PCR-Based Identification of Hyperthermophilic Archaea of the Family Thermococcaceae

A method for rapid detection and identification of hyperthermophilic archaea of the family Thermococcaceae based on PCR amplification of 16S rRNA gene fragments with primers TcPc 173F (5′-TCCCCCATAGGYCTGRGGTACTGGAAGGTC-3′) and TcPc 589R (5′-GCCGTGRGATTTCGCCAGGGACTTACGGGC-3′) was developed and used for identification of new isolates.     

Gene Analysis of Trehalose-producing Enzymes from Hyperthermophilic Archaea in Sulfolobales

The genes encoding new trehalose-producing enzymes from S. acidocaldarius ATCC33909 were cloned to analyze the distribution of these genes in Sulfolobales. Comparison of the amino acid sequences with S. solfataricus KM1 showed approximately 50% similarity. Southern analysis suggests that homologues of the trehalose-producing enzyme genes exist widely in Sulfolobales and strains in Sulfolobales were classified into three kinds of genotypes.     

Metabolism of Pentose Sugars in the Hyperthermophilic Archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius

We have previously shown that the hyperthermophilic archaeon, Sulfolobus solfataricus, catabolizes d-glucose and d-galactose to pyruvate and glyceraldehyde via a non-phosphorylative version of the Entner-Doudoroff pathway. At each step, one enzyme is active with both C6 epimers, leading to a metabolically promiscuous pathway. On further investigation, the catalytic promiscuity of the first enzyme in this pathway, glucose dehydrogenase, has been shown to extend to the C5 sugars, d-xylose and l-arabinose. In the current paper we establish that this promiscuity for C6 and C5 metabolites is also exhibited by the third enzyme in the pathway, 2-keto-3-deoxygluconate aldolase, but that the second step requires a specific C5-dehydratase, the gluconate dehydratase being active only with C6 metabolites. The products of this pathway for the catabolism of d-xylose and l-arabinose are pyruvate and glycolaldehyde, pyruvate entering the citric acid cycle after oxidative decarboxylation to acetyl-coenzyme A. We have identified and characterized the enzymes, both native and recombinant, that catalyze the conversion of glycolaldehyde to glycolate and then to glyoxylate, which can enter the citric acid cycle via the action of malate synthase. Evidence is also presented that similar enzymes for this pentose sugar pathway are present in Sulfolobus acidocaldarius, and metabolic tracer studies in this archaeon demonstrate its in vivo operation in parallel with a route involving no aldol cleavage of the 2-keto-3-deoxy-pentanoates but direct conversion to the citric acid cycle C5-metabolite, 2-oxoglutarate.     

Constraints on Anaerobic Respiration in the Hyperthermophilic Archaea Pyrobaculum islandicum and Pyrobaculum aerophilum

Pyrobaculum islandicum uses iron, thiosulfate, and elemental sulfur for anaerobic respiration, while Pyrobaculum aerophilum uses iron and nitrate; however, the constraints on these processes and their physiological mechanisms for iron and sulfur reduction are not well understood. Growth rates on sulfur compounds are highest at pH 5 to 6 and highly reduced (<−420-mV) conditions, while growth rates on nitrate and iron are highest at pH 7 to 9 and more-oxidized (>−210-mV) conditions. Growth on iron expands the known pH range of growth for both organisms. P. islandicum differs from P. aerophilum in that it requires direct contact with insoluble iron oxide for growth, it did not produce any extracellular compounds when grown on insoluble iron, and it lacked 2,6-anthrahydroquinone disulfonate oxidase activity. Furthermore, iron reduction in P. islandicum appears to be completely independent of c-type cytochromes. Like that in P. aerophilum, NADH-dependent ferric reductase activity in P. islandicum increased significantly in iron-grown cultures relative to that in non-iron-grown cultures. Proteomic analyses showed that there were significant increases in the amounts of a putative membrane-bound thiosulfate reductase in P. islandicum cultures grown on thiosulfate relative to those in cultures grown on iron and elemental sulfur. This is the first evidence of this enzyme being used in either a hyperthermophile or an archaeon. Pyrobaculum arsenaticum and Pyrobaculum calidifontis also grew on Fe(III) citrate and insoluble iron oxide, but only P. arsenaticum could grow on insoluble iron without direct contact.     

Detection of Hyperthermophilic Archaea of the Genus Desulfurococcus by Hybridization with Oligonucleotide Probes

Based on the analysis of nucleotide sequences of 16S rRNA, oligonucleotide probes were designed for the detection and identification of representatives of the genus Desulfurococcus (kingdom Crenarchaeota of the domain Archaea). The detection procedure included obtaining PCR products on DNA isolated from pure cultures, enrichments, or natural samples with a designed Crenarchaeota-specific primer pair: Cren 7F (5-TTCCGGTTGATCCYGCCGGACC-3) and Cren 518R (5-GCTGGTWTTACCGCGGCGGCTGA-3). The PCR products were hybridized with Dig-11-dUTP–labeled oligonucleotide probes targeting the genus Desulfurococcus (Dco 198, 5-CGTTAACYCCYGCCACACC-3) and its species D. mobilis (Dco_mob 198, 5-CGTTAACCCCTGCCACACC-3) and D. amylolyticus (Dco_amy 198, 5-CGTTAACCCCCGCCACACC-3). With the use of these primers and probes, four new strains isolated from hydrotherms of Kamchatka and Kunashir Island were identified as members of the speciesDesulfurococcus amylolyticus. Desulfurococcus representatives were detected in several natural samples, including a sample taken from a marine hydrotherm at Kunashir Island; this demonstrates that representatives of this genus occur not only in terrestrial but also in marine environments.     

UV and Ethyl Methanesulfonate Effects in Hyperthermophilic Archaea and Isolation of Auxotrophic Mutants of Pyrococcus Strains

The lethal and mutagenic effects of ethyl methanesulfonate (EMS) and UV on nine archaeal strains belonging to each of the two described genera of Thermococcales, Pyrococcus and Thermococcus, were investigated. To test the efficiency of the EMS and UV mutagenesis under a variety of experimental conditions, we chose Pyrococcus abyssi strain GE5 as a model strain. We observed a strong induced mutagenicity in both cases, since the spontaneous mutation frequency (expressed as the frequency of resistance to 5-fluoroorotic acid) increased up to 150-fold with EMS and 400-fold with UV, after mutagen exposure. Although a heterogeneous response to the induced effects caused after EMS and UV exposures was detected for all the other sulfothermophilic archaea tested, an efficient mutagenicity of Pyrococcus-like isolates GE27, GE23, and GE9 was observed. Optimal procedures described for UV mutagenesis yielded a number of useful uracil auxotrophic mutant strains of Pyrococcus abyssi. Received: 2 May 1996 / Accepted: 3 July 1996     

Selective Phylogenetic Analysis Targeting 16S rRNA Genes of Hyperthermophilic Archaea in the Deep-Subsurface Hot Biosphere

International drilling projects for the study of microbial communities in the deep-subsurface hot biosphere have been expanded. Core samples obtained by deep drilling are commonly contaminated with mesophilic microorganisms in the drilling fluid, making it difficult to examine the microbial community by 16S rRNA gene clone library analysis. To eliminate mesophilic organism contamination, we previously developed a new method (selective phylogenetic analysis [SePA]) based on the strong correlation between the guanine-plus-cytosine (G+C) contents of the 16S rRNA genes and the optimal growth temperatures of prokaryotes, and we verified the method's effectiveness (H. Kimura, M. Sugihara, K. Kato, and S. Hanada, Appl. Environ. Microbiol. 72:21-27, 2006). In the present study we ascertained SePA's ability to eliminate contamination by archaeal rRNA genes, using deep-sea hydrothermal fluid (117°C) and surface seawater (29.9°C) as substitutes for deep-subsurface geothermal samples and drilling fluid, respectively. Archaeal 16S rRNA gene fragments, PCR amplified from the surface seawater, were denatured at 82°C and completely digested with exonuclease I (Exo I), while gene fragments from the deep-sea hydrothermal fluid remained intact after denaturation at 84°C because of their high G+C contents. An examination using mixtures of DNAs from the two environmental samples showed that denaturation at 84°C and digestion with Exo I completely eliminated archaeal 16S rRNA genes from the surface seawater. Our method was quite useful for culture-independent community analysis of hyperthermophilic archaea in core samples recovered from deep-subsurface geothermal environments.     

N-Linked Glycans Are Assembled on Highly Reduced Dolichol Phosphate Carriers in the Hyperthermophilic Archaea Pyrococcus furiosus

In all three domains of life, N-glycosylation begins with the assembly of glycans on phosphorylated polyisoprenoid carriers. Like eukaryotes, archaea also utilize phosphorylated dolichol for this role, yet whereas the assembled oligosaccharide is transferred to target proteins from dolichol pyrophosphate in eukaryotes, archaeal N-linked glycans characterized to date are derived from a dolichol monophosphate carrier, apart from a single example. In this study, glycan-charged dolichol phosphate from the hyperthermophile Pyrococcus furiosus was identified and structurally characterized. Normal and reverse phase liquid chromatography-electrospray ionization mass spectrometry revealed the existence of dolichol phosphate charged with the heptasaccharide recently described in in vitro studies of N-glycosylation on this species. As with other described archaeal dolichol phosphates, the α- and ω-terminal isoprene subunits of the P. furiosus lipid are saturated, in contrast to eukaryal phosphodolichols that present only a saturated α-position isoprene subunit. Interestingly, an additional 1-4 of the 12-14 isoprene subunits comprising P. furiosus dolichol phosphate are saturated, making this lipid not only the longest archaeal dolichol phosphate described to date but also the most highly saturated.     

Free Levels of Selected Organic Solutes and Cardiovascular Morbidity and Mortality in Hemodialysis Patients: Results from the Retained Organic Solutes and Clinical Outcomes (ROSCO) Investigators

Background and Objectives

Numerous substances accumulate in the body in uremia but those contributing to cardiovascular morbidity and mortality in dialysis patients are still undefined. We examined the association of baseline free levels of four organic solutes that are secreted in the native kidney — p-cresol sulfate, indoxyl sulfate, hippurate and phenylacetylglutamine — with outcomes in hemodialysis patients.

Design, Setting, Participants and Measurements

We measured these solutes in stored specimens from 394 participants of a US national prospective cohort study of incident dialysis patients. We examined the relation of each solute and a combined solute index to cardiovascular mortality and morbidity (first cardiovascular event) using Cox proportional hazards regression adjusted for demographics, comorbidities, clinical factors and laboratory tests including Kt/V_UREA.

Results

Mean age of the patients was 57 years, 65% were white and 55% were male. In fully adjusted models, a higher p-cresol sulfate level was associated with a greater risk (HR per SD increase; 95% CI) of cardiovascular mortality (1.62; 1.17–2.25; p=0.004) and first cardiovascular event (1.60; 1.23–2.08; p<0.001). A higher phenylacetylglutamine level was associated with a greater risk of first cardiovascular event (1.37; 1.18–1.58; p<0.001). Patients in the highest quintile of the combined solute index had a 96% greater risk of cardiovascular mortality (1.96; 1.05–3.68; p=0.04) and 62% greater risk of first cardiovascular event (1.62; 1.12–2.35; p=0.01) compared with patients in the lowest quintile. Results were robust in sensitivity analyses.

Conclusions

Free levels of uremic solutes that are secreted by the native kidney are associated with a higher risk of cardiovascular morbidity and mortality in incident hemodialysis patients.     

Effects of Dissolved Sulfide, pH, and Temperature on Growth and Survival of Marine Hyperthermophilic Archaea

The ability of metabolically diverse hyperthermophilic archaea to withstand high temperatures, low pHs, high sulfide concentrations, and the absence of carbon and energy sources was investigated. Close relatives of our study organisms, Methanocaldococcus jannaschii, Archaeoglobus profundus, Thermococcus fumicolans, and Pyrococcus sp. strain GB-D, are commonly found in hydrothermal vent chimney walls and hot sediments and possibly deeper in the subsurface, where highly dynamic hydrothermal flow patterns and steep chemical and temperature gradients provide an ever-changing mosaic of microhabitats. These organisms (with the possible exception of Pyrococcus strain GB-D) tolerated greater extremes of low pH, high sulfide concentration, and high temperature when actively growing and metabolizing than when starved of carbon sources and electron donors/acceptors. Therefore these organisms must be actively metabolizing in the hydrothermal vent chimneys, sediments, and subsurface in order to withstand at least 24 h of exposure to extremes of pH, sulfide, and temperature that occur in these environments.     

Comparative Physiological Studies on Hyperthermophilic Archaea Isolated from Deep-Sea Hot Vents with Emphasis on Pyrococcus Strain GB-D

Three new sulfur- or non-sulfur-dependent archaeal isolates, including a Pyrococcus strain, from Guaymas Basin hydrothermal vents (Gulf of California; depth, 2,010 m) were characterized and physiologically compared with four known hyperthermophiles, previously isolated from other vent sites, with an emphasis on growth and survival under the conditions particular to the natural habitat. Incubation under in situ pressure (200 atm [1 atm = 101.29 kPa]) did not increase the maximum growth temperature by more than 1°C for any of the organisms but did result in increases in growth rates of up to 15% at optimum growth temperatures. At in situ pressure, temperatures considerably higher than those limiting growth (i.e., > 105°C) were survived best by isolates with the highest maximum growth temperatures, but none of the organisms survived at temperatures of 150°C or higher for 5 min. Free oxygen was toxic to all isolates at growth range temperatures, but at ambient deep-sea temperature (3 to 4°C), the effect varied in different isolates, the non-sulfur-dependent isolate being the most oxygen tolerant. Hyperthermophiles could be isolated from refrigerated and oxygenated samples after 5 years of storage. Cu, Zn, and Pb ions were found to be toxic under nongrowth conditions (absence of organic substrate), with the non-sulfur-dependent isolate again being the most tolerant.     

Material Balance and Additional Effect of Second Organic Solutes in the Radiolysis of Aqueous Methionine Solution

The gamma-radiolysis of methionine in 10^?3 m aqueous solution was studied. From the yield vs. dose plots, the following values were obtained: G(?Methionine)=3.0, G(Methionine sulfoxide)=0.30, G(α- Aminobutyric acid)=0.46, G(3-Methylthio propylamine)=0.59, G(Methional)=0.08, G(Carboxylic acid)=0.24, G(Mercaptan + Disulfide)=0.6l, G(Ammonia)=1.48, and G(Carbon dioxide)=1.45. From these results, it was concluded that major reaction was deamination and decarboxylation by OH radical attack.

Addition of methanol as the second solute at concentration above 4 × 10^?3 m could not lower G(Methionine sulfoxide), suggesting the reaction of methionine with secondary radical produced from methanol.

Existence of similar reaction was suggested in the radiolysis of methionine in aqueous pork extract.     

Effect of Organic Nutrients on the Activity of Archaea of the Ferroplasmaceae Family

The effect of different organic compounds (glucose, fructose, ribose, glycine, alanine, pyruvate, acetate, citrate, and yeast extract) as well as of the wastes of food production (molasses, stillage, sweet whey), on the growth of iron-oxidizing acidophilic microorganisms and biooxidation of ferrous iron was studied. Representatives of the microorganisms predominating in biohydrometallurgical processes—archaea of the family Ferroplasmaceae (A. aeolicum V1^T, A. cupricumulans BH2^T, Acidiplasma sp. MBA-1, Ferroplasma acidiphilum B-1) and bacteria of the genus Sulfobacillus (S. thermosulfidooxidans SH 10–1, S. thermotolerans Kr1^T)—were the subjects of the study. All studied strains most actively grew and oxidized ferrous iron in the presence of yeast extract, which is probably due to the presence of a large number of different growth factors in its composition, while others substrates provided growth of microorganisms and ferrous iron oxidation.     

Transport of Compatible Solutes in Extremophiles

Salt-tolerant as well as moderately halophilic and halophilic organisms have to maintain their turgor. One strategy is to accumulate small organic compounds, compatible solutes, by de novo synthesis or uptake. From a bioenergetic point of view, uptake is preferred over biosynthesis. The transport systems catalyzing uptake of compatible solutes are of primary or secondary nature and coupled to ATP hydrolysis or ion (H+, Na+) symport. Expression of the transporter genes as well as the activity of the transporters is regulated by salinity/osmolarity and one of the key questions is how salinity or osmolarity is sensed and the signal transmitted as far as to gene expression and transporter activation. Recent studies shed light on the nature and the activation mechanisms of solute transporters in extremophiles, and this review summarizes current knowledge on the structure, function and osmo- or salt-regulation of transporters for compatible solutes in extremophiles.     

Transcriptional regulation in Archaea

During the past few decades, it has become clear that microorganisms can thrive under the most diverse conditions, including extremes of temperature, pressure, salinity and pH. Most of these extremophilic organisms belong to the third domain of life, that of the Archaea. The organisms of this domain are of particular interest because most informational systems that are associated with archaeal genomes and their expression are reminiscent of those seen in Eucarya, whereas, most of their metabolic aspects are similar to those of Bacteria. A better understanding of the regulatory mechanisms of gene expression in Archaea will, therefore, help to integrate the body of knowledge regarding the regulatory mechanisms that underlie gene expression in all three domains of life.     

Heat-shock response in Archaea

The Archaea are one of the three phylogenetic domains into which all organisms have been classified, and include extreme halophiles, extreme thermophiles and methanogens. Some of these organisms inhabit inhospitable environments on Earth, and thus have evolved stress responses to cope with the extremes of heat, pH and salinity that they encounter. Although the archaeal stress or heat-shock response bears some similarity to the heat-shock responses of other organisms, it possesses some unique features. A better understanding of this response would facilitate its exploitation in the biotechnological industries; for example, in engineering cells that exhibit an improved ability to withstand, or recover from, stress.