a Whole Genome Array Approach - Jacobs University

THESIS ABSTRACT
Since the first microbial genome has been finished in the year 1995 more than 800 sequenced
microorganisms are publicly available and many more are on their way. Sophisticated
bioinformatic (in silico) analysis of the sequence information is required to process this huge
amount of data and to generate sound hypotheses in terms of physiology and ecology of an
organism as well as to efficiently screen for candidate genes for biotechnological relevant
enzymes. Current success to directly obtain sequence information from the environment
without former cultivation (the metagenomic approach) even speeds up the process. The most
prominent in the marine field being the Venter Sargasso Sea expedition in 2004 delivering
more than 1.2 million new genes. The introduction of new sequencing technologies, such as
pyrosequencing will soon enable biologists to perform sequencing on a daily basis.
However, high-throughput lab-methods, implemented by the DNA microarray technology, are
more than ever required for the subsequent verification of initial bioinformatic findings and
hypotheses. Post-genomic approaches like DNA microarrays have revolutionised molecular
biology by enabling a new dimension of parallelism in expression profiling.
Eight years ago, under the light of the up-coming cutting-edge technologies of the genomic
era, the Max Planck Institute for Marine Microbiology in Bremen has initiated a genomics
project for the complete genome sequencing and analysis of environmental relevant marine
bacteria. Rhodopirellula baltica SH 1 T was selected as a marine representative of the globally
distributed and environmentally important bacterial phylum Planctomycetales. It is a model
organism for aerobic carbohydrate degradation in marine systems, where polysaccharides
represent the dominant components of biomass.
The complete genome sequence of R. baltica has been determined and functional annotation
was performed. However, pure in silico predictions left about 55% of the genes without
functional assignment. The availability of the whole genome sequence has already stimulated
a set of follow-up studies ranging from proteomics to protein crystallisation as well as
biotechnological applications.
This work presents the establishment of, and the results gained with, the first whole genome
microarray for a Planctomycete. It shows that massive expression profiling under defined
environmental conditions can take the challenge to bridge the gap between classical studies on
the cell biology and physiology of Planctomycetes and their active genetic repertoire.
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