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PubMed1990

An efficient system for the synthesis of bacteriorhodopsin in Halobacterium halobium.

The mechanism by which bacteriorhodopsin (BR) transports protons across the cell membrane of Halobacterium halobium is actively studied in many laboratories. Currently available systems for the synthesis of mutant proteins obtained by site-directed mutagenesis of the gene encoding BR (bop) require reconstitution of the denatured polypeptide after its synthesis Escherichia coli or yeast; this approach is technically difficult and labor intensive, and raises questions about possible differences between in vivo and in vitro folding. Using a newly described transformation system and a halobacterial plasmid vector, we show that it is possible to reintroduce the bop gene into BR- strains of H. halobium. The bop-carrying plasmid expresses native BR in amounts similar to those obtained in several wild type strains. This system allows facile site-directed mutagenesis in halophilic archaebacteria.

Bacteriorhodopsins↗
PubMed1991

Structure and organization of the gas vesicle gene cluster on the Halobacterium halobium plasmid pNRC100.

Halobacterium halobium strain NRC-1 contains intracellular gas-filled vesicles (GVs) that confer buoyancy to the cells. Cloning of the major GV protein (GvpA)-encoding gene, gvpA, and analysis of GV-deficient mutants (Vac-) of H. halobium led to the identification of a region of a 200-kb plasmid, pNRC100, important for GV synthesis. We report here the nucleotide sequence of an 8520-bp region which, including gvpA, contains twelve open reading frames (ORFs) that are organized into two divergent transcription units, gvpAC oriented rightward, and gvpD, E, F, G, H, I, J, K, L, and M located upstream from gvpAC and oriented leftward. Insertions into the gvpA promoter and gvpD and E resulted in the Vac- phenotype. The overall gene organization is highly compact with the end of one ORF overlapping with the beginning of the next in most cases. The gene cluster is bracketed by two ISH8 element copies in inverted orientation, an organization suggestive of a composite transposon. Comparison of predicted amino acid sequences showed homology between GvpA, and the gvpJ and gvpM putative gene products. The putative gvpC gene product contains eight copies of an imperfectly repeated sequence with similarity to repeats in a cyanobacterial GvpC plus a highly acidic C-terminal region not found in the cyanobacterial homologue.

Amino Acid Sequence↗
PubMed1996

Cloning and characterization of the gene encoding Halobacterium halobium adenylate kinase.

The gene (AK) encoding adenylate kinase (AK) of Halobacterium halobium was cloned. AK consisted of 648 bp and coded for 216 amino acids (aa). S1 mapping and primer extension experiments indicated that the transcription start point (tsp) was located immediately upstream from the start codon. The TAT-like promoter sequence was found at a position 20-24 bp upstream from tsp. The most striking property of the enzyme was a putative Zn finger-like structure with four cysteines. It might contribute to the structural stability of the molecule in high-salt conditions. Phylogenetic analysis indicated two lineages of the AK family, the short and long types which diverged a long time ago, possibly before the separation of prokaryotes and eukaryotes. Although the H. halobium AK belongs to the long-type AK lineage, it is located in an intermediary position between the two lineages of the phylogenetic tree, indicating early divergence of the gene along the long-type lineage.

Adenylate Kinase↗
PubMed1995

Alterations in oxidative activity and superoxide dismutase in Halobacterium halobium in response to aerobic respiratory inhibitors.

Aerobic incubation of Halobacterium halobium with low concentrations of cyanide or azide resulted in a twofold increase in activity of the Mn-containing superoxide dismutase (SOD). A similar effect was observed with antimycin A, albeit at a higher concentration. Oxygen consumption increased 100% at concentrations of cyanide, azide, and antimycin A that produced maximal SOD induction. Luminol chemiluminescence of H. halobium cells, indicative of oxidative activity, was elevated in the presence of concentrations of aerobic respiratory inhibitors that corresponded to maximal levels of SOD induction. In addition, oxidation of NADH by cell extracts was maximal at inhibitor concentrations that correlated with the peak induction of SOD. Proton fluxes for H. halobium cells also corresponded to concentration ranges of inhibitor resulting in greatest SOD levels, indicative of a potential uncoupling effect. A similar phenomenon was also observed with the uncoupler carbonyl cyanide m-chlorophenyl hydrazone. Growth was unaffected by inhibitors at the concentrations used for SOD induction. The results are interpreted as an induction of enhanced levels of SOD through a combination of increased electron flow and an increased oxidative environment.

Aerobiosis↗
PubMed2005

Crystallization of halorhodopsin from Halobacterium sp. shark.

The chloride-ion-pumping channel, halorhodopsin from Halobacterium sp. shark was detergent-solubilized and 3-D crystallized. Proteins were solubilized using the nonionic detergent n-octyl-beta-D-glucoside and were crystallized as thin-plate crystals with polyethylene glycol 4000 as a precipitant. The crystals belong to the space group P4(1)2(1)2 with unit-cell dimensions a=b=74.5 A and c=138.6 A. The diffraction pattern was slightly anisotropic. The best ordered crystal diffracted up to 3.3 A resolution along c axis with synchrotron radiation.

Crystallization↗
PubMed2006

Proteome analysis of Halobacterium salinarum and characterization of proteins related to the degradation of isopropyl alcohol.

We reported in a previous study that proteomic approach, coupled with genomic techniques, could be used to screen and develop multiple candidates for halophilic enzymes from Halobacterium salinarum. In order to evaluate the biodegradation of isopropyl alcohol (IPA) by H. salinarum, the amounts of residual IPA and acetone generated in the growth media were determined using a gas chromatography-flame ionization detector (GC-FID). The protein expression profiles of cells which had been cultured with IPA were obtained with the two-dimensional gel electrophoresis. Proteins evidencing different expression levels in the presence of 0.5% IPA were identified by electrospray ionization-quadruple-time of flight (ESI-Q-TOF) mass spectrometry. We found 12 proteins which were down-regulated, and another 12 proteins which were up-regulated, in the presence of 0.5% IPA and we further identified 17 proteins among them using ESI-TOF MS/MS. Among these identified proteins, we selected glyceraldehyde 3-phosphate dehydrogenase (GAPDH) for further characterization as a halophilic enzyme. We have demonstrated for the first time that H. salinarum possesses the ability to degrade IPA and GAPDH was both stable and active at high salt concentrations, with maximum activity occurring at 1 M NaCl, although the optimal salt concentration with regard to the growth of H. salinarum is 4.3 M.

2-Propanol↗
PubMed2005

Functional characterization of sensory rhodopsin II from Halobacterium salinarum expressed in Escherichia coli.

Sensory rhodopsin II (SRII) from Halobacterium salinarum is heterologously expressed in Escherichia coli with a yield of 3-4 mg of purified SRII per liter cell culture. UV/Vis absorption spectroscopy display bands characteristic for native SRII. The resonance Raman spectrum provides evidence for a strongly hydrogen-bonded Schiff base like in mammalian rhodopsin but unlike to the homologous pSRII from Natronobacterium pharaonis. Laser flash spectroscopy indicates that SRII in detergent as well as after reconstitution into polar lipids shows its typical photochemical properties with prolonged photocycle kinetics. The first functional heterologous expression of SRII from H. salinarum provides the basis for studies with its cognate transducer HtrII to investigate the molecular processes involved in phototransduction as well as in chemotransduction.

Electrophoresis↗
PubMed2005

Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum.

Nucleoside diphosphate kinase from the halophilic archaeon Halobacterium salinarum was crystallized in a free state and a substrate-bound form with CDP. The structures were solved to a resolution of 2.35 and 2.2A, respectively. Crystals with the apo-form were obtained with His6-tagged enzyme, whereas the untagged form was used for co-crystallization with the nucleotide. Crosslinking under different salt and pH conditions revealed a stronger oligomerization tendency for the tagged protein at low and high salt concentrations. The influence of the His6-tag on the halophilic nature of the enzyme is discussed on the basis of the observed structural properties.

Crystallization↗
PubMed2005

Refining the structure of the Halobacterium salinarum flagellar filament using the iterative helical real space reconstruction method: insights into polymorphism.

The eubacterial flagellar filament is an external, self-assembling, helical polymer approximately 220 A in diameter constructed from a highly conserved monomer, flagellin, which polymerizes externally at the distal end. The archaeal filament is only approximately 100 A in diameter, assembles at the proximal end and is constructed from different, glycosylated flagellins. Although the phenomenology of swimming is similar to that of eubacteria, the symmetry of the archebacterial filament is entirely different. Here, we extend our previous study on the flagellar coiled filament structure of strain R1M1 of Halobacterium salinarum. We use strain M175 of H.salinarum, which forms poly-flagellar bundles at high yield which, under conditions of relatively low ionic-strength (0.8 M versus 5 M) and low pH ( approximately 2.5 versus approximately 6.8), form straight filaments. We demonstrated previously that a single-particle approach to helical reconstruction has many advantages over conventional Fourier-Bessel methods when dealing with variable helical symmetry and heterogeneity. We show here that when this method is applied to the ordered helical structure of the archebacterial uncoiled flagellar filament, significant extensions in resolution can be obtained readily when compared to applying traditional helical techniques. The filament population can be separated into classes of different morphologies, which may represent polymorphic states. Using cryo-negatively stained images, a resolution of approximately 10-15 A has been achieved. Single alpha-helices can be fit into the reconstruction, supporting the proposed similarity of the structure to that of type IV bacterial pili.

Biopolymers↗
PubMed2003

Downstream coding region determinants of bacterio-opsin, muscarinic acetylcholine receptor and adrenergic receptor expression in Halobacterium salinarum.

The aim of this work is to develop a prokaryotic system capable of expressing membrane-bound receptors in quantities suitable for biochemical and biophysical studies. Our strategy exploits the endogenous high-level expression of the membrane protein bacteriorhodopsin (BR) in the Archaeon Halobacterium salinarum. We attempted to express the human muscarinic acetylcholine (M(1)) and adrenergic (a2b) receptors by fusing the coding region of the m1 and a2b genes to nucleotide sequences known to direct bacterio-opsin (bop) gene transcription. The fusions included downstream modifications to produce non-native carboxyl-terminal amino acids useful for protein identification and purification. bop mRNA and BR accumulation were found to be tightly coupled and the carboxyl-terminal coding region modifications perturbed both. m1 and a2b mRNA levels were low, and accumulation was sensitive to both the extent of the bop gene fusion and the specific carboxyl-terminal coding sequence modifications included. Functional a2b adrenergic receptor expression was observed to be dependent on the downstream coding region. This work demonstrates that a critical determinant of expression resides in the downstream coding region of the wild-type bop gene and manipulation of the downstream coding region of heterologous genes may affect their potential for expression in H. salinarum.

Amino Acid Sequence↗
PubMed1990

Glycolysis and Entner-Doudoroff pathways in Halobacterium halobium: some new observations based on 13C NMR spectroscopy.

13C NMR was used to study glucose metabolism in intact cells of Halobacterium halobium. Spectra of glucose grown cells incubated with [1-13C] glucose indicate the presence of gluconate as the initial product. The existence of glycolytic pathway is also indicated. In the extracts of these cells an NADP dependent glucose dehydrogenase was detected. Galactose grown cells failed to metabolise glucose but exhibited glucose dehydrogenase activity although about 20-50% less than that for glucose grown cells. Possible explanations of these experiments are discussed.

Carbon Isotopes↗
PubMed1991

Molecular cloning of the cytochrome aa3 gene from the archaeon (Archaebacterium) Halobacterium halobium.

A novel aa3-type cytochrome oxidase from the extremely halophilic archaeon, Halobacterium halobium, differs significantly from those of other prokaryotic and eukaryotic cytochrome oxidases (Fujiwara, T., Fukumori, Y., and Yamanaka, T. (1989) J. Biochem. 105, 287-292). In the present study, we cloned and sequenced the gene which encodes the cytochrome aa3 by using the polymerase chain reaction methods. The deduced amino acid sequence of subunit I of H. halobium cytochrome aa3 was more similar to that of subunit I of the eukaryotic cytochrome (44%, maize mitochondria) than that of the cytochrome from other bacteria (36%, Paracoccus denitrificans). The consensus sequence in putative metal binding residues is well-conserved also in H. halobium cytochrome aa3.

Amino Acid Sequence↗
PubMed1984

Photochemical intermediate of third rhodopsin-like pigment in Halobacterium halobium by simultaneous illumination with red and blue light.

We found new photochemical intermediate of third rhodopsin-like pigment (tR) or slow cycling rhodopsin-like pigment (sR) in Halobacterium halobium, which was produced by simultaneous illumination with red and blue light. This illumination is employed for measurements of negative phototaxis. The formation of this intermediate is fast. (With the instrument used, it could not be measured.) The half-time of its decay is ca 150 msec in 4 M NaCl, pH 7.0 at 20 degrees C. The maximum of absorbance is located at 510-530 nm.

Bacteriorhodopsins↗
PubMed1985

Evidence that the long-lifetime photointermediate of s-rhodopsin is a receptor for negative phototaxis in Halobacterium halobium.

The effect of blue background light on behavioral response of Halobacterium halobium to step-like stimulation with green-orange attractant light was examined. The results strongly support the previously proposed hypothesis that a long-lifetime photointermediate of s-rhodopsin is the photoreceptor for repellent light: the step-like increase in green-orange light was convertible from attractant stimulus to repellent one, when the cells were constantly illuminated with blue light. No difference of the threshold intensity of the blue background light was observed between the mutant strain that lacks both bacteriorhodopsin and halorhodopsin and the wild type strain, suggesting that the two light-driven ion pumps are not participant in sensing attractant light.

Halobacterium↗
PubMed1986

Flash spectrophotometric identification of a fourth rhodopsin-like pigment in Halobacterium halobium.

A fourth retinal-containing pigment in Halobacterium halobium cell membrane was examined by flash spectrophotometry. The absorption maximum of this pigment was at about 480 nm. Flash light caused a photoreaction cycle with a half recovery time of about 300 ms at room temperature. The photoreaction cycle involved at least two photo-intermediates. The absorption maximum of the first one was at about 350 nm and that of the second was at around 530 nm. The spectral properties of this pigment and the content of the cells correlate with the sensitivity of photo-repellent response to the light around 480 nm. We suggest a name 'phoborhodopsin' for this new pigment.

Halobacterium↗
PubMed1987

The purification and subunit structure of a membrane-bound ATPase from the Archaebacterium Halobacterium saccharovorum.

A membrane-bound ATPase from Halobacterium saccharovorum was solubilized using sodium deoxycholate and Zwittergent 3-10 and purified by hydrophobic and ammonium sulfate-mediated chromatography. The enzyme, which had a molecular mass of 350 kDa, was composed of two major (87 and 60 kDa) and two minor (29 kDa and 20 kDa) subunits. The halobacterial ATPases appear to be unlike any other ATPase described to date.

Adenosine Triphosphatases↗
PubMed1988

On the glutamate transport through cell envelope vesicles of Halobacterium halobium.

Glutamate uptake by envelope vesicles of Halobacterium halobium was measured. Previous authors showed that the glutamate uptake needs the illumination as well as Na+ gradient across the membrane. The latter is considered to be the driving force for the uptake. No satisfactory explanation for the necessity of the illumination has not been given. We found that in the absence of Cl- in the medium, only Na+ gradient was enough to induce the glutamate uptake, i.e. no illumination was needed. Glutamate uptake was measured with various strains of H. halobium. We found that the envelope vesicles prepared from strains containing no bacteriorhodopsin showed the glutamate uptake in the dark and in the presence of Cl- in the medium provided only that Na+ gradient is imposed.

Cell Membrane↗