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Shene C, Leyton A, Flores L, Chavez D, Asenjo JA, Chisti Y. Genome-scale metabolic modeling of Thraustochytrium sp. RT2316-16: Effects of nutrients on metabolism. Biotechnol Bioeng 2024. [PMID: 38500406 DOI: 10.1002/bit.28689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/17/2024] [Accepted: 02/20/2024] [Indexed: 03/20/2024]
Abstract
Marine thraustochytrids produce metabolically important lipids such as the long-chain omega-3 polyunsaturated fatty acids, carotenoids, and sterols. The growth and lipid production in thraustochytrids depends on the composition of the culture medium that often contains yeast extract as a source of amino acids. This work discusses the effects of individual amino acids provided in the culture medium as the only source of nitrogen, on the production of biomass and lipids by the thraustochytrid Thraustochytrium sp. RT2316-16. A reconstructed metabolic network based on the annotated genome of RT2316-16 in combination with flux balance analysis was used to explain the observed growth and consumption of the nutrients. The culture kinetic parameters estimated from the experimental data were used to constrain the flux via the nutrient consumption rates and the specific growth rate of the triacylglycerol-free biomass in the genome-scale metabolic model (GEM) to predict the specific rate of ATP production for cell maintenance. A relationship was identified between the specific rate of ATP production for maintenance and the specific rate of glucose consumption. The GEM and the derived relationship for the production of ATP for maintenance were used in linear optimization problems, to successfully predict the specific growth rate of RT2316-16 in different experimental conditions.
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Affiliation(s)
- Carolina Shene
- Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB), Universidad de La Frontera, Temuco, Chile
| | - Allison Leyton
- Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB), Universidad de La Frontera, Temuco, Chile
| | - Liset Flores
- Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB), Universidad de La Frontera, Temuco, Chile
| | - Daniela Chavez
- Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB), Universidad de La Frontera, Temuco, Chile
| | - Juan A Asenjo
- Department of Chemical Engineering, Biotechnology and Materials, Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Chile, Santiago, Chile
| | - Yusuf Chisti
- Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
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Razmilic V, Nouioui I, Karlyshev A, Jawad R, Trujillo ME, Igual JM, Andrews BA, Asenjo JA, Carro L, Goodfellow M. Micromonospora parastrephiae sp. nov. and Micromonospora tarensis sp. nov., isolated from the rhizosphere of a Parastrephia quadrangularis plant growing in the Salar de Tara region of the Central Andes in Chile. Int J Syst Evol Microbiol 2023; 73. [PMID: 38059605 DOI: 10.1099/ijsem.0.006189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023] Open
Abstract
Two novel Micromonospora strains, STR1-7T and STR1S-6T, were isolated from the rhizosphere of a Parastrephia quadrangularis plant growing in the Salar de Tara region of the Atacama Desert, Chile. Chemotaxonomic, cultural and phenotypic features confirmed that the isolates belonged to the genus Micromonospora. They grew from 20 to 37 °C, from pH7 to 8 and in the presence of up to 3 %, w/v NaCl. The isolates formed distinct branches in Micromonospora gene trees based on 16S rRNA gene sequences and on a multi-locus sequence analysis of conserved house-keeping genes. A phylogenomic tree generated from the draft genomes of the isolates and their closest phylogenetic neighbours showed that isolate STR1-7T is most closely related to Micromonospora orduensis S2509T, and isolate STR1S-6 T forms a distinct branch that is most closely related to 12 validly named Micromonospora species, including Micromonospora saelicesensis the earliest proposed member of the group. The isolates were separated from one another and from their closest phylogenomic neighbours using a combination of chemotaxonomic, genomic and phenotypic features, and by low average nucleotide index and digital DNA-DNA hybridization values. Consequently, it is proposed that isolates STR1-7T and STR1S-6T be recognized as representing new species in the genus Micromonospora, namely as Micromonospora parastrephiae sp. nov. and Micromonospora tarensis sp. nov.; the type strains are STR1-7T (=CECT 9665T=LMG 30768T) and STR1S-6T (=CECT 9666T=LMG 30770T), respectively. Genome mining showed that the isolates have the capacity to produce novel specialized metabolites, notably antibiotics and compounds that promote plant growth, as well as a broad-range of stress-related genes that provide an insight into how they cope with harsh abiotic conditions that prevail in high-altitude Atacama Desert soils.
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Affiliation(s)
- Valeria Razmilic
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
- Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany
| | - Andrey Karlyshev
- Department of Biomolecular Sciences, School of Life Sciences, Pharmacy and Chemistry, Faculty of Health, Science, Social Care and Education, Kingston University London, Kingston upon Thames, KT1 2EE, UK
| | - Rana Jawad
- Department of Biomolecular Sciences, School of Life Sciences, Pharmacy and Chemistry, Faculty of Health, Science, Social Care and Education, Kingston University London, Kingston upon Thames, KT1 2EE, UK
| | - Martha E Trujillo
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain
| | - Jose M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Barbara A Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
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3
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Flores L, Shene C, Asenjo JA, Chisti Y. Coenzyme Q in Thraustochytrium sp. RT2316-16: Effect of the Medium Composition. Mar Drugs 2023; 21:586. [PMID: 37999410 PMCID: PMC10672569 DOI: 10.3390/md21110586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/05/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023] Open
Abstract
Coenzyme Q (CoQ; ubiquinone) is an essential component of the respiratory chain. It is also a potent antioxidant that prevents oxidative damage to DNA, biological membranes, and lipoproteins. CoQ comprises a six-carbon ring with polar substituents that interact with electron acceptors and donors, and a hydrophobic polyisoprenoid chain that allows for its localization in cellular membranes. Human CoQ has 10 isoprenoid units (CoQ10) within the polyisoprenoid chain. Few microorganisms produce CoQ10. This work shows that Thraustochytrium sp. RT2316-16 produces CoQ10 and CoQ9. The CoQ10 content in RT2316-16 depended strongly on the composition of the growth medium and the age of the culture, whereas the CoQ9 content was less variable probably because it served a different function in the cell. Adding p-hydroxybenzoic acid to the culture media positively influenced the CoQ10 content of the cell. The absence of some B vitamins and p-aminobenzoic acid in the culture medium negatively affected the growth of RT2316-16, but reduced the decline in CoQ10 that otherwise occurred during growth. The highest content of CoQ9 and CoQ10 in the biomass were 855 μg g-1 and 10 mg g-1, respectively. The results presented here suggest that the thraustochytrid RT2316-16 can be a potential vehicle for producing CoQ10. Metabolic signals that trigger the synthesis of CoQ10 in RT2316-16 need to be determined for optimizing culture conditions.
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Affiliation(s)
- Liset Flores
- Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB), Universidad de La Frontera, Temuco 4811230, Chile;
| | - Carolina Shene
- Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB), Universidad de La Frontera, Temuco 4811230, Chile;
| | - Juan A. Asenjo
- Centre for Biotechnoloy and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Beauchef 851, Santiago 8370459, Chile;
| | - Yusuf Chisti
- Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus 21030, Terengganu, Malaysia;
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Valdebenito D, Urrutia S, Leyton A, Chisti Y, Asenjo JA, Shene C. Nitrogen Sources Affect the Long-Chain Polyunsaturated Fatty Acids Content in Thraustochytrium sp. RT2316-16. Mar Drugs 2022; 21:md21010015. [PMID: 36662188 PMCID: PMC9864179 DOI: 10.3390/md21010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
The psychrophilic marine microorganism Thraustochytrium sp. RT2316-16 can produce carotenoids as well as lipids containing the omega-3 polyunsaturated fatty acids (PUFA) eicosapentaenoic acid and docosahexaenoic acid. This work reports on the effects of the composition of the culture medium, including certain amino acids, on growth and lipid synthesis by RT2316-16. Compared with the culture on glutamate, the use of lysine, alanine, or serine, increased the content of the omega-3 PUFA in total lipids. In the media that contained yeast extract, glutamate, and glucose, lipid accumulation occurred when organic ammonium was exhausted earlier than glucose. In contrast, lipid mobilization was promoted if glucose was exhausted while organic ammonium (supplied by yeast extract and glutamate) remained in the medium. The total content of carotenoids in the lipid-free biomass decreased during the first 12 to 24 h of culture, simultaneously with a decrease in the total lipid content of the biomass. The experimental data suggested a possible interrelationship between the metabolism of carotenoids and lipids. A high content of omega-3 PUFA in the total lipids could be obtained by growing the thraustochytrid in a medium with a low glucose concentration (6 g L-1) and a high concentration of organic nitrogen (yeast extract 12 g L-1; glutamate 1.06 g L-1), after glucose was exhausted. These observations may guide the development of a strategy to enhance omega-3 PUFA in the biomass.
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Affiliation(s)
- Diego Valdebenito
- Center for Biotechnology and Bioengineering (CeBiB), Center of Food Biotechnology and Bioseparations, BIOREN and Department of Chemical Engineering, Universidad de La Frontera, Francisco Salazar 01145, Temuco 4780000, Chile
| | - Sebastián Urrutia
- Center for Biotechnology and Bioengineering (CeBiB), Center of Food Biotechnology and Bioseparations, BIOREN and Department of Chemical Engineering, Universidad de La Frontera, Francisco Salazar 01145, Temuco 4780000, Chile
| | - Allison Leyton
- Center for Biotechnology and Bioengineering (CeBiB), Center of Food Biotechnology and Bioseparations, BIOREN and Department of Chemical Engineering, Universidad de La Frontera, Francisco Salazar 01145, Temuco 4780000, Chile
| | - Yusuf Chisti
- Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus 21030, Terengganu, Malaysia
| | - Juan A. Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Beauchef 851, Santiago 8370459, Chile
| | - Carolina Shene
- Center for Biotechnology and Bioengineering (CeBiB), Center of Food Biotechnology and Bioseparations, BIOREN and Department of Chemical Engineering, Universidad de La Frontera, Francisco Salazar 01145, Temuco 4780000, Chile
- Correspondence:
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5
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Oróstica KY, Saez-Hidalgo J, de Santiago PR, Rivas S, Contreras S, Navarro G, Asenjo JA, Olivera-Nappa Á, Armisén R. Total mutational load and clinical features as predictors of the metastatic status in lung adenocarcinoma and squamous cell carcinoma patients. Lab Invest 2022; 20:373. [PMID: 35982500 PMCID: PMC9389677 DOI: 10.1186/s12967-022-03572-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 08/04/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Recently, extensive cancer genomic studies have revealed mutational and clinical data of large cohorts of cancer patients. For example, the Pan-Lung Cancer 2016 dataset (part of The Cancer Genome Atlas project), summarises the mutational and clinical profiles of different subtypes of Lung Cancer (LC). Mutational and clinical signatures have been used independently for tumour typification and prediction of metastasis in LC patients. Is it then possible to achieve better typifications and predictions when combining both data streams? METHODS In a cohort of 1144 Lung Adenocarcinoma (LUAD) and Lung Squamous Cell Carcinoma (LSCC) patients, we studied the number of missense mutations (hereafter, the Total Mutational Load TML) and distribution of clinical variables, for different classes of patients. Using the TML and different sets of clinical variables (tumour stage, age, sex, smoking status, and packs of cigarettes smoked per year), we built Random Forest classification models that calculate the likelihood of developing metastasis. RESULTS We found that LC patients different in age, smoking status, and tumour type had significantly different mean TMLs. Although TML was an informative feature, its effect was secondary to the "tumour stage" feature. However, its contribution to the classification is not redundant with the latter; models trained using both TML and tumour stage performed better than models trained using only one of these variables. We found that models trained in the entire dataset (i.e., without using dimensionality reduction techniques) and without resampling achieved the highest performance, with an F1 score of 0.64 (95%CrI [0.62, 0.66]). CONCLUSIONS Clinical variables and TML should be considered together when assessing the likelihood of LC patients progressing to metastatic states, as the information these encode is not redundant. Altogether, we provide new evidence of the need for comprehensive diagnostic tools for metastasis.
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Affiliation(s)
- Karen Y Oróstica
- Instituto de Investigación Interdisciplinaria, Vicerrectoría Académica, Universidad de Talca, 3460000, Talca, Chile
| | - Juan Saez-Hidalgo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, 8370456, Santiago, Chile.,Department of Computer Science, University of Chile, 8370459, Santiago, Chile
| | - Pamela R de Santiago
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Solange Rivas
- Department of Basic Clinical Oncology, Faculty of Medicine, University of Chile, Santiago, Chile.,Centro de Genética Y Genómica, Instituto de Ciencias E Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, 7590943, Santiago, Chile
| | - Sebastian Contreras
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, 8370456, Santiago, Chile.,Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
| | - Gonzalo Navarro
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, 8370456, Santiago, Chile.,Department of Computer Science, University of Chile, 8370459, Santiago, Chile
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, 8370456, Santiago, Chile
| | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, 8370456, Santiago, Chile.
| | - Ricardo Armisén
- Centro de Genética Y Genómica, Instituto de Ciencias E Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, 7590943, Santiago, Chile.
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6
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Medina-Ortiz D, Contreras S, Amado-Hinojosa J, Torres-Almonacid J, Asenjo JA, Navarrete M, Olivera-Nappa Á. Generalized Property-Based Encoders and Digital Signal Processing Facilitate Predictive Tasks in Protein Engineering. Front Mol Biosci 2022; 9:898627. [PMID: 35911960 PMCID: PMC9329607 DOI: 10.3389/fmolb.2022.898627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
Computational methods in protein engineering often require encoding amino acid sequences, i.e., converting them into numeric arrays. Physicochemical properties are a typical choice to define encoders, where we replace each amino acid by its value for a given property. However, what property (or group thereof) is best for a given predictive task remains an open problem. In this work, we generalize property-based encoding strategies to maximize the performance of predictive models in protein engineering. First, combining text mining and unsupervised learning, we partitioned the AAIndex database into eight semantically-consistent groups of properties. We then applied a non-linear PCA within each group to define a single encoder to represent it. Then, in several case studies, we assess the performance of predictive models for protein and peptide function, folding, and biological activity, trained using the proposed encoders and classical methods (One Hot Encoder and TAPE embeddings). Models trained on datasets encoded with our encoders and converted to signals through the Fast Fourier Transform (FFT) increased their precision and reduced their overfitting substantially, outperforming classical approaches in most cases. Finally, we propose a preliminary methodology to create de novo sequences with desired properties. All these results offer simple ways to increase the performance of general and complex predictive tasks in protein engineering without increasing their complexity.
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Affiliation(s)
- David Medina-Ortiz
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas, Chile
| | - Sebastian Contreras
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- *Correspondence: Sebastian Contreras, ; Álvaro Olivera-Nappa,
| | - Juan Amado-Hinojosa
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
- Departamento de Ingeniería Química, Biotecnología y Materiales, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Jorge Torres-Almonacid
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas, Chile
| | - Juan A. Asenjo
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
- Departamento de Ingeniería Química, Biotecnología y Materiales, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | | | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
- Departamento de Ingeniería Química, Biotecnología y Materiales, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
- *Correspondence: Sebastian Contreras, ; Álvaro Olivera-Nappa,
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Paredes P, Larama G, Flores L, Leyton A, Ili CG, Asenjo JA, Chisti Y, Shene C. Temperature Differentially Affects Gene Expression in Antarctic Thraustochytrid Oblongichytrium sp. RT2316-13. Mar Drugs 2020; 18:md18110563. [PMID: 33217919 PMCID: PMC7698632 DOI: 10.3390/md18110563] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/08/2020] [Accepted: 11/11/2020] [Indexed: 01/17/2023] Open
Abstract
Oblongichytrium RT2316-13 synthesizes lipids rich in eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). The content of these fatty acids in the total lipids depended on growth temperature. Sequencing technology was used in this work to examine the thraustochytrid's response to a decrease in growth temperature from 15 °C to 5 °C. Around 4% (2944) of the genes were differentially expressed (DE) and only a few of the DE genes (533 upregulated; 206 downregulated) had significant matches to those in the SwissProt database. Most of the annotated DE genes were related to cell membrane composition (fatty acids, sterols, phosphatidylinositol), the membrane enzymes linked to cell energetics, and membrane structure (cytoskeletal proteins and enzymes). In RT2316-13, the synthesis of long-chain polyunsaturated fatty acids occurred through ω3- and ω6-pathways. Enzymes of the alternative pathways (Δ8-desaturase and Δ9-elongase) were also expressed. The upregulation of the genes coding for a Δ5-desaturase and a Δ5-elongase involved in the synthesis of EPA and DHA, explained the enrichment of total lipid with these two long-chain fatty acids at the low temperature. This molecular response has the potential to be used for producing microbial lipids with a fatty acids profile similar to that of fish oils.
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Affiliation(s)
- Paris Paredes
- Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB), Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco 4780000, Chile; (P.P.); (L.F.); (A.L.)
| | - Giovanni Larama
- Centro de Modelación y Computación Científica, Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco 4780000, Chile;
| | - Liset Flores
- Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB), Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco 4780000, Chile; (P.P.); (L.F.); (A.L.)
| | - Allison Leyton
- Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB), Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco 4780000, Chile; (P.P.); (L.F.); (A.L.)
| | - Carmen Gloria Ili
- Centro de Excelencia en Medicina Traslacional—Scientific and Technological Bioresource Nucleus (CEMT-BIOREN), Universidad de La Frontera, Av. Alemania 0478, Temuco 4810296, Chile;
| | - Juan A. Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, Universidad de Chile, Beauchef 851, Santiago 8370459, Chile;
| | - Yusuf Chisti
- School of Engineering, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand;
| | - Carolina Shene
- Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB), Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco 4780000, Chile; (P.P.); (L.F.); (A.L.)
- Correspondence: ; Tel.: +56-45-232-5491
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Jarmusch SA, Lagos-Susaeta D, Diab E, Salazar O, Asenjo JA, Ebel R, Jaspars M. Iron-meditated fungal starvation by lupine rhizosphere-associated and extremotolerant Streptomyces sp. S29 desferrioxamine production. Mol Omics 2020; 17:95-107. [PMID: 33185220 DOI: 10.1039/d0mo00084a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Siderophores are iron-chelating compounds that aid iron uptake, one of the key strategies for microorganisms to carve out ecological niches in microbially diverse environments. Desferrioxamines are the principal siderophores produced by Streptomyces spp. Their biosynthesis has been well studied and as a consequence, the chemical potential of the pathway continues to expand. With all of this in mind, our study aimed to explore extremotolerant and lupine rhizosphere-derived Streptomyces sp. S29 for its potential antifungal capabilities. Cocultivation of isolate S29 was carried out with Aspergillus niger and Botrytis cinerea, both costly fungal phytopathogens in the wine industry, to simulate their interaction within the rhizosphere. The results indicate that not only is Streptomyces sp. S29 extraordinary at producing hydroxamate siderophores but uses siderophore production as a means to 'starve' the fungi of iron. High resolution LC-MS/MS followed by GNPS molecular networking was used to observe the datasets for desferrioxamines and guided structure elucidation of new desferrioxamine analogues. Comparing the new chemistry, using tools like molecular networking and MS2LDA, with the known biosynthesis, we show that the chemical potential of the desferrioxamine pathway has further room for exploration.
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Affiliation(s)
- Scott A Jarmusch
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen AB24 3UE, Scotland, UK.
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9
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Lagos-Susaeta D, Salazar O, Asenjo JA. openPFGE: An open source and low cost pulsed-field gel electrophoresis equipment. HardwareX 2020; 8:e00128. [PMID: 35498240 PMCID: PMC9041189 DOI: 10.1016/j.ohx.2020.e00128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 06/14/2023]
Abstract
DNA electrophoresis is a fundamental technique in molecular biology that allows the separation of DNA molecules up to ~50 Kbp. Pulsed-field gel electrophoresis [PFGE] is a variation of the conventional DNA electrophoresis technique that allows the separation of very large DNA molecules up to ~10 Mbp. PFGE equipment is very expensive and it becomes an access barrier to many laboratories. Also, just a few privative designs of the equipment are available and it becomes difficult for the community to improve or customize their functioning. Here, we provide an open source PFGE equipment capable of the separation of DNA molecules up to, at least, ~2 Mbp and at low cost: USD$850, about 3% of the price of typical commercial equipment.
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Affiliation(s)
- Diego Lagos-Susaeta
- Corresponding author at: Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Santiago, Chile.
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10
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Shene C, Paredes P, Flores L, Leyton A, Asenjo JA, Chisti Y. Dynamic flux balance analysis of biomass and lipid production by Antarctic thraustochytrid
Oblongichytrium
sp. RT2316‐13. Biotechnol Bioeng 2020; 117:3006-3017. [DOI: 10.1002/bit.27463] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 06/03/2020] [Accepted: 06/16/2020] [Indexed: 01/18/2023]
Affiliation(s)
- Carolina Shene
- Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB) Universidad de La Frontera Temuco Chile
| | - Paris Paredes
- Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB) Universidad de La Frontera Temuco Chile
| | - Liset Flores
- Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB) Universidad de La Frontera Temuco Chile
| | - Allison Leyton
- Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB) Universidad de La Frontera Temuco Chile
| | - Juan A. Asenjo
- Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB) Universidad de Chile Santiago Chile
| | - Yusuf Chisti
- School of Engineering Massey University Palmerston North New Zealand
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Cortés-Albayay C, Jarmusch SA, Trusch F, Ebel R, Andrews BA, Jaspars M, Asenjo JA. Downsizing Class II Lasso Peptides: Genome Mining-Guided Isolation of Huascopeptin Containing the First Gly1-Asp7 Macrocycle. J Org Chem 2020; 85:1661-1667. [DOI: 10.1021/acs.joc.9b02231] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Carlos Cortés-Albayay
- Centre for Biotechnology and Bioengineering, CeBiB, Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago 8370450, Chile
| | - Scott A. Jarmusch
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen AB24 3UE, Scotland, U.K
| | - Franziska Trusch
- Institute of Medical Sciences, University of Aberdeen, Foresterhill AB25 2ZD, Scotland, U.K
- Division of Plant Sciences, College of Life Science, University of Dundee (at JHI), Errol Road, Invergowrie, Dundee DD2 5DA, U.K
| | - Rainer Ebel
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen AB24 3UE, Scotland, U.K
| | - Barbara A. Andrews
- Centre for Biotechnology and Bioengineering, CeBiB, Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago 8370450, Chile
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen AB24 3UE, Scotland, U.K
| | - Juan A. Asenjo
- Centre for Biotechnology and Bioengineering, CeBiB, Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago 8370450, Chile
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12
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Contador CA, Veas-Castillo L, Tapia E, Antipán M, Miranda N, Ruiz-Tagle B, García-Araya J, Andrews BA, Marin M, Dorador C, Asenjo JA. Atacama Database: a platform of the microbiome of the Atacama Desert. Antonie Van Leeuwenhoek 2019; 113:185-195. [PMID: 31535335 DOI: 10.1007/s10482-019-01328-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/07/2019] [Indexed: 11/30/2022]
Abstract
The Atacama Desert is one of the oldest and driest places on Earth. In the last decade, microbial richness and diversity has been acknowledged as an important biological resource of this region. Owing to the value of the microbial diversity apparent in potential biotechnology applications and conservation purposes, it is necessary to catalogue these microbial communities to promote research activities and help to preserve the wide range of ecological niches of the Atacama region. A prototype Atacama Database has been designed and it provides a description of the rich microbial diversity of the Atacama Desert, and helps to visualise available literature resources. Data has been collected, curated, and organised into several categories to generate a single record for each organism in the database that covers classification, isolation metadata, morphology, physiology, genome and metabolism information. The current version of Atacama Database contains 2302 microorganisms and includes cultured and uncultured organisms retrieved from different environments within the desert between 1984 and 2016. These organisms are distributed in bacterial, archaeal or eukaryotic domains, along with those that are unclassified taxonomically. The initial prototype of the Atacama Database includes a basic search and taxonomic and advanced search tools to allow identification and comparison of microbial populations, and space distribution within this biome. A geolocation search was implemented to visualise the microbial diversity of the ecological niches defined by sectors and extract general information of the sampling sites. This effort will aid understanding of the microbial ecology of the desert, microbial population dynamics, seasonal behaviour, impact of climate change over time, and reveal further biotechnological applications of these microorganisms. The Atacama Database is freely available at: https://www.atacamadb.cl.
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Affiliation(s)
- Carolina A Contador
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile.
| | - Luis Veas-Castillo
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática (DIINF), Universidad de Santiago de Chile, Santiago, Chile
| | - Emilio Tapia
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática (DIINF), Universidad de Santiago de Chile, Santiago, Chile
| | - Marcela Antipán
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Noemi Miranda
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Benjamín Ruiz-Tagle
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática (DIINF), Universidad de Santiago de Chile, Santiago, Chile
| | - Jonathan García-Araya
- Centre for Biotechnology and Bioengineering (CeBiB), Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Barbara A Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Mauricio Marin
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática (DIINF), Universidad de Santiago de Chile, Santiago, Chile
| | - Cristina Dorador
- Centre for Biotechnology and Bioengineering (CeBiB), Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
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13
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Carro L, Castro JF, Razmilic V, Nouioui I, Pan C, Igual JM, Jaspars M, Goodfellow M, Bull AT, Asenjo JA, Klenk HP. Uncovering the potential of novel micromonosporae isolated from an extreme hyper-arid Atacama Desert soil. Sci Rep 2019; 9:4678. [PMID: 30886188 PMCID: PMC6423291 DOI: 10.1038/s41598-019-38789-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/12/2018] [Indexed: 11/29/2022] Open
Abstract
The taxonomic status, biotechnological and ecological potential of several Micromonospora strains isolated from an extreme hyper arid Atacama Desert soil were determined. Initially, a polyphasic study was undertaken to clarify the taxonomic status of five micromonosporae, strains LB4, LB19, LB32T, LB39T and LB41, isolated from an extreme hyper-arid soil collected from one of the driest regions of the Atacama Desert. All of the isolates were found to have chemotaxonomic, cultural and morphological properties consistent with their classification in the genus Micromonospora. Isolates LB32T and LB39T were distinguished from their nearest phylogenetic neighbours and proposed as new species, namely as Micromonospora arida sp. nov. and Micromonospora inaquosa sp. nov., respectively. Eluted methanol extracts of all of the isolates showed activity against a panel of bacterial and fungal indicator strains, notably against multi-drug resistant Klebsiella pneumoniae ATCC 700603 while isolates LB4 and LB41 showed pronounced anti-tumour activity against HepG2 cells. Draft genomes generated for the isolates revealed a rich source of novel biosynthetic gene clusters, some of which were unique to individual strains thereby opening up the prospect of selecting especially gifted micromonosporae for natural product discovery. Key stress-related genes detected in the genomes of all of the isolates provided an insight into how micromonosporae adapt to the harsh environmental conditions that prevail in extreme hyper-arid Atacama Desert soils.
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Affiliation(s)
- Lorena Carro
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain. .,School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK.
| | - Jean Franco Castro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK.,Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Beauchef 851, Santiago, Chile.,Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Scotland, UK
| | - Valeria Razmilic
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK.,Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Beauchef 851, Santiago, Chile
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
| | - Che Pan
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
| | - José M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain.,Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca, Unidad Asociada al CSIC, Spain
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Scotland, UK
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
| | - Alan T Bull
- School of Biosciences, University of Kent Canterbury, Canterbury, UK
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Beauchef 851, Santiago, Chile
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
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Contador CA, Rodríguez V, Andrews BA, Asenjo JA. Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora. BMC Syst Biol 2019; 13:11. [PMID: 30665399 PMCID: PMC6341766 DOI: 10.1186/s12918-019-0683-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 01/11/2019] [Indexed: 11/10/2022]
Abstract
BACKGROUND There is little published regarding metabolism of Salinispora species. In continuation with efforts performed towards this goal, this study is focused on new insights into the metabolism of the three-identified species of Salinispora using constraints-based modeling. At present, only one manually curated genome-scale metabolic model (GSM) for Salinispora tropica strain CNB-440T has been built despite the role of Salinispora strains in drug discovery. RESULTS Here, we updated, and expanded the scope of the model of Salinispora tropica CNB-440T, and GSMs were constructed for two sequenced type strains covering the three-identified species. We also constructed a Salinispora core model that contains the genes shared by 93 sequenced strains and a few non-conserved genes associated with essential reactions. The models predicted no auxotrophies for essential amino acids, which was corroborated experimentally using a defined minimal medium (DMM). Experimental observations suggest possible sulfur accumulation. The Core metabolic content shows that the biosynthesis of specialised metabolites is the less conserved subsystem. Sets of reactions were analyzed to explore the differences between the reconstructions. Unique reactions associated to each GSM were mainly due to genome sequence data except for the ST-CNB440 reconstruction. In this case, additional reactions were added from experimental evidence. This reveals that by reaction content the ST-CNB440 model is different from the other species models. The differences identified in reaction content between models gave rise to different functional predictions of essential nutrient usage by each species in DMM. Furthermore, models were used to evaluate in silico single gene knockouts under DMM and complex medium. Cluster analysis of these results shows that ST-CNB440, and SP-CNR114 models are more similar when considering predicted essential genes. CONCLUSIONS Models were built for each of the three currently identified Salinispora species, and a core model representing the conserved metabolic capabilities of Salinispora was constructed. Models will allow in silico metabolism studies of Salinispora strains, and help researchers to guide and increase the production of specialised metabolites. Also, models can be used as templates to build GSMs models of closely related organisms with high biotechnology potential.
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Affiliation(s)
- Carolina A. Contador
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
- Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Vida Rodríguez
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Barbara A. Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Juan A. Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
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Shene C, Asenjo JA, Chisti Y. Metabolic modelling and simulation of the light and dark metabolism of Chlamydomonas reinhardtii. Plant J 2018; 96:1076-1088. [PMID: 30168220 DOI: 10.1111/tpj.14078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 08/15/2018] [Accepted: 08/20/2018] [Indexed: 05/10/2023]
Abstract
A metabolic network model of the green microalga Chlamydomonas reinhardtii was used to characterize photoautotrophic and heterotrophic (i.e. growth on stored compounds) growth under light and dark, respectively. The metabolic network comprised 2514 reactions distributed among nine intracellular compartments and the extracellular space. The metabolic network included all the key biochemical pathways for synthesis and metabolism of starch and triacylglycerols (TAGs). Under light and nitrogen limitation, the model simulated the accumulation of the energy-rich compounds (TAGs and starch) in the cell. In the dark, the model could simulate cell growth and maintenance on stored compounds. The model-predicted consumption rates of storage compounds (starch or TAGs) to enable growth in the dark, were found to be greater than the rates of synthesis under light. This implied utilization of the storage compounds for cell maintenance in the dark. Under constant illumination, the simulations of cell growth and intracellular starch content agreed closely with independent experimental data. In other simulations, compared with the case without photorespiration, light uptake rate increased 1.04-fold when the ratio of the rates of oxygenation and carboxylation (Rubisco) was 0.1. Although extensive experimental work exists on culture and physiology of microalgae, it does not allow quantitative predictions of the influence of dark metabolism on the productivity of metabolites to be made. This limitation is overcome using the present model. A metabolic network model of Chlamydomonas reinhardtii is shown to simulate growth and synthesis of energy-rich compounds (triacylglycerols and starch) under light. The same model also simulates dark growth and maintenance through consumption of the stored energy-rich compounds.
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Affiliation(s)
- Carolina Shene
- Department of Chemical Engineering and Center of Food Biotechnology and Bioseparations, BIOREN, Universidad de La Frontera, Casilla 54-D, Temuco, Chile
- Centre for Biotechnology and Bioengineering (CeBiB), Universidad de La Frontera, Temuco, Chile
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, Universidad de Chile, Beauchef 851, Santiago, Chile
| | - Yusuf Chisti
- School of Engineering, Massey University, Private Bag 11 222, Palmerston North, New Zealand
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16
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Sanchez AC, Ravanal MC, Andrews BA, Asenjo JA. Heterologous expression and biochemical characterization of a novel cold-active α-amylase from the Antarctic bacteria Pseudoalteromonas sp. 2-3. Protein Expr Purif 2018; 155:78-85. [PMID: 30496815 DOI: 10.1016/j.pep.2018.11.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/20/2018] [Accepted: 11/25/2018] [Indexed: 11/27/2022]
Abstract
α-Amylase is an endo-acting enzyme which catalyzes random hydrolysis of starch. These enzymes are used in various biotechnological processes including the textile, paper, food, biofuels, detergents and pharmaceutical industries. The use of active enzymes at low temperatures has a high potential because these enzymes would avoid the demand for heating during the process thereby reducing costs. In this work, the gene of α-amylase from Pseudoalteromonas sp. 2-3 (Antarctic bacteria) has been sequenced and expressed in Escherichia coli BL21(DE3). The ORF of the α-amylase gene cloned into pET22b(+) is 1824 bp long and codes for a protein of 607 amino acid residues including a His6-tag. The mature protein has a calculated molecular mass of 68.8 kDa. Recombinant α-amylase was purified with Ni-NTA affinity chromatography. The purified enzyme is active on potato starch with a Km of 6.94 mg/ml and Vmax of 0.27 mg/ml*min. The pH optimum is 8.0 and the optimal temperature is 20 °C. This enzyme was strongly activated by Ca2+; results consistent with other α-amylases. To the best of our knowledge, this enzyme has the lowest temperature optimum so far reported for α-amylases.
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Affiliation(s)
- Anamaria C Sanchez
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile.
| | - María Cristina Ravanal
- Instituto de Ciencia y Tecnología de los Alimentos (ICYTAL), Facultad de Ciencias Agrarias, Universidad Austral de Chile, Avda. Julio Sarrazín s/n, Isla Teja, Valdivia, Chile.
| | - Barbara A Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile.
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile.
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17
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Castro JF, Nouioui I, Sangal V, Choi S, Yang SJ, Kim BY, Trujillo ME, Riesco R, Montero-Calasanz MDC, Rahmani TPD, Bull AT, Sutcliffe IC, Asenjo JA, Andrews B, Goodfellow M. Blastococcus atacamensis sp. nov., a novel strain adapted to life in the Yungay core region of the Atacama Desert. Int J Syst Evol Microbiol 2018; 68:2712-2721. [PMID: 29969090 DOI: 10.1099/ijsem.0.002828] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A polyphasic study was undertaken to establish the taxonomic status of a Blastococcus strain isolated from an extreme hyper-arid Atacama Desert soil. The isolate, strain P6T, was found to have chemotaxonomic and morphological properties consistent with its classification in the genus Blastococcus. It was shown to form a well-supported branch in the Blastococcus 16S rRNA gene tree together with the type strains of Blastococcus capsensis and Blastococcus saxobsidens and was distinguished from the latter, its close phylogenetic neighbour, by a broad range of phenotypic properties. The draft genome sequence of isolate P6T showed 84.6 % average nucleotide identity, 83.0 % average amino acid identity and a digital DNA-DNA hybridisation value of 27.8 % in comparison with the genome sequence of B. saxobsidens DSM 44509T, values consistent with its assignment to a separate species. Based on these data it is proposed that isolate P6T (NCIMB 15090T=NRRL B-65468T) be assigned to the genus Blastococcus as Blastococcus atacamensis sp. nov. Analysis of the whole genome sequence of B. atacamensis P6T, with 3778 open reading frames and a genome size of 3.9 Mb showed the presence of genes and gene clusters that encode for properties that reflect its adaptation to the extreme environmental conditions that prevail in Atacama Desert soils.
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Affiliation(s)
- Jean Franco Castro
- 1School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
- 2Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - Imen Nouioui
- 1School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Vartul Sangal
- 3Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Seonbin Choi
- 4ChunLab, Inc., 1, Gwanaka-ro, Gwanak-gu, Seoul 151015, Republic of Korea
| | - Seung-Jo Yang
- 4ChunLab, Inc., 1, Gwanaka-ro, Gwanak-gu, Seoul 151015, Republic of Korea
| | - Byung-Yong Kim
- 4ChunLab, Inc., 1, Gwanaka-ro, Gwanak-gu, Seoul 151015, Republic of Korea
| | - Martha E Trujillo
- 5Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Raul Riesco
- 4ChunLab, Inc., 1, Gwanaka-ro, Gwanak-gu, Seoul 151015, Republic of Korea
| | | | - Tara P D Rahmani
- 1School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Alan T Bull
- 6School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Iain C Sutcliffe
- 3Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Juan A Asenjo
- 2Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - Barbara Andrews
- 2Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - Michael Goodfellow
- 1School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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18
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Saavedra JM, Azócar MA, Rodríguez V, Ramírez-Sarmiento CA, Andrews BA, Asenjo JA, Parra LP. Relevance of Local Flexibility Near the Active Site for Enzymatic Catalysis: Biochemical Characterization and Engineering of Cellulase Cel5A FromBacillus agaradherans. Biotechnol J 2018; 13:e1700669. [DOI: 10.1002/biot.201700669] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/19/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Juan M. Saavedra
- Department of Chemical Engineering and Biotechnology; Centre for Biotechnology and Bioengineering (CeBiB); University of Chile; Santiago Chile
| | - Mauricio A. Azócar
- Department of Chemical Engineering and Biotechnology; Centre for Biotechnology and Bioengineering (CeBiB); University of Chile; Santiago Chile
| | - Vida Rodríguez
- Department of Chemical Engineering and Biotechnology; Centre for Biotechnology and Bioengineering (CeBiB); University of Chile; Santiago Chile
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering; Schools of Engineering,; Medicine and Biological Sciences; Pontificia Universidad Católica de Chile; Avenida Vicuña Mackenna 4860 Santiago 7820436 Chile
| | - Barbara A. Andrews
- Department of Chemical Engineering and Biotechnology; Centre for Biotechnology and Bioengineering (CeBiB); University of Chile; Santiago Chile
| | - Juan A. Asenjo
- Department of Chemical Engineering and Biotechnology; Centre for Biotechnology and Bioengineering (CeBiB); University of Chile; Santiago Chile
| | - Loreto P. Parra
- Institute for Biological and Medical Engineering; Schools of Engineering,; Medicine and Biological Sciences; Pontificia Universidad Católica de Chile; Avenida Vicuña Mackenna 4860 Santiago 7820436 Chile
- Department of Chemical and Bioprocesses Engineering; School of Engineering; Pontificia Universidad Católica de Chile; Santiago Chile
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19
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Razmilic V, Castro JF, Andrews B, Asenjo JA. Analysis of metabolic networks of Streptomyces leeuwenhoekii C34 by means of a genome scale model: Prediction of modifications that enhance the production of specialized metabolites. Biotechnol Bioeng 2018; 115:1815-1828. [PMID: 29578590 DOI: 10.1002/bit.26598] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/03/2018] [Accepted: 03/19/2018] [Indexed: 11/08/2022]
Abstract
The first genome scale model (GSM) for Streptomyces leeuwenhoekii C34 was developed to study the biosynthesis pathways of specialized metabolites and to find metabolic engineering targets for enhancing their production. The model, iVR1007, consists of 1,722 reactions, 1,463 metabolites, and 1,007 genes, it includes the biosynthesis pathways of chaxamycins, chaxalactins, desferrioxamines, ectoine, and other specialized metabolites. iVR1007 was validated using experimental information of growth on 166 different sources of carbon, nitrogen and phosphorous, showing an 83.7% accuracy. The model was used to predict metabolic engineering targets for enhancing the biosynthesis of chaxamycins and chaxalactins. Gene knockouts, such as sle03600 (L-homoserine O-acetyltransferase), and sle39090 (trehalose-phosphate synthase), that enhance the production of the specialized metabolites by increasing the pool of precursors were identified. Using the algorithm of flux scanning based on enforced objective flux (FSEOF) implemented in python, 35 and 25 over-expression targets for increasing the production of chaxamycin A and chaxalactin A, respectively, that were not directly associated with their biosynthesis routes were identified. Nineteen over-expression targets that were common to the two specialized metabolites studied, like the over-expression of the acetyl carboxylase complex (sle47660 (accA) and any of the following genes: sle44630 (accA_1) or sle39830 (accA_2) or sle27560 (bccA) or sle59710) were identified. The predicted knockouts and over-expression targets will be used to perform metabolic engineering of S. leeuwenhoekii C34 and obtain overproducer strains.
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Affiliation(s)
- Valeria Razmilic
- Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Chile, Santiago, Chile
| | - Jean F Castro
- Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Chile, Santiago, Chile
| | - Barbara Andrews
- Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Chile, Santiago, Chile
| | - Juan A Asenjo
- Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Chile, Santiago, Chile
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Castro JF, Nouioui I, Sangal V, Trujillo ME, Montero-Calasanz MDC, Rahmani T, Bull AT, Asenjo JA, Andrews BA, Goodfellow M. Geodermatophilus chilensis sp. nov., from soil of the Yungay core-region of the Atacama Desert, Chile. Syst Appl Microbiol 2018; 41:427-436. [PMID: 29789182 DOI: 10.1016/j.syapm.2018.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/14/2018] [Accepted: 03/22/2018] [Indexed: 01/20/2023]
Abstract
A polyphasic study was undertaken to establish the taxonomic status of three representative Geodermatophilus strains isolated from an extreme hyper-arid Atacama Desert soil. The strains, isolates B12T, B20 and B25, were found to have chemotaxonomic and morphological properties characteristic of the genus Geodermatophilus. The isolates shared a broad range of chemotaxonomic, cultural and physiological features, formed a well-supported branch in the Geodermatophilus 16S rRNA gene tree in which they were most closely associated with the type strain of Geodermatophilus obscurus. They were distinguished from the latter by BOX-PCR fingerprint patterns and by chemotaxonomic and other phenotypic properties. Average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between the whole genome sequences of isolate B12T and G. obscurus DSM 43160T were 89.28%, 87.27% and 37.4%, respectively, metrics consistent with its classification as a separate species. On the basis of these data, it is proposed that the isolates be assigned to the genus Geodermatophilus as Geodermatophilus chilensis sp. nov. with isolate B12T (CECT 9483T=NCIMB 15089T) as the type strain. Analysis of the whole genome sequence of G. chilensis B12T with 5341 open reading frames and a genome size of 5.5Mb highlighted genes and gene clusters that encode for properties relevant to its adaptation to extreme environmental conditions prevalent in extreme hyper-arid Atacama Desert soils.
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Affiliation(s)
- Jean Franco Castro
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom; Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, United Kingdom
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | | | - Tara Rahmani
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Alan T Bull
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, United Kingdom
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - Barbara A Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom.
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Carro L, Razmilic V, Nouioui I, Richardson L, Pan C, Golinska P, Asenjo JA, Bull AT, Klenk HP, Goodfellow M. Hunting for cultivable Micromonospora strains in soils of the Atacama Desert. Antonie Van Leeuwenhoek 2018; 111:1375-1387. [PMID: 29480426 DOI: 10.1007/s10482-018-1049-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 02/16/2018] [Indexed: 02/01/2023]
Abstract
Innovative procedures were used to selectively isolate small numbers of Micromonospora strains from extreme hyper-arid and high altitude Atacama Desert soils. Micromonosporae were recognised on isolation plates by their ability to produce filamentous microcolonies that were strongly attached to the agar. Most of the isolates formed characteristic orange colonies that lacked aerial hyphae and turned black on spore formation, whereas those from the high altitude soil were dry, blue-green and covered by white aerial hyphae. The isolates were assigned to seven multi- and eleven single-membered groups based on BOX-PCR profiles. Representatives of the groups were assigned to either multi-membered clades that also contained marker strains or formed distinct phyletic lines in the Micromonospora 16S rRNA gene tree; many of the isolates were considered to be putatively novel species of Micromonospora. Most of the isolates from the high altitude soils showed activity against wild type strains of Bacillus subtilis and Pseudomonas fluorescens while those from the rhizosphere of Parastrephia quadrangulares and from the Lomas Bayas hyper-arid soil showed resistance to UV radiation.
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Affiliation(s)
- Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK.
| | - Valeria Razmilic
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK.,Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Chile, Beauchef 850, Santiago, Chile
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Lee Richardson
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Che Pan
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Patrycja Golinska
- Department of Microbiology, Nicolaus Copernicus University, Torun, Poland
| | - Juan A Asenjo
- Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Chile, Beauchef 850, Santiago, Chile
| | - Alan T Bull
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
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Idris H, Nouioui I, Pathom-Aree W, Castro JF, Bull AT, Andrews BA, Asenjo JA, Goodfellow M. Amycolatopsis vastitatis sp. nov., an isolate from a high altitude subsurface soil on Cerro Chajnantor, northern Chile. Antonie Van Leeuwenhoek 2018; 111:1523-1533. [PMID: 29428970 DOI: 10.1007/s10482-018-1039-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 02/02/2018] [Indexed: 10/18/2022]
Abstract
The taxonomic position of a novel Amycolatopsis strain isolated from a high altitude Atacama Desert subsurface soil was established using a polyphasic approach. The strain, isolate H5T, was shown to have chemical properties typical of members of the genus Amycolatopsis such as meso-diaminopimelic acid as the diamino acid in the cell wall peptidoglycan, arabinose and galactose as diagnostic sugars and MK-9(H4) as the predominant isoprenologue. It also has cultural and morphological properties consistent with its classification in the genus, notably the formation of branching substrate hyphae which fragment into rod-like elements. 16S rRNA gene sequence analyses showed that the strain is closely related to the type strain of Amycolatopsis mediterranei but could be distinguished from this and other related Amycolatopsis strains using a broad range of phenotypic properties. It was separated readily from the type strain of Amycolatopsis balhymycina, its near phylogenetic neighbour, based on multi-locus sequence data, by low average nucleotide identity (92.9%) and in silico DNA/DNA relatedness values (51.3%) calculated from draft genome assemblies. Consequently, the strain is considered to represent a novel species of Amycolatopsis for which the name Amycolatopsis vastitatis sp. nov. is proposed. The type strain is H5T (= NCIMB 14970T = NRRL B-65279T).
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Affiliation(s)
- Hamidah Idris
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.,Biology Department, Sultan Idris Education University, 35900, Tanjung Malim, Perak, Malaysia
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Wasu Pathom-Aree
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.,Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Jean Franco Castro
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.,Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), University of Chile, Beaucheff 851, Santiago, Chile
| | - Alan T Bull
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Barbara A Andrews
- Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), University of Chile, Beaucheff 851, Santiago, Chile
| | - Juan A Asenjo
- Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), University of Chile, Beaucheff 851, Santiago, Chile
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
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Razmilic V, Castro JF, Marchant F, Asenjo JA, Andrews B. Metabolic modelling and flux analysis of microorganisms from the Atacama Desert used in biotechnological processes. Antonie van Leeuwenhoek 2018; 111:1479-1491. [DOI: 10.1007/s10482-018-1031-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 01/25/2018] [Indexed: 01/16/2023]
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Abdelkader MSA, Philippon T, Asenjo JA, Bull AT, Goodfellow M, Ebel R, Jaspars M, Rateb ME. Asenjonamides A-C, antibacterial metabolites isolated from Streptomyces asenjonii strain KNN 42.f from an extreme-hyper arid Atacama Desert soil. J Antibiot (Tokyo) 2018; 71:425-431. [PMID: 29362461 DOI: 10.1038/s41429-017-0012-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 10/27/2017] [Accepted: 11/02/2017] [Indexed: 11/09/2022]
Abstract
Bio-guided fractionation of the culture broth extract of Streptomyces asenjonii strain KNN 42.f recovered from an extreme hyper-arid Atacama Desert soil in northern Chile led to the isolation of three new bioactive β-diketones; asenjonamides A-C (1-3) in addition to the known N-(2-(1H-indol-3-yl)-2-oxoethyl)acetamide (4), a series of bioactive acylated 4-aminoheptosyl-β-N-glycosides; spicamycins A-E (5-9), and seven known diketopiperazines (10-16). All isolated compounds were characterized by HRESIMS and NMR analyses and tested for their antibacterial effect against a panel of bacteria.
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Affiliation(s)
| | - Thomas Philippon
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef, 851, Santiago, Chile
| | - Alan T Bull
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Michael Goodfellow
- School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Rainer Ebel
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Mostafa E Rateb
- School of Science and Sport, University of the West of Scotland, Paisley, PA1 2BE, UK. .,Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt.
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Abstract
The Atacama Desert of northern Chile is the oldest and most arid nonpolar environment on Earth. It is a coastal desert covering approximately 180,000 km(2), and together with the greater Atacama region it comprises a dramatically wide range of ecological niches. Long known and exploited for its mineral resources, the Atacama Desert harbors a rich microbial diversity that has only recently been discovered; the great majority of it has not yet been recovered in culture or even taxonomically identified. This review traces the progress of microbiology research in the Atacama and dispels the popular view that this region is virtually devoid of life. We examine reasons for such research activity and demonstrate that microbial life is the latest recognized and least explored resource in this inspiring biome.
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Affiliation(s)
- Alan T Bull
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, United Kingdom;
| | - Juan A Asenjo
- Center for Biotechnology and Bioengineering, University of Chile, Santiago, Chile.,Department of Chemical Engineering and Biotechnology, University of Chile, Santiago, Chile;
| | - Michael Goodfellow
- School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom;
| | - Benito Gómez-Silva
- Biochemistry Laboratory, Biomedical Department, Faculty of Health Sciences, University of Antofagasta, Chile;
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Sanchez AC, Li C, Andrews B, Asenjo JA, Samulski RJ. AAV Gene Therapy for Alcoholism: Inhibition of Mitochondrial Aldehyde Dehydrogenase Enzyme Expression in Hepatoma Cells. Hum Gene Ther 2017; 28:717-725. [PMID: 28578603 DOI: 10.1089/hum.2017.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Most ethanol is broken down in the liver in two steps by alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH2) enzymes, which metabolize down ethanol into acetaldehyde and then acetate. Some individuals from the Asian population who carry a mutation in the aldehyde dehydrogenase gene (ALDH2*2) cannot metabolize acetaldehyde as efficiently, producing strong effects, including facial flushing, dizziness, hypotension, and palpitations. This results in an aversion to alcohol intake and protection against alcoholism. The large prevalence of this mutation in the human population strongly suggests that modulation of ALDH2 expression by genetic technologies could result in a similar phenotype. scAAV2 vectors encoding ALDH2 small hairpin RNA (shRNA) were utilized to validate this hypothesis by silencing ALDH2 gene expression in human cell lines. Human cell lines HEK-293 and HepG2 were transduced with scAAV2/shRNA, showing a reduction in ALDH2 RNA and protein expression with the two viral concentration assayed (1 × 104 and 1 × 105 vg/cell) at two different time points. In both cell lines, ALDH2 RNA levels were reduced by 90% and protein expression was inhibited by 90% and 52%, respectively, 5 days post infection. Transduced HepG2 VL17A cells (ADH+) exposed to ethanol resulted in a 50% increase in acetaldehyde levels. These results suggest that gene therapy could be a useful tool for the treatment of alcoholism by knocking down ALDH2 expression using shRNA technology delivered by AAV vectors.
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Affiliation(s)
- Anamaria C Sanchez
- 1 Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile , Santiago, Chile
| | - Chengwen Li
- 2 Gene Therapy Center, University of North Carolina , Chapel Hill, North Carolina
| | - Barbara Andrews
- 1 Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile , Santiago, Chile
| | - Juan A Asenjo
- 1 Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile , Santiago, Chile
| | - R Jude Samulski
- 2 Gene Therapy Center, University of North Carolina , Chapel Hill, North Carolina
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27
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Idris H, Nouioui I, Asenjo JA, Bull AT, Goodfellow M. Lentzea chajnantorensis sp. nov., an actinobacterium from a very high altitude Cerro Chajnantor gravel soil in northern Chile. Antonie van Leeuwenhoek 2017; 110:795-802. [DOI: 10.1007/s10482-017-0851-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/23/2017] [Indexed: 10/19/2022]
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28
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Acevedo JP, Reetz MT, Asenjo JA, Parra LP. One-step combined focused epPCR and saturation mutagenesis for thermostability evolution of a new cold-active xylanase. Enzyme Microb Technol 2017; 100:60-70. [PMID: 28284313 DOI: 10.1016/j.enzmictec.2017.02.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 01/25/2017] [Accepted: 02/09/2017] [Indexed: 11/17/2022]
Abstract
Enzymes active at low temperature are of great interest for industrial bioprocesses due to their high efficiency at a low energy cost. One of the particularities of naturally evolved cold-active enzymes is their increased enzymatic activity at low temperature, however the low thermostability presented in this type of enzymes is still a major drawback for their application in biocatalysis. Directed evolution of cold-adapted enzymes to a more thermostable version, appears as an attractive strategy to fulfill the stability and activity requirements for the industry. This paper describes the recombinant expression and characterization of a new and highly active cold-adapted xylanase from the GH-family 10 (Xyl-L), and the use of a novel one step combined directed evolution technique that comprises saturation mutagenesis and focused epPCR as a feasible semi-rational strategy to improve the thermostability. The Xyl-L enzyme was cloned from a marine-Antarctic bacterium, Psychrobacter sp. strain 2-17, recombinantly expressed in E. coli strain BL21(DE3) and characterized enzymatically. Molecular dynamic simulations using a homology model of the catalytic domain of Xyl-L were performed to detect flexible regions and residues, which are considered to be the possible structural elements that define the thermolability of this enzyme. Mutagenic libraries were designed in order to stabilize the protein introducing mutations in some of the flexible regions and residues identified. Twelve positive mutant clones were found to improve the T5015 value of the enzyme, in some cases without affecting the activity at 25°C. The best mutant showed a 4.3°C increase in its T5015. The efficiency of the directed evolution approach can also be expected to work in the protein engineering of stereoselectivity.
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Affiliation(s)
- Juan Pablo Acevedo
- Facultad de Medicina y Facultad de Ingeniería y Ciencias Aplicadas, Universidad de los Andes, San Carlos de Apoquindo, 2200 Santiago, Chile
| | - Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung, 45070 Mülheim, Germany; Chemistry Department, Philipps-University, 35032 Marburg, Germany
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering, CeBiB, Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef, 851 Santiago, Chile
| | - Loreto P Parra
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna, 4860 Santiago, Chile; Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna, 4860 Santiago, Chile.
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29
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Idris H, Labeda DP, Nouioui I, Castro JF, Del Carmen Montero-Calasanz M, Bull AT, Asenjo JA, Goodfellow M. Streptomyces aridus sp. nov., isolated from a high altitude Atacama Desert soil and emended description of Streptomyces noboritoensis Isono et al. 1957. Antonie Van Leeuwenhoek 2017; 110:705-717. [PMID: 28185026 PMCID: PMC5387016 DOI: 10.1007/s10482-017-0838-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/30/2017] [Indexed: 11/27/2022]
Abstract
A polyphasic study was undertaken to determine the taxonomic status of a Streptomyces strain which had been isolated from a high altitude Atacama Desert soil and shown to have bioactive properties. The strain, isolate H9T, was found to have chemotaxonomic, cultural and morphological properties that place it in the genus Streptomyces. 16S rRNA gene sequence analyses showed that the isolate forms a distinct branch at the periphery of a well-delineated subclade in the Streptomyces 16S rRNA gene tree together with the type strains of Streptomyces crystallinus, Streptomyces melanogenes and Streptomyces noboritoensis. Multi-locus sequence analysis (MLSA) based on five house-keeping gene alleles showed that isolate H9T is closely related to the latter two type strains and to Streptomyces polyantibioticus NRRL B-24448T. The isolate was distinguished readily from the type strains of S. melanogenes, S. noboritoensis and S. polyantibioticus using a combination of phenotypic properties. Consequently, the isolate is considered to represent a new species of Streptomyces for which the name Streptomyces aridus sp. nov. is proposed; the type strain is H9T (=NCIMB 14965T=NRRL B65268T). In addition, the MLSA and phenotypic data show that the S. melanogenes and S. noboritoensis type strains belong to a single species, it is proposed that S. melanogenes be recognised as a heterotypic synonym of S. noboritoensis for which an emended description is given.
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Affiliation(s)
- Hamidah Idris
- School of Biology, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - David P Labeda
- National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL, 61604, USA
| | - Imen Nouioui
- School of Biology, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Jean Franco Castro
- School of Biology, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK.,Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), University of Chile, Beauchef 851, Santiago, Chile
| | | | - Alan T Bull
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Juan A Asenjo
- Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), University of Chile, Beauchef 851, Santiago, Chile
| | - Michael Goodfellow
- School of Biology, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK.
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30
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Sandoval G, Espinoza D, Figueroa N, Asenjo JA. Optimization of a biotechnological multiproduct batch plant design for the manufacture of four different products: A real case scenario. Biotechnol Bioeng 2017; 114:1252-1263. [PMID: 28145566 DOI: 10.1002/bit.26260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/16/2017] [Accepted: 01/22/2017] [Indexed: 11/06/2022]
Abstract
In this work a biotechnological multiproduct batch plant that manufactures four different recombinant proteins for human application is described in some detail. This batch plant design is then optimized with regards to the size of equipment using a mixed-integer linear programming (MILP) formulation recently developed by us in order to find a hypothetical new biotechnological batch plant based on the information of real known processes for the production of the four recombinant protein products. The real plant was divided for practical purposes into two sub-processes or facilities: a fermentation facility and a purification facility. Knowing the specific steps conforming the downstream processing of each product, size, and time factors were computed and used as parameters to solve the aforementioned MILP reformulation. New constraints were included to permit the selection of some equipment-such as centrifuges and membrane filters-in a discrete set of sizes. For equipment that can be built according to customer needs-such as reactors-the original formulation was retained. Computational results show the ability of this optimization methodology to deal with real data giving reliable solutions for a multi-product batch plant composed of 44 unit operations in a relatively small amount of time showing that in the case studied it is possible to save up to a 66% of the capital investment in equipment given the cost data used. Biotechnol. Bioeng. 2017;114: 1252-1263. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Gabriela Sandoval
- Centre of Biotechnology and Bioengineering, CeBiB, Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago 8370456, Chile.,Facultad de Ingeniería y Tecnologí-a, Universidad de San Sebastián, Bellavista 7, Santiago 8420524, Chile
| | - Daniel Espinoza
- Facultad de Ciencias Fí-sicas y Matemáticas, Departamento de Ingenierí-a Industrial, Universidad de Chile, Santiago, Chile
| | - Nicolas Figueroa
- Instituto de Economí-a, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan A Asenjo
- Centre of Biotechnology and Bioengineering, CeBiB, Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago 8370456, Chile
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31
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Merino MP, Andrews BA, Parada P, Asenjo JA. Characterization of Ferroplasma acidiphilum growing in pure and mixed culture with Leptospirillum ferriphilum. Biotechnol Prog 2016; 32:1390-1396. [PMID: 27535541 DOI: 10.1002/btpr.2340] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/27/2016] [Indexed: 11/07/2022]
Abstract
Biomining is defined as biotechnology for metal recovery from minerals, and is promoted by the concerted effort of a consortium of acidophile prokaryotes, comprised of members of the Bacteria and Archaea domains. Ferroplasma acidiphilum and Leptospirillum ferriphilum are the dominant species in extremely acid environments and have great use in bioleaching applications; however, the role of each species in this consortia is still a subject of research. The hypothesis of this work is that F. acidiphilum uses the organic matter secreted by L. ferriphilum for growth, maintaining low levels of organic compounds in the culture medium, preventing their toxic effects on L. ferriphilum. To test this hypothesis, a characterization of Ferroplasma acidiphilum strain BRL-115 was made with the objective of determining its optimal growth conditions. Subsequently, under the optimal conditions, L. ferriphilum and F. acidiphilum were tested growing in each other's supernatant, in order to define if there was exchange of metabolites between the species. With these results, a mixed culture in batch cyclic operation was performed to obtain main specific growth rates, which were used to evaluate a mixed metabolic model previously developed by our group. It was observed that F. acidiphilum, strain BRL-115 is a chemomixotrophic organism, and its growth is maximized with yeast extract at a concentration of 0.04% wt/vol. From the experiments of L. ferriphilum growing on F. acidiphilum supernatant and vice versa, it was observed that in both cases cell growth is favorably affected by the presence of the filtered medium of the other microorganism, proving a synergistic interaction between these species. Specific growth rates were obtained in cyclic batch operation of the mixed culture and were used as input data for a Flux Balance Analysis of the mixed metabolic model, obtaining a reasonable behavior of the metabolic fluxes and the system as a whole, therefore consolidating the model previously developed. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1390-1396, 2016.
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Affiliation(s)
- M P Merino
- Centre for Biotechnology and Bioengineering, CeBiB, Dept. of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - B A Andrews
- Centre for Biotechnology and Bioengineering, CeBiB, Dept. of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - P Parada
- Biosigma S.A, Carretera Gral. San Martín 16500, Loteo Industrial Los Libertadores, Lote 106, Colina, Chile
| | - J A Asenjo
- Centre for Biotechnology and Bioengineering, CeBiB, Dept. of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
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32
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Wichner D, Idris H, Houssen WE, McEwan AR, Bull AT, Asenjo JA, Goodfellow M, Jaspars M, Ebel R, Rateb ME. Isolation and anti-HIV-1 integrase activity of lentzeosides A-F from extremotolerant lentzea sp. H45, a strain isolated from a high-altitude Atacama Desert soil. J Antibiot (Tokyo) 2016; 70:448-453. [PMID: 27353167 DOI: 10.1038/ja.2016.78] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/10/2016] [Accepted: 05/31/2016] [Indexed: 12/29/2022]
Abstract
The extremotolerant isolate H45 was one of several actinomycetes isolated from a high-altitude Atacama Desert soil collected in northwest Chile. The isolate was identified as a new Lentzea sp. using a combination of chemotaxonomic, morphological and phylogenetic properties. Large scale fermentation of the strain in two different media followed by chromatographic purification led to the isolation of six new diene and monoene glycosides named lentzeosides A-F, together with the known compound (Z)-3-hexenyl glucoside. The structures of the new compounds were confirmed by HRESIMS and NMR analyses. Compounds 1-6 displayed moderate inhibitory activity against HIV integrase.
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Affiliation(s)
- Dominik Wichner
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Scotland, UK.,Department of Chemistry, University of Regensburg, Universitätsstraße 31, Regensburg, Germany
| | - Hamidah Idris
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Wael E Houssen
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Scotland, UK.,Institute of Medical Sciences, University of Aberdeen, Scotland, UK.,Faculty of Pharmacy, Department of Pharmacognosy, Mansoura University, Mansoura, Egypt
| | - Andrew R McEwan
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Scotland, UK.,Institute of Medical Sciences, University of Aberdeen, Scotland, UK
| | - Alan T Bull
- School of Biosciences, University of Kent, Kent, UK
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, Universidad de Chile, Santiago, Chile
| | | | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Scotland, UK
| | - Rainer Ebel
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Scotland, UK
| | - Mostafa E Rateb
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Scotland, UK.,School of Science & Sport, University of the West of Scotland, Paisley, UK.,Department of Pharmacognosy, School of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
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Campodonico MA, Vaisman D, Castro JF, Razmilic V, Mercado F, Andrews BA, Feist AM, Asenjo JA. Acidithiobacillus ferrooxidans's comprehensive model driven analysis of the electron transfer metabolism and synthetic strain design for biomining applications. Metab Eng Commun 2016; 3:84-96. [PMID: 29468116 PMCID: PMC5779729 DOI: 10.1016/j.meteno.2016.03.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 12/16/2015] [Accepted: 03/14/2016] [Indexed: 10/28/2022] Open
Abstract
Acidithiobacillus ferrooxidans is a gram-negative chemolithoautotrophic γ-proteobacterium. It typically grows at an external pH of 2 using the oxidation of ferrous ions by oxygen, producing ferric ions and water, while fixing carbon dioxide from the environment. A. ferrooxidans is of great interest for biomining and environmental applications, as it can process mineral ores and alleviate the negative environmental consequences derived from the mining processes. In this study, the first genome-scale metabolic reconstruction of A. ferrooxidans ATCC 23270 was generated (iMC507). A total of 587 metabolic and transport/exchange reactions, 507 genes and 573 metabolites organized in over 42 subsystems were incorporated into the model. Based on a new genetic algorithm approach, that integrates flux balance analysis, chemiosmotic theory, and physiological data, the proton translocation stoichiometry for a number of enzymes and maintenance parameters under aerobic chemolithoautotrophic conditions using three different electron donors were estimated. Furthermore, a detailed electron transfer and carbon flux distributions during chemolithoautotrophic growth using ferrous ion, tetrathionate and thiosulfate were determined and reported. Finally, 134 growth-coupled designs were calculated that enables Extracellular Polysaccharide production. iMC507 serves as a knowledgebase for summarizing and categorizing the information currently available for A. ferrooxidans and enables the understanding and engineering of Acidithiobacillus and similar species from a comprehensive model-driven perspective for biomining applications.
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Affiliation(s)
- Miguel A Campodonico
- Centre for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef 850, Santiago, Chile
| | - Daniela Vaisman
- Centre for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef 850, Santiago, Chile
| | - Jean F Castro
- Centre for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef 850, Santiago, Chile
| | - Valeria Razmilic
- Centre for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef 850, Santiago, Chile
| | - Francesca Mercado
- Centre for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef 850, Santiago, Chile
| | - Barbara A Andrews
- Centre for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef 850, Santiago, Chile
| | - Adam M Feist
- Department of Bioengineering, University of California, 9500 Gilman Drive # 0412, San Diego, La Jolla, CA 92093, USA
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef 850, Santiago, Chile
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34
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Elsayed SS, Trusch F, Deng H, Raab A, Prokes I, Busarakam K, Asenjo JA, Andrews BA, van West P, Bull AT, Goodfellow M, Yi Y, Ebel R, Jaspars M, Rateb ME. Chaxapeptin, a Lasso Peptide from Extremotolerant Streptomyces leeuwenhoekii Strain C58 from the Hyperarid Atacama Desert. J Org Chem 2015; 80:10252-60. [DOI: 10.1021/acs.joc.5b01878] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Somayah S. Elsayed
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
| | - Franziska Trusch
- Aberdeen
Oomycetes Laboratory, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, U.K
| | - Hai Deng
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
| | - Andrea Raab
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
| | - Ivan Prokes
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | | | - Juan A. Asenjo
- Centre
for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef 850, Santiago, Chile
| | - Barbara A. Andrews
- Centre
for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef 850, Santiago, Chile
| | - Pieter van West
- Aberdeen
Oomycetes Laboratory, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, U.K
| | - Alan T. Bull
- School
of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, U.K
| | - Michael Goodfellow
- School
of Biology, Newcastle University, Newcastle upon Tyne NE1
7RU, U.K
| | - Yu Yi
- Key Laboratory
of Combinatory Biosynthesis and Drug Discovery, School of Pharmaceutical
Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, P. R. China
| | - Rainer Ebel
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
| | - Marcel Jaspars
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
| | - Mostafa E. Rateb
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
- Pharmacognosy
Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 32514, Egypt
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Castro JF, Razmilic V, Gomez-Escribano JP, Andrews B, Asenjo JA, Bibb MJ. Identification and Heterologous Expression of the Chaxamycin Biosynthesis Gene Cluster from Streptomyces leeuwenhoekii. Appl Environ Microbiol 2015; 81:5820-31. [PMID: 26092459 PMCID: PMC4551226 DOI: 10.1128/aem.01039-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/12/2015] [Indexed: 11/20/2022] Open
Abstract
Streptomyces leeuwenhoekii, isolated from the hyperarid Atacama Desert, produces the new ansamycin-like compounds chaxamycins A to D, which possess potent antibacterial activity and moderate antiproliferative activity. We report the development of genetic tools to manipulate S. leeuwenhoekii and the identification and partial characterization of the 80.2-kb chaxamycin biosynthesis gene cluster, which was achieved by both mutational analysis in the natural producer and heterologous expression in Streptomyces coelicolor A3(2) strain M1152. Restoration of chaxamycin production in a nonproducing ΔcxmK mutant (cxmK encodes 3-amino-5-hydroxybenzoic acid [AHBA] synthase) was achieved by supplementing the growth medium with AHBA, suggesting that mutasynthesis may be a viable approach for the generation of novel chaxamycin derivatives.
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Affiliation(s)
- Jean Franco Castro
- Centre for Biotechnology and Bioengineering, Department of Chemical Engineering and Biotechnology, Universidad de Chile, Santiago, Chile Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Valeria Razmilic
- Centre for Biotechnology and Bioengineering, Department of Chemical Engineering and Biotechnology, Universidad de Chile, Santiago, Chile Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | | | - Barbara Andrews
- Centre for Biotechnology and Bioengineering, Department of Chemical Engineering and Biotechnology, Universidad de Chile, Santiago, Chile
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering, Department of Chemical Engineering and Biotechnology, Universidad de Chile, Santiago, Chile
| | - Mervyn J Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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Contador CA, Shene C, Olivera A, Yoshikuni Y, Buschmann A, Andrews BA, Asenjo JA. Analyzing redox balance in a synthetic yeast platform to improve utilization of brown macroalgae as feedstock. Metab Eng Commun 2015; 2:76-84. [PMID: 34150511 PMCID: PMC8193247 DOI: 10.1016/j.meteno.2015.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 06/19/2015] [Indexed: 11/13/2022] Open
Abstract
Macroalgae have high potential to be an efficient, and sustainable feedstock for the production of biofuels and other more valuable chemicals. Attempts have been made to enable the co-fermentation of alginate and mannitol by Saccharomyces cerevisiae to unlock the full potential of this marine biomass. However, the efficient use of the sugars derived from macroalgae depends on the equilibrium of cofactors derived from the alginate and mannitol catabolic pathways. There are a number of strong metabolic limitations that have to be tackled before this bioconversion can be carried out efficiently by engineered yeast cells. An analysis of the redox balance during ethanol fermentation from alginate and mannitol by Saccharomyces cerevisiae using metabolic engineering tools was carried out. To represent the strain designed for conversion of macroalgae carbohydrates to ethanol, a context-specific model was derived from the available yeast genome-scale metabolic reconstructions. Flux balance analysis and dynamic simulations were used to determine the flux distributions. The model indicates that ethanol production is determined by the activity of 4-deoxy-l-erythro-5-hexoseulose uronate (DEHU) reductase (DehR) and its preferences for NADH or NADPH which influences strongly the flow of cellular resources. Different scenarios were explored to determine the equilibrium between NAD(H) and NADP(H) that will lead to increased ethanol yields on mannitol and DEHU under anaerobic conditions. When rates of mannitol dehydrogenase and DehRNADH tend to be close to a ratio in the range 1–1.6, high growth rates and ethanol yields were predicted. The analysis shows a number of metabolic limitations that are not easily identified through experimental procedures such as quantifying the impact of the cofactor preference by DEHU reductase in the system, the low flux into the alginate catabolic pathway, and a detailed analysis of the redox balance. These results show that production of ethanol and other chemicals can be optimized if a redox balance is achieved. A possible methodology to achieve this balance is presented. This paper shows how metabolic engineering tools are essential to comprehend and overcome this limitation. We studied a strain designed for bioconversion of macroalgae sugars to ethanol. A genome-scale model was used to simulate biomass and by-product formation. The characterization of the current metabolic state of the strain was achieved. Biofuel production depends on the redox balance derived from alginate and mannitol. Flux split into DehR determines the redox balance, by-products and ethanol level.
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Affiliation(s)
- C A Contador
- Centre for Biotechnology and Bioengineering, CeBiB, Chile.,Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 850, Santiago, Chile
| | - C Shene
- Centre for Biotechnology and Bioengineering, CeBiB, Chile.,Department of Chemical Engineering, University of La Frontera, Temuco, Chile
| | - A Olivera
- Centre for Biotechnology and Bioengineering, CeBiB, Chile.,Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 850, Santiago, Chile
| | | | - A Buschmann
- Centre for Biotechnology and Bioengineering, CeBiB, Chile.,Consorcio BALBiofuel, Camino Chiquihue km6, Puerto Montt, Chile and Centro i-mar, Universidad de Los Lagos, Puerto Montt, Chile
| | - B A Andrews
- Centre for Biotechnology and Bioengineering, CeBiB, Chile.,Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 850, Santiago, Chile
| | - J A Asenjo
- Centre for Biotechnology and Bioengineering, CeBiB, Chile.,Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 850, Santiago, Chile
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Gomez-Escribano JP, Castro JF, Razmilic V, Chandra G, Andrews B, Asenjo JA, Bibb MJ. The Streptomyces leeuwenhoekii genome: de novo sequencing and assembly in single contigs of the chromosome, circular plasmid pSLE1 and linear plasmid pSLE2. BMC Genomics 2015; 16:485. [PMID: 26122045 PMCID: PMC4487206 DOI: 10.1186/s12864-015-1652-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/20/2015] [Indexed: 11/18/2022] Open
Abstract
Background Next Generation DNA Sequencing (NGS) and genome mining of actinomycetes and other microorganisms is currently one of the most promising strategies for the discovery of novel bioactive natural products, potentially revealing novel chemistry and enzymology involved in their biosynthesis. This approach also allows rapid insights into the biosynthetic potential of microorganisms isolated from unexploited habitats and ecosystems, which in many cases may prove difficult to culture and manipulate in the laboratory. Streptomyces leeuwenhoekii (formerly Streptomyces sp. strain C34) was isolated from the hyper-arid high-altitude Atacama Desert in Chile and shown to produce novel polyketide antibiotics. Results Here we present the de novo sequencing of the S. leeuwenhoekii linear chromosome (8 Mb) and two extrachromosomal replicons, the circular pSLE1 (86 kb) and the linear pSLE2 (132 kb), all in single contigs, obtained by combining Pacific Biosciences SMRT (PacBio) and Illumina MiSeq technologies. We identified the biosynthetic gene clusters for chaxamycin, chaxalactin, hygromycin A and desferrioxamine E, metabolites all previously shown to be produced by this strain (J Nat Prod, 2011, 74:1965) and an additional 31 putative gene clusters for specialised metabolites. As well as gene clusters for polyketides and non-ribosomal peptides, we also identified three gene clusters encoding novel lasso-peptides. Conclusions The S. leeuwenhoekii genome contains 35 gene clusters apparently encoding the biosynthesis of specialised metabolites, most of them completely novel and uncharacterised. This project has served to evaluate the current state of NGS for efficient and effective genome mining of high GC actinomycetes. The PacBio technology now permits the assembly of actinomycete replicons into single contigs with >99 % accuracy. The assembled Illumina sequence permitted not only the correction of omissions found in GC homopolymers in the PacBio assembly (exacerbated by the high GC content of actinomycete DNA) but it also allowed us to obtain the sequences of the termini of the chromosome and of a linear plasmid that were not assembled by PacBio. We propose an experimental pipeline that uses the Illumina assembled contigs, in addition to just the reads, to complement the current limitations of the PacBio sequencing technology and assembly software. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1652-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan Pablo Gomez-Escribano
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
| | - Jean Franco Castro
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom. .,Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, Universidad de Chile, Beauchef 850, Santiago, Chile.
| | - Valeria Razmilic
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom. .,Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, Universidad de Chile, Beauchef 850, Santiago, Chile.
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
| | - Barbara Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, Universidad de Chile, Beauchef 850, Santiago, Chile.
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, Universidad de Chile, Beauchef 850, Santiago, Chile.
| | - Mervyn J Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
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38
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Rodríguez V, Lascani J, Asenjo JA, Andrews BA. Production of Cell-Penetrating Peptides in Escherichia coli Using an Intein-Mediated System. Appl Biochem Biotechnol 2015; 175:3025-37. [DOI: 10.1007/s12010-015-1484-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 01/05/2015] [Indexed: 10/24/2022]
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39
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Merino MP, Andrews BA, Asenjo JA. Stoichiometric model and flux balance analysis for a mixed culture of Leptospirillum ferriphilum and Ferroplasma acidiphilum. Biotechnol Prog 2014; 31:307-15. [PMID: 25504621 DOI: 10.1002/btpr.2028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 11/20/2014] [Indexed: 11/08/2022]
Abstract
The oxidation process of sulfide minerals in natural environments is achieved by microbial communities from the Archaea and Bacteria domains. A metabolic reconstruction of two dominant species, Leptospirillum ferriphilum and Ferroplasma acidiphilum, which are always found together as a mixed culture in this natural environments, was made. The metabolic model, composed of 152 internal reactions and 29 transport reactions, describes the main interactions between these species, assuming that both use ferrous iron as energy source, and F. acidiphilum takes advantage of the organic compounds secreted by L. ferriphilum for chemomixotrophic growth. A first metabolic model for a mixed culture used in bacterial leaching is proposed in this article, which pretends to represent the characteristics of the mixed culture in a simplified manner. It was evaluated with experimental data through flux balance analysis (FBA) using as objective function the maximization of biomass. The growth yields on ferrous iron obtained for each microorganism are consistent with experimental data, and the flux distribution obtained allows understanding of the metabolic capabilities of both microorganisms growing together in a bioleaching process. The model was used to simulate the growth of F. acidiphilum on different substrates, to determine in silico which compounds maximize cell growth, and which are essential. Knockout simulations were carried out for L. ferriphilum and F. acidiphilum metabolic models, predicting key enzymes of central metabolism. The results of this analysis are consistent with experimental data from literature, showing a robust behavior of the metabolic model.
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Affiliation(s)
- M P Merino
- Dept. of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef, 850, Santiago, Chile
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40
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Parra LP, Espina G, Devia J, Salazar O, Andrews B, Asenjo JA. Identification of lipase encoding genes from Antarctic seawater bacteria using degenerate primers: expression of a cold-active lipase with high specific activity. Enzyme Microb Technol 2014; 68:56-61. [PMID: 25435506 DOI: 10.1016/j.enzmictec.2014.10.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 10/07/2014] [Accepted: 10/17/2014] [Indexed: 11/24/2022]
Abstract
Cold-active enzymes are valuable catalysts showing high activity at low and moderate temperatures and low thermostability. Among cold-active enzymes, lipases offer a great potential in detergent, cosmetic, biofuel and food or feed industries. In this paper we describe the identification of novel lipase coding genes and the expression of a lipase with high activity at low temperatures. The genomic DNA from Antarctic seawater bacteria showing lipolytic activity at 4°C was used to amplify five DNA fragments that partially encode novel lipases using specifically designed COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP). All the fragments were found to have a high identity with an α/β-hydrolase domain-containing protein identified by the sequencing of the complete genome of Shewanella frigidimarina NCIMB 400. The complete sequence of one of the lipase-coding gene fragments, lipE13, was obtained by genome walking. Considering that the other fragments had a high identity to the putative lipase from S. frigidimarina NCIMB 400, the complete lipase genes were amplified using oligonucleotide primers designed based on the 5' and 3' regions of the coding sequence of the related protein. This strategy allowed the amplification of 3 lipase-encoding genes of which one was expressed in the periplasm using the Escherichia coli BL21(DE3)/pET-22b(+) expression system. The recombinant protein was obtained with activity toward p-nitrophenyl caproate showing a high specific activity between 15 and 25°C.
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Affiliation(s)
- Loreto P Parra
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 850, Santiago, Chile; Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago, Chile
| | - Giannina Espina
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 850, Santiago, Chile
| | - Javier Devia
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 850, Santiago, Chile
| | - Oriana Salazar
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 850, Santiago, Chile
| | - Barbara Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 850, Santiago, Chile
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 850, Santiago, Chile.
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41
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Rodríguez V, Asenjo JA, Andrews BA. Design and implementation of a high yield production system for recombinant expression of peptides. Microb Cell Fact 2014; 13:65. [PMID: 24885242 PMCID: PMC4022411 DOI: 10.1186/1475-2859-13-65] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 04/01/2014] [Indexed: 11/24/2022] Open
Abstract
Background Making peptide pharmaceuticals involves challenging processes where many barriers, which include production and manufacture, need to be overcome. A non common but interesting research area is related to peptides with intracellular targets, which opens up new possibilities, allowing the modulation of processes occurring within the cell or interference with signaling pathways. However, if the bioactive sequence requires fusion to a carrier peptide to allow access into the cell, the resulting peptide could be such a length that traditional production could be difficult. The goal of the present study was the development of a flexible recombinant expression and purification system for peptides, as a contribution to the discovery and development of these potentially new drugs. Results In this work, a high throughput recombinant expression and purification system for production of cell penetrating peptides in Escherichia coli has been designed and implemented. The system designed produces target peptides in an insoluble form by fusion to a hexahistidine tagged ketosteroid isomerase which is then separated by a highly efficient thrombin cleavage reaction procedure. The expression system was tested on the anticancer peptides p53pAnt and PNC27. These peptides comprise the C-terminal region and the N-terminal region of the protein p53, respectively, fused by its carboxyl terminal extreme to the cell penetrating peptide Penetratin. High yields of purified recombinant fused peptides were obtained in both cases; nevertheless, thrombin cleavage reaction was successful only for p53pAnt peptide release. The features of the system, together with the procedure developed, allow achievement of high production yields of over 30 mg of highly pure p53pAnt peptide per g of dry cell mass. It is proposed that the system could be used for production of other peptides at a similar yield. Conclusions This study provides a system suitable for recombinant production of peptides for scientific research, including biological assays.
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Affiliation(s)
- Vida Rodríguez
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile.
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42
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Olivera-Nappa A, Reyes F, Andrews BA, Asenjo JA. Cold adaptation, ca2+ dependency and autolytic stability are related features in a highly active cold-adapted trypsin resistant to autoproteolysis engineered for biotechnological applications. PLoS One 2013; 8:e72355. [PMID: 23951314 PMCID: PMC3741176 DOI: 10.1371/journal.pone.0072355] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 07/16/2013] [Indexed: 11/23/2022] Open
Abstract
Pig trypsin is routinely used as a biotechnological tool, due to its high specificity and ability to be stored as an inactive stable zymogen. However, it is not an optimum enzyme for conditions found in wound debriding for medical uses and trypsinization processes for protein analysis and animal cell culturing, where low Ca(2+) dependency, high activity in mild conditions and easy inactivation are crucial. We isolated and thermodynamically characterized a highly active cold-adapted trypsin for medical and laboratory use that is four times more active than pig trypsin at 10(°) C and at least 50% more active than pig trypsin up to 50(°) C. Contrary to pig trypsin, this enzyme has a broad optimum pH between 7 and 10 and is very insensitive to Ca(2+) concentration. The enzyme is only distantly related to previously described cryophilic trypsins. We built and studied molecular structure models of this trypsin and performed molecular dynamic calculations. Key residues and structures associated with calcium dependency and cryophilicity were identified. Experiments indicated that the protein is unstable and susceptible to autoproteolysis. Correlating experimental results and structural predictions, we designed mutations to improve the resistance to autoproteolysis and conserve activity for longer periods after activation. One single mutation provided around 25 times more proteolytic stability. Due to its cryophilic nature, this trypsin is easily inactivated by mild denaturation conditions, which is ideal for controlled proteolysis processes without requiring inhibitors or dilution. We clearly show that cold adaptation, Ca(2+) dependency and autolytic stability in trypsins are related phenomena that are linked to shared structural features and evolve in a concerted fashion. Hence, both structurally and evolutionarily they cannot be interpreted and studied separately as previously done.
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Affiliation(s)
- Alvaro Olivera-Nappa
- Centre for Biochemical Engineering and Biotechnology, Department of Chemical Engineering and Biotechnology, University of Chile, Santiago, Chile
| | - Fernando Reyes
- Centre for Biochemical Engineering and Biotechnology, Department of Chemical Engineering and Biotechnology, University of Chile, Santiago, Chile
| | - Barbara A. Andrews
- Centre for Biochemical Engineering and Biotechnology, Department of Chemical Engineering and Biotechnology, University of Chile, Santiago, Chile
| | - Juan A. Asenjo
- Centre for Biochemical Engineering and Biotechnology, Department of Chemical Engineering and Biotechnology, University of Chile, Santiago, Chile
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Acevedo JP, Rodriguez V, Saavedra M, Muñoz M, Salazar O, Asenjo JA, Andrews BA. Cloning, expression and decoding of the cold adaptation of a new widely represented thermolabile subtilisin-like protease. J Appl Microbiol 2012; 114:352-63. [PMID: 23043619 DOI: 10.1111/jam.12033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/23/2012] [Accepted: 09/27/2012] [Indexed: 11/29/2022]
Abstract
AIMS Cloning, expression and characterization of a new cold-adapted protease with potential biotechnological application, isolated from Antarctic bacteria. METHOD AND RESULTS A subtilisin-like gene was isolated from several Antarctic bacterial genus using CODPEHOP-designed primers and a genome walking method. This gene encodes a precursor protein, which undergoes an autocatalytic cleavage resulting in a 34.6 kDa active cold-adapted protease with a maximum activity at 25-35°C and optimum pH of 8.0-9.0. It showed a higher catalytic efficiency at lower temperatures compared to its mesophilic counterpart. Heat-induced inactivation resulted in a very low melting point. Local packing analysis using the homology model indicated Ala284 as an important cold-adaptation determinant, which was corroborated by the site-directed mutagenesis. CONCLUSIONS A new thermolabile subtilisin-like protease has been successfully cloned and analysed, and an important hot spot in the evolution of the cold adaptation and substrate specificity of this enzyme was identified and tested. SIGNIFICANCE AND IMPACT OF THE STUDY This work reports a new cold-adapted protease with a vast representation amongst Antarctic genus, suggesting therefore its evolutionary success in this cold environment. Likewise, important sites for genetic potentiation have been identified, which are extrapolated to other enzymes of the same kind.
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Santhanam R, Okoro CK, Rong X, Huang Y, Bull AT, Weon HY, Andrews BA, Asenjo JA, Goodfellow M. Streptomyces atacamensis sp. nov., isolated from an extreme hyper-arid soil of the Atacama Desert, Chile. Int J Syst Evol Microbiol 2012; 62:2680-2684. [DOI: 10.1099/ijs.0.038463-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of a
Streptomyces
strain isolated from an extreme hyper-arid soil sample collected from the Atacama Desert was determined using a polyphasic approach. The strain, isolate C60T, had chemical and morphological features typical of members of the genus
Streptomyces
and formed a distinct phyletic line in the
Streptomyces
16S rRNA gene tree, together with the type strain of
Streptomyces radiopugnans
. The two strains were distinguished readily using a combination of phenotypic properties and by a DNA–DNA relatedness value of 23.17 (±0.95) %. On the basis of these genotypic and phenotypic data, it is proposed that isolate C60T ( = CGMCC 4.7018T = KACC 15492T) be classified in the genus
Streptomyces
as Streptomyces atacamensis sp. nov.
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Affiliation(s)
- Rakesh Santhanam
- School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Chinyere K. Okoro
- School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Xiaoying Rong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Alan T. Bull
- Department of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
- School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Hang-Yeon Weon
- Korean Agricultural Culture Collection, Agricultural Microbiological Team, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Barbara A. Andrews
- Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 850, Santiago, Chile
| | - Juan A. Asenjo
- Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 850, Santiago, Chile
| | - Michael Goodfellow
- School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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Clark DS, Blanch HW, Wang DI, Demain AL, Wandrey C, Hu WS, Schultz JS, Shuler ML, Hoare M, Lightfoot EN, Humphrey AE, Dordick JS, Asenjo JA. Elmer L. Gaden, Jr. Tribute. Biotechnol Bioeng 2012; 109:2417-21. [DOI: 10.1002/bit.24610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Mayolo-Deloisa K, Lienqueo ME, Andrews B, Rito-Palomares M, Asenjo JA. Hydrophobic interaction chromatography for purification of monoPEGylated RNase A. J Chromatogr A 2012; 1242:11-6. [DOI: 10.1016/j.chroma.2012.03.079] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 03/22/2012] [Accepted: 03/23/2012] [Indexed: 10/28/2022]
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Asenjo JA, Andrews BA. Aqueous two-phase systems for protein separation: Phase separation and applications. J Chromatogr A 2012; 1238:1-10. [DOI: 10.1016/j.chroma.2012.03.049] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 03/13/2012] [Accepted: 03/15/2012] [Indexed: 11/15/2022]
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Santhanam R, Okoro CK, Rong X, Huang Y, Bull AT, Andrews BA, Asenjo JA, Weon HY, Goodfellow M. Streptomyces deserti sp. nov., isolated from hyper-arid Atacama Desert soil. Antonie van Leeuwenhoek 2011; 101:575-81. [DOI: 10.1007/s10482-011-9672-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 11/01/2011] [Indexed: 11/29/2022]
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Rateb ME, Houssen WE, Harrison WTA, Deng H, Okoro CK, Asenjo JA, Andrews BA, Bull AT, Goodfellow M, Ebel R, Jaspars M. Diverse metabolic profiles of a Streptomyces strain isolated from a hyper-arid environment. J Nat Prod 2011; 74:1965-1971. [PMID: 21879726 DOI: 10.1021/np200470u] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The metabolic profile of Streptomyces sp. strain C34, isolated from the Chilean hyper-arid Atacama Desert soil, is dependent on the culture media used for its growth. The application of an OSMAC approach on this strain using a range of cultivation media resulted in the isolation and identification of three new compounds from the rare class of 22-membered macrolactone polyketides, named chaxalactins A-C (1-3). In addition, the known compounds deferroxamine E (4), hygromycin A (5), and 5″-dihydrohygromycin A (6) were detected. The isolated compounds were characterized by NMR spectroscopy and accurate mass spectrometric analysis. Compounds 1-3 displayed strong activity against Gram-positive but weak activity Gram-negative strains tested.
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Affiliation(s)
- Mostafa E Rateb
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, UK
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