Bacillus subtilis and phage SPO1
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA932315 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23373800_1.fastq.gz | Fastqsanger.gz | |||
| SRR23373800_2.fastq.gz | Fastqsanger.gz | |||
| SRR23373801_1.fastq.gz | Fastqsanger.gz | |||
| SRR23373801_2.fastq.gz | Fastqsanger.gz | |||
| SRR23373802_1.fastq.gz | Fastqsanger.gz |
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Project description:A complete 39,318-bp genome sequence containing 52 coding sequences has been determined for the Bacillus subtilis temperate phage ϕ105. In a lysogen, B. subtilis strain 1L32, the ϕ105 prophage interrupts the radC locus, a part of the competence-induced ComK regulon.
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Project description:Identification of the specific WalR (YycF) binding regions on the B. subtilis chromosome during exponential and phosphate starvation growth phases. The data serves to extend the WalRK regulon in Bacillus subtilis and its role in cell wall metabolism, as well as implying a role in several other cellular processes.
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Project description:SPP1 is a siphophage infecting the gram-positive bacterium Bacillus subtilis. The SPP1 tail electron microscopy (EM) reconstruction revealed that it is mainly constituted by conserved structural proteins such as the major tail proteins (gp17.1), the tape measure protein (gp18), the Distal tail protein (Dit, gp19.1), and the Tail associated lysin (gp21). A group of five small genes (22-24.1) follows in the genome but it remains to be elucidated whether their protein products belong or not to the tail. Noteworthy, an unassigned EM density accounting for ~245 kDa is present at the distal end of the SPP1 tail-tip. We report here the gp23.1 crystal structure at 1.6 A resolution, a protein that lacks sequence identity to any known protein. We found that gp23.1 forms a hexamer both in the crystal lattice and in solution as revealed by light scattering measurements. The gp23.1 hexamer does not fit well in the unassigned SPP1 tail-tip EM density and we hypothesize that this protein might act as a chaperone.
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Project description:Poly-?-glutamate (?-PGA) is an industrially interesting polymer secreted mainly by members of the class Bacilli which forms a shield able to protect bacteria from phagocytosis and phages. Few enzymes are known to degrade ?-PGA; among them is a phage-encoded ?-PGA hydrolase, PghP. The supposed role of PghP in phages is to ensure access to the surface of bacterial cells by dismantling the ?-PGA barrier. We identified four unannotated B. subtilis genes through similarity of their encoded products to PghP; in fact these genes reside in prophage elements of B. subtilis genome. The recombinant products of two of them demonstrate efficient polymer degradation, confirming that sequence similarity reflects functional homology. Genes encoding similar ?-PGA hydrolases were identified in phages specific for the order Bacillales and in numerous microbial genomes, not only belonging to that order. The distribution of the ?-PGA biosynthesis operon was also investigated with a bioinformatics approach; it was found that the list of organisms endowed with ?-PGA biosynthetic functions is larger than expected and includes several pathogenic species. Moreover in non-Bacillales bacteria the predicted ?-PGA hydrolase genes are preferentially found in species that do not have the genetic asset for polymer production. Our findings suggest that ?-PGA hydrolase genes might have spread across microbial genomes via horizontal exchanges rather than via phage infection. We hypothesize that, in natural habitats rich in ?-PGA supplied by producer organisms, the availability of hydrolases that release glutamate oligomers from ?-PGA might be a beneficial trait under positive selection.
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Project description:UnlabelledThe study of phage-host relationships is essential to understanding the dynamic of microbial systems. Here, we analyze genome-wide interactions of Bacillus subtilis and its lytic phage ϕ29 during the early stage of infection. Simultaneous high-resolution analysis of virus and host transcriptomes by deep RNA sequencing allowed us to identify differentially expressed bacterial genes. Phage ϕ29 induces significant transcriptional changes in about 0.9% (38/4,242) and 1.8% (76/4,242) of the host protein-coding genes after 8 and 16 min of infection, respectively. Gene ontology enrichment analysis clustered upregulated genes into several functional categories, such as nucleic acid metabolism (including DNA replication) and protein metabolism (including translation). Surprisingly, most of the transcriptional repressed genes were involved in the utilization of specific carbon sources such as ribose and inositol, and many contained promoter binding-sites for the catabolite control protein A (CcpA). Another interesting finding is the presence of previously uncharacterized antisense transcripts complementary to the well-known phage ϕ29 messenger RNAs that adds an additional layer to the viral transcriptome complexity.ImportanceThe specific virus-host interactions that allow phages to redirect cellular machineries and energy resources to support the viral progeny production are poorly understood. This study provides, for the first time, an insight into the genome-wide transcriptional response of the Gram-positive model Bacillus subtilis to phage ϕ29 infection.
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Project description:The Gram-positive bacteriumBacillus subtilisis used as a model organism to study cellular and molecular processes. Here, we announce the complete genomic sequence ofB. subtilisstrain CU1050, derived fromB. subtilisstrain 168. CU1050 has historically been used to study suppressor mutations and phage biology, especially the lysogenic phage SPβ.
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Project description:Identification of the specific WalR (YycF) binding regions on the B. subtilis chromosome during exponential and phosphate starvation growth phases. The data serves to extend the WalRK regulon in Bacillus subtilis and its role in cell wall metabolism, as well as implying a role in several other cellular processes. For each sample analyzed in this study three biological replicates were performed. Three different samples were taken from a strain expressing the WalR-SPA protein as well as from wild-type (168) without a tagged WalR. Samples were taken from exponentially growing cells in low phosphate medium (LPDM) as well as from phosphate-limited cells (T2). Each sample compares ChIP DNA vs. Total DNA from the same cells.
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Project description:Henry2009 - Genome-scale metabolic network of
Bacillus subtilis (iBsu1103)
This model is described in the article:
iBsu1103: a new genome-scale
metabolic model of Bacillus subtilis based on SEED
annotations.
Henry CS, Zinner JF, Cohoon MP,
Stevens RL.
Genome Biol. 2009; 10(6): R69
Abstract:
BACKGROUND: Bacillus subtilis is an organism of interest
because of its extensive industrial applications, its
similarity to pathogenic organisms, and its role as the model
organism for Gram-positive, sporulating bacteria. In this work,
we introduce a new genome-scale metabolic model of B. subtilis
168 called iBsu1103. This new model is based on the annotated
B. subtilis 168 genome generated by the SEED, one of the most
up-to-date and accurate annotations of B. subtilis 168
available. RESULTS: The iBsu1103 model includes 1,437 reactions
associated with 1,103 genes, making it the most complete model
of B. subtilis available. The model also includes Gibbs free
energy change (DeltarG' degrees ) values for 1,403 (97%) of the
model reactions estimated by using the group contribution
method. These data were used with an improved reaction
reversibility prediction method to identify 653 (45%)
irreversible reactions in the model. The model was validated
against an experimental dataset consisting of 1,500 distinct
conditions and was optimized by using an improved model
optimization method to increase model accuracy from 89.7% to
93.1%. CONCLUSIONS: Basing the iBsu1103 model on the
annotations generated by the SEED significantly improved the
model completeness and accuracy compared with the most recent
previously published model. The enhanced accuracy of the
iBsu1103 model also demonstrates the efficacy of the improved
reaction directionality prediction method in accurately
identifying irreversible reactions in the B. subtilis
metabolism. The proposed improved model optimization
methodology was also demonstrated to be effective in minimally
adjusting model content to improve model accuracy.
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2015-07-30 | MODEL1507180015 | BioModels