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Lim CK, Villada JC, Chalifour A, Duran MF, Lu H, Lee PKH. Designing and Engineering Methylorubrum extorquens AM1 for Itaconic Acid Production. Front Microbiol 2019; 10:1027. [PMID: 31143170 PMCID: PMC6520949 DOI: 10.3389/fmicb.2019.01027] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/24/2019] [Indexed: 01/05/2023] Open
Abstract
Methylorubrum extorquens (formerly Methylobacterium extorquens) AM1 is a methylotrophic bacterium with a versatile lifestyle. Various carbon sources including acetate, succinate and methanol are utilized by M. extorquens AM1 with the latter being a promising inexpensive substrate for use in the biotechnology industry. Itaconic acid (ITA) is a high-value building block widely used in various industries. Given that no wildtype methylotrophic bacteria are able to utilize methanol to produce ITA, we tested the potential of M. extorquens AM1 as an engineered host for this purpose. In this study, we successfully engineered M. extorquens AM1 to express a heterologous codon-optimized gene encoding cis-aconitic acid decarboxylase. The engineered strain produced ITA using acetate, succinate and methanol as the carbon feedstock. The highest ITA titer in batch culture with methanol as the carbon source was 31.6 ± 5.5 mg/L, while the titer and productivity were 5.4 ± 0.2 mg/L and 0.056 ± 0.002 mg/L/h, respectively, in a scaled-up fed-batch bioreactor under 60% dissolved oxygen saturation. We attempted to enhance the carbon flux toward ITA production by impeding poly-β-hydroxybutyrate accumulation, which is used as carbon and energy storage, via mutation of the regulator gene phaR. Unexpectedly, ITA production by the phaR mutant strain was not higher even though poly-β-hydroxybutyrate concentration was lower. Genome-wide transcriptomic analysis revealed that phaR mutation in the ITA-producing strain led to complex rewiring of gene transcription, which might result in a reduced carbon flux toward ITA production. Besides poly-β-hydroxybutyrate metabolism, we found evidence that PhaR might regulate the transcription of many other genes including those encoding other regulatory proteins, methanol dehydrogenases, formate dehydrogenases, malate:quinone oxidoreductase, and those synthesizing pyrroloquinoline quinone and thiamine co-factors. Overall, M. extorquens AM1 was successfully engineered to produce ITA using acetate, succinate and methanol as feedstock, further supporting this bacterium as a feasible host for use in the biotechnology industry. This study showed that PhaR could have a broader regulatory role than previously anticipated, and increased our knowledge of this regulator and its influence on the physiology of M. extorquens AM1.
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Affiliation(s)
- Chee Kent Lim
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Juan C Villada
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Annie Chalifour
- Department of Chemistry, City University of Hong Kong, Hong Kong, China
| | - Maria F Duran
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Hongyuan Lu
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
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Grate JW, Liu B, Kelly RT, Anheier NC, Schmidt TM. Microfluidic Sensors with Impregnated Fluorophores for Simultaneous Imaging of Spatial Structure and Chemical Oxygen Gradients. ACS Sens 2019; 4:317-325. [PMID: 30609370 DOI: 10.1021/acssensors.8b00924] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Interior surfaces of polystyrene microfluidic structures were impregnated with the oxygen sensing dye Pt(II) tetra(pentafluorophenyl)porphyrin (PtTFPP) using a solvent-induced fluorophore impregnation (SIFI) method. Using this technique, microfluidic oxygen sensors are obtained that enable simultaneous imaging of both chemical oxygen gradients and the physical structure of the microfluidic interior. A gentle method of fluorophore impregnation using acetonitrile solutions of PtTFPP at 50 °C was developed leading to a 10-μm-deep region containing fluorophore. This region is localized at the surface to sense oxygen in the interior fluid during use. Regions of the device that do not contact the interior fluid pathways lack fluorophores and are dark in fluorescent imaging. The technique was demonstrated on straight microchannel and pore network devices, the latter having pillars of 300 μm diameter spaced center to center at 340 μm providing pore throats of 40 μm. Sensing within channels or pores and imaging across the pore network devices were performed using a Lambert LIFA-P frequency domain fluorescence lifetime imaging system on a Leica microscope platform. Calibrations of different devices prepared by the SIFI method were indistinguishable. Gradient imaging showed fluorescent regions corresponding to the fluid pore network, dark pillars, and fluorescent lifetime varying across the gradient, thus providing both physical and chemical imaging. More generally, the SIFI technique can impregnate the interior surfaces of other polystyrene containers, such as cuvettes or cell and tissue culture containers, to enable sensing of interior conditions.
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Affiliation(s)
- Jay W. Grate
- Pacific Northwest
National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Bingwen Liu
- Pacific Northwest
National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Ryan T. Kelly
- Pacific Northwest
National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Norman C. Anheier
- Pacific Northwest
National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Thomas M. Schmidt
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
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Deng J, Dhummakupt A, Samson PC, Wikswo JP, Shor LM. Dynamic Dosing Assay Relating Real-Time Respiration Responses of Staphylococcus aureus Biofilms to Changing Microchemical Conditions. Anal Chem 2013; 85:5411-9. [DOI: 10.1021/ac303711m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jinzi Deng
- Department of Chemical & Biomolecular Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Adit Dhummakupt
- Department of Molecular Genetics & Microbiology, University of Florida College of Medicine, Gainesville, Florida, United States
| | - Philip C. Samson
- Vanderbilt
Institute for Integrative
Biosytems Research and Education (VIIBRE), Vanderbilt University, Nashville, Tennessee 37235, United States
| | - John P. Wikswo
- Vanderbilt
Institute for Integrative
Biosytems Research and Education (VIIBRE), Vanderbilt University, Nashville, Tennessee 37235, United States
- Departments of Biomedical Engineering, Physics & Astronomy, and Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Leslie M. Shor
- Department of Chemical & Biomolecular Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
- Center
for Environmental Sciences
and Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
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Grate JW, Kelly RT, Suter J, Anheier NC. Silicon-on-glass pore network micromodels with oxygen-sensing fluorophore films for chemical imaging and defined spatial structure. LAB ON A CHIP 2012; 12:4796-4801. [PMID: 22995983 DOI: 10.1039/c2lc40776k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Pore network microfluidic models were fabricated by a silicon-on-glass technique that provides the precision advantage of dry etched silicon while creating a structure that is transparent across all microfluidic channels and pores, and can be imaged from either side. A silicon layer is bonded to an underlying borosilicate glass substrate and thinned to the desired height of the microfluidic channels and pores. The silicon is then patterned and through-etched by deep reactive ion etching (DRIE), with the underlying glass serving as an etch stop. After bonding on a transparent glass cover plate, one obtains a micromodel in oxygen impermeable materials with water-wet surfaces where the microfluidic channels are transparent and structural elements such as the pillars creating the pore network are opaque. The advantageous features of this approach in a chemical imaging application are demonstrated by incorporating a Pt porphyrin fluorophore in a PDMS film serving as the oxygen-sensing layer and a bonding surface, or in a polystyrene film coated with a PDMS layer for bonding. The sensing of a dissolved oxygen gradient was demonstrated using fluorescence lifetime imaging, and it is shown that different matrix polymers lead to optimal use in different ranges of oxygen concentration. Imaging with the opaque pillars in between the observation direction and the continuous fluorophore film yields images that retain defined spatial structure in the sensor image.
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Affiliation(s)
- Jay W Grate
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA.
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Strovas TJ, McQuaide SC, Anderson JB, Nandakumar V, Kalyuzhnaya MG, Burgess LW, Holl MR, Meldrum DR, Lidstrom ME. Direct measurement of oxygen consumption rates from attached and unattached cells in a reversibly sealed, diffusionally isolated sample chamber. ACTA ACUST UNITED AC 2010; 5:398-408. [PMID: 21546993 DOI: 10.4236/abb.2010.15053] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Oxygen consumption is a fundamental component of metabolic networks, mitochondrial function, and global carbon cycling. To date there is no method available that allows for replicate measurements on attached and unattached biological samples without compensation for extraneous oxygen leaking into the system. Here we present the Respiratory Detection System, which is compatible with virtually any biological sample. The RDS can be used to measure oxygen uptake in microliter-scale volumes with a reversibly sealed sample chamber, which contains a porphyrin-based oxygen sensor. With the RDS, one can maintain a diffusional seal for up to three hours, allowing for the direct measurement of respiratory function of samples with fast or slow metabolic rates. The ability to easily measure oxygen uptake in small volumes with small populations or dilute samples has implications in cell biology, environmental biology, and clinical diagnostics.
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Affiliation(s)
- Timothy J Strovas
- Department of Electrical Engineering, University of Washington, Seattle, USA
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Dragavon J, Molter T, Young C, Strovas T, McQuaide S, Holl M, Zhang M, Cookson B, Jen A, Lidstrom M, Meldrum D, Burgess L. A cellular isolation system for real-time single-cell oxygen consumption monitoring. J R Soc Interface 2008; 5 Suppl 2:S151-9. [PMID: 18522927 DOI: 10.1098/rsif.2008.0106.focus] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The development of a cellular isolation system (CIS) that enables the monitoring of single-cell oxygen consumption rates in real time is presented. The CIS was developed through a multidisciplinary effort within the Microscale Life Sciences Center (MLSC) at the University of Washington. The system comprises arrays of microwells containing Pt-porphyrin-embedded polystyrene microspheres as the reporter chemistry, a lid actuator system and a gated intensified imaging camera, all mounted on a temperature-stabilized confocal microscope platform. Oxygen consumption determination experiments were performed on RAW264.7 mouse macrophage cells as proof of principle. Repeatable and consistent measurements indicate that the oxygen measurements did not adversely affect the physiological state of the cells measured. The observation of physiological rates in real time allows studies of cell-to-cell heterogeneity in oxygen consumption rate to be performed. Such studies have implications in understanding the role of mitochondrial function in the progression of inflammatory-based diseases, and in diagnosing and treating such diseases.
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Affiliation(s)
- Joe Dragavon
- Department of Chemistry, University of Washington, Seattle, WA 98195-2180, USA.
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