Composition of ribosomes of an extremely halophilic bacterium

Sequence of the 16S Ribosomal RNA from Halobacterium volcanii, an Archaebacterium

The sequence of the 16S ribosomal RNA (rRNA) from the archaebacterium Halobacterium volcanii has been determined by DNA sequencing methods. The archaebacterial rRNA is similar to its eubacterial counterpart in secondary structure. Although it is closer in sequence to the eubacterial 16S rRNA than to the eukaryotic 16S-like rRNA, the H. volcanii sequence also shows certain points of specific similarity to its eukaryotic counterpart. Since the H. volcanii sequence is closer to both the eubacterial and the eukaryotic sequences than these two are to one another, it follows that the archaebacterial sequence resembles their common ancestral sequence more closely than does either of the other two versions.

Control of ribosome turnover during growth of the haloalkaliphilic archaeon Natronococcus occultus

The metabolism of ribosomes during growth of the haloalkaliphilic archaeon Natronococcus occultus was examined. The ribosome content was higher during exponential growth and diminished to 35% of the maximum in the stationary stage. The incorporation of H3-orotic acid and C14-uracil into rRNA was higher during exponential growth. After that, it decreased to 39% of the maximum in the stationary stage. The labeling of non-ribosomal RNA took place almost exclusively in the exponential stage. From loss of radioactivity, the half-life of rRNA was 11.43, 14.85, 5.28 and 7.14 h during the initial, exponential, late exponential and stationary growth stages, respectively. These results suggested that increased synthesis combined with diminished degradation were responsible for the high ribosome content displayed by Ncc. occultus during exponential growth. In contrast, diminished synthesis together with increased degradation provoked its posterior loss.

Absolute requirement of ammonium sulfate for reconstitution of active 70S ribosomes from the extreme halophilic archaeon Haloferax mediterranei

Active 70S ribosomes from the halophilic archaeon Haloferax mediterranei have been reconstituted from their isolated rRNAs and proteins. The reconstitution procedure consists of a two-step incubation; first with 1 M ammonium sulfate and 100 mM magnesium acetate for 1 h at 42 degrees C, followed by a 90-min incubation at 50 degrees C after increasing the ammonium sulfate to 2 M final concentration. The total reconstitution of halophilic 70S ribosomes is a process with its own identity, which does not correspond to the conditions required for the reconstitution of the isolated subunits. Ammonium sulfate is the only salt capable of promoting the assembly of active ribosomes. The increase of ammonium sulfate salts in the second incubation step is obligatory for the isolation of functional particles.

Crystallography of halophilic ribosome: the isolation of an internal ribonucleoprotein complex

Crystals of 50S ribosomal subunits from Haloarcula marismortui diffracting to 2.9 A resolution were grown. Because of their large unit cells and the extremely weak diffracting power, almost all X-ray crystallographic analysis of these crystals must be performed with intense synchrotron radiation. At ambient temperature, all ribosomal crystals decay upon the first instance of X-irradiation. To overcome this severe sensitivity, procedures for data collection at cryo temperature were developed. Under these conditions the crystals can be irradiated for periods sufficient for the collection of more than one data set from an individual crystal (days or weeks) with no observable damage. They also can be stored for months, to resume interrupted measurements. To assist the interpretation of the anticipated electron density map, a specific internal nucleoprotein complex of protein HmaL1 and a stretch of H23S rRNA was isolated from the halophilic ribosome. The fragments of the 23S rRNA protected by the protein from nuclease digestion were sequenced. Alignment of the sequences of some archaebacterial L1-specific RNA fragments to the corresponding parts of eubacterial and eukaryotic rDNAs, localized the sequence identities to two distinct regions. Chimeric complexes were reconstituted with the corresponding E. coli ribosomal components, indicating a rather high homology, despite the evolution distance. A feasible secondary structure of the rRNA stretch participating in this complex was found to be compatible with the one proposed for the corresponding part in the E. coli ribosomal RNA.

In vitro reassembly of active large ribosomal subunits of the halophilic archaebacterium Haloferax mediterranei

The large ribosomal subunits of the halophilic archaebacterium Haloferax mediterranei have been reconstituted in vitro from the dissociated RNA and protein components. Efficient reassembly of particles fully active in poly(U)-directed polyphenylalanine synthesis requires a 2-h incubation at 42 degrees C in the presence of no less than 2.5 M concentrations of monovalent cations and of 60 mM magnesium. K+ and NH4+ ions are equally effective in promoting subunit reconstitution; however, maximal efficiency is attained when they are combined in a 1:2 molar ratio. The reassembly process requires no heat activation step, as under the appropriate ionic conditions it takes place spontaneously within the temperature range optimal for growth of H. mediterranei cells (40-45 degrees C).

Lack of detectable polyamines in an extremely halophilic bacterium

Polyamines (putrescine, spermidine, spermine and other analogs) were not detectable by the dansylation procedure coupled with HPLC analysis in an extremely halophilic bacterium, Halobacterium halobium. Based on the detection limit of this analytical method, we estimated that the polyamine content in H. halobium, if present, was less than 0.06% of that of E. coli. Putrescine uptake and the metabolic conversion of ornithine or arginine to polyamines were negligible in this bacterium. In a H. halobium cell-free extract, a saturated amount of KC1 was needed for poly(U) directed polyphenylalanine synthesis; neither putrescine nor spermidine could replace KC1. These results suggest that polyamines may play an insignificant role in the growth of this halophilic bacterium.

The effect of high hydrostatic pressure on eukaryotic protein synthesis

The pressure response of two eukaryotic protein synthesizing systems has been characterized. The rabbit reticulocyte system has been tested, both in vivo and in vitro, using endogenous polysomes and polyuridylic acid (poly U). In addition, the poly U-directed polyphenylalanine synthesizing system obtained from wheat germ was utilized. The effect of pressure on eukaryotic protein synthesis has been found to be basically similar to that observed in prokaryotic systems, although the response of the eukaryotic protein synthesizing system is somewhat more complex signifying a greater influence of overlapping reactions. Magnesium was found to affect eukaryotic systems in much the same way as has been reported for prokaryotic systems, i.e., increasing the Mg2+ concentration in a protein synthesizing system increases the barotolerance exhibited by the system. Under conditions of high Mg2+ concentration, however, extreme (up to 160%) stimulation of protein synthesis at lower pressure levels was observed in the eukaryotic systems. Such high stimulation is not apparent in prokaryotic systems. The poly U-directed wheat germ system exhibited the most barotolerant polypeptide synthesis ever seen in our laboratory. This extreme barotolerance was only slightly decreased when the system was tested at reduced concentrations of magnesium.

The N-terminal sequence of the ribosomal 'A' protein from two moderate halophiles, Vibrio costicola and an unidentified moderate (NRCC 11227)

The 'A' protein, equivalent to ribosomal protein EL7/L12 from Escherichia coli, has been isolated and purified from two moderate halophiles Vibrio costicola and NRCC 11227. The 'A' protein from V. costicola contained an N-terminal serine and separated into two forms on DEAE-cellulose and two-dimensional electrophoresis while the equivalent protein in NRCC 11227 contained an N-terminal alanine residue and was present in only one form. The amino acid composition and mobility on two-dimensional gels indicated these proteins were very similar to EL7/L12. The first 38 residues of the 'A' proteins were sequenced and compared to the equivalent protein from E. coli and the extreme halophile Halobacterium cutirubrum. The N-terminal region of the 'A' protein from both moderate halophiles showed substantial homology to EL 12 (75--80%) but no evidence of any homology to the equivalent protein from the extreme halophile. The ribosomal proteins equivalent to ES1A in E. coli were also isolated and their amino acid compositions determined.

Properties of the halophilic nuclease of a moderate halophile, Micrococcus varians subsp. halophilus

The halophilic nuclease of Micrococcus varians ATCC 21971 hydrolyzed thymidine 5'-monophospho-p-nitrophenyl ester at a rate that increased with the NaCl concentration up to saturation. The nuclease attacked RNA and DNA exonucleolytically and processively, producing 5'-mononucleotides. The molecular weight of the enzyme as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis was 99,000, approximately the same as that previously determined for the native enzyme. Examination of amino acid composition showed that acidic amino acids were in high excess over basic amino acids.

Role of the 30S ribosomal subunit, initiation factors, and specific ion concentration in barotolerant protein synthesis in Pseudomonas bathycetes

Washed (1 M NH4Cl) ribosomes from Pseudomonas bathycetes, Pseudomonas fluorescens, and Escherichia coli were tested for their ability to synthesize protein or polypeptide at high pressure when used as such, when recombined with homologous initiation factors, and when recombined with heterologous initiation factors. The responses of natural messenger ribonucleic acid (MS-2)-directed systems to pressure were independent of the source of initiation factors and paralleled those of the washed ribosomes in polyuridylate-directed systems. In all cases, the responses to pressure were parallel to those obtained when unwashed ribosomes were utilized; therefore, we concluded that the initiation factors were interchangeable among these organisms, and that these factors did not play a critical role in determining the pressure responses of the protein-synthesizing systems. P. bathycetes ribosomal subunits were isolated under a variety of ionic conditions. These were tested for their ability to synthesize protein and polyphenylalanine at a variety of pressures when used in reconstituted P. bathycetes homologous systems and in hybrid systems with ribosomal subunits from E. coli and P. fluorescens. O. bathycetes 30S subunits, isolated in a buffer solution containing 0 mM NaCl and O mM KC] were functional at any pressure; those isolated in the presence of 150 mM NaCl and 0 mM KCl were functional at 1 atmosphere but barosensitive, and those isolated in the presence of O mM NaCl and 150 mM KCl retained the ion-mediated barotolerance characteristic of crude P. bathycetes ribosome preparations. The 50S subunit remained functional regardless of the method of isolation, and it had no effect on pressure sensitivity.

The properties of ribosomal proteins from a moderate halophile

The ribosomes from the extreme halophile Halobacterium cutirubrum are unusual in that their ribosomal proteins are acidic rather than basic as is the case with almost all bacterial ribosomes (Bayley, S.T. (1966) J. Mol. Biol. 15, 420-427). To determine whether the ribosomes of a moderate halophile show similar properties the ribosomal proteins from an unidentified moderate halophile, which grows over a wide range of NaCl concentrations (0.04-4.3 M), were compared to those of Escherichia coli and H. cutirubrum. The proteins are slightly more acidic than those of E. coli but much less acidic than those from the extreme halophile as judged by their mobility on polyacrylamide gels and their amino acid composition. The electrophoretic profile on polyacrylamide gels of the ribosomal proteins from the moderate halophile is similar whether the cells are grown in 0.5 M or 4.25 M NaCl.

Temperature related alterations in the acidic alanine-rich "A" protein from the 50S ribosomal particle of the extreme halophile, Halobacterium cutirubrum

50-S ribosomal subunits from the extreme halophilic bacterium, Halobacterium cutirubrum, contain an alanine-rich acidic "A" protein which resembles the L7--L12 multimer (Kaltschmidt and Wittmann, 1970) found in the 50-S ribosomal subunit of Escherichia coli cells. The protein contains 24 mole % alanine and is devoid of histidine, tryptophan and cysteine. Unlike E. coli which has two forms of the "A" protein distinguished solely by the acetylation state of the serine amino terminus. H. cutirubrum 50-S subunits contain only one unsubstituted form of the "A" protein in vivo. However, during purification of ribosomes from cells grown between 25 and 37 degrees C the latter "A" protein undergoes rapid, specific, in vitro enzymatic alteration at its carboxy-terminal end. When the halophile is grown in the temperature range of 40 to 42 degrees C the cleaving enzyme is not active and only one form of the "A" protein is found on the ribosomes.

Halobacterium cutirubrum ribosomes. Properties of the ribosomal proteins and ribonucleic acid

1. The 30S ribosomal subunit of the extreme halophile Halobacterium cutirubrum is unstable and loses 75% of its ribosomal protein when the 70S ribosome is dissociated into the two subunits. A stable 30S subunit is obtained if the dissociation of the 70S particle is carried out in the presence of the soluble fraction. 2. A fractionation procedure was developed for the selective removal of groups of proteins from the 30S and 50S subunits. When the ribosomes, which are stable in 4m-K(+) and 0.1m-Mg(2+), were extracted with low-ionic-strength buffer 75-80% of the 30S proteins and 60-65% of the 50S proteins as well as the 5S rRNA were released. The proteins in this fraction are the most acidic of the H. cutirubrum ribosomal proteins. Further extraction with Li(+)-EDTA releases additional protein, leaving a core particle containing either 16S rRNA or 23S rRNA and about 5% of the total ribosomal protein. The amino acid composition, mobility on polyacrylamide gels at pH4.5 and 8.7, and the molecular-weight distribution of the various protein fractions were determined. 3. The s values of the rRNA are 5S, 16S and 23S. The C+G contents of the 16S and 23S rRNA were 56.1 and 58.8% respectively and these are higher than C+G contents of the corresponding Escherichia coli rRNA (53.8 and 54.1%).

Isolation and properties of highly purified Halobacterium cutirubrum deoxyribonucleic acid-dependent ribonucleic acid polymerase

1. The subunits alpha and beta of Halobacterium cutirubrum DNA-dependent RNA polymerase have been purified to electrophoretic homogeneity. Both have mol.wt. 18000 and they are required in equimolar amounts for optimum activity. 2. The instability of the complete enzyme, alphabeta, in the absence of salt is due to the rapid inactivation of the beta subunit in these conditions. 3. Nearest-neighbour analysis of the product formed on poly[d(A-T)] as template shows that the enzyme copies the latter accurately. 4. The enzyme initiates new chains with purine nucleoside triphosphates exclusively. 5. The product obtained in the standard assay conditions contains some high mol.wt. (>16S) material, but consists primarily of short chains, of average length 70-80 nucleotide units. 6. The template specificity of the complete enzyme has been studied at high and low ionic strength. Its extreme dependence on salt concentration is unrelated to the gross overall base composition of the DNA used. 7. T(7) DNA is transcribed asymmetrically and the enzyme selectively copies the T(7) ;early' genes. 8. Preliminary amino acid analyses of alpha and beta subunits show that their overall content of acidic, basic and neutral amino acids does not differ appreciably from that of Escherichia coli RNA polymerase.

Characterization of ribosomes from the myxomycete Physarum rigidum grown in pure culture

The plasmodial phase of the myxomycete Physarum rigidum, analyzed during the period of rapid growth, attained a ribonucleic acid (RNA) and protein content of 9.8 and 60.0%, respectively, on a dry weight basis. It possessed ribosomes of the 80S class which, especially in the absence of magnesium ions, partially dissociated to 60S and 40S subunit classes. Electron micrographs of ribosomes treated with uranyl acetate-lead citrate revealed a number of surface features. Nucleotide analyses of both ribosomal and total RNA disclosed that they were composed of 51.0 and 52.5% guanylic and cytidylic acids, respectively. Consistent with most reports on other organisms, guanylic acid was the most abundant nucleotide found in the various types of RNA and cytidylic acid was the least abundant. The S(0) (20,w) values of the total RNA classes, in 0.01 sodium acetate (pH 4.6) containing 0.10 m NaCl, were 5.2, 18.1, and 27.3 in S units. Changing the ionic environment of the RNA (0.017 molal potassium phosphate, pH 7.0, containing 0.01 m disodium ethylenediaminetetraacetate) resulted in a reduction of the S(0) (20,w) values to 4.2, 16.6, and 22.6 in S units, which is indicative of molecular conformational transitions. In general, the amino acid composition of the ribosomal proteins was similar to the data available on ribosomal proteins from other biological sources.

Further characterization of particulate fractions from lysed cell envelopes of Halobacterium halobium and isolation of gas vacuole membranes

Lysates of cell envelopes from Halobacterium halobium have been separated into four fractions. A soluble, colorless fraction (I) containing protein, hexosamines, and no lipid is apparently derived from the cell wall. A red fraction (II), containing approximately 40 per cent lipid, 60 per cent protein, and a small amount of hexosamines consists of cell membrane disaggregated into fragments of small size. A third fraction (III) of purple color consists of large membrane sheets and has a very similar composition to II, containing the same classes of lipids but no hexosamines; its buoyant density is 1.18 g/ml. The fourth fraction (IV) has a buoyant density of 1.23 g/ml and contains the "intracytoplasmic membranes." These consist mainly of protein, and no lipid can be extracted with chloroform-methanol. Fractions I and II, which result from disaggregation of cell wall and cell membrane during lysis, contain a high proportion of dicarboxyl amino acids; this is in good agreement with the assumption that disruption of the cell envelope upon removal of salt is due to the high charge density. The intracytoplasmic membranes (IV) represent the gas vacuole membranes in the collapsed state. In a number of mutants that have lost the ability to form gas vacuoles, no vacuole membranes or any structure that could be related to them has been found.

A morphological study of Halobacterium halobium and its lysis in media of low salt concentration

The reported absence of a cell wall in halobacteria cannot be confirmed. Improved fixation techniques clearly show a cell wall-like structure on the surface of these cells. A stepwise reduction of the salt concentration causes the release of cell wall material before the cell membrane begins to disintegrate. The cell membrane breaks up into fragments of variable but rather small size, which are clearly different from a 4S component reported by others to be the major breakdown product of the cell membrane. It appears more likely that the 4S component arises from the dissolution of the cell wall. A residue of large membranous sheets remains even after prolonged exposure of halobacteria envelopes to distilled water. The lipids in these sheets do not differ significantly from the lipids in the lysed part of the cell membrane. The sheets, however, contain a purple-colored substance, which is not present in the lysed part. The easily sedimentable residue that remains after lysis of the cells or envelopes in distilled water also contains "intracytoplasmic membranes" with unusual structural characteristics. They can also be identified in sections through intact bacteria or envelope preparations. Their function is at present unknown but seems to be related to the formation of gas vacuoles in these organisms.