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A Survey of Spontaneous Antibiotic-Resistant Mutants of the Halophilic, Thermophilic Bacterium Rhodothermus marinus. Antibiotics (Basel) 2021; 10:antibiotics10111384. [PMID: 34827322 PMCID: PMC8614978 DOI: 10.3390/antibiotics10111384] [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: 09/19/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 11/17/2022] Open
Abstract
Rhodothermus marinus is a halophilic extreme thermophile, with potential as a model organism for studies of the structural basis of antibiotic resistance. In order to facilitate genetic studies of this organism, we have surveyed the antibiotic sensitivity spectrum of R. marinus and identified spontaneous antibiotic-resistant mutants. R. marinus is naturally insensitive to aminoglycosides, aminocylitols and tuberactinomycins that target the 30S ribosomal subunit, but is sensitive to all 50S ribosomal subunit-targeting antibiotics examined, including macrolides, lincosamides, streptogramin B, chloramphenicol, and thiostrepton. It is also sensitive to kirromycin and fusidic acid, which target protein synthesis factors. It is sensitive to rifampicin (RNA polymerase inhibitor) and to the fluoroquinolones ofloxacin and ciprofloxacin (DNA gyrase inhibitors), but insensitive to nalidixic acid. Drug-resistant mutants were identified using rifampicin, thiostrepton, erythromycin, spiramycin, tylosin, lincomycin, and chloramphenicol. The majority of these were found to have mutations that are similar or identical to those previously found in other species, while several novel mutations were identified. This study provides potential selectable markers for genetic manipulations and demonstrates the feasibility of using R. marinus as a model system for studies of ribosome and RNA polymerase structure, function, and evolution.
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Kristjansdottir T, Ron EYC, Molins-Delgado D, Fridjonsson OH, Turner C, Bjornsdottir SH, Gudmundsson S, van Niel EWJ, Karlsson EN, Hreggvidsson GO. Engineering the carotenoid biosynthetic pathway in Rhodothermus marinus for lycopene production. Metab Eng Commun 2020; 11:e00140. [PMID: 32793416 PMCID: PMC7414004 DOI: 10.1016/j.mec.2020.e00140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/25/2020] [Accepted: 07/20/2020] [Indexed: 11/20/2022] Open
Abstract
Rhodothermus marinus has the potential to be well suited for biorefineries, as an aerobic thermophile that produces thermostable enzymes and is able to utilize polysaccharides from different 2nd and 3rd generation biomass. The bacterium produces valuable chemicals such as carotenoids. However, the native carotenoids are not established for industrial production and R. marinus needs to be genetically modified to produce higher value carotenoids. Here we genetically modified the carotenoid biosynthetic gene cluster resulting in three different mutants, most importantly the lycopene producing mutant TK-3 (ΔtrpBΔpurAΔcruFcrtB::trpBcrtBT.thermophilus). The genetic modifications and subsequent structural analysis of carotenoids helped clarify the carotenoid biosynthetic pathway in R. marinus. The nucleotide sequences encoding the enzymes phytoene synthase (CrtB) and the previously unidentified 1′,2′-hydratase (CruF) were found fused together and encoded by a single gene in R. marinus. Deleting only the cruF part of the gene did not result in an active CrtB enzyme. However, by deleting the entire gene and inserting the crtB gene from Thermus thermophilus, a mutant strain was obtained, producing lycopene as the sole carotenoid. The lycopene produced by TK-3 was quantified as 0.49 g/kg CDW (cell dry weight). Genetically engineered Rhodothermus marinus produces lycopene instead of native γ-carotenoids. A gene encoding 1′,2′-hydratase (cruF) was identified in the genome, fused with the gene encoding phytoene synthase (crtB). Marker-replacement of the cruF-crtB gene with the crtB from Thermus thermophilus resulted in the R. marinus mutant TK-3. The mutant strain TK-3 produced lycopene as the sole carotenoid (0.49 g/kg CDW).
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Affiliation(s)
- Thordis Kristjansdottir
- Matis, Vinlandsleid 12, 113 Reykjavik, Iceland.,University of Iceland, Department of Computer Science, School of Engineering and Natural Sciences, Dunhagi 5, 107 Reykjavik, Iceland
| | - Emanuel Y C Ron
- Lund University, Department of Chemistry, Division of Biotechnology, Box 124, 221 00, Lund, Sweden
| | - Daniel Molins-Delgado
- Lund University, Department of Chemistry, Centre for Analysis and Synthesis, Box 124, 221 00, Lund, Sweden
| | | | - Charlotta Turner
- Lund University, Department of Chemistry, Centre for Analysis and Synthesis, Box 124, 221 00, Lund, Sweden
| | - Snaedis H Bjornsdottir
- University of Iceland, Department of Biology, School of Engineering and Natural Sciences, Sturlugata 7, 102 Reykjavík, Iceland
| | - Steinn Gudmundsson
- University of Iceland, Department of Computer Science, School of Engineering and Natural Sciences, Dunhagi 5, 107 Reykjavik, Iceland
| | - Ed W J van Niel
- Lund University, Department of Chemistry, Division of Applied Microbiology, Box 124, 221 00, Lund, Sweden
| | - Eva Nordberg Karlsson
- Lund University, Department of Chemistry, Division of Biotechnology, Box 124, 221 00, Lund, Sweden
| | - Gudmundur O Hreggvidsson
- Matis, Vinlandsleid 12, 113 Reykjavik, Iceland.,University of Iceland, Department of Biology, School of Engineering and Natural Sciences, Sturlugata 7, 102 Reykjavík, Iceland
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Ron EYC, Sardari RRR, Anthony R, van Niel EWJ, Hreggvidsson GO, Nordberg-Karlsson E. Cultivation technology development of Rhodothermus marinus DSM 16675. Extremophiles 2019; 23:735-745. [PMID: 31522265 PMCID: PMC6801211 DOI: 10.1007/s00792-019-01129-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 08/14/2019] [Indexed: 12/17/2022]
Abstract
This work presents an evaluation of batch, fed-batch, and sequential batch cultivation techniques for production of R. marinus DSM 16675 and its exopolysaccharides (EPSs) and carotenoids in a bioreactor, using lysogeny broth (LB) and marine broth (MB), respectively, in both cases supplemented with 10 g/L maltose. Batch cultivation using LB supplemented with maltose (LBmalt) resulted in higher cell density (OD620 = 6.6) than use of MBmalt (OD620 = 1.7). Sequential batch cultivation increased the cell density threefold (OD620 = 20) in LBmalt and eightfold (OD620 = 14) in MBmalt. In both single and sequential batches, the production of carotenoids and EPSs using LBmalt was detected in the exponential phase and stationary phase, respectively, while in MBmalt formation of both products was detectable in both the exponential and stationary phases of the culture. Heteropolymeric EPSs were produced with an overall volumetric productivity (QE) of 0.67 (mg/L h) in MBmalt and the polymer contained xylose. In LB, QE was lower (0.1 mg/L h) and xylose could not be detected in the composition of the produced EPSs. In conclusion, this study showed the importance of a process design and medium source for production of R. marinus DSM 16675 and its metabolites.
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Affiliation(s)
- Emanuel Y C Ron
- Division of Biotechnology, Department of Chemistry, Lund University, Naturvetarvägen 14, 22100, Lund, Sweden
| | - Roya R R Sardari
- Division of Biotechnology, Department of Chemistry, Lund University, Naturvetarvägen 14, 22100, Lund, Sweden.
| | - Richard Anthony
- Division of Biotechnology, Department of Chemistry, Lund University, Naturvetarvägen 14, 22100, Lund, Sweden
| | - Ed W J van Niel
- Division of Applied Microbiology, Department of Chemistry, Lund University, Naturvetarvägen 14, 22100, Lund, Sweden
| | | | - Eva Nordberg-Karlsson
- Division of Biotechnology, Department of Chemistry, Lund University, Naturvetarvägen 14, 22100, Lund, Sweden
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Edrada-Ebel R, Ævarsson A, Polymenakou P, Hentschel U, Carettoni D, Day J, Green D, Hreggviðsson GÓ, Harvey L, McNeil B. SeaBioTech: From Seabed to Test-Bed: Harvesting the Potential of Marine Biodiversity for Industrial Biotechnology. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Ron EYC, Plaza M, Kristjansdottir T, Sardari RRR, Bjornsdottir SH, Gudmundsson S, Hreggvidsson GO, Turner C, van Niel EWJ, Nordberg-Karlsson E. Characterization of carotenoids in Rhodothermus marinus. Microbiologyopen 2017; 7. [PMID: 29045010 PMCID: PMC5822342 DOI: 10.1002/mbo3.536] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/10/2017] [Accepted: 08/18/2017] [Indexed: 11/13/2022] Open
Abstract
Rhodothermus marinus, a marine aerobic thermophile, was first isolated from an intertidal hot spring in Iceland. In recent years, the R. marinus strain PRI 493 has been genetically modified, which opens up possibilities for targeted metabolic engineering of the species, such as of the carotenoid biosynthetic pathway. In this study, the carotenoids of the R. marinus type‐strain DSM 4252T, strain DSM 4253, and strain PRI 493 were characterized. Bioreactor cultivations were used for pressurized liquid extraction and analyzed by ultra‐high performance supercritical fluid chromatography with diode array and quadropole time‐of‐flight mass spectrometry detection (UHPSFC‐DAD‐QTOF/MS). Salinixanthin, a carotenoid originally found in Salinibacter ruber and previously detected in strain DSM 4253, was identified in all three R. marinus strains, both in the hydroxylated and nonhydroxylated form. Furthermore, an additional and structurally distinct carotenoid was detected in the three strains. MS/MS fragmentation implied that the mass difference between salinixanthin and the novel carotenoid structure corresponded to the absence of a 4‐keto group on the ß‐ionone ring. The study confirmed the lack of carotenoids for the strain SB‐71 (ΔtrpBΔpurAcrtBI’::trpB) in which genes encoding two enzymes of the proposed pathway are partially deleted. Moreover, antioxidant capacity was detected in extracts of all the examined R. marinus strains and found to be 2–4 times lower for the knock‐out strain SB‐71. A gene cluster with 11 genes in two operons in the R. marinusDSM 4252T genome was identified and analyzed, in which several genes were matched with carotenoid biosynthetic pathway genes in other organisms.
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Affiliation(s)
- Emanuel Y C Ron
- Division of Biotechnology, Department of Chemistry, Lund University, Lund, Sweden
| | - Merichel Plaza
- Division of Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Lund, Sweden
| | | | - Roya R R Sardari
- Division of Biotechnology, Department of Chemistry, Lund University, Lund, Sweden
| | | | | | | | - Charlotta Turner
- Division of Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Lund, Sweden
| | - Ed W J van Niel
- Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
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Sardari RR, Kulcinskaja E, Ron EY, Björnsdóttir S, Friðjónsson ÓH, Hreggviðsson GÓ, Karlsson EN. Evaluation of the production of exopolysaccharides by two strains of the thermophilic bacterium Rhodothermus marinus. Carbohydr Polym 2017; 156:1-8. [DOI: 10.1016/j.carbpol.2016.08.062] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/18/2016] [Accepted: 08/18/2016] [Indexed: 01/27/2023]
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Gene deletion strategy to examine the involvement of the two chondroitin lyases in Flavobacterium columnare virulence. Appl Environ Microbiol 2015; 81:7394-402. [PMID: 26253667 DOI: 10.1128/aem.01586-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/06/2015] [Indexed: 11/20/2022] Open
Abstract
Flavobacterium columnare is an important bacterial pathogen of freshwater fish that causes high mortality of infected fish and heavy economic losses in aquaculture. The pathogenesis of this bacterium is poorly understood, in part due to the lack of efficient methods for genetic manipulation. In this study, a gene deletion strategy was developed and used to determine the relationship between the production of chondroitin lyases and virulence. The F. johnsoniae ompA promoter (PompA) was fused to sacB to construct a counterselectable marker for F. columnare. F. columnare carrying PompA-sacB failed to grow on media containing 10% sucrose. A suicide vector carrying PompA-sacB was constructed, and a gene deletion strategy was developed. Using this approach, the chondroitin lyase-encoding genes, cslA and cslB, were deleted. The ΔcslA and ΔcslB mutants were both partially deficient in digestion of chondroitin sulfate A, whereas a double mutant (ΔcslA ΔcslB) was completely deficient in chondroitin lyase activity. Cells of F. columnare wild-type strain G4 and of the chondroitin lyase-deficient ΔcslA ΔcslB mutant exhibited similar levels of virulence toward grass carp in single-strain infections. Coinfections, however, revealed a competitive advantage for the wild type over the chondroitin lyase mutant. The results indicate that chondroitin lyases are not essential virulence factors of F. columnare but may contribute to the ability of the pathogen to compete and cause disease in natural infections. The gene deletion method developed in this study may be employed to investigate the virulence factors of this bacterium and may have wide application in many other members of the phylum Bacteroidetes.
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