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Sensevdi ER, Sourrouille ZA, Quax TE. Host range and cell recognition of archaeal viruses. Curr Opin Microbiol 2024; 77:102423. [PMID: 38232492 DOI: 10.1016/j.mib.2023.102423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/19/2024]
Abstract
Archaea are members of a separate domain of life that have unique properties, such as the composition of their cell walls and the structure of their lipid bilayers. Consequently, archaeal viruses face different challenges to infect host cells in comparison with viruses of bacteria and eukaryotes. Despite their significant impact on shaping microbial communities, our understanding of infection processes of archaeal viruses remains limited. Several receptors used by archaeal viruses to infect cells have recently been identified. The interactions between viruses and receptors are one of the determinants of the host range of viruses. Here, we review the current literature on host ranges of archaeal viruses and factors that might impact the width of these host ranges.
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Affiliation(s)
- Emine Rabia Sensevdi
- Biology of Archaea and Viruses, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, 9747 Groningen AG, the Netherlands
| | - Zaloa Aguirre Sourrouille
- Biology of Archaea and Viruses, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, 9747 Groningen AG, the Netherlands
| | - Tessa Ef Quax
- Biology of Archaea and Viruses, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, 9747 Groningen AG, the Netherlands.
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2
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Subramanian S, Bergland Drarvik SM, Tinney KR, Parent KN. Cryo-EM structure of a Shigella podophage reveals a hybrid tail and novel decoration proteins. Structure 2024; 32:24-34.e4. [PMID: 37909043 PMCID: PMC10842012 DOI: 10.1016/j.str.2023.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/02/2023] [Accepted: 10/04/2023] [Indexed: 11/02/2023]
Abstract
There is a paucity of high-resolution structures of phages infecting Shigella, a human pathogen and a serious threat to global health. HRP29 is a Shigella podophage belonging to the Autographivirinae family, and has very low sequence identity to other known phages. Here, we resolved the structure of the entire HRP29 virion by cryo-EM. Phage HRP29 has a highly unusual tail that is a fusion of a T7-like tail tube and P22-like tailspikes mediated by interactions from a novel tailspike adaptor protein. Understanding phage tail structures is critical as they mediate hosts interactions. Furthermore, we show that the HRP29 capsid is stabilized by two novel, and essential decoration proteins, gp47 and gp48. Only one high resolution structure is currently available for Shigella podophages. The presence of a hybrid tail and an adapter protein suggests that it may be a product of horizontal gene transfer, and may be prevalent in other phages.
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Affiliation(s)
- Sundharraman Subramanian
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Silje M Bergland Drarvik
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Kendal R Tinney
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Kristin N Parent
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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3
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Zheng J, Chen W, Xiao H, Yang F, Song J, Cheng L, Liu H. Asymmetric Structure of Podophage GP4 Reveals a Novel Architecture of Three Types of Tail Fibers. J Mol Biol 2023; 435:168258. [PMID: 37660940 DOI: 10.1016/j.jmb.2023.168258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
Bacteriophage tail fibers (or called tail spikes) play a critical role in the early stage of infection by binding to the bacterial surface. Podophages with known structures usually possess one or two types of fibers. Here, we resolved an asymmetric structure of the podophage GP4 to near-atomic resolution by cryo-EM. Our structure revealed a symmetry-mismatch relationship between the components of the GP4 tail with previously unseen topologies. In detail, two dodecameric adaptors (adaptors I and II), a hexameric nozzle, and a tail needle form a conserved tail body connected to a dodecameric portal occupying a unique vertex of the icosahedral head. However, five chain-like extended fibers (fiber I) and five tulip-like short fibers (fiber II) are anchored to a 15-fold symmetric fiber-tail adaptor, encircling the adaptor I, and six bamboo-like trimeric fibers (fiber III) are connected to the nozzle. Five fibers I, each composed of five dimers of the protein gp80 linked by an elongated rope protein, are attached to the five edges of the tail vertex of the icosahedral head. In this study, we identified a new structure of the podophage with three types of tail fibers, and such phages with different types of fibers may have a broad host range and/or infect host cells with considerably high efficiency, providing evolutionary advantages in harsh environments.
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Affiliation(s)
- Jing Zheng
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha 410082, China
| | - Wenyuan Chen
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha 410082, China
| | - Hao Xiao
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha 410082, China; State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Fan Yang
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha 410082, China
| | - Jingdong Song
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Lingpeng Cheng
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha 410082, China.
| | - Hongrong Liu
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha 410082, China.
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4
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López-Pérez J, Otero J, Sánchez-Osuna M, Erill I, Cortés P, Llagostera M. Impact of mutagenesis and lateral gene transfer processes in bacterial susceptibility to phage in food biocontrol and phage therapy. Front Cell Infect Microbiol 2023; 13:1266685. [PMID: 37842006 PMCID: PMC10569123 DOI: 10.3389/fcimb.2023.1266685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction The emergence of resistance and interference mechanisms to phage infection can hinder the success of bacteriophage-based applications, but the significance of these mechanisms in phage therapy has not been determined. This work studies the emergence of Salmonella isolates with reduced susceptibility to a cocktail of three phages under three scenarios: i) Salmonella cultures (LAB), ii) biocontrol of cooked ham slices as a model of food safety (FOOD), and iii) oral phage therapy in broilers (PT). Methods S. Typhimurium ATCC 14028 RifR variants with reduced phage susceptibility were isolated from the three scenarios and conventional and molecular microbiology techniques were applied to study them. Results and discussion In LAB, 92% of Salmonella isolates lost susceptibility to all three phages 24 h after phage infection. This percentage was lower in FOOD, with 4.3% of isolates not susceptible to at least two of the three phages after seven days at 4°C following phage treatment. In PT, 9.7% and 3.3 % of isolates from untreated and treated broilers, respectively, displayed some mechanism of interference with the life cycle of some of the phages. In LAB and FOOD scenarios, resistant variants carrying mutations in rfc and rfaJ genes involved in lipopolysaccharide synthesis (phage receptor) were identified. However, in PT, the significant decrease of EOP, ECOI, and burst size observed in isolates was prompted by lateral gene transfer of large IncI1 plasmids, which may encode phage defense mechanisms. These data indicate that the acquisition of specific conjugative plasmids has a stronger impact than mutagenesis on the emergence of reduced phage-susceptibility bacteria in certain environments. In spite of this, neither mechanism seems to significantly impair the success of Salmonella biocontrol and oral phage therapy.
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Affiliation(s)
- Júlia López-Pérez
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Jennifer Otero
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- SK8 Biotech, Parc Científic de Barcelona, Barcelona, Spain
| | - Miquel Sánchez-Osuna
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ivan Erill
- Department of Biological Sciences, University of Maryland, Baltimore, MD, United States
- Departament Enginyeria de la Informació i de les Comunicacions, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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Baláž A, Kajsik M, Budiš J, Szemes T, Turňa J. PHERI-Phage Host ExploRation Pipeline. Microorganisms 2023; 11:1398. [PMID: 37374901 DOI: 10.3390/microorganisms11061398] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Antibiotic resistance is becoming a common problem in medicine, food, and industry, with multidrug-resistant bacterial strains occurring in all regions. One of the possible future solutions is the use of bacteriophages. Phages are the most abundant form of life in the biosphere, so we can highly likely purify a specific phage against each target bacterium. The identification and consistent characterization of individual phages was a common form of phage work and included determining bacteriophages' host-specificity. With the advent of new modern sequencing methods, there was a problem with the detailed characterization of phages in the environment identified by metagenome analysis. The solution to this problem may be to use a bioinformatic approach in the form of prediction software capable of determining a bacterial host based on the phage whole-genome sequence. The result of our research is the machine learning algorithm-based tool called PHERI. PHERI predicts the suitable bacterial host genus for the purification of individual viruses from different samples. In addition, it can identify and highlight protein sequences that are important for host selection.
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Affiliation(s)
- Andrej Baláž
- Geneton Ltd., Ilkovicova 8, 841 04 Bratislava, Slovakia
- Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynska dolina F1, 842 48 Bratislava, Slovakia
| | - Michal Kajsik
- Science Park, Comenius University, Ilkovicova 8, 841 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 841 04 Bratislava, Slovakia
- Medirex Group Academy n.o., Novozamocka 1, 949 05 Nitra, Slovakia
| | - Jaroslav Budiš
- Geneton Ltd., Ilkovicova 8, 841 04 Bratislava, Slovakia
- Science Park, Comenius University, Ilkovicova 8, 841 04 Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information (SCSTI), Lamacska Cesta 8/A, 811 04 Bratislava, Slovakia
| | - Tomáš Szemes
- Geneton Ltd., Ilkovicova 8, 841 04 Bratislava, Slovakia
- Science Park, Comenius University, Ilkovicova 8, 841 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 841 04 Bratislava, Slovakia
| | - Ján Turňa
- Science Park, Comenius University, Ilkovicova 8, 841 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 841 04 Bratislava, Slovakia
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6
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Isolation and Characterization of a Novel Siphoviridae Phage, vB_AbaS_TCUP2199, Infecting Multidrug-Resistant Acinetobacter baumannii. Viruses 2022; 14:v14061240. [PMID: 35746711 PMCID: PMC9228384 DOI: 10.3390/v14061240] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/02/2022] [Accepted: 06/06/2022] [Indexed: 11/29/2022] Open
Abstract
Multidrug-resistant Acinetobacter baumannii (MDRAB) is a pathogen recognized as antimicrobial-resistant bacteria involved in healthcare-associated infections. Resistance to antibiotics has made alternative therapies necessary. Bacteriophage therapy is considered a potential solution to treat MDRAB. In this study, we isolated and characterized the phage vB_AbaS_TCUP2199 (TCUP2199), which can infect MDRAB. Morphological analysis revealed that TCUP2199 belongs to the Siphoviridae family. TCUP2199 has a wide host range, can adsorb rapidly (68.28% in 2 min), and has a burst size of 196 PFU/cell. At least 16 distinct structural proteins were visualized by SDS polyacrylamide gel electrophoresis. A stability test showed that TCUP2199 was stable at 37 °C and pH 7. Genome analysis of TCUP2199 showed that it consists of a double-stranded DNA genome of 79,572 bp with a G+C content of 40.39%, which contains 98 putative open reading frames, none of which is closely related to the bacteriophage genome sequence that was found in the public database. TCUP2199 shows similarity in genomic organization and putative packaging mechanism with Achromobacter phage JWF and Pseudoalteromonas phage KB12-38 based on protein BLAST and phylogenetic analysis. Because of those unique characteristics, we consider TCUP2199 to be a novel phage that is suitable for inclusion in a phage cocktail to treat A. baumannii infection.
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7
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Johnson CN, Palacios Araya D, Schink V, Islam M, Mangalea MR, Decurtis EK, Ngo TC, Palmer KL, Duerkop BA. Genetically distant bacteriophages select for unique genomic changes in Enterococcus faecalis. Microbiologyopen 2022; 11:e1273. [PMID: 35478284 PMCID: PMC8924694 DOI: 10.1002/mbo3.1273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 11/10/2022] Open
Abstract
The human microbiota harbors diverse bacterial and bacteriophage (phage) communities. Bacteria evolve to overcome phage infection, thereby driving phage evolution to counter bacterial resistance. Understanding how phages select for genetic alterations in medically relevant bacteria is important as phages become established biologics for the treatment of multidrug-resistant (MDR) bacterial infections. Before phages can be widely used as standalone or combination antibacterial therapies, we must obtain a deep understanding of the molecular mechanisms of phage infection and how host bacteria alter their genomes to become resistant. We performed coevolution experiments using a single Enterococcus faecalis strain and two distantly related phages to determine how phage pressure impacts the evolution of the E. faecalis genome. Whole-genome sequencing of E. faecalis following continuous exposure to these two phages revealed mutations previously demonstrated to be essential for phage infection. We also identified mutations in genes previously unreported to be associated with phage infection in E. faecalis. Intriguingly, there was only one shared mutation in the E. faecalis genome that was selected by both phages tested, demonstrating that infection by two genetically distinct phages selects for diverse variants. This knowledge serves as the basis for the continued study of E. faecalis genome evolution during phage infection and can be used to inform the design of future therapeutics, such as phage cocktails, intended to target MDR E. faecalis.
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Affiliation(s)
- Cydney N. Johnson
- Department of Immunology and MicrobiologyUniversity of Colorado School of MedicineAuroraColoradoUSA
| | | | - Viviane Schink
- Department of Immunology and MicrobiologyUniversity of Colorado School of MedicineAuroraColoradoUSA
| | - Moutusee Islam
- Department of Biological SciencesUniversity of Texas at DallasRichardsonTexasUSA
| | - Mihnea R. Mangalea
- Department of Immunology and MicrobiologyUniversity of Colorado School of MedicineAuroraColoradoUSA
| | - Emily K. Decurtis
- Department of Biological SciencesUniversity of Texas at DallasRichardsonTexasUSA
| | - Tuong‐Vi C. Ngo
- Department of Biological SciencesUniversity of Texas at DallasRichardsonTexasUSA
| | - Kelli L. Palmer
- Department of Biological SciencesUniversity of Texas at DallasRichardsonTexasUSA
| | - Breck A. Duerkop
- Department of Immunology and MicrobiologyUniversity of Colorado School of MedicineAuroraColoradoUSA
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8
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Adler BA, Kazakov AE, Zhong C, Liu H, Kutter E, Lui LM, Nielsen TN, Carion H, Deutschbauer AM, Mutalik VK, Arkin AP. The genetic basis of phage susceptibility, cross-resistance and host-range in Salmonella. MICROBIOLOGY (READING, ENGLAND) 2021; 167. [PMID: 34910616 PMCID: PMC8744999 DOI: 10.1099/mic.0.001126] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Though bacteriophages (phages) are known to play a crucial role in bacterial fitness and virulence, our knowledge about the genetic basis of their interaction, cross-resistance and host-range is sparse. Here, we employed genome-wide screens in Salmonella enterica serovar Typhimurium to discover host determinants involved in resistance to eleven diverse lytic phages including four new phages isolated from a therapeutic phage cocktail. We uncovered 301 diverse host factors essential in phage infection, many of which are shared between multiple phages demonstrating potential cross-resistance mechanisms. We validate many of these novel findings and uncover the intricate interplay between RpoS, the virulence-associated general stress response sigma factor and RpoN, the nitrogen starvation sigma factor in phage cross-resistance. Finally, the infectivity pattern of eleven phages across a panel of 23 genome sequenced Salmonella strains indicates that additional constraints and interactions beyond the host factors uncovered here define the phage host range.
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Affiliation(s)
- Benjamin A Adler
- The UC Berkeley-UCSF Graduate Program in Bioengineering, Berkeley, California, USA.,Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, California, USA
| | - Alexey E Kazakov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Crystal Zhong
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
| | - Hualan Liu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Lauren M Lui
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Torben N Nielsen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Heloise Carion
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Vivek K Mutalik
- Innovative Genomics Institute, University of California, Berkeley, California, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, California, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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9
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Turzynski V, Monsees I, Moraru C, Probst AJ. Imaging Techniques for Detecting Prokaryotic Viruses in Environmental Samples. Viruses 2021; 13:2126. [PMID: 34834933 PMCID: PMC8622608 DOI: 10.3390/v13112126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/28/2022] Open
Abstract
Viruses are the most abundant biological entities on Earth with an estimate of 1031 viral particles across all ecosystems. Prokaryotic viruses-bacteriophages and archaeal viruses-influence global biogeochemical cycles by shaping microbial communities through predation, through the effect of horizontal gene transfer on the host genome evolution, and through manipulating the host cellular metabolism. Imaging techniques have played an important role in understanding the biology and lifestyle of prokaryotic viruses. Specifically, structure-resolving microscopy methods, for example, transmission electron microscopy, are commonly used for understanding viral morphology, ultrastructure, and host interaction. These methods have been applied mostly to cultivated phage-host pairs. However, recent advances in environmental genomics have demonstrated that the majority of viruses remain uncultivated, and thus microscopically uncharacterized. Although light- and structure-resolving microscopy of viruses from environmental samples is possible, quite often the link between the visualization and the genomic information of uncultivated prokaryotic viruses is missing. In this minireview, we summarize the current state of the art of imaging techniques available for characterizing viruses in environmental samples and discuss potential links between viral imaging and environmental genomics for shedding light on the morphology of uncultivated viruses and their lifestyles in Earth's ecosystems.
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Affiliation(s)
- Victoria Turzynski
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany;
| | - Indra Monsees
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany;
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky-University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany;
| | - Alexander J. Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany;
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
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10
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Sørensen AN, Woudstra C, Sørensen MCH, Brøndsted L. Subtypes of tail spike proteins predicts the host range of Ackermannviridae phages. Comput Struct Biotechnol J 2021; 19:4854-4867. [PMID: 34527194 PMCID: PMC8432352 DOI: 10.1016/j.csbj.2021.08.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 12/01/2022] Open
Abstract
Phages belonging to the Ackermannviridae family encode up to four tail spike proteins (TSPs), each recognizing a specific receptor of their bacterial hosts. Here, we determined the TSPs diversity of 99 Ackermannviridae phages by performing a comprehensive in silico analysis. Based on sequence diversity, we assigned all TSPs into distinctive subtypes of TSP1, TSP2, TSP3 and TSP4, and found each TSP subtype to be specifically associated with the genera (Kuttervirus, Agtrevirus, Limestonevirus, Taipeivirus) of the Ackermannviridae family. Further analysis showed that the N-terminal XD1 and XD2 domains in TSP2 and TSP4, hinging the four TSPs together, are preserved. In contrast, the C-terminal receptor binding modules were only conserved within TSP subtypes, except for some Kuttervirus TSP1s and TSP3s that were similar to specific TSP4s. A conserved motif in TSP1, TSP3 and TSP4 of Kuttervirus phages may allow recombination between receptor binding modules, thus altering host recognition. The receptors for numerous uncharacterized phages expressing TSPs in the same subtypes were predicted using previous host range data. To validate our predictions, we experimentally determined the host recognition of three of the four TSPs expressed by kuttervirus S117. We confirmed that S117 TSP1 and TSP2 bind to their predicted host receptors, and identified the receptor for TSP3, which is shared by 51 other Kuttervirus phages. Kuttervirus phages were thus shown encode a vast genetic diversity of potentially exchangeable TSPs influencing host recognition. Overall, our study demonstrates that comprehensive in silico and host range analysis of TSPs can predict host recognition of Ackermannviridae phages.
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Key Words
- ANI, Average nucleotide identity
- Ackermannviridae family
- Bacteriophage
- CPS, Capsular polysaccharide
- EOP, Efficiency of plating
- Escherichia coli O:157
- Host range
- LB, Luria-Bertani
- LPS, Lipopolysaccharide
- NCBI, National Center for Biotechnology Information
- O-antigen
- ORF, Open reading frame
- PFU, Plaque formation unit
- RBP, Receptor binding protein
- Receptor-binding proteins
- Salmonella
- TSP, Tail spike protein
- Tail spike proteins
- VriC, Virulence-associated protein
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Affiliation(s)
- Anders Nørgaard Sørensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Cedric Woudstra
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Martine C Holst Sørensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
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11
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Witte S, Zinsli LV, Gonzalez-Serrano R, Matter CI, Loessner MJ, van Mierlo JT, Dunne M. Structural and functional characterization of the receptor binding proteins of Escherichia coli O157 phages EP75 and EP335. Comput Struct Biotechnol J 2021; 19:3416-3426. [PMID: 34194667 PMCID: PMC8217332 DOI: 10.1016/j.csbj.2021.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 12/16/2022] Open
Abstract
Bacteriophages (phages) are widely used as biocontrol agents in food and as antibacterial agents for treatment of food production plant surfaces. An important feature of such phages is broad infectivity towards a given pathogenic species. Phages attach to the surfaces of bacterial cells using receptor binding proteins (RBPs), namely tail fibers or tailspikes (TSPs). The binding range of RBPs is the primary determinant of phage host range and infectivity, and therefore dictates a phage's suitability as an antibacterial agent. Phages EP75 and EP335 broadly infect strains of E. coli serotype O157. To better understand host recognition by both phages, here we focused on characterizing the structures and functions of their RBPs. We identified two distinct tail fibers in the genome of the podovirus EP335: gp12 and gp13. Using fluorescence microscopy, we reveal how gp13 recognizes strains of E. coli serotypes O157 and O26. Phage EP75 belongs to the Kuttervirus genus within the Ackermannviridae family and features a four TSP complex (TSPs 1-4) that is universal among such phages. We demonstrate enzymatic activity of TSP1 (gp167) and TSP2 (gp168) toward the O18A and O157 O-antigens of E. coli, respectively, as well as TSP3 activity (gp169.1) against O4, O7, and O9 Salmonella O-antigens. TSPs of EP75 present high similarity to TSPs from E. coli phages CBA120 (TSP2) and HK620 (TSP1) and Salmonella myovirus Det7 (TSP3), which helps explain the cross-genus infectivity observed for EP75.
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Affiliation(s)
- Sander Witte
- Micreos Food Safety B.V., Wageningen, Nieuwe Kanaal 7P, 6709PA, The Netherlands
| | - Léa V. Zinsli
- Institute of Food Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zürich, Switzerland
| | | | - Cassandra I. Matter
- Institute of Food Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zürich, Switzerland
| | - Martin J. Loessner
- Institute of Food Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zürich, Switzerland
| | - Joël T. van Mierlo
- Micreos Food Safety B.V., Wageningen, Nieuwe Kanaal 7P, 6709PA, The Netherlands
| | - Matthew Dunne
- Institute of Food Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zürich, Switzerland
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12
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Wang Z, Cai R, Wang G, Guo Z, Liu X, Guan Y, Ji Y, Zhang H, Xi H, Zhao R, Bi L, Liu S, Yang L, Feng X, Sun C, Lei L, Han W, Gu J. Combination Therapy of Phage vB_KpnM_P-KP2 and Gentamicin Combats Acute Pneumonia Caused by K47 Serotype Klebsiella pneumoniae. Front Microbiol 2021; 12:674068. [PMID: 33968007 PMCID: PMC8100603 DOI: 10.3389/fmicb.2021.674068] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/30/2021] [Indexed: 12/26/2022] Open
Abstract
Klebsiella pneumoniae (K. pneumoniae) is an important nosocomial and community acquired opportunistic pathogen which causes various infections. The emergence of multi-drug resistant (MDR) K. pneumoniae and carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) has brought more severe challenge to the treatment of K. pneumoniae infection. In this study, a novel bacteriophage that specifically infects K. pneumoniae was isolated and named as vB_KpnM_P-KP2 (abbreviated as P-KP2). The biological characteristics of P-KP2 and the bioinformatics of its genome were analyzed, and then the therapeutic effect of P-KP2 was tested by animal experiments. P-KP2 presents high lysis efficiency in vitro. The genome of P-KP2 shows homology with nine phages which belong to “KP15 virus” family and its genome comprises 172,138 bp and 264 ORFs. Besides, P-KP2 was comparable to gentamicin in the treatment of lethal pneumonia caused by K. pneumoniae W-KP2 (K47 serotype). Furthermore, the combined treatment of P-KP2 and gentamicin completely rescued the infected mice. Therefore, this study not only introduces a new member to the phage therapeutic library, but also serves as a reference for other phage-antibiotic combinations to combat MDR pathogens.
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Affiliation(s)
- Zijing Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Ruopeng Cai
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Gang Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zhimin Guo
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun, China
| | - Xiao Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yuan Guan
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yalu Ji
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Hao Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Hengyu Xi
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Rihong Zhao
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Lanting Bi
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Shanshan Liu
- Department of Chinese Journal of Veterinary Science, Jilin University, Changchun, China
| | - Li Yang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xin Feng
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Changjiang Sun
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Liancheng Lei
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Wenyu Han
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
| | - Jingmin Gu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
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13
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Sofy AR, El-Dougdoug NK, Refaey EE, Dawoud RA, Hmed AA. Characterization and Full Genome Sequence of Novel KPP-5 Lytic Phage against Klebsiella pneumoniae Responsible for Recalcitrant Infection. Biomedicines 2021; 9:342. [PMID: 33800632 PMCID: PMC8066614 DOI: 10.3390/biomedicines9040342] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 01/21/2023] Open
Abstract
Klebsiella pneumoniae is a hazardous opportunistic pathogen that is involved in many serious human diseases and is considered to be an important foodborne pathogen found in many food types. Multidrug resistance (MDR) K. pneumoniae strains have recently spread and increased, making bacteriophage therapy an effective alternative to multiple drug-resistant pathogens. As a consequence, this research was conducted to describe the genome and basic biological characteristics of a novel phage capable of lysing MDR K. pneumoniae isolated from food samples in Egypt. The host range revealed that KPP-5 phage had potent lytic activity and was able to infect all selected MDR K. pneumoniae strains from different sources. Electron microscopy images showed that KPP-5 lytic phage was a podovirus morphology. The one-step growth curve exhibited that KPP-5 phage had a relatively short latent period of 25 min, and the burst size was about 236 PFU/infected cells. In addition, KPP-5 phage showed high stability at different temperatures and pH levels. KPP-5 phage has a linear dsDNA genome with a length of 38,245 bp with a GC content of 50.8% and 40 predicted open reading frames (ORFs). Comparative genomics and phylogenetic analyses showed that KPP-5 is most closely associated with the Teetrevirus genus in the Autographviridae family. No tRNA genes have been identified in the KPP-5 phage genome. In addition, phage-borne virulence genes or drug resistance genes were not present, suggesting that KPP-5 could be used safely as a phage biocontrol agent.
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Affiliation(s)
- Ahmed R. Sofy
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo 11884, Egypt; (E.E.R.); (A.A.H.)
| | - Noha K. El-Dougdoug
- Botany and Microbiology Department, Faculty of Science, Benha University, Benha 13518, Egypt;
| | - Ehab E. Refaey
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo 11884, Egypt; (E.E.R.); (A.A.H.)
| | - Rehab A. Dawoud
- Virus and Phytoplasma Research Department, Plant Pathology Research Institute, Agricultural Research Center (ARC), Giza 12619, Egypt;
- Department of Biology, Faculty of Science, Jazan University, Box 114, Jazan 45142, Saudi Arabia
| | - Ahmed A. Hmed
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo 11884, Egypt; (E.E.R.); (A.A.H.)
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14
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Lukianova AA, Shneider MM, Evseev PV, Shpirt AM, Bugaeva EN, Kabanova AP, Obraztsova EA, Miroshnikov KK, Senchenkova SN, Shashkov AS, Toschakov SV, Knirel YA, Ignatov AN, Miroshnikov KA. Morphologically Different Pectobacterium brasiliense Bacteriophages PP99 and PP101: Deacetylation of O-Polysaccharide by the Tail Spike Protein of Phage PP99 Accompanies the Infection. Front Microbiol 2020; 10:3147. [PMID: 32038580 PMCID: PMC6989608 DOI: 10.3389/fmicb.2019.03147] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/29/2019] [Indexed: 01/31/2023] Open
Abstract
Soft rot caused by numerous species of Pectobacterium and Dickeya is a serious threat to the world production of potatoes. The application of bacteriophages to combat bacterial infections in medicine, agriculture, and the food industry requires the selection of comprehensively studied lytic phages and the knowledge of their infection mechanism for more rational composition of therapeutic cocktails. We present the study of two bacteriophages, infective for the Pectobacterium brasiliense strain F152. Podoviridae PP99 is a representative of the genus Zindervirus, and Myoviridae PP101 belongs to the still unclassified genomic group. The structure of O-polysaccharide of F152 was established by sugar analysis and 1D and 2D NMR spectroscopy: → 4)-α-D-Manp6Ac-(1→ 2)-α-D-Manp-(1→ 3)-β-D-Galp-(1→
3↑1α-l-6dTalpAc0−2 The recombinant tail spike protein of phage PP99, gp55, was shown to deacetylate the side chain talose residue of bacterial O-polysaccharide, thus providing the selective attachment of the phage to the cell surface. Both phages demonstrate lytic behavior, thus being prospective for therapeutic purposes.
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Affiliation(s)
- Anna A Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail M Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Peter V Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anna M Shpirt
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Anastasia P Kabanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Research Center "PhytoEngineering" Ltd., Rogachevo, Moscow, Russia
| | - Ekaterina A Obraztsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Kirill K Miroshnikov
- Winogradsky Institute of Microbiology, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia
| | - Sofiya N Senchenkova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander S Shashkov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Stepan V Toschakov
- Winogradsky Institute of Microbiology, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia
| | - Yuriy A Knirel
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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15
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Knecht LE, Veljkovic M, Fieseler L. Diversity and Function of Phage Encoded Depolymerases. Front Microbiol 2020; 10:2949. [PMID: 31998258 PMCID: PMC6966330 DOI: 10.3389/fmicb.2019.02949] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/09/2019] [Indexed: 12/14/2022] Open
Abstract
Bacteriophages of the Podoviridae family often exhibit so-called depolymerases as structural components of the virion. These enzymes appear as tail spike proteins (TSPs). After specific binding to capsular polysaccharides (CPS), exopolysaccharides (EPS) or lipopolysaccharide (LPS) of the host bacteria, polysaccharide-repeating units are specifically cleaved. Finally, the phage reaches the last barrier, the cell wall, injects its DNA, and infects the cell. Recently, similar enzymes from bacteriophages of the Ackermannviridae, Myoviridae, and Siphoviridae families were also described. In this mini-review the diversity and function of phage encoded CPS-, EPS-, and LPS-degrading depolymerases is summarized. The function of the enzymes is described in terms of substrate specificity and applications in biotechnology.
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Affiliation(s)
- Leandra E Knecht
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Marjan Veljkovic
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Lars Fieseler
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, Wädenswil, Switzerland
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16
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Gao M, Wang C, Qiang X, Liu H, Li P, Pei G, Zhang X, Mi Z, Huang Y, Tong Y, Bai C. Isolation and Characterization of a Novel Bacteriophage Infecting Carbapenem-Resistant Klebsiella pneumoniae. Curr Microbiol 2020; 77:722-729. [PMID: 31912220 DOI: 10.1007/s00284-019-01849-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/13/2019] [Indexed: 01/13/2023]
Abstract
A novel virulent phage, vB_KpnP_IME337, isolated from a hospital sewage in Beijing, China, that infects carbapenem-resistant Klebsiella pneumoniae KN2 capsular type was identified and characterized. Next-generation sequencing and genome analysis revealed that vB_KpnP_IME337 had a linear double-stranded genome with a length of 44,266 base pairs and G+C content of 53.7%. Fifty-two putative open reading frames were identified, and no transfer RNA-encoding genes were detected. BLASTn analysis revealed that phage vB_KpnP_IME337 had the highest sequence similarity with Klebsiella phage phiBO1E, with genome coverage of 79%. Based on morphology, phage vB_KpnP_IME337 was determined to belong to the family Podoviridae of the order Caudovirales. It was shown that phage vB_KpnP_IME337 had an infection duration of ~ 90 min and 10 min latent period, and a highly specific to host strain. In conclusion, phage vB_KpnP_IME337 may be a promising alternative candidate to antibiotic treatment for controlling diseases caused by drug-resistant K. pneumoniae.
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Affiliation(s)
- Mingming Gao
- Department of Graduate, Hebei North University, Zhangjiakou, 075000, China
| | - Can Wang
- Department of Respiratory and Critical Care Diseases, The Fifth Medical Center, Chinese General Hospital of the PLA, Beijing, 100071, China
| | - Xin Qiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Huiying Liu
- Department of Respiratory and Critical Care Diseases, The Fifth Medical Center, Chinese General Hospital of the PLA, Beijing, 100071, China
| | - Puyuan Li
- Department of Respiratory and Critical Care Diseases, The Fifth Medical Center, Chinese General Hospital of the PLA, Beijing, 100071, China
| | - Guangqian Pei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Zhiqiang Mi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yong Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China. .,Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Changqing Bai
- Department of Graduate, Hebei North University, Zhangjiakou, 075000, China. .,Department of Respiratory and Critical Care Diseases, The Fifth Medical Center, Chinese General Hospital of the PLA, Beijing, 100071, China. .,Shenzhen University General Hospital, Shenzhen, 518055, China.
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17
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Latka A, Leiman PG, Drulis-Kawa Z, Briers Y. Modeling the Architecture of Depolymerase-Containing Receptor Binding Proteins in Klebsiella Phages. Front Microbiol 2019; 10:2649. [PMID: 31803168 PMCID: PMC6872550 DOI: 10.3389/fmicb.2019.02649] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/30/2019] [Indexed: 11/30/2022] Open
Abstract
Klebsiella pneumoniae carries a thick polysaccharide capsule. This highly variable chemical structure plays an important role in its virulence. Many Klebsiella bacteriophages recognize this capsule with a receptor binding protein (RBP) that contains a depolymerase domain. This domain degrades the capsule to initiate phage infection. RBPs are highly specific and thus largely determine the host spectrum of the phage. A majority of known Klebsiella phages have only one or two RBPs, but phages with up to 11 RBPs with depolymerase activity and a broad host spectrum have been identified. A detailed bioinformatic analysis shows that similar RBP domains repeatedly occur in K. pneumoniae phages with structural RBP domains for attachment of an RBP to the phage tail (anchor domain) or for branching of RBPs (T4gp10-like domain). Structural domains determining the RBP architecture are located at the N-terminus, while the depolymerase is located in the center of protein. Occasionally, the RBP is complemented with an autocleavable chaperone domain at the distal end serving for folding and multimerization. The enzymatic domain is subjected to an intense horizontal transfer to rapidly shift the phage host spectrum without affecting the RBP architecture. These analyses allowed to model a set of conserved RBP architectures, indicating evolutionary linkages.
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Affiliation(s)
- Agnieszka Latka
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium.,Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wrocław, Wrocław, Poland
| | - Petr G Leiman
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, United States
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wrocław, Wrocław, Poland
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
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18
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Broeker NK, Roske Y, Valleriani A, Stephan MS, Andres D, Koetz J, Heinemann U, Barbirz S. Time-resolved DNA release from an O-antigen-specific Salmonella bacteriophage with a contractile tail. J Biol Chem 2019; 294:11751-11761. [PMID: 31189652 PMCID: PMC6682738 DOI: 10.1074/jbc.ra119.008133] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/11/2019] [Indexed: 12/20/2022] Open
Abstract
Myoviruses, bacteriophages with T4-like architecture, must contract their tails prior to DNA release. However, quantitative kinetic data on myovirus particle opening are lacking, although they are promising tools in bacteriophage-based antimicrobial strategies directed against Gram-negative hosts. For the first time, we show time-resolved DNA ejection from a bacteriophage with a contractile tail, the multi-O-antigen-specific Salmonella myovirus Det7. DNA release from Det7 was triggered by lipopolysaccharide (LPS) O-antigen receptors and notably slower than in noncontractile-tailed siphoviruses. Det7 showed two individual kinetic steps for tail contraction and particle opening. Our in vitro studies showed that highly specialized tailspike proteins (TSPs) are necessary to attach the particle to LPS. A P22-like TSP confers specificity for the Salmonella Typhimurium O-antigen. Moreover, crystal structure analysis at 1.63 Å resolution confirmed that Det7 recognized the Salmonella Anatum O-antigen via an ϵ15-like TSP, DettilonTSP. DNA ejection triggered by LPS from either host showed similar velocities, so particle opening is thus a process independent of O-antigen composition and the recognizing TSP. In Det7, at permissive temperatures TSPs mediate O-antigen cleavage and couple cell surface binding with DNA ejection, but no irreversible adsorption occurred at low temperatures. This finding was in contrast to short-tailed Salmonella podoviruses, illustrating that tailed phages use common particle-opening mechanisms but have specialized into different infection niches.
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Affiliation(s)
- Nina K Broeker
- Department of Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Yvette Roske
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Angelo Valleriani
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Mareike S Stephan
- Department of Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Dorothee Andres
- Department of Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Joachim Koetz
- Kolloidchemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
- Institut für Chemie und Biochemie, Freie Universität, Takustrasse 6, 14195 Berlin, Germany
| | - Stefanie Barbirz
- Department of Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
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19
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Cai R, Wang Z, Wang G, Zhang H, Cheng M, Guo Z, Ji Y, Xi H, Wang X, Xue Y, Ur Rahman S, Sun C, Feng X, Lei L, Tong Y, Han W, Gu J. Biological properties and genomics analysis of vB_KpnS_GH-K3, a Klebsiella phage with a putative depolymerase-like protein. Virus Genes 2019; 55:696-706. [PMID: 31254238 DOI: 10.1007/s11262-019-01681-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 06/20/2019] [Indexed: 01/21/2023]
Abstract
Bacteriophages have been recently revisited as an alternative biocontrol tool due to the limitations of antibiotic treatment. In this study, we reported on the biological characteristics and genomic information of vB_KpnS_GH-K3 (abbreviated as GH-K3), a Klebsiella phage of the Siphoviridae family, which was previously isolated from a hospital sewage system. One-step growth curve analysis indicated that the burst size of GH-K3 was 291 PFU/cell. GH-K3 maintained a stable titer in a broad range of pH values (6-10) and temperature (up to 50 °C). Based on bioinformatics analysis, GH-K3 comprises of 49,427 bp containing a total of 77 open reading frames (ORFs), which share high degree of nucleotide similarity and close evolutionary relationships with at least 12 other Klebsiella phages. Of note, GH-K3 gp32 was identified as a unique ORF. The major segment of gp32 sequence at the C-terminus (residues 351-907) was found highly variable as determined by its mismatch with the nucleotide and protein sequences available at NCBI database. Furthermore, HHpred analysis indicated that GH-K3 gp32 contains three domains (PDB ID: 5W6S_A, 3GQ8_A and 1BHE_A) similar to depolymerase (depoKP36) of Klebsiella phage KP36 suggestive of a potential depolymerase activity during host receptor-binding in the processes of phage infection. Altogether, the current data revealed a novel putative depolymerase-like protein which is most likely to play an important role in phage-host interaction.
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Affiliation(s)
- Ruopeng Cai
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Zijing Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Gang Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Hao Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Mengjun Cheng
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Zhimin Guo
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun, 130021, People's Republic of China
| | - Yalu Ji
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Hengyu Xi
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Xinwu Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Yibing Xue
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Sadeeq Ur Rahman
- College of Veterinary Sciences & Animal Husbandry, Abdul Wali Khan University, Mardan, 23200, Pakistan
| | - Changjiang Sun
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Xin Feng
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Liancheng Lei
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, People's Republic of China
| | - Wenyu Han
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Jingmin Gu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China.
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20
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Wang C, Tu J, Liu J, Molineux IJ. Structural dynamics of bacteriophage P22 infection initiation revealed by cryo-electron tomography. Nat Microbiol 2019; 4:1049-1056. [PMID: 30886360 PMCID: PMC6533119 DOI: 10.1038/s41564-019-0403-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/07/2019] [Indexed: 01/06/2023]
Abstract
For successful infection, bacteriophages must overcome multiple barriers to transport the genome and proteins across the bacterial cell envelope. We use cryo-electron tomography to study infection initiation of phage P22 in Salmonella enterica sv. Typhimurium, revealing how a channel forms to allow genome translocation into the cytoplasm. Our results show free phages initially attaching obliquely to the cell through interactions between the O antigen and two of the six tailspikes; the tail needle also abuts the cell surface. The virion then orients to the perpendicular and the needle penetrates the outer membrane. The needle is released and the internal head protein gp7* is ejected and assembles into an extra-cellular channel extending from the gp10 baseplate to the cell surface. A second protein, gp20, is ejected and assembles into a structure that extends the extra-cellular channel across the outer membrane into the periplasm. Insertion of the third ejected protein gp16 into the cytoplasmic membrane likely completes the overall trans-envelope channel into the cytoplasm. Construction of a trans-envelope channel is an essential step during infection by all short-tailed phages of Gram-negative bacteria because such virions cannot directly deliver their genome into the cell cytoplasm.
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Affiliation(s)
- Chunyan Wang
- Department of Microbial Pathogenesis, Yale University, New Haven, CT, USA.,Microbial Sciences Institute, Yale University, West Haven, CT, USA.,Department of Pathology and Laboratory Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jiagang Tu
- Department of Pathology and Laboratory Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale University, New Haven, CT, USA.,Microbial Sciences Institute, Yale University, West Haven, CT, USA.,Department of Pathology and Laboratory Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ian J Molineux
- LaMontagne Center for Infectious Disease, Institute for Cell and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
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21
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Cai R, Wu M, Zhang H, Zhang Y, Cheng M, Guo Z, Ji Y, Xi H, Wang X, Xue Y, Sun C, Feng X, Lei L, Tong Y, Liu X, Han W, Gu J. A Smooth-Type, Phage-Resistant Klebsiella pneumoniae Mutant Strain Reveals that OmpC Is Indispensable for Infection by Phage GH-K3. Appl Environ Microbiol 2018; 84:e01585-18. [PMID: 30171001 PMCID: PMC6193389 DOI: 10.1128/aem.01585-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/22/2018] [Indexed: 01/06/2023] Open
Abstract
Bacteriophage can be used as an alternative or complementary therapy to antibiotics for treating multidrug-resistant bacterial infections. However, the rapid emergence of resistant host variants during phage treatment has limited its therapeutic applications. In this study, a potential phage-resistant mechanism of Klebsiella pneumoniae was revealed. After phage GH-K3 treatment, a smooth-type colony, named K7RB, was obtained from the K. pneumoniae K7 culture. Treatment with IO4- and/or proteinase K indicated that polysaccharides of K7 played an important role in phage recruitment, and protein receptors on K7 were essential for effective infection by GH-K3. Differences in protein expression between K7 and K7RB were quantitatively analyzed by liquid chromatography-tandem mass spectrometry. Among differentially expressed proteins, OmpC, OmpN, KPN_02430, and OmpF were downregulated significantly in K7RBtrans-Complementation of OmpC in K7RB conferred rapid adsorption and sensitivity to GH-K3. In contrast, a single-base deletion mutation of ompC in K7, which resulted in OmpC silencing, led to lower adsorption efficiency and resistance to GH-K3. These assays proved that OmpC is the key receptor-binding protein for GH-K3. In addition, the native K. pneumoniae strains KPP14, KPP27, and KPP36 showed low or no sensitivity to GH-K3. However, these strains became more sensitive to GH-K3 after their native receptors were replaced by OmpC of K7, suggesting that OmpCK7 was the most suitable receptor for GH-K3. This study revealed that K7RB became resistant to GH-K3 due to gene mutation of ompC and that OmpC of K7 is essential for effective infection by GH-K3.IMPORTANCE With increased incidence of multidrug-resistant (MDR) bacterial strains, phages have regained attention as promising potential antibacterial agents. However, the rapid emergence of resistant variants during phage treatment has limited the therapeutic applications of phage. According to our trans-complementation, ompC mutation, and phage adsorption efficiency assays, we identified OmpC as the key receptor-binding protein (RBP) for phage GH-K3, which is essential for effective infection. This study revealed that the phage secondary receptor of K. pneumoniae, OmpC, is the essential RBP not only for phage infecting Gram-negative bacteria, such as Escherichia coli and Salmonella, but also for K. pneumoniae.
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Affiliation(s)
- Ruopeng Cai
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Mei Wu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Hao Zhang
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Yufeng Zhang
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Mengjun Cheng
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Zhimin Guo
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun, China
| | - Yalu Ji
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Hengyu Xi
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Xinwu Wang
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Yibing Xue
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Changjiang Sun
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Xin Feng
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Liancheng Lei
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaoyun Liu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Wenyu Han
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jingmin Gu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
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Newase S, Kapadnis BP, Shashidhar R. Isolation and Genome Sequence Characterization of Bacteriophage vB_SalM_PM10, a Cba120virus, Concurrently Infecting Salmonella enterica Serovars Typhimurium, Typhi, and Enteritidis. Curr Microbiol 2018; 76:86-94. [PMID: 30361843 DOI: 10.1007/s00284-018-1588-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 10/19/2018] [Indexed: 01/21/2023]
Abstract
The prevalence of multidrug-resistant Salmonella is ever increasing and calls for alternatives to antibiotics. The use of phages has been anticipated to reduce the multidrug-resistant human pathogens in food environment. Salmonella phage vB_SalM_PM10 (PM10) was isolated from sewage-polluted river in India. It shows an icosahedral head (94 ± 4 nm) along with a long contractile tail (106 ± 7 × 18 ± 2 nm), a morphotype of family Ackermannviridae. Additionally, the phage displayed the features resembling to existing Cba120viruses. Phage PM10 could infect S. enterica serovars Typhimurium, Typhi, and Enteritidis. The genome sequencing analysis of phage PM10 revealed circular 158.08 kb double-stranded DNA, with the GC content of 44.6%. Two hundred and nine ORFs, 171 putative promoters, 122 rho-independent terminators, and 5 transfer RNA encoding genes were found in the genome. The genome-wide comparisons and phylogenetic analyses showed that phage PM10 is closely related to Salmonella phage PhiSH19. Comparison of the tail-spike protein sequences encoded in PM10 and PhiSH19 genome showed the variation, which might have facilitated PM10's simultaneous infectivity to aforementioned S. enterica serovars. This is a varied host range than that of PhiSH19 or any other Cba120viruses.
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Affiliation(s)
- Sandeep Newase
- Department of Microbiology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India.,Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Balu P Kapadnis
- Department of Microbiology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India.
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de Jonge PA, Nobrega FL, Brouns SJJ, Dutilh BE. Molecular and Evolutionary Determinants of Bacteriophage Host Range. Trends Microbiol 2018; 27:51-63. [PMID: 30181062 DOI: 10.1016/j.tim.2018.08.006] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/07/2018] [Accepted: 08/13/2018] [Indexed: 01/12/2023]
Abstract
The host range of a bacteriophage is the taxonomic diversity of hosts it can successfully infect. Host range, one of the central traits to understand in phages, is determined by a range of molecular interactions between phage and host throughout the infection cycle. While many well studied model phages seem to exhibit a narrow host range, recent ecological and metagenomics studies indicate that phages may have specificities that range from narrow to broad. There is a growing body of studies on the molecular mechanisms that enable phages to infect multiple hosts. These mechanisms, and their evolution, are of considerable importance to understanding phage ecology and the various clinical, industrial, and biotechnological applications of phage. Here we review knowledge of the molecular mechanisms that determine host range, provide a framework defining broad host range in an evolutionary context, and highlight areas for additional research.
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Affiliation(s)
- Patrick A de Jonge
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8 3584 CH Utrecht, The Netherlands; Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9 2629 HZ, Delft, The Netherlands
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9 2629 HZ, Delft, The Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9 2629 HZ, Delft, The Netherlands; Laboratory for Microbiology, Wageningen University, Stippeneng 4 6708 WE, Wageningen, The Netherlands; These authors made equal contributions
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8 3584 CH Utrecht, The Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Geert Grooteplein Zuid 26-28, 6525GA Nijmegen, The Netherlands; These authors made equal contributions.
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