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Title: Combining transcriptomics with functional phylogenomics elucidates the ecophysiology of sulfatases in marine bacteria      
dateReleased:
03-31-2012
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
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-35832
refinement:
raw
alternateIdentifiers:
35832
keywords:
functional genomics
dateModified:
05-02-2014
availability:
available
types:
gene expression
name:
Rhodopirellula baltica
ID:
A-GEOD-7654
name:
Max Planck Institute, Whole Genome Array for Rhodopirellula baltica SH1T 7.4K version 1
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-35832/E-GEOD-35832.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-35832/E-GEOD-35832.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=GSE35832
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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