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McGalliard R, Muhamadali H, AlMasoud N, Haldenby S, Romero-Soriano V, Allman E, Xu Y, Roberts AP, Paterson S, Carrol ED, Goodacre R. Bacterial discrimination by Fourier transform infrared spectroscopy, MALDI-mass spectrometry and whole-genome sequencing. Future Microbiol 2024; 19:795-810. [PMID: 38652264 PMCID: PMC11290759 DOI: 10.2217/fmb-2024-0043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024] Open
Abstract
Aim: Proof-of-concept study, highlighting the clinical diagnostic ability of FT-IR compared with MALDI-TOF MS, combined with WGS. Materials & methods: 104 pathogenic isolates of Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus pyogenes and Staphylococcus aureus were analyzed. Results: Overall prediction accuracy was 99.6% in FT-IR and 95.8% in MALDI-TOF-MS. Analysis of N. meningitidis serogroups was superior in FT-IR compared with MALDI-TOF-MS. Phylogenetic relationship of S. pyogenes was similar by FT-IR and WGS, but not S. aureus or S. pneumoniae. Clinical severity was associated with the zinc ABC transporter and DNA repair genes in S. pneumoniae and cell wall proteins (biofilm formation, antibiotic and complement permeability) in S. aureus via WGS. Conclusion: FT-IR warrants further clinical evaluation as a promising diagnostic tool.
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Affiliation(s)
- Rachel McGalliard
- Department of Clinical Infection, Microbiology & Immunology, University of Liverpool Institute of Infection, Veterinary & Ecological Sciences, Ronald Ross Building, 8 West Derby Street, Liverpool, UK
- Department of Infectious Diseases, Alder Hey Children's NHS Foundation Trust, Eaton Road, Liverpool, UK
| | - Howbeer Muhamadali
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
- center for Metabolomics Research, Department of Biochemistry, Cell & Systems Biology, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, UK
| | - Najla AlMasoud
- College of Science, Princess Nourah Bint Abdulrahman University, Department of Chemistry, Riyadh, 11671, Saudi Arabia
| | - Sam Haldenby
- center for Genomic Research, University of Liverpool, Mersey Bio Building, Crown Street, Liverpool, UK
| | - Valeria Romero-Soriano
- center for Genomic Research, University of Liverpool, Mersey Bio Building, Crown Street, Liverpool, UK
| | - Ellie Allman
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Yun Xu
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
- center for Metabolomics Research, Department of Biochemistry, Cell & Systems Biology, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, UK
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Steve Paterson
- center for Genomic Research, University of Liverpool, Mersey Bio Building, Crown Street, Liverpool, UK
| | - Enitan D Carrol
- Department of Clinical Infection, Microbiology & Immunology, University of Liverpool Institute of Infection, Veterinary & Ecological Sciences, Ronald Ross Building, 8 West Derby Street, Liverpool, UK
- Department of Infectious Diseases, Alder Hey Children's NHS Foundation Trust, Eaton Road, Liverpool, UK
| | - Royston Goodacre
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
- center for Metabolomics Research, Department of Biochemistry, Cell & Systems Biology, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, UK
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Valle A, de la Calle ME, Muhamadali H, Hollywood KA, Xu Y, Lloyd JR, Goodacre R, Cantero D, Bolivar J. Metabolomics of Escherichia coli for Disclosing Novel Metabolic Engineering Strategies for Enhancing Hydrogen and Ethanol Production. Int J Mol Sci 2023; 24:11619. [PMID: 37511377 PMCID: PMC10380867 DOI: 10.3390/ijms241411619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
The biological production of hydrogen is an appealing approach to mitigating the environmental problems caused by the diminishing supply of fossil fuels and the need for greener energy. Escherichia coli is one of the best-characterized microorganisms capable of consuming glycerol-a waste product of the biodiesel industry-and producing H2 and ethanol. However, the natural capacity of E. coli to generate these compounds is insufficient for commercial or industrial purposes. Metabolic engineering allows for the rewiring of the carbon source towards H2 production, although the strategies for achieving this aim are difficult to foresee. In this work, we use metabolomics platforms through GC-MS and FT-IR techniques to detect metabolic bottlenecks in the engineered ΔldhΔgndΔfrdBC::kan (M4) and ΔldhΔgndΔfrdBCΔtdcE::kan (M5) E. coli strains, previously reported as improved H2 and ethanol producers. In the M5 strain, increased intracellular citrate and malate were detected by GC-MS. These metabolites can be redirected towards acetyl-CoA and formate by the overexpression of the citrate lyase (CIT) enzyme and by co-overexpressing the anaplerotic human phosphoenol pyruvate carboxykinase (hPEPCK) or malic (MaeA) enzymes using inducible promoter vectors. These strategies enhanced specific H2 production by up to 1.25- and 1.49-fold, respectively, compared to the reference strains. Other parameters, such as ethanol and H2 yields, were also enhanced. However, these vectors may provoke metabolic burden in anaerobic conditions. Therefore, alternative strategies for a tighter control of protein expression should be addressed in order to avoid undesirable effects in the metabolic network.
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Affiliation(s)
- Antonio Valle
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, Campus Universitario de Puerto Real, University of Cadiz, 11510 Puerto Real, Spain
- Institute of Viticulture and Agri-Food Research (IVAGRO)-International Campus of Excellence (ceiA3), University of Cadiz, 11510 Puerto Real, Spain
| | - Maria Elena de la Calle
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, Campus Universitario de Puerto Real, University of Cadiz, 11510 Puerto Real, Spain
- Department of Chemical Engineering and Food Technology, Campus Universitario de Puerto Real, University of Cadiz, 11510 Puerto Real, Spain
| | - Howbeer Muhamadali
- Centre for Metabolomics Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, BioSciences Building, Crown Street, Liverpool L69 7ZB, UK
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Katherine A Hollywood
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
- Department of Chemistry, Faculty of Science and Engineering, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Yun Xu
- Centre for Metabolomics Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, BioSciences Building, Crown Street, Liverpool L69 7ZB, UK
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Jonathan R Lloyd
- Williamson Research Centre, School of Earth & Environmental Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Royston Goodacre
- Centre for Metabolomics Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, BioSciences Building, Crown Street, Liverpool L69 7ZB, UK
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Domingo Cantero
- Institute of Viticulture and Agri-Food Research (IVAGRO)-International Campus of Excellence (ceiA3), University of Cadiz, 11510 Puerto Real, Spain
- Department of Chemical Engineering and Food Technology, Campus Universitario de Puerto Real, University of Cadiz, 11510 Puerto Real, Spain
| | - Jorge Bolivar
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, Campus Universitario de Puerto Real, University of Cadiz, 11510 Puerto Real, Spain
- Institute of Biomolecules (INBIO), University of Cadiz, 11510 Puerto Real, Spain
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Rebets Y, Kormanec J, Lutzhetskyy A, Bernaerts K, Anné J. Cloning and Expression of Metagenomic DNA in Streptomyces lividans and Its Subsequent Fermentation for Optimized Production. Methods Mol Biol 2023; 2555:213-260. [PMID: 36306090 DOI: 10.1007/978-1-0716-2795-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The choice of an expression system for the metagenomic DNA of interest is of vital importance for the detection of any particular gene or gene cluster. Most of the screens to date have used the Gram-negative bacterium Escherichia coli as a host for metagenomic gene libraries. However, the use of E. coli introduces a potential host bias since only 40% of the enzymatic activities may be readily recovered by random cloning in E. coli. To recover some of the remaining 60%, alternative cloning hosts such as Streptomyces spp. have been used. Streptomycetes are high-GC Gram-positive bacteria belonging to the Actinomycetales and they have been studied extensively for more than 25 years as an alternative expression system. They are extremely well suited for the expression of DNA from other actinomycetes and genomes of high GC content. Furthermore, due to its high innate, extracellular secretion capacity, Streptomyces can be a better system than E. coli for the production of many extracellular proteins. In this article, an overview is given about the materials and methods for growth and successful expression and secretion of heterologous proteins from diverse origin using Streptomyces lividans as a host. More in detail, an overview is given about the protocols of transformation, type of plasmids used and of vectors useful for integration of DNA into the host chromosome, and accompanying cloning strategies. In addition, various control elements for gene expression including synthetic promoters are discussed, and methods to compare their strength are described. Stable and efficient marker-less integration of the gene of interest under the control of the promoter of choice into S. lividans chromosome via homologous recombination using pAMR23A-based system will be explained. Finally, a basic protocol for bench-top bioreactor experiments which can form the start in the production process optimization and up-scaling will be provided.
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Affiliation(s)
| | - Jan Kormanec
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Andriy Lutzhetskyy
- Department of Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), University of Saarland, Saarbrücken, Germany
| | - Kristel Bernaerts
- Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety Division, KU Leuven, Leuven, Belgium
| | - Jozef Anné
- Department of Microbiology, Immunology and Transplantation, lab. Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium.
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Valle A, Soto Z, Muhamadali H, Hollywood KA, Xu Y, Lloyd JR, Goodacre R, Cantero D, Cabrera G, Bolivar J. Metabolomics for the design of new metabolic engineering strategies for improving aerobic succinic acid production in Escherichia coli. Metabolomics 2022; 18:56. [PMID: 35857216 PMCID: PMC9300530 DOI: 10.1007/s11306-022-01912-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 06/17/2022] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Glycerol is a byproduct from the biodiesel industry that can be biotransformed by Escherichia coli to high added-value products such as succinate under aerobic conditions. The main genetic engineering strategies to achieve this aim involve the mutation of succinate dehydrogenase (sdhA) gene and also those responsible for acetate synthesis including acetate kinase, phosphate acetyl transferase and pyruvate oxidase encoded by ackA, pta and pox genes respectively in the ΔsdhAΔack-ptaΔpox (M4) mutant. Other genetic manipulations to rewire the metabolism toward succinate consist on the activation of the glyoxylate shunt or blockage the pentose phosphate pathway (PPP) by deletion of isocitrate lyase repressor (iclR) or gluconate dehydrogenase (gnd) genes on M4-ΔiclR and M4-Δgnd mutants respectively. OBJECTIVE To deeply understand the effect of the blocking of the pentose phosphate pathway (PPP) or the activation of the glyoxylate shunt, metabolite profiles were analyzed on M4-Δgnd, M4-ΔiclR and M4 mutants. METHODS Metabolomics was performed by FT-IR and GC-MS for metabolite fingerprinting and HPLC for quantification of succinate and glycerol. RESULTS Most of the 65 identified metabolites showed lower relative levels in the M4-ΔiclR and M4-Δgnd mutants than those of the M4. However, fructose 1,6-biphosphate, trehalose, isovaleric acid and mannitol relative concentrations were increased in M4-ΔiclR and M4-Δgnd mutants. To further improve succinate production, the synthesis of mannitol was suppressed by deletion of mannitol dehydrogenase (mtlD) on M4-ΔgndΔmtlD mutant that increase ~ 20% respect to M4-Δgnd. CONCLUSION Metabolomics can serve as a holistic tool to identify bottlenecks in metabolic pathways by a non-rational design. Genetic manipulation to release these restrictions could increase the production of succinate.
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Affiliation(s)
- Antonio Valle
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, University of Cadiz, Campus Universitario de Puerto Real, 11510, Puerto Real, Cádiz, Spain.
- Institute of Viticulture and Agri-Food Research (IVAGRO) - International Campus of Excellence (ceiA3), University of Cadiz, 11510, Puerto Real, Cádiz, Spain.
| | - Zamira Soto
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, University of Cadiz, Campus Universitario de Puerto Real, 11510, Puerto Real, Cádiz, Spain
- Department of Chemical Engineering and Food Technology, University of Cadiz, Campus Universitario de Puerto Real, 11510, Puerto Real, Cádiz, Spain
- Faculty of Basic and Biomedical Sciences, Universidad Simón Bolívar, 080020, Barranquilla, Colombia
| | - Howbeer Muhamadali
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
- Department of Biochemistry and Systems Biology, Institute of Integrative Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK
| | - Katherine A Hollywood
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, UK
| | - Yun Xu
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
- Department of Biochemistry and Systems Biology, Institute of Integrative Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK
| | - Jonathan R Lloyd
- Williamson Research Centre, School of Earth & Environmental Sciences, University of Manchester, Manchester, M13 9PL, UK
| | - Royston Goodacre
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
- Department of Biochemistry and Systems Biology, Institute of Integrative Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK
| | - Domingo Cantero
- Department of Chemical Engineering and Food Technology, University of Cadiz, Campus Universitario de Puerto Real, 11510, Puerto Real, Cádiz, Spain
- Institute of Viticulture and Agri-Food Research (IVAGRO) - International Campus of Excellence (ceiA3), University of Cadiz, 11510, Puerto Real, Cádiz, Spain
| | - Gema Cabrera
- Department of Chemical Engineering and Food Technology, University of Cadiz, Campus Universitario de Puerto Real, 11510, Puerto Real, Cádiz, Spain
- Institute of Viticulture and Agri-Food Research (IVAGRO) - International Campus of Excellence (ceiA3), University of Cadiz, 11510, Puerto Real, Cádiz, Spain
| | - Jorge Bolivar
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, University of Cadiz, Campus Universitario de Puerto Real, 11510, Puerto Real, Cádiz, Spain.
- Institute of Biomolecules (INBIO), University of Cadiz, 11510, Puerto Real, Cádiz, Spain.
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Tengsuttiwat T, Kaderbhai NN, Gallagher J, Goodacre R, Muhamadali H. Metabolic Fingerprint Analysis of Cytochrome b5-producing E. coli N4830-1 Using FT-IR Spectroscopy. Front Microbiol 2022; 13:874247. [PMID: 35814704 PMCID: PMC9257212 DOI: 10.3389/fmicb.2022.874247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Optimization of recombinant protein expression in bacteria is an important task in order to increase protein yield while maintaining the structural fidelity of the product. In this study, we employ Fourier transform infrared (FT-IR) spectroscopy as a high throughput metabolic fingerprinting approach to optimize and monitor cytochrome b5 (CYT b5) production in Escherichia coli N4830-1, as the heterologous host. Cyt b5 was introduced as a plasmid with between 0 and 6 copies under a strong promoter. The FT-IR spectroscopy results combined with multivariate chemometric analysis illustrated discriminations among culture conditions as well as revealing features that correlated to the different cytb5 gene copy numbers. The second derivative of the FT-IR spectral data allowed for the quantitative detection of Cyt b5 directly inside the intact cells without the need for extraction, and highlighted changes in protein secondary structure that was directly correlated to the cytb5 gene copy number and protein content, and was in complete agreement with quantitative findings of standard traditional techniques such as SDS–PAGE and western blot analysis.
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Affiliation(s)
- Thanyaporn Tengsuttiwat
- Centre for Metabolomics Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Naheed Nazly Kaderbhai
- Institute of Biological, Environmental and Rural Sciences, Gogerddan Campus, Aberystwyth University, Aberystwyth, United Kingdom
| | - Joe Gallagher
- Institute of Biological, Environmental and Rural Sciences, Gogerddan Campus, Aberystwyth University, Aberystwyth, United Kingdom
| | - Royston Goodacre
- Centre for Metabolomics Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Howbeer Muhamadali
- Centre for Metabolomics Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- *Correspondence: Howbeer Muhamadali
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Berini F, Marinelli F, Binda E. Streptomycetes: Attractive Hosts for Recombinant Protein Production. Front Microbiol 2020; 11:1958. [PMID: 32973711 PMCID: PMC7468451 DOI: 10.3389/fmicb.2020.01958] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/24/2020] [Indexed: 01/28/2023] Open
Abstract
Enzymes are increasingly applied as biocatalysts for fulfilling industrial needs in a variety of applications and there is a bursting of interest for novel therapeutic proteins. Consequently, developing appropriate expression platforms for efficiently producing such recombinant proteins represents a crucial challenge. It is nowadays widely accepted that an ideal ‘universal microbial host’ for heterologous protein expression does not exist. Indeed, the first-choice microbes, as Escherichia coli or yeasts, possess known intrinsic limitations that inevitably restrict their applications. In this scenario, bacteria belonging to the Streptomyces genus need to be considered with more attention as promising, alternative, and versatile platforms for recombinant protein production. This is due to their peculiar features, first-of-all their natural attitude to secrete proteins in the extracellular milieu. Additionally, streptomycetes are considered robust and scalable industrial strains and a wide range of tools for their genetic manipulation is nowadays available. This mini-review includes an overview of recombinant protein production in streptomycetes, covering nearly 100 cases of heterologous proteins expressed in these Gram-positives from the 1980s to December 2019. We investigated homologous sources, heterologous hosts, and molecular tools (promoters/vectors/signal peptides) used for the expression of these recombinant proteins. We reported on their final cellular localization and yield. Thus, this analysis might represent a useful source of information, showing pros and cons of using streptomycetes as platform for recombinant protein production and paving the way for their more extensive use in future as alternative heterologous hosts.
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Affiliation(s)
- Francesca Berini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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Muhamadali H, Simoens K, Xu Y, Nicolai B, Bernaerts K, Goodacre R. Evaluation of Sample Preparation Methods for Inter-Laboratory Metabolomics Investigation of Streptomyces lividans TK24. Metabolites 2020; 10:E379. [PMID: 32972026 PMCID: PMC7569812 DOI: 10.3390/metabo10090379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 01/11/2023] Open
Abstract
In the past two decades, metabolomics has proved to be a valuable tool with many potential applications in different areas of science. However, there are still some challenges that need to be addressed, particularly for multicenter studies. These challenges are mainly attributed to various sources of fluctuation and unwanted variations that can be introduced at pre-analytical, analytical, and/or post-analytical steps of any metabolomics experiment. Thus, this study aimed at using Streptomyces lividans TK24 as the model organism in a cross-laboratory experiment in Manchester and Leuven to evaluate the reproducibility of a standard sample preparation method, and determine the optimal sample format (cell extract or quenched biomass) required to preserve the metabolic profile of the cells during cross-lab sample transportation and storage. Principal component analysis (PCA) scores plot of the gas chromatography-mass spectrometry (GC-MS) data from both laboratories displayed clear growth-dependent clustering patterns which was in agreement with the Procrustes analysis findings. In addition, the data generated in Manchester displayed tight clustering of cell pellets (quenched biomass) and metabolite extracts, confirming the stability of both sample formats during the transportation and storage period.
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Affiliation(s)
- Howbeer Muhamadali
- Department of Biochemistry and Systems Biology, Institute of Systems Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Liverpool L69 7ZB, UK; (H.M.); (Y.X.)
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Kenneth Simoens
- Bio- and Chemical Systems Technology, Reactor Engineering and Safety Section, Department of Chemical Engineering, KU Leuven (University of Leuven), Leuven Chem&Tech, Celestijnenlaan 200F Box 2424, 3001 Leuven, Belgium; (K.S.); (K.B.)
| | - Yun Xu
- Department of Biochemistry and Systems Biology, Institute of Systems Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Liverpool L69 7ZB, UK; (H.M.); (Y.X.)
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Bart Nicolai
- Division of Mechatronics, Biostatistics and Sensors (MeBioS), Department of Biosystems (BIOSYST), KU Leuven (University of Leuven), Willem de Croylaan 42 Box 2428, 3001 Leuven, Belgium;
| | - Kristel Bernaerts
- Bio- and Chemical Systems Technology, Reactor Engineering and Safety Section, Department of Chemical Engineering, KU Leuven (University of Leuven), Leuven Chem&Tech, Celestijnenlaan 200F Box 2424, 3001 Leuven, Belgium; (K.S.); (K.B.)
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology, Institute of Systems Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Liverpool L69 7ZB, UK; (H.M.); (Y.X.)
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
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Firat Duzenli O, Okay S. Promoter engineering for the recombinant protein production in prokaryotic systems. AIMS BIOENGINEERING 2020. [DOI: 10.3934/bioeng.2020007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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9
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Valverde JR, Gullón S, García-Herrero CA, Campoy I, Mellado RP. Dynamic metabolic modelling of overproduced protein secretion in Streptomyces lividans using adaptive DFBA. BMC Microbiol 2019; 19:233. [PMID: 31655540 PMCID: PMC6815373 DOI: 10.1186/s12866-019-1591-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 09/02/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Streptomyces lividans is an appealing host for the production of proteins of biotechnological interest due to its relaxed exogenous DNA restriction system and its ability to secrete proteins directly to the medium through the major Sec or the minor Tat routes. Often, protein secretion displays non-uniform time-dependent patterns. Understanding the associated metabolic changes is a crucial step to engineer protein production. Dynamic Flux Balance Analysis (DFBA) allows the study of the interactions between a modelled organism and its environment over time. Existing methods allow the specification of initial model and environment conditions, but do not allow introducing arbitrary modifications in the course of the simulation. Living organisms, however, display unexpected adaptive metabolic behaviours in response to unpredictable changes in their environment. Engineering the secretion of products of biotechnological interest has systematically proven especially difficult to model using DFBA. Accurate time-dependent modelling of complex and/or arbitrary, adaptive metabolic processes demands an extended approach to DFBA. RESULTS In this work, we introduce Adaptive DFBA, a novel, versatile simulation approach that permits inclusion of changes in the organism or the environment at any time in the simulation, either arbitrary or interactively responsive to environmental changes. This approach extends traditional DFBA to allow steering arbitrarily complex simulations of metabolic dynamics. When applied to Sec- or Tat-dependent secretion of overproduced proteins in S. lividans, Adaptive DFBA can overcome the limitations of traditional DFBA to reproduce experimental data on plasmid-free, plasmid bearing and secretory protein overproducing S. lividans TK24, and can yield useful insights on the behaviour of systems with limited experimental knowledge such as agarase or amylase overproduction in S. lividans TK21. CONCLUSIONS Adaptive DFBA has allowed us to overcome DFBA limitations and to generate more accurate models of the metabolism during the overproduction of secretory proteins in S. lividans, improving our understanding of the underlying processes. Adaptive DFBA is versatile enough to permit dynamical metabolic simulations of arbitrarily complex biotechnological processes.
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Affiliation(s)
- Jósé R. Valverde
- Scientific Computing Service, Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin 3, 28049 Madrid, Spain
| | - Sonia Gullón
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin, 3, 28049 Madrid, Spain
| | - Clara A. García-Herrero
- Scientific Computing Service, Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin 3, 28049 Madrid, Spain
| | - Iván Campoy
- Scientific Computing Service, Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin 3, 28049 Madrid, Spain
| | - Rafael P. Mellado
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin, 3, 28049 Madrid, Spain
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Liu X, Wang T, Sun X, Wang Z, Tian X, Zhuang Y, Chu J. Optimized sampling protocol for mass spectrometry-based metabolomics in Streptomyces. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0269-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
In quantitative metabolomics studies, the most crucial step was arresting snapshots of all interesting metabolites. However, the procedure customized for Streptomyces was so rare that most studies consulted the procedure from other bacteria even yeast, leading to inaccurate and unreliable metabolomics analysis. In this study, a base solution (acetone: ethanol = 1:1, mol/mol) was added to a quenching solution to keep the integrity of the cell membrane. Based on the molar transition energy (ET) of the organic solvents, five solutions were used to carry out the quenching procedures. These were acetone, isoamylol, propanol, methanol, and 60% (v/v) methanol. To the best of our knowledge, this is the first report which has utilized a quenching solution with ET values. Three procedures were also adopted for extraction. These were boiling, freezing–thawing, and grinding ethanol. Following the analysis of the mass balance, amino acids, organic acids, phosphate sugars, and sugar alcohols were measured using gas chromatography with an isotope dilution mass spectrometry. It was found that using isoamylol with a base solution (5:1, v/v) as a quenching solution and that freezing–thawing in liquid nitrogen within 50% (v/v) methanol as an extracting procedure were the best pairing for the quantitative metabolomics of Streptomyces ZYJ-6, and resulted in average recoveries of close to 100%. The concentration of intracellular metabolites obtained from this new quenching solution was between two and ten times higher than that from 60% (v/v) methanol, which until now has been the most commonly used solution. Our findings are the first systematic quantitative metabolomics tools for Streptomyces ZYJ-6 and, therefore, will be important references for research in fields such as 13C based metabolic flux analysis, multi-omic research and genome-scale metabolic model establishment, as well as for other Streptomyces.
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Production of 5-aminolevulinic Acid by Recombinant Streptomyces coelicolor Expressing hemA from Rhodobacter sphaeroides. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-018-0484-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Daniels W, Bouvin J, Busche T, Rückert C, Simoens K, Karamanou S, Van Mellaert L, Friðjónsson ÓH, Nicolai B, Economou A, Kalinowski J, Anné J, Bernaerts K. Transcriptomic and fluxomic changes in Streptomyces lividans producing heterologous protein. Microb Cell Fact 2018; 17:198. [PMID: 30577858 PMCID: PMC6302529 DOI: 10.1186/s12934-018-1040-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/26/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The Gram-positive Streptomyces lividans TK24 is an attractive host for heterologous protein production because of its high capability to secrete proteins-which favors correct folding and facilitates downstream processing-as well as its acceptance of methylated DNA and its low endogeneous protease activity. However, current inconsistencies in protein yields urge for a deeper understanding of the burden of heterologous protein production on the cell. In the current study, transcriptomics and [Formula: see text]-based fluxomics were exploited to uncover gene expression and metabolic flux changes associated with heterologous protein production. The Rhodothermus marinus thermostable cellulase A (CelA)-previously shown to be successfully overexpressed in S. lividans-was taken as an example protein. RESULTS RNA-seq and [Formula: see text]-based metabolic flux analysis were performed on a CelA-producing and an empty-plasmid strain under the same conditions. Differential gene expression, followed by cluster analysis based on co-expression and co-localization, identified transcriptomic responses related to secretion-induced stress and DNA damage. Furthermore, the OsdR regulon (previously associated with hypoxia, oxidative stress, intercellular signaling, and morphological development) was consistently upregulated in the CelA-producing strain and exhibited co-expression with isoenzymes from the pentose phosphate pathway linked to secondary metabolism. Increased expression of these isoenzymes matches to increased fluxes in the pentose phosphate pathway. Additionally, flux maps of the central carbon metabolism show increased flux through the tricarboxylic acid cycle in the CelA-producing strain. Redirection of fluxes in the CelA-producing strain leads to higher production of NADPH, which can only partly be attributed to increased secretion. CONCLUSIONS Transcriptomic and fluxomic changes uncover potential new leads for targeted strain improvement strategies which may ease the secretion stress and metabolic burden associated with heterologous protein synthesis and secretion, and may help create a more consistently performing S. lividans strain. Yet, links to secondary metabolism and redox balancing should be further investigated to fully understand the S. lividans metabolome under heterologous protein production.
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Affiliation(s)
- Wouter Daniels
- Department of Chemical Engineering, Bio- and Chemical Systems Technology, Reactor Engineering and Safety Section, KU Leuven, Celestijnenlaan 200F, box 2424, 3001, Leuven, Belgium
| | - Jeroen Bouvin
- Department of Chemical Engineering, Bio- and Chemical Systems Technology, Reactor Engineering and Safety Section, KU Leuven, Celestijnenlaan 200F, box 2424, 3001, Leuven, Belgium
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Kenneth Simoens
- Department of Chemical Engineering, Bio- and Chemical Systems Technology, Reactor Engineering and Safety Section, KU Leuven, Celestijnenlaan 200F, box 2424, 3001, Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, box 1037, 3000, Leuven, Belgium
| | - Lieve Van Mellaert
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, box 1037, 3000, Leuven, Belgium
| | | | - Bart Nicolai
- Division of Mechatronics, Biostatistics and Sensors (MeBioS), Department of Biosystems (BIOSYST), KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Anastassios Economou
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, box 1037, 3000, Leuven, Belgium
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Jozef Anné
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, box 1037, 3000, Leuven, Belgium
| | - Kristel Bernaerts
- Department of Chemical Engineering, Bio- and Chemical Systems Technology, Reactor Engineering and Safety Section, KU Leuven, Celestijnenlaan 200F, box 2424, 3001, Leuven, Belgium.
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Gamboa-Suasnavart RA, Valdez-Cruz NA, Gaytan-Ortega G, Reynoso-Cereceda GI, Cabrera-Santos D, López-Griego L, Klöckner W, Büchs J, Trujillo-Roldán MA. The metabolic switch can be activated in a recombinant strain of Streptomyces lividans by a low oxygen transfer rate in shake flasks. Microb Cell Fact 2018; 17:189. [PMID: 30486842 PMCID: PMC6260694 DOI: 10.1186/s12934-018-1035-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/21/2018] [Indexed: 12/16/2022] Open
Abstract
Background In Streptomyces, understanding the switch from primary to secondary metabolism is important for maximizing the production of secondary metabolites such as antibiotics, as well as for optimizing recombinant glycoprotein production. Differences in Streptomyces lividans bacterial aggregation as well as recombinant glycoprotein production and O-mannosylation have been reported due to modifications in the shake flask design. We hypothetized that such differences are related to the metabolic switch that occurs under oxygen-limiting conditions in the cultures. Results Shake flask design was found to affect undecylprodigiosin (RED, a marker of secondary metabolism) production; the RED yield was 12 and 385 times greater in conventional normal Erlenmeyer flasks (NF) than in baffled flasks (BF) and coiled flasks (CF), respectively. In addition, oxygen transfer rates (OTR) and carbon dioxide transfer rates were almost 15 times greater in cultures in CF and BF as compared with those in NF. Based on these data, we obtained respiration quotients (RQ) consistent with aerobic metabolism for CF and BF, but an RQ suggestive of anaerobic metabolism for NF. Conclusion Although the metabolic switch is usually related to limitations in phosphate and nitrogen in Streptomyces sp., our results reveal that it can also be activated by low OTR, dramatically affecting recombinant glycoprotein production and O-mannosylation and increasing RED synthesis in the process. Electronic supplementary material The online version of this article (10.1186/s12934-018-1035-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ramsés A Gamboa-Suasnavart
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, CP. 04510, Ciudad de México, Mexico
| | - Norma A Valdez-Cruz
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, CP. 04510, Ciudad de México, Mexico
| | - Gerardo Gaytan-Ortega
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, CP. 04510, Ciudad de México, Mexico
| | - Greta I Reynoso-Cereceda
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, CP. 04510, Ciudad de México, Mexico
| | - Daniel Cabrera-Santos
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, CP. 04510, Ciudad de México, Mexico
| | - Lorena López-Griego
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, CP. 04510, Ciudad de México, Mexico
| | - Wolf Klöckner
- Department of Biochemical Engineering (AVT.BioVT), RWTH Aachen University of Technology, Forckenbeckstraße 51, 52074, Aachen, Germany.,Bayer AG, Engineering and Technology, Chempark, 51368, Leverkusen, Germany
| | - Jochen Büchs
- Department of Biochemical Engineering (AVT.BioVT), RWTH Aachen University of Technology, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Mauricio A Trujillo-Roldán
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, CP. 04510, Ciudad de México, Mexico.
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Hamed MB, Karamanou S, Ólafsdottir S, Basílio JSM, Simoens K, Tsolis KC, Van Mellaert L, Guðmundsdóttir EE, Hreggvidsson GO, Anné J, Bernaerts K, Fridjonsson OH, Economou A. Large-scale production of a thermostable Rhodothermus marinus cellulase by heterologous secretion from Streptomyces lividans. Microb Cell Fact 2017; 16:232. [PMID: 29274637 PMCID: PMC5741968 DOI: 10.1186/s12934-017-0847-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 12/13/2017] [Indexed: 01/28/2023] Open
Abstract
Background The gene encoding a thermostable cellulase of family 12 was previously isolated from a Rhodothermus marinus through functional screening. CelA is a protein of 260 aminoacyl residues with a 28-residue amino-terminal signal peptide. Mature CelA was poorly synthesized in some Escherichia coli strains and not at all in others. Here we present an alternative approach for its heterologous production as a secreted polypeptide in Streptomyces. Results CelA was successfully over-expressed as a secreted polypeptide in Streptomyces lividans TK24. To this end, CelA was fused C-terminally to the secretory signal peptide of the subtilisin inhibitor protein (Sianidis et al. in J Biotechnol. 121: 498–507, 2006) from Streptomyces venezuelae and a new cloning strategy developed. Optimal growth media and conditions that stall biomass production promote excessive CelA secretion. Under optimal growth conditions in nutrient broth medium, significant amounts of mature CelA (50–90 mg/L or 100–120 mg/g of dry cell weight) are secreted in the spent growth media after 7 days. A protocol to rapidly purify CelA to homogeneity from culture supernatants was developed and specific anti-sera raised against it. Biophysical, biochemical and immmuno-detection analyses indicate that the enzyme is intact, stable and fully functional. CelA is the most thermostable heterologous polypeptide shown to be secreted from S. lividans. Conclusion This study further validates and extends the use of the S. lividans platform for production of heterologous enzymes of industrial importance and extends it to active thermostable enzymes. This study contributes to developing a platform for poly-omics analysis of protein secretion in S. lividans. Electronic supplementary material The online version of this article (10.1186/s12934-017-0847-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mohamed Belal Hamed
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000, Louvain, Belgium.,Department of Molecular Biology, National Research Centre, Dokki, Giza, Egypt
| | - Spyridoula Karamanou
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000, Louvain, Belgium
| | | | - Joana Sofia Martins Basílio
- Bio- & Chemical Systems Technology, Reactor Engineering and Safety Section, Department of Chemical Engineering, KU Leuven, Celestijnenlaan 200F, 3001, Louvain, Belgium
| | - Kenneth Simoens
- Bio- & Chemical Systems Technology, Reactor Engineering and Safety Section, Department of Chemical Engineering, KU Leuven, Celestijnenlaan 200F, 3001, Louvain, Belgium
| | - Kostantinos C Tsolis
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000, Louvain, Belgium
| | - Lieve Van Mellaert
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000, Louvain, Belgium
| | | | | | - Jozef Anné
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000, Louvain, Belgium
| | - Kristel Bernaerts
- Bio- & Chemical Systems Technology, Reactor Engineering and Safety Section, Department of Chemical Engineering, KU Leuven, Celestijnenlaan 200F, 3001, Louvain, Belgium
| | | | - Anastassios Economou
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000, Louvain, Belgium.
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Protein Secretion in Gram-Positive Bacteria: From Multiple Pathways to Biotechnology. Curr Top Microbiol Immunol 2017; 404:267-308. [PMID: 27885530 DOI: 10.1007/82_2016_49] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A number of Gram-positive bacteria are important players in industry as producers of a diverse array of economically interesting metabolites and proteins. As discussed in this overview, several Gram-positive bacteria are valuable hosts for the production of heterologous proteins. In contrast to Gram-negative bacteria, proteins secreted by Gram-positive bacteria are released into the culture medium where conditions for correct folding are more appropriate, thus facilitating the isolation and purification of active proteins. Although seven different protein secretion pathways have been identified in Gram-positive bacteria, the majority of heterologous proteins are produced via the general secretion or Sec pathway. Not all proteins are equally well secreted, because heterologous protein production often faces bottlenecks including hampered secretion, susceptibility to proteases, secretion stress, and metabolic burden. These bottlenecks are associated with reduced yields leading to non-marketable products. In this chapter, besides a general overview of the different protein secretion pathways, possible hurdles that may hinder efficient protein secretion are described and attempts to improve yield are discussed including modification of components of the Sec pathway. Attention is also paid to omics-based approaches that may offer a more rational approach to optimize production of heterologous proteins.
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Patejko M, Jacyna J, Markuszewski MJ. Sample preparation procedures utilized in microbial metabolomics: An overview. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1043:150-157. [PMID: 27693061 DOI: 10.1016/j.jchromb.2016.09.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 09/17/2016] [Accepted: 09/21/2016] [Indexed: 10/21/2022]
Abstract
Bacteria are remarkably diverse in terms of their size, structure and biochemical properties. Due to this fact, it is hard to develop a universal method for handling bacteria cultures during metabolomic analysis. The choice of suitable processing methods constitutes a key element in any analysis, because only appropriate selection of procedures may provide accurate results, leading to reliable conclusions. Because of that, every analytical experiment concerning bacteria requires individually and very carefully planned research methodology. Although every study varies in terms of sample preparation, there are few general steps to follow while planning experiment, like sampling, separation of cells from growth medium, stopping their metabolism and extraction. As a result of extraction, all intracellular metabolites should be washed out from cell environment. What is more, extraction method utilized cannot cause any chemical decomposition or degradation of the metabolome. Furthermore, chosen extraction method should correlate with analytical technique, so it will not disturb or prolong following sample preparation steps. For those reasons, we observe a need to summarize sample preparation procedures currently utilized in microbial metabolomic studies. In the presented overview, papers concerning analysis of extra- and intracellular metabolites, published over the last decade, have been discussed. Presented work gives some basic guidelines that might be useful while planning experiments in microbial metabolomics.
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Affiliation(s)
- Małgorzata Patejko
- Medical University of Gdańsk, Department of Biopharmaceutics and Pharmacodynamics, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
| | - Julia Jacyna
- Medical University of Gdańsk, Department of Biopharmaceutics and Pharmacodynamics, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
| | - Michał J Markuszewski
- Medical University of Gdańsk, Department of Biopharmaceutics and Pharmacodynamics, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland.
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Sayqal A, Xu Y, Trivedi DK, AlMasoud N, Ellis DI, Muhamadali H, Rattray NJW, Webb C, Goodacre R. Metabolic analysis of the response of Pseudomonas putida DOT-T1E strains to toluene using Fourier transform infrared spectroscopy and gas chromatography mass spectrometry. Metabolomics 2016; 12:112. [PMID: 27398079 PMCID: PMC4916193 DOI: 10.1007/s11306-016-1054-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/04/2016] [Indexed: 01/09/2023]
Abstract
INTRODUCTION An exceptionally interesting stress response of Pseudomonas putida strains to toxic substances is the induction of efflux pumps that remove toxic chemical substances from the bacterial cell out to the external environment. To exploit these microorganisms to their full potential a deeper understanding of the interactions between the bacteria and organic solvents is required. Thus, this study focuses on investigation of metabolic changes in P. putida upon exposure to toluene. OBJECTIVE Investigate observable metabolic alterations during interactions of three strains of P. putida (DOT-T1E, and its mutants DOT-T1E-PS28 and DOT-T1E-18) with the aromatic hydrocarbon toluene. METHODS The growth profiles were measured by taking optical density (OD) measurement at 660 nm (OD660) at various time points during incubation. For fingerprinting analysis, Fourier-transform infrared (FT-IR) spectroscopy was used to investigate any phenotypic changes resulting from exposure to toluene. Metabolic profiling analysis was performed using gas chromatography-mass spectrometry (GC-MS). Principal component-discriminant function analysis (PC-DFA) was applied to the FT-IR data while multiblock principal component analysis (MB-PCA) and N-way analysis of variance (N-way ANOVA) were applied to the GC-MS data. RESULTS The growth profiles demonstrated the effect of toluene on bacterial cultures and the results suggest that the mutant P. putida DOT-T1E-18 was more sensitive (significantly affected) to toluene compared to the other two strains. PC-DFA on FT-IR data demonstrated the differentiation between different conditions of toluene on bacterial cells, which indicated phenotypic changes associated with the presence of the solvent within the cell. Fifteen metabolites associated with this phenotypic change, in P. putida due to exposure to solvent, were from central metabolic pathways. Investigation of MB-PCA loading plots and N-way ANOVA for condition | strain × time blocking (dosage of toluene) suggested ornithine as the most significant compound that increased upon solvent exposure. CONCLUSION The combination of metabolic fingerprinting and profiling with suitable multivariate analysis revealed some interesting leads for understanding the mechanism of Pseudomonas strains response to organic solvent exposure.
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Affiliation(s)
- Ali Sayqal
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Yun Xu
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Drupad K. Trivedi
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Najla AlMasoud
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - David I. Ellis
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Howbeer Muhamadali
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Nicholas J. W. Rattray
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Carole Webb
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Royston Goodacre
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
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Muhamadali H, Weaver D, Subaihi A, AlMasoud N, Trivedi DK, Ellis DI, Linton D, Goodacre R. Chicken, beams, and Campylobacter: rapid differentiation of foodborne bacteria via vibrational spectroscopy and MALDI-mass spectrometry. Analyst 2015; 141:111-22. [PMID: 26523729 DOI: 10.1039/c5an01945a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Campylobacter species are one of the main causes of food poisoning worldwide. Despite the availability of established culturing and molecular techniques, due to the fastidious nature of these microorganisms, simultaneous detection and species differentiation still remains challenging. This study focused on the differentiation of eleven Campylobacter strains from six species, using Fourier transform infrared (FT-IR) and Raman spectroscopies, together with matrix-assisted laser desorption ionisation-time of flight-mass spectrometry (MALDI-TOF-MS), as physicochemical approaches for generating biochemical fingerprints. Cluster analysis of data from each of the three analytical approaches provided clear differentiation of each Campylobacter species, which was generally in agreement with a phylogenetic tree based on 16S rRNA gene sequences. Notably, although C. fetus subspecies fetus and venerealis are phylogenetically very closely related, using FT-IR and MALDI-TOF-MS data these subspecies were readily differentiated based on differences in the lipid (2920 and 2851 cm(-1)) and fingerprint regions (1500-500 cm(-1)) of the FT-IR spectra, and the 500-2000 m/z region of the MALDI-TOF-MS data. A finding that was further investigated with targeted lipidomics using liquid chromatography-mass spectrometry (LC-MS). Our results demonstrate that such metabolomics approaches combined with molecular biology techniques may provide critical information and knowledge related to the risk factors, virulence, and understanding of the distribution and transmission routes associated with different strains of foodborne Campylobacter spp.
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Affiliation(s)
- Howbeer Muhamadali
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
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