Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus Pelagibacter ubique

ABSTRACT: Investigation of the gene expression responses of Candidatus Pelagibacter ubique cultures to iron limitation in natural seawater media supplemented with a siderophore to chelate iron. Quantitative peptide mass spectrometry revealed that sfuC protein abundance increased 27-fold, despite an average decrease of 59% across the global proteome.

OTHER RELATED OMICS DATASETS IN: PRJNA124525

INSTRUMENT(S): LTQ Orbitrap, LTQ Orbitrap Velos

ORGANISM(S): Candidatus Pelagibacter Ubique (ncbitaxon:198252)

SUBMITTER: Stephen J. Giovannoni

PROVIDER: MSV000085445 | MassIVE | Mon May 18 21:57:00 BST 2020

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Publications

Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus pelagibacter ubique.

Smith Daniel P DP Kitner Joshua B JB Norbeck Angela D AD Clauss Therese R TR Lipton Mary S MS Schwalbach Michael S MS Steindler Laura L Nicora Carrie D CD Smith Richard D RD Giovannoni Stephen J SJ

PloS one 20100505 5

Iron is recognized as an important micronutrient that limits microbial plankton productivity over vast regions of the oceans. We investigated the gene expression responses of Candidatus Pelagibacter ubique cultures to iron limitation in natural seawater media supplemented with a siderophore to chelate iron. Microarray data indicated transcription of the periplasmic iron binding protein sfuC increased by 16-fold, and iron transporter subunits, iron-sulfur center assembly genes, and the putative f ...[more]

PMID: 20463970

Similar Datasets

Transcriptional Response to Iron Limitation in Pelagibacter ubique

Project description:We investigated the gene expression responses of Candidatus Pelagibacter ubique cultures to iron limitation. Differential expression was observed for genes in iron acquisition and incorporation operons. SfuC in particular was 16 times higher in iron-limited cultures and encodes a periplasmic iron-binding protein. Six natural seawater cultures were amended with minimal nutrients and inoculated with P. ubique. Close to maximum cell density, all carboys were supplemented with 100 nM ferrichrome (an iron-chelating siderophore) and three carboys were additionally supplemented with 1 µM FeCl3. Each of the six carboys was sampled for microarray analyses one, two, and eleven days after the ferrichrome addition.

2010-05-05 | E-GEOD-20962 | biostudies-arrayexpress

Transcriptome Profile of C. Pseudotuberculosis in Response to Iron Limitation: Differential gene expression of Iron and DtxR regulated genes

Project description:RNA-seq differential gene expression profiling of Corynebacterium pseudotuberculosis under iron limitation. We use two C. pseudotuberculosis strains, a ciuA Cp13 mutant and its parental wild type T1 strain to quantify the relative gene expression of these strains in cultures with low iron availability. The ciuA Cp13 mutant is deficient for an operon which encodes a iron siderophore uptake system. The Cp13 mutant also showed reduced virulence in CLA infection models. Due to the importance of iron for many pathogenic bacteria, our primary goal was to identified the expression profile of iron regulated genes.

2019-07-31 | GSE114125 | GEO

Transcriptomic response induced by iron limitation in the cyanobacteria Synechococcus sp. PCC 7002 (BMB04)

Project description:In this study, we characterized the homeostasis of the marine cyanobacteria Synechococcus sp. PCC7002 (BMB04) growing in chemically characterized synthetic seawater with three different levels of iron limitation representative of the modern ocean. Using transcriptomic approach, we identified the sequence of physiological responses to increasing Fe limitation. Our results showed an increase in the number of dysregulated genes and in the complexity of the response to increasing Fe limitation. Genes involved in photosynthesis were strongly down-regulated under MiFeL, while membrane transporters were up-regulated. Genes involved in regulation of energy metabolism responded under strong Fe limitation, while fine metabolic regulation of co-factors expression and activation of specific cellular mechanisms to minimize oxidative stress were only observed under severe Fe limitation. Additionally, our results demonstrate the limitations in the construct of the bioreporter BMB04 that hamper its application in areas of the ocean strongly Fe limited.

2017-01-30 | GSE77354 | GEO

Transcriptional Response to Iron Limitation in Pelagibacter ubique

2010-05-05 | GSE20962 | GEO

Clostridium difficile response to iron limitation

Project description:Clostridium difficile response to iron limitation

| PRJNA430909 | ENA

Five diatoms transcriptomes under iron limitation and oxidative stress

Project description:Divergent functions of two clades of flavodoxin in diatoms mitigate oxidative stress and iron limitation Thalassiosira pseudonana and 4 open-ocean diatoms were subjected to iron limitation or short-term oxidative stress (hydrogen peroxide). mRNA profiles of T. pseudonana (CCMP1335), Thalassiosira oceanica (CCMP1005), Amphora coffeaeformis (CCMP1405), Chaetoceros sp. (CCMP199), and Cylindrotheca closterium (CCMP340).

2022-11-07 | GSE217467 | GEO

Differential expression of genes in the WT and hupB KO strain of Mycobacterium tuberculosis H37Rv upon iron limitation

Project description:HupB is a 28 kDa in Mycobacterium tuberculosis that is co-expressed with the siderophores mycobactin and carboxymycobactin upon iron limitation. High levels of all the three components are seen in low iron (LI; 0.02 µg Fe / mL) organisms, with negligible expression in high iron organisms (HI; 8 µg Fe / mL). We generated a hupB knock out mutant of M. tuberculosis (H37Rv ∆ hupB) and studied the differential expression of genes upon iron limitation in the WT H37Rv and the mutant. The RNA transcripts of the WT H37Rv, grown under high and low iron conditions of growth were isolated and subjected to microarray analysis to identify the iron-regulated genes and second, the differential expression of genes in iron-limited H37Rv ∆ hupB vs iron-limited WT H37Rv was analysed. Microarray analysis was done commercially by Genotypic Technology (Bangalore, India), an authorised service provider for Agilent Technologies. The study revealed the up-regulation of all the mbt genes of the mycobactin biosynthetic machinery in LI - H37Rv and several other reported iron-regulated genes. The salient feature of this study is the failure of LI - H37Rv ∆ hupB to show any up-regulation of the mbt genes as compared to LI - H37Rv. Among several other genes influenced by HupB, the mutant strain showed low levels of mmpL5 and mmpS5 transcripts, whose expressed products are reported to be associated with siderophore transport and biosynthesis.

2014-03-18 | GSE53254 | GEO

Identification of Francisella tularensis genes affected by iron limitation

Project description:Three pairs of total RNA preparations from F. t. LVS grown under iron-replete and iron-restricted conditions were used in the DNA microarray. Seven arrays were used to examine the genes affected by iron limitation. Keywords: Dual Channel (Cy5/Cy3) arrays

2006-07-26 | GSE3622 | GEO

The Graded Response of Fur Regulon to Iron Limitation in Bacillus subtilis

Project description:Bacterial cells often modulate their transcriptional profiles in response to the changes in iron availability. Ferric uptake regulator (Fur), as a global iron biosensor, plays a central role in maintaining iron homeostasis in Bacillus subtilis. Here we utilized a high affinity Fe2+ efflux transporter, Listeria monocytogenes FrvA, as an inducible genetic tool to deplete intracellular iron. We then characterized the responses of the Fur, FsrA, and PerR regulons as cells transition from iron sufficiency to deficiency. Our results indicate that the Fur regulon is derepressed in three distinct waves. First, elemental iron uptake (ywbLMN), ferric citrate uptake (ymfCDEF-yhfQ), and petrobactin uptake (yclNOPQ) systems are induced to prevent iron deficiency. Second, B. subtilis synthesizes its own siderophore bacillibactin (dhbACEBF) and turns on bacillibactin uptake (feuABC-yusV) along with flavodoxin (ykuNOP) and hydroxamate siderophore uptake (fhuBCGD-yxeB) to scavenge iron from the environment. Third, as iron levels decline further, an iron sparing response (fsrA, fbpAB, and fbpC) is induced to block the translation of nonessential iron-using proteins and permit only essential iron-dependent enzymes to utilize the limited iron. ChIP experiments demonstrate that in vivo occupancy of Fur correlates with derepression of each operon, and the graded response observed here results, at least in part, from higher affinity binding of Fur to the late induced genes. These results provide insights into the distinct roles of Fur-regulated target genes as intracellular iron levels decline.

2017-06-30 | GSE100668 | GEO

Differential expression of genes in the WT and hupB KO strain of Mycobacterium tuberculosis H37Rv upon iron limitation

Project description:HupB is a 28 kDa in Mycobacterium tuberculosis that is co-expressed with the siderophores mycobactin and carboxymycobactin upon iron limitation. High levels of all the three components are seen in low iron (LI; 0.02 M-BM-5g Fe / mL) organisms, with negligible expression in high iron organisms (HI; 8 M-BM-5g Fe / mL). We generated a hupB knock out mutant of M. tuberculosis (H37Rv M-bM-^HM-^F hupB) and studied the differential expression of genes upon iron limitation in the WT H37Rv and the mutant. The RNA transcripts of the WT H37Rv, grown under high and low iron conditions of growth were isolated and subjected to microarray analysis to identify the iron-regulated genes and second, the differential expression of genes in iron-limited H37Rv M-bM-^HM-^F hupB vs iron-limited WT H37Rv was analysed. Microarray analysis was done commercially by Genotypic Technology (Bangalore, India), an authorised service provider for Agilent Technologies. The study revealed the up-regulation of all the mbt genes of the mycobactin biosynthetic machinery in LI - H37Rv and several other reported iron-regulated genes. The salient feature of this study is the failure of LI - H37Rv M-bM-^HM-^F hupB to show any up-regulation of the mbt genes as compared to LI - H37Rv. Among several other genes influenced by HupB, the mutant strain showed low levels of mmpL5 and mmpS5 transcripts, whose expressed products are reported to be associated with siderophore transport and biosynthesis. One-color experiment,Organism: Mycobacterium tuberculosis ,Custom Mycobacterium tuberculosis 8x15k Array designed byGenotypic Technology Private Limited (AMADID: 20181), Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

2014-03-18 | E-GEOD-53254 | biostudies-arrayexpress

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