Total functional genomics of the hyperthermophilic archaeon, T.kodakaraensis KOD1

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The entire genome sequence of this archaeon has been determined and annotated. Gene disruption systems have been developed and improved for rapid and multiple gene disruption. A whole genome DNA microarray has also been developed for transcriptome studies. We have been able to elucidate the function of various hypothetical proteins and identify various missing genes. T.kodakaraensis can utilize a variety of organic compounds for growth, which include poly(oligo)saccharides, peptides, amino acids and pyruvate. This archaeon utilizes the modified Embden-Meyerhof pathway for glycolysis, and we have examined the enzymes involved in the conversion of glyceraldehyde 3-phosphate to 3-phosphoglycerate, and phosphoenolpyruvate to pyruvate. In terms of gluconeogenesis, we have performed a biochemical and genetic analysis on the key enzyme fructose-1,6-bisphosphatase. Enzymes involved in the production of glycogen have also been identified, as well as a novel degradation pathway for chitin. T.kodakaraensis does not harbor a complete set of genes corresponding to the pentose phosphate pathway, necessary for pentose and nucleotide synthesis in bacteria and eukaryotes. We instead found that a reverse flux of the ribulose monophosphate pathway is responsible for pentose synthesis in this organism. Through investigations on the physiological role of Type III Rubiscos, we have identified a novel pathway that may be involved in retrieving excess pentose carbon and redirecting it back to glycolysis. In terms of amino acid metabolism, we found that the five acetyl-CoA synthetase paralogs present on the genome encode acyl-CoA synthetases with distinct substrate specificities. We have also identified the regulator that is responsible for controlling glycolytic and gluconeogenic modes of growth in T.kodakaraensis.