1
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Tan Z, Li J, Hou J, Gonzalez R. Designing artificial pathways for improving chemical production. Biotechnol Adv 2023; 64:108119. [PMID: 36764336 DOI: 10.1016/j.biotechadv.2023.108119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Metabolic engineering exploits manipulation of catalytic and regulatory elements to improve a specific function of the host cell, often the synthesis of interesting chemicals. Although naturally occurring pathways are significant resources for metabolic engineering, these pathways are frequently inefficient and suffer from a series of inherent drawbacks. Designing artificial pathways in a rational manner provides a promising alternative for chemicals production. However, the entry barrier of designing artificial pathway is relatively high, which requires researchers a comprehensive and deep understanding of physical, chemical and biological principles. On the other hand, the designed artificial pathways frequently suffer from low efficiencies, which impair their further applications in host cells. Here, we illustrate the concept and basic workflow of retrobiosynthesis in designing artificial pathways, as well as the most currently used methods including the knowledge- and computer-based approaches. Then, we discuss how to obtain desired enzymes for novel biochemistries, and how to trim the initially designed artificial pathways for further improving their functionalities. Finally, we summarize the current applications of artificial pathways from feedstocks utilization to various products synthesis, as well as our future perspectives on designing artificial pathways.
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Affiliation(s)
- Zaigao Tan
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Department of Bioengineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Jian Li
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Department of Bioengineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ramon Gonzalez
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA.
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2
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A balancing act. Nat Chem Biol 2023; 19:127-128. [PMID: 36470995 DOI: 10.1038/s41589-022-01183-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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3
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Danchin A, Huang JD. SynBio 2.0, a new era for synthetic life: Neglected essential functions for resilience. Environ Microbiol 2023; 25:64-78. [PMID: 36045561 DOI: 10.1111/1462-2920.16140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 07/16/2022] [Indexed: 01/21/2023]
Affiliation(s)
- Antoine Danchin
- School of Biomedical Sciences, Li KaShing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong
| | - Jian Dong Huang
- School of Biomedical Sciences, Li KaShing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong
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4
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Abstract
Analysis of the genes retained in the minimized Mycoplasma JCVI-Syn3A genome established that systems that repair or preempt metabolite damage are essential to life. Several genes known to have such functions were identified and experimentally validated, including 5-formyltetrahydrofolate cycloligase, coenzyme A (CoA) disulfide reductase, and certain hydrolases. Furthermore, we discovered that an enigmatic YqeK hydrolase domain fused to NadD has a novel proofreading function in NAD synthesis and could double as a MutT-like sanitizing enzyme for the nucleotide pool. Finally, we combined metabolomics and cheminformatics approaches to extend the core metabolic map of JCVI-Syn3A to include promiscuous enzymatic reactions and spontaneous side reactions. This extension revealed that several key metabolite damage control systems remain to be identified in JCVI-Syn3A, such as that for methylglyoxal.
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5
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Jeffryes JG, Lerma-Ortiz C, Liu F, Golubev A, Niehaus TD, Elbadawi-Sidhu M, Fiehn O, Hanson AD, Tyo KE, Henry CS. Chemical-damage MINE: A database of curated and predicted spontaneous metabolic reactions. Metab Eng 2021; 69:302-312. [PMID: 34958914 DOI: 10.1016/j.ymben.2021.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 10/05/2021] [Accepted: 11/23/2021] [Indexed: 01/27/2023]
Abstract
Spontaneous reactions between metabolites are often neglected in favor of emphasizing enzyme-catalyzed chemistry because spontaneous reaction rates are assumed to be insignificant under physiological conditions. However, synthetic biology and engineering efforts can raise natural metabolites' levels or introduce unnatural ones, so that previously innocuous or nonexistent spontaneous reactions become an issue. Problems arise when spontaneous reaction rates exceed the capacity of a platform organism to dispose of toxic or chemically active reaction products. While various reliable sources list competing or toxic enzymatic pathways' side-reactions, no corresponding compilation of spontaneous side-reactions exists, nor is it possible to predict their occurrence. We addressed this deficiency by creating the Chemical Damage (CD)-MINE resource. First, we used literature data to construct a comprehensive database of metabolite reactions that occur spontaneously in physiological conditions. We then leveraged this data to construct 148 reaction rules describing the known spontaneous chemistry in a substrate-generic way. We applied these rules to all compounds in the ModelSEED database, predicting 180,891 spontaneous reactions. The resulting (CD)-MINE is available at https://minedatabase.mcs.anl.gov/cdmine/#/home and through developer tools. We also demonstrate how damage-prone intermediates and end products are widely distributed among metabolic pathways, and how predicting spontaneous chemical damage helps rationalize toxicity and carbon loss using examples from published pathways to commercial products. We explain how analyzing damage-prone areas in metabolism helps design effective engineering strategies. Finally, we use the CD-MINE toolset to predict the formation of the novel damage product N-carbamoyl proline, and present mass spectrometric evidence for its presence in Escherichia coli.
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Affiliation(s)
- James G Jeffryes
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Claudia Lerma-Ortiz
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60637, USA; Department of Data Science and Learning, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Filipe Liu
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA; Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60637, USA
| | - Alexey Golubev
- Department of Carcinogenesis and Oncogerontology, N.N. Petrov National Medical Research Center of Oncology, Saint Petersburg, 197758, Russia
| | - Thomas D Niehaus
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA; Plant and Microbial Biology Department, University of Minnesota, Saint Paul, MN, 55108, USA
| | | | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, CA, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Keith Ej Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA; Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60637, USA.
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6
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Cros A, Alfaro-Espinoza G, De Maria A, Wirth NT, Nikel PI. Synthetic metabolism for biohalogenation. Curr Opin Biotechnol 2021; 74:180-193. [PMID: 34954625 DOI: 10.1016/j.copbio.2021.11.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 12/19/2022]
Abstract
The pressing need for novel bioproduction approaches faces a limitation in the number and type of molecules accessed through synthetic biology. Halogenation is widely used for tuning physicochemical properties of molecules and polymers, but traditional halogenation chemistry often lacks specificity and generates harmful by-products. Here, we pose that deploying synthetic metabolism tailored for biohalogenation represents an unique opportunity towards economically attractive and environmentally friendly organohalide production. On this background, we discuss growth-coupled selection of functional metabolic modules that harness the rich repertoire of biosynthetic and biodegradation capabilities of environmental bacteria for in vivo biohalogenation. By rationally combining these approaches, the chemical landscape of living cells can accommodate bioproduction of added-value organohalides which, as of today, are obtained by traditional chemistry.
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Affiliation(s)
- Antonin Cros
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Gabriela Alfaro-Espinoza
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; Division Biodeterioration and Reference Organisms, Federal Institute for Materials Research and Testing (BAM), 12205 Berlin, Germany
| | - Alberto De Maria
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
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7
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Griffith CM, Walvekar AS, Linster CL. Approaches for completing metabolic networks through metabolite damage and repair discovery. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 28:None. [PMID: 34957344 PMCID: PMC8669784 DOI: 10.1016/j.coisb.2021.100379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Metabolites are prone to damage, either via enzymatic side reactions, which collectively form the underground metabolism, or via spontaneous chemical reactions. The resulting non-canonical metabolites that can be toxic, are mended by dedicated "metabolite repair enzymes." Deficiencies in the latter can cause severe disease in humans, whereas inclusion of repair enzymes in metabolically engineered systems can improve the production yield of value-added chemicals. The metabolite damage and repair loops are typically not yet included in metabolic reconstructions and it is likely that many remain to be discovered. Here, we review strategies and associated challenges for unveiling non-canonical metabolites and metabolite repair enzymes, including systematic approaches based on high-resolution mass spectrometry, metabolome-wide side-activity prediction, as well as high-throughput substrate and phenotypic screens.
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Affiliation(s)
| | | | - Carole L. Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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8
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Bathe U, Leong BJ, McCarty DR, Henry CS, Abraham PE, Wilson MA, Hanson AD. The Moderately (D)efficient Enzyme: Catalysis-Related Damage In Vivo and Its Repair. Biochemistry 2021; 60:3555-3565. [PMID: 34729986 DOI: 10.1021/acs.biochem.1c00613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Enzymes have in vivo life spans. Analysis of life spans, i.e., lifetime totals of catalytic turnovers, suggests that nonsurvivable collateral chemical damage from the very reactions that enzymes catalyze is a common but underdiagnosed cause of enzyme death. Analysis also implies that many enzymes are moderately deficient in that their active-site regions are not naturally as hardened against such collateral damage as they could be, leaving room for improvement by rational design or directed evolution. Enzyme life span might also be improved by engineering systems that repair otherwise fatal active-site damage, of which a handful are known and more are inferred to exist. Unfortunately, the data needed to design and execute such improvements are lacking: there are too few measurements of in vivo life span, and existing information about the extent, nature, and mechanisms of active-site damage and repair during normal enzyme operation is too scarce, anecdotal, and speculative to act on. Fortunately, advances in proteomics, metabolomics, cheminformatics, comparative genomics, and structural biochemistry now empower a systematic, data-driven approach for identifying, predicting, and validating instances of active-site damage and its repair. These capabilities would be practically useful in enzyme redesign and improvement of in-use stability and could change our thinking about which enzymes die young in vivo, and why.
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Affiliation(s)
- Ulschan Bathe
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| | - Bryan J Leong
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| | - Donald R McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| | - Christopher S Henry
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Mark A Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, United States
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9
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Diederen T, Delabrière A, Othman A, Reid ME, Zamboni N. Metabolomics. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Glasscock CJ, Biggs BW, Lazar JT, Arnold JH, Burdette LA, Valdes A, Kang MK, Tullman-Ercek D, Tyo KEJ, Lucks JB. Dynamic Control of Gene Expression with Riboregulated Switchable Feedback Promoters. ACS Synth Biol 2021; 10:1199-1213. [PMID: 33834762 DOI: 10.1021/acssynbio.1c00015] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One major challenge in synthetic biology is the deleterious impacts of cellular stress caused by expression of heterologous pathways, sensors, and circuits. Feedback control and dynamic regulation are broadly proposed strategies to mitigate this cellular stress by optimizing gene expression levels temporally and in response to biological cues. While a variety of approaches for feedback implementation exist, they are often complex and cannot be easily manipulated. Here, we report a strategy that uses RNA transcriptional regulators to integrate additional layers of control over the output of natural and engineered feedback responsive circuits. Called riboregulated switchable feedback promoters (rSFPs), these gene expression cassettes can be modularly activated using multiple mechanisms, from manual induction to autonomous quorum sensing, allowing control over the timing, magnitude, and autonomy of expression. We develop rSFPs in Escherichia coli to regulate multiple feedback networks and apply them to control the output of two metabolic pathways. We envision that rSFPs will become a valuable tool for flexible and dynamic control of gene expression in metabolic engineering, biological therapeutic production, and many other applications.
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Affiliation(s)
- Cameron J. Glasscock
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 113 Ho Plaza, Ithaca, New York 14853, United States
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Bradley W. Biggs
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - John T. Lazar
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Jack H. Arnold
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Lisa A. Burdette
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Aliki Valdes
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Min-Kyoung Kang
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Danielle Tullman-Ercek
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Keith E. J. Tyo
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Julius B. Lucks
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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11
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Zhang C, Zheng W, Cheng M, Omenn GS, Freddolino PL, Zhang Y. Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome. J Proteome Res 2021; 20:1178-1189. [PMID: 33393786 PMCID: PMC7867644 DOI: 10.1021/acs.jproteome.0c00359] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
When the JCVI-syn3.0 genome was designed and implemented in 2016 as the minimal genome of a free-living organism, approximately one-third of the 438 protein-coding genes had no known function. Subsequent refinement into JCVI-syn3A led to inclusion of 16 additional protein-coding genes, including several unknown functions, resulting in an improved growth phenotype. Here, we seek to unveil the biological roles and protein-protein interaction (PPI) networks for these poorly characterized proteins using state-of-the-art deep learning contact-assisted structure prediction, followed by structure-based annotation of functions and PPI predictions. Our pipeline is able to confidently assign functions for many previously unannotated proteins such as putative vitamin transporters, which suggest the importance of nutrient uptake even in a minimized genome. Remarkably, despite the artificial selection of genes in the minimal syn3 genome, our reconstructed PPI network still shows a power law distribution of node degrees typical of naturally evolved bacterial PPI networks. Making use of our framework for combined structure/function/interaction modeling, we are able to identify both fundamental aspects of network biology that are retained in a minimal proteome and additional essential functions not yet recognized among the poorly annotated components of the syn3.0 and syn3A proteomes.
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Affiliation(s)
- Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Wei Zheng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Micah Cheng
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
- Departments of Internal Medicine and Human Genetics and School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Peter L Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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12
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Toward sustainable, cell-free biomanufacturing. Curr Opin Biotechnol 2021; 69:136-144. [PMID: 33453438 DOI: 10.1016/j.copbio.2020.12.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022]
Abstract
Industrial biotechnology is an attractive approach to address the need for low-cost fuels and products from sustainable resources. Unfortunately, cells impose inherent limitations on the effective synthesis and release of target products. One key constraint is that cellular survival objectives often work against the production objectives of biochemical engineers. Additionally, industrial strains release CO2 and struggle to utilize sustainable, potentially profitable feedstocks. Cell-free biotechnology, which uses biological machinery harvested from cells, can address these challenges with advantages including: (i) shorter development times, (ii) higher volumetric production rates, and (iii) tolerance to otherwise toxic molecules. In this review, we highlight recent advances in cell-free technologies toward the production of non-protein products beyond lab-scale demonstrations and describe guiding principles for designing cell-free systems. Specifically, we discuss carbon and energy sources, reaction homeostasis, and scale-up. Expanding the scope of cell-free biomanufacturing practice could enable innovative approaches for the industrial production of green chemicals.
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13
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Thioproline formation as a driver of formaldehyde toxicity in Escherichia coli. Biochem J 2020; 477:1745-1757. [PMID: 32301498 DOI: 10.1042/bcj20200198] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/14/2020] [Accepted: 04/17/2020] [Indexed: 12/14/2022]
Abstract
Formaldehyde (HCHO) is a reactive carbonyl compound that formylates and cross-links proteins, DNA, and small molecules. It is of specific concern as a toxic intermediate in the design of engineered pathways involving methanol oxidation or formate reduction. The interest in engineering these pathways is not, however, matched by engineering-relevant information on precisely why HCHO is toxic or on what damage-control mechanisms cells deploy to manage HCHO toxicity. The only well-defined mechanism for managing HCHO toxicity is formaldehyde dehydrogenase-mediated oxidation to formate, which is counterproductive if HCHO is a desired pathway intermediate. We therefore sought alternative HCHO damage-control mechanisms via comparative genomic analysis. This analysis associated homologs of the Escherichia coli pepP gene with HCHO-related one-carbon metabolism. Furthermore, deleting pepP increased the sensitivity of E. coli to supplied HCHO but not other carbonyl compounds. PepP is a proline aminopeptidase that cleaves peptides of the general formula X-Pro-Y, yielding X + Pro-Y. HCHO is known to react spontaneously with cysteine to form the close proline analog thioproline (thiazolidine-4-carboxylate), which is incorporated into proteins and hence into proteolytic peptides. We therefore hypothesized that certain thioproline-containing peptides are toxic and that PepP cleaves these aberrant peptides. Supporting this hypothesis, PepP cleaved the model peptide Ala-thioproline-Ala as efficiently as Ala-Pro-Ala in vitro and in vivo, and deleting pepP increased sensitivity to supplied thioproline. Our data thus (i) provide biochemical genetic evidence that thioproline formation contributes substantially to HCHO toxicity and (ii) make PepP a candidate damage-control enzyme for engineered pathways having HCHO as an intermediate.
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14
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Pogodaev AA, Lap TT, Huck WTS. The Dynamics of an Oscillating Enzymatic Reaction Network is Crucially Determined by Side Reactions. CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.202000033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Aleksandr A. Pogodaev
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 Nijmegen 6525 AJ The Netherlands
| | - Tijs T. Lap
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 Nijmegen 6525 AJ The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 Nijmegen 6525 AJ The Netherlands
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15
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Human ARMT1 structure and substrate specificity indicates that it is a DUF89 family damage-control phosphatase. J Struct Biol 2020; 212:107576. [PMID: 32682077 DOI: 10.1016/j.jsb.2020.107576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 07/07/2020] [Accepted: 07/10/2020] [Indexed: 11/21/2022]
Abstract
Metabolite damage control is a critical but poorly defined aspect of cellular biochemistry, which likely involves many of the so far functionally uncharacterized protein domain (domains of unknown function; DUFs). We have determined the crystal structure of the human DUF89 protein product of the C6ORF211 gene to 1.85 Å. The crystal structure shows that the protein contains a core α-β-α fold with an active site-bound metal ion and α-helical bundle N-terminal cap, which are both conserved features of subfamily III DUF89 domains. The biochemical activities of the human protein are conserved with those of a previously characterized budding yeast homolog, where an in vitro phosphatase activity is supported by divalent cations that include Co2+, Ni2+, Mn2+ or Mg2+. Full steady-state kinetics parameters of human DUF89 using a standard PNPP phosphatase assay revealed a six times higher catalytic efficiency in presence of Co2+ compared to Mg2+. The human enzyme targets a number of phosphate substrates similar to the budding yeast homolog, while it lacks a previously indicated methyltransferase activity. The highest activity on substrate was observed with fructose-1-phosphate, a potent glycating agent, and thus human DUF89 phosphatase activity may also play a role in limiting the buildup of phospho-glycan species and their related damaged metabolites.
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16
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Synthetic Biochemistry: The Bio-inspired Cell-Free Approach to Commodity Chemical Production. Trends Biotechnol 2020; 38:766-778. [DOI: 10.1016/j.tibtech.2019.12.024] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 01/26/2023]
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17
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Miller TE, Beneyton T, Schwander T, Diehl C, Girault M, McLean R, Chotel T, Claus P, Cortina NS, Baret JC, Erb TJ. Light-powered CO 2 fixation in a chloroplast mimic with natural and synthetic parts. Science 2020; 368:649-654. [PMID: 32381722 DOI: 10.1126/science.aaz6802] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/24/2020] [Indexed: 12/21/2022]
Abstract
Nature integrates complex biosynthetic and energy-converting tasks within compartments such as chloroplasts and mitochondria. Chloroplasts convert light into chemical energy, driving carbon dioxide fixation. We used microfluidics to develop a chloroplast mimic by encapsulating and operating photosynthetic membranes in cell-sized droplets. These droplets can be energized by light to power enzymes or enzyme cascades and analyzed for their catalytic properties in multiplex and real time. We demonstrate how these microdroplets can be programmed and controlled by adjusting internal compositions and by using light as an external trigger. We showcase the capability of our platform by integrating the crotonyl-coenzyme A (CoA)/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH) cycle, a synthetic network for carbon dioxide conversion, to create an artificial photosynthetic system that interfaces the natural and the synthetic biological worlds.
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Affiliation(s)
- Tarryn E Miller
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Thomas Beneyton
- University of Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac 33600, France
| | - Thomas Schwander
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Christoph Diehl
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | | | - Richard McLean
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Tanguy Chotel
- University of Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac 33600, France
| | - Peter Claus
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Niña Socorro Cortina
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Jean-Christophe Baret
- University of Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac 33600, France. .,Institut Universitaire de France, Paris 75005, France
| | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany. .,Center for Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
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18
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Burgener S, Luo S, McLean R, Miller TE, Erb TJ. A roadmap towards integrated catalytic systems of the future. Nat Catal 2020. [DOI: 10.1038/s41929-020-0429-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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19
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Structural organization of biocatalytic systems: the next dimension of synthetic metabolism. Emerg Top Life Sci 2019; 3:579-586. [PMID: 33523157 PMCID: PMC7289016 DOI: 10.1042/etls20190015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 08/20/2019] [Accepted: 08/20/2019] [Indexed: 11/17/2022]
Abstract
In natural metabolic networks, more than 2000 different biochemical reactions are operated and spatially and temporally co-ordinated in a reaction volume of <1 µm3. A similar level of control and precision has not been achieved in chemical synthesis, so far. Recently, synthetic biology succeeded in reconstructing complex synthetic in vitro metabolic networks (SIVMNs) from individual proteins in a defined fashion bottom-up. In this review, we will highlight some examples of SIVMNs and discuss how the further advancement of SIVMNs will require the structural organization of these networks and their reactions to (i) minimize deleterious side reactions, (ii) efficiently energize these networks from renewable energies, and (iii) achieve high productivity. The structural organization of synthetic metabolic networks will be a key step to create novel catalytic systems of the future and advance ongoing efforts of creating cell-like systems and artificial cells.
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20
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21
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On the importance of reaction networks for synthetic living systems. Emerg Top Life Sci 2019; 3:517-527. [DOI: 10.1042/etls20190016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/14/2019] [Accepted: 08/15/2019] [Indexed: 12/11/2022]
Abstract
The goal of creating a synthetic cell necessitates the development of reaction networks which will underlie all of its behaviours. Recent developments in in vitro systems, based upon both DNA and enzymes, have created networks capable of a range of behaviours e.g. information processing, adaptation and diffusive signalling. These networks are based upon reaction motifs that when combined together produce more complex behaviour. We highlight why it is inevitable that networks, based on enzymes or enzyme-like catalysts, will be required for the construction of a synthetic cell. We outline several of the challenges, including (a) timing, (b) regulation and (c) energy distribution, that must be overcome in order to transition from the simple networks we have today to much more complex networks capable of a variety of behaviours and which could find application one day within a synthetic cell.
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22
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Erb TJ. Back to the future: Why we need enzymology to build a synthetic metabolism of the future. Beilstein J Org Chem 2019; 15:551-557. [PMID: 30873239 PMCID: PMC6404388 DOI: 10.3762/bjoc.15.49] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/29/2019] [Indexed: 12/26/2022] Open
Abstract
Biology is turning from an analytical into a synthetic discipline. This is especially apparent in the field of metabolic engineering, where the concept of synthetic metabolism has been recently developed. Compared to classical metabolic engineering efforts, synthetic metabolism aims at creating novel metabolic networks in a rational fashion from bottom-up. However, while the theoretical design of synthetic metabolic networks has made tremendous progress, the actual realization of such synthetic pathways is still lacking behind. This is mostly because of our limitations in enzyme discovery and engineering to provide the parts required to build synthetic metabolism. Here I discuss the current challenges and limitations in synthetic metabolic engineering and elucidate how modern day enzymology can help to build a synthetic metabolism of the future.
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Affiliation(s)
- Tobias J Erb
- Max-Planck-Institute for Terrestrial Microbiology, Department of Biochemistry & Synthetic Metabolism, Karl-von-Frisch-Str. 10, D-35043 Marburg, Germany.,LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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23
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The metabolite repair enzyme Nit1 is a dual-targeted amidase that disposes of damaged glutathione in Arabidopsis. Biochem J 2019; 476:683-697. [PMID: 30692244 DOI: 10.1042/bcj20180931] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 01/16/2019] [Accepted: 01/28/2019] [Indexed: 12/19/2022]
Abstract
The tripeptide glutathione (GSH) is implicated in various crucial physiological processes including redox buffering and protection against heavy metal toxicity. GSH is abundant in plants, with reported intracellular concentrations typically in the 1-10 mM range. Various aminotransferases can inadvertently transaminate the amino group of the γ-glutamyl moiety of GSH to produce deaminated glutathione (dGSH), a metabolite damage product. It was recently reported that an amidase known as Nit1 participates in dGSH breakdown in mammals and yeast. Plants have a hitherto uncharacterized homolog of the Nit1 amidase. We show that recombinant Arabidopsis Nit1 (At4g08790) has high and specific amidase activity towards dGSH. Ablating the Arabidopsis Nit1 gene causes a massive accumulation of dGSH and other marked changes to the metabolome. All plant Nit1 sequences examined had predicted plastidial targeting peptides with a potential second start codon whose use would eliminate the targeting peptide. In vitro transcription/translation assays show that both potential translation start codons in Arabidopsis Nit1 were used and confocal microscopy of Nit1-GFP fusions in plant cells confirmed both cytoplasmic and plastidial localization. Furthermore, we show that Arabidopsis enzymes present in leaf extracts convert GSH to dGSH at a rate of 2.8 pmol min-1 mg-1 in the presence of glyoxalate as an amino acceptor. Our data demonstrate that plants have a dGSH repair system that is directed to at least two cellular compartments via the use of alternative translation start sites.
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24
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Zheng Y, Cantley LC. Toward a better understanding of folate metabolism in health and disease. J Exp Med 2019; 216:253-266. [PMID: 30587505 PMCID: PMC6363433 DOI: 10.1084/jem.20181965] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/18/2018] [Accepted: 12/03/2018] [Indexed: 12/15/2022] Open
Abstract
Folate metabolism is crucial for many biochemical processes, including purine and thymidine monophosphate (dTMP) biosynthesis, mitochondrial protein translation, and methionine regeneration. These biochemical processes in turn support critical cellular functions such as cell proliferation, mitochondrial respiration, and epigenetic regulation. Not surprisingly, abnormal folate metabolism has been causally linked with a myriad of diseases. In this review, we provide a historical perspective, delve into folate chemistry that is often overlooked, and point out various missing links and underdeveloped areas in folate metabolism for future exploration.
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Affiliation(s)
- Yuxiang Zheng
- Department of Medicine, Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Lewis C Cantley
- Department of Medicine, Meyer Cancer Center, Weill Cornell Medicine, New York, NY
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25
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Harnessing Underground Metabolism for Pathway Development. Trends Biotechnol 2019; 37:29-37. [DOI: 10.1016/j.tibtech.2018.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/17/2018] [Accepted: 08/06/2018] [Indexed: 01/13/2023]
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26
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Rudroff F. Whole-cell based synthetic enzyme cascades-light and shadow of a promising technology. Curr Opin Chem Biol 2018; 49:84-90. [PMID: 30458384 DOI: 10.1016/j.cbpa.2018.10.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/05/2018] [Accepted: 10/15/2018] [Indexed: 01/16/2023]
Abstract
Mimicking Nature by biocatalytic cascade reactions in a whole-cell environment is a revolutionary development in multistep synthesis for the production of bulk and fine chemicals. In the past decade, several proof of concept success stories demonstrated the power of those synthetic cascades and paved the road for future industrial applications. Although enzymes and their promiscuity are best suited to construct such artificial pathways, the complexity and the lack of understanding of the cellular machinery slowed down this progress significantly. In this review, recent achievements in the field of whole-cell biocatalysis are described, challenges and hidden traps that have to be overcome are depicted, and strategies are illustrated how to increase overall cascade productivity.
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Affiliation(s)
- Florian Rudroff
- TU Wien, Institute of Applied Synthetic Chemistry, Getreidemarkt 9, 163-OC, 1060 Vienna, Austria.
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27
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Escherichia coli as a host for metabolic engineering. Metab Eng 2018; 50:16-46. [DOI: 10.1016/j.ymben.2018.04.008] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 12/21/2022]
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28
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Nikel PI, de Lorenzo V. Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans-metabolism. Metab Eng 2018; 50:142-155. [DOI: 10.1016/j.ymben.2018.05.005] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 05/07/2018] [Accepted: 05/10/2018] [Indexed: 12/12/2022]
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29
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de Crécy-Lagard V, Haas D, Hanson AD. Newly-discovered enzymes that function in metabolite damage-control. Curr Opin Chem Biol 2018; 47:101-108. [PMID: 30268903 DOI: 10.1016/j.cbpa.2018.09.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 08/19/2018] [Accepted: 09/11/2018] [Indexed: 01/26/2023]
Abstract
Enzymes of unknown function are estimated to make up around 25% of the sequenced proteome. In the past decade, over 20 conserved families have been shown to function in the metabolism of 'damaged' or abnormal metabolites that are wasteful and often toxic. These newly discovered damage-control enzymes either repair or inactivate the offending metabolites, or pre-empt their formation in the first place. Comparative genomics has been of prime importance in predicting the functions of damage-control enzymes and in guiding the biochemical and genetic tests required to validate these functions.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA; Genetics Institute, University of Florida, Gainesville, FL, USA.
| | - Drago Haas
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
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30
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Schwille P, Spatz J, Landfester K, Bodenschatz E, Herminghaus S, Sourjik V, Erb TJ, Bastiaens P, Lipowsky R, Hyman A, Dabrock P, Baret JC, Vidakovic-Koch T, Bieling P, Dimova R, Mutschler H, Robinson T, Tang TYD, Wegner S, Sundmacher K. MaxSynBio: Wege zur Synthese einer Zelle aus nicht lebenden Komponenten. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802288] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Petra Schwille
- Zelluläre und molekulare Biophysik; MPI für Biochemie; Am Klopferspitz 18 82152 Martinsried Deutschland
| | - Joachim Spatz
- MPI für medizinische Forschung; Jahnstraße 29 69120 Heidelberg Deutschland
| | | | - Eberhard Bodenschatz
- MPI für Dynamik und Selbstorganisation; Am Fassberg 17 37077 Göttingen Deutschland
| | - Stephan Herminghaus
- MPI für Dynamik und Selbstorganisation; Am Fassberg 17 37077 Göttingen Deutschland
| | - Victor Sourjik
- MPI für terrestrische Mikrobiologie; Karl-von-Frisch-Str. 16 35043 Marburg Deutschland
| | - Tobias J. Erb
- MPI für terrestrische Mikrobiologie; Karl-von-Frisch-Str. 16 35043 Marburg Deutschland
| | - Philippe Bastiaens
- MPI für molekulare Physiologie; Otto-Hahn-Str. 11 44227 Dortmund Deutschland
| | - Reinhard Lipowsky
- MPI für Kolloide und Grenzflächen; Wissenschaftspark Golm 14424 Potsdam Deutschland
| | - Anthony Hyman
- MPI für molekulare Zellbiologie und Genetik; Pfotenhauerstraße 108 01307 Dresden Deutschland
| | - Peter Dabrock
- Friedrich-Alexander-Universität Erlangen-Nürnberg; Fachbereich Theologie; Kochstraße 6 91054 Erlangen Deutschland
| | - Jean-Christophe Baret
- University of Bordeaux - Centre de Recherches Paul Pascal; 115 Avenue Schweitze 33600 Pessac Frankreich
| | - Tanja Vidakovic-Koch
- MPI für Dynamik komplexer technischer Systeme; Sandtorstraße 1 39106 Magdeburg Deutschland
| | - Peter Bieling
- MPI für molekulare Physiologie; Otto-Hahn-Str. 11 44227 Dortmund Deutschland
| | - Rumiana Dimova
- MPI für Kolloide und Grenzflächen; Wissenschaftspark Golm 14424 Potsdam Deutschland
| | - Hannes Mutschler
- Zelluläre und molekulare Biophysik; MPI für Biochemie; Am Klopferspitz 18 82152 Martinsried Deutschland
| | - Tom Robinson
- MPI für Kolloide und Grenzflächen; Wissenschaftspark Golm 14424 Potsdam Deutschland
| | - T.-Y. Dora Tang
- MPI für molekulare Zellbiologie und Genetik; Pfotenhauerstraße 108 01307 Dresden Deutschland
| | - Seraphine Wegner
- MPI für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Kai Sundmacher
- MPI für Dynamik komplexer technischer Systeme; Sandtorstraße 1 39106 Magdeburg Deutschland
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31
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Schwille P, Spatz J, Landfester K, Bodenschatz E, Herminghaus S, Sourjik V, Erb TJ, Bastiaens P, Lipowsky R, Hyman A, Dabrock P, Baret JC, Vidakovic-Koch T, Bieling P, Dimova R, Mutschler H, Robinson T, Tang TYD, Wegner S, Sundmacher K. MaxSynBio: Avenues Towards Creating Cells from the Bottom Up. Angew Chem Int Ed Engl 2018; 57:13382-13392. [PMID: 29749673 DOI: 10.1002/anie.201802288] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/03/2018] [Indexed: 12/18/2022]
Abstract
A large German research consortium mainly within the Max Planck Society ("MaxSynBio") was formed to investigate living systems from a fundamental perspective. The research program of MaxSynBio relies solely on the bottom-up approach to synthetic biology. MaxSynBio focuses on the detailed analysis and understanding of essential processes of life through modular reconstitution in minimal synthetic systems. The ultimate goal is to construct a basic living unit entirely from non-living components. The fundamental insights gained from the activities in MaxSynBio could eventually be utilized for establishing a new generation of biotechnological processes, which would be based on synthetic cell constructs that replace the natural cells currently used in conventional biotechnology.
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Affiliation(s)
- Petra Schwille
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Joachim Spatz
- MPI for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany
| | | | - Eberhard Bodenschatz
- MPI for Dynamics and Self-Organization, Am Fassberg 17, 37077, Göttingen, Germany
| | - Stephan Herminghaus
- MPI for Dynamics and Self-Organization, Am Fassberg 17, 37077, Göttingen, Germany
| | - Victor Sourjik
- MPI for Terrestrial Microbiology, Karl-von-Frisch-Str. 16, 35043, Marburg, Germany
| | - Tobias J Erb
- MPI for Terrestrial Microbiology, Karl-von-Frisch-Str. 16, 35043, Marburg, Germany
| | - Philippe Bastiaens
- MPI for Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Reinhard Lipowsky
- MPI of Colloids and Interfaces, Wissenschaftspark Golm, 14424, Potsdam, Germany
| | - Anthony Hyman
- MPI of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Peter Dabrock
- Friedrich-Alexander University Erlangen-Nuremberg, Department of Theology, Kochstraße 6, 91054, Erlangen, Germany
| | - Jean-Christophe Baret
- University of Bordeaux -Centre de Recherches Paul Pascal, 115 Avenue Schweitze, 33600, Pessac, France
| | - Tanja Vidakovic-Koch
- Process Systems Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
| | - Peter Bieling
- MPI for Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Rumiana Dimova
- MPI of Colloids and Interfaces, Wissenschaftspark Golm, 14424, Potsdam, Germany
| | - Hannes Mutschler
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Tom Robinson
- MPI of Colloids and Interfaces, Wissenschaftspark Golm, 14424, Potsdam, Germany
| | - T-Y Dora Tang
- MPI of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Seraphine Wegner
- MPI for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Kai Sundmacher
- Process Systems Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
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32
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Jeffryes JG, Seaver SMD, Faria JP, Henry CS. A pathway for every product? Tools to discover and design plant metabolism. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:61-70. [PMID: 29907310 DOI: 10.1016/j.plantsci.2018.03.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/13/2018] [Accepted: 03/19/2018] [Indexed: 06/08/2023]
Abstract
The vast diversity of plant natural products is a powerful indication of the biosynthetic capacity of plant metabolism. Synthetic biology seeks to capitalize on this ability by understanding and reconfiguring the biosynthetic pathways that generate this diversity to produce novel products with improved efficiency. Here we review the algorithms and databases that presently support the design and manipulation of metabolic pathways in plants, starting from metabolic models of native biosynthetic pathways, progressing to novel combinations of known reactions, and finally proposing new reactions that may be carried out by existing enzymes. We show how these tools are useful for proposing new pathways as well as identifying side reactions that may affect engineering goals.
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Affiliation(s)
- James G Jeffryes
- Argonne National Laboratory, Mathematics and Computer Science Division, Argonne, IL, United States
| | - Samuel M D Seaver
- Argonne National Laboratory, Mathematics and Computer Science Division, Argonne, IL, United States
| | - José P Faria
- Argonne National Laboratory, Mathematics and Computer Science Division, Argonne, IL, United States
| | - Christopher S Henry
- Argonne National Laboratory, Mathematics and Computer Science Division, Argonne, IL, United States.
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33
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Genotype to phenotype mapping still needs underpinning by research in metabolism and enzymology. Biosci Rep 2018; 38:BSR20180520. [PMID: 29848765 PMCID: PMC6013700 DOI: 10.1042/bsr20180520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 05/29/2018] [Accepted: 05/29/2018] [Indexed: 11/17/2022] Open
Abstract
The article ‘Evidence that the metabolite repair enzyme NAD(P)HX epimerase has a moonlighting function’ by Niehaus et al. published in this issue illustrates a number of the problems that still arise when attempting to translate genotypes to phenotypes, such as for interpreting mutant phenotypes or building genome-scale metabolic models. In this case, the mutation concerned appears to map to an enzyme in one of the little-known but essential metabolite repair pathways that have been discovered in recent years. However, the bioinformatic and experimental evidence presented suggests that the annotated enzyme activity of the mutated gene product, whilst correct, accounts neither for the phenotype nor for the chromosomal and transcriptional associations of the gene. The bioinformatic and metabolomic evidence presented points to an additional but important role for the gene product in pyridoxal phosphate homoeostasis, thus adding the enzyme to the expanding list of those with a ‘moonlighting function’.
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34
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Vögeli B, Geyer K, Gerlinger PD, Benkstein S, Cortina NS, Erb TJ. Combining Promiscuous Acyl-CoA Oxidase and Enoyl-CoA Carboxylase/Reductases for Atypical Polyketide Extender Unit Biosynthesis. Cell Chem Biol 2018; 25:833-839.e4. [PMID: 29731424 DOI: 10.1016/j.chembiol.2018.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/22/2018] [Accepted: 04/06/2018] [Indexed: 10/17/2022]
Abstract
The incorporation of different extender units generates structural diversity in polyketides. There is significant interest in engineering substrate specificity of polyketide synthases (PKSs) to change their chemical structure. Efforts to change extender unit selectivity are hindered by the lack of simple screening methods and easily available atypical extender units. Here, we present a chemo-biosynthetic strategy that employs biocatalytic proofreading and allows access to a large variety of extender units. First, saturated acids are chemically coupled to free coenzyme A (CoA). The corresponding acyl-CoAs are then converted to alkylmalonyl-CoAs in a "one-pot" reaction through the combined action of an acyl-CoA oxidase and enoyl-CoA carboxylase/reductase. We synthesized six different extender units and used them in in vitro competition screens to investigate active site residues conferring extender unit selectivity. Our results show the importance of an uncharacterized glutamine in extender unit selectivity and open the possibility for comprehensive studies on extender incorporation in PKSs.
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Affiliation(s)
- Bastian Vögeli
- Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Kyra Geyer
- Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Patrick D Gerlinger
- Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Sarah Benkstein
- Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Niña Socorro Cortina
- Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Tobias J Erb
- Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany.
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