Sphingopyxis alaskensis RB2256
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA13907 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description: Not available
| S-EPMC3976071 | biostudies-literature
Project description:Activating the cryptic secondary metabolic gene clusters is a vital research field in Streptomyces. The marine Streptomyces sp. FJNU027 strain which could produce tirandamycins was cultured in the oligotrophic medium. Compared with normal medium, a differential product in oligotrophic culture was found by HPLC assay. After mass fermentation, 2 mg of the differential product was obtained from 30 L fermentation broth by solvent extraction, column chromatography over sephadex LH-20 and reverse phase C18, and other methods. It was identified as 4,4',5,5'-tetramethyl-[1,1'- diphenyl]-2,2'-diol by NMR and MS data. The production of this compound was enhanced with the increment of cultural time. Transcriptome sequencing analysis showed that the highest upregulated genes under oligotrophic condition were glycosidase, TraR/DksA C4-type zinc finger protein and ribonuclease encoding genes, while the expression of a MarR family transcriptional regulator was most significantly decreased under oligotrophic condition. The results indicate that oligotrophic culture is an effective method for altering the secondary metabolism of Streptomyces.
2025-12-10 | GSE278152 | GEO
Project description: Not available
| S-EPMC4528936 | biostudies-literature
Project description:Sphingopyxis alaskensis strain:BT1 13.2 Genome sequencing and assembly
| PRJNA587048 | ENA
Project description:Bacterium capable of metal corrosion
| PRJNA329 | ENA
Project description:BACKGROUND: With the aim of remaining viable, bacteria must deal with changes in environmental conditions, including increases in external osmolarity. While studies concerning bacterial response to this stress condition have focused on soil, marine and enteric species, this report is about Caulobacter crescentus, a species inhabiting freshwater oligotrophic habitats. RESULTS: A genomic analysis reported in this study shows that most of the classical genes known to be involved in intracellular solute accumulation under osmotic adaptation are missing in C. crescentus. Consistent with this observation, growth assays revealed a restricted capability of the bacterium to propagate under hyperosmotic stress, and addition of the compatible solute glycine betaine did not improve bacterial resistance. A combination of transcriptomic and proteomic analyses indicated quite similar changes triggered by the presence of either salt or sucrose, including down-regulation of many housekeeping processes and up-regulation of functions related to environmental adaptation. Furthermore, a GC-MS analysis revealed some metabolites at slightly increased levels in stressed cells, but none of them corresponding to well-established compatible solutes. CONCLUSION: Despite a clear response to hyperosmotic stress, it seems that the restricted capability of C. crescentus to tolerate this unfavorable condition is probably a consequence of the inability to accumulate intracellular solutes. This finding is consistent with the ecology of the bacterium, which inhabits aquatic environments with low nutrient concentration. Three experimental procedures, each of them performed in three replicates. A total of nine independent biological samples were used
2015-04-21 | E-GEOD-49654 | biostudies-arrayexpress
Project description:BACKGROUND: With the aim of remaining viable, bacteria must deal with changes in environmental conditions, including increases in external osmolarity. While studies concerning bacterial response to this stress condition have focused on soil, marine and enteric species, this report is about Caulobacter crescentus, a species inhabiting freshwater oligotrophic habitats. RESULTS: A genomic analysis reported in this study shows that most of the classical genes known to be involved in intracellular solute accumulation under osmotic adaptation are missing in C. crescentus. Consistent with this observation, growth assays revealed a restricted capability of the bacterium to propagate under hyperosmotic stress, and addition of the compatible solute glycine betaine did not improve bacterial resistance. A combination of transcriptomic and proteomic analyses indicated quite similar changes triggered by the presence of either salt or sucrose, including down-regulation of many housekeeping processes and up-regulation of functions related to environmental adaptation. Furthermore, a GC-MS analysis revealed some metabolites at slightly increased levels in stressed cells, but none of them corresponding to well-established compatible solutes. CONCLUSION: Despite a clear response to hyperosmotic stress, it seems that the restricted capability of C. crescentus to tolerate this unfavorable condition is probably a consequence of the inability to accumulate intracellular solutes. This finding is consistent with the ecology of the bacterium, which inhabits aquatic environments with low nutrient concentration.
2015-04-21 | GSE49654 | GEO
Project description:Polyphosphate (polyP) is a ubiquitous and evolutionarily conserved form of phosphorus (P) present in all living organisms, yet its role in cellular and biogeochemical P cycling remains poorly constrained. In P-depleted marine environments, polyP consistently represents a larger fraction of total particulate P (TPP) than in P-replete environments. This P deficiency response is paradoxical under the classical view of polyP as a luxury storage compound, highlighting a longstanding unresolved discrepancy. Whether the elevated polyP:TPP ratio reflects active accumulation under P stress or simply the persistence of this intracellular pool has never been directly tested under steady-state conditions. Using continuous cultures of the globally important marine cyanobacterium Synechococcus sp. WH8102, we address this knowledge gap. While P availability strongly affected growth rates, single-cell C:N:P stoichiometry and the expression of P-stress genes, polyP:TPP increased with decreasing growth rate, reproducing the pattern observed in oligotrophic marine environments. This shift was not driven by polyP accumulation; instead, cellular polyP concentrations remained relatively stable across growth rates (ANOVA, p = 0.16), while other intracellular P pools—including RNA, free Pi, ATP and phospholipids—were preferentially depleted with decreasing P availability (ranging from 2.6- to 11.8-fold, respectively), increasing the relative contribution of polyP to total cellular P. Gene expression analysis revealed little transcription differences between polyP-metabolism associated genes. These results indicate that cellular polyP content is maintained independently of growth rate under steady-state conditions, suggesting that P deficiency responses observed in oligotrophic environments and various microorganisms in batch culture reflect slow-growing physiology (differential pool lability over selective polyP retention), with consequences for interpreting particulate P stoichiometry and export.
2026-05-05 | GSE327000 | GEO