Physical properties of some ribosomal proteins in solution and evidence for molecular interactions between isolated ribosomal proteins

Messenger RNA recognition by fragments of ribosomal protein S4

Ribosomal protein S4 from Escherichia coli binds a large domain of 16 S ribosomal RNA and also a pseudoknot structure in the alpha operon mRNA, where it represses its own synthesis. No similarity between the two RNA binding sites has been detected. To find out whether separate protein regions are responsible for rRNA and mRNA recognition, proteins with N-terminal or C-terminal deletions have been overexpressed and purified. Protein-mRNA interactions were detected by (i) a nitrocellulose filter binding assay, (ii) inhibition of primer extension by reverse transcriptase, and (iii) a gel shift assay. Circular dichroism spectra were taken to determine whether the proteins adopted stable secondary structures. From these studies it is concluded that amino acids 48-104 make specific contacts with the mRNA, although residues 105-177 (out of 205) are required to observe the same toeprint pattern as full-length protein and may stabilize a specific portion of the mRNA structure. These results parallel ribosomal RNA binding properties of similar fragments (Conrad, R. C., and Craven, G. R. (1987) Nucleic Acids Res. 15, 10331-10343, and references therein). It appears that the same protein domain is responsible for both mRNA and rRNA binding activities.

RNA-protein interactions in 30S ribosomal subunits: folding and function of 16S rRNA

Chemical probing methods have been used to "footprint" 16S ribosomal RNA (rRNA) at each step during the in vitro assembly of twenty 30S subunit ribosomal proteins. These experiments yield information about the location of each protein relative to the structure of 16S rRNA and provide the basis for derivation of a detailed model for the three-dimensional folding of 16S rRNA. Several lines of evidence suggest that protein-dependent conformational changes in 16S rRNA play an important part in the cooperativity of ribosome assembly and in fine-tuning of the conformation and dynamics of 16S rRNA in the 30S subunit.

Acidic ribosomal proteins of Neurospora crassa

Neurospora crassa acidic ribosomal proteins from the high salt-ethanol extract of 80 S ribosomes have been fractionated by DEAE-cellulose chromatography. Six acidic ribosomal proteins were purified. All resemble Escherichia coli L7 and L12 in amino acid composition and molecular weight but each has a slightly different net charge at pH 3.2. Four have an apparent molecular weight of approx. 14 000, and two have a molecular weight of approx. 14 800. The amino acid compositions and circular dichroism (CD) spectra of the purified Neuropsora proteins are identical for the four 14 kDa proteins, but clearly distinguishable from the two 14.8 kDa proteins. The latter are also identical in amino acid composition and CD spectra. This suggests that there are two Neurospora acidic, or 'A', proteins, one of which exists in four microheterogeneous forms and the other exists in two forms.

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.

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.

Polynucleotide . ribosomal-protein complexes and their decoding properties

Polyadenylic acid, polycytidylic acid, polyuridylic acid or phage MS2 RNA, immobilized on Sepharose, form a complex with Escherichia coli ribosomal proteins. Regardless of their particular nucleotide composition, all four polynucleotides bind an invariable set of proteins consisting of S1, S3, S4, S5, S9, S13, L2 and L17. We found that these polynucleotide . protein complexes bind tRNA. Furthermore, it was possible to show that the poly(A) . protein and poly(U) . protein complexes select efficiently their cognate tRNAs, tRNALys and tRNAPhe respectively. This important functional property of the polynucleotide . protein complexes suggests that these ribosomal proteins belong in the ribosome to a functional domain responsible for the decoding of mRNA.

Shape of proteins S3 and S17 from the small subunit of Escherichia coli ribosome

The shapes of proteins S3 and S17 purified from the 30 S subunit of Escherichia coli A19 were studied by hydrodynamic methods. The proteins have s020,w values of 2.1 +/- 0.1 S and 1.2 +/- 0.1 S and D020,w values of 7.4 +/- 0.5 . 10(-7) cm2/s and 11.4 +/- 0.6 . 10(-7) cm2/s. The respective molecular weights determined by sedimentation equilibrium are 25 800 +/- 500 and 9900 +/- 300. The intrinsic viscosity values for the two proteins are 5.8 +/- 0.3 ml/g and 4.2 +/- 0.2 ml/g. From these hydrodynamic parameters a slightly elongated shape for S3 and a globular shape for S17 have been concluded.

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.

Physical studies on the conformation of ribosomal protein S4 from Escherichia coli

Proton magnetic resonance, circular dichroism and infrared spectroscopy were used to investigate the secondary and tertiary structure of the 16-S RNA binding protein S4 from Escherichia coli ribosomes. The proton magnetic resonance spectra of protein S4 in ribosomal reconstitution and low-salt buffers were identical and showed little dipolar broadening of the peaks, suggesting that the protein had an open extended structure. A ring-current-shifted apolar methyl resonance in the high-field region of the spectrum, together with a perturbation of the tyrosine ring proton resonance in the low-field region, indicated the existence of a specific tertiary fold in the polypeptide chain. This structure disappeared on lowering the pH below 5 or on heating above 30 degrees C, both processes being reversible. Circular dichroism measurements on protein S4 showed an alpha-helix content of 32% in reconstitution buffer compared with 26% in low-salt buffer. Heating the protein solution in reconstitution buffer above 35 degrees C reversibly disrupted this extra helix. Infrared studies on both solid films and solutions of protein S4 indicated the presence of little or no beta-structure. These results correlate well with the known RNA binding properties of protein S4.

A trypsin-resistant fragment from complexes of ribosomal protein S4 with 16-S RNA of Escherichia coli and from the uncomplexed protein

A fragment of ribosomal protein S4 was prepared by limited trypsin degestion of a specific complex between protein S4 and 16-S RNA. It was characterised for amino acid sequence and the N-terminal 46 amino acids were found to be absent. An intermediate fragment, cut at Arg-43, was also observed at low trypsin concentrations. Evidence is presented that the protected fragment constitutes the primary RNA-binding region of the protein. No smaller protein fragments were found that rebound to the RNA. A mechanism for the degradation of the N-terminal region of the protein is proposed and two probable functions of the excised region are given. Under milder trypsin digestion conditions than for the complex, the same fragment, cut at Arg-46, was also prepared from the free protein. This result, together with that from a control experiment, indicates that at least within this local region, the protein conformation is conserved in both the free protein and the protein-RNA complex. This is the first direct evidence for the conservation of conformation in a protein when both complexed and uncomplexed with a ribosomal RNA.

Geometry of the protein S4 from Escherichia coli ribosomes

The shape of protein S4 from Escherichia coli ribosomes in solution was determined by hydrodynamic methods and low-angle X-ray scattering. The molecular weight of 24000 determined by low-angle X-ray scattering is within 3% of that found by sedimentation equilibrium analysis and 8% of that determined by amino acid sequence work. The radius of gyration of 3.36 nm, the radius of gyration of the cross section of 0.41 nm and the hydrodynamic studies revealed that protein S4 is not spherical, but rather has a markedly extended shape. Calculations of different conformations, e.g. random coil, based on the parameters evaluated from hydrodynamic methods, revealed a rod-like structure of S4 with a length of 14 nm and a diameter of 1 nm. This is supported by a model of an equivalent scattering particle of uniform density based on all parameters obtained in this study.

Ribosomal proteins of Escherichia coli that stimulate stringent-factor-mediated pyrophosphoryl transfer in vitro

Guanosine tetra- and pentaphosphate, (p)ppGpp, can be synthesized in vitro in a reaction containing only the enzyme (stringent factor), salts, and substrates (nonribosomal system). This reaction is greatly stimulated upon addition of methanol (methanol system) or by ribosomes, mRNA, and tRNA (ribosome system). Here we show that several ribosomal proteins alone stimulate the synthesis of (p)ppGpp in the presence of stringent factor (protein system). The optimal ionic conditions for the ribosome and protein systems are identical. The concentration of ribosomes or any stimulating ribosomal protein required for saturation of a given concentration of stringent factor is similar. Fifty of 54 ribosomal proteins were tested for stimulation in the protein system; 15 proteins showed high activity, seven of these from the 30S ribosomal subunit and eight from the 50S subunit. The physiological relevance of this finding is discussed.

Molecular interactions between ribosomal proteins. Evidence for specificity of interaction between isolated proteins

The proteins S2, S3, S5, and S10 from the 30S ribosomal subunit of Escherichia coli was studied by analytical ultracentrifugation to characterize them in solution and to determine whether isolated protein-protein interactions exist. Such interactions, if specific, may therefore bear some relationship to the spatial organization of the subunit structure. It was found that protein S2 self-associates to a slight extent and that solution mixtures of S2 and S3 contain only enough dimeric species to account for the S2 dimer. Hence, no observable interaction was detected between S2 and S3. Solution mixtures of proteins S5 and S10 revealed a species of molecular weight greater than either protein. The proposal is that S5 and S10 interact with an association equilibrium constant of 7.6 X 10(-5) M-1 at 3 degrees in a Tris buffer at pH 7.4. It was also shown that solution with a 1:1:1 mixture by mass, of S2, S5, and S10 contained a species possessing a molecular weight consistent with a simple ternary complex of the three proteins.