Genomic, transcriptomic, and structural analysis of Pseudomonas virus PA5oct highlights the molecular complexity among Jumbo phages
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA534259 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Pseudomonas virus PA5oct has a large, linear, double-stranded DNA genome (286,783 bp) and is related to Escherichia phages 121Q/PBECO 4, Klebsiella phage vB_KleM-RaK2, Klebsiella phage K64-1, and Cronobacter phage vB_CsaM_GAP32. A protein-sharing network analysis highlights the conserved core genes within this clade. Combining hybrid genome sequencing, RNA-Seq and mass spectrometry analyses of its virion proteins allowed us to accurately identify genes and elucidate regulatory elements for this phage (ncRNAs, tRNAs and promoter elements). In total PA5oct encodes 449 CDS of which 93, have been identified as virion-associated based on ESI-MS/MS. The RNA-Seq-based temporal genome organization suggests a gradual take-over by viral transcripts from 21%, 69%, and 93% at 5, 15 and 25 min after infection, respectively . Like many large phages, PA5oct is not organized into contiguous regions of temporal transcription. However, although the temporal regulation of the PA5oct genome expression reveals specific genome clusters expressed in early and late infection, many genes encoding experimentally observed structural proteins surprisingly appear to remain almost untranscribed throughout the infection cycle. Within the host, operons associated with elements of a cryptic Pf1-like prophage are upregulated, as are operons responsible for Psl exopolysaccharide (pslE-J) and periplasmic nitrate reductase (napA-F) production. The characterization described here represents a crucial step towards understanding the genomic complexity as well as molecular diversity of jumbo viruses.
2020-06-04 | GSE130190 | GEO
Project description: Not available
| S-EPMC7318152 | biostudies-literature
Project description:This series represents the gene expression study of phages DT1 and 2972 during the whole process of infection. Gene expression was measured at nine time intervals (0, 2, 7, 12, 17, 22, 27, 32, 37 minutes) during phage infection.
2005-08-10 | E-GEOD-2476 | biostudies-arrayexpress
Project description:This series represents the gene expression study of phages DT1 and 2972 during the whole process of infection. Gene expression was measured at nine time intervals (0, 2, 7, 12, 17, 22, 27, 32, 37 minutes) during phage infection. Keywords: time-course
2005-08-10 | GSE2476 | GEO
Project description:The mammalian immune system implements a remarkably effective set of mechanisms for fighting pathogens. Its main actors are hematopoietic immune cells, including myeloid cells with their focus on innate immunity and lymphoid cells as enablers of adaptive immunity. Nevertheless, immune functions are not unique to hematopoietic cells, and basic mechanisms of pathogen defense are present in many other cell types. To advance our understanding of immunology outside of the hematopoietic system, we systematically investigated immune gene regulation in the three major types of structural cells: Epithelium, endothelium, and fibroblasts. We characterized these cell types across 12 organs in mice, using cellular phenotyping, transcriptome sequencing, chromatin accessibility profiling, and epigenome mapping. This comprehensive dataset uncovered a striking complexity of immune gene activity and regulation in structural cells. The observed patterns were highly organ-specific and appear to modulate interactions between structural cells and hematopoietic immune cells. Moreover, we identified an epigenetically encoded immune potential in structural cells under tissue homeostasis, which was triggered in response to systemic viral infection. This study highlights an underappreciated complexity of organ-specific immune gene regulation beyond hematopoietic cells, and it provides a high-resolution, multi-omics atlas of the epigenomic and transcription-regulatory circuitry of structural cells in the mouse.
2020-06-30 | GSE145820 | GEO
Project description:The mammalian immune system implements a remarkably effective set of mechanisms for fighting pathogens. Its main actors are hematopoietic immune cells, including myeloid cells with their focus on innate immunity and lymphoid cells as enablers of adaptive immunity. Nevertheless, immune functions are not unique to hematopoietic cells, and basic mechanisms of pathogen defense are present in many other cell types. To advance our understanding of immunology outside of the hematopoietic system, we systematically investigated immune gene regulation in the three major types of structural cells: Epithelium, endothelium, and fibroblasts. We characterized these cell types across 12 organs in mice, using cellular phenotyping, transcriptome sequencing, chromatin accessibility profiling, and epigenome mapping. This comprehensive dataset uncovered a striking complexity of immune gene activity and regulation in structural cells. The observed patterns were highly organ-specific and appear to modulate interactions between structural cells and hematopoietic immune cells. Moreover, we identified an epigenetically encoded immune potential in structural cells under tissue homeostasis, which was triggered in response to systemic viral infection. This study highlights an underappreciated complexity of organ-specific immune gene regulation beyond hematopoietic cells, and it provides a high-resolution, multi-omics atlas of the epigenomic and transcription-regulatory circuitry of structural cells in the mouse.
2020-06-30 | GSE134658 | GEO