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Jaryenneh J, Schoeniger JS, Mageeney CM. Genome sequence and characterization of a novel Pseudomonas putida phage, MiCath. Sci Rep 2023; 13:21834. [PMID: 38071193 PMCID: PMC10710427 DOI: 10.1038/s41598-023-48634-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Pseudomonads are ubiquitous bacteria with importance in medicine, soil, agriculture, and biomanufacturing. We report a novel Pseudomonas putida phage, MiCath, which is the first known phage infecting P. putida S12, a strain increasingly used as a synthetic biology chassis. MiCath was isolated from garden soil under a tomato plant using P. putida S12 as a host and was also found to infect four other P. putida strains. MiCath has a ~ 61 kbp double-stranded DNA genome which encodes 97 predicted open reading frames (ORFs); functions could only be predicted for 48 ORFs using comparative genomics. Functions include structural phage proteins, other common phage proteins (e.g., terminase), a queuosine gene cassette, a cas4 exonuclease, and an endosialidase. Restriction digestion analysis suggests the queuosine gene cassette encodes a pathway capable of modification of guanine residues. When compared to other phage genomes, MiCath shares at most 74% nucleotide identity over 2% of the genome with any sequenced phage. Overall, MiCath is a novel phage with no close relatives, encoding many unique gene products.
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Delavault A, Zoheir AE, Muller D, Hollenbach R, Rabe KS, Ochsenreither K, Rudat J, Syldatk C. Enhanced Bioactivity of Tailor-Made Glycolipid Enriched Manuka Honey. Int J Mol Sci 2022; 23:12031. [PMID: 36233331 PMCID: PMC9570014 DOI: 10.3390/ijms231912031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/21/2022] [Accepted: 07/24/2022] [Indexed: 11/16/2022] Open
Abstract
Glycolipids can be synthetized in deep eutectic solvents (DESs) as they possess low water content allowing a reversed lipase activity and thus enables ester formation. Based on this principle, honey can also serve as a media for glycolipid synthesis. Indeed, this supersaturated sugar solution is comparable in terms of physicochemical properties to the sugar-based DESs. Honey-based products being commercially available for therapeutic applications, it appears interesting to enhance its bioactivity. In the current work, we investigate if enriching medical grade honey with in situ enzymatically-synthetized glycolipids can improve the antimicrobial property of the mixture. The tested mixtures are composed of Manuka honey that is enriched with octanoate, decanoate, laurate, and myristate sugar esters, respectively dubbed GOH, GDH, GLH, and GMH. To characterize the bioactivity of those mixtures, first a qualitative screening using an agar well diffusion assay has been performed with methicillin-resistant Staphylococcus aureus, Bacillus subtilis, Candida bombicola, Escherichia coli, and Pseudomonas putida which confirmed considerably enhanced susceptibility of these micro-organisms to the different glycolipid enriched honey mixtures. Then, a designed biosensor E. coli strain that displays a stress reporter system consisting of three stress-specific inducible, red, green, and blue fluorescent proteins which respectively translate to physiological stress, genotoxicity, and cytotoxicity was used. Bioactivity was, therefore, characterized, and a six-fold enhancement of the physiological stress that was caused by GOH compared to regular Manuka honey at a 1.6% (v/v) concentration was observed. An antibacterial agar well diffusion assay with E. coli was performed as well and demonstrated an improved inhibitory potential with GOH upon 20% (v/v) concentration.
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Affiliation(s)
- André Delavault
- Technical Biology, Institute of Process Engineering in Life Sciences II, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Ahmed E. Zoheir
- Department of Genetics and Cytology, National Research Center (NRC), Cairo 12622, Egypt
- Molecular Evolution, Institute for Biological Interfaces 1 (IBG-1), Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Delphine Muller
- Technical Biology, Institute of Process Engineering in Life Sciences II, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Rebecca Hollenbach
- Technical Biology, Institute of Process Engineering in Life Sciences II, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
- Technikum Laubholz GmbH, Biotechnologische Konversion, 89143 Blaubeuren, Germany
| | - Kersten S. Rabe
- Molecular Evolution, Institute for Biological Interfaces 1 (IBG-1), Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Katrin Ochsenreither
- Technical Biology, Institute of Process Engineering in Life Sciences II, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
- Technikum Laubholz GmbH, Biotechnologische Konversion, 89143 Blaubeuren, Germany
| | - Jens Rudat
- Technical Biology, Institute of Process Engineering in Life Sciences II, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Christoph Syldatk
- Technical Biology, Institute of Process Engineering in Life Sciences II, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
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Lelchat F, Mocaer PY, Ojima T, Michel G, Sarthou G, Bucciarelli E, Cérantola S, Colliec-Jouault S, Boisset C, Baudoux AC. Viral degradation of marine bacterial exopolysaccharides. FEMS Microbiol Ecol 2020; 95:5498295. [PMID: 31125051 DOI: 10.1093/femsec/fiz079] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/23/2019] [Indexed: 11/14/2022] Open
Abstract
The identification of the mechanisms by which marine dissolved organic matter (DOM) is produced and regenerated is critical to develop robust prediction of ocean carbon cycling. Polysaccharides represent one of the main constituents of marine DOM and their degradation is mainly attributed to polysaccharidases derived from bacteria. Here, we report that marine viruses can depolymerize the exopolysaccharides (EPS) excreted by their hosts using five bacteriophages that infect the notable EPS producer, Cobetia marina DSMZ 4741. Degradation monitorings as assessed by gel electrophoresis and size exclusion chromatography showed that four out of five phages carry structural enzymes that depolymerize purified solution of Cobetia marina EPS. The depolymerization patterns suggest that these putative polysaccharidases are constitutive, endo-acting and functionally diverse. Viral adsorption kinetics indicate that the presence of these enzymes provides a significant advantage for phages to adsorb onto their hosts upon intense EPS production conditions. The experimental demonstration that marine phages can display polysaccharidases active on bacterial EPS lead us to question whether viruses could also contribute to the degradation of marine DOM and modify its bioavailability. Considering the prominence of phages in the ocean, such studies may unveil an important microbial process that affects the marine carbon cycle.
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Affiliation(s)
- F Lelchat
- Laboratoire BMM, centre Ifremer de Brest, ZI pointe du diable, 29280 Plouzané, France
| | - P Y Mocaer
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - T Ojima
- Laboratory of Marine Biotechnology and Microbiology, Graduate School of Fisheries Sciences, Hokkaido University, Minato-cho 3-1-1, Hakodate 041-8611, Japan
| | - G Michel
- Sorbonne Université, CNRS, Laboratoire de Biologie Intégrative des Modèles Marins UMR 8227, Station Biologique de Roscoff, Roscoff, France
| | - G Sarthou
- CNRS, Université de Brest, IRD, Ifremer, UMR 6539/LEMAR/IUEM, Technopôle Brest Iroise, Place Nicolas Copernic, 29280 Plouzané, France
| | - E Bucciarelli
- CNRS, Université de Brest, IRD, Ifremer, UMR 6539/LEMAR/IUEM, Technopôle Brest Iroise, Place Nicolas Copernic, 29280 Plouzané, France
| | - S Cérantola
- Service commun de résonnance magnétique nucléaire, Faculté de science de Brest, Université de Bretagne Occidentale, 6 av. Victor Le Gorgeu, 29238 Brest Cedex 3, France
| | - S Colliec-Jouault
- Laboratoire EM3B, Centre Ifremer Atlantique - Rue de l'Ile d'Yeu - 44311 Nantes, France
| | - C Boisset
- Service commun de chromatographie, CERMAV-CNRS, 601 rue de la chimie, St Martin d'Hère, 38041 Grenoble, France
| | - A-C Baudoux
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
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Magill DJ, Krylov VN, Shaburova OV, McGrath JW, Allen CCR, Quinn JP, Kulakov LA. Pf16 and phiPMW: Expanding the realm of Pseudomonas putida bacteriophages. PLoS One 2017; 12:e0184307. [PMID: 28877269 PMCID: PMC5587285 DOI: 10.1371/journal.pone.0184307] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 08/21/2017] [Indexed: 12/22/2022] Open
Abstract
We present the analysis of two novel Pseudomonas putida phages, pf16 and phiPMW. Pf16 represents a peripherally related T4-like phage, and is the first of its kind infecting a Pseudomonad, with evidence suggesting cyanophage origins. Extensive divergence has resulted in pf16 occupying a newly defined clade designated as the pf16-related phages, lying at the interface of the Schizo T-Evens and Exo T-Evens. Recombination with an ancestor of the P. putida phage AF is likely responsible for the tropism of this phage. phiPMW represents a completely novel Pseudomonas phage with a genome containing substantial genetic novelty through its many hypothetical proteins. Evidence suggests that this phage has been extensively shaped through gene transfer events and vertical evolution. Phylogenetics shows that this phage has an evolutionary history involving FelixO1-related viruses but is in itself highly distinct from this group.
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Affiliation(s)
- Damian J. Magill
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast, Northern Ireland
| | - Victor N. Krylov
- Department of Microbiology, Laboratory for Genetics of Bacteriophages, I.I. Mechnikov Research Institute for Vaccines and Sera, Moscow, Russia
| | - Olga V. Shaburova
- Department of Microbiology, Laboratory for Genetics of Bacteriophages, I.I. Mechnikov Research Institute for Vaccines and Sera, Moscow, Russia
| | - John W. McGrath
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast, Northern Ireland
| | - Christopher C. R. Allen
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast, Northern Ireland
| | - John P. Quinn
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast, Northern Ireland
| | - Leonid A. Kulakov
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast, Northern Ireland
- * E-mail:
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Pseudomonas putida and Pseudomonas fluorescens Species Group Recovery from Human Homes Varies Seasonally and by Environment. PLoS One 2015; 10:e0127704. [PMID: 26023929 PMCID: PMC4449118 DOI: 10.1371/journal.pone.0127704] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 04/17/2015] [Indexed: 02/03/2023] Open
Abstract
By shedding light on variation in time as well as in space, long-term biogeographic studies can help us define organisms' distribution patterns and understand their underlying drivers. Here we examine distributions of Pseudomonas in and around 15 human homes, focusing on the P. putida and P. fluorescens species groups. We describe recovery from 10,941 samples collected during up to 8 visits per home, occurring on average 2.6 times per year. We collected a mean of 141 samples per visit, from sites in most rooms of the house, from the surrounding yards, and from human and pet occupants. We recovered Pseudomonas in 9.7% of samples, with the majority of isolates being from the P. putida and P. fluorescens species groups (approximately 62% and 23% of Pseudomonas samples recovered respectively). Although representatives of both groups were recovered from every season, every house, and every type of environment sampled, recovery was highly variable across houses and samplings. Whereas recovery of P. putida group was higher in summer and fall than in winter and spring, P. fluorescens group isolates were most often recovered in spring. P. putida group recovery from soils was substantially higher than its recovery from all other environment types, while higher P. fluorescens group recovery from soils than from other sites was much less pronounced. Both species groups were recovered from skin and upper respiratory tract samples from healthy humans and pets, although this occurred infrequently. This study indicates that even species that are able to survive under a broad range of conditions can be rare and variable in their distributions in space and in time. For such groups, determining patterns and causes of stochastic and seasonal variability may be more important for understanding the processes driving their biogeography than the identity of the types of environments in which they can be found.
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Cornelissen A, Ceyssens PJ, Krylov VN, Noben JP, Volckaert G, Lavigne R. Identification of EPS-degrading activity within the tail spikes of the novel Pseudomonas putida phage AF. Virology 2012; 434:251-6. [PMID: 23084421 DOI: 10.1016/j.virol.2012.09.030] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/13/2012] [Accepted: 09/21/2012] [Indexed: 11/26/2022]
Abstract
We report the study of phage AF, the first member of the canonical lambdoid phage group infecting Pseudomonas putida. Its 42.6 kb genome is related to the "epsilon15-like viruses" and the "BPP-1-like viruses", a clade of bacteriophages shaped by extensive horizontal gene transfer. The AF virions display exopolysaccharide (EPS)-degrading activity, which originates from the action of the C-terminal domain of the tail spike (Gp19). This protein shows high similarity to the tail spike of the T7-like P. putida-infecting phage φ15. These unrelated phages have an identical host spectrum and EPS degradation characteristics, designating the C-terminal part of Gp19 as sole determinant for these functions. While intact AF particles have biofilm-degrading properties, Gp19 and non-infectious AF particles do not, emphasizing the role of phage amplification in biofilm degradation.
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Affiliation(s)
- Anneleen Cornelissen
- Laboratory of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, Leuven B-3001, Belgium
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Chertkov OV, Chuprov-Netochin RN, Legotskiĭ SV, Sykilinda NN, Shneider MM, Ivanova MA, Pleteneva EA, Shaburova OV, Burkal'tseva MB, Kostriukova ES, Lazarev VN, Kliachko NL, Miroshnikov KA. Properties of the peptidoglycan-degrading enzyme of the Pseudomonas aeruginosa ϕPMG1 bacteriophage. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:807-14. [PMID: 22497079 DOI: 10.1134/s1068162011060057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Cornelissen A, Ceyssens PJ, T'Syen J, Van Praet H, Noben JP, Shaburova OV, Krylov VN, Volckaert G, Lavigne R. The T7-related Pseudomonas putida phage φ15 displays virion-associated biofilm degradation properties. PLoS One 2011; 6:e18597. [PMID: 21526174 PMCID: PMC3079711 DOI: 10.1371/journal.pone.0018597] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 03/05/2011] [Indexed: 12/26/2022] Open
Abstract
Formation of a protected biofilm environment is recognized as one of the major causes of the increasing antibiotic resistance development and emphasizes the need to develop alternative antibacterial strategies, like phage therapy. This study investigates the in vitro degradation of single-species Pseudomonas putida biofilms, PpG1 and RD5PR2, by the novel phage ϕ15, a ‘T7-like virus’ with a virion-associated exopolysaccharide (EPS) depolymerase. Phage ϕ15 forms plaques surrounded by growing opaque halo zones, indicative for EPS degradation, on seven out of 53 P. putida strains. The absence of haloes on infection resistant strains suggests that the EPS probably act as a primary bacterial receptor for phage infection. Independent of bacterial strain or biofilm age, a time and dose dependent response of ϕ15-mediated biofilm degradation was observed with generally a maximum biofilm degradation 8 h after addition of the higher phage doses (104 and 106 pfu) and resistance development after 24 h. Biofilm age, an in vivo very variable parameter, reduced markedly phage-mediated degradation of PpG1 biofilms, while degradation of RD5PR2 biofilms and ϕ15 amplification were unaffected. Killing of the planktonic culture occurred in parallel with but was always more pronounced than biofilm degradation, accentuating the need for evaluating phages for therapeutic purposes in biofilm conditions. EPS degrading activity of recombinantly expressed viral tail spike was confirmed by capsule staining. These data suggests that the addition of high initial titers of specifically selected phages with a proper EPS depolymerase are crucial criteria in the development of phage therapy.
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Affiliation(s)
| | - Pieter-Jan Ceyssens
- Laboratory of Gene Technology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jeroen T'Syen
- Laboratory of Gene Technology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Helena Van Praet
- Laboratory of Gene Technology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jean-Paul Noben
- School of Life Sciences, Biomedical Research Institute and Transnational University Limburg, Hasselt University, Diepenbeek, Belgium
| | - Olga V. Shaburova
- State Institute for Genetics of Industrial Microorganisms, Moscow, Russia
| | - Victor N. Krylov
- State Institute for Genetics of Industrial Microorganisms, Moscow, Russia
| | - Guido Volckaert
- Laboratory of Gene Technology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Katholieke Universiteit Leuven, Leuven, Belgium
- * E-mail:
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Pleteneva EA, Bourkaltseva MV, Shaburova OV, Krylov SV, Pechnikova EV, Sokolova OS, Krylov VN. TL, the new bacteriophage of Pseudomonas aeruginosa and its application for the search of halo-producing bacteriophages. RUSS J GENET+ 2011. [DOI: 10.1134/s1022795411010091] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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