1
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Massier L, Musat N, Stumvoll M, Tremaroli V, Chakaroun R, Kovacs P. Tissue-resident bacteria in metabolic diseases: emerging evidence and challenges. Nat Metab 2024; 6:1209-1224. [PMID: 38898236 DOI: 10.1038/s42255-024-01065-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/13/2024] [Indexed: 06/21/2024]
Abstract
Although the impact of the gut microbiome on health and disease is well established, there is controversy regarding the presence of microorganisms such as bacteria and their products in organs and tissues. However, recent contamination-aware findings of tissue-resident microbial signatures provide accumulating evidence in support of bacterial translocation in cardiometabolic disease. The latter provides a distinct paradigm for the link between microbial colonizers of mucosal surfaces and host metabolism. In this Perspective, we re-evaluate the concept of tissue-resident bacteria including their role in metabolic low-grade tissue and systemic inflammation. We examine the limitations and challenges associated with studying low bacterial biomass samples and propose experimental and analytical strategies to overcome these issues. Our Perspective aims to encourage further investigation of the mechanisms linking tissue-resident bacteria to host metabolism and their potentially actionable health implications for prevention and treatment.
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Affiliation(s)
- Lucas Massier
- Department of Medicine (H7), Karolinska Institutet, Stockholm, Sweden
| | - Niculina Musat
- Aarhus University, Department of Biology, Section for Microbiology, Århus, Denmark
| | - Michael Stumvoll
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Rima Chakaroun
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.
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2
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Tamura A, Azam AH, Nakamura T, Lee K, Iyoda S, Kondo K, Ojima S, Chihara K, Yamashita W, Cui L, Akeda Y, Watashi K, Takahashi Y, Yotsuyanagi H, Kiga K. Synthetic phage-based approach for sensitive and specific detection of Escherichia coli O157. Commun Biol 2024; 7:535. [PMID: 38710842 DOI: 10.1038/s42003-024-06247-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
Escherichia coli O157 can cause foodborne outbreaks, with infection leading to severe disease such as hemolytic-uremic syndrome. Although phage-based detection methods for E. coli O157 are being explored, research on their specificity with clinical isolates is lacking. Here, we describe an in vitro assembly-based synthesis of vB_Eco4M-7, an O157 antigen-specific phage with a 68-kb genome, and its use as a proof of concept for E. coli O157 detection. Linking the detection tag to the C-terminus of the tail fiber protein, gp27 produces the greatest detection sensitivity of the 20 insertions sites tested. The constructed phage detects all 53 diverse clinical isolates of E. coli O157, clearly distinguishing them from 35 clinical isolates of non-O157 Shiga toxin-producing E. coli. Our efficient phage synthesis methods can be applied to other pathogenic bacteria for a variety of applications, including phage-based detection and phage therapy.
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Affiliation(s)
- Azumi Tamura
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
- Division of Infectious Diseases, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Aa Haeruman Azam
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Tomohiro Nakamura
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Kenichi Lee
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Sunao Iyoda
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Kohei Kondo
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Shinjiro Ojima
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Kotaro Chihara
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Wakana Yamashita
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
- Department of Life Science and Medical Bioscience, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke-shi, Tochigi, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Koichi Watashi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Yoshimasa Takahashi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
- Department of Life Science and Medical Bioscience, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Kotaro Kiga
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan.
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke-shi, Tochigi, Japan.
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3
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Santos‐Beneit F. What is the role of microbial biotechnology and genetic engineering in medicine? Microbiologyopen 2024; 13:e1406. [PMID: 38556942 PMCID: PMC10982607 DOI: 10.1002/mbo3.1406] [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: 01/12/2024] [Revised: 02/26/2024] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
Microbial products are essential for developing various therapeutic agents, including antibiotics, anticancer drugs, vaccines, and therapeutic enzymes. Genetic engineering techniques, functional genomics, and synthetic biology unlock previously uncharacterized natural products. This review highlights major advances in microbial biotechnology, focusing on gene-based technologies for medical applications.
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Affiliation(s)
- Fernando Santos‐Beneit
- Institute of Sustainable ProcessesValladolidSpain
- Department of Chemical Engineering and Environmental Technology, School of Industrial EngineeringUniversity of ValladolidValladolidSpain
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4
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Kanaparthi D, Lampe M, Krohn JH, Zhu B, Hildebrand F, Boesen T, Klingl A, Phapale P, Lueders T. The reproduction process of Gram-positive protocells. Sci Rep 2024; 14:7075. [PMID: 38528088 DOI: 10.1038/s41598-024-57369-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/18/2024] [Indexed: 03/27/2024] Open
Abstract
Protocells are believed to have existed on early Earth prior to the emergence of prokaryotes. Due to their rudimentary nature, it is widely accepted that these protocells lacked intracellular mechanisms to regulate their reproduction, thereby relying heavily on environmental conditions. To understand protocell reproduction, we adopted a top-down approach of transforming a Gram-positive bacterium into a lipid-vesicle-like state. In this state, cells lacked intrinsic mechanisms to regulate their morphology or reproduction, resembling theoretical propositions on protocells. Subsequently, we grew these proxy-protocells under the environmental conditions of early Earth to understand their impact on protocell reproduction. Despite the lack of molecular biological coordination, cells in our study underwent reproduction in an organized manner. The method and the efficiency of their reproduction can be explained by an interplay between the physicochemical properties of cell constituents and environmental conditions. While the overall reproductive efficiency in these top-down modified cells was lower than their counterparts with a cell wall, the process always resulted in viable daughter cells. Given the simplicity and suitability of this reproduction method to early Earth environmental conditions, we propose that primitive protocells likely reproduced by a process like the one we described below.
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Affiliation(s)
- Dheeraj Kanaparthi
- Department of Cellular and Molecular Biophysics, Max-Planck Institute for Biochemistry, Munich, Germany.
- Chair of Ecological Microbiology, BayCeer, University of Bayreuth, Bayreuth, Germany.
- Excellenzcluster Origins, Garching, Germany.
| | - Marko Lampe
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jan-Hagen Krohn
- Department of Cellular and Molecular Biophysics, Max-Planck Institute for Biochemistry, Munich, Germany
- Excellenzcluster Origins, Garching, Germany
| | - Baoli Zhu
- Chair of Ecological Microbiology, BayCeer, University of Bayreuth, Bayreuth, Germany
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions, CAS, Changsha, China
| | | | - Thomas Boesen
- Department of Biosciences, Center for Electromicrobiology, Aarhus, Denmark
| | - Andreas Klingl
- Department of Biology, LMU, Planegg-Martinsried, Germany
| | - Prasad Phapale
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tillmann Lueders
- Chair of Ecological Microbiology, BayCeer, University of Bayreuth, Bayreuth, Germany.
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5
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Tian D, Liu Y, Zhang Y, Liu Y, Xia Y, Xu B, Xu J, Yomo T. Implementation of Fluorescent-Protein-Based Quantification Analysis in L-Form Bacteria. Bioengineering (Basel) 2024; 11:81. [PMID: 38247958 PMCID: PMC10813599 DOI: 10.3390/bioengineering11010081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Cell-wall-less (L-form) bacteria exhibit morphological complexity and heterogeneity, complicating quantitative analysis of them under internal and external stimuli. Stable and efficient labeling is needed for the fluorescence-based quantitative cell analysis of L-forms during growth and proliferation. Here, we evaluated the expression of multiple fluorescent proteins (FPs) under different promoters in the Bacillus subtilis L-form strain LR2 using confocal microscopy and imaging flow cytometry. Among others, Pylb-derived NBP3510 showed a superior performance for inducing several FPs including EGFP and mKO2 in both the wild-type and L-form strains. Moreover, NBP3510 was also active in Escherichia coli and its L-form strain NC-7. Employing these established FP-labeled strains, we demonstrated distinct morphologies in the L-form bacteria in a quantitative manner. Given cell-wall-deficient bacteria are considered protocell and synthetic cell models, the generated cell lines in our work could be valuable for L-form-based research.
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Affiliation(s)
| | | | | | | | | | | | - Jian Xu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, China
| | - Tetsuya Yomo
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, China
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6
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Di Giulio M. The absence of the evolutionary state of the Prokaryote would imply a polyphyletic origin of proteins and that LUCA, the ancestor of bacteria and that of archaea were progenotes. Biosystems 2023; 233:105014. [PMID: 37652180 DOI: 10.1016/j.biosystems.2023.105014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/02/2023]
Abstract
I analysed the similarity gradient observed in protein families - of phylogenetically deep fundamental traits - of bacteria and archaea, ranging from cases such as the core of the DNA replication apparatus where there is no sequence similarity between the proteins involved, to cases in which, as in the translation initiation factors, only some proteins involved would be homologs, to cases such as for aminoacyl-tRNA synthetases in which most of the proteins involved would be homologs. This pattern of similarity between bacteria and archaea would seem to be a very clear indication of a transitional evolutionary stage that preceded both the Last Bacterial Common Ancestor and the Last Archaeal Common Ancestor, i.e. progenotic stages. Indeed, this similarity pattern would seem to exemplify an ongoing transition as all the evolutionary phases would be represented in it. Instead, in the cellular stage it is expected that these evolutionary phases should have already been overcome, i.e. completed, and therefore no longer detectable. In fact, if we had really been in the presence of the prokaryotic stage then we should not have observed this similarity pattern in proteins involved in defining the ancestral characters of bacteria and archaea, as the completion of the different cellular structures should have required a very low number of proteins to be late evolved in lineages leading to bacteria and archaea. Indeed, the already reached state of the Prokaryote would have determined complete cellular structures therefore a total absence of proteins to evolve independently in the two main phyletic lineages and able to complete the evolution of a particular character already evidently in a definitive state, which, on the other hand, does not appear to have been the case. All this would have prevented the formation of this pattern of similarity which instead would appear to be real. In conclusion, the existence of this pattern of similarity observed in the families of homologous proteins of bacteria and archaea would imply the absence of the evolutionary stage of the Prokaryote and consequently a progenotic status to be assigned to the LUCA. Indeed, the LUCA stage would have been a stage of evolutionary transition because it is belatedly marked by the presence of all the different evolutionary phases, evidently more easily interpretable within the definition of progenote than that of genote precisely because they are inherent in an evolutionary transition and not to an evolution that has already been achieved. Finally, I discuss the importance of these arguments for the polyphyletic origin of proteins.
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Affiliation(s)
- Massimo Di Giulio
- The Ionian School, Early Evolution of Life Department, Genetic Code and tRNA Origin Laboratory, Via Roma 19, 67030, Alfedena, L'Aquila, Italy.
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7
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Stojowska-Swędrzyńska K, Kuczyńska-Wiśnik D, Laskowska E. New Strategies to Kill Metabolically-Dormant Cells Directly Bypassing the Need for Active Cellular Processes. Antibiotics (Basel) 2023; 12:1044. [PMID: 37370363 DOI: 10.3390/antibiotics12061044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/09/2023] [Accepted: 06/11/2023] [Indexed: 06/29/2023] Open
Abstract
Antibiotic therapy failure is often caused by the presence of persister cells, which are metabolically-dormant bacteria capable of surviving exposure to antimicrobials. Under favorable conditions, persisters can resume growth leading to recurrent infections. Moreover, several studies have indicated that persisters may promote the evolution of antimicrobial resistance and facilitate the selection of specific resistant mutants; therefore, in light of the increasing numbers of multidrug-resistant infections worldwide, developing efficient strategies against dormant cells is of paramount importance. In this review, we present and discuss the efficacy of various agents whose antimicrobial activity is independent of the metabolic status of the bacteria as they target cell envelope structures. Since the biofilm-environment is favorable for the formation of dormant subpopulations, anti-persister strategies should also include agents that destroy the biofilm matrix or inhibit biofilm development. This article reviews examples of selected cell wall hydrolases, polysaccharide depolymerases and antimicrobial peptides. Their combination with standard antibiotics seems to be the most promising approach in combating persistent infections.
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Affiliation(s)
- Karolina Stojowska-Swędrzyńska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Dorota Kuczyńska-Wiśnik
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Ewa Laskowska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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8
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Tahara YO, Miyata M. Visualization of Peptidoglycan Structures of Escherichia coli by Quick-Freeze Deep-Etch Electron Microscopy. Methods Mol Biol 2023; 2646:299-307. [PMID: 36842124 DOI: 10.1007/978-1-0716-3060-0_24] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Peptidoglycan (PG) is an essential component of the bacterial cell wall that protects the cell from turgor pressure and maintains its shape. In diderm (gram-negative) bacteria, such as Escherichia coli, the PG layer is flexible with a thickness of a 2-6 nm, and its visualization is difficult due to the presence of the outer membrane. The quick-freeze deep-etch replica method has been widely used for the visualization of flexible structures in cell interior, such as cell organelles and membrane components. In this technique, a platinum replica on the surface of a specimen fixed by freezing is observed using a transmission electron microscope. In this chapter, we describe the application of this method for visualizing the E. coli PG layer. We expect that these methods will be useful for the visualization of the PG layer in diverse bacterial species.
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Affiliation(s)
- Yuhei O Tahara
- Graduate School of Science, Osaka City University, Osaka, Japan. .,Graduate School of Science, Osaka Metropolitan University, Osaka, Japan. .,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan. .,The OMU Advanced Research Center for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan.
| | - Makoto Miyata
- Graduate School of Science, Osaka City University, Osaka, Japan.,Graduate School of Science, Osaka Metropolitan University, Osaka, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan.,The OMU Advanced Research Center for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan
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9
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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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10
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Dissipative Particle Dynamics Simulations for Shape Change of Growing Lipid Bilayer Vesicles. Life (Basel) 2023; 13:life13020306. [PMID: 36836663 PMCID: PMC9961397 DOI: 10.3390/life13020306] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/09/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
The characteristic shape changes observed in the growth and division of L-form cells have been explained by several theoretical studies and simulations using a vesicle model in which the membrane area increases with time. In those theoretical studies, characteristic shapes such as tubulation and budding were reproduced in a non-equilibrium state, but it was not possible to incorporate deformations that would change the topology of the membrane. We constructed a vesicle model in which the area of the membrane increases using coarse-grained particles and analyzed the changes in the shape of growing membrane by the dissipative particle dynamics (DPD) method. In the simulation, lipid molecules were added to the lipid membrane at regular time intervals to increase the surface area of the lipid membrane. As a result, it was found that the vesicle deformed into a tubular shape or a budding shape depending on the conditions for adding lipid molecules. This suggests that the difference in the place where new lipid molecules are incorporated into the cell membrane during the growth of L-form cells causes the difference in the transformation pathway of L-form cells.
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11
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Kapteijn R, Shitut S, Aschmann D, Zhang L, de Beer M, Daviran D, Roverts R, Akiva A, van Wezel GP, Kros A, Claessen D. Endocytosis-like DNA uptake by cell wall-deficient bacteria. Nat Commun 2022; 13:5524. [PMID: 36138004 PMCID: PMC9500057 DOI: 10.1038/s41467-022-33054-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/31/2022] [Indexed: 11/29/2022] Open
Abstract
Horizontal gene transfer in bacteria is widely believed to occur via conjugation, transduction and transformation. These mechanisms facilitate the passage of DNA across the protective cell wall using sophisticated machinery. Here, we report that cell wall-deficient bacteria can engulf DNA and other extracellular material via an endocytosis-like process. Specifically, we show that L-forms of the filamentous actinomycete Kitasatospora viridifaciens can take up plasmid DNA, polysaccharides (dextran) and 150-nm lipid nanoparticles. The process involves invagination of the cytoplasmic membrane, leading to formation of intracellular vesicles that encapsulate extracellular material. DNA uptake is not affected by deletion of genes homologous to comEC and comEA, which are required for natural transformation in other species. However, uptake is inhibited by sodium azide or incubation at 4 °C, suggesting the process is energy-dependent. The encapsulated materials are released into the cytoplasm upon degradation of the vesicle membrane. Given that cell wall-deficient bacteria are considered a model for early life forms, our work reveals a possible mechanism for primordial cells to acquire food or genetic material before invention of the bacterial cell wall. Horizontal gene transfer in bacteria can occur through mechanisms such as conjugation, transduction and transformation, which facilitate the passage of DNA across the cell wall. Here, Kapteijn et al. show that cell wall-deficient bacteria can take up DNA and other extracellular materials via an endocytosis-like process.
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Affiliation(s)
- Renée Kapteijn
- Institute of Biology, Leiden University, Sylviusweg 72, 2333, Leiden, The Netherlands
| | - Shraddha Shitut
- Institute of Biology, Leiden University, Sylviusweg 72, 2333, Leiden, The Netherlands
| | - Dennis Aschmann
- Department of Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333, Leiden, The Netherlands
| | - Le Zhang
- Institute of Biology, Leiden University, Sylviusweg 72, 2333, Leiden, The Netherlands
| | - Marit de Beer
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Nijmegen, The Netherlands
| | - Deniz Daviran
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Nijmegen, The Netherlands
| | - Rona Roverts
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Nijmegen, The Netherlands
| | - Anat Akiva
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Nijmegen, The Netherlands
| | - Gilles P van Wezel
- Institute of Biology, Leiden University, Sylviusweg 72, 2333, Leiden, The Netherlands.
| | - Alexander Kros
- Department of Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333, Leiden, The Netherlands
| | - Dennis Claessen
- Institute of Biology, Leiden University, Sylviusweg 72, 2333, Leiden, The Netherlands.
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12
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Zhu W, Wang JZ, Liu Z, Wei JF. The bacteria inside human cancer cells: Mainly as cancer promoters. Front Oncol 2022; 12:897330. [PMID: 36033476 PMCID: PMC9411745 DOI: 10.3389/fonc.2022.897330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/14/2022] [Indexed: 11/24/2022] Open
Abstract
The roles of the microbiome in human beings have become clearer with the development of next-generation sequencing techniques. Several pieces of evidence showed strong correlations between the microbiome and human health and disease, such as metabolic disorders, infectious diseases, digestive system diseases, and cancers. Among these diverse microbiomes, the role of bacteria in human cancers, especially in cancer cells, has received extensive attention. Latest studies found that bacteria widely existed in cancers, mainly in cancer cells and immune cells. In this review, we summarize the latest advances in understanding the role of bacteria in human cancer cells. We also discuss how bacteria are transported into cancer cells and their physiological significance in cancer progression. Finally, we present the prospect of bacterial therapy in cancer treatment.
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Affiliation(s)
- Wei Zhu
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Research Division of Clinical Pharmacology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jing-Zi Wang
- Department of Urology, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Zhixian Liu
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Zhixian Liu, ; Ji-Fu Wei,
| | - Ji-Fu Wei
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Zhixian Liu, ; Ji-Fu Wei,
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13
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Borrero‐de Acuña JM, Poblete‐Castro I. Rational engineering of natural polyhydroxyalkanoates producing microorganisms for improved synthesis and recovery. Microb Biotechnol 2022; 16:262-285. [PMID: 35792877 PMCID: PMC9871526 DOI: 10.1111/1751-7915.14109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/14/2022] [Indexed: 01/27/2023] Open
Abstract
Microbial production of biopolymers derived from renewable substrates and waste streams reduces our heavy reliance on petrochemical plastics. One of the most important biodegradable polymers is the family of polyhydroxyalkanoates (PHAs), naturally occurring intracellular polyoxoesters produced for decades by bacterial fermentation of sugars and fatty acids at the industrial scale. Despite the advances, PHA production still suffers from heavy costs associated with carbon substrates and downstream processing to recover the intracellular product, thus restricting market positioning. In recent years, model-aided metabolic engineering and novel synthetic biology approaches have spurred our understanding of carbon flux partitioning through competing pathways and cellular resource allocation during PHA synthesis, enabling the rational design of superior biopolymer producers and programmable cellular lytic systems. This review describes these attempts to rationally engineering the cellular operation of several microbes to elevate PHA production on specific substrates and waste products. We also delve into genome reduction, morphology, and redox cofactor engineering to boost PHA biosynthesis. Besides, we critically evaluate engineered bacterial strains in various fermentation modes in terms of PHA productivity and the period required for product recovery.
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Affiliation(s)
| | - Ignacio Poblete‐Castro
- Biosystems Engineering LaboratoryDepartment of Chemical and Bioprocess EngineeringUniversidad de Santiago de Chile (USACH)SantiagoChile
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14
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Natsume Y. Thermo-Statistical Effects of Inclusions on Vesicles: Division into Multispheres and Polyhedral Deformation. MEMBRANES 2022; 12:membranes12060608. [PMID: 35736315 PMCID: PMC9229943 DOI: 10.3390/membranes12060608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 12/10/2022]
Abstract
The construction of simple cellular models has attracted much attention as a way to explore the origin of life or elucidate the mechanisms of cell division. In the absence of complex regulatory systems, some bacteria spontaneously divide through thermostatistically elucidated mechanisms, and incorporating these simple physical principles could help to construct primitive or artificial cells. Because thermodynamic interactions play an essential role in such mechanisms, this review discusses the thermodynamic aspects of spontaneous division models of vesicles that contain a high density of inclusions, with their membrane serving as a boundary. Vesicles with highly dense inclusions are deformed according to the volume-to-area ratio. The phase separation of beads at specific intermediate volume fractions and the associated polyhedral deformation of the membrane are considered in relation to the Alder transition. Current advances in the development of a membrane-growth vesicular model are summarized. The thermostatistical understanding of these mechanisms could become a cornerstone for the construction of vesicular models that display spontaneous cell division.
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Affiliation(s)
- Yuno Natsume
- Schoolteacher Training Course/Natural Sciences, Cooperative Faculty of Education, Utsunomiya University, Mine-machi 350, Utsunomiya 321-8505, Japan;
- Institute for Promotion of Research Center for Bioscience Research and Education, Utsunomiya University, Mine-machi 350, Utsunomiya 321-8505, Japan
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15
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Ongenae V, Mabrouk AS, Crooijmans M, Rozen D, Briegel A, Claessen D. Reversible bacteriophage resistance by shedding the bacterial cell wall. Open Biol 2022; 12:210379. [PMID: 35673854 PMCID: PMC9174709 DOI: 10.1098/rsob.210379] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Phages are highly abundant in the environment and pose a major threat for bacteria. Therefore, bacteria have evolved sophisticated defence systems to withstand phage attacks. Here, we describe a previously unknown mechanism by which mono- and diderm bacteria survive infection with diverse lytic phages. Phage exposure leads to a rapid and near-complete conversion of walled cells to a cell-wall-deficient state, which remains viable in osmoprotective conditions and can revert to the walled state. While shedding the cell wall dramatically reduces the number of progeny phages produced by the host, it does not always preclude phage infection. Altogether, these results show that the formation of cell-wall-deficient cells prevents complete eradication of the bacterial population and suggest that cell wall deficiency may potentially limit the efficacy of phage therapy, especially in highly osmotic environments or when used together with antibiotics that target the cell wall.
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Affiliation(s)
- Véronique Ongenae
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Adam Sidi Mabrouk
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Marjolein Crooijmans
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Daniel Rozen
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Ariane Briegel
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Dennis Claessen
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
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16
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Zambri MP, Williams MA, Elliot MA. How Streptomyces thrive: Advancing our understanding of classical development and uncovering new behaviors. Adv Microb Physiol 2022; 80:203-236. [PMID: 35489792 DOI: 10.1016/bs.ampbs.2022.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Streptomyces are soil- and marine-dwelling microbes that need to survive dramatic fluctuations in nutrient levels and environmental conditions. Here, we explore the advances made in understanding how Streptomyces bacteria can thrive in their natural environments. We examine their classical developmental cycle, and the intricate regulatory cascades that govern it. We discuss alternative growth strategies and behaviors, like the rapid expansion and colonization properties associated with exploratory growth, the release of membrane vesicles and S-cells from hyphal tips, and the acquisition of exogenous DNA along the lateral walls. We further investigate Streptomyces interactions with other organisms through the release of volatile compounds that impact nutrient levels, microbial growth, and insect behavior. Finally, we explore the increasingly diverse strategies employed by Streptomyces species in escaping and thwarting phage infections.
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Affiliation(s)
- Matthew P Zambri
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Michelle A Williams
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Marie A Elliot
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
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17
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Zou J, Peng B, Qu J, Zheng J. Are Bacterial Persisters Dormant Cells Only? Front Microbiol 2022; 12:708580. [PMID: 35185807 PMCID: PMC8847742 DOI: 10.3389/fmicb.2021.708580] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Abstract
Bacterial persisters are a sub-population of phenotypic variants that tolerate high concentrations of antibiotics within the genetically homogeneous cells. They resume division upon the removal of drugs. Bacterial persistence is one of major causes of antibiotic treatment failure and recurrent infection. Cell dormancy, triggered by toxin/antitoxin pair, (p)ppGpp, SOS response and ATP levels, is known to be the mechanistic basis for persistence. However, recent studies have demonstrated that bacteria with active metabolism can maintain persistence by lowering intracellular antibiotic concentration via an efflux pump. Additionally, others and our work have showed that cell wall deficient bacteria (CWDB), including both L-form and spheroplasts that produced by β-lactam antibiotics, are associated with antibiotic persistence. They are not dormant cells as their cell walls have been completely damaged. In this review, we discuss the various types of persisters and highlight the contribution of non-walled bacteria on bacterial persistence.
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Affiliation(s)
- Jin Zou
- Department of Clinical Laboratory, The Third People's Hospital of Shenzhen, Southern University of Science and Technology, National Clinical Research Center for Infectious Diseases, Shenzhen, China.,Faculty of Health Sciences, University of Macau, Zhuhai, Macau SAR, China
| | - Bo Peng
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jiuxin Qu
- Department of Clinical Laboratory, The Third People's Hospital of Shenzhen, Southern University of Science and Technology, National Clinical Research Center for Infectious Diseases, Shenzhen, China
| | - Jun Zheng
- Faculty of Health Sciences, University of Macau, Zhuhai, Macau SAR, China.,Institute of Translational Medicine, University of Macau, Zhuhai, Macau SAR, China
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18
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Was the Last Bacterial Common Ancestor a Monoderm after All? Genes (Basel) 2022; 13:genes13020376. [PMID: 35205421 PMCID: PMC8871954 DOI: 10.3390/genes13020376] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 12/20/2022] Open
Abstract
The very nature of the last bacterial common ancestor (LBCA), in particular the characteristics of its cell wall, is a critical issue to understand the evolution of life on earth. Although knowledge of the relationships between bacterial phyla has made progress with the advent of phylogenomics, many questions remain, including on the appearance or disappearance of the outer membrane of diderm bacteria (also called Gram-negative bacteria). The phylogenetic transition between monoderm (Gram-positive bacteria) and diderm bacteria, and the associated peptidoglycan expansion or reduction, requires clarification. Herein, using a phylogenomic tree of cultivated and characterized bacteria as an evolutionary framework and a literature review of their cell-wall characteristics, we used Bayesian ancestral state reconstruction to infer the cell-wall architecture of the LBCA. With the same phylogenomic tree, we further revisited the evolution of the division and cell-wall synthesis (dcw) gene cluster using homology- and model-based methods. Finally, extensive similarity searches were carried out to determine the phylogenetic distribution of the genes involved with the biosynthesis of the outer membrane in diderm bacteria. Quite unexpectedly, our analyses suggest that all cultivated and characterized bacteria might have evolved from a common ancestor with a monoderm cell-wall architecture. If true, this would indicate that the appearance of the outer membrane was not a unique event and that selective forces have led to the repeated adoption of such an architecture. Due to the lack of phenotypic information, our methodology cannot be applied to all extant bacteria. Consequently, our conclusion might change once enough information is made available to allow the use of an even more diverse organism selection.
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19
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Genome Sequence of Litorilinea aerophila, an Icelandic Intertidal Hot Springs Bacterium. Microbiol Resour Announc 2022; 11:e0120621. [PMID: 35084223 PMCID: PMC8793728 DOI: 10.1128/mra.01206-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The hot springs bacterium Litorilinea aerophila PRI-4131T (= ATCC BAA-2444T) was found in Isafjardardjup, in northwest Iceland. In this paper, we present a draft genome sequence for the type strain, with a total predicted genome length of 6,043,010 bp, 4,608 protein-coding sequences, 54 RNAs, 9 CRISPR arrays, and a G+C content of 64.61%.
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20
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Lu H, Aida H, Kurokawa M, Chen F, Xia Y, Xu J, Li K, Ying BW, Yomo T. Primordial mimicry induces morphological change in Escherichia coli. Commun Biol 2022; 5:24. [PMID: 35017623 PMCID: PMC8752768 DOI: 10.1038/s42003-021-02954-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 12/07/2021] [Indexed: 11/09/2022] Open
Abstract
The morphology of primitive cells has been the subject of extensive research. A spherical form was commonly presumed in prebiotic studies but lacked experimental evidence in living cells. Whether and how the shape of living cells changed are unclear. Here we exposed the rod-shaped bacterium Escherichia coli to a resource utilization regime mimicking a primordial environment. Oleate was given as an easy-to-use model prebiotic nutrient, as fatty acid vesicles were likely present on the prebiotic Earth and might have been used as an energy resource. Six evolutionary lineages were generated under glucose-free but oleic acid vesicle (OAV)-rich conditions. Intriguingly, fitness increase was commonly associated with the morphological change from rod to sphere and the decreases in both the size and the area-to-volume ratio of the cell. The changed cell shape was conserved in either OAVs or glucose, regardless of the trade-offs in carbon utilization and protein abundance. Highly differentiated mutations present in the genome revealed two distinct strategies of adaption to OAV-rich conditions, i.e., either directly targeting the cell wall or not. The change in cell morphology of Escherichia coli for adapting to fatty acid availability supports the assumption of the primitive spherical form. Lu et al. investigate the evolution of the shape of living cells by generating six experimental lineages of the rod-shaped E. coli under glucose-free conditions in the presence of oleic acid mimicking a primordial environment. The authors show that the morphological changes from rod to sphere accompanied fitness increases and adaptation amongst fatty acid availability supports the assumption of a primitive spherical form.
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Affiliation(s)
- Hui Lu
- Biomedical Synthetic Biology Research Center, School of Life Sciences, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, PR China
| | - Honoka Aida
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Masaomi Kurokawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Feng Chen
- School of Software Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, PR China
| | - Yang Xia
- Biomedical Synthetic Biology Research Center, School of Life Sciences, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, PR China
| | - Jian Xu
- Biomedical Synthetic Biology Research Center, School of Life Sciences, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, PR China
| | - Kai Li
- Biomedical Synthetic Biology Research Center, School of Life Sciences, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, PR China
| | - Bei-Wen Ying
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8572, Japan.
| | - Tetsuya Yomo
- Biomedical Synthetic Biology Research Center, School of Life Sciences, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, PR China.
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21
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Matsuo M, Kurihara K. Proliferating coacervate droplets as the missing link between chemistry and biology in the origins of life. Nat Commun 2021; 12:5487. [PMID: 34561428 PMCID: PMC8463549 DOI: 10.1038/s41467-021-25530-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 08/12/2021] [Indexed: 02/08/2023] Open
Abstract
The hypothesis that prebiotic molecules were transformed into polymers that evolved into proliferating molecular assemblages and eventually a primitive cell was first proposed about 100 years ago. To the best of our knowledge, however, no model of a proliferating prebiotic system has yet been realised because different conditions are required for polymer generation and self-assembly. In this study, we identify conditions suitable for concurrent peptide generation and self-assembly, and we show how a proliferating peptide-based droplet could be created by using synthesised amino acid thioesters as prebiotic monomers. Oligopeptides generated from the monomers spontaneously formed droplets through liquid-liquid phase separation in water. The droplets underwent a steady growth-division cycle by periodic addition of monomers through autocatalytic self-reproduction. Heterogeneous enrichment of RNA and lipids within droplets enabled RNA to protect the droplet from dissolution by lipids. These results provide experimental constructs for origins-of-life research and open up directions in the development of peptide-based materials.
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Affiliation(s)
- Muneyuki Matsuo
- Department of Chemistry, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro, Tokyo, Japan
- Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
| | - Kensuke Kurihara
- Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan.
- Institute of Laser Engineering, Osaka University, Suita, Osaka, Japan.
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.
- Faculty of Education, Utsunomiya University, Utsumomiya, Tochigi, Japan.
- Department of Life and Coordination-Complex Molecular Science, Biomolecular Functions, Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan.
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22
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Stotz HU, Brotherton D, Inal J. Communication is key: Extracellular vesicles as mediators of infection and defence during host-microbe interactions in animals and plants. FEMS Microbiol Rev 2021; 46:6358524. [PMID: 34448857 PMCID: PMC8767456 DOI: 10.1093/femsre/fuab044] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicles (EVs) are now understood to be ubiquitous mediators of cellular communication. In this review, we suggest that EVs have evolved into a highly regulated system of communication with complex functions including export of wastes, toxins and nutrients, targeted delivery of immune effectors and vectors of RNA silencing. Eukaryotic EVs come in different shapes and sizes and have been classified according to their biogenesis and size distributions. Small EVs (or exosomes) are released through fusion of endosome-derived multivesicular bodies with the plasma membrane. Medium EVs (or microvesicles) bud off the plasma membrane as a form of exocytosis. Finally, large EVs (or apoptotic bodies) are produced as a result of the apoptotic process. This review considers EV secretion and uptake in four eukaryotic kingdoms, three of which produce cell walls. The impacts cell walls have on EVs in plants and fungi are discussed, as are roles of fungal EVs in virulence. Contributions of plant EVs to development and innate immunity are presented. Compelling cases are sporophytic self-incompatibility and cellular invasion by haustorium-forming filamentous pathogens. The involvement of EVs in all of these eukaryotic processes is reconciled considering their evolutionary history.
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Affiliation(s)
- Henrik U Stotz
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK
| | - Dominik Brotherton
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK
| | - Jameel Inal
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK.,School of Human Sciences, London Metropolitan University, London, N7 8DB, UK
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23
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Subedi BP, Martin WF, Carbone V, Duin EC, Cronin B, Sauter J, Schofield LR, Sutherland-Smith AJ, Ronimus RS. Archaeal pseudomurein and bacterial murein cell wall biosynthesis share a common evolutionary ancestry. FEMS MICROBES 2021; 2:xtab012. [PMID: 37334239 PMCID: PMC10117817 DOI: 10.1093/femsmc/xtab012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 08/19/2021] [Indexed: 08/29/2023] Open
Abstract
Bacteria near-universally contain a cell wall sacculus of murein (peptidoglycan), the synthesis of which has been intensively studied for over 50 years. In striking contrast, archaeal species possess a variety of other cell wall types, none of them closely resembling murein. Interestingly though, one type of archaeal cell wall termed pseudomurein found in the methanogen orders Methanobacteriales and Methanopyrales is a structural analogue of murein in that it contains a glycan backbone that is cross-linked by a L-amino acid peptide. Here, we present taxonomic distribution, gene cluster and phylogenetic analyses that confirm orthologues of 13 bacterial murein biosynthesis enzymes in pseudomurein-containing methanogens, most of which are distantly related to their bacterial counterparts. We also present the first structure of an archaeal pseudomurein peptide ligase from Methanothermus fervidus DSM1088 (Mfer336) to a resolution of 2.5 Å and show that it possesses a similar overall tertiary three domain structure to bacterial MurC and MurD type murein peptide ligases. Taken together the data strongly indicate that murein and pseudomurein biosynthetic pathways share a common evolutionary history.
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Affiliation(s)
- Bishwa P Subedi
- AgResearch Ltd. Grasslands, Tennent Drive, Palmerston North 4442, New Zealand
- Massey University, Tennent Drive, Palmerston North 4442, New Zealand
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine University, Düsseldorf Universitätsstraße 1, D-40225, Germany
| | - Vincenzo Carbone
- AgResearch Ltd. Grasslands, Tennent Drive, Palmerston North 4442, New Zealand
| | - Eduardus C Duin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
| | - Bryan Cronin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
| | - Julia Sauter
- AgResearch Ltd. Grasslands, Tennent Drive, Palmerston North 4442, New Zealand
| | - Linley R Schofield
- AgResearch Ltd. Grasslands, Tennent Drive, Palmerston North 4442, New Zealand
| | | | - Ron S Ronimus
- AgResearch Ltd. Grasslands, Tennent Drive, Palmerston North 4442, New Zealand
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24
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Abstract
How mitochondria shaped the evolution of eukaryotic complexity has been controversial for decades. The discovery of the Asgard archaea, which harbor close phylogenetic ties to the eukaryotes, supports the idea that a critical endosymbiosis between an archaeal host and a bacterial endosymbiont transformed the selective constraints present at the origin of eukaryotes. Cultured Asgard archaea are typically prokaryotic in both size and internal morphology, albeit featuring extensive protrusions. The acquisition of the mitochondrial predecessor by an archaeal host cell fundamentally altered the topology of genes in relation to bioenergetic membranes. Mitochondria internalised not only the bioenergetic membranes but also the genetic machinery needed for local control of oxidative phosphorylation. Gene loss from mitochondria enabled expansion of the nuclear genome, giving rise to an extreme genomic asymmetry that is ancestral to all extant eukaryotes. This genomic restructuring gave eukaryotes thousands of fold more energy availability per gene. In principle, that difference can support more and larger genes, far more non-coding DNA, greater regulatory complexity, and thousands of fold more protein synthesis per gene. These changes released eukaryotes from the bioenergetic constraints on prokaryotes, facilitating the evolution of morphological complexity.
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Affiliation(s)
- Nick Lane
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.
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25
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Almeida C. A potential third-order role of the host endoplasmic reticulum as a contact site in interkingdom microbial endosymbiosis and viral infection. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:255-271. [PMID: 33559322 DOI: 10.1111/1758-2229.12938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
The normal functioning of eukaryotic cells depends on the compartmentalization of metabolic processes within specific organelles. Interactions among organelles, such as those between the endoplasmic reticulum (ER) - considered the largest single structure in eukaryotic cells - and other organelles at membrane contact sites (MCSs) have also been suggested to trigger synergisms, including intracellular immune responses against pathogens. In addition to the ER-endogenous functions and ER-organelle MCSs, we present the perspective of a third-order role of the ER as a host contact site for endosymbiotic microbial non-pathogens and pathogens, from endosymbiont bacteria to parasitic protists and viruses. Although understudied, ER-endosymbiont interactions have been observed in a range of eukaryotic hosts, including protists, plants, algae, and metazoans. Host ER interactions with endosymbionts could be an ER function built from ancient, conserved mechanisms selected for communicating with mutualistic endosymbionts in specific life cycle stages, and they may be exploited by pathogens and parasites. The host ER-'guest' interactome and traits in endosymbiotic biology are briefly discussed. The acknowledgment and understanding of these possible mechanisms might reveal novel evolutionary perspectives, uncover the causes of unexplained cellular disorders and suggest new pharmacological targets.
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Affiliation(s)
- Celso Almeida
- ENDOBIOS Biotech®, Praceta Progresso Clube n° 6, 2725-110 Mem-Martins, Portugal
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26
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Chang X, Kingsley KL, White JF. Chemical Interactions at the Interface of Plant Root Hair Cells and Intracellular Bacteria. Microorganisms 2021; 9:1041. [PMID: 34066008 PMCID: PMC8150332 DOI: 10.3390/microorganisms9051041] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 12/13/2022] Open
Abstract
In this research, we conducted histochemical, inhibitor and other experiments to evaluate the chemical interactions between intracellular bacteria and plant cells. As a result of these experiments, we hypothesize two chemical interactions between bacteria and plant cells. The first chemical interaction between endophyte and plant is initiated by microbe-produced ethylene that triggers plant cells to grow, release nutrients and produce superoxide. The superoxide combines with ethylene to form products hydrogen peroxide and carbon dioxide. In the second interaction between microbe and plant the microbe responds to plant-produced superoxide by secretion of nitric oxide to neutralize superoxide. Nitric oxide and superoxide combine to form peroxynitrite that is catalyzed by carbon dioxide to form nitrate. The two chemical interactions underlie hypothesized nutrient exchanges in which plant cells provide intracellular bacteria with fixed carbon, and bacteria provide plant cells with fixed nitrogen. As a consequence of these two interactions between endophytes and plants, plants grow and acquire nutrients from endophytes, and plants acquire enhanced oxidative stress tolerance, becoming more tolerant to abiotic and biotic stresses.
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Affiliation(s)
| | | | - James F. White
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA; (X.C.); (K.L.K.)
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27
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Cell division in the archaeon Haloferax volcanii relies on two FtsZ proteins with distinct functions in division ring assembly and constriction. Nat Microbiol 2021; 6:594-605. [PMID: 33903747 PMCID: PMC7611241 DOI: 10.1038/s41564-021-00894-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 03/22/2021] [Indexed: 02/02/2023]
Abstract
In bacteria, the tubulin homologue FtsZ assembles a cytokinetic ring, termed the Z ring, and plays a key role in the machinery that constricts to divide the cells. Many archaea encode two FtsZ proteins from distinct families, FtsZ1 and FtsZ2, with previously unclear functions. Here, we show that Haloferax volcanii cannot divide properly without either or both FtsZ proteins, but DNA replication continues and cells proliferate in alternative ways, such as blebbing and fragmentation, via remarkable envelope plasticity. FtsZ1 and FtsZ2 colocalize to form the dynamic division ring. However, FtsZ1 can assemble rings independent of FtsZ2, and stabilizes FtsZ2 in the ring, whereas FtsZ2 functions primarily in the constriction mechanism. FtsZ1 also influenced cell shape, suggesting it forms a hub-like platform at midcell for the assembly of shape-related systems too. Both FtsZ1 and FtsZ2 are widespread in archaea with a single S-layer envelope, but archaea with a pseudomurein wall and division septum only have FtsZ1. FtsZ1 is therefore likely to provide a fundamental recruitment role in diverse archaea, and FtsZ2 is required for constriction of a flexible S-layer envelope, where an internal constriction force might dominate the division mechanism, in contrast with the single-FtsZ bacteria and archaea that divide primarily by wall ingrowth.
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Abstract
Almost all bacteria are surrounded by a cell wall, which protects cells from environmental harm. Formation of the cell wall requires the precursor molecule lipid II, which in bacteria is universally synthesized by the conserved and essential lipid II synthase MurG. The cell wall is a stress-bearing structure and a unifying trait in bacteria. Without exception, synthesis of the cell wall involves formation of the precursor molecule lipid II by the activity of the essential biosynthetic enzyme MurG, which is encoded in the division and cell wall synthesis (dcw) gene cluster. Here, we present the discovery of a cell wall enzyme that can substitute for MurG. A mutant of Kitasatospora viridifaciens lacking a significant part of the dcw cluster, including murG, surprisingly produced lipid II and wild-type peptidoglycan. Genomic analysis identified a distant murG homologue, which encodes a putative enzyme that shares only around 31% amino acid sequence identity with MurG. We show that this enzyme can replace the canonical MurG, and we therefore designated it MglA. Orthologues of mglA are present in 38% of all genomes of Kitasatospora and members of the sister genus Streptomyces. CRISPR interference experiments showed that K. viridifaciens mglA can also functionally replace murG in Streptomyces coelicolor, thus validating its bioactivity and demonstrating that it is active in multiple genera. All together, these results identify MglA as a bona fide lipid II synthase, thus demonstrating plasticity in cell wall synthesis.
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29
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Garde S, Chodisetti PK, Reddy M. Peptidoglycan: Structure, Synthesis, and Regulation. EcoSal Plus 2021; 9:eESP-0010-2020. [PMID: 33470191 PMCID: PMC11168573 DOI: 10.1128/ecosalplus.esp-0010-2020] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Indexed: 02/06/2023]
Abstract
Peptidoglycan is a defining feature of the bacterial cell wall. Initially identified as a target of the revolutionary beta-lactam antibiotics, peptidoglycan has become a subject of much interest for its biology, its potential for the discovery of novel antibiotic targets, and its role in infection. Peptidoglycan is a large polymer that forms a mesh-like scaffold around the bacterial cytoplasmic membrane. Peptidoglycan synthesis is vital at several stages of the bacterial cell cycle: for expansion of the scaffold during cell elongation and for formation of a septum during cell division. It is a complex multifactorial process that includes formation of monomeric precursors in the cytoplasm, their transport to the periplasm, and polymerization to form a functional peptidoglycan sacculus. These processes require spatio-temporal regulation for successful assembly of a robust sacculus to protect the cell from turgor and determine cell shape. A century of research has uncovered the fundamentals of peptidoglycan biology, and recent studies employing advanced technologies have shed new light on the molecular interactions that govern peptidoglycan synthesis. Here, we describe the peptidoglycan structure, synthesis, and regulation in rod-shaped bacteria, particularly Escherichia coli, with a few examples from Salmonella and other diverse organisms. We focus on the pathway of peptidoglycan sacculus elongation, with special emphasis on discoveries of the past decade that have shaped our understanding of peptidoglycan biology.
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Affiliation(s)
- Shambhavi Garde
- These authors contributed equally
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India 500007
| | - Pavan Kumar Chodisetti
- These authors contributed equally
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India 500007
| | - Manjula Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India 500007
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30
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Mironov T, Sabaneyeva E. A Robust Symbiotic Relationship Between the Ciliate Paramecium multimicronucleatum and the Bacterium Ca. Trichorickettsia Mobilis. Front Microbiol 2020; 11:603335. [PMID: 33324385 PMCID: PMC7721670 DOI: 10.3389/fmicb.2020.603335] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 10/28/2020] [Indexed: 12/22/2022] Open
Abstract
Close reciprocal interactions in symbiotic systems have suggested the holobiont concept, in which the host and its microbiota are considered as a single entity. Ciliates are known for their ability to form symbiotic associations with prokaryotes. Relationships between the partners in such systems vary from mutualism to parasitism and differ significantly in their robustness. We assessed the viability of the ciliate Paramecium multimicronucleatum and its ability to maintain its intranuclear endosymbiont Ca. Trichorickettsia mobilis (Rickettsiaceae) after treatment with antibiotics characterized by different mode of action, such as ampicillin, streptomycin, chloramphenicol, tetracycline. The presence of endosymbionts in the host cell was determined by means of living cell observations made using differential interference contrast or fluorescence in situ hybridization with the species-specific oligonucleotide probe (FISH). Administration of antibiotics traditionally used in treatments of rickettsioses, tetracycline and chloramphenicol, depending on the concentration used and the ciliate strain treated, either caused death of both, infected and control cells, or did not affect the ability of the host to maintain the intranuclear endosymbiont. The surviving cells always manifested motile bacteria in the macronucleus. Streptomycin treatment never led to the loss of endosymbionts in any of the four infected strains, and nearly all ciliates remained viable. Ampicillin treatment never caused host cell death, but resulted in formation of filamentous and immobile oval bacterial forms. Under repeated ampicillin treatments, a part of endosymbionts was registered in the host cytoplasm, as evidenced both by FISH and transmission electron microscopy. Endosymbionts located in the host cytoplasm were enclosed in vacuoles, apparently, corresponding to autophagosomes. Nevertheless, the bacteria seemed to persist in this compartment and might cause relapse of the infection. Although the antibiotic sensitivity profile of Trichorickettsia seems to resemble that of other representatives of Rickettsiaceae, causative agents of severe diseases in humans, neither of the antibiotic treatments used in this study resulted in an aposymbiotic cell line, apparently, due to the protists’ sensitivity to tetracyclines, the drugs of preference in rickettsiosis treatment. The observed robustness of this symbiotic system makes it a good model for further elaboration of the holobiont concept.
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Affiliation(s)
- Timofey Mironov
- Department of Cytology and Histology, Biological Faculty, Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Elena Sabaneyeva
- Department of Cytology and Histology, Biological Faculty, Saint-Petersburg State University, Saint-Petersburg, Russia
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31
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Megrian D, Taib N, Witwinowski J, Beloin C, Gribaldo S. One or two membranes? Diderm Firmicutes challenge the Gram-positive/Gram-negative divide. Mol Microbiol 2020; 113:659-671. [PMID: 31975449 DOI: 10.1111/mmi.14469] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 12/24/2022]
Abstract
How, when and why the transition between cell envelopes with one membrane (Gram-positives or monoderms) and two (Gram-negative or diderms) occurred in Bacteria is a key unanswered question in evolutionary biology. Different hypotheses have been put forward, suggesting that either the monoderm or the diderm phenotype is ancestral. The existence of diderm members in the classically monoderm Firmicutes challenges the Gram-positive/Gram-negative divide and provides a great opportunity to tackle the issue. In this review, we present current knowledge on the diversity of bacterial cell envelopes, including these atypical Firmicutes. We discuss how phylogenomic analysis supports the hypothesis that the diderm cell envelope architecture is an ancestral character in the Firmicutes, and that the monoderm phenotype in this phylum arose multiple times independently by loss of the outer membrane. Given the overwhelming distribution of diderm phenotypes with respect to monoderm ones, this scenario likely extends to the ancestor of all bacteria. Finally, we discuss the recent development of genetic tools for Veillonella parvula, a diderm Firmicute member of the human microbiome, which indicates it as an emerging new experimental model to investigate fundamental aspects of the diderm/monoderm transition.
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Affiliation(s)
- Daniela Megrian
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France.,Ecole Doctorale Complexité du vivant, Sorbonne University, Paris, France
| | - Najwa Taib
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France.,Hub Bioinformatics and Biostatistics, Department of Computational Biology, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Jerzy Witwinowski
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France
| | - Christophe Beloin
- Department of Microbiology, Genetics of Biofilm Unit, Institut Pasteur, Paris, France
| | - Simonetta Gribaldo
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France
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32
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Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition. Nat Ecol Evol 2020; 4:1661-1672. [PMID: 33077930 DOI: 10.1038/s41559-020-01299-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/05/2020] [Indexed: 11/08/2022]
Abstract
The transition between cell envelopes with one membrane (Gram-positive or monoderm) and those with two membranes (Gram-negative or diderm) is a fundamental open question in the evolution of Bacteria. Evidence of the presence of two independent diderm lineages, the Halanaerobiales and the Negativicutes, within the classically monoderm Firmicutes has blurred the monoderm/diderm divide and specifically anticipated that other members with an outer membrane (OM) might exist in this phylum. Here, by screening 1,639 genomes of uncultured Firmicutes for signatures of an OM, we highlight a third and deep branching diderm clade, the Limnochordia, strengthening the hypothesis of a diderm ancestor and the occurrence of independent transitions leading to the monoderm phenotype. Phyletic patterns of over 176,000 protein families constituting the Firmicutes pan-proteome identify those that strongly correlate with the diderm phenotype and suggest the existence of new potential players in OM biogenesis. In contrast, we find practically no largely conserved core of monoderms, a fact possibly linked to different ways of adapting to repeated OM losses. Phylogenetic analysis of a concatenation of main OM components totalling nearly 2,000 amino acid positions illustrates the common origin and vertical evolution of most diderm bacterial envelopes. Finally, mapping the presence/absence of OM markers onto the tree of Bacteria shows the overwhelming presence of diderm phyla and the non-monophyly of monoderm ones, pointing to an early origin of two-membraned cells and the derived nature of the Gram-positive envelope following multiple OM losses.
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33
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Papp-Wallace KM, Mack AR, Taracila MA, Bonomo RA. Resistance to Novel β-Lactam-β-Lactamase Inhibitor Combinations: The "Price of Progress". Infect Dis Clin North Am 2020; 34:773-819. [PMID: 33011051 DOI: 10.1016/j.idc.2020.05.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Significant advances were made in antibiotic development during the past 5 years. Novel agents were added to the arsenal that target critical priority pathogens, including multidrug-resistant Pseudomonas aeruginosa and carbapenem-resistant Enterobacterales. Of these, 4 novel β-lactam-β-lactamase inhibitor combinations (ceftolozane-tazobactam, ceftazidime-avibactam, meropenem-vaborbactam, and imipenem-cilastatin-relebactam) reached clinical approval in the United States. With these additions comes a significant responsibility to reduce the possibility of emergence of resistance. Reports in the rise of resistance toward ceftolozane-tazobactam and ceftazidime-avibactam are alarming. Clinicians and scientists must make every attempt to reverse or halt these setbacks.
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Affiliation(s)
- Krisztina M Papp-Wallace
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, 151W, 10701 East Boulevard, Cleveland, OH 44106, USA.
| | - Andrew R Mack
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, 151W, 10701 East Boulevard, Cleveland, OH 44106, USA
| | - Magdalena A Taracila
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, 151W, 10701 East Boulevard, Cleveland, OH 44106, USA
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, 151W, 10701 East Boulevard, Cleveland, OH 44106, USA.
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34
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Nishida H. Factors That Affect the Enlargement of Bacterial Protoplasts and Spheroplasts. Int J Mol Sci 2020; 21:E7131. [PMID: 32992574 PMCID: PMC7582836 DOI: 10.3390/ijms21197131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 11/21/2022] Open
Abstract
Cell enlargement is essential for the microinjection of various substances into bacterial cells. The cell wall (peptidoglycan) inhibits cell enlargement. Thus, bacterial protoplasts/spheroplasts are used for enlargement because they lack cell wall. Though bacterial species that are capable of gene manipulation are limited, procedure for bacterial cell enlargement does not involve any gene manipulation technique. In order to prevent cell wall resynthesis during enlargement of protoplasts/spheroplasts, incubation media are supplemented with inhibitors of peptidoglycan biosynthesis such as penicillin. Moreover, metal ion composition in the incubation medium affects the properties of the plasma membrane. Therefore, in order to generate enlarged cells that are suitable for microinjection, metal ion composition in the medium should be considered. Experiment of bacterial protoplast or spheroplast enlargement is useful for studies on bacterial plasma membrane biosynthesis. In this paper, we have summarized the factors that influence bacterial cell enlargement.
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Affiliation(s)
- Hiromi Nishida
- Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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35
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Reporter Phage-Based Detection of Bacterial Pathogens: Design Guidelines and Recent Developments. Viruses 2020; 12:v12090944. [PMID: 32858938 PMCID: PMC7552063 DOI: 10.3390/v12090944] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/10/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
Fast and reliable detection of bacterial pathogens in clinical samples, contaminated food products, and water supplies can drastically improve clinical outcomes and reduce the socio-economic impact of disease. As natural predators of bacteria, bacteriophages (phages) have evolved to bind their hosts with unparalleled specificity and to rapidly deliver and replicate their viral genome. Not surprisingly, phages and phage-encoded proteins have been used to develop a vast repertoire of diagnostic assays, many of which outperform conventional culture-based and molecular detection methods. While intact phages or phage-encoded affinity proteins can be used to capture bacteria, most phage-inspired detection systems harness viral genome delivery and amplification: to this end, suitable phages are genetically reprogrammed to deliver heterologous reporter genes, whose activity is typically detected through enzymatic substrate conversion to indicate the presence of a viable host cell. Infection with such engineered reporter phages typically leads to a rapid burst of reporter protein production that enables highly sensitive detection. In this review, we highlight recent advances in infection-based detection methods, present guidelines for reporter phage construction, outline technical aspects of reporter phage engineering, and discuss some of the advantages and pitfalls of phage-based pathogen detection. Recent improvements in reporter phage construction and engineering further substantiate the potential of these highly evolved nanomachines as rapid and inexpensive detection systems to replace or complement traditional diagnostic approaches.
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36
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Wu LJ, Lee S, Park S, Eland LE, Wipat A, Holden S, Errington J. Geometric principles underlying the proliferation of a model cell system. Nat Commun 2020; 11:4149. [PMID: 32811832 PMCID: PMC7434903 DOI: 10.1038/s41467-020-17988-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023] Open
Abstract
Many bacteria can form wall-deficient variants, or L-forms, that divide by a simple mechanism that does not require the FtsZ-based cell division machinery. Here, we use microfluidic systems to probe the growth, chromosome cycle and division mechanism of Bacillus subtilis L-forms. We find that forcing cells into a narrow linear configuration greatly improves the efficiency of cell growth and chromosome segregation. This reinforces the view that L-form division is driven by an excess accumulation of surface area over volume. Cell geometry also plays a dominant role in controlling the relative positions and movement of segregating chromosomes. Furthermore, the presence of the nucleoid appears to influence division both via a cell volume effect and by nucleoid occlusion, even in the absence of FtsZ. Our results emphasise the importance of geometric effects for a range of crucial cell functions, and are of relevance for efforts to develop artificial or minimal cell systems.
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Affiliation(s)
- Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK.
| | - Seoungjun Lee
- grid.1006.70000 0001 0462 7212Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX UK ,grid.13097.3c0000 0001 2322 6764Present Address: Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, SE5 9RX UK
| | - Sungshic Park
- grid.1006.70000 0001 0462 7212Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX UK ,grid.1006.70000 0001 0462 7212Interdisciplinary Computing and Complex BioSystems research group, School of Computing, Newcastle University, Newcastle upon Tyne, NE4 5TG UK
| | - Lucy E. Eland
- grid.1006.70000 0001 0462 7212Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX UK ,grid.1006.70000 0001 0462 7212Interdisciplinary Computing and Complex BioSystems research group, School of Computing, Newcastle University, Newcastle upon Tyne, NE4 5TG UK
| | - Anil Wipat
- grid.1006.70000 0001 0462 7212Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX UK ,grid.1006.70000 0001 0462 7212Interdisciplinary Computing and Complex BioSystems research group, School of Computing, Newcastle University, Newcastle upon Tyne, NE4 5TG UK
| | - Séamus Holden
- grid.1006.70000 0001 0462 7212Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX UK
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK.
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37
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Maitra A, Munshi T, Healy J, Martin LT, Vollmer W, Keep NH, Bhakta S. Cell wall peptidoglycan in Mycobacterium tuberculosis: An Achilles' heel for the TB-causing pathogen. FEMS Microbiol Rev 2020; 43:548-575. [PMID: 31183501 PMCID: PMC6736417 DOI: 10.1093/femsre/fuz016] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/07/2019] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB), caused by the intracellular pathogen Mycobacterium tuberculosis, remains one of the leading causes of mortality across the world. There is an urgent requirement to build a robust arsenal of effective antimicrobials, targeting novel molecular mechanisms to overcome the challenges posed by the increase of antibiotic resistance in TB. Mycobacterium tuberculosis has a unique cell envelope structure and composition, containing a peptidoglycan layer that is essential for maintaining cellular integrity and for virulence. The enzymes involved in the biosynthesis, degradation, remodelling and recycling of peptidoglycan have resurfaced as attractive targets for anti-infective drug discovery. Here, we review the importance of peptidoglycan, including the structure, function and regulation of key enzymes involved in its metabolism. We also discuss known inhibitors of ATP-dependent Mur ligases, and discuss the potential for the development of pan-enzyme inhibitors targeting multiple Mur ligases.
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Affiliation(s)
- Arundhati Maitra
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Tulika Munshi
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Jess Healy
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Liam T Martin
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Nicholas H Keep
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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38
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Nejman D, Livyatan I, Fuks G, Gavert N, Zwang Y, Geller LT, Rotter-Maskowitz A, Weiser R, Mallel G, Gigi E, Meltser A, Douglas GM, Kamer I, Gopalakrishnan V, Dadosh T, Levin-Zaidman S, Avnet S, Atlan T, Cooper ZA, Arora R, Cogdill AP, Khan MAW, Ologun G, Bussi Y, Weinberger A, Lotan-Pompan M, Golani O, Perry G, Rokah M, Bahar-Shany K, Rozeman EA, Blank CU, Ronai A, Shaoul R, Amit A, Dorfman T, Kremer R, Cohen ZR, Harnof S, Siegal T, Yehuda-Shnaidman E, Gal-Yam EN, Shapira H, Baldini N, Langille MGI, Ben-Nun A, Kaufman B, Nissan A, Golan T, Dadiani M, Levanon K, Bar J, Yust-Katz S, Barshack I, Peeper DS, Raz DJ, Segal E, Wargo JA, Sandbank J, Shental N, Straussman R. The human tumor microbiome is composed of tumor type-specific intracellular bacteria. Science 2020; 368:973-980. [PMID: 32467386 DOI: 10.1126/science.aay9189] [Citation(s) in RCA: 1048] [Impact Index Per Article: 262.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 01/22/2020] [Accepted: 04/14/2020] [Indexed: 12/15/2022]
Abstract
Bacteria were first detected in human tumors more than 100 years ago, but the characterization of the tumor microbiome has remained challenging because of its low biomass. We undertook a comprehensive analysis of the tumor microbiome, studying 1526 tumors and their adjacent normal tissues across seven cancer types, including breast, lung, ovary, pancreas, melanoma, bone, and brain tumors. We found that each tumor type has a distinct microbiome composition and that breast cancer has a particularly rich and diverse microbiome. The intratumor bacteria are mostly intracellular and are present in both cancer and immune cells. We also noted correlations between intratumor bacteria or their predicted functions with tumor types and subtypes, patients' smoking status, and the response to immunotherapy.
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Affiliation(s)
- Deborah Nejman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Livyatan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Garold Fuks
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Nancy Gavert
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yaara Zwang
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Leore T Geller
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Roi Weiser
- Division of Surgery, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Giuseppe Mallel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Elinor Gigi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Arnon Meltser
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gavin M Douglas
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Iris Kamer
- Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
| | | | - Tali Dadosh
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Smadar Levin-Zaidman
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Sofia Avnet
- Orthopaedic Pathophysiology and Regenerative Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Tehila Atlan
- Department of Bioinformatics, Jerusalem College of Technology, Jerusalem, Israel
| | - Zachary A Cooper
- Translational Medicine, Oncology R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Reetakshi Arora
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexandria P Cogdill
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Md Abdul Wadud Khan
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gabriel Ologun
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuval Bussi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Adina Weinberger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Maya Lotan-Pompan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Ofra Golani
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Perry
- Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
| | - Merav Rokah
- Department of Thoracic Surgery, Sheba Medical Center, Ramat Gan, Israel
| | | | - Elisa A Rozeman
- Department of Medical Oncology and Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Christian U Blank
- Department of Medical Oncology and Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Anat Ronai
- Pediatric Gastroenterology Institute, Rambam Medical Center, Haifa, Israel
| | - Ron Shaoul
- Pediatric Gastroenterology Institute, Rambam Medical Center, Haifa, Israel
| | - Amnon Amit
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.,Department of Obstetrics and Gynecology, Rambam Health Care Campus, Haifa, Israel
| | - Tatiana Dorfman
- Division of General Surgery, Rambam Health Care Campus, Haifa, Israel.,Ambulatory and Breast Surgery Service, Rambam Health Care Campus, Haifa, Israel
| | - Ran Kremer
- Department of Thoracic Surgery, Rambam Health Care Campus, Haifa, Israel
| | - Zvi R Cohen
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Department of Neurosurgery, Sheba Medical Center, Ramat Gan, Israel
| | - Sagi Harnof
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Department of Neurosurgery, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - Tali Siegal
- Neuro-Oncology Unit, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | | | | | - Hagit Shapira
- Institute of Pathology, Megalab, Maccabi Healthcare Services, Rehovot, Israel
| | - Nicola Baldini
- Orthopaedic Pathophysiology and Regenerative Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Morgan G I Langille
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada.,Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Alon Ben-Nun
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Department of Thoracic Surgery, Sheba Medical Center, Ramat Gan, Israel
| | - Bella Kaufman
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
| | - Aviram Nissan
- Department of Surgical Oncology (Surgery C), Sheba Medical Center, Ramat Gan, Israel
| | - Talia Golan
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
| | - Maya Dadiani
- Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
| | - Keren Levanon
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
| | - Jair Bar
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
| | - Shlomit Yust-Katz
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Neuro-Oncology Unit, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - Iris Barshack
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Department of Pathology, Sheba Medical Center, Ramat Gan, Israel
| | - Daniel S Peeper
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Dan J Raz
- Division of Thoracic Surgery, City of Hope Medical Center, Duarte, CA, USA
| | - Eran Segal
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Judith Sandbank
- Institute of Pathology, Megalab, Maccabi Healthcare Services, Rehovot, Israel
| | - Noam Shental
- Department of Mathematics and Computer Science, The Open University of Israel, Ra'anana, Israel
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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39
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The evolution of the type VI secretion system as a disintegration weapon. PLoS Biol 2020; 18:e3000720. [PMID: 32453732 PMCID: PMC7274471 DOI: 10.1371/journal.pbio.3000720] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 06/05/2020] [Accepted: 04/30/2020] [Indexed: 12/22/2022] Open
Abstract
The type VI secretion system (T6SS) is a nanomachine used by many bacteria to drive a toxin-laden needle into other bacterial cells. Although the potential to influence bacterial competition is clear, the fitness impacts of wielding a T6SS are not well understood. Here we present a new agent-based model that enables detailed study of the evolutionary costs and benefits of T6SS weaponry during competition with other bacteria. Our model identifies a key problem with the T6SS. Because of its short range, T6SS activity becomes self-limiting, as dead cells accumulate in its way, forming “corpse barriers” that block further attacks. However, further exploration with the model presented a solution to this problem: if injected toxins can quickly lyse target cells in addition to killing them, the T6SS becomes a much more effective weapon. We tested this prediction with single-cell analysis of combat between T6SS-wielding Acinetobacter baylyi and T6SS-sensitive Escherichia coli. As predicted, delivery of lytic toxins is highly effective, whereas nonlytic toxins leave large patches of E. coli alive. We then analyzed hundreds of bacterial species using published genomic data, which suggest that the great majority of T6SS-wielding species do indeed use lytic toxins, indicative of a general principle underlying weapon evolution. Our work suggests that, in the T6SS, bacteria have evolved a disintegration weapon whose effectiveness often rests upon the ability to break up competitors. Understanding the evolutionary function of bacterial weapons can help in the design of probiotics that can both establish well and eliminate problem species. Bacteria attack each other with poison-tipped spears. This study combines theory and experiments to show that these spears (Type VI Secretion Systems) have evolved to break their targets apart with lytic toxins, as this then clears the way to rapidly stab new victims.
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40
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An Affair to Remember: How an Endosymbiont Partners with Its Host to Build a Cell Envelope. Cell 2020; 179:584-586. [PMID: 31626766 DOI: 10.1016/j.cell.2019.09.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Studying endosymbionts gives us insight into early cellular mechanisms that led to the emergence of eukaryotic organelles. In this issue of Cell, Bublitz et al. (2019) report on how a nested bacterial endosymbiont of mealybugs builds its cell wall peptidoglycan through a biosynthetic pathway that is dependent on transported host enzymes.
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41
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Tulum I, Tahara YO, Miyata M. Peptidoglycan layer and disruption processes in Bacillus subtilis cells visualized using quick-freeze, deep-etch electron microscopy. Microscopy (Oxf) 2020; 68:441-449. [PMID: 31690940 DOI: 10.1093/jmicro/dfz033] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/08/2019] [Accepted: 08/08/2019] [Indexed: 12/22/2022] Open
Abstract
Peptidoglycan, which is the main component of the bacterial cell wall, is a heterogeneous polymer of glycan strands cross-linked with short peptides and is synthesized in cooperation with the cell division cycle. Although it plays a critical role in bacterial survival, its architecture is not well understood. Herein, we visualized the architecture of the peptidoglycan surface in Bacillus subtilis at the nanometer resolution, using quick-freeze, deep-etch electron microscopy (EM). Filamentous structures were observed on the entire surface of the cell, where filaments about 11 nm wide formed concentric circles on cell poles, filaments about 13 nm wide formed a circumferential mesh-like structure on the cylindrical part and a 'piecrust' structure was observed at the boundary. When growing cells were treated with lysozyme, the entire cell mass migrated to one side and came out from the cell envelope. Fluorescence labeling showed that lysozyme preferentially bound to a cell pole and cell division site, where the peptidoglycan synthesis was not complete. Ruffling of surface structures was observed during EM. When cells were treated with penicillin, the cell mass came out from a cleft around the cell division site. Outward curvature of the protoplast at the cleft seen using EM suggested that turgor pressure was applied as the peptidoglycan was not damaged at other positions. When muropeptides were depleted, surface filaments were lost while the rod shape of the cell was maintained. These changes can be explained on the basis of the working points of the chemical structure of peptidoglycan.
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Affiliation(s)
- Isil Tulum
- Graduate School of Science, Osaka City University, Osaka 558-8585, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka 558-8585, Japan
| | - Yuhei O Tahara
- Graduate School of Science, Osaka City University, Osaka 558-8585, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka 558-8585, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka City University, Osaka 558-8585, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka 558-8585, Japan
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42
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Bateman A. Division of labour in a matrix, rather than phagocytosis or endosymbiosis, as a route for the origin of eukaryotic cells. Biol Direct 2020; 15:8. [PMID: 32345370 PMCID: PMC7187495 DOI: 10.1186/s13062-020-00260-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 02/25/2020] [Indexed: 12/13/2022] Open
Abstract
Abstract Two apparently irreconcilable models dominate research into the origin of eukaryotes. In one model, amitochondrial proto-eukaryotes emerged autogenously from the last universal common ancestor of all cells. Proto-eukaryotes subsequently acquired mitochondrial progenitors by the phagocytic capture of bacteria. In the second model, two prokaryotes, probably an archaeon and a bacterial cell, engaged in prokaryotic endosymbiosis, with the species resident within the host becoming the mitochondrial progenitor. Both models have limitations. A search was therefore undertaken for alternative routes towards the origin of eukaryotic cells. The question was addressed by considering classes of potential pathways from prokaryotic to eukaryotic cells based on considerations of cellular topology. Among the solutions identified, one, called here the “third-space model”, has not been widely explored. A version is presented in which an extracellular space (the third-space), serves as a proxy cytoplasm for mixed populations of archaea and bacteria to “merge” as a transitionary complex without obligatory endosymbiosis or phagocytosis and to form a precursor cell. Incipient nuclei and mitochondria diverge by division of labour. The third-space model can accommodate the reorganization of prokaryote-like genomes to a more eukaryote-like genome structure. Nuclei with multiple chromosomes and mitosis emerge as a natural feature of the model. The model is compatible with the loss of archaeal lipid biochemistry while retaining archaeal genes and provides a route for the development of membranous organelles such as the Golgi apparatus and endoplasmic reticulum. Advantages, limitations and variations of the “third-space” models are discussed. Reviewers This article was reviewed by Damien Devos, Buzz Baum and Michael Gray.
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Affiliation(s)
- Andrew Bateman
- Division of Experimental Medicine, Department of Medicine, McGill University, Glen Site Pavilion E, 1001 Boulevard Decarie, Montreal, Quebec, H4A 3J1, Canada. .,Centre for Translational Biology, Research Institute of McGill University Health Centre, Glen Site Pavilion E, 1001 Boulevard Decarie, Montreal, Quebec, H4A 3J1, Canada.
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43
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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44
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The evolution of spherical cell shape; progress and perspective. Biochem Soc Trans 2020; 47:1621-1634. [PMID: 31829405 PMCID: PMC6925525 DOI: 10.1042/bst20180634] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/06/2019] [Accepted: 11/11/2019] [Indexed: 01/29/2023]
Abstract
Bacterial cell shape is a key trait governing the extracellular and intracellular factors of bacterial life. Rod-like cell shape appears to be original which implies that the cell wall, division, and rod-like shape came together in ancient bacteria and that the myriad of shapes observed in extant bacteria have evolved from this ancestral shape. In order to understand its evolution, we must first understand how this trait is actively maintained through the construction and maintenance of the peptidoglycan cell wall. The proteins that are primarily responsible for cell shape are therefore the elements of the bacterial cytoskeleton, principally FtsZ, MreB, and the penicillin-binding proteins. MreB is particularly relevant in the transition between rod-like and spherical cell shape as it is often (but not always) lost early in the process. Here we will highlight what is known of this particular transition in cell shape and how it affects fitness before giving a brief perspective on what will be required in order to progress the field of cell shape evolution from a purely mechanistic discipline to one that has the perspective to both propose and to test reasonable hypotheses regarding the ecological drivers of cell shape change.
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45
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Bublitz DC, Chadwick GL, Magyar JS, Sandoz KM, Brooks DM, Mesnage S, Ladinsky MS, Garber AI, Bjorkman PJ, Orphan VJ, McCutcheon JP. Peptidoglycan Production by an Insect-Bacterial Mosaic. Cell 2019; 179:703-712.e7. [PMID: 31587897 PMCID: PMC6838666 DOI: 10.1016/j.cell.2019.08.054] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/06/2019] [Accepted: 08/28/2019] [Indexed: 01/19/2023]
Abstract
Peptidoglycan (PG) is a defining feature of bacteria, involved in cell division, shape, and integrity. We previously reported that several genes related to PG biosynthesis were horizontally transferred from bacteria to the nuclear genome of mealybugs. Mealybugs are notable for containing a nested bacteria-within-bacterium endosymbiotic structure in specialized insect cells, where one bacterium, Moranella, lives in the cytoplasm of another bacterium, Tremblaya. Here we show that horizontally transferred genes on the mealybug genome work together with genes retained on the Moranella genome to produce a PG layer exclusively at the Moranella cell periphery. Furthermore, we show that an insect protein encoded by a horizontally transferred gene of bacterial origin is transported into the Moranella cytoplasm. These results provide a striking parallel to the genetic and biochemical mosaicism found in organelles, and prove that multiple horizontally transferred genes can become integrated into a functional pathway distributed between animal and bacterial endosymbiont genomes. Mealybugs have two bacterial endosymbionts; one symbiont lives inside the other The mealybug genome has acquired some bacterial peptidoglycan (PG)-related genes This insect-symbiont mosaic pathway produces a PG layer at the innermost symbiont Endosymbionts and organelles have evolved similar levels of biochemical integration
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Affiliation(s)
- DeAnna C Bublitz
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Grayson L Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - John S Magyar
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kelsi M Sandoz
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT 59840, USA
| | - Diane M Brooks
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Stéphane Mesnage
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Mark S Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Arkadiy I Garber
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - John P McCutcheon
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA.
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46
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Claessen D, Errington J. Cell Wall Deficiency as a Coping Strategy for Stress. Trends Microbiol 2019; 27:1025-1033. [PMID: 31420127 DOI: 10.1016/j.tim.2019.07.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/02/2019] [Accepted: 07/23/2019] [Indexed: 12/22/2022]
Abstract
The cell wall is a surface layer located outside the cell membrane of almost all bacteria; it protects cells from environmental stresses and gives them their typical shape. The cell wall is highly conserved in bacteria and is the target for some of our best antibiotics. Surprisingly, some bacteria are able to shed their wall under the influence of stress, yielding cells that are cell-wall-deficient. Notably, wall-deficient cells are flexible and are able to maneuver through narrow spaces, insensitive to wall-targeting antibiotics, and capable of taking up and exchanging DNA. Moreover, given that wall-associated epitopes are often recognized by host defense systems, wall deficiency provides a plausible explanation for how some bacteria may hide in their host. In this review we focus on this paradoxical stress response, which provides cells with unique opportunities that are unavailable to walled cells.
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Affiliation(s)
- Dennis Claessen
- Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands.
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, NE2 4AX, UK.
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47
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Affiliation(s)
- Kilian Vogele
- Physik-DepartmentTechnische Universitat Munchen, TU München Garching Germany
| | - Tobias Pirzer
- Physik-DepartmentTechnische Universitat Munchen, TU München Garching Germany
| | - Friedrich C. Simmel
- Physik-DepartmentTechnische Universitat Munchen, TU München Garching Germany
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48
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Ruiz-Herrero T, Fai TG, Mahadevan L. Dynamics of Growth and Form in Prebiotic Vesicles. PHYSICAL REVIEW LETTERS 2019; 123:038102. [PMID: 31386448 DOI: 10.1103/physrevlett.123.038102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Indexed: 06/10/2023]
Abstract
The growth, form, and division of prebiotic vesicles, membraneous bags of fluid of varying components and shapes is hypothesized to have served as the substrate for the origin of life. The dynamics of these out-of-equilibrium structures is controlled by physicochemical processes that include the intercalation of amphiphiles into the membrane, fluid flow across the membrane, and elastic deformations of the membrane. To understand prebiotic vesicular forms and their dynamics, we construct a minimal model that couples membrane growth, deformation, and fluid permeation, ultimately couched in terms of two dimensionless parameters that characterize the relative rate of membrane growth and the membrane permeability. Numerical simulations show that our model captures the morphological diversity seen in extant precursor mimics of cellular life, and might provide simple guidelines for the synthesis of these complex shapes from simple ingredients.
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Affiliation(s)
- Teresa Ruiz-Herrero
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Thomas G Fai
- Department of Mathematics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - L Mahadevan
- John A. Paulson School of Engineering and Applied Sciences, Department of Physics, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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49
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Hilgemann DW, Lin MJ, Fine M, Deisl C. On the existence of endocytosis driven by membrane phase separations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183007. [PMID: 31202864 DOI: 10.1016/j.bbamem.2019.06.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/31/2019] [Accepted: 06/06/2019] [Indexed: 01/15/2023]
Abstract
Large endocytic responses can occur rapidly in diverse cell types without dynamins, clathrin, or actin remodeling. Our experiments suggest that membrane phase separations are crucial with more ordered plasma membrane domains being internalized. Not only do these endocytic processes rely on coalescence of membrane domains, they are promoted by participation of membrane proteins in such domains, one important regulatory influence being palmitoylation. Membrane actin cytoskeleton in general resists membrane phase transitions, and its remodeling may play many roles. Besides membrane 'caging' and 'pinching' roles, typically ascribed to clathrin and dynamins, cytoskeleton remodeling may modify local membrane tension and buckling, as well as the presence and location of actin- and tension-free membrane patches. Endocytosis that depends on membrane phase separations becomes activated in metabolic stress and in response to Ca and PI3 kinase signaling. Internalized membrane traffics normally, and the secretory pathway eventually resupplies membrane to the plasmalemma or directs internalized membrane to other locations, including the extracellular space as exosomes. We describe here that endocytosis driven by membrane phase transitions is regulated by the same signaling mechanisms that regulate macropinocytosis, and it may play diverse roles in cells from nutrient assimilation to membrane recycling, cell migration, and the initiation of quiescent or hibernating cell states. Membrane ordering and phase separations have been shown to promote endocytosis in diverse cell types, including fibroblasts, myocytes, glial cells, and immune cells. We propose that clathrin/dynamin-independent endocytosis represents a continuum of related mechanisms with variable but universal dependence on membrane ordering and actin remodeling. This article is part of a Special Issue entitled: Molecular biophysics of membranes and membrane proteins.
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Affiliation(s)
- Donald W Hilgemann
- University of Texas Southwestern Medical Center, Department of Physiology, 5323 Harry Hines Boulevard, Dallas, TX 75235-9040, USA.
| | - Mei-Jung Lin
- University of Texas Southwestern Medical Center, Department of Physiology, 5323 Harry Hines Boulevard, Dallas, TX 75235-9040, USA
| | - Michael Fine
- University of Texas Southwestern Medical Center, Department of Physiology, 5323 Harry Hines Boulevard, Dallas, TX 75235-9040, USA
| | - Christine Deisl
- University of Texas Southwestern Medical Center, Department of Physiology, 5323 Harry Hines Boulevard, Dallas, TX 75235-9040, USA
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50
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Reyes-Lamothe R, Sherratt DJ. The bacterial cell cycle, chromosome inheritance and cell growth. Nat Rev Microbiol 2019; 17:467-478. [DOI: 10.1038/s41579-019-0212-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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