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Viruses Jul 2021Bacteriophages vB_YpeM_fEV-1 (fEV-1) and vB_YpeM_fD1 (fD1) were isolated from incoming sewage water samples in Turku, Finland, using strains EV76 and KIM D27 as...
Bacteriophages vB_YpeM_fEV-1 (fEV-1) and vB_YpeM_fD1 (fD1) were isolated from incoming sewage water samples in Turku, Finland, using strains EV76 and KIM D27 as enrichment hosts, respectively. Genomic analysis and transmission electron microscopy established that fEV-1 is a novel type of dwarf myovirus, while fD1 is a T4-like myovirus. The genome sizes are 38 and 167 kb, respectively. To date, the morphology and genome sequences of some dwarf myoviruses have been described; however, a proteome characterization such as the one presented here, has currently been lacking for this group of viruses. Notably, fEV-1 is the first dwarf myovirus described for . The host range of fEV-1 was restricted strictly to strains, while that of fD1 also included other members of Enterobacterales such as and . In this study, we present the life cycles, genomes, and proteomes of two myoviruses, fEV-1 and fD1.
Topics: Bacteriophages; Finland; Genome, Viral; Host Specificity; Microscopy, Electron, Transmission; Proteome; Sewage; Yersinia pestis
PubMed: 34372590
DOI: 10.3390/v13071384 -
Annual Review of Virology Sep 2020Actinobacteriophages are viruses that infect bacterial hosts in the phylum . More than 17,000 actinobacteriophages have been described and over 3,000 complete genome... (Review)
Review
Actinobacteriophages are viruses that infect bacterial hosts in the phylum . More than 17,000 actinobacteriophages have been described and over 3,000 complete genome sequences reported, resulting from large-scale, high-impact, integrated research-education initiatives such as the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Sciences (SEA-PHAGES) program. Their genomic diversity is enormous; actinobacteriophages comprise many architecturally mosaic genomes with distinct DNA sequences. Their genome diversity is driven by the highly dynamic interactions between phages and their hosts, and prophages can confer a variety of systems that defend against attack by genetically distinct phages; phages can neutralize these defense systems by coding for counter-defense proteins. These phages not only provide insights into diverse and dynamic phage populations but also have provided numerous tools for mycobacterial genetics. A case study using a three-phage cocktail to treat a patient with a drug-resistant suggests that phages may have considerable potential for the therapeutic treatment of mycobacterial infections.
Topics: Actinobacteria; Bacteriophages; Base Sequence; Genetic Variation; Genome, Viral; Genomics; Mycobacterium Infections; Phage Therapy; Phylogeny
PubMed: 32991269
DOI: 10.1146/annurev-virology-122019-070009 -
Nature Aug 2022Bacteria encode myriad defences that target the genomes of infecting bacteriophage, including restriction-modification and CRISPR-Cas systems. In response, one family of...
Bacteria encode myriad defences that target the genomes of infecting bacteriophage, including restriction-modification and CRISPR-Cas systems. In response, one family of large bacteriophages uses a nucleus-like compartment to protect its replicating genomes by excluding host defence factors. However, the principal composition and structure of this compartment remain unknown. Here we find that the bacteriophage nuclear shell assembles primarily from one protein, which we name chimallin (ChmA). Combining cryo-electron tomography of nuclear shells in bacteriophage-infected cells and cryo-electron microscopy of a minimal chimallin compartment in vitro, we show that chimallin self-assembles as a flexible sheet into closed micrometre-scale compartments. The architecture and assembly dynamics of the chimallin shell suggest mechanisms for its nucleation and growth, and its role as a scaffold for phage-encoded factors mediating macromolecular transport, cytoskeletal interactions, and viral maturation.
Topics: Bacteria; Bacteriophages; Cell Compartmentation; Cryoelectron Microscopy; Viral Proteins; Virus Assembly
PubMed: 35922510
DOI: 10.1038/s41586-022-05013-4 -
Current Opinion in Virology Aug 2021Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), are influenced by the bacterial and fungal organisms found within the... (Review)
Review
Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), are influenced by the bacterial and fungal organisms found within the intestine. However, the intestine is also home to a vast number of viral particles, with most of them being viruses that infect prokaryotes, called bacteriophages. While use of bacteriophages to specifically target pathogenic bacterial species involved in IBD is currently under investigation, recent studies have also highlighted that these viral particles can impact the mammalian immune system. IBD is a chronic multi-factorial inflammatory condition with unknown etiology. This review will highlight the current investigations that have revealed that bacteriophage-mammalian immune cell interactions can influence disease processes beyond their known role for infecting bacteria, which might identify novel ways to treat or diagnose IBD.
Topics: Animals; Bacteriophages; Gastrointestinal Microbiome; Gene Expression; Host Microbial Interactions; Humans; Immune System; Inflammatory Bowel Diseases; Phage Therapy; Virome
PubMed: 34029992
DOI: 10.1016/j.coviro.2021.04.010 -
International Journal of Nanomedicine 2013Bacteriophages are traditionally used for the development of phage display technology. Recently, their nanosized dimensions and ease with which genetic modifications can... (Review)
Review
Bacteriophages are traditionally used for the development of phage display technology. Recently, their nanosized dimensions and ease with which genetic modifications can be made to their structure and function have put them in the spotlight towards their use in a variety of biosensors. In particular, the expression of any protein or peptide on the extraluminal surface of bacteriophages is possible by genetically engineering the genome. In addition, the relatively short replication time of bacteriophages offers researchers the ability to generate mass quantities of any given bacteriophage-based biosensor. Coupled with the emergence of various biomarkers in the clinic as a means to determine pathophysiological states, the development of current and novel technologies for their detection and quantification is imperative. In this review, we categorize bacteriophages by their morphology into M13-based filamentous bacteriophages and T4- or T7-based icosahedral bacteriophages, and examine how such advantages are utilized across a variety of biosensors. In essence, we take a comprehensive approach towards recent trends in bacteriophage-based biosensor applications and discuss their outlook with regards to the field of biotechnology.
Topics: Bacteria; Bacteriophages; Biological Assay; Biopolymers; Biosensing Techniques; Equipment Design; Equipment Failure Analysis; Nanotechnology; Peptide Library
PubMed: 24143096
DOI: 10.2147/IJN.S51894 -
BioMed Research International 2013Viruses specifically infecting bacteria, or bacteriophages, are the most common biological entity in the biosphere. As such, they greatly influence bacteria, both in... (Review)
Review
Viruses specifically infecting bacteria, or bacteriophages, are the most common biological entity in the biosphere. As such, they greatly influence bacteria, both in terms of enhancing their virulence and in terms of killing them. Since the first identification of bacteriophages in the beginning of the 20th century, researchers have been fascinated by these microorganisms and their ability to eradicate bacteria. In this review, we will cover the history of the Propionibacterium acnes bacteriophage research and point out how bacteriophage research has been an important part of the research on P. acnes itself. We will further discuss recent findings from phage genome sequencing and the identification of phage sequence signatures in clustered regularly interspaced short palindromic repeats (CRISPRs). Finally, the potential to use P. acnes bacteriophages as a therapeutic strategy to combat P. acnes-associated diseases will be discussed.
Topics: Animals; Bacteriophages; Cellular Microenvironment; Clustered Regularly Interspaced Short Palindromic Repeats; Genomic Islands; Humans; Prophages; Propionibacterium acnes
PubMed: 23691509
DOI: 10.1155/2013/705741 -
Proceedings of the National Academy of... Sep 2016The role of bacteriophages in influencing the structure and function of the healthy human gut microbiome is unknown. With few exceptions, previous studies have found a...
The role of bacteriophages in influencing the structure and function of the healthy human gut microbiome is unknown. With few exceptions, previous studies have found a high level of heterogeneity in bacteriophages from healthy individuals. To better estimate and identify the shared phageome of humans, we analyzed a deep DNA sequence dataset of active bacteriophages and available metagenomic datasets of the gut bacteriophage community from healthy individuals. We found 23 shared bacteriophages in more than one-half of 64 healthy individuals from around the world. These shared bacteriophages were found in a significantly smaller percentage of individuals with gastrointestinal/irritable bowel disease. A network analysis identified 44 bacteriophage groups of which 9 (20%) were shared in more than one-half of all 64 individuals. These results provide strong evidence of a healthy gut phageome (HGP) in humans. The bacteriophage community in the human gut is a mixture of three classes: a set of core bacteriophages shared among more than one-half of all people, a common set of bacteriophages found in 20-50% of individuals, and a set of bacteriophages that are either rarely shared or unique to a person. We propose that the core and common bacteriophage communities are globally distributed and comprise the HGP, which plays an important role in maintaining gut microbiome structure/function and thereby contributes significantly to human health.
Topics: Bacteriophages; Computational Biology; Feces; Gastrointestinal Microbiome; Gastrointestinal Tract; Humans; Inflammatory Bowel Diseases; Metagenomics; Microbiota
PubMed: 27573828
DOI: 10.1073/pnas.1601060113 -
Viruses Oct 2023Half a century has passed since the discovery of Pseudomonas phage phi6, the first enveloped dsRNA bacteriophage to be isolated. It remained the sole known dsRNA phage... (Review)
Review
Half a century has passed since the discovery of Pseudomonas phage phi6, the first enveloped dsRNA bacteriophage to be isolated. It remained the sole known dsRNA phage for a quarter of a century and the only recognised member of the family until the year 2018. After the initial discovery of phi6, additional dsRNA phages have been isolated from globally distant locations and identified in metatranscriptomic datasets, suggesting that this virus type is more ubiquitous in nature than previously acknowledged. Most identified dsRNA phages infect strains and utilise either pilus or lipopolysaccharide components of the host as the primary receptor. In addition to the receptor-mediated strictly lytic lifestyle, an alternative persistent infection strategy has been described for some dsRNA phages. To date, complete genome sequences of fourteen dsRNA phage isolates are available. Despite the high sequence diversity, similar sets of genes can typically be found in the genomes of dsRNA phages, suggesting shared evolutionary trajectories. This review provides a brief overview of the recognised members of the virus family and related dsRNA phage isolates, outlines the current classification of dsRNA phages, and discusses their relationships with eukaryotic RNA viruses.
Topics: Bacteriophages; Pseudomonas Phages; Pseudomonas; Genome, Viral
PubMed: 38005832
DOI: 10.3390/v15112154 -
Genomics Jan 2021Listeria monocytogenes is an important food-borne pathogen and its bacteriophages are promising tools for its control in food and surfaces. Listeria bacteriophages...
Listeria monocytogenes is an important food-borne pathogen and its bacteriophages are promising tools for its control in food and surfaces. Listeria bacteriophages belonging to the genus Pecentumvirus of the family Herelleviridae are strictly lytic, have a contractile tail and a large double stranded DNA genome (mean of 135.4 kb). We report the isolation and genome sequences of two new Pecentumvirus bacteriophages: vB_Lino_VEfB7 and vB_Liva_VAfA18. Twenty-one bacteriophages of this genus have been described and their genomes were used for the study of Pecentumvirus evolution. Analyses showed collinear genomes and gene gain and loss propensity and recombination events were distinctly found in two regions. A large potential recombination event (≈20 kB) was detected in P100 and vB_Liva_VAfA18. Phylogenetic analyses of multi-gene alignments showed that diversification events formed two groups of species distantly related.
Topics: Bacteriophages; Evolution, Molecular; Gene Deletion; Genes, Viral; Listeria monocytogenes; Phylogeny; Recombination, Genetic; Viral Proteins
PubMed: 33301894
DOI: 10.1016/j.ygeno.2020.12.003 -
The Journal of Biological Chemistry Jan 2022Technological advances in cryo-EM in recent years have given rise to detailed atomic structures of bacteriophage tail tubes-a class of filamentous protein assemblies... (Review)
Review
Technological advances in cryo-EM in recent years have given rise to detailed atomic structures of bacteriophage tail tubes-a class of filamentous protein assemblies that could previously only be studied on the atomic scale in either their monomeric form or when packed within a crystal lattice. These hollow elongated protein structures, present in most bacteriophages of the order Caudovirales, connect the DNA-containing capsid with a receptor function at the distal end of the tail and consist of helical and polymerized major tail proteins. However, the resolution of cryo-EM data for these systems differs enormously between different tail tube types, partly inhibiting the building of high-fidelity models and barring a combination with further structural biology methods. Here, we review the structural biology efforts within this field and highlight the role of integrative structural biology approaches that have proved successful for some of these systems. Finally, we summarize the structural elements of major tail proteins and conceptualize how different amounts of tail tube flexibility confer heterogeneity within cryo-EM maps and, thus, limit high-resolution reconstructions.
Topics: Bacteriophages; Capsid; Capsid Proteins; Caudovirales; Cryoelectron Microscopy; Protein Conformation; Virion
PubMed: 34890646
DOI: 10.1016/j.jbc.2021.101472