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Parra Daza LE, Suarez Medina L, Tafur Rangel AE, Fernández-Niño M, Mejía-Manzano LA, González-Valdez J, Reyes LH, González Barrios AF. Design and Assembly of a Biofactory for (2 S)-Naringenin Production in Escherichia coli: Effects of Oxygen Transfer on Yield and Gene Expression. Biomolecules 2023; 13:biom13030565. [PMID: 36979500 PMCID: PMC10046166 DOI: 10.3390/biom13030565] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/17/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
The molecule (2S)-naringenin is a scaffold molecule with several nutraceutical properties. Currently, (2S)-naringenin is obtained through chemical synthesis and plant isolation. However, these methods have several drawbacks. Thus, heterologous biosynthesis has emerged as a viable alternative to its production. Recently, (2S)-naringenin production studies in Escherichia coli have used different tools to increase its yield up to 588 mg/L. In this study, we designed and assembled a bio-factory for (2S)-naringenin production. Firstly, we used several parametrized algorithms to identify the shortest pathway for producing (2S)-naringenin in E. coli, selecting the genes phenylalanine ammonia lipase (pal), 4-coumarate: CoA ligase (4cl), chalcone synthase (chs), and chalcone isomerase (chi) for the biosynthetic pathway. Then, we evaluated the effect of oxygen transfer on the production of (2S)-naringenin at flask (50 mL) and bench (4 L culture) scales. At the flask scale, the agitation rate varied between 50 rpm and 250 rpm. At the bench scale, the dissolved oxygen was kept constant at 5% DO (dissolved oxygen) and 40% DO, obtaining the highest (2S)-naringenin titer (3.11 ± 0.14 g/L). Using genome-scale modeling, gene expression analysis (RT-qPCR) of oxygen-sensitive genes was obtained.
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Affiliation(s)
- Laura E Parra Daza
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá 110311, Colombia
| | - Lina Suarez Medina
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá 110311, Colombia
| | - Albert E Tafur Rangel
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá 110311, Colombia
| | - Miguel Fernández-Niño
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá 110311, Colombia
- Department of Bioorganic Chemistry, Leibniz-Institute of Plant Biochemistry, 06120 Halle, Germany
| | - Luis Alberto Mejía-Manzano
- Tecnológico de Monterrey, School of Engineering and Science, Av. Eugenio Garza Sada 2501 Sur, Monterrey 64849, NL, Mexico
| | - José González-Valdez
- Tecnológico de Monterrey, School of Engineering and Science, Av. Eugenio Garza Sada 2501 Sur, Monterrey 64849, NL, Mexico
| | - Luis H Reyes
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá 110311, Colombia
| | - Andrés Fernando González Barrios
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá 110311, Colombia
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2
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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3
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Sundararajan S, Muniyan R. Latent tuberculosis: interaction of virulence factors in Mycobacterium tuberculosis. Mol Biol Rep 2021; 48:6181-6196. [PMID: 34351540 DOI: 10.1007/s11033-021-06611-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/29/2021] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) remains a prominent health concern worldwide. Besides extensive research and vaccinations available, attempts to control the pandemic are cumbersome due to the complex physiology of Mycobacterium tuberculosis (Mtb). Alongside the emergence of drug-resistant TB, latent TB has worsened the condition. The tubercle bacilli are unusually behaved and successful with its strategies to modulate genes to evade host immune system and persist within macrophages. Under latent/unfavorable conditions, Mtb conceals itself from immune system and modulates its genes. Among many intracellular modulated genes, important are those involved in cell entry, fatty acid degradation, mycolic acid synthesis, phagosome acidification inhibition, inhibition of phagosome-lysosome complex and chaperon protein modulation. Though the study on these genes date back to early times of TB, an insight on their inter-relation within and to newly evolved genes are still required. This review focuses on the findings and discussions on these genes, possible mechanism, credibility as target for novel drugs and repurposed drugs and their interaction that enables Mtb in survival, pathogenesis, resistance and latency.
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Affiliation(s)
- Sadhana Sundararajan
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Rajiniraja Muniyan
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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4
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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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5
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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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6
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Baena A, Vasco E, Pastrana M, Alzate JF, Barrera LF, Martínez A. New Conjugated Compound T5 Epidioxy-Sterol-ANB Inhibits the Growth of Mycobacterium tuberculosis Affecting the Cholesterol and Folate Pathways. Front Microbiol 2020; 11:537935. [PMID: 33072006 PMCID: PMC7533559 DOI: 10.3389/fmicb.2020.537935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/13/2020] [Indexed: 11/13/2022] Open
Abstract
The upsurge and persistence of drug resistant strains of Mycobacterium tuberculosis (Mtb) is an important limitant to the battery of drugs available for the elimination of tuberculosis (TB). To avoid future scarcity of antibiotics against Mtb, it is important to discover new effective anti-mycobacterial agents. In this study, we present data from a series of experiments to determine in vitro and in vivo anti-mycobacterial activity of a library of epidioxy-sterol analogs. We test 15 compounds for their ability to reduce the viability of Mtb. We found that one compound called T5 epidioxy-sterol-ANB display significant potency against Mtb in vitro specifically inside macrophages but without effectivity in axenic cultures. A viability assay confirms that this T5 compound is less toxic for macrophages in vitro as compared to the current Mtb drug Rifampicin at higher concentrations. We use a transcriptomic analysis of Mtb inside macrophages after T5 epidioxy-sterol-ANB treatment, and we found a significant down-regulation of enzymes involved in the cholesterol and folic acid pathways. In vivo, significant differences were found in the lungs and spleen CFUs of Mtb infected mice treated with the T5 epidioxy-sterol-ANB as compared with the untreated control group, which provides additional evidence of the effectivity of the T5 compound. Altogether these results confirm the potential of this T5 epidioxy-sterol-ANB compound against Mtb.
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Affiliation(s)
- Andres Baena
- Grupo de Inmunología Celular e Inmunogenética, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Emanuel Vasco
- Grupo de Inmunología Celular e Inmunogenética, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Manuel Pastrana
- Grupo de Productos Naturales Marinos, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Medellín, Colombia
| | - Juan F Alzate
- Grupo de Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.,Centro Nacional de Secuenciación Genómica, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Luis F Barrera
- Grupo de Inmunología Celular e Inmunogenética, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Alejandro Martínez
- Grupo de Productos Naturales Marinos, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Medellín, Colombia
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7
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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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8
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López-Agudelo VA, Mendum TA, Laing E, Wu H, Baena A, Barrera LF, Beste DJV, Rios-Estepa R. A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks. PLoS Comput Biol 2020; 16:e1007533. [PMID: 32542021 PMCID: PMC7316355 DOI: 10.1371/journal.pcbi.1007533] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 06/25/2020] [Accepted: 05/08/2020] [Indexed: 01/06/2023] Open
Abstract
Metabolism underpins the pathogenic strategy of the causative agent of TB, Mycobacterium tuberculosis (Mtb), and therefore metabolic pathways have recently re-emerged as attractive drug targets. A powerful approach to study Mtb metabolism as a whole, rather than just individual enzymatic components, is to use a systems biology framework, such as a Genome-Scale Metabolic Network (GSMN) that allows the dynamic interactions of all the components of metabolism to be interrogated together. Several GSMNs networks have been constructed for Mtb and used to study the complex relationship between the Mtb genotype and its phenotype. However, the utility of this approach is hampered by the existence of multiple models, each with varying properties and performances. Here we systematically evaluate eight recently published metabolic models of Mtb-H37Rv to facilitate model choice. The best performing models, sMtb2018 and iEK1011, were refined and improved for use in future studies by the TB research community. The tuberculosis bacillus, Mycobacterium tuberculosis (Mtb), is a global killer causing millions of deaths every year and is therefore a major burden to human health. Treatment of tuberculosis requires a cocktail of antibiotics for a minimum of 6 months. Treatment failure is common and is a major driver in the upward trend of antibiotic resistance, recognized by the World Health Organization as one of top ten threats to global health. A key to the success of Mtb as a human pathogen is ascribed to its extraordinary metabolic flexibility. Understanding the metabolism of Mtb is therefore an important goal of TB researchers as metabolic pathways present attractive drug targets. A powerful approach to study metabolism is through the use of genome-scale metabolic networks which enable metabolism to be studied at the whole system level rather than one enzyme at a time. Here, we comprehensively compare available genome scale metabolic networks. Our results identify the best performing networks for a variety of modelling approaches. This work allowed us to refine these models for the TB community to use in future studies to probe the metabolism of this formidable human pathogen.
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Affiliation(s)
- Víctor A. López-Agudelo
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia UdeA, Medellín, Colombia
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Tom A. Mendum
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Emma Laing
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - HuiHai Wu
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Andres Baena
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Luis F. Barrera
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
- Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Dany J. V. Beste
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- * E-mail: (DJVB); (RRE)
| | - Rigoberto Rios-Estepa
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia UdeA, Medellín, Colombia
- * E-mail: (DJVB); (RRE)
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9
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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] [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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10
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Tuyiringire N, Tusubira D, Munyampundu JP, Tolo CU, Muvunyi CM, Ogwang PE. Application of metabolomics to drug discovery and understanding the mechanisms of action of medicinal plants with anti-tuberculosis activity. Clin Transl Med 2018; 7:29. [PMID: 30270413 PMCID: PMC6165828 DOI: 10.1186/s40169-018-0208-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/29/2018] [Indexed: 11/10/2022] Open
Abstract
Human tuberculosis (TB) is amongst the oldest and deadliest human bacterial diseases that pose major health, social and economic burden at a global level. Current regimens for TB treatment are lengthy, expensive and ineffective to emerging drug resistant strains. Thus, there is an urgent need for identification and development of novel TB drugs and drug regimens with comprehensive and specific mechanisms of action. Many medicinal plants are traditionally used for TB treatment. While some of their phytochemical composition has been elucidated, their mechanisms of action are not well understood. Insufficient knowledge on Mycobacterium tuberculosis (M.tb) biology and the complex nature of its infection limit the effectiveness of current screening-based methods used for TB drug discovery. Nonetheless, application of metabolomics tools within the 'omics' approaches, could provide an alternative method of elucidating the mechanism of action of medicinal plants. Metabolomics aims at high throughput detection, quantification and identification of metabolites in biological samples. Changes in the concentration of specific metabolites in a biological sample indicate changes in the metabolic pathways. In this paper review and discuss novel methods that involve application of metabolomics to drug discovery and the understanding of mechanisms of action of medicinal plants with anti-TB activity. Current knowledge on TB infection, anti-TB drugs and mechanisms of action are also included. We further highlight metabolism of M. tuberculosis and the potential drug targets, as well as current approaches in the development of anti-TB drugs.
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Affiliation(s)
- Naasson Tuyiringire
- Pharm-BioTechnology and Traditional Medicine Centre (PHARMBIOTRAC), Mbarara University of Science & Technology, P.O. Box, 1410 Mbarara, Uganda
- College of Medicine and Health Sciences, University of Rwanda, University Avenue, P.O. Box 56, Butare, Rwanda
| | - Deusdedit Tusubira
- Pharm-BioTechnology and Traditional Medicine Centre (PHARMBIOTRAC), Mbarara University of Science & Technology, P.O. Box, 1410 Mbarara, Uganda
- Department of Biomedicine, University of Bergen, Jonas Lies Vei 91, 5020 Bergen, Norway
| | - Jean-Pierre Munyampundu
- School of Science, College of Science and Technology, University of Rwanda, Avenue de l’Armée, P.O. Box 3900, Kigali, Rwanda
| | - Casim Umba Tolo
- Pharm-BioTechnology and Traditional Medicine Centre (PHARMBIOTRAC), Mbarara University of Science & Technology, P.O. Box, 1410 Mbarara, Uganda
| | - Claude M. Muvunyi
- College of Medicine and Health Sciences, University of Rwanda, University Avenue, P.O. Box 56, Butare, Rwanda
| | - Patrick Engeu Ogwang
- Pharm-BioTechnology and Traditional Medicine Centre (PHARMBIOTRAC), Mbarara University of Science & Technology, P.O. Box, 1410 Mbarara, Uganda
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11
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Guerrini V, Prideaux B, Blanc L, Bruiners N, Arrigucci R, Singh S, Ho-Liang HP, Salamon H, Chen PY, Lakehal K, Subbian S, O’Brien P, Via LE, Barry CE, Dartois V, Gennaro ML. Storage lipid studies in tuberculosis reveal that foam cell biogenesis is disease-specific. PLoS Pathog 2018; 14:e1007223. [PMID: 30161232 PMCID: PMC6117085 DOI: 10.1371/journal.ppat.1007223] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 07/16/2018] [Indexed: 12/16/2022] Open
Abstract
Foam cells are lipid-laden macrophages that contribute to the inflammation and tissue damage associated with many chronic inflammatory disorders. Although foam cell biogenesis has been extensively studied in atherosclerosis, how these cells form during a chronic infectious disease such as tuberculosis is unknown. Here we report that, unlike the cholesterol-laden cells of atherosclerosis, foam cells in tuberculous lung lesions accumulate triglycerides. Consequently, the biogenesis of foam cells varies with the underlying disease. In vitro mechanistic studies showed that triglyceride accumulation in human macrophages infected with Mycobacterium tuberculosis is mediated by TNF receptor signaling through downstream activation of the caspase cascade and the mammalian target of rapamycin complex 1 (mTORC1). These features are distinct from the known biogenesis of atherogenic foam cells and establish a new paradigm for non-atherogenic foam cell formation. Moreover, they reveal novel targets for disease-specific pharmacological interventions against maladaptive macrophage responses.
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Affiliation(s)
- Valentina Guerrini
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States of America
| | - Brendan Prideaux
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States of America
| | - Landry Blanc
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States of America
| | - Natalie Bruiners
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States of America
| | - Riccardo Arrigucci
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States of America
| | - Sukhwinder Singh
- Department of Pathology and Laboratory Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States of America
| | - Hsin Pin Ho-Liang
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States of America
| | - Hugh Salamon
- Knowledge Synthesis, Berkeley, CA, United States of America
| | - Pei-Yu Chen
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States of America
| | - Karim Lakehal
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States of America
| | - Selvakumar Subbian
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States of America
| | - Paul O’Brien
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States of America
| | - Laura E. Via
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Clifton E. Barry
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Véronique Dartois
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States of America
| | - Maria Laura Gennaro
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States of America
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Sanders S, Bartee D, Harrison MJ, Phillips PD, Koppisch AT, Freel Meyers CL. Growth medium-dependent antimicrobial activity of early stage MEP pathway inhibitors. PLoS One 2018; 13:e0197638. [PMID: 29771999 PMCID: PMC5957436 DOI: 10.1371/journal.pone.0197638] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 05/04/2018] [Indexed: 01/01/2023] Open
Abstract
The in vivo microenvironment of bacterial pathogens is often characterized by nutrient limitation. Consequently, conventional rich in vitro culture conditions used widely to evaluate antibacterial agents are often poorly predictive of in vivo activity, especially for agents targeting metabolic pathways. In one such pathway, the methylerythritol phosphate (MEP) pathway, which is essential for production of isoprenoids in bacterial pathogens, relatively little is known about the influence of growth environment on antibacterial properties of inhibitors targeting enzymes in this pathway. The early steps of the MEP pathway are catalyzed by 1-deoxy-d-xylulose 5-phosphate (DXP) synthase and reductoisomerase (IspC). The in vitro antibacterial efficacy of the DXP synthase inhibitor butylacetylphosphonate (BAP) was recently reported to be strongly dependent upon growth medium, with high potency observed under nutrient limitation and exceedingly weak activity in nutrient-rich conditions. In contrast, the well-known IspC inhibitor fosmidomycin has potent antibacterial activity in nutrient-rich conditions, but to date, its efficacy had not been explored under more relevant nutrient-limited conditions. The goal of this work was to thoroughly characterize the effects of BAP and fosmidomycin on bacterial cells under varied growth conditions. In this work, we show that activities of both inhibitors, alone and in combination, are strongly dependent upon growth medium, with differences in cellular uptake contributing to variance in potency of both agents. Fosmidomycin is dissimilar to BAP in that it displays relatively weaker activity in nutrient-limited compared to nutrient-rich conditions. Interestingly, while it has been generally accepted that fosmidomycin activity depends upon expression of the GlpT transporter, our results indicate for the first time that fosmidomycin can enter cells by an alternative mechanism under nutrient limitation. Finally, we show that the potency and relationship of the BAP-fosmidomycin combination also depends upon the growth medium, revealing a striking loss of BAP-fosmidomycin synergy under nutrient limitation. This change in BAP-fosmidomycin relationship suggests a shift in the metabolic and/or regulatory networks surrounding DXP accompanying the change in growth medium, the understanding of which could significantly impact targeting strategies against this pathway. More generally, our findings emphasize the importance of considering physiologically relevant growth conditions for predicting the antibacterial potential MEP pathway inhibitors and for studies of their intracellular targets.
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Affiliation(s)
- Sara Sanders
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - David Bartee
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Mackenzie J. Harrison
- Department of Chemistry, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Paul D. Phillips
- Department of Chemistry, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Andrew T. Koppisch
- Department of Chemistry, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Caren L. Freel Meyers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- * E-mail:
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