Novipirellula maiorica
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ABSTRACT:
PROVIDER: PRJNA183076 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We present a study combining gene expression analyses and bioinformatic assessment. 1120 sequences annotated as sulfatase encoding from eight Rhodopirellula strains were clustered into 173 groups of orthologous and paralogous genes. A selection of 709 sulfatase gene strains were aligned to 66 sulfatase genes of known function to check for their respective substrate specificity. Thereby, 22 major phylogenetic clusters were observed with just five being mixed clusters between Rhodopirellula and reference sequences. This indicates a huge diversity on the substrate recognition level, unexpected from conventional annotations in public databases. Exemplarily, Rhodopirellula baltica SH1T was grown on different sulfated polysaccharides. Subsequent gene expression analyses using whole genome microarrays revealed distinct sulfatase expression profiles based on substrates tested. Expression profiles strongly point towards a functional link between sulfated polysaccharides and sulfatases. Moreover, further potential functions can be deduced from the expression profiles. In silico assessment backed up in vivo findings and raised the question, whether related strains and species are even more adapted to utilizing sulfated polysaccharides present in marine environments.
2012-04-01 | GSE35832 | GEO
Project description:Expression profiling of the stress response of the marine Planctomycete Rhodopirellula baltica after a temperature up-shift. R. baltica cultures were grown at 28°C and then shifted to 6°C. Samples were taken after 10, 20, 40, 60 and 300min and compared with cultures before the up-shift (28°C).
2009-09-09 | GSE13856 | GEO
Project description:We present a study combining gene expression analyses and bioinformatic assessment. 1120 sequences annotated as sulfatase encoding from eight Rhodopirellula strains were clustered into 173 groups of orthologous and paralogous genes. A selection of 709 sulfatase gene strains were aligned to 66 sulfatase genes of known function to check for their respective substrate specificity. Thereby, 22 major phylogenetic clusters were observed with just five being mixed clusters between Rhodopirellula and reference sequences. This indicates a huge diversity on the substrate recognition level, unexpected from conventional annotations in public databases. Exemplarily, Rhodopirellula baltica SH1T was grown on different sulfated polysaccharides. Subsequent gene expression analyses using whole genome microarrays revealed distinct sulfatase expression profiles based on substrates tested. Expression profiles strongly point towards a functional link between sulfated polysaccharides and sulfatases. Moreover, further potential functions can be deduced from the expression profiles. In silico assessment backed up in vivo findings and raised the question, whether related strains and species are even more adapted to utilizing sulfated polysaccharides present in marine environments. Dual channel microarrays have been used for comparing the gene expression of R. baltica SH1T under reference condition (grown on glucose) and grown on sulfated polysaccharides as substrates of interest. Substrates tested have been: Chondroitin sulfate, lambda carrageenan and fucoidan. Control: 3 Biological replicates, Substrates tested: 2-3 Biological replicates, 2-3 replicates per array
2012-03-31 | E-GEOD-35832 | biostudies-arrayexpress
Project description:Expression profiling of the stress response of the marine Planctomycete Rhodopirellula baltica after a salinity up-shift. R. baltica cultures were grown at 28°C in mineral media with 17.5% salinity and up-shifted to 59.9%. Samples were taken after 10, 20, 40, 60 and 300min and compared with cultures before the up-shift.
2009-09-09 | GSE14075 | GEO
Project description:Expression profiling of the stress response of the marine Planctomycete Rhodopirellula baltica after a temperature up-shift. R. baltica cultures were grown at 28°C and then shifted to 37°C. Samples were taken after 10, 20, 40, 60 and 300min and compared with cultures before the up-shift (28°C). Time series experiment, whole genome array
2009-09-09 | GSE13769 | GEO
Project description:Rhodopirellula sp. PMP Genome sequencing
| PRJNA1086377 | ENA