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Schulz-Mirbach H, Müller A, Wu T, Pfister P, Aslan S, Schada von Borzyskowski L, Erb TJ, Bar-Even A, Lindner SN. On the flexibility of the cellular amination network in E coli. eLife 2022; 11:e77492. [PMID: 35876664 PMCID: PMC9436414 DOI: 10.7554/elife.77492] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/22/2022] [Indexed: 12/03/2022] Open
Abstract
Ammonium (NH4+) is essential to generate the nitrogenous building blocks of life. It gets assimilated via the canonical biosynthetic routes to glutamate and is further distributed throughout metabolism via a network of transaminases. To study the flexibility of this network, we constructed an Escherichia coli glutamate auxotrophic strain. This strain allowed us to systematically study which amino acids serve as amine sources. We found that several amino acids complemented the auxotrophy either by producing glutamate via transamination reactions or by their conversion to glutamate. In this network, we identified aspartate transaminase AspC as a major connector between many amino acids and glutamate. Additionally, we extended the transaminase network by the amino acids β-alanine, alanine, glycine, and serine as new amine sources and identified d-amino acid dehydrogenase (DadA) as an intracellular amino acid sink removing substrates from transaminase reactions. Finally, ammonium assimilation routes producing aspartate or leucine were introduced. Our study reveals the high flexibility of the cellular amination network, both in terms of transaminase promiscuity and adaptability to new connections and ammonium entry points.
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Affiliation(s)
| | - Alexandra Müller
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Tong Wu
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Pascal Pfister
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Selçuk Aslan
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Lennart Schada von Borzyskowski
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
- Institute of Biology Leiden, Leiden UniversityLeidenNetherlands
| | - Tobias J Erb
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
- Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Department of Biochemistry, Charité – Universitätsmedizin BerlinBerlinGermany
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2
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Bearne SL. Through the Looking Glass: Chiral Recognition of Substrates and Products at the Active Sites of Racemases and Epimerases. Chemistry 2020; 26:10367-10390. [DOI: 10.1002/chem.201905826] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/09/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Stephen L. Bearne
- Department of Biochemistry & Molecular BiologyDepartment of ChemistryDalhousie University Halifax, Nova Scotia B3H 4R2 Canada
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3
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Biochemical characterization and mutational analysis of alanine racemase from Clostridium perfringens. J Biosci Bioeng 2019; 128:149-155. [DOI: 10.1016/j.jbiosc.2019.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 02/03/2019] [Accepted: 02/06/2019] [Indexed: 11/24/2022]
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4
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A co-expression system to shift the equilibrium of transamination reactions toward the synthesis of enantiomerically pure amines. MOLECULAR CATALYSIS 2019. [DOI: 10.1016/j.mcat.2019.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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Mackie J, Kumar H, Bearne SL. Changes in quaternary structure cause a kinetic asymmetry of glutamate racemase-catalyzed homocysteic acid racemization. FEBS Lett 2018; 592:3399-3413. [PMID: 30194685 DOI: 10.1002/1873-3468.13248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/30/2018] [Accepted: 08/24/2018] [Indexed: 11/07/2022]
Abstract
Glutamate racemases (GR) catalyze the racemization of d- and l-glutamate and are targets for the development of antibiotics. We demonstrate that GR from the periodontal pathogen Fusobacterium nucleatum (FnGR) catalyzes the racemization of d-homocysteic acid (d-HCA), while l-HCA is a poor substrate. This enantioselectivity arises because l-HCA perturbs FnGR's monomer-dimer equilibrium toward inactive monomer. The inhibitory effect of l-HCA may be overcome by increasing the total FnGR concentration or by adding glutamate, but not by blocking access to the active site through site-directed mutagenesis, suggesting that l-HCA binds at an allosteric site. This phenomenon is also exhibited by GR from Bacillus subtilis, suggesting that enantiospecific, "substrate"-induced dissociation of oligomers to form inactive monomers may furnish a new inhibition strategy.
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Affiliation(s)
- Joanna Mackie
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada
| | - Himank Kumar
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada
| | - Stephen L Bearne
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada.,Department of Chemistry, Dalhousie University, Halifax, Canada
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6
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Building cellular pathways and programs enabled by the genetic diversity of allo-genomes and meta-genomes. Curr Opin Biotechnol 2015; 36:16-31. [DOI: 10.1016/j.copbio.2015.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/06/2015] [Accepted: 08/09/2015] [Indexed: 12/21/2022]
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7
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Liu D, Liu X, Zhang L, Jiao H, Ju J, Zhao B. Biochemical characteristics of an alanine racemase from Aeromonas hydrophil HBNUAh01. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715020071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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8
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Ju J, Xu S, Furukawa Y, Zhang Y, Misono H, Minamino T, Namba K, Zhao B, Ohnishi K. Correlation between catalytic activity and monomer-dimer equilibrium of bacterial alanine racemases. J Biochem 2010; 149:83-9. [PMID: 20971724 DOI: 10.1093/jb/mvq120] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
From the reaction mechanism and crystal structure analysis, a bacterial alanine racemase is believed to work as a homodimer with a substrate, l-alanine or d-alanine. We analysed oligomerization states of seven alanine racemases, biosynthetic and catabolic, from Escherichia coli, Salmonella typhimurium, Pseudomonas aeruginosa, P. putida and P. fluorescens, with three different methods, gel filtration chromatography, native PAGE and analytical ultracentrifugation. All alanine racemases were proved to be in a dynamic equilibrium between monomeric and dimeric form with every methods used in this study. In both biosynthetic and catabolic alanine racemases, association constants for dimerization were high for the enzymes with high V(max) values. The enzymes with low V(max) values gave the low association constants. We proposed that alanine racemases are classified into two types; the enzymes with low and high-equilibrium association constants for dimerization.
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Affiliation(s)
- Jiansong Ju
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050016, Japan
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9
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Dietrich JA, McKee AE, Keasling JD. High-throughput metabolic engineering: advances in small-molecule screening and selection. Annu Rev Biochem 2010; 79:563-90. [PMID: 20367033 DOI: 10.1146/annurev-biochem-062608-095938] [Citation(s) in RCA: 245] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Metabolic engineering for the overproduction of high-value small molecules is dependent upon techniques in directed evolution to improve production titers. The majority of small molecules targeted for overproduction are inconspicuous and cannot be readily obtained by screening. We provide a review on the development of high-throughput colorimetric, fluorescent, and growth-coupled screening techniques, enabling inconspicuous small-molecule detection. We first outline constraints on throughput imposed during the standard directed evolution workflow (library construction, transformation, and screening) and establish a screening and selection ladder on the basis of small-molecule assay throughput and sensitivity. An in-depth analysis of demonstrated screening and selection approaches for small-molecule detection is provided. Particular focus is placed on in vivo biosensor-based detection methods that reduce or eliminate in vitro assay manipulations and increase throughput. We conclude by providing our prospectus for the future, focusing on transcription factor-based detection systems as a natural microbial mode of small-molecule detection.
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Affiliation(s)
- Jeffrey A Dietrich
- UCSF-UCB Joint Graduate Group in Bioengineering, Berkeley, California 94720, USA.
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10
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Kinetic characterization and quaternary structure of glutamate racemase from the periodontal anaerobe Fusobacterium nucleatum. Arch Biochem Biophys 2009; 491:16-24. [DOI: 10.1016/j.abb.2009.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Revised: 09/11/2009] [Accepted: 09/15/2009] [Indexed: 11/17/2022]
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11
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Priyadarshi A, Lee EH, Sung MW, Nam KH, Lee WH, Kim EE, Hwang KY. Structural insights into the alanine racemase from Enterococcus faecalis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1030-40. [PMID: 19328247 DOI: 10.1016/j.bbapap.2009.03.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Revised: 02/19/2009] [Accepted: 03/04/2009] [Indexed: 11/13/2022]
Abstract
Alanine racemase (AlaR) is a bacterial enzyme that belongs to the fold-type III group of pyridoxal 5'-phosphate (PLP)-dependent enzymes. AlaR catalyzes the interconversion between L- and D-alanine, which is important for peptidoglycan biosynthesis. This enzyme is common in prokaryotes, but absent in eukaryotes, which makes it an attractive target for the design of new antibacterial drugs. Here, we report the crystal structures of both the apoenzyme and the d-cycloserine (DCS) complex of AlaR from the pathogenic bacterium Enterococcus faecalis v583, at a resolution of 2.5 A. DCS is a suicide inhibitor of AlaR and, as such, serves as an antimicrobial agent and has been used to treat tuberculosis and urinary tract infection-related diseases, and makes several hydrogen bonds with the conserved active site residues, Tyr44 and Ser207, respectively. The apoenzyme crystal structure of AlaR consists of three monomers in the asymmetric unit, including a polyethylene glycol molecule in the dimer interface that surrounds one of the His 293 residues and also sits close to one side of the His 293 residue in the opposite monomer. Our results provide structural insights into AlaR that may be used for the development of new antibiotics targeting the alanine racemase in pathogenic bacteria.
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Affiliation(s)
- Amit Priyadarshi
- Biomedical Research Center, Life Science Division, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 136-791, South Korea
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12
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Characterization of endogenous pyridoxal 5′-phosphate-dependent alanine racemase from Bacillus pseudofirmus OF4. J Biosci Bioeng 2009; 107:225-9. [DOI: 10.1016/j.jbiosc.2008.11.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Revised: 10/30/2008] [Accepted: 11/05/2008] [Indexed: 11/24/2022]
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13
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Abstract
Enzymes have become an attractive alternative to conventional catalysts in numerous industrial processes. However, their properties do not always meet the criteria of the application of interest. Directed evolution is a powerful tool for adopting the characteristics of an enzyme. However, selection of the evolved variants is a critical step, and therefore new strategies to enable selection of the desired enzymatic activity have been developed. This review focuses on these novel strategies for selecting enzymes from large libraries, in particular those that are used in the synthesis of pharmaceutical intermediates and pharmaceuticals.
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Affiliation(s)
- Ykelien L Boersma
- Department of Pharmaceutical Biology, Groningen University Institute for Drug Exploration, the Netherlands
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14
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Boersma YL, Dröge MJ, Quax WJ. Selection strategies for improved biocatalysts. FEBS J 2007. [DOI: 10.1111/j.0014-2956.2007.05782.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Matsuura T, Yomo T. In vitro evolution of proteins. J Biosci Bioeng 2006; 101:449-56. [PMID: 16935245 DOI: 10.1263/jbb.101.449] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2006] [Accepted: 05/08/2006] [Indexed: 11/17/2022]
Abstract
Consecutive rounds of diversification and selection of the fittest is believed to be the main driving force for the evolution of life. For the evolution of life to proceed, all living cells are surrounded by a lipid bilayer that separates their own genes from the external environment and from those of other organisms. In this way, the genetic information of an individual is replicated on the basis of their phenotype; thus the enrichment of the fittest will occur. Hence, evolution is based on linkage between genotype and phenotype owing to the surrounding of the genetic material with a barrier. The linkage between genotype and phenotype is also known to be essential for the directed evolution of proteins. Indeed, systems for molecular evolution, including phage display, ribosome display, and in vitro compartmentalization, all satisfy this requirement in different ways. These systems have been shown to be powerful tools for high-throughput screening for the functions of proteins, screening as many as <10(12) molecules in 1 d. These selection systems in combination with various gene libraries yield proteins with improved or altered biophysical properties, and may even allow the generation of proteins with novel functions.
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Affiliation(s)
- Tomoaki Matsuura
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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16
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Johannes TW, Zhao H. Directed evolution of enzymes and biosynthetic pathways. Curr Opin Microbiol 2006; 9:261-7. [PMID: 16621678 DOI: 10.1016/j.mib.2006.03.003] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2006] [Accepted: 03/31/2006] [Indexed: 11/19/2022]
Abstract
Directed evolution is an important tool for overcoming the limitations of natural enzymes as biocatalysts. Recent advances have focused on applying directed evolution to a variety of enzymes, such as epoxide hydrolase, glyphosate N-acetyltransferase, xylanase and phosphotriesterase, in order to improve their activity, selectivity, stability and solubility. The focus has also shifted to manipulating biosynthetic pathways for the production of many naturally synthesized compounds, as well as the production of novel 'unnatural' compounds. A combined directed evolution and computational design approach is becoming increasingly important in exploring enzyme sequence-space and creating improved or novel enzymes. Fueled by recent breakthroughs in genomics and metagenomics, these developments should help expand the use of biocatalysts in industry.
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Affiliation(s)
- Tyler W Johannes
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, IL 61801, USA
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