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Barry CP, Gillane R, Talbo GH, Plan M, Palfreyman R, Haber-Stuk AK, Power J, Nielsen LK, Marcellin E. Multi-omic characterisation of Streptomyces hygroscopicus NRRL 30439: detailed assessment of its secondary metabolic potential. Mol Omics 2022; 18:226-236. [PMID: 34989730 DOI: 10.1039/d1mo00150g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The emergence of multidrug-resistant pathogenic bacteria creates a demand for novel antibiotics with distinct mechanisms of action. Advances in next-generation genome sequencing promised a paradigm shift in the quest to find new bioactive secondary metabolites. Genome mining has proven successful for predicting putative biosynthetic elements in secondary metabolite superproducers such as Streptomycetes. However, genome mining approaches do not inform whether biosynthetic gene clusters are dormant or active under given culture conditions. Here we show that using a multi-omics approach in combination with antiSMASH, it is possible to assess the secondary metabolic potential of a Streptomyces strain capable of producing mannopeptimycin, an important cyclic peptide effective against Gram-positive infections. The genome of Streptomyces hygroscopicus NRRL 30439 was first sequenced using PacBio RSII to obtain a closed genome. A chemically defined medium was then used to elicit a nutrient stress response in S. hygroscopicus NRRL 30439. Detailed extracellular metabolomics and intracellular proteomics were used to profile and segregate primary and secondary metabolism. Our results demonstrate that the combination of genomics, proteomics and metabolomics enables rapid evaluation of a strain's performance in bioreactors for industrial production of secondary metabolites.
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Affiliation(s)
- Craig P Barry
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia.
| | - Rosemary Gillane
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia.
| | - Gert H Talbo
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
| | - Manual Plan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
| | - Robin Palfreyman
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
| | | | - John Power
- Zoetis, 333 Portage Street, Kalamazoo, MI 49007, USA
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
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Streptomyces Differentiation in Liquid Cultures as a Trigger of Secondary Metabolism. Antibiotics (Basel) 2018; 7:antibiotics7020041. [PMID: 29757948 PMCID: PMC6022995 DOI: 10.3390/antibiotics7020041] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/09/2018] [Accepted: 05/09/2018] [Indexed: 02/08/2023] Open
Abstract
Streptomyces is a diverse group of gram-positive microorganisms characterised by a complex developmental cycle. Streptomycetes produce a number of antibiotics and other bioactive compounds used in the clinic. Most screening campaigns looking for new bioactive molecules from actinomycetes have been performed empirically, e.g., without considering whether the bacteria are growing under the best developmental conditions for secondary metabolite production. These screening campaigns were extremely productive and discovered a number of new bioactive compounds during the so-called “golden age of antibiotics” (until the 1980s). However, at present, there is a worrying bottleneck in drug discovery, and new experimental approaches are needed to improve the screening of natural actinomycetes. Streptomycetes are still the most important natural source of antibiotics and other bioactive compounds. They harbour many cryptic secondary metabolite pathways not expressed under classical laboratory cultures. Here, we review the new strategies that are being explored to overcome current challenges in drug discovery. In particular, we focus on those aimed at improving the differentiation of the antibiotic-producing mycelium stage in the laboratory.
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Manteca A, Alvarez R, Salazar N, Yagüe P, Sanchez J. Mycelium differentiation and antibiotic production in submerged cultures of Streptomyces coelicolor. Appl Environ Microbiol 2008; 74:3877-86. [PMID: 18441105 PMCID: PMC2446541 DOI: 10.1128/aem.02715-07] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2007] [Accepted: 04/19/2008] [Indexed: 11/20/2022] Open
Abstract
Despite the fact that most industrial processes for secondary metabolite production are performed with submerged cultures, a reliable developmental model for Streptomyces under these culture conditions is lacking. With the exception of a few species which sporulate under these conditions, it is assumed that no morphological differentiation processes take place. In this work, we describe new developmental features of Streptomyces coelicolor A3(2) grown in liquid cultures and integrate them into a developmental model analogous to the one previously described for surface cultures. Spores germinate as a compartmentalized mycelium (first mycelium). These young compartmentalized hyphae start to form pellets which grow in a radial pattern. Death processes take place in the center of the pellets, followed by growth arrest. A new multinucleated mycelium with sporadic septa (second mycelium) develops inside the pellets and along the periphery, giving rise to a second growth phase. Undecylprodigiosin and actinorhodin antibiotics are produced by this second mycelium but not by the first one. Cell density dictates how the culture will behave in terms of differentiation processes and antibiotic production. When diluted inocula are used, the growth arrest phase, emergence of a second mycelium, and antibiotic production are delayed. Moreover, pellets are less abundant and have larger diameters than in dense cultures. This work is the first to report on the relationship between differentiation processes and secondary metabolite production in submerged Streptomyces cultures.
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Affiliation(s)
- Angel Manteca
- Area de Microbiologia, Departamento de Biologia Funcional and IUBA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain.
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Kim CJ, Lee SJ, Chang YK, Chun GT, Jeong YH, Kim SB. Repeated-batch culture of immobilizedGibberella fujikuroi B9 for gibberellic acid production: An optimization study. BIOTECHNOL BIOPROC E 2006. [DOI: 10.1007/bf02932081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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el-Naggar MY, Hassan MA, Said WYY, el-Aassar SA. Effect of support materials on antibiotic MSW2000 production by immobilized Streptomyces violatus. J GEN APPL MICROBIOL 2004; 49:235-43. [PMID: 14581992 DOI: 10.2323/jgam.49.235] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The production of an antibiotic by free and immobilized cells of Streptomyces violatus through entrapment or adsorption on different materials was investigated. S. violatus entrapped in Ca-alginate beads gave low antibiotic activity compared to the free cell or adsorbed cell, while the adsorption of S. violatus on sponge cubes yielded the highest antibiotic concentration after 4 days of incubation in static cultures. A starch concentration of 10 g/L was optimum for the production of the antibiotic by adsorbed cells. The weight and size of the sponge cubes used for immobilization influenced production of the antibiotic and the optimum weight and size of the sponge were 0.8 g and 1.0 cm(3), respectively, yielding a maximum antibiotic production of 280 mg/ml. Maximum antibiotic production was obtained at an initial pH value of 7.5 and in an inoculum size of 3 ml (spore suspension) per 50 ml. The production of the antibiotic in a fixed-bed bioreactor reached a maximum value after 2 days of incubation at a circulation rate of 30 ml/h. The immobilized cells in the bioreactor were reused seven successive times over a period of 14 days.
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Affiliation(s)
- Mousatfa Y el-Naggar
- Botany Department, Microbiology Division, Faculty of Science, Alexandria University, Alexandria, Egypt.
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Srinivasulu B, Ellaiah P, Adinarayana K. Studies on neomycin production using immobilized cells of S marinensis NUV-5 in various reactor configurations: a technical note. AAPS PharmSciTech 2003; 4:E46. [PMID: 14621978 PMCID: PMC2750639 DOI: 10.1208/pt040346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Bandi Srinivasulu
- Pharmaceutical Biotechnology Division, Department of Pharmaceutical Sciences, Andhra University, 530 003 Visakhapatnam, India
| | - Poluri Ellaiah
- Pharmaceutical Biotechnology Division, Department of Pharmaceutical Sciences, Andhra University, 530 003 Visakhapatnam, India
| | - Kunamneni Adinarayana
- Pharmaceutical Biotechnology Division, Department of Pharmaceutical Sciences, Andhra University, 530 003 Visakhapatnam, India
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Srinivasulu B, Prakasham R, Jetty A, Srinivas S, Ellaiah P, Ramakrishna S. Neomycin production with free and immobilized cells of Streptomyces marinensis in an airlift reactor. Process Biochem 2002. [DOI: 10.1016/s0032-9592(02)00182-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Kojima E. The Latest Frontiers of Bubble Columns and Slurry Bubble Columns. Perspective of the Relationship between Hydrodynamics and Reactor Performance in Bubble Column and Airlift Bioreactors. KAGAKU KOGAKU RONBUN 2001. [DOI: 10.1252/kakoronbunshu.27.419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Eiichi Kojima
- Institute of Applied Biochemistry, University of Tsukuba
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Sarrà M, Pérez-Pons JA, Gòdia F, Casas Alvero C. Importance of growth form on production of hybrid antibiotic by Streptomyces lividans TK21 by fed-batch and continuous fermentation. Appl Biochem Biotechnol 1998; 75:235-48. [PMID: 10230022 DOI: 10.1007/bf02787777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A fermentation strategy, based on the controlled feeding of growth-limiting nutrients in order to maintain metabolic activity for extended periods, has been examined in the case of the production of a hybrid antibiotic by a transformed strain of Streptomyces lividans TK21. The fed-batch operation did not improve the results obtained with batch operation. Continuous cultures on defined medium showed stable levels of biomass concentration, but antibiotic production ceased when continuous operation was started. The results obtained indicate the critical influence that morphology of the cell aggregates has on metabolic activity. The antibiotic is produced only in culture conditions providing growth in compact mycelial pellets.
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Affiliation(s)
- M Sarrà
- Departament d'Enginyeria Química, Facultat de Ciències, Universitat Autònoma de Barcelona, Spain
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