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PubMedDate not supplied

[Absorption of 14C-dicarboxylic acids by bacteria of the family Halobacteriaceae].

Cultures of the family Halobacteriaceae belonging to the species Halobacterium halobium, H. cutirubrum, H. vallismortis and Halococcus morrhuae were shown to be capable of assimilating 14C-succinate. Halobacterium salinarium lacked this ability. The transport systems of C4-dicarboxylates differed in Halobacterium halobium 996 and H. vallismortis 1398, on the one hand, and Halococcus morrhuae 1235, on the other. The differences involve the kinetic parameters and stereospecificity of transport systems, the ability to take up different labelled C4-dicarboxylates, the pH-dependence of transport, and the action of CCCP, a protonophorous uncoupling agent. Halobacteria are capable of labelled succinate uptake at a lower NaCl content in the incubation medium than it is necessary for their growth. The optimal temperature for 14C-succinate uptake by halobacteria is higher than the optimal temperature of their growth. For all of the studied cultures, the transport system of dicarboxylate was shown to differ from that of E. coli common for C4-dicarboxylates and aspartate.

Absorption↗

PubMed1993

Ch2, a novel halophilic archaeon from an Australian solar saltern.

A novel halophilic archaeon, strain Ch2, was isolated from a marine solar saltern in Geelong, Australia. The fact that this organism had a dam-methylated genome suggested that it is closely related to the taxon that includes Halobacterium saccharovorum, Halobacterium sodomense, and Halobacterium trapanicum. A sequence analysis of the 16S rRNA gene (Ch2 has three copies of this gene) showed that Ch2 is phylogenetically equidistant from the genera Haloarcula and Haloferax and closely related to H. saccharovorum. The susceptibility of both Ch2 and H. saccharovorum to the recently isolated halophage HF2 supported the hypothesis that these two organisms are closely related.

Bacterial Typing Techniques↗

PubMed2001

Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach.

By comparing the gene order in the completely sequenced archaeal genomes complemented by sequence profile analysis, we predict the existence and protein composition of the archaeal counterpart of the eukaryotic exosome, a complex of RNAses, RNA-binding proteins, and helicases that mediates processing and 3'->5' degradation of a variety of RNA species. The majority of the predicted archaeal exosome subunits are encoded in what appears to be a previously undetected superoperon. In Methanobacterium thermoautotrophicum, this predicted superoperon consists of 15 genes; in the Crenarchaea, Sulfolobus solfataricus and Aeropyrum pernix, one and two of the genes from the superoperon, respectively, are relocated in the genome, whereas in other Euryarchaeota, the superoperon is split into a variable number of predicted operons and solitary genes. Methanococcus jannaschii partially retains the superoperon, but lacks the three core exosome subunits, and in Halobacterium sp., the superoperon is divided into two predicted operons, with the same three exosome subunits missing. This suggests concerted gene loss and an alteration of the structure and function of the predicted exosome in the Methanococcus and Halobacterium lineages. Additional potential components of the exosome are encoded by partially conserved predicted small operons. Along with the orthologs of eukaryotic exosome subunits, namely an RNase PH and two RNA-binding proteins, the predicted archaeal exosomal superoperon also encodes orthologs of two protein subunits of RNase P. This suggests a functional and possibly a physical interaction between RNase P and the postulated archaeal exosome, a connection that has not been reported in eukaryotes. In a pattern of apparent gene loss complementary to that seen in Methanococcus and Halobacterium, Thermoplasma acidophilum lacks the RNase P subunits. Unexpectedly, the identified exosomal superoperon, in addition to the predicted exosome components, encodes the catalytic subunits of the archaeal proteasome, two ribosomal proteins and a DNA-directed RNA polymerase subunit. These observations suggest that in archaea, a tight functional coupling exists between translation, RNA processing and degradation, (apparently mediated by the predicted exosome) and protein degradation (mediated by the proteasome), and may have implications for cross-talk between these processes in eukaryotes.

Adenosine Triphosphatases↗

PubMed2004

Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea.

We report the complete sequence of the 4,274,642-bp genome of Haloarcula marismortui, a halophilic archaeal isolate from the Dead Sea. The genome is organized into nine circular replicons of varying G+C compositions ranging from 54% to 62%. Comparison of the genome architectures of Halobacterium sp. NRC-1 and H. marismortui suggests a common ancestor for the two organisms and a genome of significantly reduced size in the former. Both of these halophilic archaea use the same strategy of high surface negative charge of folded proteins as means to circumvent the salting-out phenomenon in a hypersaline cytoplasm. A multitiered annotation approach, including primary sequence similarities, protein family signatures, structure prediction, and a protein function association network, has assigned putative functions for at least 58% of the 4242 predicted proteins, a far larger number than is usually achieved in most newly sequenced microorganisms. Among these assigned functions were genes encoding six opsins, 19 MCP and/or HAMP domain signal transducers, and an unusually large number of environmental response regulators-nearly five times as many as those encoded in Halobacterium sp. NRC-1--suggesting H. marismortui is significantly more physiologically capable of exploiting diverse environments. In comparing the physiologies of the two halophilic archaea, in addition to the expected extensive similarity, we discovered several differences in their metabolic strategies and physiological responses such as distinct pathways for arginine breakdown in each halophile. Finally, as expected from the larger genome, H. marismortui encodes many more functions and seems to have fewer nutritional requirements for survival than does Halobacterium sp. NRC-1.

Archaeal Proteins↗

PubMed1994

Comparative analysis of the protein components from 5S rRNA.protein complexes of halophilic archaebacteria.

The 5S RNA.protein complexes have been isolated from the 50S subunit of the halophilic archaebacteria Halobacterium cutirubrum, Halobacterium halobium, Halobacterium salinarium, Haloferax mediterranei, Haloferax volcanii and Haloarcula marismortui. The 50S subunits from most of the halophiles released a multiprotein ribonucleoprotein particle similar to that previously observed with the H. cutirubrum 5S RNA.protein complex, which contained proteins from the L5 and L18 ribosomal protein families. Ribosomes from H. marismortui, however, released an RNA.protein complex containing a single protein (L18) that is homologous to the single protein found in the eukaryotic 5S ribonucleoprotein complexes. N-terminal sequence analyses of the halophilic 5S RNA-binding proteins suggest that the L18 protein primary structure is highly conserved, with only the H. marismortui protein having a sequence difference in at least the first twenty amino acids. Although the L5 group of ribosomal proteins also shows a high conservation, it appears that the proteins may have had more freedom to diverge throughout evolution.

Amino Acid Sequence↗

PubMed1992

HALOBACTERIAL A-ATP SYNTHASE IN RELATION TO V-ATPase.

The head piece separated from the A-ATP synthase of Halobacterium halobium hydrolyses ATP. This A1-ATPase is inhibited by nitrate but not by other chaotropic anions. The nitrate inhibition is noncompetitive with respect to ATP, reversible, and partially protected by chloride. In contrast, ATP synthase in situ (A1Ao-ATPase) is not inhibited by nitrate but apparently is inhibited by stronger chaotropic reagents, such as thiocyanate and trichloroacetate, which make the vesicle membrane permeable to protons. The mode of action of nitrate and chaotropic anions seems to differentiate A-ATPases from V-ATPases. Other strains of Halobacterium, Haloferax, Haloarcula, Halococcus and Natronobacterium, contain at least two polypeptides immunochemically similar to the two major subunits, (&agr;) (86x10(3 )Mr on SDS-PAGE) and &bgr; (64x10(3 )Mr), of the A-ATPase of Halobacterium halobium. When solubilized, membrane vesicles of these halobacteria hydrolyse ATP. Their ATPases are commonly sensitive to nitrate. They require high concentrations of the supporting salt but depend differently on chloride or sulfate/sulfite. The A-ATPases of Halobacteriaceae appear to diverge with respect to salt preference.

Journal Article↗

PubMed1999

Structural diversity of membrane lipids in members of Halobacteriaceae.

This minireview gives an updated and consolidated summary of taxonomic classification correlated with membrane phospholipid, glycolipid, and core lipid structural diversity within the family Halobacteriaceae. We also point out that the recently reported diversity in the membrane core lipid structure of a putative strain of Halobacterium (Halobacterium halobium strain IAM 13167) (Morita et al., Biosci. Biotechnol. Biochem., 62, 596-598, 1998) is not correct since the strain used by the authors has for some time been recognized not to be a member of the genus Halobacterium but a member of halobacteria group 2 (Grant and Larsen, Bergey's Manual of Systematic Bacteriology, Vol.3, pp. 2216-2233, 1989), which has recently been designated as a new genus, Natrinema (McGenity et al., Int. J. Syst. Bacteriol. 48, 1187-1196, 1998).

Halobacteriaceae↗

PubMedDate not supplied

[Nucleotide composition and homologies in the DNA of new extreme halophilic soil archaebacteria].

DNA nucleotide composition was studied in extreme halophilic bacteria belonging to the genera Halobacterium, Halococcus, Natronobacterium and Natronococcus. The cultures were shown to be a monolithic group of microorganisms with the content of GC pairs typical of extreme halophilic archebacteria. The difference between the content of DNA major and minor components was twice as high in Halobacterium distributus strains isolated from sulfate saline soils as compared to cultures of this species isolated from natural waters with a high salinity. DNA minor components were not found in haloalkalophilic microorganisms from soda saline soils in contrast to those from soda lakes. The results of DNA-DNA hybridization indicate that the Halobacterium genus is highly heterogeneous. The newly isolated strains of extremely halophilic H. distributus are characterized by the low homology of their DNAs both among themselves and with other species of the genus. However, the hybridization data for the collection strains H. vallismortis 1398 and H. halobium 996 from the National Collection of Microorganisms are indicative of a high homology (80-100%) which is not characteristic of cultures belonging to different species. These results as well as some phenotypical properties of H. vallismortis 1398 different from those of this species type strain support the data reported in the literature about the genetic instability of extreme halophilic archebacteria. The analysis of homologies in DNA nucleotide sequences may be used to study the taxonomy of extreme halophilic archebacteria.

Base Sequence↗

PubMed1994

Novel isoprenoid modified proteins in Halobacteria.

Incorporation of [3H]mevalonic acid-derived materials into proteins was studied with extremely halophilic archaebacteria, Halobacterium halobium and Halobacterium cutirubrum. Several labeled proteins were detected on SDS-polyacrylamide gel electrophoresis followed by fluorography. The majority of the radioactive materials released from the labeled proteins by sulfonium salt cleavage moved with a mobility similar to that of a C85 polyprenol on reverse-phase thin-layer chromatography, and no radioactive farnesol was found on the chromatography. However, a weak but significant protein farnesyltransferase activity was detected in in vitro experiments with a combination of [3H]farnesyl diphosphate and Ras precursor protein.

Alkyl and Aryl Transferases↗

PubMed1988

Archaebacterial class I and class II aldolases from extreme halophiles.

Both, class I (Schiff-base forming) and class II (metal requiring) fructose biphosphate aldolases were found to be distributed among halophilic archaebacteria. The aldolase activity from Halobacteriium halobium, H. salinarium, H. cutirubrum, H. mediterranei and H. volcanii exhibited properties of a bacterial class II aldolase as it was metal-dependent for activity and therefore inhibited by EDTA. In contrast, aldolase from H. saccharovorum, Halobacterium R-113, H. vallismortis and Halobacterium CH-1 formed a Schiff-base intermediate with the substrate and therefore resembled to eukaryotic class I type. The type of aldolase did not vary by changes in the growth medium.

Dihydroxyacetone Phosphate↗

PubMed2004

Construction of a novel shuttle vector based on an RCR-plasmid from a haloalkaliphilic archaeon and transformation into other haloarchaea.

The pNB101 is the first plasmid to be isolated from an haloalkaliphilic archaea. With insertion of the ColE1 replicon of Escherichia coli, as well as two antibiotic resistance genes at its unique Hin dIII site, a novel shuttle vector between haloarchaea and E. coli was developed. This vector, named pNB102, was successfully transformed into two non-alkaliphilic haloarchaea, Halobacterium salinarum SNOB and Haloarcula hispanica ATCC33960. The presence and stability of pNB102 in the transformants were confirmed by PCR identification, Southern blotting and restriction endonuclease digestion. Results also indicated that the presence of restriction-modification (R-M) systems in some Halobacterium species prevented this transformation. It is the first report that the replicon of pNB101 has such a wide host range, and has taken the first step for construction of the vector/host system in haloalkaliphilic archaea.

Archaea↗

PubMed1995

A novel type of protein modification by isoprenoid-derived materials. Diphytanylglycerylated proteins in Halobacteria.

Previous work from this laboratory has shown that a derivative of [3H]mevalonic acid is incorporated into a number of specific proteins in Halobacterium halobium and Halobacterium cutirubrum and that the major radioactive material released by treatment with methyl iodide was neither farnesyl nor geranylgeranyl compound, which have been generally accepted to be prenyl groups of a number of prenylated proteins found in eukaryotic cells, but an unknown compound (Sagami, H., Kikuchi, A., and Ogura, K. (1994) Biochem. Biophys. Res. Commun. 203, 972-978). In the current study, the unknown compound was prepared in a large amount from H. halobium cells and analyzed by reverse and normal phase high performance liquid chromatographies followed by mass spectrometry. The mass spectrum of this compound exhibited a parent ion peak (M+) at m/z 682, suggesting that it is a 1-methylthio-2,3-di-O-(3',7',11',15'-tetramethylhexadecyl)glycerol (diphytanylglyceryl methylthioether). Diphytanylglyceryl methyl thioether was chemically synthesized, and its mass fragmentation pattern was completely coincident with that of the mevalonic acid-derived material from H. halobium. These results indicate that Halobacteria contains specific proteins with a novel type of modification of a cysteine residue of the proteins with a diphytanylglyceryl group in thioether linkage.

Bacterial Proteins↗

PubMed1963

THE CELL ENVELOPES OF TWO EXTREMELY HALOPHILIC BACTERIA.

The cell envelope of Halobacterium halobium was seen in thin sections of permanganate-fixed cells to consist of one membrane. This membrane appeared mostly as a unit membrane but in a few preparations it resembled a 5-layered compound membrane. The cell envelope of Halobacterium salinarium at high resolution was always seen as a 5-layered structure different in appearance from the apparent compound membrane of H. halobium. The "envelopes" which were isolated in 12.5 per cent NaCl from each organism were indistinguishable from each other in the electron microscope and comprised, in each case, a single unit membrane with an over-all thickness of about 110 A. Some chemical analyses were made of isolated membranes after freeing them from salt by precipitating and washing with trichloroacetic acid. Such precipitated membranes consisted predominantly of protein, with little carbohydrate and no peptido-aminopolysaccharide (mucopeptide). Sectioned whole cells of H. halobium contained intracellular electron-opaque structures of unknown function.

Bacteria↗

PubMed2000

Characterisation of membrane phospholipids and glycolipids from a halophilic archaebacterium by high-performance liquid chromatography/electrospray mass spectrometry.

Combined high-performance liquid chromatography and electrospray mass spectrometry (LC/ES-MS) has been used for direct characterisation of the polar membrane lipids in total lipid extracts from Halobacterium salinarium, a species of halophilic archaebacterium. The principle phospholipids found were the diphytanyl archaeol phosphatidylglycerol and diphytanyl archaeol phosphatidylglycerolphosphate methyl ester. The application of LC/ES-MS revealed the additional presence of diphytanyl archaeol phosphatidylglycerol sulphate The extracts also contained an archaeol glycolipid, initially detected in preliminary offline ES-MS studies, which was further characterised by LC/ES-MS and by product ion tandem mass spectrometry (MS/MS) as a sulphate ester of diglycosyl-2,3-di-O-phytanyl-sn-glycerol. Whilst archaeol phospho- and glycolipids containing a (C(20)-C(20))-isopranyl glycerol ether core predominated, LC/ES-MS of the extracts from Halobacterium salinarium indicated the presence of an analogue containing one double bond in its isoprenyl ether core as a minor component of the phosphatidylglycerolphosphate methyl ester fraction, providing a further example of the previously recognised existence of isoprenologues of diphytanyl archaeols which occur as minor components of archaebacterial membrane lipids. The value of these techniques in compositional analysis of archaebacterial lipid extracts is discussed.

Archaea↗

PubMed1994

The archaebacterial membrane protein bacterio-opsin is expressed and N-terminally processed in the yeast Saccharomyces cerevisiae.

The bop gene codes for the membrane protein bacterio-opsin (BO), which on binding all-trans-retinal, constitutes the light-driven proton pump bacteriorhodopsin (BR) in the archaebacterium Halobacterium salinarium. This gene was cloned in a yeast multi-copy vector and expressed in Saccharomyces cerevisiae under the control of the constitutive ADH1 promoter. Both the authentic gene and a modified form lacking the precursor sequence were expressed in yeast. Both proteins are incorporated into the membrane in S. cerevisiae. The presequence is thus not required for membrane targeting and insertion of the archaebacterial protein in budding yeast, or in the fission yeast Schizosaccharomyces pombe, as has been shown previously. However, in contrast to S. pombe transformants, which take on a reddish colour when all-trans-retinal is added to the culture medium as a result of the in vivo regeneration of the pigment, S. cerevisiae cells expressing BO do not take on a red colour. The precursor of BO is processed to a protein identical in size to the mature BO found in the purple membrane of Halobacterium. The efficiency of processing in S. cerevisiae is dependent on growth phase, as well as on the composition of the medium and on the strain used. The efficiency of processing of BR is reduced in S. pombe and in a retinal-deficient strain of H. salinarium, when retinal is present in the medium.

Alcohol Dehydrogenase↗

PubMed1991

The primary structure of rat ribosomal protein L17.

The amino acid sequence of the rat 60S ribosomal subunit protein L17 was deduced from the sequence of nucleotides in two recombinant cDNAs. Ribosomal protein L17 has 184 amino acids and has a molecular weight of 21,383. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 17-19 copies of the L17 gene. The mRNA for the protein is about 720 nucleotides in length. Rat L17 is homologous to human L17 and related to Saccharomyces cerevisiae YL17, Halobacterium marismortui L23, Halobacterium halobium L22e, Escherichia coli L22 and other members of the prokaryotic L22 family.

Amino Acid Sequence↗

PubMed1989

An archaebacterial gene from Methanococcus vannielii encoding a protein homologous to the ribosomal protein L10 family.

An open reading frame upstream of the Methanococcus vannielii L12 gene has been detected. The beginning of this open reading frame agrees with the N-terminal region of a protein (MvaL10) which has been isolated from the 50 S ribosomal subunit of M. vannielii and sequenced. The length of this gene is 1008 nucleotides, coding for 336 amino acids. Excellent sequence similarities were found to the L10-like ribosomal proteins from Halobacterium halobium and man. The N-terminal part of the MvaL10 protein shows significant sequence similarities to the E. coli L10 protein. MvaL10 is more than twice as long as E. coli L10 but is of length similar to those of the homologous halobacterial and human proteins. Interestingly, the C-terminal region of MvaL10 shows exceptionally high similarity to the C-terminal sequence of the MvaL12 protein. This is not the case for the E. coli proteins but was also observed for the human, Halobacterium and Sulfolobus proteins.

Amino Acid Sequence↗

PubMed1984

Photoreactivation in pigmented and non-pigmented extreme halophiles.

The sensitivity to ultraviolet radiation (254 nm) and the photoreactivability of four pigmented and three colourless strains of the extremely halophilic bacteria Halobacterium cutirubrum and Halobacterium salinarium have been studied. The results with three pigmented/non-pigmented pairs show that the pigments play an accessory role in photoreactivation at low visible light intensities and confirm that they do not provide passive protection against ultraviolet light. Evidence is presented that photoreactivation plays an unexpected direct role in the resistance of extreme halophiles to ultraviolet radiation and that colourless mutants of H. cutirubrum NRC 34001 only arise in cultures that have been both ultraviolet-irradiated and photoreactivated. None of these extreme halophiles is capable of excision repair of ultraviolet damage to DNA.

DNA Repair↗