Bacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB13437 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Six bacterial genomes, Geobacter metallireducens GS-15, Chromohalobacter salexigens, Vibrio breoganii 1C-10, Bacillus cereus ATCC 10987, Campylobacter jejuni subsp. jejuni 81-176 and Campylobacter jejuni NCTC 11168, all of which had previously been sequenced using other platforms were re-sequenced using single-molecule, real-time (SMRT) sequencing specifically to analyze their methylomes. In every case a number of new N6-methyladenine (m6A) and N4-methylcytosine (m4C) methylation patterns were discovered and the DNA methyltransferases (MTases) responsible for those methylation patterns were assigned. In 15 cases it was possible to match MTase genes with MTase recognition sequences without further sub-cloning. Two Type I restriction systems required sub-cloning to differentiate their recognition sequences, while four MTases genes that were not expressed in the native organism were sub-cloned to test for viability and recognition sequences. No attempt was made to detect 5-methylcytosine (m5C) recognition motifs from the SMRT sequencing data because this modification produces weaker signals using current methods. However, all predicted m6A and m4C MTases were detected unambiguously. This study shows that the addition of SMRT sequencing to traditional sequencing approaches gives a wealth of useful functional information about a genome showing not only which MTase genes are active, but also revealing their recognition sequences. Examination of the methylomes of six different strains of bacteria using kinetic data from single-molecule, real-time (SMRT) sequencing on the PacBio RS.
2012-10-04 | E-GEOD-40133 | biostudies-arrayexpress
Project description:We quantified bacterial incorporation of algal-derived complex dissolved organic C (DOC) and N (DON) and net algal incorporation of remineralized C and N at the single cell level using isotope tracing and NanoSIMS for fifteen bacterial co-cultures growing with the diatom Phaeodactylum tricornutum, and examined the expressed proteins of two of the isolates when growing with P. tricornutum. Data was searched with MS-GF+ using PNNL's DMS Processing pipeline.
2022-08-24 | MSV000090201 | MassIVE
Project description:Phytoplankton blooms represent hotspots of primary production and lead to the formation of particulate organic matter composed of living and dead algal cells. These particles are characterized by steep chemical gradients, for instance in oxygen concentration, that provide diverse ecological niches for specifically adapted microbes to thrive. Particulate fractions were collected at almost daily intervals between early March and late May in 2018. Amplicon sequencing and Meta-omics was used to asses microbial community composition and functionality at different time points.
2024-04-02 | PXD035982 | Pride
Project description:Post-transcriptional modifications are important for transfer RNAs (tRNAs) to be efficient and accurate in translation on the ribosome. The m1G37 modification on a subset of tRNAs in bacteria are generated by a conserved methyltransferase TrmD and is essential for bacterial growth. Previous studies showed that m1G37 has an important role in preventing translational frameshifting and also that this modification is coupled with aminoacylation of tRNAs for proline. Here we performed suppressor screening to isolate a mutant E. coli cell that lacks TrmD but is viable, and the whole-genome sequencing revealed several mutations on prolyl-tRNA synthetase (ProRS) gene conferring cell viability in the absence of TrmD. Biochemical assays confirmed uncoupling of m1G37 modification and aminoacylation, and cell-based assays uncovered the critical role of m1G37 in supporting Wobble decoding.
2022-09-24 | E-MTAB-12178 | biostudies-arrayexpress
Project description:Genome and metagenome analysis of algal cell wall degrading bacteria
| PRJNA311641 | ENA
Project description:Phytoplankton-derived metabolites fuel a large fraction of heterotrophic bacterial production in the global ocean, yet methodological challenges have limited our knowledge of organic molecules transferred between these two microbial groups. In an experimental bloom study in which the diatom Thalassiosira pseudonana was co-cultured with three heterotrophic marine bacteria, we concurrently measured diatom endometabolites (i.e., potential exometabolite supply) by nuclear magnetic resonance (NMR) spectroscopy and bacterial gene expression (i.e., potential exometabolite uptake) by metatranscriptomic sequencing.
2021-08-31 | ST001944 | MetabolomicsWorkbench