Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Solidesulfovibrio magneticus RS-1

ABSTRACT: Desulfovibrio magneticus mutant Genome sequencing

PROVIDER: PRJNA258555 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR1561890.fastq.gz	Fastqsanger.gz
	SRR1561900.fastq.gz	Fastqsanger.gz
	SRR1561910.fastq.gz	Fastqsanger.gz
	SRR1561891.fastq.gz	Fastqsanger.gz
	SRR1561901.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 31

Similar Datasets

Solidesulfovibrio magneticus strain:ML1

Project description:Desulfovibrio magnetic ML1 genome sequencing

| PRJNA332968 | ENA

Solidesulfovibrio magneticus RS-1

Project description:This strain will be used for comparative genome analysis

| PRJDA32105 | ENA

Solidesulfovibrio magneticus str. Maddingley MBC34

Project description:Desulfovibrio magneticus str. Maddingley MBC34 Metagenomic Assembly

| PRJNA169936 | ENA

Solidesulfovibrio magneticus

Project description:Sulfate-reducing bacterium with intracellular magnetite particles

| PRJNA35755 | ENA

Solidesulfovibrio cf. magneticus IFRC170

Project description:Solidesulfovibrio cf. magneticus IFRC170 Genome sequencing

| PRJNA195833 | ENA

Solidesulfovibrio fructosivorans JJ] strain:JJ

Project description:Desulfovibrio fructosovorans JJ whole genome sequencing project

| PRJNA43359 | ENA

Solidesulfovibrio carbinoliphilus subsp. oakridgensis strain:FW1012B

Project description:GEBA Desulfovibrio sp. FW1012B genome sequencing project

| PRJNA38043 | ENA

Solidesulfovibrio magneticus strain:ATCC 700980

Project description:Sulfate-reducing bacterium with intracellular magnetite particles

| PRJNA15681 | ENA

Whole genome sequence of Desulfovibrio magneticus strain RS-1 revealed common gene clusters in magnetotactic bacteria.

Project description:Magnetotactic bacteria are ubiquitous microorganisms that synthesize intracellular magnetite particles (magnetosomes) by accumulating Fe ions from aquatic environments. Recent molecular studies, including comprehensive proteomic, transcriptomic, and genomic analyses, have considerably improved our hypotheses of the magnetosome-formation mechanism. However, most of these studies have been conducted using pure-cultured bacterial strains of alpha-proteobacteria. Here, we report the whole-genome sequence of Desulfovibrio magneticus strain RS-1, the only isolate of magnetotactic microorganisms classified under delta-proteobacteria. Comparative genomics of the RS-1 and four alpha-proteobacterial strains revealed the presence of three separate gene regions (nuo and mamAB-like gene clusters, and gene region of a cryptic plasmid) conserved in all magnetotactic bacteria. The nuo gene cluster, encoding NADH dehydrogenase (complex I), was also common to the genomes of three iron-reducing bacteria exhibiting uncontrolled extracellular and/or intracellular magnetite synthesis. A cryptic plasmid, pDMC1, encodes three homologous genes that exhibit high similarities with those of other magnetotactic bacterial strains. In addition, the mamAB-like gene cluster, encoding the key components for magnetosome formation such as iron transport and magnetosome alignment, was conserved only in the genomes of magnetotactic bacteria as a similar genomic island-like structure. Our findings suggest the presence of core genetic components for magnetosome biosynthesis; these genes may have been acquired into the magnetotactic bacterial genomes by multiple gene-transfer events during proteobacterial evolution.

| S-EPMC2765288 | biostudies-literature

Desulfovibrio magneticus RS-1 contains an iron- and phosphorus-rich organelle distinct from its bullet-shaped magnetosomes.

Project description:Intracellular magnetite crystal formation by magnetotactic bacteria has emerged as a powerful model for investigating the cellular and molecular mechanisms of biomineralization, a process common to all branches of life. Although magnetotactic bacteria are phylogenetically diverse and their crystals morphologically diverse, studies to date have focused on a few, closely related species with similar crystal habits. Here, we investigate the process of magnetite biomineralization in Desulfovibrio magneticus sp. RS-1, the only reported species of cultured magnetotactic bacteria that is outside of the alpha-Proteobacteria and that forms bullet-shaped crystals. Using a variety of high-resolution imaging and analytical tools, we show that RS-1 cells form amorphous, noncrystalline granules containing iron and phosphorus before forming magnetite crystals. Using NanoSIMS (dynamic secondary ion mass spectroscopy), we show that the iron-phosphorus granules and the magnetite crystals are likely formed through separate cellular processes. Analysis of the cellular ultrastructure of RS-1 using cryo-ultramicrotomy, cryo-electron tomography, and tomography of ultrathin sections reveals that the magnetite crystals are not surrounded by membranes but that the iron-phosphorus granules are surrounded by membranous compartments. The varied cellular paths for the formation of these two minerals lead us to suggest that the iron-phosphorus granules constitute a distinct bacterial organelle.

| S-EPMC2901430 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data