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Katsube S, Sakai K, Ando T, Tobe R, Yoneyama H. l-Alanine Exporter AlaE Functions as One of the d-Alanine Exporters in Escherichia coli. Int J Mol Sci 2023; 24:10242. [PMID: 37373388 DOI: 10.3390/ijms241210242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
d-amino acids have recently been found to be present in the extracellular milieu at millimolar levels and are therefore assumed to play a physiological function. However, the pathway (or potential pathways) by which these d-amino acids are secreted remains unknown. Recently, Escherichia coli has been found to possess one or more energy-dependent d-alanine export systems. To gain insight into these systems, we developed a novel screening system in which cells expressing a putative d-alanine exporter could support the growth of d-alanine auxotrophs in the presence of l-alanyl-l-alanine. In the initial screening, five d-alanine exporter candidates, AlaE, YmcD, YciC, YraM, and YidH, were identified. Transport assays of radiolabeled d-alanine in cells expressing these candidates indicated that YciC and AlaE resulted in lower intracellular levels of d-alanine. Further detailed transport assays of AlaE in intact cells showed that it exports d-alanine in an expression-dependent manner. In addition, the growth constraints on cells in the presence of 90 mM d-alanine were mitigated by the overexpression of AlaE, implying that AlaE could export free d-alanine in addition to l-alanine under conditions in which intracellular d/l-alanine levels are raised. This study also shows, for the first time, that YciC could function as a d-alanine exporter in intact cells.
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Affiliation(s)
- Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Keiichiro Sakai
- Laboratory of Animal Microbiology, Department of Animal Science, Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Tasuke Ando
- Laboratory of Animal Microbiology, Department of Animal Science, Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Ryuta Tobe
- Laboratory of Animal Microbiology, Department of Animal Science, Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Hiroshi Yoneyama
- Laboratory of Animal Microbiology, Department of Animal Science, Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai 980-0845, Japan
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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] [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.
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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
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Bongaerts N, Edoo Z, Abukar AA, Song X, Sosa-Carrillo S, Haggenmueller S, Savigny J, Gontier S, Lindner AB, Wintermute EH. Low-cost anti-mycobacterial drug discovery using engineered E. coli. Nat Commun 2022; 13:3905. [PMID: 35798732 PMCID: PMC9262897 DOI: 10.1038/s41467-022-31570-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 06/23/2022] [Indexed: 12/29/2022] Open
Abstract
Whole-cell screening for Mycobacterium tuberculosis (Mtb) inhibitors is complicated by the pathogen's slow growth and biocontainment requirements. Here we present a synthetic biology framework for assaying Mtb drug targets in engineered E. coli. We construct Target Essential Surrogate E. coli (TESEC) in which an essential metabolic enzyme is deleted and replaced with an Mtb-derived functional analog, linking bacterial growth to the activity of the target enzyme. High throughput screening of a TESEC model for Mtb alanine racemase (Alr) revealed benazepril as a targeted inhibitor, a result validated in whole-cell Mtb. In vitro biochemical assays indicated a noncompetitive mechanism unlike that of clinical Alr inhibitors. We establish the scalability of TESEC for drug discovery by characterizing TESEC strains for four additional targets.
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Affiliation(s)
- Nadine Bongaerts
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- CRI, Paris, France
| | - Zainab Edoo
- Sorbonne Université, Université Paris Cité, Inserm, Centre de Recherche des Cordeliers (CRC), Paris, France
| | - Ayan A Abukar
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- CRI, Paris, France
| | - Xiaohu Song
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- CRI, Paris, France
| | - Sebastián Sosa-Carrillo
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- Institut Pasteur, Inria de Paris, Université Paris Cité, InBio, Paris, France
| | - Sarah Haggenmueller
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- CRI, Paris, France
| | - Juline Savigny
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- CRI, Paris, France
| | - Sophie Gontier
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- CRI, Paris, France
| | - Ariel B Lindner
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France.
- CRI, Paris, France.
| | - Edwin H Wintermute
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France.
- CRI, Paris, France.
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4
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Kumar R, Singh N, Chauhan A, Kumar M, Bhatta RS, Singh SK. Mycobacterium tuberculosis survival and biofilm formation studies: effect of D-amino acids, D-cycloserine and its components. J Antibiot (Tokyo) 2022; 75:472-479. [PMID: 35650279 DOI: 10.1038/s41429-022-00534-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/04/2022] [Accepted: 05/13/2022] [Indexed: 11/09/2022]
Abstract
D-amino acids play an important role in cell wall peptidoglycan biosynthesis. Mycobacterium tuberculosis D-amino acid oxidase deletion led to reduced biofilm-forming ability. Other recent studies also suggest that the accumulation of D-amino acids blocks biofilm formation and could also disperse pre-formed biofilm. Biofilms are communities of bacterial cells protected by extracellular matrix and harbor drug-tolerant as well as persistent bacteria. In Mycobacterium tuberculosis, biofilm formation or its inhibition by D-amino acids is yet to be tested. In the present study, we used selected D-amino acids to study their role in the prevention of biofilm formation and also if D-cycloserine's activity was due to presence of D-Serine as a metabolite. It was observed that D-serine limits biofilm formation in Mycobacterium tuberculosis H37Ra (Mtb-Ra), but it shows no effect on pre-formed biofilm. Also, D-cycloserine and its metabolic product, hydroxylamine, individually and in combination, with D-Serine, limit biofilm formation in Mtb-Ra and also disrupts existing biofilm. In summary, we demonstrated that D-alanine, D-valine, D-phenylalanine, D-serine, and D-threonine had no disruptive effect on pre-formed biofilm of Mtb-Ra, either individually or in combination, and D-cycloserine and its metabolite hydroxylamine have potent anti-biofilm activity.
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Affiliation(s)
- Ram Kumar
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India.,Jawaharlal Nehru University, New Mehrauli Road, JNU Ring Rd, New Delhi, 110067, India
| | - Nirbhay Singh
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India.,Jawaharlal Nehru University, New Mehrauli Road, JNU Ring Rd, New Delhi, 110067, India
| | - Anu Chauhan
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Mukesh Kumar
- Jawaharlal Nehru University, New Mehrauli Road, JNU Ring Rd, New Delhi, 110067, India.,Pharmaceutics and Pharmacokinetics Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Rabi Sankar Bhatta
- Pharmaceutics and Pharmacokinetics Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Sudheer Kumar Singh
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Ashida H, Murakami K, Inagaki K, Sawa Y, Hemmi H, Iwasaki Y, Yoshimura T. Evolution and properties of alanine racemase from Synechocystis sp. PCC6803. J Biochem 2021; 171:421-428. [PMID: 34967408 DOI: 10.1093/jb/mvab155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/20/2021] [Indexed: 11/14/2022] Open
Abstract
Alanine racemase (EC 5.1.1.1) depends on pyridoxal 5'-phosphate and catalyzes the interconversion between L- and D-Ala. The enzyme is responsible for the biosynthesis of D-Ala, which is an essential component of the peptidoglycan layer of bacterial cell walls. Phylogenetic analysis of alanine racemases demonstrated that the cyanobacterial enzyme diverged before the separation of gram-positive and gram-negative enzymes. This result is interesting considering that the peptidoglycans observed in cyanobacteria seem to combine the properties of those in both gram-negative and gram-positive bacteria. We cloned the putative alanine racemase gene (slr0823) of Synechocystis sp. PCC6803 in E. coli cells, expressed and purified the enzyme protein, and studied its enzymological properties. The enzymatic properties of the Synechocystis enzyme were similar to those of other gram-positive and gram-negative bacterial enzymes. Alignment of the amino acid sequences of alanine racemase enzymes revealed that the conserved tyrosine residue in the active center of most of the gram-positive and gram-negative bacterial enzymes has been replaced with tryptophan in most of the cyanobacterial enzymes. We carried out the site-directed mutagenesis involving the corresponding residue of Synechocystis enzyme (W385), and revealed that the residue is involved in the substrate recognition by the enzyme.
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Affiliation(s)
- Hiroyuki Ashida
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Shimane University
| | - Kaho Murakami
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University
| | - Kenji Inagaki
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University
| | - Yoshihiro Sawa
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University
| | - Hisashi Hemmi
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University
| | - Yugo Iwasaki
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University
| | - Tohru Yoshimura
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University
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Martin DR, Sibuyi NR, Dube P, Fadaka AO, Cloete R, Onani M, Madiehe AM, Meyer M. Aptamer-Based Diagnostic Systems for the Rapid Screening of TB at the Point-of-Care. Diagnostics (Basel) 2021; 11:1352. [PMID: 34441287 PMCID: PMC8391981 DOI: 10.3390/diagnostics11081352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 12/17/2022] Open
Abstract
The transmission of Tuberculosis (TB) is very rapid and the burden it places on health care systems is felt globally. The effective management and prevention of this disease requires that it is detected early. Current TB diagnostic approaches, such as the culture, sputum smear, skin tuberculin, and molecular tests are time-consuming, and some are unaffordable for low-income countries. Rapid tests for disease biomarker detection are mostly based on immunological assays that use antibodies which are costly to produce, have low sensitivity and stability. Aptamers can replace antibodies in these diagnostic tests for the development of new rapid tests that are more cost effective; more stable at high temperatures and therefore have a better shelf life; do not have batch-to-batch variations, and thus more consistently bind to a specific target with similar or higher specificity and selectivity and are therefore more reliable. Advancements in TB research, in particular the application of proteomics to identify TB specific biomarkers, led to the identification of a number of biomarker proteins, that can be used to develop aptamer-based diagnostic assays able to screen individuals at the point-of-care (POC) more efficiently in resource-limited settings.
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Affiliation(s)
- Darius Riziki Martin
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa;
| | - Nicole Remaliah Sibuyi
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
| | - Phumuzile Dube
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
| | - Adewale Oluwaseun Fadaka
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa;
| | - Martin Onani
- Department of Chemistry, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa;
| | - Abram Madimabe Madiehe
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
| | - Mervin Meyer
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
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Cell Wall Anchoring of a Bacterial Chitosanase in Lactobacillus plantarum Using a Food-Grade Expression System and Two Versions of an LP TG Anchor. Int J Mol Sci 2020; 21:ijms21113773. [PMID: 32471049 PMCID: PMC7312796 DOI: 10.3390/ijms21113773] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 05/21/2020] [Accepted: 05/23/2020] [Indexed: 01/16/2023] Open
Abstract
Lactic acid bacteria (LAB) have attracted increasing interest recently as cell factories for the production of proteins as well as a carrier of proteins that are of interest for food and therapeutic applications. In this present study, we exploit a lactobacillal food-grade expression system derived from the pSIP expression vectors using the alr (alanine racemase) gene as the selection marker for the expression and cell-surface display of a chitosanase in Lactobacillus plantarum using two truncated forms of a LP × TG anchor. CsnA, a chitosanase from Bacillus subtilis 168 (ATCC23857), was fused to two different truncated forms (short-S and long-L anchors) of an LP × TG anchor derived from Lp_1229, a key-protein for mannose-specific adhesion in L. plantarum WCFS1. The expression and cell-surface display efficiency driven by the food-grade alr-based system were compared with those obtained from the erm-based pSIP system in terms of enzyme activities and their localisation on L. plantarum cells. The localization of the protein on the bacterial cell surface was confirmed by flow cytometry and immunofluorescence microscopy. The highest enzymatic activity of CsnA-displaying cells was obtained from the strain carrying the alr-based expression plasmid with short cell wall anchor S. However, the attachment of chitosanase on L. plantarum cells via the long anchor L was shown to be more stable compared with the short anchor after several repeated reaction cycles. CsnA displayed on L. plantarum cells is catalytically active and can convert chitosan into chito-oligosaccharides, of which chitobiose and chitotriose are the main products.
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8
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Biochemical characterization and mutational analysis of alanine racemase from Clostridium perfringens. J Biosci Bioeng 2019; 128:149-155. [DOI: 10.1016/j.jbiosc.2019.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 02/03/2019] [Accepted: 02/06/2019] [Indexed: 11/24/2022]
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9
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Immunoscreening of the M. tuberculosis F15/LAM4/KZN secretome library against TB patients' sera identifies unique active- and latent-TB specific biomarkers. Tuberculosis (Edinb) 2019; 115:161-170. [PMID: 30948172 DOI: 10.1016/j.tube.2019.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/01/2019] [Accepted: 03/12/2019] [Indexed: 02/03/2023]
Abstract
Tuberculosis (TB) protein biomarkers are urgently needed for the development of point-of-care diagnostics, new drugs and vaccines. Mycobacterium tuberculosis extracellular and secreted proteins play an important role in host-pathogen interactions. Antibodies produced against M. tuberculosis proteins before the onset of clinical symptoms can be used in proteomic studies to identify their target proteins. In this study, M. tuberculosis F15/LAM4/KZN strain phage secretome library was screened against immobilized polyclonal sera from active TB patients (n = 20), TST positive individuals (n = 15) and M. tuberculosis uninfected individuals (n = 20) to select and identify proteins recognized by patients' antibodies. DNA sequence analysis from randomly selected latent TB and active TB specific phage clones revealed 118 and 96 ORFs, respectively. Proteins essential for growth, virulence and metabolic pathways were identified using different TB databases. The identified active TB specific biomarkers included five proteins, namely, TrpG, Alr, TreY, BfrA and EspR, with no human homologs, whilst latent TB specific biomarkers included NarG, PonA1, PonA2 and HspR. Future studies will assess potential applications of identified protein biomarkers as TB drug or vaccine candidates/targets and diagnostic markers with the ability to discriminate LTBI from active TB.
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Kittibunchakul S, Pham ML, Tran AM, Nguyen TH. β-Galactosidase from Lactobacillus helveticus DSM 20075: Biochemical Characterization and Recombinant Expression for Applications in Dairy Industry. Int J Mol Sci 2019; 20:ijms20040947. [PMID: 30813223 PMCID: PMC6412629 DOI: 10.3390/ijms20040947] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 12/29/2022] Open
Abstract
β-Galactosidase encoding genes lacLM from Lactobacillus helveticus DSM 20075 were cloned and successfully overexpressed in Escherichia coli and Lactobacillus plantarum using different expression systems. The highest recombinant β-galactosidase activity of ∼26 kU per L of medium was obtained when using an expression system based on the T7 RNA polymerase promoter in E. coli, which is more than 1000-fold or 28-fold higher than the production of native β-galactosidase from L. helveticus DSM 20075 when grown on glucose or lactose, respectively. The overexpression in L. plantarum using lactobacillal food-grade gene expression system resulted in ∼2.3 kU per L of medium, which is approximately 10-fold lower compared to the expression in E. coli. The recombinant β-galactosidase from L. helveticus overexpressed in E. coli was purified to apparent homogeneity and subsequently characterized. The Km and vmax values for lactose and o-nitrophenyl-β-d-galactopyranoside (oNPG) were 15.7 ± 1.3 mM, 11.1 ± 0.2 µmol D-glucose released per min per mg protein, and 1.4 ± 0.3 mM, 476 ± 66 µmol o-nitrophenol released per min per mg protein, respectively. The enzyme was inhibited by high concentrations of oNPG with Ki,s = 3.6 ± 0.8 mM. The optimum pH for hydrolysis of both substrates, lactose and oNPG, is pH 6.5 and optimum temperatures for these reactions are 60 and 55 °C, respectively. The formation of galacto-oligosaccharides (GOS) in discontinuous mode using both crude recombinant enzyme from L. plantarum and purified recombinant enzyme from E. coli revealed high transgalactosylation activity of β-galactosidases from L. helveticus; hence, this enzyme is an interesting candidate for applications in lactose conversion and GOS formation processes.
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Affiliation(s)
- Suwapat Kittibunchakul
- Food Biotechnology Laboratory, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
| | - Mai-Lan Pham
- Food Biotechnology Laboratory, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
| | - Anh-Minh Tran
- Food Biotechnology Laboratory, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
- Department of Biology, Faculty of Fundamental Sciences, Ho Chi Minh City University of Medicine and Pharmacy, 217 Hong Bang, Ho Chi Minh City, Vietnam.
| | - Thu-Ha Nguyen
- Food Biotechnology Laboratory, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
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11
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Localization and Regulation of the T1 Unimolecular Spanin. J Virol 2018; 92:JVI.00380-18. [PMID: 30135120 DOI: 10.1128/jvi.00380-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/01/2018] [Indexed: 11/20/2022] Open
Abstract
Spanins are bacteriophage lysis proteins responsible for disruption of the outer membrane, the final step of Gram-negative host lysis. The absence of spanins results in a terminal phenotype of fragile spherical cells. The phage T1 employs a unimolecular spanin gp11 that has an N-terminal lipoylation signal and a C-terminal transmembrane domain. Upon maturation and localization, gp11 ends up as an outer membrane lipoprotein with a C-terminal transmembrane domain embedded in the inner membrane, thus connecting both membranes as a covalent polypeptide chain. Unlike the two-component spanins encoded by most of the other phages, including lambda, the unimolecular spanins have not been studied extensively. In this work, we show that the gp11 mutants lacking either membrane localization signal were nonfunctional and conferred a partially dominant phenotype. Translation from internal start sites within the gp11 coding sequence generated a shorter product which exhibited a negative regulatory effect on gp11 function. Fluorescence spectroscopy time-lapse videos of gp11-GFP expression showed gp11 accumulated in distinct punctate foci, suggesting localized clusters assembled within the peptidoglycan meshwork. In addition, gp11 was shown to mediate lysis in the absence of holin and endolysin function when peptidoglycan density was depleted by starvation for murein precursors. This result indicates that the peptidoglycan is a negative regulator of gp11 function. This supports a model in which gp11 acts by fusing the inner and outer membranes, a mode of action analogous to but mechanistically distinct from that proposed for the two-component spanin systems.IMPORTANCE Spanins have been proposed to fuse the cytoplasmic and outer membranes during phage lysis. Recent work with the lambda spanins Rz-Rz1, which are similar to class I viral fusion proteins, has shed light on the functional domains and requirements for two-component spanin function. Here we report, for the first time, a genetic and biochemical approach to characterize unimolecular spanins, which are structurally and mechanistically different from two-component spanins. Considering similar predicted secondary structures within the ectodomains, unimolecular spanins can be regarded as a prokaryotic version of type II viral membrane fusion proteins. This study not only adds to our understanding of regulation of phage lysis at various levels but also provides a prokaryotic genetically tractable platform for interrogating class II-like membrane fusion proteins.
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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] [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.
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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.
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13
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Ray S, Das S, Panda PK, Suar M. Identification of a new alanine racemase in Salmonella Enteritidis and its contribution to pathogenesis. Gut Pathog 2018; 10:30. [PMID: 30008809 PMCID: PMC6040060 DOI: 10.1186/s13099-018-0257-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/03/2018] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Non-typhoidal Salmonella (NTS) infections caused primarily by S. Enteritidis and S. Typhimurium particularly in immunocompromised hosts have accounted for a large percentage of fatalities in developed nations. Antibiotics have revolutionized the cure of enteric infections but have also led to the rapid emergence of pathogen resistance. New powerful therapeutics involving metabolic enzymes are expected to be potential targets for combating microbial infections and ensuring effective health management. Therefore, the need for new antimicrobials to fight such health emergencies is paramount. Enteric bacteria successfully evade the gut and colonize their hosts through specialized virulence strategies. An important player, alanine racemase is a key enzyme facilitating bacterial survival. RESULTS This study aims at understanding the contribution of alanine racemase genes alr, dadX and SEN3897 to Salmonella survival in vitro and in vivo. We have shown SEN3897 to function as a unique alanine racemase in S. Enteritidis which displayed essential alanine racemase activity. Interestingly, the sole presence of this gene in alr dadX double mutant showed a strict dependence on d-alanine supplementation both in vitro and in vivo. However, Alr complementation in d-alanine auxotrophic strain restored the alanine racemase deficiency. The Km and Vmax of SEN3897 was 89.15 ± 10.2 mM, 400 ± 25.6 µmol/(min mg) for l-alanine and 35 ± 6 mM, 132.5 ± 11.3 µmol/(min mg) for d-alanine, respectively. In vitro assays for invasion and survival as well as in vivo virulence assays involving SEN3897 mutant showed attenuated phenotypes. Further, this study also showed attenuation of d-alanine auxotrophic strain in vivo for the development of potential targets against Salmonella that can be investigated further. CONCLUSION This study identified a third alanine racemase gene unique in S. Enteritidis which had a potential effect on survival and pathogenesis in vitro and in vivo. Our results also confirmed that SEN3897 by itself wasn't able to rescue d-alanine auxotrophy in S. Enteritidis which further contributed to its virulence properties.
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Affiliation(s)
- Shilpa Ray
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha India
| | - Susmita Das
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha India
| | | | - Mrutyunjay Suar
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha India
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14
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Lohrasbi V, Talebi M, Bialvaei AZ, Fattorini L, Drancourt M, Heidary M, Darban-Sarokhalil D. Trends in the discovery of new drugs for Mycobacterium tuberculosis therapy with a glance at resistance. Tuberculosis (Edinb) 2017; 109:17-27. [PMID: 29559117 DOI: 10.1016/j.tube.2017.12.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 11/23/2017] [Accepted: 12/07/2017] [Indexed: 12/19/2022]
Abstract
Despite the low expensive and effective four-drug treatment regimen (isoniazid, rifampicin, pyrazinamide and ethambutol) was introduced 40 years ago, TB continues to cause considerable morbidity and mortality worldwide. In 2015, the WHO estimated a total of 10.4 million new tuberculosis (TB) cases worldwide. Currently, the increased number of multidrug-resistant (MDR-TB), extensively-drug resistant (XDR-TB) and in some recent reports, totally drug-resistant TB (TDR-TB) cases raises concerns about this disease. MDR-TB and XDR-TB have lower cure rates and higher mortality levels due to treatment problems. Novel drugs and regimens for all forms of TB have emerged in recent years. Moreover, scientific interest has recently increased in the field of host-directed therapies (HDTs) in order to identify new treatments for MDR-TB. In this review, we offer an update on the discovery of new drugs for TB therapy with a glance at molecular mechanisms leading to drug resistance in Mycobacterium tuberculosis.
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Affiliation(s)
- Vahid Lohrasbi
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Malihe Talebi
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Abed Zahedi Bialvaei
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Lanfranco Fattorini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Michel Drancourt
- Institut Hospital-Universitaire (IHU) Mediterranée Infection, AP-HM, Marseille, France; Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Mohsen Heidary
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Davood Darban-Sarokhalil
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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15
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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] [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.
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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
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16
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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. ENVIRONMENTAL MICROBIOLOGY REPORTS 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] [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.
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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
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17
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Soo VWC, Yosaatmadja Y, Squire CJ, Patrick WM. Mechanistic and Evolutionary Insights from the Reciprocal Promiscuity of Two Pyridoxal Phosphate-dependent Enzymes. J Biol Chem 2016; 291:19873-87. [PMID: 27474741 PMCID: PMC5025676 DOI: 10.1074/jbc.m116.739557] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Indexed: 11/06/2022] Open
Abstract
Enzymes that utilize the cofactor pyridoxal 5′-phosphate play essential roles in amino acid metabolism in all organisms. The cofactor is used by proteins that adopt at least five different folds, which raises questions about the evolutionary processes that might explain the observed distribution of functions among folds. In this study, we show that a representative of fold type III, the Escherichia coli alanine racemase (ALR), is a promiscuous cystathionine β-lyase (CBL). Furthermore, E. coli CBL (fold type I) is a promiscuous alanine racemase. A single round of error-prone PCR and selection yielded variant ALR(Y274F), which catalyzes cystathionine β-elimination with a near-native Michaelis constant (Km = 3.3 mm) but a poor turnover number (kcat ≈10 h−1). In contrast, directed evolution also yielded CBL(P113S), which catalyzes l-alanine racemization with a poor Km (58 mm) but a high kcat (22 s−1). The structures of both variants were solved in the presence and absence of the l-alanine analogue, (R)-1-aminoethylphosphonic acid. As expected, the ALR active site was enlarged by the Y274F substitution, allowing better access for cystathionine. More surprisingly, the favorable kinetic parameters of CBL(P113S) appear to result from optimizing the pKa of Tyr-111, which acts as the catalytic acid during l-alanine racemization. Our data emphasize the short mutational routes between the functions of pyridoxal 5′-phosphate-dependent enzymes, regardless of whether or not they share the same fold. Thus, they confound the prevailing model of enzyme evolution, which predicts that overlapping patterns of promiscuity result from sharing a common multifunctional ancestor.
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Affiliation(s)
- Valerie W C Soo
- From the Institute of Natural and Mathematical Sciences, Massey University, Auckland 0632
| | - Yuliana Yosaatmadja
- the School of Biological Sciences, University of Auckland, Auckland 1142, and
| | | | - Wayne M Patrick
- the Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
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18
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Katsube S, Sato K, Ando T, Isogai E, Yoneyama H. Secretion of d-alanine by Escherichia coli. Microbiology (Reading) 2016; 162:1243-1252. [DOI: 10.1099/mic.0.000305] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Satoshi Katsube
- Laboratory of Animal Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1, Amamiya-machi, Tsutsumidori, Aoba-ku, Sendai 981-8555, Japan
| | - Kazuki Sato
- Laboratory of Animal Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1, Amamiya-machi, Tsutsumidori, Aoba-ku, Sendai 981-8555, Japan
| | - Tasuke Ando
- Laboratory of Animal Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1, Amamiya-machi, Tsutsumidori, Aoba-ku, Sendai 981-8555, Japan
| | - Emiko Isogai
- Laboratory of Animal Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1, Amamiya-machi, Tsutsumidori, Aoba-ku, Sendai 981-8555, Japan
| | - Hiroshi Yoneyama
- Laboratory of Animal Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1, Amamiya-machi, Tsutsumidori, Aoba-ku, Sendai 981-8555, Japan
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19
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Hasan MA, Khan MA, Sharmin T, Hasan Mazumder MH, Chowdhury AS. Identification of putative drug targets in Vancomycin-resistant Staphylococcus aureus (VRSA) using computer aided protein data analysis. Gene 2016; 575:132-43. [DOI: 10.1016/j.gene.2015.08.044] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 08/20/2015] [Accepted: 08/23/2015] [Indexed: 02/07/2023]
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20
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Abstract
In general, phages cause lysis of the bacterial host to effect release of the progeny virions. Until recently, it was thought that degradation of the peptidoglycan (PG) was necessary and sufficient for osmotic bursting of the cell. Recently, we have shown that in Gram-negative hosts, phage lysis also requires the disruption of the outer membrane (OM). This is accomplished by spanins, which are phage-encoded proteins that connect the cytoplasmic membrane (inner membrane, IM) and the OM. The mechanism by which the spanins destroy the OM is unknown. Here we show that the spanins of the paradigm coliphage lambda mediate efficient membrane fusion. This supports the notion that the last step of lysis is the fusion of the IM and OM. Moreover, data are provided indicating that spanin-mediated fusion is regulated by the meshwork of the PG, thus coupling fusion to murein degradation by the phage endolysin. Because endolysin function requires the formation of μm-scale holes by the phage holin, the lysis pathway is seen to require dramatic dynamics on the part of the OM and IM, as well as destruction of the PG.
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21
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Guzman JD, Pesnot T, Barrera DA, Davies HM, McMahon E, Evangelopoulos D, Mortazavi PN, Munshi T, Maitra A, Lamming ED, Angell R, Gershater MC, Redmond JM, Needham D, Ward JM, Cuca LE, Hailes HC, Bhakta S. Tetrahydroisoquinolines affect the whole-cell phenotype of Mycobacterium tuberculosis by inhibiting the ATP-dependent MurE ligase. J Antimicrob Chemother 2015; 70:1691-703. [PMID: 25656411 PMCID: PMC4498294 DOI: 10.1093/jac/dkv010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/05/2015] [Indexed: 11/18/2022] Open
Abstract
Objectives (S)-Leucoxine, isolated from the Colombian Lauraceae tree Rhodostemonodaphne crenaticupula Madriñan, was found to inhibit the growth of Mycobacterium tuberculosis H37Rv. A biomimetic approach for the chemical synthesis of a wide array of 1-substituted tetrahydroisoquinolines was undertaken with the aim of elucidating a common pharmacophore for these compounds with novel mode(s) of anti-TB action. Methods Biomimetic Pictet–Spengler or Bischler–Napieralski synthetic routes were employed followed by an evaluation of the biological activity of the synthesized compounds. Results In this work, the synthesized tetrahydroisoquinolines were found to inhibit the growth of M. tuberculosis H37Rv and affect its whole-cell phenotype as well as the activity of the ATP-dependent MurE ligase, a key enzyme involved in the early stage of cell wall peptidoglycan biosynthesis. Conclusions As the correlation between the MIC and the half-inhibitory enzymatic concentration was not particularly strong, there is a credible possibility that these compounds have pleiotropic mechanism(s) of action in M. tuberculosis.
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Affiliation(s)
- Juan D Guzman
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Thomas Pesnot
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Diana A Barrera
- Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Carrera 30 No. 45-03, Bogotá, Colombia
| | - Heledd M Davies
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Eleanor McMahon
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Dimitrios Evangelopoulos
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Parisa N Mortazavi
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Tulika Munshi
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Arundhati Maitra
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Eleanor D Lamming
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Richard Angell
- Drug Discovery Group, UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Markus C Gershater
- The Advanced Centre for Biochemical Engineering, University College London, Gordon Street, London WC1H 0AH, UK
| | - Joanna M Redmond
- Department of Medicinal Chemistry, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Deborah Needham
- Department of Medicinal Chemistry, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - John M Ward
- Drug Discovery Group, UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Luis E Cuca
- Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Carrera 30 No. 45-03, Bogotá, Colombia
| | - Helen C Hailes
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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22
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Davis E, Scaletti-Hutchinson E, Opel-Reading H, Nakatani Y, Krause KL. The structure of alanine racemase from Acinetobacter baumannii. Acta Crystallogr F Struct Biol Commun 2014; 70:1199-205. [PMID: 25195891 PMCID: PMC4157418 DOI: 10.1107/s2053230x14017725] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 08/01/2014] [Indexed: 01/11/2023] Open
Abstract
Acinetobacter baumannii is an opportunistic Gram-negative bacterium which is a common cause of hospital-acquired infections. Numerous antibiotic-resistant strains exist, emphasizing the need for the development of new antimicrobials. Alanine racemase (Alr) is a pyridoxal 5'-phosphate dependent enzyme that is responsible for racemization between enantiomers of alanine. As D-alanine is an essential component of the bacterial cell wall, its inhibition is lethal to prokaryotes, making it an excellent antibiotic drug target. The crystal structure of A. baumannii alanine racemase (AlrAba) from the highly antibiotic-resistant NCTC13302 strain has been solved to 1.9 Å resolution. Comparison of AlrAba with alanine racemases from closely related bacteria demonstrates a conserved overall fold. The substrate entryway and active site of the enzymes were shown to be highly conserved. The structure of AlrAba will provide the template required for future structure-based drug-design studies.
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Affiliation(s)
- Emily Davis
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | | | - Yoshio Nakatani
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Kurt L. Krause
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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Asojo OA, Nelson SK, Mootien S, Lee Y, Rezende WC, Hyman DA, Matsumoto MM, Reiling S, Kelleher A, Ledizet M, Koski RA, Anthony KG. Structural and biochemical analyses of alanine racemase from the multidrug-resistant Clostridium difficile strain 630. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1922-33. [PMID: 25004969 PMCID: PMC4089486 DOI: 10.1107/s1399004714009419] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 04/26/2014] [Indexed: 05/04/2024]
Abstract
Clostridium difficile, a Gram-positive, spore-forming anaerobic bacterium, is the leading cause of infectious diarrhea among hospitalized patients. C. difficile is frequently associated with antibiotic treatment, and causes diseases ranging from antibiotic-associated diarrhea to life-threatening pseudomembranous colitis. The severity of C. difficile infections is exacerbated by the emergence of hypervirulent and multidrug-resistant strains, which are difficult to treat and are often associated with increased mortality rates. Alanine racemase (Alr) is a pyridoxal-5'-phosphate (PLP)-dependent enzyme that catalyzes the reversible racemization of L- and D-alanine. Since D-alanine is an essential component of the bacterial cell-wall peptidoglycan, and there are no known Alr homologs in humans, this enzyme is being tested as an antibiotic target. Cycloserine is an antibiotic that inhibits Alr. In this study, the catalytic properties and crystal structures of recombinant Alr from the virulent and multidrug-resistant C. difficile strain 630 are presented. Three crystal structures of C. difficile Alr (CdAlr), corresponding to the complex with PLP, the complex with cycloserine and a K271T mutant form of the enzyme with bound PLP, are presented. The structures are prototypical Alr homodimers with two active sites in which the cofactor PLP and cycloserine are localized. Kinetic analyses reveal that the K271T mutant CdAlr has the highest catalytic constants reported to date for any Alr. Additional studies are needed to identify the basis for the high catalytic activity. The structural and activity data presented are first steps towards using CdAlr for the development of structure-based therapeutics for C. difficile infections.
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Affiliation(s)
- Oluwatoyin A. Asojo
- National School of Tropical Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah K. Nelson
- National School of Tropical Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sara Mootien
- L Diagnostics LLC, 300 George Street, New Haven, CT 06511, USA
| | - Yashang Lee
- L Diagnostics LLC, 300 George Street, New Haven, CT 06511, USA
| | - Wanderson C. Rezende
- National School of Tropical Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel A. Hyman
- National School of Tropical Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Monica M. Matsumoto
- National School of Tropical Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Scott Reiling
- Pathology and Microbiology Department, University of Nebraska Medical Center, Omaha, NE 68105, USA
| | - Alan Kelleher
- National School of Tropical Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michel Ledizet
- L Diagnostics LLC, 300 George Street, New Haven, CT 06511, USA
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Hong W, Chen L, Xie J. Molecular basis underlying Mycobacterium tuberculosis D-cycloserine resistance. Is there a role for ubiquinone and menaquinone metabolic pathways? Expert Opin Ther Targets 2014; 18:691-701. [PMID: 24773568 DOI: 10.1517/14728222.2014.902937] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Tuberculosis remains a formidable threat to global public health. Multidrug-resistant tuberculosis presents increasing burden on the control strategy. D-Cycloserine (DCS) is an effective second-line drug against Mycobacterium tuberculosis (M. tuberculosis), the causative agent of tuberculosis. Though less potent than isoniazid (INH) and streptomycin, DCS is crucial for antibiotic-resistant tuberculosis. One advantage of DCS is that less drug-resistant M. tuberculosis is reported in comparison with first-line antituberculosis drugs such as INH and rifampin. AREAS COVERED In this review, we summarise our current knowledge of DCS, and review the drug target and low-level resistance of DCS in M. tuberculosis. We summarise the metabolism of D-alanine (D-Ala) and peptidoglycan biosynthesis in bacteria. We first compared the amino acid similarity of Mycobacterium alanine racemase and D-Ala:D-alanine ligase and quite unexpectedly found that the two enzymes are highly conserved among Mycobacterium. EXPERT OPINION We summarise the drug targets of DCS and possible mechanisms underlying its low-level resistance for the first time. One significant finding is that ubiquinone and menaquinone metabolism-related genes are novel genes underlying DCS resistance in Escherichia coli and with homologues in M. tuberculosis. Further understanding of DCS targets and basis for its low-level resistance might inspire us to improve the use of DCS or find better drug targets.
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Affiliation(s)
- Weiling Hong
- Southwest University, Institute of Modern Biopharmaceuticals, School of Life Sciences, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education , Beibei, Chongqing 400715 , China +86 23 68367 108 ; +86 23 68367 108 ;
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25
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Staudigl P, Haltrich D, Peterbauer CK. L-Arabinose isomerase and D-xylose isomerase from Lactobacillus reuteri: characterization, coexpression in the food grade host Lactobacillus plantarum, and application in the conversion of D-galactose and D-glucose. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:1617-1624. [PMID: 24443973 PMCID: PMC3931408 DOI: 10.1021/jf404785m] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/15/2014] [Accepted: 01/20/2014] [Indexed: 06/03/2023]
Abstract
The L-arabinose isomerase (L-AI) and the D-xylose isomerase (D-XI) encoding genes from Lactobacillus reuteri (DSMZ 17509) were cloned and overexpressed in Escherichia coli BL21 (DE3). The proteins were purified to homogeneity by one-step affinity chromatography and characterized biochemically. L-AI displayed maximum activity at 65 °C and pH 6.0, whereas D-XI showed maximum activity at 65 °C and pH 5.0. Both enzymes require divalent metal ions. The genes were also ligated into the inducible lactobacillal expression vectors pSIP409 and pSIP609, the latter containing a food grade auxotrophy marker instead of an antibiotic resistance marker, and the L-AI- and D-XI-encoding sequences/genes were coexpressed in the food grade host Lactobacillus plantarum . The recombinant enzymes were tested for applications in carbohydrate conversion reactions of industrial relevance. The purified L-AI converted D-galactose to D-tagatose with a maximum conversion rate of 35%, and the D-XI isomerized D-glucose to D-fructose with a maximum conversion rate of 48% at 60 °C.
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Halouska S, Fenton RJ, Zinniel DK, Marshall DD, Barletta RG, Powers R. Metabolomics analysis identifies d-Alanine-d-Alanine ligase as the primary lethal target of d-Cycloserine in mycobacteria. J Proteome Res 2013; 13:1065-76. [PMID: 24303782 DOI: 10.1021/pr4010579] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
d-Cycloserine is an effective second line antibiotic used as a last resort to treat multi (MDR)- and extensively (XDR) drug resistant strains of Mycobacterium tuberculosis . d-Cycloserine interferes with the formation of peptidoglycan biosynthesis by competitive inhibition of alanine racemase (Alr) and d-alanine-d-alanine ligase (Ddl). Although the two enzymes are known to be inhibited, the in vivo lethal target is still unknown. Our NMR metabolomics work has revealed that Ddl is the primary target of DCS, as cell growth is inhibited when the production of d-alanyl-d-alanine is halted. It is shown that inhibition of Alr may contribute indirectly by lowering the levels of d-alanine, thus allowing DCS to outcompete d-alanine for Ddl binding. The NMR data also supports the possibility of a transamination reaction to produce d-alanine from pyruvate and glutamate, thereby bypassing Alr inhibition. Furthermore, the inhibition of peptidoglycan synthesis results in a cascading effect on cellular metabolism as there is a shift toward the catabolic routes to compensate for accumulation of peptidoglycan precursors.
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Affiliation(s)
- Steven Halouska
- Department of Chemistry, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0304, United States
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27
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Xue Z, Hu Y, Xu S, Ohnishi K, Ma Y, Ju J, Zhao B. Characterization and preliminary mutation analysis of a thermostable alanine racemase from Thermoanaerobacter tengcongensis MB4. Extremophiles 2013; 17:611-21. [PMID: 23703245 DOI: 10.1007/s00792-013-0545-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 05/12/2013] [Indexed: 10/26/2022]
Abstract
A thermostable alanine racemase from Thermoanaerobacter tengcongensis MB4 was successfully expressed in Escherichia coli and characterized. The full-length gene MBalr2 (1164 bp) encodes 388 amino acid residues including 6 out of 8 highly conserved amino acid residues at the entryway to the active site of alanine racemase. Recombinant MBAlr2 and three mutants (S171A, H359Y and double mutation S171A/H359Y) of MBAlr2 were purified by His6-tag affinity column and gel filtration chromatography. The purified protein MBAlr2 was a dimeric PLP-dependent enzyme with broad substrate specificity. The optimal racemization temperature and pH were 70-75 °C and 11.0, respectively. The kinetic parameters K m and V max of MBAlr2 at 70 °C, determined by HPLC, were 20.16 mM and 1414 μmol min(-1) for L-alanine, and 9.95 mM and 702.6 μmol min(-1) for D-alanine, respectively. Enzymatic assays showed that the activity of both mutants (S171A and H359Y) was lost, but the activity of mutant S171A/H359Y was recovered to 69.8 % of wild type, which suggested that residues Ser171 and His359 might be the important residues for catalytic mechanisms of MBAlr2.
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Affiliation(s)
- Zhangwei Xue
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, China
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28
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Lee Y, Mootien S, Shoen C, Destefano M, Cirillo P, Asojo OA, Yeung KR, Ledizet M, Cynamon MH, Aristoff PA, Koski RA, Kaplan PA, Anthony KG. Inhibition of mycobacterial alanine racemase activity and growth by thiadiazolidinones. Biochem Pharmacol 2013; 86:222-30. [PMID: 23680030 DOI: 10.1016/j.bcp.2013.05.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 05/02/2013] [Accepted: 05/03/2013] [Indexed: 11/25/2022]
Abstract
The genus Mycobacterium includes non-pathogenic species such as M. smegmatis, and pathogenic species such as M. tuberculosis, the causative agent of tuberculosis (TB). Treatment of TB requires a lengthy regimen of several antibiotics, whose effectiveness has been compromised by the emergence of resistant strains. New antibiotics that can shorten the treatment course and those that have not been compromised by bacterial resistance are needed. In this study, we report that thiadiazolidinones, a relatively little-studied heterocyclic class, inhibit the activity of mycobacterial alanine racemase, an essential enzyme that converts l-alanine to d-alanine for peptidoglycan synthesis. Twelve members of the thiadiazolidinone family were evaluated for inhibition of M. tuberculosis and M. smegmatis alanine racemase activity and bacterial growth. Thiadiazolidinones inhibited M. tuberculosis and M. smegmatis alanine racemases to different extents with 50% inhibitory concentrations (IC50) ranging from <0.03 to 28μM and 23 to >150μM, respectively. The compounds also inhibited the growth of these bacteria, including multidrug resistant strains of M. tuberculosis. The minimal inhibitory concentrations (MIC) for drug-susceptible M. tuberculosis and M. smegmatis ranged from 6.25μg/ml to 100μg/ml, and from 1.56 to 6.25μg/ml for drug-resistant M. tuberculosis. The in vitro activities of thiadiazolidinones suggest that this family of compounds might represent starting points for medicinal chemistry efforts aimed at developing novel antimycobacterial agents.
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Affiliation(s)
- Yashang Lee
- L2 Diagnostics LLC, 300 George St., New Haven, CT 06511, USA
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Kaswurm V, Nguyen TT, Maischberger T, Kulbe KD, Michlmayr H. Evaluation of the food grade expression systems NICE and pSIP for the production of 2,5-diketo-D-gluconic acid reductase from Corynebacterium glutamicum. AMB Express 2013; 3:7. [PMID: 23356419 PMCID: PMC3565945 DOI: 10.1186/2191-0855-3-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Accepted: 01/21/2013] [Indexed: 11/10/2022] Open
Abstract
2,5-diketo-D-gluconic acid reductase (2,5-DKG reductase) catalyses the reduction of 2,5-diketo-D-gluconic acid (2,5-DKG) to 2-keto-L-gulonic acid (2-KLG), a direct precursor (lactone) of L-ascorbic acid (vitamin C). This reaction is an essential step in the biocatalytic production of the food supplement vitamin C from D-glucose or D-gluconic acid. As 2,5-DKG reductase is usually produced recombinantly, it is of interest to establish an efficient process for 2,5-DKG reductase production that also satisfies food safety requirements. In the present study, three recently described food grade variants of the Lactobacillales based expression systems pSIP (Lactobacillus plantarum) and NICE (Lactococcus lactis) were evaluated with regard to their effictiveness to produce 2,5-DKG reductase from Corynebacterium glutamicum. Our results indicate that both systems are suitable for 2,5-DKG reductase expression. Maximum production yields were obtained with Lb. plantarum/pSIP609 by pH control at 6.5. With 262 U per litre of broth, this represents the highest heterologous expression level so far reported for 2,5-DKG reductase from C. glutamicum. Accordingly, Lb. plantarum/pSIP609 might be an interesting alternative to Escherichia coli expression systems for industrial 2,5-DKG reductase production.
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Development of a high-throughput screening method for racemase activity and its application to the identification of alanine racemase variants with activity towards l-arginine. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.06.062] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Alanine racemase mutants of Mycobacterium tuberculosis require d-alanine for growth and are defective for survival in macrophages and mice. Microbiology (Reading) 2012; 158:319-327. [DOI: 10.1099/mic.0.054064-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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32
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M. Takacs J, C. Thacker N, Molnár-Tóth J, L. Miska J, G. Barletta R. Preparation of D-Cycloserine and 13C-Labeled D-Cycloserine. HETEROCYCLES 2012. [DOI: 10.3987/com-12-12553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Scaletti ER, Luckner SR, Krause KL. Structural features and kinetic characterization of alanine racemase from Staphylococcus aureus (Mu50). ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:82-92. [PMID: 22194336 PMCID: PMC3245724 DOI: 10.1107/s0907444911050682] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 11/25/2011] [Indexed: 11/10/2022]
Abstract
Staphylococcus aureus is an opportunistic Gram-positive bacterium which causes a wide variety of diseases ranging from minor skin infections to potentially fatal conditions such as pneumonia, meningitis and septicaemia. The pathogen is a leading cause of nosocomial acquired infections, a problem that is exacerbated by the existence of methicillin- and glycopeptide antibiotic-resistant strains which can be challenging to treat. Alanine racemase (Alr) is a pyridoxal-5'-phosphate-dependent enzyme which catalyzes reversible racemization between enantiomers of alanine. As D-alanine is an essential component of the bacterial cell-wall peptidoglycan, inhibition of Alr is lethal to prokaryotes. Additionally, while ubiquitous amongst bacteria, this enzyme is absent in humans and most eukaryotes, making it an excellent antibiotic drug target. The crystal structure of S. aureus alanine racemase (Alr(Sas)), the sequence of which corresponds to that from the highly antibiotic-resistant Mu50 strain, has been solved to 2.15 Å resolution. Comparison of the Alr(Sas) structure with those of various alanine racemases demonstrates a conserved overall fold, with the enzyme sharing most similarity to those from other Gram-positive bacteria. Structural examination indicates that the active-site binding pocket, dimer interface and active-site entryway of the enzyme are potential targets for structure-aided inhibitor design. Kinetic constants were calculated in this study and are reported here. The potential for a disulfide bond in this structure is noted. This structural and biochemical information provides a template for future structure-based drug-development efforts targeting Alr(Sas).
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Affiliation(s)
- Emma R. Scaletti
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Sylvia R. Luckner
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Kurt L. Krause
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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Zajdowicz SLW, Jones-Carson J, Vazquez-Torres A, Jobling MG, Gill RE, Holmes RK. Alanine racemase mutants of Burkholderia pseudomallei and Burkholderia mallei and use of alanine racemase as a non-antibiotic-based selectable marker. PLoS One 2011; 6:e21523. [PMID: 21720554 PMCID: PMC3123353 DOI: 10.1371/journal.pone.0021523] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 05/31/2011] [Indexed: 12/20/2022] Open
Abstract
Burkholderia pseudomallei and Burkholderia mallei are category B select agents and must be studied under BSL3 containment in the United States. They are typically resistant to multiple antibiotics, and the antibiotics used to treat B. pseudomallei or B. mallei infections may not be used as selective agents with the corresponding Burkholderia species. Here, we investigated alanine racemase deficient mutants of B. pseudomallei and B. mallei for development of non-antibiotic-based genetic selection methods and for attenuation of virulence. The genome of B. pseudomallei K96243 has two annotated alanine racemase genes (bpsl2179 and bpss0711), and B. mallei ATCC 23344 has one (bma1575). Each of these genes encodes a functional enzyme that can complement the alanine racemase deficiency of Escherichia coli strain ALA1. Herein, we show that B. pseudomallei with in-frame deletions in both bpsl2179 and bpss0711, or B. mallei with an in-frame deletion in bma1575, requires exogenous D-alanine for growth. Introduction of bpsl2179 on a multicopy plasmid into alanine racemase deficient variants of either Burkholderia species eliminated the requirement for D-alanine. During log phase growth without D-alanine, the viable counts of alanine racemase deficient mutants of B. pseudomallei and B. mallei decreased within 2 hours by about 1000-fold and 10-fold, respectively, and no viable bacteria were present at 24 hours. We constructed several genetic tools with bpsl2179 as a selectable genetic marker, and we used them without any antibiotic selection to construct an in-frame ΔflgK mutant in the alanine racemase deficient variant of B. pseudomallei K96243. In murine peritoneal macrophages, wild type B. mallei ATCC 23344 was killed much more rapidly than wild type B. pseudomallei K96243. In addition, the alanine racemase deficient mutant of B. pseudomallei K96243 exhibited attenuation versus its isogenic parental strain with respect to growth and survival in murine peritoneal macrophages.
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Affiliation(s)
- Sheryl L. W. Zajdowicz
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- Department of Biology, Metropolitan State College of Denver, Denver, Colorado, United States of America
| | - Jessica Jones-Carson
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Andres Vazquez-Torres
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Michael G. Jobling
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Ronald E. Gill
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Randall K. Holmes
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
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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] [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.
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Affiliation(s)
- Karen G Anthony
- L2 Diagnostics, LLC, New Haven, Connecticut, United States of America.
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36
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Nguyen TT, Mathiesen G, Fredriksen L, Kittl R, Nguyen TH, Eijsink VGH, Haltrich D, Peterbauer CK. A food-grade system for inducible gene expression in Lactobacillus plantarum using an alanine racemase-encoding selection marker. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:5617-5624. [PMID: 21504147 DOI: 10.1021/jf104755r] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Food-grade gene expression systems for lactic acid bacteria are useful for applications in the food industry. We describe a new food-grade host/vector system for Lactobacillus plantarum based on pSIP expression vectors and the use of the homologous alanine racemase gene (alr) as selection marker. A new series of expression vectors were constructed by exchanging the erythromycin resistance gene (erm) in pSIP vectors by the L. plantarum WCFS1 alr gene. The vectors were applied for the overexpression of β-galactosidase genes from L. reuteri L103 and L. plantarum WCFS1 in an alr deletion mutant of L. plantarum WCFS1. The expression levels obtained in this way, i.e. without the use of antibiotics, were comparable to the levels obtained with the conventional system based on selection for erythromycin resistance. The new system is suitable for the production of ingredients and additives for the food industry.
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Affiliation(s)
- Tien-Thanh Nguyen
- Department of Food Sciences and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
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Hori H, Ando T, Isogai E, Yoneyama H, Katsumata R. Identification of an l-alanine export system in Escherichia coli and isolation and characterization of export-deficient mutants. FEMS Microbiol Lett 2011; 316:83-9. [DOI: 10.1111/j.1574-6968.2010.02196.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Upregulation of MetC is essential for D-alanine-independent growth of an alr/dadX-deficient Escherichia coli strain. J Bacteriol 2010; 193:1098-106. [PMID: 21193606 DOI: 10.1128/jb.01027-10] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
D-Alanine is a central component of the cell wall in most prokaryotes. D-Alanine synthesis in Escherichia coli is carried out by two different alanine racemases encoded by the alr and dadX genes. Deletion of alr and dadX from the E. coli genome results in a D-alanine auxotrophic phenotype. However, we have observed growth of prototrophic phenotypic revertants during routine culturing of a D-alanine auxotrophic strain. We present a detailed comparison of the proteome and transcriptome profiles of the D-alanine auxotroph and a prototrophic revertant strain. Most noticeably, a general upregulation of genes involved in methionine synthesis in the revertant strain was detected. The appearance of the revertant phenotype was genetically linked to point mutations in the methionine repressor gene (metJ). Our results reveal an alternative metabolic pathway which can supply essential d-alanine for peptidoglycan synthesis of alr- and dadX-deficient E. coli mutants and provide evidence for significant alanine racemase coactivity of the E. coli cystathionine beta-lyase (MetC).
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Ju J, Xu S, Furukawa Y, Zhang Y, Misono H, Minamino T, Namba K, Zhao B, Ohnishi K. Correlation between catalytic activity and monomer-dimer equilibrium of bacterial alanine racemases. J Biochem 2010; 149:83-9. [PMID: 20971724 DOI: 10.1093/jb/mvq120] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
From the reaction mechanism and crystal structure analysis, a bacterial alanine racemase is believed to work as a homodimer with a substrate, l-alanine or d-alanine. We analysed oligomerization states of seven alanine racemases, biosynthetic and catabolic, from Escherichia coli, Salmonella typhimurium, Pseudomonas aeruginosa, P. putida and P. fluorescens, with three different methods, gel filtration chromatography, native PAGE and analytical ultracentrifugation. All alanine racemases were proved to be in a dynamic equilibrium between monomeric and dimeric form with every methods used in this study. In both biosynthetic and catabolic alanine racemases, association constants for dimerization were high for the enzymes with high V(max) values. The enzymes with low V(max) values gave the low association constants. We proposed that alanine racemases are classified into two types; the enzymes with low and high-equilibrium association constants for dimerization.
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Affiliation(s)
- Jiansong Ju
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050016, Japan
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40
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Dick T, Manjunatha U, Kappes B, Gengenbacher M. Vitamin B6 biosynthesis is essential for survival and virulence of Mycobacterium tuberculosis. Mol Microbiol 2010; 78:980-8. [PMID: 20815826 DOI: 10.1111/j.1365-2958.2010.07381.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
With 500000 cases of multidrug-resistant tuberculosis there is an urgent need for attractive targets to enable the discovery of novel antimycobacterials. The biosynthesis of essential cofactors is of particular interest as these pathways are absent in man and their inhibition is expected to affect the metabolism of Mycobacterium tuberculosis at multiple sites. Our data demonstrate that the pathogen synthesizes pyridoxal 5-phosphate (PLP), the bioactive form of vitamin B6, by a heteromeric PLP synthase composed of Pdx1 (Rv2606c) and Pdx2 (Rv2604c). Disruption of the pdx1 gene generated a strictly B6 auxotrophic M. tuberculosis mutant, Δpdx1. Removal of the cofactor during exponential growth or stationary phase demonstrated the essentiality of vitamin B6 biosynthesis for growth and survival of the pathogen in culture. In a tuberculosis dormancy model based on gradual oxygen depletion, de novo biosynthesis of PLP was required for regrowth of the bacillus after direct oxygen exposure. The Δpdx1 mutant showed a severe growth defect in immunocompetent mice: bacilli applied intranasally failed to persist in host tissues and were quickly cleared. We conclude that vitamin B6 biosynthesis is required for survival of M. tuberculosis in vivo and thus might represent a candidate pathway for the development of new antitubercular agents.
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Affiliation(s)
- Thomas Dick
- Novartis Institute for Tropical Diseases Pte. Ltd., 10 Biopolis Road, #05-01 Chromos, Singapore 138670, Singapore
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41
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Kushwaha SK, Shakya M. Protein interaction network analysis—Approach for potential drug target identification in Mycobacterium tuberculosis. J Theor Biol 2010; 262:284-94. [DOI: 10.1016/j.jtbi.2009.09.029] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2009] [Revised: 09/24/2009] [Accepted: 09/24/2009] [Indexed: 01/09/2023]
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Couñago RM, Davlieva M, Strych U, Hill RE, Krause KL. Biochemical and structural characterization of alanine racemase from Bacillus anthracis (Ames). BMC STRUCTURAL BIOLOGY 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] [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.
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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
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Riccardi G, Pasca MR, Buroni S. Mycobacterium tuberculosis: drug resistance and future perspectives. Future Microbiol 2009; 4:597-614. [PMID: 19492969 DOI: 10.2217/fmb.09.20] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
TB is still a global health problem. The selection and spread of multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis strains represents a threat for global TB control. The reappearance of TB has driven an increased interest in understanding the mechanisms of drug action and drug resistance, which could provide a significant contribution in the development of new antimicrobials. In this article, the authors describe the mode of action and the resistance mechanisms of the principal first- and second-line antitubercular agents, namely isoniazid, ethionamide, ethambutol, D-cycloserine, rifamycins, fluoroquinolones, streptomycin, linezolid and pyrazinamide. A brief outline of the seven drugs in clinical development is reported, showing how the development of new TB drugs is still required.
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Affiliation(s)
- Giovanna Riccardi
- Department of Genetics & Microbiology, University of Pavia, Via Ferrata, 1 27100 Pavia, Italy.
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Construction and characterization of an attenuated Listeria monocytogenes strain for clinical use in cancer immunotherapy. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2008; 16:96-103. [PMID: 19020110 DOI: 10.1128/cvi.00274-08] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Listeria monocytogenes has been exploited previously as a vaccine vector for the delivery of heterologous proteins such as tumor-specific antigens for active cancer immunotherapy. However, for effective use of live vector in clinics, safety is a major concern. In the present study, we describe an irreversibly attenuated and highly immunogenic L. monocytogenes platform, the L. monocytogenes dal-, dat-, and actA-deleted strain that expresses the human prostate-specific antigen (PSA) using an antibiotic resistance marker-free plasmid (the dal dat DeltaactA 142 strain expressing PSA). Despite limited in vivo survival, the dal dat DeltaactA 142 strain was able to elicit efficient immune responses required for tumor clearance. Our results showed that immunization of mice with the dal dat DeltaactA 142 strain caused the regression of the tumors established by the prostate adenocarcinoma cell line expressing PSA. An evaluation of immunologic potency indicated that the dal dat DeltaactA 142 strain elicits a high frequency of PSA-specific immune responses. Interestingly, immunization with the dal dat DeltaactA 142 strain induced significant infiltration of PSA-specific T cells in the intratumoral milieu. Collectively, our data suggest that the dal dat DeltaactA 142 strain is a safe and potent vector for clinical use and that this platform may be further exploited as a potential candidate to express other single or multiple antigens for cancer immunotherapy.
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45
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Cloning and analysis of two alanine racemase genes fromBacillus licheniformis. ANN MICROBIOL 2008. [DOI: 10.1007/bf03175331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Wu D, Hu T, Zhang L, Chen J, Du J, Ding J, Jiang H, Shen X. Residues Asp164 and Glu165 at the substrate entryway function potently in substrate orientation of alanine racemase from E. coli: Enzymatic characterization with crystal structure analysis. Protein Sci 2008; 17:1066-76. [PMID: 18434499 DOI: 10.1110/ps.083495908] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Alanine racemase (Alr) is an important enzyme that catalyzes the interconversion of L-alanine and D-alanine, an essential building block in the peptidoglycan biosynthesis. For the small size of the Alr active site, its conserved substrate entryway has been proposed as a potential choice for drug design. In this work, we fully analyzed the crystal structures of the native, the D-cycloserine-bound, and four mutants (P219A, E221A, E221K, and E221P) of biosynthetic Alr from Escherichia coli (EcAlr) and studied the potential roles in substrate orientation for the key residues involved in the substrate entryway in conjunction with the enzymatic assays. Structurally, it was discovered that EcAlr is similar to the Pseudomonas aeruginosa catabolic Alr in both overall and active site geometries. Mutation of the conserved negatively charged residue aspartate 164 or glutamate 165 at the substrate entryway could obviously reduce the binding affinity of enzyme against the substrate and decrease the turnover numbers in both D- to L-Ala and L- to D-Ala directions, especially when mutated to lysine with the opposite charge. However, mutation of Pro219 or Glu221 had only negligible or a small influence on the enzymatic activity. Together with the enzymatic and structural investigation results, we thus proposed that the negatively charged residues Asp164 and Glu165 around the substrate entryway play an important role in substrate orientation with cooperation of the positively charged Arg280 and Arg300 on the opposite monomer. Our findings are expected to provide some useful structural information for inhibitor design targeting the substrate entryway of Alr.
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Affiliation(s)
- Dalei Wu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
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Pierce KJ, Salifu SP, Tangney M. Gene cloning and characterization of a second alanine racemase from Bacillus subtilis encoded by yncD. FEMS Microbiol Lett 2008; 283:69-74. [DOI: 10.1111/j.1574-6968.2008.01151.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Ashby CR, Jodlowski TZ, Sym D. Medications for Extensively Drug-Resistant Tuberculosis: Back to the Future? J Pharm Technol 2008. [DOI: 10.1177/875512250802400205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Objective: To reexamine the existing medications for the potential treatment of extensively drug-resistant tuberculosis (XDR-TB), based on susceptibility data, and to identify potential future medications from the literature. Data Sources: Relevant information was identified through a search of MEDLINE (1966–November 2007), PubMed (1955–November 2007), American Search Premier (1975–November 2007), International Pharmaceutical Abstracts (1960–November 2007), Science Citation Index Expanded (1996–November 2007), Cochrane Databases (publications archived until November 2007), and various tertiary sources as listed in the references, using the terms extensively drug-resistant tuberculosis (XDR-TB), ethambutol, pyrazinamide, para-aminosalicylic acid, cycloserine, linezolid, diarylquinoline, nitroimidazopyran, fluoroquinolones, β-lactams, new treatments, and ethionamide alone or in combination regimens. Study Selection and Data Extraction: After identification of the relevant information, the data presented in this article were selected based on clinical relevance and value of information. Data Synthesis: Based on susceptibility data, pyrazinamide, ethambutol, para-aminosalicylic acid, cycloserine, and ethionamide may be used for the treatment of tuberculosis. However, due to the emergence of XDR-TB, many of these agents are no longer successful treatment regimens. We have found limited data supporting potential future use of β-lactams, clarithromycin, and linezolid in resistant TB infections. TMC207, nitroimidazopyran, and SQ109 compounds may also prove to be viable options in the near future for treatment of tuberculosis, especially in cases with resistance to mainstay medications. Conclusions: Extensively resistant tuberculosis appears to be a potentially catastrophic disease if allowed to spread. Due to its resistance profile, very few potentially effective agents are available, calling attention to this growing problem.
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Affiliation(s)
- Charles R Ashby
- CHARLES R ASHBY JR PhD, Professor, St. John's University College of Pharmacy and Allied Health Professions, Queens, NY
| | - Tomasz Z Jodlowski
- TOMASZ Z JODLOWSKI PharmD BCPS, Assistant Clinical Professor, St. John's University College of Pharmacy and Allied Health Professions, Queens, NY; Infectious Diseases Clinical Pharmacist, Beth Israel Medical Center, New York, NY
| | - Donna Sym
- DONNA SYM BS PharmD, Assistant Clinical Professor, St. John's University College of Pharmacy and Allied Health Professions; Clinical Preceptor, North Shore University Hospital, Manhasset, NY
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Barreteau H, Kovac A, Boniface A, Sova M, Gobec S, Blanot D. Cytoplasmic steps of peptidoglycan biosynthesis. FEMS Microbiol Rev 2008; 32:168-207. [PMID: 18266853 DOI: 10.1111/j.1574-6976.2008.00104.x] [Citation(s) in RCA: 479] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The biosynthesis of bacterial cell wall peptidoglycan is a complex process that involves enzyme reactions that take place in the cytoplasm (synthesis of the nucleotide precursors) and on the inner side (synthesis of lipid-linked intermediates) and outer side (polymerization reactions) of the cytoplasmic membrane. This review deals with the cytoplasmic steps of peptidoglycan biosynthesis, which can be divided into four sets of reactions that lead to the syntheses of (1) UDP-N-acetylglucosamine from fructose 6-phosphate, (2) UDP-N-acetylmuramic acid from UDP-N-acetylglucosamine, (3) UDP-N-acetylmuramyl-pentapeptide from UDP-N-acetylmuramic acid and (4) D-glutamic acid and dipeptide D-alanyl-D-alanine. Recent data concerning the different enzymes involved are presented. Moreover, special attention is given to (1) the chemical and enzymatic synthesis of the nucleotide precursor substrates that are not commercially available and (2) the search for specific inhibitors that could act as antibacterial compounds.
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Affiliation(s)
- Hélène Barreteau
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Univ Paris-Sud, Orsay, France
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Halouska S, Chacon O, Fenton RJ, Zinniel DK, Barletta RG, Powers R. Use of NMR metabolomics to analyze the targets of D-cycloserine in mycobacteria: role of D-alanine racemase. J Proteome Res 2007; 6:4608-14. [PMID: 17979227 DOI: 10.1021/pr0704332] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
D-Cycloserine (DCS) is only used with multidrug-resistant strains of tuberculosis because of serious side effects. DCS is known to inhibit cell wall biosynthesis, but the in vivo lethal target is still unknown. We have applied NMR-based metabolomics combined with principal component analysis to monitor the in vivo effect of DCS on Mycobacterium smegmatis. Our analysis suggests DCS functions by inhibiting multiple protein targets.
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Affiliation(s)
- Steven Halouska
- Department of Chemistry, University of Nebraska Lincoln, Lincoln, Nebraska 68522, USA
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