Insights into the Autotrophic CO ₂ Fixation Pathway of the Archaeon Ignicoccus hospitalis : Comprehensive Analysis of the Central Carbon Metabolism

Abstract

Ignicoccus hospitalis is an autotrophic hyperthermophilic archaeon that serves as a host for another parasitic/ symbiotic archaeon, Nanoarchaeum equitans. In this study, the biosynthetic pathways of I. hospitalis were investigated by in vitro enzymatic analyses, in vivo 13 C-labeling experiments, and genomic analyses. Our results suggest the operation of a so far unknown pathway of autotrophic CO 2 fixation that starts from acetyl-coenzyme A (CoA). The cyclic regeneration of acetyl-CoA, the primary CO 2 acceptor molecule, has not been clarified yet. In essence, acetyl-CoA is converted into pyruvate via reductive carboxylation by pyruvateferredoxin oxidoreductase. Pyruvate-water dikinase converts pyruvate into phosphoenolpyruvate (PEP), which is carboxylated to oxaloacetate by PEP carboxylase. An incomplete citric acid cycle is operating: citrate is synthesized from oxaloacetate and acetyl-CoA by a (re)-specific citrate synthase, whereas a 2-oxoglutarateoxidizing enzyme is lacking. Further investigations revealed that several special biosynthetic pathways that have recently been described for various archaea are operating. Isoleucine is synthesized via the uncommon citramalate pathway and lysine via the ␣-aminoadipate pathway. Gluconeogenesis is achieved via a reverse Embden-Meyerhof pathway using a novel type of fructose 1,6-bisphosphate aldolase. Pentosephosphates are formed from hexosephosphates via the suggested ribulose-monophosphate pathway, whereby formaldehyde is released from C-1 of hexose. The organism may not contain any sugar-metabolizing pathway. This comprehensive analysis of the central carbon metabolism of I. hospitalis revealed further evidence for the unexpected and unexplored diversity of metabolic pathways within the (hyperthermophilic) archaea.

Study of the distribution of autotrophic CO2 fixation cycles in Crenarchaeota

“…3). These data are in line with the presence of the biotindependent carboxylases in all Sulfolobales studied so far (Norris et al, 1989;Burton et al, 1999;Ishii et al, 1996;Chuakrut et al, 2003;Hügler et al, 2003a, b;Menendez et al, 1999) as well as with the absence of these proteins and the corresponding genes in the sequenced Desulfurococcales genomes (Hügler et al, 2003a;Jahn et al, 2007;Anderson et al, 2009;Brügger et al, 2007;Kawarabayasi et al, 1999;Podar et al, 2008;Ravin et al, 2009).…”

“…The last two pathways were described recently in the (hyper)thermophilic autotrophic Crenarchaeota and, up to now, are restricted to this group of Archaea (Norris et al, 1989;Ishii et al, 1996;Burton et al, 1999;Menendez et al, 1999;Berg et al, 2007;Jahn et al, 2007;Huber et al, 2008;Ramos-Vera et al, 2009;Hügler et al, 2003a, b).…”

“…All Crenarchaeota studied so far use either the 3-hydroxypropionate/4-hydroxybutyrate cycle or the dicarboxylate/4-hydroxybutyrate cycle, as has been experimentally shown for Metallosphaera sedula (Sulfolobales), Ignicoccus hospitalis (Desulfurococcaceae, Desulfurococcales) and Thermoproteus neutrophilus (Thermoproteales), and generalized based on whole-genome comparisons Jahn et al, 2007;Huber et al, 2008;Ramos-Vera et al, 2009). These pathways have in common the synthesis of succinyl-CoA from acetyl-CoA and two inorganic carbons, although this is accomplished in quite different ways and using different carboxylases (Fig.…”

A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis

“…The shortest generation time of the organism grown at 90°C under autotrophic conditions (H 2 , CO 2 , and elemental sulfur) is 1 h (1,4). This indicates that the specialized metabolism also is highly streamlined.…”

Synthetic biology for CO2 fixation

“…One molecule each of CO2 and Oleary, 1982), demonstrating its high affinity for HCO3 -. Notably, the doubling time of autotrophic archaea Ignicoccus hospitalis, which utilizes this CO2-fixation pathway, is only 1 h under optimal growth conditions (Jahn et al, 2007). This may be partly contributed by the strong affinity of phosphoenolpyruvate carboxylase.…”