1
|
Choi G, Kim W, Koo J. Investigating the Performance of Machine Learning Methods in Predicting Functional Properties of the Hydrogenase Variants. BIOTECHNOL BIOPROC E 2023. [DOI: 10.1007/s12257-022-0330-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
|
2
|
Shao F, Lee PW, Li H, Hsieh K, Wang TH. Emerging platforms for high-throughput enzymatic bioassays. Trends Biotechnol 2023; 41:120-133. [PMID: 35863950 PMCID: PMC9789168 DOI: 10.1016/j.tibtech.2022.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/19/2022] [Accepted: 06/14/2022] [Indexed: 12/27/2022]
Abstract
Enzymes have essential roles in catalyzing biological reactions and maintaining metabolic systems. Many in vitro enzymatic bioassays have been developed for use in industrial and research fields, such as cell biology, enzyme engineering, drug screening, and biofuel production. Of note, many of these require the use of high-throughput platforms. Although the microtiter plate remains the standard for high-throughput enzymatic bioassays, microfluidic arrays and droplet microfluidics represent emerging methods. Each has seen significant advances and offers distinct advantages; however, drawbacks in key performance metrics, including reagent consumption, reaction manipulation, reaction recovery, real-time measurement, concentration gradient range, and multiplexity, remain. Herein, we compare recent high-throughput platforms using the aforementioned metrics as criteria and provide insights into remaining challenges and future research trends.
Collapse
Affiliation(s)
- Fangchi Shao
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Pei-Wei Lee
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Hui Li
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA.
| |
Collapse
|
3
|
Koo J. Cell-Free Protein Synthesis of Metalloproteins. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 185:47-58. [PMID: 37561181 DOI: 10.1007/10_2023_233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Metalloproteins, proteins containing metal atoms or clusters within their structures, are critical for various biological functions across all domains of life. More than hundreds of different types have been discovered, which conduct various roles such as transportation of O2, catalyzing chemical reactions, sensing environmental changes, and relaying electrons. Metalloprotein molecules incorporate a variety of metal atoms, coordinated to specific amino acid residues that affect their conformation and functionality. The process of metal incorporation typically occurs during or post-protein folding, often requiring chaperones for metal ion delivery and quality control. Progress in understanding metal incorporation and metalloprotein functionality has been enhanced by cell-free protein synthesis (CFPS) methods that offer direct control over the synthesis environment. This chapter reviews the diverse applications of CFPS methods in metalloprotein research, encompassing structure-function studies, protein engineering, and creation of artificial metalloproteins. Examples demonstrating the utility and advances brought about by CFPS in synthetic biology, electrochemistry, and drug discovery are highlighted. Despite remarkable progress, challenges remain in optimizing and advancing the CFPS methods, underscoring the need for future explorations in this transformative approach to metalloprotein study and engineering.
Collapse
Affiliation(s)
- Jamin Koo
- Department of Chemical Engineering, Hongik University, Seoul, Republic of Korea.
| |
Collapse
|
4
|
King SJ, Jerkovic A, Brown LJ, Petroll K, Willows RD. Synthetic biology for improved hydrogen production in Chlamydomonas reinhardtii. Microb Biotechnol 2022; 15:1946-1965. [PMID: 35338590 PMCID: PMC9249334 DOI: 10.1111/1751-7915.14024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 12/04/2022] Open
Abstract
Hydrogen is a clean alternative to fossil fuels. It has applications for electricity generation and transportation and is used for the manufacturing of ammonia and steel. However, today, H2 is almost exclusively produced from coal and natural gas. As such, methods to produce H2 that do not use fossil fuels need to be developed and adopted. The biological manufacturing of H2 may be one promising solution as this process is clean and renewable. Hydrogen is produced biologically via enzymes called hydrogenases. There are three classes of hydrogenases namely [FeFe], [NiFe] and [Fe] hydrogenases. The [FeFe] hydrogenase HydA1 from the model unicellular algae Chlamydomonas reinhardtii has been studied extensively and belongs to the A1 subclass of [FeFe] hydrogenases that have the highest turnover frequencies amongst hydrogenases (21,000 ± 12,000 H2 s−1 for CaHydA from Clostridium acetobutyliticum). Yet to date, limitations in C. reinhardtii H2 production pathways have hampered commercial scale implementation, in part due to O2 sensitivity of hydrogenases and competing metabolic pathways, resulting in low H2 production efficiency. Here, we describe key processes in the biogenesis of HydA1 and H2 production pathways in C. reinhardtii. We also summarize recent advancements of algal H2 production using synthetic biology and describe valuable tools such as high‐throughput screening (HTS) assays to accelerate the process of engineering algae for commercial biological H2 production.
Collapse
Affiliation(s)
- Samuel J King
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ante Jerkovic
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Louise J Brown
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Kerstin Petroll
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Robert D Willows
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| |
Collapse
|
5
|
Dudley QM, Cai YM, Kallam K, Debreyne H, Carrasco Lopez JA, Patron NJ. Biofoundry-assisted expression and characterization of plant proteins. Synth Biol (Oxf) 2021; 6:ysab029. [PMID: 34693026 PMCID: PMC8529701 DOI: 10.1093/synbio/ysab029] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/25/2021] [Accepted: 09/09/2021] [Indexed: 12/29/2022] Open
Abstract
Many goals in synthetic biology, including the elucidation and refactoring of biosynthetic pathways and the engineering of regulatory circuits and networks, require knowledge of protein function. In plants, the prevalence of large gene families means it can be particularly challenging to link specific functions to individual proteins. However, protein characterization has remained a technical bottleneck, often requiring significant effort to optimize expression and purification protocols. To leverage the ability of biofoundries to accelerate design-built-test-learn cycles, we present a workflow for automated DNA assembly and cell-free expression of plant proteins that accelerates optimization and enables rapid screening of enzyme activity. First, we developed a phytobrick-compatible Golden Gate DNA assembly toolbox containing plasmid acceptors for cell-free expression using Escherichia coli or wheat germ lysates as well as a set of N- and C-terminal tag parts for detection, purification and improved expression/folding. We next optimized automated assembly of miniaturized cell-free reactions using an acoustic liquid handling platform and then compared tag configurations to identify those that increase expression. We additionally developed a luciferase-based system for rapid quantification that requires a minimal 11-amino acid tag and demonstrate facile removal of tags following synthesis. Finally, we show that several functional assays can be performed with cell-free protein synthesis reactions without the need for protein purification. Together, the combination of automated assembly of DNA parts and cell-free expression reactions should significantly increase the throughput of experiments to test and understand plant protein function and enable the direct reuse of DNA parts in downstream plant engineering workflows.
Collapse
Affiliation(s)
- Quentin M Dudley
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk UK
| | - Yao-Min Cai
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk UK
| | - Kalyani Kallam
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk UK
| | - Hubert Debreyne
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk UK
| | | | - Nicola J Patron
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk UK
| |
Collapse
|
6
|
Koo J, Yang J, Park H. Cell-free Systems: Recent Advances and Future Outlook. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0013-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
7
|
Swartz J. Opportunities toward hydrogen production biotechnologies. Curr Opin Biotechnol 2020; 62:248-255. [PMID: 32278260 DOI: 10.1016/j.copbio.2020.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 01/08/2023]
Abstract
Hydrogen is already a major commodity and process intermediate for fertilizer production, petroleum processing, and chemical synthesis. It also offers unrealized potential for energy storage. While biological production offers an expandable and sustainable source, enthusiasm has been dampened by slow research progress. Also, the very low cost of natural gas (the major current hydrogen source) imposes severe economic challenges. This discussion describes process, metabolic, and protein engineering opportunities toward cost-effective biohydrogen production. Recent progress in hydrogenase engineering and photosynthetic bacterial research now suggests a favorable risk versus reward opportunity. Although the risks are still significant, successful technologies would provide important components in an integrated energy portfolio that enables global sustainability.
Collapse
Affiliation(s)
- James Swartz
- Dept. of Chemical Engineering, Dept. of Bioengineering Stanford University, United States.
| |
Collapse
|
8
|
Lu Y, Koo J. O 2 sensitivity and H 2 production activity of hydrogenases-A review. Biotechnol Bioeng 2019; 116:3124-3135. [PMID: 31403182 DOI: 10.1002/bit.27136] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/23/2019] [Accepted: 08/05/2019] [Indexed: 01/24/2023]
Abstract
Hydrogenases are metalloproteins capable of catalyzing the interconversion between molecular hydrogen and protons and electrons. The iron-sulfur clusters within the enzyme enable rapid relay of electrons which are either consumed or generated at the active site. Their unparalleled catalytic efficiency has attracted attention, especially for potential use in H2 production and/or fuel cell technologies. However, there are limitations to using hydrogenases, especially due to their high O2 sensitivity. The subclass, called [FeFe] hydrogenases, are particularly more vulnerable to O2 but proficient in H2 production. In this review, we provide an overview of mechanistic and protein engineering studies focused on understanding and enhancing O2 tolerance of the enzyme. The emphasis is on ongoing studies that attempt to overcome O2 sensitivity of the enzyme while it catalyzes H2 production in an aerobic environment. We also discuss pioneering attempts to utilize the enzyme in biological H2 production and other industrial processes, as well as our own perspective on future applications.
Collapse
Affiliation(s)
- Yuan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Jamin Koo
- Department of Chemical Engineering, Hongik University, Seoul, Republic of Korea
| |
Collapse
|
9
|
Zhou Y, Wei W, Su H, Wang W. Sensitively fluorescent detection of H2 with resazurin hydrogenation reactions catalyzed by Pd/C nanocomposites. INORG CHEM COMMUN 2019. [DOI: 10.1016/j.inoche.2019.05.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
10
|
Ni J, Liu H, Tao F, Wu Y, Xu P. Remodeling of the Photosynthetic Chain Promotes Direct CO
2
Conversion into Valuable Aromatic Compounds. Angew Chem Int Ed Engl 2018; 57:15990-15994. [DOI: 10.1002/anie.201808402] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 09/24/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Jun Ni
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Hong‐Yu Liu
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Fei Tao
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Yu‐Tong Wu
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Ping Xu
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| |
Collapse
|
11
|
Ni J, Liu H, Tao F, Wu Y, Xu P. Remodeling of the Photosynthetic Chain Promotes Direct CO2Conversion into Valuable Aromatic Compounds. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jun Ni
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Hong‐Yu Liu
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Fei Tao
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Yu‐Tong Wu
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Ping Xu
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| |
Collapse
|
12
|
Bucci A, Dunn S, Bellachioma G, Menendez Rodriguez G, Zuccaccia C, Nervi C, Macchioni A. A Single Organoiridium Complex Generating Highly Active Catalysts for both Water Oxidation and NAD+/NADH Transformations. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02387] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alberto Bucci
- Department
of Chemistry, Biology and Biotechnology, University of Perugia and CIRCC, Via Elce di Sotto, 8, I-06123 Perugia, Italy
| | - Savannah Dunn
- Department
of Chemistry, Longwood University, 201 High Street, Farmville, Virginia 23901, United States
| | - Gianfranco Bellachioma
- Department
of Chemistry, Biology and Biotechnology, University of Perugia and CIRCC, Via Elce di Sotto, 8, I-06123 Perugia, Italy
| | - Gabriel Menendez Rodriguez
- Department
of Chemistry, Biology and Biotechnology, University of Perugia and CIRCC, Via Elce di Sotto, 8, I-06123 Perugia, Italy
| | - Cristiano Zuccaccia
- Department
of Chemistry, Biology and Biotechnology, University of Perugia and CIRCC, Via Elce di Sotto, 8, I-06123 Perugia, Italy
| | - Carlo Nervi
- Department
of Chemistry, University of Torino, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Alceo Macchioni
- Department
of Chemistry, Biology and Biotechnology, University of Perugia and CIRCC, Via Elce di Sotto, 8, I-06123 Perugia, Italy
- Department
of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg
2, CH-8093 Zürich, Switzerland
| |
Collapse
|