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Pospíšil J, Schwarz M, Ziková A, Vítovská D, Hradilová M, Kolář M, Křenková A, Hubálek M, Krásný L, Vohradský J. σ E of Streptomyces coelicolor can function both as a direct activator or repressor of transcription. Commun Biol 2024; 7:46. [PMID: 38184746 PMCID: PMC10771440 DOI: 10.1038/s42003-023-05716-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/18/2023] [Indexed: 01/08/2024] Open
Abstract
σ factors are considered as positive regulators of gene expression. Here we reveal the opposite, inhibitory role of these proteins. We used a combination of molecular biology methods and computational modeling to analyze the regulatory activity of the extracytoplasmic σE factor from Streptomyces coelicolor. The direct activator/repressor function of σE was then explored by experimental analysis of selected promoter regions in vivo. Additionally, the σE interactome was defined. Taken together, the results characterize σE, its regulation, regulon, and suggest its direct inhibitory function (as a repressor) in gene expression, a phenomenon that may be common also to other σ factors and organisms.
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Affiliation(s)
- Jiří Pospíšil
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Czech Republic.
| | - Marek Schwarz
- Laboratory of Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Alice Ziková
- Laboratory of Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Dragana Vítovská
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Miluše Hradilová
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Michal Kolář
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Alena Křenková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 542/2, 160 00, Prague 6, Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 542/2, 160 00, Prague 6, Czech Republic
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Jiří Vohradský
- Laboratory of Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Czech Republic.
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Kumar P, Rajput D, Dubey KK. Insights into the mechanism of mycelium transformation of Streptomyces toxytricini into pellet. FEMS MICROBES 2023; 4:xtad017. [PMID: 37662548 PMCID: PMC10473828 DOI: 10.1093/femsmc/xtad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/09/2023] [Accepted: 08/17/2023] [Indexed: 09/05/2023] Open
Abstract
Formation of the mycelial pellet in submerged cultivation of Streptomycetes is unwanted in industrial fermentation processes as it imposes mass transfer limitations, changes in the rheology of a medium, and affects the production of secondary metabolites. Though detailed information is not available about the factors involved in regulating mycelial morphology, it is studied that culture conditions and the genetic information of strain play a crucial role. Moreover, the proteomic study has revealed the involvement of low molecular weight proteins such as; DivIVA, FilP, ParA, Scy, and SsgA proteins in apical growth and branching of hyphae, which results in the establishment of the mycelial network. The present study proposes the mechanism of pellet formation of Streptomyces toxytricini (NRRL B-5426) with the help of microscopic and proteomic analysis. The microscopic analysis revealed that growing hyphae contain a bud-like structure behind the apical tip, which follows a certain organized path of growth and branching, which was further converted into the pellet when shake flask to the shake flask inoculation was performed. Proteomic analysis revealed the production of low molecular weight proteins ranging between 20 and 95 kDa, which are involved in apical growth and hyphae branching and can possibly participate in the regulation of pellet morphology.
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Affiliation(s)
- Punit Kumar
- Department of Morphology and Physiology, Karaganda Medical University, Karaganda 100008, Kazakhstan
| | - Deepanshi Rajput
- Biomanufacturing and Process Development Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Kashyap K Dubey
- Biomanufacturing and Process Development Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
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Selegato DM, Castro-Gamboa I. Enhancing chemical and biological diversity by co-cultivation. Front Microbiol 2023; 14:1117559. [PMID: 36819067 PMCID: PMC9928954 DOI: 10.3389/fmicb.2023.1117559] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023] Open
Abstract
In natural product research, microbial metabolites have tremendous potential to provide new therapeutic agents since extremely diverse chemical structures can be found in the nearly infinite microbial population. Conventionally, these specialized metabolites are screened by single-strain cultures. However, owing to the lack of biotic and abiotic interactions in monocultures, the growth conditions are significantly different from those encountered in a natural environment and result in less diversity and the frequent re-isolation of known compounds. In the last decade, several methods have been developed to eventually understand the physiological conditions under which cryptic microbial genes are activated in an attempt to stimulate their biosynthesis and elicit the production of hitherto unexpressed chemical diversity. Among those, co-cultivation is one of the most efficient ways to induce silenced pathways, mimicking the competitive microbial environment for the production and holistic regulation of metabolites, and has become a golden methodology for metabolome expansion. It does not require previous knowledge of the signaling mechanism and genome nor any special equipment for cultivation and data interpretation. Several reviews have shown the potential of co-cultivation to produce new biologically active leads. However, only a few studies have detailed experimental, analytical, and microbiological strategies for efficiently inducing bioactive molecules by co-culture. Therefore, we reviewed studies applying co-culture to induce secondary metabolite pathways to provide insights into experimental variables compatible with high-throughput analytical procedures. Mixed-fermentation publications from 1978 to 2022 were assessed regarding types of co-culture set-ups, metabolic induction, and interaction effects.
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Kuhl M, Rückert C, Gläser L, Beganovic S, Luzhetskyy A, Kalinowski J, Wittmann C. Microparticles enhance the formation of seven major classes of natural products in native and metabolically engineered actinobacteria through accelerated morphological development. Biotechnol Bioeng 2021; 118:3076-3093. [PMID: 33974270 DOI: 10.1002/bit.27818] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/17/2021] [Accepted: 04/30/2021] [Indexed: 11/09/2022]
Abstract
Actinobacteria provide a rich spectrum of bioactive natural products and therefore display an invaluable source towards commercially valuable pharmaceuticals and agrochemicals. Here, we studied the use of inorganic talc microparticles (hydrous magnesium silicate, 3MgO·4SiO2 ·H2 O, 10 µm) as a general supplement to enhance natural product formation in this important class of bacteria. Added to cultures of recombinant Streptomyces lividans, talc enhanced production of the macrocyclic peptide antibiotic bottromycin A2 and its methylated derivative Met-bottromycin A2 up to 109 mg L-1 , the highest titer reported so far. Hereby, the microparticles fundamentally affected metabolism. With 10 g L-1 talc, S. lividans grew to 40% smaller pellets and, using RNA sequencing, revealed accelerated morphogenesis and aging, indicated by early upregulation of developmental regulator genes such as ssgA, ssgB, wblA, sigN, and bldN. Furthermore, the microparticles re-balanced the expression of individual bottromycin cluster genes, resulting in a higher macrocyclization efficiency at the level of BotAH and correspondingly lower levels of non-cyclized shunt by-products, driving the production of mature bottromycin. Testing a variety of Streptomyces species, talc addition resulted in up to 13-fold higher titers for the RiPPs bottromycin and cinnamycin, the alkaloid undecylprodigiosin, the polyketide pamamycin, the tetracycline-type oxytetracycline, and the anthramycin-analogs usabamycins. Moreover, talc addition boosted production in other actinobacteria, outside of the genus of Streptomyces: vancomycin (Amycolatopsis japonicum DSM 44213), teicoplanin (Actinoplanes teichomyceticus ATCC 31121), and the angucyclinone-type antibiotic simocyclinone (Kitasatospora sp.). For teicoplanin, the microparticles were even crucial to activate production. Taken together, the use of talc was beneficial in 75% of all tested cases and optimized natural and heterologous hosts forming the substance of interest with clusters under native and synthetic control. Given its simplicity and broad benefits, microparticle-supplementation appears as an enabling technology in natural product research of these most important microbes.
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Affiliation(s)
- Martin Kuhl
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Selma Beganovic
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
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Kuhl M, Gläser L, Rebets Y, Rückert C, Sarkar N, Hartsch T, Kalinowski J, Luzhetskyy A, Wittmann C. Microparticles globally reprogram Streptomyces albus toward accelerated morphogenesis, streamlined carbon core metabolism, and enhanced production of the antituberculosis polyketide pamamycin. Biotechnol Bioeng 2020; 117:3858-3875. [PMID: 32808679 DOI: 10.1002/bit.27537] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 12/18/2022]
Abstract
Streptomyces spp. are a rich source for natural products with recognized industrial value, explaining the high interest to improve and streamline the performance of in these microbes. Here, we studied the production of pamamycins, macrodiolide homologs with a high activity against multiresistant pathogenic microbes, using recombinant Streptomyces albus J1074/R2. Talc particles (hydrous magnesium silicate, 3MgO·4SiO2 ·H2 O) of micrometer size, added to submerged cultures of the recombinant strain, tripled pamamycin production up to 50 mg/L. Furthermore, they strongly affected morphology, reduced the size of cell pellets formed by the filamentous microbe during the process up to sixfold, and shifted the pamamycin spectrum to larger derivatives. Integrated analysis of transcriptome and precursor (CoA thioester) supply of particle-enhanced and control cultures provided detailed insights into the underlying molecular changes. The microparticles affected the expression of 3,341 genes (56% of all genes), revealing a global and fundamental impact on metabolism. Morphology-associated genes, encoding major regulators such as SsgA, RelA, EshA, Factor C, as well as chaplins and rodlins, were found massively upregulated, indicating that the particles caused a substantially accelerated morphogenesis. In line, the pamamycin cluster was strongly upregulated (up to 1,024-fold). Furthermore, the microparticles perturbed genes encoding for CoA-ester metabolism, which were mainly activated. The altered expression resulted in changes in the availability of intracellular CoA-esters, the building blocks of pamamycin. Notably, the ratio between methylmalonyl CoA and malonyl-CoA was increased fourfold. Both metabolites compete for incorporation into pamamycin so that the altered availability explained the pronounced preference for larger derivatives in the microparticle-enhanced process. The novel insights into the behavior of S. albus in response to talc appears of general relevance to further explore and upgrade the concept of microparticle enhanced cultivation, widely used for filamentous microbes.
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Affiliation(s)
- Martin Kuhl
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Yuriy Rebets
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | | | | | | | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
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6
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Wu Y, Kang Q, Zhang LL, Bai L. Subtilisin-Involved Morphology Engineering for Improved Antibiotic Production in Actinomycetes. Biomolecules 2020; 10:biom10060851. [PMID: 32503302 PMCID: PMC7356834 DOI: 10.3390/biom10060851] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 05/27/2020] [Accepted: 05/30/2020] [Indexed: 12/27/2022] Open
Abstract
In the submerged cultivation of filamentous microbes, including actinomycetes, complex morphology is one of the critical process features for the production of secondary metabolites. Ansamitocin P-3 (AP-3), an antitumor agent, is a secondary metabolite produced by Actinosynnema pretiosum ATCC 31280. An excessive mycelial fragmentation of A. pretiosum ATCC 31280 was observed during the early stage of fermentation. Through comparative transcriptomic analysis, a subtilisin-like serine peptidase encoded gene APASM_4178 was identified to be responsible for the mycelial fragmentation. Mutant WYT-5 with the APASM_4178 deletion showed increased biomass and improved AP-3 yield by 43.65%. We also found that the expression of APASM_4178 is specifically regulated by an AdpA-like protein APASM_1021. Moreover, the mycelial fragmentation was alternatively alleviated by the overexpression of subtilisin inhibitor encoded genes, which also led to a 46.50 ± 0.79% yield increase of AP-3. Furthermore, APASM_4178 was overexpressed in salinomycin-producing Streptomyces albus BK 3-25 and validamycin-producing S. hygroscopicus TL01, which resulted in not only dispersed mycelia in both strains, but also a 33.80% yield improvement of salinomycin to 24.07 g/L and a 14.94% yield improvement of validamycin to 21.46 g/L. In conclusion, our work elucidates the involvement of a novel subtilisin-like serine peptidase in morphological differentiation, and modulation of its expression could be an effective strategy for morphology engineering and antibiotic yield improvement in actinomycetes.
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Affiliation(s)
- Yuanting Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200204, China; (Y.W.); (Q.K.)
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qianjin Kang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200204, China; (Y.W.); (Q.K.)
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Li-Li Zhang
- College of Life Science, Tarim University, Alar 843300, China;
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200204, China; (Y.W.); (Q.K.)
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- College of Life Science, Tarim University, Alar 843300, China;
- Correspondence:
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7
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van Dissel D, Willemse J, Zacchetti B, Claessen D, Pier GB, van Wezel GP. Production of poly-β-1,6-N-acetylglucosamine by MatAB is required for hyphal aggregation and hydrophilic surface adhesion by Streptomyces. MICROBIAL CELL 2018; 5:269-279. [PMID: 29850464 PMCID: PMC5972031 DOI: 10.15698/mic2018.06.635] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Streptomycetes are multicellular filamentous microorganisms, and major producers of industrial enzymes and bioactive compounds such as antibiotics and anticancer drugs. The mycelial lifestyle plays an important role in the productivity during industrial fermentations. The hyphae of liquid-grown streptomycetes can self-aggregate into pellets, which hampers their industrial exploitation. Here we show that the Mat complex, which is required for pellet formation, catalyzes the synthesis of extracellular poly-β-1,6-N-acetylglucosamine (PNAG) in the model organisms Streptomyces coelicolor and Streptomyces lividans. Extracellular accumulation of PNAG allows Streptomyces to attach to hydrophilic surfaces, while attachment to hydrophobic surfaces requires a cellulase-degradable extracellular polymer (EPS) produced by CslA. Over-expression of matAB was sufficient to restore pellet formation to cslA null mutants of S. lividans. The two EPS systems together increase the robustness of mycelial pellets. These new insights allow better control of liquid-culture morphology of streptomycetes, which may be harnessed to improve growth and industrial exploitation of these highly versatile natural product and enzyme producers.
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Affiliation(s)
- Dino van Dissel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Joost Willemse
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Boris Zacchetti
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Dennis Claessen
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Gerald B Pier
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
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Kumar P, Dubey KK. Implication of mutagenesis and precursor supplementation towards the enhancement of lipstatin (an antiobesity agent) biosynthesis through submerged fermentation using Streptomyces toxytricini. 3 Biotech 2018; 8:29. [PMID: 29291142 PMCID: PMC5742565 DOI: 10.1007/s13205-017-1049-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 12/17/2017] [Indexed: 11/28/2022] Open
Abstract
In the present study, lipstatin production was studied from different mutants of Streptomyces toxytricini which were developed using ultraviolet radiation (exposure time 30 s, 1, 2, 5 and 10 min), ethyl methane sulfonte, methyl methane sulfonate (MMS) and N-methyl-N'-intro-N-nitrosoguanidine (NTG) treatments (50, 100, 200, 500, 1000 µM, respectively). Highest yielding mutants were provided precursor supplementation of citric acid, thiamine and biotin (each 1 g/L) at idiophase for further enhancement in the production of lipstatin. Screened mutants produced biomass in the range of 5.8-7.16 g/L which were lesser than control. Screened mutants also exhibited pellet morphology in submerged culture. Out of these mutants, NTG8 mutant produced highest amount of lipstatin (1383.25 mg/L) with 9.606 mg/L/h productivity. Precursor supplementation to this mutant further increased the production to 2387.81 mg/L. Mutant was validated in 5 L bioreactor and lipstatin production was enhanced to 2519.34 mg/L.
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Affiliation(s)
- Punit Kumar
- Microbial Process Development Laboratory, University Institute of Engineering and Technology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Kashyap Kumar Dubey
- Microbial Process Development Laboratory, University Institute of Engineering and Technology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
- Department of Biotechnology, Central University of Haryana, Mahendergarh, Haryana 123031 India
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Morphology engineering of Streptomyces coelicolor M145 by sub-inhibitory concentrations of antibiotics. Sci Rep 2017; 7:13226. [PMID: 29038577 PMCID: PMC5643529 DOI: 10.1038/s41598-017-13493-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 09/25/2017] [Indexed: 11/11/2022] Open
Abstract
Growth of Streptomyces in submerged culture is characterized by the formation of complex mycelial particles, known as pellets or clumps, which strongly influence antibiotic production. Also, many bioactive molecules produced by Streptomyces have great potential to modulate soil bacteria morphological development. However, there has been no effort directed at engineering mycelial morphology using these small molecules. Here, thiostrepton was identified, using a combination of qRT-PCR, semi-preparative HPLC, and MALDI-TOF MS, as a pellet-inducing compound produced by S. laurentii ATCC31255. At sub-inhibitory concentration, thiostrepton stimulated Streptomyces coelicolor M145 pellet formation and antibiotics production were altered, with 3-fold and 2-fold decreases in actinorhodin and undecylprodigiosin yields, respectively. It was also shown that mycelial morphology can be influenced by other antibiotic class at sub-inhibitory concentrations. For instance, in the presence of spectinomycin, S. coelicolor M145, which under typical growth conditions forms large diameter pellets with many protruding hyphae, instead formed small diameter pellets with barely visible hyphae at the edge. Importantly, this morphology produced a 4-fold increase in undecylprodigiosin production and 3-fold decrease in actinorhodin production. These results indicated that these small molecules, previously identified as antimicrobials, also have great potential for influencing mycelial morphology.
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Kumar P, Dubey KK. Mycelium transformation of Streptomyces toxytricini into pellet: Role of culture conditions and kinetics. BIORESOURCE TECHNOLOGY 2017; 228:339-347. [PMID: 28088096 DOI: 10.1016/j.biortech.2017.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/31/2016] [Accepted: 01/03/2017] [Indexed: 06/06/2023]
Abstract
The present study envisages the role of different carbon sources, nitrogen sources, metals, pH, inoculum volume and agitation rate in pellet formation of S. toxytricini at shake-flask level. It was found that galactose, ammonium sulphate, sodium nitrate, Cu2+, Zn2+, higher inoculum volume (5% v/v) and agitation rate at 300rpm caused significant reduction in pellet size (up to the range of 30μm-0.5mm) but biomass formations was also reduced subsequently. Interestingly diffused type of morphology was obtained in Fe2+ supplemented medium with reduced biomass (1.5gL-1). Rheological study revealed that non-Newtonian behaviour of culture broth. Besides this, kinetics study was also made to understand the growth kinetics (0.39gL-1h-1), oxygen uptake rate (0.1146mgL-1h-1), and production of lipstatin (0.0072gh-1).
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Affiliation(s)
- Punit Kumar
- Microbial Biotechnology Laboratory, University Institute of Engineering and Technology, Maharshi Dayanand University, Rohtak 124001, Haryana, India
| | - Kashyap Kumar Dubey
- Microbial Biotechnology Laboratory, University Institute of Engineering and Technology, Maharshi Dayanand University, Rohtak 124001, Haryana, India; Department of Biotechnology, Central University of Haryana, Mahendergarh 123031, Haryana, India.
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11
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Schrempf H, Merling P. Extracellular Streptomyces lividans vesicles: composition, biogenesis and antimicrobial activity. Microb Biotechnol 2015; 8:644-58. [PMID: 25851532 PMCID: PMC4476819 DOI: 10.1111/1751-7915.12274] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 02/09/2015] [Accepted: 02/09/2015] [Indexed: 11/27/2022] Open
Abstract
We selected Streptomyces lividans to elucidate firstly the biogenesis and antimicrobial activities of extracellular vesicles that a filamentous and highly differentiated Gram-positive bacterium produces. Vesicle types range in diameter from 110 to 230 nm and 20 to 60 nm, respectively; they assemble to clusters, and contain lipids and phospholipids allowing their in situ imaging by specific fluorescent dyes. The presence of the identified secondary metabolite undecylprodigiosin provokes red fluorescence of a portion of the heterogeneous vesicle populations facilitating in vivo monitoring. Protuberances containing vesicles generate at tips, and alongside of substrate hyphae, and enumerate during late vegetative growth to droplet-like exudates. Owing to in situ imaging in the presence and absence of a green fluorescent vancomycin derivative, we conclude that protuberances comprising vesicles arise at sites with enhanced levels of peptidoglycan subunits [pentapeptide of lipid II (C55)-linked disaccharides], and reduced levels of polymerized and cross-linked peptidoglycan within hyphae. These sites correlate with enhanced levels of anionic phospholipids and lipids. Vesicles provoke pronounced damages of Aspergillus proliferans, Verticillium dahliae and induced clumping and distortion of Escherichia coli. These harmful effects are likely attributable to the action of the identified vesicular compounds including different enzyme types, components of signal transduction cascades and undecylprodigiosin. Based on our pioneering findings, we highlight novel clues with environmental implications and application potential.
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Affiliation(s)
- Hildgund Schrempf
- FB Biology/Chemistry, Applied Genetics of Microorganisms, University Osnabrück, Barbarastr. 13, D-49069, Osnabrück, Germany
| | - Philipp Merling
- FB Biology/Chemistry, Applied Genetics of Microorganisms, University Osnabrück, Barbarastr. 13, D-49069, Osnabrück, Germany
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12
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van Dissel D, Claessen D, Roth M, van Wezel GP. A novel locus for mycelial aggregation forms a gateway to improved Streptomyces cell factories. Microb Cell Fact 2015; 14:44. [PMID: 25889360 PMCID: PMC4391728 DOI: 10.1186/s12934-015-0224-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/09/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Streptomycetes produce a plethora of natural products including antibiotics and anticancer drugs, as well as many industrial enzymes. Their mycelial life style is a major bottleneck for industrial exploitation and over decades strain improvement programs have selected production strains with better growth properties. Uncovering the nature of the underlying mutations should allow the ready transfer of desirable traits to other production hosts. RESULTS Here we report that the mat gene cluster, which was identified through reverse engineering of a non-pelleting mutant selected in a chemostat, is key to pellet formation of Streptomyces lividans. Deletion of matA or matB, which encode putative polysaccharide synthases, effects mycelial metamorphosis, with very small and open mycelia. Growth rate and productivity of the matAB null mutant were increased by over 60% as compared to the wild-type strain. CONCLUSION Here, we present a way to counteract pellet formation by streptomycetes, which is one of the major bottlenecks in their industrial application. The mat locus is an ideal target for rational strain design approaches aimed at improving streptomycetes as industrial production hosts.
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Affiliation(s)
- Dino van Dissel
- Molecular Biotechnology, Institute of Biology, Leiden University, PO Box 9505, 2300RA, Leiden, The Netherlands.
| | - Dennis Claessen
- Molecular Biotechnology, Institute of Biology, Leiden University, PO Box 9505, 2300RA, Leiden, The Netherlands.
| | - Martin Roth
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Adolf-Reichwein-Str. 23, 07745, Jena, Germany.
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, PO Box 9505, 2300RA, Leiden, The Netherlands.
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13
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van Dissel D, Claessen D, van Wezel GP. Morphogenesis of Streptomyces in submerged cultures. ADVANCES IN APPLIED MICROBIOLOGY 2014; 89:1-45. [PMID: 25131399 DOI: 10.1016/b978-0-12-800259-9.00001-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Members of the genus Streptomyces are mycelial bacteria that undergo a complex multicellular life cycle and propagate via sporulation. Streptomycetes are important industrial microorganisms, as they produce a plethora of medically relevant natural products, including the majority of clinically important antibiotics, as well as a wide range of enzymes with industrial application. While development of Streptomyces in surface-grown cultures is well studied, relatively little is known of the parameters that determine morphogenesis in submerged cultures. Here, growth is characterized by the formation of mycelial networks and pellets. From the perspective of industrial fermentations, such mycelial growth is unattractive, as it is associated with slow growth, heterogeneous cultures, and high viscosity. Here, we review the current insights into the genetic and environmental factors that determine mycelial growth and morphology in liquid-grown cultures. The genetic factors include cell-matrix proteins and extracellular polymers, morphoproteins with specific roles in liquid-culture morphogenesis, with the SsgA-like proteins as well-studied examples, and programmed cell death. Environmental factors refer in particular to those dictated by process engineering, such as growth media and reactor set-up. These insights are then integrated to provide perspectives as to how this knowledge can be applied to improve streptomycetes for industrial applications.
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Affiliation(s)
- Dino van Dissel
- Molecular Biotechnology, Institute Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Dennis Claessen
- Molecular Biotechnology, Institute Biology Leiden, Leiden University, Leiden, The Netherlands.
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute Biology Leiden, Leiden University, Leiden, The Netherlands.
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Guyet A, Benaroudj N, Proux C, Gominet M, Coppée JY, Mazodier P. Identified members of the Streptomyces lividans AdpA regulon involved in differentiation and secondary metabolism. BMC Microbiol 2014; 14:81. [PMID: 24694298 PMCID: PMC4021200 DOI: 10.1186/1471-2180-14-81] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 03/27/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND AdpA is a key transcriptional regulator involved in the complex growth cycle of Streptomyces. Streptomyces are Gram-positive bacteria well-known for their production of secondary metabolites and antibiotics. Most work on AdpA has been in S. griseus, and little is known about the pathways it controls in other Streptomyces spp. We recently discovered interplay between ClpP peptidases and AdpA in S. lividans. Here, we report the identification of genes directly regulated by AdpA in S. lividans. RESULTS Microarray experiments revealed that the expression of hundreds of genes was affected in a S. lividans adpA mutant during early stationary phase cultures in YEME liquid medium. We studied the expression of the S. lividans AdpA-regulated genes by quantitative real-time PCR analysis after various times of growth. In silico analysis revealed the presence of potential AdpA-binding sites upstream from these genes; electrophoretic mobility shift assays indicated that AdpA binds directly to their promoter regions. This work identifies new pathways directly controlled by AdpA and that are involved in S. lividans development (ramR, SLI7885 also known as hyaS and SLI6586), and primary (SLI0755-SLI0754 encoding CYP105D5 and Fdx4) or secondary (cchA, cchB, and hyaS) metabolism. CONCLUSIONS We characterised six S. lividans AdpA-dependent genes whose expression is directly activated by this pleiotropic regulator. Several of these genes are orthologous to bldA-dependent genes in S. coelicolor. Furthermore, in silico analysis suggests that over hundred genes may be directly activated or repressed by S. lividans AdpA, although few have been described as being part of any Streptomyces AdpA regulons. This study increases the number of known AdpA-regulated pathways in Streptomyces spp.
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Affiliation(s)
| | | | | | | | | | - Philippe Mazodier
- Unité de Biologie des Bactéries Pathogènes à Gram-Positif, Institut Pasteur, CNRS URA 2172, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.
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Lamp J, Weber M, Cingöz G, Ortiz de Orué Lucana D, Schrempf H. A Streptomyces-specific member of the metallophosphatase superfamily contributes to spore dormancy and interaction with Aspergillus proliferans. FEMS Microbiol Lett 2013; 342:89-97. [PMID: 23480800 DOI: 10.1111/1574-6968.12121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 03/01/2013] [Accepted: 03/04/2013] [Indexed: 11/27/2022] Open
Abstract
We have identified, cloned and characterized a formerly unknown protein from Streptomyces lividans spores. The deduced protein belongs to a novel member of the metallophosphatase superfamily and contains a phosphatase domain and predicted binding sites for divalent ions. Very close relatives are encoded in the genomic DNA of many different Streptomyces species. As the deduced related homologues diverge from other known phosphatase types, we named the protein MptS (metallophosphatase type from Streptomyces). Comparative physiological and biochemical investigations and analyses by fluorescence microscopy of the progenitor strain, designed mutants carrying either a disruption of the mptS gene or the reintroduced gene as fusion with histidine codons or the egfp gene led to the following results: (i) the mptS gene is transcribed in the course of aerial mycelia formation. (ii) The MptS protein is produced during the late stages of growth, (iii) accumulates within spores, (iv) functions as an active enzyme that releases inorganic phosphate from an artificial model substrate, (v) is required for spore dormancy and (vi) MptS supports the interaction amongst Streptomyces lividans spores with conidia of the fungus Aspergillus proliferans. We discuss the possible role(s) of MptS-dependent enzymatic activity and the implications for spore biology.
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Affiliation(s)
- Jessica Lamp
- FB Biologie/Chemie, Universität Osnabrück, Osnabrück 49069, Germany
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Meschke H, Walter S, Schrempf H. Characterization and localization of prodiginines from Streptomyces lividans suppressing Verticillium dahliae in the absence or presence of Arabidopsis thaliana. Environ Microbiol 2011; 14:940-52. [DOI: 10.1111/j.1462-2920.2011.02665.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Fujimoto M, Yamada A, Kurosawa J, Kawata A, Beppu T, Takano H, Ueda K. Pleiotropic role of the Sco1/SenC family copper chaperone in the physiology of Streptomyces. Microb Biotechnol 2011; 5:477-88. [PMID: 22117562 PMCID: PMC3815325 DOI: 10.1111/j.1751-7915.2011.00319.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Antibiotic production and cell differentiation in Streptomyces is stimulated by micromolar levels of Cu(2+) . Here, we knocked out the Sco1/SenC family copper chaperone (ScoC) encoded in the conserved gene cluster 'sco' (the S treptomycescopper utilization) in Streptomyces coelicolor A3(2) and S. griseus. It is known that the Sco1/SenC family incorporates Cu(2+) into the active centre of cytochrome oxidase (cox). The knockout caused a marked delay in antibiotic production and aerial mycelium formation on solid medium, temporal pH decline in glucose-containing liquid medium, and significant reduction of cox activity in S. coelicolor. The scoC mutant produced two- to threefold higher cellular mass of the wild type exhibiting a marked cox activity in liquid medium supplied with 10 µM CuSO(4) , suggesting that ScoC is involved in not only the construction but also the deactivation of cox. The scoC mutant was defective in the monoamine oxidase activity responsible for cell aggregation and sedimentation. These features were similarly observed with regard to the scoC mutant of S. griseus. The scoC mutant of S. griseus was also defective in the extracellular activity oxidizing N,N'-dimethyl-p-phenylenediamine sulfate. Addition of 10 µM CuSO(4) repressed the activity of the conserved promoter preceding scoA and caused phenylalanine auxotrophy in some Streptomyces spp. probably because of the repression of pheA; pheA encodes prephenate dehydratase, which is located at the 3' terminus of the putative operon structure. Overall, the evidence indicates that Sco is crucial for the utilization of copper under a low-copper condition and for the activation of the multiple Cu(2+) -containing oxidases that play divergent roles in the complex physiology of Streptomyces.
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Affiliation(s)
- Masahiro Fujimoto
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Japan
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Schrempf H, Koebsch I, Walter S, Engelhardt H, Meschke H. Extracellular Streptomyces vesicles: amphorae for survival and defence. Microb Biotechnol 2011; 4:286-99. [PMID: 21342473 PMCID: PMC3818868 DOI: 10.1111/j.1751-7915.2011.00251.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 01/12/2011] [Indexed: 11/27/2022] Open
Abstract
Blue-pigmented exudates arise as droplets on sporulated lawns of Streptomyces coelicolor M110 grown on agar plates. Our electron microscopical and biochemical studies suggest that droplets contain densely packed vesicles with large assemblies of different protein types and/or the polyketide antibiotic actinorhodin. Frozen-hydrated vesicles were unilamellar with a typical bilayer membrane, and ranged from 80 to 400 nm in diameter with a preferred width of 150-300 nm. By means of cryo-electron tomography, three types were reconstructed three-dimensionally: vesicles that were filled with particulate material, likely protein assemblies, those that contained membrane-bound particles, and a vesicle that showed a higher contrast inside, but lacked particles. Our LC/MS analyses of generated tryptic peptides led to the identification of distinct proteins that carry often a predicted N-terminal signal peptide with a twin-arginine motif or lack a canonical signal sequence. The proteins are required for a range of processes: the acquisition of inorganic as well as organic phosphate, iron ions, and of distinct carbon sources, energy metabolism and redox balance, defence against oxidants and tellurites, the tailoring of actinorhodin, folding and assembly of proteins, establishment of turgor, and different signalling cascades. Our novel findings have immense implications for understanding new avenues of environmental biology of streptomycetes and for biotechnological applications.
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Affiliation(s)
- Hildgund Schrempf
- FB Biology/Chemistry, Applied Genetics of Microorganisms, University Osnabrück, Barbarastr. 13, D-49069 Osnabrück, Germany.
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