Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11748952.fastq.gz | Fastqsanger.gz | |||
| SRR11748953.fastq.gz | Fastqsanger.gz | |||
| SRR11748954.fastq.gz | Fastqsanger.gz | |||
| SRR11748955.fastq.gz | Fastqsanger.gz | |||
| SRR11748956.fastq.gz | Fastqsanger.gz |
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Project description:One of the most complex prokaryotic organelles are magnetosomes, which are formed by magnetotactic bacteria as sensors for navigation in the Earth’s magnetic field. In the alphaproteobacterium Magnetospirillum gryphiswaldense magnetosomes consist of chains of magnetite crystals (Fe3O4) that under suboxic conditions are biomineralized within membrane vesicles. To form such an intricate structure, the transcription of >30 specific structural genes clustered within the genomic magnetosome island (MAI) has to be coordinated with the expression of an as-yet unknown number of auxiliary genes encoding several generic metabolic functions. However, their global regulation and transcriptional organization in response to anoxic conditions most favorable for magnetite biomineralization are still unclear. Here, we compared transcriptional profiles of anaerobically grown magnetosome forming cells with those in which magnetosome biosynthesis has been suppressed by aerobic condition. Using whole transcriptome shotgun sequencing, we found that transcription of about 300 of the >4300 genes was significantly enhanced during magnetosome formation. The about 40 top upregulated genes are directly or indirectly linked to aerobic and anaerobic respiration (denitrification) or unknown functions. mam and mms gene clusters specifically controlling magnetosome biosynthesis were highly transcribed, but constitutively expressed irrespective of the growth condition. By Cappable-sequencing, we show that the transcriptional complexity of both the MAI and the entire genome decreased under anaerobic conditions optimal for magnetosome formation. In addition, predominant promoter structures were highly similar to sigma factor σ70 dependent promoters in other Alphaproteobacteria. Our transcriptome-wide analysis revealed that magnetite biomineralization relies on a complex interplay between generic metabolic processes such as aerobic and anaerobic respiration, cellular redox control, and the biosynthesis of specific magnetosome structures. In addition, we provide insights into global regulatory features that have remained uncharacterized in the widely studied model organism M. gryphiswaldense, including a comprehensive dataset of newly annotated transcription start sites and genome-wide operon detection as a community resource.
2022-10-19 | GSE197098 | GEO
Project description:A Transcriptomics Approach to Study the Biocompatibility and Finding out the Potential Applications of Magnetite (Fe3O4) Nanoparticles Here in this study, we examine the molecular effects of uptake of Fe3O4 nanoparticles using a whole genome microarray study in human epithelial cancer cell line. 38 genes (55%) out of 69 downregulated genes were found to be associated with TGF-beta or BMP signaling including six genes, Id1, Id2, Id3, Caspase-9, Smad6 and SMAD7, important negative regulators of these signaling pathways involved in development and tumorigenesis.
2010-03-13 | GSE15248 | GEO
Project description:Deatails of the series are available in the publications Suzuki et al., The Journal of Bacteriology “Global gene expression analysis of iron-inducible genes in Magnetospirillum magneticum AMB-1”, accepted for the publication. The gene expression profiles were categorized into 5 patterns. Abstract of the publication: "feo, tpd and ftr which encode ferrous transporters were up-regulated under iron-rich conditions.The concomitant rapid iron uptake and magnetite formation suggest that these uptake systems serve as iron supply lines for magnetosome synthesis." Keywords: iron response
2006-03-24 | GSE3914 | GEO
Project description:Iron-oxidizing bacteria are widely found in natural and man-made environments where they influence varied biogeochemical cycles. Despite their prevalence, the mechanisms and Fe(II) substrates used by these organisms remain understudied. To date, there has been limited exploration of the ability of iron-oxidizing bacteria to utilize solid minerals as electron donors. Sideroxydans lithotrophicus ES-1 is a robust, facultative iron oxidizer with multiple enzymatic pathways for iron oxidation, making it a prime candidate for evaluating extracellular electron uptake mechanisms. In this study, S. lithotrophicus ES-1 was grown on dissolved Fe(II)-citrate and three preparations of magnetite that provided different ratios of soluble and solid Fe(II). S. lithotrophicus ES-1 grew equally well on the different batches of magnetite, suggesting it can adapt to the type of iron present during growth. S. lithotrophicus ES-1 oxidized all available dissolved Fe2+ released from magnetite, and continued to build biomass when only solid Fe(II) remained. Quantitative proteomic analyses of S. lithotrophicus ES-1 grown on these substrates revealed proteome remodeling in response to electron donor and growth state, and uncovered potential proteins and metabolic pathways involved in the oxidation of solid magnetite. While the Cyc2 iron oxidases were highly expressed on both dissolved and solid substrates, the MtoAB complex was only expressed during growth on the solid magnetite, suggesting these proteins play a role in oxidation of solid minerals in S. lithotrophicus ES-1. A set of cupredoxin domain-containing proteins were also identified that were specifically expressed during solid iron oxidation. This work confirmed the iron oxidizer, S. lithotrophicus ES-1, utilized distinct extracellular electron transfer pathways when growing on solid mineral electron donors compared to dissolved Fe(II)-citrate. The presence of multiple pathways, and the ability to regulate their expression and use, could benefit iron-oxidizing bacteria that encounter various electron donors in their environments.
2024-01-04 | MSV000093770 | MassIVE
Project description:Sulfate-reducing bacterium with intracellular magnetite particles
| PRJNA15681 | ENA