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

Transcription pattern of ribosomal protein L26 during anoxia exposure in Littorina littorea

Differential screening of a hepatopancreas cDNA library derived from the marine snail Littorina littorea yielded a 421-bp clone coding for ribosomal protein L26 that was up-regulated during anoxia exposure. The deduced amino acid sequence, containing 144 residues with a predicted molecular weight of 17 kDa, showed 80% amino acid sequence identity to the mammalian ribosomal protein L26. Analysis of hepatopancreas and foot muscle samples from a time course of anoxia exposure showed a maximal transcript increase of 4- and 3-fold after 96 hr and 48 hr, respectively, relative to normoxic animals, with a subsequent decrease in transcript levels during normoxic recovery. Nuclear run-off assays confirmed the observed transcriptional up-regulation of L26 during anoxia. Organ culture experiments were performed to determine a possible pathway of up-regulation of L26, with data indicating a putative role for cGMP in signal transduction. The transcriptional up-regulation of L26 during anoxia may stabilize the existing mRNA pool, via a possible cGMP-mediated signaling cascade, until oxygen reappears and protein synthesis resumes.

Peptidyl transferase centres of rat and yeast ribosomes. Different response to modification of protein amino groups

Modification of rat liver ribosomes with dimethylmaleic anhydride, a reagent for protein amino groups, causes a large stimulation of peptidyl transferase activity assayed by the "fragment" reaction, as well as the inactivation of poly(U)-directed polyphenylalanine synthesis. In contrast to rat ribosomes, the peptidyl transferase of yeast ribosomes is little affected by modification. Although other interpretations are not excluded, these results might be due to differences between the peptidyl transferase centres of mammalian and yeast ribosomes.

Identification of proteins at the peptidyl-tRNA binding site of rat liver ribosomes

We have identified proteins involved in the peptidyl-tRNA-binding site of rat liver ribosomes, using an affinity label designed specifically to probe the P-site in eukaryotic peptidyl transferase. The label is a 3'-terminal pentanucleotide fragment of N-acetylleucyl-tRNA in which mercury atoms have been added at the C-5 position of the three cytosine residues. This mercurated fragment can bind to rat liver peptidyl transferase and function as a donor of N-acetylleucine to puromycin. Concomitant with this binding, the mercury atoms present in the fragment can form a covalent linkage with a small number of ribosomal proteins. The major proteins labeled by this reagent are L5 and L36A. Four protein spots are found labeled to a lesser extent: L10, L7/7a, L3/4 and L25/31. Each of these proteins, therefore, is implicated in the binding of the 3'-terminus of peptidyl-tRNA. The results presented here are correlated with other investigations of the structure-function aspects of rat liver peptidyl transferase. Using these data, we have constructed a model for the arrangement of proteins within this active site.

Peptidyl transferase of bacterial ribosome: resistance to proteinase K

70-S ribosomes and 50-S ribosomal subunits from Escherichia coli D10 were treated with proteinase K for increasing periods of time. Peptidyl transferase activity and sparsomycin-induced binding of (U)C-A-C-C-A-[3H]Leu-Ac were tested in the treated particles, the binding of the substrate being more sensitive to the protease than peptide bond formation. Comparison of the amounts of proteins present in the treated particles with the residual activity indicates that only proteins L3 and L14 are released at a similar rate to that at which peptidyl transferase activity is lost. Proteins related to this ribosomal activity by other techniques are lost at a faster rate than the activity itself. In addition, the results indicate that sparsomycin stimulates the binding of the substrate by a different mechanism from that which inhibits peptide bond formation.

Affinity labelling of yeast ribosomal peptidyl transferase

Using p-nitrophenylcarbamyl-phenylalanyl-tRNA (PNPC-Phe-tRNA) and N-Iodoacetylphenylalanyl-tRNA as affinity labels we have attempted to identify the components of the aminoacyl-tRNA binding sites located in the vicinity of the peptidyl transferase centre of the yeast ribosome. Both Phe-tRNA derivatives bind to the ribosomal A-site in the presence of 20 mM Mg++ ion concentration and can be translocated to the ribosomal P-site in the presence of elongation factor. After the labels have been allowed to react covalently with ribosomes they were found associated with the large ribosomal subunit. Proteins L36, L43, L42, L29, L2, L17/18, L19/20 and proteins L26, L38, L22/23, L7/9, L4/6, L36, L11, L43, L39 were labelled in samples treated with PNPC-Phe-tRNA and N-iodoacetyl-Phe-tRNA respectively. In contrast, when only the components of the ribosomal P-site were analysed by reacting the treated particles with puromycin fewer spots were labelled, corresponding to proteins L36 and L19/20 using PNPC-Phe-tRNA and proteins L4/6, L36, and L43 using N-Iodoacetyl-Phe-tRNA.

Proteins associated with rRNA in the Escherichia coli ribosome

Ribosomal proteins located near the rRNA have been identified by cross linking to [14C]spermine with 1,5-difluoro-2,4-dinitrobenzene. The polyamine binds to double-stranded rRNA; those proteins showing radioactivity covalently bound after treatment with the bifunctional reagent should therefore be located in the vicinity of these regions of rRNA. Six proteins from the small subunit, S4, S5, S9, S18, S19 and S20 and ten proteins from the large subunit L2, L6, L13, L14, L16, L17, L18, L19, L22 and L27 preferentially take up the label. The results obtained with three proteins from the large subunit, L6, L16 and L27, show a high degree of variability that could reflect differences of conformation in the subunit population. Several proteins were drastically modified by the cross-linking agent but were not detected in the two-dimensional gel electrophoresis (e.g., S1, S11, S21, L7, L8 and L12) and therefore could not be studied.

Peptidyl transferase center of rat-liver ribosome cores

Protein-deficient particles have been obtained by treating rat liver 80-S ribosomes or their 60-S subunits with 1 M NH4Cl in the presence of 50% ethanol at 0 degrees C (Po-cores) and 37 degrees C (P37-cores). The Po-cores from 80-S ribosomes are totally inactive in polyphenylalanine synthesis but fully active in the 'fragment assay' to test peptidyl transferase activity. The polymerizing activity of the cores is restored up to 40--50% of control activity by incubation in the presence of the split proteins. Three proteins are totally lost in the treatment, namely proteins L12, L40/41 ans S25. A series of up to nine different spots in the region of the L40/41 proteins are detected when the split fraction is analyzed by two-dimensional electrophoresis. This series of spots is, however, reduced to only two proteins when the second dimension is carried out in the presence of sodium dodecylsulphate. 80-S ribosome-derived P37-cores are about 80% active in the 'fragment reaction' while 60-S-subunit-derived particles are inactive in this assay. The inhibitory effect of a number of antibiotics is differentially affected by the treatment suggesting different localization of their binding sites. A comparative study of the proteins released by treatment in the two types of particles suggests the involvement in the peptidyl transferase center of the ribosome of one or more of the floolwing proteins: L21, L24, L27, L28 and L36.