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1.
Microbiol Resour Announc ; 13(6): e0018224, 2024 Jun 11.
Artigo em Inglês | MEDLINE | ID: mdl-38651927

RESUMO

Amabiko is a lytic subcluster BE2 bacteriophage that infects Streptomyces scabiei-a bacterium causing common scab in potatoes. Its 131,414 bp genome has a GC content of 49.5% and contains 245 putative protein-coding genes, 45 tRNAs, and one tmRNA. Amabiko is closely related to Streptomyces bacteriophage MindFlayer (gene content similarity: 86.5%).

2.
Microbiol Resour Announc ; 13(4): e0006824, 2024 Apr 11.
Artigo em Inglês | MEDLINE | ID: mdl-38394246

RESUMO

Here, we present bacteriophage SoJo, a siphovirus infecting Streptomyces mirabilis, with a circularly permuted genome of 39 kbp and GC content of 71.5%. Its genome length and content are similar to that of other phages in the Actinobacteriophage Database BC cluster. SoJo was isolated from soil in Columbia, MD, USA.

3.
ISME J ; 17(12): 2381-2388, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37907733

RESUMO

Satellites are mobile genetic elements that are dependent upon the replication machinery of their helper viruses. Bacteriophages have provided many examples of satellite nucleic acids that utilize their helper morphogenic genes for propagation. Here we describe two novel satellite-helper phage systems, Mulch and Flayer, that infect Streptomyces species. The satellites in these systems encode for encapsidation machinery but have an absence of key replication genes, thus providing the first example of bacteriophage satellite viruses. We also show that codon usage of the satellites matches the tRNA gene content of the helpers. The satellite in one of these systems, Flayer, does not appear to integrate into the host genome, which represents the first example of a virulent satellite phage. The Flayer satellite has a unique tail adaptation that allows it to attach to its helper for simultaneous co-infection. These findings demonstrate an ever-increasing array of satellite strategies for genetic dependence on their helpers in the evolutionary arms race between satellite and helper phages.


Assuntos
Bacteriófagos , Streptomyces , Vírus Satélites/genética , Streptomyces/genética , Virulência , Vírus Auxiliares/genética , Bacteriófagos/genética
4.
Microbiol Resour Announc ; 12(11): e0059223, 2023 Nov 16.
Artigo em Inglês | MEDLINE | ID: mdl-37830805

RESUMO

Frankenweenie is a newly isolated bacteriophage that infects Streptomyces scabiei RL-34. Frankenweenie was discovered in Gaithersburg, MD, and has 366 genes comprising a 200,048-bp genome. Frankenweenie is grouped in cluster BM and is predicted to possess a unique tailspike protein that potentially widens its host range.

5.
Viruses ; 15(2)2023 01 18.
Artigo em Inglês | MEDLINE | ID: mdl-36851489

RESUMO

Bacteriophage genomes represent an enormous level of genetic diversity and provide considerable potential to acquire new insights about viral genome evolution. In this study, the genome sequences of sixteen Bacillus-infecting bacteriophages were explored through comparative genomics approaches to reveal shared and unique characteristics. These bacteriophages are in the Salasmaviridae family with small (18,548-27,206 bp) double-stranded DNA genomes encoding 25-46 predicted open reading frames. We observe extensive nucleotide and amino acid sequence divergence among a set of core-function genes that present clear synteny. We identify two examples of sequence directed recombination within essential genes, as well as explore the expansion of gene content in these genomes through the introduction of novel open reading frames. Together, these findings highlight the complex evolutionary relationships of phage genomes that include old, common origins as well as new components introduced through mosaicism.


Assuntos
Fagos Bacilares , Bacillus , Genômica , Genoma Viral , Sequência de Aminoácidos
6.
Microbiol Resour Announc ; 11(12): e0099822, 2022 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-36326493

RESUMO

This paper reports the genome sequences of five bacteriophages that were isolated using Streptomyces scabiei. Phages Fabian, FlowerPower, Geostin, RetrieverFever, and Vorvolakos were assigned to actinobacteriophage cluster BF based on shared gene content, with each phage containing between 16 and 21 tRNA genes.

7.
Cureus ; 14(9): e29524, 2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-36312601

RESUMO

We present the case of a patient who developed an isolated palsy of the flexor pollicis longus (FPL) branch of the anterior interosseous nerve (AIN) following a fracture of the right radial shaft. The diagnosis of AIN palsy in this setting is rare, especially involving partial neuropathies of only the FPL branch. Clinical presentation in this scenario can be mistaken for other musculoskeletal pathology, and electrodiagnostic studies can be helpful in confirming the diagnosis.

8.
Microbiol Resour Announc ; 11(11): e0092222, 2022 Nov 17.
Artigo em Inglês | MEDLINE | ID: mdl-36286992

RESUMO

Seven siphoviruses were isolated from soil using Streptomyces hosts. Their genome sequences ranged from 42,730 to 57,624 bp long and had a GC content of approximately 60%. Based on their gene content similarity to actinobacteriophages, all seven phages were assigned to cluster BI. For several of these phages, multiple ribosomal frameshifts were identified.

9.
Front Microbiol ; 13: 918015, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36060776

RESUMO

Pilitropic and flagellotropic phages adsorb to bacterial pili and flagella. These phages have long been used to investigate multiple aspects of bacterial physiology, such as the cell cycle control in the Caulobacterales. Targeting cellular appendages for adsorption effectively constrains the population of infectable hosts, suggesting that phages may have developed strategies to maximize their infective yield. Brevundimonas phage vB_BsubS-Delta is a recently characterized pilitropic phage infecting the Alphaproteobacterium Brevundimonas subvibrioides. Like other Caulobacterales, B. subvibrioides divides asymmetrically and its cell cycle is governed by multiple transcriptional regulators, including the master regulator CtrA. Genomic characterization of phage vB_BsubS-Delta identified the presence of a large intergenic region with an unusually high density of putative CtrA-binding sites. A systematic analysis of the positional distribution of predicted CtrA-binding sites in complete phage genomes reveals that the highly skewed distribution of CtrA-binding sites observed in vB_BsubS-Delta is an unequivocal genomic signature that extends to other pilli- and flagellotropic phages infecting the Alphaproteobacteria. Moreover, putative CtrA-binding sites in these phage genomes localize preferentially to promoter regions and have higher scores than those detected in other phage genomes. Phylogenetic and comparative genomics analyses show that this genomic signature has evolved independently in several phage lineages, suggesting that it provides an adaptive advantage to pili/flagellotropic phages infecting the Alphaproteobacteria. Experimental results demonstrate that CtrA binds to predicted CtrA-binding sites in promoter regions and that it regulates transcription of phage genes in unrelated Alphaproteobacteria-infecting phages. We propose that this focused distribution of CtrA-binding sites reflects a fundamental new aspect of phage infection, which we term lytic deferment. Under this novel paradigm, pili- and flagellotropic phages exploit the CtrA transduction pathway to monitor the host cell cycle state and synchronize lysis with the presence of infectable cells.

10.
PLoS Comput Biol ; 17(10): e1009463, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34710081

RESUMO

Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5,000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a 10-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills.


Assuntos
Crowdsourcing/métodos , Ontologia Genética , Anotação de Sequência Molecular/métodos , Biologia Computacional , Bases de Dados Genéticas , Humanos , Proteínas/genética , Proteínas/fisiologia
11.
Viruses ; 11(12)2019 12 07.
Artigo em Inglês | MEDLINE | ID: mdl-31817897

RESUMO

Streptomyces phages WheeHeim and Forthebois are two novel members of the Tectiviridae family. These phages were isolated on cultures of the plant pathogen Streptomyces scabiei, known for its worldwide economic impact on potato crops. Transmission electron microscopy showed viral particles with double-layered icosahedral capsids, and frequent instances of protruding nanotubes harboring a collar-like structure. Mass-spectrometry confirmed the presence of lipids in the virion, and serial purification of colonies from turbid plaques and immunity testing revealed that both phages are temperate. Streptomycesphages WheeHeim and Forthebois have linear dsDNA chromosomes (18,266 bp and 18,251 bp long, respectively) with the characteristic two-segment architecture of the Tectiviridae. Both genomes encode homologs of the canonical tectiviral proteins (major capsid protein, packaging ATPase and DNA polymerase), as well as PRD1-type virion-associated transglycosylase and membrane DNA delivery proteins. Comparative genomics and phylogenetic analyses firmly establish that these two phages, together with Rhodococcusphage Toil, form a new genus within the Tectiviridae, which we have tentatively named Deltatectivirus. The identification of a cohesive clade of Actinobacteria-infecting tectiviruses with conserved genome structure but with scant sequence similarity to members of other tectiviral genera confirms that the Tectiviridae are an ancient lineage infecting a broad range of bacterial hosts.


Assuntos
Actinobacillus/virologia , Tectiviridae/classificação , Tectiviridae/fisiologia , Bacteriólise , Biologia Computacional/métodos , DNA Viral , Genoma Viral , Genômica/métodos , Especificidade de Hospedeiro , Anotação de Sequência Molecular , Filogenia , Streptomyces/virologia , Tectiviridae/isolamento & purificação , Tectiviridae/ultraestrutura
12.
Artigo em Inglês | MEDLINE | ID: mdl-30533665

RESUMO

Six double-stranded DNA Streptomyces bacteriophages, HotFries, Moozy, RavenPuff, Scap1, Rainydai, and SenditCS, were isolated using the phytopathogen Streptomyces scabiei as a host. These phages have been identified as Siphoviridae and members of cluster BI by genomic analysis.

13.
Genome Announc ; 6(25)2018 06 21.
Artigo em Inglês | MEDLINE | ID: mdl-29930035

RESUMO

Three cluster C Myoviridae bacteriophages that infect Bacillus cereus group bacteria were isolated from soil collected in the mid-Atlantic region using B. thuringiensis subsp. kurstaki as a host. Bacillus phages HonestAbe, Anthony, and Taffo16 each shared 90% or higher average nucleotide identities within their subclusters.

14.
Genome Announc ; 6(3)2018 Jan 18.
Artigo em Inglês | MEDLINE | ID: mdl-29348349

RESUMO

The Streptomyces bacteriophage Abt2graduatex2 is a double-stranded DNA (dsDNA) Siphoviridae isolated from soil collected in Baltimore, MD, and harvested using Streptomyces griseus subsp. griseus Abt2graduatex2, a cluster BG phage, encodes an HicA-like toxin.

15.
Genome Announc ; 5(31)2017 08 03.
Artigo em Inglês | MEDLINE | ID: mdl-28774974

RESUMO

The Bacillus cereus group bacteriophage Flapjack, a double-stranded DNA (dsDNA) Myoviridae isolate collected from soil collected in Washington, DC, is a member of cluster C3 and encodes an intramolecular chaperone-containing tail fiber protein previously found in Podoviridae and Siphoviridae but not annotated in the Myoviridae.

16.
Genome Announc ; 5(29)2017 07 20.
Artigo em Inglês | MEDLINE | ID: mdl-28729280

RESUMO

Three double-stranded DNA phi29-like Bacillus cereus group bacteriophages, BeachBum, Harambe, and SerPounce, were identified and characterized. BeachBum and Harambe are closely related but are remarkably different from previously identified phi29-like phages. SerPounce is substantially closer to other phi29-like phages, enabling the identification of its prohead RNA (pRNA) gene.

17.
Genome Announc ; 4(5)2016 Oct 06.
Artigo em Inglês | MEDLINE | ID: mdl-27795236

RESUMO

Streptomyces phage Nanodon is a temperate double-stranded DNA Siphoviridae belonging to cluster BD1. It was isolated from soil collected in Kilauea, HI, using Streptomyces griseus subsp. griseus as a host.

18.
Genome Announc ; 4(5)2016 Sep 29.
Artigo em Inglês | MEDLINE | ID: mdl-27688335

RESUMO

The double-stranded DNA (dsDNA) Myoviridae Bacillus cereus group bacteriophage SalinJah was isolated from soil collected in Gyeonggi-do, South Korea. SalinJah, a cluster C phage with a broad host range, suggests the need to create a new subcluster with SalinJah and Helga as founding members.

19.
Virology ; 489: 243-51, 2016 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-26773385

RESUMO

Bacillus thuringiensis Kurstaki, a bacterium that is a source of biopesticides and a safe simulant for pathogenic Bacillus species, was used to isolate seven unique bacteriophages. The phage genomes were sequenced and ranged in size from 158,100 to 163,019 bp encoding 290-299 genes, and the GC content of ~38% was similar to that of the host bacterium. All phages had terminal repeats 2-3 kb long. Three of the phages encoded tRNAs and three contained a self-splicing intron in the DNA polymerase gene. They were categorized as a single cluster (>60% nucleotide conservation) containing three subclusters (>80% nucleotide conservation), supported by genomic synteny and phylogenetic analysis. Considering the published genomes of phages that infect the genus Bacillus and noting the ability of many of the Bacillus cereus group phages to infect multiple species, a clustering system based on gene content is proposed.


Assuntos
Fagos Bacilares/genética , Bacillus thuringiensis/virologia , Myoviridae/genética , Fagos Bacilares/classificação , Fagos Bacilares/isolamento & purificação , Fagos Bacilares/fisiologia , Tamanho do Genoma , Genoma Viral , Genômica , Dados de Sequência Molecular , Myoviridae/classificação , Myoviridae/isolamento & purificação , Myoviridae/fisiologia , Filogenia , Proteínas Virais/química , Proteínas Virais/genética
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