Microarray analysis to unravel Microbial Metabolism
11 / 2003 - 11 / 2007
To understand life, we need to study it. Many processes, which are crucial for most forms of live, are conserved throughout nature. Because these processes are usually very complex, we try to study these processes in organisms, in which these processes are simplified. This automatically leads to the study of prokaryotes, which are less complex then most Eukaryotes. They also have the benefit of being unicellular and thus easier to grow and manipulate in a lab environment. Genetic based approaches are becoming more and more dominant in many studies. Here, prokaryotes also have the benefit of having a relative simple and streamlined genetic makeup and control. They do not have introns, making an one-to-one comparison between genes and proteins possible, many genes are situated in operons, small clusters of functionally related genes, making prediction of genefunction easier and the frequent positioning of transcriptional regulators in close proximity to the genes that they regulate are additional benefits of prokaryotic genome organization. In this project we have chosen to study the expression of genes using microarray technology. This technology makes it possible to have an unbiased look at the cellular gene responses that cells exhibit in different situations. This will not only give us the opportunity to understand generegulation on a cellular level, but will also give us the possibility to link genes with an unknown function to a now known function. For this project we have chosen an Archaeal model organism called Sulfolobus solfataricus. [Archaea]: Live on earth is divided in three domains: the Eukarya, the Bacteria and the Archaea. Archaea, or the third domain of life, typically inhabit extreme environments, unsuitable for Bacteria and Eukaryotes. While Archaea are prokaryotic and exhibit many bacterial like features, the molecular mechanisms of DNA replication, transcription and translation, are more like those present in eukaryotic organisms, making them a good type of organism to study these processes in a more or less simplified form. One of the Archaeal model organisms and the organism we have chosen to study is the thermophile Sulfolobus solfataricus. It grows aerobically, at an optimum temperature of 80oC and it has a pH range of 2-5. It can be found in thermal heated springs all over the world (one of those hotsprings is the Grand Prismatic Spring in Yellowstone National Park). The small 3 Mbase genome of S. solfataricus was sequenced in 2001 and recently (2004) a microarray system has been developed. Using bioinformatic tools and the newly developed microarray system, we try to understand more the about gene expression in Archaea and we try to link the expression data, obtained from the microarray experiments, to cellular processes.