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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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2
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Chernov VM, Chernova OA, Trushin MV. Human and animal intestinal commensals and probiotics vs modern challenges of biosafety: problems and prospects. ARCHIVES OF RAZI INSTITUTE 2024; 79:28-32. [PMID: 39192958 PMCID: PMC11345466 DOI: 10.32592/ari.2024.79.1.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 11/28/2023] [Indexed: 08/29/2024]
Abstract
The appearance of an array of data on the study of the intestinal microbiota in Metazoa has significantly expanded our understanding of the role of commensals in the control of a wide range of physiological functions in higher organisms in norm and pathology. In the intestine, where the microbial load significantly exceeds the number of microorganisms of other ecosystems, the components of the intestinal microbiota are a constant source of stimuli that induce activation of the host immune system. The introduction into practice of biomedical research of innovative high-resolution methods, including multi-omics technologies, has brought data that change our understanding of intestinal commensals, including probiotics with GRAS status, widely used in medicine, agriculture and biotechnology. The ability of these bacteria to induce negative processes in the host body that are beneficial for bacterial proliferation and expansion revealed a clear lack of our knowledge about the logic of their life and the mechanisms of interaction with eukaryotic cells. This determines the urgent need for comprehensive research of probiotics and the development of standardization of their safety assessment. Apriori's confidence in the exceptional benefit of the bacteria widely used in medicine, agriculture and biotechnology has determined the seriously omission in our control system today - the lack of standardization of studies for the safety assessment of bacteria with GRAS status . The moment has come when it became clear that this gap should be promptly filled and that only exact understanding the molecular base of interacting the microbes with eukaryotic cells can provide the foundation for effective practical developments in controlling the evolution of bacterial virulence and probiotic safety strategy, as well as the competent use of genetic technologies for monitoring the environment and managing infectious processes, thus avoiding the dramatic consequences of large-scale interventions in the micro and macro worlds.
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Affiliation(s)
- V M Chernov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
| | - O A Chernova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
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3
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Liu Y, Zhang Y, Kang C, Tian D, Lu H, Xu B, Xia Y, Kashiwagi A, Westermann M, Hoischen C, Xu J, Yomo T. Comparative genomics hints at dispensability of multiple essential genes in two Escherichia coli L-form strains. Biosci Rep 2023; 43:BSR20231227. [PMID: 37819245 PMCID: PMC10600066 DOI: 10.1042/bsr20231227] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/13/2023] Open
Abstract
Despite the critical role of bacterial cell walls in maintaining cell shapes, certain environmental stressors can induce the transition of many bacterial species into a wall-deficient state called L-form. Long-term induced Escherichia coli L-forms lose their rod shape and usually hold significant mutations that affect cell division and growth. Besides this, the genetic background of L-form bacteria is still poorly understood. In the present study, the genomes of two stable L-form strains of E. coli (NC-7 and LWF+) were sequenced and their gene mutation status was determined and compared with their parental strains. Comparative genomic analysis between two L-forms reveals both unique adaptions and common mutated genes, many of which belong to essential gene categories not involved in cell wall biosynthesis, indicating that L-form genetic adaptation impacts crucial metabolic pathways. Missense variants from L-forms and Lenski's long-term evolution experiment (LTEE) were analyzed in parallel using an optimized DeepSequence pipeline to investigate predicted mutation effects (α) on protein functions. We report that the two L-form strains analyzed display a frequency of 6-10% (0% for LTEE) in mutated essential genes where the missense variants have substantial impact on protein functions (α<0.5). This indicates the emergence of different survival strategies in L-forms through changes in essential genes during adaptions to cell wall deficiency. Collectively, our results shed light on the detailed genetic background of two E. coli L-forms and pave the way for further investigations of the gene functions in L-form bacterial models.
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Affiliation(s)
- Yunfei Liu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Yueyue Zhang
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Chen Kang
- School of Software Engineering, East China Normal University, Shanghai 200062, PR China
| | - Di Tian
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Hui Lu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Boying Xu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 200072, China
| | - Yang Xia
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Akiko Kashiwagi
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | - Martin Westermann
- Center for Electron Microscopy, Medical Faculty, Friedrich–Schiller–University Jena, Ziegelmühlenweg 1, D-07743 Jena, Germany
| | - Christian Hoischen
- CF Imaging, Leibniz Institute On Aging, Fritz–Lipmann–Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Jian Xu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Tetsuya Yomo
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
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4
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Ohta K, Shimizu T, Oshima T, Ichihashi N. Genetic analysis of Bacillus subtilis stable L-forms obtained via long-term cultivation. J GEN APPL MICROBIOL 2023; 69:45-52. [PMID: 36384691 DOI: 10.2323/jgam.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Various bacteria can change to a spherical cell-wall-deficient state, called L-from, in the presence of antibiotics that inhibit cell wall synthesis. L-forms are classified into two types: unstable and stable L-forms. Unstable L-forms revert to a normal walled state in the absence of antibiotics, while stable L-forms remain in their wall-deficient state. The conversion from unstable to stable L-forms has been often observed during long-term cultivation. However, the genetic cause for this conversion is not yet fully understood. Here, we obtained stable Bacillus subtilis L-form strains from unstable L-form strains via three independent long-term culturing experiments. The whole genome sequencing of the long-cultured strains identified many mutations, and some mutations were commonly found in all three long-cultured strains. The knockout strain of one of the commonly mutated genes, tagF, in the ancestral strain lost the ability to revert to walled state (rod shape), supporting that eliminating the function of tagF gene is one of the possible methods to convert unstable L forms to a stable state.
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Affiliation(s)
- Kazuki Ohta
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo
| | - Tenma Shimizu
- Graduate School of Frontier Biosciences, Osaka University
| | - Taku Oshima
- Department of Biotechnology, Toyama Prefectural University
| | - Norikazu Ichihashi
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo
- Komaba Institute for Science, The University of Tokyo
- Universal Biology Institute, Graduate School of Science, The University of Tokyo
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5
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Tsafarova B, Hodzhev Y, Yordanov G, Tolchkov V, Kalfin R, Panaiotov S. Morphology of blood microbiota in healthy individuals assessed by light and electron microscopy. Front Cell Infect Microbiol 2023; 12:1091341. [PMID: 36741978 PMCID: PMC9889553 DOI: 10.3389/fcimb.2022.1091341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 12/30/2022] [Indexed: 01/20/2023] Open
Abstract
Introduction The blood microbiome is still an enigma. The existence of blood microbiota in clinically healthy individuals was proven during the last 50 years. Indirect evidence from radiometric analysis suggested the existence of living microbial forms in erythrocytes. Recently targeted nucleic acid sequencing demonstrated rich microbial biodiversity in the blood of clinically healthy individuals. The morphology and proliferation cycle of blood microbiota in peripheral blood mononuclear cells (PBMC) isolated from freshly drawn and cultured whole blood are obscure. Methods To study the life cycle of blood microbiota we focused on light, and electron microscopy analysis. Peripheral blood mononuclear cells isolated from freshly drawn blood and stress-cultured lysed whole blood at 43°C in presence of vitamin K from healthy individuals were studied. Results Here, we demonstrated that free circulating microbiota in the PMBC fraction possess a well-defined cell wall and proliferate by budding or through a mechanism similar to the extrusion of progeny bodies. By contrast, stress-cultured lysed whole blood microbiota proliferated as cell-wall deficient microbiota by forming electron-dense or electron-transparent bodies. The electron-dense bodies proliferated by fission or produce in chains Gram-negatively stained progeny cells or enlarged and burst to release progeny cells of 180 - 200 nm size. On the other hand, electron-transparent bodies enlarged and emitted progeny cells through the membrane. A novel proliferation mechanism of blood microbiota called by us "a cell within a cell" was observed. It combines proliferation of progeny cells within a progeny cell which is growing within the "mother" cell. Discussion The rich biodiversity of eukaryotic and prokaryotic microbiota identified in blood by next-generation sequencing technologies and our microscopy results suggest different proliferation mechanisms in whole and cultured blood. Our documented evidence and conclusions provide a more comprehensive view of the existence of normal blood microbiota in healthy individuals.
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Affiliation(s)
- Borislava Tsafarova
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Yordan Hodzhev
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Georgi Yordanov
- Faculty of Chemistry and Pharmacy, Sofia University, Sofia, Bulgaria
| | - Vladimir Tolchkov
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Reni Kalfin
- Institute of Neurobiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
- Department of Health Care, South-West University “Neofit Rilski”, Blagoevgrad, Bulgaria
| | - Stefan Panaiotov
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
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6
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Cheng J, Zhang L, Huang Q, Li C, Yu J, Zhu M. Refractory Osteomyelitis Caused by Mycobacterium aubagnense and Its L-Form: Case Report and Review of the Literature. Infect Drug Resist 2022; 15:7317-7325. [DOI: 10.2147/idr.s388629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
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7
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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] [Key Words] [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
| | - Ji-Fu Wei
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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8
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Murtha AN, Kazi MI, Schargel RD, Cross T, Fihn C, Cattoir V, Carlson EE, Boll JM, Dörr T. High-level carbapenem tolerance requires antibiotic-induced outer membrane modifications. PLoS Pathog 2022; 18:e1010307. [PMID: 35130322 PMCID: PMC8853513 DOI: 10.1371/journal.ppat.1010307] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/17/2022] [Accepted: 01/26/2022] [Indexed: 12/22/2022] Open
Abstract
Antibiotic tolerance is an understudied potential contributor to antibiotic treatment failure and the emergence of multidrug-resistant bacteria. The molecular mechanisms governing tolerance remain poorly understood. A prominent type of β-lactam tolerance relies on the formation of cell wall-deficient spheroplasts, which maintain structural integrity via their outer membrane (OM), an asymmetric lipid bilayer consisting of phospholipids on the inner leaflet and a lipid-linked polysaccharide (lipopolysaccharide, LPS) enriched in the outer monolayer on the cell surface. How a membrane structure like LPS, with its reliance on mere electrostatic interactions to maintain stability, is capable of countering internal turgor pressure is unknown. Here, we have uncovered a novel role for the PhoPQ two-component system in tolerance to the β-lactam antibiotic meropenem in Enterobacterales. We found that PhoPQ is induced by meropenem treatment and promotes an increase in 4-amino-4-deoxy-L-aminoarabinose [L-Ara4N] modification of lipid A, the membrane anchor of LPS. L-Ara4N modifications likely enhance structural integrity, and consequently tolerance to meropenem, in several Enterobacterales species. Importantly, mutational inactivation of the negative PhoPQ regulator mgrB (commonly selected for during clinical therapy with the last-resort antibiotic colistin, an antimicrobial peptide [AMP]) results in dramatically enhanced tolerance, suggesting that AMPs can collaterally select for meropenem tolerance via stable overactivation of PhoPQ. Lastly, we identify histidine kinase inhibitors (including an FDA-approved drug) that inhibit PhoPQ-dependent LPS modifications and consequently potentiate meropenem to enhance lysis of tolerant cells. In summary, our results suggest that PhoPQ-mediated LPS modifications play a significant role in stabilizing the OM, promoting survival when the primary integrity maintenance structure, the cell wall, is removed. Treating an infection with an antibiotic often fails, resulting in a tremendous public health burden. One understudied likely reason for treatment failure is the development of “antibiotic tolerance”, the ability of bacteria to survive normally lethal exposure to an antibiotic. Here, we describe a molecular mechanism promoting tolerance. A bacterial stress sensor (PhoPQ) is activated in response to antibiotic (meropenem) treatment and consequently strengthens a bacterial protective “shell” to enhance survival. We also identify inhibitors of this mechanism, opening the door to developing compounds that help antibiotics work better against tolerant bacteria.
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Affiliation(s)
- Andrew N. Murtha
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Misha I. Kazi
- Department of Biology, University of Texas Arlington, Arlington, Texas, United States of America
| | - Richard D. Schargel
- Department of Biology, University of Texas Arlington, Arlington, Texas, United States of America
| | - Trevor Cross
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Conrad Fihn
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Vincent Cattoir
- Department of Clinical Microbiology and National Reference Center for Antimicrobial Resistance (Lab Enterococci), Rennes University Hospital, Rennes, France; Inserm Unit U1230, University of Rennes 1, Rennes, France
| | - Erin E. Carlson
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Molecular Pharmacology and Therapeutics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Joseph M. Boll
- Department of Biology, University of Texas Arlington, Arlington, Texas, United States of America
- * E-mail: (JMB); (TD)
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, New York, United States of America
- * E-mail: (JMB); (TD)
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9
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D'Amico F, Barone M, Tavella T, Rampelli S, Brigidi P, Turroni S. Host microbiomes in tumor precision medicine: how far are we? Curr Med Chem 2022; 29:3202-3230. [PMID: 34986765 DOI: 10.2174/0929867329666220105121754] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/13/2021] [Accepted: 11/22/2021] [Indexed: 11/22/2022]
Abstract
The human gut microbiome has received a crescendo of attention in recent years, due to the countless influences on human pathophysiology, including cancer. Research on cancer and anticancer therapy is constantly looking for new hints to improve the response to therapy while reducing the risk of relapse. In this scenario, the gut microbiome and the plethora of microbial-derived metabolites are considered a new opening in the development of innovative anticancer treatments for a better prognosis. This narrative review summarizes the current knowledge on the role of the gut microbiome in the onset and progression of cancer, as well as in response to chemo-immunotherapy. Recent findings regarding the tumor microbiome and its implications for clinical practice are also commented on. Current microbiome-based intervention strategies (i.e., prebiotics, probiotics, live biotherapeutics and fecal microbiota transplantation) are then discussed, along with key shortcomings, including a lack of long-term safety information in patients who are already severely compromised by standard treatments. The implementation of bioinformatic tools applied to microbiomics and other omics data, such as machine learning, has an enormous potential to push research in the field, enabling the prediction of health risk and therapeutic outcomes, for a truly personalized precision medicine.
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Affiliation(s)
- Federica D'Amico
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Monica Barone
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Teresa Tavella
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Patrizia Brigidi
- Microbiome Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
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10
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Levin PA, Janakiraman A. Localization, Assembly, and Activation of the Escherichia coli Cell Division Machinery. EcoSal Plus 2021; 9:eESP00222021. [PMID: 34910577 PMCID: PMC8919703 DOI: 10.1128/ecosalplus.esp-0022-2021] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/14/2021] [Indexed: 01/01/2023]
Abstract
Decades of research, much of it in Escherichia coli, have yielded a wealth of insight into bacterial cell division. Here, we provide an overview of the E. coli division machinery with an emphasis on recent findings. We begin with a short historical perspective into the discovery of FtsZ, the tubulin homolog that is essential for division in bacteria and archaea. We then discuss assembly of the divisome, an FtsZ-dependent multiprotein platform, at the midcell septal site. Not simply a scaffold, the dynamic properties of polymeric FtsZ ensure the efficient and uniform synthesis of septal peptidoglycan. Next, we describe the remodeling of the cell wall, invagination of the cell envelope, and disassembly of the division apparatus culminating in scission of the mother cell into two daughter cells. We conclude this review by highlighting some of the open questions in the cell division field, emphasizing that much remains to be discovered, even in an organism as extensively studied as E. coli.
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Affiliation(s)
- Petra Anne Levin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
- Center for Science & Engineering of Living Systems (CSELS), McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Anuradha Janakiraman
- Department of Biology, The City College of New York, New York, New York, USA
- Programs in Biology and Biochemistry, The Graduate Center of the City University of New York, New York, New York, USA
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11
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Dörr T. Understanding tolerance to cell wall-active antibiotics. Ann N Y Acad Sci 2021; 1496:35-58. [PMID: 33274447 PMCID: PMC8359209 DOI: 10.1111/nyas.14541] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 12/19/2022]
Abstract
Antibiotic tolerance-the ability of bacteria to survive for an extended time in the presence of bactericidal antibiotics-is an understudied contributor to antibiotic treatment failure. Herein, I review the manifestations, mechanisms, and clinical relevance of tolerance to cell wall-active (CWA) antibiotics, one of the most important groups of antibiotics at the forefront of clinical use. I discuss definitions of tolerance and assays for tolerance detection, comprehensively discuss the mechanism of action of β-lactams and other CWA antibiotics, and then provide an overview of how cells mitigate the potentially lethal effects of CWA antibiotic-induced cell damage to become tolerant. Lastly, I discuss evidence for a role of CWA antibiotic tolerance in clinical antibiotic treatment failure.
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Affiliation(s)
- Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Department of Microbiology, and Cornell Institute of Host–Pathogen Interactions and DiseaseCornell UniversityIthacaNew York
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12
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Pelletier JF, Sun L, Wise KS, Assad-Garcia N, Karas BJ, Deerinck TJ, Ellisman MH, Mershin A, Gershenfeld N, Chuang RY, Glass JI, Strychalski EA. Genetic requirements for cell division in a genomically minimal cell. Cell 2021; 184:2430-2440.e16. [PMID: 33784496 DOI: 10.1016/j.cell.2021.03.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 01/27/2021] [Accepted: 03/03/2021] [Indexed: 12/15/2022]
Abstract
Genomically minimal cells, such as JCVI-syn3.0, offer a platform to clarify genes underlying core physiological processes. Although this minimal cell includes genes essential for population growth, the physiology of its single cells remained uncharacterized. To investigate striking morphological variation in JCVI-syn3.0 cells, we present an approach to characterize cell propagation and determine genes affecting cell morphology. Microfluidic chemostats allowed observation of intrinsic cell dynamics that result in irregular morphologies. A genome with 19 genes not retained in JCVI-syn3.0 generated JCVI-syn3A, which presents morphology similar to that of JCVI-syn1.0. We further identified seven of these 19 genes, including two known cell division genes, ftsZ and sepF, a hydrolase of unknown substrate, and four genes that encode membrane-associated proteins of unknown function, which are required together to restore a phenotype similar to that of JCVI-syn1.0. This result emphasizes the polygenic nature of cell division and morphology in a genomically minimal cell.
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Affiliation(s)
- James F Pelletier
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Lijie Sun
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Kim S Wise
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Bogumil J Karas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, University of California-San Diego, La Jolla, CA 92037, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, University of California-San Diego, La Jolla, CA 92037, USA
| | - Andreas Mershin
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Neil Gershenfeld
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - John I Glass
- J. Craig Venter Institute, La Jolla, CA 92037, USA.
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13
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Shin J, Choe D, Ransegnola B, Hong H, Onyekwere I, Cross T, Shi Q, Cho B, Westblade LF, Brito IL, Dörr T. A multifaceted cellular damage repair and prevention pathway promotes high-level tolerance to β-lactam antibiotics. EMBO Rep 2021; 22:e51790. [PMID: 33463026 PMCID: PMC7857431 DOI: 10.15252/embr.202051790] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/17/2020] [Accepted: 12/02/2020] [Indexed: 12/27/2022] Open
Abstract
Bactericidal antibiotics are powerful agents due to their ability to convert essential bacterial functions into lethal processes. However, many important bacterial pathogens are remarkably tolerant against bactericidal antibiotics due to inducible damage repair responses. The cell wall damage response two-component system VxrAB of the gastrointestinal pathogen Vibrio cholerae promotes high-level β-lactam tolerance and controls a gene network encoding highly diverse functions, including negative control over multiple iron uptake systems. How this system contributes to tolerance is poorly understood. Here, we show that β-lactam antibiotics cause an increase in intracellular free iron levels and collateral oxidative damage, which is exacerbated in the ∆vxrAB mutant. Mutating major iron uptake systems dramatically increases ∆vxrAB tolerance to β-lactams. We propose that VxrAB reduces antibiotic-induced toxic iron and concomitant metabolic perturbations by downregulating iron uptake transporters and show that iron sequestration enhances tolerance against β-lactam therapy in a mouse model of cholera infection. Our results suggest that a microorganism's ability to counteract diverse antibiotic-induced stresses promotes high-level antibiotic tolerance and highlights the complex secondary responses elicited by antibiotics.
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Affiliation(s)
- Jung‐Ho Shin
- Weill Institute for Cell and Molecular BiologyCornell, UniversityIthacaNYUSA
- Department of MicrobiologyCornell UniversityIthacaNYUSA
| | - Donghui Choe
- Department of Biological SciencesKorea Advanced Institute of Science and TechnologyDaejeonKorea
- KI for the BioCenturyKorea Advanced Institute of Science and TechnologyDaejeonKorea
| | - Brett Ransegnola
- Weill Institute for Cell and Molecular BiologyCornell, UniversityIthacaNYUSA
- Department of MicrobiologyCornell UniversityIthacaNYUSA
| | - Hye‐Rim Hong
- Weill Institute for Cell and Molecular BiologyCornell, UniversityIthacaNYUSA
- Department of MicrobiologyCornell UniversityIthacaNYUSA
| | - Ikenna Onyekwere
- Weill Institute for Cell and Molecular BiologyCornell, UniversityIthacaNYUSA
- Department of MicrobiologyCornell UniversityIthacaNYUSA
| | - Trevor Cross
- Weill Institute for Cell and Molecular BiologyCornell, UniversityIthacaNYUSA
- Department of MicrobiologyCornell UniversityIthacaNYUSA
| | - Qiaojuan Shi
- Meinig School of Biomedical EngineeringCornell UniversityIthacaNYUSA
| | - Byung‐Kwan Cho
- Department of Biological SciencesKorea Advanced Institute of Science and TechnologyDaejeonKorea
- KI for the BioCenturyKorea Advanced Institute of Science and TechnologyDaejeonKorea
- Intelligent Synthetic Biology CenterDaejeonKorea
| | - Lars F Westblade
- Department of Pathology and Laboratory MedicineWeill Cornell MedicineNew YorkNYUSA
- Division of Infectious DiseasesDepartment of MedicineWeill Cornell MedicineNew YorkNYUSA
| | - Ilana L Brito
- Meinig School of Biomedical EngineeringCornell UniversityIthacaNYUSA
| | - Tobias Dörr
- Weill Institute for Cell and Molecular BiologyCornell, UniversityIthacaNYUSA
- Department of MicrobiologyCornell UniversityIthacaNYUSA
- Cornell Institute of Host‐Microbe Interactions and DiseaseCornell UniversityIthacaNYUSA
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14
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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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15
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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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16
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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: 1093] [Impact Index Per Article: 273.3] [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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17
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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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18
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Spheroplast-Mediated Carbapenem Tolerance in Gram-Negative Pathogens. Antimicrob Agents Chemother 2019; 63:AAC.00756-19. [PMID: 31285232 DOI: 10.1128/aac.00756-19] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/28/2019] [Indexed: 01/01/2023] Open
Abstract
Antibiotic tolerance, the ability to temporarily sustain viability in the presence of bactericidal antibiotics, constitutes an understudied and yet potentially widespread cause of antibiotic treatment failure. We have previously shown that the Gram-negative pathogen Vibrio cholerae can tolerate exposure to the typically bactericidal β-lactam antibiotics by assuming a spherical morphotype devoid of detectable cell wall material. However, it is unclear how widespread β-lactam tolerance is. Here, we tested a panel of clinically significant Gram-negative pathogens for their response to the potent, broad-spectrum carbapenem antibiotic meropenem. We show that clinical isolates of Enterobacter cloacae, Klebsiella aerogenes, and Klebsiella pneumoniae, but not Escherichia coli, exhibited moderate to high levels of tolerance of meropenem, both in laboratory growth medium and in human serum. Importantly, tolerance was mediated by cell wall-deficient spheroplasts, which readily recovered wild-type morphology and growth upon removal of antibiotic. Our results suggest that carbapenem tolerance is prevalent in clinically significant bacterial species, and we suggest that this could contribute to treatment failure associated with these organisms.
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19
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van Bel AJE, Musetti R. Sieve element biology provides leads for research on phytoplasma lifestyle in plant hosts. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3737-3755. [PMID: 30972422 DOI: 10.1093/jxb/erz172] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/26/2019] [Indexed: 06/09/2023]
Abstract
Phytoplasmas reside exclusively in sieve tubes, tubular arrays of sieve element-companion cell complexes. Hence, the cell biology of sieve elements may reveal (ultra)structural and functional conditions that are of significance for survival, propagation, colonization, and effector spread of phytoplasmas. Electron microscopic images suggest that sieve elements offer facilities for mobile and stationary stages in phytoplasma movement. Stationary stages may enable phytoplasmas to interact closely with diverse sieve element compartments. The unique, reduced sieve element outfit requires permanent support by companion cells. This notion implies a future focus on the molecular biology of companion cells to understand the sieve element-phytoplasma inter-relationship. Supply of macromolecules by companion cells is channelled via specialized symplasmic connections. Ca2+-mediated gating of symplasmic corridors is decisive for the communication within and beyond the sieve element-companion cell complex and for the dissemination of phytoplasma effectors. Thus, Ca2+ homeostasis, which affects sieve element Ca2+ signatures and induces a range of modifications, is a key issue during phytoplasma infection. The exceptional physical and chemical environment in sieve elements seems an essential, though not the only factor for phytoplasma survival.
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Affiliation(s)
- Aart J E van Bel
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus-Liebig University, Giessen, Germany
| | - Rita Musetti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
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20
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Vedyaykin AD, Ponomareva EV, Khodorkovskii MA, Borchsenius SN, Vishnyakov IE. Mechanisms of Bacterial Cell Division. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719030159] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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21
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Gheibi A, Khanahmad H, Kardar GA, Boshtam M, Rezaie S, Kazemi B, Khorramizadeh MR. Optimization and Comparison of Different Methods and Factors for Efficient Transformation of Brucella abortus RB51strain. Adv Biomed Res 2019; 8:37. [PMID: 31198771 PMCID: PMC6555225 DOI: 10.4103/abr.abr_14_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: The development of protective vaccines for Brucella spp. has been hampered by the difficulty in transformation of Brucella cells with foreign DNA for genetic manipulation. It seems that the formation of Brucella spheroplasts would increase the efficiency of transformation. The aim of this study was to devise an efficient method for the transformation of Brucella spp. Materials and Methods: At first, spheroplast of Brucella was prepared by glycine and ampicillin induction and transformed using optimized protocols of CaCl2, electroporation, and lipofection methods. Then, the efficacy of transformation was compared between the three-mentioned methods. Results: Ampicillin-induced spheroplasts from early-log phase culture of brucella when incubated in a medium-containing 0.2 M sucrose during cell recovery had higher transformation efficiency in three different methods. Comparison of the transformation efficiency of Brucella abortus RB51 using the CaCl2, lipofection, and electroporation methods revealed that the transformation efficiency with the lipofection method was significantly higher than with other two methods (P < 0.05). Conclusions: Lipofection method by lipofectamine 2000 on ampicillin-induced spheroplasts can be a suitable approach for Brucella transformation.
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Affiliation(s)
- Azam Gheibi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Gholam Ali Kardar
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, Asthma and Allergy Research Institute, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Boshtam
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sassan Rezaie
- Department of Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Bahram Kazemi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Khorramizadeh
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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22
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Kretschmer S, Ganzinger KA, Franquelim HG, Schwille P. Synthetic cell division via membrane-transforming molecular assemblies. BMC Biol 2019; 17:43. [PMID: 31126285 PMCID: PMC6533746 DOI: 10.1186/s12915-019-0665-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Reproduction, i.e. the ability to produce new individuals from a parent organism, is a hallmark of living matter. Even the simplest forms of reproduction require cell division: attempts to create a designer cell therefore should include a synthetic cell division machinery. In this review, we will illustrate how nature solves this task, describing membrane remodelling processes in general and focusing on bacterial cell division in particular. We discuss recent progress made in their in vitro reconstitution, identify open challenges, and suggest how purely synthetic building blocks could provide an additional and attractive route to creating artificial cell division machineries.
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23
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Rogolevich VV, Glushkova TV, Ponasenko AV, Ovcharenko EA. [Infective Endocarditis Causing Native and Prosthetic Heart Valve Dysfunction]. ACTA ACUST UNITED AC 2019; 59:68-77. [PMID: 30990144 DOI: 10.18087/cardio.2019.3.10245] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 04/13/2019] [Indexed: 11/18/2022]
Abstract
Infective endocarditis (IE) is the disease that has high inhospital mortality. Heart valves dysfunction - both native and prosthetic - is the primary IE complication requiring a surgical intervention. The IE causes and its course have been discussed in this review. In particular, the role of concomitant infectious foci in the formation and development of IE have been considered, the mechanisms of mutual transition of subacute and acute clinical forms have been described. Modern diagnostic principles and methods based on the Duke criteria system have been mentioned, as well as the difficulties that follow the patient's clinical status evaluation. The normobiotic microbiota participation, as well as the possibilities for their identification using blood culture and PCR technique, have been closely reviewed. According to modern researches and publications, there have been made the conclusion about the contribution of obligate anaerobic bacteria, fungi and viruses to the development of endocarditis. There have been described the hypothesis about the presumptive strategy for the cardiac dysfunction formation as a result of the IE causative agents cells metabolic activity based on a literature data analysis in the article: vegetation formed by Staphylococcus aureus can lead to the heart valve stenosis, and the influence of hyaluronidases, collagenases on a heart valve structure can lead to regurgitation. The pathogens cells ability to avoid the human immune system response is caused by the biofilms, fibrin vegetations formation and the enzymes production - cytotoxins (streptolysins, leukocidin, etc.). It has been suggested that the mediators of inflammation and leukocyte cells participate in the destruction of native and prosthetic tissues due to an IE pathogens inaccessibility for immunocompetent cells.
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Affiliation(s)
- V V Rogolevich
- Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo
| | - T V Glushkova
- Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo
| | - A V Ponasenko
- Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo
| | - E A Ovcharenko
- Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo
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