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

该古菌的全基因组序列已被确定并注释。基因破坏系统已经发展和改进，用于快速和多基因破坏。全基因组DNA微阵列也被开发用于转录组研究。我们已经能够阐明各种假设的蛋白质的功能，并确定各种缺失的基因。柯达卡拉霉可以利用多种有机化合物生长，包括聚（寡）糖、多肽、氨基酸和丙酮酸。这种古菌利用改良的Embden-Meyerhof途径进行糖酵解，我们研究了参与将3-磷酸甘油醛转化为3-磷酸甘油酸酯和磷酸烯醇丙酮酸酯转化为丙酮酸酯的酶。在糖异生方面，我们对关键酶果糖-1,6-二磷酸酶进行了生化和遗传分析。参与糖原生产的酶也已被确定，以及甲壳素的一种新的降解途径。在细菌和真核生物中，戊糖和核苷酸的合成是必需的，而T.kodakaraensis没有完整的戊糖磷酸途径对应的基因。相反，我们发现单磷酸核酮糖途径的反向通量负责该生物体的戊糖合成。通过对III型Rubiscos生理作用的研究，我们发现了一种可能涉及回收多余戊糖碳并将其重定向回糖酵解的新途径。在氨基酸代谢方面，我们发现基因组上存在的5种乙酰辅酶a合成酶类似物编码的乙酰辅酶a合成酶具有不同的底物特异性。我们还确定了负责控制T.kodakaraensis糖酵解和糖异生模式生长的调节因子。

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.