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At least 19 records
All sourcesNASA NTRSDOE OSTI
NASA NTRS1999

Archaea: From Genomics to Physiology and the Origin of Life

This document represents a report on a meeting about Archaea. The meeting had an unusually diversified mix of topics all related to Archaea highlighting their differences and similarities with other kingdoms of life. Thus, a large number of scientists from others areas of biology participated in this conference. One-third of the speakers (11 of 33) represented laboratories whose main interests have not been archaea and who have not previously participated in similar symposia or workshops. Thus, this symposium provided a unique opportunity for archaeal researchers to interact in a wider forum. Because of the broad range of topics covered, the conference also introduced many of the participants to new areas of archaeal research. The discussions of genomics, molecular mechanisms of transcription, metabolic pathways and evolution were at a very high level. Talks and posters provided detailed discussions of the state of the current knowledge in RNA processing, transcriptional initiation, chromatin structure, aminoacyl-tRNA synthetases, autotrophic CO2 fixation, Upid biosynthesis and a wide range of other topics. In addition to providing overviews, major areas of scientific argument were clearly delineated, particularly in the discussions of genomics and evolution. Some of the questions raised included: how representative are individual gene trees of organismal evolution, how prevalent is horizontal evolution, how reliable are functional assignments in genomics? On these topics, the different points of view were well represented. The future of any field depends on the enthusiasm and intellectual engagement of young scientists working in the area. Therefore, the participation of 29 graduate and postdoctoral students (out of about 135 participants) was a highlight of the meeting. This was the consequence of funding contributions by NSF and NASA.

Vothknecht, Ute C.↗
NASA NTRS1994

Transcription factor IID in the Archaea: sequences in the Thermococcus celer genome would encode a product closely related to the TATA-binding protein of eukaryotes

The first step in transcription initiation in eukaryotes is mediated by the TATA-binding protein, a subunit of the transcription factor IID complex. We have cloned and sequenced the gene for a presumptive homolog of this eukaryotic protein from Thermococcus celer, a member of the Archaea (formerly archaebacteria). The protein encoded by the archaeal gene is a tandem repeat of a conserved domain, corresponding to the repeated domain in its eukaryotic counterparts. Molecular phylogenetic analyses of the two halves of the repeat are consistent with the duplication occurring before the divergence of the archael and eukaryotic domains. In conjunction with previous observations of similarity in RNA polymerase subunit composition and sequences and the finding of a transcription factor IIB-like sequence in Pyrococcus woesei (a relative of T. celer) it appears that major features of the eukaryotic transcription apparatus were well-established before the origin of eukaryotic cellular organization. The divergence between the two halves of the archael protein is less than that between the halves of the individual eukaryotic sequences, indicating that the average rate of sequence change in the archael protein has been less than in its eukaryotic counterparts. To the extent that this lower rate applies to the genome as a whole, a clearer picture of the early genes (and gene families) that gave rise to present-day genomes is more apt to emerge from the study of sequences from the Archaea than from the corresponding sequences from eukaryotes.

NASA Discipline Exobiology↗
NASA NTRS2000

Apparent Minimum Free Energy Requirements for Methanogenic Archaea and Sulfate-Reducing Bacteria in an Anoxic Marine Sediment

Among the most fundamental constraints governing the distribution of microorganisms in the environment is the availability of chemical energy at biologically useful levels. To assess the minimum free energy yield that can support microbial metabolism in situ, we examined the thermodynamics of H2-consuming processes in anoxic sediments from Cape Lookout Bight, NC, USA. Depth distributions of H2 partial pressure, along with a suite of relevant concentration data, were determined in sediment cores collected in November (at 14.5 C) and August (at 27 C) and used to calculate free energy yields for methanogenesis and sulfate reduction. At both times of year, and for both processes, free energy yields gradually decreased (became less negative) with depth before reaching an apparent asymptote. Sulfate reducing bacteria exhibited an asymptote of -19.1 +/- 1.7 kj(mol SO4(2-)(sup -1) while methanogenic archaea were apparently supported by energy yields as small as -10.6 +/- 0.7 kj(mol CH4)(sup -1).

Hoehler, Tori M.↗
NASA NTRS1991

A definition of the domains Archaea, Bacteria and Eucarya in terms of small subunit ribosomal RNA characteristics

The number of small subunit rRNA sequences is now great enough that the three domains Archaea, Bacteria and Eucarya (Woese et al., 1990) can be reliably defined in terms of their sequence "signatures". Approximately 50 homologous positions (or nucleotide pairs) in the small subunit rRNA characterize and distinguish among the three. In addition, the three can be recognized by a variety of nonhomologous rRNA characters, either individual positions and/or higher-order structural features. The Crenarchaeota and the Euryarchaeota, the two archaeal kingdoms, can also be defined and distinguished by their characteristic compositions at approximately fifteen positions in the small subunit rRNA molecule.

NASA Program Exobiology↗
NASA NTRS1999

Transcription in archaea

Using the sequences of all the known transcription-associated proteins from Bacteria and Eucarya (a total of 4,147), we have identified their homologous counterparts in the four complete archaeal genomes. Through extensive sequence comparisons, we establish the presence of 280 predicted transcription factors or transcription-associated proteins in the four archaeal genomes, of which 168 have homologs only in Bacteria, 51 have homologs only in Eucarya, and the remaining 61 have homologs in both phylogenetic domains. Although bacterial and eukaryotic transcription have very few factors in common, each exclusively shares a significantly greater number with the Archaea, especially the Bacteria. This last fact contrasts with the obvious close relationship between the archaeal and eukaryotic transcription mechanisms per se, and in particular, basic transcription initiation. We interpret these results to mean that the archaeal transcription system has retained more ancestral characteristics than have the transcription mechanisms in either of the other two domains.

NASA Discipline Exobiology↗
NASA NTRS1996

An Archaea 5S rRNA analog is stably expressed in Escherichia coli

Mini-genes for 5S-like rRNA were constructed. These genes had a sequence which largely resembles that of the naturally occurring 5S rRNA of a bacterium, Halococcus morrhuae, which phylogenetically belongs to the Archaea. Plasmids carrying the mini-genes were transformed into Escherichia coli (Ec). Ribosomal incorporation was not a prerequisite for stable accumulation of the RNA product. However, only those constructs with a well-base-paired helix I accumulated RNA product. This result strongly implies that this aspect of the structure is likely to be an important condition for stabilizing 5S rRNA-like products. The results are consistent with our current understanding of 5S rRNA processing in Ec. When used in conjunction with rRNA probe technology, the resulting chimeric RNA may be useful as a monitoring tool for genetically engineered microorganisms or naturally occurring organisms that are released into the environment.

Non-NASA Center↗
NASA NTRS2002

Lipid Biomarkers for Methanogens in Hypersaline Cyanobacterial Mats for Guerrero Negro, Baja California Sur

Analyses of sediments from the vicinity of active methane seeps have uncovered a particular suite of lipid biomarker patterns that characterize methane consuming archaea and their syntrophic, sulfate reducing partners. These isoprenoid biomarkers, largely identified by their anomalously light carbon isotopic signatures, have been a topic of intense research activity and are recorded in numerous methane-rich environments from Holocene to Cenozoic. This phenomenon has implications for depleted kerogens at 2.7 Ga on early Earth (Hinrichs 2002). In contrast, the lipid biosignatures of methane producing archaea are not readily identified through distinct isotopic labels and have received comparably little attention in analyses of archaea in environmental samples. Indeed, environmental analyses generally detect only free archaeal lipids, not the intact, polar molecules found in the membrane of living organisms. As part of the Ames NAI, the 'Early Microbial Ecosystem Research Group' (EMERG) is working to understand microbial processes in the hypersaline cyanobacterial mats growing in the salt evaporation ponds of the Exportadora de Sal at Guerrero Negro, Baja California Sur, Mexico. The aim of this study was to develop methods by which we could identify the organisms responsible for methane generation in this environment. While the ester-bound fatty acids, hopanoids and wax esters provide a means to identify most of the bacterial components of these mats, the archaea which Ere evidently present through genomic assays and the fact of intense methane production (Hoehler et al. 200l), have not been identified through their corresponding lipid signatures. Archaeal core lipids present a number of analytical challenges. The core lipids of methanogens comprise C20, C40 and sometimes C25 isoprenoid chains, linked through ether bonds to glycerol. As well as archaeal (C20), sn-2- and sn-3-hydroxyarchaeol are associated particularly with methylotrophic methanogens. Recently, we have also identified a dihydroxyarchaeol in a hyperthermophilic methanogen (Summons et al. 2002). Additional structural diversity is encoded into the polar head groups that are attached to the glycerol ether cores. The C20 core lipids are readily analyzed by GC-MS as their volatile trimethylsilyl derivatives while compounds with intact polar head groups can only be detected using LC-MS approaches. Our approach was to utilize the alternative of an ether cleavage reagent (BBr3 vs. HI) and a hydride reducing agent to convert all ether lipids to hydrocarbon in order to provide a vertical profile of quantitative information that might be matched to methane fluxes. We have found that while conventional acid hydrolysis and HI treatment will destroy hydroxyarchaeols, molecular information remains intact through use of BBr3 for ether cleavage. This method revealed the presence of traces of biphytane and various ether alkyls associated with some sulfate reducing bacteria within the mat structure. An interesting, and potentially valuable, byproduct of the method utilizing HI was the identification of abundant homohopanoids after superhydride reduction. Evidently present as sulfur-bound diagenetic products these hopanoids are likely cyanobacterial biomarkers in the early stages of diagenetic preservation.

Jahnke, Linda L.↗
NASA NTRS2001

Sulfate- and Sulfur-Reducing Bacteria as Terrestrial Analogs for Microbial Life on Jupiter's Satellite Io

Observations from the Voyager and Galileo spacecraft have revealed Jupiter's moon Io to be the most volcanically active body of our Solar System. The Galileo Near Infrared Imaging Spectrometer (NIMS) detected extensive deposits of sulfur compounds, elemental sulfur and SO2 frost on the surface of Io. There are extreme temperature variations on Io's surface, ranging from -130 C to over 2000 C at the Pillan Patera volcanic vent. The active volcanoes, fumaroles, calderas, and lava lakes and vast sulfur deposits on this frozen moon indicate that analogs of sulfur- and sulfate-reducing bacteria might inhabit Io. Hence Io may have great significance to Astrobiology. Earth's life forms that depend on sulfur respiration are members of two domains: Bacteria and Archaea. Two basic links of the biogeochemical sulfur cycle of Earth have been studied: 1) the sulfur oxidizing process (occurring at aerobic conditions) and 2) the process of sulfur-reduction to hydrogen sulfide (anaerobic conditions). Sulfate-reducing bacteria (StRB) and sulfur-reducing bacteria (SrRB) are responsible for anaerobic reducing processes. At the present time the systematics of StRB include over 112 species distributed into 35 genera of Bacteria and Archaea. Moderately thermophilic and mesophilic SrRB belong to the Bacteria. The hyperthermophilic SrRB predominately belong to the domain Archaea and are included in the genera: Pyrodictium, Thermoproteus, Pyrobaculum, Thermophilum, Desulfurococcus, and Thermodiscus. The StRB and SrRB use a wide spectrum of substrates as electron donors for lithotrophic and heterotrophic type nutrition. The electron acceptors for the StRB include: sulfate, thiosulfate, sulfite, sulfur, arsenate, dithionite, tetrathionate, sulfur monoxide, iron, nitrite, selenite, fumarate, oxygen, carbon dioxide, and chlorine-containing phenol compounds. The Sulfate- and Sulfur-reducing bacteria are widely distributed in anaerobic ecosystems, including extreme environments like hot springs, deepsea hydrothermal vents, soda and high salinity lakes, and cryo-environments. Furthermore, the StRB and SrRB have Astrobiological significance as these anaerobic extremophiles may represent the dominant relic life forms that inhabited our planet during the extensive volcanic activity in the Earth's early evolutionary period.

Pikuta, Elena V.↗
NASA NTRS1998

Archaeal translation initiation revisited: the initiation factor 2 and eukaryotic initiation factor 2B alpha-beta-delta subunit families

As the amount of available sequence data increases, it becomes apparent that our understanding of translation initiation is far from comprehensive and that prior conclusions concerning the origin of the process are wrong. Contrary to earlier conclusions, key elements of translation initiation originated at the Universal Ancestor stage, for homologous counterparts exist in all three primary taxa. Herein, we explore the evolutionary relationships among the components of bacterial initiation factor 2 (IF-2) and eukaryotic IF-2 (eIF-2)/eIF-2B, i.e., the initiation factors involved in introducing the initiator tRNA into the translation mechanism and performing the first step in the peptide chain elongation cycle. All Archaea appear to posses a fully functional eIF-2 molecule, but they lack the associated GTP recycling function, eIF-2B (a five-subunit molecule). Yet, the Archaea do posses members of the gene family defined by the (related) eIF-2B subunits alpha, beta, and delta, although these are not specifically related to any of the three eukaryotic subunits. Additional members of this family also occur in some (but by no means all) Bacteria and even in some eukaryotes. The functional significance of the other members of this family is unclear and requires experimental resolution. Similarly, the occurrence of bacterial IF-2-like molecules in all Archaea and in some eukaryotes further complicates the picture of translation initiation. Overall, these data lend further support to the suggestion that the rudiments of translation initiation were present at the Universal Ancestor stage.

NASA Discipline Exobiology↗
NASA NTRS1997

The Evolution of Energy-Transducing Systems. Studies with an Extremely Halophilic Archaebacterium

The F-type ATPases are found in remarkably similar versions in the energy-transducing membranes of bacteria, chloroplasts and mitochondria (1). Thus, it is likely that they have originated early in the evolution of life, which is consistent with their function as key enzymes of cellular metabolism. The archaea (formerly called archaebacteria) are a group of microorganisms which, as shown by molecular sequencing and biochemical data, have diverged early from the main line of prokaryotic evolution (2). From studies of members of all three major groups of archaea, the halophiles, methanogens and thermoacidophiles, it emerged that they possess a membrane ATPase, which differs from the F-ATPases. The goal of this project was a comparison of the ATPase from the halophilic archaebacterium Halobacterium saccharovorum with the well-characterized F-type ATPases on the molecular level. The results were expected to allow a decision about the nature of archaebacterial ATPases, their classification as one of the known or, alternatively, novel enzyme complex, and possibly a deduction of events during the early evolution of energy-transducing systems.

Stan-Lotter, Helga↗
NASA NTRS1994

ATP Synthesis in the Extremely Halophilic Bacteria

The proton-translocating ATPases are multimeric enzymes that carry out a multitude of essential functions. Their origin and evolution represent a seminal event in the early evolution of life. Amino acid sequences of the two largest subunits from archaeal ATPases (A-ATPases), vacuolar ATPases (V-ATPases), and FOF1-ATP syntheses (FATPases) suggest these ATPases evolved from an ancestral vacuolar-like ATP syntheses. A necessary consequence of this notion is that the A-ATPases are ATP syntheses. With the possible exception of the A-ATPase from Halobacterium salinarium. no A-ATPase has been demonstrated to synthesize ATP. The evidence for this case is dubious since ATP synthesis occurs only when conditions are distinctively unphysiological. We demonstrated that ATP synthesis in H.saccharovorum is inconsistent with the operation of an A-type ATPase. In order to determine if this phenomenon was unique to H. saccharovorum, ATP synthesis was examined in various extremely halophilic bacteria with the goal of ascertaining if it resembled what occurred in a. saccharovorum, or was consistent with the operation of an A-type ATPase. A-, V-, and F-type ATPases respond singularly to certain inhibitors. Therefore, the effect of these inhibitors on ATP synthesis in several extreme halophiles was determined. Inhibitors that either blocked or collapsed proton-gradients inhibited the steady state synthesis of ATP thus verifying that synthesis took place at the expense of a proton gradient. Azide, an inhibitor of F-ATPases inhibited ATP synthesis. Since the arginine-dependent synthesis of ATP, which occurs by way of substrate-level phosphorylation, was unaffected by azide, it was unlikely that azide acted as an "uncoupler." N -ethylmaleimide and nitrate, which inhibit V- and A-ATPases, either did not inhibit ATP synthesis or resulted in higher steady-state levels of ATP. These results suggest there are two types of proton-motive ATPases in the extreme halophiles (and presumably in other Archaea). One, the V-like enzyme which, provides protons that are subsequently used for solute translocation. The other ATPase is the familiar and ubiquitous F-ATPase that functions as a reversible proton pump and is the ATP Synthase in the extreme halophiles. Thus, while the suggested evolution of the proton -translocating ATPases accounts for the relationship among these ATPases, this scheme does not account for the presence of F-ATPases in the Archaea. Discounting lateral gene transfer, perhaps an F-type ATPase evolved before the eucaryal-archaeal and bacterial bifurcation. The presence of V-type ATPases in the Bacterial Domain is consistent with this suggestion. Finally, it is of interest to note that if an F-type ATPase appeared before the bifurcation, an endosymbiotic event need not be invoked to explain the presence of F-ATPases in the Eucarya.

Hochstein, Lawrence I.↗
NASA NTRS2003

Autotrophic Ecosystems on the Early Earth

Ophiolite sequences, sections of lower oceanic crust and upper mantle that have been thrust onto continental craton, are located in northern and central California and provide easily accessible areas that serve as good analogs for similar, more extensive areas of the early Earth. We have begun investigating and characterizing these sites in order to understand better the processes that may be responsible for the water chemistry, mineralogy and biology of similar environments on the early Earth. The geophysical and geochemical processes in these terranes provide niches for unique communities of extremeophiles and likely provide a good analog to the location that first gave rise to life on Earth. The ophiolites found in northern and central California include the Trinity, Josephine, Coast Range and Point Sal, all of which are approximately 160 million years old. Fluids from serpentinizing springs are generally alkaline with high pH and H2 contents, indicating that the mafic rock compositions control the fluid composition through water-rock reactions during relatively low-grade hydrothermal processes. There are significant amounts of primary mineralogy remaining in the rocks, meaning that substantial alteration processes are still occurring in these terranes. The general reaction for serpentinization of olivine is given by one of the authors. olivine + H2O = serpentine + brucite + magnetite + H2. We have analyzed the mineralogical composition of several rock samples collected from the Coast Range Ophiolite near Clear Lake, CA by electron microprobe. The remnant primary mineralogy is fairly urnform in composition, with an olivine composition of Fo(sub 90), and with pyroxene compositions of En(sub 90) for orthopyroxene and En(sub 49)Wo(sub 48)Fs(sub 03) for the clinopyroxene. Other primary phases observed include chromites and other spinels. Examination of petrographic thin sections reveals that serpentinization reactions have occurred in these locations. The serpentine resulting from aqueous alteration of olivine resides in veins that are see to cross cut the primary mineral grains. There are several generations of alteration products, comprised mostly of serpentines that are magnesium rich, with magnetite, brucite and carbonates observed as accessory minerals. The formation of carbonates can be taken to indicate the presence of CO2 in the altering fluids. We collected samples from a spring in the Coast Range Ophiolite in order to determine whether the geochemical environment serves as a habitat for chemotrophic microorganisms. DNA was extracted from the sediment samples and the 16s rRNA gene was PCR amplified using universal Archaeal primers. Denaturing gradient gel electrophoresis (DGGE) was used to determine the community of Archaea thriving in these samples. Our results indicate that there were 8 different genera of Archaea from a single sample. A sequence was obtained from one of these eight. The sequence is of an organism similar to Halorubrum tibetense, and alkalophilic Archaeon. This result suggests that these environments are likely hosts for communities of organisms that are adapted for the unique chemistry provided by the alkaline spring.

Schulte, M.↗
NASA NTRS2000

Horizontal transfer of archaeal genes into the deinococcaceae: detection by molecular and computer-based approaches

Members of the Deinococcaceae (e.g., Thermus, Meiothermus, Deinococcus) contain A/V-ATPases typically found in Archaea or Eukaryotes which were probably acquired by horizontal gene transfer. Two methods were used to quantify the extent to which archaeal or eukaryotic genes have been acquired by this lineage. Screening of a Meiothermus ruber library with probes made against Thermoplasma acidophilum DNA yielded a number of clones which hybridized more strongly than background. One of these contained the prolyl tRNA synthetase (RS) gene. Phylogenetic analysis shows the M. ruber and D. radiodurans prolyl RS to be more closely related to archaeal and eukaryal forms of this gene than to the typical bacterial type. Using a bioinformatics approach, putative open reading frames (ORFs) from the prerelease version of the D. radiodurans genome were screened for genes more closely related to archaeal or eukaryotic genes. Putative ORFs were searched against representative genomes from each of the three domains using automated BLAST. ORFs showing the highest matches against archaeal and eukaryotic genes were collected and ranked. Among the top-ranked hits were the A/V-ATPase catalytic and noncatalytic subunits and the prolyl RS genes. Using phylogenetic methods, ORFs were analyzed and trees assessed for evidence of horizontal gene transfer. Of the 45 genes examined, 20 showed topologies in which D. radiodurans homologues clearly group with eukaryotic or archaeal homologues, and 17 additional trees were found to show probable evidence of horizontal gene transfer. Compared to the total number of ORFs in the genome, those that can be identified as having been acquired from Archaea or Eukaryotes are relatively few (approximately 1%), suggesting that interdomain transfer is rare.

Non-NASA Center↗
NASA NTRS2000

Cloning and characterization of ftsZ and pyrF from the archaeon Thermoplasma acidophilum

To characterize cytoskeletal components of archaea, the ftsZ gene from Thermoplasma acidophilum was cloned and sequenced. In T. acidophilum ftsZ, which is involved in cell division, was found to be in an operon with the pyrF gene, which encodes orotidine-5'-monophosphate decarboxylase (ODC), an essential enzyme in pyrimidine biosynthesis. Both ftsZ and pyrF from T. acidophilum were expressed in Escherichia coli and formed functional proteins. FtsZ expression in wild-type E. coli resulted in the filamentous phenotype characteristic of ftsZ mutants. T. acidophilum pyrF expression in an E. coli mutant lacking pyrF complemented the mutation and rescued the strain. Sequence alignments of ODCs from archaea, bacteria, and eukarya reveal five conserved regions, two of which have homology to 3-hexulose-6-phosphate synthase (HPS), suggesting a common substrate recognition and binding motif. Copyright 2000 Academic Press.

Bacterial Proteins/chemistry/genetics/metabolism↗
NASA NTRS2000

An archaeal genomic signature

Comparisons of complete genome sequences allow the most objective and comprehensive descriptions possible of a lineage's evolution. This communication uses the completed genomes from four major euryarchaeal taxa to define a genomic signature for the Euryarchaeota and, by extension, the Archaea as a whole. The signature is defined in terms of the set of protein-encoding genes found in at least two diverse members of the euryarchaeal taxa that function uniquely within the Archaea; most signature proteins have no recognizable bacterial or eukaryal homologs. By this definition, 351 clusters of signature proteins have been identified. Functions of most proteins in this signature set are currently unknown. At least 70% of the clusters that contain proteins from all the euryarchaeal genomes also have crenarchaeal homologs. This conservative set, which appears refractory to horizontal gene transfer to the Bacteria or the Eukarya, would seem to reflect the significant innovations that were unique and fundamental to the archaeal "design fabric." Genomic protein signature analysis methods may be extended to characterize the evolution of any phylogenetically defined lineage. The complete set of protein clusters for the archaeal genomic signature is presented as supplementary material (see the PNAS web site, www.pnas.org).

Non-NASA Center↗
NASA NTRS1993

An intron within the 16S ribosomal RNA gene of the archaeon Pyrobaculum aerophilum

The 16S rRNA genes of Pyrobaculum aerophilum and Pyrobaculum islandicum were amplified by the polymerase chain reaction, and the resulting products were sequenced directly. The two organisms are closely related by this measure (over 98% similar). However, they differ in that the (lone) 16S rRNA gene of Pyrobaculum aerophilum contains a 713-bp intron not seen in the corresponding gene of Pyrobaculum islandicum. To our knowledge, this is the only intron so far reported in the small subunit rRNA gene of a prokaryote. Upon excision the intron is circularized. A secondary structure model of the intron-containing rRNA suggests a splicing mechanism of the same type as that invoked for the tRNA introns of the Archaea and Eucarya and 23S rRNAs of the Archaea. The intron contains an open reading frame whose protein translation shows no certain homology with any known protein sequence.

NASA Discipline Exobiology↗