Light versus Dark gene expression in SAR11
Ontology highlight
ABSTRACT:
ORGANISM(S): Candidatus Pelagibacter ubique HTCC1062 Candidatus Pelagibacter ubique HTCC1002 Candidatus Pelagibacter sp. HTCC7211
PROVIDER: GSE24134 | GEO | 2011/12/31
SECONDARY ACCESSION(S): PRJNA130131
REPOSITORIES: GEO
Similar Datasets
Project description: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). Several components of the oxidative phosphorylation pathway were up-regulated in the dark, supporting physiological data showing higher respiration rates in darkness than in the light under starvation conditions. We also observed up-regulation of a proton translocating pyrophosphate synthase (SAR11_1040), which may be an additional energy production mechanism utilized by SAR11 cells in the dark. Finally, we noted the up-regulation of pili formation genes in the array data, consistent with the observation of pili in dark grown cells via electron microscopy. Triplicate biological replicates were collected from five growth conditions (n=15 total): 1) exponential phase, 24 hour light (n=3) 2) exponential phase, 24 hour dark (n=3) 3) stationary phase, 12:12 hour light:dark cycles (n=3) 4) stationary phase, 24 hour dark (n=3) 5) stationary phase, 6 hours after transfer to darkness (n=3)
2011-12-31 | E-GEOD-24134 | biostudies-arrayexpress
Project description:Candidatus Pelagibacter ubique SAR11 HTCC9565 Genome sequencing
| PRJNA278082 | ENA
Project description: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. However, the extent of transcriptional control in Pelagibacter is unknown. Here we show that transcriptional control is extremely low in Pelagibacter and another oligotroph (SAR92) compared to two marine copiotrophic bacterial taxa, Polaribacter MED152 and Ruegeria pomeroyi. We found that ~0.1% of protein-encoding genes in Pelagibacter are under transcriptional control compared to >10% of genes in other marine bacteria. Regardless of the growth condition, the same genes were highly expressed while most genes were always expressed at very low levels. Quantitative RNA sequencing revealed that abundances of most Pelagibacter transcripts were <0.01 copies per cell whereas transcript abundances were 1 to 10 copies per cell in some other bacteria. Our results demonstrate that Pelagibacter can change growth without shifts in transcript levels, suggesting that transcriptional control plays a minimal role in the adaptive strategy for one of the most successful organisms in the biosphere.
2015-03-03 | GSE66443 | GEO
Project description: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. However, the extent of transcriptional control in Pelagibacter is unknown. Here we show that transcriptional control is extremely low in Pelagibacter and another oligotroph (SAR92) compared to two marine copiotrophic bacterial taxa, Polaribacter MED152 and Ruegeria pomeroyi. We found that ~0.1% of protein-encoding genes in Pelagibacter are under transcriptional control compared to >10% of genes in other marine bacteria. Regardless of the growth condition, the same genes were highly expressed while most genes were always expressed at very low levels. Quantitative RNA sequencing revealed that abundances of most Pelagibacter transcripts were <0.01 copies per cell whereas transcript abundances were 1 to 10 copies per cell in some other bacteria. Our results demonstrate that Pelagibacter can change growth without shifts in transcript levels, suggesting that transcriptional control plays a minimal role in the adaptive strategy for one of the most successful organisms in the biosphere. Bacteria were grown in batch culture and sampled twice during the initial, rapid phase of exponential growth and twice during the phase of slower growth that followed.
2015-03-03 | E-GEOD-66443 | biostudies-arrayexpress
Project 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.
2013-09-01 | GSE37445 | GEO
Project 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 http://omics.pnl.gov .
2013-09-01 | E-GEOD-37445 | biostudies-arrayexpress
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.
2010-05-05 | GSE20962 | GEO
Project description:In the ocean surface layer and cell culture, the polyamine transport protein PotD of SAR11 bacteria is often one of the most abundant proteins detected. Polyamines are organic cations at seawater pH produced by all living organisms and are thought to be an important component of dissolved organic matter (DOM) produced in planktonic ecosystems. We hypothesized that SAR11 cells uptake and metabolize multiple polyamines and use them as sources of carbon and nitrogen. Metabolic footprinting and fingerprinting were used to measure the uptake of five polyamine compounds (putrescine, cadaverine, agmatine, norspermidine, and spermidine) in two SAR11 strains that represent the majority of SAR11 cells in the surface ocean environment, Ca. Pelagibacter st. HTCC7211 and C. P. ubique st. HTCC1062. Both strains took up all five polyamines and concentrated them to micromolar or millimolar intracellular concentrations. Both strains could use most of the polyamines to meet their nitrogen requirements, but polyamines did not fully substitute for their requirements of glycine (or related compounds) or pyruvate (or related compounds). Our data suggests that potABCD transports all five polyamines and that spermidine synthase, speE, is reversible, catalyzing the breakdown of spermidine and norspermidine, in addition to its usual biosynthetic role. These findings provide support for the hypothesis that enzyme multifunctionality enables streamlined cells in planktonic ecosystems to increase the range of DOM compounds they metabolize.
2021-09-09 | MTBLS3146 | MetaboLights
Project description:Light versus Dark gene expression in SAR11
| PRJNA130131 | ENA
Project description: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. Two distinct responses were observed: one as DMSP approached exhaustion, and another after the DMSP supply was depleted. The first response was characterized by increased transcription and translation of all Ca. P. ubique genes downstream of previously confirmed S-adenosyl methionine (SAM) riboswitches: bhmT, mmuM, and metY. These genes were up to 33 times more abundant during low DMSP conditions and shunt all available sulfur to methionine. The osmotically inducible organic hydroperoxidase OsmC was the most up-regulated protein as DMSP (an osmolyte) became scarce. The second response, during sulfur-depleted stationary phase, saw increased transcription of the heme c shuttle ccmC and two small genes of unknown function (SAR11_1163 and SAR11_1164) which were 6-10 times higher in sulfur-starved cultures. No known membrane transporters were up-regulated in response to sulfur limitation, suggesting that this bacterium's strategy for coping with sulfur stress focuses on intracellularly redistributing, rather than importing, organic sulfur compounds. This supports the conclusion that the few organosulfur molecules that Ca. P. ubique is able to metabolize are rarely limiting in the marine environment.
2016-06-26 | GSE31630 | GEO