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Deal I, Macauley M, Davies R. Boolean Models of the Transport, Synthesis, and Metabolism of Tryptophan in Escherichia coli. Bull Math Biol 2023; 85:29. [PMID: 36877290 DOI: 10.1007/s11538-023-01122-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 01/11/2023] [Indexed: 03/07/2023]
Abstract
The tryptophan (trp) operon in Escherichia coli codes for the proteins responsible for the synthesis of the amino acid tryptophan from chorismic acid, and has been one of the most well-studied gene networks since its discovery in the 1960s. The tryptophanase (tna) operon codes for proteins needed to transport and metabolize it. Both of these have been modeled individually with delay differential equations under the assumption of mass-action kinetics. Recent work has provided strong evidence for bistable behavior of the tna operon. The authors of Orozco-Gómez et al. (Sci Rep 9(1):5451, 2019) identified a medium range of tryptophan in which the system has two stable steady-states, and they reproduced these experimentally. In this paper, we will show how a Boolean model can capture this bistability. We will also develop and analyze a Boolean model of the trp operon. Finally, we will combine these two to create a single Boolean model of the transport, synthesis, and metabolism of tryptophan. In this amalgamated model, the bistability disappears, presumably reflecting the ability of the trp operon to produce tryptophan and drive the system toward homeostasis. All of these models have longer attractors that we call "artifacts of synchrony", which disappear in the asynchronous automata. This curiously matches the behavior of a recent Boolean model of the arabinose operon in E. coli, and we discuss some open-ended questions that arise along these lines.
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Affiliation(s)
- Isadora Deal
- School of Medicine, University of South Carolina, Columbia, SC, 29209, USA
| | - Matthew Macauley
- School of Mathematical and Statistical Sciences, Clemson University, Clemson, SC, 29634, USA.
| | - Robin Davies
- Radford University Carilion, Roanoke, VA, 24013, USA
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A Molecular Dynamic Model of Tryptophan Overproduction in Escherichia coli. FERMENTATION 2022. [DOI: 10.3390/fermentation8100560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Several deterministic models simulate the main molecular biology interactions among the numerous mechanisms controlling the dynamics of the tryptophan operon in native strains. However, no models exist to investigate bacterial tryptophan production from a biotechnological point of view. Here, we modified tryptophan models for native production to propose a biotechnological working model that incorporates the activity of tryptophan secretion systems and genetic modifications made in two reported E. coli strains. The resultant deterministic model could emulate the production of tryptophan in the same order of magnitude as those quantified experimentally by the genetically engineered E. coli strains GPT1001 and GPT1002 in shake flasks. We hope this work may contribute to the rational development of biological models that define and include the main parameters and molecular components for designing and engineering efficient biotechnological chassis to produce valuable chemicals.
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Sudan S, Flick R, Nong L, Li J. Potential Probiotic Bacillus subtilis Isolated from a Novel Niche Exhibits Broad Range Antibacterial Activity and Causes Virulence and Metabolic Dysregulation in Enterotoxic E. coli. Microorganisms 2021; 9:1483. [PMID: 34361918 PMCID: PMC8307078 DOI: 10.3390/microorganisms9071483] [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: 06/20/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
Microbial life in extreme environments, such as deserts and deep oceans, is thought to have evolved to overcome constraints of nutrient availability, temperature, and suboptimal hygiene environments. Isolation of probiotic bacteria from such niche may provide a competitive edge over traditional probiotics. Here, we tested the survival, safety, and antimicrobial effect of a recently isolated and potential novel strain of Bacillus subtilis (CP9) from desert camel in vitro. Antimicrobial assays were performed via radial diffusion, agar spot, and co-culture assays. Cytotoxic analysis was performed using pig intestinal epithelial cells (IPEC-J2). Real time-PCR was performed for studying the effect on ETEC virulence genes and metabolomic analysis was performed using LC-MS. The results showed that CP9 cells were viable in varied bile salts and in low pH environments. CP9 showed no apparent cytotoxicity in IPEC-J2 cells. CP9 displayed significant bactericidal effect against Enterotoxic E. coli (ETEC), Salmonella Typhimurium, and Methicillin-resistant Staphylococcus aureus (MRSA) in a contact inhibitory fashion. CP9 reduced the expression of ETEC virulent genes during a 5 h co-culture. Additionally, a unique emergent metabolic signature in co-culture samples was observed by LC-MS analysis. Our findings indicate that CP9 exhibits a strong antibacterial property and reveals potential mechanisms behind.
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Affiliation(s)
- Sudhanshu Sudan
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Robert Flick
- Biozone, Mass Spectrometry and Metabolomics, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada;
| | - Linda Nong
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Julang Li
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada;
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Pyridoxal 5'-Phosphate-Dependent Enzymes at the Crossroads of Host-Microbe Tryptophan Metabolism. Int J Mol Sci 2020; 21:ijms21165823. [PMID: 32823705 PMCID: PMC7461572 DOI: 10.3390/ijms21165823] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/06/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023] Open
Abstract
The chemical processes taking place in humans intersects the myriad of metabolic pathways occurring in commensal microorganisms that colonize the body to generate a complex biochemical network that regulates multiple aspects of human life. The role of tryptophan (Trp) metabolism at the intersection between the host and microbes is increasingly being recognized, and multiple pathways of Trp utilization in either direction have been identified with the production of a wide range of bioactive products. It comes that a dysregulation of Trp metabolism in either the host or the microbes may unbalance the production of metabolites with potential pathological consequences. The ability to redirect the Trp flux to restore a homeostatic production of Trp metabolites may represent a valid therapeutic strategy for a variety of pathological conditions, but identifying metabolic checkpoints that could be exploited to manipulate the Trp metabolic network is still an unmet need. In this review, we put forward the hypothesis that pyridoxal 5′-phosphate (PLP)-dependent enzymes, which regulate multiple pathways of Trp metabolism in both the host and in microbes, might represent critical nodes and that modulating the levels of vitamin B6, from which PLP is derived, might represent a metabolic checkpoint to re-orienteer Trp flux for therapeutic purposes.
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Rubio VY, Cagmat JG, Wang GP, Yost RA, Garrett TJ. Analysis of Tryptophan Metabolites in Serum Using Wide-Isolation Strategies for UHPLC-HRMS/MS. Anal Chem 2020; 92:2550-2557. [PMID: 31927994 DOI: 10.1021/acs.analchem.9b04210] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Current targeted metabolomic workflows are limited by design and thus sacrifice crucial information from a profiling standpoint that could lead to a more fundamental understanding of the metabolic processes of interest. One drawback to performing targeted analysis on ion trapping instruments is the potential for increased variability in analysis when analytes and standards are isolated and trapped individually for fragmentation. In addition, this sequential isolation process increases the duty cycle of the mass spectrometer and reduces the number of points collected across a chromatographic peak. To address this, the use of a wide-isolation window (12 Da) to encompass the target analyte and the isotope standard within a single fragmentation window ensures that fragmentation is consistent when quantitation relies on the ratio of the target to the internal standard. Additionally, the preservation of a faster scan rate ensures that optimal representation of chromatographic peaks is preserved for the purposes of both quantitative and qualitative analyses that require peak integration for statistical analysis. The use of this flexible method is promising in the investigation of pathways that require multiple targets and are highly integrated within the system. Here, we demonstrate the application of this method in a fast ultra-high performance liquid chromatography (UHPLC) analysis to integrate wide-isolation quantitative strategies for high-resolution mass spectrometry (HRMS) combined with profiling qualitative metabolomics for the analysis of tryptophan degradation metabolites in mouse serum. Analysis of tryptophan-deficient states as compared to control in both germ-free or E. coli gut microbiota states was used to quantitate pathway-specific metabolites as well as obtain full profiling information. The quantitative and qualitative results revealed the preservation of the primary pathways of degradation in the kynurenine pathway to potentially produce primary products such as nicotinamide during stress-induced dietary states.
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Affiliation(s)
- Vanessa Y Rubio
- Department of Chemistry , University of Florida , Gainesville , Florida 32610 , United States
| | - Joy G Cagmat
- Southeast Center for Integrated Metabolomics , University of Florida , Gainesville , Florida 32611 , United States
| | - Gary P Wang
- Department of Medicine, Division of Infectious Diseases and Global Medicine , University of Florida , Gainesville , Florida 32610 , United States
| | - Richard A Yost
- Department of Chemistry , University of Florida , Gainesville , Florida 32610 , United States.,Southeast Center for Integrated Metabolomics , University of Florida , Gainesville , Florida 32611 , United States.,Department of Pathology, Immunology, and Laboratory Medicine , University of Florida , Gainesville , Florida 32610 , United States
| | - Timothy J Garrett
- Southeast Center for Integrated Metabolomics , University of Florida , Gainesville , Florida 32611 , United States.,Department of Pathology, Immunology, and Laboratory Medicine , University of Florida , Gainesville , Florida 32610 , United States
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