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Title: Transcriptional Response to Nitrogen Limitation in Pelagibacter ubique      
dateReleased:
09-01-2013
description:
Nitrogen is one of the major nutrients limiting microbial productivity in the ocean, and as a result marine microorganisms have evolved specialized systems for responding to nitrogen stress. The highly abundant alphaproteobacterium Candidatus Pelagibacter ubique lacks the canonical GlnB, GlnD, and NtrB/NtrC genes for regulating nitrogen assimilation. A survey of 127 Alphaproteobacteria genomes found these genes to be highly represented in free-living and pathogenic organisms with large genomes and only missing in a subset of obligate intracellular organisms and other SAR11 strains. We examined global differences in mRNA and protein expression in Ca. P. ubique strain HTCC1062 during nitrogen-limited and nitrogen-replete stationary phase to understand how this thriving organism responds to nitrogen limitation. Transporters for ammonium (AmtB), taurine (TauA), amino acids (YhdW), and opines (OccT) were all elevated in nitrogen-limited cells, indicating they devote increased resources to the assimilation of nitrogenous compounds. Enzymes for assimilating amine into glutamine (GlnA) and glutamate (AspC, GltBD) were similarly up-regulated. Differential regulation of the transcriptional regulator NtrX in the two-component signaling system NtrY/NtrX was also observed, implicating it in the control of the nitrogen starvation response. Comparisons of the transcriptome and proteome suggest that Amt is post-transcriptionally repressed during nitrogen limitation, supporting previous studies that computationally identified a novel cis-acting riboswitch upstream of this gene. These observations support the conclusion that Ca. P. ubique has an unusually simple regulatory system that enables it to increase its capacity for the uptake of nitrogenous compounds in response to nitrogen limitation. Batch cultures of P. ubique were grown in a defined arificial seawater media. Three cultures were given no nitrogen amendment, and three other cultures received an excess concentration of NH3. Cultures were harvested for microarray analyses during log and stationary phase for the purpose of observing differences in gene expression related to nitrogen limitation. Proteomic analysis was conducted in parallel and is available at .
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-37445
refinement:
raw
alternateIdentifiers:
37445
keywords:
functional genomics
dateModified:
09-26-2013
availability:
available
types:
gene expression
name:
Candidatus Pelagibacter ubique
ID:
A-GEOD-7330
name:
Candidatus Pelagibacter ubique OSU_SAR11_affychip
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-37445/E-GEOD-37445.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-37445/E-GEOD-37445.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37445
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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