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Zarabadi MP, Couture M, Charette SJ, Greener J. A Generalized Kinetic Framework Applied to Whole‐Cell Bioelectrocatalysis in Bioflow Reactors Clarifies Performance Enhancements for
Geobacter Sulfurreducens
Biofilms. ChemElectroChem 2019. [DOI: 10.1002/celc.201900732] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Mir Pouyan Zarabadi
- Département de Chimie, Faculté des sciences et de génieUniversité Laval, Québec City, QC Canada
| | - Manon Couture
- Institut de Biologie Intégrative et des Systèmes, Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génieUniversité Laval Québec City, QC Canada
| | - Steve J. Charette
- Institut de Biologie Intégrative et des Systèmes, Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génieUniversité Laval Québec City, QC Canada
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec Québec City, QC Canada
| | - Jesse Greener
- Département de Chimie, Faculté des sciences et de génieUniversité Laval, Québec City, QC Canada
- CHU de Québec, centre de rechercheUniversité Laval, 10 rue de l'Espinay Québec, QC Canada
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2
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Vanacek P, Sebestova E, Babkova P, Bidmanova S, Daniel L, Dvorak P, Stepankova V, Chaloupkova R, Brezovsky J, Prokop Z, Damborsky J. Exploration of Enzyme Diversity by Integrating Bioinformatics with Expression Analysis and Biochemical Characterization. ACS Catal 2018. [DOI: 10.1021/acscatal.7b03523] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Pavel Vanacek
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Eva Sebestova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Petra Babkova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Sarka Bidmanova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Lukas Daniel
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Pavel Dvorak
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Veronika Stepankova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Enantis
Ltd., Biotechnology Incubator INBIT, Kamenice 34, 625 00 Brno, Czech Republic
| | - Radka Chaloupkova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Enantis
Ltd., Biotechnology Incubator INBIT, Kamenice 34, 625 00 Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Enantis
Ltd., Biotechnology Incubator INBIT, Kamenice 34, 625 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
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3
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Hossain GS, Nadarajan SP, Zhang L, Ng TK, Foo JL, Ling H, Choi WJ, Chang MW. Rewriting the Metabolic Blueprint: Advances in Pathway Diversification in Microorganisms. Front Microbiol 2018; 9:155. [PMID: 29483901 PMCID: PMC5816047 DOI: 10.3389/fmicb.2018.00155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/23/2018] [Indexed: 11/13/2022] Open
Abstract
Living organisms have evolved over millions of years to fine tune their metabolism to create efficient pathways for producing metabolites necessary for their survival. Advancement in the field of synthetic biology has enabled the exploitation of these metabolic pathways for the production of desired compounds by creating microbial cell factories through metabolic engineering, thus providing sustainable routes to obtain value-added chemicals. Following the past success in metabolic engineering, there is increasing interest in diversifying natural metabolic pathways to construct non-natural biosynthesis routes, thereby creating possibilities for producing novel valuable compounds that are non-natural or without elucidated biosynthesis pathways. Thus, the range of chemicals that can be produced by biological systems can be expanded to meet the demands of industries for compounds such as plastic precursors and new antibiotics, most of which can only be obtained through chemical synthesis currently. Herein, we review and discuss novel strategies that have been developed to rewrite natural metabolic blueprints in a bid to broaden the chemical repertoire achievable in microorganisms. This review aims to provide insights on recent approaches taken to open new avenues for achieving biochemical production that are beyond currently available inventions.
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Affiliation(s)
- Gazi Sakir Hossain
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Saravanan Prabhu Nadarajan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Lei Zhang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Tee-Kheang Ng
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Hua Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Won Jae Choi
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Agency for Science, Technology and Research (ASTAR), Institute of Chemical and Engineering Sciences, Singapore, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
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4
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Gerlt JA. Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence-Function Space and Genome Context to Discover Novel Functions. Biochemistry 2017; 56:4293-4308. [PMID: 28826221 PMCID: PMC5569362 DOI: 10.1021/acs.biochem.7b00614] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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The exponentially increasing number
of protein and nucleic acid
sequences provides opportunities to discover novel enzymes, metabolic
pathways, and metabolites/natural products, thereby adding to our
knowledge of biochemistry and biology. The challenge has evolved from
generating sequence information to mining the databases to integrating
and leveraging the available information, i.e., the availability of
“genomic enzymology” web tools. Web tools that allow
identification of biosynthetic gene clusters are widely used by the
natural products/synthetic biology community, thereby facilitating
the discovery of novel natural products and the enzymes responsible
for their biosynthesis. However, many novel enzymes with interesting
mechanisms participate in uncharacterized small-molecule metabolic
pathways; their discovery and functional characterization also can
be accomplished by leveraging information in protein and nucleic acid
databases. This Perspective focuses on two genomic enzymology web
tools that assist the discovery novel metabolic pathways: (1) Enzyme
Function Initiative-Enzyme Similarity Tool (EFI-EST) for generating
sequence similarity networks to visualize and analyze sequence–function
space in protein families and (2) Enzyme Function Initiative-Genome
Neighborhood Tool (EFI-GNT) for generating genome neighborhood networks
to visualize and analyze the genome context in microbial and fungal
genomes. Both tools have been adapted to other applications to facilitate
target selection for enzyme discovery and functional characterization.
As the natural products community has demonstrated, the enzymology
community needs to embrace the essential role of web tools that allow
the protein and genome sequence databases to be leveraged for novel
insights into enzymological problems.
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Affiliation(s)
- John A Gerlt
- Departments of Biochemistry and Chemistry, Institute for Genomic Biology, University of Illinois , Urbana-Champaign Urbana, Illinois 61801, United States
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5
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Carter CW, Chandrasekaran SN, Weinreb V, Li L, Williams T. Combining multi-mutant and modular thermodynamic cycles to measure energetic coupling networks in enzyme catalysis. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:032101. [PMID: 28191480 PMCID: PMC5272822 DOI: 10.1063/1.4974218] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 12/21/2016] [Indexed: 06/06/2023]
Abstract
We measured and cross-validated the energetics of networks in Bacillus stearothermophilus Tryptophanyl-tRNA synthetase (TrpRS) using both multi-mutant and modular thermodynamic cycles. Multi-dimensional combinatorial mutagenesis showed that four side chains from this "molecular switch" move coordinately with the active-site Mg2+ ion as the active site preorganizes to stabilize the transition state for amino acid activation. A modular thermodynamic cycle consisting of full-length TrpRS, its Urzyme, and the Urzyme plus each of the two domains deleted in the Urzyme gives similar energetics. These dynamic linkages, although unlikely to stabilize the transition-state directly, consign the active-site preorganization to domain motion, assuring coupled vectorial behavior.
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Affiliation(s)
- Charles W Carter
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7260, USA
| | - Srinivas Niranj Chandrasekaran
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7260, USA
| | - Violetta Weinreb
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7260, USA
| | - Li Li
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7260, USA
| | - Tishan Williams
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7260, USA
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Agarwal V, Miles ZD, Winter JM, Eustáquio AS, El Gamal AA, Moore BS. Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse. Chem Rev 2017; 117:5619-5674. [PMID: 28106994 PMCID: PMC5575885 DOI: 10.1021/acs.chemrev.6b00571] [Citation(s) in RCA: 248] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Naturally produced halogenated compounds are ubiquitous across all domains of life where they perform a multitude of biological functions and adopt a diversity of chemical structures. Accordingly, a diverse collection of enzyme catalysts to install and remove halogens from organic scaffolds has evolved in nature. Accounting for the different chemical properties of the four halogen atoms (fluorine, chlorine, bromine, and iodine) and the diversity and chemical reactivity of their organic substrates, enzymes performing biosynthetic and degradative halogenation chemistry utilize numerous mechanistic strategies involving oxidation, reduction, and substitution. Biosynthetic halogenation reactions range from simple aromatic substitutions to stereoselective C-H functionalizations on remote carbon centers and can initiate the formation of simple to complex ring structures. Dehalogenating enzymes, on the other hand, are best known for removing halogen atoms from man-made organohalogens, yet also function naturally, albeit rarely, in metabolic pathways. This review details the scope and mechanism of nature's halogenation and dehalogenation enzymatic strategies, highlights gaps in our understanding, and posits where new advances in the field might arise in the near future.
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Affiliation(s)
- Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Zachary D. Miles
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
| | | | - Alessandra S. Eustáquio
- College of Pharmacy, Department of Medicinal Chemistry & Pharmacognosy and Center for Biomolecular Sciences, University of Illinois at Chicago
| | - Abrahim A. El Gamal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Bradley S. Moore
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
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8
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Trautman EP, Crawford JM. Linking Biosynthetic Gene Clusters to their Metabolites via Pathway- Targeted Molecular Networking. Curr Top Med Chem 2016; 16:1705-16. [PMID: 26456470 PMCID: PMC5055756 DOI: 10.2174/1568026616666151012111046] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/25/2015] [Accepted: 09/08/2015] [Indexed: 12/16/2022]
Abstract
The connection of microbial biosynthetic gene clusters to the small molecule metabolites they encode is central to the discovery and characterization of new metabolic pathways with ecological and pharmacological potential. With increasing microbial genome sequence information being deposited into publicly available databases, it is clear that microbes have the coding capacity for many more biologically active small molecules than previously realized. Of increasing interest are the small molecules encoded by the human microbiome, as these metabolites likely mediate a variety of currently uncharacterized human-microbe interactions that influence health and disease. In this mini-review, we describe the ongoing biosynthetic, structural, and functional characterizations of the genotoxic colibactin pathway in gut bacteria as a thematic example of linking biosynthetic gene clusters to their metabolites. We also highlight other natural products that are produced through analogous biosynthetic logic and comment on some current disconnects between bioinformatics predictions and experimental structural characterizations. Lastly, we describe the use of pathway-targeted molecular networking as a tool to characterize secondary metabolic pathways within complex metabolomes and to aid in downstream metabolite structural elucidation efforts.
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Affiliation(s)
| | - Jason M Crawford
- Department of Chemistry, Faculty of Yale University, P.O. Box: 27392, West Haven, CT, 06516, USA.
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10
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Zhang R, Wong K. High performance enzyme kinetics of turnover, activation and inhibition for translational drug discovery. Expert Opin Drug Discov 2016; 12:17-37. [PMID: 27784173 DOI: 10.1080/17460441.2017.1245721] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Enzymes are the macromolecular catalysts of many living processes and represent a sizable proportion of all druggable biological targets. Enzymology has been practiced just over a century during which much progress has been made in both the identification of new enzymes and the development of novel methodologies for enzyme kinetics. Areas covered: This review aims to address several key practical aspects in enzyme kinetics in reference to translational drug discovery research. The authors first define what constitutes a high performance enzyme kinetic assay. The authors then review the best practices for turnover, activation and inhibition kinetics to derive critical parameters guiding drug discovery. Notably, the authors recommend global progress curve analysis of dose/time dependence employing an integrated Michaelis-Menten equation and global curve fitting of dose/dose dependence. Expert opinion: The authors believe that in vivo enzyme and substrate abundance and their dynamics, binding modality, drug binding kinetics and enzyme's position in metabolic networks should be assessed to gauge the translational impact on drug efficacy and safety. Integrating these factors in a systems biology and systems pharmacology model should facilitate translational drug discovery.
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Affiliation(s)
- Rumin Zhang
- a Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc. , Kenilworth , NJ , USA
| | - Kenny Wong
- a Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc. , Kenilworth , NJ , USA
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11
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Sigala PA, Morante K, Tsumoto K, Caaveiro JMM, Goldberg DE. In-Cell Enzymology To Probe His-Heme Ligation in Heme Oxygenase Catalysis. Biochemistry 2016; 55:4836-49. [PMID: 27490825 DOI: 10.1021/acs.biochem.6b00562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Heme oxygenase (HO) is a ubiquitous enzyme with key roles in inflammation, cell signaling, heme disposal, and iron acquisition. HO catalyzes the oxidative conversion of heme to biliverdin (BV) using a conserved histidine to coordinate the iron atom of bound heme. This His-heme interaction has been regarded as being essential for enzyme activity, because His-to-Ala mutants fail to convert heme to biliverdin in vitro. We probed a panel of proximal His mutants of cyanobacterial, human, and plant HO enzymes using a live-cell activity assay based on heterologous co-expression in Escherichia coli of each HO mutant and a fluorescent biliverdin biosensor. In contrast to in vitro studies with purified proteins, we observed that multiple HO mutants retained significant activity within the intracellular environment of bacteria. X-ray crystallographic structures of human HO1 H25R with bound heme and additional functional studies suggest that HO mutant activity inside these cells does not involve heme ligation by a proximal amino acid. Our study reveals unexpected plasticity in the active site binding interactions with heme that can support HO activity within cells, suggests important contributions by the surrounding active site environment to HO catalysis, and can guide efforts to understand the evolution and divergence of HO function.
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Affiliation(s)
- Paul A Sigala
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine , St. Louis, Missouri 63110, United States
| | - Koldo Morante
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo , Bunkyo-ku, Tokyo 113-8654, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo , Bunkyo-ku, Tokyo 113-8654, Japan.,Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo , Minato-ku, Tokyo 108-8639, Japan
| | - Jose M M Caaveiro
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo , Bunkyo-ku, Tokyo 113-8654, Japan
| | - Daniel E Goldberg
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine , St. Louis, Missouri 63110, United States
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