GEO DataSets

(Submitter supplied) Candidatus Pelagibacter ubique is the most abundant marine microorganism, but is unable to utilize inorganic sulfur compounds that are plentiful in the ocean. To investigate how these cells adapt to organic sulfur limitation, batch cultures were grown in defined media containing either limiting or non-limiting amounts of dimethylsulfoniopropionate (DMSP) as the sole sulfur source. Protein and mRNA expression were measured during exponential growth, immediately prior to stationary phase, and in late stationary phase. more...

Organism:

Candidatus Pelagibacter ubique HTCC1002; Candidatus Pelagibacter ubique HTCC1062; Candidatus Pelagibacter sp. HTCC7211

Type:

Expression profiling by array

Platform:

GPL7330

29 Samples

Download data: CEL

(Submitter supplied) Bacteria respond to stimuli in the environment using transcriptional control, but this may not be the case for most marine bacteria having small, streamlined genomes. Candidatus Pelagibacter ubique, a cultivated representative of the SAR11 clade, which is the most abundant clade in the oceans 4, has a small, streamlined genome and possesses an unusually small number of transcriptional regulators. This observation leads to the hypothesis that transcriptional control is low in Pelagibacter and limits its response to environmental conditions. more...

Organism:

Polaribacter sp. MED152; Candidatus Pelagibacter ubique HTCC1062; Ruegeria pomeroyi DSS-3; gamma proteobacterium HTCC2207

Type:

Expression profiling by high throughput sequencing

4 related Platforms

44 Samples

Download data: XLSX

(Submitter supplied) Recent studies have shown that Pelagibacter oxidize a wide range of one carbon (C1) and methylated compounds that are ubiquitous in the oceans. However, the metabolic pathways used to oxidize and assimilate these compounds are complex and have been only partly described. To understand the metabolism of these compounds in Pelagibacter and to identify candidate genes involved in these pathways, we used microarray to study changes in gene expression in response to five different compounds (trimethylamine N-oxide (TMAO), methylamine, dimethylsulfoniopropionate (DMSP), methanol, and glycine betaine (GBT)) in Pelagibacter strain HTCC1062.

Organism:

Candidatus Pelagibacter ubique HTCC1062; Candidatus Pelagibacter sp. HTCC7211; Candidatus Pelagibacter ubique HTCC1002

Type:

Expression profiling by array

Platform:

GPL7330

18 Samples

Download data: CEL

(Submitter supplied) Thiamine is often undetectable in ocean surface waters where Pelagibacter cells are numerically abundant. Despite this, Pelagibacter cells are missing de novo thiamine synthesis pathways. We show that an eogenous source of the thiamine precursor HMP is required for thiamine synthesis in Pelagibacter and that this precursor is abundant in the Sargasso sea.

Organism:

Candidatus Pelagibacter ubique HTCC1062; Candidatus Pelagibacter ubique HTCC1002; Candidatus Pelagibacter sp. HTCC7211

Type:

Expression profiling by array

Platform:

GPL7330

12 Samples

Download data: CEL

(Submitter supplied) Responses of Pelagibacterales strains to phosphate limitation

Organism:

Candidatus Pelagibacter ubique HTCC1002; Candidatus Pelagibacter ubique HTCC1062; Candidatus Pelagibacter sp. HTCC7211

Type:

Expression profiling by array

Platform:

GPL7330

54 Samples

Download data: CEL

(Submitter supplied) 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. more...

Organism:

Candidatus Pelagibacter ubique HTCC1002; Candidatus Pelagibacter ubique HTCC1062; Candidatus Pelagibacter ubique; Candidatus Pelagibacter sp. HTCC7211

Type:

Expression profiling by array

Platform:

GPL7330

12 Samples

Download data: CEL

(Submitter supplied) We investigated the transcriptional response of cand. Pelagibacter ubique cultures to light and dark when grown under carbon replete and deplete conditions. Results: During exponential phase, few genes were differentially transcribed between light:dark growth conditions. In stationary phase, a high proportion (9.7%) of coding sequences were found differentially expressed between treatments; 4.7% being up-regulated in the light (n=64) and 4.9% being up-regulated in the dark (n=67). more...

Organism:

Candidatus Pelagibacter sp. HTCC7211; Candidatus Pelagibacter ubique HTCC1002; Candidatus Pelagibacter ubique HTCC1062

Type:

Expression profiling by array

Platform:

GPL7330

15 Samples

Download data: CEL, CHP

(Submitter supplied) 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.

Organism:

Candidatus Pelagibacter ubique HTCC1062; Candidatus Pelagibacter sp. HTCC7211; Candidatus Pelagibacter ubique HTCC1002

Type:

Expression profiling by array

Platform:

GPL7330

18 Samples

Download data: CEL

(Submitter supplied) The primary goal of this experiment is to examine the transcription profiles of HTCC1062 when grown in the presence or absence of D-glucose (30uM final concentration). Experiment confirmed activity of predicted glycolysis operon.

Organism:

Candidatus Pelagibacter ubique HTCC1002; Candidatus Pelagibacter sp. HTCC7211; Candidatus Pelagibacter ubique HTCC1062

Type:

Expression profiling by array

Platform:

GPL7330

6 Samples

Download data: CEL, CHP

(Submitter supplied) Oligos designed using sequences from three SAR11 genomes (HTCC1062, 1002, 7211) as well as highly similar sequences from the first metagenomic GOS survey (Venter et al. 2004). No mismatch probes are included on the chip. All probes target biotin-labeled antisense-RNA. Probes hard pruned against 16s and 23s rRNA genes. Affy description of production (from website): GeneChip microarrays are a classic Silicon Valley innovation, combining several disciplines to create a new technology and more useful research tool. more...

Organism:

Candidatus Pelagibacter ubique HTCC1002; Candidatus Pelagibacter ubique HTCC1062; Candidatus Pelagibacter sp. HTCC7211

8 Series

164 Samples

Download data: CDF