1
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Rotsides P, Lee PJ, Webber N, Grasty KC, Beld J, Loll PJ. Diazirine Photoprobes for the Identification of Vancomycin-Binding Proteins. ACS BIO & MED CHEM AU 2024; 4:86-94. [PMID: 38645928 PMCID: PMC11027123 DOI: 10.1021/acsbiomedchemau.3c00067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 04/23/2024]
Abstract
Vancomycin's interactions with cellular targets drive its antimicrobial activity and also trigger expression of resistance against the antibiotic. Interaction partners for vancomycin have previously been identified using photoaffinity probes, which have proven to be useful tools for exploring vancomycin's interactome. This work seeks to develop diazirine-based vancomycin photoprobes that display enhanced specificity and bear fewer chemical modifications as compared to previous photoprobes. Using proteins fused to vancomycin's main cell-wall target, d-alanyl-d-alanine, we used mass spectrometry to show that these photoprobes specifically label known vancomycin-binding partners within minutes. In a complementary approach, we developed a Western-blot strategy targeting the vancomycin adduct of the photoprobes, eliminating the need for affinity tags and simplifying the analysis of photolabeling reactions. Together, the probes and identification strategy provide a novel and streamlined pipeline for identifying vancomycin-binding proteins.
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Affiliation(s)
- Photis Rotsides
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Paula J. Lee
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Nakoa Webber
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Kimberly C. Grasty
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Joris Beld
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Patrick J. Loll
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
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2
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Miyamoto T, Fushinobu S, Saitoh Y, Sekine M, Katane M, Sakai-Kato K, Homma H. Novel tetrahydrofolate-dependent d-serine dehydratase activity of serine hydroxymethyltransferases. FEBS J 2024; 291:308-322. [PMID: 37700610 DOI: 10.1111/febs.16953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 08/12/2023] [Accepted: 09/06/2023] [Indexed: 09/14/2023]
Abstract
d-Serine plays vital physiological roles in the functional regulation of the mammalian brain, where it is produced from l-serine by serine racemase and degraded by d-amino acid oxidase. In the present study, we identified a new d-serine metabolizing activity of serine hydroxymethyltransferase (SHMT) in bacteria as well as mammals. SHMT is known to catalyze the conversion of l-serine and tetrahydrofolate (THF) to glycine and 5,10-methylenetetrahydrofolate, respectively. In addition, we found that human and Escherichia coli SHMTs have d-serine dehydratase activity, which degrades d-serine to pyruvate and ammonia. We characterized this enzymatic activity along with canonical SHMT activity. Intriguingly, SHMT required THF to catalyze d-serine dehydration and did not exhibit dehydratase activity toward l-serine. Furthermore, SHMT did not use d-serine as a substrate in the canonical hydroxymethyltransferase reaction. The d-serine dehydratase activities of two isozymes of human SHMT were inhibited in the presence of a high concentration of THF, whereas that of E. coli SHMT was increased. The pH and temperature profiles of d-serine dehydratase and serine hydroxymethyltransferase activities of these three SHMTs were partially distinct. The catalytic efficiency (kcat /Km ) of dehydratase activity was lower than that of hydroxymethyltransferase activity. Nevertheless, the d-serine dehydratase activity of SHMT was physiologically important because d-serine inhibited the growth of an SHMT deletion mutant of E. coli, ∆glyA, more than that of the wild-type strain. Collectively, these results suggest that SHMT is involved not only in l- but also in d-serine metabolism through the degradation of d-serine.
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Affiliation(s)
- Tetsuya Miyamoto
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
| | - Yasuaki Saitoh
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Masae Sekine
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Masumi Katane
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Kumiko Sakai-Kato
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Hiroshi Homma
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
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3
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Du S, Wey M, Armstrong DW. d-Amino acids in biological systems. Chirality 2023; 35:508-534. [PMID: 37074214 DOI: 10.1002/chir.23562] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 04/20/2023]
Abstract
Investigations on the occurrence and biochemical roles of free D-amino acids and D-amino acid-containing peptides and proteins in living systems have increased in frequency and significance. Their occurrence and roles may vary substantially with progression from microbiotic to evermore advanced macrobiotic systems. We now understand many of the biosynthetic and regulatory pathways, which are outlined herein. Important uses for D-amino acids in plants, invertebrates, and vertebrates are reviewed. Given its importance, a separate section on the occurrence and role of D-amino acids in human disease is presented.
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Affiliation(s)
- Siqi Du
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas, USA
| | - Michael Wey
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas, USA
| | - Daniel W Armstrong
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas, USA
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4
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Osaki A, Aoyama M, Mita M, Hamase K, Yasui M, Sasabe J. Endogenous d-serine exists in the mammalian brain independent of synthesis by serine racemase. Biochem Biophys Res Commun 2023; 641:186-191. [PMID: 36535077 DOI: 10.1016/j.bbrc.2022.12.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 11/23/2022] [Accepted: 12/12/2022] [Indexed: 12/14/2022]
Abstract
Activation of N-methyl-d-aspartate receptors (NMDARs) requires binding of a co-agonist in addition to l-glutamate. d-serine binds to the co-agonist site on GluN1 subunits of NMDARs and modulates glutamatergic neurotransmission. While loss of GluN1 subunits in mice results in neonatal death due to respiratory failure, animals that lack a d-serine synthetic enzyme, serine racemase (SR), show grossly normal growth. However, SR-independent origins of d-serine in the brain remain unclarified. In the present study, we investigated the origin of brain d-serine in mice. Loss of SR significantly reduced d-serine in the cerebral cortex, but a portion of d-serine remained in both neonates and adults. Although d-serine was also produced by intestinal bacteria, germ-free experiments did not influence d-serine levels in the cerebral cortex. In addition, treatment of SR-knockout mice with antibiotics showed a significant reduction of intestinal d-serine, but no reduction in the brain. On the other hand, restriction of dietary intake reduced systemic circulation of d-serine and resulted in a slight decrease of d-serine in the cerebral cortex, but did not account for brain d-serine found in the SR-knockout mice. Therefore, our findings show that endogenous d-serine of non-SR origin exists in the brain. Such previously unrecognized, SR-independent, endogenous d-serine may contribute baseline activity of NMDARs, especially in developing brain, which has minimal SR expression.
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Affiliation(s)
- Akina Osaki
- Department of Pharmacology, Keio University School of Medicine, 160-8582, Tokyo, Japan
| | - Marie Aoyama
- Vita-Salute San Raffaele University, 20132, Milano, Italy
| | | | - Kenji Hamase
- Graduate School of Pharmaceutical Sciences, Kyushu University, 812-8582, Fukuoka, Japan
| | - Masato Yasui
- Department of Pharmacology, Keio University School of Medicine, 160-8582, Tokyo, Japan
| | - Jumpei Sasabe
- Department of Pharmacology, Keio University School of Medicine, 160-8582, Tokyo, Japan.
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5
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Vahdati SN, Behboudi H, Navasatli SA, Tavakoli S, Safavi M. New insights into the inhibitory roles and mechanisms of D-amino acids in bacterial biofilms in medicine, industry, and agriculture. Microbiol Res 2022; 263:127107. [PMID: 35843196 DOI: 10.1016/j.micres.2022.127107] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 11/26/2022]
Abstract
Biofilms are complex aggregates of microbes that are tightly protected by an extracellular matrix (ECM) and may attach to a surface or adhere together. A higher persistence of bacteria on biofilms makes them resistant not only to harsh conditions but also to various antibiotics which led to the emergence of problems in different applications. Recently, it has been discovered that many bacteria produce and release various D-amino acids (D-AAs) to inhibit biofilm formation, which made a great deal of interest in research into the control of bacterial biofilms in diverse fields, such as human health, industrial settings, and medical devices. D-AAs have various mechanisms to inhibit bacterial biofilms such as: (i) interfering with protein synthesis (ii) Inhibition of extracellular polymeric materials (EPS) productions (protein, eDNA, and polysaccharide) (iii) Inhibition of quorum sensing (autoinducers), and (iv) interfere with peptidoglycan synthesis, these various modes of action, enables these small molecules to inhibit both Gram-negative and Gram-positive bacterial biofilms. Since most biofilms are multi-species, D-AAs in combination with other antimicrobial agents are good choices to combat a variety of bacterial biofilms without displaying toxicity on human cells. This review article addressed the role of D-AAs in controlling several bacterial biofilms and described the possible or definite mechanisms involved in this process.
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Affiliation(s)
- Saeed Niazi Vahdati
- Institute of Biochemistry and Biophysics, Department of Biochemistry, University of Tehran, Tehran, Iran
| | - Hossein Behboudi
- Department of Biology, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran.
| | - Sepideh Aliniaye Navasatli
- Institute of Biochemistry and Biophysics, Department of Biochemistry, University of Tehran, Tehran, Iran
| | - Sara Tavakoli
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Maliheh Safavi
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, Iran
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6
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Miyamoto T, Moriya T, Katane M, Saitoh Y, Sekine M, Sakai‐Kato K, Oshima T, Homma H. Identification of a novel
d
‐amino acid aminotransferase involved in
d
‐glutamate biosynthetic pathways in the hyperthermophile
Thermotoga maritima. FEBS J 2022; 289:5933-5946. [DOI: 10.1111/febs.16452] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/22/2022] [Accepted: 04/01/2022] [Indexed: 02/02/2023]
Affiliation(s)
- Tetsuya Miyamoto
- Graduate School of Pharmaceutical Sciences Kitasato University Tokyo Japan
| | - Toshiyuki Moriya
- Institute of Environmental Microbiology Kyowa Kako Co. Tokyo Japan
| | - Masumi Katane
- Graduate School of Pharmaceutical Sciences Kitasato University Tokyo Japan
| | - Yasuaki Saitoh
- Graduate School of Pharmaceutical Sciences Kitasato University Tokyo Japan
| | - Masae Sekine
- Graduate School of Pharmaceutical Sciences Kitasato University Tokyo Japan
| | - Kumiko Sakai‐Kato
- Graduate School of Pharmaceutical Sciences Kitasato University Tokyo Japan
| | - Tairo Oshima
- Institute of Environmental Microbiology Kyowa Kako Co. Tokyo Japan
| | - Hiroshi Homma
- Graduate School of Pharmaceutical Sciences Kitasato University Tokyo Japan
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7
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Regulation of Resistance in Vancomycin-Resistant Enterococci: The VanRS Two-Component System. Microorganisms 2021; 9:microorganisms9102026. [PMID: 34683347 PMCID: PMC8541618 DOI: 10.3390/microorganisms9102026] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 01/20/2023] Open
Abstract
Vancomycin-resistant enterococci (VRE) are a serious threat to human health, with few treatment options being available. New therapeutics are urgently needed to relieve the health and economic burdens presented by VRE. A potential target for new therapeutics is the VanRS two-component system, which regulates the expression of vancomycin resistance in VRE. VanS is a sensor histidine kinase that detects vancomycin and in turn activates VanR; VanR is a response regulator that, when activated, directs expression of vancomycin-resistance genes. This review of VanRS examines how the expression of vancomycin resistance is regulated, and provides an update on one of the field’s most pressing questions: How does VanS sense vancomycin?
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8
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Identification and biochemical characterization of threonine dehydratase from the hyperthermophile Thermotoga maritima. Amino Acids 2021; 53:903-915. [PMID: 33938999 DOI: 10.1007/s00726-021-02993-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/21/2021] [Indexed: 01/14/2023]
Abstract
The peptidoglycan of the hyperthermophile Thermotoga maritima contains an unusual component, D-lysine (D-Lys), in addition to the typical D-alanine (D-Ala) and D-glutamate (D-Glu). In a previous study, we identified a Lys racemase that is presumably associated with D-Lys biosynthesis. However, our understanding of D-amino acid metabolism in T. maritima and other bacteria remains limited, although D-amino acids in the peptidoglycan are crucial for preserving bacterial cell structure and resistance to environmental threats. Herein, we characterized enzymatic and structural properties of TM0356 that shares a high amino acid sequence identity with serine (Ser) racemase. The results revealed that TM0356 forms a tetramer with each subunit containing a pyridoxal 5'-phosphate as a cofactor. The enzyme did not exhibit racemase activity toward various amino acids including Ser, and dehydratase activity was highest toward L-threonine (L-Thr). It also acted on L-Ser and L-allo-Thr, but not on the corresponding D-amino acids. The catalytic mechanism did not follow typical Michaelis-Menten kinetics; it displayed a sigmoidal dependence on substrate concentration, with highest catalytic efficiency (kcat/K0.5) toward L-Thr. Interestingly, dehydratase activity was insensitive to allosteric regulators L-valine and L-isoleucine (L-Ile) at low concentrations, while these L-amino acids are inhibitors at high concentrations. Thus, TM0356 is a biosynthetic Thr dehydratase responsible for the conversion of L-Thr to α-ketobutyrate and ammonia, which is presumably involved in the first step of the biosynthesis of L-Ile.
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9
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Miyamoto T, Homma H, Miyamoto T. D-Amino acid metabolism in bacteria. J Biochem 2021; 170:5-13. [PMID: 33788945 DOI: 10.1093/jb/mvab043] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/19/2021] [Indexed: 02/02/2023] Open
Affiliation(s)
- Tetsuya Miyamoto
- Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Hiroshi Homma
- Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Tetsuya Miyamoto
- Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
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10
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Miyamoto T, Moriya T, Homma H, Oshima T. Enzymatic properties and physiological function of glutamate racemase from Thermus thermophilus. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140461. [PMID: 32474108 DOI: 10.1016/j.bbapap.2020.140461] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/08/2020] [Accepted: 05/26/2020] [Indexed: 01/12/2023]
Abstract
d-Amino acids are physiologically important components of peptidoglycan in the bacterial cell wall, maintaining cell structure and aiding adaptation to environmental changes through peptidoglycan remodelling. Therefore, the biosynthesis of d-amino acids is essential for bacteria to adapt to different environmental conditions. The peptidoglycan of the extremely thermophilic bacterium Thermus thermophilus contains d-alanine (d-Ala) and d-glutamate (d-Glu), but its d-amino acid metabolism remains poorly understood. Here, we investigated the enzyme activity and function of the product of the TTHA1643 gene, which is annotated to be a Glu racemase in the T. thermophilus HB8 genome. Among 21 amino acids tested, TTHA1643 showed highly specific activity toward Glu as the substrate. The catalytic efficiency (kcat/Km) of TTHA1643 toward d- and l-Glu was comparable; however, the kcat value was 18-fold higher for l-Glu than for d-Glu. Temperature and pH profiles showed that the racemase activity of TTHA1643 is high under physiological conditions for T. thermophilus growth. To assess physiological relevance, we constructed a TTHA1643-deficient strain (∆TTHA1643) by replacing the TTHA1643 gene with the thermostable hygromycin resistance gene. Growth of the ∆TTHA1643 strain in synthetic medium without d-Glu was clearly diminished relative to wild type, although the TTHA1643 deletion was not lethal, suggesting that alternative d-Glu biosynthetic pathways may exist. The deterioration in growth was restored by adding d-Glu to the culture medium, showing that d-Glu is required for normal growth of T. thermophilus. Collectively, our findings show that TTHA1643 is a Glu racemase and has the physiological function of d-Glu production in T. thermophilus.
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Affiliation(s)
- Tetsuya Miyamoto
- Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Toshiyuki Moriya
- Institute of Environmental Microbiology, Kyowa Kako Co., 2-15-5 Tadao, Machida, Tokyo 194-0035, Japan
| | - Hiroshi Homma
- Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Tairo Oshima
- Institute of Environmental Microbiology, Kyowa Kako Co., 2-15-5 Tadao, Machida, Tokyo 194-0035, Japan.
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11
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Miyamoto T, Katane M, Saitoh Y, Sekine M, Homma H. Involvement of penicillin-binding proteins in the metabolism of a bacterial peptidoglycan containing a non-canonical D-amino acid. Amino Acids 2020; 52:487-497. [PMID: 32108264 DOI: 10.1007/s00726-020-02830-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/14/2020] [Indexed: 12/15/2022]
Abstract
Bacteria produce various D-amino acids, including non-canonical D-amino acids, to adapt to environmental changes and overcome a variety of threats. These D-amino acids are largely utilized as components of peptidoglycan, and they promote peptidoglycan remodeling and biofilm disassembly. The biosynthesis, maturation, and recycling of peptidoglycan are catalyzed by penicillin-binding proteins (PBPs). However, although non-canonical D-amino acids are known to be incorporated into peptidoglycan, the maturation and recycling of peptidoglycan containing such residues remain uncharacterized. Therefore, we investigated whether PBP4 and PBP5, low molecular mass (LMM) PBPs from Escherichia coli and Bacillus subtilis, are involved in these events of peptidoglycan metabolism. Enzyme assays using p-nitroaniline (pNA)-derivatized D-amino acids and peptidoglycan-mimicking peptides revealed that PBP4 and PBP5 from both species have peptidase activity toward substrates containing D-Asn, D-His, or D-Trp. These D-amino acids slowed the growth of dacA- or dacB-deficient E. coli (∆dacA or ∆dacB) relative to the wild-type strain. Additionally, these D-amino acids affected biofilm formation by the ∆dacB strain. Collectively, PBP4 and PBP5 are involved in the cleavage of peptidoglycan containing non-canonical D-amino acids, and these properties affect growth and biofilm formation.
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Affiliation(s)
- Tetsuya Miyamoto
- Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Masumi Katane
- Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Yasuaki Saitoh
- Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Masae Sekine
- Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Hiroshi Homma
- Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
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12
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Anderson EM, Sychantha D, Brewer D, Clarke AJ, Geddes-McAlister J, Khursigara CM. Peptidoglycomics reveals compositional changes in peptidoglycan between biofilm- and planktonic-derived Pseudomonas aeruginosa. J Biol Chem 2019; 295:504-516. [PMID: 31771981 DOI: 10.1074/jbc.ra119.010505] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/25/2019] [Indexed: 12/14/2022] Open
Abstract
Peptidoglycan (PG) is a critical component of the bacterial cell wall and is composed of a repeating β-1,4-linked disaccharide of N-acetylglucosamine and N-acetylmuramic acid appended with a highly conserved stem peptide. In Gram-negative bacteria, PG is assembled in the cytoplasm and exported into the periplasm where it undergoes considerable maturation, modification, or degradation depending on the growth phase or presence of environmental stressors. These modifications serve important functions in diverse processes, including PG turnover, cell elongation/division, and antibiotic resistance. Conventional methods for analyzing PG composition are complex and time-consuming. We present here a streamlined MS-based method that combines differential analysis with statistical 1D annotation approaches to quantitatively compare PGs produced in planktonic- and biofilm-cultured Pseudomonas aeruginosa We identified a core assembly of PG that is present in high abundance and that does not significantly differ between the two growth states. We also identified an adaptive PG assembly that is present in smaller amounts and fluctuates considerably between growth states in response to physiological changes. Biofilm-derived adaptive PG exhibited significant changes compared with planktonic-derived PG, including amino acid substitutions of the stem peptide and modifications that indicate changes in the activity of amidases, deacetylases, and lytic transglycosylases. The results of this work also provide first evidence of de-N-acetylated muropeptides from P. aeruginosa The method developed here offers a robust and reproducible workflow for accurately determining PG composition in samples that can be used to assess global PG fluctuations in response to changing growth conditions or external stimuli.
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Affiliation(s)
- Erin M Anderson
- Department of Molecular and Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada
| | - David Sychantha
- Department of Molecular and Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada
| | - Dyanne Brewer
- Mass Spectrometry Facility, University of Guelph, Ontario N1G 2W1, Canada
| | - Anthony J Clarke
- Department of Molecular and Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada
| | - Jennifer Geddes-McAlister
- Department of Molecular and Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada; Mass Spectrometry Facility, University of Guelph, Ontario N1G 2W1, Canada.
| | - Cezar M Khursigara
- Department of Molecular and Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada; Mass Spectrometry Facility, University of Guelph, Ontario N1G 2W1, Canada.
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13
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Panina IS, Chugunov AO, Efremov RG. Lipid II as a Target for Novel Antibiotics: Structural and Molecular Dynamics Studies. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019010126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Miyamoto T, Katane M, Saitoh Y, Sekine M, Homma H. Elucidation of the d-lysine biosynthetic pathway in the hyperthermophile Thermotoga maritima. FEBS J 2018; 286:601-614. [PMID: 30548096 DOI: 10.1111/febs.14720] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/29/2018] [Accepted: 12/03/2018] [Indexed: 12/31/2022]
Abstract
Various d-amino acids are involved in peptidoglycan and biofilm metabolism in bacteria, suggesting that these compounds are necessary for successful adaptation to environmental changes. In addition to the conventional d-alanine (d-Ala) and d-glutamate, the peptidoglycan of the hyperthermophilic bacterium Thermotoga maritima contains both l-lysine (l-Lys) and d-Lys, but not meso-diaminopimelate (meso-Dpm). d-Lys is an uncommon component of peptidoglycan, and its biosynthetic pathway remains unclear. In this study, we identified and characterized a novel Lys racemase (TM1597) and Dpm epimerase (TM1522) associated with the d-Lys biosynthetic pathway in T. maritima. The Lys racemase had a dimeric structure containing pyridoxal 5'-phosphate as a cofactor. Among the amino acids, it exhibited the highest racemase activity toward d- and l-Lys, and also had relatively high activity toward d- and l-enantiomers of ornithine and Ala. The Dpm epimerase had the highest epimerization activity toward ll- and meso-Dpm, and also measurably racemized certain amino acids, including Lys. These results suggest that Lys racemase contributes to production of d-Lys and d-Ala for use as peptidoglycan components, and that Dpm epimerase converts ll-Dpm to meso-Dpm, a precursor in the l-Lys biosynthetic pathway.
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Affiliation(s)
- Tetsuya Miyamoto
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Masumi Katane
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Yasuaki Saitoh
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Masae Sekine
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Hiroshi Homma
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
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15
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Cystathionine β-lyase is involved in d-amino acid metabolism. Biochem J 2018; 475:1397-1410. [PMID: 29592871 DOI: 10.1042/bcj20180039] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 03/23/2018] [Accepted: 03/28/2018] [Indexed: 01/07/2023]
Abstract
Non-canonical d-amino acids play important roles in bacteria including control of peptidoglycan metabolism and biofilm disassembly. Bacteria appear to produce non-canonical d-amino acids to adapt to various environmental changes, and understanding the biosynthetic pathways is important. We identified novel amino acid racemases possessing the ability to produce non-canonical d-amino acids in Escherichia coli and Bacillus subtilis in our previous study, whereas the biosynthetic pathways of these d-amino acids still remain unclear. In the present study, we demonstrated that two cystathionine β-lyases (MetC and MalY) from E. coli produce non-canonical d-amino acids including non-proteinogenic amino acids. Furthermore, MetC displayed d- and l-serine (Ser) dehydratase activity. We characterised amino acid racemase, Ser dehydratase and cysteine lyase activities, and all were higher for MetC. Interestingly, all three activities were at a comparable level for MetC, although optimal conditions for each reaction were distinct. These results indicate that MetC and MalY are multifunctional enzymes involved in l-methionine metabolism and the production of d-amino acids, as well as d- and l-Ser metabolism. To our knowledge, this is the first evidence that cystathionine β-lyase is a multifunctional enzyme with three different activities.
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16
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Aliashkevich A, Alvarez L, Cava F. New Insights Into the Mechanisms and Biological Roles of D-Amino Acids in Complex Eco-Systems. Front Microbiol 2018; 9:683. [PMID: 29681896 PMCID: PMC5898190 DOI: 10.3389/fmicb.2018.00683] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 03/22/2018] [Indexed: 01/22/2023] Open
Abstract
In the environment bacteria share their habitat with a great diversity of organisms, from microbes to humans, animals and plants. In these complex communities, the production of extracellular effectors is a common strategy to control the biodiversity by interfering with the growth and/or viability of nearby microbes. One of such effectors relies on the production and release of extracellular D-amino acids which regulate diverse cellular processes such as cell wall biogenesis, biofilm integrity, and spore germination. Non-canonical D-amino acids are mainly produced by broad spectrum racemases (Bsr). Bsr’s promiscuity allows it to generate high concentrations of D-amino acids in environments with variable compositions of L-amino acids. However, it was not clear until recent whether these molecules exhibit divergent functions. Here we review the distinctive biological roles of D-amino acids, their mechanisms of action and their modulatory properties of the biodiversity of complex eco-systems.
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Affiliation(s)
- Alena Aliashkevich
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Laura Alvarez
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Felipe Cava
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
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17
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Identification and characterization of novel broad-spectrum amino acid racemases from Escherichia coli and Bacillus subtilis. Amino Acids 2017; 49:1885-1894. [DOI: 10.1007/s00726-017-2486-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 09/06/2017] [Indexed: 12/15/2022]
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18
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Hernández SB, Cava F. Environmental roles of microbial amino acid racemases. Environ Microbiol 2015; 18:1673-85. [DOI: 10.1111/1462-2920.13072] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 09/15/2015] [Accepted: 09/27/2015] [Indexed: 02/02/2023]
Affiliation(s)
- Sara B. Hernández
- Laboratory for Molecular Infection Medicine Sweden; Department of Molecular Biology; Umeå Centre for Microbial Research; Umeå University; 90187 Umeå Sweden
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden; Department of Molecular Biology; Umeå Centre for Microbial Research; Umeå University; 90187 Umeå Sweden
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19
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Koch G, Yepes A, Förstner KU, Wermser C, Stengel ST, Modamio J, Ohlsen K, Foster KR, Lopez D. Evolution of resistance to a last-resort antibiotic in Staphylococcus aureus via bacterial competition. Cell 2014; 158:1060-1071. [PMID: 25171407 PMCID: PMC4163622 DOI: 10.1016/j.cell.2014.06.046] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 04/28/2014] [Accepted: 06/23/2014] [Indexed: 01/02/2023]
Abstract
Antibiotic resistance is a key medical concern, with antibiotic use likely being an important cause. However, here we describe an alternative route to clinically relevant antibiotic resistance that occurs solely due to competitive interactions among bacterial cells. We consistently observe that isolates of Methicillin-resistant Staphylococcus aureus diversify spontaneously into two distinct, sequentially arising strains. The first evolved strain outgrows the parent strain via secretion of surfactants and a toxic bacteriocin. The second is resistant to the bacteriocin. Importantly, this second strain is also resistant to intermediate levels of vancomycin. This so-called VISA (vancomycin-intermediate S. aureus) phenotype is seen in many hard-to-treat clinical isolates. This strain diversification also occurs during in vivo infection in a mouse model, which is consistent with the fact that both coevolved phenotypes resemble strains commonly found in clinic. Our study shows how competition between coevolving bacterial strains can generate antibiotic resistance and recapitulate key clinical phenotypes.
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Affiliation(s)
- Gudrun Koch
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
| | - Ana Yepes
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
| | - Konrad U Förstner
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Charlotte Wermser
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
| | - Stephanie T Stengel
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
| | - Jennifer Modamio
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
| | - Knut Ohlsen
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Kevin R Foster
- Department of Zoology, University of Oxford, Oxford OX1 3QU, UK; Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford OX1 3QU, UK
| | - Daniel Lopez
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany.
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20
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Alvarez L, Espaillat A, Hermoso JA, de Pedro MA, Cava F. Peptidoglycan remodeling by the coordinated action of multispecific enzymes. Microb Drug Resist 2014; 20:190-8. [PMID: 24799190 DOI: 10.1089/mdr.2014.0047] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The peptidoglycan (PG) cell wall constitutes the main defense barrier of bacteria against environmental insults and acts as communication interface. The biochemistry of this macromolecule has been well characterized throughout the years but recent discoveries have unveiled its chemical plasticity under environmental stresses. Non-canonical D-amino acids (NCDAA) are produced and released to the extracellular media by diverse bacteria. Such molecules govern cell wall adaptation to challenging environments through their incorporation into the polymer, a widespread capability among bacteria that reveals the inherent catalytic plasticity of the enzymes involved in the cell wall metabolism. Here, we analyze the recent structural and biochemical characterization of Bsr, a new family of broad spectrum racemases able to generate a wide range of NCDAA. We also discuss the necessity of a coordinated action of PG multispecific enzymes to generate adequate levels of modification in the murein sacculus. Finally, we also highlight how this catalytic plasticity of NCDAA-incorporating enzymes has allowed the development of new revolutionary methodologies for the study of PG modes of growth and in vivo dynamics.
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Affiliation(s)
- Laura Alvarez
- 1 Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University , Umeå, Sweden
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21
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Identification, purification, and characterization of a novel amino acid racemase, isoleucine 2-epimerase, from Lactobacillus species. J Bacteriol 2013; 195:5207-15. [PMID: 24039265 DOI: 10.1128/jb.00709-13] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Accumulation of d-leucine, d-allo-isoleucine, and d-valine was observed in the growth medium of a lactic acid bacterium, Lactobacillus otakiensis JCM 15040, and the racemase responsible was purified from the cells and identified. The N-terminal amino acid sequence of the purified enzyme was GKLDKASKLI, which is consistent with that of a putative γ-aminobutyrate aminotransferase from Lactobacillus buchneri. The putative γ-aminobutyrate aminotransferase gene from L. buchneri JCM 1115 was expressed in recombinant Escherichia coli and then purified to homogeneity. The enzyme catalyzed the racemization of a broad spectrum of nonpolar amino acids. In particular, it catalyzed at high rates the epimerization of l-isoleucine to d-allo-isoleucine and d-allo-isoleucine to l-isoleucine. In contrast, the enzyme showed no γ-aminobutyrate aminotransferase activity. The relative molecular masses of the subunit and native enzyme were estimated to be about 49 kDa and 200 kDa, respectively, indicating that the enzyme was composed of four subunits of equal molecular masses. The Km and Vmax values of the enzyme for l-isoleucine were 5.00 mM and 153 μmol·min(-1)·mg(-1), respectively, and those for d-allo-isoleucine were 13.2 mM and 286 μmol·min(-1)·mg(-1), respectively. Hydroxylamine and other inhibitors of pyridoxal 5'-phosphate-dependent enzymes completely blocked the enzyme activity, indicating the enzyme requires pyridoxal 5'-phosphate as a coenzyme. This is the first evidence of an amino acid racemase that specifically catalyzes racemization of nonpolar amino acids at the C-2 position.
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22
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Horcajo P, de Pedro MA, Cava F. Peptidoglycan plasticity in bacteria: stress-induced peptidoglycan editing by noncanonical D-amino acids. Microb Drug Resist 2012; 18:306-13. [PMID: 22443287 DOI: 10.1089/mdr.2012.0009] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
It has been generally assumed that the role of D-amino acids in bacterial physiology is rather limited. However, recent new evidence demonstrated that millimolar concentrations of noncanonical D-amino acids are synthesized and released to the environment by bacteria from diverse phyla. These D-amino acids help bacteria adapt to environmental challenges by modulating the structure and composition of the peptidoglycan (PG). This regulation, which appears to be well conserved among bacterial species, occurs principally through the incorporation of the D-amino acids into the terminus of the peptide moiety of muropeptides. These findings revived interest in studies investigating D-amino acids as an exciting and trendy topic in current microbiology, which considers them as fundamental players in different aspects of bacterial physiology. In this article, we provide an overview of the origins of research on the effects of D-amino acids in the biology of bacterial cell walls, including their recent implication as key factors for stress-associated PG remodeling.
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Affiliation(s)
- Pilar Horcajo
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
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23
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Pereira PM, Filipe SR, Tomasz A, Pinho MG. Fluorescence ratio imaging microscopy shows decreased access of vancomycin to cell wall synthetic sites in vancomycin-resistant Staphylococcus aureus. Antimicrob Agents Chemother 2007; 51:3627-33. [PMID: 17646417 PMCID: PMC2043281 DOI: 10.1128/aac.00431-07] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A new method of fluorescence ratio imaging microscopy was used to compare the in vivo binding capacity and the access of a fluorescent derivative of vancomycin to the cell wall synthetic sites in isogenic pairs of vancomycin-susceptible and -resistant laboratory mutants and vancomycin-intermediate and -susceptible clinical isolates of Staphylococcus aureus. Live cells of resistant strains were found to bind approximately 1.5 times more antibiotic, but there was no correlation between the increased binding capacity and the MICs of the strains. In both susceptible and resistant bacteria, the subcellular sites of wall synthesis were localized to the division septa, but the rate of diffusion of drug molecules to these sites was reduced in resistant cells. The findings allow a reinterpretation of the mechanism of vancomycin resistance in which the path of vancomycin to its lethal target (lipid II) is considered to be through the division septum and therefore is dependent on the stage of the staphylococcal cell cycle.
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Affiliation(s)
- Pedro M Pereira
- Laboratory of Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica, Av da Republica, 2781-901, Oeiras, Portugal
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24
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Magnet S, Arbeloa A, Mainardi JL, Hugonnet JE, Fourgeaud M, Dubost L, Marie A, Delfosse V, Mayer C, Rice LB, Arthur M. Specificity of L,D-transpeptidases from gram-positive bacteria producing different peptidoglycan chemotypes. J Biol Chem 2007; 282:13151-9. [PMID: 17311917 DOI: 10.1074/jbc.m610911200] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report here the first direct assessment of the specificity of a class of peptidoglycan cross-linking enzymes, the L,D-transpeptidases, for the highly diverse structure of peptidoglycan precursors of Gram-positive bacteria. The lone functionally characterized member of this new family of active site cysteine peptidases, Ldt(fm) from Enterococcus faecium, was previously shown to bypass the D,D-transpeptidase activity of the classical penicillin-binding proteins leading to high level cross-resistance to glycopeptide and beta-lactam antibiotics. Ldt(fm) homologues from Bacillus subtilis (Ldt(Bs)) and E. faecalis (Ldt(fs)) were found here to cross-link their cognate disaccharide-peptide subunits containing meso-diaminopimelic acid (mesoDAP(3)) and L-Lys(3)-L-Ala-L-Ala at the third position of the stem peptide, respectively, instead of L-Lys(3)-d-iAsn in E. faecium. Ldt(fs) differed from Ldt(fm) and Ldt(Bs) by its capacity to hydrolyze the L-Lys(3)-D-Ala(4) bond of tetrapeptide (L,D-carboxypeptidase activity) and pentapeptide (L,D-endopeptidase activity) stems, in addition to the common cross-linking activity. The three enzymes were specific for their cognate acyl acceptors in the cross-linking reaction. In contrast to Ldt(fs), which was also specific for its cognate acyl donor, Ldt(fm) tolerated substitution of L-Lys(3)-D-iAsn by L-Lys(3)-L-Ala-L-Ala. Likewise, Ldt(Bs) tolerated substitution of mesoDAP(3) by L-Lys(3)-D-iAsn and L-Lys(3)-L-Ala-L-Ala in the acyl donor. Thus, diversification of the structure of peptidoglycan precursors associated with speciation has led to a parallel evolution of the substrate specificity of the L,D-transpeptidases affecting mainly the recognition of the acyl acceptor. Blocking the assembly of the side chain could therefore be used to combat antibiotic resistance involving L,D-transpeptidases.
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25
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Manero A, Vilanova X, Cerdà-Cuéllar M, Blanch AR. Vancomycin- and erythromycin-resistant enterococci in a pig farm and its environment. Environ Microbiol 2006; 8:667-74. [PMID: 16584478 DOI: 10.1111/j.1462-2920.2005.00945.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A high prevalence of vancomycin- and erythromycin-resistant enterococci (VRE and ERE respectively) in a pig farm and its environment was observed. A similar structure and composition of enterococcal populations was detected between urban sewage and those associated with the pig environment. Enterococcus faecium was the most predominant species among VRE isolates from both animal and human origin. The high population similarity index (Sp) obtained comparing VRE and ERE isolates from urban sewage and pig slurry suggests that there are certain strains circulating through the food chain from farms to humans. Erythromycin resistance was present in a wider variety of clones and species of enterococci in both pigs and humans than vancomycin resistance.
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Affiliation(s)
- Albert Manero
- Laboratori d'Anàlisi Mediambiental, Secció Microbiologia, Aigües de Terrassa, S.A., Carrer del Nord, 88, E 08221 Terrassa (Barcelona), Catalonia, Spain
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26
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Mainardi JL, Fourgeaud M, Hugonnet JE, Dubost L, Brouard JP, Ouazzani J, Rice LB, Gutmann L, Arthur M. A novel peptidoglycan cross-linking enzyme for a beta-lactam-resistant transpeptidation pathway. J Biol Chem 2005; 280:38146-52. [PMID: 16144833 DOI: 10.1074/jbc.m507384200] [Citation(s) in RCA: 171] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The beta-lactam antibiotics remain the most commonly used to treat severe infections. Because of structural similarity between the beta-lactam ring and the d-alanyl(4)-d-alanine(5) extremity of bacterial cell wall precursors, the drugs act as suicide substrates of the dd-transpeptidases that catalyze the last cross-linking step of cell wall assembly. Here, we show that this mechanism of action can be defeated by a novel type of transpeptidase identified for the first time by reverse genetics in abeta-lactam-resistant mutant of Enterococcus faecium. The enzyme, Ldt(fm), catalyzes in vitro the cross-linking of peptidoglycan subunits in a beta-lactam-insensitive ld-transpeptidation reaction. The specificity of Ldt(fm) for the l-lysyl(3)-d-alanine(4) peptide bond of tetrapeptide donors accounts for resistance because the substrate does not mimic beta-lactams in contrast to d-alanyl(4)-d-alanine(5) in the pentapeptide donors required for dd-transpeptidation. Ldt(fm) homologues are encountered sporadically among taxonomically distant bacteria, indicating that ld-transpeptidase-mediated resistance may emerge in various pathogens.
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Affiliation(s)
- Jean-Luc Mainardi
- INSERM, U655-Laboratoire de Recherche Moléculaire sur les Antibiotiques, Université Pierre et Marie Curie, Paris, France.
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27
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Panesso D, Abadía-Patiño L, Vanegas N, Reynolds PE, Courvalin P, Arias CA. Transcriptional analysis of the vanC cluster from Enterococcus gallinarum strains with constitutive and inducible vancomycin resistance. Antimicrob Agents Chemother 2005; 49:1060-6. [PMID: 15728903 PMCID: PMC549275 DOI: 10.1128/aac.49.3.1060-1066.2005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The vanC glycopeptide resistance gene cluster encodes enzymes required for synthesis of peptidoglycan precursors ending in D-Ala-D-Ser. Enterococcus gallinarum BM4174 and SC1 are constitutively and inducibly resistant to vancomycin, respectively. Analysis of peptidoglycan precursors in both strains indicated that UDP-MurNAc-tetrapeptide and UDP-MurNAc-pentapeptide[D-Ser] were synthesized in E. gallinarum SC1 only in the presence of vancomycin (4 microg/ml), whereas the "resistance" precursors accumulated in the cytoplasm of BM4174 cells under both inducing and noninducing conditions. Northern hybridization and reverse transcription-PCR experiments revealed that all the genes from the cluster, vanC-1, vanXY(C), vanT, vanR(C), and vanS(C), were transcribed from a single promoter. In the inducible SC1 isolate, transcriptional regulation appeared to be responsible for inducible expression of resistance. Promoter mapping in E. gallinarum BM4174 revealed that the transcriptional start site was located 30 nucleotides upstream from vanC-1 and that the -10 promoter consensus sequence had high identity with that of the vanA cluster. Comparison of the deduced sequence of the vanS(C) genes from isolates with constitutive and inducible resistance revealed several amino acid substitutions located in the X box (R200L) and in the region between the F and G2 boxes (D312N, D312A, and G320S) of the putative sensor kinase proteins from isolates with constitutive resistance.
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Affiliation(s)
- Diana Panesso
- Bacterial Molecular Genetics Unit, Centro de Investigaciones, Universidad El Bosque, Bogotá, Columbia
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28
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Reynolds PE, Courvalin P. Vancomycin resistance in enterococci due to synthesis of precursors terminating in D-alanyl-D-serine. Antimicrob Agents Chemother 2005; 49:21-5. [PMID: 15616270 PMCID: PMC538887 DOI: 10.1128/aac.49.1.21-25.2005] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Peter E Reynolds
- Department of Biochemistry, University of Cambridge, Tennis Court Rd., Cambridge CB2 1QW, United Kingdom.
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29
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David V, Bozdogan B, Mainardi JL, Legrand R, Gutmann L, Leclercq R. Mechanism of intrinsic resistance to vancomycin in Clostridium innocuum NCIB 10674. J Bacteriol 2004; 186:3415-22. [PMID: 15150227 PMCID: PMC415764 DOI: 10.1128/jb.186.11.3415-3422.2004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have studied the basis for intrinsic resistance to low levels of vancomycin in Clostridium innocuum NCIB 10674 (MIC = 8 microg/ml). Analysis by high-pressure liquid chromatography (HPLC) and mass spectrometry of peptidoglycan nucleotide precursors pools revealed the presence of two types of UDP-MurNac-pentapeptide precursors constitutively produced, an UDP-MurNAc-pentapeptide with a serine at the C terminus which represented 93% of the pool and an UDP-MurNAc-pentapeptide with an alanine at the C terminus which represented the rest of the pool. C. innocuum cell wall muropeptides containing pentapeptide[Ser], either dialanine substituted on the epsilon amino group of lysine or not, were identified and represented about 10% of the monomers while only 1% of pentapeptide[D-Ala] monomers were found. The sequence of a 2,465-bp chromosomal fragment from C. innocuum was determined and revealed the presence of ddl(c. innocuum) and C. innocuum racemase genes putatively encoding homologues of D-Ala:D-X ligases and amino acid racemases, respectively. Analysis of the pool of precursors of Enterococcus faecalis JH2-2, containing cloned ddl(c. innocuum) and C. innocuum racemase genes showed in addition to the UDP-MurNAc-pentapeptide[D-Ala], the presence of an UDP-MurNAc-pentapeptide[D-Ser] precursor. However, the expression of low-level resistance to vancomycin was observed only when both genes were cloned in E. faecalis JH2-2 together with the vanXYc gene from Enterococcus gallinarum BM4174 which encodes a d,d-peptidase which eliminates preferentially the high affinity vancomycin UDP-MurNAc-pentapeptide [D-Ala] precursors produced by the host. We conclude that resistance to vancomycin in C. innocuum NCIB 10674 was related to the presence of the two chromosomal ddl(c. innocuum) and C. innocuum racemase genes allowing the synthesis of a peptidoglycan precursor terminating in serine with low affinity for vancomycin.
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Affiliation(s)
- Véronique David
- Service de Bactériologie-Virologie, Hôpital Henri Mondor-Université Paris XII, Crétil, France
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30
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Pinho MG, Errington J. Dispersed mode of Staphylococcus aureus cell wall synthesis in the absence of the division machinery. Mol Microbiol 2004; 50:871-81. [PMID: 14617148 DOI: 10.1046/j.1365-2958.2003.03719.x] [Citation(s) in RCA: 184] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have developed several new fluorescent staining procedures that enabled us to study the synthesis of cell wall material in the spherical Gram-positive bacterium Staphylococcus aureus. The results obtained support previous proposals that these cells synthesize new wall material specifically at cell division sites, in the form of a flat circular plate that is subsequently cleaved and remodelled to produce the new hemispherical poles of the daughter cells. We have shown that formation of the septal peptidoglycan is dependent on the key cell division protein FtsZ, which recruits penicillin-binding protein (PBP) 2. Unexpectedly, in FtsZ-depleted cells, the cell wall synthetic machinery becomes dispersed and new wall material is made in dispersed patches over the entire surface of the cells, which increase in volume by up to eightfold before lysing. The results have implications for understanding the nature of S. aureus morphogenesis and for inhibitors of cell division proteins as drug targets.
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Affiliation(s)
- Mariana G Pinho
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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31
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Panesso D, Ospina S, Robledo J, Vela MC, Peña J, Hernández O, Reyes J, Arias CA. First characterization of a cluster of VanA-type glycopeptide-resistant Enterococcus faecium, Colombia. Emerg Infect Dis 2002; 8:961-5. [PMID: 12194774 PMCID: PMC2732560 DOI: 10.3201/eid0809.010435] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
From August 1998 to October 1999, glycopeptide-resistant enterococci (GRE) were isolated from 23 infected patients at a teaching hospital in Medellín, Colombia. Identification at the species level and by multiplex polymerase chain reaction assay indicated that all isolates were Enterococcus faecium. The isolates were highly resistant to ampicillin, ciprofloxacin, gentamicin, penicillin, streptomycin, teicoplanin, and vancomycin; they were susceptible only to chloramphenicol, linezolid, and nitrofurantoin. Determination of glycopeptide genotype indicated the presence of the vanA gene in all isolates. Molecular typing by pulsed field gel electrophoresis showed that all isolates were closely related. This study is the first molecular characterization of GRE in Colombia.
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Affiliation(s)
| | | | - Jaime Robledo
- Centro de Investigaciones Biológicas, Medellín, Colombia
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32
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Panesso D, Ospina S, Robledo J, Vela MC, Peña J, Hernández O, Reyes J, Arias CA. First characterization of a cluster of VanA-type glycopeptide-resistant Enterococcus faecium, Colombia. Emerg Infect Dis 2002. [PMID: 12194774 PMCID: PMC2732560 DOI: 10.3201/eid0809.10.3201/eid0809.010435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
From August 1998 to October 1999, glycopeptide-resistant enterococci (GRE) were isolated from 23 infected patients at a teaching hospital in Medellín, Colombia. Identification at the species level and by multiplex polymerase chain reaction assay indicated that all isolates were Enterococcus faecium. The isolates were highly resistant to ampicillin, ciprofloxacin, gentamicin, penicillin, streptomycin, teicoplanin, and vancomycin; they were susceptible only to chloramphenicol, linezolid, and nitrofurantoin. Determination of glycopeptide genotype indicated the presence of the vanA gene in all isolates. Molecular typing by pulsed field gel electrophoresis showed that all isolates were closely related. This study is the first molecular characterization of GRE in Colombia.
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Affiliation(s)
| | | | - Jaime Robledo
- Centro de Investigaciones Biológicas, Medellín, Colombia
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Grail BM, Payne JW. Conformational analysis of bacterial cell wall peptides indicates how particular conformations have influenced the evolution of penicillin-binding proteins, beta-lactam antibiotics and antibiotic resistance mechanisms. J Mol Recognit 2002; 15:113-25. [PMID: 12203837 DOI: 10.1002/jmr.566] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Our aim was to use a conformational analysis technique developed for peptides to identify structural relationships between bacterial cell wall peptides and beta-lactam antibiotics that might help to explain their different actions as substrates and inhibitors of penicillin binding proteins (PBPs). The conformational forms of the model cell wall peptide Ac-L-Lys(Ac)-D-Ala-D-Ala are described by just a few backbone torsion combinations: three C-terminal carboxylate regions, with Tor8 (psi(i+1)) ranges of D3 region (50 degrees to 70 degrees ), D6 region (140 degrees to 170 degrees ) and D9 region (-50 degrees to -70 degrees ) are combined with either of two Tor6 (phi(i))-Tor4 (psi(i)) combinations, C4 region (-50 degrees to -80 degrees ) with B8 region (-40 degrees to -70 degrees ) or C11 region (30 degrees to 50 degrees ) with B2 region (30 degrees to 70 degrees ). From these results, and comparisons with conformational analyses of various beta-lactams and Ac-L-Lys(Ac)-D-Ala-D-Lac, it is concluded that molecular recognition of cell wall peptide substrates by PBPs requires conformers with backbone torsion angles of D3C4B8. beta-Lactam antibiotics are constrained compounds with fewer conformational forms; these match well the backbone torsions of cell wall peptides at D3C4, allowing their recognition and acylation by PBPs, whereas their unique Tor4 produces differently orientated CO and N atoms that appear to prevent subsequent deacylation, leading to their action as suicide substrates. The results are also related to the selective pressures involved in evolution of beta-lactamases from PBPs. From analysis of conformers of Ac-L-Lys(Ac)-D-Ala-D-Ala and the vancomycin-resistant analogue Ac-L-Lys(Ac)-D-Ala-D-Lac, it is concluded that vancomycin may recognise D6C11B2 conformers, giving it complementary substrate specificity to PBPs. This approach could have applications in the rational design of antibiotics targeted against PBPs and their substrates.
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Affiliation(s)
- Barry M Grail
- School of Biological Sciences, University of Wales Bangor, Bangor, Gwynedd LL57 2UW, UK
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Ambúr OH, Reynolds PE, Arias CA. D-Ala:D-Ala ligase gene flanking the vanC cluster: evidence for presence of three ligase genes in vancomycin-resistant Enterococcus gallinarum BM4174. Antimicrob Agents Chemother 2002; 46:95-100. [PMID: 11751117 PMCID: PMC126995 DOI: 10.1128/aac.46.1.95-100.2002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An open reading frame located 230 nucleotides downstream from the stop codon of vanS(c) and in the opposite direction relative to the other genes of the vanC cluster was identified in Enterococcus gallinarum BM4174. This gene (designated ddl2) encoded a protein of 343 amino acids that had significant predicted structural similarity to D-Ala:D-Ala ligases and displayed 33 and 35% amino acid identity to VanC-1 and the previously reported partial sequence of Ddl from E. gallinarum, respectively. Biochemical characterization by thin-layer chromatography confirmed that Ddl2 is a D-Ala:D-Ala ligase with no detectable D-Ala:D-Ser ligase activity. The vancomycin dependence of Enterococcus faecalis BM4320 (ddl mutant) was lost on electroporation of a plasmid construct expressing ddl2 constitutively. The latter strain was able to grow in the absence of vancomycin, and peptidoglycan precursor analysis under the same conditions indicated the synthesis of pentapeptide[D-Ala] as the main precursor, confirming the activity of Ddl2 in vivo. Expression of ddl and ddl2 in BM4174 was tested by reverse transcription-PCR: results suggested that both D-Ala:D-Ala ligases were expressed concomitantly. Our findings indicate that vancomycin-resistant E. gallinarum BM4174 is likely to express one D-Ala:D-Ser and two D-Ala:D-Ala ligase genes.
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Affiliation(s)
- Ole-Herman Ambúr
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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