1
|
Maidanik I, Kirzner S, Pekarski I, Arsenieff L, Tahan R, Carlson MCG, Shitrit D, Baran N, Goldin S, Weitz JS, Lindell D. Cyanophages from a less virulent clade dominate over their sister clade in global oceans. THE ISME JOURNAL 2022; 16:2169-2180. [PMID: 35726021 PMCID: PMC9381782 DOI: 10.1038/s41396-022-01259-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 11/18/2022]
Abstract
Environmental virus communities are highly diverse. However, the infection physiology underlying the evolution of diverse phage lineages and their ecological consequences are largely unknown. T7-like cyanophages are abundant in nature and infect the marine unicellular cyanobacteria, Synechococcus and Prochlorococcus, important primary producers in the oceans. Viruses belonging to this genus are divided into two distinct phylogenetic clades: clade A and clade B. These viruses have narrow host-ranges with clade A phages primarily infecting Synechococcus genotypes, while clade B phages are more diverse and can infect either Synechococcus or Prochlorococcus genotypes. Here we investigated infection properties (life history traits) and environmental abundances of these two clades of T7-like cyanophages. We show that clade A cyanophages have more rapid infection dynamics, larger burst sizes and greater virulence than clade B cyanophages. However, clade B cyanophages were at least 10-fold more abundant in all seasons, and infected more cyanobacteria, than clade A cyanophages in the Red Sea. Models predicted that steady-state cyanophage abundances, infection frequency, and virus-induced mortality, peak at intermediate virulence values. Our findings indicate that differences in infection properties are reflected in virus phylogeny at the clade level. They further indicate that infection properties, together with differences in subclade diversity and host repertoire, have important ecological consequences with the less aggressive, more diverse virus clade having greater ecological impacts.
Collapse
Affiliation(s)
- Ilia Maidanik
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Shay Kirzner
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Irena Pekarski
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Laure Arsenieff
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Ran Tahan
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Michael C G Carlson
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Dror Shitrit
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Nava Baran
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Svetlana Goldin
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Institut de Biologie, École Normale Supérieure, Paris, 75014, France
| | - Debbie Lindell
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel.
| |
Collapse
|
2
|
Genetic engineering of marine cyanophages reveals integration but not lysogeny in T7-like cyanophages. THE ISME JOURNAL 2022; 16:488-499. [PMID: 34429521 PMCID: PMC8776855 DOI: 10.1038/s41396-021-01085-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 02/07/2023]
Abstract
Marine cyanobacteria of the genera Synechococcus and Prochlorococcus are the most abundant photosynthetic organisms on earth, spanning vast regions of the oceans and contributing significantly to global primary production. Their viruses (cyanophages) greatly influence cyanobacterial ecology and evolution. Although many cyanophage genomes have been sequenced, insight into the functional role of cyanophage genes is limited by the lack of a cyanophage genetic engineering system. Here, we describe a simple, generalizable method for genetic engineering of cyanophages from multiple families, that we named REEP for REcombination, Enrichment and PCR screening. This method enables direct investigation of key cyanophage genes, and its simplicity makes it adaptable to other ecologically relevant host-virus systems. T7-like cyanophages often carry integrase genes and attachment sites, yet exhibit lytic infection dynamics. Here, using REEP, we investigated their ability to integrate and maintain a lysogenic life cycle. We found that these cyanophages integrate into the host genome and that the integrase and attachment site are required for integration. However, stable lysogens did not form. The frequency of integration was found to be low in both lab cultures and the oceans. These findings suggest that T7-like cyanophage integration is transient and is not part of a classical lysogenic cycle.
Collapse
|
3
|
Hoang CV, Bhaskar CK, Ma LS. A Novel Core Effector Vp1 Promotes Fungal Colonization and Virulence of Ustilago maydis. J Fungi (Basel) 2021; 7:jof7080589. [PMID: 34436129 PMCID: PMC8396986 DOI: 10.3390/jof7080589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 02/07/2023] Open
Abstract
The biotrophic fungus Ustilago maydis secretes a plethora of uncharacterized effector proteins and causes smut disease in maize. Among the effector genes that are up-regulated during the biotrophic growth in maize, we identified vp1 (virulence promoting 1), which has an expression that was up-regulated and maintained at a high level throughout the life cycle of the fungus. We characterized Vp1 by applying in silico analysis, reverse genetics, phenotypic assessment, microscopy, and protein localization and provided a fundamental understanding of the Vp1 protein in U. maydis. The reduction in fungal virulence and colonization in the vp1 mutant suggests the virulence-promoting function of Vp1. The deletion studies on the NLS (nuclear localization signal) sequence and the protein localization study revealed that the C-terminus of Vp1 is processed after secretion in plant apoplast and could localize to the plant nucleus. The Ustilago hordei ortholog UhVp1 lacks NLS localized in the plant cytoplasm, suggesting that the orthologs might have a distinct subcellular localization. Further complementation studies of the Vp1 orthologs in related smut fungi revealed that none of them could complement the virulence function of U. maydis Vp1, suggesting that UmVp1 could acquire a specialized function via sequence divergence.
Collapse
Affiliation(s)
- Cuong V. Hoang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan; (C.V.H.); (C.K.B.)
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung 402, Taiwan
| | - Chibbhi K. Bhaskar
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan; (C.V.H.); (C.K.B.)
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung 402, Taiwan
| | - Lay-Sun Ma
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan; (C.V.H.); (C.K.B.)
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei 11529, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
- Correspondence: ; Tel.: +886-2-2787-1145
| |
Collapse
|
4
|
Huang S, Sun Y, Zhang S, Long L. Temporal transcriptomes of a marine cyanopodovirus and its Synechococcus host during infection. Microbiologyopen 2020; 10:e1150. [PMID: 33377630 PMCID: PMC7885011 DOI: 10.1002/mbo3.1150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/01/2020] [Accepted: 12/07/2020] [Indexed: 12/24/2022] Open
Abstract
Marine picocyanobacteria belonging to genera Synechococcus and Prochlorococcus are genetically diverged and distributed into distinct biogeographical patterns, and both are infected by genetically closely related cyanopodoviruses. Previous studies have not fully explored whether the two virus–host systems share similar gene expression patterns during infection. Whole‐genome expression dynamics of T7‐like cyanopodovirus P‐SSP7 and its host Prochlorococcus strain MED4 have already been reported. Here, we conducted genomic and transcriptomic analyses on T7‐like cyanopodovirus S‐SBP1 during its infection on Synechococcus strain WH7803. S‐SBP1 has a latent period of 8 h and phage DNA production of 30 copies per cell. In terms of whole‐genome phylogenetic relationships and average nucleotide identity, S‐SBP1 was most similar to cyanopodovirus S‐RIP2, which also infects Synechococcus WH7803. Three hypervariable genomic islands were identified when comparing the genomes of S‐SBP1 and S‐RIP2. Single nucleotide variants were also observed in three S‐SBP1 genes, which were located within the island regions. Based on RNA‐seq analysis, S‐SBP1 genes clustered into three temporal expression classes, whose gene content was similar to that of P‐SSP7. Thirty‐two host genes were upregulated during phage infection, including those involved in carbon metabolism, ribosome components, and stress response. These upregulated genes were similar to those upregulated by Prochlorococcus MED4 in response to infection by P‐SSP7. Our study demonstrates a programmed temporal expression pattern of cyanopodoviruses and hosts during infection.
Collapse
Affiliation(s)
- Sijun Huang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Yingting Sun
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Lijuan Long
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| |
Collapse
|
5
|
Resistance in marine cyanobacteria differs against specialist and generalist cyanophages. Proc Natl Acad Sci U S A 2019; 116:16899-16908. [PMID: 31383764 PMCID: PMC6708340 DOI: 10.1073/pnas.1906897116] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Long-term coexistence between unicellular cyanobacteria and their lytic viruses (cyanophages) in the oceans is thought to be due to the presence of sensitive cells in which cyanophages reproduce, ultimately killing the cell, while other cyanobacteria survive due to resistance to infection. Here, we investigated resistance in marine cyanobacteria from the genera Synechococcus and Prochlorococcus and compared modes of resistance against specialist and generalist cyanophages belonging to the T7-like and T4-like cyanophage families. Resistance was extracellular in most interactions against specialist cyanophages irrespective of the phage family, preventing entry into the cell. In contrast, resistance was intracellular in practically all interactions against generalist T4-like cyanophages. The stage of intracellular arrest was interaction-specific, halting at various stages of the infection cycle. Incomplete infection cycles proceeded to various degrees of phage genome transcription and translation as well as phage genome replication in numerous interactions. In a particularly intriguing case, intracellular capsid assembly was observed, but the phage genome was not packaged. The cyanobacteria survived the encounter despite late-stage infection and partial genome degradation. We hypothesize that this is tolerated due to genome polyploidy, which we found for certain strains of both Synechococcus and Prochlorococcus Our findings unveil a heavy cost of promiscuous entry of generalist phages into nonhost cells that is rarely paid by specialist phages and suggests the presence of unknown mechanisms of intracellular resistance in the marine unicellular cyanobacteria. Furthermore, these findings indicate that the range for virus-mediated horizontal gene transfer extends beyond hosts to nonhost cyanobacterial cells.
Collapse
|
6
|
Ma LS, Wang L, Trippel C, Mendoza-Mendoza A, Ullmann S, Moretti M, Carsten A, Kahnt J, Reissmann S, Zechmann B, Bange G, Kahmann R. The Ustilago maydis repetitive effector Rsp3 blocks the antifungal activity of mannose-binding maize proteins. Nat Commun 2018; 9:1711. [PMID: 29703884 PMCID: PMC5923269 DOI: 10.1038/s41467-018-04149-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 04/06/2018] [Indexed: 12/22/2022] Open
Abstract
To cause disease in maize, the biotrophic fungus Ustilago maydis secretes a large arsenal of effector proteins. Here, we functionally characterize the repetitive effector Rsp3 (repetitive secreted protein 3), which shows length polymorphisms in field isolates and is highly expressed during biotrophic stages. Rsp3 is required for virulence and anthocyanin accumulation. During biotrophic growth, Rsp3 decorates the hyphal surface and interacts with at least two secreted maize DUF26-domain family proteins (designated AFP1 and AFP2). AFP1 binds mannose and displays antifungal activity against the rsp3 mutant but not against a strain constitutively expressing rsp3. Maize plants silenced for AFP1 and AFP2 partially rescue the virulence defect of rsp3 mutants, suggesting that blocking the antifungal activity of AFP1 and AFP2 by the Rsp3 effector is an important virulence function. Rsp3 orthologs are present in all sequenced smut fungi, and the ortholog from Sporisorium reilianum can complement the rsp3 mutant of U. maydis, suggesting a novel widespread fungal protection mechanism. The fungus Ustilago maydis secretes many effector proteins to cause disease in maize. Here, Ma et al. show that the repetitive effector Rsp3 is required for virulence by inhibiting the antifungal activity of two mannose-binding proteins that are secreted by the plant cells.
Collapse
Affiliation(s)
- Lay-Sun Ma
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Lei Wang
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Department of Pharmacology, Max Planck Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany
| | - Christine Trippel
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Department of Plant Cell Biology, Albrecht-von-Haller-Institute, Georg-August-University-Göttingen, 37077, Göttingen, Germany
| | - Artemio Mendoza-Mendoza
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Bio-Protection Research Centre, Lincoln University, PO Box 64, Lincoln, 7647, New Zealand
| | - Steffen Ullmann
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,, Düsseldorfer Straße 177, 45481, Mülheim an der Ruhr, Germany
| | - Marino Moretti
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Alexander Carsten
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Jörg Kahnt
- Mass Spectroscopy Facility, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Stefanie Reissmann
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Bernd Zechmann
- Center for Microscopy and Imaging (CMI), Baylor University, Waco, Texas, 76798-7046, USA
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology and Faculty of Chemistry, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Regine Kahmann
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.
| |
Collapse
|
7
|
Abstract
Viruses are integral to ecological and evolutionary processes, but we have a poor understanding of what drives variation in key traits across diverse viruses. For lytic viruses, burst size, latent period, and genome size are primary characteristics controlling host-virus dynamics. Here we synthesize data on these traits for 75 strains of phytoplankton viruses, which play an important role in global biogeochemistry. We find that primary traits of the host (genome size, growth rate) explain 40%-50% of variation in burst size and latent period. Specifically, burst size and latent period both exhibit saturating relationships versus the host∶virus genome size ratio, with both traits increasing at low genome size ratios while showing no relationship at high size ratios. In addition, latent period declines as host growth rate increases. We analyze a model of latent period evolution to explore mechanisms that could cause these patterns. The model predicts that burst size may often be set by the host genomic resources available for viral construction, while latent period evolves to permit this maximal burst size, modulated by host metabolic rate. These results suggest that general mechanisms may underlie the evolution of diverse viruses. Future extensions of this work could help explain viral regulation of host populations, viral influence on community structure and diversity, and viral roles in biogeochemical cycles.
Collapse
|
8
|
Breaking Symmetry in Viral Icosahedral Capsids as Seen through the Lenses of X-ray Crystallography and Cryo-Electron Microscopy. Viruses 2018; 10:v10020067. [PMID: 29414851 PMCID: PMC5850374 DOI: 10.3390/v10020067] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 01/26/2018] [Accepted: 01/31/2018] [Indexed: 12/19/2022] Open
Abstract
The majority of viruses on Earth form capsids built by multiple copies of one or more types of a coat protein arranged with 532 symmetry, generating an icosahedral shell. This highly repetitive structure is ideal to closely pack identical protein subunits and to enclose the nucleic acid genomes. However, the icosahedral capsid is not merely a passive cage but undergoes dynamic events to promote packaging, maturation and the transfer of the viral genome into the host. These essential processes are often mediated by proteinaceous complexes that interrupt the shell’s icosahedral symmetry, providing a gateway through the capsid. In this review, we take an inventory of molecular structures observed either internally, or at the 5-fold vertices of icosahedral DNA viruses that infect bacteria, archea and eukaryotes. Taking advantage of the recent revolution in cryo-electron microscopy (cryo-EM) and building upon a wealth of crystallographic structures of individual components, we review the design principles of non-icosahedral structural components that interrupt icosahedral symmetry and discuss how these macromolecules play vital roles in genome packaging, ejection and host receptor-binding.
Collapse
|
9
|
Quantification of diverse virus populations in the environment using the polony method. Nat Microbiol 2017; 3:62-72. [PMID: 29085077 DOI: 10.1038/s41564-017-0045-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 09/20/2017] [Indexed: 01/21/2023]
Abstract
Viruses are globally abundant and extremely diverse in their genetic make-up and in the hosts they infect. Although they influence the abundance, diversity and evolution of their hosts, current methods are inadequate for gaining a quantitative understanding of their impact on these processes. Here we report the adaptation of the solid-phase single-molecule PCR polony method for the quantification of taxonomically relevant groups of diverse viruses. Using T7-like cyanophages as our model, we found the polony method to be far superior to regular quantitative PCR methods and droplet digital PCR when degenerate primers were used to encompass the group's diversity. This method revealed that T7-like cyanophages were highly abundant in the Red Sea in spring 2013, reaching 770,000 phages ml-1, and displaying a similar depth distribution pattern to cyanobacteria. Furthermore, the abundances of two major clades within the T7-like cyanophages differed dramatically throughout the water column: clade B phages that carry the psbA photosynthesis gene and infect either Synechococcus or Prochlorococcus were at least 20-fold more abundant than clade A phages that lack psbA and infect Synechococcus hosts. Such measurements are of paramount importance for understanding virus population dynamics and the impact of viruses on different microbial taxa and for modelling viral influence on ecosystem functioning on a global scale.
Collapse
|
10
|
Weitz JS, Stock CA, Wilhelm SW, Bourouiba L, Coleman ML, Buchan A, Follows MJ, Fuhrman JA, Jover LF, Lennon JT, Middelboe M, Sonderegger DL, Suttle CA, Taylor BP, Frede Thingstad T, Wilson WH, Eric Wommack K. A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes. THE ISME JOURNAL 2015; 9:1352-64. [PMID: 25635642 PMCID: PMC4438322 DOI: 10.1038/ismej.2014.220] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 11/08/2022]
Abstract
Viral lysis of microbial hosts releases organic matter that can then be assimilated by nontargeted microorganisms. Quantitative estimates of virus-mediated recycling of carbon in marine waters, first established in the late 1990s, were originally extrapolated from marine host and virus densities, host carbon content and inferred viral lysis rates. Yet, these estimates did not explicitly incorporate the cascade of complex feedbacks associated with virus-mediated lysis. To evaluate the role of viruses in shaping community structure and ecosystem functioning, we extend dynamic multitrophic ecosystem models to include a virus component, specifically parameterized for processes taking place in the ocean euphotic zone. Crucially, we are able to solve this model analytically, facilitating evaluation of model behavior under many alternative parameterizations. Analyses reveal that the addition of a virus component promotes the emergence of complex communities. In addition, biomass partitioning of the emergent multitrophic community is consistent with well-established empirical norms in the surface oceans. At steady state, ecosystem fluxes can be probed to characterize the effects that viruses have when compared with putative marine surface ecosystems without viruses. The model suggests that ecosystems with viruses will have (1) increased organic matter recycling, (2) reduced transfer to higher trophic levels and (3) increased net primary productivity. These model findings support hypotheses that viruses can have significant stimulatory effects across whole-ecosystem scales. We suggest that existing efforts to predict carbon and nutrient cycling without considering virus effects are likely to miss essential features of marine food webs that regulate global biogeochemical cycles.
Collapse
Affiliation(s)
- Joshua S Weitz
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Charles A Stock
- Geophysical Fluid Dynamics Laboratory, NOAA, Princeton, NJ, USA
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Lydia Bourouiba
- Department of Applied Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Alison Buchan
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Luis F Jover
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Mathias Middelboe
- Marine Biological Section, University of Copenhagen, Copenhagen, Denmark
| | | | - Curtis A Suttle
- Department of Earth and Ocean Sciences, Department of Botany, and Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bradford P Taylor
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | | | | | - K Eric Wommack
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| |
Collapse
|
11
|
Chénard C, Chan AM, Vincent WF, Suttle CA. Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages. ISME JOURNAL 2015; 9:2046-58. [PMID: 25822482 DOI: 10.1038/ismej.2015.24] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 01/02/2015] [Accepted: 01/06/2015] [Indexed: 11/09/2022]
Abstract
Cyanobacteria are often the dominant phototrophs in polar freshwater communities; yet, the phages that infect them remain unknown. Here, we present a genomic and morphological characterization of cyanophage S-EIV1 that was isolated from freshwaters on Ellesmere Island (Nunavut, High Arctic Canada), and which infects the polar Synechococcus sp., strain PCCC-A2c. S-EIV1 represents a newly discovered evolutionary lineage of bacteriophages whose representatives are widespread in aquatic systems. Among the 130 predicted open reading frames (ORFs) there is no recognizable similarity to genes that encode structural proteins other than the large terminase subunit and a distant viral morphogenesis protein, indicating that the genes encoding the structural proteins of S-EIV1 are distinct from other viruses. As well, only 19 predicted coding sequences on the 79 178 bp circularly permuted genome have homology with genes encoding proteins of known function. Although S-EIV1 is divergent from other sequenced phage isolates, it shares synteny with phage genes captured on a fosmid from the deep-chlorophyll maximum in the Mediterranean Sea, as well as with an incision element in the genome of Anabaena variabilis (ATCC 29413). Sequence recruitment of metagenomic data indicates that S-EIV1-like viruses are cosmopolitan and abundant in a wide range of aquatic systems, suggesting they have an important ecological role.
Collapse
Affiliation(s)
- C Chénard
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - A M Chan
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - W F Vincent
- Département de Biologie and Centre d'études nordiques (CEN), Laval University, Quebec City, Quebec, Canada
| | - C A Suttle
- 1] Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada [2] Departments of Botany, and Microbiology & Immunology, University of British Columbia, Vancouver, British Columbia, Canada [3] Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| |
Collapse
|
12
|
Zernike phase-contrast electron cryotomography applied to marine cyanobacteria infected with cyanophages. Nat Protoc 2014; 9:2630-42. [PMID: 25321408 DOI: 10.1038/nprot.2014.176] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Advances in electron cryotomography have provided new opportunities to visualize the internal 3D structures of a bacterium. An electron microscope equipped with Zernike phase-contrast optics produces images with markedly increased contrast compared with images obtained by conventional electron microscopy. Here we describe a protocol to apply Zernike phase plate technology for acquiring electron tomographic tilt series of cyanophage-infected cyanobacterial cells embedded in ice, without staining or chemical fixation. We detail the procedures for aligning and assessing phase plates for data collection, and methods for obtaining 3D structures of cyanophage assembly intermediates in the host by subtomogram alignment, classification and averaging. Acquiring three or four tomographic tilt series takes ∼12 h on a JEM2200FS electron microscope. We expect this time requirement to decrease substantially as the technique matures. The time required for annotation and subtomogram averaging varies widely depending on the project goals and data volume.
Collapse
|
13
|
Wang Y, Wang W, Lv Y, Zheng W, Mi Z, Pei G, An X, Xu X, Han C, Liu J, Zhou C, Tong Y. Characterization and complete genome sequence analysis of novel bacteriophage IME-EFm1 infecting Enterococcus faecium. J Gen Virol 2014; 95:2565-2575. [PMID: 25078302 DOI: 10.1099/vir.0.067553-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We isolated and characterized a novel virulent bacteriophage, IME-EFm1, specifically infecting multidrug-resistant Enterococcus faecium. IME-EFm1 is morphologically similar to members of the family Siphoviridae. It was found capable of lysing a wide range of our E. faecium collections, including two strains resistant to vancomycin. One-step growth tests revealed the host lysis activity of phage IME-EFm1, with a latent time of 30 min and a large burst size of 116 p.f.u. per cell. These biological characteristics suggested that IME-EFm1 has the potential to be used as a therapeutic agent. The complete genome of IME-EFm1 was 42 597 bp, and was linear, with terminally non-redundant dsDNA and a G+C content of 35.2 mol%. The termini of the phage genome were determined with next-generation sequencing and were further confirmed by nuclease digestion analysis. To our knowledge, this is the first report of a complete genome sequence of a bacteriophage infecting E. faecium. IME-EFm1 exhibited a low similarity to other phages in terms of genome organization and structural protein amino acid sequences. The coding region corresponded to 90.7 % of the genome; 70 putative ORFs were deduced and, of these, 29 could be functionally identified based on their homology to previously characterized proteins. A predicted metallo-β-lactamase gene was detected in the genome sequence. The identification of an antibiotic resistance gene emphasizes the necessity for complete genome sequencing of a phage to ensure it is free of any undesirable genes before use as a therapeutic agent against bacterial pathogens.
Collapse
Affiliation(s)
- Yahui Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China.,School of Life Science & Technology, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, PR China
| | - Wei Wang
- Anhui Medical University, Hefei 230032, PR China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Yongqiang Lv
- Department of Laboratory, Dalian Beihai Hospital, Dalian Liaoning 116021, PR China
| | - Wangliang Zheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Zhiqiang Mi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Guangqian Pei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Xiaoping An
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Xiaomeng Xu
- Anhui Medical University, Hefei 230032, PR China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Chuanyin Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Jie Liu
- The General Hospital of Beijing Military Command, Beijing 100041, PR China
| | - Changlin Zhou
- School of Life Science & Technology, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, PR China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| |
Collapse
|
14
|
Gipson P, Baker ML, Raytcheva D, Haase-Pettingell C, Piret J, King JA, Chiu W. Protruding knob-like proteins violate local symmetries in an icosahedral marine virus. Nat Commun 2014; 5:4278. [PMID: 24985522 PMCID: PMC4102127 DOI: 10.1038/ncomms5278] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 06/03/2014] [Indexed: 02/02/2023] Open
Abstract
Marine viruses play crucial roles in shaping the dynamics of oceanic microbial communities and in the carbon cycle on Earth. Here we report a 4.7-Å structure of a cyanobacterial virus, Syn5, by electron cryo-microscopy and modelling. A Cα backbone trace of the major capsid protein (gp39) reveals a classic phage protein fold. In addition, two knob-like proteins protruding from the capsid surface are also observed. Using bioinformatics and structure analysis tools, these proteins are identified to correspond to gp55 and gp58 (each with two copies per asymmetric unit). The non 1:1 stoichiometric distribution of gp55/58 to gp39 breaks all expected local symmetries and leads to non-quasi-equivalence of the capsid subunits, suggesting a role in capsid stabilization. Such a structural arrangement has not yet been observed in any known virus structures.
Collapse
Affiliation(s)
- Preeti Gipson
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Matthew L Baker
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Desislava Raytcheva
- 1] Department of Microbiology, Northeastern University, Boston, Massachusetts 02115, USA [2] Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Cameron Haase-Pettingell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jacqueline Piret
- Department of Microbiology, Northeastern University, Boston, Massachusetts 02115, USA
| | - Jonathan A King
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Wah Chiu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| |
Collapse
|
15
|
Abstract
The marine cyanophage Syn5 can be propagated to a high titer in the laboratory on marine photosynthetic Synechococcus sp. strain WH8109. The purified particles carry a novel slender horn structure projecting from the vertex opposite the tail vertex. The genome of Syn5 includes a number of genes coding for novel proteins. Using immune-electron microscopy with gold-labeled antibodies, we show that two of these novel proteins, products of genes 53 and 54, are part of the horn structure. A third novel protein, the product of gene 58, is assembled onto the icosahedral capsid lattice. Characterization of radioactively labeled precursor procapsids by sucrose gradient centrifugation shows that there appear to be three classes of particles-procapsids, scaffold-deficient procapsids, and expanded capsids. These lack fully assembled horn appendages. The horn presumably assembles onto the virion just before or after DNA packaging. Antibodies raised to the recombinant novel Syn5 proteins did not interfere with phage infectivity, suggesting that the functions of these proteins are not directly involved in phage attachment or infection of the host WH8109. The horn structure may represent some adaption to the marine environment, whose function will require additional investigation.
Collapse
|
16
|
Prevalence of psbA-containing cyanobacterial podoviruses in the ocean. Sci Rep 2013; 3:3207. [PMID: 24220518 PMCID: PMC3826097 DOI: 10.1038/srep03207] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 10/25/2013] [Indexed: 11/29/2022] Open
Abstract
Podoviruses that infect marine picocyanobacteria are abundant and could play a significant role on regulating host populations due to their specific phage-host relationship. Genome sequencing of cyanophages has unveiled that many marine cyanophages encode certain photosynthetic genes like psbA. It appears that psbA is only present in certain groups of cyanopodovirus isolates. In order to better understand the prevalence of psbA in cyanobacterial podoviruses, we searched the marine metagenomic database (GOS, BATS, HOT and MarineVirome). Our study suggests that 89% of recruited cyanopodovirus scaffolds from the GOS database contained the psbA gene, supporting the ecological relevance of the photosynthesis gene for surface oceanic cyanophages. Diversification between Clade A and B are consistent with recent finding of two major groups of cyanopodoviruses. All the data also shows that Clade B cyanopodoviruses dominate the surface ocean water, while Clade A cyanopodoviruses become more important in the coastal and estuarine environments.
Collapse
|
17
|
Dai W, Fu C, Raytcheva D, Flanagan J, Khant HA, Liu X, Rochat RH, Haase-Pettingell C, Piret J, Ludtke SJ, Nagayama K, Schmid MF, King JA, Chiu W. Visualizing virus assembly intermediates inside marine cyanobacteria. Nature 2013; 502:707-10. [PMID: 24107993 PMCID: PMC3984937 DOI: 10.1038/nature12604] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/27/2013] [Indexed: 12/31/2022]
Abstract
Cyanobacteria are photosynthetic organisms responsible for ~25% of organic carbon fixation on earth. These bacteria began to convert solar energy and carbon dioxide into bioenergy and oxygen billions of years ago. Cyanophages, which infect these bacteria, play an important role in regulating the marine ecosystem by controlling cyanobacteria community organization and mediating lateral gene transfer. Here we visualize the maturation process of cyanophage Syn5 inside its host cell, Synechococcus, using Zernike Phase Contrast (ZPC) electron cryo-tomography (cryoET)1,2. This imaging modality yields significant enhancement of image contrast over conventional cryoET and thus facilitates the direct identification of subcellular components, including thylakoid membranes, carboxysomes and polyribosomes, as well as phages, inside the congested cytosol of the infected cell. By correlating the structural features and relative abundance of viral progeny within cells at different stages of infection, we identified distinct Syn5 assembly intermediates. Our results suggest that the procapsid releases scaffolding proteins and expands its volume at an early stage of genome packaging. Later in assembly, we detected full particles with a tail either with or without an additional horn. The morphogenetic pathway we describe herein is highly conserved and was probably established long before that of double stranded DNA (dsDNA) viruses infecting higher life forms.
Collapse
Affiliation(s)
- Wei Dai
- National Center for Macromolecular Imaging, Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Ge X, Wu Y, Wang M, Wang J, Wu L, Yang X, Zhang Y, Shi Z. Viral metagenomics analysis of planktonic viruses in East Lake, Wuhan, China. Virol Sin 2013; 28:280-90. [PMID: 24132758 DOI: 10.1007/s12250-013-3365-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 09/28/2013] [Indexed: 11/28/2022] Open
Abstract
East Lake (Lake Donghu), located in Wuhan, China, is a typical city freshwater lake that has been experiencing eutrophic conditions and algal blooming during recent years. Marine and fresh water are considered to contain a large number of viruses. However, little is known about their genetic diversity because of the limited techniques for culturing viruses. In this study, we conducted a viral metagenomic analysis using a high-throughput sequencing technique with samples collected from East Lake in Spring, Summer, Autumn, and Winter. The libraries from four samples each generated 234,669, 71,837, 12,820, and 34,236 contigs (> 90 bp each), respectively. The genetic structure of the viral community revealed a high genetic diversity covering 23 viral families, with the majority of contigs homologous to DNA viruses, including members of Myoviridae, Podoviridae, Siphoviridae, Phycodnaviridae, and Microviridae, which infect bacteria or algae, and members of Circoviridae, which infect invertebrates and vertebrates. The highest viral genetic diversity occurred in samples collected in August, then December and June, and the least diversity in March. Most contigs have low-sequence identities with known viruses. PCR detection targeting the conserved sequences of genes (g20, psbA, psbD, and DNApol) of cyanophages further confirmed that there are novel cyanophages in the East Lake. Our viral metagenomic data provide the first preliminary understanding of the virome in one freshwater lake in China and would be helpful for novel virus discovery and the control of algal blooming in the future.
Collapse
Affiliation(s)
- Xingyi Ge
- Center for Emerging Infectious Diseases, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Zhou Y, Lin J, Li N, Hu Z, Deng F. Characterization and genomic analysis of a plaque purified strain of cyanophage PP. Virol Sin 2013; 28:272-9. [PMID: 24132757 DOI: 10.1007/s12250-013-3363-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 09/23/2013] [Indexed: 11/24/2022] Open
Abstract
Cyanophages are ubiquitous and essential components of the aquatic environment and play an important role in the termination of algal blooms. As such, they have attracted widespread interest. PP was the first isolated cyanophage in China, which infects Plectonema boryanum and Phormidium foveolarum. In this study, this cyanophage was purified three times by a double-agar overlay plaque assay and characterized. Its genome was extracted, totally sequenced and analyzed. Electron microscopy revealed a particle with an icosahedral head connected to a short stubby tail. Bioassays showed that PP was quite virulent. The genome of PP is a 42,480 base pair (bp), linear, double-stranded DNA molecule with 222 bp terminal repeats. It has high similarity with the known Pf-WMP3 sequence. It contains 41 open reading frames (ORFs), 17 of which were annotated. Intriguingly, the genome can be divided into two completely different parts, which differ both in orientation and function.
Collapse
Affiliation(s)
- Yiran Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | | | | | | | | |
Collapse
|
20
|
Allers E, Moraru C, Duhaime MB, Beneze E, Solonenko N, Barrero-Canosa J, Amann R, Sullivan MB. Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses. Environ Microbiol 2013; 15:2306-18. [PMID: 23489642 PMCID: PMC3884771 DOI: 10.1111/1462-2920.12100] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 01/18/2013] [Accepted: 01/19/2013] [Indexed: 11/29/2022]
Abstract
Microbes drive the biogeochemical cycles that fuel planet Earth, and their viruses (phages) alter microbial population structure, genome repertoire, and metabolic capacity. However, our ability to understand and quantify phage–host interactions is technique-limited. Here, we introduce phageFISH – a markedly improved geneFISH protocol that increases gene detection efficiency from 40% to > 92% and is optimized for detection and visualization of intra- and extracellular phage DNA. The application of phageFISH to characterize infection dynamics in a marine podovirus–gammaproteobacterial host model system corroborated classical metrics (qPCR, plaque assay, FVIC, DAPI) and outperformed most of them to reveal new biology. PhageFISH detected both replicating and encapsidated (intracellular and extracellular) phage DNA, while simultaneously identifying and quantifying host cells during all stages of infection. Additionally, phageFISH allowed per-cell relative measurements of phage DNA, enabling single-cell documentation of infection status (e.g. early vs late stage infections). Further, it discriminated between two waves of infection, which no other measurement could due to population-averaged signals. Together, these findings richly characterize the infection dynamics of a novel model phage–host system, and debut phageFISH as a much-needed tool for studying phage–host interactions in the laboratory, with great promise for environmental surveys and lineage-specific population ecology of free phages.
Collapse
Affiliation(s)
- Elke Allers
- Department of Ecology and Evolutionary Biology, University of Arizona, Life Sciences South, 1007 East Lowell Street, Tucson, AZ 85721, USA
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Zhu B, Tabor S, Raytcheva DA, Hernandez A, King JA, Richardson CC. The RNA polymerase of marine cyanophage Syn5. J Biol Chem 2012; 288:3545-52. [PMID: 23258537 DOI: 10.1074/jbc.m112.442350] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A single subunit DNA-dependent RNA polymerase was identified and purified to apparent homogeneity from cyanophage Syn5 that infects the marine cyanobacteria Synechococcus. Syn5 is homologous to bacteriophage T7 that infects Escherichia coli. Using the purified enzyme its promoter has been identified by examining transcription of segments of Syn5 DNA and sequencing the 5'-termini of the transcripts. Only two Syn5 RNAP promoters, having the sequence 5'-ATTGGGCACCCGTAA-3', are found within the Syn5 genome. One promoter is located within the Syn5 RNA polymerase gene and the other is located close to the right genetic end of the genome. The purified enzyme and its promoter have enabled a determination of the requirements for transcription. Unlike the salt-sensitive bacteriophage T7 RNA polymerase, this marine RNA polymerase requires 160 mm potassium for maximal activity. The optimal temperature for Syn5 RNA polymerase is 24 °C, much lower than that for T7 RNA polymerase. Magnesium is required as a cofactor although some activity is observed with ferrous ions. Syn5 RNA polymerase is more efficient in utilizing low concentrations of ribonucleotides than T7 RNA polymerase.
Collapse
Affiliation(s)
- Bin Zhu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.
| | | | | | | | | | | |
Collapse
|
22
|
Parent KN, Gilcrease EB, Casjens SR, Baker TS. Structural evolution of the P22-like phages: comparison of Sf6 and P22 procapsid and virion architectures. Virology 2012; 427:177-88. [PMID: 22386055 DOI: 10.1016/j.virol.2012.01.040] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 01/10/2012] [Accepted: 01/30/2012] [Indexed: 01/07/2023]
Abstract
Coat proteins of tailed, dsDNA phages and in herpesviruses include a conserved core similar to the bacteriophage HK97 subunit. This core is often embellished with other domains such as the telokin Ig-like domain of phage P22. Eighty-six P22-like phages and prophages with sequenced genomes share a similar set of virion assembly genes and, based on comparisons of twelve viral assembly proteins (structural and assembly/packaging chaperones), these phages are classified into three groups (P22-like, Sf6-like, and CUS-3-like). We used cryo-electron microscopy and 3D image reconstruction to determine the structures of Sf6 procapsids and virions (~7Å resolution), and the structure of the entire, asymmetric Sf6 virion (16-Å resolution). The Sf6 coat protein is similar to that of P22 yet it has differences in the telokin domain and in its overall quaternary organization. Thermal stability and agarose gel experiments show that Sf6 virions are slightly less stable than those of P22. Finally, bacterial host outer membrane proteins A and C were identified in lipid vesicles that co-purify with Sf6 particles, but are not components of the capsid.
Collapse
Affiliation(s)
- Kristin N Parent
- University of California, San Diego, Department of Chemistry & Biochemistry, La Jolla, CA 92093, USA
| | | | | | | |
Collapse
|
23
|
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.
Collapse
|