1
|
Pham C, Stogios PJ, Savchenko A, Mahadevan R. Design and Characterization of a Generalist Biosensor for Indole Derivatives. ACS Synth Biol 2024; 13:2246-2252. [PMID: 38875315 DOI: 10.1021/acssynbio.3c00736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
Transcription factor (TF)-based biosensors are useful synthetic biology tools for applications in a variety of areas of biotechnology. A major challenge of biosensor circuits is the limited repertoire of identified and well-characterized TFs for applications of interest, in addition to the challenge of optimizing selected biosensors. In this work, we implement the IclR family repressor TF TtgV from Pseudomonas putida DOT-T1E as an indole-derivative biosensor in Escherichia coli. We optimize the genetic circuit utilizing different components, providing insights into biosensor design and expanding on previous studies investigating this TF. We discover novel physiologically relevant ligands of TtgV, such as skatole. The broad specificity of TtgV makes it a useful target for directed evolution and protein engineering toward desired specificity. TtgV, as an indole-derivative biosensor, is a promising genetic component for the detection of compounds with biological activities relevant to health and the gut microbiome.
Collapse
Affiliation(s)
- Chester Pham
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3H7, Canada
- The Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3H7, Canada
| |
Collapse
|
2
|
Pham C, Nasr MA, Skarina T, Di Leo R, Kwan DH, Martin VJJ, Stogios PJ, Mahadevan R, Savchenko A. Functional and structural characterization of an IclR family transcription factor for the development of dicarboxylic acid biosensors. FEBS J 2024. [PMID: 38696354 DOI: 10.1111/febs.17149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/15/2024] [Accepted: 04/17/2024] [Indexed: 05/04/2024]
Abstract
Prokaryotic transcription factors (TFs) regulate gene expression in response to small molecules, thus representing promising candidates as versatile small molecule-detecting biosensors valuable for synthetic biology applications. The engineering of such biosensors requires thorough in vitro and in vivo characterization of TF ligand response as well as detailed molecular structure information. In this work, we functionally and structurally characterize the Pca regulon regulatory protein (PcaR) transcription factor belonging to the IclR transcription factor family. Here, we present in vitro functional analysis of the ligand profile of PcaR and the construction of genetic circuits for the characterization of PcaR as an in vivo biosensor in the model eukaryote Saccharomyces cerevisiae. We report the crystal structures of PcaR in the apo state and in complex with one of its ligands, succinate, which suggests the mechanism of dicarboxylic acid recognition by this transcription factor. This work contributes key structural and functional insights enabling the engineering of PcaR for dicarboxylic acid biosensors, in addition to providing more insights into the IclR family of regulators.
Collapse
Affiliation(s)
- Chester Pham
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Mohamed A Nasr
- Centre for Applied Synthetic Biology, Concordia University, Montreal, Canada
- Department of Biology, Concordia University, Montreal, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Rosa Di Leo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - David H Kwan
- Centre for Applied Synthetic Biology, Concordia University, Montreal, Canada
- Department of Biology, Concordia University, Montreal, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Canada
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Canada
| | - Vincent J J Martin
- Centre for Applied Synthetic Biology, Concordia University, Montreal, Canada
- Department of Biology, Concordia University, Montreal, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
- The Institute of Biomedical Engineering, University of Toronto, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Canada
| |
Collapse
|
3
|
Emelianov G, Song DU, Jang N, Ko M, Kim SK, Rha E, Shin J, Kwon KK, Kim H, Lee DH, Lee H, Lee SG. Engineered Methylococcus capsulatus Bath for efficient methane conversion to isoprene. BIORESOURCE TECHNOLOGY 2024; 393:130098. [PMID: 38040299 DOI: 10.1016/j.biortech.2023.130098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023]
Abstract
Isoprene has numerous industrial applications, including rubber polymer and potential biofuel. Microbial methane-based isoprene production could be a cost-effective and environmentally benign process, owing to a reduced carbon footprint and economical utilization of methane. In this study, Methylococcus capsulatus Bath was engineered to produce isoprene from methane by introducing the exogenous mevalonate (MVA) pathway. Overexpression of MVA pathway enzymes and isoprene synthase from Populus trichocarpa under the control of a phenol-inducible promoter substantially improved isoprene production. M. capsulatus Bath was further engineered using a CRISPR-base editor to disrupt the expression of soluble methane monooxygenase (sMMO), which oxidizes isoprene to cause toxicity. Additionally, optimization of the metabolic flux in the MVA pathway and culture conditions increased isoprene production to 228.1 mg/L, the highest known titer for methanotroph-based isoprene production. The developed methanotroph could facilitate the efficient conversion of methane to isoprene, resulting in the sustainable production of value-added chemicals.
Collapse
Affiliation(s)
- Georgii Emelianov
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea.
| | - Dong-Uk Song
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Graduate School of Engineering Biology, Korea Advanced Institute of Science & Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Nulee Jang
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.
| | - Minji Ko
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea.
| | - Seong Keun Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.
| | - Eugene Rha
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.
| | - Jonghyeok Shin
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.
| | - Kil Koang Kwon
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea.
| | - Haseong Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea; Graduate School of Engineering Biology, Korea Advanced Institute of Science & Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Dae-Hee Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea; Graduate School of Engineering Biology, Korea Advanced Institute of Science & Technology (KAIST), Daejeon 34141, Republic of Korea; Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon-si, Gyeonggi-do 16419, Republic of Korea.
| | - Hyewon Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea.
| | - Seung-Goo Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea; Graduate School of Engineering Biology, Korea Advanced Institute of Science & Technology (KAIST), Daejeon 34141, Republic of Korea.
| |
Collapse
|
4
|
Hwang HG, Ye DY, Jung GY. Biosensor-guided discovery and engineering of metabolic enzymes. Biotechnol Adv 2023; 69:108251. [PMID: 37690614 DOI: 10.1016/j.biotechadv.2023.108251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Abstract
A variety of chemicals have been produced through metabolic engineering approaches, and enhancing biosynthesis performance can be achieved by using enzymes with high catalytic efficiency. Accordingly, a number of efforts have been made to discover enzymes in nature for various applications. In addition, enzyme engineering approaches have been attempted to suit specific industrial purposes. However, a significant challenge in enzyme discovery and engineering is the efficient screening of enzymes with the desired phenotype from extensive enzyme libraries. To overcome this bottleneck, genetically encoded biosensors have been developed to specifically detect target molecules produced by enzyme activity at the intracellular level. Especially, the biosensors facilitate high-throughput screening (HTS) of targeted enzymes, expanding enzyme discovery and engineering strategies with advances in systems and synthetic biology. This review examines biosensor-guided HTS systems and highlights studies that have utilized these tools to discover enzymes in diverse areas and engineer enzymes to enhance their properties, such as catalytic efficiency, specificity, and stability.
Collapse
Affiliation(s)
- Hyun Gyu Hwang
- Institute of Environmental and Energy Technology, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea.
| |
Collapse
|
5
|
Jiang J, Yang G, Ma F. Fluorescence coupling strategies in fluorescence-activated droplet sorting (FADS) for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Biotechnol Adv 2023; 66:108173. [PMID: 37169102 DOI: 10.1016/j.biotechadv.2023.108173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/17/2023] [Accepted: 05/06/2023] [Indexed: 05/13/2023]
Abstract
Fluorescence-activated droplet sorting (FADS) has emerged as a powerful tool for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Fluorescence coupling strategies (FCSs) are key to the development of new FADS methods through their coupling of analyte properties such as concentration, activities, and affinity with fluorescence signals. Over the last decade, a series of FCSs have been developed, greatly expanding applications of FADS. Here, we review recent advances in FCS for different analyte types, providing a critical comparison of the available FCSs and further classification into four categories according to their principles. We also summarize successful FADS applications employing FCSs in enzymes, metabolites, and antibodies. Further, we outline possible future developments in this area.
Collapse
Affiliation(s)
- Jingjie Jiang
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Guangyu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Fuqiang Ma
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.
| |
Collapse
|
6
|
Hwangbo M, Shao Y, Hatzinger PB, Chu KH. Acidophilic methanotrophs: Occurrence, diversity, and possible bioremediation applications. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023. [PMID: 37041665 DOI: 10.1111/1758-2229.13156] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
Methanotrophs have been identified and isolated from acidic environments such as wetlands, acidic soils, peat bogs, and groundwater aquifers. Due to their methane (CH4 ) utilization as a carbon and energy source, acidophilic methanotrophs are important in controlling the release of atmospheric CH4 , an important greenhouse gas, from acidic wetlands and other environments. Methanotrophs have also played an important role in the biodegradation and bioremediation of a variety of pollutants including chlorinated volatile organic compounds (CVOCs) using CH4 monooxygenases via a process known as cometabolism. Under neutral pH conditions, anaerobic bioremediation via carbon source addition is a commonly used and highly effective approach to treat CVOCs in groundwater. However, complete dechlorination of CVOCs is typically inhibited at low pH. Acidophilic methanotrophs have recently been observed to degrade a range of CVOCs at pH < 5.5, suggesting that cometabolic treatment may be an option for CVOCs and other contaminants in acidic aquifers. This paper provides an overview of the occurrence, diversity, and physiological activities of methanotrophs in acidic environments and highlights the potential application of these organisms for enhancing contaminant biodegradation and bioremediation.
Collapse
Affiliation(s)
- Myung Hwangbo
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, Texas, USA
| | - Yiru Shao
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, Texas, USA
| | - Paul B Hatzinger
- Aptim Federal Services, LLC, 17 Princess Road, Lawrenceville, New Jersey, USA
| | - Kung-Hui Chu
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, Texas, USA
| |
Collapse
|
7
|
Research progress on the degradation mechanism and modification of keratinase. Appl Microbiol Biotechnol 2023; 107:1003-1017. [PMID: 36633625 DOI: 10.1007/s00253-023-12360-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/23/2022] [Accepted: 12/31/2022] [Indexed: 01/13/2023]
Abstract
Keratin is regarded as the main component of feathers and is difficult to be degraded by conventional proteases, leading to substantial abandonment. Keratinase is the only enzyme with the most formidable potential for degrading feathers. Although there have been in-depth studies in recent years, the large-scale application of keratinase is still associated with many problems. It is relatively challenging to find keratinase not only with high activity but could also meet the industrial application environment, so it is urgent to exploit keratinase with high acid and temperature resistance, strong activity, and low price. Therefore, researchers have been keen to explore the degradation mechanism of keratinases and the modification of existing keratinases for decades. This review critically introduces the basic properties and mechanism of keratinase, and focuses on the current situation of keratinase modification and the direction and strategy of its future application and modification. KEY POINTS: •The research status and mechanism of keratinase were reviewed. •The new direction of keratinase application and modification is discussed. •The existing modification methods and future modification strategies of keratinases are reviewed.
Collapse
|
8
|
Recent Progress in the Development of Droplet-based Microfluidic Technologies for Phenotypic Screening using Cell-cell Interactions. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0081-1] [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]
|
9
|
Woo SG, Kim SK, Oh BR, Lee SG, Lee DH. Genetically Encoded Biosensor-Based Screening for Directed Bacteriophage T4 Lysozyme Evolution. Int J Mol Sci 2020; 21:ijms21228668. [PMID: 33212940 PMCID: PMC7698408 DOI: 10.3390/ijms21228668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/05/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022] Open
Abstract
Lysozyme is widely used as a model protein in studies of structure–function relationships. Recently, lysozyme has gained attention for use in accelerating the degradation of secondary sludge, which mainly consists of bacteria. However, a high-throughput screening system for lysozyme engineering has not been reported. Here, we present a lysozyme screening system using a genetically encoded biosensor. We first cloned bacteriophage T4 lysozyme (T4L) into a plasmid under control of the araBAD promoter. The plasmid was expressed in Escherichia coli with no toxic effects on growth. Next, we observed that increased soluble T4L expression decreased the fluorescence produced by the genetic enzyme screening system. To investigate T4L evolution based on this finding, we generated a T4L random mutation library, which was screened using the genetic enzyme screening system. Finally, we identified two T4L variants showing 1.4-fold enhanced lytic activity compared to native T4L. To our knowledge, this is the first report describing the use of a genetically encoded biosensor to investigate bacteriophage T4L evolution. Our approach can be used to investigate the evolution of other lysozymes, which will expand the applications of lysozyme.
Collapse
Affiliation(s)
- Seung-Gyun Woo
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (S.-G.W.); (S.K.K.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Seong Keun Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (S.-G.W.); (S.K.K.)
| | - Baek-Rock Oh
- Microbial Biotechnology Research Center, Jeonbuk Branch Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 56212, Korea;
| | - Seung-Goo Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (S.-G.W.); (S.K.K.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Korea
- Correspondence: (S.-G.L.); (D.-H.L.); Tel.: +82-42-860-4373 (S.-G.L.); +82-42-879-8225 (D.-H.L.)
| | - Dae-Hee Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (S.-G.W.); (S.K.K.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Korea
- Correspondence: (S.-G.L.); (D.-H.L.); Tel.: +82-42-860-4373 (S.-G.L.); +82-42-879-8225 (D.-H.L.)
| |
Collapse
|