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Ifrid E, Ouertatani-Sakouhi H, Jauslin T, Kicka S, Chiriano G, Harrison CF, Hilbi H, Scapozza L, Soldati T, Cosson P. 5-ethyl-2'-deoxyuridine fragilizes Klebsiella pneumoniae outer wall and facilitates intracellular killing by phagocytic cells. PLoS One 2022; 17:e0269093. [PMID: 36315510 PMCID: PMC9621411 DOI: 10.1371/journal.pone.0269093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 05/14/2022] [Indexed: 01/24/2023] Open
Abstract
Klebsiella pneumoniae is the causative agent of a variety of severe infections. Many K. pneumoniae strains are resistant to multiple antibiotics, and this situation creates a need for new antibacterial molecules. K. pneumoniae pathogenicity relies largely on its ability to escape phagocytosis and intracellular killing by phagocytic cells. Interfering with these escape mechanisms may allow to decrease bacterial virulence and to combat infections. In this study, we used Dictyostelium discoideum as a model phagocyte to screen a collection of 1,099 chemical compounds. Phg1A KO D. discoideum cells cannot feed upon K. pneumoniae bacteria, unless bacteria bear mutations decreasing their virulence. We identified 3 non-antibiotic compounds that restored growth of phg1A KO cells on K. pneumoniae, and we characterized the mode of action of one of them, 5-ethyl-2'-deoxyuridine (K2). K2-treated bacteria were more rapidly killed in D. discoideum phagosomes than non-treated bacteria. They were more sensitive to polymyxin and their outer membrane was more accessible to a hydrophobic fluorescent probe. These results suggest that K2 acts by rendering the membrane of K. pneumoniae accessible to antibacterial effectors. K2 was effective on three different K. pneumoniae strains, and acted at concentrations as low as 3 μM. K2 has previously been used to treat viral infections but its precise molecular mechanism of action in K. pneumoniae remains to be determined.
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Affiliation(s)
- Estelle Ifrid
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Centre Médical Universitaire, Geneva, Switzerland
| | - Hajer Ouertatani-Sakouhi
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Centre Médical Universitaire, Geneva, Switzerland
| | - Tania Jauslin
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Centre Médical Universitaire, Geneva, Switzerland
| | - Sebastien Kicka
- Department of Biochemistry, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Gianpaolo Chiriano
- Pharmaceutical Biochemistry, School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Christopher F. Harrison
- Max von Pettenkofer Institute, Department of Medicine, Ludwig-Maximilians University Munich, Munich, Germany
| | - Hubert Hilbi
- Institute of Medical Microbiology, Department of Medicine, University of Zürich, Zürich, Switzerland
| | - Leonardo Scapozza
- Pharmaceutical Biochemistry, School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Thierry Soldati
- Department of Biochemistry, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Pierre Cosson
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Centre Médical Universitaire, Geneva, Switzerland
- * E-mail:
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Chen X, Hu Y, Tian S, Han B. Understanding the Interactions between Staphylococcus aureus and the Raw-Meat-Processing Environment Isolate Klebsiella oxytoca in Dual-Species Biofilms via Discovering an Altered Metabolic Profile. Microorganisms 2021; 9:microorganisms9040672. [PMID: 33805148 PMCID: PMC8064066 DOI: 10.3390/microorganisms9040672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/02/2021] [Accepted: 03/23/2021] [Indexed: 11/24/2022] Open
Abstract
In a raw-meat-processing environment, members of the Enterobacteriaceae family can coexist with Staphylococcus aureus to form dual-species biofilms, leading to a higher risk of food contamination. However, very little is known about the effect of inter-species interactions on dual-species biofilm formation. The aim of this study was to investigate the interactions between S. aureus and raw-meat-processing environment isolates of Klebsiella oxytoca in dual-species biofilms, by employing an untargeted metabolomics tool. Crystal violet staining assay showed that the biomass of the dual-species biofilm significantly increased and reached its maximum after incubation for 21 h, compared with that of single species grown alone. The number of K. oxytoca in the dual-species biofilm was significantly higher than that of S. aureus. Field emission scanning electron microscopy (FESEM) revealed that both species were evenly distributed, and were tightly wrapped by extracellular polymeric substances in the dual-species biofilms. Ultra-high-pressure liquid chromatography equipped with a quadrupole-time-of-flight mass spectrometer (UHPLC-Q-TOF MS) analysis exhibited a total of 8184 positive ions, and 6294 negative ions were obtained from all test samples. Multivariate data analysis further described altered metabolic profiling between mono- and dual-species biofilms. Further, 18 and 21 different metabolites in the dual-species biofilm were screened as biomarkers by comparing the mono-species biofilms of S. aureus and K. oxytoca, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways that were exclusively upregulated in the dual-species biofilm included ABC transporters, amino acid metabolism, and the two-component signal transduction system. Our results contribute to a better understanding of the interactive behavior of inter-species biofilm communities, by discovering altered metabolic profiling.
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Radulović O, Stanković S, Uzelac B, Tadić V, Trifunović-Momčilov M, Lozo J, Marković M. Phenol Removal Capacity of the Common Duckweed ( Lemna minor L.) and Six Phenol-Resistant Bacterial Strains From Its Rhizosphere: In Vitro Evaluation at High Phenol Concentrations. PLANTS 2020; 9:plants9050599. [PMID: 32397144 PMCID: PMC7285011 DOI: 10.3390/plants9050599] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/26/2020] [Accepted: 04/28/2020] [Indexed: 02/07/2023]
Abstract
The main topic of this study is the bioremediation potential of the common duckweed, Lemna minor L., and selected rhizospheric bacterial strains in removing phenol from aqueous environments at extremely high initial phenol concentrations. To that end, fluorescence microscopy, MIC tests, biofilm formation, the phenol removal test (4-AAP method), the Salkowski essay, and studies of multiplication rates of sterile and inoculated duckweed in MS medium with phenol (200, 500, 750, and 1000 mg L−1) were conducted. Out of seven bacterial strains, six were identified as epiphytes or endophytes that efficiently removed phenol. The phenol removal experiment showed that the bacteria/duckweed system was more efficient during the first 24 h compared to the sterile duckweed control group. At the end of this experiment, almost 90% of the initial phenol concentration was removed by both groups, respectively. The bacteria stimulated the duckweed multiplication even at a high bacterial population density (>105 CFU mL−1) over a prolonged period of time (14 days). All bacterial strains were sensitive to all the applied antibiotics and formed biofilms in vitro. The dual bacteria/duckweed system, especially the one containing strain 43-Hafnia paralvei C32-106/3, Accession No. MF526939, had a number of characteristics that are advantageous in bioremediation, such as high phenol removal efficiency, biofilm formation, safety (antibiotic sensitivity), and stimulation of duckweed multiplication.
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Affiliation(s)
- Olga Radulović
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”–National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana, Belgrade 11060, Serbia; (B.U.); (M.T-M.); (M.M.)
- Correspondence:
| | - Slaviša Stanković
- Faculty of Biology, University of Belgrade, 16 Studentski Trg, Belgrade 11000, Serbia; (S.S.); (J.L.)
| | - Branka Uzelac
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”–National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana, Belgrade 11060, Serbia; (B.U.); (M.T-M.); (M.M.)
| | - Vojin Tadić
- Mining and Metallurgy Institute Bor, 35 Zeleni Bulevar, Bor 19210, Serbia;
| | - Milana Trifunović-Momčilov
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”–National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana, Belgrade 11060, Serbia; (B.U.); (M.T-M.); (M.M.)
| | - Jelena Lozo
- Faculty of Biology, University of Belgrade, 16 Studentski Trg, Belgrade 11000, Serbia; (S.S.); (J.L.)
| | - Marija Marković
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”–National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana, Belgrade 11060, Serbia; (B.U.); (M.T-M.); (M.M.)
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Rubin M, Miller AD, Katoh-Kurasawa M, Dinh C, Kuspa A, Shaulsky G. Cooperative predation in the social amoebae Dictyostelium discoideum. PLoS One 2019; 14:e0209438. [PMID: 30625171 PMCID: PMC6326426 DOI: 10.1371/journal.pone.0209438] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/05/2018] [Indexed: 12/05/2022] Open
Abstract
The eukaryotic amoeba Dictyostelium discoideum is commonly used to study sociality. The amoebae cooperate during development, exhibiting altruism, cheating, and kin-discrimination, but growth while preying on bacteria has been considered asocial. Here we show that Dictyostelium are cooperative predators. Using mutants that grow poorly on Gram-negative bacteria but grow well on Gram-positive bacteria, we show that growth depends on cell-density and on prey type. We also found synergy, by showing that pairwise mixes of different mutants grow well on live Gram-negative bacteria. Moreover, wild-type amoebae produce diffusible factors that facilitate mutant growth and some mutants exploit the wild type in mixed cultures. Finding cooperative predation in D. discoideum should facilitate studies of this fascinating phenomenon, which has not been amenable to genetic analysis before.
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Affiliation(s)
- Michelle Rubin
- Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, United States of America
| | - Amber D. Miller
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Mariko Katoh-Kurasawa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Christopher Dinh
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States of America
| | - Adam Kuspa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States of America
| | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
- * E-mail:
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Kundu S, Sharma R. Origin, evolution, and divergence of plant class C GH9 endoglucanases. BMC Evol Biol 2018; 18:79. [PMID: 29848310 PMCID: PMC5977491 DOI: 10.1186/s12862-018-1185-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 04/18/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glycoside hydrolases of the GH9 family encode cellulases that predominantly function as endoglucanases and have wide applications in the food, paper, pharmaceutical, and biofuel industries. The partitioning of plant GH9 endoglucanases, into classes A, B, and C, is based on the differential presence of transmembrane, signal peptide, and the carbohydrate binding module (CBM49). There is considerable debate on the distribution and the functions of these enzymes which may vary in different organisms. In light of these findings we examined the origin, emergence, and subsequent divergence of plant GH9 endoglucanases, with an emphasis on elucidating the role of CBM49 in the digestion of crystalline cellulose by class C members. RESULTS Since, the digestion of crystalline cellulose mandates the presence of a well-defined set of aromatic and polar amino acids and/or an attributable domain that can mediate this conversion, we hypothesize a vertical mode of transfer of genes that could favour the emergence of class C like GH9 endoglucanase activity in land plants from potentially ancestral non plant taxa. We demonstrated the concomitant occurrence of a GH9 domain with CBM49 and other homologous carbohydrate binding modules, in putative endoglucanase sequences from several non-plant taxa. In the absence of comparable full length CBMs, we have characterized several low strength patterns that could approximate the CBM49, thereby, extending support for digestion of crystalline cellulose to other segments of the protein. We also provide data suggestive of the ancestral role of putative class C GH9 endoglucanases in land plants, which includes detailed phylogenetics and the presence and subsequent loss of CBM49, transmembrane, and signal peptide regions in certain populations of early land plants. These findings suggest that classes A and B of modern vascular land plants may have emerged by diverging directly from CBM49 encompassing putative class C enzymes. CONCLUSION Our detailed phylogenetic and bioinformatics analysis of putative GH9 endoglucanase sequences across major taxa suggests that plant class C enzymes, despite their recent discovery, could function as the last common ancestor of classes A and B. Additionally, research into their ability to digest or inter-convert crystalline and amorphous forms of cellulose could make them lucrative candidates for engineering biofuel feedstock.
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Affiliation(s)
- Siddhartha Kundu
- Department of Biochemistry, Government of NCT of Delhi, Dr. Baba Saheb Ambedkar Medical College & Hospital, New Delhi, 110085, India. .,Crop Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Rita Sharma
- Crop Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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