Effect of NH+4 and K+ on the activity of the ribosomal subunits in the EF-G- and EF-T-dependent GTR hydrolysis

$\text{E. coli}$ 50S ribosomal subunits show in the absence of 30S subunits and at low NH₄⁺ or K⁺ high turnover activity in EF-G-dependent GTP hydrolysis which is inhibited by increasing concentrations of monovalent cations. At 80 mM NH₄⁺ or K⁺ this activity is already 70–80% inhibited. This effect is reversed by 30S which are stimulatory with an optimum at about 80 mM for NH₄⁺ and 20–40 mM for K⁺. At low NH₄⁺ or K⁺ (<5 mM) stimulation by 30S of maximal 50S activity depends on the [EF-G]/[50S]. Unlike EF-G, EF-T does not show any Phe-tRNA-dependent GTPase activity with 50S alone even at low concentrations of NH₄⁺ or K⁺.     

Effect of polyamines on in vitro reconstitution of ribosomal subunits

The effect of polyamines on in vitro reconstitution of Escherichia coli 30S and 50S ribosomal subunits has been studied. Spermidine stimulated the reconstitution of 30S particles from 16S rRNA lacking the methyl groups on two neighboring adenines and total proteins of 30S subunits at least 1.6-fold. The reconstitution of 30S particles from normal 16S rRNA and total proteins of 30S subunits exhibited only slight spermidine stimulation. However, the optimal Mg2+ concentration of the reconstitution was decreased from 20 mM to 16 mM in the presence of 3 mM spermidine. In the absence of spermidine the assembly of 30S particles from normal 16S rRNA was more rapid than the assembly from 16S rRNA lacking the methyl groups on two neighboring adenines. The reconstitution of 50S particles from 23S and 5S rRNA and total proteins of 50S subunits was not influenced greatly by spermidine. Gel electrophoresis results, from reconstitution experiments of 30S particles from 16S rRNA lacking the methyl groups on two neighboring adenines and total proteins of 30S subunits, showed that the assembly of S1 and S9 proteins to 23S core particles was stimulated by spermidine during reconstitution. The relationship of polyamine effects on in vitro ribosome assembly from its constituents to in vivo ribosome assembly is discussed. The reconstitution of Bacillus subtilis 30S particles from 16S rRNA and total proteins of 30S subunits was also stimulated approximately 1.3-fold by 3 mM spermidine.     

Loosening and unfolding of E. coli 50 S ribosomal subunits: Dependence on magnesium content and temperature

Reversible change of 50 S ribosomal subunits to 40 S particles takes place in cold buffered 0.5 M NH₄Cl solutions either containing Mg⁺⁺ (up to 0.1 M), or free from Mg⁺⁺ and even supplemented with EDTA (1 mM). The 40 S particles were stable only within a definite temperature range. Heating of the samples caused completely irreversible unflding of the 40 S particles. This melting appeared to be co-operative and took place within a very narrow range of temperature, which for samples containing Mg⁺⁺ was a linear function of the log of Mg⁺⁺ concentration.The results suggest that two types of bonds maintained the compact structure of the ribosomal subunits: ionic bonds involving Mg⁺⁺ and heat-labile weak interactions between ribosomal components.     

Partial reconstitution of 60S ribosomal subunits from yeast

Summary Ribosomal 60S subunits active in polyphenylalanine synthesis can be reconstituted from core particles lacking 20–40% of the total protein. These core particles were obtained by treatment of yeast 60S subunits with dimethylmaleic anhydride, a reagent for protein amino groups. Upon reconstitution a complementary amount of split proteins is incorporated into the ribosomal particles, which have the sedimentation coefficient of the original subunits. Ribosomal protein fractions obtained by extraction with 1.25 M NH₄Cl, 4 M LiCl, 7 M LiCl, or 67% acetic acid, are much less efficient in the reconstitution of active subunits from these core particles than the corresponding released fraction prepared with dimethylmaleic anhydride. Attempts to reconstitute active subunits from protein-deficient particles obtained with 1.25 M NH₄Cl plus different preparations of ribosomal proteins, including the fraction released with dimethylmaleic anhydride, were unsuccessful. Therefore, under our conditions, of the disassembly procedures assayed only dimethylmaleic anhydride allows partial reconstitution of active 60S subunits.Abbreviation DMMA dimethylmaleic anhydride     

Stimulation by polyamines of enzymatic methylation of two adjacent adenines near the 3′ end of 16S ribosomal RNA of Escherichia coli

Effect of polyamines on the methylation of adenine in 16S rRNA was examined using the purified methylating enzyme. When 23S core particles were used as substrate, the activity was stimulated by Mg²⁺, Ca²⁺ and monovalent cations. Even in the presence of optimal concentrations of Mg²⁺ and NH₄⁺, the addition of 1 mM spermidine stimulated the methylation approximately 1.7-fold. When 30S ribosomal subunits were used as substrate, the rate of methylation was 20% of that of the methylation of 23S core particles. The activity was not influenced significantly by Mg²⁺, Ca²⁺ or monovalent cations. The addition of spermidine inhibited the methylation.     

The effect of ammonium on assimilatory nitrate reduction in the haloarchaeon Haloferax mediterranei

Physiology, regulation and biochemical aspects of the nitrogen assimilation are well known in Prokarya or Eukarya but they are poorly described in Archaea domain. The haloarchaeon Haloferax mediterranei can use different nitrogen inorganic sources (NO₃⁻, NO₂⁻ or NH₄⁺) for growth. Different approaches were considered to study the effect of NH₄⁺ on nitrogen assimilation in Hfx. mediterranei cells grown in KNO₃ medium. The NH₄⁺ addition to KNO₃ medium caused a decrease of assimilatory nitrate (Nas) and nitrite reductases (NiR) activities. Similar effects were observed when nitrate-growing cells were transferred to NH₄⁺ media. Both activities increased when NH₄⁺ was removed from culture, showing that the negative effect of NH₄⁺ on this pathway is reversible. These results suggest that ammonium causes the inhibition of the assimilatory nitrate pathway, while nitrate exerts a positive effect. This pattern has been confirmed by RT-PCR. In the presence of both NO₃⁻ and NH₄⁺, NH₄⁺ was preferentially consumed, but NO₃⁻ uptake was not completely inhibited by NH₄⁺ at prolonged time scale. The addition of MSX to NH₄⁺ or NO₃⁻ cultures results in an increase of Nas and NiR activities, suggesting that NH₄⁺ assimilation, rather than NH₄⁺ per se, has a negative effect on assimilatory nitrate reduction in Hfx. mediterranei. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Effects of monovalent cations on the catalytic activity of pig liver phosphofructokinase.

The monovalent cations NH₄⁺, K⁺, and Rb⁺ activate pig liver phosphofructokinase by increasing the maximal velocity. In the presence of these cations the enzyme retains sigmoid kinetics with respect to fructose-6-phosphate. However, these cations bring about a decrease in the [S]_0.5 for fructose-6-phosphate to an extent directly proportional to their ionic volumes. The apparent dissociation constants of NH₄⁺, K⁺, and Rb⁺ for the enzyme at 0.5 mM ATP and 4 mM Fru6P are 0.2 mM, 8 mM, and 15 mM, respectively. The maximal velocity of the enzyme in the presence of saturating concentrations of Rb⁺ is about 70% of that seen with NH₄⁺ or K⁺. The monovalent cations Li⁺, Na⁺, and Cs⁺ inhibit the enzyme at high concentrations (> 50 mM) by decreasing the maximal velocity. Although the efficiency of inhibition by these cations qualitatively increases with decreasing size, there is no obvious quantitative relationship between efficiency of inhibition and any parameter of ionic size.     

Properties of ribosomes and RNA synthesized by Escherichia coli grown in the presence of ethionine. V. Methylation dependence on the assembly of E. coli 50 S ribosomal subunits.

An ethionine-containing submethylated particle related to the 50 S ribosomal subunit has been isolated from Escherichia coli grown in the presence of ethionine. This particle (E-50S) lacks L16, contains reduced amounts of L6, L27, L28 and L30 and possesses a more labile and flexible structure than the normal 50 S subunit. The E-50S particle has defective association properties and is incapable of peptide bond formation. It can be converted to an active 50 S ribosomal subunit when ethionine-treated bacteria are incubated under conditions which permit methylation of submethylated cellular components (presence of methionine) in the absence of de novo protein and RNA synthesis (presence of rifampicin).Total reconstitution of 50 S ribosomal subunits in vitro using normal 23 S and 5 S ribosomal RNA and proteins prepared from E-50S particles yields active subunits only if L16 is also added. The hypothesis that E-50S particles accumulate in ethionine-treated bacteria because the absence of methylation of one or more of their components blocks a late stage (L16 integration) in the normal 50 S assembly process is discussed.     

Cation requirement for the reconstitution of oligomycin-sensitive ATPase by means of soluble F1-ATPase and F1-depleted submitochondrial particles

Bovine heart submitochondrial particles depleted of F₁ by treatment with urea (‘F₁-depleted particles’) were incubated with soluble F₁-ATPase. The binding of F₁ to the particles and the concomitant conferral of oligomycin sensitivity on the ATPase activity required the presence of cations in the incubation medium. NH⁺₄, K⁺, Rb⁺, Cs⁺, Na⁺ and Li⁺ promoted reconstitution maximally at 40–74 mM, guanidinium⁺ and Tris⁺ at 20–30 mM, and Ca²⁺ and Mg²⁺ at 3–5 mM. The particles exhibited a negative ζ-potential, as determined by microelectrophoresis, and this was neutralized by mono- and divalent cations in the same concentration range as that needed to promote F₁ binding and reconstitution of oligomycin-sensitive ATPase. It is concluded that the cations act by neutralizing negative charges on the membrane surface, mainly negatively charged phospholipids. These results are discussed in relation to earlier findings reported in the literature with F₁-depleted thylakoid membranes and with submitochondrial particles depleted of both F₁ and the coupling proteins F₆ and oligomycin sensitivity-conferring protein.     

Nitrogen metabolism in haloarchaea

The nitrogen cycle (N-cycle), principally supported by prokaryotes, involves different redox reactions mainly focused on assimilatory purposes or respiratory processes for energy conservation. As the N-cycle has important environmental implications, this biogeochemical cycle has become a major research topic during the last few years. However, although N-cycle metabolic pathways have been studied extensively in Bacteria or Eukarya, relatively little is known in the Archaea. Halophilic Archaea are the predominant microorganisms in hot and hypersaline environments such as salted lakes, hot springs or salted ponds. Consequently, the denitrifying haloarchaea that sustain the nitrogen cycle under these conditions have emerged as an important target for research aimed at understanding microbial life in these extreme environments. The haloarchaeon Haloferax mediterranei was isolated 20 years ago from Santa Pola salted ponds (Alicante, Spain). It was described as a denitrifier and it is also able to grow using NO₃ ^-, NO₂ ^- or NH₄ ⁺ as inorganic nitrogen sources. This review summarizes the advances that have been made in understanding the N-cycle in halophilic archaea using Hfx mediterranei as a haloarchaeal model. The results obtained show that this microorganism could be very attractive for bioremediation applications in those areas where high salt, nitrate and nitrite concentrations are found in ground waters and soils.     

Identification of proteins functionally altered by chemical modification of the transfer RNA and polyuridylic acid binding sites of 30 S ribosomal subunits

Previous studies have shown that Rose Bengal-sensitized photo-oxidation of 30 S ribosomal subunits causes inactivation of tRNA binding and partial loss of poly(U) binding activities (Noller et al., 1971). The present studies, reconstitution of 30 S subunits from 16 S RNA, total protein from modified subunits, and purified proteins from untreated subunits, show that proteins S2 and S3 together completely restore these activities to the reconstituted subunits. The modified proteins are capable of in vitro assembly, and give rise to particles with normal sedimentation constants, showing that restoration of activity is not simply due to correction of an assembly defect.Protein S3 restores poly(U) binding and tRNA binding to the same extent, accounting for the lowered mRNA binding activity of the modified particles as well as a corresponding fraction of the tRNA binding activity. Protein S2 restores the remaining fraction of the tRNA binding activity, but has no effect on poly (U) binding. In 50 S-stimulated tRNA binding, proteins S1 and S5 are required in addition to S2 and S3 for full activity.     

Effects of NH4+ concentration on growth,morphology and NH4+ uptake kinetics of Salvinia natans

Many plants develop toxicity symptoms and have reduced growth rates when supplied with ammonium (NH₄⁺) as the only source of inorganic nitrogen. In the present study, the growth, morphology, NH₄⁺ uptake kinetics and mineral concentrations in the tissues of the free-floating aquatic plant Salvinia natans (water fern) supplied exclusively with NH₄⁺–N at concentrations of 0.25–15 mM were investigated. S. natans grew well, with relative growth rates of c. 0.25 g g^?1 d^?1 at external NH₄⁺ concentrations up to 5 mM, but at higher levels growth was suppressed and the plants had small leaves and short roots with stunted growth. The high-affinity transport system (HATS) that mediate NH₄⁺ uptake at dilute NH₄⁺ levels was downregulated at high NH₄⁺ concentrations with lower velocities of maximum uptake (V_max) and higher half-saturation constants (K_1/2). High NH₄⁺ levels also barely affected the concentrations of mineral cations and anions in the plant tissue. It is concluded that S. natans can be characterized as NH₄⁺-tolerant in line with a number of other species of wetland plants as growth was unaffected at NH₄⁺ concentrations as high as 5 mM and as symptoms of toxicity at higher concentrations were relatively mild. Depolarization of the plasma membrane to the equilibrium potential for NH₄⁺ at high external concentrations may be a mechanism used by the plant to avoid excessive futile transmembrane cycling. S. natans is tolerant to the high NH₄⁺ levels that prevail in domestic and agricultural wastewaters, and the inherent high growth rate and the ease of biomass harvesting make S. natans a primary candidate for use in constructed wetland systems for the treatment of various types of nitrogen-rich wastewaters.     

Assembly in vitro of the 50 S subunit from Escherichia coli ribosomes: proteins essential for the first heat-dependent conformational change.

An early intermediate during the assembly in vitro of the ribosomal 50 S subunit is the RI₅₀(1) particle, which undergoes a drastic change in s value to form the RI₅₀¹(1) particle. The formation of this RI₅₀¹(1) particle, which is essential for the assembly of a highly active 50 S particle, was analyzed. Total reconstitution experiments with purified proteins revealed that six ribosomal components (23 S RNA and the proteins L4, L13, L20, L22 and L24) are essential for the RI₅₀¹(1) formation. Protein L3 had a stimulatory effect, but was not essential. With these seven components, a particle with the RI₅₀¹ conformation could be formed.A comparison with assembly in vivo demonstrated that the pathways of protein assembly in vitro and in vivo are very similar at the beginning, but diverge towards the end of the process. Furthermore, the sequence in which the proteins can be split off the 50 S subunit by increasing concentrations of LiCl corresponds, to a first approximation, to the reverse of the order of assembly in vitro.     

Hepatitis E virus capsid protein assembles in 4M urea in the presence of salts

The hepatitis E virus (HEV) capsid protein has been demonstrated to be able to assemble into particles in vitro. However, this process and the mechanism of protein–protein interactions during particle assembly remain unclear. In this study, we investigated the assembly mechanism of HEV structural protein subunits, the capsid protein p239 (aa368–606), using analytical ultracentrifugation. It was the first to observe that the p239 can form particles in 4M urea as a result of supplementation with salt, including ammonium sulfate [(NH₄)₂SO₄], sodium sulfate (Na₂SO₄), sodium chloride (NaCl), and ammonium chloride (NH₄Cl). Interestingly, it is the ionic strength that determines the efficiency of promoting particle assembly. The assembly rate was affected by temperature and salt concentration. When (NH₄)₂SO₄ was used, assembling intermediates of p239 with sedimentation coefficient values of approximately 5 S, which were mostly dodecamers, were identified for the first time. A highly conserved 28‐aa region (aa368–395) of p239 was found to be critical for particle assembly, and the hydrophobic residues Leu³⁷², Leu³⁷⁵, and Leu³⁹⁵of p239 was found to be critical for particle assembly, which was revealed by site‐directed mutagenesis. This study provides new insights into the assembly mechanism of native HEV, and contributes a valuable basis for further investigations of protein assembly by hydrophobic interactions under denaturing conditions.     

Action of methanol on the assocation of ribosomal subunits and its effect on the GTPase activity of elongation factor G

Methanol causes association of 30S and 50S ribosomal subunits from $\text{E. coli}$ at MgCl₂ concentrations in which they are normally completely dissociated. The 70S ribosome formed under these conditions shows a lower sedimentation velocity and is functionally active in the EF-G GTPase. Association of ribosomal subunits in the presence as well as absence of methanol is affected by washing the ribosomes with 0.5 M NH₄Cl. Methanol reduces the Mg²⁺ concentration required for subunit association as well as for EF-G GTPase activity. The basic requirement for EF-G GTPase activity both with and without alcohol is shown to be the association of 30S and 50S subunits.     

A dominant negative mutant of the E. coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit

Escherichia coli DbpA is an ATP-dependent RNA helicase with specificity for hairpin 92 of 23S ribosomal RNA, an important part of the peptidyl transferase center. The R331A active site mutant of DbpA confers a dominant slow growth and cold sensitive phenotype when overexpressed in E. coli containing endogenous DbpA. Ribosome profiles from cells overexpressing DbpA R331A display increased levels of 50S and 30S subunits and decreased levels 70S ribosomes. Profiles run at low Mg²⁺ exhibit fewer 50S subunits and accumulate a 45S particle that contains incompletely processed and undermodified 23S rRNA in addition to reduced levels of several ribosomal proteins that bind late in the assembly pathway. Unlike mature 50S subunits, these 45S particles can stimulate the ATPase activity of DbpA, indicating that hairpin 92 has not yet been sequestered within the 50S subunit. Overexpression of the inactive DbpA R331A mutant appears to block assembly at a late stage when the peptidyl transferase center is formed, indicating a possible role for DbpA promoting this conformational change.     

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).     

Effects of Culture Conditions on Poly(β-Hydroxybutyric Acid) Production by Haloferax mediterranei

The halobacterium Haloferax mediterranei accumulates poly(β-hydroxybutyrate) (PHB) as intracellular granules. The conditions for PHB production in batch and continuous cultures have been studied and optimized. Phosphate limitation is essential for PHB accumulation in large quantities. Glucose and starch are the best carbon sources. With 2% starch, 0.00375% KH₂PO₄, and 0.2% NH₄Cl in batch culture, a production of ca. 6 g of PHB per liter was reached, being 60% of the total biomass dry weight, and giving a yield over the carbon source of 0.33 g/g. The PHB production in continuous cultures was stable over a 3-month period. Our results demonstrate that H. mediterranei is an interesting candidate for industrial production of biological polyesters.     

A comparative study on the hydrodynamic shape, conformation, and stability of E. coli ribosomal subunits in reconstitution buffer.

We have compared the hydrodynamic shape, conformation, and stabilities of active, unwashed ribosomal subunits, as well as their susceptibilities to changes in temperature and ionic strength. Both intrinsic viscosity and sedimentation velocity measurements indicate that the 30 S subunit has a more asymmetric hydrodynamic shape. The intrinsic viscosity of this subunit in reconstitution buffer has been found to be significantly larger than the value reported previously. While the RNA conformation in both subunits may be very similar as suggested by the near uv CD spectra, the average conformation of the protein in the two subunits is drastically different. The 30 S subunit has a lower T_m. The 50 S subunit is rather stable toward changes of ionic strength, whereas the 30 S subunit is quite susceptible to changes in ionic strength.     

Protein-protein proximity in the association of ribosomal subunits of Escherichia coli: crosslinking of 30 S protein S16 to 50 S proteins by glutaraldehyde or formaldehyde

The interaction of ribosomal subunits from Escherichia coli has been studied using crosslinking reagents. Radioactive ³⁵S-labeled 50 S subunits and non-radioactive 30 S subunits were allowed to reassociate to form 70 S ribosomes. The 70 S particles, containing radioactivity only in the 50 S protein moiety, were incubated with glutaraldehyde or formaldehyde. As a result of this treatment a substantial fraction of the 70 S particles did not dissociate at 1 mm-Mg²⁺. This fraction was isolated and the ribosomal proteins were extracted. The protein mixture was analyzed by the Ouchterlony double diffusion technique by using eighteen antisera prepared against single 30 S ribosomal proteins (all except those against S3, S15 and S17). As a result of the crosslinking procedure it was found that only anti-S16 co-precipitated ³⁵S-labeled 50 S protein. It is concluded that the 30 S protein S16 is at or near the site of interaction between subunits and can become crosslinked to one or more 50 S ribosomal proteins.