d-Ribose Catabolism in Archaea: Discovery of a Novel Oxidative Pathway in Haloarcula Species

Extremophiles in a changing world

Extremophiles and their products have been a major focus of research interest for over 40 years. Through this period, studies of these organisms have contributed hugely to many aspects of the fundamental and applied sciences, and to wider and more philosophical issues such as the origins of life and astrobiology. Our understanding of the cellular adaptations to extreme conditions (such as acid, temperature, pressure and more), of the mechanisms underpinning the stability of macromolecules, and of the subtleties, complexities and limits of fundamental biochemical processes has been informed by research on extremophiles. Extremophiles have also contributed numerous products and processes to the many fields of biotechnology, from diagnostics to bioremediation. Yet, after 40 years of dedicated research, there remains much to be discovered in this field. Fortunately, extremophiles remain an active and vibrant area of research. In the third decade of the twenty-first century, with decreasing global resources and a steadily increasing human population, the world's attention has turned with increasing urgency to issues of sustainability. These global concerns were encapsulated and formalized by the United Nations with the adoption of the 2030 Agenda for Sustainable Development and the presentation of the seventeen Sustainable Development Goals (SDGs) in 2015. In the run-up to 2030, we consider the contributions that extremophiles have made, and will in the future make, to the SDGs.

A conserved transcription factor controls gluconeogenesis via distinct targets in hypersaline-adapted archaea with diverse metabolic capabilities

Timely regulation of carbon metabolic pathways is essential for cellular processes and to prevent futile cycling of intracellular metabolites. In Halobacterium salinarum, a hypersaline adapted archaeon, a sugar-sensing TrmB family protein controls gluconeogenesis and other biosynthetic pathways. Notably, Hbt. salinarum does not utilize carbohydrates for energy, uncommon among Haloarchaea. We characterized a TrmB-family transcriptional regulator in a saccharolytic generalist, Haloarcula hispanica, to investigate whether the targets and function of TrmB, or its regulon, is conserved in related species with distinct metabolic capabilities. In Har. hispanica, TrmB binds to 15 sites in the genome and induces the expression of genes primarily involved in gluconeogenesis and tryptophan biosynthesis. An important regulatory control point in Hbt. salinarum, activation of ppsA and repression of pykA, is absent in Har. hispanica. Contrary to its role in Hbt. salinarum and saccharolytic hyperthermophiles, TrmB does not act as a global regulator: it does not directly repress the expression of glycolytic enzymes, peripheral pathways such as cofactor biosynthesis, or catabolism of other carbon sources in Har. hispanica. Cumulatively, these findings suggest rewiring of the TrmB regulon alongside metabolic network evolution in Haloarchaea.

Identification and characterization of a novel pathway for aldopentose degradation in Acinetobacter baumannii

The nosocomial pathogen Acinetobacter baumannii is well known for its extraordinary metabolic diversity. Recently, we demonstrated growth on L-arabinose, but the pathway remained elusive. Transcriptome analyses revealed two upregulated gene clusters that code for isoenzymes catalysing oxidation of a pentonate to α-ketoglutarate. Molecular, genetic, and biochemical experiments revealed one branch to be specific for L-arabonate oxidation, and the other for D-xylonate and D-ribonate. Both clusters also encode an uptake system and a regulator that acts as activator (L-arabonate) or repressor (D-xylonate and D-ribonate). Genes encoding the initial oxidation of pentose to pentonate were not part of the clusters, but our data are consistent with the hypothesis of a promiscous, pyrroloquinoline quinone (PQQ)-dependent, periplasmic pentose dehydrogenase, followed by the uptake of the pentonates and their degradation by specific pathways. However, there is a cross-talk between the two different pathways since the isoenzymes can replace each other. Growth on pentoses was found only in pathogenic Acinetobacter species but not in non-pathogenic such as Acinetobacter baylyi. However, mutants impaired in growth on pentoses were not affected in traits important for infection, but growth on L-arabinose was beneficial for long-term survival and desiccation resistance in A. baumannii ATCC 19606.

Discovery of a novel transcriptional regulator of sugar catabolism in archaea

The haloarchaeon Haloferax volcanii degrades D-glucose via the semiphosphorylative Entner-Doudoroff pathway and D-fructose via a modified Embden-Meyerhof pathway. Here, we report the identification of GfcR, a novel type of transcriptional regulator that functions as an activator of both D-glucose and D-fructose catabolism. We find that in the presence of D-glucose, GfcR activates gluconate dehydratase, glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase and also acts as activator of the phosphotransferase system and of fructose-1,6-bisphosphate aldolase, which are involved in uptake and degradation of D-fructose. In addition, glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase are activated by GfcR in the presence of D-fructose and also during growth on D-galactose and glycerol. Electrophoretic mobility shift assays indicate that GfcR binds directly to promoters of regulated genes. Specific intermediates of the degradation pathways of the three hexoses and of glycerol were identified as inducer molecules of GfcR. GfcR is composed of a phosphoribosyltransferase (PRT) domain with an N-terminal helix-turn-helix motif and thus shows homology to PurR of Gram-positive bacteria that is involved in the transcriptional regulation of nucleotide biosynthesis. We propose that GfcR of H. volcanii evolved from a PRT-like enzyme to attain a function as a transcriptional regulator of central sugar catabolic pathways in archaea.

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.

Glucose Metabolism and Acetate Switch in Archaea: the Enzymes in Haloferax volcanii

The halophilic archaeon Haloferax volcanii has been proposed to degrade glucose via the semiphosphorylative Entner-Doudoroff (spED) pathway. Following our previous studies on key enzymes of this pathway, we now focus on the characterization of enzymes involved in 3-phosphoglycerate conversion to pyruvate, in anaplerosis, and in acetyl coenzyme A (acetyl-CoA) formation from pyruvate. These enzymes include phosphoglycerate mutase, enolase, pyruvate kinase, phosphoenolpyruvate carboxylase, and pyruvate-ferredoxin oxidoreductase. The essential function of these enzymes were shown by transcript analyses and growth experiments with respective deletion mutants. Furthermore, we show that H. volcanii-during aerobic growth on glucose-excreted significant amounts of acetate, which was consumed in the stationary phase (acetate switch). The enzyme catalyzing the conversion of acetyl-CoA to acetate as part of the acetate overflow mechanism, an ADP-forming acetyl-CoA synthetase (ACD), was characterized. The functional involvement of ACD in acetate formation and of AMP-forming acetyl-CoA synthetases (ACSs) in activation of excreted acetate was proven by using respective deletion mutants. Together, the data provide a comprehensive analysis of enzymes of the spED pathway and of anaplerosis and report the first genetic evidence of the functional involvement of enzymes of the acetate switch in archaea.IMPORTANCE In this work, we provide a comprehensive analysis of glucose degradation via the semiphosphorylative Entner-Doudoroff pathway in the haloarchaeal model organism Haloferax volcanii The study includes transcriptional analyses, growth experiments with deletion mutants. and characterization of all enzymes involved in the conversion of 3-phosphoglycerate to acetyl coenzyme A (acetyl-CoA) and in anaplerosis. Phylogenetic analyses of several enzymes indicate various lateral gene transfer events from bacteria to haloarchaea. Furthermore, we analyzed the key players involved in the acetate switch, i.e., in the formation (overflow) and subsequent consumption of acetate during aerobic growth on glucose. Together, the data provide novel aspects of glucose degradation, anaplerosis, and acetate switch in H. volcanii and thus expand our understanding of the unusual sugar metabolism in archaea.

D-galactose catabolism in archaea: operation of the DeLey-Doudoroff pathway in Haloferax volcanii

The haloarchaeon Haloferax volcanii was found to grow on D-galactose as carbon and energy source. Here we report a comprehensive analysis of D-galactose catabolism in H. volcanii. Genome analyses indicated a cluster of genes encoding putative enzymes of the DeLey-Doudoroff pathway for D-galactose degradation including galactose dehydrogenase, galactonate dehydratase, 2-keto-3-deoxygalactonate kinase and 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) aldolase. The recombinant galactose dehydrogenase and galactonate dehydratase showed high specificity for D-galactose and galactonate, respectively, whereas KDPGal aldolase was promiscuous in utilizing KDPGal and also the C4 epimer 2-keto-3-deoxy-6-phosphogluconate as substrates. Growth studies with knock-out mutants indicated the functional involvement of galactose dehydrogenase, galactonate dehydratase and KDPGal aldolase in D-galactose degradation. Further, the transcriptional regulator GacR was identified, which was characterized as an activator of genes of the DeLey-Doudoroff pathway. Finally, genes were identified encoding components of an ABC transporter and a knock-out mutant of the substrate binding protein indicated the functional involvement of this transporter in D-galactose uptake. This is the first report of D-galactose degradation via the DeLey-Doudoroff pathway in the domain of archaea.

Enzymology of Alternative Carbohydrate Catabolic Pathways

The Embden–Meyerhof–Parnas (EMP) and Entner–Doudoroff (ED) pathways are considered the most abundant catabolic pathways found in microorganisms, and ED enzymes have been shown to also be widespread in cyanobacteria, algae and plants. In a large number of organisms, especially common strains used in molecular biology, these pathways account for the catabolism of glucose. The existence of pathways for other carbohydrates that are relevant to biomass utilization has been recognized as new strains have been characterized among thermophilic bacteria and Archaea that are able to transform simple polysaccharides from biomass to more complex and potentially valuable precursors for industrial microbiology. Many of the variants of the ED pathway have the key dehydratase enzyme involved in the oxidation of sugar derived from different families such as the enolase, IlvD/EDD and xylose-isomerase-like superfamilies. There are the variations in structure of proteins that have the same specificity and generally greater-than-expected substrate promiscuity. Typical biomass lignocellulose has an abundance of xylan, and four different pathways have been described, which include the Weimberg and Dahms pathways initially oxidizing xylose to xylono-gamma-lactone/xylonic acid, as well as the major xylose isomerase pathway. The recent realization that xylan constitutes a large proportion of biomass has generated interest in exploiting the compound for value-added precursors, but few chassis microorganisms can grow on xylose. Arabinose is part of lignocellulose biomass and can be metabolized with similar pathways to xylose, as well as an oxidative pathway. Like enzymes in many non-phosphorylative carbohydrate pathways, enzymes involved in L-arabinose pathways from bacteria and Archaea show metabolic and substrate promiscuity. A similar multiplicity of pathways was observed for other biomass-derived sugars such as L-rhamnose and L-fucose, but D-mannose appears to be distinct in that a non-phosphorylative version of the ED pathway has not been reported. Many bacteria and Archaea are able to grow on mannose but, as with other minor sugars, much of the information has been derived from whole cell studies with additional enzyme proteins being incorporated, and so far, only one synthetic pathway has been described. There appears to be a need for further discovery studies to clarify the general ability of many microorganisms to grow on the rarer sugars, as well as evaluation of the many gene copies displayed by marine bacteria.

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.