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Fu J, Xie X, Zhang S, Kang N, Zong G, Zhang P, Cao G. Rich Organic Nitrogen Impacts Clavulanic Acid Biosynthesis through the Arginine Metabolic Pathway in Streptomyces clavuligerus F613-1. Microbiol Spectr 2023; 11:e0201722. [PMID: 36515504 PMCID: PMC9927107 DOI: 10.1128/spectrum.02017-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Clavulanic acid (CA) is the preferred clinical drug for the treatment of infections by β-lactam antibiotic-resistant bacteria. CA is produced by Streptomyces clavuligerus, and although there have been many reports on the effects of carbon and nitrogen sources on CA production, the mechanisms involved remain unclear. In this study, we found that CA accumulation in S. clavuligerus F613-1 was increased significantly in MH medium, which is rich in organic nitrogen, compared with that in ML medium, which contains half the amount of organic nitrogen present in MH medium. Transcriptome analysis revealed that genes involved in CA biosynthesis, such as ceas1, ceas2, bls1, bls2, cas2, pah2, gcaS, and cad, and arginine biosynthesis, such as argB, argC, argD, argG, argH, argJ, and argR, were upregulated under rich organic nitrogen. Metabolome data revealed notable differences between cultures of F613-1 grown in MH and ML media with regard to levels of key intracellular metabolites, most of which are involved in arginine metabolic pathways, including arginine, glutamine, and glutamic acid. Additionally, supplementation of ML medium with arginine, glutamine, or glutamic acid resulted in increased CA production by S. clavuligerus F613-1. Our results indicate that rich organic nitrogen mainly affects CA biosynthesis by increasing the levels of amino acids associated with the arginine metabolic pathway and activating the expression of the CA biosynthetic gene cluster. These findings provide important insights for improving medium optimization and engineering of S. clavuligerus F613-1 for high-yield production of CA. IMPORTANCE The bacterium Streptomyces clavuligerus is used for the industrial production of the broad-spectrum β-lactamase inhibitor clavulanic acid (CA). However, much remains unknown about the factors which affect CA yields. We investigated the effects of different levels of organic nitrogen on CA production. Our analyses indicate that higher organic nitrogen levels were associated with increased CA yields and increased levels of arginine biosynthesis. Further analyses supported the relationship between arginine metabolism and CA production and demonstrated that increasing the levels of arginine or associated amino acids could boost CA yields. These findings suggest approaches for improving the production of this clinically important antibiotic.
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Affiliation(s)
- Jiafang Fu
- Biomedical Sciences College, Shandong First Medical University, Jinan, China
- NHC Key Laboratory of Biotechnology Drugs, Shandong Academy of Medical Sciences, Jinan, China
| | - Xinru Xie
- Biomedical Sciences College, Shandong First Medical University, Jinan, China
| | - Shaowei Zhang
- Biomedical Sciences College, Shandong First Medical University, Jinan, China
| | - Ni Kang
- Biomedical Sciences College, Shandong First Medical University, Jinan, China
| | - Gongli Zong
- Biomedical Sciences College, Shandong First Medical University, Jinan, China
- NHC Key Laboratory of Biotechnology Drugs, Shandong Academy of Medical Sciences, Jinan, China
| | - Peipei Zhang
- Biomedical Sciences College, Shandong First Medical University, Jinan, China
- NHC Key Laboratory of Biotechnology Drugs, Shandong Academy of Medical Sciences, Jinan, China
| | - Guangxiang Cao
- Biomedical Sciences College, Shandong First Medical University, Jinan, China
- NHC Key Laboratory of Biotechnology Drugs, Shandong Academy of Medical Sciences, Jinan, China
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Takahashi-Iñiguez T, Flores ME. mRNA levels of tricarboxylic acid cycle genes in Streptomyces coelicolor M145 cultured on glucose. Mol Biol Rep 2023; 50:719-30. [PMID: 36372816 DOI: 10.1007/s11033-022-08068-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 10/31/2022] [Indexed: 11/14/2022]
Abstract
BACKGROUND Streptomyces strains degrade many complex organic compounds and produce secondary metabolites. In aerobic organisms such as Streptomyces species, the tricarboxylic acid (TCA) cycle represents an indispensable central carbon metabolic pathway for energy generation and metabolic intermediary replenishment. Although various precursors for antibiotic biosynthesis are derived from this cycle, relatively few studies have focused on determining how a single carbon source can impact this metabolic pathway at different growth phases. In this study, we identified chromosomal genes involved in the TCA cycle in Streptomyces coelicolor and determined their mRNA levels. METHODS AND RESULTS We searched the genes involved in the TCA cycle in S. coelicolor through bioinformatic analysis. Growth, glucose concentration quantification and RNA isolation were made from cultures of S. coelicolor grown on minimal medium with glucose along 72 h. mRNA levels of all identified genes were obtained by RT-qPCR. Five enzymes encoded by a single gene each were found, while for the rest at least two genes were found. The results showed that all the genes corresponding to the TCA enzymes were transcribed at very different levels and some of them displayed growth-phase dependent expression. CONCLUSION All TCA cycle-associated genes, including paralog genes, were differentially transcribed in S. coelicolor grown in minimal medium with glucose as carbon source. Some of them, such as succinyl-CoA synthetase and succinate dehydrogenase, have low mRNA levels, which could limit the carbon flux through the TCA cycle. Our findings suggest that the genetic expansion of TCA cycle genes could confer to S. coelicolor the ability to adapt to diverse nutritional conditions and metabolic changes through different paralog genes expression.
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Gómez-Ríos D, Ramírez-Malule H, Neubauer P, Junne S, Ríos-Estepa R, Ochoa S. Tuning of fed-batch cultivation of Streptomyces clavuligerus for enhanced Clavulanic Acid production based on genome-scale dynamic modeling. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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6
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Ribeiro RMMGP, Esperança MN, Sousa APA, Neto ÁB, Cerri MO. Individual effect of shear rate and oxygen transfer on clavulanic acid production by Streptomyces clavuligerus. Bioprocess Biosyst Eng 2021; 44:1721-32. [PMID: 33821325 DOI: 10.1007/s00449-021-02555-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/17/2021] [Indexed: 10/21/2022]
Abstract
The production of biocompounds through the cultivation of filamentous microorganisms is mainly affected by Oxygen Transfer Rate (OTR) and shear rate ([Formula: see text]) conditions. Despite efforts have been made to evaluate the effect of operating variables (impeller speed, N; and airflow rate, ϕair) on clavulanic acid production, no analysis regarding the effect of OTR and [Formula: see text] was made. Then, the aim of this study was to evaluate the dissociated effect of physical phenomena such as oxygen transfer and shear rate in the production of clavulanic acid from Streptomyces clavuligerus using a stirred tank bioreactor. Streptomyces clavuligerus cultivations were performed at five different OTR and [Formula: see text] conditions by manipulating the operating conditions (N, ϕair, and gas inlet composition). Cultivations performed at equal impeller speed (600 rpm, similar [Formula: see text]) using oxygen enrichment, showed that CA productivity (ProdCA) was positively affected by OTR increase. Subsequently, the different shear conditions (achieved by varying the impeller speed) lead to an increase in CA production levels. Despite both OTR and shear rate positively enhanced CA productivity, [Formula: see text] exhibited the highest impact: an increase of 145% in OTRinitial enhanced the clavulanic acid productivity of about 29%, while an increment in the shear rate of 134% raised the ProdCA in 53%.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Fernández-Martínez LT, Hoskisson PA. Expanding, integrating, sensing and responding: the role of primary metabolism in specialised metabolite production. Curr Opin Microbiol 2019; 51:16-21. [DOI: 10.1016/j.mib.2019.03.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/22/2019] [Accepted: 03/12/2019] [Indexed: 01/30/2023]
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Gómez-Ríos D, Junne S, Neubauer P, Ochoa S, Ríos-Estepa R, Ramírez-Malule H. Characterization of the Metabolic Response of Streptomyces clavuligerus to Shear Stress in Stirred Tanks and Single-Use 2D Rocking Motion Bioreactors for Clavulanic Acid Production. Antibiotics (Basel) 2019; 8:antibiotics8040168. [PMID: 31569725 PMCID: PMC6963652 DOI: 10.3390/antibiotics8040168] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/22/2019] [Accepted: 09/25/2019] [Indexed: 12/16/2022] Open
Abstract
Streptomyces clavuligerus is a gram-positive filamentous bacterium notable for producing clavulanic acid (CA), an inhibitor of β-lactamase enzymes, which confers resistance to bacteria against several antibiotics. Here we present a comparative analysis of the morphological and metabolic response of S. clavuligerus linked to the CA production under low and high shear stress conditions in a 2D rocking-motion single-use bioreactor (CELL-tainer ®) and stirred tank bioreactor (STR), respectively. The CELL-tainer® guarantees high turbulence and enhanced volumetric mass transfer at low shear stress, which (in contrast to bubble columns) allows the investigation of the impact of shear stress without oxygen limitation. The results indicate that high shear forces do not compromise the viability of S. clavuligerus cells; even higher specific growth rate, biomass, and specific CA production rate were observed in the STR. Under low shear forces in the CELL-tainer® the mycelial diameter increased considerably (average diameter 2.27 in CELL-tainer® vs. 1.44 µm in STR). This suggests that CA production may be affected by a lower surface-to-volume ratio which would lead to lower diffusion and transport of nutrients, oxygen, and product. The present study shows that there is a strong correlation between macromorphology and CA production, which should be an important aspect to consider in industrial production of CA.
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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.
| | - Stefan Junne
- Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, D-13355 Berlin, Germany.
| | - Peter Neubauer
- Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, D-13355 Berlin, Germany.
| | - 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.
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Pinilla L, Toro LF, Laing E, Alzate JF, Ríos-Estepa R. Comparative Transcriptome Analysis of Streptomyces Clavuligerus in Response to Favorable and Restrictive Nutritional Conditions. Antibiotics (Basel) 2019; 8:E96. [PMID: 31330947 DOI: 10.3390/antibiotics8030096] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [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-Cerón S, Galindo-Betancur D, Ramírez-Malule H. Data set of in silico simulation for the production of clavulanic acid and cephamycin C by Streptomyces clavuligerus using a genome scale metabolic model. Data Brief 2019; 24:103992. [PMID: 31193725 PMCID: PMC6538926 DOI: 10.1016/j.dib.2019.103992] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 05/06/2019] [Indexed: 12/31/2022] Open
Abstract
Streptomyces clavuligerus (S. clavuligerus) is a Gram-positive bacterium which produced clavulanic acid (CA) and cephamycin C (CephC). In this data article, a curated genome scale metabolic model of S. clavuligerus is presented. A total of eighteen objective functions were evaluated for a better representation of CA and CephC production by S. clavuligerus. The different objective functions were evaluated varying the weighting factors of CA and CephC between 0, 1 y 2, whereas for the case of biomass the weight factor was varied between 1 and 2. A robustness analysis, by mean of flux balance analysis, showed five different metabolic phenotypes of S. clavuligerus as a function of oxygen uptake: (I) and (II) biomass production, (III) biomass and CephC production, (IV) simultaneous production of biomass, CA and CephC and (V) production of biomass and CA. Data of shadow prices and reduced cost are also presented.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
C–H functionalization is a chemically challenging but highly desirable transformation. 2-oxoglutarate-dependent oxygenases (2OGXs) are remarkably versatile biocatalysts for the activation of C–H bonds. In nature, they have been shown to accept both small and large molecules carrying out a plethora of reactions, including hydroxylations, demethylations, ring formations, rearrangements, desaturations, and halogenations, making them promising candidates for industrial manufacture. In this review, we describe the current status of 2OGX use in biocatalytic applications concentrating on 2OGX-catalyzed oxyfunctionalization of amino acids and synthesis of antibiotics. Looking forward, continued bioinformatic sourcing will help identify additional, practical useful members of this intriguing enzyme family, while enzyme engineering will pave the way to enhance 2OGX reactivity for non-native substrates.
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Fu J, Qin R, Zong G, Liu C, Kang N, Zhong C, Cao G. The CagRS Two-Component System Regulates Clavulanic Acid Metabolism via Multiple Pathways in Streptomyces clavuligerus F613-1. Front Microbiol 2019; 10:244. [PMID: 30837970 PMCID: PMC6382702 DOI: 10.3389/fmicb.2019.00244] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 01/29/2019] [Indexed: 11/21/2022] Open
Abstract
Streptomyces clavuligerus F613-1 produces a clinically important β-lactamase inhibitor, clavulanic acid (CA). Although the biosynthesis pathway of CA has essentially been elucidated, the global regulatory mechanisms of CA biosynthesis remain unclear. The paired genes cagS and cagR, which are annotated, respectively, as orf22 and orf23 in S. clavuligerus ATCC 27064, encode a bacterial two-component regulatory system (TCS) and were found next to the CA biosynthetic gene cluster of S. clavuligerus F613-1. To further elucidate the regulatory mechanism of CA biosynthesis, the CagRS TCS was deleted from S. clavuligerus F613-1. Deletion of cagRS resulted in decreased production of CA, but the strain phenotype was not otherwise affected. Both transcriptome and ChIP-seq data revealed that, in addition to CA biosynthesis, the CagRS TCS mainly regulates genes involved in primary metabolism, such as glyceraldehyde 3-phosphate (G3P) metabolism and arginine biosynthesis. Notably, both G3P and arginine are precursors of CA. Electrophoretic mobility shift assays demonstrated that the response regulator CagR could bind to the intergenic regions of argG, argC, oat1, oat2, ceaS1, and claR in vitro, suggesting that CagR can directly regulate genes involved in arginine and CA biosynthesis. This study indicated that CagRS is a pleiotropic regulator that can directly affect the biosynthesis of CA and indirectly affect CA production by regulating the metabolism of arginine and G3P. Our findings provide new insights into the regulation of CA biosynthetic pathways and provide an innovative approach for future metabolic engineering efforts for CA production in S. clavuligerus.
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Affiliation(s)
- Jiafang Fu
- Shandong Medicinal Biotechnology Center, Shandong Academy of Medical Sciences, Jinan, China
| | - Ronghuo Qin
- Shandong Medicinal Biotechnology Center, Shandong Academy of Medical Sciences, Jinan, China
| | - Gongli Zong
- Shandong Medicinal Biotechnology Center, Shandong Academy of Medical Sciences, Jinan, China
| | - Cheng Liu
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, China
| | - Ni Kang
- Shandong Medicinal Biotechnology Center, Shandong Academy of Medical Sciences, Jinan, China
| | - Chuanqing Zhong
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, China
| | - Guangxiang Cao
- Shandong Medicinal Biotechnology Center, Shandong Academy of Medical Sciences, Jinan, China
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Gómez-Ríos D, Ramírez-Malule H, Neubauer P, Junne S, Ríos-Estepa R. Degradation Kinetics of Clavulanic Acid in Fermentation Broths at Low Temperatures. Antibiotics (Basel) 2019; 8:E6. [PMID: 30658482 DOI: 10.3390/antibiotics8010006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/13/2019] [Accepted: 01/15/2019] [Indexed: 12/20/2022] Open
Abstract
Clavulanic acid (CA) is a β-lactam antibiotic inhibitor of β-lactamase enzymes, which confers resistance to bacteria against several antibiotics. CA is produced in submerged cultures by the filamentous Gram-positive bacterium Streptomyces clavuligerus; yield and downstream process are compromised by a degradation phenomenon, which is not yet completely elucidated. In this contribution, a study of degradation kinetics of CA at low temperatures (−80, −20, 4, and 25 °C) and pH 6.8 in chemically-defined fermentation broths is presented. Samples of CA in the fermentation broths showed a fast decline of concentration during the first 5 h followed by a slower, but stable, reaction rate in the subsequent hours. A reversible-irreversible kinetic model was applied to explain the degradation rate of CA, its dependence on temperature and concentration. Kinetic parameters for the equilibrium and irreversible reactions were calculated and the proposed kinetic model was validated with experimental data of CA degradation ranging 16.3 mg/L to 127.0 mg/L. Degradation of the chromophore CA-imidazole, which is commonly used for quantifications by High Performance Liquid Chromatography, was also studied at 4 °C and 25 °C, showing a rapid rate of degradation according to irreversible first-order kinetics. A hydrolysis reaction mechanism is proposed as the cause of CA-imidazole loss in aqueous solutions.
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Ramirez-Malule H. Bibliometric Analysis of Global Research on Clavulanic Acid. Antibiotics (Basel) 2018; 7:E102. [PMID: 30486255 DOI: 10.3390/antibiotics7040102] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Mohite OS, Weber T, Kim HU, Lee SY. Genome-Scale Metabolic Reconstruction of Actinomycetes for Antibiotics Production. Biotechnol J 2018; 14:e1800377. [DOI: 10.1002/biot.201800377] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/11/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Omkar S. Mohite
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; 2800 kongens Lyngby Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; 2800 kongens Lyngby Denmark
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Korea Advanced Institute of Science and Technology (KAIST); 291 Daehak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; 2800 kongens Lyngby Denmark
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Korea Advanced Institute of Science and Technology (KAIST); 291 Daehak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
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