2020] [Indexed: 12/31/2022] Open
Abstract
Enzymes that cleave ATP to activate carboxylic acids play essential roles in primary and secondary metabolism in all domains of life. Class I adenylate-forming enzymes share a conserved structural fold but act on a wide range of substrates to catalyze reactions involved in bioluminescence, nonribosomal peptide biosynthesis, fatty acid activation, and β-lactone formation. Despite their metabolic importance, the substrates and functions of the vast majority of adenylate-forming enzymes are unknown without tools available to accurately predict them. Given the crucial roles of adenylate-forming enzymes in biosynthesis, this also severely limits our ability to predict natural product structures from biosynthetic gene clusters. Here we used machine learning to predict adenylate-forming enzyme function and substrate specificity from protein sequences. We built a web-based predictive tool and used it to comprehensively map the biochemical diversity of adenylate-forming enzymes across >50,000 candidate biosynthetic gene clusters in bacterial, fungal, and plant genomes. Ancestral phylogenetic reconstruction and sequence similarity networking of enzymes from these clusters suggested divergent evolution of the adenylate-forming superfamily from a core enzyme scaffold most related to contemporary CoA ligases toward more specialized functions including β-lactone synthetases. Our classifier predicted β-lactone synthetases in uncharacterized biosynthetic gene clusters conserved in >90 different strains of Nocardia. To test our prediction, we purified a candidate β-lactone synthetase from Nocardia brasiliensis and reconstituted the biosynthetic pathway in vitro to link the gene cluster to the β-lactone natural product, nocardiolactone. We anticipate that our machine learning approach will aid in functional classification of enzymes and advance natural product discovery.
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Affiliation(s)
- Serina L Robinson
- BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA; Graduate Program in Bioinformatics and Computational Biology, University of Minnesota, Rochester, Minnesota, USA; Graduate Program in Microbiology, Immunology, and Cancer Biology, University of Minnesota, Minneapolis, Minnesota, USA.
| | - Barbara R Terlouw
- Bioinformatics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Megan D Smith
- BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA; Graduate Program in Microbiology, Immunology, and Cancer Biology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Sacha J Pidot
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Lawrence P Wackett
- BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA; Graduate Program in Bioinformatics and Computational Biology, University of Minnesota, Rochester, Minnesota, USA; Graduate Program in Microbiology, Immunology, and Cancer Biology, University of Minnesota, Minneapolis, Minnesota, USA
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20
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Mangas KM, Tobias NJ, Marion E, Babonneau J, Marsollier L, Porter JL, Pidot SJ, Wong CY, Jackson DC, Chua BY, Stinear TP. High antibody titres induced by protein subunit vaccines using Mycobacterium ulcerans antigens Hsp18 and MUL_3720 with a TLR-2 agonist fail to protect against Buruli ulcer in mice. PeerJ 2020; 8:e9659. [PMID: 32844063 PMCID: PMC7416718 DOI: 10.7717/peerj.9659] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/14/2020] [Indexed: 12/26/2022] Open
Abstract
Background Mycobacterium ulcerans is the causative agent of a debilitating skin and soft tissue infection known as Buruli ulcer (BU). There is no vaccine against BU. The purpose of this study was to investigate the vaccine potential of two previously described immunogenic M. ulcerans proteins, MUL_3720 and Hsp18, using a mouse tail infection model of BU. Methods Recombinant versions of the two proteins were each electrostatically coupled with a previously described lipopeptide adjuvant. Seven C57BL/6 and seven BALB/c mice were vaccinated and boosted with each of the formulations. Vaccinated mice were then challenged with M. ulcerans via subcutaneous tail inoculation. Vaccine performance was assessed by time-to-ulceration compared to unvaccinated mice. Results The MUL_3720 and Hsp18 vaccines induced high titres of antigen-specific antibodies that were predominately subtype IgG1. However, all mice developed ulcers by day-40 post-M. ulcerans challenge. No significant difference was observed in the time-to-onset of ulceration between the experimental vaccine groups and unvaccinated animals. Conclusions These data align with previous vaccine experiments using Hsp18 and MUL_3720 that indicated these proteins may not be appropriate vaccine antigens. This work highlights the need to explore alternative vaccine targets and different approaches to understand the role antibodies might play in controlling BU.
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Affiliation(s)
- Kirstie M Mangas
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Nicholas J Tobias
- Johann Wolfgang Goethe Universität Frankfurt am Main, Frankfurt, Germany.,LOEWE Centre for Translational Biodiversity in Genomics (TBG), Frankfurt, Germany
| | - Estelle Marion
- Université de Nantes, Nantes, France.,Université de Nantes, Nantes, France.,Université d'Angers, Angers, France
| | - Jérémie Babonneau
- Université de Nantes, Nantes, France.,Université d'Angers, Angers, France
| | - Laurent Marsollier
- Université de Nantes, Nantes, France.,Université d'Angers, Angers, France
| | - Jessica L Porter
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Sacha J Pidot
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Chinn Yi Wong
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - David C Jackson
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Brendon Y Chua
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
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21
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Herisse M, Ishida K, Porter JL, Howden B, Hertweck C, Stinear TP, Pidot SJ. Identification and Mobilization of a Cryptic Antibiotic Biosynthesis Gene Locus from a Human-Pathogenic Nocardia Isolate. ACS Chem Biol 2020; 15:1161-1168. [PMID: 31697466 DOI: 10.1021/acschembio.9b00763] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The genus Nocardia contains >50 human pathogenic species that cause a range of illnesses from skin and soft tissue infections to lung and brain infections. However, despite their membership in the most prominent family of secondary metabolite producers (the Actinomycetes), the ability of Nocardia species, especially those that cause human infections, to produce secondary metabolites has not been as well studied. Using genome mining, we have investigated cryptic secondary metabolite biosynthesis gene clusters from Nocardia species and identified a conserved locus within human pathogenic strains of Nocardia brasiliensis and Nocardia vulneris. Direct capture and heterologous expression in a Streptomyces host activated the biosynthetic locus, revealing it to be the source of the brasiliquinones, benz[a]anthraquinone antibiotics whose biosynthetic pathway has remained hidden for over two decades, until now. Our findings highlight these hitherto neglected human pathogenic Nocardia as a source of diverse and important natural products.
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Affiliation(s)
- Marion Herisse
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Jessica L. Porter
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Ben Howden
- Microbiological Diagnostic Unit, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
- Natural Product Chemistry, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
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22
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Bratovanov EV, Ishida K, Heinze B, Pidot SJ, Stinear TP, Hegemann JD, Marahiel MA, Hertweck C. Genome Mining and Heterologous Expression Reveal Two Distinct Families of Lasso Peptides Highly Conserved in Endofungal Bacteria. ACS Chem Biol 2020; 15:1169-1176. [PMID: 31800204 DOI: 10.1021/acschembio.9b00805] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome mining identified the fungal-bacterial endosymbiosis Rhizopus microsporus-Mycetohabitans (previously Burkholderia) rhizoxinica as a rich source of novel natural products. However, most of the predicted compounds have remained cryptic. In this study, we employed heterologous expression to isolate and characterize three ribosomally synthesized and post-translationally modified peptides with lariat topology (lasso peptides) from the endosymbiont M. rhizoxinica: burhizin-23, mycetohabin-16, and mycetohabin-15. Through coexpression experiments, it was shown that an orphan gene product results in mature mycetohabin-15, albeit encoded remotely from the core biosynthetic gene cluster. Comparative genomics revealed that mycetohabins are highly conserved among M. rhizoxinica and related endosymbiotic bacteria. Gene knockout and reinfection experiments indicated that the lasso peptides are not crucial for establishing symbiosis; instead, the peptides are exported into the environment during endosymbiosis. This is the first report on lasso peptides from endosymbiotic bacteria.
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Affiliation(s)
- Evgeni V. Bratovanov
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Beatrix Heinze
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Sacha J. Pidot
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Julian D. Hegemann
- Institute of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 124/TC2, 10623 Berlin, Germany
- Department of Chemistry and Biochemistry, Philipps University Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Mohamed A. Marahiel
- Department of Chemistry and Biochemistry, Philipps University Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
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23
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Niehs SP, Dose B, Richter S, Pidot SJ, Dahse H, Stinear TP, Hertweck C. Mining Symbionts of a Spider‐Transmitted Fungus Illuminates Uncharted Biosynthetic Pathways to Cytotoxic Benzolactones. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sarah P. Niehs
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Sophie Richter
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Sacha J. Pidot
- Department of Microbiology and Immunology Doherty Institute 792 Elizabeth Street Melbourne 3000 Australia
| | | | - Timothy P. Stinear
- Department of Microbiology and Immunology Doherty Institute 792 Elizabeth Street Melbourne 3000 Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
- Faculty of Biological Sciences Friedrich Schiller University Jena 07743 Jena Germany
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24
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Niehs SP, Dose B, Richter S, Pidot SJ, Dahse HM, Stinear TP, Hertweck C. Mining Symbionts of a Spider-Transmitted Fungus Illuminates Uncharted Biosynthetic Pathways to Cytotoxic Benzolactones. Angew Chem Int Ed Engl 2020; 59:7766-7771. [PMID: 32040253 PMCID: PMC7318616 DOI: 10.1002/anie.201916007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Indexed: 11/17/2022]
Abstract
A spider‐transmitted fungus (Rhizopus microsporus) that was isolated from necrotic human tissue was found to harbor endofungal bacteria (Burkholderia sp.). Metabolic profiling of the symbionts revealed a complex of cytotoxic agents (necroximes). Their structures were characterized as oxime‐substituted benzolactone enamides with a peptidic side chain. The potently cytotoxic necroximes are also formed in symbiosis with the fungal host and could have contributed to the necrosis. Genome sequencing and computational analyses revealed a novel modular PKS/NRPS assembly line equipped with several non‐canonical domains. Based on gene‐deletion mutants, we propose a biosynthetic model for bacterial benzolactones. We identified specific traits that serve as genetic handles to find related salicylate macrolide pathways (lobatamide, oximidine, apicularen) in various other bacterial genera. Knowledge of the biosynthetic pathway enables biosynthetic engineering and genome‐mining approaches.
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Affiliation(s)
- Sarah P Niehs
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Sophie Richter
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Sacha J Pidot
- Department of Microbiology and Immunology, Doherty Institute, 792 Elizabeth Street, Melbourne, 3000, Australia
| | | | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute, 792 Elizabeth Street, Melbourne, 3000, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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25
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Abstract
The nargenicin family of antibiotic macrolides comprise a group of bacterial natural products with a rare ether bridged cis-decalin moiety and a narrow spectrum of activity. Most family members were identified almost four decades ago and were placed on the shelf due to the numbers of broad-spectrum compounds available at the time. However, in light of rising rates of antimicrobial resistance, there has been a renewed interest in the use of narrow-spectrum antimicrobials. Here, we review the history of this family of compounds, including synthetic approaches, and highlight the recently uncovered genetic basis for nargenicin production. Given the renewed pharmaceutical interest in these compounds, we also investigate structure-activity relationships among these molecules, with a view to the future development of members of this unusual antibiotic family.
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Affiliation(s)
- Sacha J Pidot
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, 3000, Melbourne, VIC, Australia
| | - Mark A Rizzacasa
- School of Chemistry, The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 3000, Melbourne, VIC, Australia
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26
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Pidot SJ, Rizzacasa MA. Frontispiece: The Nargenicin Family of Oxa‐Bridged Macrolide Antibiotics. Chemistry 2020. [DOI: 10.1002/chem.202081362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sacha J. Pidot
- Department of Microbiology and Immunology at the Doherty Institute University of Melbourne 3000 Melbourne VIC Australia
| | - Mark A. Rizzacasa
- School of Chemistry The Bio21 Molecular Science and Biotechnology Institute University of Melbourne 3000 Melbourne VIC Australia
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27
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Lee BM, Harold LK, Almeida DV, Afriat-Jurnou L, Aung HL, Forde BM, Hards K, Pidot SJ, Ahmed FH, Mohamed AE, Taylor MC, West NP, Stinear TP, Greening C, Beatson SA, Nuermberger EL, Cook GM, Jackson CJ. Predicting nitroimidazole antibiotic resistance mutations in Mycobacterium tuberculosis with protein engineering. PLoS Pathog 2020; 16:e1008287. [PMID: 32032366 PMCID: PMC7032734 DOI: 10.1371/journal.ppat.1008287] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 02/20/2020] [Accepted: 12/16/2019] [Indexed: 12/21/2022] Open
Abstract
Our inability to predict which mutations could result in antibiotic resistance has made it difficult to rapidly identify the emergence of resistance, identify pre-existing resistant populations, and manage our use of antibiotics to effectively treat patients and prevent or slow the spread of resistance. Here we investigated the potential for resistance against the new antitubercular nitroimidazole prodrugs pretomanid and delamanid to emerge in Mycobacterium tuberculosis, the causative agent of tuberculosis (TB). Deazaflavin-dependent nitroreductase (Ddn) is the only identified enzyme within M. tuberculosis that activates these prodrugs, via an F420H2-dependent reaction. We show that the native menaquinone-reductase activity of Ddn is essential for emergence from hypoxia, which suggests that for resistance to spread and pose a threat to human health, the native activity of Ddn must be at least partially retained. We tested 75 unique mutations, including all known sequence polymorphisms identified among ~15,000 sequenced M. tuberculosis genomes. Several mutations abolished pretomanid and delamanid activation in vitro, without causing complete loss of the native activity. We confirmed that a transmissible M. tuberculosis isolate from the hypervirulent Beijing family already possesses one such mutation and is resistant to pretomanid, before being exposed to the drug. Notably, delamanid was still effective against this strain, which is consistent with structural analysis that indicates delamanid and pretomanid bind to Ddn differently. We suggest that the mutations identified in this work be monitored for informed use of delamanid and pretomanid treatment and to slow the emergence of resistance.
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Affiliation(s)
- Brendon M. Lee
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Liam K. Harold
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Deepak V. Almeida
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Livnat Afriat-Jurnou
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
- MIGAL, Galilee Research Institute, Kiryat Shmona, Israel
- Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee, Israel
| | - Htin Lin Aung
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Brian M. Forde
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Kiel Hards
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - F. Hafna Ahmed
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - A. Elaaf Mohamed
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Matthew C. Taylor
- Land and Water Flagship, The Commonwealth Scientific and Industrial Organisation, Canberra, Australian Capital Territory, Australia
| | - Nicholas P. West
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Chris Greening
- Land and Water Flagship, The Commonwealth Scientific and Industrial Organisation, Canberra, Australian Capital Territory, Australia
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Scott A. Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Eric L. Nuermberger
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Gregory M. Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Colin J. Jackson
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
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28
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Pidot SJ, Gao W, Buultjens AH, Monk IR, Guerillot R, Carter GP, Lee JYH, Lam MMC, Grayson ML, Ballard SA, Mahony AA, Grabsch EA, Kotsanas D, Korman TM, Coombs GW, Robinson JO, Gonçalves da Silva A, Seemann T, Howden BP, Johnson PDR, Stinear TP. Increasing tolerance of hospital Enterococcus faecium to handwash alcohols. Sci Transl Med 2019; 10:10/452/eaar6115. [PMID: 30068573 DOI: 10.1126/scitranslmed.aar6115] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 02/10/2018] [Accepted: 04/03/2018] [Indexed: 11/03/2022]
Abstract
Alcohol-based disinfectants and particularly hand rubs are a key way to control hospital infections worldwide. Such disinfectants restrict transmission of pathogens, such as multidrug-resistant Staphylococcus aureus and Enterococcus faecium Despite this success, health care infections caused by E. faecium are increasing. We tested alcohol tolerance of 139 hospital isolates of E. faecium obtained between 1997 and 2015 and found that E. faecium isolates after 2010 were 10-fold more tolerant to killing by alcohol than were older isolates. Using a mouse gut colonization model of E. faecium transmission, we showed that alcohol-tolerant E. faecium resisted standard 70% isopropanol surface disinfection, resulting in greater mouse gut colonization compared to alcohol-sensitive E. faecium We next looked for bacterial genomic signatures of adaptation. Alcohol-tolerant E. faecium accumulated mutations in genes involved in carbohydrate uptake and metabolism. Mutagenesis confirmed the roles of these genes in the tolerance of E. faecium to isopropanol. These findings suggest that bacterial adaptation is complicating infection control recommendations, necessitating additional procedures to prevent E. faecium from spreading in hospital settings.
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Affiliation(s)
- Sacha J Pidot
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Wei Gao
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Andrew H Buultjens
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Ian R Monk
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Romain Guerillot
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Glen P Carter
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Jean Y H Lee
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Margaret M C Lam
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - M Lindsay Grayson
- Infectious Diseases Department, Austin Health, Heidelberg, Victoria 3084, Australia.,Department of Medicine, University of Melbourne, Heidelberg, Victoria 3084, Australia.,Department of Epidemiology and Preventive Medicine, Monash University, Victoria 3800, Australia
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Andrew A Mahony
- Infectious Diseases Department, Austin Health, Heidelberg, Victoria 3084, Australia
| | - Elizabeth A Grabsch
- Infectious Diseases Department, Austin Health, Heidelberg, Victoria 3084, Australia
| | - Despina Kotsanas
- Monash Infectious Diseases, Monash Health, Clayton, Victoria 3168, Australia
| | - Tony M Korman
- Monash Infectious Diseases, Monash Health, Clayton, Victoria 3168, Australia
| | - Geoffrey W Coombs
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia.,Department of Microbiology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Murdoch, Western Australia 6150, Australia
| | - J Owen Robinson
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia.,Department of Microbiology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Murdoch, Western Australia 6150, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Torsten Seemann
- Melbourne Bioinformatics, University of Melbourne, Carlton, Victoria 3053, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia.,Infectious Diseases Department, Austin Health, Heidelberg, Victoria 3084, Australia.,Department of Medicine, University of Melbourne, Heidelberg, Victoria 3084, Australia.,Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Paul D R Johnson
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia. .,Infectious Diseases Department, Austin Health, Heidelberg, Victoria 3084, Australia.,Department of Medicine, University of Melbourne, Heidelberg, Victoria 3084, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia.
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Niehs SP, Dose B, Scherlach K, Pidot SJ, Stinear TP, Hertweck C. Genome Mining Reveals Endopyrroles from a Nonribosomal Peptide Assembly Line Triggered in Fungal-Bacterial Symbiosis. ACS Chem Biol 2019; 14:1811-1818. [PMID: 31283172 DOI: 10.1021/acschembio.9b00406] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bacterial endosymbiont (Burkholderia rhizoxinica) of the rice seedling blight fungus (Rhizopus microsporus) harbors a large number of cryptic biosynthesis gene clusters. Genome mining and sequence similarity networks based on an encoded nonribosomal peptide assembly line and the associated pyrrole-forming enzymes in the symbiont indicated that the encoded metabolites are unique among a large number of tentative pyrrole natural products in diverse and unrelated bacterial phyla. By performing comparative metabolic profiling using a mutant generated with an improved pheS Burkholderia counterselection marker, we found that the symbionts' biosynthetic pathway is mainly activated under salt stress and exclusively in symbiosis with the fungal host. The cryptic metabolites were fully characterized as novel pyrrole-substituted depsipeptides (endopyrroles). A broader survey showed that endopyrrole production is a hallmark of geographically distant endofungal bacteria, which produce the peptides solely under symbiotic conditions.
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Affiliation(s)
- Sarah P. Niehs
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, 792 Elizabeth Street, Melbourne 3000, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, 792 Elizabeth Street, Melbourne 3000, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
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30
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Hermenau R, Mehl JL, Ishida K, Dose B, Pidot SJ, Stinear TP, Hertweck C. Genomics‐Driven Discovery of NO‐Donating Diazeniumdiolate Siderophores in Diverse Plant‐Associated Bacteria. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906326] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Ron Hermenau
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Jule L. Mehl
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Sacha J. Pidot
- Department of Microbiology and Immunology at the Doherty Institute University of Melbourne Melbourne VIC 3000 Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology at the Doherty Institute University of Melbourne Melbourne VIC 3000 Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
- Natural Product Chemistry Faculty of Biological Sciences Friedrich Schiller University Jena 07743 Jena Germany
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31
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Hermenau R, Mehl JL, Ishida K, Dose B, Pidot SJ, Stinear TP, Hertweck C. Genomics-Driven Discovery of NO-Donating Diazeniumdiolate Siderophores in Diverse Plant-Associated Bacteria. Angew Chem Int Ed Engl 2019; 58:13024-13029. [PMID: 31276269 PMCID: PMC6771848 DOI: 10.1002/anie.201906326] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/05/2019] [Indexed: 01/13/2023]
Abstract
Siderophores are key players in bacteria–host interactions, with the main function to provide soluble iron for their producers. Gramibactin from rhizosphere bacteria expands siderophore function and diversity as it delivers iron to the host plant and features an unusual diazeniumdiolate moiety for iron chelation. By mutational analysis of the grb gene cluster, we identified genes (grbD and grbE) necessary for diazeniumdiolate formation. Genome mining using a GrbD‐based network revealed a broad range of orthologous gene clusters in mainly plant‐associated Burkholderia/Paraburkholderia species. Two new types of diazeniumdiolate siderophores, megapolibactins and plantaribactin were fully characterized. In vitro assays and in vivo monitoring experiments revealed that the iron chelators also liberate nitric oxide (NO) in plant roots. This finding is important since NO donors are considered as biofertilizers that maintain iron homeostasis and increase overall plant fitness.
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Affiliation(s)
- Ron Hermenau
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Jule L Mehl
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Sacha J Pidot
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany.,Natural Product Chemistry, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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32
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Monk IR, Shaikh N, Begg SL, Gajdiss M, Sharkey LKR, Lee JYH, Pidot SJ, Seemann T, Kuiper M, Winnen B, Hvorup R, Collins BM, Bierbaum G, Udagedara SR, Morey JR, Pulyani N, Howden BP, Maher MJ, McDevitt CA, King GF, Stinear TP. Zinc-binding to the cytoplasmic PAS domain regulates the essential WalK histidine kinase of Staphylococcus aureus. Nat Commun 2019; 10:3067. [PMID: 31296851 PMCID: PMC6624279 DOI: 10.1038/s41467-019-10932-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 06/05/2019] [Indexed: 01/23/2023] Open
Abstract
WalKR (YycFG) is the only essential two-component regulator in the human pathogen Staphylococcus aureus. WalKR regulates peptidoglycan synthesis, but this function alone does not explain its essentiality. Here, to further understand WalKR function, we investigate a suppressor mutant that arose when WalKR activity was impaired; a histidine to tyrosine substitution (H271Y) in the cytoplasmic Per-Arnt-Sim (PASCYT) domain of the histidine kinase WalK. Introducing the WalKH271Y mutation into wild-type S. aureus activates the WalKR regulon. Structural analyses of the WalK PASCYT domain reveal a metal-binding site, in which a zinc ion (Zn2+) is tetrahedrally-coordinated by four amino acids including H271. The WalKH271Y mutation abrogates metal binding, increasing WalK kinase activity and WalR phosphorylation. Thus, Zn2+-binding negatively regulates WalKR. Promoter-reporter experiments using S. aureus confirm Zn2+ sensing by this system. Identification of a metal ligand recognized by the WalKR system broadens our understanding of this critical S. aureus regulon.
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Affiliation(s)
- Ian R Monk
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia.
| | - Nausad Shaikh
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4067, Australia
| | - Stephanie L Begg
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Mike Gajdiss
- University Clinics of Bonn, Institute of Medical Microbiology, Immunology and Parasitology, 53127, Bonn, Germany
| | - Liam K R Sharkey
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Jean Y H Lee
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Sacha J Pidot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia.,Melbourne Bioinformatics, University of Melbourne, Melbourne, VIC, 3000, Australia
| | | | | | - Rikki Hvorup
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4067, Australia
| | - Brett M Collins
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4067, Australia
| | - Gabriele Bierbaum
- University Clinics of Bonn, Institute of Medical Microbiology, Immunology and Parasitology, 53127, Bonn, Germany
| | - Saumya R Udagedara
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Jacqueline R Morey
- Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Neha Pulyani
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Megan J Maher
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Christopher A McDevitt
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia.,Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4067, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia.
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Pidot SJ, Herisse M, Sharkey L, Atkin L, Porter JL, Seemann T, Howden BP, Rizzacasa MA, Stinear TP. Biosynthesis and Ether‐Bridge Formation in Nargenicin Macrolides. Angew Chem Int Ed Engl 2019; 58:3996-4001. [DOI: 10.1002/anie.201900290] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Sacha J. Pidot
- Department of Microbiology and Immunology at the Doherty InstituteUniversity of Melbourne Melbourne VIC 3000 Australia
| | - Marion Herisse
- Department of Microbiology and Immunology at the Doherty InstituteUniversity of Melbourne Melbourne VIC 3000 Australia
| | - Liam Sharkey
- Department of Microbiology and Immunology at the Doherty InstituteUniversity of Melbourne Melbourne VIC 3000 Australia
| | - Liselle Atkin
- School of ChemistryThe Bio21 Molecular Science and Biotechnology InstituteUniversity of Melbourne Melbourne VIC 3000 Australia
| | - Jessica L. Porter
- Department of Microbiology and Immunology at the Doherty InstituteUniversity of Melbourne Melbourne VIC 3000 Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology at the Doherty InstituteUniversity of Melbourne Melbourne VIC 3000 Australia
- Microbioloigical Diagnostic UnitUniversity of Melbourne Melbourne VIC 3000 Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology at the Doherty InstituteUniversity of Melbourne Melbourne VIC 3000 Australia
- Microbioloigical Diagnostic UnitUniversity of Melbourne Melbourne VIC 3000 Australia
| | - Mark A. Rizzacasa
- School of ChemistryThe Bio21 Molecular Science and Biotechnology InstituteUniversity of Melbourne Melbourne VIC 3000 Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology at the Doherty InstituteUniversity of Melbourne Melbourne VIC 3000 Australia
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Pidot SJ, Herisse M, Sharkey L, Atkin L, Porter JL, Seemann T, Howden BP, Rizzacasa MA, Stinear TP. Biosynthesis and Ether‐Bridge Formation in Nargenicin Macrolides. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sacha J. Pidot
- Department of Microbiology and Immunology at the Doherty InstituteUniversity of Melbourne Melbourne VIC 3000 Australia
| | - Marion Herisse
- Department of Microbiology and Immunology at the Doherty InstituteUniversity of Melbourne Melbourne VIC 3000 Australia
| | - Liam Sharkey
- Department of Microbiology and Immunology at the Doherty InstituteUniversity of Melbourne Melbourne VIC 3000 Australia
| | - Liselle Atkin
- School of ChemistryThe Bio21 Molecular Science and Biotechnology InstituteUniversity of Melbourne Melbourne VIC 3000 Australia
| | - Jessica L. Porter
- Department of Microbiology and Immunology at the Doherty InstituteUniversity of Melbourne Melbourne VIC 3000 Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology at the Doherty InstituteUniversity of Melbourne Melbourne VIC 3000 Australia
- Microbioloigical Diagnostic UnitUniversity of Melbourne Melbourne VIC 3000 Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology at the Doherty InstituteUniversity of Melbourne Melbourne VIC 3000 Australia
- Microbioloigical Diagnostic UnitUniversity of Melbourne Melbourne VIC 3000 Australia
| | - Mark A. Rizzacasa
- School of ChemistryThe Bio21 Molecular Science and Biotechnology InstituteUniversity of Melbourne Melbourne VIC 3000 Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology at the Doherty InstituteUniversity of Melbourne Melbourne VIC 3000 Australia
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35
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Gebel J, Gemein S, Kampf G, Pidot SJ, Buetti N, Exner M. Isopropanol at 60% and at 70% are effective against 'isopropanol-tolerant' Enterococcus faecium. J Hosp Infect 2019; 103:e88-e91. [PMID: 30711531 DOI: 10.1016/j.jhin.2019.01.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/28/2019] [Indexed: 02/06/2023]
Abstract
The bactericidal activity of isopropanol was determined against Enterococcus faecium ATCC 6057, ST 796 (isopropanol-tolerant strain) and Enterococcus hirae ATCC 10541 (EN 13727). Isopropanol at 60% and 70% were effective (≥5.38 log10-reduction) in 15 s against all strains but 23% isopropanol was not (<0.99 log10-reduction in ≤15 min). Isopropanol at 70% was tested against E. faecium in the four-field test. Eight millilitres was not effective enough in 1 min (<5 log10-reduction), whilst 16 mL was effective (≥5.85 log10-reduction). Healthcare workers can be reassured that 60% and 70% isopropanol with an appropriate volume are effective against E. faecium.
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Affiliation(s)
- J Gebel
- Institute for Hygiene and Public Health, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany.
| | - S Gemein
- Institute for Hygiene and Public Health, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - G Kampf
- Institute for Hygiene and Environmental Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, 17475 Greifswald, Germany
| | - S J Pidot
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - N Buetti
- Department of Infectious Diseases, Bern University Hospital, Bern, Switzerland
| | - M Exner
- Institute for Hygiene and Public Health, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
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Guérillot R, Li L, Baines S, Howden B, Schultz MB, Seemann T, Monk I, Pidot SJ, Gao W, Giulieri S, Gonçalves da Silva A, D’Agata A, Tomita T, Peleg AY, Stinear TP, Howden BP. Comprehensive antibiotic-linked mutation assessment by resistance mutation sequencing (RM-seq). Genome Med 2018; 10:63. [PMID: 30165908 PMCID: PMC6117896 DOI: 10.1186/s13073-018-0572-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/24/2018] [Indexed: 12/15/2022] Open
Abstract
Mutation acquisition is a major mechanism of bacterial antibiotic resistance that remains insufficiently characterised. Here we present RM-seq, a new amplicon-based deep sequencing workflow based on a molecular barcoding technique adapted from Low Error Amplicon sequencing (LEA-seq). RM-seq allows detection and functional assessment of mutational resistance at high throughput from mixed bacterial populations. The sensitive detection of very low-frequency resistant sub-populations permits characterisation of antibiotic-linked mutational repertoires in vitro and detection of rare resistant populations during infections. Accurate quantification of resistance mutations enables phenotypic screening of mutations conferring pleiotropic phenotypes such as in vivo persistence, collateral sensitivity or cross-resistance. RM-seq will facilitate comprehensive detection, characterisation and surveillance of resistant bacterial populations ( https://github.com/rguerillot/RM-seq ).
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Affiliation(s)
- Romain Guérillot
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Lucy Li
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Sarah Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Brian Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Mark B. Schultz
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
- Doherty Applied Microbial Genomics, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Torsten Seemann
- Doherty Applied Microbial Genomics, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Victoria Australia
| | - Ian Monk
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Wei Gao
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Stefano Giulieri
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Anders Gonçalves da Silva
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
- Doherty Applied Microbial Genomics, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Anthony D’Agata
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Takehiro Tomita
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Anton Y. Peleg
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria Australia
- Infection and Immunity Theme, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
- Doherty Applied Microbial Genomics, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
- Doherty Applied Microbial Genomics, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
- Infectious Diseases Department, Austin Health, Heidelberg, Victoria Australia
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Herisse M, Porter JL, Guerillot R, Tomita T, Goncalves Da Silva A, Seemann T, Howden BP, Stinear TP, Pidot SJ. The ΦBT1 large serine recombinase catalyzes DNA integration at pseudo- attB sites in the genus Nocardia. PeerJ 2018; 6:e4784. [PMID: 29740520 PMCID: PMC5937489 DOI: 10.7717/peerj.4784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/27/2018] [Indexed: 12/17/2022] Open
Abstract
Plasmid vectors based on bacteriophage integrases are important tools in molecular microbiology for the introduction of foreign DNA, especially into bacterial species where other systems for genetic manipulation are limited. Site specific integrases catalyze recombination between phage and bacterial attachment sites (attP and attB, respectively) and the best studied integrases in the actinomycetes are the serine integrases from the Streptomyces bacteriophages ΦC31 and ΦBT1. As this reaction is unidirectional and highly stable, vectors containing phage integrase systems have been used in a number of genetic engineering applications. Plasmids bearing the ΦBT1 integrase have been used to introduce DNA into Streptomyces and Amycolatopsis strains; however, they have not been widely studied in other actinobacterial genera. Here, we show that vectors based on ΦBT1 integrase can stably integrate into the chromosomes of a range of Nocardia species, and that this integration occurs despite the absence of canonical attB sites in these genomes. Furthermore, we show that a ΦBT1 integrase-based vector can insert at multiple pseudo-attB sites within a single strain and we determine the sequence of a pseudo-attB motif. These data suggest that ΦBT1 integrase-based vectors can be used to readily and semi-randomly introduce foreign DNA into the genomes of a range of Nocardia species. However, the precise site of insertion will likely require empirical determination in each species to avoid unexpected off-target effects.
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Affiliation(s)
- Marion Herisse
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Jessica L Porter
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Romain Guerillot
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Takehiro Tomita
- Microbiological Diagnostic Unit, University of Melbourne, Melbourne, VIC, Australia
| | - Anders Goncalves Da Silva
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, VIC, Australia.,Microbiological Diagnostic Unit, University of Melbourne, Melbourne, VIC, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, VIC, Australia.,Microbiological Diagnostic Unit, University of Melbourne, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, VIC, Australia.,Microbiological Diagnostic Unit, University of Melbourne, Melbourne, VIC, Australia.,Doherty Applied Microbial Genomics, University of Melbourne, Melbourne, VIC, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, VIC, Australia.,Microbiological Diagnostic Unit, University of Melbourne, Melbourne, VIC, Australia.,Doherty Applied Microbial Genomics, University of Melbourne, Melbourne, VIC, Australia
| | - Sacha J Pidot
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, VIC, Australia
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Tobias NJ, Wolff H, Djahanschiri B, Grundmann F, Kronenwerth M, Shi YM, Simonyi S, Grün P, Shapiro-Ilan D, Pidot SJ, Stinear TP, Ebersberger I, Bode HB. Natural product diversity associated with the nematode symbionts Photorhabdus and Xenorhabdus. Nat Microbiol 2017; 2:1676-1685. [PMID: 28993611 DOI: 10.1038/s41564-017-0039-9] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 09/08/2017] [Indexed: 12/25/2022]
Abstract
Xenorhabdus and Photorhabdus species dedicate a large amount of resources to the production of specialized metabolites derived from non-ribosomal peptide synthetase (NRPS) or polyketide synthase (PKS). Both bacteria undergo symbiosis with nematodes, which is followed by an insect pathogenic phase. So far, the molecular basis of this tripartite relationship and the exact roles that individual metabolites and metabolic pathways play have not been well understood. To close this gap, we have significantly expanded the database for comparative genomics studies in these bacteria. Clustering the genes encoded in the individual genomes into hierarchical orthologous groups reveals a high-resolution picture of functional evolution in this clade. It identifies groups of genes-many of which are involved in secondary metabolite production-that may account for the niche specificity of these bacteria. Photorhabdus and Xenorhabdus appear very similar at the DNA sequence level, which indicates their close evolutionary relationship. Yet, high-resolution mass spectrometry analyses reveal a huge chemical diversity in the two taxa. Molecular network reconstruction identified a large number of previously unidentified metabolite classes, including the xefoampeptides and tilivalline. Here, we apply genomic and metabolomic methods in a complementary manner to identify and elucidate additional classes of natural products. We also highlight the ability to rapidly and simultaneously identify potentially interesting bioactive products from NRPSs and PKSs, thereby augmenting the contribution of molecular biology techniques to the acceleration of natural product discovery.
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Affiliation(s)
- Nicholas J Tobias
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Hendrik Wolff
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Bardya Djahanschiri
- Department of Applied Bioinformatics, Institute for Cell Biology and Neuroscience, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Florian Grundmann
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Max Kronenwerth
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Yi-Ming Shi
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Svenja Simonyi
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Peter Grün
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - David Shapiro-Ilan
- USDA-ARS, SEA, SE Fruit and Tree Nut Research Unit, 21 Dunbar Road, Byron, GA, 31008, USA
| | - Sacha J Pidot
- Department of Microbiology and Immunology, University of Melbourne, at the Doherty Institute for Infection and Immunity, Parkville, Victoria, 3010, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, University of Melbourne, at the Doherty Institute for Infection and Immunity, Parkville, Victoria, 3010, Australia
| | - Ingo Ebersberger
- Department of Applied Bioinformatics, Institute for Cell Biology and Neuroscience, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany.,Senckenberg Climate and Research Centre (BIK-F), Frankfurt am Main, 60325, Germany
| | - Helge B Bode
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany. .,Buchmann Institute for Molecular Life Sciences, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany.
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Wallace JR, Mangas KM, Porter JL, Marcsisin R, Pidot SJ, Howden B, Omansen TF, Zeng W, Axford JK, Johnson PDR, Stinear TP. Mycobacterium ulcerans low infectious dose and mechanical transmission support insect bites and puncturing injuries in the spread of Buruli ulcer. PLoS Negl Trop Dis 2017; 11:e0005553. [PMID: 28410412 PMCID: PMC5406025 DOI: 10.1371/journal.pntd.0005553] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 04/26/2017] [Accepted: 04/04/2017] [Indexed: 11/18/2022] Open
Abstract
Addressing the transmission enigma of the neglected disease Buruli ulcer (BU) is a World Health Organization priority. In Australia, we have observed an association between mosquitoes harboring the causative agent, Mycobacterium ulcerans, and BU. Here we tested a contaminated skin model of BU transmission by dipping the tails from healthy mice in cultures of the causative agent, Mycobacterium ulcerans. Tails were exposed to mosquito (Aedes notoscriptus and Aedes aegypti) blood feeding or punctured with sterile needles. Two of 12 of mice with M. ulcerans contaminated tails exposed to feeding A. notoscriptus mosquitoes developed BU. There were no mice exposed to A. aegypti that developed BU. Eighty-eight percent of mice (21/24) subjected to contaminated tail needle puncture developed BU. Mouse tails coated only in bacteria did not develop disease. A median incubation time of 12 weeks, consistent with data from human infections, was noted. We then specifically tested the M. ulcerans infectious dose-50 (ID50) in this contaminated skin surface infection model with needle puncture and observed an ID50 of 2.6 colony-forming units. We have uncovered a biologically plausible mechanical transmission mode of BU via natural or anthropogenic skin punctures.
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Affiliation(s)
- John R. Wallace
- Department of Biology, Millersville University, Millersville, PA, United States of America
| | - Kirstie M. Mangas
- Department of Microbiology and Immunology, at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Jessica L. Porter
- Department of Microbiology and Immunology, at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Renee Marcsisin
- Department of Microbiology and Immunology, at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Brian Howden
- Department of Microbiology and Immunology, at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Till F. Omansen
- Department of Microbiology and Immunology, at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
- Department of Internal Medicine, University of Groningen, Groningen, RB, The Netherlands
| | - Weiguang Zeng
- Department of Microbiology and Immunology, at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Jason K. Axford
- Pest and Environmental Adaptation Research Group, Bio21 Institute and School of BioSciences, University of Melbourne, Parkville, Vic, Australia
| | - Paul D. R. Johnson
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
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Cai X, Shi YM, Pöhlmann N, Revermann O, Bahner I, Pidot SJ, Wesche F, Lackner H, Büchel C, Kaiser M, Richter C, Schwalbe H, Stinear TP, Zeeck A, Bode HB. Structure and Biosynthesis of Isatropolones, Bioactive Amine-Scavenging Fluorescent Natural Products from Streptomyces Gö66. Angew Chem Int Ed Engl 2017; 56:4945-4949. [PMID: 28371116 DOI: 10.1002/anie.201701223] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Indexed: 01/09/2023]
Abstract
The natural products isatropolone A-C (1-3) were reisolated from Streptomyces Gö66, with 1 and 3 showing potent activity against Leishmania donovani. They contain a rare tropolone ring derived from a type II polyketide biosynthesis pathway. Their biosynthesis was elucidated by labeling experiments, analysis of the biosynthesis gene cluster, its partial heterologous expression, and structural characterization of various intermediates. Owing to their 1,5-diketone moiety, they can react with ammonia, amines, lysine, and lysine-containing peptides and proteins, which results in the formation of a covalent bond and subsequent pyridine ring formation. Their fluorescence properties change upon amine binding, enabling the simple visualization of reacted amines including proteins.
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Affiliation(s)
- Xiaofeng Cai
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe-Universität Frankfurt, Max-von-Laue-Strasse 9, 60438, Frankfurt am Main, Germany
| | - Yi-Ming Shi
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe-Universität Frankfurt, Max-von-Laue-Strasse 9, 60438, Frankfurt am Main, Germany
| | - Nicole Pöhlmann
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Germany
| | - Ole Revermann
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Germany
| | - Isabel Bahner
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Germany
| | - Sacha J Pidot
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Australia
| | - Frank Wesche
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe-Universität Frankfurt, Max-von-Laue-Strasse 9, 60438, Frankfurt am Main, Germany
| | - Helmut Lackner
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Germany
| | - Claudia Büchel
- Institute of Molecular Biosciences, Goethe-Universität Frankfurt, Germany
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Parasite Chemotherapy, Basel, Switzerland.,University of Basel, Switzerland
| | - Christian Richter
- Institut für Organische Chemie und Chemische Biologie, Zentrum für Biomolekulare Magnetische Resonanz, Goethe-Universität Frankfurt, Germany
| | - Harald Schwalbe
- Institut für Organische Chemie und Chemische Biologie, Zentrum für Biomolekulare Magnetische Resonanz, Goethe-Universität Frankfurt, Germany
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Australia
| | - Axel Zeeck
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Germany
| | - Helge B Bode
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe-Universität Frankfurt, Max-von-Laue-Strasse 9, 60438, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, Germany
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41
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Cai X, Shi YM, Pöhlmann N, Revermann O, Bahner I, Pidot SJ, Wesche F, Lackner H, Büchel C, Kaiser M, Richter C, Schwalbe H, Stinear TP, Zeeck A, Bode HB. Struktur und Biosynthese der Isatropolone, bioaktiver und Amin-reaktiver fluoreszierender Naturstoffe aus Streptomyces
Gö66. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Xiaofeng Cai
- Merck Stiftungsprofessur für Molekulare Biotechnologie; Fachbereich Biowissenschaften; Goethe-Universität Frankfurt; Max-von-Laue-Straße 9 60438 Frankfurt am Main Deutschland
| | - Yi-Ming Shi
- Merck Stiftungsprofessur für Molekulare Biotechnologie; Fachbereich Biowissenschaften; Goethe-Universität Frankfurt; Max-von-Laue-Straße 9 60438 Frankfurt am Main Deutschland
| | - Nicole Pöhlmann
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Deutschland
| | - Ole Revermann
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Deutschland
| | - Isabel Bahner
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Deutschland
| | - Sacha J. Pidot
- Department of Microbiology and Immunology; The Peter Doherty Institute for Infection and Immunity; The University of Melbourne; Australien
| | - Frank Wesche
- Merck Stiftungsprofessur für Molekulare Biotechnologie; Fachbereich Biowissenschaften; Goethe-Universität Frankfurt; Max-von-Laue-Straße 9 60438 Frankfurt am Main Deutschland
| | - Helmut Lackner
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Deutschland
| | - Claudia Büchel
- Institut für Molekulare Biowissenschaften; Goethe-Universität Frankfurt; Deutschland
| | - Marcel Kaiser
- Schweizerisches Tropen- und Public Health-Institut; Parasite Chemotherapy; Basel Schweiz
- Universität Basel; Schweiz
| | - Christian Richter
- Institut für Organische Chemie und Chemische Biologie; Zentrum für Biomolekulare Magnetische Resonanz; Goethe-Universität Frankfurt; Deutschland
| | - Harald Schwalbe
- Institut für Organische Chemie und Chemische Biologie; Zentrum für Biomolekulare Magnetische Resonanz; Goethe-Universität Frankfurt; Deutschland
| | - Timothy P. Stinear
- Department of Microbiology and Immunology; The Peter Doherty Institute for Infection and Immunity; The University of Melbourne; Australien
| | - Axel Zeeck
- Institut für Organische und Biomolekulare Chemie; Georg-August-Universität Göttingen; Deutschland
| | - Helge B. Bode
- Merck Stiftungsprofessur für Molekulare Biotechnologie; Fachbereich Biowissenschaften; Goethe-Universität Frankfurt; Max-von-Laue-Straße 9 60438 Frankfurt am Main Deutschland
- Buchmann Institute for Molecular Life Sciences (BMLS); Goethe-Universität Frankfurt; Deutschland
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42
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Lee JYH, Monk IR, Pidot SJ, Singh S, Chua KYL, Seemann T, Stinear TP, Howden BP. Functional analysis of the first complete genome sequence of a multidrug resistant sequence type 2 Staphylococcus epidermidis. Microb Genom 2016; 2:e000077. [PMID: 28785416 PMCID: PMC5537629 DOI: 10.1099/mgen.0.000077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/05/2016] [Indexed: 12/31/2022] Open
Abstract
Staphylococcus epidermidis is a significant opportunistic pathogen of humans. The ST2 lineage is frequently multidrug-resistant and accounts for most of the clinical disease worldwide. However, there are no publically available, closed ST2 genomes and pathogenesis studies have not focused on these strains. We report the complete genome and methylome of BPH0662, a multidrug-resistant, hospital-adapted, ST2 S. epidermidis, and describe the correlation between resistome and phenotype, as well as demonstrate its relationship to publically available, international ST2 isolates. Furthermore, we delineate the methylome determined by the two type I restriction modification systems present in BPH0662 through heterologous expression in Escherichia coli, allowing the assignment of each system to its corresponding target recognition motif. As the first, to our knowledge, complete ST2 S. epidermidis genome, BPH0662 provides a valuable reference for future genomic studies of this clinically relevant lineage. Defining the methylome and the construction of these E. coli hosts provides the foundation for the development of molecular tools to bypass restriction modification systems in this lineage that has hitherto proven intractable.
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Affiliation(s)
- Jean Y. H. Lee
- Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
| | - Ian R. Monk
- Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
| | - Sacha J. Pidot
- Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
| | | | - Kyra Y. L. Chua
- Microbiology Department, Austin Health, Melbourne, Australia
| | - Torsten Seemann
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
- Victorian Life Sciences Computation Inititative, University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
| | - Benjamin P. Howden
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
- Infectious Diseases Department, Austin Health, Melbourne, Australia
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Shabuer G, Ishida K, Pidot SJ, Roth M, Dahse HM, Hertweck C. Plant pathogenic anaerobic bacteria use aromatic polyketides to access aerobic territory. Science 2015; 350:670-4. [PMID: 26542569 DOI: 10.1126/science.aac9990] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Around 25% of vegetable food is lost worldwide because of infectious plant diseases, including microbe-induced decay of harvested crops. In wet seasons and under humid storage conditions, potato tubers are readily infected and decomposed by anaerobic bacteria (Clostridium puniceum). We found that these anaerobic plant pathogens harbor a gene locus (type II polyketide synthase) to produce unusual polyketide metabolites (clostrubins) with dual functions. The clostrubins, which act as antibiotics against other microbial plant pathogens, enable the anaerobic bacteria to survive an oxygen-rich plant environment.
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Affiliation(s)
- Gulimila Shabuer
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Sacha J Pidot
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany. Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, VIC 3010, Australia
| | - Martin Roth
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany. Department of Natural Product Chemistry, Friedrich Schiller University, Jena, Germany.
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44
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Letzel AC, Pidot SJ, Hertweck C. Genome mining for ribosomally synthesized and post-translationally modified peptides (RiPPs) in anaerobic bacteria. BMC Genomics 2014; 15:983. [PMID: 25407095 PMCID: PMC4289311 DOI: 10.1186/1471-2164-15-983] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 09/23/2014] [Indexed: 02/04/2023] Open
Abstract
Background Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a diverse group of biologically active bacterial molecules. Due to the conserved genomic arrangement of many of the genes involved in their synthesis, these secondary metabolite biosynthetic pathways can be predicted from genome sequence data. To date, however, despite the myriad of sequenced genomes covering many branches of the bacterial phylogenetic tree, such an analysis for a broader group of bacteria like anaerobes has not been attempted. Results We investigated a collection of 211 complete and published genomes, focusing on anaerobic bacteria, whose potential to encode RiPPs is relatively unknown. We showed that the presence of RiPP-genes is widespread among anaerobic representatives of the phyla Actinobacteria, Proteobacteria and Firmicutes and that, collectively, anaerobes possess the ability to synthesize a broad variety of different RiPP classes. More than 25% of anaerobes are capable of producing RiPPs either alone or in conjunction with other secondary metabolites, such as polyketides or non-ribosomal peptides. Conclusion Amongst the analyzed genomes, several gene clusters encode uncharacterized RiPPs, whilst others show similarity with known RiPPs. These include a number of potential class II lanthipeptides; head-to-tail cyclized peptides and lactococcin 972-like RiPP. This study presents further evidence in support of anaerobic bacteria as an untapped natural products reservoir. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-983) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology HKI, Beutenbergstr, 11a, Jena 07745, Germany.
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45
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Roupie V, Pidot SJ, Einarsdottir T, Van Den Poel C, Jurion F, Stinear TP, Huygen K. Analysis of the vaccine potential of plasmid DNA encoding nine mycolactone polyketide synthase domains in Mycobacterium ulcerans infected mice. PLoS Negl Trop Dis 2014; 8:e2604. [PMID: 24392169 PMCID: PMC3879250 DOI: 10.1371/journal.pntd.0002604] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/07/2013] [Indexed: 11/18/2022] Open
Abstract
There is no effective vaccine against Buruli ulcer. In experimental footpad infection of C57BL/6 mice with M. ulcerans, a prime-boost vaccination protocol using plasmid DNA encoding mycolyltransferase Ag85A of M. ulcerans and a homologous protein boost has shown significant, albeit transient protection, comparable to the one induced by M. bovis BCG. The mycolactone toxin is an obvious candidate for a vaccine, but by virtue of its chemical structure, this toxin is not immunogenic in itself. However, antibodies against some of the polyketide synthase domains involved in mycolactone synthesis, were found in Buruli ulcer patients and healthy controls from the same endemic region, suggesting that these domains are indeed immunogenic. Here we have analyzed the vaccine potential of nine polyketide synthase domains using a DNA prime/protein boost strategy. C57BL/6 mice were vaccinated against the following domains: acyl carrier protein 1, 2, and 3, acyltransferase (acetate) 1 and 2, acyltransferase (propionate), enoylreductase, ketoreductase A, and ketosynthase load module. As positive controls, mice were vaccinated with DNA encoding Ag85A or with M. bovis BCG. Strongest antigen specific antibodies could be detected in response to acyltransferase (propionate) and enoylreductase. Antigen-specific Th1 type cytokine responses (IL-2 or IFN-γ) were induced by vaccination against all antigens, and were strongest against acyltransferase (propionate). Finally, vaccination against acyltransferase (propionate) and enoylreductase conferred some protection against challenge with virulent M. ulcerans 1615. However, protection was weaker than the one conferred by vaccination with Ag85A or M. bovis BCG. Combinations of these polyketide synthase domains with the vaccine targeting Ag85A, of which the latter is involved in the integrity of the cell wall of the pathogen, and/or with live attenuated M. bovis BCG or mycolactone negative M. ulcerans may eventually lead to the development of an efficacious BU vaccine.
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Affiliation(s)
- Virginie Roupie
- Service Immunology, Scientific Institute of Public Health (WIV-ISP Site Ukkel), Brussels, Belgium
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
| | - Tobba Einarsdottir
- Service Immunology, Scientific Institute of Public Health (WIV-ISP Site Ukkel), Brussels, Belgium
| | - Christophe Van Den Poel
- Service Immunology, Scientific Institute of Public Health (WIV-ISP Site Ukkel), Brussels, Belgium
| | - Fabienne Jurion
- Service Immunology, Scientific Institute of Public Health (WIV-ISP Site Ukkel), Brussels, Belgium
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
| | - Kris Huygen
- Service Immunology, Scientific Institute of Public Health (WIV-ISP Site Ukkel), Brussels, Belgium
- * E-mail:
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Porter JL, Tobias NJ, Pidot SJ, Falgner S, Tuck KL, Vettiger A, Hong H, Leadlay PF, Stinear TP. The cell wall-associated mycolactone polyketide synthases are necessary but not sufficient for mycolactone biosynthesis. PLoS One 2013; 8:e70520. [PMID: 23894666 PMCID: PMC3720922 DOI: 10.1371/journal.pone.0070520] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 06/26/2013] [Indexed: 11/23/2022] Open
Abstract
Mycolactones are polyketide-derived lipid virulence factors made by the slow-growing human pathogen, Mycobacterium ulcerans. Three unusually large and homologous plasmid-borne genes (mlsA1: 51 kb, mlsB: 42 kb and mlsA2: 7 kb) encode the mycolactone type I polyketide synthases (PKS). The extreme size and low sequence diversity of these genes has posed significant barriers for exploration of the genetic and biochemical basis of mycolactone synthesis. Here, we have developed a truncated, more tractable 3-module version of the 18-module mycolactone PKS and we show that this engineered PKS functions as expected in the natural host M. ulcerans to produce an additional polyketide; a triketide lactone (TKL). Cell fractionation experiments indicated that this 3-module PKS and the putative accessory enzymes encoded by mup045 and mup038 associated with the mycobacterial cell wall, a finding supported by confocal microscopy. We then assessed the capacity of the faster growing, Mycobacterium marinum to harbor and express the 3-module Mls PKS and accessory enzymes encoded by mup045 and mup038. RT-PCR, immunoblotting, and cell fractionation experiments confirmed that the truncated Mls PKS multienzymes were expressed and also partitioned with the cell wall material in M. marinum. However, this heterologous host failed to produce TKL. The systematic deconstruction of the mycolactone PKS presented here suggests that the Mls multienzymes are necessary but not sufficient for mycolactone synthesis and that synthesis is likely to occur (at least in part) within the mycobacterial cell wall. This research is also the first proof-of-principle demonstration of the potential of this enzyme complex to produce tailored small molecules through genetically engineered rearrangements of the Mls modules.
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Affiliation(s)
- Jessica L. Porter
- Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
| | - Nicholas J. Tobias
- Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
| | - Steffen Falgner
- Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
| | - Kellie L. Tuck
- School of Chemistry, Monash University, Clayton, Victoria, Australia
| | - Andrea Vettiger
- Molecular Immunology Unit, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Hui Hong
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Peter F. Leadlay
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
- * E-mail:
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Abstract
A total of 211 complete and published genomes from anaerobic bacteria are analysed for the presence of secondary metabolite biosynthesis gene clusters, in particular those tentatively coding for polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS). We investigate the distribution of these gene clusters according to bacterial phylogeny and, if known, correlate these to the type of metabolic pathways they encode. The potential of anaerobes as secondary metabolite producers is highlighted.
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Affiliation(s)
- Anne-Catrin Letzel
- Leibniz Institute for Natural Product Research and Infection Biology HKI, Beutenbergstr. 11a, Jena, 07745, Germany
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Pidot SJ, Porter JL, Marsollier L, Chauty A, Migot-Nabias F, Badaut C, Bénard A, Ruf MT, Seemann T, Johnson PDR, Davies JK, Jenkin GA, Pluschke G, Stinear TP. Serological evaluation of Mycobacterium ulcerans antigens identified by comparative genomics. PLoS Negl Trop Dis 2010; 4:e872. [PMID: 21072233 PMCID: PMC2970529 DOI: 10.1371/journal.pntd.0000872] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 10/06/2010] [Indexed: 01/17/2023] Open
Abstract
A specific and sensitive serodiagnostic test for Mycobacterium ulcerans infection would greatly assist the diagnosis of Buruli ulcer and would also facilitate seroepidemiological surveys. By comparative genomics, we identified 45 potential M. ulcerans specific proteins, of which we were able to express and purify 33 in E. coli. Sera from 30 confirmed Buruli ulcer patients, 24 healthy controls from the same endemic region and 30 healthy controls from a non-endemic region in Benin were screened for antibody responses to these specific proteins by ELISA. Serum IgG responses of Buruli ulcer patients were highly variable, however, seven proteins (MUP045, MUP057, MUL_0513, Hsp65, and the polyketide synthase domains ER, AT propionate, and KR A) showed a significant difference between patient and non-endemic control antibody responses. However, when sera from the healthy control subjects living in the same Buruli ulcer endemic area as the patients were examined, none of the proteins were able to discriminate between these two groups. Nevertheless, six of the seven proteins showed an ability to distinguish people living in an endemic area from those in a non-endemic area with an average sensitivity of 69% and specificity of 88%, suggesting exposure to M. ulcerans. Further validation of these six proteins is now underway to assess their suitability for use in Buruli ulcer seroepidemiological studies. Such studies are urgently needed to assist efforts to uncover environmental reservoirs and understand transmission pathways of the M. ulcerans. Buruli ulcer is a slowly progressive but potentially devastating disease of skin and subcutaneous tissue caused by the bacterium Mycobacterium ulcerans. The disease is widespread throughout West and Central Africa, and some countries in the region have established Buruli ulcer control programs. Buruli ulcer is difficult to distinguish from other chronic skin conditions that require different treatments, and there is an urgent need for an accurate point-of-care diagnostic test. In this study, we have used genomic techniques to identify 45 potential M. ulcerans–specific antigens, 33 of which we have been able to produce and purify. We tested these proteins against sera from patients, healthy people living in the same region as the patients and from individuals living in a region with no cases of Buruli ulcer. We found that seven proteins were able to elicit antibody responses that were significantly different between patients and the control subjects from the non-endemic region but not from the healthy individuals in the same Buruli ulcer endemic region. Further analysis showed that six of these M. ulcerans proteins might be useful as markers of exposure to M. ulcerans and could be developed into tools to uncover environmental reservoirs and understand transmission pathways of the bacterium.
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Affiliation(s)
- Sacha J. Pidot
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
| | - Jessica L. Porter
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
| | - Laurent Marsollier
- Groupe d'Étude des Interactions Hôte-Pathogène, Université d'Angers, Angers, France
| | - Annick Chauty
- Centre de Dépistage et de Traitement de l'ulcère de Buruli, Pobè, Benin
| | - Florence Migot-Nabias
- Institut de Recherche pour le Développement UMR216, Mère et enfant face aux infections tropicales, Paris, France
- Faculté de Pharmacie, Université Paris Descartes, Paris, France
| | - Cyril Badaut
- Institut de Recherche pour le Développement UMR216, Mère et enfant face aux infections tropicales, Paris, France
- Faculté de Pharmacie, Université Paris Descartes, Paris, France
| | - Angèle Bénard
- Swiss Tropical Public Health Institute, Basel, Switzerland
| | | | - Torsten Seemann
- Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria, Australia
| | - Paul D. R. Johnson
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - John K. Davies
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Grant A. Jenkin
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
| | - Gerd Pluschke
- Swiss Tropical Public Health Institute, Basel, Switzerland
| | - Timothy P. Stinear
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
- * E-mail:
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Pidot SJ, Porter JL, Tobias NJ, Anderson J, Catmull D, Seemann T, Kidd S, Davies JK, Reynolds E, Dashper S, Stinear TP. Regulation of the 18 kDa heat shock protein in Mycobacterium ulcerans: an alpha-crystallin orthologue that promotes biofilm formation. Mol Microbiol 2010; 78:1216-31. [PMID: 21091506 DOI: 10.1111/j.1365-2958.2010.07401.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Mycobacterium ulcerans is the causative agent of the debilitating skin disease Buruli ulcer, which is most prevalent in Western and Central Africa. M. ulcerans shares >98% DNA sequence identity with Mycobacterium marinum, however, M. marinum produces granulomatous, but not ulcerative, lesions in humans and animals. Here we report the differential expression of a small heat shock protein (Hsp18) between strains of M. ulcerans (Hsp18(+) ) and M. marinum (Hsp18(-) ) and describe the molecular basis for this difference. We show by gene deletion and GFP reporter assays in M. marinum that a divergently transcribed gene called hspR_2, immediately upstream of hsp18, encodes a MerR-like regulatory protein that represses hsp18 transcription while promoting its own expression. Naturally occurring mutations within a 70 bp segment of the 144 bp hspR_2-hsp18 intergenic region among M. ulcerans strains inhibit hspR_2 transcription and explain the Hsp18(+) phenotype. We also propose a biological role for Hsp18, as we show that this protein significantly enhances bacterial attachment or aggregation during biofilm formation. This study has uncovered a new member of the MerR family of transcriptional regulators and suggests that upregulation of hsp18 expression was an important pathoadaptive response in the evolution of M. ulcerans from a M. marinum-like ancestor.
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Affiliation(s)
- Sacha J Pidot
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
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