Purification of ribosomal proteins from Escherichia coli under nondenaturing conditions

Distance measurement by energy transfer. Ribosomal proteins L6, L10 and L11 of Escherichia coli

Ribosomal proteins L6, L11 and the complex [(L12)4 X L10] were labelled specifically at their respective single thiol groups, either with the acetylaminoethyl-dansyl or with the acetamidofluorescein fluorophore. The labelled proteins were then reconstituted, singly or in pairs, into ribosomal 50S subunits; the presence of the label had no observable effect on the composition, shape or activity of the reconstituted subunits. The distances between the labelled thiol groups were measured by a fluorescence energy transfer method detailed elsewhere [Epe, B. et al. (1983) Proc. Natl Acad. Sci. USA, 80, 2579-2583] and were found to be: for L6-L10, 60 A (6.0 nm); for L6-L11, 46 A (4.6 nm); for L10-L11, 56 A (5.6 nm). Reversal of the direction of energy transfer by exchanging labels gave duplicate distances which differed, on average, by about 4%. The distance between the fluorescent labels on L10 and L11 in the [23 S-RNA X L10 X L11 X (L12)4] ribonucleoprotein complex was the same as in the 50S subunit, but all three distances were greater in 50S subunits which had been reconstituted without the final activation step (incubation at 50 degrees C). This suggests a tightening of the L6/L10/L11 domain of the 50S subunit during the activation step.

Immunological studies of Escherichia coli mutants lacking one or two ribosomal proteins

A battery of immunological tests were used to investigate mutants which had been determined as lacking one or two ribosomal proteins on the basis of two-dimensional polyacrylamide gels. Proteins which were confirmed as missing from the ribosome in one or more mutants were large subunit proteins L1, L15, L19, L24, L27, L28, L30 and L33 and small subunit proteins S1, S9, S17 and S20. Cross-reacting material (CRM) was also absent from the post-ribosomal supernatant except in the case of protein S1. Since mutants lacking protein L11 have been previously described, any one of 13 of the 52 ribosomal proteins can be missing. None of these 13 proteins, except S1, can therefore have an indispensable role in ribosome function or assembly. In several mutants in which a protein was not missing but altered, it was present as several moieties of differing charge and size.

Immunoelectron microscopy of ribosomes carrying a fluorescence label in a defined position. Location of proteins S17 and L6 in the ribosome of Escherichia coli

By coupling fluorescein to a defined amino acid of a single ribosomal protein and incorporating this protein into the ribosome, we have obtained ribosomes labelled at a single, defined position. A fluorescein-specific antibody preparation was used to locate the fluorescein residues bound to the two cysteines at positions 58 and 63 of protein S17 and to the cysteine at position 86 of protein L6. This study demonstrates the advantages which accrue from the combination of electron microscopy and fluorimetry.

500-MHz 1H-NMR studies of ribosomal proteins isolated from 70-S ribosomes of Escherichia coli

A method for the large-scale isolation of ribosomal proteins is described avoiding pre-separation of 30-S and 50-S subunits. Five proteins isolated in this way were studied with high-resolution 1H NMR at 500 MHz. These are S21, L18, L25, L30 and L33. The results show that L18, L25 and L30 exhibit tertiary structure in solution and indications for secondary structure in S21 are found. Protein L33 appears to be a random coil. Several resonances in the 1H NMR spectra are assigned to particular protons of amino acid residues, e.g. the aromatic ring protons of tyrosines and histidines, and epsilon-protons of lysines.

Dissociation of nucleoprotein complexes by chaotropic salts

The effect of various anions in destabilizing yeast nucleoprotein complexes followed the order F- less than Cl- less than Br- less than ClO-4 congruent to Cl3CCOO-. Treatment of yeast nucleoproteins with 0.5 M NaClO4 resulted in removal of 80% of RNA. Based on the results, a simple method for effective separation of RNA from ribosomal particles is proposed and the mechanism of RNA dissociation by anions is also discussed.

Physical properties of ribosomal proteins isolated under different conditions from the Escherichia coli 50 S subunit

Physical properties of ribosomal proteins obtained with or without denaturating agents were compared. CD measurements and NMR studies have shown that proteins L2, L19, L24 and L30 isolated under denaturing conditions have the same properties as those prepared avoiding denaturating agents. CD and NMR spectra of proteins L1, L6, L11, L23, L25 and L29 obtained by us under denaturating conditions practically coincide with the data for the same proteins reported under 'mild' conditions. These findings suggest that the differences of reported physical properties can be due to different procedures of protein renaturation rather than to the methods of their isolation.

Localization of polyamine enhancement of protein synthesis to subcellular components of Escherichia coli and Pseudomonas sp. strain Kim

At 5 mM Mg2+, spermidine stimulation of polyphenylalanine synthesis by cell-free extracts of Escherichia coli was found to be about 30 times greater than that by extracts of Pseudomonas sp. strain Kim, a unique organism which lacks detectable levels of spermidine. By means of reconstitution experiments, the target of spermidine stimulation was localized to the protein fraction of the highspeed supernatant component (S-100) of E. coli and was absent from, or deficient in, the S-100 fraction of Pseudomonas sp. strain Kim. The spermidine stimulation did not appear to be due to the presence in the E. coli S-100 fraction of ribosomal protein S1, elongation factors, or E. coli aminoacyl-tRNA synthetases. The failure to observe spermidine stimulation by the Pseudomonas sp. strain Kim S-100 fraction was also not due to a spermidine-enhanced polyuridylic acid degradation. The synthesis of polyphenylalanine by Pseudomonas sp. strain Kim extracts was stimulated by putrescine and by S-(+)-2-hydroxyputrescine to a greater degree than was synthesis by E. coli extracts. The enhancement by putrescine and by S-(+)-2-hydroxyputrescine with Pseudomonas sp. strain Kim extracts was found to be due to effects on its ribosomes.

Structural and functional studies on protein S20 from the 30-S subunit of the Escherichia coli ribosome

Fragments resistant to proteolysis have been obtained from the ribosomal protein S20. They provide evidence for a structural domain stretching from the middle of the protein to its C terminus. With the exception of a large fragment of this protein lacking only 14 residues at the N terminus, all fragments had lost their ability to bind to 16-S rRNA. The protein in the S20 . 16-S-RNA complex was highly protected against enzymic digestion, indicating that the entire protein is involved in interaction with the nucleic acid. Circular dichroism showed a high alpha helix content (36%) for the intact protein and a low alpha helix content (2%) for the large fragment. Intrinsic fluorescence studies demonstrated that the single tyrosine residue in protein S20 is exposed to the solvent in the intact protein and is not exposed in the S20 . 16-S-RNA complex. Irreversible thermal denaturation of the protein was followed by fluorescence of the tyrosine and was found between 50 degrees C and 70 degrees C.

Distance measurement by energy transfer: the 3' end of 16-S RNA and proteins S4 and S17 of the ribosome of Escherichia coli

Escherichia coli ribosomal proteins S4 and S17 were specifically labelled at their thiol groups with the acetylaminoethyl-dansyl and/or bimane fluorophores. Each formed a complex with 16-S RNA and, when the other 30-S ribosomal proteins were added, a complete 30-S subunit with at least partial activity. If the 3' end of the RNA was also labelled (with fluorescein) then the distance between the two fluorophores could be measured by Förster-type energy transfer. The result for S4 was 6.0 nm (60 A) in the ribonucleoprotein complex and 5.6 nm (56 A) in the 30-S subunit, and for S17 6.3 nm (63 A) in the complex and 6.2 nm (62 A) in the subunit. There is no evidence for a major change in the relative disposition of the 3' and 5' ends of the 16-S RNA during formation of the 30-S subunit. Sources of error are discussed, including the question of multiple labelling. In order to measure more accurately the extent of energy transfer a procedure based upon enzymic digestion was developed and is detailed in this paper.

Ribosomal protein S20 purified under mild conditions almost completely inhibits its own translation

The efficiency of ribosomal protein S20 to act as repressor of its own synthesis in an in vitro system was found to depend greatly on the procedures employed to purify this protein. Whilst conventionally purified r-protein S20 inhibited its own synthesis by some 30%, up to 90% inhibition was observed if "milder" purification conditions were used. Evidence is presented that the latter preparation shows also a higher binding affinity to 16S rRNA.

Structure of ribosomal protein L6 from Escherichia coli. A fluorescence study

Protein L6 from the 50-S ribosomal subunit has been investigated using fluorimetric techniques. The intrinsic fluorophore Trp-61 and fluorescent labels (acetylaminoethyl-dansyl and acetylaminofluorescein) attached to the residue Cys-124 were used. It proved possible to incorporate fluorescence-labelled L6 into the 50-S ribosome. Trp-61 is exposed to solvent, as shown by its emission wavelength and by quenching experiments; the latter also show that it lies in a pocket with a high positive charge due to the basic residues in the N-terminal fragment. Cys-124 lies in a less strongly positive region. Upon incorporation into the 50-S subunit, the label on Cys-124 becomes less accessible for quenching but its positive potential rises, showing the absence of direct contact with 23-S RNA. Analysis of anisotropy data indicates a considerable degree of asphericity of free L6. Energy transfer between Trp-61 and the dansyl label on Cys-124, measured by donor quenching and acceptor enhancement, reveals a separation of 3.5 +/- 0.4 nm (35 +/- 4 A) between fluorophores.

Structure and evolution of ribosomes

Ribosomes are the only cell organelles occurring in all organisms. E. coli ribosomes, which are the best characterized particles, consist of three RNAs and 53 proteins. All components have been isolated and characterized by chemical, physical and immunological methods. The primary structures of the RNAs and of all the proteins are known. Information about the secondary structure of the proteins derives from circular dichroism measurements and from secondary structure prediction methods. The tertiary structure is being studied by limited proteolysis, proton magnetic resonance and crystallization followed by X-ray analysis. Various methods are being used to elucidate the architecture of the ribosomal particle: three-dimensional image reconstruction of crystals of bacterial ribosomes and/or their subunits; immune electron microscopy; neutron scattering; protein-protein, protein-RNA and RNA-RNA crosslinking; total reconstitution of ribosomal subunits. The results from these studies yield valuable information on the architecture of the ribosomal particle. Many mutants have been isolated in which one or a few ribosomal proteins are altered or even deleted. The genetic and biochemical characterization of these mutants allows conclusions about the importance of these proteins for the function of the ribosome. Ribosomal proteins from various prokaryotic and eukaryotic species have been compared by two-dimensional gel electrophoresis, immunological methods, reconstitution and amino acid sequence analysis. These studies show a strong homology among prokaryotic ribosomal proteins but only a weak homology between proteins from prokaryotic and eukaryotic ribosomes. Comparison of the primary and secondary structures of the ribosomal RNAs from various organisms shows that the secondary structure of the RNA molecules has been strongly conserved throughout evolution.

Preparation and characterization of fluorescent 50S ribosomes. Specific labeling of ribosomal proteins L7/L12 and L10 of Escherichia coli

So that the topographic and dynamic properties of the L7/L12--L10 complex in the 50S ribosome of Escherichia coli could be studied, methods and reagents were developed in order to introduce fluorescent groups at specific positions of these proteins. In the case of L7/L12, this was done by attaching an aldehyde group to Lys-51 of the protein by using 4-(4-formylphenoxy)butyrimidate or by converting the amino terminus of L12 into an aldehyde group by periodate oxidation. Subsequent reaction of the aldehyde groups with newly developed hydrazine derivatives of fluorescein and coumarin resulted in specifically labeled L7/L12 derivatives. L10 was modified at the single cysteine residue with N-[7-(dimethylamino)-4-methylcoumarinyl]maleimide. The fluorescent proteins L10 and L7/L12 could be reconstituted into 50S ribosomes. The resulting specifically labeled 50S ribosomes show 25--100% activity in elongation factor G dependent GTPase as well as in polyphenylalanine synthesis. The fluorescent properties of the labeled 50S ribosomes show that these fluorescent derivatives are suitable for energy transfer studies.

Concerning the mode of action of micrococcin upon bacterial protein synthesis

The antibiotic, micrococcin, binds to complexes formed between bacterial 23-S ribosomal RNA and ribosomal protein L11 and, in doing so, inhibits of thiostrepton. In assay systems simulating partial reaction of protein synthesis, micrococcin inhibits a number of processes believed to involve the ribosomal A site while stimulating GTP hydrolysis dependent upon ribosomes and elongation factor EF-G. The latter effect is not observed upon ribosomes lacking a protein homologous with protein L11. Nor is it apparent upon those containing 23-S RNA previously subjected to the action of a specific methylase known to render ribosomes resistant to thiostrepton. It is concluded that stimulation by micrococcin of factor-dependent GTP hydrolysis results from the binding of the drug to its normal target site which involves 23-S RNA and protein L11.

Functional studies on ribosomes lacking protein L1 from mutant Escherichia coli

The function of protein L1 in protein biosynthesis has been examined using ribosomes from two independently derived mutants of Escherichia coli, both of which lacked this protein. In systems in vitro with phage MS2 RNA or poly(U) as message, the mutant ribosomes showed from 40% to 60% of the activity of wild-type ribosomes. The reduction in activity was apparent in the kinetics of [14C]phenylalanine incorporation throughout the incubation period. The activities were restored fully to the wild-type level by the addition of purified protein L1. These results show on the one hand that protein L1 is not essential for protein biosynthesis but, on the other, its presence can significantly increase the overall rate of this process. The data further indicate it as likely that protein L1 exerts its effect at the elongation step

Recovery of pure ribosomal proteins from stained gels. A fast method of purification of active proteins

A simple technique has been developed for eluting ribosomal proteins from stained gels in the presence of an acetic acid solution. The ribosomal proteins are then separated from the dye by anion-exchange chromatography under dissociating conditions. Ribosomal proteins purified by these methods give total cross-reaction with proteins obtained by standard procedures, when tested by immunodiffusion against their corresponding antibodies, and show the same electrophoretic mobility as standard proteins in bidimensional polyacrylamide gel systems. Ribosomal proteins L7/L12, recovered from stained gels and purified by these methods, are able to reconstitute the elongation-factor-G-dependent GTPase activity of ribosomal particles deprived of these proteins. Radioactive protein L1, recovered in the same way, is incorporated into a total reconstituted 50-S subunit, competing with an excess of standard L1 present in the pool of total proteins from 50-S subunits used for reconstitution. These results suggest that bidimensional electrophoresis can be considered an alternative system of purification of active proteins from complex mixtures.

Structure and evolution of ribosomes

Ribosomes are multicomponent particles on which biosynthesis of proteins occurs in all organisms. The best-known ribosome, namely that of E. coli, consists of three RNA's and 53 different proteins. All proteins have been isolated and characterized by chemical, physical, and immunological methods. the primary sequences of 49 E. coli ribosomal proteins have so far been determined. Studies of the shape, as well as of the secondary and tertiary structure, of the proteins are in progress. Various techniques, 3.g., immune electron microscopy and cross-linking of neighboring components in situ, give information about the architecture of the ribosomal particle. The first technique resulted in illustrative and detailed knowledge now only on the shape of the ribosomal subunits but also about the location of many proteins on the surface of the particles. The analysis of cross-links between ribosomal proteins and/or RNA's has in several cases been pursued to the level of elucidating which amino acids and/or nucleotides are cross-linked together in situ. Reconstitution of a fully active E. coli 50S ribosomal subunit from its isolated RNA and protein components can be accomplished by means of a two-step incubation procedure. From the analysis of the intermediates occurring during the reconstitution process it has been concluded that the in vitro reconstitution process resembles that in vivo assembly of 50S subunits in many respects. E. coli mutants with alterations in almost all ribosomal proteins have been isolated. Their biochemical and genetic analyses are very useful tools for obtaining information about the structure, function, and biosynthesis of ribosomes, as well as about the location of the genes for these proteins on the chromosome. From comparative electrophoretic, immunological, protein-chemical, and reconstitution studies on ribosomes from various species it has become clear that their is little homology between ribosomal proteins from prokaryotes and those from eukaryotes. This finding is surprising since there is no essential difference in the way in which pro-and eukaryotic ribosomes function in protein biosynthesis.

Assembly map of the 50-S subunit from Escherichia coli ribosomes, covering the proteins present in the first reconstitution intermediate particle

Highly purified proteins and 23-S RNA from the 50-S subunit of Escherichia coli ribosomes were used to study the assembly dependences of the early assembly proteins. The proteins under observation and the RNA were incubated at 4 mM Mg2+ and 44 degrees C, the unbound proteins were separated by sucrose gradient centrifugation, the RNA . protein complex was precipitated with trichloroacetic acid, and the complex-bound proteins was identified by means of sodium dodecylsulfate gel electrophoresis. A systematic analysis led to the establishment of an assembly map including 17 proteins which represent the protein moiety of the first reconstitution intermediate particle.

50-S subunit from Escherichia coli ribosomes. Isolation of active ribosomal proteins and protein complexes

A method is described for the isolation of highly purified proteins from the 50-S subunit of Escherichia coli ribosomes. All the proteins from the large subunit could be isolated with the exception of L14, L26, L31 and L34. The isolated proteins are functionally active in reconstituted particles. The method consists of successive NH4Cl/EtOH and LiCl washing steps, which split off distinct groups of proteins from the ribosome. The protein groups are further separated by a combination of gel filtration (Sephadex G-100) and ion-exchange chromatography (carboxymethylcellulose) in the presence of 6 M urea, at neutral pH and 4 degrees C. The purity of the proteins was analyzed by two-dimensional gel electrophoresis. In addition, ten protein complexes were isolated and identified.