THE ISOLATION, CHARACTERIZATION AND ACID-BASE PROPERTIES OF RIBONUCLEIC ACID FROM RABBIT-RETICULOCYTE RIBOSOMES

Properties of ribosomal proteins from two mammalian sources

1. Ribosomal protein fractions from rabbit reticulocytes and rat liver were prepared by extracting ribosomes with 0.2n-hydrochloric acid or guanidinium chloride and subsequent dialysis. 2. Treatment for 2.5hr. or less with 0.2n-hydrochloric acid dissolved 46-54% of the proteins, which were richer in arginine and lysine and in N-terminal alanine groups and poorer in aspartic acid and glutamic acid and in N-terminal glycine groups than the acid-insoluble proteins. 3. Protein fractions prepared from the guanidinium chloride extract of ribosomes from rat liver were usually more basic than those from rabbit reticulocytes. 4. The ratios lysine: arginine of fractions in the guanidinium chloride extracts were appreciably higher for proteins from rabbit reticulocytes than from rat liver. 5. The concentration of urea and the pH of the gel affected the rate of migration and number of bands in starch-gel electrophoresis.

Synthesis of messenger ribonucleic acid in excised pea-seedling root segments. Separation of the messenger from microsomes by electrophoresis

1. Electrophoresis on cellulose acetate membrane in a tris-pyrophosphate buffer was used to separate microsomal fractions into three components: (1) the lipoprotein; (2) the nucleoprotein (termed the beta-band); (3) traces of free RNA (termed the alpha-band). In tris buffer containing Mg(2+) the alpha-band was not obtained. 2. The incorporation of uridine and phosphate into RNA by excised pea-seedling root segments was studied by using this electrophoretic technique. 3. It was shown that after a short (;pulse') incubation in the radioactive precursor and a longer (;chase') incubation in the non-radioactive precursor most of the incorporation was into the RNA of the alpha-band and little into that of the beta-band. Previous work showed that in roots of whole seedlings the incorporation is mostly into the ribosomal RNA, corresponding to the material in the beta-band. 4. A pulse-labelled RNA has also been found; this seems to be a cell fraction distinct from the microsomes or ribosomes. 5. The apparent base compositions of labelled RNA in the alpha-band and small amounts of labelled RNA in the beta-band and of unfractionated RNA were very different from the composition of ribosomal or transfer RNA, and somewhat like that of DNA. 6. It is suggested that the excised root segment synthesizes a messenger-RNA fraction labelled after a pulse incubation and a distinct messenger RNA labelled after a pulse and chase incubation, but no ribosomal or transfer RNA. The system is thus similar to the ;step-down' culture conditions in bacteria.

Further observations on the polynucleotide-induced stimulation of protein synthesis by cell-free preparations from rabbit reticulocytes

1. The effect of high-molecular-weight RNA from reticulocyte polyribosomes (messenger RNA) on protein synthesis by subcellular fractions derived from reticulocytes, reported by Arnstein, Cox & Hunt (1964), has now been studied in detail. Optimum response of the cell-free system requires 30-50mm-K(+) and approx. 5mm-Mg(2+) in the pH range 7.4-7.6. 2. RNA stimulates the incorporation into protein of both free amino acids and of aminoacyl residues from s-RNA. Stimulation by either RNA or polyuridylic acid is dependent on a labile factor or enzyme, which is present in the ;pH5 fraction' and may be concerned with the formation of new polysomes. Quantitatively the response of the cell-free system to RNA is similar to that of polyuridylic acid, and there appears to be competition between messenger RNA and polyuridylic acid or polyadenylic acid.

Electrophoresis of extracts of Paramecium aurelia containing metagons

Methods are described for subjecting microsomal and RNA extracts of mate-killer paramecia ( Paramecium aurelia , stock 540) to electrophoresis on cellulose acetate paper. Material in the bands thus obtained is eluted from the paper and tested for ability to infect paramecia with metagons—cytoplasmic products of genes M 1 or M 2 —originally derived from mate-killer paramecia. Following successful infection the recipient paramecia are able to maintain growth of the symbiotic mu particles which determine mate-killing. It has been found that the potential biological activity of metagons is retained throughout the various steps in the procedure: homogenization, fractional centrifugation, separation of ENA from protein, paper electrophoresis and elution. The metagons are found initially to be associated with ribosomes, but can be dissociated from the latter by electrophoresis in a low Mg 2+ buffer. Metagon activity is found in bands containing free RNA. The base composition of the metagon-containing band has been compared with that of the DNA of P. aurelia.

ISOLATION AND CHARACTERIZATION OF RIBOSOMAL RIBONUCLEIC ACID

1. Ribosomal RNA has been prepared by extracting tissues with a phenol-cresol mixture, and ribosomal RNA can be selectively precipitated with m-cresol. No rapidly labelled RNA was associated with this material. 2. However, if RNA and DNA are extracted with 4-aminosalicylate and phenol-cresol mixture and the nucleic acids precipitated, DNA, glycogen and s-RNA (transfer RNA) can be extracted with 3m-sodium acetate and in this case rapidly labelled RNA remains associated with the ribosomal RNA. 3. The ribosomal RNA is stable in the presence of concentrated salt solution and, although the secondary structure is lost by heating at 70 degrees in 10mm-sodium acetate, it can be re-formed in the presence of 200mm-sodium acetate. 4. The 28s and 18s components have been separated and their base compositions determined.

TERMINAL-SEQUENCE STUDIES OF HIGH-MOLECULAR-WEIGHT RIBONUCLEIC. THE REACTION OF PERIODATE-OXIDIZED RIBONUCLEOSIDES , 5'-RIBONUCLEOTIDES AND RIBONUCLEIC ACID WITH ISONIAZID

1. The reaction products of isoniazid with periodate-oxidized ribonucleosides and 5'-ribonucleotides have been characterized as the monohydrazones. 2. The stability, chromatographic and electrophoretic properties of the hydrazones are described. 3. (3)H-labelled isoniazid was shown to react with the 5'-linked terminal adenosine and cytidine groups of periodate-oxidized Escherichia coli transfer RNA. One mole of isoniazid reacts with 27x10(3)g. of the transfer RNA. 4. One mole of (3)H-labelled isoniazid reacts with approx. 10(6)g. of rabbit-reticulocyte ribosomal RNA. After fractionation of the RNA into its two components and treating the fractionated material with pancreatic ribonuclease and ribonuclease T(1) evidence is presented for the existence of two 5'-linked terminal sequences in the 30s fraction and only one sequence in the 17s fraction. 5. The application of this method to determining terminal sequences of high-molecular-weight RNA is discussed.

A microsystem to evaluate the synthesis of [3H]leucine labeled proteins by macrophages

A method is described for evaluating protein synthesis by adherent M phi by measuring the incorporation of [3H]leucine into TCA precipitable material. By using guanidine-HCl it was possible to remove completely the radiolabeled proteins from the adherent cells that were cultured in microwells, and retain TCA precipitable material. This procedure enabled us to harvest the TCA precipitable proteins with a semiautomatic cell harvester. The guanidine-HCl treatment did not affect the recovery of the radioactive proteins and did not alter the sensitivity of the assay. This method is very simple and rapid and, since it is suitable for processing microcultures, permits detailed studies on the biology of small numbers of M phi.

Studies on the secondary structure of nuclear ribonucleic acids

Rat liver nuclei were separated into two fractions, the nucleolus and the nucleoplasm, by a combined salt-enzymic extraction. RNA was purified from both sources and analysed on sucrose density gradients. In both fractions a prominent heterogeneous RNA class with mean sedimentation coefficient of 18S was found. This material was analysed by measuring the rate of reaction with formaldehyde, the ultraviolet absorbance-temperature profile, the spectrophotometric observation of conformational changes as a function of pH, the spectrophotometric titration of uracil and guanine residues and the effect of both temperature and ionic strength on the spectrophotometric titration of cytosine residues. Nucleoplasmic 18S RNA fraction exhibited, on heating and also by adjustment of the pH to 2.5, a hyperchromicity of about 16%, close to that observed, in control experiments, for ribosomal RNA (22%). Titration of cytosine residues in solutions containing 1mm-NaCl and 0.1m-NaCl yielded pK values equal to 4.41 and 3.84 respectively. These results suggest that this RNA fraction is composed of structurally complex polymers. The hypochromicity of the nucleolar 18S RNA fraction determined by heating or adjusting the pH to 2.5, was not greater than 6% of the initial value. The rate of reaction with formaldehyde was 88% of that observed for the hydrolysed 18S fraction which suggested only 12% hydrogen bonding. pK values for uracil and guanine residues were 10.1 and 10.05 respectively. Titration of cytosine residues yielded a pK of 4.10, which was found to be independent of temperature and ionic strength variations.

A spectrophotometric study of the secondary structure of ribonucleic acid isolated from the smaller and larger ribosomal subparticles of rabbit reticulocytes

The spectrum of RNA from the smaller and larger subparticles of rabbit reticulocyte ribosomes was studied as a function of pH, ionic strength, urea concentration and temperature. It was inferred that both RNA species form short double-helical segments of not more than about 10 base-pairs in length. Not more than about 70% of the base residues may be located in double-helical segments. RNA from the larger subparticle is richer in guanine and cytosine residues and its secondary structure is the more stable. These conclusions are based on the use of double-helical RNA from virus-like particles and of unfractionated Escherichia coli tRNA as model systems.

The effect of pancreatic ribonuclease on rabbit reticulocyte ribosomes and its interpretation in terms of ribosome structure

1. Parts of the 16s and 30s RNA species of reticulocytes are readily hydrolysed by pancreatic ribonuclease. The biological activity of the ribosomes is diminished after treatment with low concentrations of the enzyme (e.g. 1ng. of ribonuclease/2.5mg. of polyribosome fraction/ml.). A high proportion of the chain scissions are ;hidden' owing to the secondary structure of the RNA moiety. 2. As the concentration of ribonuclease is increased RNA is lost from the ribosome. About 20-30% of the RNA may be removed from the ribosome without altering appreciably its sedimentation coefficient or its appearance in the electron microscope. 3. The amount of RNA removed from the ribosome is not increased by raising the concentration of enzyme from about 1mug. to 2.5mg. of ribonuclease/2.5mg. of polyribosome fraction/ml., or by increasing the temperature from 0 degrees to 30 degrees , or by first converting the RNA moiety into a single-stranded form before exposure to ribonuclease. 4. Untreated polyribosomes aggregate at about 75 degrees , whereas ribosomes treated with ribonuclease aggregate at about 45 degrees . The aggregates that are found on heating ribosomes after enzymic hydrolysis contain about 40-50% of the complement of RNA of intact ribosomes. 5. From the size of the fragments of RNA isolated from RNA-depleted ribosomes it is inferred that there is one site/60-100 nucleotides that is sensitive to ribonuclease. 6. The RNA moiety of RNA-depleted ribosomes has some double-helical character as shown by the optical properties and X-ray-diffraction pattern of ribonuclease-treated ribosomes and by the ;melting' properties of the isolated RNA. 7. Subparticles prepared by titration with an excess of EDTA are readily hydrolysed by ribonuclease to fragments of S(20,w) less than 4s, in contrast with the intact particle.

A possible structure of the rabbit reticulocyte ribosome. An exercise in model building

It is suggested that the location of each of the diverse ribosomal proteins in the ribosome, or in the ribosomal subparticles in their native or derived forms, is determined by the nucleotide sequence of the 16s and 23-30s RNA moieties, i.e. that the 16s and 23-30s RNA species provide a unique binding site for each species of ribosomal protein. The ways of assembling such a thread into a ribosome-like structure appear limited if the ribosome is largely stabilized by protein-protein interactions. The nucleoprotein thread was built into a structure, having the general features of a hollow cylinder, that is consistent with the known dimensions and properties of the rabbit reticulocyte ribosome. It appears possible to test the model by experiment.

The preparation of ribosomal ribonucleic acid from whole bacteria

1. A simple method for the preparation of ribonuclease-free ribosomal RNA is described in which ribonuclease-deficient bacteria are treated with acetone and the RNA is extracted with phenol and purified by precipitating it with potassium acetate. The treatment with acetone appears to render the cell wall permeable to RNA but not to DNA during the extraction with phenol. The method thus avoids the need to disrupt the bacteria and greatly simplifies the subsequent purification. 2. The method has been used successfully with ribonuclease-deficient strains of Escherichia coli, Pseudomonas fluorescens and Staphylococcus epidermidis. The recovered purified RNA accounts for about 70% of the total ribosomal RNA and shows the normal sedimentation pattern of the 16s and 23s components in the analytical centrifuge.

A study of the hydrolysis of unfractionated reticulocyte ribosomal ribonucleic acid by pancreatic ribonuclease and its relevance to secondary structure

1. Unfractionated RNA from reticulocyte ribosomes was hydrolysed with pancreatic ribonuclease at 25 degrees . The molecular weight decreased rapidly to about 3s when about 6% of the residues were soluble in 0.5n-perchloric acid. In the early stages 60-80% of the hydrolysed linkages were ;hidden'. The denaturation spectrum was affected. Continued hydrolysis led to slow changes in S value, in the electrophoresis pattern in polyacrylamide gels and in the denaturation spectrum. 2. Hydrolysis of RNA with alkali to fragments of between 2.8s and 5.9s led to changes in the denaturation spectrum similar to those observed in the early stages of enzymic hydrolysis. 3. A theory was developed to relate changes in secondary structure with main-chain scission. 4. The results agree with the ;hairpin-loop' model for RNA. The denaturation studies are consistent with the presence of more than one species of hairpin loop that differ in their denaturation spectra. The average length of the hairpin loop was estimated to be 10-20 residues and an upper limit of 35 residues was established. 5. It is inferred, on the basis of studies with model compounds, that the stability of single-stranded stacked structures is hardly dependent on salt concentration. 6. The denaturation spectrum of the fragments obtained on hydrolysis became less dependent on ionic strength, suggesting that double-helical structures revert to a single-stranded stacked form on denaturation.

The fractionation of high-molecular-weight ribonucleic acid by polyacrylamide-gel electrophoresis

1. Gels were prepared with recrystallized acrylamide and bisacrylamide. Electrophoresis was in tris-sodium acetate-EDTA buffer for 0.5 to 3hr. Gels were scanned at 280 or 265mmu. Techniques are described for slicing and radioactive counting. 2. The mobility of RNA was inversely related to the sedimentation coefficient and varied with gel concentration. Electrophoresis in 2.2-2.6% gels gives a fractionation similar to density-gradient centrifugation. It shows the two ribosomal RNA components, the 45s precursor, transfer RNA and minor components. In 5% and 7.5% gels, 4s and 5s RNA separated and ribosomal RNA was excluded. 3. The resolution is greater and more detailed than by centrifugation, and many samples can be analysed simultaneously and rapidly.

A possible method for characterizing the secondary structure of ribonucleic acids

The E(280)/E(260) ratio was found to be suitable for following the ionization of cytosine residues of polynucleotides on the basis of studies with model compounds such as oligoguanylic acid, oligocytidylic acid, a complex formed between polyadenylic acid and polyuridylic acid, and a copolymer of guanylic acid and cytidylic acid, provided that changes in secondary structure were taken into account. The pK of cytosine residues of a polynucleotide in the amorphous form was found to be 4.70 at 25 degrees in 0.1m-sodium phosphate on the basis of titration at 75-85 degrees and on the assumption that the heat of ionization was the same as the value (5.2kcal./mole) found for CMP. In contrast, the pK of cytosine residues in the double-helical form of DNA was found to be about 3.25. These observations were utilized in estimating the fraction of cytosine residues in helical segments of ribosomal RNA, a copolymer of guanylic acid and cytidylic acid, and a copolymer of adenylic acid, guanylic acid, uridylic acid and cytidylic acid. The ionization of guanine and uracil residues was estimated from changes in the E(270)/E(260) ratio and E(230)/E(260) ratio respectively. In the amorphous form of RNA both residues had the same pK, whereas in the double-helical form ionization was suppressed. The fraction of guanine and uracil residues in amorphous segments may be estimated from the titration curves. The difference in the denaturation spectrum of adenine--uracil and guanine--cytosine base pairs at 280mmu was enhanced in acidic solutions whereas E(260) was hardly affected. Hence a comparison of the increments in E(280) and E(260) obtained on increasing the temperature at constant pH may be used to distinguish the melting ranges of helical domains differing in nucleotide composition. In alkaline solutions comparison of the increments in E(260) and E(270) yields similar information. In acidic solutions the fraction of cytosine residues involved in helical secondary structure, the degree of ionization of cytosine residues and the fraction of adenine--uracil base pairs denatured may be estimated from DeltaE(265) and DeltaE(280). In alkaline solutions the fractions of guanine and uracil residues involved in secondary structure and the degrees of ionization of these residues may be estimated from DeltaE(230), DeltaE(245), DeltaE(260) and DeltaE(280).

Factors controlling amino acid incorporation by ribosomes from krebs II mouse ascites-tumour cells

1. A ribosome-cell sap system capable of supporting the incorporation of (14)C-labelled amino acids into protein has been prepared from Krebs II mouse ascites-tumour cells. The requirements of this system for optimum activity and response to added messenger RNA have been investigated. One such system has been obtained for which amino acid incorporation is almost wholly dependent on the addition of suitable messenger RNA. 2. Ribosomes of widely different but predictable activities in the cell-free system have been prepared from Krebs cells pretreated in a variety of ways. The factors in the pretreatment of the cells responsible for these differences have been investigated. 3. The structural and functional properties of these different ribosome preparations and their response to exogenous messenger RNA have been examined and are discussed in the light of modern concepts of the control of protein synthesis.

The secondary structure of ribosomal ribonucleic acid in solution

1. The u.v.-absorption spectrum of ribosomal RNA from rabbit reticulocytes was studied as a function of temperature at different pH values. The changes in the spectrum over the range 220-320mmu were interpreted on the basis of the assumption that the effect of denaturation and ionization are additive. The results suggest that in neutral salt solutions the secondary structure of the ribosomal RNA samples studied is due to two species of helical segments stabilized principally, if not solely, by complementary base pairs but differing in nucleotide composition: each species appears to be heterogeneous in other respects in view of the breadth of the melting ranges. 2. The number of base pairs per helical segment was estimated to be small (between 4 and 17) on the basis of the relation between melting temperature and chain length previously established by Lipsett and others for model compounds. Small fragments (about 2s) obtained by alkaline hydrolysis appeared to form the same helical segments as the intact molecule in accord with the estimated size of these segments. 3. Specific nucleotide sequences appear necessary to account for the hysteresis observed on titrating ribosomal RNA with acid or alkali within the range pH3.0-7.0 since this phenomenon was less pronounced for Escherichia coli transfer RNA and for RNA from turnip yellow-mosaic virus.