1
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Han J, Lim HJ, Park J, Han DH, Kim DM, Park JK. On-chip microfluidic dual detection of amino acid metabolism disorders using cell-free protein synthesis. Biosens Bioelectron 2023; 222:114936. [PMID: 36455376 DOI: 10.1016/j.bios.2022.114936] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/27/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022]
Abstract
Various metabolic diseases are associated with the accumulation of specific amino acids due to abnormal metabolic pathways, and thus can be diagnosed by measuring the level of amino acids in body fluids. However, present methods for amino acid analysis are not readily accessible because they require a complex experimental setup, expensive equipment, and a long processing time. Here, we present a dual sensing microfluidic device that enables fast, portable, and quantitative analysis of target amino acids, harnessing the biological mechanism of protein synthesis. In this device, the working principle of a finger-actuated pumping unit is applied, and the microchannels are designed to perform cell-free synthesis of a reporter protein in response to the target amino acids in the assay samples. Multiple steps required for the translational assay are controlled by the simple operation of two pushbuttons on the device. It is demonstrated that the developed microfluidic device provides precise quantification of two amino acids (methionine and phenylalanine) within 30 min at room temperature. We expect that the application of the presented device can be readily extended to the point-of-care testing of other metabolic compounds.
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Affiliation(s)
- Jieun Han
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hye Jin Lim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Juhwan Park
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Dong Hyun Han
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea.
| | - Je-Kyun Park
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
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2
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Dhyani R, Jain S, Bhatt A, Kumar P, Navani NK. Genetic regulatory element based whole-cell biosensors for the detection of metabolic disorders. Biosens Bioelectron 2021; 199:113869. [PMID: 34915213 DOI: 10.1016/j.bios.2021.113869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 11/29/2022]
Abstract
Clinicians require simple, and cost-effective diagnostic tools for the quantitative determination of amino acids in physiological fluids for the detection of metabolic disorder diseases. Besides, amino acids also act as biological markers for different types of cancers and cardiovascular diseases. Herein, we applied an in-silico based approach to identify potential amino acid-responsive genetic regulatory elements for the detection of metabolic disorders in humans. Identified sequences were further transcriptionally fused with GFP, thus generating an optical readout in response to their cognate targets. Screening of genetic regulatory elements led us to discover two promoter elements (pmetE::GFP and ptrpL::GFP) that showed a significant change in the fluorescence response to homocysteine and tryptophan, respectively. The developed biosensors respond specifically and sensitively with a limit of detection of 3.8 μM and 3 μM for homocysteine and tryptophan, respectively. Furthermore, the clinical utility of this assay was demonstrated by employing it to identify homocystinuria and tryptophanuria diseases through the quantification of homocysteine and tryptophan in plasma and urine samples within 5 h. The precision and accuracy of the biosensors for disease diagnosis were well within an acceptable range. The general strategy used in this system can be expanded to screen different genetic regulatory elements present in other gram-negative and gram-positive bacteria for the detection of metabolic disorders.
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Affiliation(s)
- Rajat Dhyani
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
| | - Shubham Jain
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
| | - Ankita Bhatt
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
| | - Piyush Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
| | - Naveen Kumar Navani
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India.
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3
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Dhyani R, Srivastava SK, Shankar K, Ghosh T, Beniwal A, Navani NK. A chemical genetic approach using genetically encoded reporters to detect and assess the toxicity of plant secondary metabolites against bacterial pathogens. JOURNAL OF HAZARDOUS MATERIALS 2021; 418:126399. [PMID: 34329040 DOI: 10.1016/j.jhazmat.2021.126399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 05/25/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
Plant secondary metabolites are emerging as attractive alternatives in the development of therapeutics against infectious and chronic diseases. Due to the present pandemic, therapeutics showing toxicity against bacterial pathogens and viruses are gaining interest. Plant metabolites of terpenoid and phenylpropanoid categories have known antibacterial and antiviral properties. These metabolites have also been associated with toxicity to eukaryotic cells in terms of carcinogenicity, hepatotoxicity, and neurotoxicity. Sensing methods that can report the exact antibacterial dosage, formation, and accumulation of these antibacterial compounds are needed. The whole-cell reporters for such antibacterial metabolites are cost-effective and easy to maintain. In the present study, battery of toxicity sensors containing fluorescent transcriptional bioreporters was constructed, followed by fine-tuning the response using gene-debilitated E. coli mutants. This study shows that by combining regulatory switches with chemical genetics strategy, it may be possible to detect and elucidate the mode of action of effective antibacterial plant secondary metabolites - thymol, cinnamaldehyde, eugenol, and carvacrol in both pure and complex formats. Apart from the detection of adulteration of pure compounds present in complex mixture of essential oils, this approach will be useful to detect authenticity of essential oils and thus reduce unintended harmful effects on human and animal health.
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Affiliation(s)
- Rajat Dhyani
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | | | - Krishna Shankar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Tamoghna Ghosh
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Arun Beniwal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Naveen Kumar Navani
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247667, India.
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4
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Ahn HT, Jang IS, Dang TV, Kim YH, Lee DH, Choi HS, Yu BJ, Kim MI. Effective Cryopreservation of a Bioluminescent Auxotrophic Escherichia coli-Based Amino Acid Array to Enable Long-Term Ready-to-Use Applications. BIOSENSORS-BASEL 2021; 11:bios11080252. [PMID: 34436054 PMCID: PMC8393857 DOI: 10.3390/bios11080252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/24/2021] [Accepted: 07/25/2021] [Indexed: 11/16/2022]
Abstract
Amino acid arrays comprising bioluminescent amino acid auxotrophic Escherichia coli are effective systems to quantitatively determine multiple amino acids. However, there is a need to develop a method for convenient long-term preservation of the array to enable its practical applications. Here, we reported a potential strategy to efficiently maintain cell viability within the portable array. The method involves immobilization of cells within agarose gel supplemented with an appropriate cryoprotectant in individual wells of a 96-well plate, followed by storage under freezing conditions. Six cryoprotectants, namely dimethyl sulfoxide, glycerol, ethylene glycol, polyethylene glycol, sucrose, and trehalose, were tested in the methionine (Met) auxotroph-based array. Carbohydrate-type cryoprotectants (glycerol, sucrose, and trehalose) efficiently preserved the linearity of determination of Met concentration. In particular, the array with 5% trehalose exhibited the best performance. The Met array with 5% trehalose could determine Met concentration with high linearity (R2 value = approximately 0.99) even after storage at −20 °C for up to 3 months. The clinical utilities of the Met and Leu array, preserved at −20 °C for 3 months, were also verified by successfully quantifying Met and Leu in spiked blood serum samples for the diagnosis of the corresponding metabolic diseases. This long-term preservation protocol enables the development of a ready-to-use bioluminescent E. coli-based amino acid array to quantify multiple amino acids and can replace the currently used laborious analytical methods.
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Affiliation(s)
- Hee Tae Ahn
- Department of BioNano Technology, Gachon University, 1342 Seongnamdae-ro, Sujeong-gu, Seongnam 13120, Korea; (H.T.A.); (T.V.D.); (D.H.L.)
| | - In Seung Jang
- Green and Sustainable Materials R&D Department, Research Institute of Clean Manufacturing System, Korea Institute of Industrial Technology (KITECH), Cheonan 31056, Korea; (I.S.J.); (Y.H.K.); (H.S.C.)
| | - Thinh Viet Dang
- Department of BioNano Technology, Gachon University, 1342 Seongnamdae-ro, Sujeong-gu, Seongnam 13120, Korea; (H.T.A.); (T.V.D.); (D.H.L.)
| | - Yi Hyang Kim
- Green and Sustainable Materials R&D Department, Research Institute of Clean Manufacturing System, Korea Institute of Industrial Technology (KITECH), Cheonan 31056, Korea; (I.S.J.); (Y.H.K.); (H.S.C.)
| | - Dong Hoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnamdae-ro, Sujeong-gu, Seongnam 13120, Korea; (H.T.A.); (T.V.D.); (D.H.L.)
| | - Hyeun Seok Choi
- Green and Sustainable Materials R&D Department, Research Institute of Clean Manufacturing System, Korea Institute of Industrial Technology (KITECH), Cheonan 31056, Korea; (I.S.J.); (Y.H.K.); (H.S.C.)
| | - Byung Jo Yu
- Green and Sustainable Materials R&D Department, Research Institute of Clean Manufacturing System, Korea Institute of Industrial Technology (KITECH), Cheonan 31056, Korea; (I.S.J.); (Y.H.K.); (H.S.C.)
- Correspondence: (B.J.Y.); (M.I.K.); Tel.: +82-41-589-8456 (B.J.Y.); +82-31-750-8563 (M.I.K.)
| | - Moon Il Kim
- Department of BioNano Technology, Gachon University, 1342 Seongnamdae-ro, Sujeong-gu, Seongnam 13120, Korea; (H.T.A.); (T.V.D.); (D.H.L.)
- Correspondence: (B.J.Y.); (M.I.K.); Tel.: +82-41-589-8456 (B.J.Y.); +82-31-750-8563 (M.I.K.)
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5
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Jang YJ, Lee KH, Yoo TH, Kim DM. Complementary Cell-Free Translational Assay for Quantification of Amino Acids. Anal Chem 2017; 89:9638-9642. [PMID: 28776976 DOI: 10.1021/acs.analchem.7b01956] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In this study, we present a simple and economical method that enables rapid quantification of amino acids based on their polymerization into a signal-generating protein. This method harnesses amino acid-deficient cell-free protein synthesis systems that generate fluorescence signals in response to exogenous amino acids. When premixed with assay samples containing the amino acids in question, incubation of the cell-free synthesis reaction mixture rapidly resulted in the production of sfGFP, the fluorescence intensity of which was linearly proportional to the concentration of the amino acids. The assay method achieved a limit of detection as low as ∼100 nM and was successfully applied to the quantification of disease-related amino acids in biological samples. Compared with standard methods in current use that require chemical derivatization of amino acids and chromatographic equipment, the complementation assay method developed in this work enables the direct translation of amino acid titer into measurable biofluorescence intensity in a much shorter period, providing a more affordable and flexible option for the quantification of amino acids.
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Affiliation(s)
- Yeon-Jae Jang
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University , 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Kyung-Ho Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University , 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University , 206 Worldcup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University , 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
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6
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Translation-dependent bioassay for amino acid quantification using auxotrophic microbes as biocatalysts of protein synthesis. Appl Microbiol Biotechnol 2016; 101:2523-2531. [DOI: 10.1007/s00253-016-8027-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/20/2016] [Accepted: 11/23/2016] [Indexed: 10/20/2022]
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7
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Woo MA, Park JH, Cho D, Sim SJ, Kim MI, Park HG. A Whole-Cell Surface Plasmon Resonance Sensor Based on a Leucine Auxotroph of Escherichia coli Displaying a Gold-Binding Protein: Usefulness for Diagnosis of Maple Syrup Urine Disease. Anal Chem 2016; 88:2871-6. [DOI: 10.1021/acs.analchem.5b04648] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Min-Ah Woo
- Department
of Chemical and Biomolecular Engineering (BK21+ Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Food
Safety Research Group, Korea Food Research Institute, Baekhyun-dong, Bundang-gu,
Seongnam-si, Gyeonggi-do 463-746, Republic of Korea
| | - Jung Hun Park
- Department
of Chemical and Biomolecular Engineering (BK21+ Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Daeyeon Cho
- LabGenomics Co., Ltd., 1571-17 Seocho3-dong, Seocho-gu, Seoul 137-874, Republic of Korea
| | - Sang Jun Sim
- Department
of Chemical and Biological Engineering, Korea University, Anam-Dong
5-1, Seongbuk-Gu, Seoul 136-713, Republic of Korea
| | - Moon Il Kim
- Department
of BioNano Technology, Gachon University, 1342 Seongnamdae-ro, Sujeong-gu, Seongnam-si, Gyeonggi-do 461-701, Republic of Korea
| | - Hyun Gyu Park
- Department
of Chemical and Biomolecular Engineering (BK21+ Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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8
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Jung YL, Park JH, Kim MI, Park HG. Label-free colorimetric detection of biological thiols based on target-triggered inhibition of photoinduced formation of AuNPs. NANOTECHNOLOGY 2016; 27:055501. [PMID: 26671249 DOI: 10.1088/0957-4484/27/5/055501] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A label-free colorimetric method for the detection of biological thiols (biothiols) was developed. This method is based on prevention of the photoinduced reduction of auric ions (Au(III)) in the presence of amino acids (acting as a reducing agent) by biothiols; the photoinduced reduction is inhibited due to the strong interaction of the biothiols with Au(III). In this method, the sample was first incubated in an assay solution containing Au(III) and threonine; the sample solution was then exposed to 254 nm UV light. For samples without biothiols, this process led to the photoreduction of Au(III) followed by growth of gold nanoparticles accompanied by the visually detectable development of a red coloration typified by an absorption peak at ca 530 nm. Conversely, in the presence of biothiols, reduction of Au(III) to Au(0) was prevented by entrapment of Au(III) within the biothiols via the thiol group. The solution thus remained colorless even after UV irradiation, which was used as an indicator of the presence of biothiols. Using this strategy, biothiols were very conveniently analyzed by monitoring color changes of the samples with the naked eye or a UV-vis spectrometer. The strategy based on this interesting phenomenon exhibited high selectivity toward biothiols over common amino acids and was successfully employed for reliable quantification of biothiols present in human plasma, demonstrating its great potential for clinical applications.
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Affiliation(s)
- Ye Lim Jung
- Department of Chemical and Biomolecular Engineering (BK21+ Program), KAIST, Daejeon 305-701, Korea. Department of Business Opportunity Analysis, Technology Innovation Analysis Center, Korea Institute of Science and Technology Information (KISTI), Seoul 130-741, Korea
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9
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Recent Advances in Genetic Technique of Microbial Report Cells and Their Applications in Cell Arrays. BIOMED RESEARCH INTERNATIONAL 2015; 2015:182107. [PMID: 26436087 PMCID: PMC4576000 DOI: 10.1155/2015/182107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/26/2015] [Indexed: 11/21/2022]
Abstract
Microbial cell arrays have attracted consistent attention for their ability to provide unique global data on target analytes at low cost, their capacity for readily detectable and robust cell growth in diverse environments, their high degree of convenience, and their capacity for multiplexing via incorporation of molecularly tailored reporter cells. To highlight recent progress in the field of microbial cell arrays, this review discusses research on genetic engineering of reporter cells, technologies for patterning live cells on solid surfaces, cellular immobilization in different polymers, and studies on their application in environmental monitoring, disease diagnostics, and other related fields. On the basis of these results, we discuss current challenges and future prospects for novel microbial cell arrays, which show promise for use as potent tools for unraveling complex biological processes.
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10
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Liu W, Jiang R. Combinatorial and high-throughput screening approaches for strain engineering. Appl Microbiol Biotechnol 2015; 99:2093-104. [DOI: 10.1007/s00253-015-6400-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 01/09/2015] [Accepted: 01/10/2015] [Indexed: 12/31/2022]
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11
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Kim MI, Park TJ, Heo NS, Woo MA, Cho D, Lee SY, Park HG. Cell-based method utilizing fluorescent Escherichia coli auxotrophs for quantification of multiple amino acids. Anal Chem 2014; 86:2489-96. [PMID: 24475885 DOI: 10.1021/ac403429s] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A cell-based assay system for simultaneous quantification of the three amino acids, phenylalanine (Phe), methionine (Met), and leucine (Leu) in a single biological sample, was developed and applied in the multiplex diagnosis of three key metabolic diseases of newborn babies. The assay utilizes three Escherichia coli auxotrophs, which grow only in the presence of the corresponding target amino acids and which contain three different fluorescent reporter plasmids that produce distinguishable fluorescence signals (red, green, and cyan) in concert with cell growth. To mixtures of the three auxotrophs, immobilized on agarose gels arrayed on a well plate, is added a test sample. Following incubation, the concentrations of the three amino acids in the sample are simultaneously determined by measuring the intensities of three fluorescence signals that correspond to the reporter plasmids. The clinical utility of this assay system was demonstrated by employing it to identify metabolic diseases of newborn babies through the quantification of Phe, Met, and Leu in clinically derived dried blood spot specimens. The general strategy developed in this effort should be applicable to the design of new assay systems for the quantification of multiple amino acids derived from complex biological samples and, as such, to expand the utilization of cell-based analytical systems that replace conventional, yet laborious methods currently in use.
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Affiliation(s)
- Moon Il Kim
- Department of Chemical & Biomolecular Engineering (BK21+ Program), KAIST , 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
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12
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Woo MA, Kim MI, Cho D, Park HG. Cell-Based Galactosemia Diagnosis System Based on a Galactose Assay Using a Bioluminescent Escherichia coli Array. Anal Chem 2013; 85:11083-9. [DOI: 10.1021/ac4027912] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Min-Ah Woo
- Department
of Chemical and Biomolecular Engineering (BK21 Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
- Food Safety Research
Group, Korea Food Research Institute, Baekhyun-dong, Bundang-gu, Seongnam-si, Gyeonggi-do 463-746, Republic of Korea
| | - Moon Il Kim
- Department
of Chemical and Biomolecular Engineering (BK21 Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Daeyeon Cho
- LabGenomics Co., Ltd., 1571-17 Seocho3-dong, Seocho-gu, Seoul 137-874, Republic of Korea
| | - Hyun Gyu Park
- Department
of Chemical and Biomolecular Engineering (BK21 Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
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13
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Bertels F, Merker H, Kost C. Design and characterization of auxotrophy-based amino acid biosensors. PLoS One 2012; 7:e41349. [PMID: 22829942 PMCID: PMC3400592 DOI: 10.1371/journal.pone.0041349] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 06/20/2012] [Indexed: 01/20/2023] Open
Abstract
Efficient and inexpensive methods are required for the high-throughput quantification of amino acids in physiological fluids or microbial cell cultures. Here we develop an array of Escherichia coli biosensors to sensitively quantify eleven different amino acids. By using online databases, genes involved in amino acid biosynthesis were identified that - upon deletion - should render the corresponding mutant auxotrophic for one particular amino acid. This rational design strategy suggested genes involved in the biosynthesis of arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, threonine, tryptophan, and tyrosine as potential genetic targets. A detailed phenotypic characterization of the corresponding single-gene deletion mutants indeed confirmed that these strains could neither grow on a minimal medium lacking amino acids nor transform any other proteinogenic amino acid into the focal one. Site-specific integration of the egfp gene into the chromosome of each biosensor decreased the detection limit of the GFP-labeled cells by 30% relative to turbidometric measurements. Finally, using the biosensors to determine the amino acid concentration in the supernatants of two amino acid overproducing E. coli strains (i.e. ΔhisL and ΔtdcC) both turbidometrically and via GFP fluorescence emission and comparing the results to conventional HPLC measurements confirmed the utility of the developed biosensor system. Taken together, our study provides not only a genotypically and phenotypically well-characterized set of publicly available amino acid biosensors, but also demonstrates the feasibility of the rational design strategy used.
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Affiliation(s)
- Felix Bertels
- Research Group Experimental Ecology and Evolution, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Holger Merker
- Research Group Experimental Ecology and Evolution, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Christian Kost
- Research Group Experimental Ecology and Evolution, Max Planck Institute for Chemical Ecology, Jena, Germany
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14
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Woo MA, Kim MI, Yu BJ, Cho D, Kim NJ, Cho JH, Choi BO, Chang HN, Park HG. Cell-Based Quantification of Homocysteine Utilizing Bioluminescent Escherichia coli Auxotrophs. Anal Chem 2011; 83:3089-95. [DOI: 10.1021/ac103350y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Min-Ah Woo
- Department of Chemical and Biomolecular Engineering (BK21 Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Moon Il Kim
- Department of Chemical and Biomolecular Engineering (BK21 Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Byung Jo Yu
- MD Science Inc., 258-1 Munji-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Daeyeon Cho
- LabGenomics Co., Ltd., 1571-17 Seocho3-dong, Seocho-gu, Seoul 137-874, Republic of Korea
| | - Nag-Jong Kim
- Department of Chemical and Biomolecular Engineering (BK21 Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - June Hyoung Cho
- MD Science Inc., 258-1 Munji-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Byung-Ok Choi
- Department of Neurology, College of Medicine, Ewha Womans University, Mokdong Hospital, 911-1 Mokdong, Yangcheon-gu, Seoul 158-710, Republic of Korea
| | - Ho Nam Chang
- Department of Chemical and Biomolecular Engineering (BK21 Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21 Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
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15
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Tepper N, Shlomi T. Computational design of auxotrophy-dependent microbial biosensors for combinatorial metabolic engineering experiments. PLoS One 2011; 6:e16274. [PMID: 21283695 PMCID: PMC3025009 DOI: 10.1371/journal.pone.0016274] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2010] [Accepted: 12/13/2010] [Indexed: 12/18/2022] Open
Abstract
Combinatorial approaches in metabolic engineering work by generating genetic diversity in a microbial population followed by screening for strains with improved phenotypes. One of the most common goals in this field is the generation of a high rate chemical producing strain. A major hurdle with this approach is that many chemicals do not have easy to recognize attributes, making their screening expensive and time consuming. To address this problem, it was previously suggested to use microbial biosensors to facilitate the detection and quantification of chemicals of interest. Here, we present novel computational methods to: (i) rationally design microbial biosensors for chemicals of interest based on substrate auxotrophy that would enable their high-throughput screening; (ii) predict engineering strategies for coupling the synthesis of a chemical of interest with the production of a proxy metabolite for which high-throughput screening is possible via a designed bio-sensor. The biosensor design method is validated based on known genetic modifications in an array of E. coli strains auxotrophic to various amino-acids. Predicted chemical production rates achievable via the biosensor-based approach are shown to potentially improve upon those predicted by current rational strain design approaches. (A Matlab implementation of the biosensor design method is available via http://www.cs.technion.ac.il/~tomersh/tools).
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Affiliation(s)
- Naama Tepper
- Department of Computer Science, Technion-IIT, Haifa, Israel
- * E-mail: (NT); (TS)
| | - Tomer Shlomi
- Department of Computer Science, Technion-IIT, Haifa, Israel
- * E-mail: (NT); (TS)
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