Identification and partial purification of DnaK homologue from extremely halophilic archaebacteria, Halobacterium cutirubrum

The levels of synthesis of six proteins were increased at elevated growth temperature of the extremely halophilic archaebacterium Halobacterium cutirubrum. One of these proteins, with an apparent molecular mass of 97 kDa on sodium dodecylsulfate–polyacrylamide gel electrophoresis (SDS–PAGE), bound to an ATP-agarose column in the presence of 4 M NaCl, but not in the absence of salt, indicating that this protein retained its ATP-binding activity only at high salt concentration. The NH₂-terminal sequence of this protein and the internal sequences of the tryptic peptides covering 1/3 of the total number of residues coincided with that deduced from the nucleotide sequence of the dnaK gene isolated from H. cutirubrum. The results strongly suggest that this apparent 97-kDa protein is the gene product of dnaK, although the molecular mass calculated from the nucleotide sequence is only 68,495, much smaller than the value of this protein determined by SDS–PAGE. Ferguson plot analysis indicated that this protein showed anomalous mobility on SDS–PAGE. We have purified DnaK homologue to greater than 90% homogeneity with stepwise elution from an ATP-agarose column.     

Cellular morphogenesis in a halophilic archaebacterium

Cultures of a red halophilic archaebacterium exhibiting a complex morphology and cellular morphogenesis were obtained on a medium containingHalobacterium cutirubrum cell lysate. On primary culture the organism grew as an amorphous cellular mass 20 or more micrometers in diameter and underwent multiple internal cellular subdivision to produce a multicellular structure consisting of cuboidal cells of submicron dimensions. These disaggregated, elongated, cells became motile and multiplied by budding, thereby resembling the eubacteriumGeodermatophilus. The new isolates are identified as archaebacteria on the basis of their response to antibiotics, probable absence of peptidoglycan, and the presence of ether-linked lipids.     

The fate of thymine-containing dimers in ultraviolet-irradiated Halobacterium cutirubrum

Extremely halophilic bacteria do not recover in the dark from the effects of ultraviolet radiation, although they can be completely photoreactivated, thus proving that pyrimidine dimers are the cytotoxic photoproducts. We have now shown, by studying the fate of thymine-containing dimers during dark liquid-holding of Halobacterium cutirubrum, that the lack of dark repair in these bacteria is due to their inability to excise such lesions, in contrast to Escherichia coli B. Nevertheless, extensive nonspecific degradation of DNA occurs in H. cutirubrum following ultraviolet irradiation, so the lack of dimer excision is not due to a generalised inability to degrade DNA after such treatment. These findings raise interesting questions concerning the basis of the resistance of halophiles to ultraviolet radiation.     

Isolation of salt-sensitive mutants of the moderately halophilic eubacteriumVibrio costicola

A protocol is described for the first isolation of salt-sensitive mutants from a moderately halophilic eubacterium, namelyVibrio costicola, which normally can grow in up to 3.4M NaCl. Four groups of mutants, which are all unable to grow at high (i.e., 2.5–3.0M) concentrations of NaCl, have been characterized on the basis of their salt and temperature sensitivities. The acquisition of these mutants will be helpful in clarifying the role of membrane lipid changes in haloadaptation.     

Osmometric and microscopic studies on bilayers of polar lipids from the extreme halophile, halobacterium cutirubrum

The major membrane polar lipid components in Halobacterium cutirubrum are the diphytanyl ether analogues of phosphatidylglycerol phosphate, glycolipid sulfate, phosphatidylglycerol and phosphatidylglycerol sulfate. Dispersions of total polar lipids in water formed large birefringent liposomes showing concentric lipid bilayers in the elctron microscope; they behaved as ideal osmometers in KCl or NaCl solutions in the concentration range 0.005–0.2 M. At concentrations above 0.2 M KCl the liposomes shrank to spherical particles which were much less birefringent, showed no distinct bilayer structures by electron microscopy, and no longer behaved as ideal osmometers. Dispersions of phosphatidylglycerol phosphate, phosphatidylglycerol or phosphatidylglycerol sulfate alone did not behave as osmometers at any concentration of KCl or NaCl, but glycolipid sulfate alone or mixed with phosphatidylglycerol phosphate or phosphatidylglycerol phosphate + phosphatidylglycerol sulfate showed ideal osmometer behavior in 0.005–0.2 M KCl or NaCl. The highly negatively charged total polar lipids of H. cutirubrum thus can form stable lipid bilayers only at low ionic concentrations (0.005–0.2 M), much lower than the salt concentration (4 M) of the growth medium, and the presence of glycolipid sulfate is essential. Stability of the membrane in 4 M salt appears to require direct participation of the protein components.     

Ecophysiology of Bacteriophage S5100 Infecting Halobacterium cutirubrum

Increasing salinity reduces burst size and increases the latent period of infection of Halobacterium cutirubrum by lytic bacteriophage S5100. Cells become reversibly and persistently infected at saturation-level concentrations of NaCl. We propose that high salinity provides a natural refuge for sensitive host bacteria and that phage S5100 acts as a scavenger, proliferating when host viability is threatened by dilution of the environment.     

Formation and regeneration ofHalobacterium spheroplasts

Spheroplasts ofHalobacterium cutirubrum were formed upon suspension of cell pellets in 0.1M MES buffer, pH 7.0, containing 0.5M sucrose, 0.25M NaCl, and 0.01M MgCl₂. The spheroplasts regenerated into rod-shaped bacteria when plated on a complex medium containing 15% (wt/vol) sucrose, undergoing several divisions as spherical bodies before the rod shape developed. The frequency of regeneration was approximately 5% of the total spheroplasts plated. The yield of regenerants was increased significantly (to approximately 35%) when bovine serum albumin was present in the spheroplasting buffer and dilution media. The conditions for spheroplast formation and regeneration inH. cutirubrum were also found effective forHalobacterium salinarium but not forHalobacterium halobium.NRCC Paper no. 23080.     

The effect of salinity on the composition of fatty acid double-bond isomers andsn-1/sn-2 positional distribution in membrane phospholipids of a moderately halophilic eubacterium

We report the first study of the effect of NaCl on the double-bond isomeric composition of fatty acids and theirsn-1/sn-2 positional distribution in the membrane phospholipids of a moderately halophilic eubacterium. The major phospholipids, phosphatidylethanolamine and phosphatidylglycerol, ofVibrio costicola grown in 1M or 3M NaCl both have ansn-1 saturated,sn-2 unsaturated distribution of fatty acids. There is a greater effect of salinity on the fatty acid composition of phosphatidylglycerol compared with phosphatidylethanolamine. The fatty acids in phosphatidylethanolamine of cultures grown in 1M compared with 3M NaCl have the same unsaturation index and average chain length, but different double-bond isomeric compositions. In comparison, the fatty acid composition of phosphatidylglycerol is more unsaturated, with a different double-bond isomeric distribution, and has a shorter average chain length in cultures grown in 3M compared with 1M NaCl. The pattern of fatty acid isomers of 16:1 and 18:1 shows thatV. costicola uses the anaerobic pathway of fatty acid biosynthesis. The presence of the isomers 16:1c11 and 18:1c13 in the phospholipids of cultures grown in 3M but not in 1M NaCl indicates that external salinity affects the specificity of fatty acid synthetase in this moderately halophilic bacterium.     

Biochemical characterisation of LigN, an NAD+-dependent DNA ligase from the halophilic euryarchaeon Haloferax volcanii that displays maximal in vitro activity at high salt concentrations

Background  

DNA ligases are required for DNA strand joining in all forms of cellular life. NAD⁺-dependent DNA ligases are found primarily in eubacteria but also in some eukaryotic viruses, bacteriophage and archaea. Among the archaeal NAD⁺-dependent DNA ligases is the LigN enzyme of the halophilic euryarchaeon Haloferax volcanii, the gene for which was apparently acquired by Hfx.volcanii through lateral gene transfer (LGT) from a halophilic eubacterium. Genetic studies show that the LGT-acquired LigN enzyme shares an essential function with the native Hfx.volcanii ATP-dependent DNA ligase protein LigA.     

Halobacterium volcanii spec. nov., a Dead Sea halobacterium with a moderate salt requirement

A halophilic bacterium was isolated from bottom sediment from the Dead Sea. The organism possessed the properties of the halobacteria, but differed from the known species in two important respects, 1) the cells were disc-shaped and often cupped when grown under optimum conditions, 2) the optimum requirements for sodium chloride was in the range 1.7–2.5 molar which is about half of that generally reported for the halobacteria. The organism was assigned to the genus Halobacterium and described as Halobacterium volcanii spec.nov. The optimum sodium chloride concentration for growth was close to that found in the Dead Sea. The tolerance for magnesium chloride was very high; the organism grew well in media containing magnesium chloride in the concentrations found in the Dead Sea. Halobacterium volcanii is therefore remarkably well fitted for life in the Dead Sea.     

The genome of the thermoacidophilic archaebacterium Sulfolobus acidocaldarius does not contain repetitive sequences

Characteristics of genome organization in the sulfur-dependent thermoacidophilic archaebacterium Sulfolobus acidocaldarius have been studied. By means of hybridization analysis it is shown that the genome of S. acidocaldarius, unlike the genome of the extremely halophilic archaebacterium Halobacterium halobium, does not contain repetitive sequences.     

Amino acid sequences of ribosomal proteins S11 from Bacillus stearothermophilus and S19 from Halobacterium marismortui Comparison of the ribosomal protein S11 family

The complete amino acid sequences of ribosomal proteins S11 from the Gram-positive eubacterium Bacillus stearothermophilus and of S19 from the archaebacterium Halobacterium marismortui have been determined. A search for homologous sequences of these proteins revealed that they belong to the ribosomal protein S11 family. Homologous proteins have previously been sequenced from Escherichia coli as well as from chloroplast, yeast and mammalian ribosomes. A pairwise comparison of the amino acid sequences showed that Bacillus protein S11 shares 68% identical residues with S11 from Escherichia coli and a slightly lower homology (52%) with the homologous chloroplast protein. The halophilic protein S19 is more related to the eukaryotic (45–49%) than to the eubacterial counterparts (35%)     

Regulation of cell volume and ion concentrations in a Halobacterium.

Changes in cell volume and ion content of a Halobacterium species are described in terms of the NaCl concentration (0.5--3.5M) and pH(4-8) of the suspending medium. Cell volume, per unit content of protein of bacteria in stationary phase cultures, rose as the [NaCl] of the growth medium was increased. Logarithmic-phase bacteria shrank as the pH fell from 7 to 5.5. These changes are characteristic of bacteria with a moderate or rapid rate of O2 consumption. Starving (i.e. nonmetabolizing) bacteria, on the other hand, did not change in size within the above ranges of [NaCl] and pH. At lower values, however, such bacteria swelled and eventually lysed. Effects of low pH on cell ions are compared in metabolizing and starving bacteria, and it is shown that changes in the state of the cell K are correlated with movements of cell Na. It appears that the cell K is used to maintain cell [Na] below the NaCl concentration of the medium. The results are explained in terms of a model involving interactions between polyelectrolytes, salts and water in the concentrated cytoplasm of these halophilic organisms.     

Lysis of Halobacteria in Bacto-Peptone by Bile Acids

All tested strains of halophilic archaebacteria of the genera Halobacterium, Haloarcula, Haloferax, and Natronobacterium lysed in 1% Bacto-Peptone (Difco) containing 25% NaCl, whereas no lysis was observed with other strains belonging to archaebacteria of the genera Halococcus, Natronococcus, and Sulfolobus, methanogenic bacteria, and moderately halophilic eubacteria. Substances in Bacto-Peptone which caused lysis of halobacteria were purified and identified as taurocholic acid and glycocholic acid. High-performance liquid chromatography analyses of peptones revealed that Bacto-Peptone contained nine different bile acids, with a total content of 9.53 mg/g, whereas much lower amounts were found in Peptone Bacteriological Technical (Difco) and Oxoid Peptone. Different kinds of peptones can be used to distinguish halophilic eubacteria and archaebacteria in mixed cultures from hypersaline environments.     

Polyadenylated RNA isolated from the archaebacterium Halobacterium halobium.

Polyadenylated [poly(A)+] RNA has been isolated from the halophilic archaebacterium Halobacterium halobium by binding, at 4 degrees C, to oligo(dT)-cellulose. H. halobium contains approximately 12 times more poly(A) per unit of RNA than does the methanogenic archaebacterium Methanococcus vannielii. The 3' poly(A) tracts in poly(A)+ RNA molecules are approximately twice as long (average length of 20 nucleotides) in H. halobium as in M. vannielii. In both archaebacterial species, poly(A)+ RNAs are unstable.     

Magnesium, manganese and mutual depletion systems in halophilic bacteria

Abstract The multi-ionic equilibria between enzymes, substrates and monovalent and divalent cations are related in such a way that a change in concentration of one element modifies the repartition of all the concentrations of the other elements, leading to a mutual depletion system. The pyruvate kinase reaction is a good application of the mutual depletion model: this cytoplasmic enzyme utilizes magnesium (Mg) and potassium (K) as cofactors and reacts with free phosphoenolpyruvate and MgADP, substrates involved in the binding of protons, K⁺ and Mg²⁺. Pyruvate kinase from Vibrio costicola , a moderately halophilic eubacterium, obeys the mutual depletion system and is competitively inhibited by physiological concentrations of potassium ions. This effect is relieved by manganese which forms more stable complexes than magnesium. Pyruvate kinase from Halobacterium cutirubrum cannot be described unambiguously by the mutual depletion model.
Cytoplasmic concentrations of potassium ions are elevated in halophilic bacteria and may thus inhibit the formation of the divalent cation complexes necessary in the enzymatic machinery of halophilic bacteria. Accordingly, the contents of the most abundant divalent cation, Mg²⁺, and of the trace element manganese, Mn²⁺, are higher in the halophilic bacteria, V. costicola, Halobacterium volcanii , and H. cutirubrum , and their increase is proportional to the ionic strength of the extracellular media. The Mn²⁺ increase is more marked than the Mg²⁺ increase, although the Mn²⁺ content is about two orders of magnitude lower than the Mg²⁺ content.     

Glucose transport into the extremely halophilic archaebacteria

Penetration of glucose into cells of several extremely halophilic archaebacteria of the Halobacterium and Haloferax genera (Halobacterium saccharovorum and Halobacterium salinarium, Haloferax volcanii and Haloferax mediterranei) has been studied. Some characteristics of transport systems of carbohydrate-utilizing halobacteria Halobacterium saccharovorum, Haloferax mediterranei and Haloferax volcanii (pH and temperature optima, stereospecificity, kinetic parameters) have been determined. Inability of H. salinarium cells for active glucose transport has been shown. The dependence of glucose transport on the Na⁺ ions gradient (on the whole cells and membrane vesicles) has been demonstrated. Cells or membrane vesicles of carbohydrate-utilizing halobacteria grown in media containing this sugar indicated the activation of glucose transport, whereas cells grown in media without sugars did not. This fact has allowed us to conclude that corresponding transport systems are inducible.     

A thermophilic amyloglucosidase fromHalobacterium sodomense,a halophilic bacterium from the Dead Sea

Halobacterium sodomense, a halophilic bacterium from the Dead Sea, degraded starch to glucose by means of an extracellular amyloglucosidase with a temperature optimum of around 65°C in the presence of 1.4 M NaCl, and around 75°C in the presence of 3.9 M NaCl. The enzyme required salt concentrations higher than 1 M for optimal activity, NaCl, KCl, and MgCl₂ being equally suitable as activators. The optimum pH was 7.5.H. sodomense culture supernatants showed only a very low maltose degrading activity. H. sodomense excreted amyloglucosidase constitutively, and relatively high activities were found in cultures grown in the absence of starch; when glucose was added to the growth medium, the amount of enzyme excreted into the medium decreased.     

The sequences of heat shock protein 40 (DnaJ) homologs provide evidence for a close evolutionary relationship between the Deinococcus- Thermus group and cyanobacteria

The genes encoding for heat shock protein 40 (Hsp40 or DnaJ) homologs were cloned and sequenced from the archaebacterium Halobacterium cutirubrum and the eubacterium Deinococcus proteolyticus to add to sequences from the gene banks. These genes were identified downstream of the Hsp70 (or DnaK) genes in genomic fragments spanning this region and, as in other prokaryotic species, Hsp70-Hsp40 genes are likely part of the same operon. The Hsp40 homolog from D. proteolyticus was found to be lacking a central 204 base pair region present in H. cutirubrum that encodes for the four cysteine-rich domains of the repeat consensus sequence CxxCxGxG (where x is any amino acid), present in most Hsp40 homologs. The available sequences from various archaebacteria, eubacteria, and eukaryotes show that the same deletion is also present in the homologs from Thermus aquaticus and two cyanobacteria, but in no other species tested. This unique deletion and the clustering of homologs from the Deinococcus–Thermus group and cyanobacterial species in the Hsp40 phylogenetic trees suggest a close evolutionary relationship between these groups as was also shown recently for Hsp70 sequences (R.S. Gupta et al., J Bacteriol 179:345–357, 1997). Sequence comparisons indicate that the Hsp40 homologs are not as conserved as the Hsp70 sequences. Phylogenetic analysis provides no reliable information concerning evolutionary relationship between prokaryotes and eukaryotes and their usefulness in this regard is limited. However, in phylogenetic trees based on Hsp40 sequences, the two archaebacterial homologs showed a polyphyletic branching within Gram-positive bacteria, similar to that seen with Hsp70 sequences. Received: 30 January 1997 / Accepted: 22 March 1997