Genome-wide survey of gene functionality for the methanogenic archaeon Methanococcus maripaludis

Abstract

Methanogens are obligately anaerobic Archaea that obtain most of their energy required for growth from the biosynthesis of methane, or methanogenesis, a process performed only by these prokaryotes. In addition to this distinctive metabolism, methanogens exhibit many other features unique to this group of microorganisms. As one of the earliest forms of life on our planet, the study of methanogens and their particular physiology, biochemistry and genetics is not only necessary to understand this specific biological group and the Archaea domain but also provides clues about the origin and the evolutionary history of all other forms of life. A comprehensive whole-genome survey of gene function was performed in the hydrogenotrophic methanogen Methanococcus maripaludis by the Tn-seq methodology. About 30% of the genome was classified as possibly essential or strongly advantageous for growth in rich medium. Many of these genes were homologous to eukaryotic genes that encode fundamental processes in replication, transcription and translation, providing direct evidence for a close relationship between Archaea and Eukaryotes in the information processing system. However, some genes classified as possibly essential were unique to the archaeal or methanococcal lineages. Of special interest, the gene polD encoding a unique replicative DNA polymerase found in archaea was essential, indicating that it is the major replicative polymerase. In contrast, the archaeal homolog to the gene encoding the ubiquitous DNA polymerase B was not essential for growth. Interestingly, PolD is absent from the genomes of the crenarchaeotes, suggesting a clear evolutionary division within the archaeal domain. These results demonstrate a fundamental change in the replication mechanism among domains and suggest an unanticipated variability in archaeal DNA replication. Additionally, the Tn-seq technology was used to identify unknown genes involved in specific metabolic processes of M. maripaludis. Some genes possibly involved in biosynthesis of vitamins and coenzymes and the aromatic amino acids aminotransferase, among others, were detected. To get the complete picture, the next step is to corroborate the involvement of these genes in the proposed pathways by detailed genetic and biochemical studies.