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Li S, Xu M, Yang D, Yang M, Wu H, Li X, Yang C, Fang Z, Wu Q, Tan L, Xiao W, Weng Q. Characterization and genomic analysis of a lytic Stenotrophomonas maltophilia short-tailed phage A1432 revealed a new genus of the family Mesyanzhinovviridae. Front Microbiol 2024; 15:1400700. [PMID: 38993489 PMCID: PMC11236537 DOI: 10.3389/fmicb.2024.1400700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 06/14/2024] [Indexed: 07/13/2024] Open
Abstract
Stenotrophomonas maltophilia (S. maltophilia) is an emerging opportunistic pathogen that exhibits resistant to a majority of commonly used antibiotics. Phages have the potential to serve as an alternative treatment for S. maltophilia infections. In this study, a lytic phage, A1432, infecting S. maltophilia YCR3A-1, was isolated and characterized from a karst cave. Transmission electron microscopy revealed that phage A1432 possesses an icosahedral head and a shorter tail. Phage A1432 demonstrated a narrow host range, with an optimal multiplicity of infection of 0.1. The one-step growth curve indicated a latent time of 10 min, a lysis period of 90 min, a burst size of 43.2 plaque-forming units per cell. In vitro bacteriolytic activity test showed that phage A1432 was capable to inhibit the growth of S. maltophilia YCR3A-1 in an MOI-dependent manner after 2 h of co-culture. BLASTn analysis showed that phage A1432 genome shares the highest similarity (81.46%) with Xanthomonas phage Xoo-sp2 in the NCBI database, while the query coverage was only 37%. The phage contains double-stranded DNA with a genome length of 61,660 bp and a GC content of 61.92%. It is predicted to have 79 open reading frames and one tRNA, with no virulence or antibiotic resistance genes. Phylogenetic analysis using terminase large subunit and DNA polymerase indicated that phage A1432 clustered with members of the Bradleyvirinae subfamily but diverged into a distinct branch. Further phylogenetic comparison analysis using Average Nucleotide Identity, proteomic phylogenetic analysis, genomic network analysis confirmed that phage A1432 belongs to a novel genus within the Bradleyvirinae subfamily, Mesyanzhinovviridae family. Additionally, phylogenetic analysis of the so far isolated S. maltophilia phages revealed significant genetic diversity among these phages. The results of this research will contribute valuable information for further studies on their morphological and genetic diversity, will aid in elucidating the evolutionary mechanisms that give rise to them.
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Affiliation(s)
- Shixia Li
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Man Xu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Deying Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Mei Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Hejing Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Xuelian Li
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Changzhou Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Zheng Fang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Qingshan Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Leitao Tan
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Wei Xiao
- Yunnan Institute of Microbiology, Yunnan International Joint Laboratory of Virology and Immunology, Yunnan University, Kunming, China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, China
- Qiannan Normal University for Nationalities, Duyun, China
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2
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Zhang C, Quan X, Lian W, Liu R, Wen Q, Chen X. Phenotypic characterization and genomic analysis of Limosilactobacillus fermentum phage. Curr Res Food Sci 2024; 8:100748. [PMID: 38764976 PMCID: PMC11098726 DOI: 10.1016/j.crfs.2024.100748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 04/14/2024] [Accepted: 04/22/2024] [Indexed: 05/21/2024] Open
Abstract
Limosilactobacillus (L.) fermentum is widely utilized for its beneficial properties, but lysogenic phages can integrate into its genome and can be induced to enter the lysis cycle under certain conditions, thus accomplishing lysis of host cells, resulting in severe economic losses. In this study, a lysogenic phage, LFP03, was induced from L. fermentum IMAU 32510 by UV irradiation for 70 s. The electron microscopy showed that this phage belonged to Caudoviricetes class. Its genome size was 39,556 bp with a GC content of 46.08%, which includes 20 functional proteins. Compared with other L. fermentum phages, the genome of phage LFP03 exhibited deletions, inversions and translocations. Biological analysis showed that its optimal multiplicity of infection was 0.1, with a burst size of 133.5 ± 4.9 PFU/infective cell. Phage LFP03 was sensitive to temperature and pH value, with a survival rate of 48.98% at 50 °C. It could be completely inactivated under pH 2. The adsorption ability of this phage was minimally affected by temperature and pH value, with adsorption rates reaching 80% under all treated conditions. Divalent cations could accelerate phage adsorption, while chloramphenicol expressed little influence. This study might expand the related knowledge of L. fermentum phages, and provide some theoretical basis for improving the stability of related products and establishing phage control measures.
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Affiliation(s)
- Can Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, 010018, PR China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, 010018, PR China
| | - Xingyu Quan
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, 010018, PR China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, 010018, PR China
| | - Weiqi Lian
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, 010018, PR China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, 010018, PR China
| | - Runze Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, 010018, PR China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, 010018, PR China
| | - Qiannan Wen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, 010018, PR China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, 010018, PR China
| | - Xia Chen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, 010018, PR China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, 010018, PR China
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3
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Jain S, Uritskiy G, Mahalingam M, Batra H, Chand S, Trinh HV, Beck C, Shin WH, Alsalmi W, Kijak G, Eller LA, Kim J, Kihara D, Tovanabutra S, Ferrari G, Robb ML, Rao M, Rao VB. A remarkable genetic shift in a transmitted/founder virus broadens antibody responses against HIV-1. eLife 2024; 13:RP92379. [PMID: 38619110 PMCID: PMC11018346 DOI: 10.7554/elife.92379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024] Open
Abstract
A productive HIV-1 infection in humans is often established by transmission and propagation of a single transmitted/founder (T/F) virus, which then evolves into a complex mixture of variants during the lifetime of infection. An effective HIV-1 vaccine should elicit broad immune responses in order to block the entry of diverse T/F viruses. Currently, no such vaccine exists. An in-depth study of escape variants emerging under host immune pressure during very early stages of infection might provide insights into such a HIV-1 vaccine design. Here, in a rare longitudinal study involving HIV-1 infected individuals just days after infection in the absence of antiretroviral therapy, we discovered a remarkable genetic shift that resulted in near complete disappearance of the original T/F virus and appearance of a variant with H173Y mutation in the variable V2 domain of the HIV-1 envelope protein. This coincided with the disappearance of the first wave of strictly H173-specific antibodies and emergence of a second wave of Y173-specific antibodies with increased breadth. Structural analyses indicated conformational dynamism of the envelope protein which likely allowed selection of escape variants with a conformational switch in the V2 domain from an α-helix (H173) to a β-strand (Y173) and induction of broadly reactive antibody responses. This differential breadth due to a single mutational change was also recapitulated in a mouse model. Rationally designed combinatorial libraries containing 54 conformational variants of V2 domain around position 173 further demonstrated increased breadth of antibody responses elicited to diverse HIV-1 envelope proteins. These results offer new insights into designing broadly effective HIV-1 vaccines.
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Affiliation(s)
- Swati Jain
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
| | - Gherman Uritskiy
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
| | - Marthandan Mahalingam
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
| | - Himanshu Batra
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
| | - Subhash Chand
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
| | - Hung V Trinh
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaUnited States
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of ResearchSilver SpringUnited States
| | - Charles Beck
- Department of Molecular Genetics and Microbiology, Duke UniversityDurhamUnited States
| | - Woong-Hee Shin
- Department of Biological Sciences, Purdue UniversityWest LafayetteUnited States
- Department of Chemistry Education, Sunchon National UniversitySuncheonRepublic of Korea
- Department of Advanced Components and Materials Engineering, Sunchon National UniversitySuncheonRepublic of Korea
| | - Wadad Alsalmi
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
| | - Gustavo Kijak
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaUnited States
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of ResearchSilver SpringUnited States
| | - Leigh A Eller
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaUnited States
| | - Jerome Kim
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of ResearchSilver SpringUnited States
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue UniversityWest LafayetteUnited States
- Department of Computer Science, Purdue UniversityWest LafayetteUnited States
| | - Sodsai Tovanabutra
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaUnited States
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of ResearchSilver SpringUnited States
| | - Guido Ferrari
- Department of Molecular Genetics and Microbiology, Duke UniversityDurhamUnited States
| | - Merlin L Robb
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaUnited States
| | - Mangala Rao
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of ResearchSilver SpringUnited States
| | - Venigalla B Rao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
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4
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Ragonis-Bachar P, Axel G, Blau S, Ben-Tal N, Kolodny R, Landau M. What can AlphaFold do for antimicrobial amyloids? Proteins 2024; 92:265-281. [PMID: 37855235 DOI: 10.1002/prot.26618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/05/2023] [Accepted: 10/05/2023] [Indexed: 10/20/2023]
Abstract
Amyloids, protein, and peptide assemblies in various organisms are crucial in physiological and pathological processes. Their intricate structures, however, present significant challenges, limiting our understanding of their functions, regulatory mechanisms, and potential applications in biomedicine and technology. This study evaluated the AlphaFold2 ColabFold method's structure predictions for antimicrobial amyloids, using eight antimicrobial peptides (AMPs), including those with experimentally determined structures and AMPs known for their distinct amyloidogenic morphological features. Additionally, two well-known human amyloids, amyloid-β and islet amyloid polypeptide, were included in the analysis due to their disease relevance, short sequences, and antimicrobial properties. Amyloids typically exhibit tightly mated β-strand sheets forming a cross-β configuration. However, certain amphipathic α-helical subunits can also form amyloid fibrils adopting a cross-α structure. Some AMPs in the study exhibited a combination of cross-α and cross-β amyloid fibrils, adding complexity to structure prediction. The results showed that the AlphaFold2 ColabFold models favored α-helical structures in the tested amyloids, successfully predicting the presence of α-helical mated sheets and a hydrophobic core resembling the cross-α configuration. This implies that the AI-based algorithms prefer assemblies of the monomeric state, which was frequently predicted as helical, or capture an α-helical membrane-active form of toxic peptides, which is triggered upon interaction with lipid membranes.
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Affiliation(s)
| | - Gabriel Axel
- George S. Wise Faculty of Life Sciences, Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel
| | - Shahar Blau
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Nir Ben-Tal
- George S. Wise Faculty of Life Sciences, Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel
| | - Rachel Kolodny
- Department of Computer Science, University of Haifa, Haifa, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- The Center for Experimental Medicine, Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany
- European Molecular Biology Laboratory (EMBL), Hamburg, Germany
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5
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Dasgupta S, Thomas JA, Ray K. Mechanism of Viral DNA Packaging in Phage T4 Using Single-Molecule Fluorescence Approaches. Viruses 2024; 16:192. [PMID: 38399968 PMCID: PMC10893049 DOI: 10.3390/v16020192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
In all tailed phages, the packaging of the double-stranded genome into the head by a terminase motor complex is an essential step in virion formation. Despite extensive research, there are still major gaps in the understanding of this highly dynamic process and the mechanisms responsible for DNA translocation. Over the last fifteen years, single-molecule fluorescence technologies have been applied to study viral nucleic acid packaging using the robust and flexible T4 in vitro packaging system in conjunction with genetic, biochemical, and structural analyses. In this review, we discuss the novel findings from these studies, including that the T4 genome was determined to be packaged as an elongated loop via the colocalization of dye-labeled DNA termini above the portal structure. Packaging efficiency of the TerL motor was shown to be inherently linked to substrate structure, with packaging stalling at DNA branches. The latter led to the design of multiple experiments whose results all support a proposed torsional compression translocation model to explain substrate packaging. Evidence of substrate compression was derived from FRET and/or smFRET measurements of stalled versus resolvase released dye-labeled Y-DNAs and other dye-labeled substrates relative to motor components. Additionally, active in vivo T4 TerS fluorescent fusion proteins facilitated the application of advanced super-resolution optical microscopy toward the visualization of the initiation of packaging. The formation of twin TerS ring complexes, each expected to be ~15 nm in diameter, supports a double protein ring-DNA synapsis model for the control of packaging initiation, a model that may help explain the variety of ring structures reported among pac site phages. The examination of the dynamics of the T4 packaging motor at the single-molecule level in these studies demonstrates the value of state-of-the-art fluorescent tools for future studies of complex viral replication mechanisms.
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Affiliation(s)
- Souradip Dasgupta
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Julie A. Thomas
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA;
| | - Krishanu Ray
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
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6
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Prokhorov NS, Davis C, Maruthi K, Yang Q, Sherman M, Woodson M, White M, Miller LM, Jarrold M, Catalano C, Morais M. Biophysical and structural characterization of a multifunctional viral genome packaging motor. Nucleic Acids Res 2024; 52:831-843. [PMID: 38084901 PMCID: PMC10810279 DOI: 10.1093/nar/gkad1135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 01/26/2024] Open
Abstract
The large dsDNA viruses replicate their DNA as concatemers consisting of multiple covalently linked genomes. Genome packaging is catalyzed by a terminase enzyme that excises individual genomes from concatemers and packages them into preassembled procapsids. These disparate tasks are catalyzed by terminase alternating between two distinct states-a stable nuclease that excises individual genomes and a dynamic motor that translocates DNA into the procapsid. It was proposed that bacteriophage λ terminase assembles as an anti-parallel dimer-of-dimers nuclease complex at the packaging initiation site. In contrast, all characterized packaging motors are composed of five terminase subunits bound to the procapsid in a parallel orientation. Here, we describe biophysical and structural characterization of the λ holoenzyme complex assembled in solution. Analytical ultracentrifugation, small angle X-ray scattering, and native mass spectrometry indicate that 5 subunits assemble a cone-shaped terminase complex. Classification of cryoEM images reveals starfish-like rings with skewed pentameric symmetry and one special subunit. We propose a model wherein nuclease domains of two subunits alternate between a dimeric head-to-head arrangement for genome maturation and a fully parallel arrangement during genome packaging. Given that genome packaging is strongly conserved in both prokaryotic and eukaryotic viruses, the results have broad biological implications.
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Affiliation(s)
- Nikolai S Prokhorov
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Christal R Davis
- Program in Structural Biology and Biochemistry, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kashyap Maruthi
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Qin Yang
- Department of Pharmaceutical Chemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Campus, Aurora, CO 80045, USA
| | - Michael B Sherman
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Michael Woodson
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Mark A White
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Lohra M Miller
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Martin F Jarrold
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Carlos E Catalano
- Program in Structural Biology and Biochemistry, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pharmaceutical Chemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Campus, Aurora, CO 80045, USA
| | - Marc C Morais
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
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7
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Hawkins DEDP, Godwin OC, Antson AA. Viral Genomic DNA Packaging Machinery. Subcell Biochem 2024; 104:181-205. [PMID: 38963488 DOI: 10.1007/978-3-031-58843-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Tailed double-stranded DNA bacteriophage employs a protein terminase motor to package their genome into a preformed protein shell-a system shared with eukaryotic dsDNA viruses such as herpesviruses. DNA packaging motor proteins represent excellent targets for antiviral therapy, with Letermovir, which binds Cytomegalovirus terminase, already licensed as an effective prophylaxis. In the realm of bacterial viruses, these DNA packaging motors comprise three protein constituents: the portal protein, small terminase and large terminase. The portal protein guards the passage of DNA into the preformed protein shell and acts as a protein interaction hub throughout viral assembly. Small terminase recognises the viral DNA and recruits large terminase, which in turn pumps DNA in an ATP-dependent manner. Large terminase also cleaves DNA at the termination of packaging. Multiple high-resolution structures of each component have been resolved for different phages, but it is only more recently that the field has moved towards cryo-EM reconstructions of protein complexes. In conjunction with highly informative single-particle studies of packaging kinetics, these structures have begun to inspire models for the packaging process and its place among other DNA machines.
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Affiliation(s)
- Dorothy E D P Hawkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
| | - Owen C Godwin
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
- Structural Biology, The Francis Crick Institute, London, UK
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
- Structural Biology, The Francis Crick Institute, London, UK.
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8
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Jagtap AD, Geraghty RJ, Wang Z. Inhibiting HCMV pUL89-C Endonuclease with Metal-Binding Compounds. J Med Chem 2023; 66:13874-13887. [PMID: 37827528 DOI: 10.1021/acs.jmedchem.3c01280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Human cytomegalovirus (HCMV) infects individuals of all ages and establishes a lifelong latency. Current antiviral drugs are suboptimal in efficacy and safety and ineffective against resistant/refractory HCMV. Therefore, there is an unmet clinical need for efficacious, safe, and mechanistically novel HCMV drugs. The recent Food and Drug Administration (FDA) approval of letermovir (LTV) validated the HCMV terminase complex as a new target for antiviral development. LTV targets terminase subunit pUL56 but not the main endonuclease enzymatic function housed in the C terminus of subunit pUL89 (pUL89-C). Structurally and mechanistically, pUL89-C is an RNase H-like viral endonuclease entailing two divalent metal ions at the active site. In recent years, numerous studies have extensively explored pUL89-C inhibition using metal-chelating chemotypes, an approach previously used for inhibiting HIV ribonuclease H (RNase H) and integrase strand transfer (INST). Collectively, the work summarized herein validates the use of metal-binding scaffolds for designing potent and specific pUL89-C inhibitors.
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Affiliation(s)
- Ajit Dhananjay Jagtap
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Robert J Geraghty
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
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9
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Guérin M, Shawky M, Zedan A, Octave S, Avalle B, Maffucci I, Padiolleau-Lefèvre S. Lyme borreliosis diagnosis: state of the art of improvements and innovations. BMC Microbiol 2023; 23:204. [PMID: 37528399 PMCID: PMC10392007 DOI: 10.1186/s12866-023-02935-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/04/2023] [Indexed: 08/03/2023] Open
Abstract
With almost 700 000 estimated cases each year in the United States and Europe, Lyme borreliosis (LB), also called Lyme disease, is the most common tick-borne illness in the world. Transmitted by ticks of the genus Ixodes and caused by bacteria Borrelia burgdorferi sensu lato, LB occurs with various symptoms, such as erythema migrans, which is characteristic, whereas others involve blurred clinical features such as fatigue, headaches, arthralgia, and myalgia. The diagnosis of Lyme borreliosis, based on a standard two-tiered serology, is the subject of many debates and controversies, since it relies on an indirect approach which suffers from a low sensitivity depending on the stage of the disease. Above all, early detection of the disease raises some issues. Inappropriate diagnosis of Lyme borreliosis leads to therapeutic wandering, inducing potential chronic infection with a strong antibody response that fails to clear the infection. Early and proper detection of Lyme disease is essential to propose an adequate treatment to patients and avoid the persistence of the pathogen. This review presents the available tests, with an emphasis on the improvements of the current diagnosis, the innovative methods and ideas which, ultimately, will allow more precise detection of LB.
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Affiliation(s)
- Mickaël Guérin
- Unité de Génie Enzymatique Et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, 60203, Compiègne, France
| | - Marc Shawky
- Connaissance Organisation Et Systèmes TECHniques (COSTECH), EA 2223, Université de Technologie de Compiègne, 60203, Compiègne, France
| | - Ahed Zedan
- Polyclinique Saint Côme, 7 Rue Jean Jacques Bernard, 60204, Compiègne, France
| | - Stéphane Octave
- Unité de Génie Enzymatique Et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, 60203, Compiègne, France
| | - Bérangère Avalle
- Unité de Génie Enzymatique Et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, 60203, Compiègne, France
| | - Irene Maffucci
- Unité de Génie Enzymatique Et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, 60203, Compiègne, France
| | - Séverine Padiolleau-Lefèvre
- Unité de Génie Enzymatique Et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, 60203, Compiègne, France.
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10
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Chechik M, Greive SJ, Antson AA, Jenkins HT. Structure of HK97 small terminase:DNA complex unveils a novel DNA binding mechanism by a circular protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549218. [PMID: 37503206 PMCID: PMC10370121 DOI: 10.1101/2023.07.17.549218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
DNA recognition is critical for assembly of double-stranded DNA viruses, in particular for the initiation of packaging the viral genome into the capsid. DNA packaging has been extensively studied for three archetypal bacteriophage systems: cos, pac and phi29. We identified the minimal site within the cos region of bacteriophage HK97 specifically recognised by the small terminase and determined a cryoEM structure for the small terminase:DNA complex. This nonameric circular protein utilizes a previously unknown mechanism of DNA binding. While DNA threads through the central tunnel, unexpectedly, DNA-recognition is generated at its exit by a substructure formed by the N- and C-terminal segments of two adjacent protomers of the terminase which are unstructured in the absence of DNA. Such interaction ensures continuous engagement of the small terminase with DNA, allowing sliding along DNA while simultaneously checking the DNA sequence. This mechanism allows locating and instigating packaging initiation and termination precisely at the cos site.
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Affiliation(s)
- Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | | | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
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Megat Mazhar Khair MH, Tee AN, Wahab NF, Othman SS, Goh YM, Masarudin MJ, Chong CM, In LLA, Gan HM, Song AAL. Comprehensive Characterization of a Streptococcus agalactiae Phage Isolated from a Tilapia Farm in Selangor, Malaysia, and Its Potential for Phage Therapy. Pharmaceuticals (Basel) 2023; 16:ph16050698. [PMID: 37242481 DOI: 10.3390/ph16050698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
The Streptococcus agalactiae outbreak in tilapia has caused huge losses in the aquaculture industry worldwide. In Malaysia, several studies have reported the isolation of S. agalactiae, but no study has reported the isolation of S. agalactiae phages from tilapia or from the culture pond. Here, the isolation of the S. agalactiae phage from infected tilapia is reported and it is named as vB_Sags-UPM1. Transmission electron micrograph (TEM) revealed that this phage showed characteristics of a Siphoviridae and it was able to kill two local S. agalactiae isolates, which were S. agalactiae smyh01 and smyh02. Whole genome sequencing (WGS) of the phage DNA showed that it contained 42,999 base pairs with 36.80% GC content. Bioinformatics analysis predicted that this phage shared an identity with the S. agalactiae S73 chromosome as well as several other strains of S. agalactiae, presumably due to prophages carried by these hosts, and it encodes integrase, which suggests that it was a temperate phage. The endolysin of vB_Sags-UPM1 termed Lys60 showed killing activity on both S. agalactiae strains with varying efficacy. The discovery of the S. agalactiae temperate phage and its antimicrobial genes could open a new window for the development of antimicrobials to treat S. agalactiae infection.
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Affiliation(s)
- Megat Hamzah Megat Mazhar Khair
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - An Nie Tee
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Nurul Fazlin Wahab
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Siti Sarah Othman
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Yong Meng Goh
- Department of Veterinary Preclinical Sciences, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Mas Jaffri Masarudin
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Nanomaterials Synthesis and Characterisation Laboratory, Institute of Nanoscience and Nanotechnology, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Chou Min Chong
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Lionel Lian Aun In
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur 56000, Selangor, Malaysia
| | - Han Ming Gan
- Patriot Biotech, Sunway Geo Avenue, Bandar Sunway, Subang Jaya 47500, Selangor, Malaysia
| | - Adelene Ai-Lian Song
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
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12
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Shan J, Jia Y, Hickenbotham P, Teulières L, Clokie MRJ. Combining citizen science and molecular diagnostic methods to investigate the prevalence of Borrelia burgdorferi s.l. and Borrelia miyamotoi in tick pools across Great Britain. Front Microbiol 2023; 14:1126498. [PMID: 37180256 PMCID: PMC10169747 DOI: 10.3389/fmicb.2023.1126498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 03/31/2023] [Indexed: 05/16/2023] Open
Abstract
Lyme disease is the most common tick-borne disease and is caused by a group of bacteria known as Borrelia burgdorferi sensu lato (s.l.) complex. Sharing the same genus as B. burgdorferi, Borrelia miyamotoi is a distinct genotype that causes relapsing fever disease. This emerging tick-borne disease is increasingly becoming a concern in public health. To investigate the prevalence of B. burgdorferi s.l. and B. miyamotoi in ticks first, we developed a PCR (Bmer-qPCR) that targets the phage terminase large subunit (terL) gene carried by B. miyamotoi. A similar approach had been used successfully in developing Ter-qPCR for detecting B. burgdorferi s.l. The terL protein functions as an enzyme in packaging phage DNA. Analytical validation of the Bmer-qPCR confirmed its specificity, efficiency and sensitivity. Second, we designed a citizen science-based approach to detect 838 ticks collected from numerous sites across Great Britain. Finally, we applied Bmer-qPCR and Ter-qPCR to 153 tick pools and revealed that the prevalence of B. burgdorferi s.l. and B. miyamotoi was dependent on their geographical locations, i.e. Scotland showed a higher rate of B. burgdorferi s.l. and lower rate of B. miyamotoi carriage as compared to those of the England data. A pattern of diminishing rate of B. miyamotoi carriage from southern England to northern Scotland was visible. Together, the citizen science-based approach provided an estimation of the carriage rate of B. burgdorferi s.l. and B. miyamotoi in tick pools and a potential spreading pattern of B. miyamotoi from the south to the north of Great Britain. Our findings underscore the power of combining citizen science with the molecular diagnostic method to reveal hidden pattern of pathogen-host-environment interplay. Our approach can provide a powerful tool to elucidate the ecology of tick-borne diseases and may offer guidance for pathogen control initiatives. In an era of limited resources, monitoring pathogens requires both field and laboratory support. Citizen science approaches provide a method to empower the public for sample collection. Coupling citizen science approaches with laboratory diagnostic tests can make real-time monitoring of pathogen distribution and prevalence possible.
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Affiliation(s)
- Jinyu Shan
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Ying Jia
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Peter Hickenbotham
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | | | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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13
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Rao VB, Fokine A, Fang Q, Shao Q. Bacteriophage T4 Head: Structure, Assembly, and Genome Packaging. Viruses 2023; 15:527. [PMID: 36851741 PMCID: PMC9958956 DOI: 10.3390/v15020527] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 02/16/2023] Open
Abstract
Bacteriophage (phage) T4 has served as an extraordinary model to elucidate biological structures and mechanisms. Recent discoveries on the T4 head (capsid) structure, portal vertex, and genome packaging add a significant body of new literature to phage biology. Head structures in unexpanded and expanded conformations show dramatic domain movements, structural remodeling, and a ~70% increase in inner volume while creating high-affinity binding sites for the outer decoration proteins Soc and Hoc. Small changes in intercapsomer interactions modulate angles between capsomer planes, leading to profound alterations in head length. The in situ cryo-EM structure of the symmetry-mismatched portal vertex shows the remarkable structural morphing of local regions of the portal protein, allowing similar interactions with the capsid protein in different structural environments. Conformational changes in these interactions trigger the structural remodeling of capsid protein subunits surrounding the portal vertex, which propagate as a wave of expansion throughout the capsid. A second symmetry mismatch is created when a pentameric packaging motor assembles at the outer "clip" domains of the dodecameric portal vertex. The single-molecule dynamics of the packaging machine suggests a continuous burst mechanism in which the motor subunits adjusted to the shape of the DNA fire ATP hydrolysis, generating speeds as high as 2000 bp/s.
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Affiliation(s)
- Venigalla B. Rao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | - Andrei Fokine
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Qianglin Fang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Qianqian Shao
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
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14
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Karaynir A, Salih H, Bozdoğan B, Güçlü Ö, Keskin D. Isolation and characterization of Brochothrix phage ADU4. Virus Res 2022; 321:198902. [PMID: 36064042 DOI: 10.1016/j.virusres.2022.198902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/22/2022] [Accepted: 08/25/2022] [Indexed: 12/24/2022]
Abstract
B. thermosphacta is a psychrotrophic bacterium that often forms the predominant part of the spoilage microflora of aerobically and anaerobically stored meats. Bacteriophages are natural enemies of bacteria and their potential for use in environmentally friendly biocontrol of specific pathogens in food is being intensively studied. In this study, we reported the isolation and characterization of the newly isolated lytic Brochothrix phage ADU4, which is capable of infecting the B. thermosphacta bacterium. For the characterization of Brochothrix phage ADU4; host range, multiplicity of infection values (MOI), phage growth parameters (latent period and burst size), stability at various temperatures and pH, reduction growth of bacteria, effect on biofilm, and molecular characterization were investigated. The spot-test analysis showed positivity with B. thermosphacta strains, while no infection was observed in any other species and genera of bacteria tested. The optimal MOI value of the phage was determined as 0.1. The phage latent period and burst sizes were 40-50 min and 311 PFU/ml per infected host cell, respectively by one-step growth curve analysis. Brochothrix phage ADU4 reduced bacteria immediately after infection, which is shown by optical density (OD) measurement and colony counting (<10 CFU/ml) for 3 days. The degradation of B. thermosphacta in biofilm by Brochothrix phage ADU4 was analyzed and it was found that high titer phage breakdown the existing biofilm and also persistently inhibited biofilm formation. Brochothrix phage ADU4 genome was found to be 127,819 bp, and GC content 41.65%. The genome contains 217 putative open reading frames (ORFs), 4 tRNAs, and additionally, no known virulence and antibiotic resistance genes (AMR) were identified. Brochothrix phage ADU4 showed a high identity (96.09%) to the A9 phage that belongs to the Herelleviridae family. Nevertheless, the assembly module and its around appeared less conserved, and some DNA fragments in Brochothrix phage ADU4 genome were not found in A9 genome and vice versa. A9 contains TnpB, a transposase accessory protein involved in lysogenicity which is absent in Brochothrix phage ADU4. In contrary Brochothrix phage ADU4 had auxiliary metabolic genes (AMG) mostly carried by lytic phages. All these results showed that the Brochothrix phage ADU4 has excellent properties such as strong antibacterial activity, short latent period, high burst size, stability in different conditions, inhibition of biofilms, and absence of virulence and AMR genes. Based on all these features, this newly isolated phage is promising to control B. thermosphacta contamination in meat and meat products, and has the potential to be used alone or in combination with phage cocktails.
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Affiliation(s)
- Abdulkerim Karaynir
- Recombinant DNA and Recombinant Protein Research Center (REDPROM), Aydın Adnan Menderes University, Turkey
| | - Hanife Salih
- Recombinant DNA and Recombinant Protein Research Center (REDPROM), Aydın Adnan Menderes University, Turkey
| | - Bülent Bozdoğan
- Recombinant DNA and Recombinant Protein Research Center (REDPROM), Aydın Adnan Menderes University, Turkey; Medicine Faculty, Department of Medical Microbiology, Aydın Adnan Menderes University, Turkey
| | - Özgür Güçlü
- Recombinant DNA and Recombinant Protein Research Center (REDPROM), Aydın Adnan Menderes University, Turkey; Sultanhisar Vocational School, Aydın Adnan Menderes University, Köşk- AYDIN, Turkey
| | - Dilek Keskin
- Recombinant DNA and Recombinant Protein Research Center (REDPROM), Aydın Adnan Menderes University, Turkey; Köşk Vocational School, Aydın Adnan Menderes University, Köşk- AYDIN, Turkey.
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15
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Lokareddy RK, Hou CFD, Doll SG, Li F, Gillilan RE, Forti F, Horner DS, Briani F, Cingolani G. Terminase Subunits from the Pseudomonas-Phage E217. J Mol Biol 2022; 434:167799. [PMID: 36007626 PMCID: PMC10026623 DOI: 10.1016/j.jmb.2022.167799] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022]
Abstract
Pseudomonas phages are increasingly important biomedicines for phage therapy, but little is known about how these viruses package DNA. This paper explores the terminase subunits from the Myoviridae E217, a Pseudomonas-phage used in an experimental cocktail to eradicate P. aeruginosa in vitro and in animal models. We identified the large (TerL) and small (TerS) terminase subunits in two genes ∼58 kbs away from each other in the E217 genome. TerL presents a classical two-domain architecture, consisting of an N-terminal ATPase and C-terminal nuclease domain arranged into a bean-shaped tertiary structure. A 2.05 Å crystal structure of the C-terminal domain revealed an RNase H-like fold with two magnesium ions in the nuclease active site. Mutations in TerL residues involved in magnesium coordination had a dominant-negative effect on phage growth. However, the two ions identified in the active site were too far from each other to promote two-metal-ion catalysis, suggesting a conformational change is required for nuclease activity. We also determined a 3.38 Å cryo-EM reconstruction of E217 TerS that revealed a ring-like decamer, departing from the most common nonameric quaternary structure observed thus far. E217 TerS contains both N-terminal helix-turn-helix motifs enriched in basic residues and a central channel lined with basic residues large enough to accommodate double-stranded DNA. Overexpression of TerS caused a more than a 4-fold reduction of E217 burst size, suggesting a catalytic amount of the protein is required for packaging. Together, these data expand the molecular repertoire of viral terminase subunits to Pseudomonas-phages used for phage therapy.
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Affiliation(s)
- Ravi K Lokareddy
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Chun-Feng David Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Steven G Doll
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Fenglin Li
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Richard E Gillilan
- Macromolecular Diffraction Facility, Cornell High Energy Synchrotron Source (MacCHESS), Cornell University, 161 Synchrotron Drive, Ithaca, NY 14853, USA
| | - Francesca Forti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - David S Horner
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA.
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16
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Lokareddy RK, Hou CFD, Li F, Yang R, Cingolani G. Viral Small Terminase: A Divergent Structural Framework for a Conserved Biological Function. Viruses 2022; 14:v14102215. [PMID: 36298770 PMCID: PMC9611059 DOI: 10.3390/v14102215] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/07/2022] Open
Abstract
The genome packaging motor of bacteriophages and herpesviruses is built by two terminase subunits, known as large (TerL) and small (TerS), both essential for viral genome packaging. TerL structure, composition, and assembly to an empty capsid, as well as the mechanisms of ATP-dependent DNA packaging, have been studied in depth, shedding light on the chemo-mechanical coupling between ATP hydrolysis and DNA translocation. Instead, significantly less is known about the small terminase subunit, TerS, which is dispensable or even inhibitory in vitro, but essential in vivo. By taking advantage of the recent revolution in cryo-electron microscopy (cryo-EM) and building upon a wealth of crystallographic structures of phage TerSs, in this review, we take an inventory of known TerSs studied to date. Our analysis suggests that TerS evolved and diversified into a flexible molecular framework that can conserve biological function with minimal sequence and quaternary structure conservation to fit different packaging strategies and environmental conditions.
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17
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A viral genome packaging ring-ATPase is a flexibly coordinated pentamer. Nat Commun 2021; 12:6548. [PMID: 34772936 PMCID: PMC8589836 DOI: 10.1038/s41467-021-26800-z] [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: 04/02/2021] [Accepted: 10/21/2021] [Indexed: 01/13/2023] Open
Abstract
Multi-subunit ring-ATPases carry out a myriad of biological functions, including genome packaging in viruses. Though the basic structures and functions of these motors have been well-established, the mechanisms of ATPase firing and motor coordination are poorly understood. Here, using single-molecule fluorescence, we determine that the active bacteriophage T4 DNA packaging motor consists of five subunits of gp17. By systematically doping motors with an ATPase-defective subunit and selecting single motors containing a precise number of active or inactive subunits, we find that the packaging motor can tolerate an inactive subunit. However, motors containing one or more inactive subunits exhibit fewer DNA engagements, a higher failure rate in encapsidation, reduced packaging velocity, and increased pausing. These findings suggest a DNA packaging model in which the motor, by re-adjusting its grip on DNA, can skip an inactive subunit and resume DNA translocation, suggesting that strict coordination amongst motor subunits of packaging motors is not crucial for function.
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18
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Abstract
Although the process of genome encapsidation is highly conserved in tailed bacteriophages and eukaryotic double-stranded DNA viruses, there are two distinct packaging pathways that these viruses use to catalyze ATP-driven translocation of the viral genome into a preassembled procapsid shell. One pathway is used by ϕ29-like phages and adenoviruses, which replicate and subsequently package a monomeric, unit-length genome covalently attached to a virus/phage-encoded protein at each 5'-end of the dsDNA genome. In a second, more ubiquitous packaging pathway characterized by phage lambda and the herpesviruses, the viral DNA is replicated as multigenome concatemers linked in a head-to-tail fashion. Genome packaging in these viruses thus requires excision of individual genomes from the concatemer that are then translocated into a preassembled procapsid. Hence, the ATPases that power packaging in these viruses also possess nuclease activities that cut the genome from the concatemer at the beginning and end of packaging. This review focuses on proposed mechanisms of genome packaging in the dsDNA viruses using unit-length ϕ29 and concatemeric λ genome packaging motors as representative model systems.
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Affiliation(s)
- Carlos E Catalano
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, CO, United States.
| | - Marc C Morais
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, TX, United States
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19
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Wangchuk J, Chatterjee A, Patil S, Madugula SK, Kondabagil K. The coevolution of large and small terminases of bacteriophages is a result of purifying selection leading to phenotypic stabilization. Virology 2021; 564:13-25. [PMID: 34598064 DOI: 10.1016/j.virol.2021.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
Genome packaging in many dsDNA phages requires a series of precisely coordinated actions of two phage-coded proteins, namely, large terminase (TerL) and small terminase (TerS) with DNA and ATP, and with each other. Despite the strict functional conservation, TerL and TerS homologs exhibit large sequence variations. We investigated the sequence variability across eight phage types and observed a coevolutionary framework wherein the genealogy of TerL homologs mirrored that of the corresponding TerS homologs. Furthermore, a high purifying selection observed (dN/dS«1) indicated strong structural constraints on both TerL and TerS, and identify coevolving residues in TerL and TerS of phage T4 and lambda. Using the highly coevolving (correlation coefficient of 0.99) TerL and TerS of phage N4, we show that their biochemical features are similar to the phylogenetically divergent phage λ terminases. We also demonstrate using the Surface Plasma Resonance (SPR) technique that phage N4 TerL transiently interacts with TerS.
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Affiliation(s)
- Jigme Wangchuk
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Anirvan Chatterjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Supriya Patil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Santhosh Kumar Madugula
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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20
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Yang M, Xia Q, Du S, Zhang Z, Qin F, Zhao Y. Genomic Characterization and Distribution Pattern of a Novel Marine OM43 Phage. Front Microbiol 2021; 12:651326. [PMID: 33841378 PMCID: PMC8024684 DOI: 10.3389/fmicb.2021.651326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/04/2021] [Indexed: 11/21/2022] Open
Abstract
Bacteriophages have a significant impact on the structure and function of marine microbial communities. Phages of some major bacterial lineages have recently been shown to dominate the marine viral communities. However, phages that infect many important bacterial clades still remained unexplored. Members of the marine OM43 clade are methylotrophs that play important roles in C1 metabolism. OM43 phages (phages that infect the OM43 bacteria) represent an understudied viral group with only one known isolate. In this study, we describe the genomic characterization and biogeography of an OM43 phage that infects the strain HTCC2181, designated MEP301. MEP301 has a genome size of 34,774 bp. We found that MEP301 is genetically distinct from other known phage isolates and only displays significant sequence similarity with some metagenomic viral genomes (MVGs). A total of 12 MEP301-type MVGs were identified from metagenomic datasets. Comparative genomic and phylogenetic analyses revealed that MEP301-type phages can be separated into two subgroups (subgroup I and subgroup II). We also performed a metagenomic recruitment analysis to determine the relative abundance of reads mapped to these MEP301-type phages, which suggested that subgroup I MEP301-type phages are present predominantly in the cold upper waters with lower salinity. Notably, subgroup II phages have an inverse different distribution pattern, implying that they may infect hosts from a distinct OM43 subcluster. Our study has expanded the knowledge about the genomic diversity of marine OM43 phages and identified a new phage group that is widespread in the ocean.
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Affiliation(s)
- Mingyu Yang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qian Xia
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sen Du
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zefeng Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fang Qin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanlin Zhao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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21
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Shan J, Jia Y, Teulières L, Patel F, Clokie MRJ. Targeting Multicopy Prophage Genes for the Increased Detection of Borrelia burgdorferi Sensu Lato (s.l.), the Causative Agents of Lyme Disease, in Blood. Front Microbiol 2021; 12:651217. [PMID: 33790883 PMCID: PMC8005754 DOI: 10.3389/fmicb.2021.651217] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/16/2021] [Indexed: 11/20/2022] Open
Abstract
The successful treatment of Lyme disease (LD) is contingent on accurate diagnosis. However, current laboratory detection assays lack sensitivity in the early stages of the disease. Because delayed diagnosis of LD incurs high healthcare costs and great suffering, new highly sensitive tests are in need. To overcome these challenges, we developed an internally controlled quantitative PCR (Ter-qPCR) that targets the multicopy terminase large subunit (terL) gene encoded by prophages that are only found in LD-causing bacteria. The terL protein helps phages pack their DNA. Strikingly, the detection limit of the Ter-qPCR was analytically estimated to be 22 copies and one bacterial cell in bacteria spiked blood. Furthermore, significant quantitative differences was observed in terms of the amount of terL detected in healthy individuals and patients with either early or late disease. Together, the data suggests that the prophage-targeting PCR has significant power to improve success detection for LD. After rigorous clinical validation, this new test could deliver a step-change in the detection of LD. Prophage encoded markers are prevalent in many other pathogenic bacteria rendering this approach highly applicable to bacterial identification in general.
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Affiliation(s)
- Jinyu Shan
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Ying Jia
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Louis Teulières
- PhelixRD Charity 230 Rue du Faubourg St Honoré, Paris, France
| | - Faizal Patel
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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22
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Niazi M, Florio TJ, Yang R, Lokareddy RK, Swanson NA, Gillilan RE, Cingolani G. Biophysical analysis of Pseudomonas-phage PaP3 small terminase suggests a mechanism for sequence-specific DNA-binding by lateral interdigitation. Nucleic Acids Res 2020; 48:11721-11736. [PMID: 33125059 PMCID: PMC7672466 DOI: 10.1093/nar/gkaa866] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 09/19/2020] [Accepted: 10/21/2020] [Indexed: 12/17/2022] Open
Abstract
The genome packaging motor of tailed bacteriophages and herpesviruses is a powerful nanomachine built by several copies of a large (TerL) and a small (TerS) terminase subunit. The motor assembles transiently at the portal vertex of an empty precursor capsid (or procapsid) to power genome encapsidation. Terminase subunits have been studied in-depth, especially in classical bacteriophages that infect Escherichia coli or Salmonella, yet, less is known about the packaging motor of Pseudomonas-phages that have increasing biomedical relevance. Here, we investigated the small terminase subunit from three Podoviridae phages that infect Pseudomonas aeruginosa. We found TerS is polymorphic in solution but assembles into a nonamer in its high-affinity heparin-binding conformation. The atomic structure of Pseudomonas phage PaP3 TerS, the first complete structure for a TerS from a cos phage, reveals nine helix-turn-helix (HTH) motifs asymmetrically arranged around a β-stranded channel, too narrow to accommodate DNA. PaP3 TerS binds DNA in a sequence-specific manner in vitro. X-ray scattering and molecular modeling suggest TerS adopts an open conformation in solution, characterized by dynamic HTHs that move around an oligomerization core, generating discrete binding crevices for DNA. We propose a model for sequence-specific recognition of packaging initiation sites by lateral interdigitation of DNA.
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Affiliation(s)
- Marzia Niazi
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Tyler J Florio
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Ruoyu Yang
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Ravi K Lokareddy
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Nicholas A Swanson
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Richard E Gillilan
- Macromolecular Diffraction Facility, Cornell High Energy Synchrotron Source (MacCHESS), Cornell University, 161 Synchrotron Drive, Ithaca, NY 14853, USA
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
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23
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Thiroux S, Dupont S, Nesbø CL, Bienvenu N, Krupovic M, L'Haridon S, Marie D, Forterre P, Godfroy A, Geslin C. The first head-tailed virus, MFTV1, infecting hyperthermophilic methanogenic deep-sea archaea. Environ Microbiol 2020; 23:3614-3626. [PMID: 33022088 DOI: 10.1111/1462-2920.15271] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/20/2020] [Accepted: 10/03/2020] [Indexed: 11/27/2022]
Abstract
Deep-sea hydrothermal vents are inhabited by complex communities of microbes and their viruses. Despite the importance of viruses in controlling the diversity, adaptation and evolution of their microbial hosts, to date, only eight bacterial and two archaeal viruses isolated from abyssal ecosystems have been described. Thus, our efforts focused on gaining new insights into viruses associated with deep-sea autotrophic archaea. Here, we provide the first evidence of an infection of hyperthermophilic methanogenic archaea by a head-tailed virus, Methanocaldococcus fervens tailed virus 1 (MFTV1). MFTV1 has an isometric head of 50 nm in diameter and a 150 nm-long non-contractile tail. Virions are released continuously without causing a sudden drop in host growth. MFTV1 infects Methanocaldococcus species and is the first hyperthermophilic head-tailed virus described thus far. The viral genome is a double-stranded linear DNA of 31 kb. Interestingly, our results suggest potential strategies adopted by the plasmid pMEFER01, carried by M. fervens, to spread horizontally in hyperthermophilic methanogens. The data presented here open a new window of understanding on how the abyssal mobilome interacts with hyperthermophilic marine archaea.
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Affiliation(s)
- Sarah Thiroux
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| | - Samuel Dupont
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| | - Camilla L Nesbø
- Biozone, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G2R3, 12, Canada
| | - Nadège Bienvenu
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, 75015, France
| | - Stéphane L'Haridon
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| | - Dominique Marie
- UPMC Univ Paris 06, INSU-CNRS, UMR 7144, Station Biologique de Roscoff, Sorbonne University, Roscoff, 29680, France
| | - Patrick Forterre
- Archaeal Virology Unit, Institut Pasteur, Paris, 75015, France.,Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS., Gif-sur-Yvette, 91198, France
| | - Anne Godfroy
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| | - Claire Geslin
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
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24
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Lu H, Yan P, Xiong W, Wang J, Liu X. Genomic characterization of a novel virulent phage infecting Shigella fiexneri and isolated from sewage. Virus Res 2020; 283:197983. [PMID: 32325115 DOI: 10.1016/j.virusres.2020.197983] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/15/2020] [Accepted: 04/15/2020] [Indexed: 11/24/2022]
Abstract
Shigella fiexneri phage SGF2 is a novel lytic phage isolated from a sewage sample. Morphological characterization indicates that phage SGF2 is a member of the Podoviridae family, producing virions with an isometric head (82.6 ± 8 nm diameter) and a short non-contractile tail (length 52 ± 8 nm). This phage specifically infected the Shigella fiexneri. One-step growth curves indicated that the burst period of phage SGF2 is 30 min, with an approximate burst size of 38. The full-length genome was sequenced and potential virulence genes were detected. We will discuss the potential application of phage SGF2 in phage therapy.
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Affiliation(s)
- Han Lu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Peihan Yan
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Wenbin Xiong
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Jingwei Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Xinchun Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 101408, China.
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25
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Hayes JA, Hilbert BJ, Gaubitz C, Stone NP, Kelch BA. A thermophilic phage uses a small terminase protein with a fixed helix-turn-helix geometry. J Biol Chem 2020; 295:3783-3793. [PMID: 32014998 DOI: 10.1074/jbc.ra119.012224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/30/2020] [Indexed: 11/06/2022] Open
Abstract
Tailed bacteriophages use a DNA-packaging motor to encapsulate their genome during viral particle assembly. The small terminase (TerS) component of this DNA-packaging machinery acts as a molecular matchmaker that recognizes both the viral genome and the main motor component, the large terminase (TerL). However, how TerS binds DNA and the TerL protein remains unclear. Here we identified gp83 of the thermophilic bacteriophage P74-26 as the TerS protein. We found that TerSP76-26 oligomerizes into a nonamer that binds DNA, stimulates TerL ATPase activity, and inhibits TerL nuclease activity. A cryo-EM structure of TerSP76-26 revealed that it forms a ring with a wide central pore and radially arrayed helix-turn-helix domains. The structure further showed that these helix-turn-helix domains, which are thought to bind DNA by wrapping the double helix around the ring, are rigidly held in an orientation distinct from that seen in other TerS proteins. This rigid arrangement of the putative DNA-binding domain imposed strong constraints on how TerSP76-26 can bind DNA. Finally, the TerSP76-26 structure lacked the conserved C-terminal β-barrel domain used by other TerS proteins for binding TerL. This suggests that a well-ordered C-terminal β-barrel domain is not required for TerSP76-26 to carry out its matchmaking function. Our work highlights a thermophilic system for studying the role of small terminase proteins in viral maturation and presents the structure of TerSP76-26, revealing key differences between this thermophilic phage and its mesophilic counterparts.
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Affiliation(s)
- Janelle A Hayes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Brendan J Hilbert
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Christl Gaubitz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Nicholas P Stone
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Brian A Kelch
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655
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26
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Identification of the First Gene Transfer Agent (GTA) Small Terminase in Rhodobacter capsulatus and Its Role in GTA Production and Packaging of DNA. J Virol 2019; 93:JVI.01328-19. [PMID: 31534034 PMCID: PMC6854486 DOI: 10.1128/jvi.01328-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/10/2019] [Indexed: 12/17/2022] Open
Abstract
Genetic exchange mediated by viruses of bacteria (bacteriophages) is the primary driver of rapid bacterial evolution. The priority of viruses is usually to propagate themselves. Most bacteriophages use the small terminase protein to identify their own genome and direct its inclusion into phage capsids. Gene transfer agents (GTAs) are descended from bacteriophages, but they instead package fragments of the entire bacterial genome without preference for their own genes. GTAs do not selectively target specific DNA, and no GTA small terminases are known. Here, we identified the small terminase from the model Rhodobacter capsulatus GTA, which then allowed prediction of analogues in other species. We examined the role of the small terminase in GTA production and propose a structural basis for random DNA packaging.IMPORTANCE Random transfer of any and all genes between bacteria could be influential in the spread of virulence or antimicrobial resistance genes. Discovery of the true prevalence of GTAs in sequenced genomes is hampered by their apparent similarity to bacteriophages. Our data allowed the prediction of small terminases in diverse GTA producer species, and defining the characteristics of a "GTA-type" terminase could be an important step toward novel GTA identification. Importantly, the GTA small terminase shares many features with its phage counterpart. We propose that the GTA terminase complex could become a streamlined model system to answer fundamental questions about double-stranded DNA (dsDNA) packaging by viruses that have not been forthcoming to date.
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27
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Identification of Novel Bacteriophages with Therapeutic Potential That Target Enterococcus faecalis. Infect Immun 2019; 87:IAI.00512-19. [PMID: 31451618 PMCID: PMC6803325 DOI: 10.1128/iai.00512-19] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/13/2019] [Indexed: 12/14/2022] Open
Abstract
The Gram-positive opportunistic pathogen Enterococcus faecalis is frequently responsible for nosocomial infections in humans and represents one of the most common bacteria isolated from recalcitrant endodontic (root canal) infections. E. faecalis is intrinsically resistant to several antibiotics routinely used in clinical settings (such as cephalosporins and aminoglycosides) and can acquire resistance to vancomycin (vancomycin-resistant enterococci). The resistance of E. faecalis to several classes of antibiotics and its capacity to form biofilms cause serious therapeutic problems. Here, we report the isolation of several bacteriophages that target E. faecalis strains isolated from the oral cavity of patients suffering root canal infections. All phages isolated were Siphoviridae with similar tail lengths (200 to 250 nm) and icosahedral heads. The genome sequences of three isolated phages were highly conserved with the exception of predicted tail protein genes that diverge in sequence, potentially reflecting the host range. The properties of the phage with the broadest host range (SHEF2) were further characterized. We show that this phage requires interaction with components of the major and variant region enterococcal polysaccharide antigen to engage in lytic infection. Finally, we explored the therapeutic potential of this phage and show that it can eradicate E. faecalis biofilms formed in vitro on a standard polystyrene surface but also on a cross-sectional tooth slice model of endodontic infection. We also show that SHEF2 cleared a lethal infection of zebrafish when applied in the circulation. We therefore propose that the phage described here could be used to treat a broad range of antibiotic-resistant E. faecalis infections.
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28
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Dixit AB, Ray K, Black LW. A viral small terminase subunit (TerS) twin ring pac synapsis DNA packaging model is supported by fluorescent fusion proteins. Virology 2019; 536:39-48. [PMID: 31400548 PMCID: PMC6760839 DOI: 10.1016/j.virol.2019.07.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 11/23/2022]
Abstract
A bacteriophage T4 DNA "synapsis model" proposes that the bacteriophage T4 terminase small subunit (TerS) apposes two pac site containing dsDNA homologs to gauge concatemer maturation adequate for packaging initiation. N-terminus, C-terminus, or both ends modified fusion Ter S proteins retain function. Replacements of the TerS gene in the T4 genome with fusion genes encoding larger (18-45 kDa) TerS-eGFP and TerS-mCherry fluorescent fusion proteins function without significant change in phenotype. Co-infection and co-expression by T4 phages encoding TerS-eGFP and TerS-mCherry shows in vivo FRET in infected bacteria comparable to that of the purified, denatured and then renatured, mixed fusion proteins in vitro. FRET of purified, denatured-renatured, mixed temperature sensitive and native TerS fusion proteins at low and high temperature in vitro shows that TerS ring-like oligomer formation is essential for function in vivo. Super-resolution STORM and PALM microscopy of intercalating dye YOYO-1 DNA and photoactivatable TerS-PAmCherry-C1 fusions support accumulation of TerS dimeric or multiple ring-like oligomer structures containing DNA and gp16-mCherry in vivo as well as in vitro to regulate pac site cutting.
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Affiliation(s)
- Aparna Banerjee Dixit
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Krishanu Ray
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA; Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Lindsay W Black
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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29
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Wang J, Zhao F, Sun H, Wang Q, Zhang C, Liu W, Zou L, Pan Q, Ren H. Isolation and characterization of the Staphylococcus aureus bacteriophage vB_SauS_SA2. AIMS Microbiol 2019; 5:285-307. [PMID: 31663062 PMCID: PMC6787349 DOI: 10.3934/microbiol.2019.3.285] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 09/25/2019] [Indexed: 12/28/2022] Open
Abstract
A novel bacteriophage vB_SauS_SA2 (hereafter designated SA2) that infects Staphylococcus aureus was isolated. At a multiplicity of infection (MOI) of 0.1, phage SA2 had a latent period of about 10 min with a burst size of 293 PFUs/infected cell (PFU, plaque forming unit). Phage SA2 had a double-stranded DNA genome with a length of 89,055 bp and a G + C content of 31.9%. The genome contained 130 open reading frames (ORFs), 28 of which had assigned functions, and 18 were unique. One tRNA gene (tRNAAsn ) was discovered, and no virulence genes were identified. Its genome showed very low similarity with phage genomes deposited in public databases (75% nucleotide identity and 7% query coverage). The unique characteristics of phage SA2 led to the proposal of a new Siphoviridae genus named 'SA2likevirus'.
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Affiliation(s)
- Jia Wang
- Qingdao Agricultural University, College of Veterinary Medicine, Shandong 266109, China
| | - Feiyang Zhao
- Qingdao Agricultural University, College of Veterinary Medicine, Shandong 266109, China
| | - Huzhi Sun
- Qingdao Phagepharm Bio-tech Co, Ltd, Shandong 266109, China
| | - Qian Wang
- Qingdao Agricultural University, College of Veterinary Medicine, Shandong 266109, China
| | - Can Zhang
- Qingdao Agricultural University, College of Veterinary Medicine, Shandong 266109, China
| | - Wenhua Liu
- Qingdao Agricultural University, College of Veterinary Medicine, Shandong 266109, China
| | - Ling Zou
- Qingdao Agricultural University, College of Veterinary Medicine, Shandong 266109, China
| | - Qiang Pan
- Qingdao Phagepharm Bio-tech Co, Ltd, Shandong 266109, China
| | - Huiying Ren
- Qingdao Agricultural University, College of Veterinary Medicine, Shandong 266109, China
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30
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Weiditch SA, Seraphim TV, Houry WA, Kanelis V. Strategies for purification of the bacteriophage HK97 small and large terminase subunits that yield pure and homogeneous samples that are functional. Protein Expr Purif 2019; 160:45-55. [DOI: 10.1016/j.pep.2019.03.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/30/2019] [Accepted: 03/30/2019] [Indexed: 02/06/2023]
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31
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Genomic and biological characterization of the Vibrio alginolyticus-infecting “Podoviridae” bacteriophage, vB_ValP_IME271. Virus Genes 2019; 55:218-226. [DOI: 10.1007/s11262-018-1622-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 12/03/2018] [Indexed: 10/27/2022]
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32
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da Silva Duarte V, Giaretta S, Campanaro S, Treu L, Armani A, Tarrah A, Oliveira de Paula S, Giacomini A, Corich V. A Cryptic Non-Inducible Prophage Confers Phage-Immunity on the Streptococcus thermophilus M17PTZA496. Viruses 2018; 11:v11010007. [PMID: 30583530 PMCID: PMC6356513 DOI: 10.3390/v11010007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/14/2018] [Accepted: 12/19/2018] [Indexed: 12/26/2022] Open
Abstract
Streptococcus thermophilus is considered one of the most important species for the dairy industry. Due to their diffusion in dairy environments, bacteriophages can represent a threat to this widely used bacterial species. Despite the presence of a CRISPR-Cas system in the S. thermophilus genome, some lysogenic strains harbor cryptic prophages that can increase the phage-host resistance defense. This characteristic was identified in the dairy strain S. thermophilus M17PTZA496, which contains two integrated prophages 51.8 and 28.3 Kb long, respectively. In the present study, defense mechanisms, such as a lipoprotein-encoding gene and Siphovirus Gp157, the last associated to the presence of a noncoding viral DNA element, were identified in the prophage M17PTZA496 genome. The ability to overexpress genes involved in these defense mechanisms under specific stressful conditions, such as phage attack, has been demonstrated. Despite the addition of increasing amounts of Mitomycin C, M17PTZA496 was found to be non-inducible. However, the transcriptional activity of the phage terminase large subunit was detected in the presence of the antagonist phage vB_SthS-VA460 and of Mitomycin C. The discovery of an additional immune mechanism, associated with bacteriophage-insensitive strains, is of utmost importance, for technological applications and industrial processes. To our knowledge, this is the first study reporting the capability of a prophage integrated into the S. thermophilus genome expressing different phage defense mechanisms. Bacteriophages are widespread entities that constantly threaten starter cultures in the dairy industry. In cheese and yogurt manufacturing, the lysis of Streptococcus thermophilus cultures by viral attacks can lead to huge economic losses. Nowadays S. thermophilus is considered a well-stablished model organism for the study of natural adaptive immunity (CRISPR-Cas) against phage and plasmids, however, the identification of novel bacteriophage-resistance mechanisms, in this species, is strongly desirable. Here, we demonstrated that the presence of a non-inducible prophage confers phage-immunity to an S. thermophilus strain, by the presence of ltp and a viral noncoding region. S. thermophilus M17PTZA496 arises as an unconventional model to study phage resistance and potentially represents an alternative starter strain for dairy productions.
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Affiliation(s)
- Vinícius da Silva Duarte
- Department of Microbiology, Universidade Federal de Viçosa, Av. Peter Henry Rolfs, s/n, Campus Universitário, Viçosa-MG 36570-900, Brazil.
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
| | - Sabrina Giaretta
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
| | | | - Laura Treu
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
- Department of Biology, University of Padova, 35121 Padova, Italy.
| | - Andrea Armani
- Venetian Institute of Molecular Medicine, 35129 Padova, Italy.
| | - Armin Tarrah
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
| | | | - Alessio Giacomini
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
| | - Viviana Corich
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
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33
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Hydroxypyridonecarboxylic Acids as Inhibitors of Human Cytomegalovirus pUL89 Endonuclease. ChemMedChem 2018; 13:1658-1663. [DOI: 10.1002/cmdc.201800283] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/22/2018] [Indexed: 11/07/2022]
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34
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Zhang H, Yang Z, Zhou Y, Bao H, Wang R, Li T, Pang M, Sun L, Zhou X. Application of a phage in decontaminating Vibrio parahaemolyticus in oysters. Int J Food Microbiol 2018; 275:24-31. [DOI: 10.1016/j.ijfoodmicro.2018.03.027] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/24/2018] [Accepted: 03/26/2018] [Indexed: 11/25/2022]
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35
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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.
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36
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Neuber S, Wagner K, Messerle M, Borst EM. The C-terminal part of the human cytomegalovirus terminase subunit pUL51 is central for terminase complex assembly. J Gen Virol 2018; 99:119-134. [DOI: 10.1099/jgv.0.000984] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Sebastian Neuber
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Karen Wagner
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Martin Messerle
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Eva Maria Borst
- Institute of Virology, Hannover Medical School, Hannover, Germany
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37
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Lin S, Alam TI, Kottadiel VI, VanGessel CJ, Tang WC, Chemla YR, Rao VB. Altering the speed of a DNA packaging motor from bacteriophage T4. Nucleic Acids Res 2017; 45:11437-11448. [PMID: 28981683 PMCID: PMC5737356 DOI: 10.1093/nar/gkx809] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/31/2017] [Indexed: 11/14/2022] Open
Abstract
The speed at which a molecular motor operates is critically important for the survival of a virus or an organism but very little is known about the underlying mechanisms. Tailed bacteriophage T4 employs one of the fastest and most powerful packaging motors, a pentamer of gp17 that translocates DNA at a rate of up to ∼2000-bp/s. We hypothesize, guided by structural and genetic analyses, that a unique hydrophobic environment in the catalytic space of gp17-adenosine triphosphatase (ATPase) determines the rate at which the 'lytic water' molecule is activated and OH- nucleophile is generated, in turn determining the speed of the motor. We tested this hypothesis by identifying two hydrophobic amino acids, M195 and F259, in the catalytic space of gp17-ATPase that are in a position to modulate motor speed. Combinatorial mutagenesis demonstrated that hydrophobic substitutions were tolerated but polar or charged substitutions resulted in null or cold-sensitive/small-plaque phenotypes. Quantitative biochemical and single-molecule analyses showed that the mutant motors exhibited 1.8- to 2.5-fold lower rate of ATP hydrolysis, 2.5- to 4.5-fold lower DNA packaging velocity, and required an activator protein, gp16 for rapid firing of ATPases. These studies uncover a speed control mechanism that might allow selection of motors with optimal performance for organisms' survival.
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Affiliation(s)
- Siying Lin
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Tanfis I Alam
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Vishal I Kottadiel
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Carl J VanGessel
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Wei-Chun Tang
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Yann R Chemla
- Department of Physics, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Venigalla B Rao
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
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Chand S, Messina EL, AlSalmi W, Ananthaswamy N, Gao G, Uritskiy G, Padilla-Sanchez V, Mahalingam M, Peachman KK, Robb ML, Rao M, Rao VB. Glycosylation and oligomeric state of envelope protein might influence HIV-1 virion capture by α4β7 integrin. Virology 2017; 508:199-212. [PMID: 28577856 PMCID: PMC5526109 DOI: 10.1016/j.virol.2017.05.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 05/22/2017] [Indexed: 10/19/2022]
Abstract
The α4ß7 integrin present on host cells recognizes the V1V2 domain of the HIV-1 envelope protein. This interaction might be involved in virus transmission. Administration of α4ß7-specific antibodies inhibit acquisition of SIV in a macaque challenge model. But the molecular details of V1V2: α4ß7 interaction are unknown and its importance in HIV-1 infection remains controversial. Our biochemical and mutational analyses show that glycosylation is a key modulator of V1V2 conformation and binding to α4ß7. Partially glycosylated, but not fully glycosylated, envelope proteins are preferred substrates for α4ß7 binding. Surprisingly, monomers of the envelope protein bound strongly to α4ß7 whereas trimers bound poorly. Our results suggest that a conformationally flexible V1V2 domain allows binding of the HIV-1 virion to the α4ß7 integrin, which might impart selectivity for the poorly glycosylated HIV-1 envelope containing monomers to be more efficiently captured by α4ß7 integrin present on mucosal cells at the time of HIV-1 transmission.
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Affiliation(s)
- Subhash Chand
- Department of Biology, The Catholic University of America, Washington DC 20064
| | - Emily L Messina
- Department of Biology, The Catholic University of America, Washington DC 20064
| | - Wadad AlSalmi
- Department of Biology, The Catholic University of America, Washington DC 20064
| | - Neeti Ananthaswamy
- Department of Biology, The Catholic University of America, Washington DC 20064
| | - Guofen Gao
- Department of Biology, The Catholic University of America, Washington DC 20064
| | - Gherman Uritskiy
- Department of Biology, The Catholic University of America, Washington DC 20064
| | | | | | - Kristina K Peachman
- Henry M Jackson Foundation for the Advancement of Military Medicine, Silver Spring, MD 20910; US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Merlin L Robb
- Henry M Jackson Foundation for the Advancement of Military Medicine, Silver Spring, MD 20910; US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Mangala Rao
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Venigalla B Rao
- Department of Biology, The Catholic University of America, Washington DC 20064.
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Hilbert BJ, Hayes JA, Stone NP, Xu RG, Kelch BA. The large terminase DNA packaging motor grips DNA with its ATPase domain for cleavage by the flexible nuclease domain. Nucleic Acids Res 2017; 45:3591-3605. [PMID: 28082398 PMCID: PMC5389665 DOI: 10.1093/nar/gkw1356] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/05/2017] [Indexed: 01/07/2023] Open
Abstract
Many viruses use a powerful terminase motor to pump their genome inside an empty procapsid shell during virus maturation. The large terminase (TerL) protein contains both enzymatic activities necessary for packaging in such viruses: the adenosine triphosphatase (ATPase) that powers DNA translocation and an endonuclease that cleaves the concatemeric genome at both initiation and completion of genome packaging. However, how TerL binds DNA during translocation and cleavage remains mysterious. Here we investigate DNA binding and cleavage using TerL from the thermophilic phage P74-26. We report the structure of the P74-26 TerL nuclease domain, which allows us to model DNA binding in the nuclease active site. We screened a large panel of TerL variants for defects in binding and DNA cleavage, revealing that the ATPase domain is the primary site for DNA binding, and is required for nuclease activity. The nuclease domain is dispensable for DNA binding but residues lining the active site guide DNA for cleavage. Kinetic analysis of DNA cleavage suggests flexible tethering of the nuclease domains during DNA cleavage. We propose that interactions with the procapsid during DNA translocation conformationally restrict the nuclease domain, inhibiting cleavage; TerL release from the capsid upon completion of packaging unlocks the nuclease domains to cleave DNA.
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Affiliation(s)
- Brendan J. Hilbert
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Janelle A. Hayes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nicholas P. Stone
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Rui-Gang Xu
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Brian A. Kelch
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA,To whom correspondence should be addressed. Tel: +1 508 856 8322; Fax: +1 508 856 6464;
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Inhibition of Human Cytomegalovirus pUL89 Terminase Subunit Blocks Virus Replication and Genome Cleavage. J Virol 2017; 91:JVI.02152-16. [PMID: 27881652 DOI: 10.1128/jvi.02152-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 11/11/2016] [Indexed: 01/09/2023] Open
Abstract
The human cytomegalovirus terminase complex cleaves concatemeric genomic DNA into unit lengths during genome packaging and particle assembly. This process is an attractive drug target because cleavage of concatemeric DNA is not required in mammalian cell DNA replication, indicating that drugs targeting the terminase complex could be safe and selective. One component of the human cytomegalovirus terminase complex, pUL89, provides the endonucleolytic activity for genome cleavage, and the domain responsible is reported to have an RNase H-like fold. We hypothesize that the pUL89 endonuclease activity is inhibited by known RNase H inhibitors. Using a novel enzyme-linked immunosorbent assay (ELISA) format as a screening assay, we found that a hydroxypyridonecarboxylic acid compound, previously reported to be an inhibitor of human immunodeficiency virus RNase H, inhibited pUL89 endonuclease activity at low-micromolar concentrations. Further characterization revealed that this pUL89 endonuclease inhibitor blocked human cytomegalovirus replication at a relatively late time point, similarly to other reported terminase complex inhibitors. Importantly, this inhibitor also prevented the cleavage of viral genomic DNA in infected cells. Taken together, these results substantiate our pharmacophore hypothesis and validate our ligand-based approach toward identifying novel inhibitors of pUL89 endonuclease. IMPORTANCE Human cytomegalovirus infection in individuals lacking a fully functioning immune system, such as newborns and transplant patients, can have severe and debilitating consequences. The U.S. Food and Drug Administration-approved anti-human cytomegalovirus drugs mainly target the viral polymerase, and resistance to these drugs has appeared. Therefore, anti-human cytomegalovirus drugs from novel targets are needed for use instead of, or in combination with, current polymerase inhibitors. pUL89 is a viral ATPase and endonuclease and is an attractive target for anti-human cytomegalovirus drug development. We identified and characterized an inhibitor of pUL89 endonuclease activity that also inhibits human cytomegalovirus replication in cell culture. pUL89 endonuclease, therefore, should be explored as a potential target for antiviral development against human cytomegalovirus.
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Djacem K, Tavares P, Oliveira L. Bacteriophage SPP1 pac Cleavage: A Precise Cut without Sequence Specificity Requirement. J Mol Biol 2017; 429:1381-1395. [PMID: 28082080 DOI: 10.1016/j.jmb.2017.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 12/23/2016] [Accepted: 01/05/2017] [Indexed: 01/23/2023]
Abstract
In many tailed bacteriophages, DNA packaging is initiated by recognition and cleavage of a specific sequence pac by the small (TerS) and large (TerL) terminase subunits. It was previously shown that the SPP1 pac region has two sequences where TerS binds (pacR and pacL), flanking the segment where TerL cleaves the SPP1 DNA (pacC). However, the pac-specific sequences required to achieve this endonucleolytic cut were not established. Their characterization is essential to understand the underlying mechanism. We show that the pacR sequence localized within 35bp downstream of the pac cut can be extensively degenerated, including its c1 and c2 repeats, and that only a disruption of a 5-bp polyadenine tract impairs the pac cleavage. This result together with deletion analysis of pacL shows that the specific DNA sequences required for targeting the terminase for pac cleavage are considerably shorter than the large region bound by TerS. Furthermore, extensive degeneration of the 6-bp target sequence within pacC where pac cleavage occurs reveals that TerL maintains, remarkably, its precise position of cleavage. Studies with SPP1-related phages show the conservation of the cut position, irrespective of the sequence variation in pacC and in pacR or the changes in pacL-pacC distance. Mechanistically, our data are compatible with a model in which TerS interactions with part of the pacL sequence and a poly-A tract in pacR are sufficient to orient very accurately the TerL nuclease to a defined pacC position. They also demonstrate that the resulting precise cut at pacC is independent of the targeted DNA sequence.
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Affiliation(s)
- Karima Djacem
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Paulo Tavares
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France.
| | - Leonor Oliveira
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France.
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42
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Ahi YS, Mittal SK. Components of Adenovirus Genome Packaging. Front Microbiol 2016; 7:1503. [PMID: 27721809 PMCID: PMC5033970 DOI: 10.3389/fmicb.2016.01503] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/08/2016] [Indexed: 12/29/2022] Open
Abstract
Adenoviruses (AdVs) are icosahedral viruses with double-stranded DNA (dsDNA) genomes. Genome packaging in AdV is thought to be similar to that seen in dsDNA containing icosahedral bacteriophages and herpesviruses. Specific recognition of the AdV genome is mediated by a packaging domain located close to the left end of the viral genome and is mediated by the viral packaging machinery. Our understanding of the role of various components of the viral packaging machinery in AdV genome packaging has greatly advanced in recent years. Characterization of empty capsids assembled in the absence of one or more components involved in packaging, identification of the unique vertex, and demonstration of the role of IVa2, the putative packaging ATPase, in genome packaging have provided compelling evidence that AdVs follow a sequential assembly pathway. This review provides a detailed discussion on the functions of the various viral and cellular factors involved in AdV genome packaging. We conclude by briefly discussing the roles of the empty capsids, assembly intermediates, scaffolding proteins, portal vertex and DNA encapsidating enzymes in AdV assembly and packaging.
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Affiliation(s)
- Yadvinder S Ahi
- Department of Comparative Pathobiology, Purdue UniversityWest Lafayette, IN, USA; Purdue University Center for Cancer Research, Purdue UniversityWest Lafayette, IN, USA
| | - Suresh K Mittal
- Department of Comparative Pathobiology, Purdue UniversityWest Lafayette, IN, USA; Purdue University Center for Cancer Research, Purdue UniversityWest Lafayette, IN, USA; Purdue Institute for Immunology, Inflammation and Infectious Diseases, Purdue UniversityWest Lafayette, IN, USA
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43
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Thermodynamic Interrogation of the Assembly of a Viral Genome Packaging Motor Complex. Biophys J 2016; 109:1663-75. [PMID: 26488657 DOI: 10.1016/j.bpj.2015.08.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 08/20/2015] [Accepted: 08/21/2015] [Indexed: 11/21/2022] Open
Abstract
Viral terminase enzymes serve as genome packaging motors in many complex double-stranded DNA viruses. The functional motors are multiprotein complexes that translocate viral DNA into a capsid shell, powered by a packaging ATPase, and are among the most powerful molecular motors in nature. Given their essential role in virus development, the structure and function of these biological motors is of considerable interest. Bacteriophage λ-terminase, which serves as a prototypical genome packaging motor, is composed of one large catalytic subunit tightly associated with two DNA recognition subunits. This protomer assembles into a functional higher-order complex that excises a unit length genome from a concatemeric DNA precursor (genome maturation) and concomitantly translocates the duplex into a preformed procapsid shell (genome packaging). While the enzymology of λ-terminase has been well described, the nature of the catalytically competent nucleoprotein intermediates, and the mechanism describing their assembly and activation, is less clear. Here we utilize analytical ultracentrifugation to determine the thermodynamic parameters describing motor assembly and define a minimal thermodynamic linkage model that describes the effects of salt on protomer assembly into a tetrameric complex. Negative stain electron microscopy images reveal a symmetric ring-like complex with a compact stem and four extended arms that exhibit a range of conformational states. Finally, kinetic studies demonstrate that assembly of the ring tetramer is directly linked to activation of the packaging ATPase activity of the motor, thus providing a direct link between structure and function. The implications of these results with respect to the assembly and activation of the functional packaging motor during a productive viral infection are discussed.
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44
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Jobe O, Trinh HV, Kim J, Alsalmi W, Tovanabutra S, Ehrenberg PK, Peachman KK, Gao G, Thomas R, Kim JH, Michael NL, Alving CR, Rao VB, Rao M. Effect of cytokines on Siglec-1 and HIV-1 entry in monocyte-derived macrophages: the importance of HIV-1 envelope V1V2 region. J Leukoc Biol 2016; 99:1089-106. [PMID: 26667473 PMCID: PMC4952014 DOI: 10.1189/jlb.2a0815-361r] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 10/29/2015] [Accepted: 11/17/2015] [Indexed: 02/02/2023] Open
Abstract
Monocytes and monocyte-derived macrophages express relatively low levels of CD4. Despite this, macrophages can be effectively infected with human immunodeficiency virus type 1. Macrophages have a critical role in human immunodeficiency virus type 1 transmission; however, the mechanism or mechanisms of virus infection are poorly understood. We report that growth factors, such as granulocyte macrophage colony-stimulating factor and macrophage colony-stimulating factor affect the phenotypic profile and permissiveness of macrophages to human immunodeficiency virus type 1. Human immunodeficiency virus type 1 infection of monocyte-derived macrophages derived from granulocyte macrophage and macrophage colony-stimulating factors was predominantly facilitated by the sialic acid-binding immunoglobulin-like lectin-1. The number of sialic acid-binding immunoglobulin-like lectin receptors on macrophage colony-stimulating factor-derived monocyte-derived macrophages was significantly greater than on granulocyte macrophage colony-stimulating factor-derived monocyte-derived macrophages, and correspondingly, human immunodeficiency virus type 1 infection was greater in the macrophage colony-stimulating factor-derived monocyte-derived macrophages. Single-genome analysis and quantitative reverse transcriptase-polymerase chain reaction revealed that the differences in infectivity was not due to differences in viral fitness or in viral variants with differential infectivity but was due to reduced viral entry into the granulocyte macrophage colony-stimulating factor-derived monocyte-derived macrophages. Anti-sialic acid-binding immunoglobulin-like lectin, trimeric glycoprotein 145, and scaffolded V1V2 proteins were bound to sialic acid-binding immunoglobulin-like lectin and significantly reduced human immunodeficiency virus type 1 entry and infection. Furthermore, sialic acid residues present in the V1V2 region of the envelope protein mediated human immunodeficiency virus type 1 interaction with sialic acid-binding immunoglobulin-like lectin and entry into macrophage colony-stimulating factor-derived monocyte-derived macrophages. Removal of sialic acid residues or glycans from scaffolded V1V2 protein decreased human immunodeficiency virus type 1 infectivity. These results highlight the importance of sialic acids on the V1V2 region in binding to sialic acid-binding immunoglobulin-like lectin and suggest that the unusually long surface-exposed sialic acid-binding immunoglobulin-like lectin might aid in the capture and entry of human immunodeficiency virus type 1 into monocyte-derived macrophages.
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Affiliation(s)
- Ousman Jobe
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA; Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Hung V Trinh
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA; Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Jiae Kim
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA; Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Wadad Alsalmi
- Department of Biology, The Catholic University of America, Washington, DC, USA
| | - Sodsai Tovanabutra
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA; Laboratory of Molecular Virology and Pathogenesis, Viral Sequencing Core, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; and
| | - Philip K Ehrenberg
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA; Host Genetics Section, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; and
| | - Kristina K Peachman
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA; Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Guofen Gao
- Department of Biology, The Catholic University of America, Washington, DC, USA
| | - Rasmi Thomas
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA; Host Genetics Section, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; and
| | - Jerome H Kim
- Laboratory of Molecular Virology and Pathogenesis, Viral Sequencing Core, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; and
| | - Nelson L Michael
- Laboratory of Molecular Virology and Pathogenesis, Viral Sequencing Core, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; and
| | - Carl R Alving
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Venigalla B Rao
- Department of Biology, The Catholic University of America, Washington, DC, USA
| | - Mangala Rao
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA;
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45
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Gao S, Zhang L, Rao VB. Exclusion of small terminase mediated DNA threading models for genome packaging in bacteriophage T4. Nucleic Acids Res 2016; 44:4425-39. [PMID: 26984529 PMCID: PMC4872099 DOI: 10.1093/nar/gkw184] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/04/2016] [Indexed: 11/17/2022] Open
Abstract
Tailed bacteriophages and herpes viruses use powerful molecular machines to package their genomes. The packaging machine consists of three components: portal, motor (large terminase; TerL) and regulator (small terminase; TerS). Portal, a dodecamer, and motor, a pentamer, form two concentric rings at the special five-fold vertex of the icosahedral capsid. Powered by ATPase, the motor ratchets DNA into the capsid through the portal channel. TerS is essential for packaging, particularly for genome recognition, but its mechanism is unknown and controversial. Structures of gear-shaped TerS rings inspired models that invoke DNA threading through the central channel. Here, we report that mutations of basic residues that line phage T4 TerS (gp16) channel do not disrupt DNA binding. Even deletion of the entire channel helix retained DNA binding and produced progeny phage in vivo. On the other hand, large oligomers of TerS (11-mers/12-mers), but not small oligomers (trimers to hexamers), bind DNA. These results suggest that TerS oligomerization creates a large outer surface, which, but not the interior of the channel, is critical for function, probably to wrap viral genome around the ring during packaging initiation. Hence, models involving TerS-mediated DNA threading may be excluded as an essential mechanism for viral genome packaging.
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Affiliation(s)
- Song Gao
- Department of Biology, The Catholic University of America, 620 Michigan Avenue Northeast, Washington, DC 20064, USA Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Huaihai Institute of Technology, Lianyungang 222005, China
| | - Liang Zhang
- Department of Biology, The Catholic University of America, 620 Michigan Avenue Northeast, Washington, DC 20064, USA
| | - Venigalla B Rao
- Department of Biology, The Catholic University of America, 620 Michigan Avenue Northeast, Washington, DC 20064, USA
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Abstract
During progeny assembly, viruses selectively package virion genomes from a nucleic acid pool that includes host nucleic acids. For large dsDNA viruses, including tailed bacteriophages and herpesviruses, immature viral DNA is recognized and translocated into a preformed icosahedral shell, the prohead. Recognition involves specific interactions between the viral packaging enzyme, terminase, and viral DNA recognition sites. Generally, viral DNA is recognized by terminase’s small subunit (TerS). The large terminase subunit (TerL) contains translocation ATPase and endonuclease domains. In phage lambda, TerS binds a sequence repeated three times in cosB, the recognition site. TerS binding to cosB positions TerL to cut the concatemeric DNA at the adjacent nicking site, cosN. TerL introduces staggered nicks in cosN, generating twelve bp cohesive ends. Terminase separates the cohesive ends and remains bound to the cosB-containing end, in a nucleoprotein structure called Complex I. Complex I docks on the prohead’s portal vertex and translocation ensues. DNA topology plays a role in the TerSλ-cosBλ interaction. Here we show that a site, I2, located between cosN and cosB, is critically important for an early DNA packaging step. I2 contains a complex static bend. I2 mutations block DNA packaging. I2 mutant DNA is cut by terminase at cosN in vitro, but in vivo, no cos cleavage is detected, nor is there evidence for Complex I. Models for what packaging step might be blocked by I2 mutations are presented.
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47
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Sankhala RS, Lokareddy RK, Cingolani G. Divergent Evolution of Nuclear Localization Signal Sequences in Herpesvirus Terminase Subunits. J Biol Chem 2016; 291:11420-33. [PMID: 27033706 DOI: 10.1074/jbc.m116.724393] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Indexed: 11/06/2022] Open
Abstract
The tripartite terminase complex of herpesviruses assembles in the cytoplasm of infected cells and exploits the host nuclear import machinery to gain access to the nucleus, where capsid assembly and genome-packaging occur. Here we analyzed the structure and conservation of nuclear localization signal (NLS) sequences previously identified in herpes simplex virus 1 (HSV-1) large terminase and human cytomegalovirus (HCMV) small terminase. We found a monopartite NLS at the N terminus of large terminase, flanking the ATPase domain, that is conserved only in α-herpesviruses. In contrast, small terminase exposes a classical NLS at the far C terminus of its helical structure that is conserved only in two genera of the β-subfamily and absent in α- and γ-herpesviruses. In addition, we predicted a classical NLS in the third terminase subunit that is partially conserved among herpesviruses. Bioinformatic analysis revealed that both location and potency of NLSs in terminase subunits evolved more rapidly than the rest of the amino acid sequence despite the selective pressure to keep terminase gene products active and localized in the nucleus. We propose that swapping NLSs among terminase subunits is a regulatory mechanism that allows different herpesviruses to regulate the kinetics of terminase nuclear import, reflecting a mechanism of virus:host adaptation.
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Affiliation(s)
- Rajeshwer S Sankhala
- From the Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107 and
| | - Ravi K Lokareddy
- From the Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107 and
| | - Gino Cingolani
- From the Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107 and Institute of Biomembranes and Bioenergetics, National Research Council, Via Amendola 165/A, 70126 Bari, Italy
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48
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Greive SJ, Fung HKH, Chechik M, Jenkins HT, Weitzel SE, Aguiar PM, Brentnall AS, Glousieau M, Gladyshev GV, Potts JR, Antson AA. DNA recognition for virus assembly through multiple sequence-independent interactions with a helix-turn-helix motif. Nucleic Acids Res 2015; 44:776-89. [PMID: 26673721 PMCID: PMC4737164 DOI: 10.1093/nar/gkv1467] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/30/2015] [Indexed: 11/14/2022] Open
Abstract
The helix-turn-helix (HTH) motif features frequently in protein DNA-binding assemblies. Viral pac site-targeting small terminase proteins possess an unusual architecture in which the HTH motifs are displayed in a ring, distinct from the classical HTH dimer. Here we investigate how such a circular array of HTH motifs enables specific recognition of the viral genome for initiation of DNA packaging during virus assembly. We found, by surface plasmon resonance and analytical ultracentrifugation, that individual HTH motifs of the Bacillus phage SF6 small terminase bind the packaging regions of SF6 and related SPP1 genome weakly, with little local sequence specificity. Nuclear magnetic resonance chemical shift perturbation studies with an arbitrary single-site substrate suggest that the HTH motif contacts DNA similarly to how certain HTH proteins contact DNA non-specifically. Our observations support a model where specificity is generated through conformational selection of an intrinsically bent DNA segment by a ring of HTHs which bind weakly but cooperatively. Such a system would enable viral gene regulation and control of the viral life cycle, with a minimal genome, conferring a major evolutionary advantage for SPP1-like viruses.
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Affiliation(s)
- Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Herman K H Fung
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK Department of Biology, University of York, York YO10 5DD, UK
| | - Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Huw T Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Stephen E Weitzel
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Pedro M Aguiar
- Department of Chemistry, University of York, York YO10 5DD, UK
| | | | - Matthieu Glousieau
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Grigory V Gladyshev
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119234, Russian Federation
| | | | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
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Feiss M, Young Min J, Sultana S, Patel P, Sippy J. DNA Packaging Specificity of Bacteriophage N15 with an Excursion into the Genetics of a Cohesive End Mismatch. PLoS One 2015; 10:e0141934. [PMID: 26633301 PMCID: PMC4669245 DOI: 10.1371/journal.pone.0141934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 10/14/2015] [Indexed: 11/17/2022] Open
Abstract
During DNA replication by the λ-like bacteriophages, immature concatemeric DNA is produced by rolling circle replication. The concatemers are processed into mature chromosomes with cohesive ends, and packaged into prohead shells, during virion assembly. Cohesive ends are generated by the viral enzyme terminase, which introduces staggered nicks at cos, an approx. 200 bp-long sequence containing subsites cosQ, cosN and cosB. Interactions of cos subsites of immature concatemeric DNA with terminase orchestrate DNA processing and packaging. To initiate DNA packaging, terminase interacts with cosB and nicks cosN. The cohesive ends of N15 DNA differ from those of λ at 2/12 positions. Genetic experiments show that phages with chromosomes containing mismatched cohesive ends are functional. In at least some infections, the cohesive end mismatch persists through cyclization and replication, so that progeny phages of both allelic types are produced in the infected cell. N15 possesses an asymmetric packaging specificity: N15 DNA is not packaged by phages λ or 21, but surprisingly, N15-specific terminase packages λ DNA. Implications for genetic interactions among λ-like bacteriophages are discussed.
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Affiliation(s)
- Michael Feiss
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52242, United States of America
| | - Jea Young Min
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52242, United States of America
| | - Sawsan Sultana
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52242, United States of America
| | - Priyal Patel
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52242, United States of America
| | - Jean Sippy
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52242, United States of America
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An RNA Domain Imparts Specificity and Selectivity to a Viral DNA Packaging Motor. J Virol 2015; 89:12457-66. [PMID: 26423956 DOI: 10.1128/jvi.01895-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/28/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED During assembly, double-stranded DNA viruses, including bacteriophages and herpesviruses, utilize a powerful molecular motor to package their genomic DNA into a preformed viral capsid. An integral component of the packaging motor in the Bacillus subtilis bacteriophage ϕ29 is a viral genome-encoded pentameric ring of RNA (prohead RNA [pRNA]). pRNA is a 174-base transcript comprised of two domains, domains I and II. Early studies initially isolated a 120-base form (domain I only) that retains high biological activity in vitro; hence, no function could be assigned to domain II. Here we define a role for this domain in the packaging process. DNA packaging using restriction digests of ϕ29 DNA showed that motors with the 174-base pRNA supported the correct polarity of DNA packaging, selectively packaging the DNA left end. In contrast, motors containing the 120-base pRNA had compromised specificity, packaging both left- and right-end fragments. The presence of domain II also provides selectivity in competition assays with genomes from related phages. Furthermore, motors with the 174-base pRNA were restrictive, in that they packaged only one DNA fragment into the head, whereas motors with the 120-base pRNA packaged several fragments into the head, indicating multiple initiation events. These results show that domain II imparts specificity and stringency to the motor during the packaging initiation events that precede DNA translocation. Heteromeric rings of pRNA demonstrated that one or two copies of domain II were sufficient to impart this selectivity/stringency. Although ϕ29 differs from other double-stranded DNA phages in having an RNA motor component, the function provided by pRNA is carried on the motor protein components in other phages. IMPORTANCE During virus assembly, genome packaging involves the delivery of newly synthesized viral nucleic acid into a protein shell. In the double-stranded DNA phages and herpesviruses, this is accomplished by a powerful molecular motor that translocates the viral DNA into a preformed viral shell. A key event in DNA packaging is recognition of the viral DNA among other nucleic acids in the host cell. Commonly, a DNA-binding protein mediates the interaction of viral DNA with the motor/head shell. Here we show that for the bacteriophage ϕ29, this essential step of genome recognition is mediated by a viral genome-encoded RNA rather than a protein. A domain of the prohead RNA (pRNA) imparts specificity and stringency to the motor by ensuring the correct orientation of DNA packaging and restricting initiation to a single event. Since this assembly step is unique to the virus, DNA packaging is a novel target for the development of antiviral drugs.
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