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Leavitt JC, Woodbury BM, Gilcrease EB, Bridges CM, Teschke CM, Casjens SR. Bacteriophage P22 SieA-mediated superinfection exclusion. mBio 2024; 15:e0216923. [PMID: 38236051 PMCID: PMC10883804 DOI: 10.1128/mbio.02169-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 11/10/2023] [Indexed: 01/19/2024] Open
Abstract
Many temperate phages encode prophage-expressed functions that interfere with superinfection of the host bacterium by external phages. Salmonella phage P22 has four such systems that are expressed from the prophage in a lysogen that are encoded by the c2 (repressor), gtrABC, sieA, and sieB genes. Here we report that the P22-encoded SieA protein is necessary and sufficient for exclusion by the SieA system and that it is an inner membrane protein that blocks DNA injection by P22 and its relatives, but has no effect on infection by other tailed phage types. The P22 virion injects its DNA through the host cell membranes and periplasm via a conduit assembled from three "ejection proteins" after their release from the virion. Phage P22 mutants that overcome the SieA block were isolated, and they have amino acid changes in the C-terminal regions of the gene 16 and 20 encoded ejection proteins. Three different single-amino acid changes in these proteins are required to obtain nearly full resistance to SieA. Hybrid P22 phages that have phage HK620 ejection protein genes are also partially resistant to SieA. There are three sequence types of extant phage-encoded SieA proteins that are less than 30% identical to one another, yet comparison of two of these types found no differences in phage target specificity. Our data strongly suggest a model in which the inner membrane protein SieA interferes with the assembly or function of the periplasmic gp20 and membrane-bound gp16 DNA delivery conduit.IMPORTANCEThe ongoing evolutionary battle between bacteria and the viruses that infect them is a critical feature of bacterial ecology on Earth. Viruses can kill bacteria by infecting them. However, when their chromosomes are integrated into a bacterial genome as a prophage, viruses can also protect the host bacterium by expressing genes whose products defend against infection by other viruses. This defense property is called "superinfection exclusion." A significant fraction of bacteria harbor prophages that encode such protective systems, and there are many different molecular strategies by which superinfection exclusion is mediated. This report is the first to describe the mechanism by which bacteriophage P22 SieA superinfection exclusion protein protects its host bacterium from infection by other P22-like phages. The P22 prophage-encoded inner membrane SieA protein prevents infection by blocking transport of superinfecting phage DNA across the inner membrane during injection.
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Affiliation(s)
- Justin C Leavitt
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Brianna M Woodbury
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Eddie B Gilcrease
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Charles M Bridges
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Carolyn M Teschke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Sherwood R Casjens
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah, USA
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2
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Iglesias SM, Lokareddy RK, Yang R, Li F, Yeggoni DP, David Hou CF, Leroux MN, Cortines JR, Leavitt JC, Bird M, Casjens SR, White S, Teschke CM, Cingolani G. Molecular Architecture of Salmonella Typhimurium Virus P22 Genome Ejection Machinery. J Mol Biol 2023; 435:168365. [PMID: 37952769 PMCID: PMC10842050 DOI: 10.1016/j.jmb.2023.168365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/04/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Bacteriophage P22 is a prototypical member of the Podoviridae superfamily. Since its discovery in 1952, P22 has become a paradigm for phage transduction and a model for icosahedral viral capsid assembly. Here, we describe the complete architecture of the P22 tail apparatus (gp1, gp4, gp10, gp9, and gp26) and the potential location and organization of P22 ejection proteins (gp7, gp20, and gp16), determined using cryo-EM localized reconstruction, genetic knockouts, and biochemical analysis. We found that the tail apparatus exists in two equivalent conformations, rotated by ∼6° relative to the capsid. Portal protomers make unique contacts with coat subunits in both conformations, explaining the 12:5 symmetry mismatch. The tail assembles around the hexameric tail hub (gp10), which folds into an interrupted β-propeller characterized by an apical insertion domain. The tail hub connects proximally to the dodecameric portal protein and head-to-tail adapter (gp4), distally to the trimeric tail needle (gp26), and laterally to six trimeric tailspikes (gp9) that attach asymmetrically to gp10 insertion domain. Cryo-EM analysis of P22 mutants lacking the ejection proteins gp7 or gp20 and biochemical analysis of purified recombinant proteins suggest that gp7 and gp20 form a molecular complex associated with the tail apparatus via the portal protein barrel. We identified a putative signal transduction pathway from the tailspike to the tail needle, mediated by three flexible loops in the tail hub, that explains how lipopolysaccharide (LPS) is sufficient to trigger the ejection of the P22 DNA in vitro.
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Affiliation(s)
- Stephano M Iglesias
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locus Street, Philadelphia, PA 19107, USA
| | - Ravi K Lokareddy
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA
| | - Ruoyu Yang
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locus Street, Philadelphia, PA 19107, USA
| | - Fenglin Li
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locus Street, Philadelphia, PA 19107, USA
| | - Daniel P Yeggoni
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locus Street, Philadelphia, PA 19107, USA
| | - Chun-Feng David Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locus Street, Philadelphia, PA 19107, USA
| | - Makayla N Leroux
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Road, Storrs, CT 06269, USA
| | - Juliana R Cortines
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Road, Storrs, CT 06269, USA; Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21590-902, Brazil
| | - Justin C Leavitt
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Mary Bird
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Road, Storrs, CT 06269, USA
| | - Sherwood R Casjens
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Simon White
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Road, Storrs, CT 06269, USA
| | - Carolyn M Teschke
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Road, Storrs, CT 06269, USA; Department of Chemistry, University of Connecticut, 91 N. Eagleville Road, Storrs, CT 06269, USA
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locus Street, Philadelphia, PA 19107, USA; Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA.
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Villanueva Valencia JR, Li D, Casjens SR, Evilevitch A. 'SAXS-osmometer' method provides measurement of DNA pressure in viral capsids and delivers an empirical equation of state. Nucleic Acids Res 2023; 51:11415-11427. [PMID: 37889048 PMCID: PMC10681747 DOI: 10.1093/nar/gkad852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/21/2023] [Accepted: 09/30/2023] [Indexed: 10/28/2023] Open
Abstract
We present a novel method that provides a measurement of DNA pressure in viral capsids using small angle X-ray scattering (SAXS). This method, unlike our previous assay, does not require triggering genome release with a viral receptor. Thus, it can be used to determine the existence of a pressurized genome state in a wide range of virus systems, even if the receptor is not known, leading to a better understanding of the processes of viral genome uncoating and encapsidation in the course of infection. Furthermore, by measuring DNA pressure for a collection of bacteriophages with varying DNA packing densities, we derived an empirical equation of state (EOS) that accurately predicts the relation between the capsid pressure and the packaged DNA density and includes the contribution of both DNA-DNA interaction energy and DNA bending stress to the total DNA pressure. We believe that our SAXS-osmometer method and the EOS, combined, provide the necessary tools to investigate physico-chemical properties of confined DNA condensates and mechanisms of infection, and may also provide essential data for the design of viral vectors in gene therapy applications and development of antivirals that target the pressurized genome state.
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Affiliation(s)
| | - Dong Li
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Alex Evilevitch
- Department of Experimental Medical Science and NanoLund, Lund University, Box 124, Lund, Sweden
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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Leavitt JC, Woodbury BM, Gilcrease EB, Bridges CM, Teschke CM, Casjens SR. Bacteriophage P22 SieA mediated superinfection exclusion. bioRxiv 2023:2023.08.15.553423. [PMID: 37645741 PMCID: PMC10461980 DOI: 10.1101/2023.08.15.553423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Many temperate phages encode prophage-expressed functions that interfere with superinfection of the host bacterium by external phages. Salmonella phage P22 has four such systems that are expressed from the prophage in a lysogen that are encoded by the c2 (repressor), gtrABC, sieA, and sieB genes. Here we report that the P22-encoded SieA protein is the only phage protein required for exclusion by the SieA system, and that it is an inner membrane protein that blocks DNA injection by P22 and its relatives, but has no effect on infection by other tailed phage types. The P22 virion injects its DNA through the host cell membranes and periplasm via a conduit assembled from three "ejection proteins" after their release from the virion. Phage P22 mutants were isolated that overcome the SieA block, and they have amino acid changes in the C-terminal regions of the gene 16 and 20 encoded ejection proteins. Three different single amino acid changes in these proteins are required to obtain nearly full resistance to SieA. Hybrid P22 phages that have phage HK620 ejection protein genes are also partially resistant to SieA. There are three sequence types of extant phage-encoded SieA proteins that are less than 30% identical to one another, yet comparison of two of these types found no differences in target specificity. Our data are consistent with a model in which the inner membrane protein SieA interferes with the assembly or function of the periplasmic gp20 and membrane-bound gp16 DNA delivery conduit.
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Affiliation(s)
- Justin C. Leavitt
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112 USA
- Current address: Green Raccoon Scientific, Gunlock UT 84733 USA
| | - Brianna M. Woodbury
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
- Current address: York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Eddie B. Gilcrease
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
- Current address: Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT 84112 USA
| | - Charles M. Bridges
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Carolyn M. Teschke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
- Department of Chemistry, University of Connecticut, Storrs, CT 06269 USA
| | - Sherwood R. Casjens
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112 USA
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
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Mohammed M, Casjens SR, Millard AD, Harrison C, Gannon L, Chattaway MA. Genomic analysis of Anderson typing phages of Salmonella Typhimrium: towards understanding the basis of bacteria-phage interaction. Sci Rep 2023; 13:10484. [PMID: 37380724 PMCID: PMC10307801 DOI: 10.1038/s41598-023-37307-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/20/2023] [Indexed: 06/30/2023] Open
Abstract
The Anderson phage typing scheme has been successfully used worldwide for epidemiological surveillance of Salmonella enterica serovar Typhimurium. Although the scheme is being replaced by whole genome sequence subtyping methods, it can provide a valuable model system for study of phage-host interaction. The phage typing scheme distinguishes more than 300 definitive types of Salmonella Typhimurium based on their patterns of lysis to a unique collection of 30 specific Salmonella phages. In this study, we sequenced the genomes of 28 Anderson typing phages of Salmonella Typhimurium to begin to characterize the genetic determinants that are responsible for the differences in these phage type profiles. Genomic analysis of typing phages reveals that Anderson phages can be classified into three different groups, the P22-like, ES18-like and SETP3-like clusters. Most Anderson phages are short tailed P22-like viruses (genus Lederbergvirus); but phages STMP8 and STMP18 are very closely related to the lambdoid long tailed phage ES18, and phages STMP12 and STMP13 are related to the long noncontractile tailed, virulent phage SETP3. Most of these typing phages have complex genome relationships, but interestingly, two phage pairs STMP5 and STMP16 as well as STMP12 and STMP13 differ by a single nucleotide. The former affects a P22-like protein involved in DNA passage through the periplasm during its injection, and the latter affects a gene whose function is unknown. Using the Anderson phage typing scheme would provide insights into phage biology and the development of phage therapy for the treatment of antibiotic resistant bacterial infections.
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Affiliation(s)
- Manal Mohammed
- Genomics and Infectious Diseases Research Group, School of Life Sciences, University of Westminster, 115 New Cavendish Street, London, W1W 6UW, UK.
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, University of Utah, Salt Lake City, UT, 84112, USA
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Andrew D Millard
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Christian Harrison
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Lucy Gannon
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
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6
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Gilcrease EB, Casjens SR, Bhattacharjee A, Goel R. A Klebsiella pneumoniae NDM-1+ bacteriophage: Adaptive polyvalence and disruption of heterogenous biofilms. Front Microbiol 2023; 14:1100607. [PMID: 36876079 PMCID: PMC9983693 DOI: 10.3389/fmicb.2023.1100607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/30/2023] [Indexed: 02/22/2023] Open
Abstract
Bacteriophage KL-2146 is a lytic virus isolated to infect Klebsiella pneumoniae BAA2146, a pathogen carrying the broad range antibiotic resistance gene New Delhi metallo-betalactamase-1 (NDM-1). Upon complete characterization, the virus is shown to belong to the Drexlerviridae family and is a member of the Webervirus genus located within the (formerly) T1-like cluster of phages. Its double-stranded (dsDNA) genome is 47,844 bp long and is predicted to have 74 protein-coding sequences (CDS). After challenging a variety of K. pneumoniae strains with phage KL-2146, grown on the NDM-1 positive strain BAA-2146, polyvalence was shown for a single antibiotic-sensitive strain, K. pneumoniae 13,883, with a very low initial infection efficiency in liquid culture. However, after one or more cycles of infection in K. pneumoniae 13,883, nearly 100% infection efficiency was achieved, while infection efficiency toward its original host, K. pneumoniae BAA-2146, was decreased. This change in host specificity is reversible upon re-infection of the NDM-1 positive strain (BAA-2146) using phages grown on the NDM-1 negative strain (13883). In biofilm infectivity experiments, the polyvalent nature of KL-2146 was demonstrated with the killing of both the multidrug-resistant K. pneumoniae BAA-2146 and drug-sensitive 13,883 in a multi-strain biofilm. The ability to infect an alternate, antibiotic-sensitive strain makes KL-2146 a useful model for studying phages infecting the NDM-1+ strain, K. pneumoniae BAA-2146. GRAPHICAL ABSTRACT.
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Affiliation(s)
- Eddie B Gilcrease
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT, United States
| | - Sherwood R Casjens
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States.,Division of Microbiology and Immunology, Pathology Department, University of Utah, Salt Lake City, UT, United States
| | - Ananda Bhattacharjee
- Department of Environmental Sciences, University of California, Riverside, CA, United States
| | - Ramesh Goel
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT, United States
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Rudenko N, Golovchenko M, Horak A, Grubhoffer L, Mongodin EF, Fraser CM, Qiu W, Luft BJ, Morgan RG, Casjens SR, Schutzer SE. Genomic Confirmation of Borrelia garinii, United States. Emerg Infect Dis 2023; 29:64-69. [PMID: 36573553 PMCID: PMC9796223 DOI: 10.3201/eid2901.220930] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Lyme disease is a multisystem disorder primarily caused by Borrelia burgdorferi sensu lato. However, B. garinii, which has been identified on islands off the coast of Newfoundland and Labrador, Canada, is a cause of Lyme disease in Eurasia. We report isolation and whole-genome nucleotide sequencing of a B. garinii isolate from a cotton mouse (Peromyscus gossypinus) in South Carolina, USA. We identified a second B. garinii isolate from the same repository. Phylogenetic analysis does not associate these isolates with the previously described isolates of B. garinii from Canada.
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8
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Feiss M, Young R, Ramsey J, Adhya S, Georgopoulos C, Hendrix RW, Hatfull GF, Gilcrease EB, Casjens SR. Hybrid Vigor: Importance of Hybrid λ Phages in Early Insights in Molecular Biology. Microbiol Mol Biol Rev 2022; 86:e0012421. [PMID: 36165780 PMCID: PMC9799177 DOI: 10.1128/mmbr.00124-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Laboratory-generated hybrids between phage λ and related phages played a seminal role in establishment of the λ model system, which, in turn, served to develop many of the foundational concepts of molecular biology, including gene structure and control. Important λ hybrids with phages 21 and 434 were the earliest of such phages. To understand the biology of these hybrids in full detail, we determined the complete genome sequences of phages 21 and 434. Although both genomes are canonical members of the λ-like phage family, they both carry unsuspected bacterial virulence gene types not previously described in this group of phages. In addition, we determined the sequences of the hybrid phages λ imm21, λ imm434, and λ h434 imm21. These sequences show that the replacements of λ DNA by nonhomologous segments of 21 or 434 DNA occurred through homologous recombination in adjacent sequences that are nearly identical in the parental phages. These five genome sequences correct a number of errors in published sequence fragments of the 21 and 434 genomes, and they point out nine nucleotide differences from Sanger's original λ sequence that are likely present in most extant λ strains in laboratory use today. We discuss the historical importance of these hybrid phages in the development of fundamental tenets of molecular biology and in some of the earliest gene cloning vectors. The 434 and 21 genomes reinforce the conclusion that the genomes of essentially all natural λ-like phages are mosaics of sequence modules from a pool of exchangeable segments.
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Affiliation(s)
- Michael Feiss
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Ryland Young
- Center for Phage Technology, Texas A&M AgriLife Research, College Station, Texas, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Jolene Ramsey
- Center for Phage Technology, Texas A&M AgriLife Research, College Station, Texas, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Sankar Adhya
- Laboratory of Molecular Biology, Center for Cancer Research, The National Cancer Institute, Bethesda, Maryland, USA
| | - Costa Georgopoulos
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Roger W. Hendrix
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Eddie B. Gilcrease
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, Utah, USA
| | - Sherwood R. Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah, USA
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
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9
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Casjens SR, Davidson AR, Grose JH. The small genome, virulent, non-contractile tailed bacteriophages that infect Enterobacteriales hosts. Virology 2022; 573:151-166. [DOI: 10.1016/j.virol.2022.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 05/07/2022] [Accepted: 06/01/2022] [Indexed: 11/25/2022]
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10
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Cranston A, Danielson P, Arens DK, Barker A, Birch EK, Brown H, Carr E, Cero P, Chow J, Correa E, Dean J, Dunn M, Eberhard N, Egbert A, Foster K, Gaertner R, Gleave A, Gomez A, Gordon JB, Harris EB, Heaps C, Hyer M, Johnson A, Johnson L, Kim M, Kruger JL, Leonard T, LeSueur A, Lima S, Marshall N, Moulton R, Newey CR, Owen D, Packard A, Rolfson A, Suorsa AR, Rodriguez W, Sandoval C, Sharma R, Smith A, Sork C, Soule C, Soule S, Stewart J, Stoker T, Thompson DW, Thurgood T, Walker J, Zaugg E, Casjens SR, Grose JH. Genome Sequences of 22 T1-like Bacteriophages That Infect Enterobacteriales. Microbiol Resour Announc 2022; 11:e0122121. [PMID: 35389258 PMCID: PMC9119101 DOI: 10.1128/mra.01221-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/12/2022] [Indexed: 11/20/2022] Open
Abstract
Here, the full genome sequences of 22 T1-like bacteriophages isolated from wastewater are reported. Eight (BlueShadow, Brooksby, Devorator, ElisaCorrea, Reinasaurus, SorkZaugg, Supreme284, ZeroToHero) were isolated on Citrobacter, six on Klebsiella (Chell, FairDinkum, HazelMika, Opt-817, P528, PeteCarol), and eight on Escherichia (Fulano1, Mishu, Opt-719, PhleaSolo, Punny, Poky, Phunderstruck, Sadiya).
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Affiliation(s)
- Alyssa Cranston
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Parker Danielson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Daniel K. Arens
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Austin Barker
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Elisabeth K. Birch
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Hannah Brown
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Emilee Carr
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Paige Cero
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Jacob Chow
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Elisa Correa
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Jeremy Dean
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Matthew Dunn
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Nathaniel Eberhard
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Ashley Egbert
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Kent Foster
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Rochelle Gaertner
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Austen Gleave
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Alex Gomez
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - J. Ben Gordon
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Evan B. Harris
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Corden Heaps
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Matthew Hyer
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Austin Johnson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Liam Johnson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Minji Kim
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Jared L. Kruger
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Thomas Leonard
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Austin LeSueur
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Sophia Lima
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Naomi Marshall
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Rebecca Moulton
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Colleen R. Newey
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Daniel Owen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Audra Packard
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Alexis Rolfson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Aurora R. Suorsa
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Walter Rodriguez
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Claudia Sandoval
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Ruchira Sharma
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Ashley Smith
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Carson Sork
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Coby Soule
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Silvia Soule
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Jared Stewart
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Tyson Stoker
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Daniel W. Thompson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Trever Thurgood
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Jamison Walker
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Ethan Zaugg
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Sherwood R. Casjens
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Julianne H. Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
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11
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Evans S, Cobbley H, Davis K, Divis T, Eberhard N, Flor S, Harris EB, Gordon JB, Hyer M, Larson W, Suorsa AR, Sharma R, Sork C, Thompson DW, Wells L, Casjens SR, Grose JH. Complete Genome Sequences of Five Bacteriophages That Infect Enterobacteriales Hosts. Microbiol Resour Announc 2022; 11:e0122321. [PMID: 35343780 PMCID: PMC9022592 DOI: 10.1128/mra.01223-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 03/13/2022] [Indexed: 11/25/2022] Open
Abstract
Full genome sequences of five bacteriophages that were isolated from raw sewage samples and infect Enterobacteriales hosts are presented. Brookers is a P22-like Proteus phage, OddieOddie is a 9g-like Escherichia coli phage, Diencephelon is a Kp3-like Klebsiella phage, and Rgz1 and Lilpapawes are classic T4-like and T7-like virulent Proteus phages, respectively.
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Affiliation(s)
- Seth Evans
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Hunter Cobbley
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Kye Davis
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Tyler Divis
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Nathaniel Eberhard
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Samuel Flor
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Evan B. Harris
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - J. Ben Gordon
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Matthew Hyer
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Weston Larson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Aurora R. Suorsa
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Ruchira Sharma
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Carson Sork
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Daniel W. Thompson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Lauren Wells
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Sherwood R. Casjens
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Julianne H. Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
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12
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Cobbley HK, Evans SI, Brown HMF, Eberhard B, Eberhard N, Kim M, Moe HM, Schaeffer D, Sharma R, Thompson DW, Casjens SR, Grose JH. Complete Genome Sequences of Six Chi-Like Bacteriophages That Infect Proteus and Klebsiella. Microbiol Resour Announc 2022; 11:e0121521. [PMID: 35297681 PMCID: PMC9022528 DOI: 10.1128/mra.01215-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/01/2022] [Indexed: 11/20/2022] Open
Abstract
Proteus mirabilis and Klebsiella aerogenes are Gram-negative opportunistic pathogens that are responsible for nosocomial and health care-associated infections, including urinary tract infections. Here, the full genome sequences of six Chi-like Proteus (DanisaurMW, DoubleBarrel, Inception, Jing313, and NotEvenPhaged) or Klebsiella (Phraden) bacteriophages are announced, contributing to the understanding of Chi-like phages.
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Affiliation(s)
- Hunter K Cobbley
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Seth I Evans
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Hannah M F Brown
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Braden Eberhard
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Nathaniel Eberhard
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Minji Kim
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Haley Mickelsen Moe
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Daniel Schaeffer
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Ruchira Sharma
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Daniel W Thompson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Sherwood R Casjens
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Julianne H Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
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13
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Purnell MG, Andersen K, Bell A, Briscoe JT, Brown HMF, Carr EL, Doney J, Folsom PF, Green C, Harris EH, Huhem E, Jensen RM, Johnson L, Jones C, Lambert AS, Loertscher E, Newey CR, Porter M, Rallison J, Sharma R, Sork C, Soule S, Stewart JB, Stoker T, Tayler S, Thompson DW, Thurgood TL, Walker J, Breakwell DP, Casjens SR, Grose JH. Complete Genome Sequences of Five SO-1-Like Siphoviridae Bacteriophages That Infect Enterobacteriales. Microbiol Resour Announc 2022; 11:e0122421. [PMID: 35293823 PMCID: PMC9022532 DOI: 10.1128/mra.01224-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/01/2022] [Indexed: 11/20/2022] Open
Abstract
The Enterobacteriales order is composed of Gram-negative bacteria that range from harmless symbionts to well-studied pathogens. We announce complete genome sequences of five related SO-1-like Enterobacteriales bacteriophages (also known as the Dhillonvirus genus) isolated from wastewater that infect Escherichia coli (Opt-212, Over9000, Pubbukkers, and Teewinot) or Shigella boydii (StarDew).
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Affiliation(s)
- Madelyn G. Purnell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Kyle Andersen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Adam Bell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Jared T. Briscoe
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Hannah M. F. Brown
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Emilee L. Carr
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Justen Doney
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Parker F. Folsom
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Cheyanne Green
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Evan H. Harris
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Elisa Huhem
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - R. Matthew Jensen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Liberty Johnson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Carter Jones
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Andrew S. Lambert
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Emily Loertscher
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Colleen R. Newey
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Matthew Porter
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Jonah Rallison
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Ruchira Sharma
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Carson Sork
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Silvia Soule
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Jared B. Stewart
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Tyson Stoker
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Sadie Tayler
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Daniel W. Thompson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Trever L. Thurgood
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Jamison Walker
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Donald P. Breakwell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Sherwood R. Casjens
- Department of Biology, University of Utah, Salt Lake City, Utah, USA
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Julianne H. Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
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14
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Zaworski J, McClung C, Ruse C, Weigele PR, Hendrix RW, Ko CC, Edgar R, Hatfull GF, Casjens SR, Raleigh EA. Genome analysis of Salmonella enterica serovar Typhimurium bacteriophage L, indicator for StySA (StyLT2III) restriction-modification system action. G3 (Bethesda) 2021; 11:6044188. [PMID: 33561243 PMCID: PMC8022706 DOI: 10.1093/g3journal/jkaa037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/07/2020] [Indexed: 01/10/2023]
Abstract
Bacteriophage L, a P22-like phage of Salmonella enterica sv Typhimurium LT2, was important for definition of mosaic organization of the lambdoid phage family and for characterization of restriction-modification systems of Salmonella. We report the complete genome sequences of bacteriophage L cI–40 13–am43 and L cII–101; the deduced sequence of wildtype L is 40,633 bp long with a 47.5% GC content. We compare this sequence with those of P22 and ST64T, and predict 72 Coding Sequences, 2 tRNA genes and 14 intergenic rho-independent transcription terminators. The overall genome organization of L agrees with earlier genetic and physical evidence; for example, no secondary immunity region (immI: ant, arc) or known genes for superinfection exclusion (sieA and sieB) are present. Proteomic analysis confirmed identification of virion proteins, along with low levels of assembly intermediates and host cell envelope proteins. The genome of L is 99.9% identical at the nucleotide level to that reported for phage ST64T, despite isolation on different continents ∼35 years apart. DNA modification by the epigenetic regulator Dam is generally incomplete. Dam modification is also selectively missing in one location, corresponding to the P22 phase-variation-sensitive promoter region of the serotype-converting gtrABC operon. The number of sites for SenLTIII (StySA) action may account for stronger restriction of L (13 sites) than of P22 (3 sites).
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Affiliation(s)
- Julie Zaworski
- Research Department, New England Biolabs, Ipswich, MA 01938-2723, USA
| | - Colleen McClung
- Research Department, New England Biolabs, Ipswich, MA 01938-2723, USA
| | - Cristian Ruse
- Research Department, New England Biolabs, Ipswich, MA 01938-2723, USA
| | - Peter R Weigele
- Research Department, New England Biolabs, Ipswich, MA 01938-2723, USA
| | - Roger W Hendrix
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ching-Chung Ko
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Robert Edgar
- Bioengineering Department, University of Pittsburgh, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.,School of Biological Science, University of Utah, Salt Lake City, UT 84112, USA
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15
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Schwartz I, Margos G, Casjens SR, Qiu WG, Eggers CH. Multipartite Genome of Lyme Disease Borrelia: Structure, Variation and Prophages. Curr Issues Mol Biol 2020; 42:409-454. [PMID: 33328355 DOI: 10.21775/cimb.042.409] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
All members of the Borrelia genus that have been examined harbour a linear chromosome that is about 900 kbp in length, as well as a plethora of both linear and circular plasmids in the 5-220 kbp size range. Genome sequences for 27 Lyme disease Borrelia isolates have been determined since the elucidation of the B. burgdorferi B31 genome sequence in 1997. The chromosomes, which carry the vast majority of the housekeeping genes, appear to be very constant in gene content and organization across all Lyme disease Borrelia species. The content of the plasmids, which carry most of the genes that encode the differentially expressed surface proteins that interact with the spirochete's arthropod and vertebrate hosts, is much more variable. Lyme disease Borrelia isolates carry between 7-21 different plasmids, ranging in size from 5-84 kbp. All strains analyzed to date harbor three plasmids, cp26, lp54 and lp17. The plasmids are unusual, as compared to most bacterial plasmids, in that they contain many paralogous sequences, a large number of pseudogenes, and, in some cases, essential genes. In addition, a number of the plasmids have features indicating that they are prophages. Numerous methods have been developed for Lyme disease Borrelia strain typing. These have proven valuable for clinical and epidemiological studies, as well as phylogenomic and population genetic analyses. Increasingly, these approaches have been displaced by whole genome sequencing techniques. Some correlations between genome content and pathogenicity have been deduced, and comparative whole genome analyses promise future progress in this arena.
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Affiliation(s)
- Ira Schwartz
- Department of Microbiology and Immunology, New York Medical College, Valhalla, NY USA
| | - Gabriele Margos
- National Reference Centre for Borrelia and Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Wei-Gang Qiu
- Department of Biological Sciences, Hunter College of the City University of New York, New York, NY USA
| | - Christian H Eggers
- Department of Biomedical Sciences, Quinnipiac University, Hamden, CT, USA
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16
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Gilcrease EB, Leavitt JC, Casjens SR. Genome Sequence of Salmonella enterica Serovar Typhimurium Bacteriophage MG40. Microbiol Resour Announc 2020; 9:e00905-20. [PMID: 32912919 PMCID: PMC7484078 DOI: 10.1128/mra.00905-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 08/17/2020] [Indexed: 11/20/2022] Open
Abstract
We report the complete genome sequence of P22-like Salmonella enterica serovar Typhimurium phage MG40, whose prophage repressor specificity is different from that of other known temperate phages.
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Affiliation(s)
- Eddie B Gilcrease
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Justin C Leavitt
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, USA
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
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17
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Thompson DW, Casjens SR, Sharma R, Grose JH. Genomic comparison of 60 completely sequenced bacteriophages that infect Erwinia and/or Pantoea bacteria. Virology 2019; 535:59-73. [PMID: 31276862 DOI: 10.1016/j.virol.2019.06.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022]
Abstract
Erwinia and Pantoea are closely related bacterial plant pathogens in the Gram negative Enterobacteriales order. Sixty tailed bacteriophages capable of infecting these pathogens have been completely sequenced by investigators around the world and are in the current databases, 30 of which were sequenced by our lab. These 60 were compared to 991 other Enterobacteriales bacteriophage genomes and found to be, on average, just over twice the overall average length. These Erwinia and Pantoea phages comprise 20 clusters based on nucleotide and protein sequences. Five clusters contain only phages that infect the Erwinia and Pantoea genera, the other 15 clusters are closely related to bacteriophages that infect other Enterobacteriales; however, within these clusters the Erwinia and Pantoea phages tend to be distinct, suggesting ecological niche may play a diversification role. The failure of many of their encoded proteins to have predicted functions highlights the need for further study of these phages.
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Affiliation(s)
- Daniel W Thompson
- Department of Microbiology and Molecular Biology, Brigham Young University, Utah, USA
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, University of Utah, Salt Lake City, UT, 84112, USA; School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Ruchira Sharma
- Department of Microbiology and Molecular Biology, Brigham Young University, Utah, USA
| | - Julianne H Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Utah, USA.
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18
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Newcomer RL, Schrad JR, Gilcrease EB, Casjens SR, Feig M, Teschke CM, Alexandrescu AT, Parent KN. The phage L capsid decoration protein has a novel OB-fold and an unusual capsid binding strategy. eLife 2019; 8:e45345. [PMID: 30945633 PMCID: PMC6449081 DOI: 10.7554/elife.45345] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 03/20/2019] [Indexed: 12/15/2022] Open
Abstract
The major coat proteins of dsDNA tailed phages (order Caudovirales) and herpesviruses form capsids by a mechanism that includes active packaging of the dsDNA genome into a precursor procapsid, followed by expansion and stabilization of the capsid. These viruses have evolved diverse strategies to fortify their capsids, such as non-covalent binding of auxiliary 'decoration' (Dec) proteins. The Dec protein from the P22-like phage L has a highly unusual binding strategy that distinguishes between nearly identical three-fold and quasi-three-fold sites of the icosahedral capsid. Cryo-electron microscopy and three-dimensional image reconstruction were employed to determine the structure of native phage L particles. NMR was used to determine the structure/dynamics of Dec in solution. The NMR structure and the cryo-EM density envelope were combined to build a model of the capsid-bound Dec trimer. Key regions that modulate the binding interface were verified by site-directed mutagenesis.
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Affiliation(s)
- Rebecca L Newcomer
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsUnited States
| | - Jason R Schrad
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingUnited States
| | - Eddie B Gilcrease
- Division of Microbiology and Immunology, Department of PathologyUniversity of Utah School of MedicineSalt Lake CityUnited States
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Department of PathologyUniversity of Utah School of MedicineSalt Lake CityUnited States
| | - Michael Feig
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingUnited States
| | - Carolyn M Teschke
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsUnited States
| | - Andrei T Alexandrescu
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsUnited States
| | - Kristin N Parent
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingUnited States
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19
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McNulty R, Cardone G, Gilcrease EB, Baker TS, Casjens SR, Johnson JE. Cryo-EM Elucidation of the Structure of Bacteriophage P22 Virions after Genome Release. Biophys J 2019; 114:1295-1301. [PMID: 29590587 DOI: 10.1016/j.bpj.2018.01.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 12/24/2017] [Accepted: 01/17/2018] [Indexed: 11/19/2022] Open
Abstract
Genome ejection proteins are required to facilitate transport of bacteriophage P22 double-stranded DNA safely through membranes of Salmonella. The structures and locations of all proteins in the context of the mature virion are known, with the exception of three ejection proteins. Furthermore, the changes that occur to the proteins residing in the mature virion upon DNA release are not fully understood. We used cryogenic electron microscopy to obtain what is, to our knowledge, the first asymmetric reconstruction of mature bacteriophage P22 after double-stranded DNA has been extruded from the capsid-a state representative of one step during viral infection. Results of icosahedral and asymmetric reconstructions at estimated resolutions of 7.8 and 12.5 Å resolutions, respectively, are presented. The reconstruction shows tube-like protein density extending from the center of the tail assembly. The portal protein does not revert to the more contracted, procapsid state, but instead maintains an extended and splayed barrel structure. These structural details contribute to our understanding of the molecular mechanism of P22 phage infection and also set the foundation for future exploitation serving engineering purposes.
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Affiliation(s)
- Reginald McNulty
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, California.
| | - Giovanni Cardone
- Department of Chemistry and BiochemistryUniversity of California, San Diego, La Jolla, California
| | - Eddie B Gilcrease
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah
| | - Timothy S Baker
- Department of Chemistry and BiochemistryUniversity of California, San Diego, La Jolla, California; Division of Biological Sciences, University of California, San Diego, La Jolla, California
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah
| | - John E Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California.
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20
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Gogokhia L, Buhrke K, Bell R, Hoffman B, Brown DG, Hanke-Gogokhia C, Ajami NJ, Wong MC, Ghazaryan A, Valentine JF, Porter N, Martens E, O'Connell R, Jacob V, Scherl E, Crawford C, Stephens WZ, Casjens SR, Longman RS, Round JL. Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis. Cell Host Microbe 2019; 25:285-299.e8. [PMID: 30763538 PMCID: PMC6885004 DOI: 10.1016/j.chom.2019.01.008] [Citation(s) in RCA: 295] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 10/23/2018] [Accepted: 01/15/2019] [Indexed: 02/07/2023]
Abstract
Bacteriophages are the most abundant members of the microbiota and have the potential to shape gut bacterial communities. Changes to bacteriophage composition are associated with disease, but how phages impact mammalian health remains unclear. We noted an induction of host immunity when experimentally treating bacterially driven cancer, leading us to test whether bacteriophages alter immune responses. Treating germ-free mice with bacteriophages leads to immune cell expansion in the gut. Lactobacillus, Escherichia, and Bacteroides bacteriophages and phage DNA stimulated IFN-γ via the nucleotide-sensing receptor TLR9. The resultant immune responses were both phage and bacteria specific. Additionally, increasing bacteriophage levels exacerbated colitis via TLR9 and IFN-γ. Similarly, ulcerative colitis (UC) patients responsive to fecal microbiota transplantation (FMT) have reduced phages compared to non-responders, and mucosal IFN-γ positively correlates with bacteriophage levels. Bacteriophages from active UC patients induced more IFN-γ compared to healthy individuals. Collectively, these results indicate that bacteriophages can alter mucosal immunity to impact mammalian health.
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Affiliation(s)
- Lasha Gogokhia
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Joan and Sanford I. Weill Department of Medicine, Jill Roberts Center and Institute for Research in Inflammatory Bowel Disease, Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Kate Buhrke
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Rickesha Bell
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Brenden Hoffman
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - D Garrett Brown
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Christin Hanke-Gogokhia
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew C Wong
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arevik Ghazaryan
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - John F Valentine
- Department of Internal Medicine, Division of Gastroenterology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Nathan Porter
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Eric Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ryan O'Connell
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Vinita Jacob
- Joan and Sanford I. Weill Department of Medicine, Jill Roberts Center and Institute for Research in Inflammatory Bowel Disease, Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ellen Scherl
- Joan and Sanford I. Weill Department of Medicine, Jill Roberts Center and Institute for Research in Inflammatory Bowel Disease, Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Carl Crawford
- Joan and Sanford I. Weill Department of Medicine, Jill Roberts Center and Institute for Research in Inflammatory Bowel Disease, Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, NY 10021, USA
| | - W Zac Stephens
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Sherwood R Casjens
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Randy S Longman
- Joan and Sanford I. Weill Department of Medicine, Jill Roberts Center and Institute for Research in Inflammatory Bowel Disease, Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, NY 10021, USA
| | - June L Round
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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21
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Bohm K, Porwollik S, Chu W, Dover JA, Gilcrease EB, Casjens SR, McClelland M, Parent KN. Genes affecting progression of bacteriophage P22 infection in Salmonella identified by transposon and single gene deletion screens. Mol Microbiol 2018; 108:288-305. [PMID: 29470858 PMCID: PMC5912970 DOI: 10.1111/mmi.13936] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2018] [Indexed: 12/20/2022]
Abstract
Bacteriophages rely on their hosts for replication, and many host genes critically determine either viral progeny production or host success via phage resistance. A random insertion transposon library of 240,000 mutants in Salmonella enterica serovar Typhimurium was used to monitor effects of individual bacterial gene disruptions on bacteriophage P22 lytic infection. These experiments revealed candidate host genes that alter the timing of phage P22 propagation. Using a False Discovery Rate of < 0.1, mutations in 235 host genes either blocked or delayed progression of P22 lytic infection, including many genes for which this role was previously unknown. Mutations in 77 genes reduced the survival time of host DNA after infection, including mutations in genes for enterobacterial common antigen (ECA) synthesis and osmoregulated periplasmic glucan (OPG). We also screened over 2000 Salmonella single gene deletion mutants to identify genes that impacted either plaque formation or culture growth rates. The gene encoding the periplasmic membrane protein YajC was newly found to be essential for P22 infection. Targeted mutagenesis of yajC shows that an essentially full-length protein is required for function, and potassium efflux measurements demonstrated that YajC is critical for phage DNA ejection across the cytoplasmic membrane.
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Affiliation(s)
- Kaitlynne Bohm
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Steffen Porwollik
- Department of Microbiology and Molecular Genetics, University of California, School of Medicine, Irvine, California 92697, USA
| | - Weiping Chu
- Department of Microbiology and Molecular Genetics, University of California, School of Medicine, Irvine, California 92697, USA
| | - John A Dover
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Eddie B Gilcrease
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California, School of Medicine, Irvine, California 92697, USA
| | - Kristin N Parent
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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22
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Abstract
Roger W. Hendrix was at the forefront of bacteriophage biology for nearly 50 years and was central to our understanding of both viral capsid assembly and phage genomic diversity and evolution. Roger's warm and gentle demeanor belied a razor-sharp mind and warmed him to numerous highly productive collaborations that amplified his scientific impact. Roger was always completely open with scientific ideas while at the same time quietly agitating with a stream of new ways of thinking about problems and nudging our communities to search for innovative solutions: a gentle but highly effective provocateur.
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Affiliation(s)
- Sherwood R Casjens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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23
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Casjens SR, Di L, Akther S, Mongodin EF, Luft BJ, Schutzer SE, Fraser CM, Qiu WG. Primordial origin and diversification of plasmids in Lyme disease agent bacteria. BMC Genomics 2018; 19:218. [PMID: 29580205 PMCID: PMC5870499 DOI: 10.1186/s12864-018-4597-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 03/12/2018] [Indexed: 12/19/2022] Open
Abstract
Background With approximately one-third of their genomes consisting of linear and circular plasmids, the Lyme disease agent cluster of species has the most complex genomes among known bacteria. We report here a comparative analysis of plasmids in eleven Borreliella (also known as Borrelia burgdorferi sensu lato) species. Results We sequenced the complete genomes of two B. afzelii, two B. garinii, and individual B. spielmanii, B. bissettiae, B. valaisiana and B. finlandensis isolates. These individual isolates carry between seven and sixteen plasmids, and together harbor 99 plasmids. We report here a comparative analysis of these plasmids, along with 70 additional Borreliella plasmids available in the public sequence databases. We identify only one new putative plasmid compatibility type (the 30th) among these 169 plasmid sequences, suggesting that all or nearly all such types have now been discovered. We find that the linear plasmids in the non-B. burgdorferi species have undergone the same kinds of apparently random, chaotic rearrangements mediated by non-homologous recombination that we previously discovered in B. burgdorferi. These rearrangements occurred independently in the different species lineages, and they, along with an expanded chromosomal phylogeny reported here, allow the identification of several whole plasmid transfer events among these species. Phylogenetic analyses of the plasmid partition genes show that a majority of the plasmid compatibility types arose early, most likely before separation of the Lyme agent Borreliella and relapsing fever Borrelia clades, and this, with occasional cross species plasmid transfers, has resulted in few if any species-specific or geographic region-specific Borreliella plasmid types. Conclusions The primordial origin and persistent maintenance of the Borreliella plasmid types support their functional indispensability as well as evolutionary roles in facilitating genome diversity. The improved resolution of Borreliella plasmid phylogeny based on conserved partition-gene clusters will lead to better determination of gene orthology which is essential for prediction of biological function, and it will provide a basis for inferring detailed evolutionary mechanisms of Borreliella genomic variability including homologous gene and plasmid exchanges as well as non-homologous rearrangements. Electronic supplementary material The online version of this article (10.1186/s12864-018-4597-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sherwood R Casjens
- Division of Microbiology and Immunology, Pathology Department and Biology Department, University of Utah School of Medicine, Salt Lake City, UT, USA. .,Biology Department, University of Utah, Salt Lake City, UT, USA. .,Pathology Department, University of Utah School of Medicine, Room 2200K Emma Eccles Jones Medical Research Building, 15 North Medical Drive East, Salt Lake City, UT, 84112, USA.
| | - Lia Di
- Department of Biological Sciences and Center for Translational and Basic Research, Hunter College of the City University of New York, New York, NY, USA
| | - Saymon Akther
- Department of Biology, The Graduate Center, City University of New York, New York, NY, USA
| | - Emmanuel F Mongodin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Benjamin J Luft
- Department of Medicine, Health Science Center, Stony Brook University, Stony Brook, NY, USA
| | - Steven E Schutzer
- Department of Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Claire M Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Wei-Gang Qiu
- Department of Biology, The Graduate Center, City University of New York, New York, NY, USA. .,Department of Biological Sciences and Center for Translational and Basic Research, Hunter College of the City University of New York, New York, NY, USA. .,Department of Physiology and Biophysics & Institute for Computational Biomedicine, Weil Cornell Medical College, New York, USA.
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24
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Gilcrease EB, Casjens SR. The genome sequence of Escherichia coli tailed phage D6 and the diversity of Enterobacteriales circular plasmid prophages. Virology 2018; 515:203-214. [PMID: 29304472 PMCID: PMC5800970 DOI: 10.1016/j.virol.2017.12.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/15/2017] [Accepted: 12/17/2017] [Indexed: 11/29/2022]
Abstract
The temperate Escherichia coli bacteriophage D6 can exist as a circular plasmid prophage, and we report here its 91,159bp complete genome sequence. It is a distant relative of the well-studied phage P1, but it is sufficiently different that it typifies a previously undescribed tailed phage type or cluster. Examination of the database of bacterial genome sequences revealed that phage P1 and D6 prophage plasmids are common in the Enterobacteriales, and in addition, previously described Salmonella phage SSU5 represents a different type of temperate tailed phage with a circular plasmid prophage that is also very common in this host order. This analysis also discovered additional divergent clusters of putative circular plasmid prophages within the two larger P1 and SSU5 groups (superclusters) that inhabit the Enterobacteriales as well as bacteria in several other orders in the Gamma-proteobacteria class. Very few of these sequences are annotated as putative prophages.
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Affiliation(s)
- Eddie B Gilcrease
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Biology Department, University of Utah, Salt Lake City, UT 84112, USA.
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25
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Bhattacharjee AS, Motlagh AM, Gilcrease EB, Islam MI, Casjens SR, Goel R. Complete genome sequence of lytic bacteriophage RG-2014 that infects the multidrug resistant bacterium Delftia tsuruhatensis ARB-1. Stand Genomic Sci 2017; 12:82. [PMID: 29270250 PMCID: PMC5735904 DOI: 10.1186/s40793-017-0290-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/24/2017] [Indexed: 01/10/2023] Open
Abstract
A lytic bacteriophage RG-2014 infecting a biofilm forming multidrug resistant bacterium Delftia tsuruhatensis strain ARB-1 as its host was isolated from a full-scale municipal wastewater treatment plant. Lytic phage RG-2014 was isolated for developing phage based therapeutic approaches against Delftia tsuruhatensis strain ARB-1. The strain ARB-1 belongs to the Comamonadaceae family of the Betaproteobacteria class. RG-2014 was characterized for its type, burst size, latent and eclipse time periods of 150 ± 9 PFU/cell, 10-min, <5-min, respectively. The phage was found to be a dsDNA virus belonging to the Podoviridae family. It has an isometric icosahedrally shaped capsid with a diameter of 85 nm. The complete genome of the isolated phage was sequenced and determined to be 73.8 kbp in length with a G + C content of 59.9%. Significant similarities in gene homology and order were observed between Delftia phage RG-2014 and the E. coli phage N4 indicating that it is a member of the N4-like phage group.
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Affiliation(s)
- Ananda Shankar Bhattacharjee
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT USA.,Bigelow Laboratory for Ocean Science, 60 Bigelow Dr., East Boothbay, ME USA
| | - Amir Mohaghegh Motlagh
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT USA.,Department of Civil, Environmental, and Construction Engineering, University of Central Florida, 12800 Pegasus Dr., Room 340, Orlando, FL USA
| | - Eddie B Gilcrease
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Md Imdadul Islam
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT USA
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT USA.,Department of Biology, University of Utah, Salt Lake City, UT USA
| | - Ramesh Goel
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT USA
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26
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Motlagh AM, Bhattacharjee AS, Coutinho FH, Dutilh BE, Casjens SR, Goel RK. Insights of Phage-Host Interaction in Hypersaline Ecosystem through Metagenomics Analyses. Front Microbiol 2017; 8:352. [PMID: 28316597 PMCID: PMC5334351 DOI: 10.3389/fmicb.2017.00352] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/20/2017] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages, as the most abundant biological entities on Earth, place significant predation pressure on their hosts. This pressure plays a critical role in the evolution, diversity, and abundance of bacteria. In addition, phages modulate the genetic diversity of prokaryotic communities through the transfer of auxiliary metabolic genes. Various studies have been conducted in diverse ecosystems to understand phage-host interactions and their effects on prokaryote metabolism and community composition. However, hypersaline environments remain among the least studied ecosystems and the interaction between the phages and prokaryotes in these habitats is poorly understood. This study begins to fill this knowledge gap by analyzing bacteriophage-host interactions in the Great Salt Lake, the largest prehistoric hypersaline lake in the Western Hemisphere. Our metagenomics analyses allowed us to comprehensively identify the bacterial and phage communities with Proteobacteria, Firmicutes, and Bacteroidetes as the most dominant bacterial species and Siphoviridae, Myoviridae, and Podoviridae as the most dominant viral families found in the metagenomic sequences. We also characterized interactions between the phage and prokaryotic communities of Great Salt Lake and determined how these interactions possibly influence the community diversity, structure, and biogeochemical cycles. In addition, presence of prophages and their interaction with the prokaryotic host was studied and showed the possibility of prophage induction and subsequent infection of prokaryotic community present in the Great Salt Lake environment under different environmental stress factors. We found that carbon cycle was the most susceptible nutrient cycling pathways to prophage induction in the presence of environmental stresses. This study gives an enhanced snapshot of phage and prokaryote abundance and diversity as well as their interactions in a hypersaline complex ecosystem, which can pave the way for further research studies.
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Affiliation(s)
- Amir Mohaghegh Motlagh
- Department of Civil and Environmental Engineering, University of Utah Salt Lake, UT, USA
| | - Ananda S Bhattacharjee
- Department of Civil and Environmental Engineering, University of Utah Salt Lake, UT, USA
| | - Felipe H Coutinho
- Instituto de Biologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil; Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics, Radboud University Medical CentreNijmegen, Netherlands
| | - Bas E Dutilh
- Instituto de Biologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil; Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics, Radboud University Medical CentreNijmegen, Netherlands; Theoretical Biology and Bioinformatics, Utrecht UniversityUtrecht, Netherlands
| | | | - Ramesh K Goel
- Department of Civil and Environmental Engineering, University of Utah Salt Lake, UT, USA
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27
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Casjens SR, Gilcrease EB, Vujadinovic M, Mongodin EF, Luft BJ, Schutzer SE, Fraser CM, Qiu WG. Plasmid diversity and phylogenetic consistency in the Lyme disease agent Borrelia burgdorferi. BMC Genomics 2017; 18:165. [PMID: 28201991 PMCID: PMC5310021 DOI: 10.1186/s12864-017-3553-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 02/03/2017] [Indexed: 01/13/2023] Open
Abstract
Background Bacteria from the genus Borrelia are known to harbor numerous linear and circular plasmids. We report here a comparative analysis of the nucleotide sequences of 236 plasmids present in fourteen independent isolates of the Lyme disease agent B. burgdorferi. Results We have sequenced the genomes of 14 B. burgdorferi sensu stricto isolates that carry a total of 236 plasmids. These individual isolates carry between seven and 23 plasmids. Their chromosomes, the cp26 and cp32 circular plasmids, as well as the lp54 linear plasmid, are quite evolutionarily stable; however, the remaining plasmids have undergone numerous non-homologous and often duplicative recombination events. We identify 32 different putative plasmid compatibility types among the 236 plasmids, of which 15 are (usually) circular and 17 are linear. Because of past rearrangements, any given gene, even though it might be universally present in these isolates, is often found on different linear plasmid compatibility types in different isolates. For example, the arp gene and the vls cassette region are present on plasmids of four and five different compatibility types, respectively, in different isolates. A majority of the plasmid types have more than one organizationally different subtype, and the number of such variants ranges from one to eight among the 18 linear plasmid types. In spite of this substantial organizational diversity, the plasmids are not so variable that every isolate has a novel version of every plasmid (i.e., there appears to be a limited number of extant plasmid subtypes). Conclusions Although there have been many past recombination events, both homologous and nonhomologous, among the plasmids, particular organizational variants of these plasmids correlate with particular chromosomal genotypes, suggesting that there has not been rapid horizontal transfer of whole linear plasmids among B. burgdorferi lineages. We argue that plasmid rearrangements are essentially non-revertable and are present at a frequency of only about 0.65% that of single nucleotide changes, making rearrangement-derived novel junctions (mosaic boundaries) ideal phylogenetic markers in the study of B. burgdorferi population structure and plasmid evolution and exchange. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3553-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sherwood R Casjens
- Division of Microbiology and Immunology, Pathology Department and Biology Department, University of Utah School of Medicine, Room 2200 K Emma Eccles Jones Medical Research Building, 15 North Medical Drive East, Salt Lake City, UT, 84112, USA. .,Biology Department, University of Utah, Salt Lake City, UT, USA.
| | - Eddie B Gilcrease
- Division of Microbiology and Immunology, Pathology Department and Biology Department, University of Utah School of Medicine, Room 2200 K Emma Eccles Jones Medical Research Building, 15 North Medical Drive East, Salt Lake City, UT, 84112, USA
| | - Marija Vujadinovic
- Division of Microbiology and Immunology, Pathology Department and Biology Department, University of Utah School of Medicine, Room 2200 K Emma Eccles Jones Medical Research Building, 15 North Medical Drive East, Salt Lake City, UT, 84112, USA.,Present Address: Janssen Disease and Vaccines, Pharmaceutical Companies of Johnson and Johnson, Leiden, The Netherlands
| | - Emmanuel F Mongodin
- Institute for Genome Sciences, University of Maryland BioPark, Baltimore, MD, USA
| | - Benjamin J Luft
- Department of Medicine, Health Science Center, Stony Brook University, Stony Brook, NY, USA
| | - Steven E Schutzer
- Department of Medicine, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ, 07103, USA
| | - Claire M Fraser
- Institute for Genome Sciences, University of Maryland BioPark, Baltimore, MD, USA
| | - Wei-Gang Qiu
- Department of Biology, The Graduate Center, City University of New York City, New York, NY, USA.,Department of Biological Sciences and Center for Translational and Basic Research, Hunter College of the City University of New York City, New York, NY, USA
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28
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Casjens SR, Grose JH. Contributions of P2- and P22-like prophages to understanding the enormous diversity and abundance of tailed bacteriophages. Virology 2016; 496:255-276. [PMID: 27372181 DOI: 10.1016/j.virol.2016.05.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 05/25/2016] [Accepted: 05/26/2016] [Indexed: 11/24/2022]
Abstract
We identified 9371 tailed phage prophages of 20 known types in reported complete genome sequences of 3298 bacteria in the Salmonella genus. These include 4758 P2 type and 744 P22 type prophages. The latter prophage types were found in the genome sequences of 127 and 24 bacterial host genera, increasing the known host ranges of phages in these groups by 114 and 20 genera, respectively. These prophage nucleotide sequences displayed much more diversity than was previously known from the 48 P2 and 24 P22 type authentic phages whose genomes have been sequenced. More detailed analysis of these prophage sequences indicated that major capsid protein (MCP) gene exchange between tailed phage clusters or types is extremely rare and that P22 prophage-encoded tailspikes correspond perfectly with their hosts' surface polysaccharide structure; thus, MCP and tailspike sequences accurately predict tailed phage type (and thus lifestyle) and host cell surface polysaccharide structure, respectively.
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Affiliation(s)
- Sherwood R Casjens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, University of Utah, Salt Lake City, UT 84112, United States; Department of Biology, University of Utah, Salt Lake City, UT 84112, United States.
| | - Julianne H Grose
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, UT 84602, United States.
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29
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Bhardwaj A, Sankhala RS, Olia AS, Brooke D, Casjens SR, Taylor DJ, Prevelige PE, Cingolani G. Structural Plasticity of the Protein Plug That Traps Newly Packaged Genomes in Podoviridae Virions. J Biol Chem 2015; 291:215-26. [PMID: 26574546 DOI: 10.1074/jbc.m115.696260] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Indexed: 02/05/2023] Open
Abstract
Bacterial viruses of the P22-like family encode a specialized tail needle essential for genome stabilization after DNA packaging and implicated in Gram-negative cell envelope penetration. The atomic structure of P22 tail needle (gp26) crystallized at acidic pH reveals a slender fiber containing an N-terminal "trimer of hairpins" tip. Although the length and composition of tail needles vary significantly in Podoviridae, unexpectedly, the amino acid sequence of the N-terminal tip is exceptionally conserved in more than 200 genomes of P22-like phages and prophages. In this paper, we used x-ray crystallography and EM to investigate the neutral pH structure of three tail needles from bacteriophage P22, HK620, and Sf6. In all cases, we found that the N-terminal tip is poorly structured, in stark contrast to the compact trimer of hairpins seen in gp26 crystallized at acidic pH. Hydrogen-deuterium exchange mass spectrometry, limited proteolysis, circular dichroism spectroscopy, and gel filtration chromatography revealed that the N-terminal tip is highly dynamic in solution and unlikely to adopt a stable trimeric conformation at physiological pH. This is supported by the cryo-EM reconstruction of P22 mature virion tail, where the density of gp26 N-terminal tip is incompatible with a trimer of hairpins. We propose the tail needle N-terminal tip exists in two conformations: a pre-ejection extended conformation, which seals the portal vertex after genome packaging, and a postejection trimer of hairpins, which forms upon its release from the virion. The conformational plasticity of the tail needle N-terminal tip is built in the amino acid sequence, explaining its extraordinary conservation in nature.
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Affiliation(s)
- Anshul Bhardwaj
- From the Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Rajeshwer S Sankhala
- From the Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Adam S Olia
- the Department of Biochemistry & Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Dewey Brooke
- the Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Sherwood R Casjens
- the Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Derek J Taylor
- the Department of Pharmacology, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106, and
| | - Peter E Prevelige
- the Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Gino Cingolani
- From the Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, the Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, Italy
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Molloy EM, Casjens SR, Cox CL, Maxson T, Ethridge NA, Margos G, Fingerle V, Mitchell DA. Identification of the minimal cytolytic unit for streptolysin S and an expansion of the toxin family. BMC Microbiol 2015. [PMID: 26204951 PMCID: PMC4513790 DOI: 10.1186/s12866-015-0464-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Streptolysin S (SLS) is a cytolytic virulence factor produced by the human pathogen Streptococcus pyogenes and other Streptococcus species. Related "SLS-like" toxins have been characterized in select strains of Clostridium and Listeria, with homologous clusters bioinformatically identified in a variety of other species. SLS is a member of the thiazole/oxazole-modified microcin (TOMM) family of natural products. The structure of SLS has yet to be deciphered and many questions remain regarding its structure-activity relationships. RESULTS In this work, we assessed the hemolytic activity of a series of C-terminally truncated SLS peptides expressed in SLS-deficient S. pyogenes. Our data indicate that while the N-terminal poly-heterocyclizable (NPH) region of SLS substantially contributes to its bioactivity, the variable C-terminal region of the toxin is largely dispensable. Through genome mining we identified additional SLS-like clusters in diverse Firmicutes, Spirochaetes and Actinobacteria. Among the Spirochaete clusters, naturally truncated SLS-like precursors were found in the genomes of three Lyme disease-causing Borrelia burgdorferi sensu lato (Bbsl) strains. Although unable to restore hemolysis in SLS-deficient S. pyogenes, a Bbsl SLS-like precursor peptide was converted to a cytolysin using purified SLS biosynthetic enzymes. A PCR-based screen demonstrated that SLS-like clusters are substantially more prevalent in Bbsl than inferred from publicly available genome sequences. CONCLUSIONS The mutagenesis data described herein indicate that the minimal cytolytic unit of SLS encompasses the NPH region of the core peptide. Interestingly, this region is found in all characterized TOMM cytolysins, as well as the novel putative TOMM cytolysins we discovered. We propose that this conserved region represents the defining feature of the SLS-like TOMM family. We demonstrate the cytolytic potential of a Bbsl SLS-like precursor peptide, which has a core region of similar length to the SLS minimal cytolytic unit, when modified with purified SLS biosynthetic enzymes. As such, we speculate that some Borrelia have the potential to produce a TOMM cytolysin, although the biological significance of this finding remains to be determined. In addition to providing new insight into the structure-activity relationships of SLS, this study greatly expands the cytolysin group of TOMMs.
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Affiliation(s)
- Evelyn M Molloy
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah Medical School, Salt Lake City, UT, 84112, USA.
| | - Courtney L Cox
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Tucker Maxson
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Nicole A Ethridge
- School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Gabriele Margos
- Bavarian Health and Food Safety Authority, National Reference Centre for Borrelia, Oberschleissheim, Germany.
| | - Volker Fingerle
- Bavarian Health and Food Safety Authority, National Reference Centre for Borrelia, Oberschleissheim, Germany.
| | - Douglas A Mitchell
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Abstract
Molecular genetic research on bacteriophage lambda carried out during its golden age from the mid-1950s to mid-1980s was critically important in the attainment of our current understanding of the sophisticated and complex mechanisms by which the expression of genes is controlled, of DNA virus assembly and of the molecular nature of lysogeny. The development of molecular cloning techniques, ironically instigated largely by phage lambda researchers, allowed many phage workers to switch their efforts to other biological systems. Nonetheless, since that time the ongoing study of lambda and its relatives has continued to give important new insights. In this review we give some relevant early history and describe recent developments in understanding the molecular biology of lambda's life cycle.
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Affiliation(s)
- Sherwood R Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Emma Eccles Jones Medical Research Building, 15 North Medical Drive East, Salt Lake City, UT 84112, USA; Biology Department, University of Utah, Salt Lake City, UT 84112, USA.
| | - Roger W Hendrix
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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32
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Grose JH, Casjens SR. Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae. Virology 2015; 468-470:421-443. [PMID: 25240328 DOI: 10.1016/j.virol.2014.08.024] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 08/18/2014] [Accepted: 08/22/2014] [Indexed: 02/03/2023]
Abstract
Bacteriophages are the predominant biological entity on the planet. The recent explosion of sequence information has made estimates of their diversity possible. We describe the genomic comparison of 337 fully sequenced tailed phages isolated on 18 genera and 31 species of bacteria in the Enterobacteriaceae. These phages were largely unambiguously grouped into 56 diverse clusters (32 lytic and 24 temperate) that have syntenic similarity over >50% of the genomes within each cluster, but substantially less sequence similarity between clusters. Most clusters naturally break into sets of more closely related subclusters, 78% of which are correlated with their host genera. The largest groups of related phages are superclusters united by genome synteny to lambda (81 phages) and T7 (51 phages). This study forms a robust framework for understanding diversity and evolutionary relationships of existing tailed phages, for relating newly discovered phages and for determining host/phage relationships.
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Affiliation(s)
- Julianne H Grose
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, UT 84602, USA.
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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33
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Parent KN, Tang J, Cardone G, Gilcrease EB, Janssen ME, Olson NH, Casjens SR, Baker TS. Three-dimensional reconstructions of the bacteriophage CUS-3 virion reveal a conserved coat protein I-domain but a distinct tailspike receptor-binding domain. Virology 2014; 464-465:55-66. [PMID: 25043589 DOI: 10.1016/j.virol.2014.06.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 06/12/2014] [Accepted: 06/15/2014] [Indexed: 01/21/2023]
Abstract
CUS-3 is a short-tailed, dsDNA bacteriophage that infects serotype K1 Escherichia coli. We report icosahedrally averaged and asymmetric, three-dimensional, cryo-electron microscopic reconstructions of the CUS-3 virion. Its coat protein structure adopts the "HK97-fold" shared by other tailed phages and is quite similar to that in phages P22 and Sf6 despite only weak amino acid sequence similarity. In addition, these coat proteins share a unique extra external domain ("I-domain"), suggesting that the group of P22-like phages has evolved over a very long time period without acquiring a new coat protein gene from another phage group. On the other hand, the morphology of the CUS-3 tailspike differs significantly from that of P22 or Sf6, but is similar to the tailspike of phage K1F, a member of the extremely distantly related T7 group of phages. We conclude that CUS-3 obtained its tailspike gene from a distantly related phage quite recently.
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Affiliation(s)
- Kristin N Parent
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, United States.
| | - Jinghua Tang
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, United States
| | - Giovanni Cardone
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, United States
| | - Eddie B Gilcrease
- University of Utah School of Medicine, Division of Microbiology and Immunology, Department of Pathology, Salt Lake City, UT 84112, United States
| | - Mandy E Janssen
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, United States
| | - Norman H Olson
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, United States
| | - Sherwood R Casjens
- University of Utah School of Medicine, Division of Microbiology and Immunology, Department of Pathology, Salt Lake City, UT 84112, United States.
| | - Timothy S Baker
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, United States; University of California, San Diego, Division of Biological Sciences, La Jolla, CA, 92093, United States.
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34
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Di L, Pagan PE, Packer D, Martin CL, Akther S, Ramrattan G, Mongodin EF, Fraser CM, Schutzer SE, Luft BJ, Casjens SR, Qiu WG. BorreliaBase: a phylogeny-centered browser of Borrelia genomes. BMC Bioinformatics 2014; 15:233. [PMID: 24994456 PMCID: PMC4094996 DOI: 10.1186/1471-2105-15-233] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 06/26/2014] [Indexed: 11/29/2022] Open
Abstract
Background The bacterial genus Borrelia (phylum Spirochaetes) consists of two groups of pathogens represented respectively by B. burgdorferi, the agent of Lyme borreliosis, and B. hermsii, the agent of tick-borne relapsing fever. The number of publicly available Borrelia genomic sequences is growing rapidly with the discovery and sequencing of Borrelia strains worldwide. There is however a lack of dedicated online databases to facilitate comparative analyses of Borrelia genomes. Description We have developed BorreliaBase, an online database for comparative browsing of Borrelia genomes. The database is currently populated with sequences from 35 genomes of eight Lyme-borreliosis (LB) group Borrelia species and 7 Relapsing-fever (RF) group Borrelia species. Distinct from genome repositories and aggregator databases, BorreliaBase serves manually curated comparative-genomic data including genome-based phylogeny, genome synteny, and sequence alignments of orthologous genes and intergenic spacers. Conclusions With a genome phylogeny at its center, BorreliaBase allows online identification of hypervariable lipoprotein genes, potential regulatory elements, and recombination footprints by providing evolution-based expectations of sequence variability at each genomic locus. The phylo-centric design of BorreliaBase (http://borreliabase.org) is a novel model for interactive browsing and comparative analysis of bacterial genomes online.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Wei-Gang Qiu
- Department of Biological Sciences, Hunter College, The City University of New York, 10065 New York, NY, USA.
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35
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Parent KN, Erb ML, Cardone G, Nguyen K, Gilcrease EB, Porcek NB, Pogliano J, Baker TS, Casjens SR. OmpA and OmpC are critical host factors for bacteriophage Sf6 entry in Shigella. Mol Microbiol 2014; 92:47-60. [PMID: 24673644 DOI: 10.1111/mmi.12536] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2014] [Indexed: 12/26/2022]
Abstract
Despite being essential for successful infection, the molecular cues involved in host recognition and genome transfer of viruses are not completely understood. Bacterial outer membrane proteins A and C co-purify in lipid vesicles with bacteriophage Sf6, implicating both outer membrane proteins as potential host receptors. We determined that outer membrane proteins A and C mediate Sf6 infection by dramatically increasing its rate and efficiency. We performed a combination of in vivo studies with three omp null mutants of Shigella flexneri, including classic phage plaque assays and time-lapse fluorescence microscopy to monitor genome ejection at the single virion level. Cryo-electron tomography of phage 'infecting' outer membrane vesicles shows the tail needle contacting and indenting the outer membrane. Lastly, in vitro ejection studies reveal that lipopolysaccharide and outer membrane proteins are both required for Sf6 genome release. We conclude that Sf6 phage entry utilizes either outer membrane proteins A or C, with outer membrane protein A being the preferred receptor.
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Affiliation(s)
- Kristin N Parent
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA; Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
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36
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Bearson BL, Allen HK, Brunelle BW, Lee IS, Casjens SR, Stanton TB. The agricultural antibiotic carbadox induces phage-mediated gene transfer in Salmonella. Front Microbiol 2014; 5:52. [PMID: 24575089 PMCID: PMC3920066 DOI: 10.3389/fmicb.2014.00052] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 01/23/2014] [Indexed: 12/23/2022] Open
Abstract
Antibiotics are used for disease therapeutic or preventative effects in humans and animals, as well as for enhanced feed conversion efficiency in livestock. Antibiotics can also cause undesirable effects in microbial populations, including selection for antibiotic resistance, enhanced pathogen invasion, and stimulation of horizontal gene transfer. Carbadox is a veterinary antibiotic used in the US during the starter phase of swine production for improved feed efficiency and control of swine dysentery and bacterial swine enteritis. Carbadox has been shown in vitro to induce phage-encoded Shiga toxin in Shiga toxin-producing Escherichia coli (STEC) and a phage-like element transferring antibiotic resistance genes in Brachyspira hyodysenteriae, but the effect of carbadox on prophages in other bacteria is unknown. This study examined carbadox exposure on prophage induction and genetic transfer in Salmonella enterica serovar Typhimurium, a human foodborne pathogen that frequently colonizes swine without causing disease. S. Typhimurium LT2 exposed to carbadox induced prophage production, resulting in bacterial cell lysis and release of virions that were visible by electron microscopy. Carbadox induction of phage-mediated gene transfer was confirmed by monitoring the transduction of a sodCIII::neo cassette in the Fels-1 prophage from LT2 to a recipient Salmonella strain. Furthermore, carbadox frequently induced generalized transducing phages in multidrug-resistant phage type DT104 and DT120 isolates, resulting in the transfer of chromosomal and plasmid DNA that included antibiotic resistance genes. Our research indicates that exposure of Salmonella to carbadox induces prophages that can transfer virulence and antibiotic resistance genes to susceptible bacterial hosts. Carbadox-induced, phage-mediated gene transfer could serve as a contributing factor in bacterial evolution during animal production, with prophages being a reservoir for bacterial fitness genes in the environment.
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Affiliation(s)
- Bradley L Bearson
- Agroecosystems Management Research Unit, National Laboratory for Agriculture and the Environment, ARS, USDA Ames, IA, USA
| | - Heather K Allen
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, ARS, USDA Ames, IA, USA
| | - Brian W Brunelle
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, ARS, USDA Ames, IA, USA
| | - In Soo Lee
- Agroecosystems Management Research Unit, National Laboratory for Agriculture and the Environment, ARS, USDA Ames, IA, USA ; Department of Biological Sciences and Biotechnology, Hannam University Daejeon, South Korea
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah Salt Lake City, UT, USA
| | - Thaddeus B Stanton
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, ARS, USDA Ames, IA, USA
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37
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Bhardwaj A, Casjens SR, Cingolani G. Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography. Acta Crystallogr D Biol Crystallogr 2014; 70:342-53. [PMID: 24531468 PMCID: PMC3940195 DOI: 10.1107/s1399004713027685] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/09/2013] [Indexed: 11/10/2022]
Abstract
Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20-35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.
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Affiliation(s)
- Anshul Bhardwaj
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
| | - Sherwood R. Casjens
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
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38
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Mongodin EF, Casjens SR, Bruno JF, Xu Y, Drabek EF, Riley DR, Cantarel BL, Pagan PE, Hernandez YA, Vargas LC, Dunn JJ, Schutzer SE, Fraser CM, Qiu WG, Luft BJ. Inter- and intra-specific pan-genomes of Borrelia burgdorferi sensu lato: genome stability and adaptive radiation. BMC Genomics 2013; 14:693. [PMID: 24112474 PMCID: PMC3833655 DOI: 10.1186/1471-2164-14-693] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 09/26/2013] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Lyme disease is caused by spirochete bacteria from the Borrelia burgdorferi sensu lato (B. burgdorferi s.l.) species complex. To reconstruct the evolution of B. burgdorferi s.l. and identify the genomic basis of its human virulence, we compared the genomes of 23 B. burgdorferi s.l. isolates from Europe and the United States, including B. burgdorferi sensu stricto (B. burgdorferi s.s., 14 isolates), B. afzelii (2), B. garinii (2), B. "bavariensis" (1), B. spielmanii (1), B. valaisiana (1), B. bissettii (1), and B. "finlandensis" (1). RESULTS Robust B. burgdorferi s.s. and B. burgdorferi s.l. phylogenies were obtained using genome-wide single-nucleotide polymorphisms, despite recombination. Phylogeny-based pan-genome analysis showed that the rate of gene acquisition was higher between species than within species, suggesting adaptive speciation. Strong positive natural selection drives the sequence evolution of lipoproteins, including chromosomally-encoded genes 0102 and 0404, cp26-encoded ospC and b08, and lp54-encoded dbpA, a07, a22, a33, a53, a65. Computer simulations predicted rapid adaptive radiation of genomic groups as population size increases. CONCLUSIONS Intra- and inter-specific pan-genome sizes of B. burgdorferi s.l. expand linearly with phylogenetic diversity. Yet gene-acquisition rates in B. burgdorferi s.l. are among the lowest in bacterial pathogens, resulting in high genome stability and few lineage-specific genes. Genome adaptation of B. burgdorferi s.l. is driven predominantly by copy-number and sequence variations of lipoprotein genes. New genomic groups are likely to emerge if the current trend of B. burgdorferi s.l. population expansion continues.
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Affiliation(s)
- Emmanuel F Mongodin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.
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Leavitt JC, Gogokhia L, Gilcrease EB, Bhardwaj A, Cingolani G, Casjens SR. The tip of the tail needle affects the rate of DNA delivery by bacteriophage P22. PLoS One 2013; 8:e70936. [PMID: 23951045 PMCID: PMC3741392 DOI: 10.1371/journal.pone.0070936] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 06/25/2013] [Indexed: 02/01/2023] Open
Abstract
The P22-like bacteriophages have short tails. Their virions bind to their polysaccharide receptors through six trimeric tailspike proteins that surround the tail tip. These short tails also have a trimeric needle protein that extends beyond the tailspikes from the center of the tail tip, in a position that suggests that it should make first contact with the host’s outer membrane during the infection process. The base of the needle serves as a plug that keeps the DNA in the virion, but role of the needle during adsorption and DNA injection is not well understood. Among the P22-like phages are needle types with two completely different C-terminal distal tip domains. In the phage Sf6-type needle, unlike the other P22-type needle, the distal tip folds into a “knob” with a TNF-like fold, similar to the fiber knobs of bacteriophage PRD1 and Adenovirus. The phage HS1 knob is very similar to that of Sf6, and we report here its crystal structure which, like the Sf6 knob, contains three bound L-glutamate molecules. A chimeric P22 phage with a tail needle that contains the HS1 terminal knob efficiently infects the P22 host, Salmonella enterica, suggesting the knob does not confer host specificity. Likewise, mutations that should abrogate the binding of L-glutamate to the needle do not appear to affect virion function, but several different other genetic changes to the tip of the needle slow down potassium release from the host during infection. These findings suggest that the needle plays a role in phage P22 DNA delivery by controlling the kinetics of DNA ejection into the host.
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Affiliation(s)
- Justin C. Leavitt
- Biology Department, University of Utah, Salt Lake City, Utah, United States of America
| | - Lasha Gogokhia
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Eddie B. Gilcrease
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Anshul Bhardwaj
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Sherwood R. Casjens
- Biology Department, University of Utah, Salt Lake City, Utah, United States of America
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- * E-mail:
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40
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Leavitt JC, Gilcrease EB, Wilson K, Casjens SR. Function and horizontal transfer of the small terminase subunit of the tailed bacteriophage Sf6 DNA packaging nanomotor. Virology 2013; 440:117-33. [PMID: 23562538 DOI: 10.1016/j.virol.2013.02.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 02/22/2013] [Accepted: 02/26/2013] [Indexed: 11/27/2022]
Abstract
Bacteriophage Sf6 DNA packaging series initiate at many locations across a 2kbp region. Our in vivo studies show that Sf6 small terminase subunit (TerS) protein recognizes a specific packaging (pac) site near the center of this region, that this site lies within the portion of the Sf6 gene that encodes the DNA-binding domain of TerS protein, that this domain of the TerS protein is responsible for the imprecision in Sf6 packaging initiation, and that the DNA-binding domain of TerS must be covalently attached to the domain that interacts with the rest of the packaging motor. The TerS DNA-binding domain is self-contained in that it apparently does not interact closely with the rest of the motor and it binds to a recognition site that lies within the DNA that encodes the domain. This arrangement has allowed the horizontal exchange of terS genes among phages to be very successful.
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Affiliation(s)
- Justin C Leavitt
- Biology Department, University of Utah, Salt Lake City, UT 84112, USA
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41
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Wiles TJ, Norton JP, Smith SN, Lewis AJ, Mobley HLT, Casjens SR, Mulvey MA. A phyletically rare gene promotes the niche-specific fitness of an E. coli pathogen during bacteremia. PLoS Pathog 2013; 9:e1003175. [PMID: 23459509 PMCID: PMC3573123 DOI: 10.1371/journal.ppat.1003175] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 12/19/2012] [Indexed: 12/17/2022] Open
Abstract
In bacteria, laterally acquired genes are often concentrated within chromosomal regions known as genomic islands. Using a recently developed zebrafish infection model, we set out to identify unique factors encoded within genomic islands that contribute to the fitness and virulence of a reference urosepsis isolate—extraintestinal pathogenic Escherichia coli strain CFT073. By screening a series of deletion mutants, we discovered a previously uncharacterized gene, neaT, that is conditionally required by the pathogen during systemic infections. In vitro assays indicate that neaT can limit bacterial interactions with host phagocytes and alter the aggregative properties of CFT073. The neaT gene is localized within an integrated P2-like bacteriophage in CFT073, but was rarely found within other proteobacterial genomes. Sequence-based analyses revealed that neaT homologues are present, but discordantly conserved, within a phyletically diverse set of bacterial species. In CFT073, neaT appears to be unameliorated, having an exceptionally A+T-rich composition along with a notably altered codon bias. These data suggest that neaT was recently brought into the proteobacterial pan-genome from an extra-phyletic source. Interestingly, even in G+C-poor genomes, as found within the Firmicutes lineage, neaT-like genes are often unameliorated. Sequence-level features of neaT homologues challenge the common supposition that the A+T-rich nature of many recently acquired genes reflects the nucleotide composition of their genomes of origin. In total, these findings highlight the complexity of the evolutionary forces that can affect the acquisition, utilization, and assimilation of rare genes that promote the niche-dependent fitness and virulence of a bacterial pathogen. Bacterial pathogens, even those belonging to the same species, can be incredibly diverse with regard to the genes they carry. However, the design of vaccines and antibiotics typically relies upon identification of general molecular features shared by the targeted organisms. Thus, we have traditionally focused on broadly conserved characteristics of pathogenic bacteria, often ignoring the genes that account for their individuality. In this article we report the discovery of a unique gene, neaT, that promotes the fitness of a pathogenic Escherichia coli isolate in zebrafish and mouse models of systemic blood infections. Surprisingly, neaT is rarely found in other related strains of E. coli and appears to have been recently acquired from distant lineages of bacteria via a process known as ‘lateral gene transfer’ that is used by microbes to swap genetic material. Expression of the neaT gene appears to help pathogens avoid interactions with host immune cells, possibly by altering bacterial surface structures. This work provides an interesting example of how the lateral acquisition of a rare gene can impact the niche-specific virulence properties of a pathogen, shedding light on the mechanisms that drive pathogen evolution and diversity.
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Affiliation(s)
- Travis J. Wiles
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - J. Paul Norton
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Sara N. Smith
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Adam J. Lewis
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Harry L. T. Mobley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Sherwood R. Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Matthew A. Mulvey
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- * E-mail:
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Padilla-Meier GP, Gilcrease EB, Weigele PR, Cortines JR, Siegel M, Leavitt JC, Teschke CM, Casjens SR. Unraveling the role of the C-terminal helix turn helix of the coat-binding domain of bacteriophage P22 scaffolding protein. J Biol Chem 2012; 287:33766-80. [PMID: 22879595 DOI: 10.1074/jbc.m112.393132] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many viruses encode scaffolding and coat proteins that co-assemble to form procapsids, which are transient precursor structures leading to progeny virions. In bacteriophage P22, the association of scaffolding and coat proteins is mediated mainly by ionic interactions. The coat protein-binding domain of scaffolding protein is a helix turn helix structure near the C terminus with a high number of charged surface residues. Residues Arg-293 and Lys-296 are particularly important for coat protein binding. The two helices contact each other through hydrophobic side chains. In this study, substitution of the residues of the interface between the helices, and the residues in the β-turn, by aspartic acid was used examine the importance of the conformation of the domain in coat binding. These replacements strongly affected the ability of the scaffolding protein to interact with coat protein. The severity of the defect in the association of scaffolding protein to coat protein was dependent on location, with substitutions at residues in the turn and helix 2 causing the most significant effects. Substituting aspartic acid for hydrophobic interface residues dramatically perturbs the stability of the structure, but similar substitutions in the turn had much less effect on the integrity of this domain, as determined by circular dichroism. We propose that the binding of scaffolding protein to coat protein is dependent on angle of the β-turn and the orientation of the charged surface on helix 2. Surprisingly, formation of the highly complex procapsid structure depends on a relatively simple interaction.
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Affiliation(s)
- G Pauline Padilla-Meier
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
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Parent KN, Deedas CT, Egelman EH, Casjens SR, Baker TS, Teschke CM. Stepwise molecular display utilizing icosahedral and helical complexes of phage coat and decoration proteins in the development of robust nanoscale display vehicles. Biomaterials 2012; 33:5628-37. [PMID: 22575828 DOI: 10.1016/j.biomaterials.2012.04.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Accepted: 04/08/2012] [Indexed: 01/18/2023]
Abstract
A stepwise addition protocol was developed to display cargo using bacteriophage P22 capsids and the phage decoration (Dec) protein. Three-dimensional image reconstructions of frozen-hydrated samples of P22 particles with nanogold-labeled Dec bound to them revealed the locations of the N- and C-termini of Dec. Each terminus is readily accessible for molecular display through affinity tags such as nickel-nitrilotriacetic acid, providing a total of 240 cargo-binding sites. Dec was shown by circular dichroism to be a β-sheet rich protein, and fluorescence anisotropy binding experiments demonstrated that Dec binds to P22 heads with high (~110 nm) affinity. Dec also binds to P22 nanotubes, which are helically symmetric assemblies that form when the P22 coat protein contains the F170A amino acid substitution. Several classes of tubes with Dec bound to them were visualized by cryo-electron microscopy and their three-dimensional structures were determined by helical reconstruction methods. In all instances, Dec trimers bound to P22 capsids and nanotubes at positions where three neighboring capsomers (oligomers of six coat protein subunits) lie in close proximity to one another. Stable interactions between Dec and P22 allow for the development of robust, nanoscale size, display vehicles.
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Affiliation(s)
- Kristin N Parent
- Department of Chemistry & Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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Casjens SR, Mongodin EF, Qiu WG, Luft BJ, Schutzer SE, Gilcrease EB, Huang WM, Vujadinovic M, Aron JK, Vargas LC, Freeman S, Radune D, Weidman JF, Dimitrov GI, Khouri HM, Sosa JE, Halpin RA, Dunn JJ, Fraser CM. Genome stability of Lyme disease spirochetes: comparative genomics of Borrelia burgdorferi plasmids. PLoS One 2012; 7:e33280. [PMID: 22432010 PMCID: PMC3303823 DOI: 10.1371/journal.pone.0033280] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 02/06/2012] [Indexed: 11/21/2022] Open
Abstract
Lyme disease is the most common tick-borne human illness in North America. In order to understand the molecular pathogenesis, natural diversity, population structure and epizootic spread of the North American Lyme agent, Borrelia burgdorferi sensu stricto, a much better understanding of the natural diversity of its genome will be required. Towards this end we present a comparative analysis of the nucleotide sequences of the numerous plasmids of B. burgdorferi isolates B31, N40, JD1 and 297. These strains were chosen because they include the three most commonly studied laboratory strains, and because they represent different major genetic lineages and so are informative regarding the genetic diversity and evolution of this organism. A unique feature of Borrelia genomes is that they carry a large number of linear and circular plasmids, and this work shows that strains N40, JD1, 297 and B31 carry related but non-identical sets of 16, 20, 19 and 21 plasmids, respectively, that comprise 33–40% of their genomes. We deduce that there are at least 28 plasmid compatibility types among the four strains. The B. burgdorferi ∼900 Kbp linear chromosomes are evolutionarily exceptionally stable, except for a short ≤20 Kbp plasmid-like section at the right end. A few of the plasmids, including the linear lp54 and circular cp26, are also very stable. We show here that the other plasmids, especially the linear ones, are considerably more variable. Nearly all of the linear plasmids have undergone one or more substantial inter-plasmid rearrangements since their last common ancestor. In spite of these rearrangements and differences in plasmid contents, the overall gene complement of the different isolates has remained relatively constant.
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Affiliation(s)
- Sherwood R Casjens
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America.
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45
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Parent KN, Gilcrease EB, Casjens SR, Baker TS. Structural evolution of the P22-like phages: comparison of Sf6 and P22 procapsid and virion architectures. Virology 2012; 427:177-88. [PMID: 22386055 DOI: 10.1016/j.virol.2012.01.040] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 01/10/2012] [Accepted: 01/30/2012] [Indexed: 01/07/2023]
Abstract
Coat proteins of tailed, dsDNA phages and in herpesviruses include a conserved core similar to the bacteriophage HK97 subunit. This core is often embellished with other domains such as the telokin Ig-like domain of phage P22. Eighty-six P22-like phages and prophages with sequenced genomes share a similar set of virion assembly genes and, based on comparisons of twelve viral assembly proteins (structural and assembly/packaging chaperones), these phages are classified into three groups (P22-like, Sf6-like, and CUS-3-like). We used cryo-electron microscopy and 3D image reconstruction to determine the structures of Sf6 procapsids and virions (~7Å resolution), and the structure of the entire, asymmetric Sf6 virion (16-Å resolution). The Sf6 coat protein is similar to that of P22 yet it has differences in the telokin domain and in its overall quaternary organization. Thermal stability and agarose gel experiments show that Sf6 virions are slightly less stable than those of P22. Finally, bacterial host outer membrane proteins A and C were identified in lipid vesicles that co-purify with Sf6 particles, but are not components of the capsid.
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Affiliation(s)
- Kristin N Parent
- University of California, San Diego, Department of Chemistry & Biochemistry, La Jolla, CA 92093, USA
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Abstract
Tailed dsDNA bacteriophage virions bind to susceptible cells with the tips of their tails and then deliver their DNA through the tail into the cells to initiate infection. This chapter discusses what is known about this process in the short-tailed phages (Podoviridae). Their short tails require that many of these virions adsorb to the outer layers of the cell and work their way down to the outer membrane surface before releasing their DNA. Interestingly, the receptor-binding protein of many short-tailed phages (and some with long tails) has an enzymatic activity that cleaves their polysaccharide receptors. Reversible adsorption and irreversible adsorption to primary and secondary receptors are discussed, including how sequence divergence in tail fiber and tailspike proteins leads to different host specificities. Upon reaching the outer membrane of Gram-negative cells, some podoviral tail machines release virion proteins into the cell that help the DNA efficiently traverse the outer layers of the cell and/or prepare the cell cytoplasm for phage genome arrival. Podoviruses utilize several rather different variations on this theme. The virion DNA is then released into the cell; the energetics of this process is discussed. Phages like T7 and N4 deliver their DNA relatively slowly, using enzymes to pull the genome into the cell. At least in part this mechanism ensures that genes in late-entering DNA are not expressed at early times. On the other hand, phages like P22 probably deliver their DNA more rapidly so that it can be circularized before the cascade of gene expression begins.
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Affiliation(s)
- Sherwood R Casjens
- Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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Cortines JR, Weigele PR, Gilcrease EB, Casjens SR, Teschke CM. Decoding bacteriophage P22 assembly: identification of two charged residues in scaffolding protein responsible for coat protein interaction. Virology 2011; 421:1-11. [PMID: 21974803 DOI: 10.1016/j.virol.2011.09.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 08/15/2011] [Accepted: 09/08/2011] [Indexed: 11/17/2022]
Abstract
Proper assembly of viruses must occur through specific interactions between capsid proteins. Many double-stranded DNA viruses and bacteriophages require internal scaffolding proteins to assemble their coat proteins into icosahedral capsids. The 303 amino acid bacteriophage P22 scaffolding protein is mostly helical, and its C-terminal helix-turn-helix (HTH) domain binds to the coat protein during virion assembly, directing the formation of an intermediate structure called the procapsid. The interaction between coat and scaffolding protein HTH domain is electrostatic, but the amino acids that form the protein-protein interface have yet to be described. In the present study, we used alanine scanning mutagenesis of charged surface residues of the C-terminal HTH domain of scaffolding protein. We have determined that P22 scaffolding protein residues R293 and K296 are crucial for binding to coat protein and that the neighboring charges are not essential but do modulate the affinity between the two proteins.
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Affiliation(s)
- Juliana R Cortines
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
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Bhardwaj A, Molineux IJ, Casjens SR, Cingolani G. Atomic structure of bacteriophage Sf6 tail needle knob. J Biol Chem 2011; 286:30867-30877. [PMID: 21705802 PMCID: PMC3162447 DOI: 10.1074/jbc.m111.260877] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 06/22/2011] [Indexed: 11/06/2022] Open
Abstract
Podoviridae are double-stranded DNA bacteriophages that use short, non-contractile tails to adsorb to the host cell surface. Within the tail apparatus of P22-like phages, a dedicated fiber known as the "tail needle" likely functions as a cell envelope-penetrating device to promote ejection of viral DNA inside the host. In Sf6, a P22-like phage that infects Shigella flexneri, the tail needle presents a C-terminal globular knob. This knob, absent in phage P22 but shared in other members of the P22-like genus, represents the outermost exposed tip of the virion that contacts the host cell surface. Here, we report a crystal structure of the Sf6 tail needle knob determined at 1.0 Å resolution. The structure reveals a trimeric globular domain of the TNF fold structurally superimposable with that of the tail-less phage PRD1 spike protein P5 and the adenovirus knob, domains that in both viruses function in receptor binding. However, P22-like phages are not known to utilize a protein receptor and are thought to directly penetrate the host surface. At 1.0 Å resolution, we identified three equivalents of l-glutamic acid (l-Glu) bound to each subunit interface. Although intimately bound to the protein, l-Glu does not increase the structural stability of the trimer nor it affects its ability to self-trimerize in vitro. In analogy to P22 gp26, we suggest the tail needle of phage Sf6 is ejected through the bacterial cell envelope during infection and its C-terminal knob is threaded through peptidoglycan pores formed by glycan strands.
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Affiliation(s)
- Anshul Bhardwaj
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Ian J Molineux
- Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas 78712
| | - Sherwood R Casjens
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107.
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Casjens SR, Thuman-Commike PA. Evolution of mosaically related tailed bacteriophage genomes seen through the lens of phage P22 virion assembly. Virology 2011; 411:393-415. [PMID: 21310457 DOI: 10.1016/j.virol.2010.12.046] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 12/20/2010] [Accepted: 12/23/2010] [Indexed: 01/06/2023]
Abstract
The mosaic composition of the genomes of dsDNA tailed bacteriophages (Caudovirales) is well known. Observations of this mosaicism have generally come from comparisons of small numbers of often rather distantly related phages, and little is known about the frequency or detailed nature of the processes that generate this kind of diversity. Here we review and examine the mosaicism within fifty-seven clusters of virion assembly genes from bacteriophage P22 and its "close" relatives. We compare these orthologous gene clusters, discuss their surprising diversity and document horizontal exchange of genetic information between subgroups of the P22-like phages as well as between these phages and other phage types. We also point out apparent restrictions in the locations of mosaic sequence boundaries in this gene cluster. The relatively large sample size and the fact that phage P22 virion structure and assembly are exceptionally well understood make the conclusions especially informative and convincing.
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Affiliation(s)
- Sherwood R Casjens
- Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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Wywial E, Haven J, Casjens SR, Hernandez YA, Singh S, Mongodin EF, Fraser-Liggett CM, Luft BJ, Schutzer SE, Qiu WG. Fast, adaptive evolution at a bacterial host-resistance locus: the PFam54 gene array in Borrelia burgdorferi. Gene 2009; 445:26-37. [PMID: 19505540 DOI: 10.1016/j.gene.2009.05.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 05/15/2009] [Accepted: 05/31/2009] [Indexed: 10/20/2022]
Abstract
Microbial pathogens have evolved sophisticated mechanisms for evasion of host innate and adaptive immunities. PFam54 is the largest paralogous gene family in the genomes of Borrelia burgdorferi, the Lyme disease bacterium. One member of PFam54, the complement-regulator acquiring surface proteins 1 (BbCrasp-1), is able to abort the alternative pathway of complement activation via binding human complement-regulator factor H (FH). The gene coding for BbCRASP-1 exists in a tandem array of PFam54 genes in the B. burgdorferi genome, a result apparently of repeated gene duplications. To help elucidate the functions of the large number of PFam54 genes, we performed phylogenomic and structural analyses of the PFam54 gene array from ten B. burgdorferi genomes. Analyses based on gene tree, genome synteny, and structural models revealed rapid adaptive evolution of this array through gene duplication, gene loss, and functional diversification. Individual PFam54 genes, however, do not show high intra-population sequence polymorphisms as genes providing evasion from adaptive immunity generally do. PFam54 members able to bind human FH are not monophyletic, suggesting that human FH affinity, however strong, is an incidental rather than main function of these PFam54 proteins. The large number of PFam54 genes existing in any single B. burgdorferi genome may target different innate-immunity proteins of a single host species or the same immune protein of a variety of host species. Genetic variability of the PFam54 gene array suggests that universally present PFam54 lineages such as BBA64, BBA65, BBA66, and BBA73 may be better candidates for the development of broad-spectrum vaccines or drugs than strain-restricted lineages such as BbCRASP-1.
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Affiliation(s)
- Ewa Wywial
- Department of Biology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
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