Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1086847 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:CRISPR-Cas constitutes an adaptive prokaryotic defence system against invasive nucleic acids like viruses and plasmids. Beyond their role in immunity, CRISPR-Cas systems have been shown to closely interact with components of cellular DNA repair pathways either by regulating their expression or via direct protein-protein contact or enzymatic activity. The integrase Cas1 is usually involved in the adaptation phase of CRISPR-Cas immunity but its function in cellular DNA repair pathways has been proposed before. Here, we analysed the capacity of an archaeal Cas1 from Haloferax volcanii to compensate DNA damage induced by oxidative stress and found that a deletion of the cas1 gene led to severe growth defects after stress induction. In addition, our results indicate that Cas1 is directly involved in DNA damage repair as the enzymatically active site of the protein is crucial for growth rescue under oxidative conditions. Based on biochemical cleavage assays, we propose a mechanism in which Cas1 exerts a similar function like the DNA repair protein Fen1 by resolving branched repair intermediate structures. Overall, the present study broadens our understanding of the functional link between CRISPR-Cas immunity and DNA repair by demonstrating that Cas1 and Fen1 display commutable roles during archaeal DNA damage repair.
2022-05-20 | PXD029952 | Pride
Project description:CRISPR loci are found in bacterial and archaeal genomes where they provide the molecular machinery for acquisition of immunity against foreign DNA. In addition to the cas genes fundamentally required for CRISPR activity, a second class of genes is associated with the CRISPR loci, of which many have no reported function in CRISPR-mediated immunity. Here, we characterize MM_0565 of Methanosarcina mazei Gö1 associated to the type I-B CRISPR-locus providing evidence for its relevance in regulating this system. We show that MM_0565 is composed of a modified Rossmann-like fold and a winged helix-turn-helix domain and forms a dimer in solution. While direct effects on CRISPR-Cas transcription were not detected by genetic approaches, binding to the leader region of both CRISPR-Cas systems was observed by microscale thermophoresis and electromobility shift assays. Overexpression of MM_0565 however, strongly induced transcription of the cas1-solo gene located in the recently reported casposon, the gene product of which shows high similarity to classical Cas1 proteins. Based on our findings we hypothesize that Cas1-solo is involved in the adaptation of CRISPR-mediated immunity in M. mazei, and that MM_0565 modulates the activity of the CRISPR systems amongst potential other hypnotized actions by activating the transcription of the cas1-solo gene.
2020-09-08 | GSE151372 | GEO
Project description:Key to CRISPR-Cas adaptive immunity is maintaining an ongoing record of invading nucleic acids that are encountered, a process carried out by the Cas1-Cas2 complex that integrates short segments of foreign genetic material (spacers) into the CRISPR locus. It is hypothesized that Cas1 evolved from casposases, a novel class of transposases. We show here that casposase integration in vitro recapitulates several properties of CRISPR-Cas integrases. The X-ray structure of Methanosarcina mazei casposase bound to DNA representing the product of integration reveals a tetramer with target DNA bound snugly between two dimers in which single-stranded casposon end binding resembles that of spacer 3'-overhangs. The differences between transposase and CRISPR-Cas integrase are largely architectural, and it appears that evolutionary change involved changes in protein-protein interactions to favor Cas2 binding over tetramerization and the separation of Cas1 dimers. This, in turn, led to preferred integration of single spacers over two transposon ends.
2020-02-03 | GSE139037 | GEO
Project description:Prokaryotic Cas1-Cas2 protein complexes generate adaptive immunity to mobile genetic elements (MGEs), by capture and integration of MGE DNA in to CRISPR sites. De novo immunity relies on Cas1-Cas2 targeting MGE DNA, without the aid of pre-existing immunity complexes, through mechanisms of ‘naive adaptation’ that are not clear. Using E. coli we show that the chaperone DnaK inhibits Cas1-Cas2 from DNA binding and integration, and that DnaK expression prevents naïve adaptation from chromosomal self-targeting. We show that that inhibition of naïve adaptation is reversible by eliminating DnaK from cells, by mutation of the DnaK substrate binding domain, and by expression of an MGE (phage )protein. We show that a fluorescently labelled Cas1 fusion can be visualised in living cells. Formation of foci depends on active DNA replication, and that the number of foci per cell is much increased in cells lacking DnaK. We discuss a model in which DnaK provides a mechanism for restraining naïve adaptation from self-targeting. This restraint is released once MGE DNA is present in the cell.
2023-05-18 | PXD042090 | Pride
Project description:Transcriptome sequencing was carried out on an Illumina HiSeq platform to investigate the activation of CRISPR-Cas and DNA repair systems by Csa3a in Sulfolobus islandicus Rey15A. We compared the differently expressed genes in Sulfolobus islandicus Rey15A strain with csa3a overexpression vs. Sulfolobus islandicus Rey15A strain carrying an empty expression vector, cas1 deletion strain with csa3a overexpression vs. cas1 deletion strain carrying an empty expression vector, as well as interference-deficient strain with csa3a overexpression vs. interference-deficient strain carrying an empty expression vector. We find that cas genes (SiRe_0760, SiRe_0761, SiRe_0762, SiRe_0763), nucleotidyltransferase domain of DNA polymerase beta (SiRe_0459), chromosome segregation protein (SMC)-related ATPase (SiRe_0649), SMC-related protein (SiRe_1142) and three HerA helicases involved in DNA double break repair (encoded by SiRe_0064 and SiRe_0095 of nurA-herA operons, and SiRe_1857) were significantly up-regulated. Our data indicated that the Csa3a regulator couples transcriptional activation of spacer acquisition genes, CRISPR RNA transcription, DNA repair and genome stability genes.
2017-10-31 | GSE99099 | GEO
Project description:Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign DNA for degradation. Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this strategy by leveraging DNA synthesis instead. We and others recently showed that DRT2 systems use an RNA template to assemble a de novo gene, leading to expression of an antiviral effector protein, Neo. It remains unknown whether similar mechanisms of defense are employed by other related DRT families. Focusing on DRT9, here we uncover an unprecedented mechanism of DNA homopolymer synthesis, in which viral infection triggers polydeoxyadenylate (poly-dA) accumulation in the cell to drive abortive infection and population-level immunity. Cryo-EM structures reveal how a conserved noncoding RNA serves as both a structural scaffold and reverse transcription template to direct hexameric complex assembly and RNA-templated poly-dA synthesis. Remarkably, biochemical and functional experiments identify conserved tyrosine residues within the reverse transcriptase itself that prime DNA synthesis, leading to the formation of high-molecular weight protein-DNA covalent adducts. Synthesis of poly-dA in vivo is regulated by the competing activities of phage-encoded triggers and host-encoded silencers of DRT9. Collectively, our work unveils a novel nucleic acid-driven defense system that expands the paradigm of bacterial immunity and broadens the known functions of reverse transcriptases.
2025-05-09 | GSE295895 | GEO
Project description:Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign DNA for degradation. Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this strategy by leveraging DNA synthesis instead. We and others recently showed that DRT2 systems use an RNA template to assemble a de novo gene, leading to expression of an antiviral effector protein, Neo. It remains unknown whether similar mechanisms of defense are employed by other related DRT families. Focusing on DRT9, here we uncover an unprecedented mechanism of DNA homopolymer synthesis, in which viral infection triggers polydeoxyadenylate (poly-dA) accumulation in the cell to drive abortive infection and population-level immunity. Cryo-EM structures reveal how a conserved noncoding RNA serves as both a structural scaffold and reverse transcription template to direct hexameric complex assembly and RNA-templated poly-dA synthesis. Remarkably, biochemical and functional experiments identify conserved tyrosine residues within the reverse transcriptase itself that prime DNA synthesis, leading to the formation of high-molecular weight protein-DNA covalent adducts. Synthesis of poly-dA in vivo is regulated by the competing activities of phage-encoded triggers and host-encoded silencers of DRT9. Collectively, our work unveils a novel nucleic acid-driven defense system that expands the paradigm of bacterial immunity and broadens the known functions of reverse transcriptases.
2025-05-09 | GSE295896 | GEO