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Ścigaczewska A, Boruta T, Bizukojć M. Morphological-metabolic analysis in Streptomyces rimosus microparticle-enhanced cultivations (MPEC). Bioprocess Biosyst Eng 2024; 47:891-902. [PMID: 38664238 PMCID: PMC11101530 DOI: 10.1007/s00449-024-03015-2] [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: 09/14/2023] [Accepted: 04/05/2024] [Indexed: 05/19/2024]
Abstract
Streptomyces produce a broad spectrum of biologically active molecules such as oxytetracycline and rimocidin, which are widely used in human and animal treatments. microparticle-enhanced cultivation (MPEC) is one of the tools used for Streptomyces bioprocesses intensification by the control of mycelial morphology. In the present work, morphological changes of Streptomyces rimosus caused by the addition of 10 µm talc microparticles in MPEC were correlated with the biosynthetic activity of the microorganism. Comparing the runs with and without microparticles, major morphological changes were observed in MPEC, including the deformation of pellets, variation of their size, appearance of hyphae and clumps as well as the aggregation of mycelial objects. The presence of talc microparticles also influenced the levels of the studied secondary metabolites produced by S. rimosus. Comparing control and MPEC runs, the addition of talc microparticles increased the amounts of oxytetracycline (9-fold), 2-acetyl-2-decarboxamido-oxytetracycline (7-fold), milbemycin A3+4[O] (3-fold) and CE 108 (1.5-fold), while rimocidin (27-ethyl) and milbemycin β11+4[O] production was reduced. In summary, the addition of talc microparticles to S. rimosus cultivations led to the development of smaller morphological forms like hyphae and clumps as well as to the changes in the amounts of secondary metabolites.
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Affiliation(s)
- Anna Ścigaczewska
- Faculty of Process and Environmental Engineering, Department of Bioprocess Engineering, Lodz University of Technology, ul. Wolczanska 213, 93-005, Lodz, Poland.
| | - Tomasz Boruta
- Faculty of Process and Environmental Engineering, Department of Bioprocess Engineering, Lodz University of Technology, ul. Wolczanska 213, 93-005, Lodz, Poland
| | - Marcin Bizukojć
- Faculty of Process and Environmental Engineering, Department of Bioprocess Engineering, Lodz University of Technology, ul. Wolczanska 213, 93-005, Lodz, Poland
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Fontana C, de Meirelles JL, Verli H. Theoretical models of staurosporine and analogs uncover detailed structural information in biological solution. J Mol Graph Model 2024; 126:108653. [PMID: 37922640 DOI: 10.1016/j.jmgm.2023.108653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 11/07/2023]
Abstract
Staurosporine and its analogs (STA-analogs) are indolocarbazoles (ICZs) compounds able to inhibit kinase proteins in a non-specific way, while present antimicrobial and cytostatic properties. The knowledge of molecular features associated to the complexation, including the ligand shape in solution and thermodynamics of complexation, is substantial to the development of new bioactive ICZs with improved therapeutic properties. In this context, the empirical approach of GROMOS force field is able to accurately reproduce condensed phase physicochemical properties of molecular systems after parameterization. Hence, through parameterization under GROMOS force field and molecular simulations, we assessed STA-analogs dynamics in aqueous solution, as well as its interaction with water to probe conformational and structural features involved in complexation to therapeutic targets. The coexistence of multiple conformers observed in simulations, and confirmed by metadynamics calculations, expanding the conformational space knowledge of these ligands with potential implications in understanding the ligand conformational selection during complexation. Also, changes in availability to H-bonding concerning the different substituents and water can reflect on effects at complexation free energy due to variation at the desolvation energetic costs. Based on these results, we expect the obtained structural data provide systemic framework for rational chemical modification of STA-analogs.
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Affiliation(s)
- Crisciele Fontana
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Av. Bento Gonçalves, 9500 (Caixa Postal 15005), Porto Alegre, CEP 91501-970, RS, Brazil
| | - João Luiz de Meirelles
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Av. Bento Gonçalves, 9500 (Caixa Postal 15005), Porto Alegre, CEP 91501-970, RS, Brazil
| | - Hugo Verli
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Av. Bento Gonçalves, 9500 (Caixa Postal 15005), Porto Alegre, CEP 91501-970, RS, Brazil.
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Schrader M, Schrinner K, Polomsky L, Ivanov D, Kampen I, Schilde C, Krull R, Kwade A. Quantification and modeling of macroparticle-induced mechanical stress for varying shake flask cultivation conditions. Front Bioeng Biotechnol 2023; 11:1254136. [PMID: 37731767 PMCID: PMC10507416 DOI: 10.3389/fbioe.2023.1254136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/08/2023] [Indexed: 09/22/2023] Open
Abstract
In biotechnological processes, filamentous microorganisms are known for their broad product spectrum and complex cellular morphology. Product formation and cellular morphology are often closely linked, requiring a well-defined level of mechanical stress to achieve high product concentrations. Macroparticles were added to shake flask cultures of the filamentous actinomycete Lentzea aerocolonigenes to find these optimal cultivation conditions. However, there is currently no model concept for the dependence of the strength and frequency of the bead-induced stress on the process parameters. Therefore, shake flask simulations were performed for combinations of bead size, bead concentration, bead density and shaking frequency. Contact analysis showed that the highest shear stresses were caused by bead-bottom contacts. Based on this, a newly generated characteristic parameter, the stress area ratio (SAR), was defined, which relates the bead wall shear and normal stresses to the total shear area. Comparison of the SAR with previous cultivation results revealed an optimum pattern for product concentration and mean product-to-biomass related yield coefficient. Thus, this model is a suitable tool for future optimization, comparison and scaling up of shear-sensitive microorganism cultivation. Finally, the simulation results were validated using high-speed recordings of the bead motion on the bottom of the shake flask.
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Affiliation(s)
- Marcel Schrader
- Institute for Particle Technology, Technische Universität Braunschweig, Braunschweig, Germany
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Kathrin Schrinner
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Laura Polomsky
- Institute for Particle Technology, Technische Universität Braunschweig, Braunschweig, Germany
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Dimitri Ivanov
- Institute for Particle Technology, Technische Universität Braunschweig, Braunschweig, Germany
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Ingo Kampen
- Institute for Particle Technology, Technische Universität Braunschweig, Braunschweig, Germany
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Carsten Schilde
- Institute for Particle Technology, Technische Universität Braunschweig, Braunschweig, Germany
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Rainer Krull
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Arno Kwade
- Institute for Particle Technology, Technische Universität Braunschweig, Braunschweig, Germany
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
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Dinius A, Kozanecka ZJ, Hoffmann KP, Krull R. Intensification of bioprocesses with filamentous microorganisms. PHYSICAL SCIENCES REVIEWS 2023. [DOI: 10.1515/psr-2022-0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Abstract
Many industrial biotechnological processes use filamentous microorganisms to produce platform chemicals, proteins, enzymes and natural products. Product formation is directly linked to their cellular morphology ranging from dispersed mycelia over loose clumps to compact pellets. Therefore, the adjustment and control of the filamentous cellular morphology pose major challenges for bioprocess engineering. Depending on the filamentous strain and desired product, optimal morphological shapes for achieving high product concentrations vary. However, there are currently no overarching strain- or product-related correlations to improve process understanding of filamentous production systems. The present book chapter summarizes the extensive work conducted in recent years in the field of improving product formation and thus intensifying biotechnological processes with filamentous microorganisms. The goal is to provide prospective scientists with an extensive overview of this scientifically diverse, highly interesting field of study. In the course of this, multiple examples and ideas shall facilitate the combination of their acquired expertise with promising areas of future research. Therefore, this overview describes the interdependence between filamentous cellular morphology and product formation. Moreover, the currently most frequently used experimental techniques for morphological structure elucidation will be discussed in detail. Developed strategies of morphology engineering to increase product formation by tailoring and controlling cellular morphology and thus to intensify processes with filamentous microorganisms will be comprehensively presented and discussed.
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Affiliation(s)
- Anna Dinius
- Institute of Biochemical Engineering , Technische Universität Braunschweig , Rebenring 56 , 38106 Braunschweig , Germany
- Center of Pharmaceutical Engineering , Technische Universität Braunschweig , Franz-Liszt-Str. 35a , 38106 Braunschweig , Germany
| | - Zuzanna J. Kozanecka
- Institute of Biochemical Engineering , Technische Universität Braunschweig , Rebenring 56 , 38106 Braunschweig , Germany
- Center of Pharmaceutical Engineering , Technische Universität Braunschweig , Franz-Liszt-Str. 35a , 38106 Braunschweig , Germany
| | - Kevin P. Hoffmann
- Institute of Biochemical Engineering , Technische Universität Braunschweig , Rebenring 56 , 38106 Braunschweig , Germany
- Center of Pharmaceutical Engineering , Technische Universität Braunschweig , Franz-Liszt-Str. 35a , 38106 Braunschweig , Germany
| | - Rainer Krull
- Institute of Biochemical Engineering , Technische Universität Braunschweig , Rebenring 56 , 38106 Braunschweig , Germany
- Center of Pharmaceutical Engineering , Technische Universität Braunschweig , Franz-Liszt-Str. 35a , 38106 Braunschweig , Germany
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Xiao S, Wang Z, Wang B, Hou B, Cheng J, Bai T, Zhang Y, Wang W, Yan L, Zhang J. Expanding the application of tryptophan: Industrial biomanufacturing of tryptophan derivatives. Front Microbiol 2023; 14:1099098. [PMID: 37032885 PMCID: PMC10076799 DOI: 10.3389/fmicb.2023.1099098] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/08/2023] [Indexed: 04/11/2023] Open
Abstract
Tryptophan derivatives are various aromatic compounds produced in the tryptophan metabolic pathway, such as 5-hydroxytryptophan, 5-hydroxytryptamine, melatonin, 7-chloro-tryptophan, 7-bromo-tryptophan, indigo, indirubin, indole-3-acetic acid, violamycin, and dexoyviolacein. They have high added value, widely used in chemical, food, polymer and pharmaceutical industry and play an important role in treating diseases and improving life. At present, most tryptophan derivatives are synthesized by biosynthesis. The biosynthesis method is to combine metabolic engineering with synthetic biology and system biology, and use the tryptophan biosynthesis pathway of Escherichia coli, Corynebacterium glutamicum and other related microorganisms to reconstruct the artificial biosynthesis pathway, and then produce various tryptophan derivatives. In this paper, the characteristics, applications and specific biosynthetic pathways and methods of these derivatives were reviewed, and some strategies to increase the yield of derivatives and reduce the production cost on the basis of biosynthesis were introduced in order to make some contributions to the development of tryptophan derivatives biosynthesis industry.
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Affiliation(s)
- Shujian Xiao
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Zhen Wang
- College of Science and Technology, Hebei Agricultural University, Cangzhou, China
| | - Bangxu Wang
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Bo Hou
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Jie Cheng
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, China
- *Correspondence: Jie Cheng, ; Lixiu Yan, ; Jiamin Zhang,
| | - Ting Bai
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Yin Zhang
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Wei Wang
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Lixiu Yan
- Chongqing Academy of Metrology and Quality Inspection, Chongqing, China
- *Correspondence: Jie Cheng, ; Lixiu Yan, ; Jiamin Zhang,
| | - Jiamin Zhang
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, China
- *Correspondence: Jie Cheng, ; Lixiu Yan, ; Jiamin Zhang,
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Dinius A, Schrinner K, Schrader M, Kozanecka ZJ, Brauns H, Klose L, Weiß H, Kwade A, Krull R. Morphology engineering for novel antibiotics: Effect of glass microparticles and soy lecithin on rebeccamycin production and cellular morphology of filamentous actinomycete Lentzea aerocolonigenes. Front Bioeng Biotechnol 2023; 11:1171055. [PMID: 37091334 PMCID: PMC10116066 DOI: 10.3389/fbioe.2023.1171055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/21/2023] [Indexed: 04/25/2023] Open
Abstract
Lentzea aerocolonigenes, as an actinomycete, is a natural producer of the antibiotic and antitumoral drug rebeccamycin. Due to the filamentous cellular morphology handling in cultivations is challenging; therefore, morphology engineering techniques are mandatory to enhance productivity. One promising approach described in the literature is the addition of mineral particles in the micrometer range to precisely adjust cellular morphology and the corresponding product synthesis (microparticle-enhanced cultivation, MPEC). Glass microparticles are introduced in this study as a novel supplementation type for bioprocess intensification in filamentous organisms. Several investigations were conducted to screen for an optimal particle setup, including particle size and concentration regarding their impact and effects on enhanced productivity, microparticle incorporation behavior into the biopellets, the viability of pellets, and morphological changes. Glass microparticles (10 g·L-1) with a median diameter of 7.9 µm, for instance, induced an up to fourfold increase in product synthesis accompanied by overall enhanced viability of biomass. Furthermore, structural elucidations showed that biopellets isolated from MPEC tend to have lower hyphal density than unsupplemented control pellets. In this context, oxygen microprofiling was conducted to better understand how internal structural changes interwind with oxygen supply into the pellets. Here, the resulting oxygen profiles are of a contradictive trend of steeper oxygen consumption with increasing glass microparticle supplementation. Eventually, MPEC was combined with another promising cultivation strategy, the supplementation of soy lecithin (7.5 g·L-1), to further increase the cultivation performance. A combination of both techniques in an optimized setup resulted in a rebeccamycin concentration of 213 mg·L-1 after 10 days of cultivation, the highest value published so far for microparticle-supplemented shake flask cultivations of L. aerocolonigenes.
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Affiliation(s)
- Anna Dinius
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Kathrin Schrinner
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Marcel Schrader
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Institute for Particle Technology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Zuzanna Justyna Kozanecka
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Henry Brauns
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Institute for Particle Technology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Leon Klose
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Institute for Particle Technology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Hannah Weiß
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Arno Kwade
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Institute for Particle Technology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Rainer Krull
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- *Correspondence: Rainer Krull,
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Timoumi A, Nguyen TC, Le T, Kraiem H, Cescut J, Anne-Archard D, Gorret N, Molina-Jouve C, To KA, Fillaudeau L. Comparison of methods to explore the morphology and granulometry of biological particles with complex shapes: Interpretation and limitations. POWDER TECHNOL 2022. [DOI: 10.1016/j.powtec.2022.118067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Zhai G, Gong R, Lin Y, Zhang M, Li J, Deng Z, Sun J, Chen W, Zhang Z. Structural Insight into the Catalytic Mechanism of Non-Heme Iron Halogenase AdaV in 2′-Chloropentostatin Biosynthesis. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guoqing Zhai
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Rong Gong
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Yaxin Lin
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Meng Zhang
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Jiahui Li
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Zixin Deng
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Jiazhong Sun
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Wenqing Chen
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Abichem Biotech Joint Center for Pharmaceutical Innovation, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Zhengyu Zhang
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
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Discovery of unusual dimeric piperazyl cyclopeptides encoded by a Lentzea flaviverrucosa DSM 44664 biosynthetic supercluster. Proc Natl Acad Sci U S A 2022; 119:e2117941119. [PMID: 35439047 PMCID: PMC9169926 DOI: 10.1073/pnas.2117941119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Actinomycetes produce many clinically useful drugs, especially antibiotics and anticancer agents. Rare actinomycetes are known to produce bioactive molecules but they remain underexplored compared to more common Streptomyces spp. Natural molecules having piperazate building blocks are often bioactive, and genome analyses previously indicated the rare actinomycete Lentzea flaviverrucosa DSM 44664 may encode for the production of such molecules. To discover these from complex fermentation mixtures, we devised and employed a targeted metabolomic approach that revealed petrichorin A, an unusual heterodimeric biaryl-cyclohexapeptide. Its structure was determined by using multi-dimensional nuclear magnetic resonance, theoretical calculations, and strain mutagenesis, and its biosynthesis implicated an atypical cytochrome p450 heterodimerization event. Petrichorin A demonstrated potent cytotoxicity, highlighting heterodimeric-biaryls as interesting features for future drug design. Rare actinomycetes represent an underexploited source of new bioactive compounds. Here, we report the use of a targeted metabologenomic approach to identify piperazyl compounds in the rare actinomycete Lentzea flaviverrucosa DSM 44664. These efforts to identify molecules that incorporate piperazate building blocks resulted in the discovery and structural elucidation of two dimeric biaryl-cyclohexapeptides, petrichorins A and B. Petrichorin B is a symmetric homodimer similar to the known compound chloptosin, but petrichorin A is unique among known piperazyl cyclopeptides because it is an asymmetric heterodimer. Due to the structural complexity of petrichorin A, solving its structure required a combination of several standard chemical methods plus in silico modeling, strain mutagenesis, and solving the structure of its biosynthetic intermediate petrichorin C for confident assignment. Furthermore, we found that the piperazyl cyclopeptides comprising each half of the petrichorin A heterodimer are made via two distinct nonribosomal peptide synthetase (NRPS) assembly lines, and the responsible NRPS enzymes are encoded within a contiguous biosynthetic supercluster on the L. flaviverrucosa chromosome. Requiring promiscuous cytochrome p450 crosslinking events for asymmetric and symmetric biaryl production, petrichorins A and B exhibited potent in vitro activity against A2780 human ovarian cancer, HT1080 fibrosarcoma, PC3 human prostate cancer, and Jurkat human T lymphocyte cell lines with IC50 values at low nM levels. Cyclic piperazyl peptides and their crosslinked derivatives are interesting drug leads, and our findings highlight the potential for heterodimeric bicyclic peptides such as petrichorin A for inclusion in future pharmaceutical design and discovery programs.
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Manisha, Gupta SS, Dhiman AK, Sharma U. Rh(III)‐Catalyzed Selective C7 Halogenation of Indolines. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100964] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Manisha
- Chemical Technology Division CSIR-Institute of Himalayan and Bioresource Technology Palampur Himachal Pradesh 176 061 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Shiv Shankar Gupta
- Chemical Technology Division CSIR-Institute of Himalayan and Bioresource Technology Palampur Himachal Pradesh 176 061 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Ankit Kumar Dhiman
- Chemical Technology Division CSIR-Institute of Himalayan and Bioresource Technology Palampur Himachal Pradesh 176 061 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Upendra Sharma
- Chemical Technology Division CSIR-Institute of Himalayan and Bioresource Technology Palampur Himachal Pradesh 176 061 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
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Kolling D, Stierhof M, Lasch C, Myronovskyi M, Luzhetskyy A. A Promiscuous Halogenase for the Derivatization of Flavonoids. Molecules 2021; 26:molecules26206220. [PMID: 34684801 PMCID: PMC8539768 DOI: 10.3390/molecules26206220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 11/17/2022] Open
Abstract
Halogenation often improves the bioactive properties of natural products and is used in pharmaceutical research for the generation of new potential drug leads. High regio- and stereospecificity, simple reaction conditions and straightforward downstream processing are the main advantages of halogenation using enzymatic biocatalysts compared to chemical synthetic approaches. The identification of new promiscuous halogenases for the modification of various natural products is of great interest in modern drug discovery. In this paper, we report the identification of a new promiscuous FAD-dependent halogenase, DklH, from Frankia alni ACN14a. The identified halogenase readily modifies various flavonoid compounds, including those with well-studied biological activities. This halogenase has been demonstrated to modify not only flavones and isoflavones, but also flavonols, flavanones and flavanonols. The structural requirements for DklH substrate recognition were determined using a feeding approach. The homology model of DklH and the mechanism of substrate recognition are also proposed in this paper.
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Affiliation(s)
- Dominik Kolling
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (D.K.); (M.S.); (C.L.); (M.M.)
| | - Marc Stierhof
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (D.K.); (M.S.); (C.L.); (M.M.)
| | - Constanze Lasch
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (D.K.); (M.S.); (C.L.); (M.M.)
| | - Maksym Myronovskyi
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (D.K.); (M.S.); (C.L.); (M.M.)
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (D.K.); (M.S.); (C.L.); (M.M.)
- AMEG Department, Helmholtz Institute for Pharmaceutical Research Saarland, 66123 Saarbruecken, Germany
- Correspondence: ; Tel.: +49-681-302-70200
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Schrinner K, Schrader M, Niebusch J, Althof K, Schwarzer FA, Nowka PF, Dinius A, Kwade A, Krull R. Macroparticle-enhanced cultivation of Lentzea aerocolonigenes: Variation of mechanical stress and combination with lecithin supplementation for a significantly increased rebeccamycin production. Biotechnol Bioeng 2021; 118:3984-3995. [PMID: 34196390 DOI: 10.1002/bit.27875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 06/19/2021] [Indexed: 11/06/2022]
Abstract
The actinomycete Lentzea aerocolonigenes produces the antitumor antibiotic rebeccamycin. In previous studies the rebeccamycin production was significantly increased by the addition of glass beads during cultivation in different diameters between 0.5 and 2 mm and the induced mechanical stress by the glass beads was proposed to be responsible for the increased production. Thus, this study was conducted to be a systematic investigation of different parameters for macroparticle addition, such as bead diameter, concentration, and density (glass and ceramic) as well as shaking frequency, for a better understanding of the particle-induced stress on L. aerocolonigenes. The induced stress for optimal rebeccamycin production can be estimated by a combination of stress energy and stress frequency. In addition, the macroparticle-enhanced cultivation of L. aerocolonigenes was combined with soy lecithin addition to further increase the rebeccamycin concentration. With 100 g L-1 glass beads in a diameter of 969 µm and 5 g L-1 soy lecithin a concentration of 388 mg L-1 rebeccamycin was reached after 10 days of cultivation, which corresponds to the highest rebeccamycin concentrations achieved in shake flask cultivations of L. aerocolonigenes stated in literature so far.
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Affiliation(s)
- Kathrin Schrinner
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany.,Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Marcel Schrader
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany.,Institute for Particle Technology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jana Niebusch
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Kristin Althof
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Friederike A Schwarzer
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Paul-Frederik Nowka
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Anna Dinius
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany.,Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Arno Kwade
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany.,Institute for Particle Technology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Rainer Krull
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany.,Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
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Mohan CD, Rangappa S, Nayak SC, Jadimurthy R, Wang L, Sethi G, Garg M, Rangappa KS. Bacteria as a treasure house of secondary metabolites with anticancer potential. Semin Cancer Biol 2021; 86:998-1013. [PMID: 33979675 DOI: 10.1016/j.semcancer.2021.05.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/03/2021] [Accepted: 05/03/2021] [Indexed: 12/27/2022]
Abstract
Cancer stands in the frontline among leading killers worldwide and the annual mortality rate is expected to reach 16.4 million by 2040. Humans suffer from about 200 different types of cancers and many of them have a small number of approved therapeutic agents. Moreover, several types of major cancers are diagnosed at advanced stages as a result of which the existing therapies have limited efficacy against them and contribute to a dismal prognosis. Therefore, it is essential to develop novel potent anticancer agents to counteract cancer-driven lethality. Natural sources such as bacteria, plants, fungi, and marine microorganisms have been serving as an inexhaustible source of anticancer agents. Notably, over 13,000 natural compounds endowed with different pharmacological properties have been isolated from different bacterial sources. In the present article, we have discussed about the importance of natural products, with special emphasis on bacterial metabolites for cancer therapy. Subsequently, we have comprehensively discussed the various sources, mechanisms of action, toxicity issues, and off-target effects of clinically used anticancer drugs (such as actinomycin D, bleomycin, carfilzomib, doxorubicin, ixabepilone, mitomycin C, pentostatin, rapalogs, and romidepsin) that have been derived from different bacteria. Furthermore, we have also discussed some of the major secondary metabolites (antimycins, chartreusin, elsamicins, geldanamycin, monensin, plicamycin, prodigiosin, rebeccamycin, salinomycin, and salinosporamide) that are currently in the clinical trials or which have demonstrated potent anticancer activity in preclinical models. Besides, we have elaborated on the application of metagenomics in drug discovery and briefly described about anticancer agents (bryostatin 1 and ET-743) identified through the metagenomics approach.
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Affiliation(s)
| | - Shobith Rangappa
- Adichunchanagiri Institute for Molecular Medicine, Adichunchanagiri University, BG Nagara, 571448, Nagamangala Taluk, India
| | - S Chandra Nayak
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysore, 570006, India
| | - Ragi Jadimurthy
- Department of Studies in Molecular Biology, University of Mysore, Manasagangotri, Mysore, 570006, India
| | - Lingzhi Wang
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Uttar Pradesh, Noida, 201313, India
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Böl M, Schrinner K, Tesche S, Krull R. Challenges of influencing cellular morphology by morphology engineering techniques and mechanical induced stress on filamentous pellet systems-A critical review. Eng Life Sci 2021; 21:51-67. [PMID: 33716605 PMCID: PMC7923580 DOI: 10.1002/elsc.202000060] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 11/30/2022] Open
Abstract
Filamentous microorganisms are main producers of organic acids, enzymes, and pharmaceutical agents such as antibiotics and other active pharmaceutical ingredients. With their complex cell morphology, ranging from dispersed mycelia to dense pellets, the cultivation is challenging. In recent years, various techniques for tailor-made cell morphologies of filamentous microorganisms have been developed to increase product formation and have been summarised under the term morphology engineering. These techniques, namely microparticle-enhanced cultivation, macroparticle-enhanced cultivation, and alteration of the osmolality of the culture medium by addition of inorganic salts, the salt-enhanced cultivation, are presented and discussed in this review. These techniques have already proven to be useful and now await further proof-of-concept. Furthermore, the mechanical behaviour of individual pellets is of special interest for a general understanding of pellet mechanics and the productivity of biotechnological processes with filamentous microorganisms. Correlating them with substrate uptake and finally with productivity would be a breakthrough not to be underestimated for the comprehensive characterisation of filamentous systems. So far, this research field is under-represented. First results on filamentous pellet mechanics are discussed and important future aspects, which the filamentous expert community should deal with, will be presented and critically discussed.
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Affiliation(s)
- Markus Böl
- Institute of Mechanics and AdaptronicsTechnische Universität BraunschweigBraunschweigGermany
- Center of Pharmaceutical Engineering (PVZ)Technische Universität BraunschweigBraunschweigGermany
| | - Kathrin Schrinner
- Center of Pharmaceutical Engineering (PVZ)Technische Universität BraunschweigBraunschweigGermany
- Institute of Biochemical EngineeringTechnische Universität BraunschweigBraunschweigGermany
| | - Sebastian Tesche
- Center of Pharmaceutical Engineering (PVZ)Technische Universität BraunschweigBraunschweigGermany
- Institute of Biochemical EngineeringTechnische Universität BraunschweigBraunschweigGermany
| | - Rainer Krull
- Center of Pharmaceutical Engineering (PVZ)Technische Universität BraunschweigBraunschweigGermany
- Institute of Biochemical EngineeringTechnische Universität BraunschweigBraunschweigGermany
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Tesche S, Krull R. An image analysis method to quantify heterogeneous filamentous biomass based on pixel intensity values – Interrelation of macro- and micro-morphology in Actinomadura namibiensis. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2020.107865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Watkins-Dulaney E, Straathof S, Arnold F. Tryptophan Synthase: Biocatalyst Extraordinaire. Chembiochem 2021; 22:5-16. [PMID: 32677310 PMCID: PMC7935429 DOI: 10.1002/cbic.202000379] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/15/2020] [Indexed: 12/23/2022]
Abstract
Tryptophan synthase (TrpS) has emerged as a paragon of noncanonical amino acid (ncAA) synthesis and is an ideal biocatalyst for synthetic and biological applications. TrpS catalyzes an irreversible, C-C bond-forming reaction between indole and serine to make l-tryptophan; native TrpS complexes possess fairly broad specificity for indole analogues, but are difficult to engineer to extend substrate scope or to confer other useful properties due to allosteric constraints and their heterodimeric structure. Directed evolution freed the catalytically relevant TrpS β-subunit (TrpB) from allosteric regulation by its TrpA partner and has enabled dramatic expansion of the enzyme's substrate scope. This review examines the long and storied career of TrpS from the perspective of its application in ncAA synthesis and biocatalytic cascades.
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Affiliation(s)
- Ella Watkins-Dulaney
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Sabine Straathof
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Frances Arnold
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
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Schrinner K, Althof K, Ebersbach AT, Grosch J, Krull R. XAD Resins for Increased Rebeccamycin Productivity in Cultivations of
Lentzea aerocolonigenes. CHEM-ING-TECH 2020. [DOI: 10.1002/cite.202000131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Kathrin Schrinner
- Technische Universität Braunschweig Institute of Biochemical Engineering Rebenring 56 38106 Braunschweig Germany
- Technische Universität Braunschweig Center of Pharmaceutical Engineering Franz-Liszt-Straße 35a 38106 Braunschweig Germany
| | - Kristina Althof
- Technische Universität Braunschweig Institute of Biochemical Engineering Rebenring 56 38106 Braunschweig Germany
| | - Anna Theresia Ebersbach
- Technische Universität Braunschweig Institute of Biochemical Engineering Rebenring 56 38106 Braunschweig Germany
| | - Jan‐Hendrik Grosch
- Technische Universität Braunschweig Institute of Biochemical Engineering Rebenring 56 38106 Braunschweig Germany
- Technische Universität Braunschweig Center of Pharmaceutical Engineering Franz-Liszt-Straße 35a 38106 Braunschweig Germany
| | - Rainer Krull
- Technische Universität Braunschweig Institute of Biochemical Engineering Rebenring 56 38106 Braunschweig Germany
- Technische Universität Braunschweig Center of Pharmaceutical Engineering Franz-Liszt-Straße 35a 38106 Braunschweig Germany
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Schrinner K, Veiter L, Schmideder S, Doppler P, Schrader M, Münch N, Althof K, Kwade A, Briesen H, Herwig C, Krull R. Morphological and physiological characterization of filamentous Lentzea aerocolonigenes: Comparison of biopellets by microscopy and flow cytometry. PLoS One 2020; 15:e0234125. [PMID: 32492063 PMCID: PMC7269266 DOI: 10.1371/journal.pone.0234125] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/19/2020] [Indexed: 12/27/2022] Open
Abstract
Cell morphology of filamentous microorganisms is highly interesting during cultivations as it is often linked to productivity and can be influenced by process conditions. Hence, the characterization of cell morphology is of major importance to improve the understanding of industrial processes with filamentous microorganisms. For this purpose, reliable and robust methods are necessary. In this study, pellet morphology and physiology of the rebeccamycin producing filamentous actinomycete Lentzea aerocolonigenes were investigated by microscopy and flow cytometry. Both methods were compared regarding their applicability. To achieve different morphologies, a cultivation with glass bead addition (Ø = 969 μm, 100 g L-1) was compared to an unsupplemented cultivation. This led to two different macro-morphologies. Furthermore, glass bead addition increased rebeccamycin titers after 10 days of cultivation (95 mg L-1 with glass beads, 38 mg L-1 without glass beads). Macro-morphology and viability were investigated through microscopy and flow cytometry. For viability assessment fluorescent staining was used additionally. Smaller, more regular pellets were found for glass bead addition. Pellet diameters resulting from microscopy followed by image analysis were 172 μm without and 106 μm with glass beads, diameters from flow cytometry were 170 and 100 μm, respectively. These results show excellent agreement of both methods, each considering several thousand pellets. Furthermore, the pellet viability obtained from both methods suggested an enhanced metabolic activity in glass bead treated pellets during the exponential production phase. However, total viability values differ for flow cytometry (0.32 without and 0.41 with glass beads) and confocal laser scanning microscopy of single stained pellet slices (life ratio in production phase of 0.10 without and 0.22 with glass beads), which is probably caused by the different numbers of investigated pellets. In confocal laser scanning microscopy only one pellet per sample could be investigated while flow cytometry considered at least 50 pellets per sample, resulting in an increased statistical reliability.
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Affiliation(s)
- Kathrin Schrinner
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Technische Universität Braunschweig, Center of Pharmaceutical Engineering, Braunschweig, Germany
| | - Lukas Veiter
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Vienna, Austria
- Competence Center CHASE GmbH, Linz, Austria
| | - Stefan Schmideder
- School of Life Sciences, Chair of Process Systems Engineering, Technische Universität München, Freising, Germany
| | - Philipp Doppler
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Vienna, Austria
| | - Marcel Schrader
- Technische Universität Braunschweig, Center of Pharmaceutical Engineering, Braunschweig, Germany
- Institute for Particle Technology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nadine Münch
- School of Life Sciences, Chair of Process Systems Engineering, Technische Universität München, Freising, Germany
| | - Kristin Althof
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Arno Kwade
- Technische Universität Braunschweig, Center of Pharmaceutical Engineering, Braunschweig, Germany
- Institute for Particle Technology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Heiko Briesen
- School of Life Sciences, Chair of Process Systems Engineering, Technische Universität München, Freising, Germany
| | - Christoph Herwig
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Vienna, Austria
| | - Rainer Krull
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Technische Universität Braunschweig, Center of Pharmaceutical Engineering, Braunschweig, Germany
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The influence of salt-enhanced cultivation on the micromechanical behaviour of filamentous pellets. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.04.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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