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Ramirez-Malule H, López-Agudelo VA, Gómez-Ríos D, Ochoa S, Ríos-Estepa R, Junne S, Neubauer P. TCA Cycle and Its Relationship with Clavulanic Acid Production: A Further Interpretation by Using a Reduced Genome-Scale Metabolic Model of Streptomyces clavuligerus. Bioengineering (Basel) 2021; 8:103. [PMID: 34436106 PMCID: PMC8389198 DOI: 10.3390/bioengineering8080103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/04/2021] [Accepted: 07/16/2021] [Indexed: 11/26/2022] Open
Abstract
Streptomyces clavuligerus (S. clavuligerus) has been widely studied for its ability to produce clavulanic acid (CA), a potent inhibitor of β-lactamase enzymes. In this study, S. clavuligerus cultivated in 2D rocking bioreactor in fed-batch operation produced CA at comparable rates to those observed in stirred tank bioreactors. A reduced model of S. clavuligerus metabolism was constructed by using a bottom-up approach and validated using experimental data. The reduced model was implemented for in silico studies of the metabolic scenarios arisen during the cultivations. Constraint-based analysis confirmed the interrelations between succinate, oxaloacetate, malate, pyruvate, and acetate accumulations at high CA synthesis rates in submerged cultures of S. clavuligerus. Further analysis using shadow prices provided a first view of the metabolites positive and negatively associated with the scenarios of low and high CA production.
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Affiliation(s)
| | | | - David Gómez-Ríos
- Grupo de Investigación en Simulación, Diseño, Control y Optimización de Procesos (SIDCOP), Departamento de Ingeniería Química, Universidad de Antioquia UdeA, Medellín 050010, Colombia; (D.G.-R.); (S.O.)
| | - Silvia Ochoa
- Grupo de Investigación en Simulación, Diseño, Control y Optimización de Procesos (SIDCOP), Departamento de Ingeniería Química, Universidad de Antioquia UdeA, Medellín 050010, Colombia; (D.G.-R.); (S.O.)
| | - Rigoberto Ríos-Estepa
- Escuela de Biociencias, Universidad Nacional de Colombia sede Medellín, Medellín 050010, Colombia;
| | - Stefan Junne
- Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, D-13355 Berlin, Germany; (S.J.); (P.N.)
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, D-13355 Berlin, Germany; (S.J.); (P.N.)
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Beyß M, Parra-Peña VD, Ramirez-Malule H, Nöh K. Robustifying Experimental Tracer Design for 13C-Metabolic Flux Analysis. Front Bioeng Biotechnol 2021; 9:685323. [PMID: 34239861 PMCID: PMC8258161 DOI: 10.3389/fbioe.2021.685323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/19/2021] [Indexed: 11/25/2022] Open
Abstract
13C metabolic flux analysis (MFA) has become an indispensable tool to measure metabolic reaction rates (fluxes) in living organisms, having an increasingly diverse range of applications. Here, the choice of the13C labeled tracer composition makes the difference between an information-rich experiment and an experiment with only limited insights. To improve the chances for an informative labeling experiment, optimal experimental design approaches have been devised for13C-MFA, all relying on some a priori knowledge about the actual fluxes. If such prior knowledge is unavailable, e.g., for research organisms and producer strains, existing methods are left with a chicken-and-egg problem. In this work, we present a general computational method, termed robustified experimental design (R-ED), to guide the decision making about suitable tracer choices when prior knowledge about the fluxes is lacking. Instead of focusing on one mixture, optimal for specific flux values, we pursue a sampling based approach and introduce a new design criterion, which characterizes the extent to which mixtures are informative in view of all possible flux values. The R-ED workflow enables the exploration of suitable tracer mixtures and provides full flexibility to trade off information and cost metrics. The potential of the R-ED workflow is showcased by applying the approach to the industrially relevant antibiotic producer Streptomyces clavuligerus, where we suggest informative, yet economic labeling strategies.
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Affiliation(s)
- Martin Beyß
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, Aachen, Germany
| | | | | | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
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López-Agudelo VA, Gómez-Ríos D, Ramirez-Malule H. Clavulanic Acid Production by Streptomyces clavuligerus: Insights from Systems Biology, Strain Engineering, and Downstream Processing. Antibiotics (Basel) 2021; 10:84. [PMID: 33477401 PMCID: PMC7830376 DOI: 10.3390/antibiotics10010084] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/16/2022] Open
Abstract
Clavulanic acid (CA) is an irreversible β-lactamase enzyme inhibitor with a weak antibacterial activity produced by Streptomyces clavuligerus (S. clavuligerus). CA is typically co-formulated with broad-spectrum β‑lactam antibiotics such as amoxicillin, conferring them high potential to treat diseases caused by bacteria that possess β‑lactam resistance. The clinical importance of CA and the complexity of the production process motivate improvements from an interdisciplinary standpoint by integrating metabolic engineering strategies and knowledge on metabolic and regulatory events through systems biology and multi-omics approaches. In the large-scale bioprocessing, optimization of culture conditions, bioreactor design, agitation regime, as well as advances in CA separation and purification are required to improve the cost structure associated to CA production. This review presents the recent insights in CA production by S. clavuligerus, emphasizing on systems biology approaches, strain engineering, and downstream processing.
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Affiliation(s)
| | - David Gómez-Ríos
- Grupo de Investigación en Simulación, Diseño, Control y Optimización de Procesos (SIDCOP), Departamento de Ingeniería Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín 050010, Colombia;
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Gómez S, Ramírez-Malule H, Cardona-G W, Osorio E, Restrepo A. Double-Ring Epimerization in the Biosynthesis of Clavulanic Acid. J Phys Chem A 2020; 124:9413-9426. [PMID: 33135896 DOI: 10.1021/acs.jpca.0c05427] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
All reaction steps during the biosynthesis of suicidal clavulanic acid (coformulated with β-lactam antibiotics and used to fight bacterial infections) are known, except for the crucial 3S,5S → 3R,5R double epimerization needed to produce a biologically active stereoisomer, for which mechanistic hypothesis is subject to debate. In this work, we provide evidence for a reaction channel for the double inversion of configuration that involves a total of six reaction steps. When mediated by an enzyme with a terminal S-H bond, this highly complex reaction is spontaneous in the absence of solvents. Polarizable continuum models introduce reaction barriers in aqueous environments because of the strong destabilization of the first transition state. Molecular geometries and electronic structures in both cases indicate that solvent-free spontaneity and aqueous medium barriers are both firmly rooted in a substantial reorganization of the electron density right at the onset of the reaction, mostly involving a cyclic evolution/involution of large regions of π delocalization used to stabilize the excess charge left after the initial proton abstraction.
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Affiliation(s)
- Sara Gómez
- Instituto de Quı́mica, Universidad de Antioquia UdeA, Calle 70 No. 52-21, 50010 Medellı́n, Colombia.,Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Howard Ramírez-Malule
- Escuela de Ingenierı́a Quı́mica, Universidad del Valle, A.A. 25360, 76001 Cali, Colombia
| | - Wilson Cardona-G
- Instituto de Quı́mica, Universidad de Antioquia UdeA, Calle 70 No. 52-21, 50010 Medellı́n, Colombia
| | - Edison Osorio
- Facultad de Ciencias Naturales y Matemáticas, Universidad de Ibagué, Carrera 22 Calle 67, 73001 Ibagué, Colombia
| | - Albeiro Restrepo
- Instituto de Quı́mica, Universidad de Antioquia UdeA, Calle 70 No. 52-21, 50010 Medellı́n, Colombia
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Gómez-Ríos D, López-Agudelo VA, Ramírez-Malule H, Neubauer P, Junne S, Ochoa S, Ríos-Estepa R. A Genome-Scale Insight into the Effect of Shear Stress During the Fed-Batch Production of Clavulanic Acid by Streptomyces Clavuligerus. Microorganisms 2020; 8:E1255. [PMID: 32824882 PMCID: PMC7569809 DOI: 10.3390/microorganisms8091255] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/26/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022] Open
Abstract
Streptomyces clavuligerus is a filamentous Gram-positive bacterial producer of the β-lactamase inhibitor clavulanic acid. Antibiotics biosynthesis in the Streptomyces genus is usually triggered by nutritional and environmental perturbations. In this work, a new genome scale metabolic network of Streptomyces clavuligerus was reconstructed and used to study the experimentally observed effect of oxygen and phosphate concentrations on clavulanic acid biosynthesis under high and low shear stress. A flux balance analysis based on experimental evidence revealed that clavulanic acid biosynthetic reaction fluxes are favored in conditions of phosphate limitation, and this is correlated with enhanced activity of central and amino acid metabolism, as well as with enhanced oxygen uptake. In silico and experimental results show a possible slowing down of tricarboxylic acid (TCA) due to reduced oxygen availability in low shear stress conditions. In contrast, high shear stress conditions are connected with high intracellular oxygen availability favoring TCA activity, precursors availability and clavulanic acid (CA) production.
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Affiliation(s)
- David Gómez-Ríos
- Grupo de Investigación en Simulación, Diseño, Control y Optimización de Procesos (SIDCOP), Departamento de Ingeniería Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín 050010, Colombia;
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia (UdeA), Calle 70 No. 52-21, Medellín 050010, Colombia;
| | - Victor A. López-Agudelo
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia (UdeA), Calle 70 No. 52-21, Medellín 050010, Colombia;
| | - Howard Ramírez-Malule
- Escuela de Ingeniería Química, Universidad del Valle, A.A. 25360, Cali 76001, Colombia;
| | - Peter Neubauer
- Technische Universität Berlin, Institute of Biotechnology, Chair of Bioprocess Engineering, Ackerstr. 76, ACK 24, D-13355 Berlin, Germany; (P.N.); (S.J.)
| | - Stefan Junne
- Technische Universität Berlin, Institute of Biotechnology, Chair of Bioprocess Engineering, Ackerstr. 76, ACK 24, D-13355 Berlin, Germany; (P.N.); (S.J.)
| | - Silvia Ochoa
- Grupo de Investigación en Simulación, Diseño, Control y Optimización de Procesos (SIDCOP), Departamento de Ingeniería Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín 050010, Colombia;
| | - Rigoberto Ríos-Estepa
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia (UdeA), Calle 70 No. 52-21, Medellín 050010, Colombia;
- Escuela de Biociencias, Universidad Nacional de Colombia sede Medellín, Calle 59 A 63-20, Medellín 050010, Colombia
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Comparative Transcriptome Analysis of Streptomyces Clavuligerus in Response to Favorable and Restrictive Nutritional Conditions. Antibiotics (Basel) 2019; 8:antibiotics8030096. [PMID: 31330947 PMCID: PMC6784218 DOI: 10.3390/antibiotics8030096] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/05/2019] [Accepted: 07/09/2019] [Indexed: 12/17/2022] Open
Abstract
Background: Clavulanic acid (CA), a β-lactamase inhibitor, is industrially produced by the fermentation of Streptomyces clavuligerus. The efficiency of CA production is associated with media composition, culture conditions and physiological and genetic strain characteristics. However, the molecular pathways that govern CA regulation in S. clavuligerus remain unknown. Methods and Results: Here we used RNA-seq to perform a comparative transcriptome analysis of S. clavuligerus ATCC 27064 wild-type strain grown in both a favorable soybean-based medium and in limited media conditions to further contribute to the understanding of S. clavuligerus metabolism and its regulation. A total of 350 genes were found to be differentially expressed between conditions; 245 genes were up-regulated in favorable conditions compared to unfavorable. Conclusion: The up-regulated expression of many regulatory and biosynthetic CA genes was positively associated with the favorable complex media condition along with pleiotropic regulators, including proteases and some genes whose biological function have not been previously reported. Knowledge from differences between transcriptomes from complex/defined media represents an advance in the understanding of regulatory paths involved in S. clavuligerus’ metabolic response, enabling the rational design of future experiments.
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Gómez-Ríos D, Ramírez-Malule H, Neubauer P, Junne S, Ríos-Estepa R. Data of clavulanic acid and clavulanate-imidazole stability at low temperatures. Data Brief 2019; 23:103775. [PMID: 31372423 PMCID: PMC6660515 DOI: 10.1016/j.dib.2019.103775] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 12/27/2022] Open
Abstract
Clavulanic acid (CA) is a β-lactam antibiotic with a strong inhibitory effect on β-lactamase enzymes. CA is produced in submerged cultures by the filamentous Gram-positive bacterium Streptomyces clavuligerus (S. clavuligerus). CA is an unstable molecule in aqueous solution and its stability depends strongly on temperature and concentration. In this contribution, the experimental data of CA stability, produced in chemically defined media and exposed to temperatures between −80 and 25 °C, are presented. The chromophore clavulanate-imidazole (CAI) is commonly used for analysis and quantification of CA samples by High Performance Liquid Chromatography (HPLC); nevertheless, this molecule is also susceptible to suffer degradation in aqueous solution, potentially affecting the quantification of CA. Data of CAI concentration for samples conserved at 4 °C and 25 °C are also presented. A reversible-irreversible kinetic model was applied to estimate the degradation rate of CA. Data from numerical simulations of CA degradation using the proposed kinetic model are also graphically presented. The data show the clavulanic acid instability in fermentation broths, in a range of temperatures of interest for bioprocess operation, downstream processing, samples quantification, conservation and storage.
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Affiliation(s)
- David Gómez-Ríos
- Universidad de Antioquia, Departamento de Ingeniería Química, Grupo de Bioprocesos, Calle 70 No. 52-21, Medellín 050010, Colombia
| | - Howard Ramírez-Malule
- Universidad del Valle, Escuela de Ingeniería Química, A.A. 25360, Cali 76001, Colombia
| | - Peter Neubauer
- Technische Universität Berlin, Department of Biotechnology, Bioprocess Engineering, Ackerstr. 76, ACK 24, Berlin 13355, Germany
| | - Stefan Junne
- Technische Universität Berlin, Department of Biotechnology, Bioprocess Engineering, Ackerstr. 76, ACK 24, Berlin 13355, Germany
| | - Rigoberto Ríos-Estepa
- Universidad de Antioquia, Departamento de Ingeniería Química, Grupo de Bioprocesos, Calle 70 No. 52-21, Medellín 050010, Colombia
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Bibliometric Analysis of Global Research on Clavulanic Acid. Antibiotics (Basel) 2018; 7:antibiotics7040102. [PMID: 30486255 PMCID: PMC6316524 DOI: 10.3390/antibiotics7040102] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/18/2018] [Accepted: 10/18/2018] [Indexed: 11/17/2022] Open
Abstract
Clavulanic acid (CA), a potent inhibitor of the β-lactam, ase enzyme, is frequently co-formulated with a broad spectrum of antibiotics to treat infections caused by β-lactamase-producing pathogens. In order to evaluate the impact and the progress of CA studies in the last four decades, a bibliometric analysis of the global scientific production of CA was carried out. A total of 39,758 records in the field of CA were indexed in the Scopus database for a 43-year period of study (1975⁻2017). The results indicated that CA studies have grown, showing three phases (1975⁻1999, 2000⁻2003 and 2004⁻2017) based on records of publications; the results showed a sigmoidal profile. Medicine was the main subject area for CA studies, whereas biochemistry, genetics and molecular biology were areas of research for CA production by Streptomyces clavuligerus (S. clavuligerus). Nevertheless, chemical engineering (as a subject area) had the highest increase in the percentage of publications related to CA production by S. clavuligerus. The United States, France, the United Kingdom, Spain and Brazil were the leading countries in the scientific production of studies on both CA and CA related to S. clavuligerus. This analysis allowed the identification of the area of knowledge with the highest impact on CA studies, the top researchers and their geographic distribution, and also helped to highlight the existence of antibiotic-resistant bacteria as an emergent area in CA research.
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Viana Marques DDA, Machado SEF, Ebinuma VCS, Duarte CDAL, Converti A, Porto ALF. Production of β-Lactamase Inhibitors by Streptomyces Species. Antibiotics (Basel) 2018; 7:E61. [PMID: 30018235 PMCID: PMC6163296 DOI: 10.3390/antibiotics7030061] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/07/2018] [Accepted: 07/12/2018] [Indexed: 12/11/2022] Open
Abstract
β-Lactamase inhibitors have emerged as an effective alternative to reduce the effects of resistance against β-lactam antibiotics. The Streptomyces genus is known for being an exceptional natural source of antimicrobials and β-lactamase inhibitors such as clavulanic acid, which is largely applied in clinical practice. To protect against the increasing prevalence of multidrug-resistant bacterial strains, new antibiotics and β-lactamase inhibitors need to be discovered and developed. This review will cover an update about the main β-lactamase inhibitors producers belonging to the Streptomyces genus; advanced methods, such as genetic and metabolic engineering, to enhance inhibitor production compared with wild-type strains; and fermentation and purification processes. Moreover, clinical practice and commercial issues are discussed. The commitment of companies and governments to develop innovative strategies and methods to improve the access to new, efficient, and potentially cost-effective microbial products to combat the antimicrobial resistance is also highlighted.
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Affiliation(s)
- Daniela de Araújo Viana Marques
- Campus Serra Talhada, University of Pernambuco, Avenida Custódio Conrado, 600, AABB, Serra Talhada, Pernambuco 56912-550, Brazil.
| | - Suellen Emilliany Feitosa Machado
- Department of Antibiotics, Federal University of Pernambuco, Avenida da Engenharia, 2° andar, Cidade Universitária, Recife, Pernambuco 50740-600, Brazil.
| | - Valéria Carvalho Santos Ebinuma
- Department of Bioprocesses and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Rodovia Araraquara-Jaú/Km 01, Araraquara 14800-903, Brazil.
| | | | - Attilio Converti
- Department of Civil, Chemical and Environmental Engineering, Chemical Pole, University of Genoa, Via Opera Pia 15, 16145 Genoa, Italy.
| | - Ana Lúcia Figueiredo Porto
- Department of Morphology and Animal Physiology, Federal Rural University of Pernambuco, Av. Dom Manoel de Medeiros, Recife, Pernambuco 52171-900, Brazil.
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Streptomyces clavuligerus shows a strong association between TCA cycle intermediate accumulation and clavulanic acid biosynthesis. Appl Microbiol Biotechnol 2018. [PMID: 29523936 DOI: 10.1007/s00253-018-8841-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Clavulanic acid (CA) is produced by Streptomyces clavuligerus (S. clavuligerus) as a secondary metabolite. Knowledge about the carbon flux distribution along the various routes that supply CA precursors would certainly provide insights about metabolic performance. In order to evaluate metabolic patterns and the possible accumulation of tricarboxylic acid (TCA) cycle intermediates during CA biosynthesis, batch and subsequent continuous cultures with steadily declining feed rates were performed with glycerol as the main substrate. The data were used to in silico explore the metabolic capabilities and the accumulation of metabolic intermediates in S. clavuligerus. While clavulanic acid accumulated at glycerol excess, it steadily decreased at declining dilution rates; CA synthesis stopped when glycerol became the limiting substrate. A strong association of succinate, oxaloacetate, malate, and acetate accumulation with CA production in S. clavuligerus was observed, and flux balance analysis (FBA) was used to describe the carbon flux distribution in the network. This combined experimental and numerical approach also identified bottlenecks during the synthesis of CA in a batch and subsequent continuous cultivation and demonstrated the importance of this type of methodologies for a more advanced understanding of metabolism; this potentially derives valuable insights for future successful metabolic engineering studies in S. clavuligerus.
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