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PubMed2005

Posttranslational protein modification in Archaea.

One of the first hurdles to be negotiated in the postgenomic era involves the description of the entire protein content of the cell, the proteome. Such efforts are presently complicated by the various posttranslational modifications that proteins can experience, including glycosylation, lipid attachment, phosphorylation, methylation, disulfide bond formation, and proteolytic cleavage. Whereas these and other posttranslational protein modifications have been well characterized in Eucarya and Bacteria, posttranslational modification in Archaea has received far less attention. Although archaeal proteins can undergo posttranslational modifications reminiscent of what their eucaryal and bacterial counterparts experience, examination of archaeal posttranslational modification often reveals aspects not previously observed in the other two domains of life. In some cases, posttranslational modification allows a protein to survive the extreme conditions often encountered by Archaea. The various posttranslational modifications experienced by archaeal proteins, the molecular steps leading to these modifications, and the role played by posttranslational modification in Archaea form the focus of this review.

Archaea↗
PubMed2002

Common evolutionary origins of mechanosensitive ion channels in Archaea, Bacteria and cell-walled Eukarya.

The ubiquity of mechanosensitive (MS) channels triggered a search for their functional homologs in Archaea. Archaeal MS channels were found to share a common ancestral origin with bacterial MS channels of large and small conductance, and sequence homology with several proteins that most likely function as MS ion channels in prokaryotic and eukaryotic cell-walled organisms. Although bacterial and archaeal MS channels differ in conductive and mechanosensitive properties, they share similar gating mechanisms triggered by mechanical force transmitted via the lipid bilayer. In this review, we suggest that MS channels of Archaea can bridge the evolutionary gap between bacterial and eukaryotic MS channels, and that MS channels of Bacteria, Archaea and cell-walled Eukarya may serve similar physiological functions and may have evolved to protect the fragile cellular membranes in these organisms from excessive dilation and rupture upon osmotic challenge.

Animals↗
PubMed2005

Higher-level classification of the Archaea: evolution of methanogenesis and methanogens.

We used a phylogenetic approach to analyze the evolution of methanogenesis and methanogens. We show that 23 vertically transmitted ribosomal proteins do not support the monophyly of methanogens, and propose instead that there are two distantly related groups of extant archaea that produce methane, which we have named Class I and Class II. Based on this finding, we subsequently investigated the uniqueness of the origin of methanogenesis by studying both the enzymes of methanogenesis and the proteins that synthesize its specific coenzymes. We conclude that hydrogenotrophic methanogenesis appeared only once during evolution. Genes involved in the seven central steps of the methanogenic reduction of carbon dioxide (CO(2)) are ubiquitous in methanogens and share a common history. This suggests that, although extant methanogens produce methane from various substrates (CO(2), formate, acetate, methylated C-1 compounds), these archaea have a core of conserved enzymes that have undergone little evolutionary change. Furthermore, this core of methanogenesis enzymes seems to originate (as a whole) from the last ancestor of all methanogens and does not appear to have been horizontally transmitted to other organisms or between members of Class I and Class II. The observation of a unique and ancestral form of methanogenesis suggests that it was preserved in two independent lineages, with some instances of specialization or added metabolic flexibility. It was likely lost in the Halobacteriales, Thermoplasmatales and Archaeoglobales. Given that fossil evidence for methanogenesis dates back 2.8 billion years, a unique origin of this process makes the methanogenic archaea a very ancient taxon.

Archaea↗
PubMed2004

Archaea recruited D-Tyr-tRNATyr deacylase for editing in Thr-tRNA synthetase.

Aminoacyl-tRNA synthetases (AARSs) are key players in the maintenance of the genetic code through correct pairing of amino acids with their cognate tRNA molecules. To this end, some AARSs, as well as seeking to recognize the correct amino acid during synthesis of aminoacyl-tRNA, enhance specificity through recognition of mischarged aminoacyl-tRNA molecules in a separate editing reaction. Recently, an editing domain, of uncertain provenance, idiosyncratic to some archaeal ThrRSs has been characterized. Here, sequence analyses and molecular modeling are reported that clearly show a relationship of the archaea-specific ThrRS editing domains with d-Tyr-tRNATyr deacylases (DTDs). The model enables the identification of the catalytic site and other substrate binding residues, as well as the proposal of a likely catalytic mechanism. Interestingly, typical DTD sequences, common in bacteria and eukaryotes, are entirely absent in archaea, consistent with an evolutionary scheme in which DTD was co-opted to serve as a ThrRS editing domain in archaea soon after their divergence from eukaryotes. A group of present-day archaebacteria contain a ThrRS obtained from a bacterium by horizontal gene transfer. In some of these cases a vestigial version of the original archaeal ThrRS, of potentially novel function, is maintained.

Amino Acid Sequence↗
PubMed1998

The euryarchaeotes, a subdomain of Archaea, survive on a single DNA polymerase: fact or farce?

Archaea is now recognized as the third domain of life. Since their discovery, much effort has been directed towards understanding the molecular biology and biochemistry of Archaea. The objective is to comprehend the complete structure and the depth of the phylogenetic tree of life. DNA replication is one of the most important events in living organisms and DNA polymerase is the key enzyme in the molecular machinery which drives the process. All archaeal DNA polymerases were thought to belong to family B. This was because all of the products of pol genes that had been cloned showed amino acid sequence similarities to those of this family, which includes three eukaryal DNA replicases and Escherichia coli DNA polymerase II. Recently, we found a new heterodimeric DNA polymerase from the hyperthermophilic archaeon, Pyrococcus furiosus. The genes coding for the subunits of this DNA polymerase are conserved in the euryarchaeotes whose genomes have been completely sequenced. The biochemical characteristics of the novel DNA polymerase family suggest that its members play an important role in DNA replication within euryarchaeal cells. We review here our current knowledge on DNA polymerases in Archaea with emphasis on the novel DNA polymerase discovered in Euryarchaeota.

Amino Acid Sequence↗
PubMed2002

Origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria supported by the newly clarified origin of functional genes.

In the previous report, we demonstrated the origin of eukaryotic cell nuclei as the symbiosis of Archaea in Bacteria by the newly developed "Homology-Hit Analysis". In that case, we counted yeast Open Reading Frames (ORFs) showing the highest similarity to a bacterial ORF as orthologous ORFs (Orthologous ORFs were produced by speciation from a common ancestor, and have the highest similarity to each other.) by comparing whole ORFs of yeast with those of individual bacteria. However, we could not count all yeast ORFs showing the highest similarity to a bacterial ORF in functional categories of yeast. Therefore, the origin of ORFs in the functional categories of yeast could not be inferred strictly. Here, we have improved the method for detecting orthologous ORFs. In this method, we count the numbers of ORF with the highest similarity between individual yeast functional categories and individual bacteria as orthologous ORFs. By this method, it was possible to detect the correct orthologous ORFs and to infer the origins of the functional categories in eukaryotic cells. As a result, two categories, assembly of protein complexes and DNA repair were newly judged to be of Archaeal origin, while five categories, lipid (fatty-acid and isoprenoid) metabolism, protein folding and stabilization, signal transduction, organization of the plasma membrane and organization of the cytoplasm, were newly judged to be of Bacterial origin. On the other hand, the origins of two categories (meiosis and cellular import, which were determined in the previous analysis) could not be judged. It is considered that functional categories related to the nucleus have origins common to Archaea, while those related to the cytoplasm have origins common to Bacteria. From these data including the origin of plasma membrane, it was further clarified that cell nucleus originated by the symbiosis of Archaea in Bacteria.

Archaea↗
PubMed2004

Osmoadaptation and osmoregulation in archaea: update 2004.

The response of archaea to changes in external NaCl is reviewed and compared to what is known about osmoadaptation and osmoregulation in bacteria and eukaryotes. Cells placed in altered external NaCl exhibit short term and long term responses. The earliest events are likely to be water movement through aquaporin-like channels (efflux if external NaCl has been increased, influx into the cell if the external NaCl has been decreased) and ion movement (e.g., K+ moving in the direction opposite to water flow) through channels sensitive to osmotic pressure. A brief discussion of recent structures of homologues of these membrane proteins is presented. Accumulation of organic solutes, either by uptake from the medium or de novo synthesis, is triggered after these initial changes. Archaea have some unique organic solutes (osmolytes) that are not used by other organisms. These as well as other more common solutes have a role in stabilizing macromolecules from denaturation. Many osmolytes are distinguished by their stability in the cell and their lack of strong interactions with cellular components. A cell may respond by accumulating one or more temporary osmolytes, then over time readjust the intracellular solute distribution to what is optimal for cell growth under the new conditions. Coupled with the movement and accumulation of solutes is the induction of stress proteins (e.g., chaperonins) and, in some cases, transcriptional regulation of key enzymes. The response to NaCl stress of Methanococcus thermolithotrophicus is presented as an example of how one particular archaeon responds and adapts to altered osmotic pressure. The detailed response of many other archaea to osmotic stress will be needed in order to identify features (aside from some of the organic osmolytes) unique to the organisms in this kingdom.

Adaptation, Physiological↗
PubMed2001

The molecular chaperone system and other anti-stress mechanisms in archaea.

This article presents a brief review of stressors, their cellular and intracellular targets, stress proteins, molecular chaperones, and other anti-stress mechanisms. New data are reported on cochaperones and multicellular structures in archaea. The molecular chaperoning systems of bacteria and eukaryotes have been studied for many years and are relatively well known in terms of their components and mechanisms of action, although many details remain to be elucidated and almost certainly other components will be discovered in the future. By comparison, the molecular chaperoning system of archaea is still unexplored. Since archaea have some molecular genetic and physiologic features similar to those of bacteria and some resembling those of eukaryotes, extrapolation from what is known of organisms from these two phylogenetic domains to archaeal species is unwarranted. For example, the components of the molecular chaperone machine, Hsp70(DnaK), Hsp40(DnaJ), and GrpE, in the archaeal species that have it, are closely related to bacterial counterparts, whereas the archaeal chaperonins are like the eukaryotic equivalents. Furthermore, many archaeal species lack the chaperone machine, in contrast to bacteria and eukaryotes that have it without any known exception. A search for the cochaperones trigger factor, Hop, Hip, BAG-1, and NAC in archaeal genomes demonstrated no conserved equivalents, but two families of archaeal molecules were identified that might be related to NAC and Hop, respectively. Multicellular structures with a single species such as packet and lamina are formed by Methanosarcina species, among which the best studied is M. mazeii. Multispecies multicellular structures are formed by a variety of archaeal organisms, which are either flat (biofilm) or globular (granule) and constitute a functional association or consortium. Details of morphology, formation, and internal organization are described for representative examples of multicellular structures. These may be seen as the result of primitive histogenesis reflecting primeval mechanisms of differentiation-development that might have evolved driven by environmental stressors. Cells in these complex threedimensional arrangements are not only positioned so they can interact with each other for more efficient functioning as in a tissue or organ, but are also protected from stressors. Single cells lacking the protective shield of other cells packed together with intercellular connective material, which is typical of multicellular structures, are directly exposed to environmental stressors and, thus, are at a disadvantage from the evolutionary standpoint. It seems reasonable to argue that differentiation-development leading to histogenesis might have arisen in primeval times as a consequence of the harsh conditions that primitive life forms had to endure, and that the ability to form tissue-like structures was a primary characteristic that ensured positive selection.

Acute-Phase Proteins↗
PubMed2000

Osmoadaptation and osmoregulation in archaea.

The response of archaea to changes in external NaCl is reviewed and compared to what is known about osmoadaptation and osmoregulation in bacteria and eukaryotes. Cells placed in altered external NaCl exhibit short term and long term responses. The earliest events are likely to be water movement through aquaporin-like channels (efflux if external NaCl has been increased, influx into the cell if the external NaCl has been decreased) and ion movement (e.g., K+ moving in the direction opposite to water flow) through channels sensitive to osmotic pressure. Accumulation of organic solutes, either by uptake from the medium or de novo synthesis, is triggered after these initial changes. Archaea have some unique organic solutes (osmolytes) that are not used by other organisms. These as well as other more common solutes have a role in stabilizing macromolecules from denaturation. Many osmolytes are distinguished by their stability in the cell and their lack of strong interactions with cellular components. A cell may respond by accumulating one or more temporary osmolytes, then over time readjust the intracellular solute distribution to what is optimal for cell growth under the new conditions. Coupled with the movement and accumulation of solutes is the induction of stress proteins (e.g., chaperonins) and, in some cases, transcriptional regulation of key enzymes. The response to NaCl stress of Methanococcus thermolithotrophicus is presented as an example of how one particular archaeon responds and adapts to altered osmotic pressure. Clearly, the detailed response of other archaea to osmotic stress will be needed in order to identify features (aside from some of the organic osmolytes) unique to the organisms in this kingdom.

Adaptation, Physiological↗
PubMedDate not supplied

Birth of the domains Bacteria, Archaea and Eucarya and of major taxa within them: a hypothesis.

A hypothesis to explain how the birth of the Bacteria, Archaea and Eucarya domains and of major taxa within them took place is presented. It is proposed that the birth of each domain was an independent event consisting in the genetic isolation of a particular cell from a very diverse pool of "primitive cells". Cells within this pool have a dynamic pattern of cell fusion followed by mostly illegitimate DNA recombination. It is postulated that genetic isolation was achieved: a) by evolution of the peptidoglycan layer in Bacteria, b) by evolution of a glycoproteic cell wall in Archaea, and c) by evolution of the nuclear membrane in Eucarya. It is also postulated that, within each domain, branching was a consequence of sporadic events of fusion between two cells of different phylogenetic lineages, followed by mostly illegitimate DNA recombination and cell wall regeneration. The two fusing cells may have belonged to the same domain, to different domains or even one may have belonged to one of the domains and the other to the pool of "primitive cells". In this last case, new complex phenotypes, previously absent from all the domains, were suddenly introduced in one of them (e.g.: photosynthesis in Bacteria, methanogenesis in Archaea). A corollary of this theory is that genes should have a phylogenetic tree with defined nodes while organisms are characterized by discontinuities instead of nodes.

Animals↗
PubMedDate not supplied

[Susceptibility of archaea to the antibiotic effect of the parasporal inclusion proteins from Bacillus thuringiensis subspecies].

The proteins of parasporal inclusions from three Bacillus thuringiensis subspecies (kurstaki, amagiensis, and monterrey) inhibited growth of methanogenic archaea of two species belonging to two genera, Methanobrevibacter arboriphilus and Methanosarcina barkeri. The minimal inhibitory concentrations of these proteins were 20 to 50 micrograms/ml. Lysozyme exhibited similar bactericidal effect on archaea. The perspective of comparative studies on the effect of polyfunctional proteins on bacteria and archaea is discussed.

Archaea↗
PubMed2002

Facile distinction of neutral and acidic tetraether lipids in archaea membrane by halogen atom adduct ions in electrospray ionization mass spectrometry.

Calditocaldarchaeol (neutral tetraether lipid) from Sulfolobus acidocaldarius (acidothermophilic archaea) and intact total lipid from the thermoacidophilic archaea Sulfolobus sp. was examined by electrospray ionization time-of-flight mass spectrometry in the negative-ion mode using high resolution. When the sample was injected as a solution in a 3:1 mixture of methanol (MeOH) and chloroform (CHCl(3)) using an infusion system, the total ether lipid afforded molecular-related ions as [M - H](-) for acidic polar lipids containing a phosphoric or sulfuric group, and as [M + Cl](-) ion for neutral glycolipids. The attachment of chloride was confirmed by the observation of [M + Br](-) ion, instead of [M + Cl](-) ion, when a 3:1 mixture of MeOH and CHBr(3) was used in place of MeOH-CHCl(3) as the solvent. The composition of tetraether neutral glycolipids that are different from each other only in the number of five-membered rings in the isoprenoid chain was determined on the basis of the isotope-resolved mass spectrum of [M + Cl](-) ions. As for acidic tetraether lipids, molecular-related ions [M - H](-)) were not observed when the 3:1 MeOH-CHBr(3) mixture was used as the solvent. These results together afforded a facile method of distinguishing neutral from acidic tetraether lipids in intact total lipids of acidothermophilic archaea. This method was applied to determine the difference of the number of five-membered rings in isoprenyl chains of neutral tetraether glycolipids yielded by the Sulfolobus sp. grown at different temperatures. Discrimination of neutral tetraether glycolipids from acidic tetraether lipids in the total lipids obtained from Thermoplasma sp. was also achieved by this method.

Animals↗
PubMed2003

The 492-bp RM07 DNA fragment from the halophilic Archaea confers promoter activity in all three domains of life.

A 492-bp DNA fragment, designated RM07, was isolated from the chromosomal DNA of the halophilic Archaea, Halobacterium halobium, and was shown to confer promoter activity in Escherichia coli. Sequence analysis revealed that RM07 contained three consensus sequences of the archaeal distal promoter element as well as the typical -35 and -10 box sequences of bacterial promoters. Promoter probe analysis confirmed that RM07 conferred promoter activity in all three domains of life: Archaea (Haloferax volcanii), Eukarya (Saccharomyces cerevisiae) and Bacteria (Escherichia coli). Deletion analysis and site-directed mutagenesis further identified the functional regions within RM07 required for promoter activity. This is the first report of a DNA fragment from Archaea that confers promoter activity in all three domains of life, suggesting that the promoter structure and activity may be viewed as a bridge narrowing the gaps among the different domains of life.

Artificial Gene Fusion↗
PubMed2006

Survival and growth of two heterotrophic hydrothermal vent archaea, Pyrococcus strain GB-D and Thermococcus fumicolans, under low pH and high sulfide concentrations in combination with high temperature and pressure regimes.

Growth and survival of hyperthermophilic archaea in their extreme hydrothermal vent and subsurface environments are controlled by chemical and physical key parameters. This study examined the effects of elevated sulfide concentrations, temperature, and acidic pH on growth and survival of two hydrothermal vent archaea (Pyrococcus strain GB-D and Thermococcus fumicolans) under high temperature and pressure regimes. These two strains are members of the Thermococcales, a family of hyperthermophilic, heterotrophic, sulfur-reducing archaea that occur in high densities at vent sites. As actively growing cells, these two strains tolerated regimes of pH, pressure, and temperature that were in most cases not tolerated under severe substrate limitation. A moderate pH of 5.5-7 extends their survival and growth range over a wider range of sulfide concentrations, temperature and pressure, relative to lower pH conditions. T. fumicolans and Pyrococcus strain GB-D grew under very high pressures that exceeded in-situ pressures typical of hydrothermal vent depths, and included deep subsurface pressures. However, under the same conditions, but in the absence of carbon substrates and electron acceptors, survival was generally lower, and decreased rapidly when low pH stress was combined with high pressure and high temperature.

Hot Temperature↗
PubMed1997

Shuttle vectors for hyperthermophilic archaea.

Progress in understanding the basic molecular, biochemical, and physiological characteristics of archaeal hyperthermophiles has been limited by the lack of suitable expression vectors. Here, we report the construction of versatile shuttle vectors that can be maintained, and selected for, in both archaea and bacteria. The primary construct, pAG1, was produced by ligating portions of the archaeal cryptic plasmid pGT5 and the bacterial plasmid pUC19, both of which exhibit high copy numbers. A second vector construct, pAG2, was generated, with a reduced copy number in Escherichia coli, by introducing the Rom/Rop gene from pBR322 into pAG1. After transformation, both pAG1 and pAG2 were stably maintained and propagated in the euryarchaeote Pyrococcus furiosus, the crenarchaeote Sulfolobus acidocaldarius, and in Escherichia coli. An archaeal selective marker, the alcohol dehydrogenase gene from Sulfolobus solfataricus, was isolated by polymerase chain reaction (PCR) amplification and cloned into the two constructs. They were stably maintained and expressed in the two archaea and conferred resistance to butanol and benzyl alcohol. However, the vector pAG21, deriving from pAG2, proved the more stable in E. coli probably due to its lower copy number in the bacterium. Conditions are presented for the use of the vectors which, potentially, can be used for other hyperthermophilic archaea.

Alcohol Dehydrogenase↗
PubMed2004

Phylogenetic analysis of archaea in three fractions of cow rumen based on the 16S rDNA sequence.

Phylogenetic analysis of archaea in the rumen ecosystem was analysed by PCR of 16S rDNA from the bovine rumen using archaea-specific primers. The libraries were constructed from rumen fluid (AF), rumen solid (AS), and rumen epithelium (AE) from a rumen-fistulated Korean cow (Hanwoo). The 45 AF clones could be divided into three groups and the largest group was affiliated with the Methanomicrobiaceae family (96% of clones). The AF clones contained a high proportion of unidentifiable clones (67%). The 39 AE clones could be divided into two groups and the largest group was also affiliated with the Methanomicrobiaceae family (95% of clones). The AE clones contained a low proportion of unidentifiable clones (5%). The 20 AS clones could be divided into two groups that were affiliated with either the Methanobacteriaceae family (55%) or the Methanomicrobiaceae family (45%). The AS clones contained a moderate proportion of unidentifiable clones (40%). The predominant family of whole rumen archaea was found to belong to the Methanomicrobiaceae (85%). Methanomicrobiaceae were predominant in the rumen epithelium and the rumen fluid while Methanobacteriaceae were predominant in the rumen solid. One clone from the rumen fluid and two clones from the rumen epithelium contained rDNA sequences of Non-Thermophilic-Crenarchaeota (NTC) and Thermophilic-Crenarchaeota (TC), respectively, which have not previously been described from the rumen.

Journal Article↗
PubMed2006

Phylogenetic diversity of planktonic archaea in the estuarine region of East China Sea.

To examine the diversity and structure of archaeal communities in the Yangtze River estuarine region of East China Sea (ECS), the 16S rRNA gene clone libraries of two typical sites were constructed with the archaea-specific primers. In total, 71 clones randomly selected were screened by PCR-restriction fragment length polymorphism (PCR-RFLP) analysis and 21 clones with unique RFLP pattern were sequenced. All the sequences are clustered into the two groups of Marine Group I (MGI) and Marine Group II (MGII) which are affiliated with the phyla Crenarchaeota and Euryarchaeota, respectively. MGI clones dominate both libraries with 20 MGI sequences obtained. The majority of sequences are closely related to uncultured marine archaea except for two sequences of which the nearest neighbor is a newly identified isolate of nitrifying marine archaeon Nitrosopumilus maritimus (98% identity). The results indicate that ECS coastal waters are inhabited by archaeal community with low dominance and high diversity corresponding to the complex estuarine environments, suggesting that archaea may perform an important role in the estuarine ecosystem.

Biodiversity↗
PubMed1999

The first determination of pseudouridine residues in 23S ribosomal RNA from hyperthermophilic Archaea Sulfolobus acidocaldarius.

We describe the first identification of pseudouridine (Psi) residues in ribosomal RNA (23S rRNA) of an hyperthermophilic Archaea Sulfolobus acidocaldarius. In contrast to Eucarya rRNA, only six Psi residues were detected, which is rather close to the situation in Bacteria. However, three modified positions (Psi(2479), Psi(2535) and Psi(2550)) are unique for S. acidocaldarius. Two Psi residues at positions 2060 and 2594 are universally conserved, while one other Psi (position 2066) is also common to Eucarya. Taken together the results argue against the conservation of Psi-synthases between Archaea and Bacteria and provide a basis for the search of snoRNA-like guides for Psi formation in Archaea.

Base Sequence↗