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Kohm K, Basu S, Nawaz MM, Hertel R. Chances and limitations when uncovering essential and non-essential genes of Bacillus subtilis phages with CRISPR-Cas9. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:934-944. [PMID: 34465000 DOI: 10.1111/1758-2229.13005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/21/2021] [Indexed: 06/13/2023]
Abstract
Virulent bacterial viruses, also known as phages or bacteriophages, are considered as a potential option to fight antibiotic-resistant bacteria. However, their biology is still poorly understood, and only a fraction of phage genes is assigned with a function. To enable the first classification, we explored new options to test phage genes for their requirement on viral replication. As a model, we used the smallest known Bacillus subtilis phage Goe1, and the Cas9-based mutagenesis vector pRH030 as a genetic tool. All phage genes were specifically disrupted, and individual survival rates and mutant genotypes were investigated. Surviving phages relied on the genome integrity through host intrinsic non-homologues end joining system or a natural alteration of the Cas9 target sequence. Quantification of phage survivors and verifying the underlying genetic situation enables the classification of genes in essential or non-essential sets for viral replication. We also observed structural genes to hold more natural mutations than genes of the genome replication machinery.
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Affiliation(s)
- Katharina Kohm
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, 37077, Germany
| | - Syamantak Basu
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
| | - Muhammad M Nawaz
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
| | - Robert Hertel
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, 37077, Germany
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2
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Absinta M, Maric D, Gharagozloo M, Garton T, Smith MD, Jin J, Fitzgerald KC, Song A, Liu P, Lin JP, Wu T, Johnson KR, McGavern DB, Schafer DP, Calabresi PA, Reich DS. A lymphocyte-microglia-astrocyte axis in chronic active multiple sclerosis. Nature 2021; 597:709-714. [PMID: 34497421 PMCID: PMC8719282 DOI: 10.1038/s41586-021-03892-7] [Citation(s) in RCA: 298] [Impact Index Per Article: 99.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 08/10/2021] [Indexed: 12/20/2022]
Abstract
Multiple sclerosis (MS) lesions that do not resolve in the months after they form harbour ongoing demyelination and axon degeneration, and are identifiable in vivo by their paramagnetic rims on MRI scans1-3. Here, to define mechanisms underlying this disabling, progressive neurodegenerative state4-6 and foster development of new therapeutic agents, we used MRI-informed single-nucleus RNA sequencing to profile the edge of demyelinated white matter lesions at various stages of inflammation. We uncovered notable glial and immune cell diversity, especially at the chronically inflamed lesion edge. We define 'microglia inflamed in MS' (MIMS) and 'astrocytes inflamed in MS', glial phenotypes that demonstrate neurodegenerative programming. The MIMS transcriptional profile overlaps with that of microglia in other neurodegenerative diseases, suggesting that primary and secondary neurodegeneration share common mechanisms and could benefit from similar therapeutic approaches. We identify complement component 1q (C1q) as a critical mediator of MIMS activation, validated immunohistochemically in MS tissue, genetically by microglia-specific C1q ablation in mice with experimental autoimmune encephalomyelitis, and therapeutically by treating chronic experimental autoimmune encephalomyelitis with C1q blockade. C1q inhibition is a potential therapeutic avenue to address chronic white matter inflammation, which could be monitored by longitudinal assessment of its dynamic biomarker, paramagnetic rim lesions, using advanced MRI methods.
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Affiliation(s)
- Martina Absinta
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
- IRCCS San Raffaele Hospital and Vita-Salute San Raffaele University, Milan, Italy.
| | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Marjan Gharagozloo
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas Garton
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Matthew D Smith
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jing Jin
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kathryn C Fitzgerald
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anya Song
- Department of Neurobiology and the Brudnik Neuropsychiatry Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Poching Liu
- DNA Sequencing and Genomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jing-Ping Lin
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Tianxia Wu
- Clinical Trials Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Kory R Johnson
- Bioinformatics Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Dorian B McGavern
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Dorothy P Schafer
- Department of Neurobiology and the Brudnik Neuropsychiatry Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Peter A Calabresi
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel S Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
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3
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Farley MM, Tu J, Kearns DB, Molineux IJ, Liu J. Ultrastructural analysis of bacteriophage Φ29 during infection of Bacillus subtilis. J Struct Biol 2016; 197:163-171. [PMID: 27480510 DOI: 10.1016/j.jsb.2016.07.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 07/26/2016] [Accepted: 07/28/2016] [Indexed: 12/13/2022]
Abstract
Recent advances in cryo-electron tomography (cryo-ET) have allowed direct visualization of the initial interactions between bacteriophages and their hosts. Previous studies focused on phage infection in Gram-negative bacteria but it is of particular interest how phages penetrate the thick, highly cross-linked Gram-positive cell wall. Here we detail structural intermediates of phage Φ29 during infection of Bacillus subtilis. Use of a minicell-producing strain facilitated in situ tomographic reconstructions of infecting phage particles. Φ29 initially contacts the cell wall at an angle through a subset of the twelve appendages, which are attached to the collar at the head proximal portion of the tail knob. The appendages are flexible and switch between extended and downward conformations during this stage of reversible adsorption; appendages enzymatically hydrolyze wall teichoic acids to bring the phage closer to the cell. A cell wall-degrading enzyme at the distal tip of the tail knob locally digests peptidoglycan, facilitating penetration of the tail further into the cell wall, and the phage particle reorients so that the tail becomes perpendicular to the cell surface. All twelve appendages attain the same "down" conformation during this stage of adsorption. Once the tail has become totally embedded in the cell wall, the tip can fuse with the cytoplasmic membrane. The membrane bulges out, presumably to facilitate genome ejection into the cytoplasm, and the deformation remains after complete ejection. This study provides the first visualization of the structural changes occurring in a phage particle during adsorption and genome transfer into a Gram-positive bacterium.
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Affiliation(s)
- Madeline M Farley
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Jiagang Tu
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Daniel B Kearns
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA
| | - Ian J Molineux
- Center for Infectious Disease, Department of Molecular Biosciences, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Jun Liu
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030, USA.
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4
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Volozhantsev NV, Oakley BB, Morales CA, Verevkin VV, Bannov VA, Krasilnikova VM, Popova AV, Zhilenkov EL, Garrish JK, Schegg KM, Woolsey R, Quilici DR, Line JE, Hiett KL, Siragusa GR, Svetoch EA, Seal BS. Molecular characterization of podoviral bacteriophages virulent for Clostridium perfringens and their comparison with members of the Picovirinae. PLoS One 2012; 7:e38283. [PMID: 22666499 PMCID: PMC3362512 DOI: 10.1371/journal.pone.0038283] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 05/02/2012] [Indexed: 01/21/2023] Open
Abstract
Clostridium perfringens is a Gram-positive, spore-forming anaerobic bacterium responsible for human food-borne disease as well as non-food-borne human, animal and poultry diseases. Because bacteriophages or their gene products could be applied to control bacterial diseases in a species-specific manner, they are potential important alternatives to antibiotics. Consequently, poultry intestinal material, soil, sewage and poultry processing drainage water were screened for virulent bacteriophages that lysed C. perfringens. Two bacteriophages, designated ΦCPV4 and ΦZP2, were isolated in the Moscow Region of the Russian Federation while another closely related virus, named ΦCP7R, was isolated in the southeastern USA. The viruses were identified as members of the order Caudovirales in the family Podoviridae with short, non-contractile tails of the C1 morphotype. The genomes of the three bacteriophages were 17.972, 18.078 and 18.397 kbp respectively; encoding twenty-six to twenty-eight ORF's with inverted terminal repeats and an average GC content of 34.6%. Structural proteins identified by mass spectrometry in the purified ΦCP7R virion included a pre-neck/appendage with putative lyase activity, major head, tail, connector/upper collar, lower collar and a structural protein with putative lysozyme-peptidase activity. All three podoviral bacteriophage genomes encoded a predicted N-acetylmuramoyl-L-alanine amidase and a putative stage V sporulation protein. Each putative amidase contained a predicted bacterial SH3 domain at the C-terminal end of the protein, presumably involved with binding the C. perfringens cell wall. The predicted DNA polymerase type B protein sequences were closely related to other members of the Podoviridae including Bacillus phage Φ29. Whole-genome comparisons supported this relationship, but also indicated that the Russian and USA viruses may be unique members of the sub-family Picovirinae.
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Affiliation(s)
- Nikolay V. Volozhantsev
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, Russian Federation
- * E-mail: (NV); (BS)
| | - Brian B. Oakley
- Poultry Microbiology Safety Research Unit, Richard B. Russell Agricultural Research Center, Agricultural Research Service, USDA, Athens, Georgia, United States of America
| | - Cesar A. Morales
- Poultry Microbiology Safety Research Unit, Richard B. Russell Agricultural Research Center, Agricultural Research Service, USDA, Athens, Georgia, United States of America
| | - Vladimir V. Verevkin
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, Russian Federation
| | - Vasily A. Bannov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, Russian Federation
| | - Valentina M. Krasilnikova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, Russian Federation
| | - Anastasia V. Popova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, Russian Federation
| | - Eugeni L. Zhilenkov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, Russian Federation
| | - Johnna K. Garrish
- Poultry Microbiology Safety Research Unit, Richard B. Russell Agricultural Research Center, Agricultural Research Service, USDA, Athens, Georgia, United States of America
| | - Kathleen M. Schegg
- Nevada Proteomics Center, University of Nevada, Reno, Nevada, United States of America
| | - Rebekah Woolsey
- Nevada Proteomics Center, University of Nevada, Reno, Nevada, United States of America
| | - David R. Quilici
- Nevada Proteomics Center, University of Nevada, Reno, Nevada, United States of America
| | - J. Eric Line
- Poultry Microbiology Safety Research Unit, Richard B. Russell Agricultural Research Center, Agricultural Research Service, USDA, Athens, Georgia, United States of America
| | - Kelli L. Hiett
- Poultry Microbiology Safety Research Unit, Richard B. Russell Agricultural Research Center, Agricultural Research Service, USDA, Athens, Georgia, United States of America
| | | | - Edward A. Svetoch
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, Russian Federation
| | - Bruce S. Seal
- Poultry Microbiology Safety Research Unit, Richard B. Russell Agricultural Research Center, Agricultural Research Service, USDA, Athens, Georgia, United States of America
- * E-mail: (NV); (BS)
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5
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Xiang Y, Leiman PG, Li L, Grimes S, Anderson DL, Rossmann MG. Crystallographic insights into the autocatalytic assembly mechanism of a bacteriophage tail spike. Mol Cell 2009; 34:375-86. [PMID: 19450535 DOI: 10.1016/j.molcel.2009.04.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 03/04/2009] [Accepted: 04/08/2009] [Indexed: 11/26/2022]
Abstract
The tailed bacteriophage phi29 has 12 "appendages" (gene product 12, gp12) attached to its neck region that participate in host cell recognition and entry. In the cell, monomeric gp12 undergoes proteolytic processing that releases the C-terminal domain during assembly into trimers. We report here crystal structures of the protein before and after catalytic processing and show that the C-terminal domain of gp12 is an "autochaperone" that aids trimerization. We also show that autocleavage of the C-terminal domain is a posttrimerization event that is followed by a unique ATP-dependent release. The posttranslationally modified N-terminal part has three domains that function to attach the appendages to the phage, digest the cell wall teichoic acids, and bind irreversibly to the host, respectively. Structural and sequence comparisons suggest that some eukaryotic and bacterial viruses as well as bacterial adhesins might have a similar maturation mechanism as is performed by phi29 gp12 for Bacillus subtilis.
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Affiliation(s)
- Ye Xiang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
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6
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Abstract
I have dedicated the past 46 years of my life to science and I expect to be active in research for many more years. I have been lucky in my professional life. During my postdoctoral years I discovered two proteins that I showed to be involved in the initiation of protein synthesis. Working with bacteriophage ø29 for the past 40 years, we have made many interesting findings. Among them is the discovery of a protein covalently linked to the 5′ ends of ø29 DNA that we later showed to be the primer for the initiation of ø29 DNA replication. Also, the finding of the ø29 DNA polymerase with its properties of high processivity, strand displacement, and high fidelity has been very rewarding. The ø29 DNA polymerase has become the ideal enzyme for DNA amplification, both rolling circle and whole-genome amplification. I also am happy because I have worked with many brilliant students and collaborators over the years, most of whom have become excellent scientists.
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Affiliation(s)
- Margarita Salas
- Instituto de Biología Molecular Eladio Viñuela (CSIC), Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain.
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7
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Shu D, Huang L, Guo P. A simple mathematical formula for stoichiometry quantification of viral and nanobiological assemblage using slopes of log/log plot curves. J Virol Methods 2004; 115:19-30. [PMID: 14656457 DOI: 10.1016/j.jviromet.2003.08.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In nanotechnology, biomolecular assemblies serve not only as model systems for the construction of nanodevices, but they can also be used directly as templates for the formation of nanostructures. Biological nano-building blocks can either be isolated as complete functional units from living cells or viruses (biological "Top down" approach) or formed by biomolecular assembly from recombinant or synthetic components ("Bottom up" approach). In both cases, rational design of nanostructures requires knowledge of the stoichiometry of the biological structures, which frequently occur as multimers, i.e., the morphological complex is composed of multiple copies of one or more macromolecules. In this paper, a method is described for the stoichiometric quantification of molecules in bio-nanostructures. The method is based on using dilution factors and relative concentrations rather than absolute quantities, which are often difficult to determine, especially in short-lived assembly intermediates. The approach exploits the fact that the larger the stoichiometry of the component is, the more dramatic is the influence of the dilution factor (decrease in concentration) on the reaction. We established and used the method to determine the stoichiometry of components of bacterial virus phi29. The log of dilution factors was plotted against the log of reaction yield. The stoichiometry Z was determined with the equation Z=-1.58+2.4193T-0.001746T(2) [T in (0,1000), or 90 degree angle alpha in (0 degrees, 89.9 degrees )], where T is the slope of the curve (tangent of 90 degree angle alpha, which is the angle between the x-axis and the concentration dependent curve). Z can also be determined from a standard table given in this report. With the bacteriophage phi29 in vitro assembly system, up to 5x10(8) infectious virions per ml can be assembled from 11 purified components, giving our method a sensitivity of nine orders of magnitude. We confirmed the stoichiometries of phi29 components that were determined previously with microscopic approaches. The described method also responded to programmed stoichiometry changes, which were generated by assembling the phi29 DNA packaging motor from modified pRNA (DNA-packaging RNA) molecules forming a trimer of dimers or a dimer of trimers, instead of the wild-type hexamer.
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Affiliation(s)
- Dan Shu
- Department of Pathobiology and Purdue Cancer Research Center, B-36 Hansen Life Science Research Building, Purdue University, West Lafayette, IN 47907, USA
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8
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Abstract
Continuous research spanning more than three decades has made the Bacillus bacteriophage phi29 a paradigm for several molecular mechanisms of general biological processes, such as DNA replication, regulation of transcription, phage morphogenesis, and phage DNA packaging. The genome of bacteriophage phi29 consists of a linear double-stranded DNA (dsDNA), which has a terminal protein (TP) covalently linked to its 5' ends. Initiation of DNA replication, carried out by a protein-primed mechanism, has been studied in detail and is considered to be a model system for the protein-primed DNA replication that is also used by most other linear genomes with a TP linked to their DNA ends, such as other phages, linear plasmids, and adenoviruses. In addition to a continuing progress in unraveling the initiation of DNA replication mechanism and the role of various proteins involved in this process, major advances have been made during the last few years, especially in our understanding of transcription regulation, the head-tail connector protein, and DNA packaging. Recent progress in all these topics is reviewed. In addition to phi29, the genomes of several other Bacillus phages consist of a linear dsDNA with a TP molecule attached to their 5' ends. These phi29-like phages can be divided into three groups. The first group includes, in addition to phi29, phages PZA, phi15, and BS32. The second group comprises B103, Nf, and M2Y, and the third group contains GA-1 as its sole member. Whereas the DNA sequences of the complete genomes of phi29 (group I) and B103 (group II) are known, only parts of the genome of GA-1 (group III) were sequenced. We have determined the complete DNA sequence of the GA-1 genome, which allowed analysis of differences and homologies between the three groups of phi29-like phages, which is included in this review.
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Affiliation(s)
- W J Meijer
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
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9
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Abstract
Continuous research spanning more than three decades has made the Bacillus bacteriophage phi29 a paradigm for several molecular mechanisms of general biological processes, such as DNA replication, regulation of transcription, phage morphogenesis, and phage DNA packaging. The genome of bacteriophage phi29 consists of a linear double-stranded DNA (dsDNA), which has a terminal protein (TP) covalently linked to its 5' ends. Initiation of DNA replication, carried out by a protein-primed mechanism, has been studied in detail and is considered to be a model system for the protein-primed DNA replication that is also used by most other linear genomes with a TP linked to their DNA ends, such as other phages, linear plasmids, and adenoviruses. In addition to a continuing progress in unraveling the initiation of DNA replication mechanism and the role of various proteins involved in this process, major advances have been made during the last few years, especially in our understanding of transcription regulation, the head-tail connector protein, and DNA packaging. Recent progress in all these topics is reviewed. In addition to phi29, the genomes of several other Bacillus phages consist of a linear dsDNA with a TP molecule attached to their 5' ends. These phi29-like phages can be divided into three groups. The first group includes, in addition to phi29, phages PZA, phi15, and BS32. The second group comprises B103, Nf, and M2Y, and the third group contains GA-1 as its sole member. Whereas the DNA sequences of the complete genomes of phi29 (group I) and B103 (group II) are known, only parts of the genome of GA-1 (group III) were sequenced. We have determined the complete DNA sequence of the GA-1 genome, which allowed analysis of differences and homologies between the three groups of phi29-like phages, which is included in this review.
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Affiliation(s)
- W J Meijer
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
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Nikolskaya AN, Pitkin JW, Schaeffer HJ, Ahn JH, Walton JD. EXG1p, a novel exo-beta1,3-glucanase from the fungus Cochliobolus carbonum, contains a repeated motif present in other proteins that interact with polysaccharides. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1425:632-6. [PMID: 9838227 DOI: 10.1016/s0304-4165(98)00117-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Genomic and cDNA copies of EXG1, a gene encoding an exo-beta1, 3-glucanase from the plant pathogenic fungus Cochliobolus carbonum, were isolated. The gene contains two introns of 50 and 53 bp, and the mRNA has a 5'-untranslated region of 90 nt and a 3'-untranslated region of 159 nt. The deduced protein product, EXG1p, has a predicted signal peptide of 17 amino acids, but based on the known N-terminus of the mature protein is further processed to remove an additional 25 amino acids. The sequence of EXG1p is not closely related to any other known protein, but has a low similarity (29% overall amino acid identity) to BGN13.1, an endo-beta1,3-glucanase from the mycoparasitic fungus Trichoderma harzianum. EXG1p contains two imperfect copies of a 23-amino acid motif that is found in several other proteins that interact with polysaccharides, including plant and bacterial polygalacturonases, phage neck appendage protein, phage endoneuramidase, and bacterial mannuronan epimerase.
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Affiliation(s)
- A N Nikolskaya
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
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11
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Barthelemy I, Salas M, Mellado RP. In vivo transcription of bacteriophage phi 29 DNA: transcription termination. J Virol 1987; 61:1751-5. [PMID: 3033305 PMCID: PMC254171 DOI: 10.1128/jvi.61.5.1751-1755.1987] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The main early and late transcription termination sites in vivo in bacteriophage phi 29 DNA were determined by nuclease S1 mapping. Transcription of the phi 29 early genes located at the left end of the viral genome terminated at the very end of the DNA molecule and within the HindIII G fragment of the viral DNA. Transcription termination of the early genes located at the right end of the genome and that of the late viral genes overlapped in a specific region of the phi 29 DNA within the EcoRI D fragment. Stem-loop structures followed by uridine-rich tails could be derived close to the 3' ends of early and late mRNAs, suggesting Rho-independent transcription termination in phi 29 DNA.
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12
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Carrascosa J, Carazo J, García N. Structural localizaton of the proteins of the head to tail connecting region of bacteriophage φ29. Virology 1983. [DOI: 10.1016/0042-6822(83)90296-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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13
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Carrascosa JL, Viñuela E, García N, Santisteban A. Structure of the head-tail connector of bacteriophage phi 29. J Mol Biol 1982; 154:311-24. [PMID: 6804634 DOI: 10.1016/0022-2836(82)90066-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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14
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Villanueva N, Lázaro JM, Salas M. Purification, properties and assembly of the neck-appendage protein of the Bacillus subtilis phage phi 29. EUROPEAN JOURNAL OF BIOCHEMISTRY 1981; 117:499-505. [PMID: 6793359 DOI: 10.1111/j.1432-1033.1981.tb06365.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The purification of the neck appendage protein of phi 29, p12*, which is involved in the adsorption of the phage to Bacillus subtilis, is described. The purified native protein is in a dimeric form and can be assembled, in vitro, onto purified 12- particles that lack the neck appendages, suggesting that the incorporation of p12* to the rest of the phage structure is a self-assembly process. The assembly of protein p12* in vitro follows cooperative kinetics and it occurs with an efficiency of about 4%.
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