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Peramuna T, Kim CM, Aguila LKT, Wendt KL, Wood GE, Cichewicz RH. Iron(III) Binding Properties of PF1140, a Fungal N-Hydroxypyridone, and Activity against Mycoplasma genitalium. JOURNAL OF NATURAL PRODUCTS 2024; 87:1746-1753. [PMID: 38958274 DOI: 10.1021/acs.jnatprod.4c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Mycoplasma genitalium is a sexually transmitted bacterium associated with urogenital disease syndromes in the US and worldwide. The global rise in drug resistance in M. genitalium necessitates the development of novel drugs to treat this pathogen. To address this need, we have screened extracts from a library of fungal isolates assembled through the University of Oklahoma Citizen Science Soil Collection Program. Analysis of one of the bioactive extracts using bioassay-guided fractionation led to the purification of the compound PF1140 (1) along with a new and several other known pyridones. The N-hydroxy pyridones are generally regarded as siderophores with high binding affinity for iron(III) under physiological conditions. Results from UV-vis absorption spectroscopy-based titration experiments revealed that 1 complexes with Fe3+. As M. genitalium does not utilize iron, we propose that the PF1140-iron complex induces cytotoxicity by facilitating the cellular uptake of iron, which reacts with endogenous hydrogen peroxide to produce toxic hydroxyl radicals.
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Affiliation(s)
- Thilini Peramuna
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Caroline M Kim
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington 98104, United States
| | - Laarni Kendra T Aguila
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington 98104, United States
| | - Karen L Wendt
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Gwendolyn E Wood
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington 98104, United States
| | - Robert H Cichewicz
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
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2
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Shao J, Zhao Y, Wei W, Vaisman II. AGRAMP: machine learning models for predicting antimicrobial peptides against phytopathogenic bacteria. Front Microbiol 2024; 15:1304044. [PMID: 38516021 PMCID: PMC10955071 DOI: 10.3389/fmicb.2024.1304044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/12/2024] [Indexed: 03/23/2024] Open
Abstract
Introduction Antimicrobial peptides (AMPs) are promising alternatives to traditional antibiotics for combating plant pathogenic bacteria in agriculture and the environment. However, identifying potent AMPs through laborious experimental assays is resource-intensive and time-consuming. To address these limitations, this study presents a bioinformatics approach utilizing machine learning models for predicting and selecting AMPs active against plant pathogenic bacteria. Methods N-gram representations of peptide sequences with 3-letter and 9-letter reduced amino acid alphabets were used to capture the sequence patterns and motifs that contribute to the antimicrobial activity of AMPs. A 5-fold cross-validation technique was used to train the machine learning models and to evaluate their predictive accuracy and robustness. Results The models were applied to predict putative AMPs encoded by intergenic regions and small open reading frames (ORFs) of the citrus genome. Approximately 7% of the 10,000-peptide dataset from the intergenic region and 7% of the 685,924-peptide dataset from the whole genome were predicted as probable AMPs. The prediction accuracy of the reported models range from 0.72 to 0.91. A subset of the predicted AMPs was selected for experimental test against Spiroplasma citri, the causative agent of citrus stubborn disease. The experimental results confirm the antimicrobial activity of the selected AMPs against the target bacterium, demonstrating the predictive capability of the machine learning models. Discussion Hydrophobic amino acid residues and positively charged amino acid residues are among the key features in predicting AMPs by the Random Forest Algorithm. Aggregation propensity appears to be correlated with the effectiveness of the AMPs. The described models would contribute to the development of effective AMP-based strategies for plant disease management in agricultural and environmental settings. To facilitate broader accessibility, our model is publicly available on the AGRAMP (Agricultural Ngrams Antimicrobial Peptides) server.
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Affiliation(s)
- Jonathan Shao
- Statistics and Bioinformatics Group - Northeast Area, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
- School of Systems Biology, George Mason University, Manassas, VA, United States
| | - Yan Zhao
- Molecular Plant Pathology Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Wei Wei
- Molecular Plant Pathology Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Iosif I. Vaisman
- School of Systems Biology, George Mason University, Manassas, VA, United States
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3
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Ramírez AS, Poveda JB, Dijkman R, Poveda C, Suárez-Pérez A, Rosales RS, Feberwee A, Szostak MP, Ressel L, Viver T, Calabuig P, Catania S, Gobbo F, Timofte D, Spergser J. Mycoplasma bradburyae sp. nov. isolated from the trachea of sea birds. Syst Appl Microbiol 2023; 46:126472. [PMID: 37839385 DOI: 10.1016/j.syapm.2023.126472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 10/17/2023]
Abstract
In the search for mollicutes in wild birds, six Mycoplasma strains were isolated from tracheal swabs taken from four different species of seabirds. Four strains originated from three Yellow-legged gulls (Larus michahellis) and a Cory's shearwater (Calonectris borealis) from Spain, one from a South African Kelp gull (Larus dominicanus), and one from an Italian Black-headed gull (Chroicocephalus ridibundus). These Mycoplasma strains presented 99 % 16S rRNA gene sequence similarity values with Mycoplasma (M.) gallisepticum. Phylogenetic analyses of marker genes (16S rRNA gene and rpoB) confirmed the close relationship of the strains to M. gallisepticum and M. tullyi. The seabirds' strains grew well in modified Hayflick medium, and colonies showed typical fried egg morphology. They produced acid from glucose and mannose but did not hydrolyze arginine or urea. Transmission electron microscopy revealed a cell morphology characteristic of mycoplasmas, presenting spherical to flask-shaped cells with an attachment organelle. Gliding motility was also observed. Furthermore, serological tests, MALDI-ToF mass spectrometry and genomic studies demonstrated that the strains were different to any known Mycoplasma species, for which the name Mycoplasma bradburyae sp. nov. is proposed; the type strain is T158T (DSM 110708 = NCTC 14398).
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Affiliation(s)
- Ana S Ramírez
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - José B Poveda
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain.
| | - Remco Dijkman
- GD Animal Health, Arnsbergstraat 7, 7418 EZ, Deventer, the Netherlands
| | - Carlos Poveda
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Alejandro Suárez-Pérez
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Rubén S Rosales
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Anneke Feberwee
- GD Animal Health, Arnsbergstraat 7, 7418 EZ, Deventer, the Netherlands
| | - Michael P Szostak
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Lorenzo Ressel
- University of Liverpool, Institute of Veterinary Science, Leahurst Campus, Neston CH64 7TE, UK
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), 07190, Esporles, Spain
| | - Pascual Calabuig
- Centro de Recuperación de Fauna Silvestre, Cabildo de Gran Canaria, Spain
| | - Salvatore Catania
- Mycoplasma Unit - SCT1-Verona, WOAH Reference Laboratory for Avian Mycoplasmosis, Istituto Zooprofilattico Sperimentale delle Venezie, 37060 Buttapietra (VR), Italy
| | - Federica Gobbo
- Mycoplasma Unit - SCT1-Verona, WOAH Reference Laboratory for Avian Mycoplasmosis, Istituto Zooprofilattico Sperimentale delle Venezie, 37060 Buttapietra (VR), Italy
| | - Dorina Timofte
- University of Liverpool, Institute of Veterinary Science, Leahurst Campus, Neston CH64 7TE, UK
| | - Joachim Spergser
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
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4
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Thorsen J, Li XJ, Peng S, Sunde RB, Shah SA, Bhattacharyya M, Poulsen CS, Poulsen CE, Leal Rodriguez C, Widdowson M, Neumann AU, Trivedi U, Chawes B, Bønnelykke K, Bisgaard H, Sørensen SJ, Stokholm J. The airway microbiota of neonates colonized with asthma-associated pathogenic bacteria. Nat Commun 2023; 14:6668. [PMID: 37863895 PMCID: PMC10589220 DOI: 10.1038/s41467-023-42309-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/06/2023] [Indexed: 10/22/2023] Open
Abstract
Culture techniques have associated colonization with pathogenic bacteria in the airways of neonates with later risk of childhood asthma, whereas more recent studies utilizing sequencing techniques have shown the same phenomenon with specific anaerobic taxa. Here, we analyze nasopharyngeal swabs from 1 month neonates in the COPSAC2000 prospective birth cohort by 16S rRNA gene sequencing of the V3-V4 region in relation to asthma risk throughout childhood. Results are compared with previous culture results from hypopharyngeal aspirates from the same cohort and with hypopharyngeal sequencing data from the later COPSAC2010 cohort. Nasopharyngeal relative abundance values of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis are associated with the same species in the hypopharyngeal cultures. A combined pathogen score of these bacteria's abundance values is associated with persistent wheeze/asthma by age 7. No other taxa are associated. Compared to the hypopharyngeal aspirates from the COPSAC2010 cohort, the anaerobes Veillonella and Prevotella, which have previously been implicated in asthma development, are less commonly detected in the COPSAC2000 nasopharyngeal samples, but correlate with the pathogen score, hinting at latent community structures that bridge current and previous results. These findings have implications for future asthma prevention efforts.
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Affiliation(s)
- Jonathan Thorsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Xuan Ji Li
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Shuang Peng
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Rikke Bjersand Sunde
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Pediatrics, Slagelse Hospital, Slagelse, Denmark
| | - Shiraz A Shah
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Madhumita Bhattacharyya
- Chair of Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany
| | - Casper Sahl Poulsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Christina Egeø Poulsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Cristina Leal Rodriguez
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Michael Widdowson
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Avidan Uriel Neumann
- Chair of Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany
- Institute of Environmental Medicine, Helmholtz Munich, Munich, Germany
| | - Urvish Trivedi
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Bo Chawes
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Søren J Sørensen
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.
| | - Jakob Stokholm
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.
- Department of Pediatrics, Slagelse Hospital, Slagelse, Denmark.
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark.
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5
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Lee JW, Collins JE, Hulverson MA, Aguila LKT, Kim CM, Wendt KL, Chakrabarti D, Ojo KK, Wood GE, Van Voorhis WC, Cichewicz RH. Appraisal of Fungus-Derived Xanthoquinodins as Broad-Spectrum Anti-Infectives Targeting Phylogenetically Diverse Human Pathogens. JOURNAL OF NATURAL PRODUCTS 2023; 86:1596-1605. [PMID: 37276438 PMCID: PMC10797637 DOI: 10.1021/acs.jnatprod.3c00283] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Xanthoquinodins make up a distinctive class of xanthone-anthraquinone heterodimers reported as secondary metabolites from several fungal species. Through a collaborative multi-institutional screening program, a fungal extract prepared from a Trichocladium sp. was identified that exhibited strong inhibitory effects against several human pathogens (Mycoplasma genitalium, Plasmodium falciparum, Cryptosporidium parvum, and Trichomonas vaginalis). This report focuses on one of the unique samples that exhibited a desirable combination of biological effects: namely, it inhibited all four test pathogens and demonstrated low levels of toxicity toward HepG2 (human liver) cells. Fractionation and purification of the bioactive components and their congeners led to the identification of six new compounds [xanthoquinodins NPDG A1-A5 (1-5) and B1 (6)] as well as several previously reported natural products (7-14). The chemical structures of 1-14 were determined based on interpretation of their 1D and 2D NMR, HRESIMS, and electronic circular dichroism (ECD) data. Biological testing of the purified metabolites revealed that they possessed widely varying levels of inhibitory activity against a panel of human pathogens. Xanthoquinodins A1 (7) and A2 (8) exhibited the most promising broad-spectrum inhibitory effects against M. genitalium (EC50 values: 0.13 and 0.12 μM, respectively), C. parvum (EC50 values: 5.2 and 3.5 μM, respectively), T. vaginalis (EC50 values: 3.9 and 6.8 μM, respectively), and P. falciparum (EC50 values: 0.29 and 0.50 μM, respectively) with no cytotoxicity detected at the highest concentration tested (HepG2 EC50 > 25 μM).
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Affiliation(s)
- Jin Woo Lee
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Jennifer E Collins
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Matthew A Hulverson
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 358061, 750 Republican Street, Seattle, Washington 98109, United States
| | - Laarni Kendra T Aguila
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington 98104, United States
| | - Caroline M Kim
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington 98104, United States
| | - Karen L Wendt
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Debopam Chakrabarti
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Kayode K Ojo
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 358061, 750 Republican Street, Seattle, Washington 98109, United States
| | - Gwendolyn E Wood
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington 98104, United States
| | - Wesley C Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 358061, 750 Republican Street, Seattle, Washington 98109, United States
| | - Robert H Cichewicz
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
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Wood GE, Kim CM, Aguila LKT, Cichewicz RH. In Vitro Susceptibility and Resistance of Mycoplasma genitalium to Nitroimidazoles. Antimicrob Agents Chemother 2023; 67:e0000623. [PMID: 37070857 PMCID: PMC10112249 DOI: 10.1128/aac.00006-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023] Open
Abstract
Mycoplasma genitalium is a sexually transmitted reproductive tract pathogen of men and women. M. genitalium infections are increasingly difficult to treat due to poor efficacy of doxycycline and acquired resistance to azithromycin and moxifloxacin. A recent clinical trial suggested that metronidazole may improve cure rates for women with pelvic inflammatory disease and reduced the detection of M. genitalium when included with standard doxycycline plus ceftriaxone treatment. As data regarding susceptibility of mycoplasmas to nitroimidazoles are lacking in the scientific literature, we determined the in vitro susceptibility of 10 M. genitalium strains to metronidazole, secnidazole, and tinidazole. MICs ranged from 1.6 to 12.5 μg/mL for metronidazole, 3.1 to 12.5 μg/mL for secnidazole, and 0.8 to 6.3 μg/mL for tinidazole. None of these agents was synergistic with doxycycline in checkerboard broth microdilution assays. Tinidazole was superior to metronidazole and secnidazole in terms of MIC and time-kill kinetics and was bactericidal (>99.9% killing) at concentrations below reported serum concentrations. Mutations associated with nitroimidazole resistance were identified by whole-genome sequencing of spontaneous resistant mutants, suggesting a mechanism for reductive activation of the nitroimidazole prodrug by a predicted NAD(P)H-dependent flavin mononucleotide (FMN) oxidoreductase. The presence of oxygen did not affect MICs of wild-type M. genitalium, but a nitroimidazole-resistant mutant was defective for growth under anaerobic conditions, suggesting that resistant mutants may have a fitness disadvantage in anaerobic genital sites. Clinical studies are needed to determine if nitroimidazoles, especially tinidazole, are effective for eradicating M. genitalium infections in men and women.
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Affiliation(s)
- Gwendolyn E Wood
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Caroline M Kim
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Laarni Kendra T Aguila
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Robert H Cichewicz
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
- Natural Products Discovery Group, University of Oklahoma, Norman, Oklahoma, USA
- Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, Oklahoma, USA
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7
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Comparison of Five Commercial Molecular Assays for Mycoplasma Testing of Cellular Therapy Products. J Clin Microbiol 2023; 61:e0149822. [PMID: 36688643 PMCID: PMC9945500 DOI: 10.1128/jcm.01498-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Testing of cellular therapy products for Mycoplasma is a regulatory requirement by the United States Food and Drug Administration (FDA) to ensure the sterility and safety of the product prior to release for patient infusion. The risk of Mycoplasma contamination in cell culture is high. Gold standard testing follows USP <63> which requires a 28-day agar and broth cultivation method that is impractical for short shelf-life biologics. Several commercial molecular platforms have been marketed for faster raw material and product release testing; however, little performance data are available in the literature. In this study, we performed a proof-of-principle analysis to evaluate the performance of five commercial molecular assays, including the MycoSEQ Mycoplasma detection kit (Life Technologies), the MycoTOOL Mycoplasma real-time detection kit (Roche), the VenorGEM qOneStep kit (Minerva Biolabs), the ATCC universal Mycoplasma detection kit, and the Biofire Mycoplasma assay (bioMérieux Industry) using 10 cultured Mollicutes spp., with each at four log-fold dilutions (1,000 CFU/mL to 1 CFU/mL) in biological duplicates with three replicates per condition (n = 6) to assess limit of detection (LOD) and repeatability. Additional testing was performed in the presence of tumor infiltrating lymphocytes (TILs). Based on LOD alone, the Biofire Mycoplasma assay was most sensitive followed by the MycoSEQ and MycoTOOL which were comparable. We showed that not all assays were capable of meeting the ≤10 CFU/mL LOD to replace culture-based methods according to European and Japanese pharmacopeia standards. No assay interference was observed when testing in the presence of TILs.
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Aguila LKT, Patton DL, Gornalusse GG, Vojtech LN, Murnane RD, Wood GE. Ascending Reproductive Tract Infection in Pig-Tailed Macaques Inoculated with Mycoplasma genitalium. Infect Immun 2022; 90:e0013122. [PMID: 35583346 PMCID: PMC9202418 DOI: 10.1128/iai.00131-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/02/2022] [Indexed: 11/27/2022] Open
Abstract
Mycoplasma genitalium is a sexually transmitted bacterial pathogen that causes urogenital disease in men and women. M. genitalium infections can persist for months to years and can ascend to the upper reproductive tract in women where it is associated with serious sequelae including pelvic inflammatory disease, tubal factor infertility, and preterm birth. An animal model is needed to understand immune evasion strategies that allow persistence, mechanisms of ascending infection, and factors associated with clearance. In earlier studies, we determined that pig-tailed macaques are susceptible to cervical infection; however, not all primates were successfully infected, persistence varied between animals, and ascension to the upper reproductive tract was not observed after 4 or 8 weeks of follow-up. Building on our previous findings, we refined our inoculation methods to increase infection rates, extended observation to 18 weeks, and comprehensively sampled the upper reproductive tract to detect ascending infection. With these improvements, we established infection in all (3/3) primates inoculated with M. genitalium and demonstrated lower tract persistence for 16 to 18 weeks. Ascension to the upper reproductive tract at endpoint was observed in two out of three primates. All three primates developed serum and local antibodies reacting primarily to the MgpB and MgpC adherence proteins. Elevated genital polymorphonuclear leukocytes (PMNs) and inflammatory cytokines and chemokines, erythema of the ectocervix in one primate, and histologic evidence of vaginitis and endocervicitis in two primates suggest a mild to moderate inflammatory response to infection. This model will be valuable to understand the natural history of M. genitalium infection including mechanisms of persistence, immune evasion, and ascension to the upper reproductive tract.
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Affiliation(s)
- Laarni Kendra T. Aguila
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Dorothy L. Patton
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, USA
| | - German G. Gornalusse
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, USA
| | - Lucia N. Vojtech
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, USA
| | - Robert D. Murnane
- Washington National Primate Research Center, Department of Comparative Medicine, University of Washington, Seattle, Washington, USA
| | - Gwendolyn E. Wood
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
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Sagouti T, Belabess Z, Rhallabi N, Barka EA, Tahiri A, Lahlali R. Citrus Stubborn Disease: Current Insights on an Enigmatic Problem Prevailing in Citrus Orchards. Microorganisms 2022; 10:183. [PMID: 35056632 PMCID: PMC8779666 DOI: 10.3390/microorganisms10010183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/05/2022] [Accepted: 01/12/2022] [Indexed: 12/29/2022] Open
Abstract
Citrus stubborn was initially observed in California in 1915 and was later proven as a graft-transmissible disease in 1942. In the field, diseased citrus trees have compressed and stunted appearances, and yield poor-quality fruits with little market value. The disease is caused by Spiroplasma citri, a phloem-restricted pathogenic mollicute, which belongs to the Spiroplasmataceae family (Mollicutes). S. citri has the largest genome of any Mollicutes investigated, with a genome size of roughly 1780 Kbp. It is a helical, motile mollicute that lacks a cell wall and peptidoglycan. Several quick and sensitive molecular-based and immuno-enzymatic pathogen detection technologies are available. Infected weeds are the primary source of transmission to citrus, with only a minor percentage of transmission from infected citrus to citrus. Several phloem-feeding leafhopper species (Cicadellidae, Hemiptera) support the natural spread of S. citri in a persistent, propagative manner. S. citri-free buds are used in new orchard plantings and bud certification, and indexing initiatives have been launched. Further, a quarantine system for newly introduced types has been implemented to limit citrus stubborn disease (CSD). The present state of knowledge about CSD around the world is summarized in this overview, where recent advances in S. citri detection, characterization, control and eradication were highlighted to prevent or limit disease spread through the adoption of best practices.
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Affiliation(s)
- Tourya Sagouti
- Laboratoire de Virologie, Microbiologie et Qualité/Ecotoxicologie et Biodiversité, Faculté des Sciences et Techniques de Mohammedia, Mohammedia 20650, Morocco; (T.S.); (N.R.)
| | - Zineb Belabess
- Plant Protection Laboratory, Regional Center of Agricultural Research of Oujda, National Institute of Agricultural Research, Avenue Mohamed VI, BP428 Oujda, Oujda 60000, Morocco;
| | - Naima Rhallabi
- Laboratoire de Virologie, Microbiologie et Qualité/Ecotoxicologie et Biodiversité, Faculté des Sciences et Techniques de Mohammedia, Mohammedia 20650, Morocco; (T.S.); (N.R.)
| | - Essaid Ait Barka
- Unité de Recherche Résistance Induite et Bio-Protection des Plantes-EA 4707, Université de Reims Champagne-Ardenne, 51100 Reims, France
| | - Abdessalem Tahiri
- Phytopathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknès, Meknes 50001, Morocco;
| | - Rachid Lahlali
- Phytopathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknès, Meknes 50001, Morocco;
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Feng M, Schaff AC, Balish MF. Mycoplasma pneumoniae biofilms grown in vitro: traits associated with persistence and cytotoxicity. MICROBIOLOGY-SGM 2021; 166:629-640. [PMID: 32421492 DOI: 10.1099/mic.0.000928] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The atypical bacterial pathogen Mycoplasma pneumoniae is a leading etiological agent of community-acquired pneumonia in humans; infections are often recalcitrant, recurrent and resistant to antibiotic treatment. These characteristics suggest a mechanism that facilitates long-term colonization in hosts. In an in vitro setting, M. pneumoniae forms biofilms that are unusual in that motility plays no more than a very limited role in their formation and development. Given the unusual nature of M. pneumoniae biofilms, open questions remain concerning phenotypes associated with persistence, such as what properties might favour the bacteria while minimizing host damage. M. pneumoniae also produces several cytotoxic molecules including community-acquired respiratory distress syndrome (CARDS) toxin, H2S and H2O2, but how it deploys these agents during growth is unknown. Whereas several biochemical techniques for biofilm disruption were ineffective, sonication was required for disruption of M. pneumoniae biofilms to generate individual cells for comparative studies, suggesting unusual physical properties likely related to the atypical cell envelope. Nonetheless, like for other bacteria, biofilms were less susceptible to antibiotic inhibition and complement killing than dispersed cells, with resistance increasing as the biofilms matured. CARDS toxin levels and enzymatic activities associated with H2S and H2O2 production were highest during early biofilm formation and decreased over time, suggesting attenuation of virulence in connection with chronic infection. Collectively, these findings result in a model of how M. pneumoniae biofilms contribute to both the establishment and propagation of M. pneumoniae infections, and how both biofilm towers and individual cells participate in persistence and chronic disease.
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Affiliation(s)
- Monica Feng
- Present address: Department of Medicine, Albert Einstein Medical College, Bronx, NY 10461, USA
| | - Andrew C Schaff
- Present address: Hudson College of Public Health, Department of Biostatistics and Epidemiology, University of Oklahoma Health Schiences Center, Oklahoma City, OK 73104, USA
| | - Mitchell F Balish
- Department of Microbiology, Miami University, 212 Pearson Hall, Oxford, OH 45056, USA
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11
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Microbial Prevalence and Antimicrobial Sensitivity in Equine Endometritis in Field Conditions. Animals (Basel) 2021; 11:ani11051476. [PMID: 34065566 PMCID: PMC8160901 DOI: 10.3390/ani11051476] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 11/17/2022] Open
Abstract
Endometritis is one of the main causes of infertility in mares. In the present study, 363 mares with a history of repetitive infertility, and positive endometrial cytology and/or vaginal discharge were included. An endometrial swab for microbiological purposes plus sensitivity test was obtained from each mare. A positive culture was obtained in 89% of mares. The main isolated genera were Staphylococcus (25.1%), Streptococcus (18.2%), Escherichia (17.3%) and Pseudomonas (12.1%). With regard to species, the most isolated microorganism was Escherichia coli (17.3%), Staphylococcus spp. (15.6%) and Streptococcus spp. (13.5%). Sensitivity tests showed that the most efficient antimicrobial was amikacin (57.3% of cultures), followed by cefoxitin (48.6%) and gentamicin (48.3%). When sensitivity test was analyzed in terms of Gram+ and Gram- bacteria, Gram+ were highly resistant to cephaloridine (77.3% of cultures), apramycin (70.8%) and penicillin (62.3%), whereas Gram- were highly resistant to penicillin (85.8%), followed by cephaloridine (78.9%). In conclusion, the present study shows the most prevalent microorganisms isolated from equine endometritis, which were found to be resistant to β-lactam antimicrobials. Likewise, these results highlight the significance of performing microbiological analyses as well as sensitivity tests prior to applying an antimicrobial therapy.
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12
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Abdul-Wahab OMS, Al-Shyarba MH, Mardassi BBA, Sassi N, Al Fayi MSS, Otifi H, Al Murea AH, Mlik B, Yacoub E. Molecular detection of urogenital mollicutes in patients with invasive malignant prostate tumor. Infect Agent Cancer 2021; 16:6. [PMID: 33472649 PMCID: PMC7816065 DOI: 10.1186/s13027-021-00344-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/08/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The etiology of prostate cancer (PCa) is multiple and complex. Among the causes recently cited are chronic infections engendered by microorganisms that often go unnoticed. A typical illustration of such a case is infection due to mollicutes bacteria. Generally known by their lurking nature, urogenital mollicutes are the most incriminated in PCa. This study was thus carried out in an attempt to establish the presence of these mollicutes by PCR in biopsies of confirmed PCa patients and to evaluate their prevalence. METHODS A total of 105 Formalin-Fixed Paraffin-Embedded prostate tissues collected from 50 patients suffering from PCa and 55 with benign prostate hyperplasia were subjected to PCR amplification targeting species-specific genes of 5 urogenital mollicutes species, Mycoplasma genitalium, M. hominis, M. fermentans, Ureaplasma parvum, and U. urealyticum. PCR products were then sequenced to confirm species identification. Results significance was statistically assessed using Chi-square and Odds ratio tests. RESULTS PCR amplification showed no positive results for M. genitalium, M. hominis, and M. fermentans in all tested patients. Strikingly, Ureaplasma spp. were detected among 30% (15/50) of PCa patients. Nucleotide sequencing further confirmed the identified ureaplasma species, which were distributed as follows: 7 individuals with only U. parvum, 5 with only U. urealyticum, and 3 co-infection cases. Association of the two ureaplasma species with PCa cases proved statistically significant (P < 0.05), and found to represent a risk factor. Of note, Ureaplasma spp. were mostly identified in patients aged 60 and above with prostatic specific antigen (PSA) level > 4 ng/ml and an invasive malignant prostate tumor (Gleason score 8-10). CONCLUSIONS This study uncovered a significant association of Ureaplasma spp. with PCa arguing in favour of their potential involvement in this condition. Yet, this finding, though statistically supported, warrants a thorough investigation at a much larger scale.
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Affiliation(s)
| | - Mishari H Al-Shyarba
- Department of Surgery, College of Medicine, King Khalid University, P.O. Box 641, Abha, 61421, Saudi Arabia
| | - Boutheina Ben Abdelmoumen Mardassi
- Specialized Unit of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - Nessrine Sassi
- Specialized Unit of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - Majed Saad Shaya Al Fayi
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, King Khalid University, P.O. Box 641, Abha, 61421, Saudi Arabia
| | - Hassan Otifi
- Department of Pathology, College of Medicine, King Khalid University, P.O. Box 641, Abha, 61421, Saudi Arabia
| | | | - Béhija Mlik
- Specialized Unit of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - Elhem Yacoub
- Specialized Unit of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia.
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13
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Distinct Mycoplasma pneumoniae Interactions with Sulfated and Sialylated Receptors. Infect Immun 2020; 88:IAI.00392-20. [PMID: 32839185 DOI: 10.1128/iai.00392-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/14/2020] [Indexed: 11/20/2022] Open
Abstract
Mycoplasma pneumoniae is a cell wall-less bacterial pathogen of the conducting airways, causing bronchitis and atypical or "walking" pneumonia in humans. M. pneumoniae recognizes sialylated and sulfated oligosaccharide receptors to colonize the respiratory tract, but the contribution of the latter is particularly unclear. We used chamber slides coated with sulfatide (3-O-sulfogalactosylceramide) to provide a baseline for M. pneumoniae binding and gliding motility. As expected, M. pneumoniae bound to surfaces coated with sulfatide in a manner that was dependent on sulfatide concentration and incubation temperature and inhibited by competing dextran sulfate. However, mycoplasmas bound to sulfatide exhibited no gliding motility, regardless of receptor density. M. pneumoniae also bound lactose 3'-sulfate ligated to an inert polymer scaffold, and binding was inhibited by competing dextran sulfate. The major adhesin protein P1 mediates adherence to terminal sialic acids linked α-2,3, but P1-specific antibodies that blocked M. pneumoniae hemadsorption (HA) and binding to the sialylated glycoprotein laminin by 95% failed to inhibit mycoplasma binding to sulfatide, suggesting that P1 does not mediate binding to sulfated galactose. Consistent with this conclusion, the M. pneumoniae HA-negative mutant II-3 failed to bind to sialylated receptors but adhered to sulfatide in a temperature-dependent manner.
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14
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Huang W, Reyes-Caldas P, Mann M, Seifbarghi S, Kahn A, Almeida RPP, Béven L, Heck M, Hogenhout SA, Coaker G. Bacterial Vector-Borne Plant Diseases: Unanswered Questions and Future Directions. MOLECULAR PLANT 2020; 13:1379-1393. [PMID: 32835885 PMCID: PMC7769051 DOI: 10.1016/j.molp.2020.08.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 06/01/2023]
Abstract
Vector-borne plant diseases have significant ecological and economic impacts, affecting farm profitability and forest composition throughout the world. Bacterial vector-borne pathogens have evolved sophisticated strategies to interact with their hemipteran insect vectors and plant hosts. These pathogens reside in plant vascular tissue, and their study represents an excellent opportunity to uncover novel biological mechanisms regulating intracellular pathogenesis and to contribute to the control of some of the world's most invasive emerging diseases. In this perspective, we highlight recent advances and major unanswered questions in the realm of bacterial vector-borne disease, focusing on liberibacters, phytoplasmas, spiroplasmas, and Xylella fastidiosa.
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Affiliation(s)
- Weijie Huang
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Paola Reyes-Caldas
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Marina Mann
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Shirin Seifbarghi
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Alexandra Kahn
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Laure Béven
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE, Villenave d'Ornon 33882 France
| | - Michelle Heck
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA; Boyce Thompson Institute, Ithaca, NY 14853, USA; Emerging Pests and Pathogens Research Unit, Robert W. Holley Center, USDA ARS, Ithaca, NY 14853, USA
| | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA.
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15
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Beam JP, Becraft ED, Brown JM, Schulz F, Jarett JK, Bezuidt O, Poulton NJ, Clark K, Dunfield PF, Ravin NV, Spear JR, Hedlund BP, Kormas KA, Sievert SM, Elshahed MS, Barton HA, Stott MB, Eisen JA, Moser DP, Onstott TC, Woyke T, Stepanauskas R. Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN. Front Microbiol 2020; 11:1848. [PMID: 33013724 PMCID: PMC7507113 DOI: 10.3389/fmicb.2020.01848] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/15/2020] [Indexed: 12/21/2022] Open
Abstract
Recent discoveries suggest that the candidate superphyla Patescibacteria and DPANN constitute a large fraction of the phylogenetic diversity of Bacteria and Archaea. Their small genomes and limited coding potential have been hypothesized to be ancestral adaptations to obligate symbiotic lifestyles. To test this hypothesis, we performed cell-cell association, genomic, and phylogenetic analyses on 4,829 individual cells of Bacteria and Archaea from 46 globally distributed surface and subsurface field samples. This confirmed the ubiquity and abundance of Patescibacteria and DPANN in subsurface environments, the small size of their genomes and cells, and the divergence of their gene content from other Bacteria and Archaea. Our analyses suggest that most Patescibacteria and DPANN in the studied subsurface environments do not form specific physical associations with other microorganisms. These data also suggest that their unusual genomic features and prevalent auxotrophies may be a result of ancestral, minimal cellular energy transduction mechanisms that lack respiration, thus relying solely on fermentation for energy conservation.
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Affiliation(s)
- Jacob P Beam
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Eric D Becraft
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Jessica K Jarett
- Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Oliver Bezuidt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Nicole J Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Kayla Clark
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - John R Spear
- Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
| | - Brian P Hedlund
- School of Life Sciences - Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Hazel A Barton
- Department of Biology, University of Akron, Akron, OH, United States
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jonathan A Eisen
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, Genome Center, University of California, Davis, Davis, CA, United States
| | - Duane P Moser
- Desert Research Institute, Las Vegas, NV, United States
| | - Tullis C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkeley, CA, United States
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16
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Season of Birth Impacts the Neonatal Nasopharyngeal Microbiota. CHILDREN-BASEL 2020; 7:children7050045. [PMID: 32403236 PMCID: PMC7278723 DOI: 10.3390/children7050045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 05/06/2020] [Indexed: 11/16/2022]
Abstract
Objective: Pathogenic airway bacteria colonizing the neonatal airway increase the risk of childhood asthma, but little is known about the determinants of the establishment and dynamics of the airway microbiota in early life. We studied associations between perinatal risk factors and bacterial richness of the commensal milieu in the neonatal respiratory tract. Methods: Three hundred and twenty-eight children from the Copenhagen Prospective Studies on Asthma in the Childhood2000 (COPSAC2000) at-risk birth cohort were included in this study. The bacterial richness in each of the nasopharynxes of the 1-month old, asymptomatic neonates was analyzed by use of a culture-independent technique (T-RFLP). Information on perinatal risk factors included predisposition to asthma, allergy and eczema; social status of family; maternal exposures during pregnancy; mode of delivery; and postnatal exposures. The risk factor analysis was done by conventional statistics and partial least square discriminant analysis (PLSDA). Results: The nasopharyngeal bacterial community at 1-month displayed an average of 35 (IQR: 14-55, range 1-161) phylogenetically different bacteria groups. Season of birth was associated with nasopharyngeal bacterial richness at 1-month of age with a higher bacterial richness (p = 0.003) and more abundant specific bacterial profiles representing Gram-negative alpha-proteobacteria and Gram-positive Bacilli in the nasopharynx of summer-born children. Conclusion: Early postnatal bacterial colonization of the upper airways is significantly affected by birth season, emphasizing a future focus on the seasonality aspect in modelling the impact of early dynamic changes in airway bacterial communities in relation to later disease development.
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17
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Chen J, Arafat Y, Ud Din I, Yang B, Zhou L, Wang J, Letuma P, Wu H, Qin X, Wu L, Lin S, Zhang Z, Lin W. Nitrogen Fertilizer Amendment Alter the Bacterial Community Structure in the Rhizosphere of Rice ( Oryza sativa L.) and Improve Crop Yield. Front Microbiol 2019; 10:2623. [PMID: 31798559 PMCID: PMC6868037 DOI: 10.3389/fmicb.2019.02623] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 10/28/2019] [Indexed: 01/01/2023] Open
Abstract
Availability of nitrogen (N) in soil changes the composition and activities of microbial community, which is critical for the processing of soil organic matter and health of crop plants. Inappropriate application of N fertilizer can alter the rhizosphere microbial community and disturb the soil N homeostasis. The goal of this study was to assess the effect of different ratio of N fertilizer at various early to late growth stages of rice, while keeping the total N supply constant on rice growth performance, microbial community structure, and soil protein expression in rice rhizosphere. Two different N regimes were applied, i.e., traditional N application (NT) consists of three sessions including 60, 30 and 10% at pre-transplanting, tillering and panicle initiation stages, respectively, while efficient N application (NF) comprises of four sessions, i.e., 30, 30, 30, and 10%), where the fourth session was extended to anthesis stage. Soil metaproteomics combined with Terminal Restriction Fragment Length Polymorphism (T-RFLP) were used to determine the rhizosphere biological process. Under NF application, soil enzymes, nitrogen utilization efficiency and rice yield were significantly higher compared to NT application. T-RFLP and qPCR analysis revealed differences in rice rhizosphere bacterial diversity and structure. NF significantly decreased the specific microbes related to denitrification, but opposite result was observed for bacteria associated with nitrification. Furthermore, soil metaproteomics analysis showed that 88.28% of the soil proteins were derived from microbes, 5.74% from plants, and 6.25% from fauna. Specifically, most of the identified microbial proteins were involved in carbohydrate, amino acid and protein metabolisms. Our experiments revealed that NF positively regulates the functioning of the rhizosphere ecosystem and further enabled us to put new insight into microbial communities and soil protein expression in rice rhizosphere.
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Affiliation(s)
- Jun Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yasir Arafat
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Genetic Breeding and Comprehensive Utilization of the Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Israr Ud Din
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Bo Yang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liuting Zhou
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Juanying Wang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Puleng Letuma
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hongmiao Wu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xianjin Qin
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Linkun Wu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sheng Lin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhixing Zhang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenxiong Lin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
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18
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Labroussaa F, Baby V, Rodrigue S, Lartigue C. [Whole genome transplantation: bringing natural or synthetic bacterial genomes back to life]. Med Sci (Paris) 2019; 35:761-770. [PMID: 31625898 DOI: 10.1051/medsci/2019154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The development of synthetic genomics (SG) allowed the emergence of several groundbreaking techniques including the synthesis, assembly and engineering of whole bacterial genomes. The successful implantation of those methods, which culminated in the creation of JCVI-syn3.0 the first nearly minimal bacterium with a synthetic genome, mainly results from the use of the yeast Saccharomyces cerevisiae as a transient host for bacterial genome replication and modification. Another method played a key role in the resounding success of this project: bacterial genome transplantation (GT). GT consists in the transfer of bacterial genomes cloned in yeast, back into a cellular environment suitable for the expression of their genetic content. While successful using many mycoplasma species, a complete understanding of the factors governing GT will most certainly help unleash the power of the entire SG pipeline to other genetically intractable bacteria.
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Affiliation(s)
- Fabien Labroussaa
- Institute of Veterinary Bacteriology, University of Bern, PO Box, CH-3001 Bern, Suisse
| | - Vincent Baby
- UMR 1332 Biologie du fruit et pathologie, INRA Bordeaux-Aquitaine, 71 avenue E. Bourlaux, 33882 Villenave d'Ornon, France
| | - Sébastien Rodrigue
- Département de biologie, Université de Sherbrooke, 2500 boulevard de l'université, Sherbrooke, Québec, Canada
| | - Carole Lartigue
- UMR 1332 Biologie du fruit et pathologie, INRA Bordeaux-Aquitaine, 71 avenue E. Bourlaux, 33882 Villenave d'Ornon, France
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19
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Schumacher M, Nicholson P, Stoffel MH, Chandran S, D’Mello A, Ma L, Vashee S, Jores J, Labroussaa F. Evidence for the Cytoplasmic Localization of the L-α-Glycerophosphate Oxidase in Members of the " Mycoplasma mycoides Cluster". Front Microbiol 2019; 10:1344. [PMID: 31275271 PMCID: PMC6593217 DOI: 10.3389/fmicb.2019.01344] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/29/2019] [Indexed: 12/15/2022] Open
Abstract
Members of the "Mycoplasma mycoides cluster" are important animal pathogens causing diseases including contagious bovine pleuropneumonia and contagious caprine pleuropneumonia, which are of utmost importance in Africa or Asia. Even if all existing vaccines have shortcomings, vaccination of herds is still considered the best way to fight mycoplasma diseases, especially with the recent and dramatic increase of antimicrobial resistance observed in many mycoplasma species. A new generation of vaccines will benefit from a better understanding of the pathogenesis of mycoplasmas, which is very patchy up to now. In particular, surface-exposed virulence traits are likely to induce a protective immune response when formulated in a vaccine. The candidate virulence factor L-α-glycerophosphate oxidase (GlpO), shared by many mycoplasmas including Mycoplasma pneumoniae, was suggested to be a surface-exposed enzyme in Mycoplasma mycoides subsp. mycoides responsible for the production of hydrogen peroxide directly into the host cells. We produced a glpO isogenic mutant GM12::YCpMmyc1.1-ΔglpO using in-yeast synthetic genomics tools including the tandem-repeat endonuclease cleavage (TREC) technique followed by the back-transplantation of the engineered genome into a mycoplasma recipient cell. GlpO localization in the mutant and its parental strain was assessed using scanning electron microscopy (SEM). We obtained conflicting results and this led us to re-evaluate the localization of GlpO using a combination of in silico and in vitro techniques, such as Triton X-114 fractionation or tryptic shaving followed by immunoblotting. Our in vitro results unambiguously support the finding that GlpO is a cytoplasmic protein throughout the "Mycoplasma mycoides cluster." Thus, the use of GlpO as a candidate vaccine antigen is unlikely to induce a protective immune response.
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Affiliation(s)
- Melanie Schumacher
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Pamela Nicholson
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | | | | | - Adonis D’Mello
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Li Ma
- J. Craig Venter Institute, Rockville, MD, United States
| | - Sanjay Vashee
- J. Craig Venter Institute, Rockville, MD, United States
| | - Joerg Jores
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Fabien Labroussaa
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
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20
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Palomar AM, Premchand-Branker S, Alberdi P, Belova OA, Moniuszko-Malinowska A, Kahl O, Bell-Sakyi L. Isolation of known and potentially pathogenic tick-borne microorganisms from European ixodid ticks using tick cell lines. Ticks Tick Borne Dis 2019; 10:628-638. [PMID: 30819609 PMCID: PMC6446187 DOI: 10.1016/j.ttbdis.2019.02.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/07/2019] [Accepted: 02/18/2019] [Indexed: 12/14/2022]
Abstract
Ticks harbour and, in many cases transmit to their vertebrate hosts, a wide variety of pathogenic, apathogenic and endosymbiotic microorganisms. Recent molecular analyses have greatly increased the range of bacterial species potentially associated with ticks, but in most cases cannot distinguish between surface contaminants, microorganisms present in the remains of the previous blood meal and truly intracellular or tissue-associated bacteria. Here we demonstrate how tick cell lines, primary cell cultures and organ cultures can be used to isolate and propagate bacteria from within embryonic and adult Ixodes ricinus, Dermacentor marginatus and Dermacentor reticulatus ticks originating from different parts of Europe. We isolated and partially characterised four new strains of Spiroplasma from The Netherlands, Spain and Poland, two new strains of Rickettsia raoultii from Russia and Poland, one strain of Rickettsia slovaca from Spain and a species of Mycobacterium from the UK. Comparison with published sequences showed that the Spiroplasma strains were closely related to Spiroplasma ixodetis and the Mycobacterium isolate belonged to the Mycobacterium chelonae complex, while the R. raoultii and R. slovaca strains were similar to previously-validated species.
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Affiliation(s)
- Ana M Palomar
- Centre of Rickettsiosis and Arthropod-Borne Diseases, CIBIR, C/ Piqueras, 98, Logroño 26006, La Rioja, Spain; The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK.
| | - Shonnette Premchand-Branker
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK; Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK.
| | - Pilar Alberdi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
| | - Oxana A Belova
- Chumakov Institute of Poliomyelitis and Viral Encephalitides (Chumakov FSC R&D IBP RAS), prem. 8, k.17, pos. Institut Poliomyelita, poselenie Moskovskiy, Moscow 108819, Russia; Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 20-1 Malaya Pirogovskaya St., Moscow 119435, Russia.
| | - Anna Moniuszko-Malinowska
- Department of Infectious Diseases and Neuroinfections, Medical University in Białystok, Zurawia 14, 15-540 Białystok, Poland.
| | - Olaf Kahl
- Tick-radar GmbH, 10555 Berlin, Germany.
| | - Lesley Bell-Sakyi
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK; The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK; Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool Science Park IC2, 146 Brownlow Hill, Liverpool L3 5RF, UK.
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21
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Thu MJ, Qiu Y, Kataoka-Nakamura C, Sugimoto C, Katakura K, Isoda N, Nakao R. Isolation of Rickettsia, Rickettsiella, and Spiroplasma from Questing Ticks in Japan Using Arthropod Cells. Vector Borne Zoonotic Dis 2019; 19:474-485. [PMID: 30779681 DOI: 10.1089/vbz.2018.2373] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ticks are blood-sucking ectoparasites that transmit zoonotic pathogens to humans and animals. Ticks harbor not only pathogenic microorganisms but also endosymbionts. Although some tick endosymbionts are known to be essential for the survival of ticks, their roles in ticks remain poorly understood. The main aim of this study was to isolate and characterize tick-borne microorganisms from field-collected ticks using two arthropod cell lines derived from Ixodes scapularis embryos (ISE6) and Aedes albopictus larvae (C6/36). A total of 170 tick homogenates originating from 15 different tick species collected in Japan were inoculated into each cell line. Bacterial growth was confirmed by PCR amplification of 16S ribosomal DNA (rDNA) of eubacteria. During the 8-week observation period, bacterial isolation was confirmed in 14 and 4 samples using ISE6 and C6/36 cells, respectively. The sequencing analysis of the 16S rDNA PCR products indicated that they were previously known tick-borne pathogens/endosymbionts in three different genera: Rickettsia, Rickettsiella, and Spiroplasma. These included four previously validated rickettsial species namely Rickettsia asiatica (n = 2), Rickettsia helvetica (n = 3), Rickettsia monacensis (n = 2), and Rickettsia tamurae (n = 3) and one uncharacterized genotype Rickettsia sp. LON (n = 2). Four isolates of Spiroplasma had the highest similarity with previously reported Spiroplasma isolates: Spiroplasma ixodetis obtained from ticks in North America and Spiroplasma sp. Bratislava 1 obtained from Ixodes ricinus in Europe, while two isolates of Rickettsiella showed 100% identity with Rickettsiella sp. detected from Ixodes uriae at Grimsey Island in Iceland. To the best of our knowledge, this is the first report on successful isolation of Rickettsiella from ticks. The isolates obtained in this study can be further analyzed to evaluate their pathogenic potential in animals and their roles as symbionts in ticks.
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Affiliation(s)
- May June Thu
- 1 Laboratory of Parasitology, Faculty of Veterinary Medicine, Graduate School of Infectious Diseases, Hokkaido University, Sapporo, Japan.,2 Unit of Risk Analysis and Management, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Yongjin Qiu
- 3 Hokudai Center for Zoonosis Control in Zambia, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Chikako Kataoka-Nakamura
- 2 Unit of Risk Analysis and Management, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,4 Surveillance Section, Biomedical Science Center, Seto Center, Kanonji Institute, The Research Foundation for Microbial Diseases of Osaka University, Kagawa, Japan
| | - Chihiro Sugimoto
- 5 Division of Collaboration and Education, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,6 Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
| | - Ken Katakura
- 1 Laboratory of Parasitology, Faculty of Veterinary Medicine, Graduate School of Infectious Diseases, Hokkaido University, Sapporo, Japan
| | - Norikazu Isoda
- 2 Unit of Risk Analysis and Management, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,6 Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
| | - Ryo Nakao
- 1 Laboratory of Parasitology, Faculty of Veterinary Medicine, Graduate School of Infectious Diseases, Hokkaido University, Sapporo, Japan
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22
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Boudet JF, Mathelié-Guinlet M, Vilquin A, Douliez JP, Béven L, Kellay H. Large variability in the motility of spiroplasmas in media of different viscosities. Sci Rep 2018; 8:17138. [PMID: 30459324 PMCID: PMC6244147 DOI: 10.1038/s41598-018-35326-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/27/2018] [Indexed: 11/09/2022] Open
Abstract
Spiroplasmas are bacteria that do not possess flagella and their motility is linked to kink propagation coupled to changes in the cell body helicity. While the motility of bacteria with flagellar motion has been studied extensively, less work has been devoted to the motility of spiroplasmas. We first show that the motility of such bacteria has large variability from individual to individual as well as large fluctuations in time. The Brownian motion of such bacteria both in orientation and translation is also highlighted. We propose a simple model to disentangle the different components of this motility by examining trajectories of single bacteria in different viscosity solvents. The mean velocity of the bacteria turns out to depend on the viscosity of the medium as it increases with viscosity. Further, the temporal fluctuations of the bacteria motility turn out to be very strong with a direct link to tumbling events particular to this bacteria.
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Affiliation(s)
- J F Boudet
- U. Bordeaux, Laboratoire Ondes et Matière d'Aquitaine, UMR 5798 CNRS/U. Bordeaux, 33405, Talence, France
| | - M Mathelié-Guinlet
- U. Bordeaux, Laboratoire Ondes et Matière d'Aquitaine, UMR 5798 CNRS/U. Bordeaux, 33405, Talence, France
| | - A Vilquin
- U. Bordeaux, Laboratoire Ondes et Matière d'Aquitaine, UMR 5798 CNRS/U. Bordeaux, 33405, Talence, France
| | - J P Douliez
- UMR 1332, Biologie du Fruit et Pathologie, Univ. Bordeaux, INRA, 33882, Villenave d'Ornon, France
| | - L Béven
- UMR 1332, Biologie du Fruit et Pathologie, Univ. Bordeaux, INRA, 33882, Villenave d'Ornon, France
| | - H Kellay
- U. Bordeaux, Laboratoire Ondes et Matière d'Aquitaine, UMR 5798 CNRS/U. Bordeaux, 33405, Talence, France.
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23
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Williams CR, Chen L, Driver AD, Arnold EA, Sheppard ES, Locklin J, Krause DC. Sialylated Receptor Setting Influences Mycoplasma pneumoniae Attachment and Gliding Motility. Mol Microbiol 2018; 109:735-744. [PMID: 29885004 DOI: 10.1111/mmi.13997] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2018] [Indexed: 01/21/2023]
Abstract
Mycoplasma pneumoniae is a common cause of human respiratory tract infections, including bronchitis and atypical pneumonia. M. pneumoniae binds glycoprotein receptors having terminal sialic acid residues via the P1 adhesin protein. Here, we explored the impact of sialic acid presentation on M. pneumoniae adherence and gliding on surfaces coated with sialylated glycoproteins, or chemically functionalized with α-2,3- and α-2,6-sialyllactose ligated individually or in combination to a polymer scaffold in precisely controlled densities. In both models, gliding required a higher receptor density threshold than adherence, and receptor density influenced gliding frequency but not gliding speed. However, very high densities of α-2,3-sialyllactose actually reduced gliding frequency over peak levels observed at lower densities. Both α-2,3- and α-2,6-sialyllactose supported M. pneumoniae adherence, but gliding was only observed on the former. Finally, gliding on α-2,3-sialyllactose was inhibited on surfaces also conjugated with α-2,6-sialyllactose, suggesting that both moieties bind P1 despite the inability of the latter to support gliding. Our results indicate that the nature and density of host receptor moieties profoundly influences M. pneumoniae gliding, which could affect pathogenesis and infection outcome. Furthermore, precise functionalization of polymer scaffolds shows great promise for further analysis of sialic acid presentation and M. pneumoniae adherence and gliding.
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Affiliation(s)
| | - Li Chen
- Department of Chemistry, College of Engineering, and New Materials Institute, University of Georgia, Athens, Georgia, USA
| | - Ashley D Driver
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Edward A Arnold
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Edward S Sheppard
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Jason Locklin
- Department of Chemistry, College of Engineering, and New Materials Institute, University of Georgia, Athens, Georgia, USA
| | - Duncan C Krause
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
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24
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Variable Membrane Protein A of Flavescence Dorée Phytoplasma Binds the Midgut Perimicrovillar Membrane of Euscelidius variegatus and Promotes Adhesion to Its Epithelial Cells. Appl Environ Microbiol 2018; 84:AEM.02487-17. [PMID: 29439985 DOI: 10.1128/aem.02487-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/30/2018] [Indexed: 01/27/2023] Open
Abstract
Phytoplasmas are uncultivated plant pathogens and cell wall-less bacteria and are transmitted from plant to plant by hemipteran insects. The phytoplasma's circulative propagative cycle in insects requires the crossing of the midgut and salivary glands, and primary adhesion to cells is an initial step toward the invasion process. The flavescence dorée (FD) phytoplasma possesses a set of variable membrane proteins (Vmps) exposed on its surface, and this pathogen is suspected to interact with insect cells. The results showed that VmpA is expressed by the flavescence dorée phytoplasma present in the midgut and salivary glands. Phytoplasmas cannot be cultivated at present, and no mutant can be produced to investigate the putative role of Vmps in the adhesion of phytoplasma to insect cells. To overcome this difficulty, we engineered the Spiroplasma citri mutant G/6, which lacks the ScARP adhesins, for VmpA expression and used VmpA-coated fluorescent beads to determine if VmpA acts as an adhesin in ex vivo adhesion assays and in vivo ingestion assays. VmpA specifically interacted with Euscelidius variegatus insect cells in culture and promoted the retention of VmpA-coated beads to the midgut of E. variegatus In this latest case, VmpA-coated fluorescent beads were localized and embedded in the perimicrovillar membrane of the insect midgut. Thus, VmpA functions as an adhesin that could be essential in the colonization of the insect by the FD phytoplasmas.IMPORTANCE Phytoplasmas infect a wide variety of plants, ranging from wild plants to cultivated species, and are transmitted by different leafhoppers, planthoppers, and psyllids. The specificity of the phytoplasma-insect vector interaction has a major impact on the phytoplasma plant host range. As entry into insect cells is an obligate process for phytoplasma transmission, the bacterial adhesion to insect cells is a key step. Thus, studying surface-exposed proteins of phytoplasma will help to identify the adhesins implicated in the specific recognition of insect vectors. In this study, it is shown that the membrane protein VmpA of the flavescence dorée (FD) phytoplasma acts as an adhesin that is able to interact with cells of Euscelidius variegatus, the experimental vector of the FD phytoplasma.
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25
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In Vitro Culture of the Insect Endosymbiont Spiroplasma poulsonii Highlights Bacterial Genes Involved in Host-Symbiont Interaction. mBio 2018; 9:mBio.00024-18. [PMID: 29559567 PMCID: PMC5874924 DOI: 10.1128/mbio.00024-18] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Endosymbiotic bacteria associated with eukaryotic hosts are omnipresent in nature, particularly in insects. Studying the bacterial side of host-symbiont interactions is, however, often limited by the unculturability and genetic intractability of the symbionts. Spiroplasma poulsonii is a maternally transmitted bacterial endosymbiont that is naturally associated with several Drosophila species. S. poulsonii strongly affects its host’s physiology, for example by causing male killing or by protecting it against various parasites. Despite intense work on this model since the 1950s, attempts to cultivate endosymbiotic Spiroplasma in vitro have failed so far. Here, we developed a method to sustain the in vitro culture of S. poulsonii by optimizing a commercially accessible medium. We also provide a complete genome assembly, including the first sequence of a natural plasmid of an endosymbiotic Spiroplasma species. Last, by comparing the transcriptome of the in vitro culture to the transcriptome of bacteria extracted from the host, we identified genes putatively involved in host-symbiont interactions. This work provides new opportunities to study the physiology of endosymbiotic Spiroplasma and paves the way to dissect insect-endosymbiont interactions with two genetically tractable partners. The discovery of insect bacterial endosymbionts (maternally transmitted bacteria) has revolutionized the study of insects, suggesting novel strategies for their control. Most endosymbionts are strongly dependent on their host to survive, making them uncultivable in artificial systems and genetically intractable. Spiroplasma poulsonii is an endosymbiont of Drosophila that affects host metabolism, reproduction, and defense against parasites. By providing the first reliable culture medium that allows a long-lasting in vitro culture of Spiroplasma and by elucidating its complete genome, this work lays the foundation for the development of genetic engineering tools to dissect endosymbiosis with two partners amenable to molecular study. Furthermore, the optimization method that we describe can be used on other yet uncultivable symbionts, opening new technical opportunities in the field of host-microbes interactions.
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26
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Krause DC, Chen S, Shi J, Jensen AJ, Sheppard ES, Jensen GJ. Electron cryotomography of Mycoplasma pneumoniae mutants correlates terminal organelle architectural features and function. Mol Microbiol 2018; 108:306-318. [PMID: 29470845 DOI: 10.1111/mmi.13937] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2018] [Indexed: 11/28/2022]
Abstract
The Mycoplasma pneumoniae terminal organelle functions in adherence and gliding motility and is comprised of at least eleven substructures. We used electron cryotomography to correlate impaired gliding and adherence function with changes in architecture in diverse terminal organelle mutants. All eleven substructures were accounted for in the prkC, prpC and P200 mutants, and variably so for the HMW3 mutant. Conversely, no terminal organelle substructures were evident in HMW1 and HMW2 mutants. The P41 mutant exhibits a terminal organelle detachment phenotype and lacked the bowl element normally present at the terminal organelle base. Complementation restored this substructure, establishing P41 as either a component of the bowl element or required for its assembly or stability, and that this bowl element is essential to anchor the terminal organelle but not for leverage in gliding. Mutants II-3, III-4 and topJ exhibited a visibly lower density of protein knobs on the terminal organelle surface. Mutants II-3 and III-4 lack accessory proteins required for a functional adhesin complex, while the topJ mutant lacks a DnaJ-like co-chaperone essential for its assembly. Taken together, these observations expand our understanding of the roles of certain terminal organelle proteins in the architecture and function of this complex structure.
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Affiliation(s)
- Duncan C Krause
- Department of Microbiology, University of Georgia, Athens, GA
| | - Songye Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Jian Shi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Ashley J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | | | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA
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27
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Bahar MH, Wist TJ, Bekkaoui DR, Hegedus DD, Olivier CY. Aster leafhopper survival and reproduction, and Aster yellows transmission under static and fluctuating temperatures, using ddPCR for phytoplasma quantification. Sci Rep 2018; 8:227. [PMID: 29321551 PMCID: PMC5762862 DOI: 10.1038/s41598-017-18437-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 12/12/2017] [Indexed: 01/14/2023] Open
Abstract
Aster yellows (AY) is an important disease of Brassica crops and is caused by Candidatus Phytoplasma asteris and transmitted by the insect vector, Aster leafhopper (Macrosteles quadrilineatus). Phytoplasma-infected Aster leafhoppers were incubated at various constant and fluctuating temperatures ranging from 0 to 35 °C with the reproductive host plant barley (Hordium vulgare). At 0 °C, leafhopper adults survived for 18 days, but failed to reproduce, whereas at 35 °C insects died within 18 days, but successfully reproduced before dying. Temperature fluctuation increased thermal tolerance in leafhoppers at 25 °C and increased fecundity of leafhoppers at 5 and 20 °C. Leafhopper adults successfully infected and produced AY-symptoms in canola plants after incubating for 18 days at 0-20 °C on barley, indicating that AY-phytoplasma maintains its virulence in this temperature range. The presence and number of AY-phytoplasma in insects and plants were confirmed by droplet digital PCR (ddPCR) quantification. The number of phytoplasma in leafhoppers increased over time, but did not differ among temperatures. The temperatures associated with a typical crop growing season on the Canadian Prairies will not limit the spread of AY disease by their predominant insect vector. Also, ddPCR quantification is a useful tool for early detection and accurate quantification of phytoplasma in plants and insects.
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Affiliation(s)
- Md H Bahar
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, 440 University Avenue, Charlottetown, PE, C1A 4N6, Canada.
| | - Tyler J Wist
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 7 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada
| | - Diana R Bekkaoui
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 7 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada
| | - Dwayne D Hegedus
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 7 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada
| | - Chrystel Y Olivier
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 7 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada
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28
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Prince OA, Krunkosky TM, Sheppard ES, Krause DC. Modelling persistent Mycoplasma pneumoniae infection of human airway epithelium. Cell Microbiol 2017; 20. [PMID: 29155483 DOI: 10.1111/cmi.12810] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/09/2017] [Accepted: 11/14/2017] [Indexed: 12/31/2022]
Abstract
Mycoplasma pneumoniae is a human respiratory tract pathogen causing acute and chronic airway disease states that can include long-term carriage and extrapulmonary spread. The mechanisms of persistence and migration beyond the conducting airways, however, remain poorly understood. We previously described an acute exposure model using normal human bronchial epithelium (NHBE) in air-liquid interface culture, showing that M. pneumoniae gliding motility is essential for initial colonisation and subsequent spread, including localisation to epithelial cell junctions. We extended those observations here, characterizing M. pneumoniae infection of NHBE for up to 4 weeks. Colonisation of the apical surface was followed by pericellular invasion of the basolateral compartment and migration across the underlying transwell membrane. Despite fluctuations in transepithelial electrical resistance and increased NHBE cell desquamation, barrier function remained largely intact. Desquamation was accompanied by epithelial remodelling that included cytoskeletal reorganisation and development of deep furrows in the epithelium. Finally, M. pneumoniae strains S1 and M129 differed with respect to invasion and histopathology, consistent with contrasting virulence in experimentally infected mice. In summary, this study reports pericellular invasion, NHBE cytoskeletal reorganisation, and tissue remodelling with persistent infection in a human airway epithelium model, providing clear insight into the likely route for extrapulmonary spread.
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Affiliation(s)
- Oliver A Prince
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Thomas M Krunkosky
- Department of Veterinary Biosciences and Diagnostic Imaging, University of Georgia, Athens, GA, USA
| | | | - Duncan C Krause
- Department of Microbiology, University of Georgia, Athens, GA, USA
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29
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Chen L, Leman D, Williams CR, Brooks K, Krause DC, Locklin J. Versatile Methodology for Glycosurfaces: Direct Ligation of Nonderivatized Reducing Saccharides to Poly(pentafluorophenyl acrylate) Grafted Surfaces via Hydrazide Conjugation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:8821-8828. [PMID: 28492327 PMCID: PMC5833976 DOI: 10.1021/acs.langmuir.7b00779] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this work, we report a convenient and versatile strategy for surface-grafted glycopolymer constructs with the goal of surface modification that controls the chemical presentation and grafting density of carbohydrate side chains. This approach employs a difunctional hydrazine linker, chemically modified to an active ester containing poly(pentafluorophenyl acrylate) grafted scaffold, to conjugate a variety of saccharides through the reducing end. The successive conjugation steps are carried out under mild conditions and yield high surface densities of sugars, as high as 4.8 nmol·cm-2, capable of multivalency, with an intact structure and retained bioactivity. We also demonstrate that this glycosylated surface can bind specific lectins according to the structure of its pendant carbohydrate. To demonstrate bioactivity, this surface platform is used to study the binding events of a human respiratory tract pathogen, Mycoplasma pneumoniae, on surfaces conjugated with sialylated sugars.
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Affiliation(s)
- Li Chen
- Department of Chemistry and College of Engineering, University of Georgia, Athens, Georgia 30602, United States
- New Materials Institute, University of Georgia, Athens, Georgia 30602, United States
| | - Deborah Leman
- Department of Chemistry and College of Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Caitlin R. Williams
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, United States
| | - Karson Brooks
- Department of Chemistry and College of Engineering, University of Georgia, Athens, Georgia 30602, United States
- New Materials Institute, University of Georgia, Athens, Georgia 30602, United States
| | - Duncan C. Krause
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, United States
| | - Jason Locklin
- Department of Chemistry and College of Engineering, University of Georgia, Athens, Georgia 30602, United States
- New Materials Institute, University of Georgia, Athens, Georgia 30602, United States
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30
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Dubrana MP, Guéguéniat J, Bertin C, Duret S, Arricau-Bouvery N, Claverol S, Lartigue C, Blanchard A, Renaudin J, Béven L. Proteolytic Post-Translational Processing of Adhesins in a Pathogenic Bacterium. J Mol Biol 2017; 429:1889-1902. [PMID: 28501585 DOI: 10.1016/j.jmb.2017.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 04/25/2017] [Accepted: 05/04/2017] [Indexed: 11/29/2022]
Abstract
Mollicutes, including mycoplasmas and spiroplasmas, have been considered as good representatives of the « minimal cell » concept: these wall-less bacteria are small in size and possess a minimal genome and restricted metabolic capacities. However, the recent discovery of the presence of post-translational modifications unknown so far, such as the targeted processing of membrane proteins of mycoplasma pathogens for human and swine, revealed a part of the hidden complexity of these microorganisms. In this study, we show that in the phytopathogen, insect-vectored Spiroplasma citri GII-3 adhesion-related protein (ScARP) adhesins are post-translationally processed through an ATP-dependent targeted cleavage. The cleavage efficiency could be enhanced in vitro when decreasing the extracellular pH or upon the addition of polyclonal antibodies directed against ScARP repeated units, suggesting that modification of the surface charge and/or ScARP conformational changes could initiate the cleavage. The two major sites for primary cleavage are localized within predicted disordered regions and do not fit any previously reported cleavage motif; in addition, the inhibition profile and the metal ion requirements indicate that this post-translational modification involves at least one non-conventional protease. Such a proteolytic process may play a role in S. citri colonization of cells of the host insect. Furthermore, our work indicates that post-translational cleavage of adhesins represents a common feature to mollicutes colonizing distinct hosts and that processing of surface antigens could represent a way to make the most out of a minimal genome.
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Affiliation(s)
| | - Julia Guéguéniat
- UMR BFP 1332, Univ. Bordeaux, INRA, Villenave d'Ornon, 33882 France
| | - Clothilde Bertin
- UMR BFP 1332, Univ. Bordeaux, INRA, Villenave d'Ornon, 33882 France
| | - Sybille Duret
- UMR BFP 1332, Univ. Bordeaux, INRA, Villenave d'Ornon, 33882 France
| | | | | | - Carole Lartigue
- UMR BFP 1332, Univ. Bordeaux, INRA, Villenave d'Ornon, 33882 France
| | - Alain Blanchard
- UMR BFP 1332, Univ. Bordeaux, INRA, Villenave d'Ornon, 33882 France
| | - Joël Renaudin
- UMR BFP 1332, Univ. Bordeaux, INRA, Villenave d'Ornon, 33882 France
| | - Laure Béven
- UMR BFP 1332, Univ. Bordeaux, INRA, Villenave d'Ornon, 33882 France.
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Taylor-Robinson D. Mollicutes in vaginal microbiology: Mycoplasma hominis, Ureaplasma urealyticum, Ureaplasma parvum and Mycoplasma genitalium. Res Microbiol 2017; 168:875-881. [PMID: 28263902 DOI: 10.1016/j.resmic.2017.02.009] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 02/22/2017] [Accepted: 02/22/2017] [Indexed: 11/19/2022]
Abstract
Mycoplasma hominis was isolated in 1937 from the human genital tract, followed 17 years later by Ureaplasma urealyticum and 27 years after that by Mycoplasma genitalium. The first two proved relatively easy to culture but the latter required a polymerase chain reaction assay for further studies. In sexually mature women, M. hominis may be found in the vagina/cervix of about 20-50%, ureaplasmas in 40-80% and M. genitalium in 0-5%. Some heterogeneity has been found among strains of all these species, sufficient to divide ureaplasmas into two species, namely U. urealyticum and Ureaplasma parvum. Studies in female mice show that sex hormones have a profound influence on colonization, multiplication and persistence of mycoplasmas/ureaplasmas in the genital tract and provoke the question, unanswered, of whether there is such an effect in the human tract. In women, there is no evidence that any of the mycoplasmal species stimulate an inflammatory vaginitis. M. hominis organisms increase hugely in number in the case of bacterial vaginosis (BV), and to a lesser extent so do ureaplasmas. Despite this, they have not been incriminated as a sole cause of BV. Evidence for the involvement of M. genitalium remains controversial. The strong association of BV with preterm birth raises the possibility that the genital mycoplasmas might play a part, but assurance that any do will be difficult to obtain. Detailed examination of the vaginal microbiome has not yet provided an answer.
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Affiliation(s)
- David Taylor-Robinson
- Section of Infectious Diseases, Wright-Fleming Institute, Faculty of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK.
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Experimental Infection of Pig-Tailed Macaques (Macaca nemestrina) with Mycoplasma genitalium. Infect Immun 2017; 85:IAI.00738-16. [PMID: 27872239 DOI: 10.1128/iai.00738-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/07/2016] [Indexed: 11/20/2022] Open
Abstract
Mycoplasma genitalium is an underappreciated cause of human reproductive tract disease, characterized by persistent, often asymptomatic, infection. Building on our previous experiments using a single female pig-tailed macaque as a model for M. genitalium infection (G. E. Wood, S. L. Iverson-Cabral, D. L. Patton, P. K. Cummings, Y. T. Cosgrove Sweeney, and P. A. Totten, Infect Immun 81:2938-2951, 2013, https://doi.org/10.1128/IAI.01322-12), we cervically inoculated eight additional animals, two of which were simultaneously inoculated in salpingeal tissue autotransplanted into abdominal pockets. Viable M. genitalium persisted in the lower genital tract for 8 weeks in three animals, 4 weeks in two, and 1 week in one; two primates resisted infection. In both animals inoculated in salpingeal pockets, viable M. genitalium was recovered for 2 weeks. Recovery of viable M. genitalium from lower genital tract specimens was improved by diluting the specimen in broth and by Vero cell coculture. Ascension to upper reproductive tract tissues was not detected, even among three persistently infected animals. M. genitalium-specific serum antibodies targeting the immunodominant MgpB and MgpC proteins appeared within 1 week in three animals inoculated both cervically and in salpingeal pockets and in one of three persistently infected animals inoculated only in the cervix. M. genitalium-specific IgG, but not IgA, was detected in cervical secretions of serum antibody-positive animals, predominantly against MgpB and MgpC, but was insufficient to clear M. genitalium lower tract infection. Our findings further support female pig-tailed macaques as a model of M. genitalium infection, persistence, and immune evasion.
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Killiny N. Generous hosts: What makes Madagascar periwinkle (Catharanthus roseus) the perfect experimental host plant for fastidious bacteria? PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 109:28-35. [PMID: 27620272 DOI: 10.1016/j.plaphy.2016.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 08/23/2016] [Accepted: 09/01/2016] [Indexed: 05/03/2023]
Abstract
Although much attention has been paid to the metabolism and biosynthesis of monoterpene alkaloids in Catharanthus roseus, its value as an experimental host for a variety of agriculturally and economically important phytopathogenic bacteria warrants further study. In the present study, we evaluated the chemical composition of the phloem and xylem saps of C. roseus to infer the nutritional requirements of phloem- and xylem-limited phytopathogens. Periwinkle phloem sap consisted of a rich mixture of sugars, organic acids, amino acids, amines, fatty acids, sugar acids and sugar alcohols while xylem contained similar compounds in lesser concentrations. Plant sap analysis may lead to a better understanding of the biology of fastidious Mollicutes and their complex nutritional requirements, and to successful culture of phytoplasmas and other uncultured phloem-restricted bacteria such as Candidatus Liberibacter asiaticus, the causal agent of huanglongbing in citrus.
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Affiliation(s)
- Nabil Killiny
- Department of Plant Pathology, Citrus Research and Education Center, University of Florida, 700 Experiment Station Rd., Lake Alfred, FL 33850, USA.
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Labroussaa F, Lebaudy A, Baby V, Gourgues G, Matteau D, Vashee S, Sirand-Pugnet P, Rodrigue S, Lartigue C. Impact of donor-recipient phylogenetic distance on bacterial genome transplantation. Nucleic Acids Res 2016; 44:8501-11. [PMID: 27488189 PMCID: PMC5041484 DOI: 10.1093/nar/gkw688] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/22/2016] [Accepted: 07/25/2016] [Indexed: 12/22/2022] Open
Abstract
Genome transplantation (GT) allows the installation of purified chromosomes into recipient cells, causing the resulting organisms to adopt the genotype and the phenotype conferred by the donor cells. This key process remains a bottleneck in synthetic biology, especially for genome engineering strategies of intractable and economically important microbial species. So far, this process has only been reported using two closely related bacteria, Mycoplasma mycoides subsp. capri (Mmc) and Mycoplasma capricolum subsp. capricolum (Mcap), and the main factors driving the compatibility between a donor genome and a recipient cell are poorly understood. Here, we investigated the impact of the evolutionary distance between donor and recipient species on the efficiency of GT. Using Mcap as the recipient cell, we successfully transplanted the genome of six bacteria belonging to the Spiroplasma phylogenetic group but including species of two distinct genera. Our results demonstrate that GT efficiency is inversely correlated with the phylogenetic distance between donor and recipient bacteria but also suggest that other species-specific barriers to GT exist. This work constitutes an important step toward understanding the cellular factors governing the GT process in order to better define and eventually extend the existing genome compatibility limit.
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Affiliation(s)
- Fabien Labroussaa
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France University of Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Anne Lebaudy
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France University of Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Vincent Baby
- Université de Sherbrooke, Département de biologie, 2500 boulevard Université Sherbrooke (Québec), J1K 2R1, Canada
| | - Géraldine Gourgues
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France University of Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Dominick Matteau
- Université de Sherbrooke, Département de biologie, 2500 boulevard Université Sherbrooke (Québec), J1K 2R1, Canada
| | | | - Pascal Sirand-Pugnet
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France University of Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Sébastien Rodrigue
- Université de Sherbrooke, Département de biologie, 2500 boulevard Université Sherbrooke (Québec), J1K 2R1, Canada
| | - Carole Lartigue
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France University of Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
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35
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Dubrana MP, Béven L, Arricau-Bouvery N, Duret S, Claverol S, Renaudin J, Saillard C. Differential expression of Spiroplasma citri surface protein genes in the plant and insect hosts. BMC Microbiol 2016; 16:53. [PMID: 27005573 PMCID: PMC4804543 DOI: 10.1186/s12866-016-0666-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 03/07/2016] [Indexed: 11/10/2022] Open
Abstract
Background Spiroplasma citri is a cell wall-less, plant pathogenic bacteria that colonizes two distinct hosts, the leafhopper vector and the host plant. Given the absence of a cell wall, surface proteins including lipoproteins and transmembrane polypeptides are expected to play key roles in spiroplasma/host interactions. Important functions in spiroplasma/insect interactions have been shown for a few surface proteins such as the major lipoprotein spiralin, the transmembrane S. citri adhesion-related proteins (ScARPs) and the sugar transporter subunit Sc76. S. citri efficient transmission from the insect to the plant is expected to rely on its ability to adapt to the different environments and more specifically to regulate the expression of genes encoding surface-exposed proteins. Results Genes encoding S. citri lipoproteins and ScARPs were investigated for their expression level in axenic medium, in the leafhopper vector Circulifer haematoceps and in the host plant (periwinkle Catharanthus roseus) either insect-infected or graft-inoculated. The vast majority of the lipoprotein genes tested (25/28) differentially responded to the various host environments. Considering their relative expression levels in the different environments, the possible involvement of the targeted genes in spiroplasma host adaptation was discussed. In addition, two S. citri strains differing notably in their ability to express adhesin ScARP2b and pyruvate dehydrogenase E1 component differed in their capacity to multiply in the two hosts, the plant and the leafhopper vector. Conclusions This study provided us with a list of genes differentially expressed in the different hosts, leading to the identification of factors that are thought to be involved in the process of S. citri host adaptation. The identification of such factors is a key step for further understanding of S. citri pathogenesis. Moreover the present work highlights the high capacity of S. citri in tightly regulating the expression level of a large set of surface protein genes, despite the small size of its genome. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0666-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marie-Pierre Dubrana
- UMR 1332 Biologie du Fruit et Pathologie, INRA, F-33882, Villenave d'Ornon, France.,UMR 1332 Biologie du Fruit et Pathologie, Université de Bordeaux, F-33882, Villenave d'Ornon, France
| | - Laure Béven
- UMR 1332 Biologie du Fruit et Pathologie, INRA, F-33882, Villenave d'Ornon, France. .,UMR 1332 Biologie du Fruit et Pathologie, Université de Bordeaux, F-33882, Villenave d'Ornon, France.
| | - Nathalie Arricau-Bouvery
- UMR 1332 Biologie du Fruit et Pathologie, INRA, F-33882, Villenave d'Ornon, France.,UMR 1332 Biologie du Fruit et Pathologie, Université de Bordeaux, F-33882, Villenave d'Ornon, France
| | - Sybille Duret
- UMR 1332 Biologie du Fruit et Pathologie, INRA, F-33882, Villenave d'Ornon, France.,UMR 1332 Biologie du Fruit et Pathologie, Université de Bordeaux, F-33882, Villenave d'Ornon, France
| | - Stéphane Claverol
- Plateforme Protéome, CGFB, Université de Bordeaux, F-33076, Bordeaux, France
| | - Joël Renaudin
- UMR 1332 Biologie du Fruit et Pathologie, INRA, F-33882, Villenave d'Ornon, France.,UMR 1332 Biologie du Fruit et Pathologie, Université de Bordeaux, F-33882, Villenave d'Ornon, France
| | - Colette Saillard
- UMR 1332 Biologie du Fruit et Pathologie, INRA, F-33882, Villenave d'Ornon, France.,UMR 1332 Biologie du Fruit et Pathologie, Université de Bordeaux, F-33882, Villenave d'Ornon, France
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36
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Mueller NJ, Tini GM, Weber A, Gaspert A, Husmann L, Bloemberg G, Boehler A, Benden C. Hepatitis From Spiroplasma sp. in an Immunocompromised Patient. Am J Transplant 2015; 15:2511-6. [PMID: 25832127 DOI: 10.1111/ajt.13254] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 02/03/2015] [Accepted: 02/04/2015] [Indexed: 01/25/2023]
Abstract
A 70-year-old lung transplant recipient patient was admitted with fever, nausea, abdominal pain, peripheral edema and pronounced weakness. An initial work-up for presumed infection revealed cholestatic hepatitis, leukocytosis and thrombocytopenia, but failed to detect a pathogen. An increased glucose uptake exclusively in the liver was demonstrated by positron emission tomography. Liver biopsy showed basophilic inclusions in the cytoplasm of hepatocytes. Broad- range 16S rRNA gene PCR followed by sequence analysis yielded Spiroplasma sp. in two independent blood samples and the liver biopsy, confirming Spiroplasma sp. as the causative agent. Antibiotic treatment with doxycycline and azithromycin led to complete recovery.
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Affiliation(s)
- N J Mueller
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - G M Tini
- Division of Pulmonary Medicine, University Hospital Zurich, Zurich, Switzerland
| | - A Weber
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - A Gaspert
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - L Husmann
- Institute of Diagnostic and Interventional Radiology, University Hospital Zurich, Zurich, Switzerland
| | - G Bloemberg
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - A Boehler
- Division of Pulmonary Medicine, University Hospital Zurich, Zurich, Switzerland
| | - C Benden
- Division of Pulmonary Medicine, University Hospital Zurich, Zurich, Switzerland
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37
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Bell-Sakyi L, Palomar AM, Kazimirova M. Isolation and propagation of a Spiroplasma sp. from Slovakian Ixodes ricinus ticks in Ixodes spp. cell lines. Ticks Tick Borne Dis 2015; 6:601-6. [PMID: 26003954 PMCID: PMC4518060 DOI: 10.1016/j.ttbdis.2015.05.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/02/2015] [Accepted: 05/03/2015] [Indexed: 11/30/2022]
Abstract
Ixodes spp. ticks are known to occasionally harbour spiroplasmas – helical mycoplasmas in the class Mollicutes; a previous study in Slovakia reported an overall prevalence of Spiroplasma ixodetis of 3% in Ixodes ricinus. In the present study, extracts of unfed adult I. ricinus ticks collected from vegetation in south-western Slovakia were added to a panel of cell lines derived from I. ricinus and Ixodes scapularis embryos. The cultures were monitored by preparation and examination of Giemsa-stained cytocentrifuge smears at intervals over the subsequent 16–18 months. Spiroplasma-like microorganisms were detected in cultures of both tick species after 2–3 months and subcultured onto fresh, uninfected cells of the appropriate cell line up to seven times. Molecular analysis using PCR assays targeting fragments of the 16S rRNA, ITS and rpoB genes confirmed the identity of the microorganisms as a Spiroplasma sp., with between 98.9% and 99.5% similarity to S. ixodetis. The sequences of the spiroplasmas isolated from three different pools of ticks collected on two different occasions were identical for all three genes tested.
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Affiliation(s)
- Lesley Bell-Sakyi
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK.
| | - Ana M Palomar
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK; CIBIR, C/Piqueras, 98, Logroño 26006, La Rioja, Spain
| | - Maria Kazimirova
- Institute of Zoology, Slovak Academy of Sciences, 84506 Bratislava, Slovakia
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38
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Renaudin J, Béven L, Batailler B, Duret S, Desqué D, Arricau-Bouvery N, Malembic-Maher S, Foissac X. Heterologous expression and processing of the flavescence dorée phytoplasma variable membrane protein VmpA in Spiroplasma citri. BMC Microbiol 2015; 15:82. [PMID: 25879952 PMCID: PMC4392738 DOI: 10.1186/s12866-015-0417-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/18/2015] [Indexed: 11/21/2022] Open
Abstract
Background Flavescence dorée (FD) of grapevine is a phloem bacterial disease that threatens European vineyards. The disease is associated with a non-cultivable mollicute, a phytoplasma that is transmitted by the grapevine leafhopper Scaphoideus titanus in a persistent, propagative manner. The specificity of insect transmission is presumably mediated through interactions between the host tissues and phytoplasma surface proteins comprising the so-called variable membrane proteins (Vmps). Plant spiroplasmas and phytoplasmas share the same ecological niches, the phloem sieve elements of host plants and the hemocoel of insect vectors. Unlike phytoplasmas, however, spiroplasmas, and Spiroplasma citri in particular, can be grown in cell-free media and genetically engineered. As a new approach for studying phytoplasmas-insect cell interactions, we sought to mimic phytoplasmas through the construction of recombinant spiroplasmas exhibiting FD phytoplasma Vmps at the cell surface. Results Here, we report the expression of the FD phytoplasma VmpA in S. citri. Transformation of S. citri with plasmid vectors in which the vmpA coding sequence was under the control of the S. citri tuf gene promoter resulted in higher accumulation of VmpA than with the native promoter. Expression of VmpA at the spiroplasma surface was achieved by fusing the vmpA coding sequence to the signal peptide sequence of the S. citri adhesin ScARP3d, as revealed by direct colony immunoblotting and immunogold labelling electron microscopy. Anchoring of VmpA to the spiroplasma membrane was further demonstrated by Triton X-114 protein partitioning and Western immunoblotting. Using the same strategy, the secretion of free, functionally active β-lactamase (used as a model protein) into the culture medium by recombinant spiroplasmas was achieved. Conclusions Construction of recombinant spiroplasmas harbouring the FD phytoplasma variable membrane protein VmpA at their surface was achieved, which provides a new biological approach for studying interactions of phytoplasma surface proteins with host cells. Likewise, the secretion of functional β-lactamase by recombinant spiroplasmas established the considerable promise of the S. citri expression system for delivering phytoplasma effector proteins into host cells. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0417-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joël Renaudin
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, France. .,Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, France.
| | - Laure Béven
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, France. .,Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, France.
| | - Brigitte Batailler
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, France. .,Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, France. .,Université de Bordeaux, UMS3420, Bordeaux Imaging Center, Bordeaux, France. .,CNRS, Bordeaux Imaging Center, UMS 3420, Bordeaux, France. .,INSERM, Bordeaux Imaging Center, US 004, Bordeaux, France.
| | - Sybille Duret
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, France. .,Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, France.
| | - Delphine Desqué
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, France. .,Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, France.
| | - Nathalie Arricau-Bouvery
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, France. .,Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, France.
| | - Sylvie Malembic-Maher
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, France. .,Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, France.
| | - Xavier Foissac
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, France. .,Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, France.
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Suzuki Y, Assad-Garcia N, Kostylev M, Noskov VN, Wise KS, Karas BJ, Stam J, Montague MG, Hanly TJ, Enriquez NJ, Ramon A, Goldgof GM, Richter RA, Vashee S, Chuang RY, Winzeler EA, Hutchison CA, Gibson DG, Smith HO, Glass JI, Venter JC. Bacterial genome reduction using the progressive clustering of deletions via yeast sexual cycling. Genome Res 2015; 25:435-44. [PMID: 25654978 PMCID: PMC4352883 DOI: 10.1101/gr.182477.114] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The availability of genetically tractable organisms with simple genomes is critical for the rapid, systems-level understanding of basic biological processes. Mycoplasma bacteria, with the smallest known genomes among free-living cellular organisms, are ideal models for this purpose, but the natural versions of these cells have genome complexities still too great to offer a comprehensive view of a fundamental life form. Here we describe an efficient method for reducing genomes from these organisms by identifying individually deletable regions using transposon mutagenesis and progressively clustering deleted genomic segments using meiotic recombination between the bacterial genomes harbored in yeast. Mycoplasmal genomes subjected to this process and transplanted into recipient cells yielded two mycoplasma strains. The first simultaneously lacked eight singly deletable regions of the genome, representing a total of 91 genes and ∼10% of the original genome. The second strain lacked seven of the eight regions, representing 84 genes. Growth assay data revealed an absence of genetic interactions among the 91 genes under tested conditions. Despite predicted effects of the deletions on sugar metabolism and the proteome, growth rates were unaffected by the gene deletions in the seven-deletion strain. These results support the feasibility of using single-gene disruption data to design and construct viable genomes lacking multiple genes, paving the way toward genome minimization. The progressive clustering method is expected to be effective for the reorganization of any mega-sized DNA molecules cloned in yeast, facilitating the construction of designer genomes in microbes as well as genomic fragments for genetic engineering of higher eukaryotes.
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Affiliation(s)
- Yo Suzuki
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA;
| | - Nacyra Assad-Garcia
- Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - Maxim Kostylev
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Vladimir N Noskov
- Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - Kim S Wise
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA; Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri 65212, USA
| | - Bogumil J Karas
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Jason Stam
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Michael G Montague
- Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - Timothy J Hanly
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Nico J Enriquez
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Adi Ramon
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Gregory M Goldgof
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA; University of California, San Diego, School of Medicine, La Jolla, California 92093, USA
| | - R Alexander Richter
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Sanjay Vashee
- Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - Ray-Yuan Chuang
- Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - Elizabeth A Winzeler
- University of California, San Diego, School of Medicine, La Jolla, California 92093, USA
| | - Clyde A Hutchison
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Daniel G Gibson
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Hamilton O Smith
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - John I Glass
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA; Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - J Craig Venter
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA; Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
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40
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Scientific Opinion on the pest categorisation of Spiroplasma citri. EFSA J 2014. [DOI: 10.2903/j.efsa.2015.3925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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41
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Frølund M, Björnelius E, Lidbrink P, Ahrens P, Jensen JS. Comparison between culture and a multiplex quantitative real-time polymerase chain reaction assay detecting Ureaplasma urealyticum and U. parvum. PLoS One 2014; 9:e102743. [PMID: 25047036 PMCID: PMC4105565 DOI: 10.1371/journal.pone.0102743] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/23/2014] [Indexed: 11/23/2022] Open
Abstract
A novel multiplex quantitative real-time polymerase chain reaction (qPCR) for simultaneous detection of U. urealyticum and U. parvum was developed and compared with quantitative culture in Shepard's 10 C medium for ureaplasmas in urethral swabs from 129 men and 66 women, and cervical swabs from 61 women. Using culture as the gold standard, the sensitivity of the qPCR was 96% and 95% for female urethral and cervical swabs, respectively. In male urethral swabs the sensitivity was 89%. The corresponding specificities were 100%, 87% and 99%. The qPCR showed a linear increasing DNA copy number with increasing colour-changing units. Although slightly less sensitive than culture, this multiplex qPCR assay detecting U. urealyticum and U. parvum constitutes a simple and fast alternative to the traditional methods for identification of ureaplasmas and allows simultaneous species differentiation and quantitation in clinical samples. Furthermore, specimens overgrown by other bacteria using the culture method can be evaluated in the qPCR.
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Affiliation(s)
- Maria Frølund
- Department of Microbiology and Infection control, Sexually Transmitted Infections, Research and Development, Statens Serum Institut, Copenhagen, Denmark
| | - Eva Björnelius
- Department of Dermatovenereology, Huddinge University Hospital, Karolinska Institutet, Huddinge, Sweden
| | - Peter Lidbrink
- Department of Dermatovenereology, Huddinge University Hospital, Karolinska Institutet, Huddinge, Sweden
| | - Peter Ahrens
- Department of Microbiology and Infection control, Sexually Transmitted Infections, Research and Development, Statens Serum Institut, Copenhagen, Denmark
| | - Jørgen Skov Jensen
- Department of Microbiology and Infection control, Sexually Transmitted Infections, Research and Development, Statens Serum Institut, Copenhagen, Denmark
- * E-mail:
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Lartigue C, Lebaudy A, Blanchard A, El Yacoubi B, Rose S, Grosjean H, Douthwaite S. The flavoprotein Mcap0476 (RlmFO) catalyzes m5U1939 modification in Mycoplasma capricolum 23S rRNA. Nucleic Acids Res 2014; 42:8073-82. [PMID: 24939895 PMCID: PMC4081110 DOI: 10.1093/nar/gku518] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 05/23/2014] [Accepted: 05/24/2014] [Indexed: 01/26/2023] Open
Abstract
Efficient protein synthesis in all organisms requires the post-transcriptional methylation of specific ribosomal ribonucleic acid (rRNA) and transfer RNA (tRNA) nucleotides. The methylation reactions are almost invariably catalyzed by enzymes that use S-adenosylmethionine (AdoMet) as the methyl group donor. One noteworthy exception is seen in some bacteria, where the conserved tRNA methylation at m5U54 is added by the enzyme TrmFO using flavin adenine dinucleotide together with N5,N10-methylenetetrahydrofolate as the one-carbon donor. The minimalist bacterium Mycoplasma capricolum possesses two homologs of trmFO, but surprisingly lacks the m5U54 tRNA modification. We created single and dual deletions of the trmFO homologs using a novel synthetic biology approach. Subsequent analysis of the M. capricolum RNAs by mass spectrometry shows that the TrmFO homolog encoded by Mcap0476 specifically modifies m5U1939 in 23S rRNA, a conserved methylation catalyzed by AdoMet-dependent enzymes in all other characterized bacteria. The Mcap0476 methyltransferase (renamed RlmFO) represents the first folate-dependent flavoprotein seen to modify ribosomal RNA.
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Affiliation(s)
- Carole Lartigue
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France Université de Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Anne Lebaudy
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France Université de Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Alain Blanchard
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France Université de Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Basma El Yacoubi
- Department of Microbiology and Cell Science, University of Florida, FL 32611, USA
| | - Simon Rose
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Henri Grosjean
- Centre de Génétique Moléculaire, UPR3404, CNRS, Associée à l'Université Paris Sud 11, FRC 3115, F-91190 Gif-sur-Yvette, France
| | - Stephen Douthwaite
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
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Transferring whole genomes from bacteria to yeast spheroplasts using entire bacterial cells to reduce DNA shearing. Nat Protoc 2014; 9:743-50. [PMID: 24603933 DOI: 10.1038/nprot.2014.045] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Direct cell-to-cell transfer of genomes from bacteria to yeast facilitates genome engineering for bacteria that are not amenable to genetic manipulation by allowing instead for the utilization of the powerful yeast genetic tools. Here we describe a protocol for transferring whole genomes from bacterial cells to yeast spheroplasts without any DNA purification process. The method is dependent on the treatment of the bacterial and yeast cellular mixture with PEG, which induces cell fusion, engulfment, aggregation or lysis. Over 80% of the bacterial genomes transferred in this way are complete, on the basis of structural and functional tests. Excluding the time required for preparing starting cultures and for incubating cells to form final colonies, the protocol can be completed in 3 h.
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44
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Vanyushkina AA, Fisunov GY, Gorbachev AY, Kamashev DE, Govorun VM. Metabolomic analysis of three Mollicute species. PLoS One 2014; 9:e89312. [PMID: 24595068 PMCID: PMC3942410 DOI: 10.1371/journal.pone.0089312] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 01/22/2014] [Indexed: 01/19/2023] Open
Abstract
We present a systematic study of three bacterial species that belong to the class Mollicutes, the smallest and simplest bacteria, Spiroplasma melliferum, Mycoplasma gallisepticum, and Acholeplasma laidlawii. To understand the difference in the basic principles of metabolism regulation and adaptation to environmental conditions in the three species, we analyzed the metabolome of these bacteria. Metabolic pathways were reconstructed using the proteogenomic annotation data provided by our lab. The results of metabolome, proteome and genome profiling suggest a fundamental difference in the adaptation of the three closely related Mollicute species to stress conditions. As the transaldolase is not annotated in Mollicutes, we propose variants of the pentose phosphate pathway catalyzed by annotated enzymes for three species. For metabolite detection we employed high performance liquid chromatography coupled with mass spectrometry. We used liquid chromatography method - hydrophilic interaction chromatography with silica column - as it effectively separates highly polar cellular metabolites prior to their detection by mass spectrometer.
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Affiliation(s)
| | - Gleb Y. Fisunov
- Russian Institute of Physico-Chemical Medicine, Moscow, Russian Federation
| | | | - Dmitri E. Kamashev
- Russian Institute of Physico-Chemical Medicine, Moscow, Russian Federation
- Russian Research Center Kurchatov Institute, Moscow, Russian Federation
- * E-mail:
| | - Vadim M. Govorun
- Russian Institute of Physico-Chemical Medicine, Moscow, Russian Federation
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, Russian Federation
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45
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Functional characterization of osmotically inducible protein C (MG_427) from Mycoplasma genitalium. J Bacteriol 2013; 196:1012-9. [PMID: 24363346 DOI: 10.1128/jb.00954-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Mycoplasma genitalium is the smallest self-replicating bacterium and an important human pathogen responsible for a range of urogenital infections and pathologies. Due to its limited genome size, many genes conserved in other bacteria are missing in M. genitalium. Genes encoding catalase and superoxide dismutase are absent, and how this pathogen overcomes oxidative stress remains poorly understood. In this study, we characterized MG_427, a homolog of the conserved osmC, which encodes hydroperoxide peroxidase, shown to protect bacteria against oxidative stress. We found that recombinant MG_427 protein reduced organic and inorganic peroxide substrates. Also, we showed that a deletion mutant of MG_427 was highly sensitive to killing by tert-butyl hydroperoxide and H2O2 compared to the sensitivity of the wild type. Further, the fully complemented mutant strain reversed its oxidative sensitivity. Examination of the expression pattern of MG_427 during osmotic shock, oxidative stress, and other stress conditions revealed its lack of induction, distinguishing MG_427 from other previously characterized osmC genes.
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46
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In vitro spatial and temporal analysis of Mycoplasma pneumoniae colonization of human airway epithelium. Infect Immun 2013; 82:579-86. [PMID: 24478073 DOI: 10.1128/iai.01036-13] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycoplasma pneumoniae is an important cause of respiratory disease, especially in school-age children and young adults. We employed normal human bronchial epithelial (NHBE) cells in air-liquid interface culture to study the interaction of M. pneumoniae with differentiated airway epithelium. These airway cells, when grown in air-liquid interface culture, polarize, form tight junctions, produce mucus, and develop ciliary function. We examined both qualitatively and quantitatively the role of mycoplasma gliding motility in the colonization pattern of developing airway cells, comparing wild-type M. pneumoniae and mutants thereof with moderate to severe defects in gliding motility. Adherence assays with radiolabeled mycoplasmas demonstrated a dramatic reduction in binding for all strains with airway cell polarization, independent of acquisition of mucociliary function. Adherence levels dropped further once NHBE cells achieved terminal differentiation, with mucociliary activity strongly selecting for full gliding competence. Analysis over time by confocal microscopy demonstrated a distinct colonization pattern that appeared to originate primarily with ciliated cells, but lateral spread from the base of the cilia was slower than expected. The data support a model in which the mucociliary apparatus impairs colonization yet cilia provide a conduit for mycoplasma access to the host cell surface and suggest acquisition of a barrier function, perhaps associated with tethered mucin levels, with NHBE cell polarization.
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Krishnakumar R, Prat L, Aerni HR, Ling J, Merryman C, Glass JI, Rinehart J, Söll D. Transfer RNA misidentification scrambles sense codon recoding. Chembiochem 2013; 14:1967-72. [PMID: 24000185 DOI: 10.1002/cbic.201300444] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Indexed: 12/22/2022]
Abstract
Sense codon recoding is the basis for genetic code expansion with more than two different noncanonical amino acids. It requires an unused (or rarely used) codon, and an orthogonal tRNA synthetase:tRNA pair with the complementary anticodon. The Mycoplasma capricolum genome contains just six CGG arginine codons, without a dedicated tRNA(Arg). We wanted to reassign this codon to pyrrolysine by providing M. capricolum with pyrrolysyl-tRNA synthetase, a synthetic tRNA with a CCG anticodon (tRNA(Pyl)(CCG)), and the genes for pyrrolysine biosynthesis. Here we show that tRNA(Pyl)(CCG) is efficiently recognized by the endogenous arginyl-tRNA synthetase, presumably at the anticodon. Mass spectrometry revealed that in the presence of tRNA(Pyl)(CCG), CGG codons are translated as arginine. This result is not unexpected as most tRNA synthetases use the anticodon as a recognition element. The data suggest that tRNA misidentification by endogenous aminoacyl-tRNA synthetases needs to be overcome for sense codon recoding.
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Affiliation(s)
- Radha Krishnakumar
- Synthetic Biology and Bioenergy, J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850 (USA)
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48
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Hamasuna R. Mycoplasma genitaliumin male urethritis: Diagnosis and treatment in Japan. Int J Urol 2013; 20:676-84. [DOI: 10.1111/iju.12152] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 03/05/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Ryoichi Hamasuna
- Department of Urology; University of Occupational and Environmental Health; Kitakyushu; Japan
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49
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Protein kinase/phosphatase function correlates with gliding motility in Mycoplasma pneumoniae. J Bacteriol 2013; 195:1750-7. [PMID: 23396910 DOI: 10.1128/jb.02277-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycoplasma pneumoniae exhibits a novel form of gliding motility that is mediated by the terminal organelle, a differentiated polar structure. Given that genes known to be involved in gliding in other organisms are absent in M. pneumoniae, random transposon mutagenesis was employed to generate mutants with gliding-deficient phenotypes. Transposon insertions in the only annotated Ser/Thr protein kinase gene (prkC; MPN248) and its cognate phosphatase gene (prpC; MPN247) in M. pneumoniae resulted in significant and contrasting effects on gliding frequencies. prkC mutant cells glided at approximately half the frequency of wild-type cells, while prpC mutant cells glided more than twice as frequently as wild-type cells. Phosphoprotein staining confirmed the association between phosphorylation of the cytoskeletal proteins HMW1 and HMW2 and membrane protein P1 and the gliding phenotype. When the prpC mutant was complemented by transposon delivery of a wild-type copy of the prpC allele, gliding frequencies and phosphorylation levels returned to the wild-type standard. Surprisingly, delivery of the recombinant wild-type prkC allele dramatically increased gliding frequency to a level approximately 3-fold greater than that of wild-type in the prkC mutant. Collectively, these data suggest that PrkC and PrpC work in opposition in M. pneumoniae to influence gliding frequency.
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50
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Abstract
Eighty Ixodes ricinus ticks collected in the Rovinka forest in Slovakia were tested by real-time and routine single-step PCR for the presence of different pathogenic and endosymbiotic bacteria. No evidence of Coxiella burnetii, Diplorickettsia massiliensis, or Bartonella spp. was found. However, we identified, as the pathogenic bacteria, Anaplasma phagocytophilum in 8%, Rickettsia helvetica in 11%, Borrelia afzelii in 9%, Bo. garinii in 8%, Bo. burgdorferi sensu stricto in 5%, Bo. valaisiana in 3%, and Bo. miyamotoi in 1% of ticks. Other bacteria with unknown or suspected pathogenicity for humans were also identified: Arsenophonus nasoniae in 25%, Spiroplasma ixodetis in 3%, Candidatus Midichloria mitochondrii in 4%, Wolbachia aff. pipientis in 14%, and Ehrlichia muris in 3% of ticks. A. nasoniae was found almost exclusively in nymphs, and E. muris was only found in adult ticks. In total, 65% of ticks contained at least one species of bacteria, and 16% contained 2 or more species.
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