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At least 19 records
All sourcesNASA NTRSDOE OSTI
NASA NTRS1980

Lipids as a principle for the identification of Archaebacteria

The 'Archaebacteria' consist of several distinct subgroups including methanogens, extreme halophiles and specific thermoacidophiles. These bacteria are distinct from other bacteria with respect to their characteristic RNA compositions, the absence of muramic acid in the cell walls and the predominance of nonsaponifable lipids. The lipid composition of the Archaebacteria consists of isoprenoid and hydroisoprenoid hydrocarbons and isopranyl glycerol ether lipids. The pathways for the biosynthesis of the lipid components are those shared by most microorganisms and demonstrate a close relationship; however, an independent line of descent is indicated by the formation of the isopranyl glycerol ether lipids. This discontinuity formulates a point for delineating the early stages of biological evolution and for dividing bacteria into two subgroups.

Tornabene, T. G.↗
NASA NTRS1987

A possible biochemical missing link among archaebacteria

The characteristics of the newly discovered strain of archaebacteria, VC-16, the only archaebacterium known to reduce sulfate, suggest that VC-16 might represent a transitional form between an anaerobic thermophilic sulfur-based type of metabolism and methanogenesis. It is shown here, using a matrix of evolutionary distances derived from an alignment of various archaebacterial 16S rRNAs and the phylogenetic tree derived from these evolutionary distances, that the lineage represented by strain VC-16 arises from the archaebacterial tree precisely where such an interpretation would predict that it would, between the Methanococcus lineage and that of Thermococcus.

Achenbach-Richter, Laurie↗
NASA NTRS1988

The ribosomal gene spacer region in archaebacteria

Sequences for the spacer regions that separate the 16S and 23S ribosomal RNA genes have been determined for four more (strategically placed) archaebacteria. These confirm the general rule that methanogens and extreme halophiles have spacers that contain a single tRNAala gene, while tRNA genes are not found in the spacer region of the true extreme thermophiles. The present study also shows that the spacer regions from the sulfate reducing Archaeglobus and the extreme thermophile Thermococcus (both of which cluster phylogenetically with the methanogens and extreme halophiles) contain each a tRNAala gene. Thus, not only all methanogens and extreme halophiles show this characteristic, but all organisms on the "methanogen branch" of the archaebacterial tree appear to do so. The finding of a tRNA gene in the spacer region of the extreme thermophile Thermococcus celer is the first known phenotypic property that links this organism with its phylogenetic counterparts, the methanogens, rather than with its phenotypic counterparts, the sulfur-dependent extreme thermophiles.

Non-NASA Center↗
NASA NTRS1979

Squalenes, phytanes and other isoprenoids as major neutral lipids of methanogenic and thermoacidophilic 'archaebacteria'

The neutral lipids from nine species of methanogenic bacteria (five methanobacilli, two methanococci, a methanospirillum and a methanosarcina) and two thermoacidophilic bacteria (Thermo-plasma and Sulfolobus) have been analyzed. The neutral lipids were found to comprise a wide range (C14 to C30) of polyisoprenyl hydrocarbons with varying degrees of saturation. The principal components represented the three major isoprenoid series (C20 phytanyl, C25 pentaisoprenyl, and C30 squalenyl), in contrast with the neutral lipids of extreme halophiles, which consist predominantly of C2O (phytanyl, geranylgeraniol), C30 (squalenes), C40 (carotenes) and C50 (bacterioruberins compounds), as reported by Kates (1978). These results, which indicate strong general similarities between genetically diverse organisms, support the classification of these organisms in a separate phylogenetic group. The occurrence of similar isoprenoid compounds in petroleum and ancient sediments and the fact that the methanogens, halophiles and thermoacidophiles live in conditions presumed to have prevailed in archaen times suggest that the isoprenoid compounds in petroleum compounds and sediment may have been directly synthesized by organisms of this type

Tornabene, T. G.↗
NASA NTRS1989

Electrophoresis and isoelectric focusing of whole cell and membrane proteins from the extremely halophilic archaebacteria

The subunits from two purified halobacterial membrane enzymes (ATPase and nitrate reductase) behaved differently with respect to isoelectric focusing, silver staining and interaction with ampholytes. Differential behavior was also observed in whole cell proteins from Halobacterium saccharovorum regarding resolution in two-dimensional gels and silver staining. It is proposed that these differences reflect the existence of two classes of halobacterial proteins.

Stan-Lotter, Helga↗
NASA NTRS1993

The evolution of energy-transducing systems: Studies with archaebacteria

N-ethylmaleimide (NEM) inhibits the ATPase of H. saccharovorum in a nucleotide protectable manner. The bulk of 14C-NEM is incorporated into subunit 1. Inhibition kinetics indicated a single binding site. To determine the sequence around this site, cyanogen bromide peptides of NEM-labeled ATPase enzyme were prepared and separated on Tris-Tricine gels. Autoradiography indicated that the NEM binding site is probably located in a fragment of Mr 10-12 K. This result will be confirmed by N-terminal sequencing of the peptide. Since the cysteinyl residue, to which NEM is bound, may be located at the C-terminal end, purification and proteolytic treatment of the 10 K peptide will be required. One inhibitor of V-type ATPases, fluoresceinisothiocyanate (FITC) inhibited also the ATPase of H. saccharovorum. Preliminary results indicated protection against inhibition by nucleotides. Localization of the binding sited to the major subunits is in progress. An extraction procedure for the membrane sector of the ATPase complex of H. saccharovorum yielded a preparation which was enriched in a peptide of Mr 5 500. Experiments to test the immunological crossreaction with subunit c from the Escherichia coli F-type ATPase and the labeling with 14C-DCCD are currently carried out. Polyclonal antiserum to the smaller of the major subunits of the ATPase from H. saccharovorum (subunit ll) reacts in Western blots strongly with the alpha and beta subunits of the F1 ATPase of E. coli, suggesting highly conserved regions on both types of ATPases. To elucidate further the regions of homology, cyanogen bromide peptides of the beta subunits were prepared for sequence analysis.

Stan-Lotter, Helga↗
NASA NTRS1994

The evolution of energy-transducing systems. Studies with archaebacteria

N-ethylmaleimide (NEM) inhibits the ATPase of H. saccharovorum in a nucleotide protectable manner. The bulk of C-14 NEM is incorporated into subunit one. Cyanogen bromide cleavage of labeled subunit one indicated that NEM bound to a peptide of a Mr of about 8,900. Thus, Cys 262 (H. salinarium numbering) may be the NEM binding site. Cyanogen bromide fragments have been submitted for sequencing. To prove the presence of three Cys residues in subunit one, alkaline cleavage following treatment with NTCB was carried out. Thiol reagents such as p-chloro mercuri phenyl sulfonate also inhibited the ATPase. However, this inhibition was not nucleotide-protectable, suggesting a different location and role for the PCMS-sensitive Cys. The proteolipid which was extracted with chloroform/methanol from the membranes of H. saccharovorum cross-reacted with an antiserum against subunit c (the DCCD-binding protein) of Escherichia coli. Following labeling of membranes from H. saccharovorum with C-14 DCCD under conditions, which inhibited ATP synthesis, the isotope was incorporated into one protein of Mr of about 6,500. Thus, the proteolipid of H. saccharovorum and the DCCD-labeled peptide may be identical. If so, these results suggest that the proteolipid is a component of the membrane sector of an archaeal F-type ATP synthase.

Stan-Lotter, Helga↗
NASA NTRS1996

The Evolution of Energy-Transducing Systems. Studies with Archaebacteria

The dicyclohexyl carbodiimide (DCCD)- binding site of the membrane ATPase from Halobacterium saccharovorum was investigated during earlier periods of this Cooperative Agreement and was localized to a cyanogen bromide fragment of subunit 2 from amino acids 379 (Glu) to 442 (Met). Although the exact position of the reactive amino acid (probably a glutamic acid) has not yet been determined, the data, together with recently obtained immuno reactions and sequences of Cyanogen Bromide (CNBr) fragments from E.coli F-ATPase, suggested subunit interactions in the halobacterial ATPase which had not been recognized before. They also provided evidence for the presence of a gamma subunit in the halobacterial ATPase, and for a stretch of a amino acids similar to the 'catch' between beta and gamma in bovine F-ATPase. The evolutionary implications of these findings are twofold: first, halobacterial (or archaebacterial) ATPases appear as complex as those from higher organisms - no simpler versions of these membrane enzymes are known to date; second, a monophyletic origin of the energy-transducing ATPases is becoming more apparent, and - together with other data - the split into V- and F-ATPases may have occurred much later than had been previously thought (i.e., after the split into Archaea and Bacteria). Other work included the characterization of an extremely halophilic isolate (Halococcus salifodinae ) from Permian salt sediments. This organism appeared to be an autotrophic halobacterium; its incorporation of C02 was investigated.

Stan-Lotter, Helga↗
NASA NTRS1986

Archaebacterial phylogeny: perspectives on the urkingdoms

Comparisons of complete 16S ribosomal RNA sequences have been used to confirm, refine and extend earlier concepts of archaebacterial phylogeny. The archaebacteria fall naturally into two major branches or divisions, I--the sulfur-dependent thermophilic archaebacteria, and II--the methanogenic archaebacteria and their relatives. Division I comprises a relatively closely related and phenotypically homogeneous collection of thermophilic sulfur-dependent species--encompassing the genera Sulfolobus, Thermoproteus, Pyrodictium and Desulfurococcus. The organisms of Division II, however, form a less compact grouping phylogenetically, and are also more diverse in phenotype. All three of the (major) methanogen groups are found in Division II, as are the extreme halophiles and two types of thermoacidophiles, Thermoplasma acidophilum and Thermococcus celer. This last species branches sufficiently deeply in the Division II line that it might be considered to represent a separate, third Division. However, both the extreme halophiles and Tp. acidophilum branch within the cluster of methanogens. The extreme halophiles are specifically related to the Methanomicrobiales, to the exclusion of both the Methanococcales and the Methanobacteriales. Tp. acidophilum is peripherally related to the halophile-Methanomicrobiales group. By 16S rRNA sequence measure the archaebacteria constitute a phylogenetically coherent grouping (clade), which excludes both the eubacteria and the eukaryotes--a conclusion that is supported by other sequence evidence as well. Alternative proposals for archaebacterial phylogeny, not based upon sequence evidence, are discussed and evaluated. In particular, proposals to rename (reclassify) various subgroups of the archaebacteria as new kingdoms are found wanting, for both their lack of proper experimental support and the taxonomic confusion they introduce.

NASA Discipline Exobiology↗
NASA NTRS1983

Evolutionary connections of biological kingdoms based on protein and nucleic acid sequence evidence

Prokaryotic and eukaryotic evolutionary trees are developed from protein and nucleic-acid sequences by the methods of numerical taxonomy. Trees are presented for bacterial ferredoxins, 5S ribosomal RNA, c-type cytochromes , cytochromes c2 and c', and 5.8S ribosomal RNA; the implications for early evolution are discussed; and a composite tree showing the branching of the anaerobes, aerobes, archaebacteria, and eukaryotes is shown. Single lines are found for all oxygen-evolving photosynthetic forms and for the salt-loving and high-temperature forms of archaebacteria. It is argued that the eukaryote mitochondria, chloroplasts, and cytoplasmic host material are descended from free-living prokaryotes that formed symbiotic associations, with more than one symbiotic event involved in the evolution of each organelle.

Dayhoff, M. O.↗
NASA NTRS1992

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 eubacteria, chloroplasts, and mitochondria. 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 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. From studies of members of all three major groups of archaebacteria - 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. Amino acid sequences of critical regions of the enzyme were to be determined, as well as immunoreactions of single subunits in the search for common epitopes. 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 complexes, and possibly deduction of events during the early evolution of energy-transducing systems.

Stan-Lotter, Helga↗
NASA NTRS1988

Rooting the archaebacterial tree: the pivotal role of Thermococcus celer in archaebacterial evolution

The sequence of the 16S ribosomal RNA gene from the archaebacterium Thermococcus celer shows the organism to be related to the methanogenic archaebacteria rather than to its phenotypic counterparts, the extremely thermophilic archaebacteria. This conclusion turns on the position of the root of the archaebacterial phylogenetic tree, however. The problems encountered in rooting this tree are analyzed in detail. Under conditions that suppress evolutionary noise both the parsimony and evolutionary distance methods yield a root location (using a number of eubacterial or eukaryotic outgroup sequences) that is consistent with that determined by an "internal rooting" method, based upon an (approximate) determination of relative evolutionary rates.

Non-NASA Center↗
NASA NTRS1997

Determining divergence times with a protein clock: update and reevaluation

A recent study of the divergence times of the major groups of organisms as gauged by amino acid sequence comparison has been expanded and the data have been reanalyzed with a distance measure that corrects for both constraints on amino acid interchange and variation in substitution rate at different sites. Beyond that, the availability of complete genome sequences for several eubacteria and an archaebacterium has had a great impact on the interpretation of certain aspects of the data. Thus, the majority of the archaebacterial sequences are not consistent with currently accepted views of the Tree of Life which cluster the archaebacteria with eukaryotes. Instead, they are either outliers or mixed in with eubacterial orthologs. The simplest resolution of the problem is to postulate that many of these sequences were carried into eukaryotes by early eubacterial endosymbionts about 2 billion years ago, only very shortly after or even coincident with the divergence of eukaryotes and archaebacteria. The strong resemblances of these same enzymes among the major eubacterial groups suggest that the cyanobacteria and Gram-positive and Gram-negative eubacteria also diverged at about this same time, whereas the much greater differences between archaebacterial and eubacterial sequences indicate these two groups may have diverged between 3 and 4 billion years ago.

NASA Discipline Exobiology↗
DOE OSTI2022

Thylakoid Assembly and Folded Protein Transport by the Tat Pathway

Assembly of functional photosystems complete with necessary intrinsic and extrinsic proteins requires the function of at least three protein transport pathways in thylakoid membranes. Our research focuses on one of those pathways, a unique and essential protein transport pathway found in the chloroplasts of plants, bacteria, and some archaebacteria, the Twin arginine translocation (Tat) system. The chloroplast Tat (cpTat) system is thought to be responsible for the proper localization of ~50% of thylakoid lumen proteins, several of which are necessary for proper photosystem assembly, maintenance, and function. For example, two components of the extrinsic oxygen evolving complex, PsbP and PsbQ, are transported to the thylakoid lumen via the cpTat system. PsbP and PsbQ have been shown to be important in photosystem II function and maintenance (Yi et al. 2006; Yi et al. 2007). The current project addresses the issues of what forms the translocation conduit, how the translocon complex is arranged and what role Hcf106 and cpTatC may have in the process of forming the conduit.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Exploring Marine Planktonic Archaea: Then and Now

In 1977, Woese and Fox leveraged molecular phylogenetic analyses of ribosomal RNAs and identified a new microbial domain of life on Earth, the Archaebacteria (now known as Archaea). At the time of their discovery, only one archaebacterial group, the strictly anaerobic methanogens, was known. But soon, other phenotypically unrelated microbial isolates were shown to belong to the Archaea, many originating from extreme habitats, including extreme halophiles, extreme thermophiles, and thermoacidophiles. Since most Archaea seemed to inhabit extreme or strictly anoxic habitats, it came as a surprise in 1992 when two new lineages of archaea were reported to be abundant in oxygen rich, temperate marine coastal waters and the deep ocean. Since that time, studies of marine planktonic archaea have revealed many more surprises, including their unexpected ubiquity, unusual symbiotic associations, unpredicted physiologies and biogeochemistry, and global abundance. In this Perspective, early work conducted on marine planktonic Archaea by my lab group and others is discussed in terms of the relevant historical context, some of the original research motivations, and surprises and discoveries encountered along the way.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1978

Are extreme halophiles actually 'bacteria'

Comparative cataloging of the 16S rRNA of Halobacterium halobium indicates that the organism did not arise, as a halophilic adaptation, from some typical bacterium. Rather, H. halobium is a member of the Archaebacteria, an ancient group of organisms that are no more related to typical bacteria than they are to eucaryotes.

Magrum, L. J.↗
NASA NTRS1982

Evolution of major metabolic innovations in the Precambrian

A combination of information on the metabolic capabilities of prokaryotes with a composite phylogenetic tree depicting an overview of prokaryote evolution based on the sequences of bacterial ferredoxin, 2Fe-2S ferredoxin, 5S ribosomal RNA, and c-type cytochromes shows three zones of major metabolic innovation in the Precambrian. The middle of these, which reflects the genesis of oxygen-releasing photosynthesis and aerobic respiration, links metabolic innovations of the anaerobic stem on the one hand and, on the other, proliferation of aerobic bacteria and the symbiotic associations leading to the eukaryotes. Those pathways where information on the structure of the enzymes is known are especially considered. Halobacterium and Thermoplasma (archaebacteria) do not belong to a totally independent line on the basis of the composite tree but branch from the eukaryote cytoplasmic line.

Barnabas, J.↗
NASA NTRS1985

Distribution and abundance of organic thiols

The role of glutathione (GSH) in protecting against the toxicity of oxygen and oxygen by products is well established for all eukaryotes studied except Entamoeba histolytica which lacks mitochrondria, chloroplasts, and microtubules. The GSH is not universal among prokaryotes. Entamoeba histolytica does not produce GSH or key enzymes of GSH metabolism. A general method of thiol analysis based upon fluorescent labeling with monobromobimane and HPLC separation of the resulting thiol derivatives was developed to determine the occurrence of GSH and other low molecular weight thiols in bacteria. Glutathione is the major thiol in cyanobacteria and in most bacteria closely related to the purple photosynthetic bacteria, but GSH was not found in archaebacteria, green bacteria, or GRAM positive bacteria. It suggested that glutathione metabolism was incorporated into eukaryotes at the time that mitochondria and chloroplasts were acquired by endosymbiosis. In Gram positive aerobes, coenzyme A occurs at millimolar levels and CoA disulfide reductases are identified. The CoA, rather than glutathione, may function in the oxygen detoxification processes of these organisms.

Fahey, R.↗