Biochemical and genetic examination of two aminotransferases from the hyperthermophilic archaeon Thermococcus kodakarensis

Exploration of formate as a liquid organic hydrogen carrier in biohydrogen production through evolutionary and process engineering of hyperthermophilic archaeon

Hydrogen (H2) is considered a promising renewable energy source, but its storage and delivery present significant challenges. Liquid organic hydrogen carriers (LOHC) offer a potential solution to this problem, with formate as a top candidate for LOHC. This study focused on developing technology for biological H2 production from formate by utilizing the hyperthermophilic archaeon Thermococcus onnurineus NA1. An engineered strain, WTF-350 T, was developed through adaptive evolution using formate and exhibited 3.6-4.0 times enhanced cell growth, formate consumption, and H2 production compared to the wild-type strain. Optimizing fermentation processes through pH-stat, fed-batch mode, and pyruvate supplementation led to a 2.0-2.5 times increase in cell density and H2 production rate. Moreover, formic acid, produced by the electroreduction of carbon dioxide (CO2), was found to be an effective feedstock for biohydrogen production. This study successfully demonstrated the potential of integrating CO2 electroreduction and biohydrogen production for a sustainable hydrogen economy.

TK2268 encodes the major aminotransferase involved in the conversion from oxaloacetic acid to aspartic acid in Thermococcus kodakarensis

Amino acid metabolism in archaea in many cases differs from those reported in bacteria and eukaryotes. The hyperthermophilic archaeon Thermococcus kodakarensis possesses an incomplete tricarboxylic cycle, and the biosynthesis pathway of aspartate is unknown. Here, four Class I aminotransferases in T. kodakarensis encoded by TK0186, TK0548, TK1094, and TK2268 were examined to identify the enzyme(s) responsible for the conversion of oxaloacetate to aspartate. Among the four proteins, the TK2268 protein (TK2268p) was the only protein to recognize oxaloacetate as the amino acceptor. With oxaloacetate, TK2268p only recognized glutamate as the amino donor. The protein also catalyzed the reverse reaction, the transamination between aspartate and 2-oxoglutarate. Substrate inhibition was observed in the presence of high concentrations of oxaloacetate or 2-oxoglutarate. Aminotransferase activity between oxaloacetate and glutamate was observed in cell extracts of the T. kodakarensis host strain KU216. Among the individual gene disruption strains of the four aminotransferases, a significant decrease in activity was only observed in the ΔTK2268 strain. T. kodakarensis KU216 does not display growth in synthetic amino acid medium when aspartate/asparagine are absent. Growth was restored upon the addition of both oxaloacetate and glutamate. Although this restoration in growth was maintained in ΔTK0186, ΔTK0548, and ΔTK1094, growth was not observed in the ΔTK2268 strain. Our results suggest that TK2268p is the predominant aminotransferase responsible for the conversion of oxaloacetate to aspartate. The growth experiments and tracer-based metabolomics using 13C3-pyruvate indicated that pyruvate is a precursor of aspartate and that this conversion is dependent on TK2268p.

IMPORTANCE

Based on genome sequence, the hyperthermophilic archaeon Thermococcus kodakarensis possesses an incomplete tricarboxylic cycle, raising questions on how this organism carries out the biosynthesis of aspartate and glutamate. The results of this study clarify two main points related to aspartate biosynthesis. We show that aspartate can be produced from oxaloacetate and identify TK2268p as the aminotransferase responsible for this reaction. The other point demonstrated in this study is that pyruvate can act as the precursor for oxaloacetate synthesis. Together with previous results, we can propose some of the roles of the individual aminotransferases in T. kodakarensis. TK0548p and TK0186p are involved in amino acid catabolism, with the latter along with TK1094p involved in the conversion of glyoxylate to glycine. TK2268p is responsible for the biosynthesis of aspartate from oxaloacetate.

Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA structure

In eukaryotes, structural maintenance of chromosomes (SMC) complexes form topologically associating domains (TADs) by extruding DNA loops and being stalled by roadblock proteins. It remains unclear whether a similar mechanism of domain formation exists in prokaryotes. Using high-resolution chromosome conformation capture sequencing, we show that an archaeal homolog of the bacterial Smc-ScpAB complex organizes the genome of Thermococcus kodakarensis into TAD-like domains. We find that TrmBL2, a nucleoid-associated protein that forms a stiff nucleoprotein filament, stalls the T. kodakarensis SMC complex and establishes a boundary at the site-specific recombination site dif. TrmBL2 stalls the SMC complex at tens of additional non-boundary loci with lower efficiency. Intriguingly, the stalling efficiency is correlated with structural properties of underlying DNA sequences. Our study illuminates a eukaryotic-like mechanism of domain formation in archaea and a role of intrinsic DNA structure in large-scale genome organization.

An energy-conserving reaction in amino acid metabolism catalyzed by arginine synthetase

All forms of life are presumed to synthesize arginine from citrulline via a two-step pathway consisting of argininosuccinate synthetase and argininosuccinate lyase using citrulline, adenosine 5'-triphosphate (ATP), and aspartate as substrates. Conversion of arginine to citrulline predominantly proceeds via hydrolysis. Here, from the hyperthermophilic archaeon Thermococcus kodakarensis, we identified an enzyme which we designate "arginine synthetase". In arginine synthesis, the enzyme converts citrulline, ATP, and free ammonia to arginine, adenosine 5'-diphosphate (ADP), and phosphate. In the reverse direction, arginine synthetase conserves the energy of arginine deimination and generates ATP from ADP and phosphate while releasing ammonia. The equilibrium constant of this reaction at pH 7.0 is [Cit][ATP][NH3]/[Arg][ADP][Pi] = 10.1 ± 0.7 at 80 °C, corresponding to a ΔG°' of -6.8 ± 0.2 kJ mol-1. Growth of the gene disruption strain was compared to the host strain in medium composed of amino acids. The results suggested that arginine synthetase is necessary in providing ornithine, the precursor for proline biosynthesis, as well as in generating ATP. Growth in medium supplemented with citrulline indicated that arginine synthetase can function in the direction of arginine synthesis. The enzyme is widespread in nature, including bacteria and eukaryotes, and catalyzes a long-overlooked energy-conserving reaction in microbial amino acid metabolism. Along with ornithine transcarbamoylase and carbamate kinase, the pathway identified here is designated the arginine synthetase pathway.

Removal of phosphoglycolate in hyperthermophilic archaea

Many organisms that utilize the Calvin-Benson-Bassham (CBB) cycle for autotrophic growth harbor metabolic pathways to remove and/or salvage 2-phosphoglycolate, the product of the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). It has been presumed that the occurrence of 2-phosphoglycolate salvage is linked to the CBB cycle, and in particular, the C2 pathway to the CBB cycle and oxygenic photosynthesis. Here, we examined 2-phosphoglycolate salvage in the hyperthermophilic archaeon Thermococcus kodakarensis, an obligate anaerobe that harbors a Rubisco that functions in the pentose bisphosphate pathway. T. kodakarensis harbors enzymes that have the potential to convert 2-phosphoglycolate to glycine and serine, and their genes were identified by biochemical and/or genetic analyses. 2-phosphoglycolate phosphatase activity increased 1.6-fold when cells were grown under microaerobic conditions compared to anaerobic conditions. Among two candidates, TK1734 encoded a phosphatase specific for 2-phosphoglycolate, and the enzyme was responsible for 80% of the 2-phosphoglycolate phosphatase activity in T. kodakarensis cells. The TK1734 disruption strain displayed growth impairment under microaerobic conditions, which was relieved upon addition of sodium sulfide. In addition, glycolate was detected in the medium when T. kodakarensis was grown under microaerobic conditions. The results suggest that T. kodakarensis removes 2-phosphoglycolate via a phosphatase reaction followed by secretion of glycolate to the medium. As the Rubisco in T. kodakarensis functions in the pentose bisphosphate pathway and not in the CBB cycle, mechanisms to remove 2-phosphoglycolate in this archaeon emerged independent of the CBB cycle.

Draft genome sequence of Thermococcus waiotapuensis WT1T, a thermophilic sulfur-dependent archaeon from the order Thermococcales

Thermococcus waiotapuensis WT1T is a thermophilic, peptide, and amino acid-fermenting archaeon from the order Thermococcales. It was isolated from Waiotapu, Aotearoa-New Zealand, and has a genome size of 1.80 Mbp. The genome contains 2,000 total genes, of which 1,913 encode proteins and 46 encode tRNA.