A Phosphofructokinase Homolog from Pyrobaculum calidifontis Displays Kinase Activity towards Pyrimidine Nucleosides and Ribose 1-Phosphate

Antagonistic Activity of Oroxylin A against Fusarium graminearum and Its Inhibitory Effect on Zearalenone Production

Fusarium graminearum produces zearalenone (ZEA), a mycotoxin that is widely found in food and feed products and is toxic to humans and livestock. Piper sarmentosum extract (PSE) inhibits F. graminearum, and Oroxylin A appears to be a major antifungal compound in PSE. The aim of this study is to quantify the Oroxylin A content in PSE using UPLC-QTOF-MS/MS, and to investigate the antagonistic activity of Oroxylin A against F. graminearum and its inhibitory effect on ZEA production. The results indicate that Oroxylin A inhibits both fungal growth and ZEA production in a dose-dependent manner. Oroxylin A treatment downregulated the mRNA expression of zearalenone biosynthesis protein 1 (ZEB1) and zearalenone biosynthesis protein 2 (ZEB2). The metabolomics analysis of F. graminearum mycelia indicated that the level of ribose 5-phosphate (R5P) deceased (p < 0.05) after Oroxylin A treatment (64-128 ng/mL). Moreover, as the Oroxylin A treatment content increased from 64 to 128 ng/mL, the levels of cis-aconitate (p < 0.05) and fumarate (p < 0.01) were upregulated successively. A correlation analysis further showed that the decreased R5P level was positively correlated with ZEB1 and ZEB2 expression, while the increased cis-aconitate and fumarate levels were negatively correlated with ZEB1 and ZEB2 expression. These findings demonstrate the potential of Oroxylin A as a natural agent to control toxigenic fungi and their mycotoxin.

Screening the Thermotoga maritima genome for new wide-spectrum nucleoside and nucleotide kinases

Enzymes from thermophilic organisms are interesting biocatalysts for a wide variety of applications in organic synthesis, biotechnology and molecular biology. Next to an increased stability at elevated temperatures, they were described to show a wider substrate spectrum than their mesophilic counterparts. To identify thermostable biocatalysts for the synthesis of nucleotide analogs, we performed a database search on the carbohydrate and nucleotide metabolism of T. maritima. After expression and purification of 13 enzyme candidates involved in nucleotide synthesis, these enzymes were screened for their substrate scope. We found that the synthesis of 2'-deoxynucleoside 5'-monophosphates (dNMPs) and uridine 5'-monophosphate from nucleosides was catalyzed by the already known wide-spectrum thymidine kinase (TK) and the ribokinase. In contrast, no NMP-forming activity was detected for adenosine-specific kinase, uridine kinase or nucleotidase. The NMP kinases (NMPKs) and the pyruvate-phosphate-dikinase of T. maritima exhibited a rather specific substrate spectrum for the phosphorylation of NMPs, while pyruvate kinase, acetate kinase and three of the NMPKs showed a broad substrate scope with (2'-deoxy)nucleoside 5'-diphosphates as substrates. Based on these promising results, TmNMPKs were applied in enzymatic cascade reactions for nucleoside 5'-triphosphate synthesis using four modified pyrimidine nucleosides and four purine NMPs as substrates, and we determined that base- and sugar-modified substrates were accepted. In summary, besides the already reported TmTK, NMPKs of T. maritima were identified to be interesting enzyme candidates for the enzymatic production of modified nucleotides.

A non-carboxylating pentose bisphosphate pathway in halophilic archaea

Bacteria and Eucarya utilize the non-oxidative pentose phosphate pathway to direct the ribose moieties of nucleosides to central carbon metabolism. Many archaea do not possess this pathway, and instead, Thermococcales utilize a pentose bisphosphate pathway involving ribose-1,5-bisphosphate (R15P) isomerase and ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco). Intriguingly, multiple genomes from halophilic archaea seem only to harbor R15P isomerase, and do not harbor Rubisco. In this study, we identify a previously unrecognized nucleoside degradation pathway in halophilic archaea, composed of guanosine phosphorylase, ATP-dependent ribose-1-phosphate kinase, R15P isomerase, RuBP phosphatase, ribulose-1-phosphate aldolase, and glycolaldehyde reductase. The pathway converts the ribose moiety of guanosine to dihydroxyacetone phosphate and ethylene glycol. Although the metabolic route from guanosine to RuBP via R15P is similar to that of the pentose bisphosphate pathway in Thermococcales, the downstream route does not utilize Rubisco and is unique to halophilic archaea.

Molecular cloning, expression in Escherichia coli and structural-functional analysis of a pyruvate kinase from Pyrobaculum calidifontis

This manuscript describes recombinant production, characterization and structural analysis of wild-type and mutant Pcal_0029, a pyruvate kinase from Pyrobaculum calidifontis. Recombinant Pcal_0029 was produced in soluble and highly active form in Escherichia coli. Purified protein exhibited divalent metal-dependent activity which increased with the increase in temperature till 85 °C. Recombinant Pcal_0029 was highly thermostable with no significant loss in activity even after an incubation of 120 min at 100 °C. The enzyme exhibited apparent S_0.5 and V_max values of 0.44 ± 0.05 mM and 840 ± 39 units, respectively, towards phosphoenolpyruvate. These values towards adenosine-5'-diphosphate were 0.5 ± 0.07 mM and 870 ± 26 units, respectively. In silico structural analysis and comparison with the characterized enzymes revealed the presence of eight conserved regions. Two substitutions, K130E and S155G, resulted in a 10-fold decrease in activity. Secondary structure analysis indicated similar structures for the wild-type and the mutant enzymes. Bioinformatics analysis revealed disruption of interatomic interactions and hydrogen bond formation, leading to a decreased flexibility and solvent accessibility, which may have led to decrease in activity. To the best of our knowledge, Pcal_0029 is the most thermostable pyruvate kinase reported so far. Moreover, this is the first study on the role of non-catalytic residues in a pyruvate kinase.

Structural analysis and functional study of phosphofructokinase B (PfkB) from Mycobacterium marinum

Phosphofructokinase B (PfkB) belongs to the ribokinase family, which uses the phosphorylated sugar as substrate, and catalyzes fructose-6-phosphate into fructose-1,6-diphosphate. However, the structural basis of Mycobacterium marinum PfkB is not clear. Here, we found that the PfkB protein was monomeric in solution, which was different from most enzymes in this family. The crystal structure of PfkB protein from M. marinum was solved at a resolution of 2.21 Å. The PfkB structure consists of two domains, a major three-layered α/β/α sandwich-like domain characteristic of the ribokinase-like superfamily, and a second domain composed of four-stranded β sheets. Structural comparison analysis suggested that residues G236, A237, G238, and D239 could be critical for ATP catalysis and substrate binding of PfkB. Our current work provides new insights into understanding the mechanism of the glycolysis in M. marinum.

Identification and Enzymatic Analysis of an Archaeal ATP-Dependent Serine Kinase from the Hyperthermophilic Archaeon Staphylothermus marinus

Serine kinase catalyzes the phosphorylation of free serine (Ser) to produce O-phosphoserine (Sep). An ADP-dependent Ser kinase in the hyperthermophilic archaeon Thermococcus kodakarensis (Tk-SerK) is involved in cysteine (Cys) biosynthesis and most likely Ser assimilation. An ATP-dependent Ser kinase in the mesophilic bacterium Staphylococcus aureus is involved in siderophore biosynthesis. Although proteins displaying various degrees of similarity with Tk-SerK are distributed in a wide range of organisms, it is unclear if they are actually Ser kinases. Here, we examined proteins from Desulfurococcales species in Crenarchaeota that display moderate similarity with Tk-SerK from Euryarchaeota (42 to 45% identical). Tk-serK homologs from Staphylothermus marinus (Smar_0555), Desulfurococcus amylolyticus (DKAM_0858), and Desulfurococcus mucosus (Desmu_0904) were expressed in Escherichia coli. All three partially purified recombinant proteins exhibited Ser kinase activity utilizing ATP rather than ADP as a phosphate donor. Purified Smar_0555 protein displayed activity for l-Ser but not other compounds, including d-Ser, l-threonine, and l-homoserine. The enzyme utilized ATP, UTP, GTP, CTP, and the inorganic polyphosphates triphosphate and tetraphosphate as phosphate donors. Kinetic analysis indicated that the Smar_0555 protein preferred nucleoside 5'-triphosphates over triphosphate as a phosphate donor. Transcript levels and Ser kinase activity in S. marinus cells grown with or without serine suggested that the Smar_0555 gene is constitutively expressed. The genes encoding Ser kinases examined here form an operon with genes most likely responsible for the conversion between Sep and 3-phosphoglycerate of central sugar metabolism, suggesting that the ATP-dependent Ser kinases from Desulfurococcales play a role in the assimilation of Ser. IMPORTANCE Homologs of the ADP-dependent Ser kinase from the archaeon Thermococcus kodakarensis (Tk-SerK) include representatives from all three domains of life. The results of this study show that even homologs from the archaeal order Desulfurococcales, which are the most structurally related to the ADP-dependent Ser kinases from the Thermococcales, are Ser kinases that utilize ATP, and in at least some cases inorganic polyphosphates, as the phosphate donor. The differences in properties between the Desulfurococcales and Thermococcales enzymes raise the possibility that Tk-SerK homologs constitute a group of kinases that phosphorylate free serine with a wide range of phosphate donors.

Pentose degradation in archaea: Halorhabdus species degrade D-xylose, L-arabinose and D-ribose via bacterial-type pathways

The degradation of the pentoses D-xylose, L-arabinose and D-ribose in the domain of archaea, in Haloferax volcanii and in Haloarcula and Sulfolobus species, has been shown to proceed via oxidative pathways to generate α-ketoglutarate. Here, we report that the haloarchaeal Halorhabdus species utilize the bacterial-type non-oxidative degradation pathways for pentoses generating xylulose-5-phosphate. The genes of these pathways are each clustered and were constitutively expressed. Selected enzymes involved in D-xylose degradation, xylose isomerase and xylulokinase, and those involved in L-arabinose degradation, arabinose isomerase and ribulokinase, were characterized. Further, D-ribose degradation in Halorhabdus species involves ribokinase, ribose-5-phosphate isomerase and D-ribulose-5-phosphate-3-epimerase. Ribokinase of Halorhabdus tiamatea and ribose-5-phosphate isomerase of Halorhabdus utahensis were characterized. This is the first report of pentose degradation via the bacterial-type pathways in archaea, in Halorhabdus species that likely acquired these pathways from bacteria. The utilization of bacterial-type pathways of pentose degradation rather than the archaeal oxidative pathways generating α-ketoglutarate might be explained by an incomplete gluconeogenesis in Halorhabdus species preventing the utilization of α-ketoglutarate in the anabolism.

The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism

Ribosyl 1,5-bisphosphate (PRibP) was discovered 65 years ago and was believed to be an important intermediate in ribonucleotide metabolism, a role immediately taken over by its "big brother" phosphoribosyldiphosphate. Only recently has PRibP come back into focus as an important player in the metabolism of ribonucleotides with the discovery of the pentose bisphosphate pathway that comprises, among others, the intermediates PRibP and ribulose 1,5-bisphosphate (cf. ribose 5-phosphate and ribulose 5-phosphate of the pentose phosphate pathway). Enzymes of several pathways produce and utilize PRibP not only in ribonucleotide metabolism but also in the catabolism of phosphonates, i.e., compounds containing a carbon-phosphorus bond. Pathways for PRibP metabolism are found in all three domains of life, most prominently among organisms of the archaeal domain, where they have been identified either experimentally or by bioinformatic analysis within all of the four main taxonomic groups, Euryarchaeota, TACK, DPANN, and Asgard. Advances in molecular genetics of archaea have greatly improved the understanding of the physiology of PRibP metabolism, and reconciliation of molecular enzymology and three-dimensional structure analysis of enzymes producing or utilizing PRibP emphasize the versatility of the compound. Finally, PRibP is also an effector of several metabolic activities in many organisms, including higher organisms such as mammals. In the present review, we describe all aspects of PRibP metabolism, with emphasis on the biochemical, genetic, and physiological aspects of the enzymes that produce or utilize PRibP. The inclusion of high-resolution structures of relevant enzymes that bind PRibP provides evidence for the flexibility and importance of the compound in metabolism.