Abstract
DNA microarray technology allows for a quick and easy comparison of complete transcriptomes, resulting in improved molecular insight in fluctuations of gene expression. After emergence of the microarray technology about a decade ago, the technique has now matured and has become routine in many molecular biology laboratories. Numerous studies have been performed that have provided global transcription patterns of many organisms under a wide range of conditions. Initially, implementation of this high-throughput technology has lead to high expectations for ground breaking discoveries. Here an evaluation is performed of the insight that transcriptome analysis has brought about in the field of hyperthermophilic archaea. The examples that will be discussed have been selected on the basis of their impact, in terms of either biological insight or technological progress.
Highlights
Thermophilic organisms can be found in watercontaining geothermally heated environments
The comparative analysis of the genome of the hyperthermophilic bacterium Thermotoga maritima to Pyrococcus furiosus (both isolated from shallow thermal vents at the same beach (Volcano, Italy)) led to the conclusion that horizontal gene transfer substantially contributes to the apparent high degree of genome flexibility [13, 14]
As biochemical pathways of archaea can be very different from their bacterial/eukaryotic counterparts, DNA microarrays in combination with the currently established gene disruption techniques for Sulfolobus spp. [117] and Thermococcus kodakaraensis [118] may provide a solid basis for subsequent analyses
Summary
Forty years ago it was generally accepted that life was not possible at temperatures higher than 60◦C. Progress in culturing thermophilic archaea and in the revolution of DNA sequencing technology has resulted in a rapidly increasing amount of (meta)genomic data on these extreme microorganisms. This has led to the discovery of robust biocatalysts and to fundamental insight into (i) physiology: including unique metabolic enzymes, pathways, and regulation [5,6,7], (ii) biochemistry: the molecular basis of thermostability of biomolecules [8,9,10], and (iii) phylogeny: theories on the evolution of the eukaryotic cell [11]. Obvious targets of comparative and functional analysis of archaeal genomes are the numerous missing links in metabolic pathways as well as the largely unknown regulatory systems with either eukaryal or bacterial characteristics [5, 6]
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