1
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Putnik R, Zhou J, Irnov I, Garner E, Liu M, Bersch KL, Jacobs-Wagner C, Grimes CL. Synthesis of a Borrelia burgdorferi-Derived Muropeptide Standard Fragment Library. Molecules 2024; 29:3297. [PMID: 39064876 PMCID: PMC11279244 DOI: 10.3390/molecules29143297] [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: 05/29/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
The interplay between the human innate immune system and bacterial cell wall components is pivotal in understanding diseases such as Crohn's disease and Lyme arthritis. Lyme disease, caused by Borrelia burgdorferi, is the most prevalent tick-borne illness in the United States, with a substantial number of cases reported annually. While antibiotic treatments are generally effective, approximately 10% of Lyme disease cases develop persistent arthritis, suggesting a dysregulated host immune response. We have previously identified a link between the immunogenic B. burgdorferi peptidoglycan (PG) and Lyme arthritis and showed that this pathogen sheds significant amounts of PG fragments during growth. Here, we synthesize these PG fragments, including ornithine-containing monosaccharides and disaccharides, to mimic the unique composition of Borrelia cell walls, using reproducible and rigorous synthetic methods. This synthetic approach allows for the modular preparation of PG derivatives, providing a diverse library of well-defined fragments. These fragments will serve as valuable tools for investigating the role of PG-mediated innate immune response in Lyme disease and aid in the development of improved diagnostic methods and treatment strategies.
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Affiliation(s)
- Rachel Putnik
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Junhui Zhou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Irnov Irnov
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Elise Garner
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Min Liu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Klare L. Bersch
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Christine Jacobs-Wagner
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Catherine Leimkuhler Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
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2
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Hoyos P, Perona A, Juanes O, Rumbero Á, Hernáiz MJ. Synthesis of Glycodendrimers with Antiviral and Antibacterial Activity. Chemistry 2021; 27:7593-7624. [PMID: 33533096 DOI: 10.1002/chem.202005065] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Indexed: 12/27/2022]
Abstract
Glycodendrimers are an important class of synthetic macromolecules that can be used to mimic many structural and functional features of cell-surface glycoconjugates. Their carbohydrate moieties perform key important functions in bacterial and viral infections, often regulated by carbohydrate-protein interactions. Several studies have shown that the molecular structure, valency and spatial organisation of carbohydrate epitopes in glycoconjugates are key factors in the specificity and avidity of carbohydrate-protein interactions. Choosing the right glycodendrimers almost always helps to interfere with such interactions and blocks bacterial or viral adhesion and entry into host cells as an effective strategy to inhibit bacterial or viral infections. Herein, the state of the art in the design and synthesis of glycodendrimers employed for the development of anti-adhesion therapy against bacterial and viral infections is described.
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Affiliation(s)
- Pilar Hoyos
- Chemistry in Pharmaceutical Sciences Department, Complutense University of Madrid, Plaza Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Almudena Perona
- Chemistry in Pharmaceutical Sciences Department, Complutense University of Madrid, Plaza Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Olga Juanes
- Organic Chemistry Department, Autónoma University of Madrid, Francisco Tomás y Valiente 7, 28049, Madrid, Spain
| | - Ángel Rumbero
- Organic Chemistry Department, Autónoma University of Madrid, Francisco Tomás y Valiente 7, 28049, Madrid, Spain
| | - María J Hernáiz
- Chemistry in Pharmaceutical Sciences Department, Complutense University of Madrid, Plaza Ramón y Cajal s/n, 28040, Madrid, Spain
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3
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Zhang L, Zeng F, McKay CP, Navarro-González R, Sun HJ. Optimizing Chiral Selectivity in Practical Life-Detection Instruments. ASTROBIOLOGY 2021; 21:505-510. [PMID: 33885325 DOI: 10.1089/ast.2020.2381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Preferential uptake of either levorotatory (L) or dextrorotatory (D) enantiomer of a chiral molecule is a potential planetary life-detection method. On Earth, bacteria, as a rule, metabolize D-sugars and L-amino acids. Here, we use growth experiments to identify exceptions to the rule and their potential impact on the method's reliability. Our experiments involve six strains of Bacillus and collective uptake of the sugars glucose and arabinose, and the amino acids alanine, glutamic acid, leucine, cysteine, and serine-all of which are highly soluble. We find that selective uptake is not evident unless (1) each sugar is tested individually and (2) multiple amino acids are tested together in a mixture. Combining sugars should be avoided because, as we show in Bacillus bacteria, the same organisms may catabolize one sugar, glucose, in D-form and another sugar, arabinose, in L-form. Single amino acids should be avoided because bacteria can access certain proteinogenically incompatible enantiomers using specific racemases. Specifically, bacteria contain an alanine acid racemase and can catabolize D-alanine if no other D-amino acids are present. The proposed improvements would reliably separate nonselective chemical reactions from biological reactions and, if life is indicated, inform whether the selective patterns for amino acids and sugars are the same as on Earth.
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Affiliation(s)
- Ling Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Desert Plant Roots Ecology and Vegetation Restoration Laboratory, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, Xinjiang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fanjiang Zeng
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Desert Plant Roots Ecology and Vegetation Restoration Laboratory, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, Xinjiang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Christopher P McKay
- Space Science Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Rafael Navarro-González
- Laboratorio de Química de Plasmas y Estudios Planetarios, Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Henry J Sun
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas, Nevada, USA
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4
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Crump GM, Zhou J, Mashayekh S, Grimes CL. Revisiting peptidoglycan sensing: interactions with host immunity and beyond. Chem Commun (Camb) 2020; 56:13313-13322. [PMID: 33057506 PMCID: PMC7642115 DOI: 10.1039/d0cc02605k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The interaction between host immunity and bacterial cells plays a pivotal role in a variety of human diseases. The bacterial cell wall component peptidoglycan (PG) is known to stimulate an immune response, which makes PG a distinctive recognition element for unveiling these complicated molecular interactions. Pattern recognition receptor (PRR) proteins are among the critical components of this system that initially recognize molecular patterns associated with microorganisms such as bacteria and fungi. These molecular patterns are mostly embedded in the bacterial or fungal cell wall structure and can be released and presented to the immune system in various situations. Nonetheless, detailed knowledge of this recognition is limited due to the diversity among the PG polymer and its fragments; the subsequent responses by multiple hosts add more complexity. Here, we discuss how our understanding of the role and molecular mechanisms of the well-studied PRR, the NOD-like receptors (NLRs), in the human immune system has evolved in recent years. We highlight the instances of other classes of proteins with similar behavior in the recognition of PG that have been identified in other microorganisms such as yeasts. These proteins are particularly interesting because a network of cellular interactions exists between human host cells, bacteria and yeast as a part of the normal human flora. To support our understanding of these interactions, we provide insight into the chemist's toolbox of peptidoglycan probes that aid in the investigations of the behaviors of these proteins and other biological contexts relevant to the sensing and recognition of peptidoglycan. The importance of these interactions in human health for the development of biomarkers and biotherapy is highlighted.
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Affiliation(s)
- Geneva Maddison Crump
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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5
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Mashayekh S, Bersch KL, Ramsey J, Harmon T, Prather B, Genova LA, Grimes CL. Synthesis of Bacterial-Derived Peptidoglycan Cross-Linked Fragments. J Org Chem 2020; 85:16243-16253. [PMID: 33108204 DOI: 10.1021/acs.joc.0c01852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Peptidoglycan (PG) is the core structural motif of the bacterial cell wall. Fragments released from the PG serve as fundamental recognition elements for the immune system. The structure of the PG, however, encompasses a variety of chemical modifications among different bacterial species. Here, the applicability of organic synthetic methods to address this chemical diversity is explored, and the synthesis of cross-linked PG fragments, carrying biologically relevant amino acid modifications and peptide cross-linkages, is presented using solution and solid phase approaches.
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Affiliation(s)
- Siavash Mashayekh
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Klare L Bersch
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Jared Ramsey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Thomas Harmon
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Benjamin Prather
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Lauren A Genova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Catherine L Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.,Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, United States
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6
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DeMeester KE, Liang H, Zhou J, Wodzanowski KA, Prather BL, Santiago CC, Grimes CL. Metabolic Incorporation of N-Acetyl Muramic Acid Probes into Bacterial Peptidoglycan. ACTA ACUST UNITED AC 2020; 11:e74. [PMID: 31763799 DOI: 10.1002/cpch.74] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacterial cells utilize small carbohydrate building blocks to construct peptidoglycan (PG), a highly conserved mesh-like polymer that serves as a protective coat for the cell. PG production has long been a target for antibiotics, and its breakdown is a source for human immune recognition. A key component of bacterial PG, N-acetyl muramic acid (NAM), is a vital element in many synthetically derived immunostimulatory compounds. However, the exact molecular details of these structures and how they are generated remain unknown due to a lack of chemical probes surrounding the NAM core. A robust synthetic strategy to generate bioorthogonally tagged NAM carbohydrate units is implemented. These molecules serve as precursors for PG biosynthesis and recycling. Escherichia coli cells are metabolically engineered to incorporate the bioorthogonal NAM probes into their PG network. The probes are subsequently modified using copper-catalyzed azide-alkyne cycloaddition to install fluorophores directly into the bacterial PG, as confirmed by super-resolution microscopy and high-resolution mass spectrometry. Here, synthetic notes for key elements of this process to generate the sugar probes as well as streamlined user-friendly metabolic labeling strategies for both microbiology and immunological applications are described. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Synthesis of peracetylated 2-azido glucosamine Basic Protocol 2: Synthesis of 2-azido and 2-alkyne NAM Basic Protocol 3: Synthesis of 3-azido NAM methyl ester Basic Protocol 4: Incorporation of NAM probes into bacterial peptidoglycan Basic Protocol 5: Confirmation of bacterial cell wall remodeling by mass spectrometry.
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Affiliation(s)
- Kristen E DeMeester
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware
| | - Hai Liang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware.,Cutaneous Microbiome and Inflammation Section, Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland
| | - Junhui Zhou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware
| | | | - Benjamin L Prather
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware
| | - Cintia C Santiago
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware.,Center for the Study of Organic Compounds, CEDECOR-UNLP-CIC, Department of Chemistry, Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
| | - Catherine L Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware.,Department of Biological Sciences, University of Delaware, Newark, Delaware
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7
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Wodzanowski KA, Cassel SE, Grimes CL, Kloxin AM. Tools for probing host-bacteria interactions in the gut microenvironment: From molecular to cellular levels. Bioorg Med Chem Lett 2020; 30:127116. [PMID: 32223923 PMCID: PMC7476074 DOI: 10.1016/j.bmcl.2020.127116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/28/2020] [Accepted: 03/15/2020] [Indexed: 12/31/2022]
Abstract
Healthy function of the gut microenvironment is dependent on complex interactions between the bacteria of the microbiome, epithelial and immune (host) cells, and the surrounding tissue. Misregulation of these interactions is implicated in disease. A range of tools have been developed to study these interactions, from mechanistic studies to therapeutic evaluation. In this Digest, we highlight select tools at the cellular and molecular level for probing specific cell-microenvironment interactions. Approaches are overviewed for controlling and probing cell-cell interactions, from transwell and microfluidic devices to engineered bacterial peptidoglycan fragments, and cell-matrix interactions, from three-dimensional scaffolds to chemical handles for in situ modifications.
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Affiliation(s)
| | - Samantha E Cassel
- Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States
| | - Catherine L Grimes
- Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Biological Sciences, University of Delaware, Newark, DE 19716, United States.
| | - April M Kloxin
- Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States; Materials Science and Engineering, University of Delaware, Newark, DE 19716, United States.
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8
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García‐Oliva C, Cabanillas AH, Perona A, Hoyos P, Rumbero Á, Hernáiz MJ. Efficient Synthesis of Muramic and Glucuronic Acid Glycodendrimers as Dengue Virus Antagonists. Chemistry 2020; 26:1588-1596. [DOI: 10.1002/chem.201903788] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/17/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Cecilia García‐Oliva
- Departamento de Química en Ciencias FarmacéuticasFacultad de FarmaciaUniversidad Complutense de Madrid 28040 Madrid Spain
| | | | - Almudena Perona
- Departamento de Química en Ciencias FarmacéuticasFacultad de FarmaciaUniversidad Complutense de Madrid 28040 Madrid Spain
| | - Pilar Hoyos
- Departamento de Química en Ciencias FarmacéuticasFacultad de FarmaciaUniversidad Complutense de Madrid 28040 Madrid Spain
| | - Ángel Rumbero
- Departamento de Química OrgánicaUniversidad Autónoma de Madrid 28049 Madrid Spain
| | - María J. Hernáiz
- Departamento de Química en Ciencias FarmacéuticasFacultad de FarmaciaUniversidad Complutense de Madrid 28040 Madrid Spain
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9
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Modulation of the NOD-like receptors NOD1 and NOD2: A chemist's perspective. Bioorg Med Chem Lett 2019; 29:1153-1161. [PMID: 30890292 DOI: 10.1016/j.bmcl.2019.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/13/2022]
Abstract
The innate immune system is the body's first defense against invading microorganisms, relying on the recognition of bacterial-derived small molecules by host protein receptors. This recognition event and downstream immune response rely heavily on the specific chemical features of both the innate immune receptors and their bacterial derived ligands. This review presents a chemist's perspective on some of the most crucial and complex components of two receptors (NOD1 and NOD2): starting from the structural and chemical characteristics of bacterial-derived small molecules, to the specific proposed models of molecular recognition of these molecules by immune receptors, to the subsequent post-translational modifications that ultimately dictate downstream immune signaling. Recent advances in the field are discussed, as well as the potential for the development of targeted therapeutics.
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10
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Burch JM, Mashayekh S, Wykoff DD, Grimes CL. Bacterial Derived Carbohydrates Bind Cyr1 and Trigger Hyphal Growth in Candida albicans. ACS Infect Dis 2018; 4:53-58. [PMID: 29040806 PMCID: PMC5800403 DOI: 10.1021/acsinfecdis.7b00154] [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] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The dimorphic yeast Candida albicans is the most common pathogenic fungus found in humans. While this species is normally commensal, a morphological switch from budding yeast to filamentous hyphae allows the fungi to invade epithelial cells and cause infections. The phenotypic change is controlled by the adenylyl cyclase, Cyr1. Interestingly, this protein contains a leucine-rich repeat (LRR) domain, which is commonly found in innate immune receptors from plants and animals. A functional and pure LRR domain was obtained in high yields from E. coli expression. Utilizing a surface plasmon resonance assay, the LRR was found to bind diverse bacterial derived carbohydrates with high affinity. This domain is capable of binding fragments of peptidoglycan, a carbohydrate polymer component of the bacterial cell wall, as well as anthracyclines produced by Streptomyces, leading to hyphae formation. These findings add another dimension to the human microbiome, taking into account yeast-bacteria interactions that occur in the host.
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Affiliation(s)
- Jason M. Burch
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Siavash Mashayekh
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Dennis D. Wykoff
- Department of Biology, Villanova University, Villanova, Pennsylvania 19085, United States
| | - Catherine L. Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, United States
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11
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Awad R, Gans P, Reiser JB. Structural insights into the substrate recognition and reaction specificity of the PLP-dependent fold-type I isoleucine 2-epimerase from Lactobacillus buchneri. Biochimie 2017; 137:165-173. [DOI: 10.1016/j.biochi.2017.03.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 02/02/2017] [Accepted: 03/21/2017] [Indexed: 02/02/2023]
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12
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Liang H, DeMeester KE, Hou CW, Parent MA, Caplan JL, Grimes CL. Metabolic labelling of the carbohydrate core in bacterial peptidoglycan and its applications. Nat Commun 2017; 8:15015. [PMID: 28425464 PMCID: PMC5411481 DOI: 10.1038/ncomms15015] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 02/20/2017] [Indexed: 02/07/2023] Open
Abstract
Bacterial cells are surrounded by a polymer known as peptidoglycan (PG), which protects the cell from changes in osmotic pressure and small molecule insults. A component of this material, N-acetyl-muramic acid (NAM), serves as a core structural element for innate immune recognition of PG fragments. We report the synthesis of modifiable NAM carbohydrate derivatives and the installation of these building blocks into the backbone of Gram-positive and Gram-negative bacterial PG utilizing metabolic cell wall recycling and biosynthetic machineries. Whole cells are labelled via click chemistry and visualized using super-resolution microscopy, revealing higher resolution PG structural details and allowing the cell wall biosynthesis, as well as its destruction in immune cells, to be tracked. This study will assist in the future identification of mechanisms that the immune system uses to recognize bacteria, glean information about fundamental cell wall architecture and aid in the design of novel antibiotics. N-acetyl-muramic acid (NAM) is a core component of the bacterial peptidoglycan (PG) cell wall, and is recognised by the innate immune system. Here the authors engineer Gram-negative and Gram-positive bacteria to incorporate a modified NAM into the backbone of PG, which can be labelled with click chemistry for imaging and tracking.
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Affiliation(s)
- Hai Liang
- Department of Chemistry and Biochemistry, University of Delaware, 134 Brown Lab, Newark, Delaware 19716, USA
| | - Kristen E DeMeester
- Department of Chemistry and Biochemistry, University of Delaware, 134 Brown Lab, Newark, Delaware 19716, USA
| | - Ching-Wen Hou
- Department of Chemistry and Biochemistry, University of Delaware, 134 Brown Lab, Newark, Delaware 19716, USA
| | - Michelle A Parent
- Department of Medical Laboratory Sciences, University of Delaware, Newark, Delaware 19716, USA.,Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, USA
| | - Jeffrey L Caplan
- Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, USA.,Bioimaging Center, Delaware Biotechnology Institute, Newark, Delaware 19716, USA
| | - Catherine L Grimes
- Department of Chemistry and Biochemistry, University of Delaware, 134 Brown Lab, Newark, Delaware 19716, USA.,Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, USA
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13
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Racemization in reverse: evidence that D-amino acid toxicity on Earth is controlled by bacteria with racemases. PLoS One 2014; 9:e92101. [PMID: 24647559 PMCID: PMC3960212 DOI: 10.1371/journal.pone.0092101] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 02/17/2014] [Indexed: 11/19/2022] Open
Abstract
D-amino acids are toxic for life on Earth. Yet, they form constantly due to geochemical racemization and bacterial growth (the cell walls of which contain D-amino acids), raising the fundamental question of how they ultimately are recycled. This study provides evidence that bacteria use D-amino acids as a source of nitrogen by running enzymatic racemization in reverse. Consequently, when soils are inundated with racemic amino acids, resident bacteria consume D- as well as L-enantiomers, either simultaneously or sequentially depending on the level of their racemase activity. Bacteria thus protect life on Earth by keeping environments D-amino acid free.
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14
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Caillet S, Ursachi L, Shareck F, Lacroix M. Effect of gamma radiation and oregano essential oil on murein and ATP concentration of Staphylococcus aureus. J Food Sci 2010; 74:M499-508. [PMID: 20492121 DOI: 10.1111/j.1750-3841.2009.01368.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The study was carried out to evaluate the effects of gamma-irradiation alone or in combination with oregano essential oil on murein composition of Staphylococcus aureus and on the intracellular and extracellular concentration of ATP. The bacterial strain was treated with 3 irradiation doses: 1.2 kGy to induce cell damage, 2.9 kGy to obtain a viable but nonculturable state, and 3.5 kGy to cause cell death. Oregano essential oil was used at 0.010% and 0.013% (w/v), which is the minimum inhibitory concentration (MIC). All treatments had a significant effect (P < or = 0.05) on the murein composition, although some muropeptides did not seem to be affected by the treatment. Each treatment influenced differently the relative percentage and number of muropeptides. There was a significant (P < or = 0.05) correlation between the reduction of intracellular ATP and increase in extracellular ATP following treatment of the cells with oregano oil. The reduction of intracellular ATP was even more important when essential oil was combined with irradiation. Also, irradiation alone of S. aureus induced a significant decrease (P < or = 0.05) of the internal ATP and a significant increase (P < or = 0.05) of the external ATP. However, no significant difference (P > 0.05) was observed in ATP concentrations between different radiation doses. Transmission electron microscopic observation revealed that oregano oil and irradiation have an effect on cell wall structure.
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Affiliation(s)
- Stéphane Caillet
- Canadian Irradiation Center and Research Laboratories in Sciences Applied to Food, Canada
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15
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Sun HJ, Saccomanno V, Hedlund B, McKay CP. Stereo-specific glucose consumption may be used to distinguish between chemical and biological reactivity on Mars: a preliminary test on Earth. ASTROBIOLOGY 2009; 9:443-446. [PMID: 19566424 DOI: 10.1089/ast.2008.0315] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Two alternative hypotheses explain the degradation of organics in the Viking Labeled Release experiment on Mars. Either martian soil contains live indigenous microorganisms or it is sterile but chemically reactive. These two possibilities could be distinguished by the use of pure preparations of glucose isomers. In the laboratory, selected eukaryotes, bacteria, and archaea consumed only D-glucose, not L-glucose, while permanganate oxidized both isomers. On Mars, selective consumption of either D- or L-glucose would constitute evidence for biological activity.
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Affiliation(s)
- Henry J Sun
- Division of Earth and Ecosystem Sciences, Desert Research Institute , Las Vegas, Nevada 89119, USA.
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16
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Caillet S, Lacroix M. Effect of gamma radiation and oregano essential oil on murein and ATP concentration of Listeria monocytogenes. J Food Prot 2006; 69:2961-9. [PMID: 17186665 DOI: 10.4315/0362-028x-69.12.2961] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The effects of gamma radiation and of oregano essential oil alone or in combination with radiation on murein composition of Listeria monocytogenes and on the intracellular and extracellular concentration of ATP were evaluated. The bacterial strain was treated with two radiation doses, 1.2 kGy to induce cell damage and 3.5 kGy to cause cell death. Oregano essential oil was used at 0.020 and 0.025% (wt/vol), which is the MIC. All treatments had a significant effect (P < or = 0.05) on the murein composition, although some muropeptides did not seem to be affected by the treatment. Each treatment influenced differently the relative percentage and number of muropeptides. There was a significant correlation (P < or = 0.05) between the reduction of intracellular ATP and increase in extracellular ATP, following treatment of the cells with oregano oil. The reduction of intracellular ATP was even more important when essential oil was combined with irradiation, but irradiation of L. monocytogenes alone induced a significant decrease (P < or = 0.05) of the internal ATP without affecting the external ATP. Transmission electron microscopic observation revealed that oregano oil and irradiation have an effect on cell wall structure.
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Affiliation(s)
- Stéphane Caillet
- Canadian Irradiation Center (CIC), 531 Boulevard des Prairies, Laval, Québec, Canada H7V 1B7
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Nau R, Eiffert H. Modulation of release of proinflammatory bacterial compounds by antibacterials: potential impact on course of inflammation and outcome in sepsis and meningitis. Clin Microbiol Rev 2002; 15:95-110. [PMID: 11781269 PMCID: PMC118062 DOI: 10.1128/cmr.15.1.95-110.2002] [Citation(s) in RCA: 173] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several bacterial components (endotoxin, teichoic and lipoteichoic acids, peptidoglycan, DNA, and others) can induce or enhance inflammation and may be directly toxic for eukaryotic cells. Bactericidal antibiotics which inhibit bacterial protein synthesis release smaller quantities of proinflammatory/toxic bacterial compounds than B-lactams and other cell wall-active drugs. Among the B-lactams, compounds binding to penicillin-binding protein 2 (PBP-2) release smaller amounts of bacterial substances than antibacterials inhibiting PBP-3. Generally, high antibiotic concentrations (more than 10 times the MIC) induce the release of fewer bacterial proinflammatory/toxic compounds than concentrations close to the MIC. In several in vitro and in vivo systems, bacteria treated with protein synthesis inhibitors or B-lactams inhibiting PBP-2 induce less inflammation than bacteria treated with PBP-3-active B-lactams. In mouse models of Escherichia coli peritonitis sepsis and of Streptococcus pneumoniae meningitis, lower release of proinflammatory bacterial compounds was associated with reduced mortality. In conclusion, sufficient evidence for the validity of the concept of modulating the release of proinflammatory bacterial compounds by antibacterials has been accumulated in vitro and in animal experiments to justify clinical trials in sepsis and meningitis. A properly conducted study addressing the potential benefit of bacterial protein synthesis inhibitors versus B-lactam antibiotics will require both strict selection and inclusion of a large number of patients. The benefit of this approach should be greatest in patients with a high bacterial load.
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Affiliation(s)
- Roland Nau
- Department of Neurology, University of Goettingen, Goettingen, Germany.
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McCarthy MD, Hedges JI, Benner R. Major bacterial contribution to marine dissolved organic nitrogen. Science 1998; 281:231-4. [PMID: 9657711 DOI: 10.1126/science.281.5374.231] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Next to N2 gas, the largest pool of reduced nitrogen in the ocean resides in the enormous reservoir of dissolved organic nitrogen (DON). The chemical identity of most of this material, and the mechanisms by which it is cycled, remain fundamental questions in contemporary oceanography. Amino acid enantiomeric ratios in the high molecular weight fraction of DON from surface and deep water in three ocean basins show substantial enrichment in D enantiomers of four amino acids. The magnitude and pattern of these D/L enrichments indicate that peptidoglycan remnants derived from bacterial cell walls constitute a major source of DON throughout the sea. These observations suggest that structural properties of specific bacterial biopolymers, and the mechanisms for their accumulation, are among the central controls on long-term cycling of dissolved organic nitrogen in the sea.
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Affiliation(s)
- MD McCarthy
- M. D. McCarthy and J. I. Hedges, University of Washington, School of Oceanography, Box 357940, Seattle, WA 98195, USA. R. Benner, University of Texas, Marine Science Institute, Port Aransas, TX 78373, USA
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McCarthy M, Pratum T, Hedges J, Benner R. Chemical composition of dissolved organic nitrogen in the ocean. Nature 1997. [DOI: 10.1038/36535] [Citation(s) in RCA: 211] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Dean CR, Ward OP. Nature of Escherichia coli cell lysis by culture supernatants of Bacillus species. Appl Environ Microbiol 1991; 57:1893-8. [PMID: 1892379 PMCID: PMC183496 DOI: 10.1128/aem.57.7.1893-1898.1991] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Escherichia coli cells were found to be sensitive to lysis by the supernatants of a variety of protease-positive Bacillus species when treated at 45 degrees C but not when treated at 37 degrees C. Different E. coli strains manifested different lysis sensitivities when treated at 45 degrees C. When the lysis rates of E. coli cells at various stages of growth were investigated, post-exponential-phase cells were shown to be most sensitive to lysis. The lysis rate was inversely related to cell viability, and susceptibility appeared to be at least partly due to lysis of dead E. coli cells. A close relation was observed between levels of lysis activity and proteolytic activity. A Bacillus subtilis mutant lacking alkaline and neutral protease activity failed to lyse E. coli cells. It was concluded that Bacillus proteases played a major role in the observed E. coli lysis.
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Affiliation(s)
- C R Dean
- Department of Biology, University of Waterloo, Ontario, Canada
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Ruby EG, Rittenberg SC. Attachment of diaminopimelic acid to bdelloplast peptidoglycan during intraperiplasmic growth of Bdellovibrio bacteriovorus 109J. J Bacteriol 1984; 158:597-602. [PMID: 6202674 PMCID: PMC215470 DOI: 10.1128/jb.158.2.597-602.1984] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
An early event in the predatory lifestyle of Bdellovibrio bacteriovorus 109J is the attachment of diaminopimelic acid (DAP) to the peptidoglycan of its prey. Attachment occurs over the first 60 min of the growth cycle and is mediated by an extracellular activity(s) produced by the bdellovibrio. Some 40,000 DAP residues are incorporated into the Escherichia coli bdelloplast wall, amounting to ca. 2 to 3% of the total initial DAP content of its prey cells. Incorporation of DAP occurs when E. coli, Pseudomonas putida, or Spirillum serpens are the prey organisms. The structurally similar compounds lysine, ornithine, citrulline, and 2,4-diaminobutyric acid are not attached. The attachment process is not affected by heat-killing the prey nor by the addition of inhibitors of either energy generation (cyanide, azide, or arsenate), protein or RNA synthesis (chloramphenicol and rifamycin), or de novo synthesis of cell wall (penicillin or vancomycin). Approximately one-third of the incorporated DAP is exchangeable with exogenously added unlabeled DAP, whereas the remaining incorporated DPA is solubilized only during the lysis of the bdelloplast wall. Examination of DAP incorporation at low prey cell densities suggests that bdellovibrios closely couple the incorporation to an independent, enzymatic solubilization of DAP by a peptidase. The data indicate that DAP incorporation is a novel process, representing the second example of the ability of the bdellovibrio to biosynthetically modify the wall of its prey.
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Heymer B, Spanel R, Haferkamp O. Experimental models of arthritis. CURRENT TOPICS IN PATHOLOGY. ERGEBNISSE DER PATHOLOGIE 1982; 71:123-52. [PMID: 7116947 DOI: 10.1007/978-3-642-68382-4_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Humphries M, Thompson JS. Crosslinkage analysis of bacterial cell walls using dual-isotope labeling of N-terminal groups with fluorodinitrobenzene: a method of general application for microdetermination of free amino groups in peptides. Anal Biochem 1981; 113:398-406. [PMID: 7025702 DOI: 10.1016/0003-2697(81)90094-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Beveridge TJ. Ultrastructure, chemistry, and function of the bacterial wall. INTERNATIONAL REVIEW OF CYTOLOGY 1981; 72:229-317. [PMID: 6166584 DOI: 10.1016/s0074-7696(08)61198-5] [Citation(s) in RCA: 327] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Lapidot A, Irving CS. Comparative in vivo nitrogen-15 nuclear magnetic resonance study of the cell wall components of five Gram-positive bacteria. Biochemistry 1979; 18:704-14. [PMID: 105756 DOI: 10.1021/bi00571a024] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The proton-decoupled 9.12 MHz 15N NMR spectra of 15N-labeled Bacillus subtilis, Bacillus licheniformis, Staphylococcus auresu, Streptococcus faecalis, and Micrococcus lysodeikticus intact cells, isolated cells walls, and cell wall digests have been examined. The general characteristics of Gram-positive bacteria 15N NMR spectra and described and spectral assignments are provided, which allow in vivo 15N NMR to be applied to a wide range of problems in bacterial cell wall research. The qualitative similarity of the intact cell and cell wall spectra found in each bacteria allowed the 15 N resonances observed in the proton broad-band noise-decoupled 15N NMR spectra of intact cells to be assigned to cell wall components. Each of the five Gram-positive bacteria displayed a unique set of cell wall 15N resonances, which reflected variations in the primary structure of peptidoglycans and the amounts of teichoic acid and teichuronic acid in the cell wall, as well as the dynamic properties of the cell wall polymers. Spectral assignments of cell wall 15 N resonances assigned to teichoic D-Ala residues, teichuronic acid and acetamido groups, and peptidoglycan acetamido, amide, peptide, and free amino groups have been made on the basis of specific isotopic labeling and dilution experiments, comparison of chemical shifts to literature values, determination of pH titration shifts, cell wall fractionation experiments, and comparative analysis of the cell wall lysozyme digest spectra in terms of the known primary sequences of peptide chains. All the peptidoglycan 15N peptide resonances observed in the intact cells and isolated cell walls could be accounted for by residues in the bridge or crossbar regions of the peptide chains, which indicated that only the cross-linking groups had a high degree of motional freedom. Thermal- and pH-induced conformational changes around the cross-linking D-Ala residues were detected in the B. licheniformis cell wall lysozyme digest products. Comparison of the proton broad-band noise-decoupled and gated decoupled intact cell and cell wall 15N spectra indicated that broad-band proton decoupling resulted in nulling of cytoplasmic resonances and enhancement of the cell wall resonances by the 15N [1H5 nuclear Overhauser effect.
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Virudachalam R, Rao VSR. Theoretical studies on peptidoglycans. I. Effect ofL-alanyl,D-butyl, orD-valyl residuces at the positions 4 or 5 of the pentapeptide moiety of peptidoglycan on the cross-linking reaction. Biopolymers 1978. [DOI: 10.1002/bip.1978.360170917] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Oldmixon EH, Dezélée P, Ziskin MC, Shockman GD. Monomer addition as a mechanism of forming peptide cross-links in the cell-wall peptidoglycan of Streptococcus faecalis ATCC 9790. EUROPEAN JOURNAL OF BIOCHEMISTRY 1976; 68:271-80. [PMID: 823022 DOI: 10.1111/j.1432-1033.1976.tb10786.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The relative amounts of radioactively labelled disaccharide-peptide monomers and peptide-cross-linked dimers and trimers found in the peptidoglycan of Streptococcus faecalis ATCC 9790 were compared to the relative amounts to be expected from two different polymerization mechanisms (random condensation and monomer addition). Data from continuously-labeled, exponentially-growing cells are consistent with a monomer addition cross-linking process, not with a random condensation cross-linking mechanism. This conclusion was supported by data obtained from analyses of cells labeled during valine starvation (and wall thickening), recovery from valine starvation, and pulse and pulse-chase labeling of walls from exponentially-growing cultures.
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Abstract
The steady-state concentration of cell wall turnover products in the medium of Bacillus subtilis 168 growing exponentially on a casein hydrolysate-supplemented medium is equivalent to an overall rate of turnover of less than 10% per generation. After transfer of a steady-labeled culture to nonradioactive medium, the rate of release of labeled turnover products increased exponentially for up to two generations. The rate of turnover finally attained by this culture reached an apparently first-order rate of about 50% per generation. The addition of soluble autolytic activity to growing cultures of a mutant possessing a reduced rate of wall turnover resulted in a marked stimulation in the rate of solubilization of the cell wall fraction. The increased rate of solubilization produced was proportional to the concentration of added enzyme and remained constant until less than 20% of the wall originally present was left. Autolytic activity added under these conditions was bound entirely to wall at least one generation old. The results are interpreted in terms of a model for cell wall growth in which wall two or more generations old covers a total surface area at least four times larger than that occupied at the time of synthesis, forming a shallow outer layer (overlying newer wall) from which all turnover takes place. The model is discussed in relation to previous attempts to determine the pattern of surface expansion in bacilli.
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Giesbrecht P, Wecke J, Reinicke B. On the morphogenesis of the cell wall of staphylococci. INTERNATIONAL REVIEW OF CYTOLOGY 1976; 44:225-318. [PMID: 770370 DOI: 10.1016/s0074-7696(08)61651-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Guymon LF, Sparling PF. Altered crystal violet permeability and lytic behavior in antibiotic-resistant and -sensitive mutants of Neisseria gonorrhoeae. J Bacteriol 1975; 124:757-63. [PMID: 810481 PMCID: PMC235965 DOI: 10.1128/jb.124.2.757-763.1975] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Wild-type, antibiotic-resistant and hypersensitive isogenic strains of Neisseria gonorrhoeae were studied for uptake of crystal violet, rates of autolysis, and response to lysozyme. Total uptake of crystal violet was similar in all strains at 0 C but varied significantly at 37 C. Mutation at the nonspecific resistance locus ery resulted in relative impermeability to crystal violet at 37 C, as compared to wild type. The penetration barrier to crystal violet at 37 C was overcome by addition of 5 mM ethylenediaminetetraacetic acid. Mutation at ery also resulted in reduced rates of autolysis and reduced sensitivity to high concentrations of lysozyme under conditions of divalent cation (Mg2+) depletion. In contrast, mutation at the nonspecific drug hypersensitivity locus env resulted in increased uptake of crystal violet at 37 C, due to increased binding of dye to crude envelope as well as increased penetration into cytoplasm. The env mutants were also more rapidly autolytic and more sensitive to lysozyme than wild type in the absence of Mg2+. These results suggest that the cell envelopes of ery mutants are more stable and less permeable and those of env mutants are less stable and more permeable than wild-type strains.
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Braun V. Covalent lipoprotein from the outer membrane of Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA 1975; 415:335-77. [PMID: 52377 DOI: 10.1016/0304-4157(75)90013-1] [Citation(s) in RCA: 481] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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