Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 15 de 15
Filtrar
Mais filtros

Base de dados
Tipo de documento
Intervalo de ano de publicação
1.
Bioinformatics ; 37(16): 2464-2466, 2021 08 25.
Artigo em Inglês | MEDLINE | ID: mdl-33226064

RESUMO

SUMMARY: Bacteriophages (phages) are incredibly abundant and genetically diverse. The volume of phage genomics data is rapidly increasing, driven in part by the SEA-PHAGES program, which isolates, sequences and manually annotates hundreds of phage genomes each year. With an ever-expanding genomics dataset, there are many opportunities for generating new biological insights through comparative genomic and bioinformatic analyses. As a result, there is a growing need to be able to store, update, explore and analyze phage genomics data. The package pdm_utils provides a collection of tools for MySQL phage database management designed to meet specific needs in the SEA-PHAGES program and phage genomics generally. AVAILABILITY AND IMPLEMENTATION: https://pypi.org/project/pdm-utils/.


Assuntos
Bacteriófagos , Bacteriófagos/genética , Biologia Computacional , Genoma Viral , Genômica , Filogenia
2.
Mol Cell ; 41(4): 480-92, 2011 Feb 18.
Artigo em Inglês | MEDLINE | ID: mdl-21329885

RESUMO

Hundreds of different proteins regulate and implement transcription in Saccharomyces. Yet their interrelationships have not been investigated on a comprehensive scale. Here we determined the genome-wide binding locations of 200 transcription-related proteins, under normal and acute heat-shock conditions. This study distinguishes binding between distal versus proximal promoter regions as well as the 3' ends of genes for nearly all mRNA and tRNA genes. This study reveals (1) a greater diversity and specialization of regulation associated with the SAGA transcription pathway compared to the TFIID pathway, (2) new regulators enriched at tRNA genes, (3) a global co-occupancy network of >20,000 unique regulator combinations that show a high degree of regulatory interconnections among lowly expressed genes, (4) regulators of the SAGA pathway located largely distal to the core promoter and regulators of the TFIID pathway located proximally, and (5) distinct mobilization of SAGA- versus TFIID-linked regulators during acute heat shock.


Assuntos
Cromatina/metabolismo , Proteínas de Ligação a DNA/metabolismo , Genoma Fúngico , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/genética , Cromatina/genética , Imunoprecipitação da Cromatina , Proteínas de Ligação a DNA/genética , Regulação Fúngica da Expressão Gênica , Regiões Promotoras Genéticas , RNA Polimerase II/genética , RNA Polimerase II/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Fator de Transcrição TFIID/genética , Fator de Transcrição TFIID/metabolismo
3.
Mol Microbiol ; 101(4): 625-44, 2016 08.
Artigo em Inglês | MEDLINE | ID: mdl-27146086

RESUMO

More than 180 individual phages infecting hosts in the phylum Actinobacteria have been sequenced and grouped into Cluster A because of their similar overall nucleotide sequences and genome architectures. These Cluster A phages are either temperate or derivatives of temperate parents, and most have an integration cassette near the centre of the genome containing an integrase gene and attP. However, about 20% of the phages lack an integration cassette, which is replaced by a 1.4 kbp segment with predicted partitioning functions, including plasmid-like parA and parB genes. Phage RedRock forms stable lysogens in Mycobacterium smegmatis in which the prophage replicates at 2.4 copies/chromosome and the partitioning system confers prophage maintenance. The parAB genes are expressed upon RedRock infection of M. smegmatis, but are downregulated once lysogeny is established by binding of RedRock ParB to parS-L, one of two centromere-like sites flanking the parAB genes. The RedRock parS-L and parS-R sites are composed of eight directly repeated copies of an 8 bp motif that is recognized by ParB. The actinobacteriophage parABS cassettes span considerable sequence diversity and specificity, providing a suite of tools for use in mycobacterial genetics.


Assuntos
Actinobacteria/virologia , Bacteriófagos/genética , Proteínas de Bactérias/metabolismo , Bacteriófagos/metabolismo , Sequência de Bases/genética , Sequência de Bases/fisiologia , Centrômero/metabolismo , Segregação de Cromossomos/genética , Cromossomos Bacterianos , Lisogenia , Mutagênese Insercional , Plasmídeos/genética , Análise de Sequência de DNA
4.
BMC Microbiol ; 17(1): 225, 2017 Dec 02.
Artigo em Inglês | MEDLINE | ID: mdl-29197343

RESUMO

BACKGROUND: Mycobacteriophages are viruses that infect Mycobacterium hosts. A large collection of phages known to infect the same bacterial host strain - Mycobacterium smegmatis mc2155 - exhibit substantial diversity and characteristically mosaic architectures. The well-studied lytic mycobacteriophage D29 appears to be a deletion derivative of a putative temperate parent, although its parent has yet to be identified. RESULTS: Here we describe three newly-isolated temperate phages - Kerberos, Pomar16 and StarStuff - that are related to D29, and are predicted to be very close relatives of its putative temperate parent, revealing the repressor and additional genes that are lost in D29. Transcriptional profiles show the patterns of both lysogenic and lytic gene expression and identify highly-expressed, abundant, stable, small non-coding transcripts made from the Pleft early lytic promoter, and which are toxic to M. smegmatis. CONCLUSIONS: Comparative genomics of phages D29, Kerberos, Pomar16 and StarStuff provide insights into bacteriophage evolution, and comparative transcriptomics identifies the pattern of lysogenic and lytic expression with unusual features including highly expressed, small, non-coding RNAs.


Assuntos
Evolução Molecular , Regulação Viral da Expressão Gênica , Genoma Viral/genética , Micobacteriófagos/genética , RNA não Traduzido/genética , Sequência de Bases , DNA Viral , Perfilação da Expressão Gênica , Lisogenia/genética , Mutação , Mycobacterium smegmatis/virologia , RNA Viral , Alinhamento de Sequência , Análise de Sequência de RNA , Interferência Viral
5.
Genome Res ; 22(6): 1098-106, 2012 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-22434426

RESUMO

Dictyostelium discoideum is an amoebozoa that exists in both a free-living unicellular and a multicellular form. It is situated in a deep branch in the evolutionary tree and is particularly noteworthy in having a very A/T-rich genome. Dictyostelium provides an ideal system to examine the extreme to which nucleotide bias may be employed in organizing promoters, genes, and nucleosomes across a genome. We find that Dictyostelium genes are demarcated precisely at their 5' ends by poly-T tracts and precisely at their 3' ends by poly-A tracts. These tracts are also associated with nucleosome-free regions and are embedded with precisely positioned TATA boxes. Homo- and heteropolymeric tracts of A and T demarcate nucleosome border regions. Together, these findings reveal the presence of a variety of functionally distinct polymeric A/T elements. Strikingly, Dictyostelium chromatin may be organized in di-nucleosome units but is otherwise organized as in animals. This includes a +1 nucleosome in a position that predicts the presence of a paused RNA polymerase II. Indeed, we find a strong phylogenetic relationship between the presence of the NELF pausing factor and positioning of the +1 nucleosome. Pausing and +1 nucleosome positioning may have coevolved in animals.


Assuntos
Cromatina/genética , Dictyostelium/genética , Nucleossomos/genética , Poli A/genética , Poli T/genética , Animais , Genes , Filogenia , Regiões Promotoras Genéticas , RNA Polimerase II/genética , TATA Box/genética , Fatores de Transcrição/genética
6.
Nature ; 453(7193): 358-62, 2008 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-18408708

RESUMO

Comparative genomics of nucleosome positions provides a powerful means for understanding how the organization of chromatin and the transcription machinery co-evolve. Here we produce a high-resolution reference map of H2A.Z and bulk nucleosome locations across the genome of the fly Drosophila melanogaster and compare it to that from the yeast Saccharomyces cerevisiae. Like Saccharomyces, Drosophila nucleosomes are organized around active transcription start sites in a canonical -1, nucleosome-free region, +1 arrangement. However, Drosophila does not incorporate H2A.Z into the -1 nucleosome and does not bury its transcriptional start site in the +1 nucleosome. At thousands of genes, RNA polymerase II engages the +1 nucleosome and pauses. How the transcription initiation machinery contends with the +1 nucleosome seems to be fundamentally different across major eukaryotic lines.


Assuntos
Drosophila melanogaster/genética , Genoma de Inseto/genética , Nucleossomos/genética , Nucleossomos/metabolismo , Animais , Sequência Conservada/genética , Drosophila melanogaster/embriologia , Drosophila melanogaster/enzimologia , Regulação da Expressão Gênica/genética , Genes de Insetos/genética , Histonas/metabolismo , Regiões Promotoras Genéticas/genética , RNA Polimerase II/metabolismo , Saccharomyces cerevisiae/genética , Sítio de Iniciação de Transcrição , Transcrição Gênica/genética
7.
Nature ; 446(7135): 572-6, 2007 Mar 29.
Artigo em Inglês | MEDLINE | ID: mdl-17392789

RESUMO

The nucleosome is the fundamental building block of eukaryotic chromosomes. Access to genetic information encoded in chromosomes is dependent on the position of nucleosomes along the DNA. Alternative locations just a few nucleotides apart can have profound effects on gene expression. Yet the nucleosomal context in which chromosomal and gene regulatory elements reside remains ill-defined on a genomic scale. Here we sequence the DNA of 322,000 individual Saccharomyces cerevisiae nucleosomes, containing the histone variant H2A.Z, to provide a comprehensive map of H2A.Z nucleosomes in functionally important regions. With a median 4-base-pair resolution, we identify new and established signatures of nucleosome positioning. A single predominant rotational setting and multiple translational settings are evident. Chromosomal elements, ranging from telomeres to centromeres and transcriptional units, are found to possess characteristic nucleosomal architecture that may be important for their function. Promoter regulatory elements, including transcription factor binding sites and transcriptional start sites, show topological relationships with nucleosomes, such that transcription factor binding sites tend to be rotationally exposed on the nucleosome surface near its border. Transcriptional start sites tended to reside about one helical turn inside the nucleosome border. These findings reveal an intimate relationship between chromatin architecture and the underlying DNA sequence it regulates.


Assuntos
Montagem e Desmontagem da Cromatina , Genoma Fúngico/genética , Histonas/metabolismo , Nucleossomos/genética , Nucleossomos/metabolismo , Saccharomyces cerevisiae/genética , DNA Fúngico/química , DNA Fúngico/genética , DNA Fúngico/metabolismo , Regulação da Expressão Gênica/genética , Nucleossomos/química , Regiões Promotoras Genéticas/genética , Rotação , Transcrição Gênica/genética
8.
PLoS One ; 15(6): e0234636, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32555720

RESUMO

The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to ~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics.


Assuntos
Actinobacteria/virologia , Bacteriófagos/genética , Variação Genética , Genoma Viral , Bacteriófagos/classificação , Bacteriófagos/isolamento & purificação , Composição de Bases , DNA Viral/genética , Genes Virais , Genômica , Filogenia , Proteínas Virais de Fusão/genética
9.
mBio ; 10(3)2019 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-31164468

RESUMO

Temperate phages encode an immunity system to control lytic gene expression during lysogeny. This gene regulatory circuit consists of multiple interacting genetic elements, and although it is essential for controlling phage growth, it is subject to conflicting evolutionary pressures. During superinfection of a lysogen, the prophage's circuit interacts with the superinfecting phage's circuit and prevents lytic growth if the two circuits are closely related. The circuitry is advantageous since it provides the prophage with a defense mechanism, but the circuitry is also disadvantageous since it limits the phage's host range during superinfection. Evolutionarily related phages have divergent, orthogonal immunity systems that no longer interact and are heteroimmune, but we do not understand how immunity systems evolve new specificities. Here, we use a group of Cluster A mycobacteriophages that exhibit a spectrum of genetic diversity to examine how immunity system evolution impacts superinfection immunity. We show that phages with mesotypic (i.e., genetically related but distinct) immunity systems exhibit asymmetric and incomplete superinfection phenotypes. They form complex immunity networks instead of well-defined immunity groups, and mutations conferring escape (i.e., virulence) from homotypic or mesotypic immunity have various escape specificities. Thus, virulence and the evolution of new immune specificities are shaped by interactions with homotypic and mesotypic immunity systems.IMPORTANCE Many aspects regarding superinfection, immunity, virulence, and the evolution of immune specificities are poorly understood due to the lack of large collections of isolated and sequenced phages with a spectrum of genetic diversity. Using a genetically diverse collection of Cluster A phages, we show that the classical and relatively straightforward patterns of homoimmunity, heteroimmunity, and virulence result from interactions between homotypic and heterotypic phages at the extreme edges of an evolutionary continuum of immune specificities. Genetic interactions between mesotypic phages result in more complex mesoimmunity phenotypes and virulence profiles. These results highlight that the evolution of immune specificities can be shaped by homotypic and mesotypic interactions and may be more dynamic than previously considered.


Assuntos
Evolução Molecular , Micobacteriófagos/classificação , Micobacteriófagos/imunologia , Superinfecção/imunologia , Genoma Viral , Filogenia , Prófagos/genética , Prófagos/imunologia , Virulência
10.
Genetics ; 212(3): 711-728, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31092540

RESUMO

The Polymerase Associated Factor 1 complex (Paf1C) is a multifunctional regulator of eukaryotic gene expression important for the coordination of transcription with chromatin modification and post-transcriptional processes. In this study, we investigated the extent to which the functions of Paf1C combine to regulate the Saccharomyces cerevisiae transcriptome. While previous studies focused on the roles of Paf1C in controlling mRNA levels, here, we took advantage of a genetic background that enriches for unstable transcripts, and demonstrate that deletion of PAF1 affects all classes of Pol II transcripts including multiple classes of noncoding RNAs (ncRNAs). By conducting a de novo differential expression analysis independent of gene annotations, we found that Paf1 positively and negatively regulates antisense transcription at multiple loci. Comparisons with nascent transcript data revealed that many, but not all, changes in RNA levels detected by our analysis are due to changes in transcription instead of post-transcriptional events. To investigate the mechanisms by which Paf1 regulates protein-coding genes, we focused on genes involved in iron and phosphate homeostasis, which were differentially affected by PAF1 deletion. Our results indicate that Paf1 stimulates phosphate gene expression through a mechanism that is independent of any individual Paf1C-dependent histone modification. In contrast, the inhibition of iron gene expression by Paf1 correlates with a defect in H3 K36 trimethylation. Finally, we showed that one iron regulon gene, FET4, is coordinately controlled by Paf1 and transcription of upstream noncoding DNA. Together, these data identify roles for Paf1C in controlling both coding and noncoding regions of the yeast genome.


Assuntos
Regulação Fúngica da Expressão Gênica , Proteínas Nucleares/genética , Proteínas de Saccharomyces cerevisiae/genética , Transcriptoma , Cromatina/metabolismo , Proteínas de Transporte de Cobre/genética , Proteínas de Transporte de Cobre/metabolismo , Histonas/metabolismo , Proteínas de Ligação ao Ferro/genética , Proteínas de Ligação ao Ferro/metabolismo , Proteínas Nucleares/metabolismo , Processamento de Proteína Pós-Traducional , RNA não Traduzido/genética , RNA não Traduzido/metabolismo , Saccharomyces cerevisiae , Proteínas de Saccharomyces cerevisiae/metabolismo
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA