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Sharma P, Vaiwala R, Gopinath AK, Chockalingam R, Ayappa KG. Structure of the Bacterial Cell Envelope and Interactions with Antimicrobials: Insights from Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:7791-7811. [PMID: 38451026 DOI: 10.1021/acs.langmuir.3c03474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Bacteria have evolved over 3 billion years, shaping our intrinsic and symbiotic coexistence with these single-celled organisms. With rising populations of drug-resistant strains, the search for novel antimicrobials is an ongoing area of research. Advances in high-performance computing platforms have led to a variety of molecular dynamics simulation strategies to study the interactions of antimicrobial molecules with different compartments of the bacterial cell envelope of both Gram-positive and Gram-negative species. In this review, we begin with a detailed description of the structural aspects of the bacterial cell envelope. Simulations concerned with the transport and associated free energy of small molecules and ions through the outer membrane, peptidoglycan, inner membrane and outer membrane porins are discussed. Since surfactants are widely used as antimicrobials, a section is devoted to the interactions of surfactants with the cell wall and inner membranes. The review ends with a discussion on antimicrobial peptides and the insights gained from the molecular simulations on the free energy of translocation. Challenges involved in developing accurate molecular models and coarse-grained strategies that provide a trade-off between atomic details with a gain in sampling time are highlighted. The need for efficient sampling strategies to obtain accurate free energies of translocation is also discussed. Molecular dynamics simulations have evolved as a powerful tool that can potentially be used to design and develop novel antimicrobials and strategies to effectively treat bacterial infections.
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Affiliation(s)
- Pradyumn Sharma
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| | - Rakesh Vaiwala
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| | - Amar Krishna Gopinath
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| | - Rajalakshmi Chockalingam
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| | - K Ganapathy Ayappa
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
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2
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Nanninga N. Molecular Cytology of 'Little Animals': Personal Recollections of Escherichia coli (and Bacillus subtilis). Life (Basel) 2023; 13:1782. [PMID: 37629639 PMCID: PMC10455606 DOI: 10.3390/life13081782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/09/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
This article relates personal recollections and starts with the origin of electron microscopy in the sixties of the previous century at the University of Amsterdam. Novel fixation and embedding techniques marked the discovery of the internal bacterial structures not visible by light microscopy. A special status became reserved for the freeze-fracture technique. By freeze-fracturing chemically fixed cells, it proved possible to examine the morphological effects of fixation. From there on, the focus switched from bacterial structure as such to their cell cycle. This invoked bacterial physiology and steady-state growth combined with electron microscopy. Electron-microscopic autoradiography with pulses of [3H] Dap revealed that segregation of replicating DNA cannot proceed according to a model of zonal growth (with envelope-attached DNA). This stimulated us to further investigate the sacculus, the peptidoglycan macromolecule. In particular, we focused on the involvement of penicillin-binding proteins such as PBP2 and PBP3, and their role in division. Adding aztreonam (an inhibitor of PBP3) blocked ongoing divisions but not the initiation of new ones. A PBP3-independent peptidoglycan synthesis (PIPS) appeared to precede a PBP3-dependent step. The possible chemical nature of PIPS is discussed.
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Affiliation(s)
- Nanne Nanninga
- Molecular Cytology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, 1098 XH Amsterdam, The Netherlands
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3
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Zaidi S, Ali K, Chawla YM, Khan AU. mltG gene deletion mitigated virulence potential of Streptococcus mutans: An in-vitro, ex-situ and in-vivo study. AMB Express 2023; 13:19. [PMID: 36806997 PMCID: PMC9941400 DOI: 10.1186/s13568-023-01526-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/22/2023] Open
Abstract
Bacterial cells are surrounded by a peptidoglycan (PG) cell wall, which is essential for cell integrity and intrinsic biogenesis pathways; hence, the cell wall is a potential target for several antibiotics. Among several lytic transglycosylases (LTs), the mltG gene plays a crucial role in the synthesis of peripheral PG. It localises the re-modelled PGs for septum formation and cleavage across the bacterial cell wall during daughter cells separation. However, the role of mltG gene in bacterial virulence, particularly in Gram-positive bacteria during dentine biofilm and caries development, has remained unexplored. Hence, we exploited Gram-positive Streptococcus mutans cells for the very first time to construct a mltG knock-out bacterial strain, e.g., ΔmltG S. mutans. Systematic comparative investigations revealed that doubling time (Td), survival, enzymatic efficiencies, pH tolerance, bio-synthesise of lipid, proteins and DNA, biofilm formation and dentine lesions were significantly (p < 0.001) compromised in case of ΔmltG S. mutans than wild type strain. The qRT-PCR based gene expression profiling revealed that transcriptional expression of critically important genes involved in biofilm, metabolism, and stress response were dysregulated in the mutant. Besides, an incredible reduction in dentine caries development was found in the molar teeth of Wistar rats and also in human extracted teeth. Concisely, these trends obtained evidently advocated the fact that the deletion of mltG gene can be a potential target to impair the S. mutans virulence through severe growth retardation, thereby reducing the virulence potential of S. mutans.
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Affiliation(s)
- Sahar Zaidi
- grid.411340.30000 0004 1937 0765Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary, Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002 UP India
| | - Khursheed Ali
- grid.411340.30000 0004 1937 0765Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary, Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002 UP India
| | - Yadya M. Chawla
- grid.425195.e0000 0004 0498 7682ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Asad U. Khan
- grid.411340.30000 0004 1937 0765Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary, Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002 UP India
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Differentiating interactions of antimicrobials with Gram-negative and Gram-positive bacterial cell walls using molecular dynamics simulations. Biointerphases 2022; 17:061008. [PMID: 36511523 DOI: 10.1116/6.0002087] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Developing molecular models to capture the complex physicochemical architecture of the bacterial cell wall and to study the interaction with antibacterial molecules is an important aspect of assessing and developing novel antimicrobial molecules. We carried out molecular dynamics simulations using an atomistic model of peptidoglycan to represent the architecture for Gram-positive S. aureus. The model is developed to capture various structural features of the Staphylococcal cell wall, such as the peptide orientation, area per disaccharide, glycan length distribution, cross-linking, and pore size. A comparison of the cell wall density and electrostatic potentials is made with a previously developed cell wall model of Gram-negative bacteria, E. coli, and properties for both single and multilayered structures of the Staphylococcal cell wall are studied. We investigated the interactions of the antimicrobial peptide melittin with peptidoglycan structures. The depth of melittin binding to peptidoglycan is more pronounced in E. coli than in S. aureus, and consequently, melittin has greater contacts with glycan units of E. coli. Contacts of melittin with the amino acids of peptidoglycan are comparable across both the strains, and the D-Ala residues, which are sites for transpeptidation, show enhanced interactions with melittin. A low energetic barrier is observed for translocation of a naturally occurring antimicrobial thymol with the four-layered peptidoglycan model. The molecular model developed for Gram-positive peptidoglycan allows us to compare and contrast the cell wall penetrating properties with Gram-negative strains and assess for the first time binding and translocation of antimicrobial molecules for Gram-positive cell walls.
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Gabanyi I, Lepousez G, Wheeler R, Vieites-Prado A, Nissant A, Wagner S, Moigneu C, Dulauroy S, Hicham S, Polomack B, Verny F, Rosenstiel P, Renier N, Boneca IG, Eberl G, Lledo PM, Chevalier G. Bacterial sensing via neuronal Nod2 regulates appetite and body temperature. Science 2022; 376:eabj3986. [PMID: 35420957 DOI: 10.1126/science.abj3986] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Gut bacteria influence brain functions and metabolism. We investigated whether this influence can be mediated by direct sensing of bacterial cell wall components by brain neurons. In mice, we found that bacterial peptidoglycan plays a major role in mediating gut-brain communication via the Nod2 receptor. Peptidoglycan-derived muropeptides reach the brain and alter the activity of a subset of brain neurons that express Nod2. Activation of Nod2 in hypothalamic inhibitory neurons is essential for proper appetite and body temperature control, primarily in females. This study identifies a microbe-sensing mechanism that regulates feeding behavior and host metabolism.
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Affiliation(s)
- Ilana Gabanyi
- Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Perception and Memory Unit, F-75015 Paris, France
- Institut Pasteur, Université Paris Cité, INSERM U1224, Microenvironment and Immunity Unit, F-75015 Paris, France
| | - Gabriel Lepousez
- Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Perception and Memory Unit, F-75015 Paris, France
| | - Richard Wheeler
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Biology and Genetics of the Bacterial Cell Wall Unit, F-75015 Paris, France
| | - Alba Vieites-Prado
- Sorbonne Université, Paris Brain Institute-ICM, INSERM U1127, CNRS UMR7225, AP-HP, Hôpital de la Pitié Salpêtrière, F-75013 Paris, France
| | - Antoine Nissant
- Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Perception and Memory Unit, F-75015 Paris, France
| | - Sébastien Wagner
- Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Perception and Memory Unit, F-75015 Paris, France
| | - Carine Moigneu
- Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Perception and Memory Unit, F-75015 Paris, France
| | - Sophie Dulauroy
- Institut Pasteur, Université Paris Cité, INSERM U1224, Microenvironment and Immunity Unit, F-75015 Paris, France
| | - Samia Hicham
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Biology and Genetics of the Bacterial Cell Wall Unit, F-75015 Paris, France
| | - Bernadette Polomack
- Institut Pasteur, Université Paris Cité, INSERM U1224, Microenvironment and Immunity Unit, F-75015 Paris, France
| | - Florine Verny
- Sorbonne Université, Paris Brain Institute-ICM, INSERM U1127, CNRS UMR7225, AP-HP, Hôpital de la Pitié Salpêtrière, F-75013 Paris, France
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Nicolas Renier
- Sorbonne Université, Paris Brain Institute-ICM, INSERM U1127, CNRS UMR7225, AP-HP, Hôpital de la Pitié Salpêtrière, F-75013 Paris, France
| | - Ivo Gomperts Boneca
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Biology and Genetics of the Bacterial Cell Wall Unit, F-75015 Paris, France
| | - Gérard Eberl
- Institut Pasteur, Université Paris Cité, INSERM U1224, Microenvironment and Immunity Unit, F-75015 Paris, France
| | - Pierre-Marie Lledo
- Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Perception and Memory Unit, F-75015 Paris, France
| | - Grégoire Chevalier
- Institut Pasteur, Université Paris Cité, INSERM U1224, Microenvironment and Immunity Unit, F-75015 Paris, France
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6
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Yang B, Gao H, Qi H, Chen Y, Ross RP, Stanton C, Zhao J, Zhang H, Chen H, Chen W. Linoleate Isomerase Complex Contributes to Metabolism and Remission of DSS-Induced Colitis in Mice of Lactobacillus plantarum ZS2058. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8160-8171. [PMID: 34281339 DOI: 10.1021/acs.jafc.1c02944] [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: 06/13/2023]
Abstract
A linoleate isomerase complex including myosin-cross-reactive antigen, short-chain dehydrogenase/oxidoreductase, and acetoacetate decarboxylase has been confirmed as the pivotal factor for conjugated linoleic acid (CLA) production in Lactobacillus plantarum. However, its role in the metabolism and health-associated benefits of Lactobacillus remain unclear. In the current study, the mild type, knockout, and complemented mutants of the linoleate isomerase complex of L. plantarum ZS2058 were used to investigate those putative effects. The metabonomic results showed that a linoleate isomerase complex could significantly influence the glycol-metabolism, lipid metabolism, and antioxidant compounds. Especially, with the stress of linoleic acid, linoleate isomerase complex knockout mutants induced the increase of several antioxidant compounds, such as glutamic acid, glycine, l-cysteine, glycerol, and l-sorbosone. Moreover, the linoleate isomerase complex played a pivotal role in ameliorating DSS-induced colitis. The knockout mutants showed effects similar to those in the DSS group, whereas complementation of the corresponding gene in the knockout mutants could restore the anti-inflammatory activity, wherein the integrity of a mucus layer was repaired, the level of pro-inflammatory cytokines decreased, and the amount of anti-inflammatory cytokines increased significantly. All the results indicated that the linoleate isomerase complex plays a key role in CLA production and metabolism as well as the health-associated benefits of L. plantarum ZS2058. These results are conducive to promote clinical trials and product development of probiotics for colitis.
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Affiliation(s)
- Bo Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - He Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hui Qi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yang Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - R Paul Ross
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi 214122, Jiangsu, China
- APC Microbiome Ireland, University College Cork, Cork T12 K8AF, Ireland
| | - Catherine Stanton
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi 214122, Jiangsu, China
- APC Microbiome Ireland, University College Cork, Cork T12 K8AF, Ireland
- Teagasc Food Research Centre, Moorepark, Co. Cork P61 C996, Ireland
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
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7
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Gao H, Yang B, Stanton C, Ross RP, Zhang H, Chen H, Chen W. Linoleic acid induces different metabolic modes in two Bifidobacterium breve strains with different conjugated linoleic acid-producing abilities. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.110974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Gilmore MC, Ritzl-Rinkenberger B, Cava F. An updated toolkit for exploring bacterial cell wall structure and dynamics. Fac Rev 2021; 10:14. [PMID: 33659932 PMCID: PMC7894271 DOI: 10.12703/r/10-14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The bacterial cell wall is made primarily from peptidoglycan, a complex biomolecule which forms a bag-like exoskeleton that envelops the cell. As it is unique to bacteria and typically essential for their growth and survival, it represents one of the most successful targets for antibiotics. Although peptidoglycan has been studied intensively for over 50 years, the past decade has seen major steps in our understanding of this molecule because of the advent of new analytical and imaging methods. Here, we outline the most recent developments in tools that have helped to elucidate peptidoglycan structure and dynamics.
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Affiliation(s)
- Michael C Gilmore
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Barbara Ritzl-Rinkenberger
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
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9
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Garde S, Chodisetti PK, Reddy M. Peptidoglycan: Structure, Synthesis, and Regulation. EcoSal Plus 2021; 9:eESP-0010-2020. [PMID: 33470191 PMCID: PMC11168573 DOI: 10.1128/ecosalplus.esp-0010-2020] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Indexed: 02/06/2023]
Abstract
Peptidoglycan is a defining feature of the bacterial cell wall. Initially identified as a target of the revolutionary beta-lactam antibiotics, peptidoglycan has become a subject of much interest for its biology, its potential for the discovery of novel antibiotic targets, and its role in infection. Peptidoglycan is a large polymer that forms a mesh-like scaffold around the bacterial cytoplasmic membrane. Peptidoglycan synthesis is vital at several stages of the bacterial cell cycle: for expansion of the scaffold during cell elongation and for formation of a septum during cell division. It is a complex multifactorial process that includes formation of monomeric precursors in the cytoplasm, their transport to the periplasm, and polymerization to form a functional peptidoglycan sacculus. These processes require spatio-temporal regulation for successful assembly of a robust sacculus to protect the cell from turgor and determine cell shape. A century of research has uncovered the fundamentals of peptidoglycan biology, and recent studies employing advanced technologies have shed new light on the molecular interactions that govern peptidoglycan synthesis. Here, we describe the peptidoglycan structure, synthesis, and regulation in rod-shaped bacteria, particularly Escherichia coli, with a few examples from Salmonella and other diverse organisms. We focus on the pathway of peptidoglycan sacculus elongation, with special emphasis on discoveries of the past decade that have shaped our understanding of peptidoglycan biology.
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Affiliation(s)
- Shambhavi Garde
- These authors contributed equally
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India 500007
| | - Pavan Kumar Chodisetti
- These authors contributed equally
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India 500007
| | - Manjula Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India 500007
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10
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Vaiwala R, Sharma P, Puranik M, Ayappa KG. Developing a Coarse-Grained Model for Bacterial Cell Walls: Evaluating Mechanical Properties and Free Energy Barriers. J Chem Theory Comput 2020; 16:5369-5384. [DOI: 10.1021/acs.jctc.0c00539] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Rakesh Vaiwala
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Pradyumn Sharma
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Mrinalini Puranik
- Unilever Research & Development, 64 Main Road, Whitefield, Bangalore 560066, India
| | - K. Ganapathy Ayappa
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
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11
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A Theoretical Framework for Evolutionary Cell Biology. J Mol Biol 2020; 432:1861-1879. [PMID: 32087200 DOI: 10.1016/j.jmb.2020.02.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/20/2020] [Accepted: 02/04/2020] [Indexed: 11/24/2022]
Abstract
One of the last uncharted territories in evolutionary biology concerns the link with cell biology. Because all phenotypes ultimately derive from events at the cellular level, this connection is essential to building a mechanism-based theory of evolution. Given the impressive developments in cell biological methodologies at the structural and functional levels, the potential for rapid progress is great. The primary challenge for theory development is the establishment of a quantitative framework that transcends species boundaries. Two approaches to the problem are presented here: establishing the long-term steady-state distribution of mean phenotypes under specific regimes of mutation, selection, and drift and evaluating the energetic costs of cellular structures and functions. Although not meant to be the final word, these theoretical platforms harbor potential for generating insight into a diversity of unsolved problems, ranging from genome structure to cellular architecture to aspects of motility in organisms across the Tree of Life.
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12
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Vigouroux A, Cordier B, Aristov A, Alvarez L, Özbaykal G, Chaze T, Oldewurtel ER, Matondo M, Cava F, Bikard D, van Teeffelen S. Class-A penicillin binding proteins do not contribute to cell shape but repair cell-wall defects. eLife 2020; 9:e51998. [PMID: 31904338 PMCID: PMC7002073 DOI: 10.7554/elife.51998] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/04/2020] [Indexed: 01/06/2023] Open
Abstract
Cell shape and cell-envelope integrity of bacteria are determined by the peptidoglycan cell wall. In rod-shaped Escherichia coli, two conserved sets of machinery are essential for cell-wall insertion in the cylindrical part of the cell: the Rod complex and the class-A penicillin-binding proteins (aPBPs). While the Rod complex governs rod-like cell shape, aPBP function is less well understood. aPBPs were previously hypothesized to either work in concert with the Rod complex or to independently repair cell-wall defects. First, we demonstrate through modulation of enzyme levels that aPBPs do not contribute to rod-like cell shape but are required for mechanical stability, supporting their independent activity. By combining measurements of cell-wall stiffness, cell-wall insertion, and PBP1b motion at the single-molecule level, we then present evidence that PBP1b, the major aPBP, contributes to cell-wall integrity by repairing cell wall defects.
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Affiliation(s)
- Antoine Vigouroux
- Microbial Morphogenesis and Growth LaboratoryInstitut PasteurParisFrance
- Synthetic Biology LaboratoryInstitut PasteurParisFrance
- Université Paris Descartes, Sorbonne-Paris-CitéParisFrance
| | - Baptiste Cordier
- Microbial Morphogenesis and Growth LaboratoryInstitut PasteurParisFrance
| | - Andrey Aristov
- Microbial Morphogenesis and Growth LaboratoryInstitut PasteurParisFrance
| | - Laura Alvarez
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular BiologyUmeå UniversityUmeåSweden
| | - Gizem Özbaykal
- Microbial Morphogenesis and Growth LaboratoryInstitut PasteurParisFrance
- Université Paris Diderot, Sorbonne-Paris-CitéParisFrance
| | | | | | | | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular BiologyUmeå UniversityUmeåSweden
| | - David Bikard
- Synthetic Biology LaboratoryInstitut PasteurParisFrance
| | - Sven van Teeffelen
- Microbial Morphogenesis and Growth LaboratoryInstitut PasteurParisFrance
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13
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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: 15] [Impact Index Per Article: 2.5] [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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Gupta A, Ahmad A, Chothwe D, Madhu MK, Srivastava S, Sharma VK. Genome-scale metabolic reconstruction and metabolic versatility of an obligate methanotroph Methylococcus capsulatus str. Bath. PeerJ 2019; 7:e6685. [PMID: 31316867 PMCID: PMC6613435 DOI: 10.7717/peerj.6685] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 02/13/2019] [Indexed: 12/27/2022] Open
Abstract
The increase in greenhouse gases with high global warming potential such as methane is a matter of concern and requires multifaceted efforts to reduce its emission and increase its mitigation from the environment. Microbes such as methanotrophs can assist in methane mitigation. To understand the metabolic capabilities of methanotrophs, a complete genome-scale metabolic model (GSMM) of an obligate methanotroph, Methylococcus capsulatus str. Bath was reconstructed. The model contains 535 genes, 899 reactions and 865 metabolites and is named iMC535. The predictive potential of the model was validated using previously-reported experimental data. The model predicted the Entner–Duodoroff pathway to be essential for the growth of this bacterium, whereas the Embden–Meyerhof–Parnas pathway was found non-essential. The performance of the model was simulated on various carbon and nitrogen sources and found that M. capsulatus can grow on amino acids. The analysis of network topology of the model identified that six amino acids were in the top-ranked metabolic hubs. Using flux balance analysis, 29% of the metabolic genes were predicted to be essential, and 76 double knockout combinations involving 92 unique genes were predicted to be lethal. In conclusion, we have reconstructed a GSMM of a methanotroph Methylococcus capsulatus str. Bath. This is the first high quality GSMM of a Methylococcus strain which can serve as an important resource for further strain-specific models of the Methylococcus genus, as well as identifying the biotechnological potential of M. capsulatus Bath.
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Affiliation(s)
- Ankit Gupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Ahmad Ahmad
- Systems Biology for Biofuels Group, International Centre For Genetic Engineering And Biotechnology, New Delhi, India.,Department of Biotechnology, Noida International University, Noida, India
| | - Dipesh Chothwe
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Midhun K Madhu
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Shireesh Srivastava
- Systems Biology for Biofuels Group, International Centre For Genetic Engineering And Biotechnology, New Delhi, India
| | - Vineet K Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
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Vos AM, Heijboer A, Boschker HTS, Bonnet B, Lugones LG, Wösten HAB. Microbial biomass in compost during colonization of Agaricus bisporus. AMB Express 2017; 7:12. [PMID: 28050852 PMCID: PMC5209305 DOI: 10.1186/s13568-016-0304-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 12/11/2016] [Indexed: 11/10/2022] Open
Abstract
Agaricus bisporus mushrooms are commercially produced on a microbe rich compost. Here, fungal and bacterial biomass was quantified in compost with and without colonization by A. bisporus. Chitin content, indicative of total fungal biomass, increased during a 26-day period from 576 to 779 nmol N-acetylglucosamine g-1 compost in the absence of A. bisporus (negative control). A similar increase was found in the presence of this mushroom forming fungus. The fungal phospholipid-derived fatty acid (PLFA) marker C18:2ω6, indicative of the living fraction of the fungal biomass, decreased from 575 to 280 nmol g-1 compost in the negative control. In contrast, it increased to 1200 nmol g-1 compost in the presence of A. bisporus. Laccase activity was absent throughout culturing in the negative control, while it correlated with the fungal PLFA marker in the presence of A. bisporus. PLFA was also used to quantify living bacterial biomass. In the negative control, the bacterial markers remained constant at 3000-3200 nmol PLFA g-1 compost. In contrast, they decreased to 850 nmol g-1 compost during vegetative growth of A. bisporus, implying that bacterial biomass decreased from 17.7 to 4.7 mg g-1 compost. The relative amount of the Gram positive associated PLFA markers a15:0 and a17:0 and the Gram negative PLFA associated markers cy17:0 and cy19:0 increased and decreased, respectively, suggesting that Gram negative bacteria are more suppressed by A. bisporus. Together, these data indicate that fungal biomass can make up 6.8% of the compost after A. bisporus colonization, 57% of which being dead. Moreover, results show that A. bisporus impacts biomass and composition of bacteria in compost.
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Dik DA, Marous DR, Fisher JF, Mobashery S. Lytic transglycosylases: concinnity in concision of the bacterial cell wall. Crit Rev Biochem Mol Biol 2017. [PMID: 28644060 DOI: 10.1080/10409238.2017.1337705] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The lytic transglycosylases (LTs) are bacterial enzymes that catalyze the non-hydrolytic cleavage of the peptidoglycan structures of the bacterial cell wall. They are not catalysts of glycan synthesis as might be surmised from their name. Notwithstanding the seemingly mundane reaction catalyzed by the LTs, their lytic reactions serve bacteria for a series of astonishingly diverse purposes. These purposes include cell-wall synthesis, remodeling, and degradation; for the detection of cell-wall-acting antibiotics; for the expression of the mechanism of cell-wall-acting antibiotics; for the insertion of secretion systems and flagellar assemblies into the cell wall; as a virulence mechanism during infection by certain Gram-negative bacteria; and in the sporulation and germination of Gram-positive spores. Significant advances in the mechanistic understanding of each of these processes have coincided with the successive discovery of new LTs structures. In this review, we provide a systematic perspective on what is known on the structure-function correlations for the LTs, while simultaneously identifying numerous opportunities for the future study of these enigmatic enzymes.
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Affiliation(s)
- David A Dik
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
| | - Daniel R Marous
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
| | - Jed F Fisher
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
| | - Shahriar Mobashery
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
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17
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Abstract
Peptidoglycan recycling is a metabolic process by which Gram-negative bacteria reutilize up to half of their cell wall within one generation during vegetative growth. Whether peptidoglycan recycling also occurs in Gram-positive bacteria has so far remained unclear. We show here that three Gram-positive model organisms, Staphylococcus aureus, Bacillus subtilis, and Streptomyces coelicolor, all recycle the sugar N-acetylmuramic acid (MurNAc) of their peptidoglycan during growth in rich medium. They possess MurNAc-6-phosphate (MurNAc-6P) etherase (MurQ in E. coli) enzymes, which are responsible for the intracellular conversion of MurNAc-6P to N-acetylglucosamine-6-phosphate and d-lactate. By applying mass spectrometry, we observed accumulation of MurNAc-6P in MurNAc-6P etherase deletion mutants but not in either the isogenic parental strains or complemented strains, suggesting that MurQ orthologs are required for the recycling of cell wall-derived MurNAc in these bacteria. Quantification of MurNAc-6P in ΔmurQ cells of S. aureus and B. subtilis revealed small amounts during exponential growth phase (0.19 nmol and 0.03 nmol, respectively, per ml of cells at an optical density at 600 nm [OD600] of 1) but large amounts during transition (0.56 nmol and 0.52 nmol) and stationary (0.53 nmol and 1.36 nmol) phases. The addition of MurNAc to ΔmurQ cultures greatly increased the levels of intracellular MurNAc-6P in all growth phases. The ΔmurQ mutants of S. aureus and B. subtilis showed no growth deficiency in rich medium compared to the growth of the respective parental strains, but intriguingly, they had a severe survival disadvantage in late stationary phase. Thus, although peptidoglycan recycling is apparently not essential for the growth of Gram-positive bacteria, it provides a benefit for long-term survival. IMPORTANCE The peptidoglycan of the bacterial cell wall is turned over steadily during growth. As peptidoglycan fragments were found in large amounts in spent medium of exponentially growing Gram-positive bacteria, their ability to recycle these fragments has been questioned. We conclusively showed recycling of the peptidoglycan component MurNAc in different Gram-positive model organisms and revealed that a MurNAc-6P etherase (MurQ or MurQ ortholog) enzyme is required in this process. We further demonstrated that recycling occurs predominantly during the transition to stationary phase in S. aureus and B. subtilis, explaining why peptidoglycan fragments are found in the medium during exponential growth. We quantified the intracellular accumulation of recycling products in MurNAc-6P etherase gene mutants, revealing that about 5% and 10% of the MurNAc of the cell wall per generation is recycled in S. aureus and B. subtilis, respectively. Importantly, we showed that MurNAc recycling and salvaging does not sustain growth in these bacteria but is used to enhance survival during late stationary phase.
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de la Torre A, Metivier A, Chu F, Laurens LML, Beck DAC, Pienkos PT, Lidstrom ME, Kalyuzhnaya MG. Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1). Microb Cell Fact 2015; 14:188. [PMID: 26607880 PMCID: PMC4658805 DOI: 10.1186/s12934-015-0377-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 11/03/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Methane-utilizing bacteria (methanotrophs) are capable of growth on methane and are attractive systems for bio-catalysis. However, the application of natural methanotrophic strains to large-scale production of value-added chemicals/biofuels requires a number of physiological and genetic alterations. An accurate metabolic model coupled with flux balance analysis can provide a solid interpretative framework for experimental data analyses and integration. RESULTS A stoichiometric flux balance model of Methylomicrobium buryatense strain 5G(B1) was constructed and used for evaluating metabolic engineering strategies for biofuels and chemical production with a methanotrophic bacterium as the catalytic platform. The initial metabolic reconstruction was based on whole-genome predictions. Each metabolic step was manually verified, gapfilled, and modified in accordance with genome-wide expression data. The final model incorporates a total of 841 reactions (in 167 metabolic pathways). Of these, up to 400 reactions were recruited to produce 118 intracellular metabolites. The flux balance simulations suggest that only the transfer of electrons from methanol oxidation to methane oxidation steps can support measured growth and methane/oxygen consumption parameters, while the scenario employing NADH as a possible source of electrons for particulate methane monooxygenase cannot. Direct coupling between methane oxidation and methanol oxidation accounts for most of the membrane-associated methane monooxygenase activity. However the best fit to experimental results is achieved only after assuming that the efficiency of direct coupling depends on growth conditions and additional NADH input (about 0.1-0.2 mol of incremental NADH per one mol of methane oxidized). The additional input is proposed to cover loss of electrons through inefficiency and to sustain methane oxidation at perturbations or support uphill electron transfer. Finally, the model was used for testing the carbon conversion efficiency of different pathways for C1-utilization, including different variants of the ribulose monophosphate pathway and the serine cycle. CONCLUSION We demonstrate that the metabolic model can provide an effective tool for predicting metabolic parameters for different nutrients and genetic perturbations, and as such, should be valuable for metabolic engineering of the central metabolism of M. buryatense strains.
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Affiliation(s)
- Andrea de la Torre
- Biology Department, San Diego State University, North Life Science Room 406, San Diego, CA, 92182-4614, USA.
| | - Aisha Metivier
- Biology Department, San Diego State University, North Life Science Room 406, San Diego, CA, 92182-4614, USA.
| | - Frances Chu
- Department of Chemical Engineering, University of Washington, Seattle, USA.
| | - Lieve M L Laurens
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, USA.
| | - David A C Beck
- Department of Chemical Engineering, University of Washington, Seattle, USA.
- eScience Institute, University of Washington, Seattle, USA.
| | - Philip T Pienkos
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, USA.
| | - Mary E Lidstrom
- Department of Chemical Engineering, University of Washington, Seattle, USA.
- Department of Microbiology, University of Washington, Seattle, USA.
| | - Marina G Kalyuzhnaya
- Biology Department, San Diego State University, North Life Science Room 406, San Diego, CA, 92182-4614, USA.
- Viral Information Institute, San Diego State University, San Diego, USA.
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de Pedro MA, Cava F. Structural constraints and dynamics of bacterial cell wall architecture. Front Microbiol 2015; 6:449. [PMID: 26005443 PMCID: PMC4424881 DOI: 10.3389/fmicb.2015.00449] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 04/25/2015] [Indexed: 12/23/2022] Open
Abstract
The peptidoglycan wall (PG) is a unique structure which confers physical strength and defined shape to bacteria. It consists of a net-like macromolecule of peptide interlinked glycan chains overlying the cell membrane. The structure and layout of the PG dictates that the wall has to be continuously modified as bacteria go through division, morphological differentiation, and adaptive responses. The PG is poorly known in structural terms. However, to understand morphogenesis a precise knowledge of glycan strand arrangement and of local effects of the different kinds of subunits is essential. The scarcity of data led to a conception of the PG as a regular, highly ordered structure which strongly influenced growth models. Here, we review the structure of the PG to define a more realistic conceptual framework. We discuss the consequences of the plasticity of murein architecture in morphogenesis and try to define a set of minimal structural constraints that must be fulfilled by any model to be compatible with present day information.
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Affiliation(s)
- Miguel A de Pedro
- Centro de Biología Molecular "Severo Ochoa" - Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid Madrid, Spain ; Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Center for Microbial Research, Umeå University, Umeå Sweden
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Center for Microbial Research, Umeå University, Umeå Sweden
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20
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Gumbart JC, Beeby M, Jensen GJ, Roux B. Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations. PLoS Comput Biol 2014; 10:e1003475. [PMID: 24586129 PMCID: PMC3930494 DOI: 10.1371/journal.pcbi.1003475] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 01/05/2014] [Indexed: 12/24/2022] Open
Abstract
Bacteria face the challenging requirement to maintain their shape and avoid rupture due to the high internal turgor pressure, but simultaneously permit the import and export of nutrients, chemical signals, and virulence factors. The bacterial cell wall, a mesh-like structure composed of cross-linked strands of peptidoglycan, fulfills both needs by being semi-rigid, yet sufficiently porous to allow diffusion through it. How the mechanical properties of the cell wall are determined by the molecular features and the spatial arrangement of the relatively thin strands in the larger cellular-scale structure is not known. To examine this issue, we have developed and simulated atomic-scale models of Escherichia coli cell walls in a disordered circumferential arrangement. The cell-wall models are found to possess an anisotropic elasticity, as known experimentally, arising from the orthogonal orientation of the glycan strands and of the peptide cross-links. Other features such as thickness, pore size, and disorder are also found to generally agree with experiments, further supporting the disordered circumferential model of peptidoglycan. The validated constructs illustrate how mesoscopic structure and behavior emerge naturally from the underlying atomic-scale properties and, furthermore, demonstrate the ability of all-atom simulations to reproduce a range of macroscopic observables for extended polymer meshes. The structure of the bacterial cell wall has been a point of controversy and contention since it was first discovered. Although the basic chemical composition of peptidoglycan, the key constituent of the cell wall, is now well established, its long-range organization is not. This dearth of information at the mesoscopic scale is a result of the inability of experimental imaging techniques to simultaneously visualize both the atomic-level detail of the peptidoglycan network and its macroscopic arrangement around the bacterium. Now, using molecular dynamics (MD) simulations, we have carefully constructed and validated models of sections of the Escherichia coli cell wall in full atomic detail. By comparing various properties of these models, including elasticity, pore size, and thickness with experiments, we can discriminate between them, resolving which best represents the native wall structure. In doing so, our study provides approaches for connecting measurements made in atomic-scale MD simulations with large-scale and even macroscopic properties.
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Affiliation(s)
- James C. Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail: (JCG); (BR)
| | - Morgan Beeby
- Imperial College London, South Kensington Campus, London, United Kingdom
| | - Grant J. Jensen
- California Institute of Technology and Howard Hughes Medical Institute, Pasadena, California, United States of America
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology and Gordon Center for Integrative Science, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (JCG); (BR)
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21
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Bhamidi S, Scherman MS, Jones V, Crick DC, Belisle JT, Brennan PJ, McNeil MR. Detailed structural and quantitative analysis reveals the spatial organization of the cell walls of in vivo grown Mycobacterium leprae and in vitro grown Mycobacterium tuberculosis. J Biol Chem 2011; 286:23168-77. [PMID: 21555513 PMCID: PMC3123084 DOI: 10.1074/jbc.m110.210534] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 04/08/2011] [Indexed: 11/06/2022] Open
Abstract
The cell wall of mycobacteria consists of an outer membrane, analogous to that of gram-negative bacteria, attached to the peptidoglycan (PG) via a connecting polysaccharide arabinogalactan (AG). Although the primary structure of these components is fairly well deciphered, issues such as the coverage of the PG layer by covalently attached mycolates in the outer membrane and the spatial details of the mycolic acid attachment to the arabinan have remained unknown. It is also not understood how these components work together to lead to the classical acid-fast staining of mycobacteria. Because the majority of Mycobacterium tuberculosis bacteria in established experimental animal infections are acid-fast negative, clearly cell wall changes are occurring. To address both the spatial properties of mycobacterial cell walls and to begin to study the differences between bacteria grown in animals and cultures, the cell walls of Mycobacterium leprae grown in armadillos was characterized and compared with that of M. tuberculosis grown in culture. Most fundamentally, it was determined that the cell wall of M. leprae contained significantly more mycolic acids attached to PG than that of in vitro grown M. tuberculosis (mycolate:PG ratios of 21:10 versus 16:10, respectively). In keeping with this difference, more arabinogalactan (AG) molecules, linking the mycolic acids to PG, were found. Differences in the structures of the AG were also found; the AG of M. leprae is smaller than that of M. tuberculosis, although the same basic structural motifs are retained.
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Affiliation(s)
- Suresh Bhamidi
- From the Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Michael S. Scherman
- From the Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Victoria Jones
- From the Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Dean C. Crick
- From the Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - John T. Belisle
- From the Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Patrick J. Brennan
- From the Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Michael R. McNeil
- From the Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523
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Hynninen A, Touzé T, Pitkänen L, Mengin-Lecreulx D, Virta M. An efflux transporter PbrA and a phosphatase PbrB cooperate in a lead-resistance mechanism in bacteria. Mol Microbiol 2009; 74:384-94. [PMID: 19737357 DOI: 10.1111/j.1365-2958.2009.06868.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The gene cluster pbrTRABCD from Cupriavidus metallidurans CH34 is thought to encode a unique, specific resistance mechanism for lead. However, the exact functions of these genes are unknown. In this study we examine the metal specificity and functions of pbrABCD by expressing these genes in different combinations and comparing their ability to restore Pb(2+), Zn(2+) and Cd(2+) resistance in a metal-sensitive C. metallidurans strain DN440. We show that lead resistance in C. metallidurans is achieved through the cooperation of the Zn/Cd/Pb-translocating ATPase PbrA and the undecaprenyl pyrophosphate phosphatase PbrB. While PbrA non-specifically exported Pb(2+), Zn(2+) and Cd(2+), a specific increase in lead resistance was observed when PbrA and PbrB were coexpressed. As a model of action for PbrA and PbrB we propose a mechanism where Pb(2+) is exported from the cytoplasm by PbrA and then sequestered as a phosphate salt with the inorganic phosphate produced by PbrB. Similar operons containing genes for heavy metal translocating ATPases and phosphatases were found in several different bacterial species, suggesting that lead detoxification through active efflux and sequestration is a common lead-resistance mechanism.
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Affiliation(s)
- Anu Hynninen
- Department of Applied Chemistry and Microbiology, University of Helsinki, FIN-00014 Helsinki, Finland
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23
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Zheng Y, Struck DK, Young R. Purification and functional characterization of phiX174 lysis protein E. Biochemistry 2009; 48:4999-5006. [PMID: 19379010 PMCID: PMC3100163 DOI: 10.1021/bi900469g] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two classes of bacteriophages, the single-stranded DNA Microviridae and the single-stranded RNA Alloleviviridae, accomplish lysis by expressing "protein antibiotics", or polypeptides that inhibit cell wall biosynthesis. Previously, we have provided genetic and physiological evidence that E, a 91-amino acid membrane protein encoded by the prototype microvirus, varphiX174, is a specific inhibitor of the translocase MraY, an essential membrane-embedded enzyme that catalyzes the formation of the murein precursor, Lipid I, from UDP-N-acetylmuramic acid-pentapeptide and the lipid carrier, undecaprenol phosphate. Here we report the first purification of E, which has been refractory to overexpression because of its lethality to Escherichia coli. Moreover, using a fluorescently labeled analogue of the sugar-nucleotide substrate, we demonstrate that E acts as a noncompetitive inhibitor of detergent-solubilized MraY, with respect to both soluble and lipid substrates. In addition, we show that the E sensitivity of five MraY mutant proteins, produced from alleles selected for resistance to E, can be correlated to the apparent affinities determined by in vivo multicopy suppression experiments. These results are inconsistent with previous reports that E inhibited membrane-embedded MraY but not the detergent-solubilized enzyme, which led to a model in which E functions by binding MraY and blocking the formation of an essential heteromultimeric complex involving MraY and other murein biosynthesis enzymes. We discuss a new model in which E binds to MraY at a site composed of the two transmembrane domains within which the E resistance mutations map and the fact that the result of this binding is a conformational change that inactivates the enzyme.
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Affiliation(s)
- Yi Zheng
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station TX 77843-2128
| | - Douglas K. Struck
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station TX 77843-2128
| | - Ry Young
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station TX 77843-2128
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The peptidoglycan sacculus of Myxococcus xanthus has unusual structural features and is degraded during glycerol-induced myxospore development. J Bacteriol 2008; 191:494-505. [PMID: 18996994 DOI: 10.1128/jb.00608-08] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Upon nutrient limitation cells of the swarming soil bacterium Myxococcus xanthus form a multicellular fruiting body in which a fraction of the cells develop into myxospores. Spore development includes the transition from a rod-shaped vegetative cell to a spherical myxospore and so is expected to be accompanied by changes in the bacterial cell envelope. Peptidoglycan is the shape-determining structure in the cell envelope of most bacteria, including myxobacteria. We analyzed the composition of peptidoglycan isolated from M. xanthus. While the basic structural elements of peptidoglycan in myxobacteria were identical to those in other gram-negative bacteria, the peptidoglycan of M. xanthus had unique structural features. meso- or LL-diaminopimelic acid was present in the stem peptides, and a new modification of N-acetylmuramic acid was detected in a fraction of the muropeptides. Peptidoglycan formed a continuous, bag-shaped sacculus in vegetative cells. The sacculus was degraded during the transition from vegetative cells to glycerol-induced myxospores. The spherical, bag-shaped coats isolated from glycerol-induced spores contained no detectable muropeptides, but they contained small amounts of N-acetylmuramic acid and meso-diaminopimelic acid.
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Den Blaauwen T, de Pedro MA, Nguyen-Distèche M, Ayala JA. Morphogenesis of rod-shaped sacculi. FEMS Microbiol Rev 2008; 32:321-44. [DOI: 10.1111/j.1574-6976.2007.00090.x] [Citation(s) in RCA: 232] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Affiliation(s)
- Waldemar Vollmer
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne, UK.
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27
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Joseleau-Petit D, Liébart JC, Ayala JA, D'Ari R. Unstable Escherichia coli L forms revisited: growth requires peptidoglycan synthesis. J Bacteriol 2007; 189:6512-20. [PMID: 17586646 PMCID: PMC2045188 DOI: 10.1128/jb.00273-07] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Growing bacterial L forms are reputed to lack peptidoglycan, although cell division is normally inseparable from septal peptidoglycan synthesis. To explore which cell division functions L forms use, we established a protocol for quantitatively converting a culture of a wild-type Escherichia coli K-12 strain overnight to a growing L-form-like state by use of the beta-lactam cefsulodin, a specific inhibitor of penicillin-binding proteins (PBPs) 1A and 1B. In rich hypertonic medium containing cefsulodin, all cells are spherical and osmosensitive, like classical L forms. Surprisingly, however, mutant studies showed that colony formation requires d-glutamate, diaminopimelate, and MurA activity, all of which are specific to peptidoglycan synthesis. High-performance liquid chromatography analysis confirmed that these L-form-like cells contain peptidoglycan, with 7% of the normal amount. Moreover, the beta-lactam piperacillin, a specific inhibitor of the cell division protein PBP 3, rapidly blocks the cell division of these L-form-like cells. Similarly, penicillin-induced L-form-like cells, which grow only within the agar layers of rich hypertonic plates, also require d-glutamate, diaminopimelate, and MurA activity. These results strongly suggest that cefsulodin- and penicillin-induced L-form-like cells of E. coli-and possibly all L forms-have residual peptidoglycan synthesis which is essential for their growth, probably being required for cell division.
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Vollmer W, Bertsche U. Murein (peptidoglycan) structure, architecture and biosynthesis in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1778:1714-34. [PMID: 17658458 DOI: 10.1016/j.bbamem.2007.06.007] [Citation(s) in RCA: 316] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2007] [Revised: 06/11/2007] [Accepted: 06/11/2007] [Indexed: 10/23/2022]
Abstract
The periplasmic murein (peptidoglycan) sacculus is a giant macromolecule made of glycan strands cross-linked by short peptides completely surrounding the cytoplasmic membrane to protect the cell from lysis due to its internal osmotic pressure. More than 50 different muropeptides are released from the sacculus by treatment with a muramidase. Escherichia coli has six murein synthases which enlarge the sacculus by transglycosylation and transpeptidation of lipid II precursor. A set of twelve periplasmic murein hydrolases (autolysins) release murein fragments during cell growth and division. Recent data on the in vitro murein synthesis activities of the murein synthases and on the interactions between murein synthases, hydrolases and cell cycle related proteins are being summarized. There are different models for the architecture of murein and for the incorporation of new precursor into the sacculus. We present a model in which morphogenesis of the rod-shaped E. coli is driven by cytoskeleton elements competing for the control over the murein synthesis multi-enzyme complexes.
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Affiliation(s)
- Waldemar Vollmer
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Catherine Cookson Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK.
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Ubbink J, Schär-Zammaretti P. Probing bacterial interactions: integrated approaches combining atomic force microscopy, electron microscopy and biophysical techniques. Micron 2005; 36:293-320. [PMID: 15857770 DOI: 10.1016/j.micron.2004.11.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Revised: 11/24/2004] [Accepted: 11/25/2004] [Indexed: 11/27/2022]
Abstract
Recent developments in the application of Atomic Force Microscopy (AFM) and other biophysical techniques for the study of bacterial interactions and adhesion are discussed in the light of established biological and microscopic approaches. Whereas molecular-biological techniques combined with electron microscopy allow the identification and localization of surface constituents mediating bacterial interactions, with AFM it has become possible to actually measure the forces involved in bacterial interactions. Combined with the flexibility of AFM in probing various types of physical interactions, such as electrostatic interactions, specific ligand-receptor interactions and the elastic forces of deformation and extension of bacterial surface polymers and cell wall, this provides prospects for the elucidation of the biophysical mechanism of bacterial interaction. However, because of the biochemical and a biophysical complexity of the bacterial cell wall, integrated approaches combining AFM with electron microscopy and biophysical techniques are needed to elucidate the mechanism by which a bacterium interacts with a host or material surface. The literature on electron microscopy of the bacterial cell wall is reviewed, with particular emphasis on the staining of specific classes of cell-wall constituents. The application of AFM in the analysis of bacterial surfaces is discussed, including AFM operating modes, sample preparation methods and results obtained on various strains. For various bacterial strains, the integration of EM and AFM data is discussed. Various biophysical aspects of the analysis of bacterial surface structure and interactions are discussed, including the theory of colloidal interactions and Bell's theory of cell-to-cell adhesion. An overview is given of biophysical techniques used in the analysis of the properties of bacterial surfaces and bacterial surface constituents and their integration with AFM. Finally, we discuss recent progress in the understanding of the role of bacterial interactions in medicine within the framework of the techniques and concepts discussed in the paper.
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Affiliation(s)
- Job Ubbink
- Nestlé Research Center, Vers-chez-les-Blanc, P.O. Box 44, CH-1000 Lausanne 26, Switzerland.
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Vollmer W, Höltje JV. The architecture of the murein (peptidoglycan) in gram-negative bacteria: vertical scaffold or horizontal layer(s)? J Bacteriol 2004; 186:5978-87. [PMID: 15342566 PMCID: PMC515156 DOI: 10.1128/jb.186.18.5978-5987.2004] [Citation(s) in RCA: 159] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Waldemar Vollmer
- Universität Tübingen, Fakultät für Biologie, Lehrbereich Mikrobielle Genetik, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
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Dmitriev BA, Toukach FV, Schaper KJ, Holst O, Rietschel ET, Ehlers S. Tertiary structure of bacterial murein: the scaffold model. J Bacteriol 2003; 185:3458-68. [PMID: 12754246 PMCID: PMC155389 DOI: 10.1128/jb.185.11.3458-3468.2003] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although the chemical structure and physical properties of peptidoglycan have been elucidated for some time, the precise three-dimensional organization of murein has remained elusive. Earlier published computer simulations of the bacterial murein architecture modeled peptidoglycan strands in either a regular (D. Pink, J. Moeller, B. Quinn, M. Jericho, and T. Beveridge, J. Bacteriol. 182: 5925-5930, 2000) or an irregular (A. Koch, J. Theor. Biol. 204: 533-541, 2000) parallel orientation with respect to the plasma membrane. However, after integrating published experimental data on glycan chain length distribution and the degree of peptide side chain cross-linking into this computer simulation, we now report that the proposed planar network of murein appears largely dysfunctional. In contrast, a scaffold model of murein architecture, which assumes that glycan strands extend perpendicularly to the plasma membrane, was found to accommodate published experimental evidence and yield a viable stress-bearing matrix. Moreover, this model is in accordance with the well-established principle of murein assembly in vivo, i.e., sequential attachment of strands to the preexisting structure. For the first time, the phenomenon of division plane alternation in dividing bacteria can be reconciled with a computer model of the molecular architecture of murein.
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Affiliation(s)
- Boris A Dmitriev
- N. F. Gamaleya Institute for Epidemiology and Microbiology, Moscow, Russia
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32
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Borruat G, Roten CA, Fay LB, Karamata D. A high-performance liquid chromatography method for the detection of diaminopimelic acid in urine. Anal Biochem 2001; 291:11-6. [PMID: 11262151 DOI: 10.1006/abio.2001.5016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We describe a quantitative assay for diaminopimelic acid (DAP) in urine. It involves (i) hydrolysis of urine samples, (ii) purification by several different liquid chromatography steps, and (iii) analysis by high-performance liquid chromatography on a reversed-phase C18 column. Tritiated-DAP, the internal standard, allows one to precisely follow the DAP-containing fractions and to determine the yield during purification. Sensitive and relatively accurate quantification of DAP, with a threshold of 50 fmol, is based on ion-pairing properties of eluants and ortho-phthaldialdehyde derivatization. The presence of DAP in relevant fractions was confirmed by combined gas chromatography and mass spectrometry. The DAP concentration in adult human urine pooled over 24 h ranges from 0.69 to 2.01 microM, a result in fair agreement with previously published values obtained by ninhydrin derivatization or gas chromatography.
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Affiliation(s)
- G Borruat
- Institut de Génétique et de Biologie Microbiennes, Rue César-Roux 19, CH-1005 Lausanne, Switzerland
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Pink D, Moeller J, Quinn B, Jericho M, Beveridge T. On the architecture of the gram-negative bacterial murein sacculus. J Bacteriol 2000; 182:5925-30. [PMID: 11004199 PMCID: PMC94722 DOI: 10.1128/jb.182.20.5925-5930.2000] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2000] [Accepted: 07/18/2000] [Indexed: 11/20/2022] Open
Abstract
The peptidoglycan network of the murein sacculus must be porous so that nutrients, waste products, and secreted proteins can pass through. Using Escherichia coli and Pseudomonas aeruginosa as a baseline for gram-negative sacculi, the hole size distribution in the peptidoglycan network has been modeled by computer simulation to deduce the network's properties. By requiring that the distribution of glycan chain lengths predicted by the model be in accord with the distribution observed, we conclude that the holes are slits running essentially perpendicular to the local axis of the glycan chains (i. e., the slits run along the long axis of the cell). This result is in accord with previous permeability measurements of Beveridge and Jack and Demchik and Koch. We outline possible advantages that might accrue to the bacterium via this architecture and suggest ways in which such defect structures might be detected. Certainly, large molecules do penetrate the peptidoglycan layer of gram-negative bacteria, and the small slits that we suggest might be made larger by the bacterium.
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Affiliation(s)
- D Pink
- TPI, Physics Department, St. Francis Xavier University, Antigonish, Nova Scotia, Canada B2G 2W5.
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Yao X, Jericho M, Pink D, Beveridge T. Thickness and elasticity of gram-negative murein sacculi measured by atomic force microscopy. J Bacteriol 1999; 181:6865-75. [PMID: 10559150 PMCID: PMC94159 DOI: 10.1128/jb.181.22.6865-6875.1999] [Citation(s) in RCA: 216] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Atomic force microscopy was used to measure the thickness of air-dried, collapsed murein sacculi from Escherichia coli K-12 and Pseudomonas aeruginosa PAO1. Air-dried sacculi from E. coli had a thickness of 3.0 nm, whereas those from P. aeruginosa were 1.5 nm thick. When rehydrated, the sacculi of both bacteria swelled to double their anhydrous thickness. Computer simulation of a section of a model single-layer peptidoglycan network in an aqueous solution with a Debye shielding length of 0.3 nm gave a mass distribution full width at half height of 2.4 nm, in essential agreement with these results. When E. coli sacculi were suspended over a narrow groove that had been etched into a silicon surface and the tip of the atomic force microscope used to depress and stretch the peptidoglycan, an elastic modulus of 2.5 x 10(7) N/m(2) was determined for hydrated sacculi; they were perfectly elastic, springing back to their original position when the tip was removed. Dried sacculi were more rigid with a modulus of 3 x 10(8) to 4 x 10(8) N/m(2) and at times could be broken by the atomic force microscope tip. Sacculi aligned over the groove with their long axis at right angles to the channel axis were more deformable than those with their long axis parallel to the groove axis, as would be expected if the peptidoglycan strands in the sacculus were oriented at right angles to the long cell axis of this gram-negative rod. Polar caps were not found to be more rigid structures but collapsed to the same thickness as the cylindrical portions of the sacculi. The elasticity of intact E. coli sacculi is such that, if the peptidoglycan strands are aligned in unison, the interstrand spacing should increase by 12% with every 1 atm increase in (turgor) pressure. Assuming an unstressed hydrated interstrand spacing of 1.3 nm (R. E. Burge, A. G. Fowler, and D. A. Reaveley, J. Mol. Biol. 117:927-953, 1977) and an internal turgor pressure of 3 to 5 atm (or 304 to 507 kPa) (A. L. Koch, Adv. Microbial Physiol. 24:301-366, 1983), the natural interstrand spacing in cells would be 1.6 to 2.0 nm. Clearly, if large macromolecules of a diameter greater than these spacings are secreted through this layer, the local ordering of the peptidoglycan must somehow be disrupted.
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Affiliation(s)
- X Yao
- Department of Physics, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J1
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35
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Ehmann DE, Gehring AM, Walsh CT. Lysine biosynthesis in Saccharomyces cerevisiae: mechanism of alpha-aminoadipate reductase (Lys2) involves posttranslational phosphopantetheinylation by Lys5. Biochemistry 1999; 38:6171-7. [PMID: 10320345 DOI: 10.1021/bi9829940] [Citation(s) in RCA: 137] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A key step in fungal biosynthesis of lysine, enzymatic reduction of alpha-aminoadipate at C6 to the semialdehyde, requires two gene products in Saccharomyces cerevisiae, Lys2 and Lys5. Here, we show that the 31-kDa Lys5 is a specific posttranslational modification catalyst, using coenzyme A (CoASH) as a cosubstrate to phosphopantetheinylate Ser880 of the 155-kDa Lys2 and activate it for catalysis. Lys2 was subcloned from S. cerevisiae and expressed in and purified from Escherichia coli as a full-length 155-kDa enzyme, as a 105-kDa adenylation/peptidyl carrier protein (A/PCP) fragment (residues 1-924), and as a 14-kDa PCP fragment (residues 809-924). The apo-PCP fragment was covalently modified to phosphopantetheinylated holo-PCP by pure Lys5 and CoASH with a Km of 1 microM and kcat of 3 min-1 for both the PCP and CoASH substrates. The adenylation domain of the A/PCP fragment activated S-carboxymethyl-L-cysteine (kcat/Km = 840 mM-1 min-1) at 16% the efficiency of L-alpha-aminoadipate in [32P]PPi/ATP exchange assays. The holo form of the A/PCP 105-kDa fragment of Lys2 covalently aminoacylated itself with [35S]S-carboxymethyl-L-cysteine. Addition of NADPH discharged the covalent acyl-S-PCP Lys2, consistent with a reductive cleavage of the acyl-S-enzyme intermediate. These results identify the Lys5/Lys2 pair as a two-component system in which Lys5 covalently primes Lys2, allowing alpha-aminoadipate reductase activity by holo-Lys2 with catalytic cycles of autoaminoacylation and reductive cleavage. This is a novel mechanism for a fungal enzyme essential for amino acid metabolism.
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Affiliation(s)
- D E Ehmann
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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36
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Abstract
The shape of Escherichia coli is strikingly simple compared to those of higher eukaryotes. In fact, the end result of E. coli morphogenesis is a cylindrical tube with hemispherical caps. It is argued that physical principles affect biological forms. In this view, genes code for products that contribute to the production of suitable structures for physical factors to act upon. After introduction of a physical model, the discussion is focused on the shape-maintaining (peptidoglycan) layer of E. coli. This is followed by a detailed analysis of the structural relationship of the cellular interior to the cytoplasmic membrane. A basic theme of this review is that the transcriptionally active nucleoid and the cytoplasmic translation machinery form a structural continuity with the growing cellular envelope. An attempt has been made to show how this dynamic relationship during the cell cycle affects cell polarity and how it leads to cell division.
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Affiliation(s)
- N Nanninga
- Institute for Molecular Cell Biology, BioCentrum Amsterdam, University of Amsterdam, The Netherlands.
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Höltje JV. Growth of the stress-bearing and shape-maintaining murein sacculus of Escherichia coli. Microbiol Mol Biol Rev 1998; 62:181-203. [PMID: 9529891 PMCID: PMC98910 DOI: 10.1128/mmbr.62.1.181-203.1998] [Citation(s) in RCA: 874] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
To withstand the high intracellular pressure, the cell wall of most bacteria is stabilized by a unique cross-linked biopolymer called murein or peptidoglycan. It is made of glycan strands [poly-(GlcNAc-MurNAc)], which are linked by short peptides to form a covalently closed net. Completely surrounding the cell, the murein represents a kind of bacterial exoskeleton known as the murein sacculus. Not only does the sacculus endow bacteria with mechanical stability, but in addition it maintains the specific shape of the cell. Enlargement and division of the murein sacculus is a prerequisite for growth of the bacterium. Two groups of enzymes, hydrolases and synthases, have to cooperate to allow the insertion of new subunits into the murein net. The action of these enzymes must be well coordinated to guarantee growth of the stress-bearing sacculus without risking bacteriolysis. Protein-protein interaction studies suggest that this is accomplished by the formation of a multienzyme complex, a murein-synthesizing machinery combining murein hydrolases and synthases. Enlargement of both the multilayered murein of gram-positive and the thin, single-layered murein of gram-negative bacteria seems to follow an inside-to-outside growth strategy. New material is hooked in a relaxed state underneath the stress-bearing sacculus before it becomes inserted upon cleavage of covalent bonds in the layer(s) under tension. A model is presented that postulates that maintenance of bacterial shape is achieved by the enzyme complex copying the preexisting murein sacculus that plays the role of a template.
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Affiliation(s)
- J V Höltje
- Max-Planck-Institut für Entwicklungsbiologie, Abteilung Biochemie, Tübingen, Germany.
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38
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Abstract
During hyperosmotic shock, the protoplast and stretched-out peptidoglycan layer first shrink together until the turgor pressure in the cell is relieved. Being non-compressible, the outer and inner membranes must fold their superfluous surfaces. While the protoplast contracts further, the inner membrane rearranges into plasmolysis spaces visible by phase-contrast microscopy. Two opposing theories predict a similar positioning of spaces in dividing cells and filaments: the 'periseptal annulus model', based on adhesion zones, involved in the predetermination of the division site; and a 'restricted, random model', based on physical properties of the protoplast. Strong osmotic shock causes retraction of the inner membrane over almost the entire surface forming the so-called 'Bayer bridges'. These tubular adhesion sites are preserved by chemical fixation, and can be destroyed by cryofixation and freeze-substitution of unfixed cells. Both the regular positioning of the plasmolysis spaces and the occurrence of tubular adhesion sites can be explained on the basis of physical properties of the membrane which necessitate rearrangements by membrane flow during shrinkage of the protoplast.
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Affiliation(s)
- C L Woldringh
- Department of Molecular Cell Biology, BioCentrum Amsterdam, University of Amsterdam, The Netherlands
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39
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Caparrós M, Quintela JC, de Pedro MA. Variability of peptidoglycan surface density in Escherichia coli. FEMS Microbiol Lett 1994; 121:71-6. [PMID: 8082828 DOI: 10.1111/j.1574-6968.1994.tb07077.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Murein synthesis in Escherichia coli can be partially inhibited by D-methionine without concomitant alterations in growth and morphology. D-Methionine-treated cultures grow steadily for an indefinite time, therefore murein surface density should be reduced. Determination of this parameter in control and D-methionine-treated cells showed a severe reduction in the latter. Murein surface density increases drastically in resting cells, irrespective of the presence of D-methionine. Mutants in ponB are hypersensitive to D-methionine. Analysis of ponB strains revealed an important reduction in murein surface density. An approximately two-fold reduction in average surface density is apparently compatible with normal growth and division.
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Affiliation(s)
- M Caparrós
- Centro de Biología Molecular Severo Ochoa CSIC-UAM, Facultad de Ciencias (Biología), Madrid, Spain
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40
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Labischinski H, Maidhof H. Chapter 2 Bacterial peptidoglycan: overview and evolving concepts. BACTERIAL CELL WALL 1994. [DOI: 10.1016/s0167-7306(08)60405-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Licht J, Gally D, Henderson T, Young K, Cooper S. Effect of mecillinam on peptidoglycan synthesis during the division cycle of Salmonella typhimurium 2616. Res Microbiol 1993; 144:423-33. [PMID: 8190989 DOI: 10.1016/0923-2508(93)90050-c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The effects of mecillinam, ampicillin and cephalexin on peptidoglycan synthesis in Salmonella typhimurium 2616 have been studied at equivalent concentrations or "isoactivities". Using antibiotics at isoactivities allows a direct comparison of the biochemical effects of different antibiotics. When mecillinam was added at different times during the division cycle at a concentration that produced 50% inhibition of peptidoglycan synthesis in an exponential culture over a short period of time, the inhibition of synthesis was greatest in the newborn cells and least in the dividing cells. Antibiotic competition experiments showed that mecillinam preferentially bound to penicillin-binding protein 2 in S. typhimurium 2616. High performance liquid chromatography analysis of the residual peptidoglycan synthesized in the presence of mecillinam showed an unexpected increase in pentapeptides and a significant increase in cross-linking. Other antibiotics added at equivalent activities did not show an increase in cross-linking.
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Affiliation(s)
- J Licht
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109-0620
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42
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Park JT. Turnover and recycling of the murein sacculus in oligopeptide permease-negative strains of Escherichia coli: indirect evidence for an alternative permease system and for a monolayered sacculus. J Bacteriol 1993; 175:7-11. [PMID: 8416911 PMCID: PMC196091 DOI: 10.1128/jb.175.1.7-11.1993] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Turnover of murein in oligopeptide permease-negative Escherichia coli cells appeared to be minimal or nonexistent. In one strain in which it was possible to measure turnover during the first generation of chase, it was found that the rate of turnover was constant throughout a chase of three generations. This result suggests that an "inside-to-outside" mode of growth of the sacculus does not occur in E. coli. Turnover, though minimal, was significantly higher from cells labeled uniformly than from cells labeled only in the lateral wall, suggesting that a significant portion of the observed turnover is related to cell separation. Actually, turnover only appeared to be minimal in opp mutant strains. Tripeptides were being released by turnover at a rate of about 50% per generation and then were efficiently recycled. This suggests that in addition to opp, a low-affinity uptake system for tripeptide derived from the sacculus may exist.
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Affiliation(s)
- J T Park
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts 02111
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43
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Roten CA, Karamata D. Endogenous synthesis of peptidoglycan in eukaryotic cells; a novel concept involving its essential role in cell division, tumor formation and the biological clock. EXPERIENTIA 1992; 48:921-31. [PMID: 1426143 DOI: 10.1007/bf01919139] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Degradation products of peptidoglycan, the universal bacterial cell wall constituent, were previously found in animal tissues and urine. Reassessment and quantitative analysis of available data lead to an original concept, i.e. that eukaryotic cells synthesize peptidoglycan. We present a model in which this endogenously synthesized peptidoglycan is essential for the processes of eukaryotic cell division and sleep induction in animals. Genes for peptidoglycan metabolism, like those for lysine biosynthesis in plants, are probably inherited from endosymbiotic bacteria, the ancestors of mitochondria and chloroplasts. Corollaries of this concept, i.e. roles for peptidoglycan metabolism in tumor formation and in the biological clock, are supported by abundant evidence. We propose that many interactions between bacteria and eukaryotes are conditioned by their common genetic heritage.
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Affiliation(s)
- C A Roten
- Institut de génétique et de biologie microbiennes, Lausanne, Switzerland
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Keller R, Gustafson JE, Keist R. The macrophage response to bacteria. Modulation of macrophage functional activity by peptidoglycan from Moraxella (Branhamella) catarrhalis. Clin Exp Immunol 1992; 89:384-9. [PMID: 1516255 PMCID: PMC1554470 DOI: 10.1111/j.1365-2249.1992.tb06967.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Moraxella (Branhamella) catarrhalis organisms have been shown to be particularly efficient in inducing in a pure population of bone marrow-derived mononuclear phagocytes secretory and cellular activities. In the present study, the ability of peptidoglycan from this Gram-negative organism to trigger a macrophage response was compared with that elicited by peptidoglycan from Staphylococcus aureus and Bacillus subtilis. The results show that the three peptidoglycans were similarly active in triggering the secretion of tumour necrosis factor and tumouricidal activity but differed considerably in their ability to induce the generation of nitrite in macrophages; in this respect, peptidoglycan from M. catarrhalis was particularly potent. The impressive capacity of M. catarrhalis peptidoglycan to induce in low concentration the secretion of tumour necrosis factor and nitrite and tumouricidal activity may, in addition to its lipopolysaccharide, contribute to the extraordinary potential of this organism to trigger the functional activities of macrophages.
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Affiliation(s)
- R Keller
- Immunobiology Research Group, University of Zürich, Switzerland
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45
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Gayda RC, Henk MC, Leong D. C-shaped cells caused by expression of an ftsA mutation in Escherichia coli. J Bacteriol 1992; 174:5362-70. [PMID: 1644763 PMCID: PMC206374 DOI: 10.1128/jb.174.16.5362-5370.1992] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A plasmid, pDLL4, was isolated from a Tn5tac1 mutagenesis experiment with plasmid pZAQ. When pDLL4 was transformed into wild-type rod-shaped cells, it caused cells in the population to become curved (C-shaped or convoluted). The Tn5tac1 transposon was integrated within the carboxyl end of the ftsA gene in pDLL4. This mutation was designated ftsAc. Subcloning ftsAc DNA into another plasmid vector verified that the curved-cell phenotype was caused by the expression of this altered gene. DNA sequence analysis of the ftsAc mutation revealed that the transposition event changed the DNA so that the last 28 amino acids of the FtsA protein were lost and 5 new amino acids were added. A radioactive peptide band corresponding to this truncated FtsAc protein was identified by a T7 promoter-T7 polymerase protein labeling system. Observations of thin sections of these curved cells with an electron microscope revealed aggregates of striated cylindrical structures traversing the cytoplasm. The ends of these aggregates appear to be at or near the cell membrane. The linear periodicity of the cylinders was approximately 11 nm, and the diameter of a cylinder was about 15 nm. Aggregates of as many as five cylinders were arrayed diagonally to the long axis of the curved cells, a finding that suggests that some type of internal organization may be causing the curved cell shape.
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Affiliation(s)
- R C Gayda
- Department of Microbiology, Louisiana State University, Baton Rouge
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46
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Abstract
Preparations of purified peptidoglycan of Escherichia coli (i.e., sacculi) were studied by low-angle laser light scattering. Control experiments and theoretical calculations based on the Rayleigh-Gans theory showed that the mean sacculus surface area could be accurately inferred from measurements with our apparatus by using computer routines developed previously. Large changes in the mean saccular surface area resulted from alterations in the stress caused by varying the net charge on the sacculi. The net charge was affected by altering the suspending medium pH, causing carboxyl and amino groups in the peptidoglycan to gain or lose protons, or by acetylation or succinylation of the amino groups. A preponderance of either plus or minus charges caused an expansion of the mean sacculus surface area. The largest increase in area probably represents the elastic limit of the peptidoglycan and was 300% above the area of isoionic sacculi. This degree of expansion is consistent with possible conformations of the intact peptidoglycan structure without necessitating rupture of the wall fabric. Our findings concerning saccular elasticity provide support for the surface stress theory. It provides a mechanism so that bacteria can grow and divide while maintaining turgor pressure, without the necessity of having and using proteins to do the mechanical work.
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Affiliation(s)
- A L Koch
- Department of Biology, Indiana University, Bloomington 47405
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