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Rath P, Hermann A, Schaefer R, Agustoni E, Vonach JM, Siegrist M, Miscenic C, Tschumi A, Roth D, Bieniossek C, Hiller S. High-throughput screening of BAM inhibitors in native membrane environment. Nat Commun 2023; 14:5648. [PMID: 37704632 PMCID: PMC10499997 DOI: 10.1038/s41467-023-41445-w] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 09/02/2023] [Indexed: 09/15/2023] Open
Abstract
The outer membrane insertase of Gram-negative bacteria, BAM, is a key target for urgently needed novel antibiotics. Functional reconstitutions of BAM have so far been limited to synthetic membranes and with low throughput capacity for inhibitor screening. Here, we describe a BAM functional assay in native membrane environment capable of high-throughput screening. This is achieved by employing outer membrane vesicles (OMVs) to present BAM directly in native membranes. Refolding of the model substrate OmpT by BAM was possible from the chaperones SurA and Skp, with the required SurA concentration three times higher than Skp. In the OMVs, the antibiotic darobactin had a tenfold higher potency than in synthetic membranes, highlighting the need for native conditions in antibiotics development. The assay is successfully miniaturized for 1536-well plates and upscaled using large scale fermentation, resulting in high-throughput capacities to screen large commercial compound libraries. Our OMV-based assay thus lays the basis for discovery, hit validation and lead expansion of antibiotics targeting BAM.
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Affiliation(s)
- Parthasarathi Rath
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Adrian Hermann
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Ramona Schaefer
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Elia Agustoni
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Jean-Marie Vonach
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Martin Siegrist
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Christian Miscenic
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Andreas Tschumi
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Doris Roth
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Christoph Bieniossek
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland.
| | - Sebastian Hiller
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland.
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Dal Molin M, Selchow P, Schäfle D, Tschumi A, Ryckmans T, Laage-Witt S, Sander P. Identification of novel scaffolds targeting Mycobacterium tuberculosis. J Mol Med (Berl) 2019; 97:1601-1613. [PMID: 31728550 DOI: 10.1007/s00109-019-01840-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 04/25/2019] [Revised: 09/13/2019] [Accepted: 09/26/2019] [Indexed: 10/25/2022]
Abstract
Drug resistance in Mycobacterium tuberculosis is relentlessly progressing while only a handful of novel drug candidates are developed. Here we describe a GFP-based high-throughput screening of 386,496 diverse compounds to identify putative tuberculosis drug candidates. In an exploratory analysis of the model organism M. bovis BCG and M. smegmatis and the subsequent screening of the main library, we identified 6354 compounds with anti-mycobacterial activity. These hit compounds were predominantly selective for mycobacteria while dozens had activity in the low μM range. We tested toxicity against the human monocyte/macrophage cell line THP-1 and elaborated activity against M. tuberculosis growing in liquid broth, under unique conditions such as non-replicating persistence or inhibition of M. tuberculosis residing in macrophages. Finally, spontaneous compound-resistant M. tuberculosis mutants were selected and subsequently analyzed by whole genome sequencing. In addition to compounds targeting the well-described proteins Pks13 and MmpL3, we identified two novel scaffolds targeting the bifunctional guanosine pentaphosphate synthetase/ polyribonucleotide nucleotidyltransferase GpsI, or interacting with the aminopeptidase PepB, a probable pro-drug activator. KEY MESSAGES: A newly identified scaffold targets the bifunctional enzyme GpsI. The aminopeptidase PepB is interacting with a second novel scaffold. Phenotypic screenings regularly identify novel compounds targeting Pks13 and MmpL3.
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Affiliation(s)
- Michael Dal Molin
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006, Zürich, Switzerland
| | - Petra Selchow
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006, Zürich, Switzerland
| | - Daniel Schäfle
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006, Zürich, Switzerland
| | - Andreas Tschumi
- Roche Pharma Research and Early Development, Infectious Diseases, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070, Basel, Switzerland
| | - Thomas Ryckmans
- Roche Pharma Research and Early Development, Infectious Diseases, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070, Basel, Switzerland
| | - Stephan Laage-Witt
- Roche Pharma Research and Early Development, Infectious Diseases, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070, Basel, Switzerland
| | - Peter Sander
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006, Zürich, Switzerland. .,Nationales Zentrum für Mykobakterien, 8006, Zürich, Switzerland.
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Lepore M, Kalinichenko A, Colone A, Paleja B, Singhal A, Tschumi A, Lee B, Poidinger M, Zolezzi F, Quagliata L, Sander P, Newell E, Bertoletti A, Terracciano L, De Libero G, Mori L. Erratum: Corrigendum: Parallel T-cell cloning and deep sequencing of human MAIT cells reveal stable oligoclonal TCRβ repertoire. Nat Commun 2014. [DOI: 10.1038/ncomms5493] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Brülle JK, Tschumi A, Sander P. Lipoproteins of slow-growing Mycobacteria carry three fatty acids and are N-acylated by apolipoprotein N-acyltransferase BCG_2070c. BMC Microbiol 2013; 13:223. [PMID: 24093492 PMCID: PMC3850990 DOI: 10.1186/1471-2180-13-223] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [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: 07/10/2013] [Accepted: 09/30/2013] [Indexed: 12/20/2022] Open
Abstract
Background Lipoproteins are virulence factors of Mycobacterium tuberculosis. Bacterial lipoproteins are modified by the consecutive action of preprolipoprotein diacylglyceryl transferase (Lgt), prolipoprotein signal peptidase (LspA) and apolipoprotein N- acyltransferase (Lnt) leading to the formation of mature triacylated lipoproteins. Lnt homologues are found in Gram-negative and high GC-rich Gram-positive, but not in low GC-rich Gram-positive bacteria, although N-acylation is observed. In fast-growing Mycobacterium smegmatis, the molecular structure of the lipid modification of lipoproteins was resolved recently as a diacylglyceryl residue carrying ester-bound palmitic acid and ester-bound tuberculostearic acid and an additional amide-bound palmitic acid. Results We exploit the vaccine strain Mycobacterium bovis BCG as model organism to investigate lipoprotein modifications in slow-growing mycobacteria. Using Escherichia coli Lnt as a query in BLASTp search, we identified BCG_2070c and BCG_2279c as putative lnt genes in M. bovis BCG. Lipoproteins LprF, LpqH, LpqL and LppX were expressed in M. bovis BCG and BCG_2070c lnt knock-out mutant and lipid modifications were analyzed at molecular level by matrix-assisted laser desorption ionization time-of-flight/time-of-flight analysis. Lipoprotein N-acylation was observed in wildtype but not in BCG_2070c mutants. Lipoprotein N- acylation with palmitoyl and tuberculostearyl residues was observed. Conclusions Lipoproteins are triacylated in slow-growing mycobacteria. BCG_2070c encodes a functional Lnt in M. bovis BCG. We identified mycobacteria-specific tuberculostearic acid as further substrate for N-acylation in slow-growing mycobacteria.
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Affiliation(s)
- Juliane K Brülle
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 30/32, CH-8006, Zurich, Switzerland.
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Widdick DA, Hicks MG, Thompson BJ, Tschumi A, Chandra G, Sutcliffe IC, Brülle JK, Sander P, Palmer T, Hutchings MI. Dissecting the complete lipoprotein biogenesis pathway in Streptomyces scabies. Mol Microbiol 2011; 80:1395-412. [PMID: 21477129 DOI: 10.1111/j.1365-2958.2011.07656.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Following translocation, bacterial lipoproteins are lipidated by lipoprotein diacylglycerol transferase (Lgt) and cleaved of their signal peptides by lipoprotein signal peptidase (Lsp). In Gram-negative bacteria and mycobacteria, lipoproteins are further lipidated by lipoprotein N-acyl transferase (Lnt), to give triacylated lipoproteins. Streptomyces are unusual amongst Gram-positive bacteria because they export large numbers of lipoproteins via the twin arginine protein transport (Tat) pathway. Furthermore, some Streptomyces species encode two Lgt homologues and all Streptomyces species encode two homologues of Lnt. Here we characterize lipoprotein biogenesis in the plant pathogen Streptomyces scabies and report that lgt and lsp mutants are defective in growth and development while only moderately affected in virulence. Lipoproteins are lost from the membrane in an S. scabies lgt mutant but restored by expression of Streptomyces coelicolor lgt1 or lgt2 confirming that both encode functional Lgt enzymes. Furthermore, lipoproteins are N-acylated in Streptomyces with efficient N-acylation dependent on Lnt1 and Lnt2. However, deletion of lnt1 and lnt2 has no effect on growth, development or virulence. We thus present a detailed study of lipoprotein biogenesis in Streptomyces, the first study of Lnt function in a monoderm bacterium and the first study of bacterial lipoproteins as virulence factors in a plant pathogen.
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Affiliation(s)
- David A Widdick
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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Brülle JK, Grau T, Tschumi A, Auchli Y, Burri R, Polsfuss S, Keller PM, Hunziker P, Sander P. Cloning, expression and characterization of Mycobacterium tuberculosis lipoprotein LprF. Biochem Biophys Res Commun 2009; 391:679-84. [PMID: 19944079 DOI: 10.1016/j.bbrc.2009.11.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Accepted: 11/19/2009] [Indexed: 01/13/2023]
Abstract
Lipoproteins are well known virulence factors of bacterial pathogens in general and of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, in particular. Lipoprotein lipidation between Gram-positive and Gram-negative bacteria differs significantly as these are di- and triacylated, respectively. Little is known about the lipid anchor of mycobacterial lipoproteins. We reported recently that mycobacterial LppX, a lipoprotein involved in synthesis of cell wall components is triacylated, although mycobacteria are classified as GC-rich Gram-positive bacteria. We here exploited the model organism Mycobacterium smegmatis for the expression of Mtb LprF and characterized N-terminal modifications at the molecular level. LprF is a putative lipoprotein of Mtb involved in signaling of potassium-dependent osmotic stress. LprF is extensively modified in a mycobacterium-specific manner by a thioether-linked diacylglyceryl residue with one ester-bound tuberculostearic- and one C16:0 fatty acid and additionally by a third N-linked C16:0 fatty acid, and a hexose.
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Affiliation(s)
- Juliane K Brülle
- Institute of Medical Microbiology, University of Zurich, Gloriastr 30/32, CH-8006 Zurich, Switzerland
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Tschumi A, Nai C, Auchli Y, Hunziker P, Gehrig P, Keller P, Grau T, Sander P. Identification of apolipoprotein N-acyltransferase (Lnt) in mycobacteria. J Biol Chem 2009; 284:27146-56. [PMID: 19661058 DOI: 10.1074/jbc.m109.022715] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lipoproteins of Gram-negative and Gram-positive bacteria carry a thioether-bound diacylglycerol but differ by a fatty acid amide bound to the alpha-amino group of the universally conserved cysteine. In Escherichia coli the N-terminal acylation is catalyzed by the N-acyltransferase Lnt. Using E. coli Lnt as a query in a BLASTp search, we identified putative lnt genes also in Gram-positive mycobacteria. The Mycobacterium tuberculosis lipoprotein LppX, heterologously expressed in Mycobacterium smegmatis, was N-acylated at the N-terminal cysteine, whereas LppX expressed in a M. smegmatis lnt::aph knock-out mutant was accessible for N-terminal sequencing. Western blot analyses of a truncated and tagged form of LppX indicated a smaller size of about 0.3 kDa in the lnt::aph mutant compared with the parental strain. Matrix-assisted laser desorption ionization time-of-flight/time-of-flight analyses of a trypsin digest of LppX proved the presence of the diacylglycerol modification in both strains, the parental strain and lnt::aph mutant. N-Acylation was found exclusively in the M. smegmatis parental strain. Complementation of the lnt::aph mutant with M. tuberculosis ppm1 restored N-acylation. The substrate for N-acylation is a C16 fatty acid, whereas the two fatty acids of the diacylglycerol residue were identified as C16 and C19:0 fatty acid, the latter most likely tuberculostearic acid. We demonstrate that mycobacterial lipoproteins are triacylated. For the first time to our knowledge, we identify Lnt activity in Gram-positive bacteria and assigned the responsible genes. In M. smegmatis and M. tuberculosis the open reading frames are annotated as MSMEG_3860 and M. tuberculosis ppm1, respectively.
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Affiliation(s)
- Andreas Tschumi
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, CH-8006 Zurich, Switzerland
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Abstract
Lipoproteins are a functionally diverse class of secreted bacterial proteins characterized by an N-terminal lipid moiety. The lipid moiety serves to anchor these proteins to the cell surface. Lipoproteins are synthesized as pre-prolipoproteins and mature by post-translational modifications. The post-translational modifications are directed by the lipobox motif located within the signal peptide. Enzymes involved in lipoprotein synthesis are essential in Gram-negative bacteria but not in Gram-positive bacteria. Inactivation of genes involved in lipoprotein synthesis attenuates a variety of Gram-positive pathogens, including Mycobacterium tuberculosis. The attenuated phenotype of these mutants indicates an important role of lipoproteins and lipoprotein synthesis in bacterial virulence. M. tuberculosis, the causative agent of tuberculosis, is one of the most devastating pathogens in the world. This article reviews recent findings on the synthesis, localization and function of lipoproteins in mycobacteria.
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Affiliation(s)
- Mandana Rezwan
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 32, CH-8006 Zürich, Switzerland
| | - Thomas Grau
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 32, CH-8006 Zürich, Switzerland
| | - Andreas Tschumi
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 32, CH-8006 Zürich, Switzerland
| | - Peter Sander
- Nationales Zentrum für Mykobakterien, Gloriastrasse 30, CH-8006 Zürich, Switzerland
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 32, CH-8006 Zürich, Switzerland
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Tschumi A, Zingg T, Güntherodt HJ. Electronic Transport Properties of Glassy and Quasicrystalline Pd60U20Si20*. Z PHYS CHEM 1988. [DOI: 10.1524/zpch.1988.157.part_2.855] [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: 11/24/2022]
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Schneider A, Tschumi A, Egloff B, Ott F, Fanconi A. [Malignant atrophic papulosis (Degos' syndrome) in a suckling infant]. Helv Paediatr Acta 1986; 41:447-54. [PMID: 3818332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The clinical and histological diagnosis of Degos' syndrome could be made in a 8-month-old infant with scarring skin lesions. Some weeks later the baby developed severe intestinal symptoms and died from perforations of multiple necrotic lesions of the small bowel. Autopsy revealed in addition to the skin and gut lesions a haemorrhagic cortical infarction of the brain and fibrotic areas in the myocardium. In all these lesions characteristic stenotic endovascular proliferations were seen. Malignant atrophic papulosis is an extremely rare disease in infancy (our patient is the fifth reported case) with a well defined clinical picture, characteristic histological appearance of obliterating vasculitis, but unknown aetiology.
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Schaad UB, Flüeler U, Schaub H, Suter H, Vischer D, Caflisch U, Tschumi A, Wick H, Vest M, Durrer D. [Disease (Lyme disease) in pediatric patients in Switzerland caused by spirochetes (Borrelia burgdorferi) of Ixodes ricinus]. Schweiz Med Wochenschr 1986; 116:1426-30. [PMID: 3787225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Lyme disease in children is studied in the light of questionnaires sent out twice to departments and divisions of pediatrics in Switzerland. Thirty-six serologically proven cases were collected. The 48 clinical signs attributed to Lyme disease involved the skin in 40%, the nervous system in 40%, and the joints in 20%. They were erythema chronicum migrans (13), lymphocytoma (4), acrodermatitis chronica atrophicans (2), peripheral facial palsy (14), sensomotor radiculoneuritis (2), meningoencephalitis (3) and arthritis (10, 7 of which were monoarthritic). Only half the patients had a history of tick-bite. Antibiotic therapy, usually with penicillin, reduced both the duration of symptoms and frequency of secondary disease. Cardiac involvement and chronic stages with residua were not observed in this series.
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Litschgi M, Tschumi A. [Diagnostic criteria of neonatal acidosis during the first 60 minutes postpartum]. Schweiz Med Wochenschr 1980; 110:85-9. [PMID: 7394505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Normal deliveries (without intra-partum warning signs or symptoms of neonatal asphyxia) were selected to form a normal population of newborns from which normal values were calculated for the pH of umbilical artery and heel prick blood at birth and 15, 30 and 60 minutes after delivery. The following lower limits were found: (formula: see text) These limits were checked for usefulness in a random population. In the light of this information the Swiss Group for Neonatology has redefined the terms "intrapartum warning signs" and "neonatal asphyxia".
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Tschumi A, Colombo JP, Moser H. [Wilson's disease in Switzerland. Clinical, genetic and biochemical studies]. Schweiz Med Wochenschr 1973; 103:140-5 concl. [PMID: 4683728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Tschumi A, Colombo JP, Moser H. [Wilson's disease in Switzerland. Clinical, genetic and biochemical studies]. Schweiz Med Wochenschr 1973; 103:89-95. [PMID: 4683518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Bernhardt JP, Mahaim CH, Tschumi A. [Several cardiac insufficiency: a "relative" contraindication for a periodic hemodialysis]. Schweiz Med Wochenschr 1970; 100:1882-4. [PMID: 5474061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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