Preparation of E. coli ribosomal subunits without loss of biological activity

Protein synthesis using a reconstituted cell-free system

Most cell-free protein-synthesis systems are based on cell extracts, which often contain undesirable activities. Reconstituted systems, by contrast, are composed of a defined number of purified and recombinant components with minimal nuclease and protease activities. This unit describes the use of a particular commercial reconstituted system, PURExpress. This system allows in vitro synthesis of proteins from mRNA and circular and linear DNA templates, as well as co-translational labeling of proteins. Unique to this system, all recombinant protein components of the system are His-tagged, allowing purification of the synthesized untagged protein by removing the rest of the system's components. Newly synthesized proteins can often be visible on an SDS-PAGE gel and directly assayed for their functions without labeling and purification. Certain components of the system, such as ribosomes or release factors, can be omitted for specific applications. Such "delta" versions of the system are well suited for studies of bacterial translation, assays of ribosome function, incorporation of unnatural amino acids, and ribosome display of protein libraries.

Late steps of ribosome assembly in E. coli are sensitive to a severe heat stress but are assisted by the HSP70 chaperone machine

The late stages of 30S and 50S ribosomal subunits biogenesis have been studied in a wild-type (wt) strain of Escherichia coli (MC4100) subjected to a severe heat stress (45–46°C). The 32S and 45S ribosomal particles (precursors to 50S subunits) and 21S ribosomal particles (precursors to 30S subunits) accumulate under these conditions. They are authentic precursors, not degraded or dead-end particles. The 21S particles are shown, by way of a modified 3′5′ RACE procedure, to contain 16S rRNA unprocessed, or processed at its 5′ end, and not at the 3′ end. This implies that maturation of 16S rRNA is ordered and starts at its 5′-terminus, and that the 3′-terminus is trimmed at a later step. This observation is not limited to heat stress conditions, but it also can be verified in bacteria growing at a normal temperature (30°C), supporting the idea that this is the general pathway. Assembly defects at very high temperature are partially compensated by plasmid-driven overexpression of the DnaK/DnaJ chaperones. The ribosome assembly pattern in wt bacteria under a severe heat stress is therefore reminiscent of that observed at lower temperatures in E. coli mutants lacking the chaperones DnaK or DnaJ.

Artemin is an RNA-binding protein with high thermal stability and potential RNA chaperone activity

Encysted embryos of the crustacean, Artemia franciscana, are among the most stress-resistant of all multicellular eukaryotes, due in part to massive amounts of p26, a small heat shock protein, that acts as a molecular chaperone. These embryos contain equally large amounts of another protein called artemin, of previously unknown function, that we report on here. Its thermal stability allows large-scale purification in about a day, using ammonium sulfate fractionation and incubation at 70 degrees C for 7 min, followed by gel filtration. The latter yields an artemin-RNA complex from which the pure protein, apo-artemin, was obtained by anion-exchange chromatography. We evaluated the possibility that artemin acts as a molecular chaperone for proteins, but obtained no evidence for that in vitro. The association of RNA with apo-artemin occurs at high temperatures and, although it is not yet clear whether artemin has a specific role as an RNA chaperone, it does bind non-polyadenylated RNAs which are then translated in vitro. Artemin-RNA is thermostable, some molecules resisting destruction after 30 min at 90 degrees C. The first order rate constant for denaturation and aggregation of artemin-RNA at 85 degrees C is 8.5 x 10(-3)min(-1), which compares well with other thermostable proteins of similar size ( approximately 500 kDa) such as the ferritins with which artemin has amino acid sequence similarity. The amount of artemin extracted from embryos that had been stored dry, under laboratory conditions, since 1951 is comparable to the amount in contemporary embryos, indicating its stability in situ, and supporting the in vitro heating studies.

Interaction of ribosome recycling factor and elongation factor EF-G with E. coli ribosomes studied by the surface plasmon resonance technique

BACKGROUND

Ribosome recycling factor (RRF), in concert with elongation factor EF-G, is required for disassembly of the post-termination complex of a ribosome after the release of polypeptides. How RRF dissociates the complex has long been puzzling. Crystal structures of RRF molecules have been solved recently and shown to mimic a transfer RNA (tRNA) shape, which prompted us to examine whether RRF binds to the ribosome as tRNA does.

RESULTS

The formation of ribosome complexes on the surface-coupled RRF and elongation factor EF-G of Escherichia coli was monitored in real time with a BIACORE 2000 instrument based on the surface plasmon resonance technique. RRF interacted with 70S ribosomes as well as 50S and 30S subunits, although it interacted preferentially with 50S subunits, which was clearly seen under high but physiological ionic conditions. This 50S interaction was diminished by a single amino acid substitutions for Arg132 of RRF, which did not appreciably affect the protein folding but nullified the activity in vivo and in vitro. Moreover, a set of antibiotics that inhibited the RRF-50S interaction were also inhibitory to the polysome breakdown activity of RRF in vitro. The BIACORE technique also worked very well in demonstrating the action of the antibiotics thiostrepton and fusidic acid, which are inhibitory to the RRF function by freezing the pre- and post-translocation intermediates catalysed by EF-G.

CONCLUSIONS

These results suggest that the preferential interplay of RRF with the 50S subunit may be of biological significance, probably reflecting the mode of RRF action. The BIACORE technique proved useful for real-time monitoring of the interaction between the ribosome and translation factors, as well as for screening of potential inhibitors for ribosome recycling factor.

The FtsJ/RrmJ heat shock protein of Escherichia coli is a 23 S ribosomal RNA methyltransferase

Ribosomal RNAs undergo several nucleotide modifications including methylation. We identify FtsJ, the first encoded protein of the ftsJ-hflB heat shock operon, as an Escherichia coli methyltransferase of the 23 S rRNA. The methylation reaction requires S-adenosylmethionine as donor of methyl groups, purified FtsJ or a S(150) supernatant from an FtsJ-producing strain, and ribosomes from an FtsJ-deficient strain. In vitro, FtsJ does not efficiently methylate ribosomes purified from a strain producing FtsJ, suggesting that these ribosomes are already methylated in vivo by FtsJ. FtsJ is active on ribosomes and on the 50 S ribosomal subunit, but is inactive on free rRNA, suggesting that its natural substrate is ribosomes or a pre-ribosomal ribonucleoprotein particle. We identified the methylated nucleotide as 2'-O-methyluridine 2552, by reverse phase high performance liquid chromatography analysis, boronate affinity chromatography, and hybridization-protection experiments. In view of its newly established function, FtsJ is renamed RrmJ and its encoding gene, rrmJ.

Ribosomal protein methylation in Escherichia coli: the gene prmA, encoding the ribosomal protein L11 methyltransferase, is dispensable

The prmA gene, located at 72 min on the Escherichia coli chromosome, is the genetic determinant of ribosomal protein L11-methyltransferase activity. Mutations at this locus, prmA1 and prmA3, result in a severely undermethylated form of L11. No effect, other than the lack of methyl groups on L11, has been ascribed to these mutations. DNA sequence analysis of the mutant alleles prmA1 and prmA3 detected point mutations near the C-terminus of the protein and plasmids overproducing the wild-type and the two mutant proteins have been constructed. The wild-type PrmA protein could be crosslinked to its radiolabelled substrate, S-adenosyl-L-methionine (SAM), by u.v. irradiation indicating that it is the gene for the methyltransferase rather than a regulatory protein. One of the mutant proteins, PrmA3, was also weakly crosslinked to SAM. Both mutant enzymes when expressed from the overproducing plasmids were capable of catalysing the incorporation of 3H-labelled methyl groups from SAM to L11 in vitro. This confirmed the observation that the mutant proteins possess significant residual activity which could account for their lack of growth phenotype. However, a strain carrying an in vitro-constructed null mutation of the prmA gene, transferred to the E. coli chromosome by homologous recombination, was perfectly viable.

Mutant DnaK chaperones cause ribosome assembly defects in Escherichia coli

To determine whether the biogenesis of ribosomes in Escherichia coli is the result of the self-assembly of their different constituents or involves the participation of additional factors, we have studied the influence of a chaperone, the product of the gene dnaK, on ribosome assembly in vivo. Using three thermosensitive (ts) mutants carrying the mutations dnaK756-ts, dnaK25-ts, and dnaK103-ts, we have observed the accumulation at nonpermissive temperature (45 degrees C) of ribosomal particles with different sedimentation constants--namely, 45S, 35S, and 25S along with the normal 30S and 50S ribosomal subunits. This is the result of a defect not in thermostability but in ribosome assembly at the nonpermissive temperature. These abnormal ribosomal particles are rescued if the mutant cells are returned to 30 degrees C. Thus, the product of the dnaK gene is implicated in ribosome biogenesis at high temperature.

Protective ribosomal preparation from Shigella sonnei as a parenteral candidate vaccine

A parenteral Shigella ribosomal vaccine (SRV) was investigated in animals for safety, antibody-inducing capacity, and protective activity. Ribosomal preparations from a Shigella sonnei phase I avirulent strain were obtained and shown to possess chemical, sedimentation, and other properties typical of bacterial ribosomes. No endotoxin contamination was revealed by a ketodeoxyoctonate assay, although the presence of some kind of O antigen was evidenced by serological findings and the high activity of SRV in inducing the O-antibody response and immunological memory in animals. SRV was nontoxic in mice, guinea pigs, and monkeys and induced no local reactions when injected subcutaneously in reasonable doses. Significant protection against a local Shigella infection (Sereny test) was seen in guinea pigs injected with SRV (efficiency index, about 60%) and the specificity of the protection was evident from cross-challenge experiments. The protective efficiency of SRV was especially high in rhesus monkeys challenged orally with virulent Shigella cells (89%, as calculated from the summarized data of several experiments in 71 animals). Protection in monkeys was long lasting and could be demonstrated several months after injection of SRV. An inexpensive technique can be used for the production of SRV on a large scale. The high immunogenicity of SRV is discussed in terms of the amplifying effect of the ribosome, which serves as a delivery system for polysaccharide O antigen. Further study of SRV as a candidate vaccine for humans seems justified by the data obtained.

A comparative study of ribosomal and DNA binding protein II from two thermophilic bacteria, Bacillus caldolyticus strain EP 00275 and Bacillus stearothermophilus

Ribosomal and DNA binding proteins (DNA bp II) from an extreme thermophilic bacterium, B. caldolyticus strain EP 00275, were investigated for stability and crystallization and compared to the homologous proteins from B. stearothermophilus. Two-dimensional gel electrophoresis of both types of proteins, the amino acid composition and the sequences of some of the peptides of DNA bp II revealed a close relationship between each other. The physico-chemical characteristics of DNA bp II were similar but different from homologous proteins from T. thermophilus and C. pasteurineum. From our results we conclude: B. stearothermophilus and B. caldolyticus strain EP 00275 are similar organisms with regard to their ribosomal and DNA binding proteins.

The anti-Shine-Dalgarno region in Escherichia coli 16S ribosomal RNA is not essential for the correct selection of translational starts

Plasmid pPM114, which contains the Escherichia coli 16S rRNA gene under control of a T7 promoter, was linearized upstream of the 3' end of the gene and used in an in vitro transcription assay to yield a 16S rRNA lacking about 30 nucleotides at its 3' end. This truncated 16S rRNA was assembled into 30S subunits which contain the full complement of 30S proteins, including S21, but were impaired in their capacity to associate to the 50S subunits. This impairment was paralleled by a decrease in their protein synthesis activity under the direction of natural or artificial messengers. However, although the anti-Shine-Dalgarno sequence was missing, the initiation step was not specifically affected, and the mutated ribosomes could initiate translation at the correct start sites. This supports previous suggestions that the translational efficiency and the selection of translational starts are not solely controlled by the Shine-Dalgarno interaction. A novel interpretation of the role of protein S21 is also proposed which is independent of the activation by this protein of the base-pairing potential of the anti-Shine-Dalgarno sequence of 16S rRNA.

Nuclear omnipotent suppressors of premature termination codons in mitochondrial genes affect the 37S mitoribosomal subunit

nam3 and R705, yeast nuclear omnipotent suppressors of mitochondrial mit- mutations, reverse the superimposed spectrum of trans-recessive splicing defects by affecting the protein composition of the small mitoribosomal subunit. Analysis of the suppressor's interaction suggests that suppression results from mutations in the mitoribosomal polypeptides. These data indicate an obligatory connection between mitoribosome function and splicing of introns bI2, bI4 and aI1 in yeast mitochondria.

Comparison of active and inactive forms of the E. coli 30S ribosomal subunits

Dissociation of E. Coli 70S ribosomes in the presence of 0.1 mM Mg++ yields partially inactivated 30S and 50S subunits. This inactivation can be avoided by dissociating the 70S ribosome in a medium containing 10 mM Mg++. 400 mM Na+. Comparison of the active and inactive forms of the 30S and 50S subunits has led to the following conclusions: 1) The two forms possess identical (50S subunits) or very similar (30S subunits) hydrodynamic properties. No differences in their morphologies is detectable by electron microscopy. 2) They possess the same protein compositions except for the presence of a larger amount of protein S1 in the inactive than in the active form of the 30S subunit. 3) They differ significantly in functional properties: more efficient association of the active than of the inactive forms with the complementary subunit; extensive dimerization of inactive 30S subunits in the presence of 10 mM Mg++; no dimerization of active 30S subunits under the same conditions; six-fold higher peptidyl transferase activity of active as compared to inactive 50S subunits.

mim3 and nam3 omnipotent suppressor genes similarly affect the polypeptide composition of yeast mitoribosomes

Yeast informational suppressors of mit- mutations coded for by nuclear (nam3-1, nam3-2) or by mitochondrial DNA (mim3-1) affect the mitoribosome. Nuclear mutations result in the appearance of an additional polypeptide called SI in the small mitoribosomal subunit. An identical polypeptide, not detected in the wild type 37S subunit, is present in crude preparations of mitoribosomes isolated from a mim3-1 suppressor carrying strain. Traces of the SI polypeptide may be found in highly purified small subunits from the mim3-1 strain. Therefore, mutations affecting either mitochondrial rRNA (mim3-1) or mitochondrial r-proteins (nam3-1, nam3-2) could be followed by similar changes in overall mitoribosome structure. This may explain the functional similarity of nuclear and mitochondrially coded suppressors.

Substitution of uridine in vivo by the intrinsic photoactivable probe 4-thiouridine in Escherichia coli RNA. Its use for E. coli ribosome structural analysis

In vivo incorporation of the uridine-photoactivable analogue, 4-thiouridine, into the ribosomal RNA of an Escherichia coli pyrD strain has been demonstrated. It is highly dependent on the exogenous uridine and 4-thiouridine concentrations as well as on temperature. We have defined conditions allowing the substitution of 13 +/- 2% of the uridine residues in bulk RNA by 4-thiouridine. On a high-Mg2+ sucrose gradient, 33 +/- 3% of ribonucleic particles sediment as 70S ribosomes, the remaining being in the form of non-associated 50S and 30S particles containing immature rRNA. The thiolated 70S ribosomes tolerate a 4-5% substitution level (40 thiouridine molecules/particle). Surprisingly, 3-4% of ribosomal proteins, about two protein molecules/particle, were spontaneously covalently bound to 4-thiouridine-substituted rRNA. Specific 366-nm photoactivation increased this proportion to 10-12%, i.e. up to six or seven ribosomal protein molecules/particle. The photochemical cross-linking proceeds with apparent first-order kinetics with a quantum yield close to 5 X 10(-3). Although extensive photodynamic breakage of rRNA occurs under aerobic conditions, both the kinetics and yield of ribosomal protein cross-linking were independent of oxygenation conditions. The thiolated (4.5%) 70S ribosomes allowed the poly(U)-directed poly(Phe)synthesis at 48% the control rate. Photoactivation decreased this activity to 28% and 10% when performed under nitrogen and in aerated conditions, respectively.

About the specificity of photoinduced affinity labeling of Escherichia coli ribosomes by dihydrorosaramicin, a macrolide related to erythromycin

Photoactivation of the [3H]dihydrorosaramicin chromophore at a wavelength above 300 nm allows the covalent attachment of the macrolide antibiotic to the bacterial ribosome. Bidimensional electrophoresis shows that the radioactivity is mainly associated with proteins L1, L5, L6, L15, L18, L19, S1, S3, S4, S5 and S9. When photoincorporation of the drug is conducted in the presence of puromycin as effector of [3H]dihydrorosaramicin-binding sites, a decrease in the labeling of most proteins is observed, except for L18 and L19, which are radiolabeled to a larger extent. These results allow us to speculate that L18 and L19 belong to the high-affinity binding site of rosaramicin antibiotic.

Comparison of fortimicins with other aminoglycosides and effects on bacterial ribosome and protein synthesis

Fortimicins are bicyclic aminoglycoside antibiotics that contain a fortamine moiety instead of the deoxystreptamine found in other aminoglysides. Fortimicin A had a bactericidal effect on Escherichia coli and Staphylococcus epidermidis and was found to inhibit protein synthesis in vivo. In vitro, fortimicin A inhibited polyuridylic acid-directed phenylalanine polymerization and induced misreading, as shown by leucine incorporation. In contrast, fortimicin B had no effect on either polymerization or misreading. In assays programmed with natural mRNA, only a weak polymerization inhibition effect was observed with fortimicin A, whereas a strong stimulation was seen in the presence of fortimicin B. Both fortimicins A and B inhibited dissociation of 70S ribosomes into their subunits and neither was able to displace [3H]dihydrostreptomycin, [3H]tobramycin, or [3H]gentamicin from their respective binding sites on the 70S particle.

Effect of P and A site substrates on the binding of a macrolide to ribosomes. Analysis of the puromycin-induced stimulation

The puromycin-induced stimulation of [3H]dihydrorosaramicin binding is due to a twofold increase in affinity of the macrolide antibiotic, with no change in the number of binding sites. Conversely, the binding of [3H]puromycin (A site) is stimulated by rosaramicin. The synergistic effect observed between the two antibiotics can be explained by a conformational change with positive effect, which occurs at the level of their binding sites. Various effectors of [3H]dihydrorosaramicin binding have been tested. Adenosine and dimethyladenosine stimulate the binding; phenylalanine, uridine and gougerotin (A site) have no effect whereas AMP, ADP, ATP, GTP, puromycin 5'-phosphate and lincomycin (P site) are inhibitors. These results point to the importance of the purine moiety in the stimulatory effect and of the phosphate function in reversing this effect. It is concluded that rosaramicin binds to the ribosomal P site and that the synergism observed between rosaramicin and puromycin may be related to interactions between the A and P sites.

Structural differences between active and inactive 30 S ribosomal subunits revealed by RNA-protein crosslinking

30 S protein-16 S rRNA crosslinking by reaction with 1-ethyl-3-dimethylaminopropylcarbodiimide is more efficient in the active than in the inactive form of the E. coli 30 S ribosomal subunit. This difference is particularly striking in the case of protein S8.

Precise localization of several covalent RNA-RNA cross-link in Escherichia coli 16S RNA

The RNA-RNA cross-linking reagent N-acetyl-N'-(p-glyoxylyl-benzoyl)cystamine, which reacts via its glyoxal residue with guanines not involved in G X C base pairs, has been used to introduce reversible RNA-RNA cross-links into Escherichia coli 16S rRNA. A two-dimensional gel method has been devised for the separation of the cross-linked oligonucleotides, and the precise location of guanines involved in four of these cross-links has been determined by sequencing the oligonucleotides. One cross-link involves guanosines 1315 and 1360 situated in two hairpin end loops of domain III. The other cross-links involves pairs of guanosine situated within the same hairpin end loops.

Concerning the thermal stability of E. coli 23S ribosomal RNA

Total RNA prepared from E. coli by several extraction procedures behaves as a mixture of covalently continuous heat stable 23S, 16S and 4-5S components. 16S rRNA remains heat stable after isolation from such preparations, whereas isolated 23S rRNA is heat labile but becomes heat stable after EDTA treatment. This and other evidence leads to the conclusion that heat lability of purified 23S rRNA is due, not to nuclease contamination of the type observed in earlier studies of the stability of this RNA, but to polyvalent cation catalyzed temperature-dependent scission of phosphodiester bonds. Heat stability of 23S rRNA in total RNA is due to the presence in these preparations of a contaminant which appears to act as a chelator of polyvalent cations. This material is similar or identical to the pyrogenic E. coli lipopolysaccharide described by Westphal and coll.

Photo-induced labelling of Escherichia coli ribosomes by a tobramycin analog

An [3H]azidobenzyl derivative of tobramycin, a 4,6-disubstituted 2-deoxystreptamine aminoglycoside, has been synthesized, and its ability to label Escherichia coli 70-S ribosomes under photoactivation has been studied. Two concentrations of the photolabel, corresponding to the saturation of the two classes of tobramycin sites on the ribosomes, were used. The results show that, at high antibiotic concentrations which induce maximal misreading during protein synthesis, most of the ribosomal proteins are labelled. At low antibiotic concentration, which results in the saturation of the first-class sites, a few proteins of both subunits are labelled, including L6, S4, S5, and, to a lesser extent, L2, L13 and S18. The 30-S subunit is, on the whole, labelled more efficiently than the 50-S subunit.

A ribonucleoprotein fragment of the 30 S ribosome of E. coli: evidence for long range RNA-RNA interactions

A stable homogeneous ribonucleoprotein fragment of the 30 S ribosomal subunit of E. coli has been prepared by mild nuclease digestion and heating in a constant ionic environment. The fragment contains about half of the 16 S ribosomal RNa and six proteins: S4, S7, S9, S13, S16 and S19. The RNA moiety contains the reported binding sites of all six proteins. After deproteinization, 80% of the RNA migrated as two major electrophoretic bands, which were isolated and sequenced. Each band contained sequences from the 5' and 3' thirds of the 16 S RNA but none from the central third. That these two noncontiguous RNA domains migrated together electrophoretically in Mg++-containing gels after deproteinization constitutes direct evidence that the 16 S RNA is folded in the intact ribosome so as to bring the two domains close together and that there are RNA-RNA interactions between them in the presence of Mg++.

Partial deproteinization of ribosomal subunits by treatment with high concentrations of sodium chloride: physical and chemical characterization of protein depleted particles

Sedimentation of E. coli ribosomal subunits through sucrose gradients containing high concentrations of NaCl (0.1 - 1.0 M) brings about removal of a specific fraction of their proteins. The alterations in the structural properties of the subunits caused by dissociation of these proteins are studied. They appear to be, at least partly the result of removal of constraints on RNA conformation imposed by the released proteins.

Effects of partial deproteinization on the functional properties of 50S ribosomal subunits of E. coli

Sedimentation of E. coli 50S ribosomal subunits through sucrose gradients containing 10 mM Mg2+ and high concentrations of NaCl (0.1-1.0 M) leads to removal of proteins L16 and L25. Analyses of the structural and functional properties of the protein depleted particles shows that removal of L16 and L25 from the 50S subunit causes loss of its ability to bind tRNA, to associate with the 30S subunit and to catalyze peptide bond formation. Reassociation of both L16 and L25 with core particles lacking these proteins is necessary for recovery of peptidyl transferase activity.

Mechanism of action of a 16-membered macrolide. Binding of rosaramicin to the Escherichia coli ribosome and its subunits

Rosaramicin is a new macrolide antibiotic with activity similar to that of erythromycin. In this paper, we describe the synthesis of [3H]dihydrorosaramicin and show by sucrose gradient centrifugation, gel exclusion chromatography and equilibrium dialysis that rosaramicin and its dihydroderivative bind specifically to the 70-S ribosome and 50-S ribosomal subunit of Escherichia coli. Binding to the 30-S subunit is not detectable. The parameters of the binding interaction were evaluated by equilibrium dialysis. The affinities of E. coli ribosomes for rosaramicin and dihydrorosaramicin are in good agreement with the minimal inhibitory concentration of these drugs for microorganisms.

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.

30-S ribosomal subunit proteins of an Escherichia coli mutant in which assembly of the small ribosomal subunit is temperature-sensitive

Escherichia coli 219ts2, a temperature-sensitive streptomycin-independent revertant of the streptomycin-dependent strain E. coli 209 is defective in 30-S ribosomal subunit assembly at 42 degrees C. Total 30-S ribosomal subunit proteins of this strain contain two additional components one of which (alpha) migrates below and the other (beta) to the right of protein S7 in two-dimensional polyacrylamide gel analyses carried out according to Kaltschmidt and Wittmann. These two components are also resolved from normal 30-S subunit proteins by chromatography on phosphocellulose. Tryptic fingerprinting of proteins alpha and beta identifies alpha as protein S7B, the form of S7 found in B strains of E. coli and beta as a mutant form of protein S4 produced by deletion of about 20 amino acids from the COOH terminus of the wild-type protein.

[Purification of the bacterial ribosome using chloramphenicol and erythromycin columns]

Chloramphenicol and erythromycin are antibiotics whose target is the bacterial ribosome. We have studied the possibility of isolating the bacterial ribosome by affinity chromatography on chloramphenicol and erythromycin columns. Several columns have been prepared using different spacers and methods of attachment of the ligands (cyanogen bromide, bis-expoxyde). The efficiency and specificity of these columns is discussed. Ethylene diamine is not always suitable as a spacer, because it presents non specific affinity for the ribosome. Pure tight ribosomes have been prepared by ultracentrifugation. They have been compared to ribosomes from affinity columns. These columns have no denaturing effect on ribosomes. They allow a good purification of ribosomes starting from crude bacterial extracts, but the separation of tight couples from loose subunits is not possible.

Synthesis and properties of N-acetyl-N'-(p-glyoxylylbenzoyl)cystamine, a new reagent for RNA-RNA and RNA-protein cross-linking

The synthesis of N-acetyl-N'-(p-glyoxylylbenzoyl)cystamine (Gbz-Cyn2-Ac) is described. Like other glyoxal-type reagents it reacts with guanine and arginine. The kinetics and pH dependence of these reactions are studied. (Gbz-Cyn2-Ac) reacts with non-base-paired guanines at about 20 sites in 16-S rRNA. After reduction of disulfide bonds each derivatized guanine residue carries a free -- SH group which can be used to create RNA-RNA bridges or, after introducing an additional photoactivatable derivative, RNA-protein bridges.

Mechanism of action of aminoglycoside antibiotics. Binding studies of tobramycin and its 6'-N-acetyl derivative to the bacterial ribosome and its subunits

6'-N-[14C]Acetyl-tobramycin and [3H]tobramycin were synthesized and their binding to Escherichia coli ribosomes and ribosomal subunits studied using equilibrium dialysis. THE 70-S ribosome, as well as its 50-S and 30-S subunits, bound tightly to 6'-N-acetyl-tobramycin. The binding of [3H]tobramycin to ribosomes was quite different. The 70-S ribosome was observed to possess several classes of binding sites; of these, one was determined to be of higher affinity and lower capacity, the 6'-N-[14C]acetyl-tobramycin site. The isotopic dilution method was used to define the specificity of the interaction. The selective binding of 6'-N-[14C]acetyl-tobramycin was highly reversible by tobramycin, kanamycins A, B, C and neomycin, but not by streptomycin or erythromycin. Gentamicin C1a was a poor inhibitor. This suggested that either the kanosamin or garosamin rings might be determinant in the binding of these molecules, as well as the 6'-amino group.

Reconstitution of active 30-S ribosomal subunits in vitro using heat-denatured 16-S rRNA

30-S ribosomal subunits which have been reconstituted using heat-denatured 16-S rRNA can participate in the synthesis of lysosyme in vitro. Therefore all the information contributed by 16-S rRNA to the reconstitution process is carried in the primary sequence of this RNA. The specific protein-synthesizing activity of 30-S subunits reconstituted from 30-S subunit proteins and heat-denatured 16-S rRNA is about one third of that observed if unheated 16-S rRNA is used and is comparable to the activity of 30-S particles isolated after dissociation of 70-S ribosomes in the presence of 0.1 mM Mg2+.

The polysomal proteins of L cells. Discrimination between the structural ribosomal proteins, the exchangeable ribosomal proteins and the non-ribosomal proteins by two-dimensional dodecylsulfate electrophoresis and autoradiography

Three groups of proteins can be clearly discriminated in the total protein of L cell polysomes by selective labelling in the presence of low doses of actinomycin D and two-dimensional polyacrylamide/dodecylsulfate gel electrophoresis followed by autoradiography: (a) structural ribosomal proteins which are not labelled in the presence of actinomycin D and form stained non-radioactive spot in gels; (b) exchangeable ribosomal proteins which are labelled in the presence of actinomycin D and stained radioactive spots; (c) non-ribosomal proteins which are detectable only by autoradiography of gels. The large and small subunits of L cell ribosomes contain respectively 45 and 34 ribosomal proteins with molecular weights less than or equal to 50 000; seven of the large subunit proteins and nine of the small subunit proteins are exchangeable. Most of the non-ribosomal proteins migrate in the region of the related to the separation of the ribosomal proteins of mammalian cells and the possible significance of the presence of non-ribosomal proteins in polysomes are discussed.

A large nucleoprotein fragment of the 50-S ribosomal subunit of Escherichia coli

A large nucleoprotein fragment was isolated from a nuclease digest of Escherichia coli 50-S ribosomes and purified to gel electrophoretic homogeneity. Conditions were employed under which the fragmentation pattern was reproducible and the various fragment fractions were stable and maintained their sedimentation and electrophoretic properties throughout the several preparative and analytical procedures used. Fractions that appeared homogeneous in sucrose gradient centrifugation were found to be heterogeneous by gel electrophoresis. The large fragment was purified to homogeneity by preparative gel electrophoresis. It contained 21 proteins, the 5-S RNA, and two large oligonucleotides which together total about two thirds the molecular weight of the 23-S RNA. Because it can be prepared reproducibly in large quantities and because of its size and stability, the fragment appears suitable for functional and structural studies and as the starting material for further fractionation. An important contributing factor to the observed stability and reproducibility was the maintenance of an unchanging ionic environment. A single buffer was employed throughout all the procedures, and the fragments produced by nuclease digestion were dissociated from each other by heat rather than by changing the medium.

Ribosomal subunits from Tetrahymena pyriformis. Isolation and properties of active 40-S and 60-S subunits

Tetrahymena pyriformis ribosomal subunits were obtained by incubation of post-mitochondrial supernatant in the presence of 0.2 mM GTP and 0.1 mM puromycin for 45 min at 28 degrees C, followed by sucrose density gradient centrifugation. Isolated 40-S subunits were able to reassociate in vitro in the presence of 5 mM MgCl2 and 50 mM KCl and to perform poly(U)-dependent protein synthesis. The 60-S subunit carries the peptidyl transferase activity. The number of proteins in T. pyriformis ribosomal subunits was determined by two-dimensional polyacrylamide gel electrophoresis. The 40-S subunit contains 30 different protein species (including two acidic proteins). The 60-S subunit contains 35 different protein species (including two acidic proteins). The proteins were numbered following the system of Kaltschmidt and Wittmann.

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.