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Miyamoto T, Saitoh Y, Katane M, Sekine M, Sakai-Kato K, Homma H. Acetylornithine aminotransferase TM1785 performs multiple functions in the hyperthermophile Thermotoga maritima. FEBS Lett 2021; 595:2931-2941. [PMID: 34747014 DOI: 10.1002/1873-3468.14222] [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: 09/25/2021] [Revised: 10/29/2021] [Accepted: 10/31/2021] [Indexed: 02/02/2023]
Abstract
The hyperthermophilic bacterium Thermotoga maritima peptidoglycan contains unusual d-lysine alongside typical d-alanine and d-glutamate. We previously identified lysine racemase and threonine dehydratase, but knowledge of d-amino acid metabolism remains limited. Herein, we identified and characterized T. maritima acetylornithine aminotransferase TM1785. The enzyme was most active towards acetyl-l-ornithine, but also utilized l-glutamate, l-ornithine and acetyl-l-lysine as amino donors, and 2-oxoglutarate was the preferred amino acceptor. TM1785 also displayed racemase activity towards four amino acids and lyase activity towards l-cysteine, but no dehydratase activity towards l-serine, l-threonine or corresponding d-amino acids. Catalytic efficiency (kcat /Km ) was highest for aminotransferase activity and lowest for racemase activity. TM1785 is a novel acetylornithine aminotransferase associated with l-arginine biosynthesis that possesses two additional distinct activities.
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Affiliation(s)
- Tetsuya Miyamoto
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Yasuaki Saitoh
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Masumi Katane
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Masae Sekine
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Kumiko Sakai-Kato
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Hiroshi Homma
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
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Identification and biochemical characterization of threonine dehydratase from the hyperthermophile Thermotoga maritima. Amino Acids 2021; 53:903-915. [PMID: 33938999 DOI: 10.1007/s00726-021-02993-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/21/2021] [Indexed: 01/14/2023]
Abstract
The peptidoglycan of the hyperthermophile Thermotoga maritima contains an unusual component, D-lysine (D-Lys), in addition to the typical D-alanine (D-Ala) and D-glutamate (D-Glu). In a previous study, we identified a Lys racemase that is presumably associated with D-Lys biosynthesis. However, our understanding of D-amino acid metabolism in T. maritima and other bacteria remains limited, although D-amino acids in the peptidoglycan are crucial for preserving bacterial cell structure and resistance to environmental threats. Herein, we characterized enzymatic and structural properties of TM0356 that shares a high amino acid sequence identity with serine (Ser) racemase. The results revealed that TM0356 forms a tetramer with each subunit containing a pyridoxal 5'-phosphate as a cofactor. The enzyme did not exhibit racemase activity toward various amino acids including Ser, and dehydratase activity was highest toward L-threonine (L-Thr). It also acted on L-Ser and L-allo-Thr, but not on the corresponding D-amino acids. The catalytic mechanism did not follow typical Michaelis-Menten kinetics; it displayed a sigmoidal dependence on substrate concentration, with highest catalytic efficiency (kcat/K0.5) toward L-Thr. Interestingly, dehydratase activity was insensitive to allosteric regulators L-valine and L-isoleucine (L-Ile) at low concentrations, while these L-amino acids are inhibitors at high concentrations. Thus, TM0356 is a biosynthetic Thr dehydratase responsible for the conversion of L-Thr to α-ketobutyrate and ammonia, which is presumably involved in the first step of the biosynthesis of L-Ile.
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Miyamoto T, Homma H, Miyamoto T. D-Amino acid metabolism in bacteria. J Biochem 2021; 170:5-13. [PMID: 33788945 DOI: 10.1093/jb/mvab043] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/19/2021] [Indexed: 02/02/2023] Open
Affiliation(s)
- Tetsuya Miyamoto
- Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Hiroshi Homma
- Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Tetsuya Miyamoto
- Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
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Miyamoto T, Moriya T, Homma H, Oshima T. Enzymatic properties and physiological function of glutamate racemase from Thermus thermophilus. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140461. [PMID: 32474108 DOI: 10.1016/j.bbapap.2020.140461] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/08/2020] [Accepted: 05/26/2020] [Indexed: 01/12/2023]
Abstract
d-Amino acids are physiologically important components of peptidoglycan in the bacterial cell wall, maintaining cell structure and aiding adaptation to environmental changes through peptidoglycan remodelling. Therefore, the biosynthesis of d-amino acids is essential for bacteria to adapt to different environmental conditions. The peptidoglycan of the extremely thermophilic bacterium Thermus thermophilus contains d-alanine (d-Ala) and d-glutamate (d-Glu), but its d-amino acid metabolism remains poorly understood. Here, we investigated the enzyme activity and function of the product of the TTHA1643 gene, which is annotated to be a Glu racemase in the T. thermophilus HB8 genome. Among 21 amino acids tested, TTHA1643 showed highly specific activity toward Glu as the substrate. The catalytic efficiency (kcat/Km) of TTHA1643 toward d- and l-Glu was comparable; however, the kcat value was 18-fold higher for l-Glu than for d-Glu. Temperature and pH profiles showed that the racemase activity of TTHA1643 is high under physiological conditions for T. thermophilus growth. To assess physiological relevance, we constructed a TTHA1643-deficient strain (∆TTHA1643) by replacing the TTHA1643 gene with the thermostable hygromycin resistance gene. Growth of the ∆TTHA1643 strain in synthetic medium without d-Glu was clearly diminished relative to wild type, although the TTHA1643 deletion was not lethal, suggesting that alternative d-Glu biosynthetic pathways may exist. The deterioration in growth was restored by adding d-Glu to the culture medium, showing that d-Glu is required for normal growth of T. thermophilus. Collectively, our findings show that TTHA1643 is a Glu racemase and has the physiological function of d-Glu production in T. thermophilus.
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Affiliation(s)
- Tetsuya Miyamoto
- Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Toshiyuki Moriya
- Institute of Environmental Microbiology, Kyowa Kako Co., 2-15-5 Tadao, Machida, Tokyo 194-0035, Japan
| | - Hiroshi Homma
- Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Tairo Oshima
- Institute of Environmental Microbiology, Kyowa Kako Co., 2-15-5 Tadao, Machida, Tokyo 194-0035, Japan.
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Miyamoto T, Katane M, Saitoh Y, Sekine M, Homma H. Elucidation of the d-lysine biosynthetic pathway in the hyperthermophile Thermotoga maritima. FEBS J 2018; 286:601-614. [PMID: 30548096 DOI: 10.1111/febs.14720] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/29/2018] [Accepted: 12/03/2018] [Indexed: 12/31/2022]
Abstract
Various d-amino acids are involved in peptidoglycan and biofilm metabolism in bacteria, suggesting that these compounds are necessary for successful adaptation to environmental changes. In addition to the conventional d-alanine (d-Ala) and d-glutamate, the peptidoglycan of the hyperthermophilic bacterium Thermotoga maritima contains both l-lysine (l-Lys) and d-Lys, but not meso-diaminopimelate (meso-Dpm). d-Lys is an uncommon component of peptidoglycan, and its biosynthetic pathway remains unclear. In this study, we identified and characterized a novel Lys racemase (TM1597) and Dpm epimerase (TM1522) associated with the d-Lys biosynthetic pathway in T. maritima. The Lys racemase had a dimeric structure containing pyridoxal 5'-phosphate as a cofactor. Among the amino acids, it exhibited the highest racemase activity toward d- and l-Lys, and also had relatively high activity toward d- and l-enantiomers of ornithine and Ala. The Dpm epimerase had the highest epimerization activity toward ll- and meso-Dpm, and also measurably racemized certain amino acids, including Lys. These results suggest that Lys racemase contributes to production of d-Lys and d-Ala for use as peptidoglycan components, and that Dpm epimerase converts ll-Dpm to meso-Dpm, a precursor in the l-Lys biosynthetic pathway.
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Affiliation(s)
- Tetsuya Miyamoto
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Masumi Katane
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Yasuaki Saitoh
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Masae Sekine
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Hiroshi Homma
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
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Radkov AD, Moe LA. A Broad Spectrum Racemase in Pseudomonas putida KT2440 Plays a Key Role in Amino Acid Catabolism. Front Microbiol 2018; 9:1343. [PMID: 30008699 PMCID: PMC6034422 DOI: 10.3389/fmicb.2018.01343] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 05/31/2018] [Indexed: 02/02/2023] Open
Abstract
The broad-spectrum amino acid racemase (Alr) of Pseudomonas putida KT2440 preferentially interconverts the l- and d-stereoisomers of Lys and Arg. Despite conservation of broad-spectrum racemases among bacteria, little is known regarding their physiological role. Here we explore potential functional roles for Alr in P. putida KT2440. We demonstrate through cellular fractionation that Alr enzymatic activity is found in the periplasm, consistent with its putative periplasm targeting sequence. Specific activity of Alr is highest during exponential growth, and this activity corresponds with an increased accumulation of d-Lys in the growth medium. An alr gene knockout strain (Δalr) was generated and used to assess potential roles for the alr gene in peptidoglycan structure, producing soluble signaling compounds, and amino acid metabolism. The stationary phase peptidoglycan structure did not differ between wild-type and Δalr strains, indicating that products resulting from Alr activity are not incorporated into peptidoglycan under these conditions. RNA-seq was used to assess differences in the transcriptome between the wild-type and Δalr strains. Genes undergoing differential expression were limited to those involved in amino acid metabolism. The Δalr strain exhibited a limited capacity for catabolism of l-Lys and l-Arg as the sole source of carbon and nitrogen. This is consistent with a predicted role for Alr in catabolism of l-Lys by virtue of its ability to convert l-Lys to d-Lys, which is further catabolized through the l-pipecolate pathway. The metabolic profiles here also implicate Alr in catabolism of l-Arg, although the pathway by which d-Arg is further catabolized is not clear at this time. Overall, data presented here describe the primary role of Alr as important for basic amino acid metabolism.
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Affiliation(s)
- Atanas D Radkov
- Department of Plant and Soil Sciences, College of Agriculture, University of Kentucky, Lexington, KY, United States
| | - Luke A Moe
- Department of Plant and Soil Sciences, College of Agriculture, University of Kentucky, Lexington, KY, United States
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Cystathionine β-lyase is involved in d-amino acid metabolism. Biochem J 2018; 475:1397-1410. [PMID: 29592871 DOI: 10.1042/bcj20180039] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 03/23/2018] [Accepted: 03/28/2018] [Indexed: 01/07/2023]
Abstract
Non-canonical d-amino acids play important roles in bacteria including control of peptidoglycan metabolism and biofilm disassembly. Bacteria appear to produce non-canonical d-amino acids to adapt to various environmental changes, and understanding the biosynthetic pathways is important. We identified novel amino acid racemases possessing the ability to produce non-canonical d-amino acids in Escherichia coli and Bacillus subtilis in our previous study, whereas the biosynthetic pathways of these d-amino acids still remain unclear. In the present study, we demonstrated that two cystathionine β-lyases (MetC and MalY) from E. coli produce non-canonical d-amino acids including non-proteinogenic amino acids. Furthermore, MetC displayed d- and l-serine (Ser) dehydratase activity. We characterised amino acid racemase, Ser dehydratase and cysteine lyase activities, and all were higher for MetC. Interestingly, all three activities were at a comparable level for MetC, although optimal conditions for each reaction were distinct. These results indicate that MetC and MalY are multifunctional enzymes involved in l-methionine metabolism and the production of d-amino acids, as well as d- and l-Ser metabolism. To our knowledge, this is the first evidence that cystathionine β-lyase is a multifunctional enzyme with three different activities.
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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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Efficient Production of Enantiopure d-Lysine from l-Lysine by a Two-Enzyme Cascade System. Catalysts 2016. [DOI: 10.3390/catal6110168] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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Hernández SB, Cava F. Environmental roles of microbial amino acid racemases. Environ Microbiol 2015; 18:1673-85. [DOI: 10.1111/1462-2920.13072] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 09/15/2015] [Accepted: 09/27/2015] [Indexed: 02/02/2023]
Affiliation(s)
- Sara B. Hernández
- Laboratory for Molecular Infection Medicine Sweden; Department of Molecular Biology; Umeå Centre for Microbial Research; Umeå University; 90187 Umeå Sweden
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden; Department of Molecular Biology; Umeå Centre for Microbial Research; Umeå University; 90187 Umeå Sweden
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Bacterial synthesis of D-amino acids. Appl Microbiol Biotechnol 2014; 98:5363-74. [PMID: 24752840 DOI: 10.1007/s00253-014-5726-3] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/22/2014] [Accepted: 03/25/2014] [Indexed: 12/30/2022]
Abstract
Recent work has shed light on the abundance and diversity of D-amino acids in bacterial extracellular/periplasmic molecules, bacterial cell culture, and bacteria-rich environments. Within the extracellular/periplasmic space, D-amino acids are necessary components of peptidoglycan, and disruption of their synthesis leads to cell death. As such, enzymes responsible for D-amino acid synthesis are promising targets for antibacterial compounds. Further, bacteria are shown to incorporate a diverse collection of D-amino acids into their peptidoglycan, and differences in D-amino acid incorporation may occur in response to differences in growth conditions. Certain D-amino acids can accumulate to millimolar levels in cell culture, and their synthesis is proposed to foretell movement from exponential growth phase into stationary phase. While enzymes responsible for synthesis of D-amino acids necessary for peptidoglycan (D-alanine and D-glutamate) have been characterized from a number of different bacteria, the D-amino acid synthesis enzymes characterized to date cannot account for the diversity of D-amino acids identified in bacteria or bacteria-rich environments. Free D-amino acids are synthesized by racemization or epimerization at the α-carbon of the corresponding L-amino acid by amino acid racemase or amino acid epimerase enzymes. Additionally, D-amino acids can be synthesized by stereospecific amination of α-ketoacids. Below, we review the roles of D-amino acids in bacterial physiology and biotechnology, and we describe the known mechanisms by which they are synthesized by bacteria.
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Gauthier NP, Soufi B, Walkowicz WE, Pedicord VA, Mavrakis KJ, Macek B, Gin DY, Sander C, Miller ML. Cell-selective labeling using amino acid precursors for proteomic studies of multicellular environments. Nat Methods 2013; 10:768-73. [PMID: 23817070 PMCID: PMC4002004 DOI: 10.1038/nmeth.2529] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 05/08/2013] [Indexed: 11/23/2022]
Abstract
To address limitations of current high-throughput methods for studying cell-cell communication and determining the cell-of-origin of proteins in multicellular environments, we have developed a technique that selectively and continuously labels the proteome of individual cell types in co-culture. Through transgenic expression of exogenous amino acid biosynthesis enzymes, vertebrate cells overcome their dependence on essential amino acids and can be selectively labeled through metabolic incorporation of amino acids produced from heavy isotope-labeled precursors. We have named this method Type specific labeling with Amino acid Precursors (CTAP). Testing CTAP in several human and mouse cell lines, we were able to differentially label the proteome of distinct cell populations in co-culture and determine the relative expression of proteins by quantitative mass spectrometry. In addition, CTAP successfully identified the cell-of-origin of extracellular proteins in co-culture, highlighting its potential use in biomarker discovery for linking secreted factors to their cellular source.
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Affiliation(s)
- Nicholas P Gauthier
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.
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Wu HM, Kuan YC, Chu CH, Hsu WH, Wang WC. Crystal structures of lysine-preferred racemases, the non-antibiotic selectable markers for transgenic plants. PLoS One 2012; 7:e48301. [PMID: 23118975 PMCID: PMC3485190 DOI: 10.1371/journal.pone.0048301] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 09/24/2012] [Indexed: 11/18/2022] Open
Abstract
Lysine racemase, a pyridoxal 5′-phosphate (PLP)-dependent amino acid racemase that catalyzes the interconversion of lysine enantiomers, is valuable to serve as a novel non-antibiotic selectable marker in the generation of transgenic plants. Here, we have determined the first crystal structure of a lysine racemase (Lyr) from Proteus mirabilis BCRC10725, which shows the highest activity toward lysine and weaker activity towards arginine. In addition, we establish the first broad-specificity amino acid racemase (Bar) structure from Pseudomonas putida DSM84, which presents not only the highest activity toward lysine but also remarkably broad substrate specificity. A complex structure of Bar-lysine is also established here. These structures demonstrate the similar fold of alanine racemase, which is a head-to-tail homodimer with each protomer containing an N-terminal (α/β)8 barrel and a C-terminal β-stranded domain. The active-site residues are located at the protomer interface that is a funnel-like cavity with two catalytic bases, one from each protomer, and the PLP binding site is at the bottom of this cavity. Structural comparisons, site-directed mutagenesis, kinetic, and modeling studies identify a conserved arginine and an adjacent conserved asparagine that fix the orientation of the PLP O3 atom in both structures and assist in the enzyme activity. Furthermore, side chains of two residues in α-helix 10 have been discovered to point toward the cavity and define the substrate specificity. Our results provide a structural foundation for the design of racemases with pre-determined substrate specificity and for the development of the non-antibiotic selection system in transgenic plants.
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Affiliation(s)
- Hsin-Mao Wu
- Institute of Molecular and Cellular Biology and Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Chia Kuan
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Chia-Han Chu
- Biomedical Science and Engineering Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Wen-Hwei Hsu
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Wen-Ching Wang
- Institute of Molecular and Cellular Biology and Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
- Biomedical Science and Engineering Center, National Tsing Hua University, Hsinchu, Taiwan
- * E-mail:
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