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Hogan AM, Motnenko A, Rahman ASMZ, Cardona ST. Cell envelope structural and functional contributions to antibiotic resistance in Burkholderia cenocepacia. J Bacteriol 2024; 206:e0044123. [PMID: 38501654 PMCID: PMC11025338 DOI: 10.1128/jb.00441-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
Antibiotic activity is limited by the physical construction of the Gram-negative cell envelope. Species of the Burkholderia cepacia complex (Bcc) are known as intrinsically multidrug-resistant opportunistic pathogens with low permeability cell envelopes. Here, we re-examined a previously performed chemical-genetic screen of barcoded transposon mutants in B. cenocepacia K56-2, focusing on cell envelope structural and functional processes. We identified structures mechanistically important for resistance to singular and multiple antibiotic classes. For example, susceptibility to novobiocin, avibactam, and the LpxC inhibitor, PF-04753299, was linked to the BpeAB-OprB efflux pump, suggesting these drugs are substrates for this pump in B. cenocepacia. Defects in peptidoglycan precursor synthesis specifically increased susceptibility to cycloserine and revealed a new putative amino acid racemase, while defects in divisome accessory proteins increased susceptibility to multiple β-lactams. Additionally, disruption of the periplasmic disulfide bond formation system caused pleiotropic defects on outer membrane integrity and β-lactamase activity. Our findings highlight the layering of resistance mechanisms in the structure and function of the cell envelope. Consequently, we point out processes that can be targeted for developing antibiotic potentiators.IMPORTANCEThe Gram-negative cell envelope is a double-layered physical barrier that protects cells from extracellular stressors, such as antibiotics. The Burkholderia cell envelope is known to contain additional modifications that reduce permeability. We investigated Burkholderia cell envelope factors contributing to antibiotic resistance from a genome-wide view by re-examining data from a transposon mutant library exposed to an antibiotic panel. We identified susceptible phenotypes for defects in structures and functions in the outer membrane, periplasm, and cytoplasm. Overall, we show that resistance linked to the cell envelope is multifaceted and provides new targets for the development of antibiotic potentiators.
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Affiliation(s)
- Andrew M. Hogan
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Anna Motnenko
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Silvia T. Cardona
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
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2
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Vahdati SN, Behboudi H, Navasatli SA, Tavakoli S, Safavi M. New insights into the inhibitory roles and mechanisms of D-amino acids in bacterial biofilms in medicine, industry, and agriculture. Microbiol Res 2022; 263:127107. [PMID: 35843196 DOI: 10.1016/j.micres.2022.127107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 11/26/2022]
Abstract
Biofilms are complex aggregates of microbes that are tightly protected by an extracellular matrix (ECM) and may attach to a surface or adhere together. A higher persistence of bacteria on biofilms makes them resistant not only to harsh conditions but also to various antibiotics which led to the emergence of problems in different applications. Recently, it has been discovered that many bacteria produce and release various D-amino acids (D-AAs) to inhibit biofilm formation, which made a great deal of interest in research into the control of bacterial biofilms in diverse fields, such as human health, industrial settings, and medical devices. D-AAs have various mechanisms to inhibit bacterial biofilms such as: (i) interfering with protein synthesis (ii) Inhibition of extracellular polymeric materials (EPS) productions (protein, eDNA, and polysaccharide) (iii) Inhibition of quorum sensing (autoinducers), and (iv) interfere with peptidoglycan synthesis, these various modes of action, enables these small molecules to inhibit both Gram-negative and Gram-positive bacterial biofilms. Since most biofilms are multi-species, D-AAs in combination with other antimicrobial agents are good choices to combat a variety of bacterial biofilms without displaying toxicity on human cells. This review article addressed the role of D-AAs in controlling several bacterial biofilms and described the possible or definite mechanisms involved in this process.
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Affiliation(s)
- Saeed Niazi Vahdati
- Institute of Biochemistry and Biophysics, Department of Biochemistry, University of Tehran, Tehran, Iran
| | - Hossein Behboudi
- Department of Biology, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran.
| | - Sepideh Aliniaye Navasatli
- Institute of Biochemistry and Biophysics, Department of Biochemistry, University of Tehran, Tehran, Iran
| | - Sara Tavakoli
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Maliheh Safavi
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, Iran
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3
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Koper K, Han SW, Pastor DC, Yoshikuni Y, Maeda HA. Evolutionary Origin and Functional Diversification of Aminotransferases. J Biol Chem 2022; 298:102122. [PMID: 35697072 PMCID: PMC9309667 DOI: 10.1016/j.jbc.2022.102122] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022] Open
Abstract
Aminotransferases (ATs) are pyridoxal 5′-phosphate–dependent enzymes that catalyze the transamination reactions between amino acid donor and keto acid acceptor substrates. Modern AT enzymes constitute ∼2% of all classified enzymatic activities, play central roles in nitrogen metabolism, and generate multitude of primary and secondary metabolites. ATs likely diverged into four distinct AT classes before the appearance of the last universal common ancestor and further expanded to a large and diverse enzyme family. Although the AT family underwent an extensive functional specialization, many AT enzymes retained considerable substrate promiscuity and multifunctionality because of their inherent mechanistic, structural, and functional constraints. This review summarizes the evolutionary history, diverse metabolic roles, reaction mechanisms, and structure–function relationships of the AT family enzymes, with a special emphasis on their substrate promiscuity and multifunctionality. Comprehensive characterization of AT substrate specificity is still needed to reveal their true metabolic functions in interconnecting various branches of the nitrogen metabolic network in different organisms.
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Affiliation(s)
- Kaan Koper
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Sang-Woo Han
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Yasuo Yoshikuni
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Global Center for Food, Land, and Water Resources, Research Faculty of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
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4
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Zhang L, Zeng F, McKay CP, Navarro-González R, Sun HJ. Optimizing Chiral Selectivity in Practical Life-Detection Instruments. ASTROBIOLOGY 2021; 21:505-510. [PMID: 33885325 DOI: 10.1089/ast.2020.2381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Preferential uptake of either levorotatory (L) or dextrorotatory (D) enantiomer of a chiral molecule is a potential planetary life-detection method. On Earth, bacteria, as a rule, metabolize D-sugars and L-amino acids. Here, we use growth experiments to identify exceptions to the rule and their potential impact on the method's reliability. Our experiments involve six strains of Bacillus and collective uptake of the sugars glucose and arabinose, and the amino acids alanine, glutamic acid, leucine, cysteine, and serine-all of which are highly soluble. We find that selective uptake is not evident unless (1) each sugar is tested individually and (2) multiple amino acids are tested together in a mixture. Combining sugars should be avoided because, as we show in Bacillus bacteria, the same organisms may catabolize one sugar, glucose, in D-form and another sugar, arabinose, in L-form. Single amino acids should be avoided because bacteria can access certain proteinogenically incompatible enantiomers using specific racemases. Specifically, bacteria contain an alanine acid racemase and can catabolize D-alanine if no other D-amino acids are present. The proposed improvements would reliably separate nonselective chemical reactions from biological reactions and, if life is indicated, inform whether the selective patterns for amino acids and sugars are the same as on Earth.
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Affiliation(s)
- Ling Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Desert Plant Roots Ecology and Vegetation Restoration Laboratory, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, Xinjiang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fanjiang Zeng
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Desert Plant Roots Ecology and Vegetation Restoration Laboratory, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, Xinjiang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Christopher P McKay
- Space Science Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Rafael Navarro-González
- Laboratorio de Química de Plasmas y Estudios Planetarios, Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Henry J Sun
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas, Nevada, USA
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5
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Sidiq KR, Chow MW, Zhao Z, Daniel RA. Alanine metabolism in Bacillus subtilis. Mol Microbiol 2020; 115:739-757. [PMID: 33155333 DOI: 10.1111/mmi.14640] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/30/2022]
Abstract
Both isomeric forms of alanine play a crucial role in bacterial growth and viability; the L-isomer of this amino acid is one of the building blocks for protein synthesis, and the D-isomer is incorporated into the bacterial cell wall. Despite a long history of genetic manipulation of Bacillus subtilis using auxotrophic markers, the genes involved in alanine metabolism have not been characterized fully. In this work, we genetically characterized the major enzymes involved in B. subtilis alanine biosynthesis and identified an alanine permease, AlaP (YtnA), which we show has a major role in the assimilation of D-alanine from the environment. Our results provide explanations for the puzzling fact that growth of B. subtilis does not result in the significant accumulation of extracellular D-alanine. Interestingly, we find that in B. subtilis, unlike E. coli where multiple enzymes have a biochemical activity that can generate alanine, the primary synthetic enzyme for alanine is encoded by alaT, although a second gene, dat, can support slow growth of an L-alanine auxotroph. However, our results also show that Dat mediates the synthesis of D-alanine and its activity is influenced by the abundance of L-alanine. This work provides valuable insights into alanine metabolism that suggests that the relative abundance of D- and L-alanine might be linked with cytosolic pool of D and L-glutamate, thereby coupling protein and cell envelope synthesis with the metabolic status of the cell. The results also suggest that, although some of the purified enzymes involved in alanine biosynthesis have been shown to catalyze reversible reactions in vitro, most of them function unidirectionally in vivo.
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Affiliation(s)
- Karzan R Sidiq
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical Faculty, Newcastle University, Newcastle Upon Tyne, UK
| | - Man W Chow
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical Faculty, Newcastle University, Newcastle Upon Tyne, UK
| | - Zhao Zhao
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical Faculty, Newcastle University, Newcastle Upon Tyne, UK
| | - Richard A Daniel
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical Faculty, Newcastle University, Newcastle Upon Tyne, UK
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Wang R, Zhang Z, Sun J, Jiao N. Differences in bioavailability of canonical and non-canonical D-amino acids for marine microbes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 733:139216. [PMID: 32454292 DOI: 10.1016/j.scitotenv.2020.139216] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/22/2020] [Accepted: 05/03/2020] [Indexed: 06/11/2023]
Abstract
Dissolved organic matter (DOM) accounts for >95% of total marine organic matter, and >95% of marine DOM is refractory to biodegradation. The recalcitrancy of DOM determines its residence time and thus is of great concern regarding to carbon sequestration in the ocean. However, the recalcitrancy of DOM not only varies among different compounds but also within different conformations of a same molecule such as L-amino acids (L-AAs) and D-amino acids (D-AAs). While the former is labile, the latter is refractory and used as a proxy for estimation of bacterial refractory DOM in the ocean. However, some D-AAs are also reported to be bioavailable. To clarify the controversy, we examined the bioavailability of two types of D-AAs: canonical D-AAs, which mainly present as bacterial cell wall components, and non-canonical D-AAs (NCDAAs), which are secreted by various bacteria as signaling molecules in bacterial physiology. Bioassay experiments were conducted with nine marine bacterial strains and a natural microbial community. D-AAs were poorly utilized by the strains as sole carbon or nitrogen sources compared with L-AAs, in addition, NCDAAs were barely used compared with canonical D-AAs. In comparison, the microbial community consumed all three canonical D-AAs (D-alanine, D-aspartic acid and D-glutamic acid) as efficiently as their corresponding L-AAs when supplied separately; however, L-AAs were preferentially used over D-AAs when both forms were provided simultaneously. Remarkably, two NCDAAs, D-methionine and D-leucine, were poorly utilized regardless of the presence of the L-enantiomers. It was found for the first time that NCDAAs are relatively more refractory than canonical D-AAs to microbial utilization. This novel recognition of difference in recalcitrancy between NCDAAs and canonical D-AAs lays the foundation for a better understanding of carbon cycling and more accurate estimation of carbon storage in the ocean.
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Affiliation(s)
- Rui Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China; Institute of Marine Microbes and Ecospheres, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, People's Republic of China
| | - Zilian Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China; Institute of Marine Microbes and Ecospheres, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, People's Republic of China.
| | - Jia Sun
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China; Institute of Marine Microbes and Ecospheres, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, People's Republic of China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China; Institute of Marine Microbes and Ecospheres, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, People's Republic of China.
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7
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Lin JC, Wang XZ, Shen T, Zhang JY. iTRAQ-based quantitative analysis reveals the mechanism underlying the changes in physiological activity in a glutamate racemase mutant strain of Streptococcus mutans UA159. Mol Biol Rep 2020; 47:3719-3733. [PMID: 32338332 DOI: 10.1007/s11033-020-05463-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/17/2020] [Indexed: 11/30/2022]
Abstract
Streptococcus mutans UA159 is responsible for human dental caries with robust cariogenic potential. Our previous study noted that a glutamate racemase (MurI) mutant strain (designated S. mutans FW1718), with the hereditary background of UA159, displayed alterations of morphogenesis, attenuated stress tolerance, and weakened biofilm-forming capabilities, accompanying with unclear mechanisms. In this study, we applied isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics to characterize the proteome profiles of the murI mutant strain vs. the wild-type strain in chemically defined media to elucidate the mechanisms by which S. mutans copes with MurI deficiency. Whole-cell proteins of S. mutans FW1718 and UA159 were assessed by iTRAQ-coupled LC-ESI-MS/MS. Furthermore, differentially expressed proteins (DEPs) were identified by Mascot, Gene Ontology (GO) annotation, Cluster of Orthologous Groups of proteins (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Finally, a protein-protein interaction (PPI) network was established using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING). Among 1173 total bacterial proteins identified, 112 DEPs exhibited altered expression patterns in S. mutans UA159 with or without the murI mutation. The ΔmurI cells displayed an increase in the relative expression of 93 proteins (fold change ≥ 1.2, p < 0.05) and a decrease in 29 proteins (fold change ≤ 0.833, p < 0.05) compared with the wild-type cells. PPI analysis revealed a complex network of DEPs containing 191 edges and 122 nodes. The DEPs significantly upregulated after murI knockout had roles in diverse functional processes spanning cell-wall biosynthesis, energy production, and DNA replication and repair. We identified distinct variations and diverse modulators caused by murI mutation in the proteome of S. mutans, indicating that the modification of cell membrane structure, redistribution of energy metabolism and enhanced nucleic acid machinery contributed to the S. mutans response to specific environmental contexts.
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Affiliation(s)
- Jia-Cheng Lin
- Department of Pediatric Dentistry, Guanghua School of Stomatology, Affiliated Stomatological Hospital, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiang-Zhu Wang
- Operative Dentistry and Endodontics, Xiangya School of Stomatology, Xiangya Stomatological Hospital, Central South University, Changsha, Hunan, China
| | - Ting Shen
- Operative Dentistry and Endodontics, Xiangya School of Stomatology, Xiangya Stomatological Hospital, Central South University, Changsha, Hunan, China
| | - Jian-Ying Zhang
- Operative Dentistry and Endodontics, Xiangya School of Stomatology, Xiangya Stomatological Hospital, Central South University, Changsha, Hunan, China.
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8
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Muhammad M, Bai J, Alhassan AJ, Sule H, Ju J, Zhao B, Liu D. Significance of Glutamate Racemase for the Viability and Cell Wall Integrity of Streptococcus iniae. BIOCHEMISTRY (MOSCOW) 2020; 85:248-256. [PMID: 32093601 DOI: 10.1134/s0006297920020121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Streptococcus iniae is a pathogenic and zoonotic bacterium responsible for human diseases and mortality of many fish species. Recently, this bacterium has demonstrated an increasing trend for antibiotics resistance, which has warranted a search for new approaches to tackle its infection. Glutamate racemase (MurI) is a ubiquitous enzyme of the peptidoglycan synthesis pathway that plays an important role in the cell wall integrity maintenance; however, the significance of this enzyme differs in different species. In this study, we knocked out the MurI gene in S. iniae in order to elucidate the role of glutamate racemase in maintaining cell wall integrity in this bacterial species. We also cloned, expressed, and purified MurI and determined its biochemical characteristics. Biochemical analysis revealed that the MurI gene in S. iniae encodes a functional enzyme with a molecular weight of 30 kDa, temperature optimum at 35°C, and pH optimum at 8.5. Metal ions, such as Cu2+, Mn2+, Co2+ and Zn2+, inhibited the enzyme activity. MurI was found to be essential for the viability and cell wall integrity of S. iniae. The optimal growth of the MurI-deficient S. iniae mutant can be achieved only by adding a high concentration of D-glutamate to the medium. Membrane permeability assay of the mutant showed an increasing extent of the cell wall damage with time upon D-glutamate starvation. Moreover, the mutant lost its virulence when incubated in fish blood. Our results demonstrated that the MurI knockout leads to the generation of S. iniae auxotroph with damaged cell walls.
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Affiliation(s)
- M Muhammad
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China.,Kano University of Science and Technology, Department of Biochemistry, Wudil, Nigeria
| | - J Bai
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - A J Alhassan
- Bayero University Kano, Department of Biochemistry, Kano, Nigeria
| | - H Sule
- Bayero University Kano, Department of Medical Laboratory Science, Kano, Nigeria
| | - J Ju
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - B Zhao
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China.
| | - D Liu
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China.
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9
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Halmschlag B, Steurer X, Putri SP, Fukusaki E, Blank LM. Tailor-made poly-γ-glutamic acid production. Metab Eng 2019; 55:239-248. [DOI: 10.1016/j.ymben.2019.07.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/16/2019] [Accepted: 07/20/2019] [Indexed: 10/26/2022]
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10
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Xue YP, Cao CH, Zheng YG. Enzymatic asymmetric synthesis of chiral amino acids. Chem Soc Rev 2018; 47:1516-1561. [DOI: 10.1039/c7cs00253j] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This review summarizes the progress achieved in the enzymatic asymmetric synthesis of chiral amino acids from prochiral substrates.
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Affiliation(s)
- Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Cheng-Hao Cao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
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11
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Mortuza R, Aung HL, Taiaroa G, Opel-Reading HK, Kleffmann T, Cook GM, Krause KL. Overexpression of a newly identified d-amino acid transaminase inMycobacterium smegmatiscomplements glutamate racemase deletion. Mol Microbiol 2017; 107:198-213. [DOI: 10.1111/mmi.13877] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Roman Mortuza
- Department of Biochemistry; University of Otago; Otago New Zealand
- Department of Microbiology and Immunology; University of Otago; Otago New Zealand
| | - Htin Lin Aung
- Department of Microbiology and Immunology; University of Otago; Otago New Zealand
| | - George Taiaroa
- Department of Microbiology and Immunology; University of Otago; Otago New Zealand
| | | | | | - Gregory M. Cook
- Department of Microbiology and Immunology; University of Otago; Otago New Zealand
| | - Kurt L. Krause
- Department of Biochemistry; University of Otago; Otago New Zealand
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12
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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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13
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Doroshenko VG, Livshits VA, Airich LG, Shmagina IS, Savrasova EA, Ovsienko MV, Mashko SV. Metabolic engineering of Escherichia coli for the production of phenylalanine and related compounds. APPL BIOCHEM MICRO+ 2015. [DOI: 10.1134/s0003683815070017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Oh SY, Richter SG, Missiakas DM, Schneewind O. Glutamate Racemase Mutants of Bacillus anthracis. J Bacteriol 2015; 197:1854-61. [PMID: 25777674 PMCID: PMC4420906 DOI: 10.1128/jb.00070-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/06/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED D-Glutamate is an essential component of bacterial peptidoglycan and a building block of the poly-γ-D-glutamic acid (PDGA) capsule of Bacillus anthracis, the causative agent of anthrax. Earlier work suggested that two glutamate racemases, encoded by racE1 and racE2, are each essential for growth of B. anthracis, supplying D-glutamic acid for the synthesis of peptidoglycan and PDGA capsule. Earlier work could not explain, however, why two enzymes that catalyze the same reaction may be needed for bacterial growth. Here, we report that deletion of racE1 or racE2 did not prevent growth of B. anthracis Sterne (pXO1(+) pXO2(-)), the noncapsulating vaccine strain, or of B. anthracis Ames (pXO1(+) pXO2(+)), a fully virulent, capsulating isolate. While mutants with deletions in racE1 and racE2 were not viable, racE2 deletion delayed vegetative growth of B. anthracis following spore germination and caused aberrant cell shapes, phenotypes that were partially restored by exogenous D-glutamate. Deletion of racE1 or racE2 from B. anthracis Ames did not affect the production or stereochemical composition of the PDGA capsule. A model is presented whereby B. anthracis, similar to Bacillus subtilis, utilizes two functionally redundant racemase enzymes to synthesize D-glutamic acid for peptidoglycan synthesis. IMPORTANCE Glutamate racemases, enzymes that convert L-glutamate to D-glutamate, are targeted for antibiotic development. Glutamate racemase inhibitors may be useful for the treatment of bacterial infections such as anthrax, where the causative agent, B. anthracis, requires d-glutamate for the synthesis of peptidoglycan and poly-γ-D-glutamic acid (PDGA) capsule. Here we show that B. anthracis possesses two glutamate racemase genes that can be deleted without abolishing either bacterial growth or PDGA synthesis. These data indicate that drug candidates must inhibit both glutamate racemases, RacE1 and RacE2, in order to block B. anthracis growth and achieve therapeutic efficacy.
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Affiliation(s)
- So-Young Oh
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Stefan G Richter
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Dominique M Missiakas
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Olaf Schneewind
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA Department of Microbiology, University of Chicago, Chicago, Illinois, USA
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Morayya S, Awasthy D, Yadav R, Ambady A, Sharma U. Revisiting the essentiality of glutamate racemase in Mycobacterium tuberculosis. Gene 2014; 555:269-76. [PMID: 25447907 DOI: 10.1016/j.gene.2014.11.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/04/2014] [Accepted: 11/10/2014] [Indexed: 01/25/2023]
Abstract
Glutamate racemase (MurI) converts l-glutamate into d-glutamate which is an essential component of peptidoglycan in bacteria. The gene encoding glutamate racemase, murI has been shown to be essential for the growth of a number of bacterial species including Escherichia coli. However, in some Gram-positive species d-amino acid transaminase (Dat) can also convert l-glutamate into d-glutamate thus rendering MurI non-essential for growth. In a recent study the murI gene of Mycobacterium tuberculosis was shown to be non-essential. As d-glutamate is an essential component of peptidoglycan of M. tuberculosis, either Dat or MurI has to be essential for its survival. Since, a Dat encoding gene has not been reported in M. tuberculosis genome sequence, the reported non-essentiality of murI was unexplainable. In order to resolve this dilemma we tried to knockout murI in the presence of single and two copies of murI, in wild type and merodiploid strains respectively. It was found that murI could not be inactivated in the wild type background indicating that it could be an essential gene. Also, inactivation of murI could not be achieved in the presence of externally supplied d-glutamate in 7H9 medium suggesting that M. tuberculosis is unable to take up d-glutamate under the conditions tested. However we could generate murI knockout strains at high frequency when two copies of the gene were present indicating that at least one murI gene is required for cellular viability. The essential nature of MurI in M. tuberculosis H37Rv suggests that it could be a potential drug target.
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Affiliation(s)
- Sapna Morayya
- Present address: Biocon Bristol Myer squib R&D Centre, Biocon Park, Jigani Link Road, Bommasandra, Bangalore, India
| | - Disha Awasthy
- Present address: Strand Center for Genomics & Personalized Medicine, Strand Life Sciences Pvt. Ltd., Veterinary College Campus, Bellary Road, Bangalore, India
| | - Reena Yadav
- AstraZeneca India Pvt. Ltd., "Avishkar", Bellary Road, Hebbal, Bangalore, India
| | - Anisha Ambady
- Present address: Biocon Bristol Myer squib R&D Centre, Biocon Park, Jigani Link Road, Bommasandra, Bangalore, India
| | - Umender Sharma
- Present address: GangaGen Biotechnologies Pvt. Ltd, No 12, 5th Cross, Raghavendra Layout, Tumkur Road, Yeshwantpur, Bangalore, India.
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16
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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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Jomrit J, Summpunn P, Meevootisom V, Wiyakrutta S. Sensitive non-radioactive determination of aminotransferase stereospecificity for C-4′ hydrogen transfer on the coenzyme. Biochem Biophys Res Commun 2011; 405:626-31. [DOI: 10.1016/j.bbrc.2011.01.080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 01/21/2011] [Indexed: 10/18/2022]
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Martínez-Rodríguez S, Martínez-Gómez A, Rodríguez-Vico F, Clemente-Jiménez J, Las Heras-Vázquez F. Natural Occurrence and Industrial Applications of d-Amino Acids: An Overview. Chem Biodivers 2010; 7:1531-48. [DOI: 10.1002/cbdv.200900245] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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van der Veen S, Abee T, de Vos WM, Wells-Bennik MH. Genome-wide screen forListeria monocytogenesgenes important for growth at high temperatures. FEMS Microbiol Lett 2009; 295:195-203. [DOI: 10.1111/j.1574-6968.2009.01586.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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20
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Hanson RL, Davis BL, Goldberg SL, Johnston RM, Parker WL, Tully TP, Montana MA, Patel RN. Enzymatic Preparation of a d-Amino Acid from a Racemic Amino Acid or Keto Acid. Org Process Res Dev 2008. [DOI: 10.1021/op800149q] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ronald L. Hanson
- Process Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, U.S.A
| | - Brian L. Davis
- Process Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, U.S.A
| | - Steven L. Goldberg
- Process Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, U.S.A
| | - Robert M. Johnston
- Process Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, U.S.A
| | - William L. Parker
- Process Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, U.S.A
| | - Thomas P. Tully
- Process Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, U.S.A
| | - Michael A. Montana
- Process Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, U.S.A
| | - Ramesh N. Patel
- Process Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, U.S.A
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21
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Fisher SL. Glutamate racemase as a target for drug discovery. Microb Biotechnol 2008; 1:345-60. [PMID: 21261855 PMCID: PMC3815242 DOI: 10.1111/j.1751-7915.2008.00031.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Revised: 01/11/2008] [Accepted: 02/15/2008] [Indexed: 11/28/2022] Open
Abstract
The bacterial cell wall is a highly cross-linked polymeric structure consisting of repeating peptidoglycan units, each of which contains a novel pentapeptide substitution which is cross-linked through transpeptidation. The incorporation of D-glutamate as the second residue is strictly conserved across the bacterial kingdom. Glutamate racemase, a member of the cofactor-independent, two-thiol-based family of amino acid racemases, has been implicated in the production and maintenance of sufficient d-glutamate pool levels required for growth. The subject of over four decades of research, it is now evident that the enzyme is conserved and essential for growth across the bacterial kingdom and has a conserved overall topology and active site architecture; however, several different mechanisms of regulation have been observed. These traits have recently been targeted in the discovery of both narrow and broad spectrum inhibitors. This review outlines the biological history of this enzyme, the recent biochemical and structural characterization of isozymes from a wide range of species and developments in the identification of inhibitors that target the enzyme as possible therapeutic agents.
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Affiliation(s)
- Stewart L Fisher
- Infection Discovery, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA.
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Barreteau H, Kovac A, Boniface A, Sova M, Gobec S, Blanot D. Cytoplasmic steps of peptidoglycan biosynthesis. FEMS Microbiol Rev 2008; 32:168-207. [PMID: 18266853 DOI: 10.1111/j.1574-6976.2008.00104.x] [Citation(s) in RCA: 479] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The biosynthesis of bacterial cell wall peptidoglycan is a complex process that involves enzyme reactions that take place in the cytoplasm (synthesis of the nucleotide precursors) and on the inner side (synthesis of lipid-linked intermediates) and outer side (polymerization reactions) of the cytoplasmic membrane. This review deals with the cytoplasmic steps of peptidoglycan biosynthesis, which can be divided into four sets of reactions that lead to the syntheses of (1) UDP-N-acetylglucosamine from fructose 6-phosphate, (2) UDP-N-acetylmuramic acid from UDP-N-acetylglucosamine, (3) UDP-N-acetylmuramyl-pentapeptide from UDP-N-acetylmuramic acid and (4) D-glutamic acid and dipeptide D-alanyl-D-alanine. Recent data concerning the different enzymes involved are presented. Moreover, special attention is given to (1) the chemical and enzymatic synthesis of the nucleotide precursor substrates that are not commercially available and (2) the search for specific inhibitors that could act as antibacterial compounds.
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Affiliation(s)
- Hélène Barreteau
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Univ Paris-Sud, Orsay, France
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23
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Dodd D, Reese JG, Louer CR, Ballard JD, Spies MA, Blanke SR. Functional comparison of the two Bacillus anthracis glutamate racemases. J Bacteriol 2007; 189:5265-75. [PMID: 17496086 PMCID: PMC1951872 DOI: 10.1128/jb.00352-07] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2007] [Accepted: 05/01/2007] [Indexed: 11/20/2022] Open
Abstract
Glutamate racemase activity in Bacillus anthracis is of significant interest with respect to chemotherapeutic drug design, because L-glutamate stereoisomerization to D-glutamate is predicted to be closely associated with peptidoglycan and capsule biosynthesis, which are important for growth and virulence, respectively. In contrast to most bacteria, which harbor a single glutamate racemase gene, the genomic sequence of B. anthracis predicts two genes encoding glutamate racemases, racE1 and racE2. To evaluate whether racE1 and racE2 encode functional glutamate racemases, we cloned and expressed racE1 and racE2 in Escherichia coli. Size exclusion chromatography of the two purified recombinant proteins suggested differences in their quaternary structures, as RacE1 eluted primarily as a monomer, while RacE2 demonstrated characteristics of a higher-order species. Analysis of purified recombinant RacE1 and RacE2 revealed that the two proteins catalyze the reversible stereoisomerization of L-glutamate and D-glutamate with similar, but not identical, steady-state kinetic properties. Analysis of the pH dependence of L-glutamate stereoisomerization suggested that RacE1 and RacE2 both possess two titratable active site residues important for catalysis. Moreover, directed mutagenesis of predicted active site residues resulted in complete attenuation of the enzymatic activities of both RacE1 and RacE2. Homology modeling of RacE1 and RacE2 revealed potential differences within the active site pocket that might affect the design of inhibitory pharmacophores. These results suggest that racE1 and racE2 encode functional glutamate racemases with similar, but not identical, active site features.
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Affiliation(s)
- Dylan Dodd
- Department of Microbiology, Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
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24
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Lundqvist T, Fisher SL, Kern G, Folmer RHA, Xue Y, Newton DT, Keating TA, Alm RA, de Jonge BLM. Exploitation of structural and regulatory diversity in glutamate racemases. Nature 2007; 447:817-22. [PMID: 17568739 DOI: 10.1038/nature05689] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Accepted: 02/14/2007] [Indexed: 11/09/2022]
Abstract
Glutamate racemase is an enzyme essential to the bacterial cell wall biosynthesis pathway, and has therefore been considered as a target for antibacterial drug discovery. We characterized the glutamate racemases of several pathogenic bacteria using structural and biochemical approaches. Here we describe three distinct mechanisms of regulation for the family of glutamate racemases: allosteric activation by metabolic precursors, kinetic regulation through substrate inhibition, and D-glutamate recycling using a d-amino acid transaminase. In a search for selective inhibitors, we identified a series of uncompetitive inhibitors specifically targeting Helicobacter pylori glutamate racemase that bind to a cryptic allosteric site, and used these inhibitors to probe the mechanistic and dynamic features of the enzyme. These structural, kinetic and mutational studies provide insight into the physiological regulation of these essential enzymes and provide a basis for designing narrow-spectrum antimicrobial agents.
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Affiliation(s)
- Tomas Lundqvist
- AstraZeneca Global Structural Chemistry, AstraZeneca R&D Mölndal, SE-431 83, Mölndal, Sweden
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25
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Lee SG, Hong SP, Song JJ, Kim SJ, Kwak MS, Sung MH. Functional and structural characterization of thermostable D-amino acid aminotransferases from Geobacillus spp. Appl Environ Microbiol 2006; 72:1588-94. [PMID: 16461714 PMCID: PMC1392904 DOI: 10.1128/aem.72.2.1588-1594.2006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
D-amino acid aminotransferases (D-AATs) from Geobacillus toebii SK1 and Geobacillus sp. strain KLS1 were cloned and characterized from a genetic, catalytic, and structural aspect. Although the enzymes were highly thermostable, their catalytic capability was approximately one-third of that of highly active Bacilli enzymes, with respective turnover rates of 47 and 55 s(-1) at 50 degrees C. The Geobacillus enzymes were unique and shared limited sequence identities of below 45% with D-AATs from mesophilic and thermophilic Bacillus spp., except for a hypothetical protein with a 72% identity from the G. kaustophilus genome. Structural alignments showed that most key residues were conserved in the Geobacillus enzymes, although the conservative residues just before the catalytic lysine were distinctively changed: the 140-LRcD-143 sequence in Bacillus D-AATs was 144-EYcY-147 in the Geobacillus D-AATs. When the EYcY sequence from the SK1 enzyme was mutated into LRcD, a 68% increase in catalytic activity was observed, while the binding affinity toward alpha-ketoglutarate decreased by half. The mutant was very close to the wild-type in thermal stability, indicating that the mutations did not disturb the overall structure of the enzyme. Homology modeling also suggested that the two tyrosine residues in the EYcY sequence from the Geobacillus D-AATs had a pi/pi interaction that was replaceable with the salt bridge interaction between the arginine and aspartate residues in the LRcD sequence.
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Affiliation(s)
- Seung-Goo Lee
- Laboratory of Microbial Function, KRIBB, Daejeon, Korea
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26
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Kimura K, Tran LSP, Itoh Y. Roles and regulation of the glutamate racemase isogenes, racE and yrpC, in Bacillus subtilis. Microbiology (Reading) 2004; 150:2911-2920. [PMID: 15347750 DOI: 10.1099/mic.0.27045-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many bacteria, including Escherichia coli, have a unique gene that encodes glutamate racemase. This enzyme catalyses the formation of d-glutamate, which is necessary for cell wall peptidoglycan synthesis. However, Bacillus subtilis has two glutamate racemase genes, named racE and yrpC. Since racE appears to be indispensable for growth in rich medium, the role of yrpC in d-amino acid synthesis is vague. Experiments with racE- and yrpC-knockout mutants confirmed that racE is essential for growth in rich medium but showed that this gene was dispensable for growth in minimal medium, where yrpC executes the anaplerotic role of racE. LacZ fusion assays demonstrated that racE was expressed in both types of media but yrpC was expressed only in minimal medium, which accounted for the absence of yrpC function in rich medium. Neither racE nor yrpC was required for B. subtilis cells to synthesize poly-γ-dl-glutamate (γ-PGA), a capsule polypeptide of d- and l-glutamate linked through a γ-carboxylamide bond. Wild-type cells degraded the capsule during the late stationary phase without accumulating the degradation products, d-glutamate and l-glutamate, in the medium. In contrast, racE or yrpC mutant cells accumulated significant amounts of d- but not l-glutamate. Exogenous d-glutamate utilization was somewhat defective in the mutants and the double mutation of race and yrpc severely impaired d-amino acid utilization. Thus, both racemase genes appear necessary to complete the catabolism of exogenous d-glutamate generated from γ-PGA.
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Affiliation(s)
- Keitarou Kimura
- Division of Applied Microbiology, National Food Research Institute, Kannondai 2-1-12, Tsukuba, Ibaraki 305-8642, Japan
| | - Lam-Son Phan Tran
- Division of Applied Microbiology, National Food Research Institute, Kannondai 2-1-12, Tsukuba, Ibaraki 305-8642, Japan
| | - Yoshifumi Itoh
- Akita Research Institute of Food and Brewing, Sanuki 4-26, Araya-machi, Akita 010-1623, Japan
- Division of Applied Microbiology, National Food Research Institute, Kannondai 2-1-12, Tsukuba, Ibaraki 305-8642, Japan
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27
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Li T, Kootstra AB, Fotheringham IG. Nonproteinogenic α-Amino Acid Preparation Using Equilibrium Shifted Transamination. Org Process Res Dev 2002. [DOI: 10.1021/op025518x] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tao Li
- Great Lakes Fine Chemicals, 601 East Kensington Rd, Mt. Prospect, Illinois 60056, U.S.A
| | - Anna B. Kootstra
- Great Lakes Fine Chemicals, 601 East Kensington Rd, Mt. Prospect, Illinois 60056, U.S.A
| | - Ian G. Fotheringham
- Great Lakes Fine Chemicals, 601 East Kensington Rd, Mt. Prospect, Illinois 60056, U.S.A
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Nishizawa T, Asayama M, Shirai M. Cyclic heptapeptide microcystin biosynthesis requires the glutamate racemase gene. MICROBIOLOGY (READING, ENGLAND) 2001; 147:1235-1241. [PMID: 11320126 DOI: 10.1099/00221287-147-5-1235] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
It was demonstrated previously that the operon consisting of the non-ribosomal peptide synthetase (NRPS) gene coupled with the polyketide synthase (PKS) gene involved in cyclic heptapeptide microcystin synthesis includes two different D-amino acid synthetase genes, an epimerization domain at the 3' end of module 2, and the racemase gene mcyF. To determine the role of mcyF in microcystin synthesis, gene-disruption and complementation analyses were carried out. Insertional mutagenesis in the mcyF gene, generated by homologous recombination, abolished only microcystin synthesis, but did not influence cell growth. Furthermore, McyF supported D-Glu-independent growth of a strain of Escherichia coli defective in D-Glu synthesis. It is concluded that mcyF is the glutamic acid racemase gene involved in the synthesis of D-Glu residues in the microcystin molecule. This is the first report of the racemase in prokaryotic NRPS.
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Affiliation(s)
- Tomoyasu Nishizawa
- The United Graduate School, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan3
- Laboratory of Molecular Genetics, School of Agriculture1, and Gene Research Center2, Ibaraki University, Ami, Ibaraki 300-0393, Japan
| | - Munehiko Asayama
- Laboratory of Molecular Genetics, School of Agriculture1, and Gene Research Center2, Ibaraki University, Ami, Ibaraki 300-0393, Japan
| | - Makoto Shirai
- Laboratory of Molecular Genetics, School of Agriculture1, and Gene Research Center2, Ibaraki University, Ami, Ibaraki 300-0393, Japan
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29
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Novel biosynthetic routes to non-proteinogenic amino acids as chiral pharmaceutical intermediates. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s1381-1177(00)00055-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Kim WC, Rhee HI, Park BK, Suk KH, Cha SH. Isolation of peptide ligands that inhibit glutamate racemase activity from a random phage display library. JOURNAL OF BIOMOLECULAR SCREENING 2000; 5:435-40. [PMID: 11598461 DOI: 10.1177/108705710000500606] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Several new antibacterial agents are currently being developed in response to the emergence of bacterial resistance to existing antibiotic substances. The new agents include compounds that interfere with bacterial membrane function. The peptidoglycan component of the bacterial cell wall is synthesized by glutamate racemase, and this enzyme is responsible for the biosynthesis of d-glutamate, which is an essential component of cell wall peptidoglycan. In this study, we screened a phage display library expressing random dodecapeptides on the surface of bacteriophage against an Escherichia coli glutamate racemase, and isolated specific peptide sequences that bind to the enzyme. Twenty-seven positive phage clones were analyzed, and seven different peptide sequences were obtained. Among them, the peptide sequence His-Pro-Trp-His-Lys-Lys-His-Pro-Asp-Arg-Lys-Thr was found most frequently, suggesting that this peptide might have the highest affinity to glutamate racemase. The positive phage clones and HPWHKKHPDRKT synthetic peptide were able to inhibit glutamate racemase activity in vitro, implying that our peptide inhibitors may be utilized for the molecular design of new potential antibacterial agents targeting cell wall synthesis.
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Affiliation(s)
- W C Kim
- Division of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chunchon 200-701, South Korea
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31
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Oguri S, Kumazaki M, Kitou R, Nonoyama H, Tooda N. Elucidation of intestinal absorption of D,L-amino acid enantiomers and aging in rats. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1472:107-14. [PMID: 10572931 DOI: 10.1016/s0304-4165(99)00110-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
At the present time, the origin of protein bound D-amino acid (AA) has been fairly well elucidated, but that of free D-AA is still not well understood. To gain greater understanding of this, intestinal absorption in rats of free D,L-AA enantiomers (arginine, alanine and aspartic acid as models for basic, neutral and acidic AAs, respectively, in this study) and the relationship between age and absorption were investigated. The degree of rat intestinal absorption of free D,L-AAs was evaluated using apparent membrane permeability coefficients (Papp) which were obtained from an in situ intestinal single-pass perfusion method with Krebs-Ringer bicarbonate buffer (pH 7.4) solution containing D,L-AA enantiomers. Determinations of D,L-AA enantiomers in perfusion (in- and outflow) solutions were carried out by the in-capillary derivatization high-performance capillary electrophoretic methods (ICD-HPCE methods) that were previously developed by our group. Collectively, our observations suggest: (1) that the Papp of L-AA is higher than that of the D-isomer; (2) that D-AA can be absorbed as well as L-AA using a sodium ion-dependent transporter that is located on the brush border membrane of rat intestinal epithelial cells; (3) that Papp reached a maximum at 8 weeks of age, but were measured at decreased amounts at 52 and 104 weeks of age. These results suggest that free D-AA in a mammalian body originates from 'exogenous sources'.
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Affiliation(s)
- S Oguri
- Department of Home Economics, Aichi-Gakusen University, Okazaki-city, Japan.
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32
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Fotheringham IG, Grinter N, Pantaleone DP, Senkpeil RF, Taylor PP. Engineering of a novel biochemical pathway for the biosynthesis of L-2-aminobutyric acid in Escherichia coli K12. Bioorg Med Chem 1999; 7:2209-13. [PMID: 10579528 DOI: 10.1016/s0968-0896(99)00153-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
L-2-Aminobutyric acid was synthesised in a transamination reaction from L-threonine and L-aspartic acid as substrates in a whole cell biotransformation using recombinant Escherichia coli K12. The cells contained the cloned genes tyrB, ilvA and alsS which respectively encode tyrosine aminotransferase of E. coli, threonine deaminase of E. coli and alpha-acetolactate synthase of B. subtilis 168. The 2-aminobutyric acid was produced by the action of the aminotransferase on 2-ketobutyrate and L-aspartate. The 2-ketobutyrate is generated in situ from L-threonine by the action of the deaminase, and the pyruvate by-product is eliminated by the acetolactate synthase. The concerted action of the three enzymes offers significant yield and purity advantages over the process using the transaminase alone with an eight to tenfold increase in the ratio of product to the major impurity.
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33
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Friedman M. Chemistry, nutrition, and microbiology of D-amino acids. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 1999; 47:3457-3479. [PMID: 10552672 DOI: 10.1021/jf990080u] [Citation(s) in RCA: 254] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Exposure of food proteins to certain processing conditions induces two major chemical changes: racemization of all L-amino acids to D-isomers and concurrent formation of cross-linked amino acids such as lysinoalanine. Racemization of L-amino acids residues to their D-isomers in food and other proteins is pH-, time-, and temperature-dependent. Although racemization rates of the 18 different L-amino acid residues in a protein vary, the relative rates in different proteins are similar. The diet contains both processing-induced and naturally formed D-amino acids. The latter include those found in microorganisms, plants, and marine invertebrates. Racemization impairs digestibility and nutritional quality. The nutritional utilization of different D-amino acids varies widely in animals and humans. In addition, some D-amino acids may be both beneficial and deleterious. Thus, although D-phenylalanine in an all-amino-acid diet is utilized as a nutritional source of L-phenylalanine, high concentrations of D-tyrosine in such diets inhibit the growth of mice. Both D-serine and lysinoalanine induce histological changes in the rat kidney. The wide variation in the utilization of D-amino acids is illustrated by the fact that whereas D-methionine is largely utilized as a nutritional source of the L-isomer, D-lysine is totally devoid of any nutritional value. Similarly, although L-cysteine has a sparing effect on L-methionine when fed to mice, D-cysteine does not. Because D-amino acids are consumed by animals and humans as part of their normal diets, a need exists to develop a better understanding of their roles in nutrition, food safety, microbiology, physiology, and medicine. To contribute to this effort, this multidiscipline-oriented overview surveys our present knowledge of the chemistry, nutrition, safety, microbiology, and pharmacology of D-amino acids. Also covered are the origin and distribution of D-amino acids in the food chain and in body fluids and tissues and recommendations for future research in each of these areas. Understanding of the integrated, beneficial effects of D-amino acids against cancer, schizophrenia, and infection, and overlapping aspects of the formation, occurrence, and biological functions of D-amino should lead to better foods and improved human health.
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Affiliation(s)
- M Friedman
- Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 800 Buchanan Street, Albany, California 94710, USA.
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