Soil gene cassette metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA485646 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:A ELMSeq reporter cassette was created to monitor Dam levels by methylation, and introduced in the genome. Some regions upstream dam were randomized to see their effect on gene expression. So the cassette consists in: 4xGATC sites - (promoter) - random region - dam. The amplicon was spanning the whole cassette, including some bases inside the dam. The cassette was introduced in Mycoplasma pneumoniae.
2017-11-08 | E-MTAB-5365 | biostudies-arrayexpress
Project description:Integrons are genetic platforms that acquire new genes encoded in integron cassettes (ICs), building arrays of adaptive functions for bacteria. ICs generally encode promoterless genes, whose expression relies on the PC promoter within the integron platform. Cassette arrays are assumed to be operon-like structures in which expression is dependent on the distance to the Pc. This is especially relevant in large sedentary chromosomal integrons (SCIs,) like the ones in Vibrio species. We have identified 29 gene-less cassettes in 4 Vibrio SCIs, and explored whether their function could be related to regulating the transcription of adjacent ICs. We show that most gene-less cassettes have promoter activity on the sense strand, enhancing the expression of downstream cassettes. Accordingly, we found that most of the superintegron in Vibrio cholerae is not silent. These promoter cassettes can trigger the expression of a silent dfrB9 resistance cassette downstream, increasing trimethoprim resistance >512-fold in V. cholerae and Escherichia coli. Additionally, one cassette had an antisense promoter capable of reducing trimethoprim resistance through transcriptional interference. Our findings highlight the regulatory role of gene-less cassettes in the expression of adjacent cassettes, emphasizing their significance in large SCIs and their clinical importance if captured by mobile integrons.
2023-04-17 | GSE229776 | GEO
Project description:A ELMSeq reporter cassette was created to monitor Dam levels by methylation, and introduced in the genome. The regions of 6 nt upstream and 6 nt downstream the stop codon were randomized to study their effect on gene expression. The ELMSeq reporter cassette was composed of: promoter - dam - random N6 - stop codon TAA - random N6 - spacer - 4xGATC. The amplicon was spanning the C-terminal region. The cassette was introduced in Mycoplasma pneumoniae.
2020-05-04 | E-MTAB-8223 | biostudies-arrayexpress
Project description:In order to determine the effect of neoR gene in Q175 locus, miRNASeq was performed to compare the transcriptional signatures of zQ175 knock-in neo-in (z_Q175 KI) (CHDI-81003003) and zQ175 KI neo-out (Z_Q175 (neo -) KI) (CHDI-81003019) mouse lines. The z_Q175 KI is a knock-in mouse line with humanized exon 1 (190-200 pure CAG repeats) derived from Q140 KI colony. It contains floxed neo cassette upstream of exon 1. The Z_Q175 KI (neo -) KI was generated by crossing the Z-Q175 KI line with a zp3-cre transgenic line to delete out the neo cassette.
2018-12-19 | GSE123664 | GEO
Project description:DNA-seq of ELMSeq reporter cassette
| PRJEB23364 | ENA
Project description:Precision genome-editing approaches have long been available in budding yeast, enabling introduction of gene deletions, epitope tag fusions, and promoter swaps through a selection-based strategy. Such approaches allow loci to be modified without disruption of coding or regulatory sequences of neighboring genes. Use of this approach to delete DBP1 however, led to silencing of expression and the resultant loss of function for the neighboring gene MRP51. We found that insertion of a resistance cassette to delete DBP1, drove a 5' extended alternative transcript for MRP51 which dampened Mrp51 protein synthesis. Misregulation of MRP51 occurred through an integrated transcriptional and translational repressive long undecoded transcript isoform (LUTI)-based mechanism that was recently shown to naturally regulate gene expression in yeast and other organisms. Cassette-induced MRP51 repression drove all mutant phenotypes we detected in cells deleted for DBP1. Selection cassette-mediated aberrant transcription events are not specific to this locus or a unique cassette but can be prevented by insertion of transcription insulators flanking the cassette. Our study suggests the existence of confounding off-target mutant phenotypes resulting from misregulated neighboring loci following genome edits in yeast. Furthermore, features of LUTI-based regulation are broadly conserved to eukaryotic organisms which indicates the potential that similar misregulation could be unnoticed in other edited organisms as well.
2022-06-24 | MSV000089724 | MassIVE
Project description:In order to determine the effect of neoR gene in Q175 locus, mRNASeq was performed to compare the transcriptional signatures of zQ175 knock-in neo-in (z_Q175 KI) (CHDI-81003003) and zQ175 KI neo-out (Z_Q175 (neo -) KI) (CHDI-81003019) mouse lines. The z_Q175 KI is a knock-in mouse line with humanized exon 1 (190-200 pure CAG repeats) derived from Q140 KI colony. It contains floxed neo cassette upstream of exon 1. The Z_Q175 KI (neo -) KI was generated by crossing the Z-Q175 KI line with a zp3-cre transgenic line to delete out the neo cassette.
2018-12-19 | GSE123657 | GEO
Project description:Using two forest soils, we previously constructed two fosmid libraries containing 113,700 members in total. The libraries were screened to select active antifungal clones using Saccharomyces cerevisiae as a target fungus. One clone from the Yuseong pine tree rhizosphere soil library, pEAF66, showed S. cerevisiae growth inhibition. Despite an intensive effort, active chemicals were not isolated. DNA sequence analysis and transposon mutagenesis of pEAF66 revealed 39 open reading frames (ORFs) and indicated that eight ORFs, probably in one transcriptional unit, might be directly involved in the expression of antifungal activity in Escherichia coli. The deduced amino acid sequences of eight ORFs were similar to those of the core genes encoding type II family polyketide synthases, such as the acyl carrier protein (ACP), ACP synthases, aminotransferase, and ACP reductase. The gene cluster involved in antifungal activity was similar in organization to the putative antibiotic production locus of Pseudomonas putida KT2440, although we could not select a similar active clone from the KT2440 genomic DNA library in E. coli. ORFs encoding ATP binding cassette transporters and membrane proteins were located at both ends of the antifungal gene cluster. Upstream ORFs encoding an IclR family response regulator and a LysR family response regulator were involved in the positive regulation of antifungal gene expression. Our results suggested the metagenomic approach as an alternative to search for novel antifungal antibiotics from unculturable soil bacteria. This is the first report of an antifungal gene cluster obtained from a soil metagenome using S. cerevisiae as a target fungus.
| S-EPMC2227728 | biostudies-literature
Project description:The metagenomes of complex microbial communities are rich sources of novel biocatalysts. We exploited the metagenome of a mixed microbial population for isolation of more than 15 different genes encoding novel biocatalysts by using a combined cultivation and direct cloning strategy. A 16S rRNA sequence analysis revealed the presence of hitherto uncultured microbes closely related to the genera Pseudomonas, Agrobacterium, Xanthomonas, Microbulbifer, and Janthinobacterium. Total genomic DNA from this bacterial community was used to construct cosmid DNA libraries, which were functionally searched for novel enzymes of biotechnological value. Our searches in combination with cosmid sequencing resulted in identification of four clones encoding 12 putative agarase genes, most of which were organized in clusters consisting of two or three genes. Interestingly, nine of these agarase genes probably originated from gene duplications. Furthermore, we identified by DNA sequencing several other biocatalyst-encoding genes, including genes encoding a putative stereoselective amidase (amiA), two cellulases (gnuB and uvs080), an alpha-amylase (amyA), a 1,4-alpha-glucan branching enzyme (amyB), and two pectate lyases (pelA and uvs119). Also, a conserved cluster of two lipase genes was identified, which was linked to genes encoding a type I secretion system. The novel gene aguB was overexpressed in Escherichia coli, and the enzyme activities were determined. Finally, we describe more than 162 kb of DNA sequence that provides a strong platform for further characterization of this microbial consortium.
| S-EPMC201203 | biostudies-literature
Project description:A miRNA Cassette Reprograms Smooth Muscle Cells into Endothelial Cells
| PRJNA753869 | ENA