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Shymialevich D, Wójcicki M, Wardaszka A, Świder O, Sokołowska B, Błażejak S. Application of Lytic Bacteriophages and Their Enzymes to Reduce Saprophytic Bacteria Isolated from Minimally Processed Plant-Based Food Products-In Vitro Studies. Viruses 2022; 15:9. [PMID: 36680050 PMCID: PMC9865725 DOI: 10.3390/v15010009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/16/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
The aim of this study was to isolate phage enzymes and apply them in vitro for eradication of the dominant saprophytic bacteria isolated from minimally processed food. Four bacteriophages-two Enterobacter-specific and two Serratia-specific, which produce lytic enzymes-were used in this research. Two methods of phage enzyme isolation were tested, namely precipitation with acetone and ultracentrifugation. It was found that the number of virions could be increased almost 100 times due to the extension of the cultivation time (72 h). The amplification of phage particles and lytic proteins was dependent on the time of cultivation. Considering the influence of isolated enzymes on the growth kinetics of bacterial hosts, proteins isolated with acetone after 72-hour phage propagation exhibited the highest inhibitory effect. The reduction of bacteria count was dependent on the concentration of enzymes in the lysates. The obtained results indicate that phages and their lytic enzymes could be used in further research aiming at the improvement of microbiological quality and safety of minimally processed food products.
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Affiliation(s)
- Dziyana Shymialevich
- Culture Collection of Industrial Microorganisms—Microbiological Resources Center, Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Michał Wójcicki
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Artur Wardaszka
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Olga Świder
- Department of Food Safety and Chemical Analysis, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Barbara Sokołowska
- Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Stanisław Błażejak
- Department of Biotechnology and Food Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences (WULS–SGGW), Nowoursynowska 166 Street, 02-776 Warsaw, Poland
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2
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MDR Pumps as Crossroads of Resistance: Antibiotics and Bacteriophages. Antibiotics (Basel) 2022; 11:antibiotics11060734. [PMID: 35740141 PMCID: PMC9220107 DOI: 10.3390/antibiotics11060734] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 05/21/2022] [Accepted: 05/26/2022] [Indexed: 01/27/2023] Open
Abstract
At present, antibiotic resistance represents a global problem in modern medicine. In the near future, humanity may face a situation where medicine will be powerless against resistant bacteria and a post-antibiotic era will come. The development of new antibiotics is either very expensive or ineffective due to rapidly developing bacterial resistance. The need to develop alternative approaches to the treatment of bacterial infections, such as phage therapy, is beyond doubt. The cornerstone of bacterial defense against antibiotics are multidrug resistance (MDR) pumps, which are involved in antibiotic resistance, toxin export, biofilm, and persister cell formation. MDR pumps are the primary non-specific defense of bacteria against antibiotics, while drug target modification, drug inactivation, target switching, and target sequestration are the second, specific line of their defense. All bacteria have MDR pumps, and bacteriophages have evolved along with them and use the bacteria’s need for MDR pumps to bind and penetrate into bacterial cells. The study and understanding of the mechanisms of the pumps and their contribution to the overall resistance and to the sensitivity to bacteriophages will allow us to either seriously delay the onset of the post-antibiotic era or even prevent it altogether due to phage-antibiotic synergy.
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3
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Swanson NA, Hou CFD, Cingolani G. Viral Ejection Proteins: Mosaically Conserved, Conformational Gymnasts. Microorganisms 2022; 10:microorganisms10030504. [PMID: 35336080 PMCID: PMC8954989 DOI: 10.3390/microorganisms10030504] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 11/16/2022] Open
Abstract
Bacterial viruses (or bacteriophages) have developed formidable ways to deliver their genetic information inside bacteria, overcoming the complexity of the bacterial-cell envelope. In short-tailed phages of the Podoviridae superfamily, genome ejection is mediated by a set of mysterious internal virion proteins, also called ejection or pilot proteins, which are required for infectivity. The ejection proteins are challenging to study due to their plastic structures and transient assembly and have remained less characterized than classical components such as the phage coat protein or terminase subunit. However, a spate of recent cryo-EM structures has elucidated key features underscoring these proteins' assembly and conformational gymnastics that accompany their expulsion from the virion head through the portal protein channel into the host. In this review, we will use a phage-T7-centric approach to critically review the status of the literature on ejection proteins, decipher the conformational changes of T7 ejection proteins in the pre- and post-ejection conformation, and predict the conservation of these proteins in other Podoviridae. The challenge is to relate the structure of the ejection proteins to the mechanisms of genome ejection, which are exceedingly complex and use the host's machinery.
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Affiliation(s)
- Nicholas A. Swanson
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA; (N.A.S.); (C.-F.D.H.)
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
| | - Chun-Feng D. Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA; (N.A.S.); (C.-F.D.H.)
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA; (N.A.S.); (C.-F.D.H.)
- Correspondence: ; Tel.: +01-(215)-503-4573
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4
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Structural changes in bacteriophage T7 upon receptor-induced genome ejection. Proc Natl Acad Sci U S A 2021; 118:2102003118. [PMID: 34504014 DOI: 10.1073/pnas.2102003118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2021] [Indexed: 12/11/2022] Open
Abstract
Many tailed bacteriophages assemble ejection proteins and a portal-tail complex at a unique vertex of the capsid. The ejection proteins form a transenvelope channel extending the portal-tail channel for the delivery of genomic DNA in cell infection. Here, we report the structure of the mature bacteriophage T7, including the ejection proteins, as well as the structures of the full and empty T7 particles in complex with their cell receptor lipopolysaccharide. Our near-atomic-resolution reconstruction shows that the ejection proteins in the mature T7 assemble into a core, which comprises a fourfold gene product 16 (gp16) ring, an eightfold gp15 ring, and a putative eightfold gp14 ring. The gp15 and gp16 are mainly composed of helix bundles, and gp16 harbors a lytic transglycosylase domain for degrading the bacterial peptidoglycan layer. When interacting with the lipopolysaccharide, the T7 tail nozzle opens. Six copies of gp14 anchor to the tail nozzle, extending the nozzle across the lipopolysaccharide lipid bilayer. The structures of gp15 and gp16 in the mature T7 suggest that they should undergo remarkable conformational changes to form the transenvelope channel. Hydrophobic α-helices were observed in gp16 but not in gp15, suggesting that gp15 forms the channel in the hydrophilic periplasm and gp16 forms the channel in the cytoplasmic membrane.
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5
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Scaling Theory of a Polymer Ejecting from a Cavity into a Semi-Space. Polymers (Basel) 2020; 12:polym12123014. [PMID: 33339450 PMCID: PMC7766115 DOI: 10.3390/polym12123014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 12/23/2022] Open
Abstract
A two-stage model is developed in order to understand the scaling behaviors of single polymers ejecting from a spherical cavity through a nanopore. The dynamics of ejection is derived by balancing the free energy change with the energy dissipation during a process. The ejection velocity is found to vary with the number of monomers in the cavity, m, as mz1/(Nx1D3z1) at the confined stage, and it turns to be m−z2 at the non-confined stage, where N is the chain length and D the cavity diameter. The exponents are shown to be z1=(3ν−1)−1, z2=2ν and x1=1/3, with ν being the Flory exponent. The profile of the velocity is carefully verified by performing Langevin dynamics simulations. The simulations further reveal that, at the starting point, the decreasing of m can be stalled for a good moment. It suggests the existence of a pre-stage that can be explained by using the concept of a classical nucleation theory. By trimming the pre-stage, the ejection time are properly studied by varying N, D, and ϕ0 (the initial volume fraction). The scaling properties of the nucleation time are also analyzed. The results fully support the predictions of the theory. The physical pictures are given for various ejection conditions that cover the entire parameter space.
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6
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Cheng L, Wang J, Zhao X, Yin H, Fang H, Lin C, Zhang S, Shen Z, Zhao C. An antiphage Escherichia coli mutant for higher production of L-threonine obtained by atmospheric and room temperature plasma mutagenesis. Biotechnol Prog 2020; 36:e3058. [PMID: 32735374 DOI: 10.1002/btpr.3058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 12/21/2022]
Abstract
Phage infection is common during the production of L-threonine by E. coli, and low L-threonine production and glucose conversion percentage are bottlenecks for the efficient commercial production of L-threonine. In this study, 20 antiphage mutants producing high concentration of L-threonine were obtained by atmospheric and room temperature plasma (ARTP) mutagenesis, and an antiphage E. coli variant was characterized that exhibited the highest production of L-threonine Escherichia coli ([E. coli] TRFC-AP). The elimination of fhuA expression in E. coli TRFC-AP was responsible for phage resistance. The biomass and cell growth of E. coli TRFC-AP showed no significant differences from those of the parent strain (E. coli TRFC), and the production of L-threonine (159.3 g L-1 ) and glucose conversion percentage (51.4%) were increased by 10.9% and 9.1%, respectively, compared with those of E. coli TRFC. During threonine production (culture time of 20 h), E. coli TRFC-AP exhibited higher activities of key enzymes for glucose utilization (hexokinase, glucose phosphate dehydrogenase, phosphofructokinase, phosphoenolpyruvate carboxylase, and PYK) and threonine synthesis (glutamate synthase, aspartokinase, homoserine dehydrogenase, homoserine kinase and threonine synthase) compared to those of E. coli TRFC. The analysis of metabolic flux distribution indicated that the flux of threonine with E. coli TRFC-AP reached 69.8%, an increase of 16.0% compared with that of E. coli TRFC. Overall, higher L-threonine production and glucose conversion percentage were obtained with E. coli TRFC-AP due to increased activities of key enzymes and improved carbon flux for threonine synthesis.
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Affiliation(s)
- Likun Cheng
- Shandong Research Center of High Cell Density Fermentation and Efficient Expression Technology, Shandong Lvdu Bio-science and Technology Co., Ltd, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Jing Wang
- Department of Critical Care Medicine, Affiliated Hospital of Binzhou Medical University, Binzhou, China
| | - Xiubao Zhao
- Shandong Research Center of High Cell Density Fermentation and Efficient Expression Technology, Shandong Lvdu Bio-science and Technology Co., Ltd, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Huanhuan Yin
- Shandong Research Center of High Cell Density Fermentation and Efficient Expression Technology, Shandong Lvdu Bio-science and Technology Co., Ltd, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Haitian Fang
- Research and Development Center, Ningxia Eppen Biotech Co., Ltd, Yinchuan, China.,Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Agriculture, Ningxia University, Yinchuan, China
| | - Chuwen Lin
- Shandong Research Center of High Cell Density Fermentation and Efficient Expression Technology, Shandong Lvdu Bio-science and Technology Co., Ltd, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Shasha Zhang
- Shandong Research Center of High Cell Density Fermentation and Efficient Expression Technology, Shandong Lvdu Bio-science and Technology Co., Ltd, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Zhiqiang Shen
- Shandong Research Center of High Cell Density Fermentation and Efficient Expression Technology, Shandong Lvdu Bio-science and Technology Co., Ltd, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Chunguang Zhao
- Research and Development Center, Ningxia Eppen Biotech Co., Ltd, Yinchuan, China.,Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Agriculture, Ningxia University, Yinchuan, China
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7
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Tkacova A, Orieskova M, Halgasova N, Bocanova L, Bukovska G. Identification of Brevibacterium flavum genes related to receptors involved in bacteriophage BFK20 adsorption. Virus Res 2019; 274:197775. [PMID: 31600527 DOI: 10.1016/j.virusres.2019.197775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/28/2019] [Accepted: 10/04/2019] [Indexed: 12/27/2022]
Abstract
Phage infection of bacterial cells is a process requiring the interaction between phage receptor binding proteins and receptors on the bacterial cell surface. We prepared a Brevibacterium flavum CCM 251 EZ-Tn5 transposon insertional library and isolated phage-resistant mutants. Analysis of the DNA fragments produced by single-primer PCR was used to determine the EZ-Tn5 transposon insertion sites in the genomes of phage-resistant B. flavum mutants. Seven disrupted genes were identified in forty B. flavum mutants. The phage resistance of these mutants was demonstrated by cultivation analysis in the presence of BFK20, and the adsorption rate of BFK20 to these mutants was tested. B. flavum mutants displayed significantly reduced adsorption rates; the lowest rate was observed for mutants containing interrupted major facilitator superfamily (MFS) protein and glycosyltransferase genes. Uninterrupted forms of these genes were cloned into corynebacterial vector pJUP06 and used for in trans complementation of the corresponding B. flavum mutants. The growth of these complemented mutants when infected with BFK20 closely resembled that of wild-type B. flavum. These complemented mutants also exhibited similar BFK20 adsorption as the wild-type control. We infer that the disrupted MFS protein and glycosyltransferase genes are responsible for the phage-resistant phenotype of these B. flavum transposition mutants.
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Affiliation(s)
- Adela Tkacova
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Maria Orieskova
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Nora Halgasova
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Lucia Bocanova
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Gabriela Bukovska
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovakia.
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8
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Temperature-Dependent Nanomechanics and Topography of Bacteriophage T7. J Virol 2018; 92:JVI.01236-18. [PMID: 30089696 DOI: 10.1128/jvi.01236-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 07/30/2018] [Indexed: 01/10/2023] Open
Abstract
Viruses are nanoscale infectious agents which may be inactivated by heat treatment. The global molecular mechanisms of virus inactivation and the thermally induced structural changes in viruses are not fully understood. In this study, we measured the heat-induced changes in the properties of T7 bacteriophage particles exposed to a two-stage (65°C and 80°C) thermal effect, by using atomic force microscopy (AFM)-based nanomechanical and topographical measurements. We found that exposure to 65°C led to the release of genomic DNA and to the loss of the capsid tail; hence, the T7 particles became destabilized. Further heating to 80°C surprisingly led to an increase in mechanical stability, due likely to partial denaturation of the capsomeric proteins kept within the global capsid arrangement.IMPORTANCE Even though the loss of DNA, caused by heat treatment, destabilizes the T7 phage, its capsid is remarkably able to withstand high temperatures with a more or less intact global topographical structure. Thus, partial denaturation within the global structural constraints of the viral capsid may have a stabilizing effect. Understanding the structural design of viruses may help in constructing artificial nanocapsules for the packaging and delivery of materials under harsh environmental conditions.
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9
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Kellermayer MSZ, Vörös Z, Csík G, Herényi L. Forced phage uncorking: viral DNA ejection triggered by a mechanically sensitive switch. NANOSCALE 2018; 10:1898-1904. [PMID: 29318247 DOI: 10.1039/c7nr05897g] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The foremost event of bacteriophage infection is the ejection of genomic material into the host bacterium after virus binding to surface receptor sites. How ejection is triggered is yet unknown. Here we show, in single mature T7 phage particles, that tapping the capsid wall with an oscillating atomic-force-microscope cantilever triggers rapid DNA ejection via the tail complex. The triggering rate increases exponentially as a function of force, following transition-state theory, across an activation barrier of 23 kcal mol-1 at 1.2 nm along the reaction coordinate. The conformation of the ejected DNA molecule revealed that it had been exposed to a propulsive force. This force, arising from intra-capsid pressure, assists in initiating the ejection process and the transfer of DNA across spatial dimensions beyond that of the virion. Chemical immobilization of the tail fibers also resulted in enhanced DNA ejection, suggesting that the triggering process might involve a conformational switch that can be mechanically activated either by external forces or via the tail-fiber complex.
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Affiliation(s)
- Miklós S Z Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, Budapest H-1094, Hungary.
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10
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Milrot E, Shimoni E, Dadosh T, Rechav K, Unger T, Van Etten JL, Minsky A. Structural studies demonstrating a bacteriophage-like replication cycle of the eukaryote-infecting Paramecium bursaria chlorella virus-1. PLoS Pathog 2017; 13:e1006562. [PMID: 28850602 PMCID: PMC5593192 DOI: 10.1371/journal.ppat.1006562] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 09/11/2017] [Accepted: 07/31/2017] [Indexed: 11/18/2022] Open
Abstract
A fundamental stage in viral infection is the internalization of viral genomes in host cells. Although extensively studied, the mechanisms and factors responsible for the genome internalization process remain poorly understood. Here we report our observations, derived from diverse imaging methods on genome internalization of the large dsDNA Paramecium bursaria chlorella virus-1 (PBCV-1). Our studies reveal that early infection stages of this eukaryotic-infecting virus occurs by a bacteriophage-like pathway, whereby PBCV-1 generates a hole in the host cell wall and ejects its dsDNA genome in a linear, base-pair-by-base-pair process, through a membrane tunnel generated by the fusion of the virus internal membrane with the host membrane. Furthermore, our results imply that PBCV-1 DNA condensation that occurs shortly after infection probably plays a role in genome internalization, as hypothesized for the infection of some bacteriophages. The subsequent perforation of the host photosynthetic membranes presumably enables trafficking of viral genomes towards host nuclei. Previous studies established that at late infection stages PBCV-1 generates cytoplasmic organelles, termed viral factories, where viral assembly takes place, a feature characteristic of many large dsDNA viruses that infect eukaryotic organisms. PBCV-1 thus appears to combine a bacteriophage-like mechanism during early infection stages with a eukaryotic-like infection pathway in its late replication cycle. Although extensively studied, the mechanisms responsible for internalization of viral genomes into their host cells remain unclear. A particularly interesting case of genome release and internalization is provided by the large Paramecium bursaria chlorella virus-1 (PBCV-1), which infects unicellular eukaryotic photosynthetic chlorella cells. In order to release its long dsDNA genome and to enable its translocation to the host nucleus, PBCV-1 must overcome multiple hurdles, including a thick host cell wall and multilayered chloroplast membranes that surround the host cytoplasm. Our observations indicate that these obstacles are dealt with perforations of the host wall, the host cellular membrane, and the host photosynthetic membranes by viral-encoded proteins. Furthermore, our results highlight a bacteriophage-like nature of early PBCV-1 infection stages, thus implying that this virus uniquely combines bacteriophage-like and eukaryotic-like pathways to accomplish its replication cycle.
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Affiliation(s)
- Elad Milrot
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (EM); (AM)
| | - Eyal Shimoni
- Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Tali Dadosh
- Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Katya Rechav
- Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Unger
- Proteomics, The Weizmann Institute of Science, Rehovot, Israel
| | - James L. Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska, Lincoln, NE, United States of America
| | - Abraham Minsky
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (EM); (AM)
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11
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Visualizing Adsorption of Cyanophage P-SSP7 onto Marine Prochlorococcus. Sci Rep 2017; 7:44176. [PMID: 28281671 PMCID: PMC5345008 DOI: 10.1038/srep44176] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 02/06/2017] [Indexed: 12/17/2022] Open
Abstract
Marine cyanobacteria perform roughly a quarter of global carbon fixation, and cyanophages that infect them liberate some of this carbon during infection and cell lysis. Studies of the cyanobacterium Prochlorococcus MED4 and its associated cyanophage P-SSP7 have revealed complex gene expression dynamics once infection has begun, but the initial cyanophage-host interactions remain poorly understood. Here, we used single particle cryo-electron tomography (cryo-ET) to investigate cyanophage-host interactions in this model system, based on 170 cyanophage-to-host adsorption events. Subtomogram classification and averaging revealed three main conformations characterized by different angles between the phage tail and the cell surface. Namely, phage tails were (i) parallel to, (ii) ~45 degrees to, or (iii) perpendicular to the cell surface. Furthermore, different conformations of phage tail fibers correlated with the aforementioned orientations of the tails. We also observed density beyond the tail tip in vertically-oriented phages that had penetrated the cell wall, capturing the final stage of adsorption. Together, our data provide a quantitative characterization of the orientation of phages as they adsorb onto cells, and suggest that cyanophages that abut their cellular targets are only transiently in the “perpendicular” orientation required for successful infection.
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12
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The T7 ejection nanomachine components gp15-gp16 form a spiral ring complex that binds DNA and a lipid membrane. Virology 2015; 486:263-71. [PMID: 26476287 DOI: 10.1016/j.virol.2015.09.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 09/18/2015] [Accepted: 09/25/2015] [Indexed: 11/20/2022]
Abstract
Bacteriophage T7 initiates infection by ejecting several internal capsid proteins into the host cell; these proteins then assemble into a nanomachine that translocates the viral genome from the phage head into the cytoplasm. The ejected proteins are thought to partially unfold as they pass through the lumen of the portal and the short stubby T7 tail during their entry into the cell. In vivo, the internal proteins gp15 and gp16 assemble into a tubular structure that spans the periplasm and cytoplasmic membrane. We show here that purified gp15 and gp16 can refold from a partially denatured state in vitro, and that gp15 interacts with gp16 to form a spiral ring structure. Purified gp15 binds to DNA, whereas gp16 binds protein-free liposomes; the gp15-gp16 complex binds both DNA and liposomes. Limited proteolysis of the liposome-bound gp16 reveals that its C-terminal region is protected, suggesting a partial membrane insertion of the protein.
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13
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Casjens SR, Hendrix RW. Bacteriophage lambda: Early pioneer and still relevant. Virology 2015; 479-480:310-30. [PMID: 25742714 PMCID: PMC4424060 DOI: 10.1016/j.virol.2015.02.010] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/13/2015] [Accepted: 02/05/2015] [Indexed: 12/14/2022]
Abstract
Molecular genetic research on bacteriophage lambda carried out during its golden age from the mid-1950s to mid-1980s was critically important in the attainment of our current understanding of the sophisticated and complex mechanisms by which the expression of genes is controlled, of DNA virus assembly and of the molecular nature of lysogeny. The development of molecular cloning techniques, ironically instigated largely by phage lambda researchers, allowed many phage workers to switch their efforts to other biological systems. Nonetheless, since that time the ongoing study of lambda and its relatives has continued to give important new insights. In this review we give some relevant early history and describe recent developments in understanding the molecular biology of lambda's life cycle.
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Affiliation(s)
- Sherwood R Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Emma Eccles Jones Medical Research Building, 15 North Medical Drive East, Salt Lake City, UT 84112, USA; Biology Department, University of Utah, Salt Lake City, UT 84112, USA.
| | - Roger W Hendrix
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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14
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Yasar S, Podgornik R, Valle-Orero J, Johnson MR, Parsegian VA. Continuity of states between the cholesteric → line hexatic transition and the condensation transition in DNA solutions. Sci Rep 2014; 4:6877. [PMID: 25371012 PMCID: PMC4220286 DOI: 10.1038/srep06877] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 09/12/2014] [Indexed: 11/25/2022] Open
Abstract
A new method of finely temperature-tuning osmotic pressure allows one to identify the cholesteric → line hexatic transition of oriented or unoriented long-fragment DNA bundles in monovalent salt solutions as first order, with a small but finite volume discontinuity. This transition is similar to the osmotic pressure-induced expanded → condensed DNA transition in polyvalent salt solutions at small enough polyvalent salt concentrations. Therefore there exists a continuity of states between the two. This finding, together with the corresponding empirical equation of state, effectively relates the phase diagram of DNA solutions for monovalent salts to that for polyvalent salts and sheds some light on the complicated interactions between DNA molecules at high densities.
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Affiliation(s)
- Selcuk Yasar
- Department of Physics, University of Massachusetts, Amherst, MA 01003, United States
| | - Rudolf Podgornik
- 1] Department of Physics, University of Massachusetts, Amherst, MA 01003, United States [2] Department of Theoretical Physics, J. Stefan Institute, SI-1000 Ljubljana, Slovenia [3] Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Jessica Valle-Orero
- 1] Institut Laue Langevin, BP 156, 6, rue Jules Horowitz 38042 Grenoble Cedex 9, France [2] Laboratoire de Physique, Ecole Normale Superiéure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - Mark R Johnson
- Institut Laue-Langevin, 6 rue Jules Horowitz, BP156 38042, Grenoble, France
| | - V Adrian Parsegian
- Department of Physics, University of Massachusetts, Amherst, MA 01003, United States
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15
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Abedon ST. Lysis from without. BACTERIOPHAGE 2014; 1:46-49. [PMID: 21687534 DOI: 10.4161/bact.1.1.13980] [Citation(s) in RCA: 243] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/19/2010] [Accepted: 10/20/2010] [Indexed: 01/21/2023]
Abstract
In this commentary I consider use of the term "lysis from without" (LO) along with the phenomenon's biological relevance. LO originally described an early bacterial lysis induced by high-multiplicity virion adsorption and that occurs without phage production (here indicated as LO(V)). Notably, this is more than just high phage multiplicities of adsorption leading to bacterial killing. The action on bacteria of exogenously supplied phage lysin, too, has been described as a form of LO (here, LO(L)). LO(V) has been somewhat worked out mechanistically for T4 phages, has been used to elucidate various phage-associated phenomena including discovery of the phage eclipse, may be relevant to phage ecology, and, with resistance to LO (LO(R)), is blocked by certain phage gene products. Speculation as to the impact of LO(V) on phage therapy also is fairly common. Since LO(V) assays are relatively easily performed and not all phages are able to induce LO(V), a phage's potential to lyse bacteria without first infecting should be subject to at least in vitro experimental confirmation before the LO(V) label is applied. The term "abortive infection" may be used more generally to describe non-productive phage infections that kill bacteria.
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Affiliation(s)
- Stephen T Abedon
- Department of Microbiology; The Ohio State University; Mansfield, OH USA
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16
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Infection cycles of large DNA viruses: Emerging themes and underlying questions. Virology 2014; 466-467:3-14. [DOI: 10.1016/j.virol.2014.05.037] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 05/28/2014] [Accepted: 05/30/2014] [Indexed: 11/20/2022]
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17
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Agarkova I, Hertel B, Zhang X, Lane L, Tchourbanov A, Dunigan DD, Thiel G, Rossmann MG, Van Etten JL. Dynamic attachment of Chlorovirus PBCV-1 to Chlorella variabilis. Virology 2014; 466-467:95-102. [PMID: 25240455 PMCID: PMC4254200 DOI: 10.1016/j.virol.2014.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 05/29/2014] [Accepted: 07/01/2014] [Indexed: 11/27/2022]
Abstract
Chloroviruses infect their hosts by specifically binding to and degrading the cell wall of their algal hosts at the site of attachment, using an intrinsic digesting enzyme(s). Chlorovirus PBCV-1 stored as a lysate survived longer than virus alone, suggesting virus attachment to cellular debris may be reversible. Ghost cells (algal cells extracted with methanol) were used as a model to study reversibility of PBCV-1 attachment because ghost cells are as susceptible to attachment and wall digestion as are live cells. Reversibility of attachment to ghost cells was examined by releasing attached virions with a cell wall degrading enzyme extract. The majority of the released virions retained infectivity even after re-incubating the released virions with ghost cells two times. Thus the chloroviruses appear to have a dynamic attachment strategy that may be beneficial in indigenous environments where cell wall debris can act as a refuge until appropriate host cells are available.
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Affiliation(s)
- Irina Agarkova
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583-0722, United States; Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, United States
| | - Brigitte Hertel
- Technische Universität Darmstadt, Department of Biology, Plant Membrane Biophysics, 64287 Darmstadt, Germany
| | - Xinzheng Zhang
- Department of Biological Sciences, Purdue University, 240 South Martin Jischke Drive, West Lafayette, IN 47907-2032, United States
| | - Les Lane
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583-0722, United States
| | - Alexander Tchourbanov
- Genetics Core, University of Arizona, 246B Biological Science West, 1041 East Lowell St, Tucson, AZ 85721-0499, United States
| | - David D Dunigan
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583-0722, United States; Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, United States
| | - Gerhard Thiel
- Technische Universität Darmstadt, Department of Biology, Plant Membrane Biophysics, 64287 Darmstadt, Germany
| | - Michael G Rossmann
- Department of Biological Sciences, Purdue University, 240 South Martin Jischke Drive, West Lafayette, IN 47907-2032, United States
| | - James L Van Etten
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583-0722, United States; Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, United States.
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18
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Happonen LJ, Erdmann S, Garrett RA, Butcher SJ. Adenosine triphosphatases of thermophilic archaeal double-stranded DNA viruses. Cell Biosci 2014; 4:37. [PMID: 25105011 PMCID: PMC4124505 DOI: 10.1186/2045-3701-4-37] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 06/13/2014] [Indexed: 12/02/2022] Open
Abstract
Adenosine triphosphatases (ATPases) of double-stranded (ds) DNA archaeal viruses are structurally related to the AAA+ hexameric helicases and translocases. These ATPases have been implicated in viral life cycle functions such as DNA entry into the host, and viral genome packaging into preformed procapsids. We summarize bioinformatical analyses of a wide range of archaeal ATPases, and review the biochemical and structural properties of those archaeal ATPases that have measurable ATPase activity. We discuss their potential roles in genome delivery into the host, virus assembly and genome packaging in comparison to hexameric helicases and packaging motors from bacteriophages.
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Affiliation(s)
- Lotta J Happonen
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, SE-221 84 Lund, Sweden
| | - Susanne Erdmann
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Roger A Garrett
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Sarah J Butcher
- Institute of Biotechnology, University of Helsinki, (Viikinkaari 1), P.O. Box 65, FI-00014 Helsinki, Finland
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19
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Mutations in Ralstonia solanacearum loci involved in lipopolysaccharide biogenesis, phospholipid trafficking and peptidoglycan recycling render bacteriophage infection. Arch Microbiol 2014; 196:667-74. [DOI: 10.1007/s00203-014-1002-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 05/13/2014] [Accepted: 05/30/2014] [Indexed: 10/25/2022]
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20
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Abedon ST. Phage therapy: eco-physiological pharmacology. SCIENTIFICA 2014; 2014:581639. [PMID: 25031881 PMCID: PMC4054669 DOI: 10.1155/2014/581639] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 02/10/2014] [Indexed: 06/03/2023]
Abstract
Bacterial virus use as antibacterial agents, in the guise of what is commonly known as phage therapy, is an inherently physiological, ecological, and also pharmacological process. Physiologically we can consider metabolic properties of phage infections of bacteria and variation in those properties as a function of preexisting bacterial states. In addition, there are patient responses to pathogenesis, patient responses to phage infections of pathogens, and also patient responses to phage virions alone. Ecologically, we can consider phage propagation, densities, distribution (within bodies), impact on body-associated microbiota (as ecological communities), and modification of the functioning of body "ecosystems" more generally. These ecological and physiological components in many ways represent different perspectives on otherwise equivalent phenomena. Comparable to drugs, one also can view phages during phage therapy in pharmacological terms. The relatively unique status of phages within the context of phage therapy as essentially replicating antimicrobials can therefore result in a confluence of perspectives, many of which can be useful towards gaining a better mechanistic appreciation of phage therapy, as I consider here. Pharmacology more generally may be viewed as a discipline that lies at an interface between organism-associated phenomena, as considered by physiology, and environmental interactions as considered by ecology.
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Affiliation(s)
- Stephen T. Abedon
- Department of Microbiology, The Ohio State University, Mansfield, OH 44906, USA
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21
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Seul A, Müller JJ, Andres D, Stettner E, Heinemann U, Seckler R. Bacteriophage P22 tailspike: structure of the complete protein and function of the interdomain linker. ACTA ACUST UNITED AC 2014; 70:1336-45. [PMID: 24816102 DOI: 10.1107/s1399004714002685] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 02/05/2014] [Indexed: 12/31/2022]
Abstract
Attachment of phages to host cells, followed by phage DNA ejection, represents the first stage of viral infection of bacteria. Salmonella phage P22 has been extensively studied, serving as an experimental model for bacterial infection by phages. P22 engages bacteria by binding to the sugar moiety of lipopolysaccharides using the viral tailspike protein for attachment. While the structures of the N-terminal particle-binding domain and the major receptor-binding domain of the tailspike have been analyzed individually, the three-dimensional organization of the intact protein, including the highly conserved linker region between the two domains, remained unknown. A single amino-acid exchange in the linker sequence made it possible to crystallize the full-length protein. Two crystal structures of the linker region are presented: one attached to the N-terminal domain and the other present within the complete tailspike protein. Both retain their biological function, but the mutated full-length tailspike displays a retarded folding pathway. Fitting of the full-length tailspike into a published cryo-electron microscopy map of the P22 virion requires an elastic distortion of the crystal structure. The conservation of the linker suggests a role in signal transmission from the distal tip of the molecule to the phage head, eventually leading to DNA ejection.
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Affiliation(s)
- Anaït Seul
- Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Jürgen J Müller
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Dorothee Andres
- Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Eva Stettner
- Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Robert Seckler
- Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
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22
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Habann M, Leiman PG, Vandersteegen K, Van den Bossche A, Lavigne R, Shneider MM, Bielmann R, Eugster MR, Loessner MJ, Klumpp J. Listeriaphage A511, a model for the contractile tail machineries of SPO1-related bacteriophages. Mol Microbiol 2014; 92:84-99. [DOI: 10.1111/mmi.12539] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Matthias Habann
- Institute of Food, Nutrition and Health; ETH Zurich; 8092 Zurich Switzerland
| | - Petr G. Leiman
- Institut de Physique des Systèmes Biologiques; EPF Lausanne; 1015 Lausanne Switzerland
| | | | - An Van den Bossche
- Division of Gene Technology; Katholieke Universiteit Leuven; 3001 Leuven Belgium
| | - Rob Lavigne
- Division of Gene Technology; Katholieke Universiteit Leuven; 3001 Leuven Belgium
| | - Mikhail M. Shneider
- Institut de Physique des Systèmes Biologiques; EPF Lausanne; 1015 Lausanne Switzerland
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; 117997 Moscow Russia
| | - Regula Bielmann
- Institute of Food, Nutrition and Health; ETH Zurich; 8092 Zurich Switzerland
| | - Marcel R. Eugster
- Institute of Food, Nutrition and Health; ETH Zurich; 8092 Zurich Switzerland
| | - Martin J. Loessner
- Institute of Food, Nutrition and Health; ETH Zurich; 8092 Zurich Switzerland
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health; ETH Zurich; 8092 Zurich Switzerland
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23
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Hanhijärvi KJ, Ziedaite G, Pietilä MK, Hæggström E, Bamford DH. DNA ejection from an archaeal virus--a single-molecule approach. Biophys J 2013; 104:2264-72. [PMID: 23708366 DOI: 10.1016/j.bpj.2013.03.061] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 03/12/2013] [Accepted: 03/15/2013] [Indexed: 10/26/2022] Open
Abstract
The translocation of genetic material from the viral capsid to the cell is an essential part of the viral infection process. Whether the energetics of this process is driven by the energy stored within the confined nucleic acid or cellular processes pull the genome into the cell has been the subject of discussion. However, in vitro studies of genome ejection have been limited to a few head-tailed bacteriophages with a double-stranded DNA genome. Here we describe a DNA release system that operates in an archaeal virus. This virus infects an archaeon Haloarcula hispanica that was isolated from a hypersaline environment. The DNA-ejection velocity of His1, determined by single-molecule experiments, is comparable to that of bacterial viruses. We found that the ejection process is modulated by the external osmotic pressure (polyethylene glycol (PEG)) and by increased ion (Mg(2+) and Na(+)) concentration. The observed ejection was unidirectional, randomly paused, and incomplete, which suggests that cellular processes are required to complete the DNA transfer.
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Affiliation(s)
- K J Hanhijärvi
- Department of Physics, University of Helsinki, Helsinki, Finland.
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24
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Leavitt JC, Gogokhia L, Gilcrease EB, Bhardwaj A, Cingolani G, Casjens SR. The tip of the tail needle affects the rate of DNA delivery by bacteriophage P22. PLoS One 2013; 8:e70936. [PMID: 23951045 PMCID: PMC3741392 DOI: 10.1371/journal.pone.0070936] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 06/25/2013] [Indexed: 02/01/2023] Open
Abstract
The P22-like bacteriophages have short tails. Their virions bind to their polysaccharide receptors through six trimeric tailspike proteins that surround the tail tip. These short tails also have a trimeric needle protein that extends beyond the tailspikes from the center of the tail tip, in a position that suggests that it should make first contact with the host’s outer membrane during the infection process. The base of the needle serves as a plug that keeps the DNA in the virion, but role of the needle during adsorption and DNA injection is not well understood. Among the P22-like phages are needle types with two completely different C-terminal distal tip domains. In the phage Sf6-type needle, unlike the other P22-type needle, the distal tip folds into a “knob” with a TNF-like fold, similar to the fiber knobs of bacteriophage PRD1 and Adenovirus. The phage HS1 knob is very similar to that of Sf6, and we report here its crystal structure which, like the Sf6 knob, contains three bound L-glutamate molecules. A chimeric P22 phage with a tail needle that contains the HS1 terminal knob efficiently infects the P22 host, Salmonella enterica, suggesting the knob does not confer host specificity. Likewise, mutations that should abrogate the binding of L-glutamate to the needle do not appear to affect virion function, but several different other genetic changes to the tip of the needle slow down potassium release from the host during infection. These findings suggest that the needle plays a role in phage P22 DNA delivery by controlling the kinetics of DNA ejection into the host.
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Affiliation(s)
- Justin C. Leavitt
- Biology Department, University of Utah, Salt Lake City, Utah, United States of America
| | - Lasha Gogokhia
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Eddie B. Gilcrease
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Anshul Bhardwaj
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Sherwood R. Casjens
- Biology Department, University of Utah, Salt Lake City, Utah, United States of America
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- * E-mail:
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25
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Bauer DW, Huffman JB, Homa FL, Evilevitch A. Herpes virus genome, the pressure is on. J Am Chem Soc 2013; 135:11216-21. [PMID: 23829592 DOI: 10.1021/ja404008r] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Herpes simplex virus type 1 (HSV-1) packages its micrometers-long double-stranded DNA genome into a nanometer-scale protein shell, termed the capsid. Upon confinement within the capsid, neighboring DNA strands experience repulsive electrostatic and hydration forces as well as bending stress associated with the tight curvature required of packaged DNA. By osmotically suppressing DNA release from HSV-1 capsids, we provide the first experimental evidence of a high internal pressure of tens of atmospheres within a eukaryotic human virus, resulting from the confined genome. Furthermore, the ejection is progressively suppressed by increasing external osmotic pressures, which reveals that internal pressure is capable of powering ejection of the entire genome from the viral capsid. Despite billions of years of evolution separating eukaryotic viruses and bacteriophages, pressure-driven DNA ejection has been conserved. This suggests it is a key mechanism for viral infection and thus presents a new target for antiviral therapies.
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Affiliation(s)
- David W Bauer
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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26
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Abstract
Sixty years after Hershey and Chase showed that nucleic acid is the major component of phage particles that is ejected into cells, we still do not fully understand how the process occurs. Advances in electron microscopy have revealed the structure of the condensed DNA confined in a phage capsid, and the mechanisms and energetics of packaging a phage genome are beginning to be better understood. Condensing DNA subjects it to high osmotic pressure, which has been suggested to provide the driving force for its ejection during infection. However, forces internal to a phage capsid cannot, alone, cause complete genome ejection into cells. Here, we describe the structure of the DNA inside mature phages and summarize the current models of genome ejection, both in vitro and in vivo.
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Affiliation(s)
- Ian J Molineux
- Molecular Genetics and Microbiology, Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA.
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27
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Lemay SG, Panja D, Molineux IJ. Role of osmotic and hydrostatic pressures in bacteriophage genome ejection. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:022714. [PMID: 23496555 DOI: 10.1103/physreve.87.022714] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Indexed: 06/01/2023]
Abstract
A critical step in the bacteriophage life cycle is genome ejection into host bacteria. The ejection process for double-stranded DNA phages has been studied thoroughly in vitro, where after triggering with the cellular receptor the genome ejects into a buffer. The experimental data have been interpreted in terms of the decrease in free energy of the densely packed DNA associated with genome ejection. Here we detail a simple model of genome ejection in terms of the hydrostatic and osmotic pressures inside the phage, a bacterium, and a buffer solution or culture medium. We argue that the hydrodynamic flow associated with the water movement from the buffer solution into the phage capsid and further drainage into the bacterial cytoplasm, driven by the osmotic gradient between the bacterial cytoplasm and culture medium, provides an alternative mechanism for phage genome ejection in vivo; the mechanism is perfectly consistent with phage genome ejection in vitro.
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Affiliation(s)
- Serge G Lemay
- MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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28
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Ghosal S. Capstan friction model for DNA ejection from bacteriophages. PHYSICAL REVIEW LETTERS 2012; 109:248105. [PMID: 23368388 PMCID: PMC3707003 DOI: 10.1103/physrevlett.109.248105] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Indexed: 06/01/2023]
Abstract
Bacteriophages infect cells by attaching to the outer membrane and injecting their DNA into the cell. The phage DNA is then transcribed by the cell's transcription machinery. A number of physical mechanisms by which DNA can be translocated from the phage capsid into the cell have been identified. A fast ejection driven by the elastic and electrostatic potential energy of the compacted DNA within the viral capsid appears to be used by most phages, at least to initiate infection. In recent in vitro experiments, the speed of DNA translocation from a λ phage capsid has been measured as a function of ejected length over the entire duration of the event. Here, a mechanical model is proposed that is able to explain the observed dependence of exit velocity on ejected length, and that is also consistent with the accepted picture of the geometric arrangement of DNA within the viral capsid.
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Affiliation(s)
- Sandip Ghosal
- Department of Physics, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom.
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29
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Reyes-Cortés R, Martínez-Peñafiel E, Martínez-Pérez F, de la Garza M, Kameyama L. A novel strategy to isolate cell-envelope mutants resistant to phage infection: bacteriophage mEp213 requires lipopolysaccharides in addition to FhuA to enter Escherichia coli K-12. Microbiology (Reading) 2012; 158:3063-3071. [DOI: 10.1099/mic.0.060970-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ruth Reyes-Cortés
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, Av. Instituto Politécnico Nacional No. 2508, C.P. 7360, México D.F., Mexico
| | - Eva Martínez-Peñafiel
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Av. Instituto Politécnico Nacional No. 2508, C.P. 7360, México D.F., Mexico
| | - Francisco Martínez-Pérez
- Laboratorio de Microbiología y Mutagénesis Ambiental, Escuela de Biología, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Mireya de la Garza
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, Av. Instituto Politécnico Nacional No. 2508, C.P. 7360, México D.F., Mexico
| | - Luis Kameyama
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Av. Instituto Politécnico Nacional No. 2508, C.P. 7360, México D.F., Mexico
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30
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Casjens SR, Molineux IJ. Short noncontractile tail machines: adsorption and DNA delivery by podoviruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 726:143-79. [PMID: 22297513 DOI: 10.1007/978-1-4614-0980-9_7] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Tailed dsDNA bacteriophage virions bind to susceptible cells with the tips of their tails and then deliver their DNA through the tail into the cells to initiate infection. This chapter discusses what is known about this process in the short-tailed phages (Podoviridae). Their short tails require that many of these virions adsorb to the outer layers of the cell and work their way down to the outer membrane surface before releasing their DNA. Interestingly, the receptor-binding protein of many short-tailed phages (and some with long tails) has an enzymatic activity that cleaves their polysaccharide receptors. Reversible adsorption and irreversible adsorption to primary and secondary receptors are discussed, including how sequence divergence in tail fiber and tailspike proteins leads to different host specificities. Upon reaching the outer membrane of Gram-negative cells, some podoviral tail machines release virion proteins into the cell that help the DNA efficiently traverse the outer layers of the cell and/or prepare the cell cytoplasm for phage genome arrival. Podoviruses utilize several rather different variations on this theme. The virion DNA is then released into the cell; the energetics of this process is discussed. Phages like T7 and N4 deliver their DNA relatively slowly, using enzymes to pull the genome into the cell. At least in part this mechanism ensures that genes in late-entering DNA are not expressed at early times. On the other hand, phages like P22 probably deliver their DNA more rapidly so that it can be circularized before the cascade of gene expression begins.
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Affiliation(s)
- Sherwood R Casjens
- Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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31
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Häuser R, Blasche S, Dokland T, Haggård-Ljungquist E, von Brunn A, Salas M, Casjens S, Molineux I, Uetz P. Bacteriophage protein-protein interactions. Adv Virus Res 2012; 83:219-98. [PMID: 22748812 PMCID: PMC3461333 DOI: 10.1016/b978-0-12-394438-2.00006-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Bacteriophages T7, λ, P22, and P2/P4 (from Escherichia coli), as well as ϕ29 (from Bacillus subtilis), are among the best-studied bacterial viruses. This chapter summarizes published protein interaction data of intraviral protein interactions, as well as known phage-host protein interactions of these phages retrieved from the literature. We also review the published results of comprehensive protein interaction analyses of Pneumococcus phages Dp-1 and Cp-1, as well as coliphages λ and T7. For example, the ≈55 proteins encoded by the T7 genome are connected by ≈43 interactions with another ≈15 between the phage and its host. The chapter compiles published interactions for the well-studied phages λ (33 intra-phage/22 phage-host), P22 (38/9), P2/P4 (14/3), and ϕ29 (20/2). We discuss whether different interaction patterns reflect different phage lifestyles or whether they may be artifacts of sampling. Phages that infect the same host can interact with different host target proteins, as exemplified by E. coli phage λ and T7. Despite decades of intensive investigation, only a fraction of these phage interactomes are known. Technical limitations and a lack of depth in many studies explain the gaps in our knowledge. Strategies to complete current interactome maps are described. Although limited space precludes detailed overviews of phage molecular biology, this compilation will allow future studies to put interaction data into the context of phage biology.
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Affiliation(s)
- Roman Häuser
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
- Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Sonja Blasche
- Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Terje Dokland
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Albrecht von Brunn
- Max-von-Pettenkofer-Institut, Lehrstuhl Virologie, Ludwig-Maximilians-Universität, München, Germany
| | - Margarita Salas
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Cantoblanco, Madrid, Spain
| | - Sherwood Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah
| | - Ian Molineux
- Molecular Genetics and Microbiology, Institute for Cell and Molecular Biology, University of Texas–Austin, Austin, Texas, USA
| | - Peter Uetz
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, USA
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32
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Siber A, Božič AL, Podgornik R. Energies and pressures in viruses: contribution of nonspecific electrostatic interactions. Phys Chem Chem Phys 2011; 14:3746-65. [PMID: 22143065 DOI: 10.1039/c1cp22756d] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We summarize some aspects of electrostatic interactions in the context of viruses. A simplified but, within well defined limitations, reliable approach is used to derive expressions for electrostatic energies and the corresponding osmotic pressures in single-stranded RNA viruses and double-stranded DNA bacteriophages. The two types of viruses differ crucially in the spatial distribution of their genome charge which leads to essential differences in their free energies, depending on the capsid size and total charge in a quite different fashion. Differences in the free energies are trailed by the corresponding characteristics and variations in the osmotic pressure between the inside of the virus and the external bathing solution.
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33
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Freeman GS, Hinckley DM, de Pablo JJ. A coarse-grain three-site-per-nucleotide model for DNA with explicit ions. J Chem Phys 2011; 135:165104. [PMID: 22047269 PMCID: PMC3221706 DOI: 10.1063/1.3652956] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 09/28/2011] [Indexed: 12/26/2022] Open
Abstract
The "three sites per nucleotide" (3SPN) model provides a coarse-grained representation of nucleic acids for simulation of molecular processes. Previously, this model has relied on an implicit representation of the surrounding ionic environment at the level of Debye-Hückel theory. In this work, we eliminate this limitation and present an explicit representation of ions, both monovalent and divalent. The coarse-grain ion-ion and ion-phosphate potential energy functions are inferred from all-atom simulations and parameterized to reproduce key features of the local structure and organization of ions in bulk water and in the presence of DNA. The resulting model, 3SPN.1-I, is capable of reproducing the local structure observed in detailed atomistic simulations, as well as the experimental melting temperature of DNA for a range of DNA oligonucleotide lengths, CG-content, Na(+) concentration, and Mg(2+) concentration.
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Affiliation(s)
- Gordon S Freeman
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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34
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A novel cyanophage with a cyanobacterial nonbleaching protein A gene in the genome. J Virol 2011; 86:236-45. [PMID: 22031930 DOI: 10.1128/jvi.06282-11] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A cyanophage, PaV-LD, has been isolated from harmful filamentous cyanobacterium Planktothrix agardhii in Lake Donghu, a shallow freshwater lake in China. Here, we present the cyanophage's genomic organization and major structural proteins. The genome is a 95,299-bp-long, linear double-stranded DNA and contains 142 potential genes. BLAST searches revealed 29 proteins of known function in cyanophages, cyanobacteria, or bacteria. Thirteen major structural proteins ranging in size from 27 kDa to 172 kDa were identified by SDS-PAGE and mass-spectrometric analysis. The genome lacks major genes that are necessary to the tail structure, and the tailless PaV-LD has been confirmed by an electron microscopy comparison with other tail cyanophages and phages. Phylogenetic analysis of the major capsid proteins also reveals an independent branch of PaV-LD that is quite different from other known tail cyanophages and phages. Moreover, the unique genome carries a nonbleaching protein A (NblA) gene (open reading frame [ORF] 022L), which is present in all phycobilisome-containing organisms and mediates phycobilisome degradation. Western blot detection confirmed that 022L was expressed after PaV-LD infection in the host filamentous cyanobacterium. In addition, its appearance was companied by a significant decline of phycocyanobilin content and a color change of the cyanobacterial cells from blue-green to yellow-green. The biological function of PaV-LD nblA was further confirmed by expression in a model cyanobacterium via an integration platform, by spectroscopic analysis and electron microscopy observation. The data indicate that PaV-LD is an exceptional cyanophage of filamentous cyanobacteria, and this novel cyanophage will also provide us with a new vision of the cyanophage-host interactions.
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35
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Visualization of bacteriophage P1 infection by cryo-electron tomography of tiny Escherichia coli. Virology 2011; 417:304-11. [PMID: 21745674 DOI: 10.1016/j.virol.2011.06.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 06/07/2011] [Accepted: 06/08/2011] [Indexed: 11/21/2022]
Abstract
Bacteriophage P1 has a contractile tail that targets the conserved lipopolysaccharide on the outer membrane surface of the host for initial adsorption. The mechanism by which P1 DNA enters the host cell is not well understood, mainly because the transient molecular interactions between bacteriophage and bacteria have been difficult to study by conventional approaches. Here, we engineered tiny E. coli host cells so that the initial stages of P1-host interactions could be captured in unprecedented detail by cryo-electron tomography. Analysis of three-dimensional reconstructions of frozen-hydrated specimens revealed three predominant configurations: an extended tail stage with DNA present in the phage head, a contracted tail stage with DNA, and a contracted tail stage without DNA. Comparative analysis of various conformations indicated that there is uniform penetration of the inner tail tube into the E. coli periplasm and a significant movement of the baseplate away from the outer membrane during tail contraction.
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36
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Goulet A, Lai-Kee-Him J, Veesler D, Auzat I, Robin G, Shepherd DA, Ashcroft AE, Richard E, Lichière J, Tavares P, Cambillau C, Bron P. The opening of the SPP1 bacteriophage tail, a prevalent mechanism in Gram-positive-infecting siphophages. J Biol Chem 2011; 286:25397-405. [PMID: 21622577 DOI: 10.1074/jbc.m111.243360] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The SPP1 siphophage uses its long non-contractile tail and tail tip to recognize and infect the Gram-positive bacterium Bacillus subtilis. The tail-end cap and its attached tip are the critical components for host recognition and opening of the tail tube for genome exit. In the present work, we determined the cryo-electron microscopic (cryo-EM) structure of a complex formed by the cap protein gp19.1 (Dit) and the N terminus of the downstream protein of gp19.1 in the SPP1 genome, gp21(1-552) (Tal). This complex assembles two back-to-back stacked gp19.1 ring hexamers, interacting loosely, and two gp21(1-552) trimers interacting with gp19.1 at both ends of the stack. Remarkably, one gp21(1-552) trimer displays a "closed" conformation, whereas the second is "open" delineating a central channel. The two conformational states dock nicely into the EM map of the SPP1 cap domain, respectively, before and after DNA release. Moreover, the open/closed conformations of gp19.1-gp21(1-552) are consistent with the structures of the corresponding proteins in the siphophage p2 baseplate, where the Tal protein (ORF16) attached to the ring of Dit (ORF15) was also found to adopt these two conformations. Therefore, the present contribution allowed us to revisit the SPP1 tail distal-end architectural organization. Considering the sequence conservation among Dit and the N-terminal region of Tal-like proteins in Gram-positive-infecting Siphoviridae, it also reveals the Tal opening mechanism as a hallmark of siphophages probably involved in the generation of the firing signal initiating the cascade of events that lead to phage DNA release in vivo.
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Affiliation(s)
- Adeline Goulet
- Centre de Biochimie Structurale, INSERM UMR 1054/CNRS UMR 5048 and Universités Montpellier I & II, 29 rue de Navacelles, Montpellier 34090, France
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37
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Casjens SR, Thuman-Commike PA. Evolution of mosaically related tailed bacteriophage genomes seen through the lens of phage P22 virion assembly. Virology 2011; 411:393-415. [PMID: 21310457 DOI: 10.1016/j.virol.2010.12.046] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 12/20/2010] [Accepted: 12/23/2010] [Indexed: 01/06/2023]
Abstract
The mosaic composition of the genomes of dsDNA tailed bacteriophages (Caudovirales) is well known. Observations of this mosaicism have generally come from comparisons of small numbers of often rather distantly related phages, and little is known about the frequency or detailed nature of the processes that generate this kind of diversity. Here we review and examine the mosaicism within fifty-seven clusters of virion assembly genes from bacteriophage P22 and its "close" relatives. We compare these orthologous gene clusters, discuss their surprising diversity and document horizontal exchange of genetic information between subgroups of the P22-like phages as well as between these phages and other phage types. We also point out apparent restrictions in the locations of mosaic sequence boundaries in this gene cluster. The relatively large sample size and the fact that phage P22 virion structure and assembly are exceptionally well understood make the conclusions especially informative and convincing.
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Affiliation(s)
- Sherwood R Casjens
- Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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38
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Abstract
Bacteriophages, phages for short, are viruses of bacteria. The majority of phages contain a double-stranded DNA genome packaged in a capsid at a density of ∼500 mg ml(-1). This high density requires substantial compression of the normal B-form helix, leading to the conjecture that DNA in mature phage virions is under significant pressure, and that pressure is used to eject the DNA during infection. A large number of theoretical, computer simulation and in vitro experimental studies surrounding this conjecture have revealed many--though often isolated and/or contradictory--aspects of packaged DNA. This prompts us to present a unified view of the statistical physics and thermodynamics of DNA packaged in phage capsids. We argue that the DNA in a mature phage is in a (meta)stable state, wherein electrostatic self-repulsion is balanced by curvature stress due to confinement in the capsid. We show that in addition to the osmotic pressure associated with the packaged DNA and its counterions, there are four different pressures within the capsid: pressure on the DNA, hydrostatic pressure, the pressure experienced by the capsid and the pressure associated with the chemical potential of DNA ejection. Significantly, we analyze the mechanism of force transmission in the packaged DNA and demonstrate that the pressure on DNA is not important for ejection. We derive equations showing a strong hydrostatic pressure difference across the capsid shell. We propose that when a phage is triggered to eject by interaction with its receptor in vitro, the (thermodynamic) incentive of water molecules to enter the phage capsid flushes the DNA out of the capsid. In vivo, the difference between the osmotic pressures in the bacterial cell cytoplasm and the culture medium similarly results in a water flow that drags the DNA out of the capsid and into the bacterial cell.
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Affiliation(s)
- Debabrata Panja
- Institute for Theoretical Physics, Universiteit van Amsterdam, Science Park 904, Postbus 94485, 1090 GL Amsterdam, The Netherlands.
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39
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Wu D, Van Valen D, Hu Q, Phillips R. Ion-dependent dynamics of DNA ejections for bacteriophage lambda. Biophys J 2010; 99:1101-9. [PMID: 20712993 DOI: 10.1016/j.bpj.2010.06.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 06/08/2010] [Accepted: 06/09/2010] [Indexed: 10/19/2022] Open
Abstract
We studied the control parameters that govern the dynamics of in vitro DNA ejection in bacteriophage lambda. Previous work demonstrated that bacteriophage DNA is highly pressurized, and this pressure has been hypothesized to help drive DNA ejection. Ions influence this process by screening charges on DNA; however, a systematic variation of salt concentrations to explore these effects has not been undertaken. To study the nature of the forces driving DNA ejection, we performed in vitro measurements of DNA ejection in bulk and at the single-phage level. We present measurements on the dynamics of ejection and on the self-repulsion force driving ejection. We examine the role of ion concentration and identity in both measurements, and show that the charge of counterions is an important control parameter. These measurements show that the mobility of ejecting DNA is independent of ionic concentrations for a given amount of DNA in the capsid. We also present evidence that phage DNA forms loops during ejection, and confirm that this effect occurs using optical tweezers.
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Affiliation(s)
- David Wu
- Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, California, USA
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40
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Schmidt MT, Olejnik-Schmidt AK, Zaręba A, Pezacki M, Wojewoda I, Grajek W. Induction of Loci Mutation duringLactococcus lactisSpontaneous Conversion to Bacteriophage-Insensitive Phenotype. FOOD BIOTECHNOL 2010. [DOI: 10.1080/08905436.2010.524470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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41
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42
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Thomas JA, Weintraub ST, Hakala K, Serwer P, Hardies SC. Proteome of the large Pseudomonas myovirus 201 phi 2-1: delineation of proteolytically processed virion proteins. Mol Cell Proteomics 2010; 9:940-51. [PMID: 20233846 DOI: 10.1074/mcp.m900488-mcp200] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pseudomonas chlororaphis phage 201 phi 2-1 produces a large structurally complex virion, including the products of 89 phage genes. Many of these proteins are modified by proteolysis during virion maturation. To delineate the proteolytic maturation process, 46 slices from an SDS-polyacrylamide gel were subjected to tryptic digestion and then HPLC-electrospray ionization-tandem mass spectrometry analysis. The scale of the experiment allowed high sequence coverage and detection of mass spectra assigned to peptides with one end produced by trypsin and the other end derived from a maturation cleavage (semitryptic peptides). Nineteen cleavage sites were detected in this way. From these sites, a cleavage motif was defined and used to predict the remaining cleavages required to explain the gel mobility of the processed polypeptide species. Profiling the gel with spectrum counts for specific polypeptide regions was found to be helpful in deducing the patterns of proteolysis. A total of 29 cleaved polypeptides derived from 19 gene products were thus detected in the mature 201 phi 2-1 virion. When combined with bioinformatics analyses, these results revealed the presence of head protein-encoding gene modules. Most of the propeptides that were removed from the virion after processing were acidic, whereas the mature domain remaining in the virion was nearly charge-neutral. For four of these processed virion proteins, the portions remaining in the mature virion were mutually homologous. Spectrum counts were found to overestimate the relative quantity of minor polypeptide species in the virion. The resulting sensitivity for minor species made it possible to observe a small amount of general proteolysis that also affected the virions.
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Affiliation(s)
- Julie A Thomas
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, Texas 78229-3900, USA
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43
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Thiel G, Moroni A, Dunigan D, Van Etten JL. Initial Events Associated with Virus PBCV-1 Infection of Chlorella NC64A. PROGRESS IN BOTANY. FORTSCHRITTE DER BOTANIK 2010; 71:169-183. [PMID: 21152366 PMCID: PMC2997699 DOI: 10.1007/978-3-642-02167-1_7] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chlorella viruses (or chloroviruses) are very large, plaque-forming viruses. The viruses are multilayered structures containing a large double-stranded DNA genome, a lipid bilayered membrane, and an outer icosahedral capsid shell. The viruses replicate in certain isolates of the coccal green alga, Chlorella. Sequence analysis of the 330-kbp genome of Paramecium bursaria Chlorella virus 1 (PBCV-1), the prototype of the virus family Phycodnaviridae, reveals <365 protein-encoding genes and 11 tRNA genes. Products of about 40% of these genes resemble proteins of known function, including many that are unexpected for a virus. Among these is a virus-encoded protein, called Kcv, which forms a functional K(+) channel. This chapter focuses on the initial steps in virus infection and provides a plausible role for the function of the viral K(+) channel in lowering the turgor pressure of the host. This step appears to be a prerequisite for delivery of the viral genome into the host.
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Affiliation(s)
- Gerhard Thiel
- Institute of Botany, Technische Universitat Darmstadt, 64287, Darmstadt, Germany
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44
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Chang CY, Kemp P, Molineux IJ. Gp15 and gp16 cooperate in translocating bacteriophage T7 DNA into the infected cell. Virology 2009; 398:176-86. [PMID: 20036409 DOI: 10.1016/j.virol.2009.12.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2009] [Revised: 10/16/2009] [Accepted: 12/01/2009] [Indexed: 10/20/2022]
Abstract
Loss of up to four amino acids from the C terminus of the 1318 residue bacteriophage T7 gp16 allows plaque formation at normal efficiencies. Loss of five residues results in non-infective virions, and loss of twelve prevents assembly of stable particles. However, replacing the C-terminal seven with nineteen non-native residues allows assembly of non-infective virions. The latter adsorb and eject internal core proteins into the cell envelope but no phage DNA enters the cytoplasm. Extragenic suppressors of the defective gene 16 lie in gene 15; the mutant gp15 proteins not only re-establish infectivity, they fully restore the kinetics of genome internalization to those exhibited by wild-type phage. After ejection from the infecting particle, gp15 and gp16 thus function together in ratcheting the leading end of the T7 genome into the cytoplasm of the infected cell.
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Affiliation(s)
- Chung-Yu Chang
- Section of Molecular Genetics and Microbiology, and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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45
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Grayson P, Han L, Winther T, Phillips R. Real-time observations of single bacteriophage lambda DNA ejections in vitro. Proc Natl Acad Sci U S A 2007; 104:14652-7. [PMID: 17804798 PMCID: PMC1976217 DOI: 10.1073/pnas.0703274104] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Indexed: 11/18/2022] Open
Abstract
The physical, chemical, and structural features of bacteriophage genome release have been the subject of much recent attention. Many theoretical and experimental studies have centered on the internal forces driving the ejection process. Recently, Mangenot et al. [Mangenot S, Hochrein M, Rädler J, Letellier L (2005) Curr Biol 15:430-435.] reported fluorescence microscopy of phage T5 ejections, which proceeded stepwise between DNA nicks, reaching a translocation speed of 75 kbp/s or higher. It is still unknown how high the speed actually is. This paper reports real-time measurements of ejection from phage lambda, revealing how the speed depends on key physical parameters such as genome length and ionic state of the buffer. Except for a pause before DNA is finally released, the entire 48.5-kbp genome is translocated in approximately 1.5 s without interruption, reaching a speed of 60 kbp/s. The process gives insights particularly into the effects of two parameters: a shorter genome length results in lower speed but a shorter total time, and the presence of divalent magnesium ions (replacing sodium) reduces the pressure, increasing ejection time to 8-11 s. Pressure caused by DNA-DNA interactions within the head affects the initiation of ejection, but the close packing is also the dominant source of friction: more tightly packed phages initiate ejection earlier, but with a lower initial speed. The details of ejection revealed in this study are probably generic features of DNA translocation in bacteriophages and have implications for the dynamics of DNA in other biological systems.
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Affiliation(s)
| | - Lin Han
- Applied Physics, California Institute of Technology, Pasadena, CA 91125
| | - Tabita Winther
- Applied Physics, California Institute of Technology, Pasadena, CA 91125
| | - Rob Phillips
- Applied Physics, California Institute of Technology, Pasadena, CA 91125
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46
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Castelnovo M, Evilevitch A. DNA ejection from bacteriophage: towards a general behavior for osmotic-suppression experiments. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2007; 24:9-18. [PMID: 17762912 DOI: 10.1140/epje/i2007-10205-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Accepted: 07/09/2007] [Indexed: 05/17/2023]
Abstract
We present in this work in vitro measurements of the force ejecting DNA from two distinct bacteriophages (T5 and lambda using the osmotic-suppression technique. Our data are analyzed by revisiting the current theories of DNA packaging in spherical capsids. In particular we show that a simplified analytical model based on bending considerations only is able to account quantitatively for the experimental findings. Physical and biological consequences are discussed.
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Affiliation(s)
- M Castelnovo
- Laboratoire Joliot-Curie et Laboratoire de Physique, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon cedex 07, France.
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47
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Roos WH, Ivanovska IL, Evilevitch A, Wuite GJL. Viral capsids: mechanical characteristics, genome packaging and delivery mechanisms. Cell Mol Life Sci 2007; 64:1484-97. [PMID: 17440680 PMCID: PMC2771126 DOI: 10.1007/s00018-007-6451-1] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The main functions of viral capsids are to protect, transport and deliver their genome. The mechanical properties of capsids are supposed to be adapted to these tasks. Bacteriophage capsids also need to withstand the high pressures the DNA is exerting onto it as a result of the DNA packaging and its consequent confinement within the capsid. It is proposed that this pressure helps driving the genome into the host, but other mechanisms also seem to play an important role in ejection. DNA packaging and ejection strategies are obviously dependent on the mechanical properties of the capsid. This review focuses on the mechanical properties of viral capsids in general and the elucidation of the biophysical aspects of genome packaging mechanisms and genome delivery processes of double-stranded DNA bacteriophages in particular.
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Affiliation(s)
- W. H. Roos
- Fysica van complexe systemen, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - I. L. Ivanovska
- Fysica van complexe systemen, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - A. Evilevitch
- Department of Biochemistry, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - G. J. L. Wuite
- Fysica van complexe systemen, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
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48
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Grayson P, Molineux IJ. Is phage DNA 'injected' into cells--biologists and physicists can agree. Curr Opin Microbiol 2007; 10:401-9. [PMID: 17714979 PMCID: PMC2064038 DOI: 10.1016/j.mib.2007.04.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2007] [Accepted: 04/17/2007] [Indexed: 12/31/2022]
Abstract
The double-stranded DNA inside bacteriophages is packaged at a density of approximately 500 mg/ml and exerts an osmotic pressure of tens of atmospheres. This pressure is commonly assumed to cause genome ejection during infection. Indeed, by the addition of their natural receptors, some phages can be induced in vitro to completely expel their genome from the virion. However, the osmotic pressure of the bacterial cytoplasm exerts an opposing force, making it impossible for the pressure of packaged DNA to cause complete genome ejection in vivo. Various processes for complete genome ejection are discussed, but we focus on a novel proposal suggesting that the osmotic gradient between the extracellular environment and the cytoplasm results in fluid flow through the phage virion at the initiation of infection. The phage genome is thereby sucked into the cell by hydrodynamic drag.
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Affiliation(s)
- Paul Grayson
- Department of Physics, California Institute of Technology, Pasadena, CA 91125
| | - Ian J. Molineux
- Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712
- * Corresponding author. Phone: 512–471–3143
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49
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Raspaud E, Forth T, São-José C, Tavares P, de Frutos M. A kinetic analysis of DNA ejection from tailed phages revealing the prerequisite activation energy. Biophys J 2007; 93:3999-4005. [PMID: 17675351 PMCID: PMC2084231 DOI: 10.1529/biophysj.107.111435] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
All tailed bacteriophages follow the same general scheme of infection: they bind to their specific host receptor and then transfer their genome into the bacterium. DNA translocation is thought to be initiated by the strong pressure due to DNA packing inside the capsid. However, the exact mechanism by which each phage controls its DNA ejection remains unknown. Using light scattering, we analyzed the kinetics of in vitro DNA release from phages SPP1 and lambda (Siphoviridae family) and found a simple exponential decay. The ejection characteristic time was studied as a function of the temperature and found to follow an Arrhenius law, allowing us to determine the activation energy that governs DNA ejection. A value of 25-30 kcal/mol is obtained for SPP1 and lambda, comparable to the one measured in vitro for T5 (Siphoviridae) and in vivo for T7 (Podoviridae). This suggests similar mechanisms of DNA ejection control. In all tailed phages, the opening of the connector-tail channel is needed for DNA release and could constitute the limiting step. The common value of the activation energy likely reflects the existence for all phages of an optimum value, ensuring a compromise between efficient DNA delivery and high stability of the virus.
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Affiliation(s)
- Eric Raspaud
- Laboratoire de Physique des Solides, Université Paris-Sud, CNRS, UMR 8502, F-91405 Orsay cedex, France
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Alcorlo M, González-Huici V, Hermoso JM, Meijer WJJ, Salas M. The phage phi29 membrane protein p16.7, involved in DNA replication, is required for efficient ejection of the viral genome. J Bacteriol 2007; 189:5542-9. [PMID: 17526715 PMCID: PMC1951806 DOI: 10.1128/jb.00402-07] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Accepted: 05/14/2007] [Indexed: 11/20/2022] Open
Abstract
It is becoming clear that in vivo phage DNA ejection is not a mere passive process. In most cases, both phage and host proteins seem to be involved in pulling at least part of the viral DNA inside the cell. The DNA ejection mechanism of Bacillus subtilis bacteriophage phi29 is a two-step process where the linear DNA penetrates the cell with a right-left polarity. In the first step approximately 65% of the DNA is pushed into the cell. In the second step, the remaining DNA is actively pulled into the cytoplasm. This step requires protein p17, which is encoded by the right-side early operon that is ejected during the first push step. The membrane protein p16.7, also encoded by the right-side early operon, is known to play an important role in membrane-associated phage DNA replication. In this work we show that, in addition, p16.7 is required for efficient execution of the second pull step of DNA ejection.
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Affiliation(s)
- Martín Alcorlo
- Instituto de Biología Molecular Eladio Viñuela, Centro de Biología Molecular Severo Ochoa, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
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