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Trisrivirat D, Hughes JMX, Hoeven R, Faulkner M, Toogood H, Chaiyen P, Scrutton NS. Promoter engineering for microbial bio-alkane gas production. Synth Biol (Oxf) 2020; 5:ysaa022. [PMID: 33263086 PMCID: PMC7680561 DOI: 10.1093/synbio/ysaa022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 12/29/2022] Open
Abstract
Successful industrial biotechnological solutions to biofuels and other chemicals production rely on effective competition with existing lower-cost natural sources and synthetic chemistry approaches enabled by adopting low-cost bioreactors and processes. This is achievable by mobilizing Halomonas as a next generation industrial chassis, which can be cultivated under non-sterile conditions. To increase the cost effectiveness of an existing sustainable low carbon bio-propane production strategy, we designed and screened a constitutive promoter library based on the known strong porin promoter from Halomonas. Comparative studies were performed between Escherichia coli and Halomonas using the reporter gene red fluorescent protein (RFP). Later studies with a fatty acid photodecarboxylase-RFP fusion protein demonstrated tuneable propane production in Halomonas and E. coli, with an ∼8-fold improvement in yield over comparable isopropyl-β-D-thiogalactoside-inducible systems. This novel set of promoters is a useful addition to the synthetic biology toolbox for future engineering of Halomonas to make chemicals and fuels.
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Affiliation(s)
- Duangthip Trisrivirat
- Department of Chemistry, School of Natural Sciences, EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.,School of Biomolecular Science and Engineering, Vidyasirimedhi Inistitute of Science and Technology (VISTEC), Rayong 21210, Thailand.,Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - John M X Hughes
- Department of Chemistry, School of Natural Sciences, EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Robin Hoeven
- Department of Chemistry, School of Natural Sciences, EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Matthew Faulkner
- Department of Chemistry, School of Natural Sciences, EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Helen Toogood
- Department of Chemistry, School of Natural Sciences, EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Inistitute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Nigel S Scrutton
- Department of Chemistry, School of Natural Sciences, EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.,School of Biomolecular Science and Engineering, Vidyasirimedhi Inistitute of Science and Technology (VISTEC), Rayong 21210, Thailand
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Berlanga M, Gomez-Perez L, Guerrero R. Biofilm formation and antibiotic susceptibility in dispersed cells versus planktonic cells from clinical, industry and environmental origins. Antonie van Leeuwenhoek 2017; 110:1691-1704. [PMID: 28770446 DOI: 10.1007/s10482-017-0919-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/25/2017] [Indexed: 12/14/2022]
Abstract
We examined the cell-surface physicochemical properties, the biofilm formation capability and the antibiotic susceptibility in dispersed cells (from an artificial biofilm of alginate beads) and compared with their planktonic (free-swimming) counterparts. The strains used were from different origins, such as clinical (Acinetobacter baumannii AB4), cosmetic industry (Klebsiella oxytoca EU213, Pseudomonas aeruginosa EU190), and environmental (Halomonas venusta MAT28). In general, dispersed cells adhered better to surfaces (measured as the "biofilm index") and had a greater hydrophobicity [measured as the microbial affinity to solvents (MATS)] than planktonic cells. The susceptibility to two antibiotics (ciprofloxacin and tetracycline) of dispersed cells was higher compared with that of their planktonic counterparts (tested by the "bactericidal index"). Dispersed and planktonic cells exhibited differences in cell permeability, especially in efflux pump activity, which could be related to the differences observed in susceptibility to antibiotics. At 1 h of biofilm formation in microtiter plates, dispersed cells treated with therapeutic concentration of ciprofloxacin yielded a lower biofilm index than the control dispersed cells without ciprofloxacin. With respect to the planktonic cells, the biofilm index was similar with and without the ciprofloxacin treatment. In both cases there were a reduction of the number of bacteria measured as viable count of the supernatant. The lower biofilm formation in dispersed cells with ciprofloxacin treatment may be due to a significant increase of biofilm disruption with respect to the biofilm from planktonic cells. From a clinical point of view, biofilms formed on medical devices such as catheters, cells that can be related to an infection were the dispersed cells. Our results showed that early treatment with ciprofloxacin of dispersed cells could diminishe bacterial dispersion and facilitate the partial elimination of the new biofilm formed.
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Affiliation(s)
- Mercedes Berlanga
- Department of Biology, Environment and Health, Section Microbiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Av. Joan XXIII 27-31, 08028, Barcelona, Spain.
| | - Laura Gomez-Perez
- Department of Biology, Environment and Health, Section Microbiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Av. Joan XXIII 27-31, 08028, Barcelona, Spain
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Ricardo Guerrero
- Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona, IDIBELL, Barcelona, Spain
- Barcelona Knowledge Hub, Academia Europaea, Barcelona, Spain
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Yin J, Chen JC, Wu Q, Chen GQ. Halophiles, coming stars for industrial biotechnology. Biotechnol Adv 2014; 33:1433-42. [PMID: 25447783 DOI: 10.1016/j.biotechadv.2014.10.008] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/10/2014] [Accepted: 10/19/2014] [Indexed: 10/24/2022]
Abstract
Industrial biotechnology aims to produce chemicals, materials and biofuels to ease the challenges of shortage on petroleum. However, due to the disadvantages of bioprocesses including energy consuming sterilization, high fresh water consumption, discontinuous fermentation to avoid microbial contamination, highly expensive stainless steel fermentation facilities and competing substrates for human consumption, industrial biotechnology is less competitive compared with chemical processes. Recently, halophiles have shown promises to overcome these shortcomings. Due to their unique halophilic properties, some halophiles are able to grow in high pH and high NaCl containing medium under higher temperature, allowing fermentation processes to run contamination free under unsterile conditions and continuous way. At the same time, genetic manipulation methods have been developed for halophiles. So far, halophiles have been used to produce bioplastics polyhydroxyalkanoates (PHA), ectoines, enzymes, and bio-surfactants. Increasing effects have been made to develop halophiles into a low cost platform for bioprocessing with advantages of low energy, less fresh water consumption, low fixed capital investment, and continuous production.
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Affiliation(s)
- Jin Yin
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jin-Chun Chen
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiong Wu
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guo-Qiang Chen
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China.
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Development of an enhanced chromosomal expression system based on porin synthesis operon for halophile Halomonas sp. Appl Microbiol Biotechnol 2014; 98:8987-97. [DOI: 10.1007/s00253-014-5959-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/11/2014] [Accepted: 07/14/2014] [Indexed: 01/26/2023]
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Tokunaga H, Furukawa M, Arakawa T, Tokunaga M. Channel forming outer membrane porin protein in halophile: Expressed as a soluble form in Escherichia coli. Int J Biol Macromol 2013; 54:44-50. [DOI: 10.1016/j.ijbiomac.2012.11.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 11/26/2012] [Accepted: 11/26/2012] [Indexed: 11/27/2022]
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Halophilic beta-lactamase as a new solubility- and folding-enhancing tag protein: production of native human interleukin 1alpha and human neutrophil alpha-defensin. Appl Microbiol Biotechnol 2009; 86:649-58. [PMID: 19902204 DOI: 10.1007/s00253-009-2325-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 10/09/2009] [Accepted: 10/20/2009] [Indexed: 10/20/2022]
Abstract
The amino acid composition of halophilic enzymes is characterized by an abundant content of acidic amino acid, which confers to the halophilic enzymes extensive negative charges at neutral pH and high aqueous solubility. This negative charge prevents protein aggregation when denatured and thereby leads to highly efficient protein refolding. Beta-lactamase from periplasmic space of moderate halophile (BLA), a typical halophilic enzyme, can be readily expressed as a native, active form in Escherichia coli cytoplasm. Similar to other halophilic enzymes, BLA is soluble upon denaturation by heat or urea treatments and, hence, can be efficiently refolded. Such high solubility and refolding efficiency make BLA a potential fusion partner for expression of aggregation-prone heterologous proteins to be expressed in E. coli. Here, we succeeded in the soluble expression of several "difficult-to-express" proteins as a BLA fusion protein and verified biological activities of human interleukin 1alpha and human neutrophil alpha-defensin, HNP-1.
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Oren A, Larimer F, Richardson P, Lapidus A, Csonka LN. How to be moderately halophilic with broad salt tolerance: clues from the genome of Chromohalobacter salexigens. Extremophiles 2005; 9:275-9. [PMID: 15902510 DOI: 10.1007/s00792-005-0442-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2004] [Accepted: 02/18/2005] [Indexed: 11/26/2022]
Abstract
We analyzed the amino acid composition of different categories of proteins of the moderately halophilic bacterium Chromohalobacter salexigens, as deduced from its genome sequence. Comparison with non-halophilic representatives of the gamma-Proteobacteria (Escherichia coli, Pseudomonas aeruginosa, Vibrio cholerae) shows only a slight excess of acidic residues in the cytoplasmic proteins, and no significant differences were found in the acidity of membrane-bound proteins. In contrast, a very pronounced difference in mean pI value was observed for the periplasmic binding proteins of the ABC transport systems of C. salexigens and the non-halophiles E. coli and P. aeruginosa. V. cholerae, which is adapted to life in brackish water, showed intermediate values. The findings suggest that there is a major difference between the proteins of the moderate halophile C. salexigens and non-halophilic bacteria in their periplasmic proteins, exemplified by the substrate binding proteins of transport systems. The highly acidic nature of these proteins may enable them to function at high salt concentrations. The evolution of highly salt-tolerant prokaryotes may have depended on an increase in acidity of the proteins located external to the cytoplasmic membrane, enabling effective transport of nutrients into the cell.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, and the Moshe Shilo Minerva Center for Marine Biogeochemistry, The Hebrew University of Jerusalem, Israel.
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