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Nilsson AS. Cocktail, a Computer Program for Modelling Bacteriophage Infection Kinetics. Viruses 2022; 14:v14112483. [PMID: 36366581 PMCID: PMC9695944 DOI: 10.3390/v14112483] [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] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 11/11/2022] Open
Abstract
Cocktail is an easy-to-use computer program for mathematical modelling of bacteriophage (phage) infection kinetics in a chemostat. The infection of bacteria by phages results in complicated dynamic processes as both have the ability to multiply and change during the course of an infection. There is a need for a simple way to visualise these processes, not least due to the increased interest in phage therapy. Cocktail is completely self-contained and runs on a Windows 64-bit operating system. By changing the publicly available source code, the program can be developed in the directions that users see fit. Cocktail's models consist of coupled differential equations that describe the infection of a bacterium in a vessel by one or two (interfering) phages. In the models, the bacterial population can be controlled by sixteen parameters, for example, through different growth rates, phage resistance, metabolically inactive cells or biofilm formation. The phages can be controlled by eight parameters each, such as different adsorption rates or latency periods. As the models in Cocktail describe the infection kinetics of phages in vitro, the program is primarily intended to generate hypotheses, but the results can however be indicative in the application of phage therapy.
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Affiliation(s)
- Anders S Nilsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
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Koonjan S, Cardoso Palacios C, Nilsson AS. Population Dynamics of a Two Phages–One Host Infection System Using Escherichia coli Strain ECOR57 and Phages vB_EcoP_SU10 and vB_EcoD_SU57. Pharmaceuticals (Basel) 2022; 15:ph15030268. [PMID: 35337066 PMCID: PMC8953519 DOI: 10.3390/ph15030268] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/09/2022] [Accepted: 02/18/2022] [Indexed: 02/01/2023] Open
Abstract
In this study, we looked at the population dynamics of a two phages-one host system using phages vB_EcoP_SU10 (SU10) and vB_EcoD_SU57 (SU57) and the bacteria Escherichia coli, strain ECOR57. Phage-specific growth curves were observed where infections by SU10 resulted in a moderate production of phages and infections by SU57 resulted in a fast and extensive production of phage progeny. Sequentially adding SU10 followed by SU57 did not produce a significant change in growth rates, whereas adding SU57 followed by SU10 resulted in a decrease in SU10 titer The efficiency of the plating assays showed that ECOR57 exhibited a resistance spectrum after infection by both the single and combined phages. Phage-resistant bacteria exhibited four different morphotypes (i.e., normal, slimy, edgy, and pointy). The normal and edgy morphotypes had a high frequency of developing resistance. Bacterial growth and biofilm assays indicated that the edgy and pointy morphotypes reached a stationary phase faster and produced more biofilm compared to the wild type. These findings suggest that the dynamic structure of phage–bacteria communities dictate resistance evolution and development. Understanding when and how resistances arise and phage(s)–hosts interactions could aid in the design of phage therapy treatments.
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Affiliation(s)
- Shazeeda Koonjan
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden;
- Correspondence: (S.K.); (A.S.N.)
| | - Carlos Cardoso Palacios
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden;
- Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences, SE-739 93 Riddarhyttan, Sweden
| | - Anders S. Nilsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden;
- Correspondence: (S.K.); (A.S.N.)
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Koonjan S, Cooper CJ, Nilsson AS. Complete Genome Sequence of vB_EcoP_SU7, a Podoviridae Coliphage with the Rare C3 Morphotype. Microorganisms 2021; 9:microorganisms9081576. [PMID: 34442655 PMCID: PMC8399022 DOI: 10.3390/microorganisms9081576] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 11/16/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) strains are an important cause of bacterial diarrheal illness in humans and animals. Infections arising from ETEC could potentially be treated through the use of bacteriophage (phage) therapy, as phages encode for enzymes capable of bacterial cell lysis. vB_EcoP_SU7 was isolated from the Käppala wastewater treatment plant in Stockholm, Sweden, and propagated on an ETEC strain exhibiting the O:139 serovar. Transmission electron microscopy confirmed that vB_EcoP_SU7 belongs to the Podoviridae family and has the rare C3 morphotype of an elongated head. Bioinformatic analyses showed that the genome was 76,626 base pairs long and contained 35 genes with predicted functions. A total of 81 open reading frames encoding proteins with hypothetical function and two encoding proteins of no significant similarity were also found. A putative tRNA gene, which may aid in vB_EcoP_SU7’s translation, was also identified. Phylogenetic analyses showed that compared to other Podoviridae, vB_EcoP_SU7 is a rare Kuravirus and is closely related to E. coli phages with the uncommon C3 morphotype, such as ECBP2, EK010, vB_EcoP_EcoN5, and vB_EcoP_SU10. Phage vB_EcoP_SU7 has a narrow host range, infecting 11 out of the 137 E. coli strains tested, a latency period of 30 min, a burst size of 12 PFU/cell, and an adsorption rate of 8.78 × 10−9 mL/min five minutes post infection. With a limited host range and poor infection kinetics, it is unlikely that SU7 can be a standalone phage used for therapeutic purposes; rather, it must be used in combination with other phages for broad-spectrum therapeutic success.
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Affiliation(s)
- Shazeeda Koonjan
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden;
- Correspondence:
| | - Callum J. Cooper
- School of Pharmacy, Pharmaceutical and Cosmetic Sciences, Faculty of Health Sciences and Wellbeing, University of Sunderland, Sunderland SR13SD, UK;
| | - Anders S. Nilsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden;
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Koonjan S, Seijsing F, Cooper CJ, Nilsson AS. Infection Kinetics and Phylogenetic Analysis of vB_EcoD_SU57, a Virulent T1-Like Drexlerviridae Coliphage. Front Microbiol 2020; 11:565556. [PMID: 33329423 PMCID: PMC7718038 DOI: 10.3389/fmicb.2020.565556] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 05/28/2020] [Accepted: 09/11/2020] [Indexed: 12/13/2022] Open
Abstract
The morphology, infection kinetics, genome sequence and phylogenetic characterization of the previously isolated bacteriophage vB_EcoD_SU57 are presented. The phage vB_EcoD_SU57 was isolated on Escherichia coli strain ECOR57 from the E. coli reference collection and was shown to produce four mm clear plaques with halos. Infection kinetics, as assessed by one-step growth analyses, suggest that vB_EcoD_SU57 is a virulent phage with an adsorption rate of 8.5 × 10–10 mL × min–1, a latency period of 14 min, and a burst size of 13 PFU per bacterium. Transmission electron microscopy confirmed vB_EcoD_SU57 to be a phage that used to be classified as a Siphoviridae phage. Bioinformatics analyses showed that the genome was 46,150 base pairs long, contained 29 genes with predicted protein functions, and 51 open reading frames encoding proteins with unknown function, many of which were gathered in clusters. A putative tRNA gene was also identified. Phylogenetic analyses showed that vB_EcoD_SU57 is a Braunvirinae phage of the newly formed Drexlerviridae family and closely related to T1-like E. coli phages vB_EcoS_ACG-M12 (Guelphvirus) and Rtp (Rtpvirus) as well as the unclassified phages vB_EcoS_CEB_EC3a and ECH1.
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Affiliation(s)
- Shazeeda Koonjan
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Fredrik Seijsing
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Callum J Cooper
- School of Pharmacy, Pharmaceutical and Cosmetic Sciences, Faculty of Health Sciences and Wellbeing, University of Sunderland, Sunderland, United Kingdom
| | - Anders S Nilsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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Abstract
Clinical trial results of phage treatment of bacterial infections show a low to moderate efficacy, and the variation in infection clearance between subjects within studies is often large. Phage therapy is complicated and introduces many additional components of variance as compared to antibiotic treatment. A large part of the variation is due to in vivo pharmacokinetics and pharmacodynamics being virtually unknown, but also to a lack of standardisation. This is a consequence of the great variation of phages, bacteria, and infections, which results in different experiments or trials being impossible to compare, and difficulties in estimating important parameter values in a quantitative and reproducible way. The limitations of phage therapy will have to be recognised and future research focussed on optimising infection clearance rates by e.g. selecting phages, bacteria, and target bacterial infections where the prospects of high efficacy can be anticipated, and by combining information from new mathematical modelling of in vivo pharmacokinetic and pharmacodynamic processes and quantitatively assessed experiments.
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Affiliation(s)
- Anders S. Nilsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol 2019. [PMID: 31285584 DOI: 10.1038/s41564-019-04904-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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Affiliation(s)
- Robert A Edwards
- Department of Biology, San Diego State University, San Diego, CA, USA.
- The Viral Information Institute, San Diego State University, San Diego, CA, USA.
| | - Alejandro A Vega
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Holly M Norman
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Maria Ohaeri
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Kyle Bibby
- Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Patrick A de Jonge
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Christelle Desnues
- MEPHI, Aix-Marseille Université, IRD, AP-HM, CNRS, IHU Méditerranée Infection, Marseille, France
- Mediterranean Institute of Oceanography, Aix-Marseille Université, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Samuel L Díaz Muñoz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - David T McCarthy
- EPHM Lab, Civil Engineering Department, Monash University, Clayton, Victoria, Australia
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - German Tapia
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Huechuraba, Chile
| | - Alexander V Tyakht
- Laboratory of Bioinformatics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Department of Informational Technologies, ITMO University, Saint Petersburg, Russia
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Frank M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Josefa Anton
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Abigail Asangba
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emma K Billings
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Vito Adrian Cantu
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Tess Condeff
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Mike Cranfield
- Wildlife Health Center, University of California, Davis, Davis, CA, USA
| | - Daniel A Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michael P Doane
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Bashir Mukhtar Elwasila
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Charles Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Elodie Ghedin
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Kristen M Gulino
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - John M Haggerty
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Steven R Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Rene S Hendriksen
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
| | - Heikki Hyöty
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL, USA
| | - Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Randall E Junge
- Department of Animal Health, Columbus Zoo and Aquarium, Powell, OH, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Martin Kowalewski
- Department Estacion Biologica Corrientes, Institution Museo Arg. Cs. Naturales-CONICET, Corrientes, Argentina
| | - Deepak Kumaresan
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA
| | - David Lipson
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Julia M Maritz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Shahar Molshanski-Mor
- Clinical Microbiology & Immunology, Sackler school of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Silvia Monteiro
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Megan Morris
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Lawrence Mugisha
- CEHA, Kampala, Uganda
- COVAB, Makerere University, Kampala, Uganda
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Nam-Phuong Nguyen
- Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivia D Nigro
- College of Natural and Computational Sciences, Hawai'i Pacific University, Kaneohe, HI, USA
| | - Anders S Nilsson
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Taylor O'Connell
- Biological and Medical Informatics Program, San Diego State University, San Diego, CA, USA
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Andrew Oliver
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aaron J Prussin Ii
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Petra Rainetova
- Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | | | | | - Kim Reasor
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Alessandro Rossi
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Biology, University of Padova, Padova, Italy
| | - Ricardo Santos
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - John Shimashita
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Elyse N Stachler
- Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars C Stene
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ronan Strain
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Rebecca Stumpf
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Alan Twaddle
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - MaryAnn Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria
| | - Nicolás Villagra
- Escuela de Tecnología Médica, Universidad Andres Bello, Santiago, Chile
| | - Stephen Wandro
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Bryan White
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy Whiteley
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Katrine L Whiteson
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Henrike Zschach
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
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Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol 2019; 4:1727-1736. [PMID: 31285584 DOI: 10.1101/527796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 10/14/2018] [Accepted: 05/22/2019] [Indexed: 05/26/2023]
Abstract
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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Affiliation(s)
- Robert A Edwards
- Department of Biology, San Diego State University, San Diego, CA, USA.
- The Viral Information Institute, San Diego State University, San Diego, CA, USA.
| | - Alejandro A Vega
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Holly M Norman
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Maria Ohaeri
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Kyle Bibby
- Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Patrick A de Jonge
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Christelle Desnues
- MEPHI, Aix-Marseille Université, IRD, AP-HM, CNRS, IHU Méditerranée Infection, Marseille, France
- Mediterranean Institute of Oceanography, Aix-Marseille Université, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Samuel L Díaz Muñoz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - David T McCarthy
- EPHM Lab, Civil Engineering Department, Monash University, Clayton, Victoria, Australia
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - German Tapia
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Huechuraba, Chile
| | - Alexander V Tyakht
- Laboratory of Bioinformatics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Department of Informational Technologies, ITMO University, Saint Petersburg, Russia
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Frank M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Josefa Anton
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Abigail Asangba
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emma K Billings
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Vito Adrian Cantu
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Tess Condeff
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Mike Cranfield
- Wildlife Health Center, University of California, Davis, Davis, CA, USA
| | - Daniel A Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michael P Doane
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Bashir Mukhtar Elwasila
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Charles Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Elodie Ghedin
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Kristen M Gulino
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - John M Haggerty
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Steven R Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Rene S Hendriksen
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
| | - Heikki Hyöty
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL, USA
| | - Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Randall E Junge
- Department of Animal Health, Columbus Zoo and Aquarium, Powell, OH, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Martin Kowalewski
- Department Estacion Biologica Corrientes, Institution Museo Arg. Cs. Naturales-CONICET, Corrientes, Argentina
| | - Deepak Kumaresan
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA
| | - David Lipson
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Julia M Maritz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Shahar Molshanski-Mor
- Clinical Microbiology & Immunology, Sackler school of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Silvia Monteiro
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Megan Morris
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Lawrence Mugisha
- CEHA, Kampala, Uganda
- COVAB, Makerere University, Kampala, Uganda
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Nam-Phuong Nguyen
- Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivia D Nigro
- College of Natural and Computational Sciences, Hawai'i Pacific University, Kaneohe, HI, USA
| | - Anders S Nilsson
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Taylor O'Connell
- Biological and Medical Informatics Program, San Diego State University, San Diego, CA, USA
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Andrew Oliver
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aaron J Prussin Ii
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Petra Rainetova
- Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | | | | | - Kim Reasor
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Alessandro Rossi
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Biology, University of Padova, Padova, Italy
| | - Ricardo Santos
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - John Shimashita
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Elyse N Stachler
- Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars C Stene
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ronan Strain
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Rebecca Stumpf
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Alan Twaddle
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - MaryAnn Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria
| | - Nicolás Villagra
- Escuela de Tecnología Médica, Universidad Andres Bello, Santiago, Chile
| | - Stephen Wandro
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Bryan White
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy Whiteley
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Katrine L Whiteson
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Henrike Zschach
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
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Hjelm LC, Nilvebrant J, Nygren PÅ, Nilsson AS, Seijsing J. Lysis of Staphylococcal Cells by Modular Lysin Domains Linked via a Non-covalent Barnase-Barstar Interaction Bridge. Front Microbiol 2019; 10:558. [PMID: 30967850 PMCID: PMC6439198 DOI: 10.3389/fmicb.2019.00558] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/04/2019] [Indexed: 01/21/2023] Open
Abstract
Bacteriophage endolysins and bacterial exolysins are capable of enzymatic degradation of the cell wall peptidoglycan layer and thus show promise as a new class of antimicrobials. Both exolysins and endolysins often consist of different modules, which are responsible for enzymatic functions and cell wall binding, respectively. Individual modules from different endo- or exolysins with different binding and enzymatic activities, can via gene fusion technology be re-combined into novel variants for investigations of arrangements of potential clinical interest. The aim of this study was to investigate if separately produced cell wall binding and enzyme modules could be assembled into a functional lysin via a non-covalent affinity interaction bridge composed of the barnase ribonuclease from Bacillus amyloliquefaciens and its cognate inhibitor barstar, known to form a stable heterodimeric complex. In a proof-of-principle study, using surface plasmon resonance, flow cytometry and turbidity reduction assays, we show that separately produced modules of a lysin cysteine/histidine-dependent amidohydrolase/peptidase (CHAP) from Staphylococcus aureus bacteriophage K endolysin (LysK) fused to barnase and a cell wall binding Src homology 3 domain (SH3b) from the S. simulans exolysin lysostaphin fused to barstar can be non-covalently assembled into a functional lysin showing both cell wall binding and staphylolytic activity. We hypothesize that the described principle for assembly of functional lysins from separate modules through appended hetero-dimerization domains has a potential for investigations of also other combinations of enzymatically active and cell wall binding domains for desired applications.
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Affiliation(s)
- Linnea C Hjelm
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Johan Nilvebrant
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Per-Åke Nygren
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anders S Nilsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Johan Seijsing
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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Cooper CJ, Koonjan S, Nilsson AS. Enhancing Whole Phage Therapy and Their Derived Antimicrobial Enzymes through Complex Formulation. Pharmaceuticals (Basel) 2018; 11:ph11020034. [PMID: 29671806 PMCID: PMC6027540 DOI: 10.3390/ph11020034] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/11/2018] [Accepted: 04/17/2018] [Indexed: 12/11/2022] Open
Abstract
The resurgence of research into phage biology and therapy is, in part, due to the increasing need for novel agents to treat multidrug-resistant infections. Despite a long clinical history in Eastern Europe and initial success within the food industry, commercialized phage products have yet to enter other sectors. This relative lack of success is, in part, due to the inherent biological limitations of whole phages. These include (but are not limited to) reaching target sites at sufficiently high concentrations to establish an infection which produces enough progeny phages to reduce the bacterial population in a clinically meaningful manner and the limited host range of some phages. Conversely, parallels can be drawn between antimicrobial enzymes derived from phages and conventional antibiotics. In the current article the biological limitations of whole phage-based therapeutics and their derived antimicrobial enzymes will be discussed. In addition, the ability of more complex formulations to address these issues, in the context of medical and non-medical applications, will also be included.
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Affiliation(s)
- Callum J Cooper
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden.
| | - Shazeeda Koonjan
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden.
| | - Anders S Nilsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden.
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Khan Mirzaei M, Haileselassie Y, Navis M, Cooper C, Sverremark-Ekström E, Nilsson AS. Corrigendum: Morphologically Distinct Escherichia coli Bacteriophages Differ in Their Efficacy and Ability to Stimulate Cytokine Release In Vitro. Front Microbiol 2017; 7:2145. [PMID: 28053602 PMCID: PMC5209331 DOI: 10.3389/fmicb.2016.02145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 12/20/2016] [Indexed: 11/28/2022] Open
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Khan Mirzaei M, Haileselassie Y, Navis M, Cooper C, Sverremark-Ekström E, Nilsson AS. Response: Commentary: Morphologically Distinct Escherichia coli Bacteriophages Differ in Their Efficacy and Ability to Stimulate Cytokine Release In Vitro. Front Microbiol 2016; 7:1974. [PMID: 28018310 PMCID: PMC5145895 DOI: 10.3389/fmicb.2016.01974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/25/2016] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Yeneneh Haileselassie
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm UniversityStockholm, Sweden
| | - Marit Navis
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm UniversityStockholm, Sweden
| | - Callum Cooper
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm UniversityStockholm, Sweden
| | - Eva Sverremark-Ekström
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm UniversityStockholm, Sweden
| | - Anders S. Nilsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm UniversityStockholm, Sweden
- *Correspondence: Anders S. Nilsson
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Abstract
The global rise of multi-drug resistant bacteria has resulted in the notion that an "antibiotic apocalypse" is fast approaching. This has led to a number of well publicized calls for global funding initiatives to develop new antibacterial agents. The long clinical history of phage therapy in Eastern Europe, combined with more recent in vitro and in vivo success, demonstrates the potential for whole phage or phage based antibacterial agents. To date, no whole phage or phage derived products are approved for human therapeutic use in the EU or USA. There are at least three reasons for this: (i) phages possess different biological, physical, and pharmacological properties compared to conventional antibiotics. Phages need to replicate in order to achieve a viable antibacterial effect, resulting in complex pharmacodynamics/pharmacokinetics. (ii) The specificity of individual phages requires multiple phages to treat single species infections, often as part of complex cocktails. (iii) The current approval process for antibacterial agents has evolved with the development of chemically based drugs at its core, and is not suitable for phages. Due to similarities with conventional antibiotics, phage derived products such as endolysins are suitable for approval under current processes as biological therapeutic proteins. These criteria render the approval of phages for clinical use theoretically possible but not economically viable. In this review, pitfalls of the current approval process will be discussed for whole phage and phage derived products, in addition to the utilization of alternative approval pathways including adaptive licensing and "Right to try" legislation.
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Affiliation(s)
- Callum J Cooper
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University Stockholm, Sweden
| | - Mohammadali Khan Mirzaei
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University Stockholm, Sweden
| | - Anders S Nilsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University Stockholm, Sweden
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Khan Mirzaei M, Haileselassie Y, Navis M, Cooper C, Sverremark-Ekström E, Nilsson AS. Morphologically Distinct Escherichia coli Bacteriophages Differ in Their Efficacy and Ability to Stimulate Cytokine Release In Vitro. Front Microbiol 2016; 7:437. [PMID: 27065990 PMCID: PMC4814447 DOI: 10.3389/fmicb.2016.00437] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 12/15/2015] [Accepted: 03/18/2016] [Indexed: 11/13/2022] Open
Abstract
Due to a global increase in the range and number of infections caused by multi-resistant bacteria, phage therapy is currently experiencing a resurgence of interest. However, there are a number of well-known concerns over the use of phages to treat bacterial infections. In order to address concerns over safety and the poorly understood pharmacokinetics of phages and their associated cocktails, immunological characterization is required. In the current investigation, the immunogenicity of four distinct phages (taken from the main families that comprise the Caudovirales order) and their interaction with donor derived peripheral blood mononuclear cells and immortalized cell lines (HT-29 and Caco-2 intestinal epithelial cells) were investigated using standard immunological techniques. When exposed to high phage concentrations (10(9) PFU/well), cytokine driven inflammatory responses were induced from all cell types. Although phages appeared to inhibit the growth of intestinal epithelial cell lines, they also appear to be non-cytotoxic. Despite co-incubation with different cell types, phages maintained a high killing efficiency, reducing extended-spectrum beta-lactamase-producing Escherichia coli numbers by 1-4 log10 compared to untreated controls. When provided with a suitable bacterial host, phages were also able to actively reproduce in the presence of human cells resulting in an approximately 2 log10 increase in phage titer compared to the initial inoculum. Through an increased understanding of the complex pharmacokinetics of phages, it may be possible to address some of the safety concerns surrounding phage preparations prior to creating new therapeutic strategies.
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Affiliation(s)
- Mohammadali Khan Mirzaei
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University Stockholm, Sweden
| | - Yeneneh Haileselassie
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University Stockholm, Sweden
| | - Marit Navis
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University Stockholm, Sweden
| | - Callum Cooper
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University Stockholm, Sweden
| | - Eva Sverremark-Ekström
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University Stockholm, Sweden
| | - Anders S Nilsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University Stockholm, Sweden
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Mirzaei MK, Nilsson AS. Correction: Isolation of phages for phage therapy: a comparison of spot tests and efficiency of plating analyses for determination of host range and efficacy. PLoS One 2015; 10:e0127606. [PMID: 25950830 PMCID: PMC4423996 DOI: 10.1371/journal.pone.0127606] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Eriksson H, Maciejewska B, Latka A, Majkowska-Skrobek G, Hellstrand M, Melefors Ö, Wang JT, Kropinski AM, Drulis-Kawa Z, Nilsson AS. A suggested new bacteriophage genus, "Kp34likevirus", within the Autographivirinae subfamily of Podoviridae. Viruses 2015; 7:1804-22. [PMID: 25853484 PMCID: PMC4411677 DOI: 10.3390/v7041804] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/22/2015] [Accepted: 03/27/2015] [Indexed: 12/17/2022] Open
Abstract
Klebsiella pneumoniae phages vB_KpnP_SU503 (SU503) and vB_KpnP_SU552A (SU552A) are virulent viruses belonging to the Autographivirinae subfamily of Podoviridae that infect and kill multi-resistant K. pneumoniae isolates. Phages SU503 and SU552A show high pairwise nucleotide identity to Klebsiella phages KP34 (NC_013649), F19 (NC_023567) and NTUH-K2044-K1-1 (NC_025418). Bioinformatic analysis of these phage genomes show high conservation of gene arrangement and gene content, conserved catalytically active residues of their RNA polymerase, a common and specific lysis cassette, and form a joint cluster in phylogenetic analysis of their conserved genes. Also, we have performed biological characterization of the burst size, latent period, host specificity (together with KP34 and NTUH-K2044-K1-1), morphology, and structural genes as well as sensitivity testing to various conditions. Based on the analyses of these phages, the creation of a new phage genus is suggested within the Autographivirinae, called "Kp34likevirus" after their type phage, KP34. This genus should encompass the recently genome sequenced Klebsiella phages KP34, SU503, SU552A, F19 and NTUH-K2044-K1-1.
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Affiliation(s)
- Harald Eriksson
- Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm 106 91, Sweden; E-Mails: (H.E.); (M.H.)
| | - Barbara Maciejewska
- Institute of Genetics and Microbiology, University of Wroclaw, Wroclaw 51-148, Poland; E-Mails: (B.M.); (A.L.); (G.M.-S.); (Z.D.-K.)
| | - Agnieszka Latka
- Institute of Genetics and Microbiology, University of Wroclaw, Wroclaw 51-148, Poland; E-Mails: (B.M.); (A.L.); (G.M.-S.); (Z.D.-K.)
| | - Grazyna Majkowska-Skrobek
- Institute of Genetics and Microbiology, University of Wroclaw, Wroclaw 51-148, Poland; E-Mails: (B.M.); (A.L.); (G.M.-S.); (Z.D.-K.)
| | - Marios Hellstrand
- Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm 106 91, Sweden; E-Mails: (H.E.); (M.H.)
| | - Öjar Melefors
- Department of Microbiology, Public Health Agency of Sweden, Solna 171 82, Sweden; E-Mail:
| | - Jin-Town Wang
- Department of Microbiology, National Taiwan University, College of Medicine, Taipei 10051, Taiwan; E-Mail:
| | - Andrew M. Kropinski
- Departments of Food Science, Molecular & Cellular Biology, and Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada; E-Mail:
| | - Zuzanna Drulis-Kawa
- Institute of Genetics and Microbiology, University of Wroclaw, Wroclaw 51-148, Poland; E-Mails: (B.M.); (A.L.); (G.M.-S.); (Z.D.-K.)
| | - Anders S. Nilsson
- Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm 106 91, Sweden; E-Mails: (H.E.); (M.H.)
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16
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Khan Mirzaei M, Nilsson AS. Isolation of phages for phage therapy: a comparison of spot tests and efficiency of plating analyses for determination of host range and efficacy. PLoS One 2015; 10:e0118557. [PMID: 25761060 PMCID: PMC4356574 DOI: 10.1371/journal.pone.0118557] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 01/20/2015] [Indexed: 11/18/2022] Open
Abstract
Phage therapy, treating bacterial infections with bacteriophages, could be a future alternative to antibiotic treatment of bacterial infections. There are, however, several problems to be solved, mainly associated to the biology of phages, the interaction between phages and their bacterial hosts, but also to the vast variation of pathogenic bacteria which implies that large numbers of different phages are going to be needed. All of these phages must under present regulation of medical products undergo extensive clinical testing before they can be applied. It will consequently be of great economic importance that effective and versatile phages are selected and collected into phage libraries, i.e., the selection must be carried out in a way that it results in highly virulent phages with broad host ranges. We have isolated phages using the Escherichia coli reference (ECOR) collection and compared two methods, spot testing and efficiency of plating (EOP), which are frequently used to identify phages suitable for phage therapy. The analyses of the differences between the two methods show that spot tests often overestimate both the overall virulence and the host range and that the results are not correlated to the results of EOP assays. The conclusion is that single dilution spot tests cannot be used for identification and selection of phages to a phage library and should be replaced by EOP assays. The difference between the two methods can be caused by many factors. We have analysed if the differences and lack of correlation could be caused by lysis from without, bacteriocins in the phage lysate, or by the presence of prophages harbouring genes coding for phage resistance systems in the genomes of the bacteria in the ECOR collection.
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Affiliation(s)
- Mohammadali Khan Mirzaei
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Anders S. Nilsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- * E-mail:
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17
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Nilsson H, Cardoso-Palacios C, Haggård-Ljungquist E, Nilsson AS. Phylogenetic structure and evolution of regulatory genes and integrases of P2-like phages. Bacteriophage 2014; 1:207-218. [PMID: 23050214 PMCID: PMC3448106 DOI: 10.4161/bact.1.4.18470] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The phylogenetic relationships and structural similarities of the proteins encoded within the regulatory region (containing the integrase gene and the lytic–lysogenic transcriptional switch genes) of P2-like phages were analyzed, and compared with the phylogenetic relationship of P2-like phages inferred from four structural genes. P2-like phages are thought to be one of the most genetically homogenous phage groups but the regulatory region nevertheless varies extensively between different phage genomes.
The analyses showed that there are many types of regulatory regions, but two types can be clearly distinguished; regions similar either to the phage P2 or to the phage 186 regulatory regions. These regions were also found to be most frequent among the sequenced P2-like phage or prophage genomes, and common in phages using Escherichia coli as a host. Both the phylogenetic and the structural analyses showed that these two regions are related. The integrases as well as the cox/apl genes show a common monophyletic origin but the immunity repressor genes, the type P2 C gene and the type 186 cI gene, are likely of different origin. There was no indication of recombination between the P2–186 types of regulatory genes but the comparison of the phylogenies of the regulatory region with the phylogeny based on four structural genes revealed recombinational events between the regulatory region and the structural genes.
Less common regulatory regions were phylogenetically heterogeneous and typically contained a fusion of genes from distantly related or unknown phages and P2-like genes.
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Affiliation(s)
- Hanna Nilsson
- Department of Genetics, Microbiology, and Toxicology; Stockholm University; Stockholm, Sweden
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18
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Abstract
The rise of antibiotic-resistant bacterial strains, causing intractable infections, has resulted in an increased interest in phage therapy. Phage therapy preceded antibiotic treatment against bacterial infections and involves the use of bacteriophages, bacterial viruses, to fight bacteria. Virulent phages are abundant and have proven to be very effective in vitro, where they in most cases lyse any bacteria within the hour. Clinical trials on animals and humans show promising results but also that the treatments are not completely effective. This is partly due to the studies being carried out with few phages, and with limited experimental groups, but also the fact that phage therapy has limitations in vivo. Phages are large compared with small antibiotic molecules, and each phage can only infect one or a few bacterial strains. A very large number of different phages are needed to treat infections as these are caused by genetically different strains of bacteria. Phages are effective only if enough of them can reach the bacteria and increase in number in situ. Taken together, this entails high demands on resources for the construction of phage libraries and the testing of individual phages. The effectiveness and host range must be characterized, and immunological risks must be assessed for every single phage.
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Affiliation(s)
- Anders S. Nilsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
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19
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Lavigne R, Darius P, Summer EJ, Seto D, Mahadevan P, Nilsson AS, Ackermann HW, Kropinski AM. Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiol 2009; 9:224. [PMID: 19857251 PMCID: PMC2771037 DOI: 10.1186/1471-2180-9-224] [Citation(s) in RCA: 207] [Impact Index Per Article: 13.8] [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] [Received: 01/16/2009] [Accepted: 10/26/2009] [Indexed: 11/30/2022] Open
Abstract
Background We advocate unifying classical and genomic classification of bacteriophages by integration of proteomic data and physicochemical parameters. Our previous application of this approach to the entirely sequenced members of the Podoviridae fully supported the current phage classification of the International Committee on Taxonomy of Viruses (ICTV). It appears that horizontal gene transfer generally does not totally obliterate evolutionary relationships between phages. Results CoreGenes/CoreExtractor proteome comparison techniques applied to 102 Myoviridae suggest the establishment of three subfamilies (Peduovirinae, Teequatrovirinae, the Spounavirinae) and eight new independent genera (Bcep781, BcepMu, FelixO1, HAP1, Bzx1, PB1, phiCD119, and phiKZ-like viruses). The Peduovirinae subfamily, derived from the P2-related phages, is composed of two distinct genera: the "P2-like viruses", and the "HP1-like viruses". At present, the more complex Teequatrovirinae subfamily has two genera, the "T4-like" and "KVP40-like viruses". In the genus "T4-like viruses" proper, four groups sharing >70% proteins are distinguished: T4-type, 44RR-type, RB43-type, and RB49-type viruses. The Spounavirinae contain the "SPO1-"and "Twort-like viruses." Conclusion The hierarchical clustering of these groupings provide biologically significant subdivisions, which are consistent with our previous analysis of the Podoviridae.
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Affiliation(s)
- Rob Lavigne
- Biosystems Department, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, Leuven, B-3001, Belgium.
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20
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Nilsson AS, Haggård-Ljungquist E. Evolution of P2-like phages and their impact on bacterial evolution. Res Microbiol 2007; 158:311-7. [PMID: 17490863 DOI: 10.1016/j.resmic.2007.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Revised: 02/13/2007] [Accepted: 02/14/2007] [Indexed: 10/23/2022]
Abstract
The structural genes of P2-like phages are almost identical between different isolates of Escherichia coli, whereas the regulatory genes and host integration sites are more variable. The variation in P2-like phages infecting other gamma-proteobacteria is broader, but their structural genes seem to follow the evolution of their host bacteria. Taken together, this suggests that P2-like phages and their hosts are coevolving.
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Affiliation(s)
- Anders S Nilsson
- Department of Genetics, Microbiology, and Toxicology, University of Stockholm, SE-10691 Stockholm, Sweden.
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21
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Melik W, Nilsson AS, Johansson M. Detection strategies of tick-borne encephalitis virus in Swedish Ixodes ricinus reveal evolutionary characteristics of emerging tick-borne flaviviruses. Arch Virol 2007; 152:1027-34. [PMID: 17277902 DOI: 10.1007/s00705-006-0922-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Accepted: 12/11/2006] [Indexed: 11/28/2022]
Abstract
The flaviviral tick-borne encephalitis virus (TBEV) is a human pathogen having significant impact on public health. The geographical distribution of TBEV and TBEV-like viruses is increasing, which makes it important to characterise the natural virus populations. Here we present four RT-PCR strategies designed for detection of broad types of tick-borne flaviviruses. Sequence information on more than 32% of a TBEV genome was generated from a small pool of ticks collected in the Stockholm archipelago on the island of Torö. The sequences were characterised and compared with those of other tick-borne flaviviruses, which classified the virus as Western European TBEV.
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Affiliation(s)
- W Melik
- School of Life Sciences, Södertörns University College, Huddinge, Sweden
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22
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Karlsson JL, Cardoso-Palacios C, Nilsson AS, Haggård-Ljungquist E. Evolution of immunity and host chromosome integration site of P2-like coliphages. J Bacteriol 2006; 188:3923-35. [PMID: 16707684 PMCID: PMC1482927 DOI: 10.1128/jb.01953-05] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Accepted: 03/14/2006] [Indexed: 11/20/2022] Open
Abstract
The amount and distribution of variation in the genomic region containing the genes in the lytic-lysogenic genetic switch and the sequence that determines the integration site into the host chromosome were analyzed for 38 P2-like phages from Escherichia coli. The genetic switch consists of two convergent mutually exclusive promoters, Pe and Pc, and two repressors, C and Cox. The immunity repressor C blocks the early Pe promoter, leading to the establishment of lysogeny. The Cox repressor blocks expression of Pc, allowing lytic growth. Phylogenetic analyses showed that the C and Cox proteins were distributed into seven distinct classes. The phylogenetic relationship differed between the two proteins, and we showed that homologous recombination plays a major role in creating alterations in the genetic switch, leading to new immunity classes. Analyses of the host integration site for these phages resulted in the discovery of a previously unknown site, and there were at least four regular integration sites. Interestingly, we found no case where phages of the same immunity class had different host attachment sites. The evolution of immunity and integration sites is complex, since it involves interactions both between the phages themselves and between phages and hosts, and often, both regulatory proteins and target DNA must change.
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Affiliation(s)
- Joakim L Karlsson
- Department of Genetics, Microbiology and Toxicology, Stockholm University, S-106 91 Stockholm, Sweden
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23
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Odegrip R, Nilsson AS, Haggård-Ljungquist E. Identification of a gene encoding a functional reverse transcriptase within a highly variable locus in the P2-like coliphages. J Bacteriol 2006; 188:1643-7. [PMID: 16452449 PMCID: PMC1367236 DOI: 10.1128/jb.188.4.1643-1647.2006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Accepted: 11/18/2005] [Indexed: 11/20/2022] Open
Abstract
The P2-like coliphages are highly similar; the structural genes show at least 96% identity. However, at two loci they have genes believed to be horizontally transferred. We show that the genetic content at the second loci, the TO region, contains six completely different sequences with high AT contents and with different open reading frames. The product of one of them exhibits reverse transcriptase activity and blocks infection of phage T5.
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Affiliation(s)
- Richard Odegrip
- Department of Genetics, Microbiology and Toxicology, Stockholm University, S-106 91 Stockholm, Sweden
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24
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Li W, Terenius O, Hirai M, Nilsson AS, Faye I. Cloning, expression and phylogenetic analysis of Hemolin, from the Chinese oak silkmoth, Antheraea pernyi. Dev Comp Immunol 2005; 29:853-64. [PMID: 15978282 DOI: 10.1016/j.dci.2005.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2004] [Revised: 02/09/2005] [Accepted: 02/16/2005] [Indexed: 05/03/2023]
Abstract
The Chinese oak silk moth Antheraea pernyi is an important silk producer. To understand microbial resistance of this moth, we cloned Hemolin, encoding a multifunctional immune protein belonging to the immunoglobulin superfamily, and examined the expression in gonads and fat body. The ApHemolin amino acid sequence was compared to other Hemolin sequences in order to predict functional sites. Several sites were conserved; among them a phosphate binding site, which according to 3D structure modelling does not appear in neuroglian, the phylogenetically closest related protein. In addition, two conserved KDG sequences in the C-C' loop of immunoglobulin domains 1 and 3, give rise to gamma-turns, which is a common motif in the C'-C'' loop of the hypervariable region L2 in vertebrate immunoglobulins. The comparisons also show variable regions of specific interest for future studies of hemolin and its interaction with microbial entities.
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Affiliation(s)
- Wenli Li
- Department of Genetics, Microbiology and Toxicology, Stockholm University, Svante Arrheniuse v. 16E, SE-106 91 Stockholm, Sweden
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25
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Nilsson AS, Karlsson JL, Haggård-Ljungquist E. Site-specific recombination links the evolution of P2-like coliphages and pathogenic enterobacteria. Mol Biol Evol 2004; 21:1-13. [PMID: 12949155 DOI: 10.1093/molbev/msg223] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The genome of the tailed temperate coliphage P2 (Myoviridae) contains some genes that probably are horizontally transferred additions to the genome. One of these genes, the Z/fun gene, was recently found intact in the genome of Neisseria meningitidis. We have investigated the presence of P2-like phages, and the genetic variation at the position corresponding to the phage P2 Z/fun locus, in the Escherichia coli reference collection (ECOR). P2-like phages are common in E. coli since they are present in about 30% of the ECOR strains. Hybridizations and PCR amplifications indicate that the overall variation among these phages is small. Amplification of the region corresponding to the phage P2 Z/fun locus in 11 prophages revealed that this is a multivariable locus. Sequencing of the region resulted in 10 completely different sequences but with a similar high AT-content as the Z/fun gene. All sequences contained at least one open reading frame with good transcription and translation signals. All sequences were also surrounded by a highly similar, previously undiscovered, inverted repeat (IR). We also found this IR in genetically unstable regions in pathogenic enterobacteria. This demonstrates that P2-like phages are important factors in the evolution of bacteria, not only because they carry a diversity of lysogenic conversion genes but also because they can act as vectors for single genes. The genes found between the IRs have unknown functions, and only a few clearly similar genes have been found in other bacteria.
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Affiliation(s)
- Anders S Nilsson
- Department of Genetics, University of Stockholm, Stockholm, Sweden.
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26
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Abstract
Bacteriophage P1 encodes a single-stranded DNA-binding protein (SSB-P1), which shows 66% amino acid sequence identity to the SSB protein of the host bacterium Escherichia coli. A phylogenetic analysis indicated that the P1 ssb gene coexists with its E. coli counterpart as an independent unit and does not represent a recent acquisition of the phage. The P1 and E. coli SSB proteins are fully functionally interchangeable. SSB-P1 is nonessential for phage growth in an exponentially growing E. coli host, and it is sufficient to promote bacterial growth in the absence of the E. coli SSB protein. Expression studies showed that the P1 ssb gene is transcribed only, in an rpoS-independent fashion, during stationary-phase growth in E. coli. Mixed infection experiments demonstrated that a wild-type phage has a selective advantage over an ssb-null mutant when exposed to a bacterial host in the stationary phase. These results reconciled the observed evolutionary conservation with the seemingly redundant presence of ssb genes in many bacteriophages and conjugative plasmids.
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Affiliation(s)
- Jannick Dyrløv Bendtsen
- Department of Genetics and Biochemistry, Institute of Microbiology, Ernst-Moritz-Arndt-Universität Greifswald, D-17487 Greifswald, Germany
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27
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Abstract
Sequencing of five late genes from 18 isolates of P2-like bacteriophages showed that these are at least 96% identical to the genes of phage P2. A maximum-parsimony phylogenetic analysis of these genes showed excess homoplasy of a magnitude three to six times higher than that expected. Examination of the distribution of the number of homoplasies at parsimoniously informative sites and incompatibility matrices of such sites revealed a pattern typical for extensive recombination. It has been shown that phage P2 probably incorporated some functionally complete genes or gene modules by recombination with other phages or with different hosts, but homologous recombination within genes has previously not been shown. In this paper we demonstrate that homologous recombination between P2-like bacteriophages occurs randomly at multiple breakpoints in five late genes. The rate of recombination is high but, since some phages were sampled decades apart and in different parts of the world, this has to be viewed on an evolutionary time scale. The applicability of different methods used for detection of recombination breakpoints and estimation of rates of recombination in bacteriophages is discussed.
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Affiliation(s)
- A S Nilsson
- Department of Genetics, University of Stockholm, S-106 91 Stockholm, Sweden.
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28
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Erfurth EM, Nilsson AS. Effects of growth hormone treatment in a woman with growth hormone deficiency. BJOG 2000; 107:290-1. [PMID: 10688517 DOI: 10.1111/j.1471-0528.2000.tb11704.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- E M Erfurth
- Department of Internal Medicine, University Hospital, Lund, Sweden
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29
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Johansson E, Sollén Hansson A, Nilsson AS, Engervall P. Vascular access devices used during harvest of peripheral blood stem cells: high complication rate in patients with a long-term dialysis central venous catheter. Bone Marrow Transplant 1999; 24:793-7. [PMID: 10516684 DOI: 10.1038/sj.bmt.1701988] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
PBSC harvesting requires good quality venous access. The efficacy and complication rate of the venous access devices used during stem cell harvest in 101 consecutive patients were examined. Four different categories of venous access were used: (1) long-term dialysis central venous catheter (dCVC), (2) short-term dCVC, (3) peripheral venous cannulae (PVC), and (4) PVC and conventional central venous catheter. The number of harvest occasions per patient or harvest days per occasion were similar between the various categories of access. Complications during harvest occurred in 13 out of 48 (27%) occasions using a long-term dCVC compared to six out of 97 (6%) in the other three categories pooled together (P < 0.01). Forty-two of the 101 patients received a long-term dCVC to facilitate the harvest. The long-term dCVC was planned to stay in place and also be used as a conventional i.v. line during the following high-dose treatment. Twenty-one (50%) of the long-term dCVCs were removed due to complication. Thirteen (31%) of the long-term dCVCs were usable throughout the entire treatment period. In conclusion, we recommend that PBSC harvesting is performed through peripheral venous catheters when practically possible, otherwise via short-term dCVC.
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Affiliation(s)
- E Johansson
- Division of Haematology and Infectious Diseases, Department of Medicine, Karolinska Hospital, Stockholm, Sweden
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30
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Abstract
A novel member of the neurotrophin family, zebrafish neurotrophin-7 (zNT-7), was isolated from the zebrafish Danio rerio. The amino acid sequence of zNT-7 is more closely related to that of fish nerve growth factor (NGF) and neurotrophin-6 (NT-6) than to that of any other neurotrophin. zNT-7 is, however, equally related to fish NGF and NT-6 (65% and 63% amino acid sequence identity, respectively) indicating that it represents a distinct neurotrophin sequence. zNT-7 contains a 15 amino acid residue insertion in a beta-turn region in the middle of the mature protein. Recombinant zNT-7 was able to bind to the human p75 neurotrophin receptor and to induce tyrosine phosphorylation of the rat TrkA receptor tyrosine kinase, albeit less efficiently than rat NGF. zNT-7 did not interact with rat TrkB or TrkC, indicating a similar receptor specificity as NGF. We propose that a diversification of the NGF subfamily in the neurotrophin evolutionary tree occurred during the evolution of teleost fishes which resulted in the appearance of several additional members, such as zNT-7 and NT-6, structurally and functionally related to NGF.
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Affiliation(s)
- A S Nilsson
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
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31
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Westman K, Salmonson EC, Nilsson AS, Eskilsson J, Erfurth EM. Growth hormone treatment increases kidney size in a woman with growth hormone deficiency--a case report. Pediatr Nephrol 1997; 11:528-9. [PMID: 9260263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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32
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Trupp M, Arenas E, Fainzilber M, Nilsson AS, Sieber BA, Grigoriou M, Kilkenny C, Salazar-Grueso E, Pachnis V, Arumäe U. Functional receptor for GDNF encoded by the c-ret proto-oncogene. Nature 1996; 381:785-9. [PMID: 8657281 DOI: 10.1038/381785a0] [Citation(s) in RCA: 580] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Glial-cell-line-derived neutrophic factor (GDNF) promotes the survival and phenotype of central dopaminergic noradrenergic and motor neurons, as well as various subpopulations of peripheral sensory and sympathetic neurons. GDNF is structurally related to members of the transforming growth factor (TGF)-beta superfamily, several members of which have well-characterized receptor systems; however, GDNF receptors still remain undefined. Here we show that GDNF binds to, and induces tyrosine phosphorylation of, the product of the c-ret proto-oncogene, an orphan receptor tyrosine kinase, in a GDNF-responsive motor-neuron cell line. Ret protein could also bind GDNF and mediate survival and growth responses to GDNF upon transfection into naive fibroblasts. Moreover, high levels of c-ret mRNA expression were found in dopaminergic neurons of the adult substantia nigra, where exogenous GDNF protected Ret-positive neurons from 6-hydroxydopamine-induced cell death. Thus the product of the c-ret proto-oncogene encodes a functional receptor for GDNF that may mediate its neurotrophic effects on motor and dopaminergic neurons.
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Affiliation(s)
- M Trupp
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
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Kashuba VI, Szeles A, Allikmets R, Nilsson AS, Bergerheim US, Modi W, Grafodatsky A, Dean M, Stanbridge EJ, Winberg G. A group of NotI jumping and linking clones cover 2.5 Mb in the 3p21-p22 region suspected to contain a tumor suppressor gene. Cancer Genet Cytogenet 1995; 81:144-50. [PMID: 7621411 DOI: 10.1016/0165-4608(94)00215-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The chromosomal region 3p21.2-p22 has been shown to be involved in the development of several forms of solid tumors. Such deletions, translocations, and rearrangements presumably result in the disturbance or loss of a critical gene function. Pulsed-field gel electrophoresis (PFGE), using NotI linking clones as a probe represent a powerful tool for analyzing such rearrangements. A NotI linking clone, AP20 (D3S1641), was localized by in situ hybridization to 3p21.3-p22. Two NotI jumping clones adjacent to this clone were isolated, clone J32-612 covering 0.5 Mb and clone J31-611 covering approximately 1 Mb. Clone J31-611 crosses the border of the deletion present in hybrid cell line MCH939.2, which contains a deleted 3p21 region. For these jumping clones, corresponding NotI linking clones, NLJ3 (D3S1642) and NL3-003, were isolated. Altogether, linking and jumping clones from the AP20 locus hybridize to NotI fragments totaling 2.5 Mb in length. These NotI-containing clones detect expressed sequences in several human tissues. Clone NLJ3 possesses homology to the human platelet-derived endothelial cell growth factor gene and may represent a new member of this gene family. Another clone (AP20) revealed 66% sequence similarity to rat skeletal muscle voltage-sensitive sodium channel subtype 2. Therefore, this group of clones will be useful not only for analyzing rearrangements in tumors, but also for the isolation of new genes from the 3p21.3-p22 region.
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Affiliation(s)
- V I Kashuba
- Department of Tumor Biology, Karolinska Institute, Stockholm, Sweden
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Boldog FL, Gemmill RM, Wilke CM, Glover TW, Nilsson AS, Chandrasekharappa SC, Brown RS, Li FP, Drabkin HA. Positional cloning of the hereditary renal carcinoma 3;8 chromosome translocation breakpoint. Proc Natl Acad Sci U S A 1993; 90:8509-13. [PMID: 7690964 PMCID: PMC47386 DOI: 10.1073/pnas.90.18.8509] [Citation(s) in RCA: 49] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The chromosome (p14.2;q24.1) translocation t(3;8) has been associated with hereditary renal cancer in one family. Based on cytogenetic analyses and loss-of-heterozygosity experiments, the 3p14 region has been independently implicated as harboring a tumor suppressor gene critical to kidney and lung cancer development. The 3p14.2 region also contains FRA3B, the most sensitive fragile site induced by aphidicolin. A chromosome 3 probe, R7K145, derived from a radiation-reduced hybrid was positioned between the t(3;8) breakpoint and an aphidicolin-induced 3p14 breakpoint. A yeast artificial chromosome (YAC) contig containing R7K145 was developed that crossed the aphidicolin-induced breakpoint on its telomeric side. A subsequent chromosome walk identified a YAC that crossed the 3;8 translocation breakpoint. A lambda sublibrary allowed isolation of clones spanning the rearrangement. Unique and evolutionarily conserved DNA sequences were used to screen a kidney cDNA library. We have identified a gene, referred to as HRCA1 (hereditary renal cancer associated 1), that maps immediately adjacent to the breakpoint. On the basis of its chromosomal position, HRCA1 may be a candidate tumor suppressor gene.
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Affiliation(s)
- F L Boldog
- University of Colorado Cancer Center, Division of Medical Oncology, Denver 80262
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