1
|
Coppinger MN, Laramore K, Popham DL, Stabb EV. A prototrophic suppressor of a Vibrio fischeri D-glutamate auxotroph reveals a member of the periplasmic broad-spectrum racemase family (BsrF). J Bacteriol 2024; 206:e0033323. [PMID: 38411059 PMCID: PMC10955857 DOI: 10.1128/jb.00333-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/04/2024] [Indexed: 02/28/2024] Open
Abstract
Although bacterial peptidoglycan (PG) is highly conserved, some natural variations in PG biosynthesis and structure have evolved. Understanding the mechanisms and limits of such variation will inform our understanding of antibiotic resistance, innate immunity, and the evolution of bacteria. We have explored the constraints on PG evolution by blocking essential steps in PG biosynthesis in Vibrio fischeri and then selecting mutants with restored prototrophy. Here, we attempted to select prototrophic suppressors of a D-glutamate auxotrophic murI racD mutant. No suppressors were isolated on unsupplemented lysogeny broth salts (LBS), despite plating >1011 cells, nor were any suppressors generated through mutagenesis with ethyl methanesulfonate. A single suppressor was isolated on LBS supplemented with iso-D-gln, although the iso-D-gln subsequently appeared irrelevant. This suppressor has a genomic amplification formed by the creation of a novel junction that fuses proB to a gene encoding a putative broad-spectrum racemase of V. fischeri, bsrF. An engineered bsrF allele lacking the putative secretion signal (ΔSS-bsrF) also suppressed D-glu auxotrophy, resulting in PG that was indistinguishable from the wild type. The ΔSS-bsrF allele similarly suppressed the D-alanine auxotrophy of an alr mutant and restored prototrophy to a murI alr double mutant auxotrophic for both D-ala and D-glu. The ΔSS-bsrF allele increased resistance to D-cycloserine but had no effect on sensitivity to PG-targeting antibiotics penicillin, ampicillin, or vancomycin. Our work helps define constraints on PG evolution and reveals a periplasmic broad-spectrum racemase in V. fischeri that can be co-opted for PG biosynthesis, with concomitant D-cycloserine resistance. IMPORTANCE D-Amino acids are used and produced by organisms across all domains of life, but often, their origins and roles are not well understood. In bacteria, D-ala and D-glu are structural components of the canonical peptidoglycan cell wall and are generated by dedicated racemases Alr and MurI, respectively. The more recent discovery of additional bacterial racemases is broadening our view and deepening our understanding of D-amino acid metabolism. Here, while exploring alternative PG biosynthetic pathways in Vibrio fischeri, we unexpectedly shed light on an unusual racemase, BsrF. Our results illustrate a novel mechanism for the evolution of antibiotic resistance and provide a new avenue for exploring the roles of non-canonical racemases and D-amino acids in bacteria.
Collapse
Affiliation(s)
- Macey N. Coppinger
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
- Department of Biological Sciences, University of Illinois, Chicago, Illinois, USA
| | - Kathrin Laramore
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - David L. Popham
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Eric V. Stabb
- Department of Biological Sciences, University of Illinois, Chicago, Illinois, USA
| |
Collapse
|
2
|
Hao M, Wang M, Tang T, Zhao D, Yin S, Shi Y, Liu X, Wudong G, Yang Y, Zhang M, Qi L, Zhou D, Liu W, Jin Y, Wang A. Regulation of the Gene for Alanine Racemase Modulates Amino Acid Metabolism with Consequent Alterations in Cell Wall Properties and Adhesive Capability in Brucella spp. Int J Mol Sci 2023; 24:16145. [PMID: 38003334 PMCID: PMC10671322 DOI: 10.3390/ijms242216145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/24/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Brucella, a zoonotic facultative intracellular pathogenic bacterium, poses a significant threat both to human health and to the development of the livestock industry. Alanine racemase (Alr), the enzyme responsible for alanine racemization, plays a pivotal role in regulating virulence in this bacterium. Moreover, Brucella mutants with alr gene deletions (Δalr) exhibit potential as vaccine candidates. However, the mechanisms that underlie the detrimental effects of alr knockouts on Brucella pathogenicity remain elusive. Here, initially, we conducted a bioinformatics analysis of Alr, which demonstrated a high degree of conservation of the protein within Brucella spp. Subsequent metabolomics studies unveiled alterations in amino acid pathways following deletion of the alr gene. Furthermore, alr deletion in Brucella suis S2 induced decreased resistance to stress, antibiotics, and other factors. Transmission electron microscopy of simulated macrophage intracellular infection revealed damage to the cell wall in the Δalr strain, whereas propidium iodide staining and alkaline phosphatase and lactate dehydrogenase assays demonstrated alterations in cell membrane permeability. Changes in cell wall properties were revealed by measurements of cell surface hydrophobicity and zeta potential. Finally, the diminished adhesion capacity of the Δalr strain was shown by immunofluorescence and bacterial enumeration assays. In summary, our findings indicate that the alr gene that regulates amino acid metabolism in Brucella influences the properties of the cell wall, which modulates bacterial adherence capability. This study is the first demonstration that Alr impacts virulence by modulating bacterial metabolism, thereby providing novel insights into the pathogenic mechanisms of Brucella spp.
Collapse
Affiliation(s)
- Mingyue Hao
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Minghui Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Ting Tang
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Danyu Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Shurong Yin
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Yong Shi
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Xiaofang Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Gaowa Wudong
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Yuanhao Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Mengyu Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Lin Qi
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Dong Zhou
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Wei Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Yaping Jin
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Aihua Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| |
Collapse
|
3
|
Van Wieren A, Durrant JD, Majumdar S. Computational and experimental analyses of alanine racemase suggest new avenues for developing allosteric small-molecule antibiotics. Drug Dev Res 2023; 84:999-1007. [PMID: 37129190 PMCID: PMC10524904 DOI: 10.1002/ddr.22068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/23/2023] [Accepted: 04/10/2023] [Indexed: 05/03/2023]
Abstract
Given the ever-present threat of antibacterial resistance, there is an urgent need to identify new antibacterial drugs and targets. One such target is alanine racemase (Alr), an enzyme required for bacterial cell-wall biosynthesis. Alr is an attractive drug target because it is essential for bacterial survival but is absent in humans. Existing drugs targeting Alr lack specificity and have severe side effects. We here investigate alternative mechanisms of Alr inhibition. Alr functions exclusively as an obligate homodimer, so we probed seven conserved interactions on the dimer interface, distant from the enzymatic active site, to identify possible allosteric influences on activity. Using the Alr from Mycobacterium tuberculosis (MT) as a model, we found that the Lys261/Asp135 salt bridge is critical for catalytic activity. The Lys261Ala mutation completely inactivated the enzyme, and the Asp135Ala mutation reduced catalytic activity eight-fold. Further investigation suggested a potential drug-binding site near the Lys261/Asp135 salt bridge that may be useful for allosteric drug discovery.
Collapse
Affiliation(s)
- Arie Van Wieren
- Madia Department of Chemistry, Biochemistry, Physics and Engineering, Indiana University of Pennsylvania, Indiana, PA 15705
- Current address: The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Sudipta Majumdar
- Madia Department of Chemistry, Biochemistry, Physics and Engineering, Indiana University of Pennsylvania, Indiana, PA 15705
| |
Collapse
|
4
|
Harshaw NS, Meyer MD, Stella NA, Lehner KM, Kowalski RP, Shanks RMQ. The Short-chain Fatty Acid Propionic Acid Activates the Rcs Stress Response System Partially through Inhibition of d-Alanine Racemase. mSphere 2023; 8:e0043922. [PMID: 36645277 PMCID: PMC9942566 DOI: 10.1128/msphere.00439-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 12/16/2022] [Indexed: 01/17/2023] Open
Abstract
The Enterobacterial Rcs stress response system reacts to envelope stresses through a complex two-component phosphorelay system to regulate a variety of environmental response genes, such as capsular polysaccharide and flagella biosynthesis genes. However, beyond Escherichia coli, the stresses that activate Rcs are not well-understood. In this study, we used a Rcs system-dependent luminescent transcriptional reporter to screen a library of over 240 antimicrobial compounds for those that activated the Rcs system in Serratia marcescens, a Yersiniaceae family bacterium. Using an isogenic rcsB mutant to establish specificity, both new and expected activators were identified, including the short-chain fatty acid propionic acid, which is found at millimolar levels in the human gut. Propionic acid did not reduce the bacterial intracellular pH, as was hypothesized for its antibacterial mechanism. Instead, data suggest that the Rcs-activation by propionic acid is due, in part, to an inactivation of alanine racemase. This enzyme is responsible for the biosynthesis of d-alanine, which is an amino-acid that is required for the generation of bacterial cell walls. Consistent with what was observed in S. marcescens, in E. coli, alanine racemase mutants demonstrated elevated expression of the Rcs-reporter in a d-alanine-dependent and RcsB-dependent manner. These results suggest that host gut short-chain fatty acids can influence bacterial behavior via the activation of the Rcs stress response system. IMPORTANCE The Rcs bacterial stress response system responds to envelope stresses by globally altering gene expression to profoundly impact host-pathogen interactions, virulence, and antibiotic tolerance. In this study, a luminescent Rcs-reporter plasmid was used to screen a library of compounds for activators of Rcs. Among the strongest inducers was the short-chain fatty acid propionic acid, which is found at high concentrations in the human gut. This study suggests that gut short-chain fatty acids can affect both bacterial virulence and antibiotic tolerance via the induction of the Rcs system.
Collapse
Affiliation(s)
- Nathaniel S. Harshaw
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mitchell D. Meyer
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Nicholas A. Stella
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kara M. Lehner
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Regis P. Kowalski
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Robert M. Q. Shanks
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
5
|
Arjes HA, Willis L, Gui H, Xiao Y, Peters J, Gross C, Huang KC. Three-dimensional biofilm colony growth supports a mutualism involving matrix and nutrient sharing. eLife 2021; 10:e64145. [PMID: 33594973 PMCID: PMC7925131 DOI: 10.7554/elife.64145] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Life in a three-dimensional biofilm is typical for many bacteria, yet little is known about how strains interact in this context. Here, we created essential gene CRISPR interference knockdown libraries in biofilm-forming Bacillus subtilis and measured competitive fitness during colony co-culture with wild type. Partial knockdown of some translation-related genes reduced growth rates and led to out-competition. Media composition led some knockdowns to compete differentially as biofilm versus non-biofilm colonies. Cells depleted for the alanine racemase AlrA died in monoculture but survived in a biofilm colony co-culture via nutrient sharing. Rescue was enhanced in biofilm colony co-culture with a matrix-deficient parent due to a mutualism involving nutrient and matrix sharing. We identified several examples of mutualism involving matrix sharing that occurred in three-dimensional biofilm colonies but not when cultured in two dimensions. Thus, growth in a three-dimensional colony can promote genetic diversity through sharing of secreted factors and may drive evolution of mutualistic behavior.
Collapse
Affiliation(s)
- Heidi A Arjes
- Department of Bioengineering, Stanford University School of MedicineStanfordUnited States
| | - Lisa Willis
- Department of Bioengineering, Stanford University School of MedicineStanfordUnited States
| | - Haiwen Gui
- Department of Bioengineering, Stanford University School of MedicineStanfordUnited States
| | - Yangbo Xiao
- Department of Bioengineering, Stanford University School of MedicineStanfordUnited States
| | - Jason Peters
- Department of Cell and Tissue Biology, University of California San FranciscoSan FranciscoUnited States
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-MadisonMadisonUnited States
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-MadisonMadisonUnited States
- Department of Bacteriology, University of Wisconsin-MadisonMadisonUnited States
- Department of Medical Microbiology and Immunology, University of Wisconsin-MadisonMadisonUnited States
| | - Carol Gross
- Department of Cell and Tissue Biology, University of California San FranciscoSan FranciscoUnited States
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University School of MedicineStanfordUnited States
- Department of Microbiology & Immunology, Stanford University School of MedicineStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| |
Collapse
|
6
|
Hoegl A, Nodwell MB, Kirsch VC, Bach NC, Pfanzelt M, Stahl M, Schneider S, Sieber SA. Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics. Nat Chem 2018; 10:1234-1245. [PMID: 30297752 PMCID: PMC6252082 DOI: 10.1038/s41557-018-0144-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/03/2018] [Indexed: 02/01/2023]
Abstract
Pyridoxal phosphate (PLP) is an enzyme cofactor required for the chemical transformation of biological amines in many central cellular processes. PLP-dependent enzymes (PLP-DEs) are ubiquitous and evolutionarily diverse, making their classification based on sequence homology challenging. Here we present a chemical proteomic method for reporting on PLP-DEs using functionalized cofactor probes. We synthesized pyridoxal analogues modified at the 2'-position, which are taken up by cells and metabolized in situ. These pyridoxal analogues are phosphorylated to functional cofactor surrogates by cellular pyridoxal kinases and bind to PLP-DEs via an aldimine bond which can be rendered irreversible by NaBH4 reduction. Conjugation to a reporter tag enables the subsequent identification of PLP-DEs using quantitative, label-free mass spectrometry. Using these probes we accessed a significant portion of the Staphylococcus aureus PLP-DE proteome (73%) and annotate uncharacterized proteins as novel PLP-DEs. We also show that this approach can be used to study structural tolerance within PLP-DE active sites and to screen for off-targets of the PLP-DE inhibitor D-cycloserine.
Collapse
Affiliation(s)
- Annabelle Hoegl
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Matthew B Nodwell
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Volker C Kirsch
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Nina C Bach
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Martin Pfanzelt
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Matthias Stahl
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Sabine Schneider
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Stephan A Sieber
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany.
| |
Collapse
|
7
|
Dong H, Han Q, Guo Y, Ju J, Wang S, Yuan C, Long W, He X, Xu S, Li S. Enzymatic characterization and crystal structure of biosynthetic alanine racemase from Pseudomonas aeruginosa PAO1. Biochem Biophys Res Commun 2018; 503:2319-2325. [PMID: 29964014 DOI: 10.1016/j.bbrc.2018.06.155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 06/27/2018] [Indexed: 02/02/2023]
Abstract
Alanine racemase is a pyridoxal-5'-phosphate (PLP)-dependent enzyme that reversibly catalyzes the conversion of l-alanine to d-alanine. d-alanine is an essential constituent in many prokaryotic cell structures. Inhibition of alanine racemase is lethal to prokaryotes, creating an attractive target for designing antibacterial drugs. Here we report the crystal structure of biosynthetic alanine racemase (Alr) from a pathogenic bacteria Pseudomonas aeruginosa PAO1. Structural studies showed that P. aeruginosa Alr (PaAlr) adopts a conserved homodimer structure. A guest substrate d-lysine was observed in the active site and refined to dual-conformation. Two buffer ions, malonate and acetate, were bound in the proximity to d-lysine. Biochemical characterization revealed the optimal reaction conditions for PaAlr.
Collapse
Affiliation(s)
- Hui Dong
- Key Laboratory of Tianjin Radiation and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300192, China
| | - Qingqing Han
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Yu Guo
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jiansong Ju
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Shanshan Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Chao Yuan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Wei Long
- Key Laboratory of Tianjin Radiation and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300192, China
| | - Xin He
- Key Laboratory of Tianjin Radiation and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300192, China
| | - Shujing Xu
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China.
| | - Sheng Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
| |
Collapse
|
8
|
Nakatani Y, Opel-Reading HK, Merker M, Machado D, Andres S, Kumar SS, Moradigaravand D, Coll F, Perdigão J, Portugal I, Schön T, Nair D, Devi KRU, Kohl TA, Beckert P, Clark TG, Maphalala G, Khumalo D, Diel R, Klaos K, Aung HL, Cook GM, Parkhill J, Peacock SJ, Swaminathan S, Viveiros M, Niemann S, Krause KL, Köser CU. Role of Alanine Racemase Mutations in Mycobacterium tuberculosis d-Cycloserine Resistance. Antimicrob Agents Chemother 2017; 61:e01575-17. [PMID: 28971867 PMCID: PMC5700341 DOI: 10.1128/aac.01575-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/25/2017] [Indexed: 11/23/2022] Open
Abstract
A screening of more than 1,500 drug-resistant strains of Mycobacterium tuberculosis revealed evolutionary patterns characteristic of positive selection for three alanine racemase (Alr) mutations. We investigated these mutations using molecular modeling, in vitro MIC testing, as well as direct measurements of enzymatic activity, which demonstrated that these mutations likely confer resistance to d-cycloserine.
Collapse
Affiliation(s)
- Yoshio Nakatani
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
| | - Helen K Opel-Reading
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Borstel-Lübeck, Germany
| | - Diana Machado
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Sönke Andres
- Division of Mycobacteriology (National Tuberculosis Reference Laboratory), Research Center Borstel, Borstel, Germany
| | - S Siva Kumar
- National Institute for Research in Tuberculosis, Chennai, India
| | | | - Francesc Coll
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - João Perdigão
- Med.ULisboa-Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Portugal
- Med.ULisboa-Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Thomas Schön
- Department of Clinical and Experimental Medicine, Division of Medical Microbiology, Linköping University, Linköping, Sweden
- Department of Clinical Microbiology and Infectious Diseases, Kalmar County Hospital, Kalmar, Sweden
| | - Dina Nair
- National Institute for Research in Tuberculosis, Chennai, India
| | - K R Uma Devi
- National Institute for Research in Tuberculosis, Chennai, India
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Patrick Beckert
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Borstel-Lübeck, Germany
| | - Taane G Clark
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Gugu Maphalala
- National Reference Laboratory, Ministry of Health, Mbabane, Swaziland
| | - Derrick Khumalo
- National Tuberculosis Control Program, Ministry of Health, Manzini, Swaziland
| | - Roland Diel
- Institute of Epidemiology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Kadri Klaos
- Tartu University Hospital, United Laboratories, Mycobacteriology, Tartu, Estonia
| | - Htin Lin Aung
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | | | - Sharon J Peacock
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Soumya Swaminathan
- Department of Health Research and Director General, Indian Council of Medical Research, New Delhi, India
| | - Miguel Viveiros
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Borstel-Lübeck, Germany
| | - Kurt L Krause
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
| | - Claudio U Köser
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
9
|
Duque E, Daddaoua A, Cordero BF, De la Torre J, Antonia Molina-Henares M, Ramos JL. Identification and elucidation of in vivo function of two alanine racemases from Pseudomonas putida KT2440. Environ Microbiol Rep 2017; 9:581-588. [PMID: 28799718 DOI: 10.1111/1758-2229.12576] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/03/2017] [Indexed: 06/07/2023]
Abstract
The genome of Pseudomonas putida KT2440 contains two open reading frames (ORFs), PP_3722 and PP_5269, that encode proteins with a Pyridoxal phosphate binding motif and a high similarity to alanine racemases. Alanine racemases play a key role in the biosynthesis of D-alanine, a crucial amino acid in the peptidoglycan layer. For these ORFs, we generated single and double mutants and found that inactivation of PP_5269 resulted in D-alanine auxotrophy, while inactivation of PP_3722 did not. Furthermore, as expected, the PP_3722/PP_5269 double mutant was a strict auxotroph for D-alanine. These results indicate that PP_5269 is an alr allele and that it is the essential alanine racemase in P. putida. We observed that the PP_5269 mutant grew very slowly, while the double PP_5269/PP_3722 mutant did not grow at all. This suggests that PP_3722 may replace PP_5269 in vivo. In fact, when the ORF encoding PP_3772 was cloned into a wide host range expression vector, ORF PP_3722 successfully complemented P. putida PP_5269 mutants. We purified both proteins to homogeneity and while they exhibit similar KM values, the Vmax of PP_5269 is fourfold higher than that of PP_3722. Here, we propose that PP_5269 and PP_3722 encode functional alanine racemases and that these genes be named alr-1 and alr-2 respectively.
Collapse
Affiliation(s)
- Estrella Duque
- Department of Environmental Protection, CSIC-Estación Experimental del Zaidín, Granada, Spain
| | - Abdelali Daddaoua
- Department of Environmental Protection, CSIC-Estación Experimental del Zaidín, Granada, Spain
| | - Baldo F Cordero
- Department of Environmental Protection, CSIC-Estación Experimental del Zaidín, Granada, Spain
| | - Jesús De la Torre
- Department of Environmental Protection, CSIC-Estación Experimental del Zaidín, Granada, Spain
| | | | - Juan-Luis Ramos
- Department of Environmental Protection, CSIC-Estación Experimental del Zaidín, Granada, Spain
| |
Collapse
|
10
|
Wei Y, Qiu W, Zhou XD, Zheng X, Zhang KK, Wang SD, Li YQ, Cheng L, Li JY, Xu X, Li MY. Alanine racemase is essential for the growth and interspecies competitiveness of Streptococcus mutans. Int J Oral Sci 2016; 8:231-238. [PMID: 27740612 PMCID: PMC5168415 DOI: 10.1038/ijos.2016.34] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2016] [Indexed: 02/05/2023] Open
Abstract
D-alanine (D-Ala) is an essential amino acid that has a key role in bacterial cell wall synthesis. Alanine racemase (Alr) is a unique enzyme that interconverts L-alanine and D-alanine in most bacteria, making this enzyme a potential target for antimicrobial drug development. Streptococcus mutans is a major causative factor of dental caries. The factors involved in the survival, virulence and interspecies interactions of S. mutans could be exploited as potential targets for caries control. The current study aimed to investigate the physiological role of Alr in S. mutans. We constructed alr mutant strain of S. mutans and evaluated its phenotypic traits and interspecies competitiveness compared with the wild-type strain. We found that alr deletion was lethal to S. mutans. A minimal supplement of D-Ala (150 μg·mL-1) was required for the optimal growth of the alr mutant. The depletion of D-alanine in the growth medium resulted in cell wall perforation and cell lysis in the alr mutant strain. We also determined the compromised competitiveness of the alr mutant strain relative to the wild-type S. mutans against other oral streptococci (S. sanguinis or S. gordonii), demonstrated using either conditioned medium assays or dual-species fluorescent in situ hybridization analysis. Given the importance and necessity of alr to the growth and competitiveness of S. mutans, Alr may represent a promising target to modulate the cariogenicity of oral biofilms and to benefit the management of dental caries.
Collapse
Affiliation(s)
- Yuan Wei
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Wei Qiu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xue-Dong Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xin Zheng
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ke-Ke Zhang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shi-Da Wang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yu-Qing Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Lei Cheng
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ji-Yao Li
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xin Xu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ming-Yun Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| |
Collapse
|
11
|
Sun X, He G, Wang X, Xu S, Ju J, Xu X. Crystal Structure of a Thermostable Alanine Racemase from Thermoanaerobacter tengcongensis MB4 Reveals the Role of Gln360 in Substrate Selection. PLoS One 2015. [PMID: 26218070 PMCID: PMC4517790 DOI: 10.1371/journal.pone.0133516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Pyridoxal 5’-phosphate (PLP) dependent alanine racemase catalyzes racemization of L-Ala to D-Ala, a key component of the peptidoglycan network in bacterial cell wall. It has been extensively studied as an important antimicrobial drug target due to its restriction in eukaryotes. However, many marketed alanine racemase inhibitors also act on eukaryotic PLP-dependent enzymes and cause side effects. A thermostable alanine racemase (AlrTt) from Thermoanaerobacter tengcongensis MB4 contains an evolutionarily non-conserved residue Gln360 in inner layer of the substrate entryway, which is supposed to be a key determinant in substrate specificity. Here we determined the crystal structure of AlrTt in complex with L-Ala at 2.7 Å resolution, and investigated the role of Gln360 by saturation mutagenesis and kinetic analysis. Compared to typical bacterial alanine racemase, presence of Gln360 and conformational changes of active site residues disrupted the hydrogen bonding interactions necessary for proper PLP immobilization, and decreased both the substrate affinity and turnover number of AlrTt. However, it could be complemented by introduction of hydrophobic amino acids at Gln360, through steric blocking and interactions with a hydrophobic patch near active site pocket. These observations explained the low racemase activity of AlrTt, revealed the essential role of Gln360 in substrate selection, and its preference for hydrophobic amino acids especially Tyr in bacterial alanine racemization. Our work will contribute new insights into the alanine racemization mechanism for antimicrobial drug development.
Collapse
Affiliation(s)
- Xiaoliang Sun
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Guangzheng He
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Xiaoyan Wang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Shujing Xu
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Jiansong Ju
- College of Life Science, Hebei Normal University, Shijiazhuang, China
- * E-mail: (JSJ); (XLX)
| | - Xiaoling Xu
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
- * E-mail: (JSJ); (XLX)
| |
Collapse
|
12
|
Deng Y, Nagachar N, Fang L, Luan X, Catchmark JM, Tien M, Kao TH. Isolation and characterization of two cellulose morphology mutants of Gluconacetobacter hansenii ATCC23769 producing cellulose with lower crystallinity. PLoS One 2015; 10:e0119504. [PMID: 25790428 PMCID: PMC4366249 DOI: 10.1371/journal.pone.0119504] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/13/2015] [Indexed: 11/25/2022] Open
Abstract
Gluconacetobacter hansenii, a Gram-negative bacterium, produces and secrets highly crystalline cellulose into growth medium, and has long been used as a model system for studying cellulose synthesis in higher plants. Cellulose synthesis involves the formation of β-1,4 glucan chains via the polymerization of glucose units by a multi-enzyme cellulose synthase complex (CSC). These glucan chains assemble into ordered structures including crystalline microfibrils. AcsA is the catalytic subunit of the cellulose synthase enzymes in the CSC, and AcsC is required for the secretion of cellulose. However, little is known about other proteins required for the assembly of crystalline cellulose. To address this question, we visually examined cellulose pellicles formed in growth media of 763 individual colonies of G. hansenii generated via Tn5 transposon insertion mutagenesis, and identified 85 that produced cellulose with altered morphologies. X-ray diffraction analysis of these 85 mutants identified two that produced cellulose with significantly lower crystallinity than wild type. The gene disrupted in one of these two mutants encoded a lysine decarboxylase and that in the other encoded an alanine racemase. Solid-state NMR analysis revealed that cellulose produced by these two mutants contained increased amounts of non-crystalline cellulose and monosaccharides associated with non-cellulosic polysaccharides as compared to the wild type. Monosaccharide analysis detected higher percentages of galactose and mannose in cellulose produced by both mutants. Field emission scanning electron microscopy showed that cellulose produced by the mutants was unevenly distributed, with some regions appearing to contain deposition of non-cellulosic polysaccharides; however, the width of the ribbon was comparable to that of normal cellulose. As both lysine decarboxylase and alanine racemase are required for the integrity of peptidoglycan, we propose a model for the role of peptidoglycan in the assembly of crystalline cellulose.
Collapse
Affiliation(s)
- Ying Deng
- Department of Biochemistry and Molecular Biology, the Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Nivedita Nagachar
- Department of Biochemistry and Molecular Biology, the Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Lin Fang
- Department of Agricultural and Biological Engineering, the Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Xin Luan
- Department of Biochemistry and Molecular Biology, the Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Jeffrey M. Catchmark
- Department of Agricultural and Biological Engineering, the Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Ming Tien
- Department of Biochemistry and Molecular Biology, the Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Teh-hui Kao
- Department of Biochemistry and Molecular Biology, the Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
13
|
Flynn JM, Downs DM. In the absence of RidA, endogenous 2-aminoacrylate inactivates alanine racemases by modifying the pyridoxal 5'-phosphate cofactor. J Bacteriol 2013; 195:3603-9. [PMID: 23749972 PMCID: PMC3754577 DOI: 10.1128/jb.00463-13] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 05/31/2013] [Indexed: 11/20/2022] Open
Abstract
Members of the RidA (YjgF/YER057c/UK114) protein family are broadly conserved across the domains of life. In vitro, these proteins deaminate 3- or 4-carbon enamines that are generated as mechanistic intermediates of pyridoxal 5'-phosphate (PLP)-dependent serine/threonine dehydratases. The three-carbon enamine 2-aminoacrylate can inactivate some enzymes by forming a covalent adduct via a mechanism that has been well characterized in vitro. The biochemical activity of RidA suggested that the phenotypes of ridA mutant strains were caused by the accumulation of reactive enamine metabolites. The data herein show that in ridA mutant strains of Salmonella enterica, a stable 2-aminoacrylate (2-AA)/PLP adduct forms on the biosynthetic alanine racemase, Alr, indicating the presence of 2-aminoacrylate in vivo. This study confirms the deleterious effect of 2-aminoacrylate generated by metabolic enzymes and emphasizes the need for RidA to quench this reactive metabolite.
Collapse
Affiliation(s)
- Jeffrey M. Flynn
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | |
Collapse
|
14
|
Melkonian LO, Avetisova GE, Ambartsumian AA, Chakhalian AK, Sagian AS. [Regulation of key enzymes of L-alanine biosynthesis by Brevibacterium flavum producer strains]. Prikl Biokhim Mikrobiol 2013; 49:144-148. [PMID: 23795472 DOI: 10.7868/s0555109913020098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The mechanisms of L-alanine overproduction by Brevibacterium flavum producer strains were studied. It was shown that beta-CI-L-alanine is an inhibitor of some key enzymes involved in the synthesis of L-alanine, including alanine transaminase and valine-pyruvate transaminase. Two highly active B. flavum GL1 and GL1 8 producer strains, which are resistant to the inhibitory effect of beta-Cl-L-alanine, were obtained using a parental B. flavum AA5 producer strain, characterized by a reduced activity of alanine racemase (>or=98%). It was demonstrated that the increased L-alanine synthesis efficiency observed in the producer strains developed in this work is associated with the absence of inhibition of alanine transaminase by the end product of the biosynthesis reaction, as well as with the effect of derepression of both alanine transaminase and valine-pyruvate transaminase synthesis by the studied compound.
Collapse
|
15
|
Liu JL, Liu XQ, Shi YW. Expression, purification, and characterization of alanine racemase from Pseudomonas putida YZ-26. World J Microbiol Biotechnol 2011; 28:267-74. [PMID: 22806802 DOI: 10.1007/s11274-011-0816-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Accepted: 06/07/2011] [Indexed: 12/26/2022]
Abstract
Alanine racemase catalyzes the interconversion of D: - and L: -alanine and plays an important role in supplying D: -alanine, a component of peptidoglycan biosynthesis, to most bacteria. Alanine racemase exists mostly in prokaryotes and is generally absent in higher eukaryotes; this makes it an attractive target for the design of new antibacterial drugs. Here, we present the cloning and characterization of a new gene-encoding alanine racemase from Pseudomonas putida YZ-26. An open reading frame (ORF) of 1,230 bp, encoding a protein of 410 amino acids with a calculated molecular weight of 44,217.3 Da, was cloned into modified vector pET32M to form the recombinant plasmid pET-alr. After introduction into E.coli BL21, the strain pET-alr/E.coli BL21 expressed His(6)-tagged alanine racemase. The recombinant alanine racemase was efficiently purified to homogeneity using Ni(2+)-NTA and a gel filtration column, with 82.5% activity recovery. The amino acid sequence deduced from the alanine racemase gene revealed identity similarities of 97.0, 93, 23, and 22.0% with from P. putida F1, P. putida200, P. aeruginosa, and Salmonella typhimurium, respectively. The recombinant alanine racemase is a monomeric protein with a molecular mass of 43 kDa. The enzyme exhibited activity with L: -alanine and L: -isoleucine, and showed higher specificity for the former compared with the latter. The enzyme was stable from pH 7.0-11.0; its optimum pH was at 9.0. The optimum temperature for the enzyme was 37°C, and its activity was rapidly lost at temperatures above 40°C. Divalent metals, including Sr(2+), Mn(2+), Co(2+), and Ni(2+) obviously enhanced enzymatic activity, while the Cu(2+) ion showed inhibitory effects.
Collapse
Affiliation(s)
- Jun-Lin Liu
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, 92 Wucheng Road, Taiyuan, People's Republic of China
| | | | | |
Collapse
|
16
|
Anthony KG, Strych U, Yeung KR, Shoen CS, Perez O, Krause KL, Cynamon MH, Aristoff PA, Koski RA. New classes of alanine racemase inhibitors identified by high-throughput screening show antimicrobial activity against Mycobacterium tuberculosis. PLoS One 2011; 6:e20374. [PMID: 21637807 PMCID: PMC3102704 DOI: 10.1371/journal.pone.0020374] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 05/01/2011] [Indexed: 11/30/2022] Open
Abstract
Background In an effort to discover new drugs to treat tuberculosis (TB) we chose alanine racemase as the target of our drug discovery efforts. In Mycobacterium tuberculosis, the causative agent of TB, alanine racemase plays an essential role in cell wall synthesis as it racemizes L-alanine into D-alanine, a key building block in the biosynthesis of peptidoglycan. Good antimicrobial effects have been achieved by inhibition of this enzyme with suicide substrates, but the clinical utility of this class of inhibitors is limited due to their lack of target specificity and toxicity. Therefore, inhibitors that are not substrate analogs and that act through different mechanisms of enzyme inhibition are necessary for therapeutic development for this drug target. Methodology/Principal Findings To obtain non-substrate alanine racemase inhibitors, we developed a high-throughput screening platform and screened 53,000 small molecule compounds for enzyme-specific inhibitors. We examined the ‘hits’ for structural novelty, antimicrobial activity against M. tuberculosis, general cellular cytotoxicity, and mechanism of enzyme inhibition. We identified seventeen novel non-substrate alanine racemase inhibitors that are structurally different than any currently known enzyme inhibitors. Seven of these are active against M. tuberculosis and minimally cytotoxic against mammalian cells. Conclusions/Significance This study highlights the feasibility of obtaining novel alanine racemase inhibitor lead compounds by high-throughput screening for development of new anti-TB agents.
Collapse
Affiliation(s)
- Karen G Anthony
- L2 Diagnostics, LLC, New Haven, Connecticut, United States of America.
| | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Abstract
The existence of multiple, alternative pathways for polyamine biosynthesis, and the presence of alternative polyamine structural analogs, is an indication of the physiological importance of polyamines and their long evolutionary history. Polyamine biosynthesis is modular: diamines are synthesized directly or indirectly from amino acids, and triamines are synthesized from diamines by transfer of aminopropyl, carboxyaminopropyl, or aminobutyl groups to the diamine. Diversification of polyamine biosynthesis has depended on gene duplication and functional divergence, on gene fusion, and on horizontal gene transfer. Four examples of polyamine biosynthetic diversification are presented here with a discussion of methodological and conceptual approaches for identification of new pathways.
Collapse
Affiliation(s)
- Anthony J Michael
- Department of Pharmacology, University of Texas Southwestern Medical Center, Forest Park, Dallas, TX, USA
| |
Collapse
|
18
|
Couñago RM, Davlieva M, Strych U, Hill RE, Krause KL. Biochemical and structural characterization of alanine racemase from Bacillus anthracis (Ames). BMC Struct Biol 2009; 9:53. [PMID: 19695097 PMCID: PMC2743695 DOI: 10.1186/1472-6807-9-53] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Accepted: 08/20/2009] [Indexed: 12/04/2022]
Abstract
BACKGROUND Bacillus anthracis is the causative agent of anthrax and a potential bioterrorism threat. Here we report the biochemical and structural characterization of B. anthracis (Ames) alanine racemase (AlrBax), an essential enzyme in prokaryotes and a target for antimicrobial drug development. We also compare the native AlrBax structure to a recently reported structure of the same enzyme obtained through reductive lysine methylation. RESULTS B. anthracis has two open reading frames encoding for putative alanine racemases. We show that only one, dal1, is able to complement a D-alanine auxotrophic strain of E. coli. Purified Dal1, which we term AlrBax, is shown to be a dimer in solution by dynamic light scattering and has a Vmax for racemization (L- to D-alanine) of 101 U/mg. The crystal structure of unmodified AlrBax is reported here to 1.95 A resolution. Despite the overall similarity of the fold to other alanine racemases, AlrBax makes use of a chloride ion to position key active site residues for catalysis, a feature not yet observed for this enzyme in other species. Crystal contacts are more extensive in the methylated structure compared to the unmethylated structure. CONCLUSION The chloride ion in AlrBax is functioning effectively as a carbamylated lysine making it an integral and unique part of this structure. Despite differences in space group and crystal form, the two AlrBax structures are very similar, supporting the case that reductive methylation is a valid rescue strategy for proteins recalcitrant to crystallization, and does not, in this case, result in artifacts in the tertiary structure.
Collapse
Affiliation(s)
- Rafael M Couñago
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Milya Davlieva
- Department of Biochemistry Rice University, Houston, TX, USA
| | - Ulrich Strych
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Ryan E Hill
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Kurt L Krause
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| |
Collapse
|
19
|
Priyadarshi A, Lee EH, Sung MW, Nam KH, Lee WH, Kim EE, Hwang KY. Structural insights into the alanine racemase from Enterococcus faecalis. Biochim Biophys Acta 2009; 1794:1030-40. [PMID: 19328247 DOI: 10.1016/j.bbapap.2009.03.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Revised: 02/19/2009] [Accepted: 03/04/2009] [Indexed: 11/13/2022]
Abstract
Alanine racemase (AlaR) is a bacterial enzyme that belongs to the fold-type III group of pyridoxal 5'-phosphate (PLP)-dependent enzymes. AlaR catalyzes the interconversion between L- and D-alanine, which is important for peptidoglycan biosynthesis. This enzyme is common in prokaryotes, but absent in eukaryotes, which makes it an attractive target for the design of new antibacterial drugs. Here, we report the crystal structures of both the apoenzyme and the d-cycloserine (DCS) complex of AlaR from the pathogenic bacterium Enterococcus faecalis v583, at a resolution of 2.5 A. DCS is a suicide inhibitor of AlaR and, as such, serves as an antimicrobial agent and has been used to treat tuberculosis and urinary tract infection-related diseases, and makes several hydrogen bonds with the conserved active site residues, Tyr44 and Ser207, respectively. The apoenzyme crystal structure of AlaR consists of three monomers in the asymmetric unit, including a polyethylene glycol molecule in the dimer interface that surrounds one of the His 293 residues and also sits close to one side of the His 293 residue in the opposite monomer. Our results provide structural insights into AlaR that may be used for the development of new antibiotics targeting the alanine racemase in pathogenic bacteria.
Collapse
Affiliation(s)
- Amit Priyadarshi
- Biomedical Research Center, Life Science Division, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 136-791, South Korea
| | | | | | | | | | | | | |
Collapse
|
20
|
Au K, Ren J, Walter TS, Harlos K, Nettleship JE, Owens RJ, Stuart DI, Esnouf RM. Structures of an alanine racemase from Bacillus anthracis (BA0252) in the presence and absence of (R)-1-aminoethylphosphonic acid (L-Ala-P). Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:327-33. [PMID: 18453697 PMCID: PMC2376406 DOI: 10.1107/s1744309108007252] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Accepted: 03/17/2008] [Indexed: 11/11/2022]
Abstract
Bacillus anthracis, the causative agent of anthrax, has been targeted by the Oxford Protein Production Facility to validate high-throughput protocols within the Structural Proteomics in Europe project. As part of this work, the structures of an alanine racemase (BA0252) in the presence and absence of the inhibitor (R)-1-aminoethylphosphonic acid (L-Ala-P) have determined by X-ray crystallography to resolutions of 2.1 and 1.47 A, respectively. Difficulties in crystallizing this protein were overcome by the use of reductive methylation. Alanine racemase has attracted much interest as a possible target for anti-anthrax drugs: not only is D-alanine a vital component of the bacterial cell wall, but recent studies also indicate that alanine racemase, which is accessible in the exosporium, plays a key role in inhibition of germination in B. anthracis. These structures confirm the binding mode of L-Ala-P but suggest an unexpected mechanism of inhibition of alanine racemase by this compound and could provide a basis for the design of improved alanine racemase inhibitors with potential as anti-anthrax therapies.
Collapse
Affiliation(s)
- Kinfai Au
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
| | - Jingshan Ren
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
| | - Thomas S. Walter
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
| | - Karl Harlos
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
| | - Joanne E. Nettleship
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
| | - Raymond J. Owens
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
| | - David I. Stuart
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
| | - Robert M. Esnouf
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
| |
Collapse
|
21
|
Oikawa T. [Occurrence of D-amino acids in higher plants and foods and the enzymes related to their metabolism]. Seikagaku 2008; 80:300-307. [PMID: 18516908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Tadao Oikawa
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-Cho, Suita-Shi, Osaka-Fu 564-8680, Japan
| |
Collapse
|
22
|
Milligan DL, Tran SL, Strych U, Cook GM, Krause KL. The alanine racemase of Mycobacterium smegmatis is essential for growth in the absence of D-alanine. J Bacteriol 2007; 189:8381-6. [PMID: 17827284 PMCID: PMC2168708 DOI: 10.1128/jb.01201-07] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alanine racemase, encoded by the gene alr, is an important enzyme in the synthesis of d-alanine for peptidoglycan biosynthesis. Strains of Mycobacterium smegmatis with a deletion mutation of the alr gene were found to require d-alanine for growth in both rich and minimal media. This indicates that alanine racemase is the only source of d-alanine for cell wall biosynthesis in M. smegmatis and confirms alanine racemase as a viable target gene for antimycobacterial drug development.
Collapse
Affiliation(s)
- Daniel L Milligan
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | | | | | | | | |
Collapse
|
23
|
Spies MA, Toney MD. Intrinsic Primary and Secondary Hydrogen Kinetic Isotope Effects for Alanine Racemase from Global Analysis of Progress Curves. J Am Chem Soc 2007; 129:10678-85. [PMID: 17691728 DOI: 10.1021/ja067643k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The pyridoxal phosphate dependent alanine racemase catalyzes the interconversion of L- and D-alanine. The latter is an essential component of peptidoglycan in cell walls of Gram-negative and -positive bacteria, making alanine racemase an attractive target for antibacterials. Global analysis of protiated and deuterated progress curves simultaneously enables determination of intrinsic kinetic and equilibrium isotope effects for alanine racemase. The intrinsic primary kinetic isotope effects for Calpha hydron abstraction are 1.57 +/- 0.05 in the D --> L direction and 1.66 +/- 0.09 in the L --> D direction. Secondary kinetic isotope effects were found for the external aldimine formation steps in both the L --> D (1.13 +/- 0.05, forward; 0.90 +/- 0.03, reverse) and D --> L (1.13 +/- 0.06, forward; 0.89 +/- 0.03, reverse) directions. The secondary equilibrium isotope effects calculated from these are 1.26 +/- 0.07 and 1.27 +/- 0.07 for the L --> D and D --> L directions, respectively. These equilibrium isotope effects imply substantial ground-state destabilization of the C-H bond via hyperconjugation with the conjugated Schiff base/pyridine ring pi system. The magnitudes of the intrinsic primary kinetic isotope effects, the lower boundary on the energy of the quinonoid intermediate, and the protonation states of the active site catalytic acids/bases (K39-epsilonNH2 and Y265-OH) suggest that the pKa of the substrate Calpha-H bond in the external aldimine lies between those of the two catalytic bases, such that the proton abstraction transition state is early in the D --> L direction and late in the L --> D direction.
Collapse
Affiliation(s)
- M Ashley Spies
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA
| | | |
Collapse
|
24
|
Ito T, Takahashi K, Naka T, Hemmi H, Yoshimura T. Enzymatic assay of D-serine using D-serine dehydratase from Saccharomyces cerevisiae. Anal Biochem 2007; 371:167-72. [PMID: 17869212 DOI: 10.1016/j.ab.2007.07.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Revised: 07/30/2007] [Accepted: 07/31/2007] [Indexed: 10/23/2022]
Abstract
D-Serine is localized in the mammalian forebrain and modulates brain functions as a coagonist of an N-methyl-D-aspartate receptor. D-Serine is also found in human urine, although its physiological meaning is unclear. A method for rapid and simple assay of D-serine is probably useful for studying its physiological role and clinical relevance. Currently, D-serine is assayed by high-performance liquid chromatography after derivatization of the amino acid to a diastereomer. The method is time consuming and requires expensive equipment. In this study, we developed a rapid and simple method for the D-serine assay using D-serine dehydratase newly found in Saccharomyces cerevisiae. The yeast d-serine dehydratase acts dominantly on d-serine, in contrast with previously reported bacterial enzymes that act on both D- and L-serine. In our method, pyruvate produced from D-serine by the dehydratase reaction is assayed with lactic dehydrogenase and reduced nicotinamide adenine dinucleotide or with 2,4-dinitrophenylhydrazine. Our enzymatic method could be used for the quantitative determination of D-serine in human urine.
Collapse
Affiliation(s)
- Tomokazu Ito
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | | | | | | | | |
Collapse
|
25
|
Major DT, Gao J. A combined quantum mechanical and molecular mechanical study of the reaction mechanism and alpha-amino acidity in alanine racemase. J Am Chem Soc 2007; 128:16345-57. [PMID: 17165790 DOI: 10.1021/ja066334r] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Combined quantum mechanical/molecular mechanical simulations have been carried out to investigate the origin of the carbon acidity enhancement in the alanine racemization reaction catalyzed by alanine racemase (AlaR). The present study shows that the enhancement of carbon acidity of alpha-amino acids by the cofactor pyridoxal 5'-phosphate (PLP) with an unusual, unprotonated pyridine is mainly due to solvation effects, in contrast to the intrinsic electron-withdrawing stabilization by the pyridinium ion to form a quinonoid intermediate. Alanine racemase further lowers the alpha-proton acidity and provides an overall 14-17 kcal/mol transition-state stabilization. The second key finding of this study is that the mechanism of racemization of an alanine zwitterion in water is altered from an essentially concerted process to a stepwise reaction by formation of an external aldimine adduct with the PLP cofactor. Finally, we have used a centroid path integral method to determine the intrinsic kinetic isotope effects for the two proton abstraction reactions, which are somewhat greater than the experimental estimates.
Collapse
Affiliation(s)
- Dan Thomas Major
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | | |
Collapse
|
26
|
Abstract
First-order rate constants for deprotonation of the alpha-imino carbon of the adduct between 5'-deoxypyridoxal (1) and glycine were determined as the rate constants for Claisen-type addition of glycine to 1 where deprotonation is rate determining for product formation. There is no significant deprotonation at pH 7.1 of the form of the 1-glycine iminium ion with the pyridine nitrogen in the basic form. The value of kHO for hydroxide ion-catalyzed deprotonation of the alpha-imino carbon increases from 7.5 x 10(2) to 3.8 x 10(5) to 3.0 x 10(7) M(-1) s(-1), respectively, with protonation of the pyridine nitrogen, the phenoxide oxyanion, and the carboxylate anion of the 1-glycine iminium ion. There is a corresponding decrease in the pKas for deprotonation of the alpha-imino carbon from 17 to 11 to 6. It is proposed that enzymes selectively bind and catalyze the reaction of the iminium ion with pKa = 17. A comparison of kB = 1.7 x 10(-3) s(-1) for deprotonation of the alpha-imino carbon of this cofactor-glycine adduct (pKa = 17 by HPO4(2-) with k(cat)/K(m) = 4 x 10(5) M(-1) s(-1) for catalysis of amino-acid racemization by alanine racemase shows that the enzyme causes a ca 2 x 10(8)-fold acceleration of the rate of deprotonation the alpha-imino carbon. This corresponds to about one-half of the burden borne by alanine racemase in catalysis of deprotonation of alanine.
Collapse
Affiliation(s)
- Krisztina Toth
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260, USA
| | | |
Collapse
|
27
|
Francois JA, Kappock TJ. Alanine racemase from the acidophile Acetobacter aceti. Protein Expr Purif 2007; 51:39-48. [PMID: 16843006 DOI: 10.1016/j.pep.2006.05.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Revised: 05/26/2006] [Accepted: 05/27/2006] [Indexed: 11/21/2022]
Abstract
Acetobacter aceti converts ethanol to acetic acid, and survives acetic acid exposure by tolerating cytoplasmic acidification. Alanine racemase (Alr) is a pyridoxal 5' phosphate (PLP) -dependent enzyme that catalyzes the interconversion of the d- and l-isomers of alanine and has a basic pH optimum. Since d-alanine is essential for peptidoglycan biosynthesis, Alr must somehow function in the acidic cytoplasm of A. aceti. We report the partial purification of native A. aceti Alr (AaAlr) and evidence that it is a rather stable enzyme. The C-terminus of AaAlr has a strong resemblance to the ssrA-encoded protein degradation signal, which thwarted initial protein expression experiments. High-activity AaAlr forms lacking a protease recognition sequence were expressed in Escherichia coli and purified. Biophysical and enzymological experiments confirm that AaAlr is intrinsically acid-resistant, yet has the catalytic properties of an ordinary Alr.
Collapse
Affiliation(s)
- Julie A Francois
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | |
Collapse
|
28
|
Yan X, Gai Y, Liang L, Liu G, Tan H. A gene encoding alanine racemase is involved in spore germination in Bacillus thuringiensis. Arch Microbiol 2006; 187:371-8. [PMID: 17165028 DOI: 10.1007/s00203-006-0201-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2006] [Revised: 11/16/2006] [Accepted: 11/20/2006] [Indexed: 10/23/2022]
Abstract
Alanine racemase is a major component of the exosporium of Bacillus cereus spores. A gene homologous to that of alanine racemase (alrA) was cloned from Bacillus thuringiensis subsp. kurstaki, and RT-PCR showed that alrA was transcribed only in the sporulating cells. Disruption of alrA did not affect the growth and sporulation of B. thuringiensis, but promoted L-alanine-induced spore germination. When the spore germination rate was measured by monitoring DPA release, complementation of the alrA disruptant reduced the rate of L-alanine-induced spore germination below that of even wild-type spores. As previously reported for spores of other Bacillus species, D-alanine was an effective and competitive inhibitor of L-alanine-induced germination of B. thuringiensis spores. D-cycloserine alone stimulated inosine-induced germination of B. thuringiensis spores in addition to increasing L-alanine-induced germination by inhibiting alanine racemase. D-alanine also increased the rate of inosine-induced germination of wild-type spores. However, D-alanine inhibited inosine-induced germination of the alrA disruptant spores. It is possible that AlrA converted D-alanine to L-alanine, and this in turn, stimulated spore germination in B. thuringiensis. These results suggest that alrA plays a crucial role in moderating the germination rate of B. thuringiensis spores.
Collapse
Affiliation(s)
- Xiaohua Yan
- Center for Microbial Genetics and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, 100080 Beijing, China
| | | | | | | | | |
Collapse
|
29
|
Oikawa T, Tauch A, Schaffer S, Fujioka T. Expression of alr gene from Corynebacterium glutamicum ATCC 13032 in Escherichia coli and molecular characterization of the recombinant alanine racemase. J Biotechnol 2006; 125:503-12. [PMID: 16707184 DOI: 10.1016/j.jbiotec.2006.04.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Revised: 03/18/2006] [Accepted: 04/04/2006] [Indexed: 11/28/2022]
Abstract
We constructed the high-expression system of the alr gene from Corynebacterium glutamicum ATCC 13032 in Escherichia coli BL 21 (DE3) to characterize the enzymological and structural properties of the gene product, Alr. The Alr was expressed in the soluble fractions of the cell extract of the E. coli clone and showed alanine racemase activity. The purified Alr was a dimer with a molecular mass of 78 kDa. The Alr required pyridoxal 5'-phosphate (PLP) as a coenzyme and contained 2 mol of PLP per mol of the enzyme. The holoenzyme showed maximum absorption at 420 nm, while the reduced form of the enzyme showed it at 310 nm. The Alr was specific for alanine, and the optimum pH was observed at about nine. The Alr was relatively thermostable, and its half-life time at 60 degrees C was estimated to be 26 min. The K(m) and V(max) values were determined as follows: l-alanine to d-alanine, K(m) (l-alanine) 5.01 mM and V(max) 306 U/mg; d-alanine to l-alanine, K(m) (d-alanine) 5.24 mM and V(max) 345 U/mg. The K(eq) value was calculated to be 1.07 and showed good agreement with the theoretical value for the racemization reaction. The high substrate specificity of the Alr from C. glutamicum ATCC 13032 is expected to be a biocatalyst for d-alanine production from the l-counter part.
Collapse
Affiliation(s)
- Tadao Oikawa
- Department of Biotechnology, Faculty of Engineering, Kansai University, 3-3-35 Yamate-Cho, Suita, Osaka-Fu 564-8680, Japan.
| | | | | | | |
Collapse
|
30
|
Kidron H, Repo S, Johnson MS, Salminen TA. Functional classification of amino acid decarboxylases from the alanine racemase structural family by phylogenetic studies. Mol Biol Evol 2006; 24:79-89. [PMID: 16997906 DOI: 10.1093/molbev/msl133] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Arginine decarboxylase (ADC) and ornithine decarboxylase (ODC) are involved in the biosynthesis of putrescine, which is the precursor of other polyamines in animals, plants, and bacteria. These pyridoxal-5'-phosphate-dependent decarboxylases belong to the alanine racemase (AR) structural family together with diaminopimelate decarboxylase (DapDC), which catalyzes the final step of lysine biosynthesis in bacteria. We have constructed a multiple-sequence alignment of decarboxylases in the AR structural family and, based on the alignment, inferred phylogenetic trees. The phylogenetic tree consists of 3 distinct clades formed by ADC, DapDC, and ODC that diverged from an ancestral decarboxylase. The ancestral decarboxylase probably was able to recognize several substrates, and in archaea and bacteria, ODC may have retained the ability to bind other amino acids. Previously, a paralogue of ODC has been proposed to account for ADC activity detected in mammalian cells. According to our results, this appears unlikely, emphasizing the need for more caution in functional assignment made using sequence data and illustrating the continuing value of phylogenetic analysis in clarifying relationships and putative functions.
Collapse
Affiliation(s)
- Heidi Kidron
- Department of Biochemistry and Pharmacy, Abo Akademi University, Turku, Finland
| | | | | | | |
Collapse
|
31
|
Panizzutti R, de Souza Leite M, Pinheiro CM, Meyer-Fernandes JR. The occurrence of free d-alanine and an alanine racemase activity inLeishmania amazonensis. FEMS Microbiol Lett 2006; 256:16-21. [PMID: 16487314 DOI: 10.1111/j.1574-6968.2006.00064.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Free D-amino acids are implicated in several biological functions. This study examined the presence of D-alanine in Leishmania amazonensis. Measuring chiral amino acid content by high-performance liquid chromatography we detected a significant amount of free D-alanine in promastigotes of these parasites. D-alanine accounts for 8.9% of total free alanine and is found primarily in the soluble fraction. Specific racemization of L-alanine to D-alanine was detected in cell lysates and this enzyme activity was inhibited by D-cycloserine, an alanine racemase inhibitor. Furthermore, we were able to decrease this pool of D-amino acid by treating our cultures with D-cycloserine. We demonstrate for the first time the existence of a significant amount of free D-alanine in L. amazonensis and an alanine racemase activity present in cell lysates. The restriction of D-alanine to bacteria, some fungi and now in L. amazonensis opens a new perspective on treatment of diseases caused by these microorganisms.
Collapse
Affiliation(s)
- Rogério Panizzutti
- Departamento de Anatomia, ICB, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | |
Collapse
|
32
|
Cao Q, Zhao Z, Zhang YZ, Wang Y, Ding JY. [Cloning, sequence analysis and expression of alanine racemase gene in Pseudomonas putida]. Wei Sheng Wu Xue Bao 2006; 46:80-4. [PMID: 16579470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Two distinct alanine racemase genes from Pseudomonas putida 200 were cloned and sequenced. DadX encodes a peptide of 357 amino acids with a calculated molecular weight of 38.82kDa. The putative product of alr gene is a peptide of 409 amino acids with molecular weight of 44.182kDa. A homology comparison revealed identities of 96.64%, 71.99%, 44.88% and 47.37% of the DadX alanine racemase to those from P. putida KT2440, Pseudomonas aeruginosa, Salmonella typhimurium and Escherichia coli, respectively. The amino acids sequence deduced from alr gene showed the homologies of 94.38%, 22.89%, 25.72% and 26.44% to those from the microorganisms above, respectively. Two motifs believed essential to the enzyme activity are found both in DadX and Alr, such as pyridoxal-5'-phosphate binding site. Both dadX and alr were expressed in E. coli TG1. Neither alanine racemase activity or serine racemase activity was detected in the host strain. Only alanine racemase activity was found in E. coli TG1/pCTD. But both E. coli TG1/pCTA and TG1/pCBA exhibit activity toward L-alanine and L-serine. Transcription of alr gene in E. coli is independent from extraneous promoter, a result confirmed by the significant enzyme activity observed in the E. coli TG1/pCBA, which indicates the presence of a possible promoter upstream the structure gene.
Collapse
Affiliation(s)
- Qin Cao
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China
| | | | | | | | | |
Collapse
|
33
|
Abstract
We have established a novel assay method based on circular dichroism that can be used for the kinetic study of the activity of amino acid racemases, such as ALR (alanine racemase). Although an enzyme-coupled assay method has been used to measure racemase activity, the CD method is superior to the enzyme assay because it can accurately determine the immediate changes of an enantiomer on racemization between its L- and D-forms. The enzyme-coupled assay requires D-amino acid oxidase, which is inactivated by an inhibitor of ALR, D-cycloserine. This indicates that the inhibitory kinetic study for ALR with D-cycloserine by the enzyme-coupled assay method is restricted to the analysis of only the reaction resulting in the formation of L-Ala from D-Ala. However, since the CD assay does not require the coupled enzyme, it can be used to comprehensively evaluate the reactions that result in the formation both of D-Ala from L-Ala and of L-Ala from D-Ala at several substrate concentrations. Streptomyces ALR also catalyses the formation of D-Ser from L-Ser and of L-Ser from D-Ser, but the catalytic constants (kcat) are 4- and 10-fold lower than those for the formation of D-Ala from L-Ala and of L-Ala from D-Ala respectively.
Collapse
Affiliation(s)
- Masafumi Noda
- *Department of Molecular Microbiology and Biotechnology, Graduate School of Biomedical Sciences, Hiroshima University, Kasumi 1-2-3, Minami-Ku, Hiroshima 734-8551, Japan
| | - Yasuyuki Matoba
- *Department of Molecular Microbiology and Biotechnology, Graduate School of Biomedical Sciences, Hiroshima University, Kasumi 1-2-3, Minami-Ku, Hiroshima 734-8551, Japan
| | - Takanori Kumagai
- *Department of Molecular Microbiology and Biotechnology, Graduate School of Biomedical Sciences, Hiroshima University, Kasumi 1-2-3, Minami-Ku, Hiroshima 734-8551, Japan
| | - Masanori Sugiyama
- *Department of Molecular Microbiology and Biotechnology, Graduate School of Biomedical Sciences, Hiroshima University, Kasumi 1-2-3, Minami-Ku, Hiroshima 734-8551, Japan
- †Frontier Center for Microbiology, Hiroshima University, Kasumi 1-2-3, Minami-Ku, Hiroshima 734-8551, Japan
- To whom correspondence should be addressed (email )
| |
Collapse
|
34
|
Zhao X, Li Z, Gu B, Frankel FR. Pathogenicity and immunogenicity of a vaccine strain of Listeria monocytogenes that relies on a suicide plasmid to supply an essential gene product. Infect Immun 2005; 73:5789-98. [PMID: 16113297 PMCID: PMC1231070 DOI: 10.1128/iai.73.9.5789-5798.2005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes is a bacterial pathogen that elicits a strong cellular immune response and thus has potential use as a vaccine vector. An attenuated strain, L. monocytogenes dal dat, produced by deletion of two genes (dal and dat) used for d-alanine synthesis, induces cytotoxic T lymphocytes and protective immunity in mice following infection in the presence of d-alanine. In order to obviate the dependence of L. monocytogenes dal dat on supplemental d-alanine yet retain its attenuation and immunogenicity, we explored mechanisms to allow transient endogenous synthesis of the amino acid. Here, we report on a derivative strain, L. monocytogenes dal dat/pRRR, that expresses a dal gene and synthesizes d-alanine under highly selective conditions. We constructed the suicide plasmid pRRR carrying a dal gene surrounded by two res1 sites and a resolvase gene, tnpR, which acts at the res1 sites. The resolvase gene is regulated by a promoter activated upon exposure to host cell cytosol. L. monocytogenes dal dat/pRRR was thus able to grow in liquid culture and to infect host cells without d-alanine supplementation. However, after infection of these cells, resolvase-mediated excision of the dal gene resulted in strong down-regulation of racemase expression. As a result, this system allowed only transient growth of L. monocytogenes dal dat/pRRR in infected cells and survival in animals for only 2 to 3 days. Nevertheless, mice immunized with L. monocytogenes dal dat/pRRR generated listeriolysin O-specific effector and memory CD8(+) T cells and were protected against lethal challenge by wild-type Listeria. This vector may be an attractive vaccine candidate for the induction of protective cellular immune responses.
Collapse
Affiliation(s)
- Xinyan Zhao
- 203C Johnson Pavilion, 3610 Hamilton Walk, Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | | | | | | |
Collapse
|
35
|
Li Z, Zhao X, Higgins DE, Frankel FR. Conditional lethality yields a new vaccine strain of Listeria monocytogenes for the induction of cell-mediated immunity. Infect Immun 2005; 73:5065-73. [PMID: 16041022 PMCID: PMC1201188 DOI: 10.1128/iai.73.8.5065-5073.2005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2005] [Revised: 02/20/2005] [Accepted: 03/10/2005] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes is a gram-positive intracellular pathogen that can enter phagocytic and nonphagocytic cells and colonize their cytosols. Taking advantage of this property to generate an intracellular vaccine delivery vector, we previously described a mutant strain of L. monocytogenes, Deltadal Deltadat, which is unable to synthesize cell wall by virtue of deletions in two genes (dal and dat) required for d-alanine synthesis. This highly attenuated strain induced long-lived protective systemic and mucosal immune responses in mice when administered in the transient presence of d-alanine. We have now increased the usefulness of this organism as a vaccine vector by use of an inducible complementation system that obviates the need for exogenous d-alanine administration. The strain expresses a copy of the Bacillus subtilis racemase gene under the control of a tightly regulated isopropyl-beta-d-thiogalactopyranoside (IPTG)-inducible promoter present on a multicopy plasmid. This bacterium demonstrates strict dose-dependent growth in the presence of IPTG. After removal of inducer, bacterial growth ceased within two replication cycles. Following infection of mice in the absence of IPTG or d-alanine, the bacterium survived in vivo for less than 3 days. Nevertheless, a single immunization elicited a state of long-lasting protective immunity against wild-type L. monocytogenes and induced a subset of effector listeriolysin O-specific CD11a(+) CD8(+) T cells in spleen and other tissues that was strongly enhanced after secondary immunization. This improved L. monocytogenes vector system may have potential use as a live vaccine against human immunodeficiency virus, other infectious diseases, and cancer.
Collapse
Affiliation(s)
- Zhongxia Li
- 203C Johnson Pavilion, 3610 Hamilton Walk, Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | | | | | | |
Collapse
|
36
|
Huang CM, Elmets CA, Tang DCC, Li F, Yusuf N. Proteomics reveals that proteins expressed during the early stage of Bacillus anthracis infection are potential targets for the development of vaccines and drugs. Genomics Proteomics Bioinformatics 2005; 2:143-51. [PMID: 15862115 PMCID: PMC5172467 DOI: 10.1016/s1672-0229(04)02020-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this review, we advance a new concept in developing vaccines and/or drugs to target specific proteins expressed during the early stage of Bacillus anthracis (anthrax) infection and address existing challenges to this concept. Three proteins (immune inhibitor A, GPR-like spore protease, and alanine racemase) initially identified by proteomics in our laboratory were found to have differential expressions during anthrax spore germination and early outgrowth. Other studies of different bacillus strains indicate that these three proteins are involved in either germination or cytotoxicity of spores, suggesting that they may serve as potential targets for the design of anti-anthrax vaccines and drugs.
Collapse
Affiliation(s)
- Chun-Ming Huang
- Department of Dermatology, University of Alabama at Birmingham, Alabama, USA.
| | | | | | | | | |
Collapse
|
37
|
Moore BC, Leigh JA. Markerless mutagenesis in Methanococcus maripaludis demonstrates roles for alanine dehydrogenase, alanine racemase, and alanine permease. J Bacteriol 2005; 187:972-9. [PMID: 15659675 PMCID: PMC545699 DOI: 10.1128/jb.187.3.972-979.2005] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Among the archaea, Methanococcus maripaludis has the unusual ability to use L- or D-alanine as a nitrogen source. To understand how this occurs, we tested the roles of three adjacent genes encoding homologs of alanine dehydrogenase, alanine racemase, and alanine permease. To produce mutations in these genes, we devised a method for markerless mutagenesis that builds on previously established genetic tools for M. maripaludis. The technique uses a negative selection strategy that takes advantage of the ability of the M. maripaludis hpt gene encoding hypoxanthine phosphoribosyltransferase to confer sensitivity to the base analog 8-azahypoxanthine. In addition, we developed a negative selection method to stably incorporate constructs into the genome at the site of the upt gene encoding uracil phosphoribosyltransferase. Mutants with in-frame deletion mutations in the genes for alanine dehydrogenase and alanine permease lost the ability to grow on either isomer of alanine, while a mutant with an in-frame deletion mutation in the gene for alanine racemase lost only the ability to grow on D-alanine. The wild-type gene for alanine dehydrogenase, incorporated into the upt site, complemented the alanine dehydrogenase mutation. Hence, the permease is required for the transport of either isomer, the dehydrogenase is specific for the L isomer, and the racemase converts the D isomer to the L isomer. Phylogenetic analysis indicated that all three genes had been acquired by lateral gene transfer from the low-moles-percent G+C gram-positive bacteria.
Collapse
Affiliation(s)
- Brian C Moore
- Department of Microbiology, University of Washington, Microbiology, Box 357242, Seattle, WA 98195-7242, USA
| | | |
Collapse
|
38
|
Kalyanaraman C, Bernacki K, Jacobson MP. Virtual Screening against Highly Charged Active Sites: Identifying Substrates of Alpha−Beta Barrel Enzymes. Biochemistry 2005; 44:2059-71. [PMID: 15697231 DOI: 10.1021/bi0481186] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have developed a virtual ligand screening method designed to help assign enzymatic function for alpha-beta barrel proteins. We dock a library of approximately 19,000 known metabolites against the active site and attempt to identify the relevant substrate based on predicted relative binding free energies. These energies are computed using a physics-based energy function based on an all-atom force field (OPLS-AA) and a generalized Born implicit solvent model. We evaluate the ability of this method to identify the known substrates of several members of the enolase superfamily of enzymes, including both holo and apo structures (11 total). The active sites of these enzymes contain numerous charged groups (lysines, carboxylates, histidines, and one or more metal ions) and thus provide a challenge for most docking scoring functions, which treat electrostatics and solvation in a highly approximate manner. Using the physics-based scoring procedure, the known substrate is ranked within the top 6% of the database in all cases, and in 8 of 11 cases, it is ranked within the top 1%. Moreover, the top-ranked ligands are strongly enriched in compounds with high chemical similarity to the substrate (e.g., different substitution patterns on a similar scaffold). These results suggest that our method can be used, in conjunction with other information including genomic context and known metabolic pathways, to suggest possible substrates or classes of substrates for experimental testing. More broadly, the physics-based scoring method performs well on highly charged binding sites and is likely to be useful in inhibitor docking against polar binding sites as well. The method is fast (<1 min per ligand), due largely to an efficient minimization algorithm based on the truncated Newton method, and thus, it can be applied to thousands of ligands within a few hours on a small Linux cluster.
Collapse
Affiliation(s)
- Chakrapani Kalyanaraman
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California 94143-2240, USA
| | | | | |
Collapse
|
39
|
Abstract
Pyridoxal phosphate enzymes catalyze a wide variety of reaction types on amines and amino acids, generally by stabilizing carbanionic intermediates. This makes them very useful in cellular metabolism, but it also creates problems in controlling the reaction pathway that a given enzyme follows, i.e., in controlling reaction specificity. Stereoelectronic effects have been proposed to play a major role in determining the bond to Calpha that gets broken in the external aldimine intermediate that is common to all PLP enzymes. Here, we discuss our work on dialkylglycine decarboxylase aimed at providing direct evidence for stereoelectronic control of external aldimine reactivity. Once a bond to Calpha has been broken to form the carbanionic intermediate, enzymes must also carefully control the fate of this reactive species. Our studies with alanine racemase suggest that the enzyme selectively destabilizes the carbanionic quinonoid intermediate to promote higher racemization specificity by avoiding transamination side reactions.
Collapse
Affiliation(s)
- Michael D Toney
- Department of Chemistry, University of California-Davis, One Shields Ave, Davis, CA 95616, USA.
| |
Collapse
|
40
|
Noda M, Kawahara Y, Ichikawa A, Matoba Y, Matsuo H, Lee DG, Kumagai T, Sugiyama M. Self-protection Mechanism in d-Cycloserine-producing Streptomyces lavendulae. J Biol Chem 2004; 279:46143-52. [PMID: 15302885 DOI: 10.1074/jbc.m404603200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An antibiotic, D-cycloserine (DCS), inhibits the catalytic activities of alanine racemase (ALR) and d-alanyl-d-alanine ligase (DDL), which are necessary for the biosynthesis of the bacterial cell wall. In this study, we cloned both genes encoding ALR and DDL, designated alrS and ddlS, respectively, from DCS-producing Streptomyces lavendulae ATCC25233. Each gene product was purified to homogeneity and characterized. Escherichia coli, transformed with a pET vector carrying alrS or ddlS, displays higher resistance to DCS than the same host carrying the E. coli ALR- or DDL-encoded gene inserted into the pET vector. Although the S. lavendulae DDL was competitively inhibited by DCS, the K(i) value (920 microM) was obviously higher (40 approximately 100-fold) than those for E. coli DdlA (9 microM) or DdlB (27 microM). The high K(i) value of the S. lavendulae DDL suggests that the enzyme may be a self-resistance determinant in the DCS-producing microorganism. Kinetic studies for the S. lavendulae ALR suggest that the time-dependent inactivation rate of the enzyme by DCS is absolutely slower than that of the E. coli ALR. We conclude that ALR from DCS-producing S. lavendulae is also one of the self-resistance determinants.
Collapse
Affiliation(s)
- Masafumi Noda
- Department of Molecular Microbiology and Biotechnology, Graduate School of Biomedical Sciences, Hiroshima University, Kasumi 1-2-3, Minami-Ku, Hiroshima 734-8551, Japan
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Bron PA, Hoffer SM, Van Swam II, De Vos WM, Kleerebezem M. Selection and characterization of conditionally active promoters in Lactobacillus plantarum, using alanine racemase as a promoter probe. Appl Environ Microbiol 2004; 70:310-7. [PMID: 14711657 PMCID: PMC321294 DOI: 10.1128/aem.70.1.310-317.2004] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This paper describes the use of the alr gene, encoding alanine racemase, as a promoter-screening tool for the identification of conditional promoters in Lactobacillus plantarum. Random fragments of the L. plantarum WCFS1 genome were cloned upstream of the promoterless alr gene of Lactococcus lactis in a low-copy-number plasmid vector. The resulting plasmid library was introduced into an L. plantarum Deltaalr strain (MD007), and 40,000 clones were selected. The genome coverage of the library was estimated to be 98%, based on nucleotide insert sequence and restriction analyses of the inserts of randomly selected clones. The library was screened for clones that were capable of complementing the D-alanine auxotroph phenotype of MD007 in media containing up to 10, 100, or 300 micro g of the competitive Alr inhibitor D-cycloserine per ml. Western blot analysis with polyclonal antibodies raised against lactococcal Alr revealed that the Alr production level required for growth increased in the presence of increasing concentrations of D-cycloserine, adding a quantitative factor to the primarily qualitative nature of the alr complementation screen. Screening of the alr complementation library for clones that could grow only in the presence of 0.8 M NaCl resulted in the identification of eight clones that upon Western blot analysis showed significantly higher Alr production under high-salt conditions than under low-salt conditions. These results established the effectiveness of the alanine racemase complementation screening method for the identification of promoters on their conditional or constitutive activity.
Collapse
Affiliation(s)
- Peter A Bron
- Wageningen Centre for Food Sciences. NIZO food research, 6710 BA Ede, The Netherlands
| | | | | | | | | |
Collapse
|
42
|
Abstract
Conservation of water molecules was identified by a cluster analysis of seven crystal structures of alanine racemase from Bacillus stearothermophilus. A total of 47 clusters of consensus water sites were determined and found to be highly localized, as indicated by their low mobilities. These clusters are located in the region of the active sites as well as at the interface between the N-terminal domain (the alpha/beta-barrel) of the first monomer and the C-terminal domain of the second monomer. The clusters located at the dimer interface form extensive hydrogen-bonding networks linked to the protein backbone. These water-mediated hydrogen bonds, and also all hydrogen-bonding interactions at the dimer interface, were monitored during a 2 ns molecular dynamics simulation and showed that when the inhibitor propionate was bound to the enzyme, some of these interactions were disrupted. The data we present here indicate that the consensus water sites identified at the interface between the two monomers of alanine racemase may play a structural role, which is to maintain and stabilize the alanine racemase dimer. A second role might be to supply the active site continuously with water molecules in order to allow rapid equilibration of active site protons with the solvent.
Collapse
Affiliation(s)
- Gabriela Mustata
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
| | | |
Collapse
|
43
|
Affiliation(s)
- Willis A Wood
- The Agouron Institute, 1055 East Colorado Blvd., Pasadena, CA 91106, USA.
| |
Collapse
|
44
|
Abstract
Alanine racemase (Alr) [EC 5.1.1.1] from Geobacillus stearothermophilus is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes the first committed step in bacterial cell wall biosynthesis. It is converted to an aldolase upon replacement of Tyr265, which normally serves as a catalytic base in the racemase reaction, with alanine. The Y265A mutation increases catalytic efficiency for cleavage of beta-phenylserine to benzaldehyde and glycine by 2.3 x 105 fold as compared to the wild-type racemase, while racemase activity is greatly decreased. Additional mutagenesis suggests that His166 may act as the base that initiates the retroaldol reaction. The Y265A mutant is highly stereoselective for (2R,3S)-phenylserine, a d-amino acid, and does not process its enantiomer. This preference is consistent with the expected binding mode of substrate in the modified active site and supports the proposal that naturally occurring d-threonine aldolases and alanine racemases derive from a common ancestor.
Collapse
Affiliation(s)
- Florian P Seebeck
- Laboratorium für Organische Chemie, Swiss Federal Institute of Technology, ETH Hönggerberg, CH-8093 Zürich, Switzerland
| | | |
Collapse
|
45
|
Abstract
Alanine racemase (EC 5.1.1.1) catalyzes the interconversion of alanine enantiomers, and thus represents the first committed step involved in bacterial cell wall biosynthesis. Cycloserine acts as a suicide inhibitor of alanine racemase and as such, serves as an antimicrobial agent. The chemical means by which cycloserine inhibits alanine racemase is unknown. Through spectroscopic assays, we show here evidence of a pyridoxal derivative (arising from either isomer of cycloserine) saturated at the C4' carbon position. We additionally report the L- and D-cycloserine inactivated crystal structures of Bacillus stearothermophilus alanine racemase, which corroborates the spectroscopy via evidence of a 3-hydroxyisoxazole pyridoxamine derivative. Upon the basis of the kinetic and structural properties of both the L- and D-isomers of the inhibitor, we propose a mechanism of alanine racemase inactivation by cycloserine. This pathway involves an initial transamination step followed by tautomerization to form a stable aromatic adduct, a scheme similar to that seen in cycloserine inactivation of aminotransferases.
Collapse
Affiliation(s)
- Timothy D Fenn
- Department of Biochemistry and Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
| | | | | | | |
Collapse
|
46
|
Spies MA, Toney MD. Multiple hydrogen kinetic isotope effects for enzymes catalyzing exchange with solvent: application to alanine racemase. Biochemistry 2003; 42:5099-107. [PMID: 12718553 DOI: 10.1021/bi0274064] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alanine racemase catalyzes the pyridoxal phosphate-dependent interconversion of the D- and L-isomers of alanine. Previous studies have shown that the enzyme employs a two-base mechanism in which Lys39 and Tyr265 are the acid/base catalysts. It is thus possible that stereoisomerization of the external aldimine intermediates occurs through a concerted double proton transfer without the existence of a distinct carbanionic intermediate. This possibility was tested by the application of multiple kinetic isotope effect (KIE) methodology to alanine racemase. The mutual dependence of primary substrate and solvent deuterium KIEs has been measured using equilibrium perturbation-type experiments. The conceptually straightforward measurement of the substrate KIE in H(2)O is complemented with a less intuitive protium washout perturbation-type measurement in D(2)O. The primary substrate KIE in the D --> L direction at 25 degrees C is reduced from 1.297 in H(2)O to 1.176 in D(2)O, while in the L --> D direction it is reduced from 1.877 in H(2)O to 1.824 in D(2)O. Similar reductions are also observed at 65 degrees C, the temperature to which the Bacillus stearothermophilus enzyme is adapted. These data strongly support a stepwise racemization of stereoisomeric aldimine intermediates in which a substrate-based carbanion is an obligatory intermediate. The ionizations observed in k(cat)/K(M) pH profiles have been definitively assigned based on the DeltaH(ion) values of the observed pK(a)'s with alanine and on the pH dependence of k(cat)/K(M) for the alternative substrate serine. The acidic pK(a) in the bell-shaped curve is due to the phenolic hydroxyl of Tyr265, which must be unprotonated for reaction with either isomer of alanine. The basic pK(a) is due to the substrate amino group, which must be protonated to react with Tyr265-unprotonated enzyme. A detailed reaction mechanism incorporating these results is proposed.
Collapse
Affiliation(s)
- M Ashley Spies
- Department of Chemistry, University of California, Davis 95616, USA
| | | |
Collapse
|
47
|
Abstract
Bacterial alanine racemases are classified into two types of subunit structure (monomer and homodimer). To clarify the catalytic unit of monomeric alanine racemases, we examined the apparent molecular mass of the monomeric alanine racemases from Shigella dysenteriae, Shigella boydii, Shigella flexneri, and Shigella sonnei by gel filtration in the presence of the substrate and inhibitor. The enzymes were eluted on gel filtration as a monomer of about 39,000 Da at low protein concentration and in the absence of L-alanine and D-cycloserine. An increase in the apparent molecular mass was induced by increasing the protein concentration or by adding the ligands in the elution buffer. The increase ratio depended on the ligand concentration, and the maximum apparent molecular masses of all enzymes were 60,000 and 76,000 Da in the presence of 100 mM L-alanine and 5 mM D-cycloserine, respectively. D-cycloserine may induce an inactive dimer and L-alanine may induce an intermediate between the monomer and dimer because of dynamic equilibrium. The apoenzyme also showed similar behavior in the presence of the ligands, but the increase ratios were lower than those of the holoenzymes. The Bacillus psychrosaccharolyticus alanine racemase, having a dimeric structure, showed a constant molecular mass irrespective of the absence or presence of the ligands. These results suggest that the monomeric Shigella Alr enzymes have a dimeric structure in the catalytic reaction. Substances that inhibit the subunit interaction of monomeric alanine racemases may be useful as a new type of antibacterial.
Collapse
Affiliation(s)
- Kumio Yokoigawa
- Department of Food Science and Nutrition, Nara Women's University, Japan.
| | | | | |
Collapse
|
48
|
Bertoldi M, Cellini B, Paiardini A, Di Salvo M, Borri Voltattorni C. Treponema denticola cystalysin exhibits significant alanine racemase activity accompanied by transamination: mechanistic implications. Biochem J 2003; 371:473-83. [PMID: 12519070 PMCID: PMC1223284 DOI: 10.1042/bj20020875] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2002] [Revised: 12/20/2002] [Accepted: 01/08/2003] [Indexed: 11/17/2022]
Abstract
To obtain information on the reaction specificity of cystalysin from the spirochaete bacterium Treponema denticola, the interaction with L- and D-alanine has been investigated. Binding of both alanine enantiomers leads to the appearance of an external aldimine absorbing at 429 nm and of a band absorbing at 498 nm, indicative of a quinonoid species. Racemization and transamination reactions were observed to occur with both alanine isomers as substrates. The steady-state kinetic parameters for racemization, k (cat) and K (m), for L-alanine are 1.05+/-0.03 s(-1) and 10+/-1 mM respectively, whereas those for D-alanine are 1.4+/-0.1 s(-1) and 10+/-1 mM. During the reaction of cystalysin with L- or D-alanine, a time-dependent loss of beta-elimination activity occurs concomitantly with the conversion of the pyridoxal 5'-phosphate (PLP) coenzyme into pyridoxamine 5'-phosphate (PMP). The catalytic efficiency of the half-transamination of L-alanine is found to be 5.3x10(-5) mM(-1) x s(-1), 5-fold higher when compared with that of D-alanine. The partition ratio between racemization and half-transamination reactions is 2.3x10(3) for L-alanine and 1.4x10(4) for D-alanine. The pH dependence of the kinetic parameters for both the reactions shows that the enzyme possesses a single ionizing residue with p K values of 6.5-6.6, which must be unprotonated for catalysis. Addition of pyruvate converts the PMP form of the enzyme back into the PLP form and causes the concomitant recovery of beta-elimination activity. In contrast with other PLP enzymes studied so far, but similar to alanine racemases, the apoform of the enzyme abstracted tritium from C4' of both (4' S)- and (4' R)-[4'-(3)H]PMP in the presence of pyruvate. Together with molecular modelling of the putative binding sites of L- and D-alanine at the active site of the enzyme, the implications of these studies for the mechanisms of the side reactions catalysed by cystalysin are discussed.
Collapse
Affiliation(s)
- Mariarita Bertoldi
- Dipartimento di Scienze Neurologiche e della Visione, Sezione di Chimica Biologica, Facoltà di Medicina e Chirurgia, Università degli Studi di Verona, Strada Le Grazie, 8, 37134 Verona, Italy
| | | | | | | | | |
Collapse
|
49
|
Paiardini A, Contestabile R, D'Aguanno S, Pascarella S, Bossa F. Threonine aldolase and alanine racemase: novel examples of convergent evolution in the superfamily of vitamin B6-dependent enzymes. Biochim Biophys Acta 2003; 1647:214-9. [PMID: 12686135 DOI: 10.1016/s1570-9639(03)00050-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Vitamin B(6)-dependent enzymes may be grouped into five evolutionarily unrelated families, each having a different fold. Within fold type I enzymes, L-threonine aldolase (L-TA) and fungal alanine racemase (AlaRac) belong to a subgroup of structurally and mechanistically closely related proteins, which specialised during evolution to perform different functions. In a previous study, a comparison of the catalytic properties and active site structures of these enzymes suggested that they have a catalytic apparatus with the same basic features. Recently, recombinant D-threonine aldolases (D-TAs) from two bacterial organisms have been characterised, their predicted amino acid sequences showing no significant similarities to any of the known B(6) enzymes. In the present work, a comparative structural analysis suggests that D-TA has an alpha/beta barrel fold and therefore is a fold type III B(6) enzyme, as eukaryotic ornithine decarboxylase (ODC) and bacterial AlaRac. The presence of both TA and AlaRac in two distinct evolutionary unrelated families represents a novel and interesting example of convergent evolution. The independent emergence of the same catalytic properties in families characterised by completely different folds may have not been determined by chance, but by the similar structural features required to catalyse pyridoxal phosphate-dependent aldolase and racemase reactions.
Collapse
Affiliation(s)
- Alessandro Paiardini
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Università degli Studi di Roma La Sapienza, Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | | | | | | | | |
Collapse
|
50
|
Kim MG, Strych U, Krause K, Benedik M, Kohn H. N(2)-substituted D,L-cycloserine derivatives: synthesis and evaluation as alanine racemase inhibitors. J Antibiot (Tokyo) 2003; 56:160-8. [PMID: 12715876 DOI: 10.7164/antibiotics.56.160] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A select series of N(2)-substituted D,L-cycloserine derivatives were prepared a ndevaluated for inhibitory activity against purified alanine racemases (alr gene product) from Escherichia coli, Staphylococcus aureus, and Mycobacterium tuberculosis, as well as in a growth inhibition assay. N(2)-Modification led to loss of enzymatic inhibitory activity in most cases consistent with a recent proposal for cycloserine function.
Collapse
Affiliation(s)
- Myoung Goo Kim
- Division of Medicinal Chemistry and Natural Products, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7360, USA
| | | | | | | | | |
Collapse
|