Natural Transformation of Bacteria by Damaged DNA
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REPOSITORIES: ENA
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Project description: Not available
| S-EPMC3856829 | biostudies-literature
Project description:In marine Vibrio species, chitin-induced natural transformation enables bacteria to take up DNA from the external environment and integrate it into their genome via homologous recombination. Expression of the master competence regulator TfoX bypasses the need for chitin induction and drives expression of the genes required for competence in several Vibrio species. Here, we show that TfoX expression in two Vibrio campbellii strains, DS40M4 and NBRC 15631, enables high frequencies of natural transformation. Conversely, transformation was not achieved in the model quorum-sensing strain V. campbellii BB120 (previously classified as Vibrio harveyi). Surprisingly, we find that quorum sensing is not required for transformation in V. campbellii DS40M4. This result is in contrast to Vibrio cholerae that requires the quorum-sensing regulator HapR to activate the competence regulator QstR. However, similar to V. cholerae, QstR is necessary for transformation in DS40M4. To investigate the difference in transformation frequencies between BB120 and DS40M4, we used previously studied V. cholerae competence genes to inform a comparative genomics analysis coupled with transcriptomics. BB120 encodes homologs of all known competence genes, but most of these genes were not induced by ectopic expression of TfoX, which likely accounts for the non-functional natural transformation in this strain. Comparison of transformation frequencies among Vibrio species indicates a wide disparity among even closely related strains, with Vibrio vulnificus having the lowest functional transformation frequency. We show that ectopic expression of both TfoX and QstR is sufficient to produce a significant increase in transformation frequency in Vibrio vulnificus.
2019-11-14 | GSE136941 | GEO
Project description:Diverse conjugative elements silence natural transformation in Legionella species
| PRJEB31835 | ENA
Project description:Diversity in natural transformation frequencies and regulation across Vibrio species
| PRJNA564094 | ENA
Project description:We report a method for bypassing restriction modification systems to increase DNA transformation in batceria and develop a high-throughput way to determine the optimal methylation pattern for DNA transformation.
2024-01-01 | GSE189864 | GEO
Project description:The bacterial world offers diverse strains for understanding medical and environmental processes and for engineering synthetic-biology chasses. However, genetically manipulating these strains has faced a long-standing bottleneck: how to efficiently transform DNA. Here we report IMPRINT, a generalized, rapid and scalable approach to overcome DNA restriction, a prominent barrier to transformation. IMPRINT utilizes cell-free systems to express DNA methyltransferases from the bacterial host’s restriction-modification systems. The expressed methyltransferases then methylate DNA in vitro to match the host DNA’s methylation pattern, circumventing restriction and enhancing transformation. Unlike established approaches, IMPRINT can be completed in under one day, readily accommodates all methyltransferase types, and avoids methylation-induced cytotoxicity. With IMPRINT, we efficiently multiplex DNA methylation and maximize plasmid transformation in gram-negative and gram-positive bacteria. We also developed a high-throughput pipeline that identifies the most consequential methyltransferases in one transformation. Overall, IMPRINT can vastly enhance DNA transformation, enabling use of increasingly sophisticated genetic manipulation tools across the bacterial world.
2024-04-07 | GSE240651 | GEO
Project description:The species Campylobacter jejuni is naturally competent for DNA uptake; nevertheless, nonnaturally transformable strains do exist. For a subset of strains we previously showed that a periplasmic DNase, encoded by dns, inhibits natural transformation in C. jejuni. In the present study, genetic factors coding for DNase activity in absence of dns were identified. DNA arrays indicated that nonnaturally transformable dns-negative strains contain putative DNA/RNA non-specific endonucleases encoded by CJE0566 and CJE1441 of strain RM1221. These genes are located on C. jejuni integrated element 2 and 4. Expression of CJE0566 and CJE1441 from strain RM1221 and a homologous gene from strain 07479 in DNase-negative Escherichia coli and C. jejuni strains indicated that these genes code for DNases. Genetic transfer of the genes to a naturally transformable C. jejuni strain resulted in a decreased efficiency of natural transformation. Modelling suggests that the C. jejuni DNases belong to the Serratia nuclease family. Overall, the data indicate that the acquisition of prophage encoded DNA/RNA non-specific endonucleases inhibits the natural transformability of C. jejuni through hydrolysis of DNA.
2009-11-14 | GSE18399 | GEO
Project description:Examine the chormatin localization of DINO in DNA damaged human U2OS cells using DINO ChIRP-seq.
2016-09-26 | GSE76418 | GEO
Project description:Parkinson disease (PD) is a neurodegenerative disease believed to initiate in the brainstem and then spread throughout the brain. The mechanism by which this occurs is not yet fully understood, but here we show that damaged mitochondrial DNA (mtDNA) plays an important role in this process, which can be initiated by dysregulation of the IFNb/IFNAR signalling pathway. We report that lack of neuronal IFNb/IFNAR, which is associated to the development of PD, causes oxidization, mutation, and deletion in mtDNA. Damaged mtDNA is subsequently extruded extracellularly and can induce PD symptoms like motor and cognitive impairments in healthy mouse brains. It even leads to neurodegeneration in brain regions far from the injection site, suggesting that damaged mtDNA triggers the propagation of PD hallmarks through the brain. We further show that the mechanism by which damaged mtDNA causes pathology in healthy neurons is independent of cGAS and IFNb/IFNAR, but it is mediated by activation of dual Toll-like receptor (TLR)4/9 pathways. Through a proteomic analysis of extracellular vesicles containing the damaged mtDNA, we identified the TLR4 activator Ribosomal Protein S3 (Rps3) and established that Rps3 is a key effector protein involved in damaged mtDNA extrusion and recognition. Collectively, these results reveal a new molecular pathway by which damaged mtDNA can initiate and propagate Parkinson's Disease, paving the way for potential new therapies or disease monitoring.
2023-09-18 | PXD038362 | Pride
Project description:The species Campylobacter jejuni is naturally competent for DNA uptake; nevertheless, nonnaturally transformable strains do exist. For a subset of strains we previously showed that a periplasmic DNase, encoded by dns, inhibits natural transformation in C. jejuni. In the present study, genetic factors coding for DNase activity in absence of dns were identified. DNA arrays indicated that nonnaturally transformable dns-negative strains contain putative DNA/RNA non-specific endonucleases encoded by CJE0566 and CJE1441 of strain RM1221. These genes are located on C. jejuni integrated element 2 and 4. Expression of CJE0566 and CJE1441 from strain RM1221 and a homologous gene from strain 07479 in DNase-negative Escherichia coli and C. jejuni strains indicated that these genes code for DNases. Genetic transfer of the genes to a naturally transformable C. jejuni strain resulted in a decreased efficiency of natural transformation. Modelling suggests that the C. jejuni DNases belong to the Serratia nuclease family. Overall, the data indicate that the acquisition of prophage encoded DNA/RNA non-specific endonucleases inhibits the natural transformability of C. jejuni through hydrolysis of DNA. The genomic diversity of 15 naturally competent or nonnaturally transformable Campylobacter jejuni strains were examined by microarray-based comparative genomic indexing (CGI) analysis. The CGI analysis allowed the assessment of CDS content for each C. jejuni strain relative to the C. jejuni DNA microarray, which comprises ORFs from strains NCTC 11168, RM1221. ORFs were spotted in duplicate. Genomic DNA from strains NCTC 11168/RM1221 were used as a reference DNA and competitively hybridized with genomic DNA from each of the other C. jejuni strains. Two replicates for each strain were performed. Data normalization was performed as in Parker et al. J Clin Microbiol 2006, 44(11):4125-4135.
2009-11-13 | E-GEOD-18399 | biostudies-arrayexpress