Spacer_acquisition_f_novicida
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB87316 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Spacer Acquisition Type V-A CRISPR-Cas system Francisella novicida
| PRJEB34159 | ENA
Project description:A whole transcriptome study was performed on Sulfolobus islandicus REY15A actively undergoing CRISPR spacer acquisition from the crenarchaeal monocaudavirus STSV2 in rich (TYS) and basal (SCV) media over a 6 day period. Spacer acquisition preceded strong host growth retardation, and changes in viral transcript abundance and virus copy numbers showed significant differences between the two media. Results showed that rich medium favoured CRISPR-Cas immunity generation.
2015-12-06 | E-MTAB-4027 | biostudies-arrayexpress
Project description:Spacer acquisition by Type III CRISPR-Cas system during bacteriophage infection of Thermus thermophilus
| PRJNA631468 | ENA
Project description:Francisella tularensis subsp. novicida U112 Genome sequencing
| PRJNA236529 | ENA
Project description:Differential expression in human peripheral blood monocytes between F. novicida-infected and uninfected, and between Francisella tularensis tularensis isolate Schu S4 and uninfected. The goal was to examine genomewide transcriptional reponses to these two strains, and identify differentially-regulated genes that may help explain the virulence of Schu S4. Experiment Overall Design: Human monocytes were infected with the Schu S4 isolate of Francisella tularensis tularensis (n=4), with F. tularensis subspecies novicida isolate U112 (n=4) or were left uninfected (n=6). Gene expression values were calculated using the gcrma package in R and BioConductor, and limma to identify differentially expressed genes. Submitted here are expression values calculated using R 2.7.1 and BioConductor 2.2 (FreeBSD/amd64) but the original were done using R 2.6.1 and BioConductor 2.1 (FreeBSD/amd64). Twelve other chips were pooled with these 14 for preprocessing.
2008-10-25 | E-GEOD-12108 | biostudies-arrayexpress
Project description:Prokaryotes create adaptive immune memories by acquiring foreign DNA snippets, known as spacers, into the CRISPR array1. In type II CRISPR-Cas systems, the RNA-guided effector Cas9 also assists the acquisition machinery by selecting spacers from protospacer adjacent motif (PAM)-flanked DNA2,3. Here, we uncover the first biological role for Cas9 that is independent of its dual RNA partners. Following depletion of crRNA and/or tracrRNA, Neisseria apoCas9 stimulates spacer acquisition efficiency. Physiologically, Cas9 senses low levels of crRNA in cells with short CRISPR arrays – such as those undergoing array neogenesis or natural array contractions – and dynamically upregulates acquisition to quickly expand the small immune memory banks. As the CRISPR array expands, rising crRNA abundance in turn reduces apoCas9 availability, thereby dampening acquisition to mitigate autoimmunity risks associate with elevated acquisition. While apoCas9’s nuclease lobe alone suffices for stimulating acquisition, only full-length Cas9 responses to crRNA levels to boost acquisition in cells with low immunity depth. Finally, we show that this activity is evolutionarily conserved across multiple type II-C Cas9 orthologs. Altogether, we establish an auto-replenishing feedback mechanism in which apoCas9 safeguards CRISPR immunity depth by acting as both a crRNA sensor and a regulator of spacer acquisition.
2025-08-29 | GSE302092 | GEO
Project description:Intra-macrophage Expression data of Francisella tularensis novicida U112
| PRJNA305059 | ENA
Project description:In many bacteria, the ability to modulate biofilm production relies on specific signaling molecules that are either self-produced or made by neighboring microbes within the ecological niche. We analyzed the potential interspecies signaling effect of the Burkholderia diffusible signal factor (BDSF) on Francisella novicida, a model organism for Francisella tularensis, and demon- strated that BDSF both inhibits the formation and causes the dispersion of Francisella biofilm. Specificity was demonstrated for the cis versus the trans form of BDSF. Using transcriptome sequencing, quantitative reverse transcription-PCR, and activity as- says, we found that BDSF altered the expression of many F. novicida genes, including genes involved in biofilm formation, such as chitinases. Using a chitinase inhibitor, the antibiofilm activity of BDSF was also shown to be chitinase dependent. In addition, BDSF caused an increase in RelA expression and increased levels of (p)ppGpp, leading to decreased biofilm production. These results support our observation that exposure of F. novicida to BDSF causes biofilm dispersal. Furthermore, BDSF upregulated the genes involved in iron acquisition (figABCD), increasing siderophore production. Thus, this study provides the first evidence for a potential role and mechanism of diffusible signal factor (DSF) signaling in the genus Francisella and suggests the possibility of interspecies signaling between Francisella and other bacteria. Overall, this study suggests that in response to the interspecies DSF signal, F. novicida can alter its gene expression and regulate its biofilm formation.
2015-08-19 | GSE72142 | GEO