a Whole Genome Array Approach - Jacobs University

Research Aims
2.2 Expression profiling of the sulphatases genes of the
planctomycete Rhodopirellula baltica grown on different sulphated
polysaccharides
The carbon cycle in natural environments depends on the remineralisation of biomass. In
marine systems biomass is mainly produced by phototrophic microorganisms in the upper
layer of the water column (annual production of 20 − 30 × 10 9 tons of carbon). Dead biomass
settles to the sediment, often aggregating as particles known as marine snow. During this
process, organic carbon is already decomposed by aerobic microorganisms (Rullkötter 1999).
Since polysaccharides are major components of biomass, carbohydrate degradation is
particularly relevant for carbon turnover. R. baltica and other members of the Planctomycetes
are considered key players in carbohydrate metabolism in marine systems, because of their
nutritional specialisation, their high abundance in the marine water column and their
association with marine snow, and also the high number of sulphatases genes found in their
genome.
The role of the sulphatases however, is still unclear. The presence of 110 sulphatase genes of
unknown physiological role in the R. baltica genome represents an ideal starting point for
further functional analysis. Expression profiling of the 110 sulphatase genes and enzymes
from associated pathways (ECF-sigma factor, sugar degradation) in R. baltica provides a
deeper view of the regulation and expression of bacterial sulphatases and their role in the
natural habitat of the organism. First expression profiling experiments on a partial genome
array were carried out with chemically labelled cDNA extracted from R. baltica cultures
grown on glucose and N-acetylglucosamine, ribose and chrondroitinsulphate A and C.
Although some differences in the expression patterns could be detected it could also be seen
that most of the sulphatases under investigation were already expressed during cultivation
with glucose (reference) (Würdemann 2006). The reason for their obvious constitutive
expression is unclear. Further microarray experiments with R. baltica cultures grown on
different oligosaccharides allow specification of the substrate preference of different
sulphatases. The different polysaccharides derived from different marine macroalgae are
provided by cooperation with the CNRS – Laboratoires GOËMAR – UPMC of Prof.
B. Kloareg in Roscoff: iota- and kappa carrageenan (Rhodophyta) (Barbeyron et al. 2000),
alginate and fucane (Phaeophyta) (Descamps et al. 2005).
Bioinformatic analysis based on the similarity comparison of the sulphatase genes found in all
available Planctomycete genomes and in the genome of the marine bacteroidetes
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