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Daitch AK, Smith EL, Goley ED. OpgH is an essential regulator of Caulobacter morphology. mBio 2024; 15:e0144324. [PMID: 39145657 DOI: 10.1128/mbio.01443-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 06/20/2024] [Indexed: 08/16/2024] Open
Abstract
Bacterial growth and division rely on intricate regulation of morphogenetic complexes to remodel the cell envelope without compromising envelope integrity. Significant progress has been made in recent years towards understanding the regulation of cell wall metabolic enzymes. However, other cell envelope components play a role in morphogenesis as well. A primary factor required to protect envelope integrity in low osmolarity environments is OpgH, the synthase of osmoregulated periplasmic glucans (OPGs). Here, we demonstrate that OpgH is essential in the α-proteobacterium Caulobacter crescentus. Unexpectedly, depletion of OpgH or attempted complementation with a catalytically dead OpgH variant results in striking asymmetric bulging and cell lysis. These shape defects are accompanied by reduced cell wall synthesis and mislocalization of morphogenetic complexes. Interestingly, overactivation of the CenKR two-component system that has been implicated in cell envelope stress homeostasis in α-proteobacteria phenocopies the morphogenetic defects associated with OpgH depletion. Each of these perturbations leads to an increase in the levels of the elongasome protein, MreB, and decreases in the levels of divisome proteins FtsZ and MipZ as well as OpgH, itself. Constitutive production of OpgH during CenKR overactivation prevents cell bulging, but cells still exhibit morphogenetic defects. We propose that OPG depletion activates CenKR, leading to changes in the expression of cell envelope-related genes, but that OPGs also exert CenKR-independent effects on morphogenesis. Our data establish a surprising function for an OpgH homolog in morphogenesis and reveal an essential role of OpgH in maintaining cell morphology in Caulobacter.IMPORTANCEBacteria must synthesize and fortify the cell envelope in a tightly regulated manner to orchestrate growth and adaptation. Osmoregulated periplasmic glucans (OPGs) are important, but poorly understood, constituents of Gram-negative cell envelopes that contribute to envelope integrity and protect against osmotic stress. Here, we determined that the OPG synthase OpgH plays a surprising, essential role in morphogenesis in Caulobacter crescentus. Loss of OpgH causes asymmetric cell bulging and lysis via misregulation of the localization and activity of morphogenetic complexes. Overactivation of the CenKR two-component system involved in envelope homeostasis phenocopies OpgH depletion, suggesting that depletion of OpgH activates CenKR. Because cell envelope integrity is critical for bacterial survival, understanding how OpgH activity contributes to morphogenesis and maintenance of envelope integrity could aid in the development of antibiotic therapies.
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Affiliation(s)
- Allison K Daitch
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Erika L Smith
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Erin D Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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2
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Janzing NBM, Senges CHR, Dietze P, Haltli B, Marchbank DH, Kerr RG, Bandow JE. Mechanism of action of pseudopteroxazole and pseudopterosin G: Diterpenes from marine origin. Proteomics 2024; 24:e2300390. [PMID: 38158717 DOI: 10.1002/pmic.202300390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
Pseudopteroxazole (Ptx) and the pseudopterosins are marine natural products with promising antibacterial potential. While Ptx has attracted interest for its antimycobacterial activity, pseudopterosins are active against several clinically relevant pathogens. Both compound classes exhibit low cytotoxicity and accessibility to targeted synthesis, yet their antibacterial mechanisms remain elusive. In this study, we investigated the modes of action of Ptx and pseudopterosin G (PsG) in Bacillus subtilis employing an unbiased approach that combines gel-based proteomics with a mathematical similarity analysis of response profiles. Proteomic responses to sublethal concentrations of Ptx and PsG were compared to a library of antibiotic stress response profiles revealing that both induce a stress response characteristic for agents targeting the bacterial cell envelope by interfering with membrane-bound steps of cell wall biosynthesis. Microscopy-based assays confirmed that both compounds compromise the integrity of the bacterial cell wall without disrupting the membrane potential. Furthermore, LC-MSE analysis showed that the greater potency of PsG against B. subtilis, reflected in a lower MIC and a more pronounced proteomic response, may be rooted in a more effective association with and penetration of B. subtilis cells. We conclude that Ptx and PsG target the integrity of the gram-positive cell wall.
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Affiliation(s)
- Niklas B M Janzing
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Christoph H R Senges
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Pascal Dietze
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Bradley Haltli
- University of Prince Edward Island, Charlottetown, PE, Canada
- Nautilus Biosciences Croda, Charlottetown, Canada
| | - Douglas H Marchbank
- University of Prince Edward Island, Charlottetown, PE, Canada
- Nautilus Biosciences Croda, Charlottetown, Canada
| | - Russell G Kerr
- University of Prince Edward Island, Charlottetown, PE, Canada
| | - Julia E Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
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3
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Zheng Y, Zhu X, Jiang M, Cao F, You Q, Chen X. Development and Applications of D-Amino Acid Derivatives-based Metabolic Labeling of Bacterial Peptidoglycan. Angew Chem Int Ed Engl 2024; 63:e202319400. [PMID: 38284300 DOI: 10.1002/anie.202319400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 01/30/2024]
Abstract
Peptidoglycan, an essential component within the cell walls of virtually all bacteria, is composed of glycan strands linked by stem peptides that contain D-amino acids. The peptidoglycan biosynthesis machinery exhibits high tolerance to various D-amino acid derivatives. D-amino acid derivatives with different functionalities can thus be specifically incorporated into and label the peptidoglycan of bacteria, but not the host mammalian cells. This metabolic labeling strategy is highly selective, highly biocompatible, and broadly applicable, which has been utilized in various fields. This review introduces the metabolic labeling strategies of peptidoglycan by using D-amino acid derivatives, including one-step and two-step strategies. In addition, we emphasize the various applications of D-amino acid derivative-based metabolic labeling, including bacterial peptidoglycan visualization (existence, biosynthesis, and dynamics, etc.), bacterial visualization (including bacterial imaging and visualization of growth and division, metabolic activity, antibiotic susceptibility, etc.), pathogenic bacteria-targeted diagnostics and treatment (positron emission tomography (PET) imaging, photodynamic therapy, photothermal therapy, gas therapy, immunotherapy, etc.), and live bacteria-based therapy. Finally, a summary of this metabolic labeling and an outlook is provided.
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Affiliation(s)
- Yongfang Zheng
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou, 350007, P.R. China
| | - Xinyu Zhu
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou, 350007, P.R. China
| | - Mingyi Jiang
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou, 350007, P.R. China
| | - Fangfang Cao
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Qing You
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
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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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George JL, Agbavor C, Cabo LF, Cahoon LA. Streptococcus pneumoniae secretion chaperones PrsA, SlrA, and HtrA are required for competence, antibiotic resistance, colonization, and invasive disease. Infect Immun 2024; 92:e0049023. [PMID: 38226817 PMCID: PMC10863415 DOI: 10.1128/iai.00490-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/19/2023] [Indexed: 01/17/2024] Open
Abstract
Streptococcus pneumoniae is a Gram-positive bacterium and a significant health threat with the populations most at risk being children, the elderly, and the immuno-compromised. To colonize and transition into an invasive infectious organism, S. pneumoniae secretes virulence factors that are translocated across the bacterial membrane and destined for surface exposure, attachment to the cell wall, or secretion into the host. The surface exposed protein chaperones PrsA, SlrA, and HtrA facilitate S. pneumoniae protein secretion; however, the distinct roles contributed by each of these secretion chaperones have not been well defined. Tandem Mass-Tagged Mass Spectrometry and virulence, adhesion, competence, and cell wall integrity assays were used to interrogate the individual and collective contributions of PrsA, SlrA, and HtrA to multiple aspects of S. pneumoniae physiology and virulence. PrsA, SlrA, and HtrA were found to play critical roles in S. pneumoniae host cell infection and competence, and the absence of each of these secretion chaperones significantly altered the S. pneumoniae secretome in distinct ways. PrsA and SlrA were additionally found to contribute to cell wall assembly and resistance to cell wall-active antimicrobials and were important for enabling S. pneumoniae host cell adhesion during colonization and invasive infection. These findings serve to further illustrate the pivotal contributions of PrsA, SlrA, and HtrA to S. pneumoniae protein secretion and virulence.
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Affiliation(s)
- Jada L. George
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Charles Agbavor
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Leah F. Cabo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Laty A. Cahoon
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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6
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Valdivieso González D, Jara J, Almendro-Vedia VG, Orgaz B, López-Montero I. Expansion microscopy applied to mono- and dual-species biofilms. NPJ Biofilms Microbiomes 2023; 9:92. [PMID: 38049404 PMCID: PMC10696089 DOI: 10.1038/s41522-023-00460-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023] Open
Abstract
Expansion microscopy (ExM) is a new super-resolution technique based on embedding the biological sample within a hydrogel and its physical expansion after swelling. This allows increasing its size by several times while preserving its structural details. Applied to prokaryotic cells, ExM requires digestion steps for efficient expansion as bacteria are surrounded by a rigid cell wall. Furthermore, bacteria can live in social groups forming biofilms, where cells are protected from environmental stresses by a self-produced matrix. The extracellular matrix represents an additional impenetrable barrier for ExM. Here we optimize the current protocols of ExM and apply them to mono- and dual-species biofilms formed by clinical isolates of Limosilactobacillus reuteri, Enterococcus faecalis, Serratia marcescens and Staphylococcus aureus. Using scanning electron microscopy for comparison, our results demonstrate that embedded bacteria expanded 3-fold. Moreover, ExM allowed visualizing the three-dimensional architecture of the biofilm and identifying the distribution of different microbial species and their interactions. We also detected the presence of the extracellular matrix after expansion with a specific stain of the polysaccharide component. The potential applications of ExM in biofilms will improve our understanding of these complex communities and have far-reaching implications for industrial and clinical research.
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Affiliation(s)
- David Valdivieso González
- Dto. Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain
- Instituto Pluridisciplinar, Universidad Complutense de Madrid, Ps. Juan XXIII 1, 28040, Madrid, Spain
- Instituto de Investigación Biomédica Hospital Doce de Octubre (Imas12), Avda. de Córdoba s/n, 28041, Madrid, Spain
| | - Josué Jara
- Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Víctor G Almendro-Vedia
- Instituto Pluridisciplinar, Universidad Complutense de Madrid, Ps. Juan XXIII 1, 28040, Madrid, Spain
- Sección Departamental de Farmacia Galénica y Tecnología Alimentaria, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain
- Instituto de Investigación Biomédica Hospital Doce de Octubre (Imas12), Avda. de Córdoba s/n, 28041, Madrid, Spain
| | - Belén Orgaz
- Sección Departamental de Farmacia Galénica y Tecnología Alimentaria, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain
| | - Iván López-Montero
- Dto. Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain.
- Instituto Pluridisciplinar, Universidad Complutense de Madrid, Ps. Juan XXIII 1, 28040, Madrid, Spain.
- Instituto de Investigación Biomédica Hospital Doce de Octubre (Imas12), Avda. de Córdoba s/n, 28041, Madrid, Spain.
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Wilson SA, Tank RKJ, Hobbs JK, Foster SJ, Garner EC. An exhaustive multiple knockout approach to understanding cell wall hydrolase function in Bacillus subtilis. mBio 2023; 14:e0176023. [PMID: 37768080 PMCID: PMC10653849 DOI: 10.1128/mbio.01760-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/03/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE In order to grow, bacterial cells must both create and break down their cell wall. The enzymes that are responsible for these processes are the target of some of our best antibiotics. Our understanding of the proteins that break down the wall- cell wall hydrolases-has been limited by redundancy among the large number of hydrolases many bacteria contain. To solve this problem, we identified 42 cell wall hydrolases in Bacillus subtilis and created a strain lacking 40 of them. We show that cells can survive using only a single cell wall hydrolase; this means that to understand the growth of B. subtilis in standard laboratory conditions, it is only necessary to study a very limited number of proteins, simplifying the problem substantially. We additionally show that the ∆40 strain is a research tool to characterize hydrolases, using it to identify three "helper" hydrolases that act in certain stress conditions.
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Affiliation(s)
- Sean A. Wilson
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
- Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Raveen K. J. Tank
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
| | - Jamie K. Hobbs
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
| | - Simon J. Foster
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Ethan C. Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
- Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA
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Lacotte PA, Denis-Quanquin S, Chatonnat E, Le Bris J, Leparfait D, Lequeux T, Martin-Verstraete I, Candela T. The absence of surface D-alanylation, localized on lipoteichoic acid, impacts the Clostridioides difficile way of life and antibiotic resistance. Front Microbiol 2023; 14:1267662. [PMID: 37965542 PMCID: PMC10642750 DOI: 10.3389/fmicb.2023.1267662] [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: 07/27/2023] [Accepted: 10/13/2023] [Indexed: 11/16/2023] Open
Abstract
Introduction The dlt operon encodes proteins responsible for the esterification of positively charged D-alanine on the wall teichoic acids and lipoteichoic acids of Gram-positive bacteria. This structural modification of the bacterial anionic surface in several species has been described to alter the physicochemical properties of the cell-wall. In addition, it has been linked to reduced sensibilities to cationic antimicrobial peptides and antibiotics. Methods We studied the D-alanylation of Clostridioides difficile polysaccharides with a complete deletion of the dltDABCoperon in the 630 strain. To look for D-alanylation location, surface polysaccharides were purified and analyzed by NMR. Properties of the dltDABCmutant and the parental strains, were determined for bacterial surface's hydrophobicity, motility, adhesion, antibiotic resistance. Results We first confirmed the role of the dltDABCoperon in D-alanylation. Then, we established the exclusive esterification of D-alanine on C. difficile lipoteichoic acid. Our data also suggest that D-alanylation modifies the cell-wall's properties, affecting the bacterial surface's hydrophobicity, motility, adhesion to biotic and abiotic surfaces,and biofilm formation. In addition, our mutant exhibitedincreased sensibilities to antibiotics linked to the membrane, especially bacitracin. A specific inhibitor DLT-1 of DltA reduces the D-alanylation rate in C. difficile but the inhibition was not sufficient to decrease the antibiotic resistance against bacitracin and vancomycin. Conclusion Our results suggest the D-alanylation of C. difficile as an interesting target to tackle C. difficile infections.
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Affiliation(s)
- Pierre-Alexandre Lacotte
- Micalis Institute, Université Paris-Saclay, INRAE AgroParisTech, Jouy-en-Josas, France
- Institut Pasteur, Université Paris Cité, UMR6047 CNRS, Laboratoire Pathogenèse des Bactéries Anaérobies, Paris, France
| | | | - Eva Chatonnat
- Institut Pasteur, Université Paris Cité, UMR6047 CNRS, Laboratoire Pathogenèse des Bactéries Anaérobies, Paris, France
| | - Julie Le Bris
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS UMR3525, Université Paris Cité, Paris, France
| | - David Leparfait
- Normandie Université, Laboratoire de Chimie Moléculaire et Thioorganique LCMT UMR6507, ENSICAEN, UNICAEN, CNRS, Caen, France
| | - Thierry Lequeux
- Normandie Université, Laboratoire de Chimie Moléculaire et Thioorganique LCMT UMR6507, ENSICAEN, UNICAEN, CNRS, Caen, France
| | - Isabelle Martin-Verstraete
- Institut Pasteur, Université Paris Cité, UMR6047 CNRS, Laboratoire Pathogenèse des Bactéries Anaérobies, Paris, France
- Institut Universitaire de France, Paris, France
| | - Thomas Candela
- Micalis Institute, Université Paris-Saclay, INRAE AgroParisTech, Jouy-en-Josas, France
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Blake MJ, Castillo HB, Curtis AE, Calhoun TR. Facilitating flip-flop: Structural tuning of molecule-membrane interactions in living bacteria. Biophys J 2023; 122:1735-1747. [PMID: 37041744 PMCID: PMC10209030 DOI: 10.1016/j.bpj.2023.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 03/17/2023] [Accepted: 04/04/2023] [Indexed: 04/13/2023] Open
Abstract
The first barrier that a small molecule must overcome before trespassing into a living cell is the lipid bilayer surrounding the intracellular content. It is imperative, therefore, to understand how the structure of a small molecule influences its fate in this region. Through the use of second harmonic generation, we show how the differing degrees of ionic headgroups, conjugated system, and branched hydrocarbon tail disparities of a series of four styryl dye molecules influence the propensity to "flip-flop" or to be further organized in the outer leaflet by the membrane. We show here that initial adsorption experiments match previous studies on model systems; however, more complex dynamics are observed over time. Aside from probe molecule structure, these dynamics also vary between cell species and can deviate from trends reported based on model membranes. Specifically, we show here that the membrane composition is an important factor to consider for headgroup-mediated small-molecule dynamics. Overall, the findings presented here on how structural variability of small molecules impacts their initial adsorption and eventual destinations within membranes in the context of living cells could have practical applications in antibiotic and drug adjuvant design.
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Affiliation(s)
- Marea J Blake
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee
| | - Hannah B Castillo
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee
| | - Anna E Curtis
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee
| | - Tessa R Calhoun
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee.
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10
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Manoj KM, Jacob VD, Kavdia M, Tamagawa H, Jaeken L, Soman V. Questioning rotary functionality in the bacterial flagellar system and proposing a murburn model for motility. J Biomol Struct Dyn 2023; 41:15691-15714. [PMID: 36970840 DOI: 10.1080/07391102.2023.2191146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/09/2023] [Indexed: 03/29/2023]
Abstract
Bacterial flagellar system (BFS) was the primary example of a purported 'rotary-motor' functionality in a natural assembly. This mandates the translation of a circular motion of components inside into a linear displacement of the cell body outside, which is supposedly orchestrated with the following features of the BFS: (i) A chemical/electrical differential generates proton motive force (pmf, including a trans-membrane potential, TMP), which is electro-mechanically transduced by inward movement of protons via BFS. (ii) Membrane-bound proteins of BFS serve as stators and the slender filament acts as an external propeller, culminating into a hook-rod that pierces the membrane to connect to a 'broader assembly of deterministically movable rotor'. We had disclaimed the purported pmf/TMP-based respiratory/photosynthetic physiology involving Complex V, which was also perceived as a 'rotary machine' earlier. We pointed out that the murburn redox logic was operative therein. We pursue the following similar perspectives in BFS-context: (i) Low probability for the evolutionary attainment of an ordered/synchronized teaming of about two dozen types of proteins (assembled across five-seven distinct phases) towards the singular agendum of rotary motility. (ii) Vital redox activity (not the gambit of pmf/TMP!) powers the molecular and macroscopic activities of cells, including flagella. (iii) Flagellar movement is noted even in ambiances lacking/countering the directionality mandates sought by pmf/TMP. (iv) Structural features of BFS lack component(s) capable of harnessing/achieving pmf/TMP and functional rotation. A viable murburn model for conversion of molecular/biochemical activity into macroscopic/mechanical outcomes is proposed herein for understanding BFS-assisted motility. HIGHLIGHTSThe motor-like functionalism of bacterial flagellar system (BFS) is analyzedProton/Ion-differential based powering of BFS is unviable in bacteriaUncouplers-sponsored effects were misinterpreted, resulting in a detour in BFS researchThese findings mandate new explanation for nano-bio-mechanical movements in BFSA minimalist murburn model for the bacterial flagella-aided movement is proposedCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kelath Murali Manoj
- Satyamjayatu, The Science & Ethics Foundation, Palakkad District, Kerala, India
| | - Vivian David Jacob
- Satyamjayatu, The Science & Ethics Foundation, Palakkad District, Kerala, India
| | - Mahendra Kavdia
- Department of Biomedical Engineering, Wayne State University, Detroit, Michigan, USA
| | - Hirohisa Tamagawa
- Department of Mechanical Engineering, Gifu University, Gifu City, Japan
| | - Laurent Jaeken
- Department of Industrial Sciences and Technology, Karel de Grote-Hogeschool, Antwerp University Association, Belgium
| | - Vidhu Soman
- Department of Bioscience & Bioengineering, IIT Bombay (& DSS Imagetech Pvt. Ltd), Mumbai, Maharashtra, India
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11
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Corona Ramírez A, Lee KS, Odriozola A, Kaminek M, Stocker R, Zuber B, Junier P. Multiple roads lead to Rome: unique morphology and chemistry of endospores, exospores, myxospores, cysts and akinetes in bacteria. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36804869 DOI: 10.1099/mic.0.001299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The production of specialized resting cells is a remarkable survival strategy developed by many organisms to withstand unfavourable environmental factors such as nutrient depletion or other changes in abiotic and/or biotic conditions. Five bacterial taxa are recognized to form specialized resting cells: Firmicutes, forming endospores; Actinobacteria, forming exospores; Cyanobacteria, forming akinetes; the δ-Proteobacterial order Myxococcales, forming myxospores; and Azotobacteraceae, forming cysts. All these specialized resting cells are characterized by low-to-absent metabolic activity and higher resistance to environmental stress (desiccation, heat, starvation, etc.) when compared to vegetative cells. Given their similarity in function, we tested the potential existence of a universal morpho-chemical marker for identifying these specialized resting cells. After the production of endospores, exospores, akinetes and cysts in model organisms, we performed the first cross-species morphological and chemical comparison of bacterial sporulation. Cryo-electron microscopy of vitreous sections (CEMOVIS) was used to describe near-native morphology of the resting cells in comparison to the morphology of their respective vegetative cells. Resting cells shared a thicker cell envelope as their only common morphological feature. The chemical composition of the different specialized resting cells at the single-cell level was investigated using confocal Raman microspectroscopy. Our results show that the different specialized cells do not share a common chemical signature, but rather each group has a unique signature with a variable conservation of the signature of the vegetative cells. Additionally, we present the validation of Raman signatures associated with calcium dipicolinic acid (CaDPA) and their variation across individual cells to develop specific sorting thresholds for the isolation of endospores. This provides a proof of concept of the feasibility of isolating bacterial spores using a Raman-activated cell-sorting platform. This cross-species comparison and the current knowledge of genetic pathways inducing the formation of the resting cells highlights the complexity of this convergent evolutionary strategy promoting bacterial survival.
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Affiliation(s)
- Andrea Corona Ramírez
- Laboratory of Microbiology, Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
| | - Kang Soo Lee
- Department of Civil, Institute for Environmental Engineering, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | | | - Marek Kaminek
- Institute of Anatomy, University of Bern, Bern, Switzerland
| | - Roman Stocker
- Department of Civil, Institute for Environmental Engineering, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Benoît Zuber
- Institute of Anatomy, University of Bern, Bern, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
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12
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Affiliation(s)
- Sven Truckenbrodt
- Convergent Research, E11 Bio. 1600 Harbor Bay Parkway, Alameda, California94502, United States
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13
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Remodeling of the Enterococcal Cell Envelope during Surface Penetration Promotes Intrinsic Resistance to Stress. mBio 2022; 13:e0229422. [PMID: 36354750 PMCID: PMC9765498 DOI: 10.1128/mbio.02294-22] [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] [Indexed: 11/12/2022] Open
Abstract
Enterococcus faecalis is a normal commensal of the human gastrointestinal tract (GIT). However, upon disruption of gut homeostasis, this nonmotile bacterium can egress from its natural niche and spread to distal organs. While this translocation process can lead to life-threatening systemic infections, the underlying mechanisms remain largely unexplored. Our prior work showed that E. faecalis migration across diverse surfaces requires the formation of matrix-covered multicellular aggregates and the synthesis of exopolysaccharides, but how enterococcal cells are reprogrammed during this process is unknown. Whether surface penetration endows E. faecalis with adaptive advantages is also uncertain. Here, we report that surface penetration promotes the generation of a metabolically and phenotypically distinct E. faecalis population with an enhanced capacity to endure various forms of extracellular stress. Surface-invading enterococci demonstrated major ultrastructural alterations in their cell envelope characterized by increased membrane glycolipid content. These changes were accompanied by marked induction of specific transcriptional programs enhancing cell envelope biogenesis and glycolipid metabolism. Notably, the surface-invading population demonstrated superior tolerance to membrane-damaging antimicrobials, including daptomycin and β-defensins produced by epithelial cells. Genetic mutations impairing glycolipid biosynthesis sensitized E. faecalis to envelope stressors and reduced the ability of this bacterium to penetrate semisolid surfaces and translocate through human intestinal epithelial cell monolayers. Our study reveals that surface penetration induces distinct transcriptional, metabolic, and ultrastructural changes that equip E. faecalis with enhanced capacity to resist external stressors and thrive in its surrounding environment. IMPORTANCE Enterococcus faecalis inhabits the GIT of multiple organisms, where its establishment could be mediated by the formation of biofilm-like aggregates. In susceptible individuals, this bacterium can overgrow and breach intestinal barriers, a process that may lead to lethal systemic infections. While the formation of multicellular aggregates promotes E. faecalis migration across surfaces, little is known about the metabolic and physiological states of the enterococci encased in these surface-penetrating structures. The present study reveals that E. faecalis cells capable of migrating through semisolid surfaces genetically reprogram their metabolism toward increased cell envelope and glycolipid biogenesis, which confers superior tolerance to membrane-damaging agents. E. faecalis's success as a pathobiont depends on its antimicrobial resistance, as well as on its rapid adaptability to overcome multiple environmental challenges. Thus, targeting adaptive genetic and/or metabolic pathways induced during E. faecalis surface penetration may be useful to better confront infections by this bacterium in the clinic.
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14
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Zhang H, Xu L, Gu X, Yu D, Li S. Amphiphilic di-cationic methylene blue for improving antibacterial photodynamic efficiency through high accumulation and low aggregation on bacterial cell surfaces. RSC Adv 2022; 13:239-250. [PMID: 36605628 PMCID: PMC9766197 DOI: 10.1039/d2ra06484g] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
The aggregation state of photosensitizers on the surface of bacterial cells is an important scientific problem for antibacterial photodynamic therapy (APDT). High accumulation and high photoactive state maintenance of photosensitizers are the prerequisite of high APDT efficiency. In this study, an amphiphilic di-cationic methylene blue photosensitizer (C12-MB) was synthesized through quaternization, and its structure, interface properties, photophysical properties and antibacterial photodynamic properties were studied. The results showed that C12-MB could reduce 4.27 log10 CFU and 4.8 log10 CFU for P. aeruginosa and S. aureus under irradiation of light at 660 nm, higher than the parent methylene blue. Through a spectroscopic study on photosensitizer adsorption over the bacterial surface, C12-MB can be accumulated with higher concentration, and the photo-active monomer content is 73% and 70% over P. aeruginosa and S. aureus, higher than those of methylene blue: 25% and 49%, respectively. The higher content of non-aggregated photo-active monomer could contribute to higher antibacterial photodynamic efficiency. For C12-MB adsorbed over bacterial surfaces, planar packing inhibition and electrostatic repulsion could contribute to lower C12-MB aggregation, which provides an useful reference for the structural design of high-efficiency photosensitizers.
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Affiliation(s)
- Hao Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University Nanjing 211816 P. R. China +86-25-58139386
| | - Lixian Xu
- Department of Dermatology, The Second Affiliated Hospital of Nanjing Medical University No. 121 Jiangjiayuan Road Nanjing 210000 P. R. China
| | - Xiaoxiao Gu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University Nanjing 211816 P. R. China +86-25-58139386
| | - Dinghua Yu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University Nanjing 211816 P. R. China +86-25-58139386
| | - Shuang Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University Nanjing 211816 P. R. China +86-25-58139386
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15
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Page EF, Blake MJ, Foley GA, Calhoun TR. Monitoring membranes: The exploration of biological bilayers with second harmonic generation. CHEMICAL PHYSICS REVIEWS 2022; 3:041307. [PMID: 36536669 PMCID: PMC9756348 DOI: 10.1063/5.0120888] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/03/2022] [Indexed: 12/23/2022]
Abstract
Nature's seemingly controlled chaos in heterogeneous two-dimensional cell membranes stands in stark contrast to the precise, often homogeneous, environment in an experimentalist's flask or carefully designed material system. Yet cell membranes can play a direct role, or serve as inspiration, in all fields of biology, chemistry, physics, and engineering. Our understanding of these ubiquitous structures continues to evolve despite over a century of study largely driven by the application of new technologies. Here, we review the insight afforded by second harmonic generation (SHG), a nonlinear optical technique. From potential measurements to adsorption and diffusion on both model and living systems, SHG complements existing techniques while presenting a large exploratory space for new discoveries.
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Affiliation(s)
- Eleanor F. Page
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Marea J. Blake
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Grant A. Foley
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Tessa R. Calhoun
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA
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16
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Fioravanti A, Mathelie-Guinlet M, Dufrêne YF, Remaut H. The Bacillus anthracis S-layer is an exoskeleton-like structure that imparts mechanical and osmotic stabilization to the cell wall. PNAS NEXUS 2022; 1:pgac121. [PMID: 36714836 PMCID: PMC9802277 DOI: 10.1093/pnasnexus/pgac121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 08/02/2022] [Indexed: 02/05/2023]
Abstract
Surface layers (S-layers) are 2D paracrystalline protein monolayers covering the cell envelope of many prokaryotes and archaea. Proposed functions include a role in cell support, as scaffolding structure, as molecular sieve, or as virulence factor. Bacillus anthracis holds two S-layers, composed of Sap or EA1, which interchange in early and late exponential growth phase. We previously found that acute disruption of B. anthracis Sap S-layer integrity, by means of nanobodies, results in severe morphological cell surface defects and cell collapse. Remarkably, this loss of function is due to the destruction of the Sap lattice structure rather than detachment of monomers from the cell surface. Here, we combine force nanoscopy and light microscopy observations to probe the contribution of the S-layer to the mechanical, structural, and functional properties of the cell envelope, which have been so far elusive. Our experiments reveal that cells with a compromised S-layer lattice show a decreased compressive stiffness and elastic modulus. Furthermore, we find that S-layer integrity is required to resist cell turgor under hypotonic conditions. These results present compelling experimental evidence indicating that the S-layers can serve as prokaryotic exoskeletons that support the cell wall in conferring rigidity and mechanical stability to bacterial cells.
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Affiliation(s)
- Antonella Fioravanti
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Marion Mathelie-Guinlet
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Han Remaut
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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17
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Kitahara Y, Oldewurtel ER, Wilson S, Sun Y, Altabe S, de Mendoza D, Garner EC, van Teeffelen S. The role of cell-envelope synthesis for envelope growth and cytoplasmic density in Bacillus subtilis. PNAS NEXUS 2022; 1:pgac134. [PMID: 36082236 PMCID: PMC9437589 DOI: 10.1093/pnasnexus/pgac134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/21/2022] [Indexed: 01/29/2023]
Abstract
All cells must increase their volumes in response to biomass growth to maintain intracellular mass density within physiologically permissive bounds. Here, we investigate the regulation of volume growth in the Gram-positive bacterium Bacillus subtilis. To increase volume, bacteria enzymatically expand their cell envelopes and insert new envelope material. First, we demonstrate that cell-volume growth is determined indirectly, by expanding their envelopes in proportion to mass growth, similarly to the Gram-negative Escherichia coli, despite their fundamentally different envelope structures. Next, we studied, which pathways might be responsible for robust surface-to-mass coupling: We found that both peptidoglycan synthesis and membrane synthesis are required for proper surface-to-mass coupling. However, surprisingly, neither pathway is solely rate-limiting, contrary to wide-spread belief, since envelope growth continues at a reduced rate upon complete inhibition of either process. To arrest cell-envelope growth completely, the simultaneous inhibition of both envelope-synthesis processes is required. Thus, we suggest that multiple envelope-synthesis pathways collectively confer an important aspect of volume regulation, the coordination between surface growth, and biomass growth.
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Affiliation(s)
- Yuki Kitahara
- Département de Microbiologie, Infectiologie, et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, QC, Canada,Université de Paris, Paris, France,Microbial Morphogenesis and Growth Lab, Institut Pasteur, Paris, France
| | - Enno R Oldewurtel
- Microbial Morphogenesis and Growth Lab, Institut Pasteur, Paris, France
| | - Sean Wilson
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, USA,Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - Yingjie Sun
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, USA,Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - Silvia Altabe
- Instituto de Biología Molecular y Celular de Rosario (IBR)-Conicet- and Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Diego de Mendoza
- Instituto de Biología Molecular y Celular de Rosario (IBR)-Conicet- and Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, USA,Center for Systems Biology, Harvard University, Cambridge, MA, USA
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18
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Bhat AV, Basha RA, Chikkaiah MD, Ananthamurthy S. Flagellar rotational features of an optically confined bacterium at high frequency and temporal resolution reveal the microorganism's response to changes in the fluid environment. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2022; 51:225-239. [PMID: 35157113 DOI: 10.1007/s00249-022-01590-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 12/23/2021] [Accepted: 01/22/2022] [Indexed: 01/17/2023]
Abstract
Rotations of the flagella control the movement of a peritrichous (multiflagellar) bacterium in fluids, the run and tumble events being caused through modulations in the flagella's collective rotation speed and pattern. Observing such modulations is a challenge in free swimming bacteria. In this work, we present a setup to measure the collective flagellar rotational features of an optically confined Bacillus subtilis bacterium. We adopt a Continuous Wavelet Technique (CWT) while monitoring the rotational patterns in frequency and time, thus achieving optimal resolution in both the domains. This enables in marking the events wherein subtle changes in the flagellar rotational pattern occur. These studies unravel a fact, hitherto unknown, that variations in swimming speed that are seen in pure run sequences are also caused by modulations in the rotating flagella. Further, we have monitored the flagellar rotation for durations over a minute and observe a gradual slowing down of the rotation before ceasing completely due to the trapping laser induced photodamage. We have observed a significant alteration in the rate of rotational fall off in real time with changes in pH or the nutrient concentration in the fluid. This work serves to demonstrate the advantage of optical confinement of a bacterium in its pristine form for carrying out such studies and can serve as a marker for work that assesses membrane photodamage in active matter. Details on the role of flagella in propulsion and on other factors influencing the rotations, can be of significance in the design of artificial microswimmers.
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Affiliation(s)
| | - Roshan Akbar Basha
- Department of Microbiology and Biotechnology, Bangalore University, Bangalore, 560056, India
| | | | - Sharath Ananthamurthy
- Department of Physics, Bangalore University, Bangalore, 560056, India. .,School of Physics, University of Hyderabad, Hyderabad, 500046, India.
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19
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Sun J, Rutherford ST, Silhavy TJ, Huang KC. Physical properties of the bacterial outer membrane. Nat Rev Microbiol 2022; 20:236-248. [PMID: 34732874 PMCID: PMC8934262 DOI: 10.1038/s41579-021-00638-0] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2021] [Indexed: 11/09/2022]
Abstract
It has long been appreciated that the Gram-negative outer membrane acts as a permeability barrier, but recent studies have uncovered a more expansive and versatile role for the outer membrane in cellular physiology and viability. Owing to recent developments in microfluidics and microscopy, the structural, rheological and mechanical properties of the outer membrane are becoming apparent across multiple scales. In this Review, we discuss experimental and computational studies that have revealed key molecular factors and interactions that give rise to the spatial organization, limited diffusivity and stress-bearing capacity of the outer membrane. These physical properties suggest broad connections between cellular structure and physiology, and we explore future prospects for further elucidation of the implications of outer membrane construction for cellular fitness and survival.
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Affiliation(s)
- Jiawei Sun
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Steven T. Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA 94080, USA,To whom correspondence should be addressed: , ,
| | - Thomas J. Silhavy
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA,To whom correspondence should be addressed: , ,
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, USA. .,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
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20
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Hurst PJ, Morris MA, Graham AA, Nowick JS, Patterson JP. Visualizing Teixobactin Supramolecular Assemblies and Cell Wall Damage in B. Subtilis Using CryoEM. ACS OMEGA 2021; 6:27412-27417. [PMID: 34693162 PMCID: PMC8529686 DOI: 10.1021/acsomega.1c04331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/24/2021] [Indexed: 05/04/2023]
Abstract
The antibiotic teixobactin targets bacterial cell walls. Previous research has proposed that the active form of teixobactin is a nano-/micron-sized supramolecular assembly. Here, we use cryogenic transmission electron microscopy to show that at 1 mg/mL, teixobactin forms sheet-like assemblies that selectively act upon the cell wall. At 4 μg/mL, teixobactin is active, and aggregates are formed either transiently or sparingly at the cell surface.
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Affiliation(s)
- Paul Joshua Hurst
- Department
of Chemistry, University of California—Irvine, Irvine, California 92697-2025, United States
| | - Michael A. Morris
- Department
of Chemistry, University of California—Irvine, Irvine, California 92697-2025, United States
| | - Annissa A. Graham
- Department
of Chemistry, University of California—Irvine, Irvine, California 92697-2025, United States
| | - James S. Nowick
- Department
of Chemistry, University of California—Irvine, Irvine, California 92697-2025, United States
| | - Joseph P. Patterson
- Department
of Chemistry, University of California—Irvine, Irvine, California 92697-2025, United States
- Department
of Materials Science and Engineering, University
of California, Irvine, California 92697, United States
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21
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Alonso-Reyes DG, Galván FS, Portero LR, Alvarado NN, Farías ME, Vazquez MP, Albarracín VH. Genomic insights into an andean multiresistant soil actinobacterium of biotechnological interest. World J Microbiol Biotechnol 2021; 37:166. [PMID: 34463818 PMCID: PMC8405860 DOI: 10.1007/s11274-021-03129-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/14/2021] [Indexed: 12/01/2022]
Abstract
Central-Andean Ecosystems (between 2000 and 6000 m above sea level (masl) are typical arid-to-semiarid environments suffering from the highest total solar and ultraviolet-B radiation on the planet but displaying numerous salt flats and shallow lakes. Andean microbial ecosystems isolated from these environments are of exceptional biodiversity enduring multiple severe conditions. Furthermore, the polyextremophilic nature of the microbes in such ecosystems indicates the potential for biotechnological applications. Within this context, the study undertaken used genome mining, physiological and microscopical characterization to reveal the multiresistant profile of Nesterenkonia sp. Act20, an actinobacterium isolated from the soil surrounding Lake Socompa, Salta, Argentina (3570 masl). Ultravioet-B, desiccation, and copper assays revealed the strain's exceptional resistance to all these conditions. Act20's genome presented coding sequences involving resistance to antibiotics, low temperatures, ultraviolet radiation, arsenic, nutrient-limiting conditions, osmotic stress, low atmospheric-oxygen pressure, heavy-metal stress, and toxic fluoride and chlorite. Act20 can also synthesize proteins and natural products such as an insecticide, bacterial cellulose, ectoine, bacterial hemoglobin, and even antibiotics like colicin V and aurachin C. We also found numerous enzymes for animal- and vegetal-biomass degradation and applications in other industrial processes. The resilience of Act20 and its biotechnologic potential were thoroughly demonstrated in this work.
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Affiliation(s)
- Daniel Gonzalo Alonso-Reyes
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica (CIME), Facultad de Agronomía y Zootecnia, UNT y CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Fátima Silvina Galván
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica (CIME), Facultad de Agronomía y Zootecnia, UNT y CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Luciano Raúl Portero
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica (CIME), Facultad de Agronomía y Zootecnia, UNT y CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Natalia Noelia Alvarado
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica (CIME), Facultad de Agronomía y Zootecnia, UNT y CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - María Eugenia Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Martín P Vazquez
- HERITAS-CONICET, Ocampo 210 bis, Predio CCT, 2000, Rosario, Santa Fe, Argentina
| | - Virginia Helena Albarracín
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica (CIME), Facultad de Agronomía y Zootecnia, UNT y CONICET, San Miguel de Tucumán, Tucumán, Argentina.
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán, Tucumán, Argentina.
- Centro Integral de Microscopía Electrónica (CIME, CONICET, UNT), Camino de Sirga s/n. FAZ, Finca El Manantial, 4107, Yerba Buena, Tucumán, Argentina.
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22
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Halladin DK, Ortega FE, Ng KM, Footer MJ, Mitić NS, Malkov SN, Gopinathan A, Huang KC, Theriot JA. Entropy-driven translocation of disordered proteins through the Gram-positive bacterial cell wall. Nat Microbiol 2021; 6:1055-1065. [PMID: 34326523 DOI: 10.1038/s41564-021-00942-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 06/28/2021] [Indexed: 02/07/2023]
Abstract
In Gram-positive bacteria, a thick cross-linked cell wall separates the membrane from the extracellular space. Some surface-exposed proteins, such as the Listeria monocytogenes actin nucleation-promoting factor ActA, remain associated with the bacterial membrane but somehow thread through tens of nanometres of cell wall to expose their amino terminus to the exterior. Here, we report that entropy enables the translocation of disordered transmembrane proteins through the Gram-positive cell wall. We build a physical model, which predicts that the entropic constraint imposed by a thin periplasm is sufficient to drive the translocation of an intrinsically disordered protein such as ActA across a porous barrier similar to a peptidoglycan cell wall. We experimentally validate our model and show that ActA translocation depends on the cell-envelope dimensions and disordered-protein length, and that translocation is reversible. We also show that disordered regions of eukaryotic proteins can translocate Gram-positive cell walls via entropy. We propose that entropic forces are sufficient to drive the translocation of specific proteins to the outer surface.
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Affiliation(s)
- David K Halladin
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Fabian E Ortega
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Katharine M Ng
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Matthew J Footer
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.,Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Nenad S Mitić
- Faculty of Mathematics, University of Belgrade, Belgrade, Serbia
| | - Saša N Malkov
- Faculty of Mathematics, University of Belgrade, Belgrade, Serbia
| | - Ajay Gopinathan
- Department of Physics, University of California, Merced, CA, USA
| | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Bioengineering, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Julie A Theriot
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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23
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Hahn J, DeSantis M, Dubnau D. Mechanisms of Transforming DNA Uptake to the Periplasm of Bacillus subtilis. mBio 2021; 12:e0106121. [PMID: 34126763 PMCID: PMC8262900 DOI: 10.1128/mbio.01061-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/05/2021] [Indexed: 11/20/2022] Open
Abstract
We demonstrate here that the acquisition of DNase resistance by transforming DNA, often assumed to indicate transport to the cytoplasm, reflects uptake to the periplasm, requiring a reevaluation of conclusions about the roles of several proteins in transformation. The new evidence suggests that the transformation pilus is needed for DNA binding to the cell surface near the cell poles and for the initiation of uptake. The cellular distribution of the membrane-anchored ComEA of Bacillus subtilis does not dramatically change during DNA uptake as does the unanchored ComEA of Vibrio and Neisseria. Instead, our evidence suggests that ComEA stabilizes the attachment of transforming DNA at localized regions in the periplasm and then mediates uptake, probably by a Brownian ratchet mechanism. Following that, the DNA is transferred to periplasmic portions of the channel protein ComEC, which plays a previously unsuspected role in uptake to the periplasm. We show that the transformation endonuclease NucA also facilitates uptake to the periplasm and that the previously demonstrated role of ComFA in the acquisition of DNase resistance derives from the instability of ComGA when ComFA is deleted. These results prompt a new understanding of the early stages of DNA uptake for transformation. IMPORTANCE Transformation is a widely distributed mechanism of bacterial horizontal gene transfer that plays a role in the spread of antibiotic resistance and virulence genes and more generally in evolution. Although transformation was discovered nearly a century ago and most, if not all the proteins required have been identified in several bacterial species, much remains poorly understood about the molecular mechanism of DNA uptake. This study uses epifluorescence microscopy to investigate the passage of labeled DNA into the compartment between the cell wall and the cell membrane of Bacillus subtilis, a necessary early step in transformation. The roles of individual proteins in this process are identified, and their modes of action are clarified.
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Affiliation(s)
- Jeanette Hahn
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Micaela DeSantis
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - David Dubnau
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
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24
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Garner EC. Toward a Mechanistic Understanding of Bacterial Rod Shape Formation and Regulation. Annu Rev Cell Dev Biol 2021; 37:1-21. [PMID: 34186006 DOI: 10.1146/annurev-cellbio-010521-010834] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
One of the most common bacterial shapes is a rod, yet we have a limited understanding of how this simple shape is constructed. While only six proteins are required for rod shape, we are just beginning to understand how they self-organize to build the micron-sized enveloping structures that define bacterial shape out of nanometer-sized glycan strains. Here, we detail and summarize the insights gained over the last 20 years into this complex problem that have been achieved with a wide variety of different approaches. We also explain and compare both current and past models of rod shape formation and maintenance and then highlight recent insights into how the Rod complex might be regulated. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA;
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25
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Erickson HP. How Teichoic Acids Could Support a Periplasm in Gram-Positive Bacteria, and Let Cell Division Cheat Turgor Pressure. Front Microbiol 2021; 12:664704. [PMID: 34040598 PMCID: PMC8141598 DOI: 10.3389/fmicb.2021.664704] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/06/2021] [Indexed: 12/17/2022] Open
Abstract
The cytoplasm of bacteria is maintained at a higher osmolality than the growth medium, which generates a turgor pressure. The cell membrane (CM) cannot support a large turgor, so there are two possibilities for transferring the pressure to the peptidoglycan cell wall (PGW): (1) the CM could be pressed directly against the PGW, or (2) the CM could be separated from the PGW by a periplasmic space that is isoosmotic with the cytoplasm. There is strong evidence for gram-negative bacteria that a periplasm exists and is isoosmotic with the cytoplasm. No comparable studies have been done for gram-positive bacteria. Here I suggest that a periplasmic space is probably essential in order for the periplasmic proteins to function, including especially the PBPs that remodel the peptidoglycan wall. I then present a semi-quantitative analysis of how teichoic acids could support a periplasm that is isoosmotic with the cytoplasm. The fixed anionic charge density of teichoic acids in the periplasm is ∼0.5 M, which would bring in ∼0.5 M Na+ neutralizing ions. This approximately balances the excess osmolality of the cytoplasm that would produce a turgor pressure of 19 atm. The 0.5 M fixed charge density is similar to that of proteoglycans in articular cartilage, suggesting a comparability ability to support pressure. An isoosmotic periplasm would be especially important for cell division, since it would allow CM constriction and PGW synthesis to avoid turgor pressure.
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Affiliation(s)
- Harold P Erickson
- Department of Cell Biology, Duke University Medical Center, Durham, NC, United States
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26
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Rumancev C, Vöpel T, Stuhr S, Gundlach AR, Senkbeil T, Osterhoff M, Sprung M, Garamus VM, Ebbinghaus S, Rosenhahn A. In Cellulo Analysis of Huntingtin Inclusion Bodies by Cryogenic Nanoprobe SAXS. CHEMSYSTEMSCHEM 2021. [DOI: 10.1002/syst.202000050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Christoph Rumancev
- Analytical Chemistry – Biointerfaces Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
| | - Tobias Vöpel
- Department of Physical Chemistry II Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
| | - Susan Stuhr
- Analytical Chemistry – Biointerfaces Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
| | - Andreas R. Gundlach
- Analytical Chemistry – Biointerfaces Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
| | - Tobias Senkbeil
- Analytical Chemistry – Biointerfaces Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
| | - Markus Osterhoff
- Deutsches Elektronen-Synchrotron DESY Notkestr. 85 22607 Hamburg Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron DESY Notkestr. 85 22607 Hamburg Germany
| | - Vasil M. Garamus
- Helmholtz-Zentrum Geesthacht: Centre for Materials and Coast Research Institute of Materials Research Max-Planck-Str. 1 21502 Geesthacht Germany
| | - Simon Ebbinghaus
- Department of Physical Chemistry II Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
- Institute of Physical and Theoretical Chemistry TU Braunschweig Rebenring 56 38106 Braunschweig Germany
| | - Axel Rosenhahn
- Analytical Chemistry – Biointerfaces Ruhr University Bochum Universitätsstr. 150 44780 Bochum Germany
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27
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Wenzel M, Dekker MP, Wang B, Burggraaf MJ, Bitter W, van Weering JRT, Hamoen LW. A flat embedding method for transmission electron microscopy reveals an unknown mechanism of tetracycline. Commun Biol 2021; 4:306. [PMID: 33686188 PMCID: PMC7940657 DOI: 10.1038/s42003-021-01809-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/05/2021] [Indexed: 12/20/2022] Open
Abstract
Transmission electron microscopy of cell sample sections is a popular technique in microbiology. Currently, ultrathin sectioning is done on resin-embedded cell pellets, which consumes milli- to deciliters of culture and results in sections of randomly orientated cells. This is problematic for rod-shaped bacteria and often precludes large-scale quantification of morphological phenotypes due to the lack of sufficient numbers of longitudinally cut cells. Here we report a flat embedding method that enables observation of thousands of longitudinally cut cells per single section and only requires microliter culture volumes. We successfully applied this technique to Bacillus subtilis, Escherichia coli, Mycobacterium bovis, and Acholeplasma laidlawii. To assess the potential of the technique to quantify morphological phenotypes, we monitored antibiotic-induced changes in B. subtilis cells. Surprisingly, we found that the ribosome inhibitor tetracycline causes membrane deformations. Further investigations showed that tetracycline disturbs membrane organization and localization of the peripheral membrane proteins MinD, MinC, and MreB. These observations are not the result of ribosome inhibition but constitute a secondary antibacterial activity of tetracycline that so far has defied discovery.
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Affiliation(s)
- Michaela Wenzel
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands.
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers - Location VUMC, 1081 HZ, Amsterdam, The Netherlands.
- Chemical Biology, Department for Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden.
| | - Marien P Dekker
- Department of Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), Neuroscience Campus Amsterdam, Amsterdam University Medical Centers - Location VUMC, 1081 HZ, Amsterdam, The Netherlands
| | - Biwen Wang
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - Maroeska J Burggraaf
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers - Location VUMC, 1081 HZ, Amsterdam, The Netherlands
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers - Location VUMC, 1081 HZ, Amsterdam, The Netherlands
- Department of Molecular Cell Biology, Amsterdam Institute for Molecules, Medicines, and Systems, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HZ, Amsterdam, The Netherlands
| | - Jan R T van Weering
- Department of Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), Neuroscience Campus Amsterdam, Amsterdam University Medical Centers - Location VUMC, 1081 HZ, Amsterdam, The Netherlands.
| | - Leendert W Hamoen
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
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28
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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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29
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Gordesli-Duatepe FP, Park BJ, Kawas LH, Abu-Lail NI. Atomic Force Microscopy Investigation of the Contributions of Listeria monocytogenes Cell-Wall Biomacromolecules to Their Adherence and Mechanics. J Phys Chem B 2020; 124:5872-5883. [PMID: 32544332 DOI: 10.1021/acs.jpcb.0c04025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, the contributions of the pathogenic Listeria monocytogenes cell-wall biomacromolecules to the bacterial mechanics and adhesion to a model inert surface of silicon nitride in water were investigated by atomic force microscopy. Chemical ethylenediaminetetraacetic acid (EDTA) and biological enzymatic trypsin treatments of cells were performed to partially or totally remove the bacterial cell-wall proteins and carbohydrates. Removal of 48.2% proteins and 29.2% of carbohydrates from the cell-wall of the bacterium by the EDTA treatment resulted in a significant decrease in the length of the bacterial cell-wall biomacromolecules and an increase in the rigidity of the bacterial cells as predicted from fitting a model of steric repulsion to the force-distance approach data and classic Hertz model to the indentation-force data, respectively. In comparison, removal of almost all the cell-wall proteins (99.5% removal) and 8.6% of cell-wall carbohydrates by the trypsin treatment resulted in an increase in the elasticity of the bacterial cells, an increase in the extension of the cell-wall biomacromolecules, and a significant decrease in their apparent grafting densities. In addition, adhesion strength of native-untreated L. monocytogenes to silicon nitride in water decreased by 30% on average after the EDTA treatment and further decreased by 60% on average after the trypsin treatment, showing a positive correlation with the% removal of cell-wall proteins by the EDTA and trypsin treatments, respectively.
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Affiliation(s)
- F Pinar Gordesli-Duatepe
- Department of Genetics and Bioengineering, Faculty of Engineering, Izmir University of Economics, 35330 Izmir, Turkey
| | - Bong J Park
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington 99164, United States
| | - Leen H Kawas
- Department of Veterinary and Comparative Anatomy, Pharmacology, and Physiology, Washington State University Pullman, Washington 99164-6520, United States
| | - Nehal I Abu-Lail
- Department of Biomedical Engineering and Chemical Engineering, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
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30
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Ultee E, van der Aart LT, Zhang L, van Dissel D, Diebolder CA, van Wezel GP, Claessen D, Briegel A. Teichoic acids anchor distinct cell wall lamellae in an apically growing bacterium. Commun Biol 2020; 3:314. [PMID: 32555532 PMCID: PMC7300013 DOI: 10.1038/s42003-020-1038-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 05/28/2020] [Indexed: 11/17/2022] Open
Abstract
The bacterial cell wall is a multicomponent structure that provides structural support and protection. In monoderm species, the cell wall is made up predominantly of peptidoglycan, teichoic acids and capsular glycans. Filamentous monoderm Actinobacteria incorporate new cell-wall material at their tips. Here we use cryo-electron tomography to reveal the architecture of the actinobacterial cell wall of Streptomyces coelicolor. Our data shows a density difference between the apex and subapical regions. Removal of teichoic acids results in a patchy cell wall and distinct lamellae. Knock-down of tagO expression using CRISPR-dCas9 interference leads to growth retardation, presumably because build-in of teichoic acids had become rate-limiting. Absence of extracellular glycans produced by MatAB and CslA proteins results in a thinner wall lacking lamellae and patches. We propose that the Streptomyces cell wall is composed of layers of peptidoglycan and extracellular polymers that are structurally supported by teichoic acids.
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Affiliation(s)
- Eveline Ultee
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Lizah T van der Aart
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Le Zhang
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Dino van Dissel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Christoph A Diebolder
- Netherlands Centre for Electron Nanoscopy (NeCEN), Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gilles P van Wezel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Dennis Claessen
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Ariane Briegel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands.
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31
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Fan Y, Lim Y, Wyss LS, Park S, Xu C, Fu H, Fei J, Hong Y, Wang B. Mechanical expansion microscopy. Methods Cell Biol 2020; 161:125-146. [PMID: 33478686 DOI: 10.1016/bs.mcb.2020.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
This chapter describes two mechanical expansion microscopy methods with accompanying step-by-step protocols. The first method, mechanically resolved expansion microscopy, uses non-uniform expansion of partially digested samples to provide the imaging contrast that resolves local mechanical properties. Examining bacterial cell wall with this method, we are able to distinguish bacterial species in mixed populations based on their distinct cell wall rigidity and detect cell wall damage caused by various physiological and chemical perturbations. The second method is mechanically locked expansion microscopy, in which we use a mechanically stable gel network to prevent the original polyacrylate network from shrinking in ionic buffers. This method allows us to use anti-photobleaching buffers in expansion microscopy, enabling detection of novel ultra-structures under the optical diffraction limit through super-resolution single molecule localization microscopy on bacterial cells and whole-mount immunofluorescence imaging in thick animal tissues. We also discuss potential applications and assess future directions.
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Affiliation(s)
- Yuhang Fan
- Department of Bioengineering, Stanford University, Stanford, CA, United States
| | - Youngbin Lim
- Department of Bioengineering, Stanford University, Stanford, CA, United States
| | - Livia S Wyss
- Department of Biology, Stanford University, Stanford, CA, United States
| | - Seongjin Park
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Cancan Xu
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, United States
| | - Huikang Fu
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, United States
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States; Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, United States
| | - Yi Hong
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, United States
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, CA, United States; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, United States.
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32
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Wang S, Zhu Y, Yang Y, Li J, Hoffmann MR. Electrochemical cell lysis of gram-positive and gram-negative bacteria: DNA extraction from environmental water samples. Electrochim Acta 2020; 338:135864. [PMID: 32255836 PMCID: PMC7063685 DOI: 10.1016/j.electacta.2020.135864] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 11/17/2022]
Abstract
Cell lysis is an essential step for the nucleic acid-based surveillance of bacteriological water quality. Recently, electrochemical cell lysis (ECL), which is based on the local generation of hydroxide at a cathode surface, has been reported to be a rapid and reagent-free method for cell lysis. Herein, we describe the development of a milliliter-output ECL device and its performance characterization with respect to the DNA extraction efficiency for gram-negative bacteria (Escherichia coli and Salmonella Typhi) and gram-positive bacteria (Enterococcus durans and Bacillus subtilis). Both gram-negative and gram-positive bacteria were successfully lysed within a short but optimal duration of 1 min at a low voltage of ∼5 V. The ECL method described herein, is demonstrated to be applicable to various environmental water sample types, including pond water, treated wastewater, and untreated wastewater with DNA extraction efficiencies similar to a commercial DNA extraction kit. The ECL system outperformed homogeneous chemical lysis in terms of reaction times and DNA extraction efficiencies, due in part to the high pH generated at the cathode surface, which was predicted by simulations of the hydroxide transport in the cathodic chamber. Our work indicates that the ECL method for DNA extraction is rapid, simplified and low-cost with no need for complex instrumentation. It has demonstrable potential as a prelude to PCR analyses of waterborne bacteria in the field, especially for the gram-negative ones.
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Affiliation(s)
| | | | | | | | - Michael R. Hoffmann
- Linde+Robinson Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
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33
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Abstract
Transformation is a widespread mechanism of horizontal gene transfer in bacteria. DNA uptake to the periplasmic compartment requires a DNA-uptake pilus and the DNA-binding protein ComEA. In the gram-negative bacteria, DNA is first pulled toward the outer membrane by retraction of the pilus and then taken up by binding to periplasmic ComEA, acting as a Brownian ratchet to prevent backward diffusion. A similar mechanism probably operates in the gram-positive bacteria as well, but these systems have been less well characterized. Transport, defined as movement of a single strand of transforming DNA to the cytosol, requires the channel protein ComEC. Although less is understood about this process, it may be driven by proton symport. In this review we also describe various phenomena that are coordinated with the expression of competence for transformation, such as fratricide, the kin-discriminatory killing of neighboring cells, and competence-mediated growth arrest.
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Affiliation(s)
- David Dubnau
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA;
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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34
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Lim Y, Shiver AL, Khariton M, Lane KM, Ng KM, Bray SR, Qin J, Huang KC, Wang B. Mechanically resolved imaging of bacteria using expansion microscopy. PLoS Biol 2019; 17:e3000268. [PMID: 31622337 PMCID: PMC6797083 DOI: 10.1371/journal.pbio.3000268] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 09/05/2019] [Indexed: 11/19/2022] Open
Abstract
Imaging dense and diverse microbial communities has broad applications in basic microbiology and medicine, but remains a grand challenge due to the fact that many species adopt similar morphologies. While prior studies have relied on techniques involving spectral labeling, we have developed an expansion microscopy method (μExM) in which bacterial cells are physically expanded prior to imaging. We find that expansion patterns depend on the structural and mechanical properties of the cell wall, which vary across species and conditions. We use this phenomenon as a quantitative and sensitive phenotypic imaging contrast orthogonal to spectral separation to resolve bacterial cells of different species or in distinct physiological states. Focusing on host-microbe interactions that are difficult to quantify through fluorescence alone, we demonstrate the ability of μExM to distinguish species through an in vitro defined community of human gut commensals and in vivo imaging of a model gut microbiota, and to sensitively detect cell-envelope damage caused by antibiotics or previously unrecognized cell-to-cell phenotypic heterogeneity among pathogenic bacteria as they infect macrophages.
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Affiliation(s)
- Youngbin Lim
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Anthony L. Shiver
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Margarita Khariton
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Keara M. Lane
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Katharine M. Ng
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Samuel R. Bray
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Jian Qin
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
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35
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Li F, Tang Y, Li C, Zheng Y, Liu X, Feng C, Zhao W, Wang F. Adsorption and sequestration of cadmium ions by polyptychial mesoporous biochar derived from Bacillus sp. biomass. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:23505-23523. [PMID: 31197673 DOI: 10.1007/s11356-019-05610-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/28/2019] [Indexed: 06/09/2023]
Abstract
Bacteria-derived biochars from Bucillus sp. biomass under different pyrolysis temperature (250 °C, 350 °C, 450 °C, and 550 °C, respectively) were prepared, forming polyptychial, mesoporous graphite-like structure. The adsorption and sequestration efficiencies of Cd2+ by these biochars were evaluated, and the underlying mechanisms were then discussed. Cd2+ sorption data could be well described by Langmuir mode while the pseudo-second-order kinetic model and Elovich model best fitted the kinetic data. The functional groups complexation, cation-π interactions, and interaction with minerals (including surface precipitation with phosphorus and ion exchange) jointly contributed to Cd2+ sorption and sequestration on biochar, but the interaction with minerals played a dominant role by forming insoluble cadmium salt composed by polycrystalline and/or amorphous phosphate-bridged ternary complex. The maximum sorption capacity of BBC350 in simulated water phase of soil for Cd2+ was 34.6 mg/g. Furthermore, the addition of bacteria-derived biochars (1%, w/w) decreased the fractions easily absorbed by plants for Cd in the test paddy soils by 1.9-26% in a 10-day time. Results of this study suggest that bacteria-derived biochar would be a promising functional material in environmental and agricultural application.
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Affiliation(s)
- Feng Li
- College of Environment Science and Resources, Xiangtan University, Xiangtan, 411105, People's Republic of China.
- Hunan Engineering Laboratory for high efficiency purification technology and its application on complex heavy metal wastewater treatment, Xiangtan, 411105, People's Republic of China.
| | - Yixin Tang
- College of Environment Science and Resources, Xiangtan University, Xiangtan, 411105, People's Republic of China
- Hunan Engineering Laboratory for high efficiency purification technology and its application on complex heavy metal wastewater treatment, Xiangtan, 411105, People's Republic of China
| | - Chengcheng Li
- College of Environment Science and Resources, Xiangtan University, Xiangtan, 411105, People's Republic of China
- Hunan Engineering Laboratory for high efficiency purification technology and its application on complex heavy metal wastewater treatment, Xiangtan, 411105, People's Republic of China
| | - Yang Zheng
- College of Environment Science and Resources, Xiangtan University, Xiangtan, 411105, People's Republic of China
- Hunan Engineering Laboratory for high efficiency purification technology and its application on complex heavy metal wastewater treatment, Xiangtan, 411105, People's Republic of China
| | - Xingwang Liu
- College of Environment Science and Resources, Xiangtan University, Xiangtan, 411105, People's Republic of China
- Hunan Engineering Laboratory for high efficiency purification technology and its application on complex heavy metal wastewater treatment, Xiangtan, 411105, People's Republic of China
| | - Chuang Feng
- College of Environment Science and Resources, Xiangtan University, Xiangtan, 411105, People's Republic of China
- Hunan Engineering Laboratory for high efficiency purification technology and its application on complex heavy metal wastewater treatment, Xiangtan, 411105, People's Republic of China
| | - Wan Zhao
- College of Environment Science and Resources, Xiangtan University, Xiangtan, 411105, People's Republic of China
- Hunan Engineering Laboratory for high efficiency purification technology and its application on complex heavy metal wastewater treatment, Xiangtan, 411105, People's Republic of China
| | - Fang Wang
- College of Environment Science and Resources, Xiangtan University, Xiangtan, 411105, People's Republic of China
- Hunan Engineering Laboratory for high efficiency purification technology and its application on complex heavy metal wastewater treatment, Xiangtan, 411105, People's Republic of China
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36
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Khanna K, Lopez-Garrido J, Zhao Z, Watanabe R, Yuan Y, Sugie J, Pogliano K, Villa E. The molecular architecture of engulfment during Bacillus subtilis sporulation. eLife 2019; 8:45257. [PMID: 31282858 PMCID: PMC6684271 DOI: 10.7554/elife.45257] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 07/04/2019] [Indexed: 01/08/2023] Open
Abstract
The study of bacterial cell biology is limited by difficulties in visualizing cellular structures at high spatial resolution within their native milieu. Here, we visualize Bacillus subtilis sporulation using cryo-electron tomography coupled with cryo-focused ion beam milling, allowing the reconstruction of native-state cellular sections at molecular resolution. During sporulation, an asymmetrically-positioned septum generates a larger mother cell and a smaller forespore. Subsequently, the mother cell engulfs the forespore. We show that the septal peptidoglycan is not completely degraded at the onset of engulfment. Instead, the septum is uniformly and only slightly thinned as it curves towards the mother cell. Then, the mother cell membrane migrates around the forespore in tiny finger-like projections, whose formation requires the mother cell SpoIIDMP protein complex. We propose that a limited number of SpoIIDMP complexes tether to and degrade the peptidoglycan ahead of the engulfing membrane, generating an irregular membrane front.
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Affiliation(s)
- Kanika Khanna
- Division of Biological SciencesUniversity of California, San DiegoLa JollaUnited States
| | - Javier Lopez-Garrido
- Division of Biological SciencesUniversity of California, San DiegoLa JollaUnited States
| | - Ziyi Zhao
- Division of Biological SciencesUniversity of California, San DiegoLa JollaUnited States
| | - Reika Watanabe
- Division of Biological SciencesUniversity of California, San DiegoLa JollaUnited States
| | - Yuan Yuan
- Division of Biological SciencesUniversity of California, San DiegoLa JollaUnited States
| | - Joseph Sugie
- Division of Biological SciencesUniversity of California, San DiegoLa JollaUnited States
| | - Kit Pogliano
- Division of Biological SciencesUniversity of California, San DiegoLa JollaUnited States
| | - Elizabeth Villa
- Division of Biological SciencesUniversity of California, San DiegoLa JollaUnited States
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37
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Porfírio S, Carlson RW, Azadi P. Elucidating Peptidoglycan Structure: An Analytical Toolset. Trends Microbiol 2019; 27:607-622. [DOI: 10.1016/j.tim.2019.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/16/2019] [Accepted: 01/29/2019] [Indexed: 01/04/2023]
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38
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Abstract
The chapter about the Gram-positive bacterial cell wall gives a brief historical background on the discovery of Gram-positive cell walls and their constituents and microscopic methods applied for studying the Gram-positive cell envelope. Followed by the description of the different chemical building blocks of peptidoglycan and the biosynthesis of the peptidoglycan layers and high turnover of peptidoglycan during bacterial growth. Lipoteichoic acids and wall teichoic acids are highlighted as major components of the cell wall. Characterization of capsules and the formation of extracellular vesicles by Gram-positive bacteria close the section on cell envelopes which have a high impact on bacterial pathogenesis. In addition, the specialized complex and unusual cell wall of mycobacteria is introduced thereafter. Next a short back view is given on the development of electron microscopic examinations for studying bacterial cell walls. Different electron microscopic techniques and methods applied to examine bacterial cell envelopes are discussed in the view that most of the illustrated methods should be available in a well-equipped life sciences orientated electron microscopic laboratory. In addition, newly developed and mostly well-established cryo-methods like high-pressure freezing and freeze-substitution (HPF-FS) and cryo-sections of hydrated vitrified bacteria (CEMOVIS, Cryo-electron microscopy of vitreous sections) are described. At last, modern cryo-methods like cryo-electron tomography (CET) and cryo-FIB-SEM milling (focus ion beam-scanning electron microscopy) are introduced which are available only in specialized institutions, but at present represent the best available methods and techniques to study Gram-positive cell walls under close-to-nature conditions in great detail and at high resolution.
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Affiliation(s)
- Manfred Rohde
- Helmholtz Centre for Infection Research, HZI, Central Facility for Microscopy, ZEIM, Braunschweig, Germany
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39
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Flores-Kim J, Dobihal GS, Fenton A, Rudner DZ, Bernhardt TG. A switch in surface polymer biogenesis triggers growth-phase-dependent and antibiotic-induced bacteriolysis. eLife 2019; 8:44912. [PMID: 30964003 PMCID: PMC6456293 DOI: 10.7554/elife.44912] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 03/11/2019] [Indexed: 01/21/2023] Open
Abstract
Penicillin and related antibiotics disrupt cell wall synthesis to induce bacteriolysis. Lysis in response to these drugs requires the activity of cell wall hydrolases called autolysins, but how penicillins misactivate these deadly enzymes has long remained unclear. Here, we show that alterations in surface polymers called teichoic acids (TAs) play a key role in penicillin-induced lysis of the Gram-positive pathogen Streptococcus pneumoniae (Sp). We find that during exponential growth, Sp cells primarily produce lipid-anchored TAs called lipoteichoic acids (LTAs) that bind and sequester the major autolysin LytA. However, penicillin-treatment or prolonged stationary phase growth triggers the degradation of a key LTA synthase, causing a switch to the production of wall-anchored TAs (WTAs). This change allows LytA to associate with and degrade its cell wall substrate, thus promoting osmotic lysis. Similar changes in surface polymer assembly may underlie the mechanism of antibiotic- and/or growth phase-induced lysis for other important Gram-positive pathogens.
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Affiliation(s)
- Josué Flores-Kim
- Department of Microbiology, Harvard Medical School, Boston, United States
| | | | - Andrew Fenton
- Department of Microbiology, Harvard Medical School, Boston, United States.,The Florey Institute, Molecular Biology Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - David Z Rudner
- Department of Microbiology, Harvard Medical School, Boston, United States
| | - Thomas G Bernhardt
- Department of Microbiology, Harvard Medical School, Boston, United States.,Howard Hughes Medical Institute, Boston, United States
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40
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Zuber B, Lučić V. Molecular architecture of the presynaptic terminal. Curr Opin Struct Biol 2019; 54:129-138. [PMID: 30925443 DOI: 10.1016/j.sbi.2019.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/11/2019] [Accepted: 01/26/2019] [Indexed: 10/27/2022]
Abstract
Neurotransmitter release at the presynaptic terminal is one of the fundamental processes in neuronal communication. It is a complex process comprising signaling pathways that exert a precise spatio-temporal coordination to prepare and bring synaptic vesicles to exocytosis. While many molecular components involved have been identified, their direct observation at different stages of the neurotransmitter release is lacking. Three-dimensional imaging by electron tomography provided remarkable views of the synaptic vesicles and the cytomatrix. Imaging fully hydrated, vitrified samples allowed a direct visualization, precise localization and a quantitative characterization of pleomorphic synaptic vesicle-bound complexes in situ, as well as the elucidation of their function in the neurotransmitter release.
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Affiliation(s)
- Benoît Zuber
- Institute of Anatomy, University of Bern, Bern 3012, Switzerland
| | - Vladan Lučić
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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41
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Christensen S, McMahon RM, Martin JL, Huston WM. Life inside and out: making and breaking protein disulfide bonds in Chlamydia. Crit Rev Microbiol 2019; 45:33-50. [PMID: 30663449 DOI: 10.1080/1040841x.2018.1538933] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Disulphide bonds are widely used among all domains of life to provide structural stability to proteins and to regulate enzyme activity. Chlamydia spp. are obligate intracellular bacteria that are especially dependent on the formation and degradation of protein disulphide bonds. Members of the genus Chlamydia have a unique biphasic developmental cycle alternating between two distinct cell types; the extracellular infectious elementary body (EB) and the intracellular replicating reticulate body. The proteins in the envelope of the EB are heavily cross-linked with disulphides and this is known to be critical for this infectious phase. In this review, we provide a comprehensive summary of what is known about the redox state of chlamydial envelope proteins throughout the developmental cycle. We focus especially on the factors responsible for degradation and formation of disulphide bonds in Chlamydia and how this system compares with redox regulation in other organisms. Focussing on the unique biology of Chlamydia enables us to provide important insights into how specialized suites of disulphide bond (Dsb) proteins cater for specific bacterial environments and lifecycles.
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Affiliation(s)
- Signe Christensen
- a Division of Chemistry and Structural Biology , Institute for Molecular Bioscience, University of Queensland , St. Lucia , QLD , Australia.,b Griffith Institute for Drug Discovery, Griffith University , Nathan , QLD , Australia
| | - Róisín M McMahon
- b Griffith Institute for Drug Discovery, Griffith University , Nathan , QLD , Australia
| | - Jennifer L Martin
- b Griffith Institute for Drug Discovery, Griffith University , Nathan , QLD , Australia
| | - Wilhelmina M Huston
- c School of Life Sciences , University of Technology Sydney , Ultimo , NSW , Australia
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42
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Velic A, Tesfamichael T, Li Z, Yarlagadda PK. Parametric Study on Nanopattern Bactericidal Activity. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.promfg.2019.02.072] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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43
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Abstract
The peptidoglycan sacculus is a net-like polymer that surrounds the cytoplasmic membrane in most bacteria. It is essential to maintain the bacterial cell shape and protect from turgor. The peptidoglycan has a basic composition, common to all bacteria, with species-specific variations that can modify its biophysical properties or the pathogenicity of the bacteria. The synthesis of peptidoglycan starts in the cytoplasm and the precursor lipid II is flipped across the cytoplasmic membrane. The new peptidoglycan strands are synthesised and incorporated into the pre-existing sacculus by the coordinated activities of peptidoglycan synthases and hydrolases. In the model organism Escherichia coli there are two complexes required for the elongation and division. Each of them is regulated by different proteins from both the cytoplasmic and periplasmic sides that ensure the well-coordinated synthesis of new peptidoglycan.
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44
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Kenward PA, Simister RL, Morgan-Lang C, Finke N, Sturm A, Hallam SJ, Crowe SA. Recovering cellular biomass from fluids using chemical flocculation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:686-694. [PMID: 30230256 DOI: 10.1111/1758-2229.12690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/31/2018] [Accepted: 09/03/2018] [Indexed: 06/08/2023]
Abstract
We developed an efficient, scalable and inexpensive method for recovering cellular biomass from complex fluid matrices that cannot be processed using conventional filtration methods. The method uses chemical flocculation with iron oxyhydroxides, is capable of recovering greater than 90% of cellular biomass from fluids with more than 103 cells ml-1 , and was validated using both mock communities and field samples. High quality DNA can be readily extracted from iron flocs using standard soil extraction kits. We applied chemical flocculation to fracing fluids from British Columbia, Canada and recovered a diversity of microbial taxa including abundant members of the Epsilon- and Deltaproteobacteria previously recovered from shale gas operations in the United States. Application of chemical flocculation presents new opportunities for scalable time-series monitoring and experimentation on complex fluid matrices including microbial community profiling and shotgun metagenomics over gas production well completion cycles.
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Affiliation(s)
- Paul A Kenward
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Earth, Ocean and Atmospheric Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rachel L Simister
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Earth, Ocean and Atmospheric Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Connor Morgan-Lang
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Niko Finke
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Earth, Ocean and Atmospheric Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Arne Sturm
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Earth, Ocean and Atmospheric Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J Hallam
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada
- Genome Sciences and Technology Training Program, University of British Columbia, Vancouver, British Columbia, Canada
- Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean A Crowe
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Earth, Ocean and Atmospheric Science, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
- Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, British Columbia, Canada
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45
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Khursigara CM, Koval SF, Moyles DM, Harris RJ. Inroads through the bacterial cell envelope: seeing is believing. Can J Microbiol 2018; 64:601-617. [DOI: 10.1139/cjm-2018-0091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A singular feature of all prokaryotic cells is the presence of a cell envelope composed of a cytoplasmic membrane and a cell wall. The introduction of bacterial cell fractionation techniques in the 1950s and 1960s along with developments in procedures for electron microscopy opened the window towards an understanding of the chemical composition and architecture of the cell envelope. This review traces the contribution of Terry Beveridge in these endeavours, beginning with his doctoral studies in the 1970s on the structure of paracrystalline surface arrays (S-layers), followed by an exploration of cryogenic methods for preserving bacteria for ultrastructural analyses. His insights are reflected in a current example of the contribution of cryo-electron microscopy to S-layer studies — the structure and assembly of the surface array of Caulobacter crescentus. The review then focuses on Terry’s contributions to imaging the ultrastructure of bacterial cell envelopes and to the development of cryo-electron microscopy techniques, including the use of CEMOVIS (Cryo-electron Microscopy of Vitreous Sections) to “see” the ultrastructure of the Gram-positive cell envelope — his last scientific endeavour.
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Affiliation(s)
- Cezar M. Khursigara
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Molecular and Cellular Imaging Facility, Advanced Analysis Centre, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Susan F. Koval
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Dianne M. Moyles
- Molecular and Cellular Imaging Facility, Advanced Analysis Centre, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Robert J. Harris
- Molecular and Cellular Imaging Facility, Advanced Analysis Centre, University of Guelph, Guelph, ON N1G 2W1, Canada
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46
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Moynihan PJ. The lasting impact of the 2013 Beveridge poster award. Can J Microbiol 2018; 64:645. [PMID: 30169129 DOI: 10.1139/cjm-2017-0458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Patrick J Moynihan
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, England.,School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, England
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47
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Holden S. Probing the mechanistic principles of bacterial cell division with super-resolution microscopy. Curr Opin Microbiol 2018; 43:84-91. [DOI: 10.1016/j.mib.2017.12.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 12/04/2017] [Accepted: 12/14/2017] [Indexed: 12/26/2022]
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48
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Abstract
Peptidoglycan is an essential component of the cell wall that protects bacteria from environmental stress. A carefully coordinated biosynthesis of peptidoglycan during cell elongation and division is required for cell viability. This biosynthesis involves sophisticated enzyme machineries that dynamically synthesize, remodel, and degrade peptidoglycan. However, when and where bacteria build peptidoglycan, and how this is coordinated with cell growth, have been long-standing questions in the field. The improvement of microscopy techniques has provided powerful approaches to study peptidoglycan biosynthesis with high spatiotemporal resolution. Recent development of molecular probes further accelerated the growth of the field, which has advanced our knowledge of peptidoglycan biosynthesis dynamics and mechanisms. Here, we review the technologies for imaging the bacterial cell wall and its biosynthesis activity. We focus on the applications of fluorescent d-amino acids, a newly developed type of probe, to visualize and study peptidoglycan synthesis and dynamics, and we provide direction for prospective research.
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Affiliation(s)
- Atanas D Radkov
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.,Current affiliation: Biophysics and Biochemistry Department, University of California, San Francisco, California 94158, USA;
| | - Yen-Pang Hsu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA; , ,
| | - Garrett Booher
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA; , ,
| | - Michael S VanNieuwenhze
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA; , ,
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49
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Li K, Yuan XX, Sun HM, Zhao LS, Tang R, Chen ZH, Qin QL, Chen XL, Zhang YZ, Su HN. Atomic Force Microscopy of Side Wall and Septa Peptidoglycan From Bacillus subtilis Reveals an Architectural Remodeling During Growth. Front Microbiol 2018; 9:620. [PMID: 29651285 PMCID: PMC5884923 DOI: 10.3389/fmicb.2018.00620] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/16/2018] [Indexed: 02/02/2023] Open
Abstract
Peptidoglycan is the fundamental structural constituent of the bacterial cell wall. Despite many years of research, the architecture of peptidoglycan is still largely elusive. Here, we report the high-resolution architecture of peptidoglycan from the model Gram-positive bacterium Bacillus subtilis. We provide high-resolution evidence of peptidoglycan architecture remodeling at different growth stages. Side wall peptidoglycan from B. subtilis strain AS1.398 changed from an irregular architecture in exponential growth phase to an ordered cable-like architecture in stationary phase. Thickness of side wall peptidoglycan was found to be related with growth stages, with a slight increase after transition to stationary phase. Septal disks were synthesized progressively toward the center, while the surface features were less clear than those imaged with side walls. Compared with previous studies, our results revealed slight differences in architecture of peptidoglycan from different B. subtilis strains, expanding our knowledge about the architectural features of B. subtilis peptidoglycan.
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Affiliation(s)
- Kang Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Xiao-Xue Yuan
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - He-Min Sun
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Long-Sheng Zhao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Ruocong Tang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Zhi-Hua Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China.,College of Marine Life Sciences, Ocean University of China, Qingdao, China
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50
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Aljabali AAA, Hussein E, Aljumaili O, Zoubi MA, Altrad B, Albatayneh K, Abd Al-razaq MA. Rapid Magnetic Nanobiosensor for the detection ofSerratia marcescen. ACTA ACUST UNITED AC 2018. [DOI: 10.1088/1757-899x/305/1/012005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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