Proton magnetic resonance studies to compare Escherichia coli ribosomal proteins prepared by two different methods

Differential effects of replacing Escherichia coli ribosomal protein L27 with its homologue from Aquifex aeolicus

The rpmA gene, which encodes 50S ribosomal subunit protein L27, was cloned from the extreme thermophile Aquifex aeolicus, and the protein was overexpressed and purified. Comparison of the A. aeolicus protein with its homologue from Escherichia coli by circular dichroism analysis and proton nuclear magnetic resonance spectroscopy showed that it readily adopts some structure in solution that is very stable, whereas the E. coli protein is unstructured under the same conditions. A mutant of E. coli that lacks L27 was found earlier to be impaired in the assembly and function of the 50S subunit; both defects could be corrected by expression of E. coli L27 from an extrachromosomal copy of the rpmA gene. When A. aeolicus L27 was expressed in the same mutant, an increase in the growth rate occurred and the "foreign" L27 protein was incorporated into E. coli ribosomes. However, the presence of A. aeolicus L27 did not promote 50S subunit assembly. Thus, while the A. aeolicus protein can apparently replace its E. coli homologue functionally in completed ribosomes, it does not assist in the assembly of E. coli ribosomes that otherwise lack L27. Possible explanations for this paradoxical behavior are discussed.

Cloning, overexpression, purification and crystallisation of ribosomal protein L9 from Bacillus stearothermophilus

The cloning, sequencing and overexpression of the gene coding for Bacillus stearothermophilus ribosomal protein L9 is described. The sequence corresponds directly to that presented for the protein itself by classical methods, differing at only a few amino acid positions. The purification and crystallisation of the corresponding L9 protein is presented. The crystals are isomorphous to those described for L9 obtained by conventional methods.

Fast preparative separation of 'native' core E coli 30S ribosomal proteins

We have developed an ion-exchange high performance liquid chromatographic method for preparative separation of 'core' proteins from E coli 30S ribosomal subunits, extracted with salt under non-denaturing conditions. This method yields individual proteins in pure and native form at high concentrations, (5 to 25 mg/ml) suitable for direct use in 1D-, 2D- or 3D-NMR studies.

The tertiary structure of salt-extracted ribosomal proteins from Escherichia coli as studied by proton magnetic resonance spectroscopy and limited proteolysis experiments

Ribosomal proteins from Escherichia coli have been isolated by a mild purification procedure. Their tertiary structure has been explored by two techniques, proton magnetic resonance and limited proteolysis. A number of proteins when subjected to limited proteolysis produce resistant fragments in good yields. In most cases this does not depend on the specificity of the enzyme used. The proteins S15, S16, S17 and L30 are not degraded at all, whereas a few proteins are very susceptible to proteolysis. 1H-NMR experiments show that the majority of the ribosomal proteins have a uniquely folded tertiary structure. This is particularly pronounced in the four proteins mentioned above which resist proteolysis. In general, a good agreement is observed between the degree of proteolytic resistance and the amount of folding indicated by NMR spectroscopy. Similar studies on a few ribosomal proteins purified under denaturing conditions show that, in contrast, these protein preparations are not structurally homogeneous and that they contain a mixture of denatured and renatured molecules. The results are interpreted in terms of a compactly folded tertiary structure for the four proteinase-resistant proteins while the majority of the other proteins appear to have two domains, one compactly folded and resistant to proteinase and the other flexible and susceptible to proteolysis. A few proteins seem to have a completely flexible structure and can therefore be easily degraded.

Ribosomal proteins and DNA-binding protein II from the extreme thermophile Bacillus caldolyticus

Crystallographic studies, presently on ribosomal and DNA-binding proteins from the moderate thermophile Bacillus stearothermophilus, can be expected to benefit from the use of even more stable proteins from extreme thermophiles. Bacillus caldolyticus, which is able to grow in the temperature range of 70-80 degrees C, appears to be a suitable candidate. We have compared the two bacilli using two criteria: the two-dimensional gel patterns of ribosomal proteins and the properties of DNA-binding protein II. The latter protein is ubiquitous in the eubacterial kingdom and can be purified in large quantities. B. caldolyticus can be grown at 75 degrees C in continuous culture with a generation time of 45-60 min. The yield of ribosomes compares favorably with that of B. stearothermophilus. The gel patterns of the ribosomal proteins are very similar but several differences, in particular among the 50S proteins, are observed. The N-terminal amino-acid sequence of the DNA-binding protein differs in 3 positions (out of 39) from B. stearothermophilus and the protein shows an increased resistance to thermal denaturation. Tetragonal and monoclinic crystals of DNA-binding protein II have been obtained which are suitable for X-ray studies and the diffraction patterns of the two crystal forms are shown.

Ribosomal proteins: their structure and spatial arrangement in prokaryotic ribosomes

During the last 15 years of ribosomal protein study, enormous progress has been made. Each of the proteins from E. coli ribosomes has been isolated, sequenced, and immunologically and physically characterized. Ribosomal proteins from other sources (e.g., from some bacteria, yeast, and rat) have been isolated and studied as well. Several proteins have recently been crystallized, and from the X-ray studies it is expected that much important information on the three-dimensional structure will be forthcoming. Many other proteins can probably be crystallized if suitable preparative procedures and crystallization conditions are found. Tremendous progress has also been made in deciphering the architecture of the ribosome. A battery of different methods has been used to provide the nearest neighbor distances of the ribosomal proteins in situ. Definitive measurements are now emanating from neutron-scattering experiments which also promise to give reasonably accurate radii of gyration of the proteins in situ. In turn, refined immune electron microscopy results supplement the neutron-scattering data and also position the proteins on the subunits themselves. This cannot be done by the other methods. Determination of the three-dimensional RNA structure within the ribosome is still in its infancy. Nonetheless, it is expected that by combining the data from protein-RNA and from RNA-RNA cross-linking studies, the structure of the RNA in situ can be unraveled. Of great interest is the fact that ribosomal subunits and ribosomes themselves have now been crystallized, and low-resolution structural maps have already been obtained. However, to grow suitable crystals and to resolve the ribosomal structure at a sufficiently high resolution remains a great challenge and task to biochemists and crystallographers.

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.

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.

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.

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.

A proton NMR study of ribosomal protein L25 from Escherichia coli

A highly folded form of the ribosomal protein L25 from Escherichia coli can be obtained from urea-denatured preparations. Proton NMR data show that this form of the molecule must have a compact, globular tertiary structure. Spectroscopically it is indistinguishable from L25 prepared by methods which avoid denaturing solvents. Thus L25 is a protein which can be reversibly denatured. The stability and solubility of the folded form of the protein are discussed and primary assignments made for a number of resonances in its NMR spectrum. The paper shows that this folded form of the protein can be characterised using NMR spectroscopy. High-resolution NMR spectroscopy provides a sensitive and general way for the characterisation of protein folds.

Purification and primary structure determination of the N-terminal blocked protein, L11, from Escherichia coli ribosomes

Protein L11 was isolated from the 50-S subunit of Escherichia coli ribosomes, using two salt extractions and two chromatographic separations on CM-cellulose. The unusual behavior of the protein when run on sodium dodecyl sulfate electrophoresis showed multiple bands. The complete primary structure of protein L11 is presented in detail. Its sequence was derived from peptides obtained by digesting the protein with trypsin, chymotrypsin, thermolysin, Staphylococcus aureus protease and, after modification, with trypsin. Chemical cleavage was performed with cyanogen bromide. Sequencing of the various peptides was achieved by manual micro-dansyl-Edman degradations and automatic methods. The N-terminal residue of the protein is blocked and was not degradable in the liquid-phase sequenator by the Edman method. It was identified by a combination of enzymatic cleavage and mass spectrometry. Protein L11 contain three methylated amino acid residues, a N alpha-trimethylalanine, and two residues of N epsilon-trimethyllysine. Their behaviour and influence in the sequence elucidation are described. The protein contains 141 amino acid residues and has a molecular weight of 14874. Secondary structure predictions of the protein are given, and its sequence is compared with those of other E. coli ribosomal proteins.

On the renaturation of ribosomal protein L11

When urea-denatured preparations of protein L11 from the ribosome of Escherichia coli are introduced into physiological buffers, two completely different configurations can be obtained. One form, by NMR criteria, shows little evidence of stable tertiary interactions; the other shows strong indications of a distinctive folding pattern. The configuration obtained depends on minor details of the method used for returning samples to non-denaturing conditions.

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.

A new method for the purification of 30S ribosomal proteins from Escherichia coli using nondenaturing conditions

A new method for the purification of Escherichia coli (A19) 30S ribosomal proteins has been developed that avoids the use of denaturing conditions such as urea, acetic acid, and lyophilization. In this way the majority of the proteins from the small ribosomal subunit can be obtained in 5--100 mg quantities and at greater than or equal to 90% purity. This has been achieved by the initial "splitting" of the proteins into two main groups with LiCl followed by fractionating on ion-exchange and gel-filtration columns, in the absence of urea and in the presence of salt. The proteins prepared by this nondenaturing procedure were soluble at high ionic strength and less soluble, being aggregated, at low salt concentrations. This behavior was exactly the opposite of that exhibited by proteins prepared with methods using denaturing conditions. These new methods have enabled additional ribosomal RNA-binding proteins to be found and potential protein-proteins complexes to be isolated. Preliminary evidence that these proteins may retain a more native structure is presented.