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Ulloa G, Quezada CP, Araneda M, Escobar B, Fuentes E, Álvarez SA, Castro M, Bruna N, Espinoza-González R, Bravo D, Pérez-Donoso JM. Phosphate Favors the Biosynthesis of CdS Quantum Dots in Acidithiobacillus thiooxidans ATCC 19703 by Improving Metal Uptake and Tolerance. Front Microbiol 2018. [PMID: 29515535 PMCID: PMC5826283 DOI: 10.3389/fmicb.2018.00234] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recently, we reported the production of Cadmium sulfide (CdS) fluorescent semiconductor nanoparticles (quantum dots, QDs) by acidophilic bacteria of the Acidithiobacillus genus. Here, we report that the addition of inorganic phosphate to Acidithiobacillus thiooxidans ATCC 19703 cultures favors the biosynthesis of CdS QDs at acidic conditions (pH 3.5). The effect of pH, phosphate and cadmium concentrations on QDs biosynthesis was studied by using Response Surface Methodology (RSM), a multivariate technique for analytical optimization scarcely used in microbiological studies to date. To address how phosphate affects intracellular biosynthesis of CdS QDs, the effect of inorganic phosphate on bacterial cadmium-uptake was evaluated. By measuring intracellular levels of cadmium we determined that phosphate influences the capacity of cells to incorporate this metal. A relation between cadmium tolerance and phosphate concentrations was also determined, suggesting that phosphate participates in the adaptation of bacteria to toxic levels of this metal. In addition, QDs-biosynthesis was also favored by the degradation of intracellular polyphosphates. Altogether, our results indicate that phosphate contributes to A. thiooxidans CdS QDs biosynthesis by influencing cadmium uptake and cadmium tolerance. These QDs may also be acting as a nucleation point for QDs formation at acidic pH. This is the first study reporting the effect of phosphates on QDs biosynthesis and describes a new cadmium-response pathway present in A. thiooxidans and most probably in other bacterial species.
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Affiliation(s)
- Giovanni Ulloa
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.,Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Carolina P Quezada
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Mabel Araneda
- Departamento de Ingeniería Química y Biotecnología, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Blanca Escobar
- Departamento de Ingeniería Química y Biotecnología, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Edwar Fuentes
- Departamento de Química Inorgánica y Analítica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Sergio A Álvarez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Matías Castro
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Nicolás Bruna
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Rodrigo Espinoza-González
- Departamento de Ingeniería Química, Biotecnología y Materiales, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Denisse Bravo
- Laboratorio de Microbiología Oral, Facultad de Odontología, Universidad de Chile, Santiago, Chile
| | - José M Pérez-Donoso
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
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Abstract
The richness and versatility of biological systems make them ideally suited to solve some of the world's most significant challenges, such as converting cheap, renewable resources into energy-rich molecules; producing high-quality, inexpensive drugs to fight disease; and remediating polluted sites. Over the years, significant strides have been made in engineering microorganisms to produce fuels, bulk chemicals, and valuable drugs from inexpensive starting materials; to detect and degrade nerve agents as well as less toxic organic pollutants; and to accumulate metals and reduce radionuclides. The components needed to engineer the chemistry inside a microbial cell are significantly different from those commonly used to overproduce pharmaceutical proteins. Synthetic biology has had and will continue to have a significant impact on the development of these components to engineer cellular metabolism and microbial chassis to host the chemistry. The ready availability of more well-characterized gene expression components and hosts for chemical synthesis, standards for the connection of these components to make larger functioning devices, computer-aided design software, and debugging tools for biological designs will decrease both the time and the support needed to construct these designs. Some of the most important tools for engineering bacterial metabolism and their use for production of the antimalarial drug artemisinin are reviewed.
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Affiliation(s)
- Jay D. Keasling
- Departments of Chemical Engineering and Bioengineering, University of California, Berkeley, Berkeley, California 94720, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
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Rangarajan ES, Nadeau G, Li Y, Wagner J, Hung MN, Schrag JD, Cygler M, Matte A. The structure of the exopolyphosphatase (PPX) from Escherichia coli O157:H7 suggests a binding mode for long polyphosphate chains. J Mol Biol 2006; 359:1249-60. [PMID: 16678853 DOI: 10.1016/j.jmb.2006.04.031] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Revised: 04/13/2006] [Accepted: 04/13/2006] [Indexed: 12/12/2022]
Abstract
Polyphosphate (polyP) is a linear polymer consisting of tens to hundreds of phosphate molecules joined together by high-energy anhydride bonds. These polymers are found in virtually all prokaryotic and eukaryotic cells and perform many functions; prominent among them are the responses to many stresses. Polyphosphate is synthesized by polyP kinase (PPK), using the terminal phosphate of ATP as the substrate, and degraded to inorganic phosphate by both endo- and exopolyphosphatases. Here we report the crystal structure and analysis of the polyphosphate phosphatase PPX from Escherichia coli O157:H7 refined at 2.2 Angstroms resolution. PPX is made of four domains. Domains I and II display structural similarity with one another and share the ribonuclease-H-like fold. Domain III bears structural similarity to the N-terminal, HD domain of SpoT. Domain IV, the smallest domain, has structural counterparts in cold-shock associated RNA-binding proteins but is of unknown function in PPX. The putative PPX active site is located at the interface between domains I and II. In the crystal structure of PPX these two domains are close together and represent the "closed" state. Comparison with the crystal structure of PPX/GPPA from Aquifex aeolicus reveals close structural similarity between domains I and II of the two enzymes, with the PPX/GPPA representing an "open" state. A striking feature of the dimer is a deep S-shaped canyon extending along the dimer interface and lined with positively charged residues. The active site region opens to this canyon. We postulate that this is a likely site of polyP binding.
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Renninger N, Knopp R, Nitsche H, Clark DS, Keasling JD. Uranyl precipitation by Pseudomonas aeruginosa via controlled polyphosphate metabolism. Appl Environ Microbiol 2005; 70:7404-12. [PMID: 15574942 PMCID: PMC535141 DOI: 10.1128/aem.70.12.7404-7412.2004] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The polyphosphate kinase gene from Pseudomonas aeruginosa was overexpressed in its native host, resulting in the accumulation of 100 times the polyphosphate seen with control strains. Degradation of this polyphosphate was induced by carbon starvation conditions, resulting in phosphate release into the medium. The mechanism of polyphosphate degradation is not clearly understood, but it appears to be associated with glycogen degradation. Upon suspension of the cells in 1 mM uranyl nitrate, nearly all polyphosphate that had accumulated was degraded within 48 h, resulting in the removal of nearly 80% of the uranyl ion and >95% of lesser-concentrated solutions. Electron microscopy, energy-dispersive X-ray spectroscopy, and time-resolved laser-induced fluorescence spectroscopy (TRLFS) suggest that this removal was due to the precipitation of uranyl phosphate at the cell membrane. TRLFS also indicated that uranyl was initially sorbed to the cell as uranyl hydroxide and was then precipitated as uranyl phosphate as phosphate was released from the cell. Lethal doses of radiation did not halt phosphate secretion from polyphosphate-filled cells under carbon starvation conditions.
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Affiliation(s)
- Neil Renninger
- Department of Chemical Engineering, University of California at Berkeley, Berkeley, CA 94720-1462, USA
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Burgard AP, Maranas CD. Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. Biotechnol Bioeng 2001; 74:364-75. [PMID: 11427938 DOI: 10.1002/bit.1127] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An optimization-based procedure for studying the response of metabolic networks after gene knockouts or additions is introduced and applied to a linear flux balance analysis (FBA) Escherichia coli model. Both the gene addition problem of optimally selecting which foreign genes to recombine into E. coli, as well as the gene deletion problem of removing a given number of existing ones, are formulated as mixed-integer optimization problems using binary 0-1 variables. The developed modeling and optimization framework is tested by investigating the effect of gene deletions on biomass production and addressing the maximum theoretical production of the 20 amino acids for aerobic growth on glucose and acetate substrates. In the gene deletion study, the smallest gene set necessary to achieve maximum biomass production in E. coli is determined for aerobic growth on glucose. The subsequent gene knockout analysis indicates that biomass production decreases monotonically, rendering the metabolic network incapable of growth after only 18 gene deletions. In the gene addition study, the E. coli flux balance model is augmented with 3,400 non-E. coli reactions from the KEGG database to form a multispecies model. This model is referred to as the Universal model. This study reveals that the maximum theoretical production of six amino acids could be improved by the addition of only one or two genes to the native amino acid production pathway of E. coli, even though the model could choose from 3,400 foreign reaction candidates. Specifically, manipulation of the arginine production pathway showed the most promise with 8.75% and 9.05% predicted increases with the addition of genes for growth on glucose and acetate, respectively. The mechanism of all suggested enhancements is either by: 1) improving the energy efficiency and/or 2) increasing the carbon conversion efficiency of the production route.
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Affiliation(s)
- A P Burgard
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Abstract
Recent advances in metabolic engineering have led to new methods for the synthesis of novel molecules, improved production of existing compounds and improved degradation of recalcitrant environmental contaminants. Increasing the flux through an existing pathway and introducing a new pathway into a host organism demand coordinated expression of the genes that encode the enzymes, tight control over gene expression and consistent expression in all cells. Although several gene-expression tools have been developed for the overproduction of proteins, they may not be ideal for pathway redirection. Metabolic engineering requires certain characteristics of gene-expression tools, and some new tools meet these needs.
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Affiliation(s)
- J D Keasling
- Department of Chemical Engineering, University of California, Berkeley, CA 94720-1462, USA.
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