Study of mammalian ribosomal protein reactivity in situ. I. - Effect of 2-methoxy-5-nitrotropone on 40S and 60S subunits

Photo-induced protein-RNA cross-linking in mammalian 60-S ribosomal subunits

Rat liver 60-S ribosomal subunits were submitted to increasing doses of radiation (253.7 nm), at 4 degrees C and 25 degrees C, as previously reported fro 40-S subunits. The existence of protein-RNA cross-linking was demonstrated by two methods. The first consisted in the separation of protein-RNA complex; the second was indirect, and took into account alteration either in the electrophoretic mobility of cross-linked proteins or the separability of 28-S RNA in a 4 M urea/3 M LiCl buffer. The peptide synthetase activity and the sedimentation characteristics of the particles irradiated at 4 degrees C were well preserved, but at 25 degrees C the large subunits were progressively inactivated and unfolded for doses higher than 2 x 10(18) quanta. The dose-dependent variations of protein cross-linkage determined by two-dimensional gel electrophoresis allowed us to distinguish those proteins which reacted at the lowest doses with a first-order reaction from those which cross-linked to RNA after a subtle modification of the subunit structure. At 25 degrees C, all proteins became low-dose reactive. The curve obtained for 28-S RNA cross-linkage was similar to that of the total protein moiety, while those obtained fro the 5-S and 5.8-S RNA (which were parallel) suggest a lower reactivity of these RNAs. As a general rule, proteins from the large subunits were more reactive to RNA than those from the small subunits. This could indicate differences in the organisation of the two subunits.

Photo-induced protein-RNA cross-linking in mammalian 40-S ribosomal subunits

RNA-protein interaction in the 40-S subunits of rat liver ribosomes were studied by measuring cross-linking of proteins to RNA induced by ultraviolet radiation. Under conditions which caused neither extensive degradation of the 40-S subunits (or 18-S RNA) nor biological inactivation, the total staining intensity of the proteins extracted from irradiated subunits was considerably reduced on the two-dimensional electrophoregrams. Convincing evidence was obtained that cross-linking of the proteins to 18-S RNA was the predominant reaction. The cross-linking extent of the individual proteins was studied as a function of the radiation dose. At 4 degree C, 13--15 proteins were found to cross-linked to RNA even at low doses of quanta. They generally correspond to proteins which have been previously shown to react poorly on the ribosomes with various chemical reagents. At 25 degree C, all the proteins became cross-linked to RNA using the same radiation doses.

Change of protein reactivity in mammalian ribosomal subunits as a function of temperature

Reductive methylation of rat liver ribosomal subunits was carried out at different temperatures and the reaction was followed as a function of time. The percentage of protein lysine residues which were methylated reached a definite plateau for each temperature, and was considerably increased by heating (four times at 40 degrees C). This increase was not observed when free ribosomal proteins were heated under the same conditions. Ribosomal subunits kept their biological activity (elongation steps of protein synthesis) even when methylated to a high extent. Half of the subunit activity was still found when 67% of the lysine residues were methylated. Proteins were divided into different classes on the basis of their alkylation in response to temperature. Those which reacted poorly within subunits even at high temperature should interact directly with rRNA. The results suggest that the protein reactivity modifications induced by heating (up to 37 degrees C), which were often totally or partially reversible, reflect a conformational change of the proteins themselves within the subunits. Besides protein unfolding, higher temperatures produced structural modification and inactivation of the subunits, which were restrained by the presence of aminoacyl tRNA.

Reductive alkylation of mammalian ribosomes

40- and 60-S ribosomal subunits and 80-S ribosomes from rat liver were highly labelled by reductive methylation using formaldehyde and sodium boro-[3H] hydride, under conditions which did not decrease their activity in poly-U-directed polyphenylalanine synthesis. Dissociation of the monosomes, subunits dimers, and polysomes into free subunits was observed after methylation. Free proteins labelled after extraction from the ribosomal subunits incorporated 7 times more radioactivity than when labelled in the subunits. Proteins extracted from methylated subunits and ribosomes were analyzed by two-dimensional gel electrophoresis, and the radioactivity of each protein was compared to that of the same free protein. A classification of the proteins was established according to their accessibility to the reagents in the subunits and the ribosomes.

Studies on proteins of animal ribosomes. XXIV. Localisation of proteins in ribosomal subunits of rat liver studied by chemical substitution with p-nitrophenyl acetate and methyl acetimidate

The reaction of [3H]p-nitrophenyl acetate (NPA) or [14C]methyl acetimidate (MAI) with amino groups of ribosomal pade between the reactivity of the proteins in situ in the ribosomal subunit with that of isolated protein mixtures. In the small subunit reactivity compared with the protein mixture was only 10-65% in the case of NPA but 45 to more than 100% in the case of MAI. In the large subunit reactivity to MAI was 10-60% that of the isas a denser structure than the small one. In agreement with earlier experiments with iodoacetamide the proteins S2, 5, 7, 8, 10 and 13 of the small subunit and L15, 17, 20, 24, 25, 27, 29, 33, 34, 35 and 38 in the large subunit are quite accessible while proteins S9, 14, 19, 20, 24, 25, 27, 29 and 30 of the small subunit and L1, 7, 8, 10, 11, 19, 28, 31, and 32 of the large one are relatively inaccessible.

Structure and function of rat-liver ribosomes. Modification by 2-methoxy-5-nitrotropone treatment

Rat liver ribosomes and 60-S ribosome subunits were treated with the primary-amino-group-specific reagent 2-methoxy-5-nitrotropone. Important differences in the sensitivity of several ribosomal activities to inactivation by the reagent were observed. While elongation-factor-dependent activities are totally abolished in the treated particles, peptidyl transferase activity is either unaffected in 60-S ribosomal subunits or even strongly stimulated in 80-S ribosomes. Analysis of the ribosomal proteins modified by nitrotropone made it possible to draw some conclusions on their accessibility in the ribosomal structure and to relate some proteins with their involvement in the ribosome active centers. Thus, proteins L3, L13, L15 and L23 seem to be in a rather well protected position while proteins L10, L35, L37, X1 and X2 are totally exposed to the reagent. The protein accessibility also depends on the ribosome conformation, proteins L14 and L17, for instance, being sensitive in 80-S ribosomes and protected in 60-S subunits. In relation to the implication of proteins in functional centers, the data presented here together with other data obtained from protein-deficient core particles seem to indicate a possible role of proteins L21 and/or L26 in the peptidyl transferase center.

Specific ribonucleoprotein fragments from 40-S ribosomal subunits

Well-defined ribonucleoprotein fragments, resulting from the action of endogenous nuclease on 40-S subunits, were able to be separated when using high concentrations of LiCl. The ribonucleoproteins obtained sedimented at 12, 17 S, 23 S and 30 S and contained 8 S, 12 S and 17 S RNA, respectively, associated with a few proteins. The proteins extracted from the fragments were [3H] labeled by reductive methylation and their molar proportion was determined. The smallest fragment (12, 17 S) contained only three proteins, S8, S9 and S24. The 23-S and 30-S materials contained some proteins in common, S15, S19, S22, S25; S16 was found mainly in 30 S. Two proteins, S26 and "protein y" were found mainly in 23 S material. Thus, these results can give information on the relative location of certain proteins in the 40-S subunits.