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Calcuttawala F, Shaw R, Sarbajna A, Dutta M, Sinha S, K. Das Gupta S. Apoptosis like symptoms associated with abortive infection of Mycobacterium smegmatis by mycobacteriophage D29. PLoS One 2022; 17:e0259480. [PMID: 35580120 PMCID: PMC9113562 DOI: 10.1371/journal.pone.0259480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 04/29/2022] [Indexed: 01/12/2023] Open
Abstract
Mycobacteriophages are phages that infect mycobacteria resulting in their killing. Although lysis is the primary mechanism by which mycobacteriophages cause cell death, others such as abortive infection may also be involved. We took recourse to perform immunofluorescence and electron microscopic studies using mycobacteriophage D29 infected Mycobacterium smegmatis cells to investigate this issue. We could observe the intricate details of the infection process using these techniques such as adsorption, the phage tail penetrating the thick mycolic acid layer, formation of membrane pores, membrane blebbing, and phage release. We observed a significant increase in DNA fragmentation and membrane depolarization using cell-biological techniques symptomatic of programmed cell death (PCD). As Toxin-Antitoxin (TA) systems mediate bacterial PCD, we measured their expression profiles with and without phage infection. Of the three TAs examined, MazEF, VapBC, and phd/doc, we found that in the case of VapBC, a significant decrease in the antitoxin (VapB): toxin (VapC) ratio was observed following phage infection, implying that high VapC may have a role to play in the induction of mycobacterial apoptotic cell death following phage infection. This study indicates that D29 infection causes mycobacteria to undergo morphological and molecular changes that are hallmarks of apoptotic cell death.
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Affiliation(s)
- Fatema Calcuttawala
- Department of Microbiology, Sister Nivedita University, Kolkata, India
- * E-mail:
| | - Rahul Shaw
- Department of Microbiology, Bose Institute, Kolkata, India
| | - Arpita Sarbajna
- Division of Electron Microscopy, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Moumita Dutta
- Division of Electron Microscopy, National Institute of Cholera and Enteric Diseases, Kolkata, India
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Turzynski V, Monsees I, Moraru C, Probst AJ. Imaging Techniques for Detecting Prokaryotic Viruses in Environmental Samples. Viruses 2021; 13:2126. [PMID: 34834933 PMCID: PMC8622608 DOI: 10.3390/v13112126] [Citation(s) in RCA: 3] [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: 09/20/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/28/2022] Open
Abstract
Viruses are the most abundant biological entities on Earth with an estimate of 1031 viral particles across all ecosystems. Prokaryotic viruses-bacteriophages and archaeal viruses-influence global biogeochemical cycles by shaping microbial communities through predation, through the effect of horizontal gene transfer on the host genome evolution, and through manipulating the host cellular metabolism. Imaging techniques have played an important role in understanding the biology and lifestyle of prokaryotic viruses. Specifically, structure-resolving microscopy methods, for example, transmission electron microscopy, are commonly used for understanding viral morphology, ultrastructure, and host interaction. These methods have been applied mostly to cultivated phage-host pairs. However, recent advances in environmental genomics have demonstrated that the majority of viruses remain uncultivated, and thus microscopically uncharacterized. Although light- and structure-resolving microscopy of viruses from environmental samples is possible, quite often the link between the visualization and the genomic information of uncultivated prokaryotic viruses is missing. In this minireview, we summarize the current state of the art of imaging techniques available for characterizing viruses in environmental samples and discuss potential links between viral imaging and environmental genomics for shedding light on the morphology of uncultivated viruses and their lifestyles in Earth's ecosystems.
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Affiliation(s)
- Victoria Turzynski
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany;
| | - Indra Monsees
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany;
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky-University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany;
| | - Alexander J. Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany;
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
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Abstract
Bacteriophages are viruses whose ubiquity in nature and remarkable specificity to their host bacteria enable an impressive and growing field of tunable biotechnologies in agriculture and public health. Bacteriophage capsids, which house and protect their nucleic acids, have been modified with a range of functionalities (e.g., fluorophores, nanoparticles, antigens, drugs) to suit their final application. Functional groups naturally present on bacteriophage capsids can be used for electrostatic adsorption or bioconjugation, but their impermanence and poor specificity can lead to inconsistencies in coverage and function. To overcome these limitations, researchers have explored both genetic and chemical modifications to enable strong, specific bonds between phage capsids and their target conjugates. Genetic modification methods involve introducing genes for alternative amino acids, peptides, or protein sequences into either the bacteriophage genomes or capsid genes on host plasmids to facilitate recombinant phage generation. Chemical modification methods rely on reacting functional groups present on the capsid with activated conjugates under the appropriate solution pH and salt conditions. This review surveys the current state-of-the-art in both genetic and chemical bacteriophage capsid modification methodologies, identifies major strengths and weaknesses of methods, and discusses areas of research needed to propel bacteriophage technology in development of biosensors, vaccines, therapeutics, and nanocarriers.
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Affiliation(s)
| | - Julie M. Goddard
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Sam R. Nugen
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
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Schmidt M, Byrne JM, Maasilta IJ. Bio-imaging with the helium-ion microscope: A review. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2021; 12:1-23. [PMID: 33489663 PMCID: PMC7801799 DOI: 10.3762/bjnano.12.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/26/2020] [Indexed: 06/01/2023]
Abstract
Scanning helium-ion microscopy (HIM) is an imaging technique with sub-nanometre resolution and is a powerful tool to resolve some of the tiniest structures in biology. In many aspects, the HIM resembles a field-emission scanning electron microscope (FE-SEM), but the use of helium ions rather than electrons provides several advantages, including higher surface sensitivity, larger depth of field, and a straightforward charge-compensating electron flood gun, which enables imaging of non-conductive samples, rendering HIM a promising high-resolution imaging technique for biological samples. Starting with studies focused on medical research, the last decade has seen some particularly spectacular high-resolution images in studies focused on plants, microbiology, virology, and geomicrobiology. However, HIM is not just an imaging technique. The ability to use the instrument for milling biological objects as small as viruses offers unique opportunities which are not possible with more conventional focused ion beams, such as gallium. Several pioneering technical developments, such as methods to couple secondary ion mass spectrometry (SIMS) or ionoluminescence with the HIM, also offer the possibility for new and exciting research on biological materials. In this review, we present a comprehensive overview of almost all currently published literature which has demonstrated the application of HIM for imaging of biological specimens. We also discuss some technical features of this unique type of instrument and highlight some of the new advances which will likely become more widely used in the years to come.
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Affiliation(s)
- Matthias Schmidt
- Helmholtz-Centre for Environmental Research GmbH - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - James M Byrne
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol BS8 1RJ, United Kingdom
| | - Ilari J Maasilta
- Nanoscience Center, Department of Physics, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
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D'Abramo F, Neumeyer S. A historical and political epistemology of microbes. CENTAURUS; INTERNATIONAL MAGAZINE OF THE HISTORY OF SCIENCE AND MEDICINE 2020; 62:321-330. [PMID: 32834061 PMCID: PMC7404376 DOI: 10.1111/1600-0498.12300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 05/26/2023]
Abstract
This article traces the historical co-evolution of microbiology, bacteriology, and virology, framed within industrial and agricultural contexts, as well as their role in colonial and national history between the end of the 19th century and the first decades of the 20th century. The epistemology of germ theory, coupled with the economic interests of European colonies, has shaped the understanding of human-microbial relationships in a reductionist way. We explore a brief history of the medical and biological sciences, focusing on microbes and the difficulty of implementing germ theory outside of biology laboratories. Furthermore, we highlight the work of Lynn Margulis, who conceptualized microbes within their ecological contexts. Such research shows the active role microbes play in handling life-sustaining biological and biochemical processes. We outline how the industrial and technological advancements of the last two centuries not only impacted almost all human societies, but also changed the world on microbial, biological, and geological levels. The narration of these histories is a complex task, and depends on how national, international, and intergovernmental institutions (such as the World Health Organization) conceive of the selective environmental pressures exerted by industry and biotechnological companies.
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Affiliation(s)
- Flavio D'Abramo
- Max Planck Institute for the History of ScienceBerlinGermany
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Debarbieux L, Forterre P, Krupovic M, Kutateladze M, Prangishvili D. Centennial celebration of the bacteriophage research. Res Microbiol 2018; 169:479-480. [PMID: 30391303 DOI: 10.1016/j.resmic.2018.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 12/16/2022]
Affiliation(s)
| | - Patrick Forterre
- Department of Microbiology, Institut Pasteur, 75015 Paris, France
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, 75015 Paris, France
| | - Mzia Kutateladze
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, Georgia
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