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PubMed2000

The cell surface glycoprotein layer of the extreme halophile Halobacterium salinarum and its relation to Haloferax volcanii: cryo-electron tomography of freeze-substituted cells and projection studies of negatively stained envelopes.

We have studied the surface layer (S-layer) of Halobacterium salinarum (formerly Halobacterium halobium), an extreme halophile requiring high concentrations of sodium, by electron microscopy of (a) isolated, negatively stained, flattened envelopes and (b) cryo-fixation of intact cells in their high-salt growth medium followed by freeze substitution and tomography of thin sections. From the negatively stained isolated envelopes we have calculated a two-dimensional, projection map that is strikingly similar to that of Haloferax volcanii, an extreme halophile requiring high concentrations of magnesium; both projection maps show the hexagonal arrangement of the morphological units with an identical center-to-center spacing of 150 A; each of the morphological units of the two species has six subunits with a similar density distribution and apparent domain organization. In contrast to the two-dimensional map, the tomographic reconstruction of Halob. salinarum does not agree in a straightforward way with the three-dimensional, electron crystallographic map of negatively stained Halof. volcanii envelopes, although the main features of the lattice and the morphological units are evident. The tomographic reconstruction of sections from epoxy-embedded material suffers from directional compression due to sectioning stress and continuous dimensional changes and mass loss due to electron irradiation. This communication consists, therefore, of three parts: (a) a comparison of the projection maps of negatively stained envelopes of Halof. volcanii and Halob. salinarum; (b) a comparison of the three-dimensional maps obtained by electron crystallography (Halof. volcanii) and low-dose cryo-tomography (Halob. salinarum); and (c) a methodological study of mass loss and dimensional changes of plastic-embedded material under low-dose conditions at room and liquid nitrogen temperatures.

Archaeal Proteins↗
PubMed1993

The fdx gene encoding the [2Fe--2S] ferredoxin of Halobacterium salinarium (H. halobium).

The gene encoding the [2Fe--2S] ferredoxin (fdx gene) was isolated from Halobacterium salinarium using two oligonucleotides deduced from the ferredoxin sequence as probes. Cosmid DNAs exhibiting hybridization were isolated, the fdx gene was localized to smaller subfragments and the nucleotide sequence determined. The 390 bp coding sequence is located in the halobacterial FI-DNA and transcribed as a 440 nucleotide mRNA. S1 mapping indicated that the 5' terminus of the mRNA maps immediately upstream of the ATG start codon. The promoter box A, centred around position -25 (5' AC-TATG 3'), and box B (TG) elements at the start of the transcript resemble the sequences of a typical archaeal promoter. The restriction pattern of an approximately 50 kb region surrounding the fdx gene is conserved in various Halobacterium species. The halobacterial ferredoxin and the major gas vesicle protein GvpA exhibit up to 70% similarity to their respective counterparts in cyanobacteria suggesting lateral gene transfer between the organisms. These similarities prompted a more detailed investigation of the relative positions of the genes in the halobacterial genome.

Amino Acid Sequence↗
PubMed1989

Expression of two gas vacuole protein genes in Halobacterium halobium and other related species.

The archaebacterium Halobacterium halobium contains two genes encoding gas vacuole proteins (vac). One resides on a large naturally occurring plasmid and encodes a protein of 76 amino acids (p-vac), while the other is a chromosomal gene that encodes a highly similar protein of 79 amino acids (c-vac). Northern analysis determined the c-vac and p-vac mRNA to be approximately 340 nucleotides in length, and S1 mapping of both transcripts indicated that the 5' terminus for each starts at the same relative nucleotide. Three other Halobacterium species producing gas vacuoles were investigated, H. spec. GN101, YC819-9, and SB3. All three contain only a chromosomal c-vac gene, and the 5' terminus of the 340 nucleotide mRNA starts at the same nucleotide as found for H. halobium. The c-vac gene region of H. spec. GN101 contains nine nucleotide exchanges, three of which occur in the coding region with no effect on the amino acid sequence. In contrast, the c-vac gene of H. spec. SB3 has an identical nucleotide sequence to the H. halobium c-vac gene. Gas vacuole production in each of these species was monitored during culture growth by phase contrast microscopy, and the vac mRNA level was determined for each time point. H. halobium p-vac deletion mutants, as well as the halobacterial species GN101 and YC819-9, start to synthesize gas vacuoles in early stationary growth phase with a maximal mRNA content in stationary phase. In contrast, H. halobium wild-type synthesizes gas vacuoles exclusively due to p-vac gene expression with a maximal mRNA level during logarithmic growth, and transcripts of the c-vac gene were not detectable.(ABSTRACT TRUNCATED AT 250 WORDS)

Archaeal Proteins↗
PubMed1988

Two genes encoding gas vacuole proteins in Halobacterium halobium.

The archaebacterium Halobacterium halobium contains two related gas vacuole protein-encoding genes (vac). One of these genes encodes a protein of 76 amino acids and resides on the major plasmid. The second gene is located on the chromosome in a (G + C)-rich DNA fraction and encodes a slightly larger but highly homologous protein consisting of 79 amino acids. The plasmid encoded vac gene is transcribed constitutively throughout the growth cycle while the chromosomal vac gene is expressed during the stationary phase of growth. Comparison of the nucleotide sequences of the two genes indicates differences in the putative promoter regions as well as 35 single base-pair exchanges within the coding regions of the two genes. The majority of the nucleotide exchanges in the coding region occur in the third position of a codon triplet generating the codon synonym. The only differences between the two encoded proteins are the exchange of 2 amino acids (positions 8 and 29) and a deletion of 3 amino acids near the carboxy-terminus of the plasmid encoded vac protein. The genomic DNAs from other halobacterial isolates (Halobacterium sp. SB3, GN101 and YC819-9) were found to contain only a chromosomal vac gene copy. There is a high conservation of the chromosomal vac gene and the genomic region surrounding it among the halobacterial strains investigated.

Amino Acid Sequence↗
PubMed1976

Passive potassium ion permeability of Halobacterium halobium cell envelope membranes.

Cell envelope vesicles, prepared from Halobacterium halobium, were loaded with 3 M KCl, suspended in 3 M NaCl, and the loss of K+ was followed at various temperatures. The Arrhenius plot of the K+-efflux rates shows a break at 30 degrees C, with higher energy of activation above the break. This temperature dependence is consistent with earlier studies of chain motions in liposomes prepared from isolated lipids. The efflux of K+ is more rapid with increasing pH between pH 5 and 7. Since these vesicles do not respire under the experimental conditions it was expected that the K+-efflux data would be related to the passive permeability of the membranes to K+. The apparent K+ permeability at 30 degrees C is 1--2 - 10(-10) cm - s-1. This value corresponds to a 5-h half-life for retained K+ in the envelope vesicles and to a probably much longer half-life in whole cells. The previously observed ability of Halobacterium to retain K+ in the absence of metabolism can thus be explained solely by the permeability characteristics of the membranes.

Cell Membrane↗
PubMed1980

The lipids of Halobacterium marismortui, an extremely halophilic bacterium in the Dead Sea.

The lipids of an extremely halophilic bacterium, Halobacterium marismortui, isolated from the Dead Sea, were found to contain 86% polar lipids and 14% non-polar lipids. Four major polar lipids were detected, all derivatives of 2,3-di-O-phytanyl-sn-glycerol: (1) a novel glycolipid, 2,3-di-O-phytanyl-1-O-[beta-D-glucopyranosyl-(1'-6')-O-alpha-D-mannopyranosyl-( 1'-2')-O-alpha-D-glucopyranosyl]-sn-glycerol (11 mol%); (2) phosphatidylglycerol (11 mol%); (3) phosphatidylglycerophosphate (62 mol%); (4) phosphatidylglycerosulfate (17 mol%). In addition, a minor glycolipid (less than 1 mol%) was detected and partially characterized. Trace levels of two other unidentified glycolipids and of two unidentified phospholipids were also detected. In contrast to Halobacterium cutirubrum and H. halobium, H. marismortui did not contain any detectable sulfated glycolipid but appeared to compensate for this deficit in sulfate by having a high content of phosphatidylglycerosulfate compared to that in H. cutirubrum. The number of negative changes per mol ionic lipid appeared to be about the same for both halophiles. The non-polar lipids in H. marismortui consisted mostly of squalenes, vitamin MK-8 and bacterioruberins with traces of beta-carotene, lycopene and retinal, as in H. cutirubrum.

Chromatography, Gas↗
PubMed1993

On the revised structure of the major phospholipid of Halobacterium salinarium.

Recent fast atom bombardment-mass spectrometry (FABMS) studies (Tsujimoto, K., Yorimitsu, S., Takahashi, T. and Ohashi, M. (1989) J. Chem. Commun. 668-670; Frederickson, H.L., De Leeuw, J.W., Tas, A.C., Van der Greef, J., LaVos, G.F. and Boon, J.J. (1989) Biomed. Environ. Mass. Spectrom. 18, 96-105; Kloppel, K.D. and Fredrickson, H.L. (1991) J. Chromatogr. 562, 369-376) have indicated that the structure of the major phospholipid of Halobacterium salinarium (formerly Halobacterium cutirubrum) is not 2,3-diphytanyl-sn-glycerol-1-phospho-3'-sn-glycerol-1'- phosphate (PGP), but the monomethylated derivative, 2,3-diphytanyl-sn-glycerol-1-phospho-3'-sn-glycerol-1'-methylphosphate (PGP-Me). We have now confirmed the structure of the major phospholipid of extremely halophilic archaebacteria as being this methylated structure (PGP-Me) by 1H- and 13C-NMR, FABMS and TLC of the native phospholipid and its product of mild acid hydrolysis PGP. The methylated structure (PGP-Me), rather than PGP itself, is also the major phospholipid in species of other genera of extreme halophiles examined so far, such as, Haloferax, Haloarcula, Halococcus, Natronobacterium and Natronococcus.

Chromatography, Thin Layer↗
PubMed1980

Amino acid sequence of 2Fe-2S ferredoxin from an extreme halophile, Halobacterium of the Dead Sea.

The primary structure of the 2Fe-2S ferredoxin from Halobacterium of the Dead Sea was determined and it consisted of 128 amino acid residues including an N epsilon-acetyllysyl residue. Due to a high degree of sequence homology between this ferredoxin and the one from Halobacterium halobium, all tryptic peptides could be aligned in order. Only 20 amino acid differences were observed between these two halobacterial ferredoxins. The distribution of cysteinyl residues involved in the iron chelation was similar to that of chloroplast-type ferredoxins.

Amino Acid Sequence↗
PubMed1980

Structural analysis by mass spectrometry and NMR spectroscopy of the glycolipid sulfate from Halobacterium salinarium and a note on its possible function.

The major glycolipid sulfate of the extreme halophile Halobacterium salinarium was isolated and characterised mainly by mass spectrometry and NMR spectroscopy. The mass spectrum of the permethylated, desulfated and trimethylsilylated derivative showed the molecule to be a trihexosyl glycerol C20-diether with the sulfate group on the terminal hexose. A 3-position of the sulfate was indicated by the mass spectrum obtained after acetylation and trimethylsilylation (solvolysis of sulfate and replacement by a trimethylsilyl group). The NMR spectrum of the desulfated permethylated glycolipid gave conclusive evidence for the presence of one beta and two alpha anomeric protons. With the knowledge of degradation data it was possible to assign the beta signal to galactose (terminal hexose), and the alpha signals to glucose and mannose. These data together make it likely that the glycolipid sulfate is identical in structure with the glycolipid from Halobacterium cutirubrum characterised previously (M. Kates and P.W. Deroo, J. Lipid Res., 14 (1973) 438). On the basis of a suggested function of cerebroside sulfate of animal origin (identical polar end with the bacterial glycolipid: beta-galactopyranose-3-sulfate) and the present knowledge of ion transport in Halobacteria, it is proposed that the bacterial glycolipid may function as a selective K+ receptor for the K+ transport from a high-Na+ and low-K+ outside medium.

Glycolipids↗
PubMed1993

Nucleotide sequence of the genes encoding the L3, L4, and L23 equivalent ribosomal proteins from the archaebacterium Halobacterium halobium.

A lambda EMBL clone containing a gene cluster coding for the ribosomal proteins L3, L4, L23 and 5' region of L2 was identified in a genomic library for the halophilic archaebacterium Halobacterium halobium using a heterologous hybridization probe from the related organism Halobacterium marismortui. The clone also contains two conserved open reading frames found in H. marismortui, although with still unknown function. Its gene organization is very similar to that of 'S10 operon' of H. marismortui. The deduced amino acid sequence of these ribosomal proteins (HhaL3, HhaL4, HhaL23 and 5' region of HhaL2) shows high similarity (64-71%) to those of the archaebacterium H. marismortui and a lesser degree of similarity to their eukaryotic (31-42%) and eubacterial (17-33%) counterparts.

Amino Acid Sequence↗
PubMed1986

Halobacterial adenosine triphosphatases and the adenosine triphosphatase from Halobacterium saccharovorum.

Membranes prepared from various members of the genus Halobacterium contained a Triton X-100 activated adenosine triphosphatase. The enzyme from Halobacterium saccharovorum was unstable in solutions of low ionic strength (< 3 M NaCl) and maximally active in the presence of 3.5 M NaCl. A variety of nucleotide triphosphates was hydrolyzed. MgADP, the product of ATP hydrolysis, was not hydrolyzed and was a competitive inhibitor with respect to MgATP. The enzyme from H. saccharovorum was composed of at least 2 and possibly 4 subunits. The 83-kDa and 60-kDa subunits represented about 90% of total protein. The 60-kDa subunit reacted with dicyclohexylcarbodiimide (DCCD) when inhibition was carried out in an acidic medium. The significance of the two minor components (28 kDa and 12 kDa is not established. The enzyme from H. saccharovorum, which differs from previously described halobacterial ATPases, possesses properties of an F1F0 as well as an E1E2 ATPase.

Adenosine Triphosphatases↗
PubMed1985

The nucleotide sequence of the gene coding for the 16S rRNA from the archaebacterium Halobacterium halobium.

The complete 1473-bp sequence of the 16S rRNA gene from the archaebacterium Halobacterium halobium has been determined. Alignment with the sequences of the 16S rRNA gene from the archaebacteria Halobacterium volcanii and Halococcus morrhua reveals similar degrees of homology, about 88%. Differences in the primary structures of H. halobium and eubacterial (Escherichia coli) 16S rRNA or eukaryotic (Dictyostelium discoideum) 18S rRNA are much higher, corresponding to 63% and 56% homology, respectively. A comparison of the nucleotide sequence of the H. halobium 16S rRNA with those of its archaebacterial counterparts generally confirms a secondary structure model of the RNA contained in the small subunit of the archaebacterial ribosome.

Archaea↗
PubMed2005

A microprobe analysis of inorganic elements in Halobacterium salinarum.

Halobacterium salinarum were grown on peptone agar containing 4.28 M NaCl, 0.036 M K and other salts. Stationary phase organisms were lifted onto carbon planchets, freeze-dried, carbon coated and examined in a scanning electron microscope equipped with an X-ray spectrometer. Intracellular element concentrations (mol/kg H(2)O) were determined using a bulk analysis program with appropriate standards. The cell K concentration was 110 times that of the medium. For Na this value was 0.3 and for Cl, 1.1. When Rb was present in the medium, its intracellular concentration was 77 times higher than the external value. The cation minus anion value suggests a high fixed negative charge, 0.72 equivalents. Intracellular apparent dielectric constants were calculated using cellular EMFs derived from the literature, and sodium concentration. The determined values ranged from 22-28 (vs 80 for normal water) suggesting phases of structured cell water. Ionic distributions in these extremophiles are treated according to the classical principles elucidated by Willard Gibbs and represents a heterogeneous system in thermodynamic equilibrium with the hypersaline environment. Factors to be considered are: (1) composition of Halobacterium and its immobile negative charge; (2) the physicochemical properties of the individual ions (charge, ionic radius, hydration energy, standard chemical potential); (3) the dielectric constant of the dispersion medium (water); and (4) the binding of ions, particularly potassium.

Chlorides↗
PubMed2005

Gas vesicles isolated from Halobacterium cells by lysis in hypotonic solution are structurally weakened.

Analysis of pressure-collapse curves of Halobacterium cells containing gas vesicles and of gas vesicles released from such cells by hypotonic lysis shows that the isolated gas vesicles are considerably weaker than those present within the cells: their mean critical collapse pressure was around 0.049-0.058 MPa, as compared to 0.082-0.095 MPa for intact cells. The hypotonic lysis procedure, which is widely used for the isolation of gas vesicles from members of the Halobacteriaceae, thus damages the mechanical properties of the vesicles. The phenomenon can possibly be attributed to the loss of one or more structural gas vesicle proteins such as GvpC, the protein that strengthens the vesicles built of GvpA subunits: Halobacterium GvpC is a highly acidic, typically "halophilic" protein, expected to denature in the absence of molar concentrations of salt.

Bacterial Proteins↗
PubMed2005

The discovery of four distinct glutamate dehydrogenase genes in a strain of Halobacterium salinarum.

In earlier work, two glutamate dehydrogenase (GDH) proteins were purified from a strain of the halophilic archaeon Halobacterium salinarum (NRC-36014). One of these, an NAD+-specific enzyme, was matched to a cloned gene from H. salinarum (GenBank accession number: X63837 S75579) by sequencing peptide fragments. Analysis of enzymatic digests of the NADP+-GDH and database searching have now established that a gene encoding this protein exists in the full genomic sequence of Halobacterium sp. NRC-1 as gdhA1, together with two other distinct gdh genes, gdhA2 and gdhB. From N-terminal sequence, it is clear that the genomic listing incorrectly assigns the start codon for gdhA1 and the corresponding protein is 43 amino acids longer than previously indicated. The three genes could be amplified by PCR either from NRC-1, as expected, or from NRC-36014 (GenBank accession numbers: YA840085-AY840087). A gene encoding the previously purified NAD+-GDH, is absent from the NRC-1 genome but can be successfully amplified from genomic DNA of NRC-36014 (GenBank accession number: AY840088). This establishes that NRC-36014 contains four gdh genes.

Amino Acid Sequence↗
PubMed1982

Unusual physical organization of the Halobacterium genome.

The genomes of the extremely halophilic bacteria, Halobacterium halobium and Halobacterium volcanii, contain many repeated sequences. These sequences comprise many families, seem to be highly mobile and are arranged in both clustered and dispersed fashions within these genomes. At least some repeated sequences are more strongly conserved between the two species than are unique sequence DNAs.

Biological Evolution↗
PubMed2004

Identification of the first archaeal Type 1 RNase H gene from Halobacterium sp. NRC-1: archaeal RNase HI can cleave an RNA-DNA junction.

All the archaeal genomes sequenced to date contain a single Type 2 RNase H gene. We found that the genome of a halophilic archaeon, Halobacterium sp. NRC-1, contains an open reading frame with similarity to Type 1 RNase H. The protein encoded by the Vng0255c gene, possessed amino acid sequence identities of 33% with Escherichia coli RNase HI and 34% with a Bacillus subtilis RNase HI homologue. The B. subtilis RNase HI homologue, however, lacks amino acid sequences corresponding to a basic protrusion region of the E. coli RNase HI, and the Vng0255c has the similar deletion. As this deletion apparently conferred a complete loss of RNase H activity on the B. subtilis RNase HI homologue protein, the Vng0255c product was expected to exhibit no RNase H activity. However, the purified recombinant Vng0255c protein specifically cleaved an RNA strand of the RNA/DNA hybrid in vitro, and when the Vng0255c gene was expressed in an E. coli strain MIC2067 it could suppress the temperature-sensitive growth defect associated with the loss of RNase H enzymes of this strain. These results in vitro and in vivo strongly indicate that the Halobacterium Vng0255c is the first archaeal Type 1 RNase H. This enzyme, unlike other Type 1 RNases H, was able to cleave an Okazaki fragment-like substrate at the junction between the 3'-side of ribonucleotide and 5'-side of deoxyribonucleotide. It is likely that the archaeal Type 1 RNase H plays a role in the removal of the last ribonucleotide of the RNA primer from the Okazaki fragment during DNA replication.

Amino Acid Sequence↗
PubMed1991

Arginine deiminase from Halobacterium salinarium. Purification and properties.

Arginine deiminase from the extreme halophilic archaebacterium Halobacterium salinarium was purified to homogeneity in a four-step procedure with a 310-fold enrichment. The enzyme consists of two identical subunits of 55 kDa; its native molecular mass is 105 kDa. The pI of 4.7 indicates that acidic nature of the protein, which is evidenced by its amino acid composition, which shows an excess of more than 15% of acidic amino acids. The N-terminal amino acid of the enzyme is lysine. Arginine deiminase from Halobacterium salinarium exhibits its highest catalytic activity in the presence of 3.5 M-NaCl, pH 7.6, and at 40 degrees C. The half-activity constant, Ks, for arginine is 3.1 mM. The enzyme is inhibited by ornithine.

Amino Acids↗