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Deletti G, Green SD, Weber C, Patterson KN, Joshi SS, Khopade TM, Coban M, Veek-Wilson J, Caulfield TR, Viswanathan R, Lane AL. Unveiling an indole alkaloid diketopiperazine biosynthetic pathway that features a unique stereoisomerase and multifunctional methyltransferase. Nat Commun 2023; 14:2558. [PMID: 37137876 PMCID: PMC10156859 DOI: 10.1038/s41467-023-38168-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 04/19/2023] [Indexed: 05/05/2023] Open
Abstract
The 2,5-diketopiperazines are a prominent class of bioactive molecules. The nocardioazines are actinomycete natural products that feature a pyrroloindoline diketopiperazine scaffold composed of two D-tryptophan residues functionalized by N- and C-methylation, prenylation, and diannulation. Here we identify and characterize the nocardioazine B biosynthetic pathway from marine Nocardiopsis sp. CMB-M0232 by using heterologous biotransformations, in vitro biochemical assays, and macromolecular modeling. Assembly of the cyclo-L-Trp-L-Trp diketopiperazine precursor is catalyzed by a cyclodipeptide synthase. A separate genomic locus encodes tailoring of this precursor and includes an aspartate/glutamate racemase homolog as an unusual D/L isomerase acting upon diketopiperazine substrates, a phytoene synthase-like prenyltransferase as the catalyst of indole alkaloid diketopiperazine prenylation, and a rare dual function methyltransferase as the catalyst of both N- and C-methylation as the final steps of nocardioazine B biosynthesis. The biosynthetic paradigms revealed herein showcase Nature's molecular ingenuity and lay the foundation for diketopiperazine diversification via biocatalytic approaches.
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Affiliation(s)
- Garrett Deletti
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA
| | - Sajan D Green
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA
| | - Caleb Weber
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA
| | - Kristen N Patterson
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Swapnil S Joshi
- Departments of Chemistry & Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, Andhra Pradesh, India
| | - Tushar M Khopade
- Departments of Chemistry & Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, Andhra Pradesh, India
| | - Mathew Coban
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - James Veek-Wilson
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA
| | - Thomas R Caulfield
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, 32224, USA
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Rajesh Viswanathan
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA.
- Departments of Chemistry & Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, Andhra Pradesh, India.
| | - Amy L Lane
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA.
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2
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Kobayashi NI, Takagi H, Yang X, Nishizawa-Yokoi A, Segawa T, Hoshina T, Oonishi T, Suzuki H, Iwata R, Toki S, Nakanishi TM, Tanoi K. Mutations in RZF1, a zinc-finger protein, reduce magnesium uptake in roots and translocation to shoots in rice. PLANT PHYSIOLOGY 2023; 192:342-355. [PMID: 36718554 PMCID: PMC10152673 DOI: 10.1093/plphys/kiad051] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 05/03/2023]
Abstract
Magnesium (Mg) homeostasis is critical for maintaining many biological processes, but little information is available to comprehend the molecular mechanisms regulating Mg concentration in rice (Oryza sativa). To make up for the lack of information, we aimed to identify mutants defective in Mg homeostasis through a forward genetic approach. As a result of the screening of 2,825 M2 seedlings mutated by ion-beam irradiation, we found a rice mutant that showed reduced Mg content in leaves and slightly increased Mg content in roots. Radiotracer 28Mg experiments showed that this mutant, named low-magnesium content 1 (LMGC1), has decreased Mg2+ influx in the root and Mg2+ translocation from root to shoot. Consequently, LMGC1 is sensitive to the low Mg condition and prone to develop chlorosis in the young mature leaf. The MutMap method identified a 7.4-kbp deletion in the LMGC1 genome leading to a loss of two genes. Genome editing using CRISPR-Cas9 further revealed that one of the two lost genes, a gene belonging to the RanBP2-type zinc-finger family that we named RanBP2-TYPE ZINC FINGER1 (OsRZF1), was the causal gene of the low Mg phenotype. OsRZF1 is a nuclear protein and may have a fundamental role in maintaining Mg homeostasis in rice plants.
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Affiliation(s)
- Natsuko I Kobayashi
- Graduate School of Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroki Takagi
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan
| | - Xiaoyu Yang
- Graduate School of Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ayako Nishizawa-Yokoi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 3-1-3 Kannondai, Tsukuba 305-8604, Japan
| | - Tenta Segawa
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan
| | - Tatsuaki Hoshina
- Graduate School of Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takayuki Oonishi
- Center for Education and Research of Community Collaboration, Utsunomiya University, Utsunomiya 321-8505, Japan
| | - Hisashi Suzuki
- National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Ren Iwata
- Cyclotron and Radioisotope Center (CYRIC), Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8572, Japan
| | - Seiichi Toki
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 3-1-3 Kannondai, Tsukuba 305-8604, Japan
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga 520-2194, Japan
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Yokohama, Kanagawa 236-0027, Japan
| | - Tomoko M Nakanishi
- Graduate School of Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Hoshi University, 2-4-41 Ebara, Shinagawa-Ku, Tokyo 142-8501, Japan
| | - Keitaro Tanoi
- Graduate School of Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Lloyd MD, Yevglevskis M, Nathubhai A, James TD, Threadgill MD, Woodman TJ. Racemases and epimerases operating through a 1,1-proton transfer mechanism: reactivity, mechanism and inhibition. Chem Soc Rev 2021; 50:5952-5984. [PMID: 34027955 PMCID: PMC8142540 DOI: 10.1039/d0cs00540a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Indexed: 12/12/2022]
Abstract
Racemases and epimerases catalyse changes in the stereochemical configurations of chiral centres and are of interest as model enzymes and as biotechnological tools. They also occupy pivotal positions within metabolic pathways and, hence, many of them are important drug targets. This review summarises the catalytic mechanisms of PLP-dependent, enolase family and cofactor-independent racemases and epimerases operating by a deprotonation/reprotonation (1,1-proton transfer) mechanism and methods for measuring their catalytic activity. Strategies for inhibiting these enzymes are reviewed, as are specific examples of inhibitors. Rational design of inhibitors based on substrates has been extensively explored but there is considerable scope for development of transition-state mimics and covalent inhibitors and for the identification of inhibitors by high-throughput, fragment and virtual screening approaches. The increasing availability of enzyme structures obtained using X-ray crystallography will facilitate development of inhibitors by rational design and fragment screening, whilst protein models will facilitate development of transition-state mimics.
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Affiliation(s)
- Matthew D Lloyd
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK.
| | - Maksims Yevglevskis
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK. and CatSci Ltd., CBTC2, Capital Business Park, Wentloog, Cardiff CF3 2PX, UK
| | - Amit Nathubhai
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK. and University of Sunderland, School of Pharmacy & Pharmaceutical Sciences, Sciences Complex, Sunderland SR1 3SD, UK
| | - Tony D James
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK and School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, People's Republic of China
| | - Michael D Threadgill
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK. and Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Aberystwyth SY23 3BY, UK
| | - Timothy J Woodman
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK.
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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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5
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Fischer C, Ahn YC, Vederas JC. Catalytic mechanism and properties of pyridoxal 5'-phosphate independent racemases: how enzymes alter mismatched acidity and basicity. Nat Prod Rep 2020; 36:1687-1705. [PMID: 30994146 DOI: 10.1039/c9np00017h] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: up to March 2019 Amino acid racemases and epimerases are key enzymes that invert the configuration of common amino acids and supply many corresponding d-isomers in living organisms. Some d-amino acids are inherently bioactive, whereas others are building blocks for important biomolecules, for example lipid II, the bacterial cell wall precursor. Peptides containing them have enhanced proteolytic stability and can act as important recognition elements in mammalian systems. Selective inhibition of certain amino acid racemases (e.g. glutamate racemase) is believed to offer a promising target for new antibacterial drugs effective against pathogens resistant to current antibiotics. Many amino acid racemases employ imine formation with pyridoxal phosphate (PLP) as a cofactor to accelerate the abstraction of the alpha proton. However, the group reviewed herein achieves racemization of free amino acids without the use of cofactors or metals, and uses a thiol/thiolate pair for deprotonation and reprotonation. All bacteria and higher plants contain such enzymes, for example diaminopimelate epimerase, which is required for lysine biosynthesis in these organisms. This process cannot be accomplished without an enzyme catalyst as the acidities of a thiol and the substrate α-hydrogen are inherently mismatched by at least 10 orders of magnitude. This review describes the structural and mechanistic studies on PLP-independent racemases and the evolving view of key enzymatic machinery that accomplishes these remarkable transformations.
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Affiliation(s)
- Conrad Fischer
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2G2.
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Cao DD, Zhang CP, Zhou K, Jiang YL, Tan XF, Xie J, Ren YM, Chen Y, Zhou CZ, Hou WT. Structural insights into the catalysis and substrate specificity of cyanobacterial aspartate racemase McyF. Biochem Biophys Res Commun 2019; 514:1108-1114. [PMID: 31101340 DOI: 10.1016/j.bbrc.2019.05.063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/07/2019] [Indexed: 11/27/2022]
Abstract
L-amino acids represent the most common amino acid form, most notably as protein residues, whereas D-amino acids, despite their rare occurrence, play significant roles in many biological processes. Amino acid racemases are enzymes that catalyze the interconversion of L- and/or D-amino acids. McyF is a pyridoxal 5'-phosphate (PLP) independent amino acid racemase that produces the substrate D-aspartate for the biosynthesis of microcystin in the cyanobacterium Microcystis aeruginosa PCC7806. Here we report the crystal structures of McyF in complex with citrate, L-Asp and D-Asp at 2.35, 2.63 and 2.80 Å, respectively. Structural analyses indicate that McyF and homologs possess highly conserved residues involved in substrate binding and catalysis. In addition, residues Cys87 and Cys195 were clearly assigned to the key catalytic residues of "two bases" that deprotonate D-Asp and L-Asp in a reaction independent of PLP. Further site-directed mutagenesis combined with enzymatic assays revealed that Glu197 also participates in the catalytic reaction. In addition, activity assays proved that McyF could also catalyze the interconversion of L-MeAsp between D-MeAsp, the precursor of another microcystin isoform. These findings provide structural insights into the catalytic mechanism of aspartate racemase and microcystin biosynthesis.
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Affiliation(s)
- Dong-Dong Cao
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui 230027, China
| | - Chun-Peng Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui 230027, China
| | - Kang Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui 230027, China
| | - Yong-Liang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui 230027, China
| | - Xiao-Feng Tan
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui 230027, China
| | - Jin Xie
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui 230027, China
| | - Yan-Min Ren
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui 230027, China
| | - Yuxing Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui 230027, China
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui 230027, China
| | - Wen-Tao Hou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui 230027, China.
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7
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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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8
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Jones RM, Popham DL, Schmidt AL, Neidle EL, Stabb EV. Vibrio fischeri DarR Directs Responses to d-Aspartate and Represents a Group of Similar LysR-Type Transcriptional Regulators. J Bacteriol 2018; 200:e00773-17. [PMID: 29437849 PMCID: PMC6040199 DOI: 10.1128/jb.00773-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 01/24/2018] [Indexed: 01/11/2023] Open
Abstract
Mounting evidence suggests that d-amino acids play previously underappreciated roles in diverse organisms. In bacteria, even d-amino acids that are absent from canonical peptidoglycan (PG) may act as growth substrates, as signals, or in other functions. Given these proposed roles and the ubiquity of d-amino acids, the paucity of known d-amino-acid-responsive transcriptional control mechanisms in bacteria suggests that such regulation awaits discovery. We found that DarR, a LysR-type transcriptional regulator (LTTR), activates transcription in response to d-Asp. The d-Glu auxotrophy of a Vibrio fischerimurI::Tn mutant was suppressed, with the wild-type PG structure maintained, by a point mutation in darR This darR mutation resulted in the overexpression of an adjacent operon encoding a putative aspartate racemase, RacD, which compensated for the loss of the glutamate racemase encoded by murI Using transcriptional reporters, we found that wild-type DarR activated racD transcription in response to exogenous d-Asp but not upon the addition of l-Asp, l-Glu, or d-Glu. A DNA sequence typical of LTTR-binding sites was identified between darR and the divergently oriented racD operon, and scrambling this sequence eliminated activation of the reporter in response to d-Asp. In several proteobacteria, genes encoding LTTRs similar to DarR are linked to genes with predicted roles in d- and/or l-Asp metabolism. To test the functional similarities in another bacterium, darR and racD mutants were also generated in Acinetobacter baylyi In V. fischeri and A. baylyi, growth on d-Asp required the presence of both darR and racD Our results suggest that multiple bacteria have the ability to sense and respond to d-Asp.IMPORTANCE d-Amino acids are prevalent in the environment and are generated by organisms from all domains of life. Although some biological roles for d-amino acids are understood, in other cases, their functions remain uncertain. Given the ubiquity of d-amino acids, it seems likely that bacteria will initiate transcriptional responses to them. Elucidating d-amino acid-responsive regulators along with the genes they control will help uncover bacterial uses of d-amino acids. Here, we report the discovery of DarR, a novel LTTR in V. fischeri that mediates a transcriptional response to environmental d-Asp and underpins the catabolism of d-Asp. DarR represents the founding member of a group of bacterial homologs that we hypothesize control aspects of aspartate metabolism in response to d-Asp and/or to d-Asp-containing peptides.
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Affiliation(s)
- Richard M Jones
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - David L Popham
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Alicia L Schmidt
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Ellen L Neidle
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Eric V Stabb
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
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9
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Expression of Pyridoxal 5'-Phosphate-Independent Racemases Can Reduce 2-Aminoacrylate Stress in Salmonella enterica. J Bacteriol 2018; 200:JB.00751-17. [PMID: 29440254 DOI: 10.1128/jb.00751-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 02/09/2018] [Indexed: 11/20/2022] Open
Abstract
The RidA protein (PF01042) from Salmonella enterica is a deaminase that quenches 2-aminoacrylate (2AA) and other reactive metabolites. In the absence of RidA, 2AA accumulates, damages cellular enzymes, and compromises the metabolic network. In vitro, RidA homologs from all domains of life deaminate 2AA, and RidA proteins from plants, bacteria, yeast, and humans complement the mutant phenotype of a ridA mutant strain of S. enterica In the present study, a methanogenic archaeon, Methanococcus maripaludis S2, was used to probe alternative mechanisms to restore metabolic balance. M. maripaludis MMP0739, which is annotated as an aspartate/glutamate racemase, complemented a ridA mutant strain and reduced the intracellular 2AA burden. The aspartate/glutamate racemase YgeA from Escherichia coli or S. enterica, when provided in trans, similarly restored wild-type growth to a ridA mutant. These results uncovered a new mechanism to ameliorate metabolic stress, and they suggest that direct quenching by RidA is not the only strategy to quench 2AA.IMPORTANCE 2-Aminoacrylate is an endogenously generated reactive metabolite that can damage cellular enzymes if not directly quenched by the conserved deaminase RidA. This study used an archaeon to identify a RidA-independent mechanism to prevent metabolic stress caused by 2AA. The data suggest that a gene product annotated as an aspartate/glutamate racemase (MMP0739) produces a metabolite that can quench 2AA, expanding our understanding of strategies available to quench reactive metabolites.
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Walton CJW, Parmeggiani F, Barber JEB, McCann JL, Turner NJ, Chica RA. Engineered Aminotransferase for the Production of d
-Phenylalanine Derivatives Using Biocatalytic Cascades. ChemCatChem 2017. [DOI: 10.1002/cctc.201701068] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Curtis J. W. Walton
- Department of Chemistry and Biomolecular Sciences; Centre for Catalysis Research and Innovation; University of Ottawa; 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada
| | - Fabio Parmeggiani
- Manchester Institute of Biotechnology; School of Chemistry; University of Manchester; 131 Princess Street M1 7DN Manchester United Kingdom
| | - Janet E. B. Barber
- Department of Chemistry and Biomolecular Sciences; Centre for Catalysis Research and Innovation; University of Ottawa; 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada
| | - Jenna L. McCann
- Department of Chemistry and Biomolecular Sciences; Centre for Catalysis Research and Innovation; University of Ottawa; 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada
| | - Nicholas J. Turner
- Manchester Institute of Biotechnology; School of Chemistry; University of Manchester; 131 Princess Street M1 7DN Manchester United Kingdom
| | - Roberto A. Chica
- Department of Chemistry and Biomolecular Sciences; Centre for Catalysis Research and Innovation; University of Ottawa; 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada
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11
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Identification and characterization of novel broad-spectrum amino acid racemases from Escherichia coli and Bacillus subtilis. Amino Acids 2017; 49:1885-1894. [DOI: 10.1007/s00726-017-2486-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 09/06/2017] [Indexed: 12/15/2022]
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12
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Cendron L, Ramazzina I, Puggioni V, Maccacaro E, Liuzzi A, Secchi A, Zanotti G, Percudani R. The Structure and Function of a Microbial Allantoin Racemase Reveal the Origin and Conservation of a Catalytic Mechanism. Biochemistry 2016; 55:6421-6432. [DOI: 10.1021/acs.biochem.6b00881] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Laura Cendron
- Department
of Biomedical Sciences, University of Padova, Padova, Italy
| | | | | | | | | | - Andrea Secchi
- Department
of Chemistry, University of Parma, Parma, Italy
| | - Giuseppe Zanotti
- Department
of Biomedical Sciences, University of Padova, Padova, Italy
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13
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Liu X, Gao F, Ma Y, Liu S, Cui Y, Yuan Z, Kang X. Crystal structure and molecular mechanism of an aspartate/glutamate racemase from Escherichia coli O157. FEBS Lett 2016; 590:1262-9. [PMID: 27001440 DOI: 10.1002/1873-3468.12148] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/13/2016] [Accepted: 03/16/2016] [Indexed: 02/02/2023]
Abstract
EcL-DER, the aspartate/glutamate racemase from the pathogen Escherichia coli O157, exhibits racemase activity for l-aspartate and l-glutamate. This study reports the crystal structures of apo-EcL-DER, the EcL-DER-l-aspartate and the EcL-DER-d-aspartate complexes. The EcL-DER structure contains two domains, forming pseudo-mirror symmetry in the active site. A unique catalytic pair consisting of Thr(83) and Cys(197) exists in the active site. The characteristic conformations of l-Asp and d-Asp in the active site provide a straight structural evidence for the racemization mechanism of EcL-DER. In addition, the diversity of catalytic pairs implies that PLP-independent amino acid racemases adopt various catalytic mechanisms and are classified into different subgroups.
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Affiliation(s)
- Xiuhua Liu
- College of Life Sciences, Hebei University, Baoding, China
| | - Fei Gao
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Yinliang Ma
- College of Life Sciences, Hebei University, Baoding, China
| | - Shuang Liu
- College of Life Sciences, Hebei University, Baoding, China
| | - Yaqi Cui
- College of Life Sciences, Hebei University, Baoding, China
| | - Zenglin Yuan
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Xianjiang Kang
- College of Life Sciences, Hebei University, Baoding, China
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