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We have developed a computational method of protein design to detect amino acid sequences that are adaptable to given main-chain coordinates of a protein. In this method, the selection of amino acid types employs a Metropolis Monte Carlo method with a scoring function in conjunction with the approximation of free energies computed from 3D structures. To compute the scoring function, a side-chain prediction using another Metropolis Monte Carlo method was performed to select structurally suitable side-chain conformations from a side-chain library. In total, two layers of Monte Carlo procedures were performed, first to select amino acid types (1st layer Monte Carlo) and then to predict side-chain conformations (2nd layers Monte Carlo). We applied this method to sequence design for the entire sequence on the SH3 domain, Protein G, and BPTI. The predicted sequences were similar to those of the wild-type proteins. We compared the results of the predictions with and without the 2nd layer Monte Carlo method. The results revealed that the two-layer Monte Carlo method produced better sequence similarity to the wild-type proteins than the one-layer method. Finally, we applied this method to neuraminidase of influenza virus. The results were consistent with the sequences identified from the isolated viruses.

Rat liver cytosol was incubated with a trace amount of rat liver 5SrRNA which was highly labeled at the 3'-end with cytidine 3',5'-[5'-32P]biphosphate, and with [35S]methionine in the presence of ATP mixture, and then with an antibody against ribosomal protein L5. The mixture was analyzed by protein A-Sepharose chromatography. The following results were obtained. (i) The eluate with glycine-HCl buffer (pH 3.0) from the protein A-Sepharose column contained an overlapping peak of 32P- and 35S-radioactivities. In a control experiment using the same amount of 32P-labeled Escherichia coli 5SrRNA with the same specific activity, no fraction of the eluate contained 32P-radioactivity. (ii) The fractions containing both 32P- and 35S-radioactivities from the protein A-Sepharose column were crosslinked by UV irradiation. The products was subjected to PAGE, and RNA in each gel slice was eluted and purified. The fraction containing both 32P- and 35S-radioactivities was present in a region of somewhat higher molecular weight than that of 5SRNP, whereas very low 32P- and 35S-radioactivities were present in this region in the control experiment without UV irradiation. This finding suggested that [35S]methionyl-tRNA interacted with 32P-labeled 5SRNP. (iii) The fraction containing overlapping 32P- and 35S-radioactivities described above was subjected to Sephadex G-150 chromatography. The component containing both radioactivities was distributed in the region corresponding to molecular weights of 10,000 to 250,000 with a peak at about 200,000, suggesting the presence of a complex containing Met-RS (Mr 108,000), 5SRNP (Mr 74,000), and methionyl-tRNA (Mr 25,000). Furthermore, this fraction showed definite Met-RS activity.(ABSTRACT TRUNCATED AT 250 WORDS)

1) Rat liver 5SrRNA enhanced the activity of methionyl-tRNA synthetase in the macromolecular aminoacyl-tRNA synthetase complex (Fraction B) purified from a rat liver supernatant. 5SrRNA-L5 protein complexes (5SrRNP) had similar effects, whereas other ribosomal RNAs and E. coli 5SrRNA had no effect. 2) 5SrRNA increased the activity of the complex for methionine-dependent ATP-PPi exchange. 3) 5SrRNA increased the activities of methionyl-, arginyl-, and isoleucyl-tRNA synthetases in the complex, but scarcely affected its leucyl-, lysyl-, and glutamyl-tRNA synthetase activities. 4) 5SrRNA increased the activities of the rat liver supernatant for the attachment of [35S]methionine, [3H]isoleucine, [3H]lysine, [3H]proline, [3H]threonine, [3H]tyrosine, and [3H]phenylalanine to endogenous tRNA markedly, and those for [3H]leucine, [3H]arginine, [3H]aspartic acid, and [3H]histidine slightly, but did not affect those for [3H]glutamic acid, [3H]glycine, [3H]valine, [3H]alanine, and [3H]tryptophan. 5) Preincubation of the rat liver supernatant with an antibody against Artemia salina ribosomal protein L5, that cross-reacted with the rat liver ribosomal protein L5, decreased the attachment of [35S]methionine and [3H]isoleucine to endogenous tRNA, and 5SrRNA and 5SRNP enhanced these activities of the supernatant preincubated with antibody. On the other hand, the antibody did not affect that for [3H]alanine. Immune dot blot analysis using the antibody against L5 showed the presence of immunologically the same protein as L5 in the liver supernatant. Northern blot analysis of RNA in the immunoprecipitate prepared from the liver supernatant incubated with the antibody against L5 indicated that 5SrRNA was complexed with L5.(ABSTRACT TRUNCATED AT 250 WORDS)

The 5SrRNA in the rat liver postmicrosomal supernatant was investigated. Acrylamide gel electrophoresis and Northern blot analysis showed that most of the 5SrRNA was present in the fractions obtained on high molecular weight regions separated by Sephadex G-200 column chromatography of the supernatant, which contained the bulk of the methionyl-tRNA synthetase (Fraction I) and tyrosyl-tRNA synthetase (Fraction II). A high molecular weight complex containing nine aminoacyl-tRNA synthetases [Mirande, M., LeCorre, D., & Waller, J.-P. (1985) Eur. J. Biochem. 147, 281-289] was purified by fractional precipitation with polyethylene glycol 6000, gel filtration on Bio-Gel A-1.5m, and finally tRNA-Sepharose column chromatography, which gave two fractions. Fraction B showed the activities of nine aminoacyl-tRNA synthetases and gave protein bands corresponding to eight previously identified enzymes on SDS-PAGE. Fraction A, eluted with a lower KCl concentration than Fraction B, showed lower activities than fraction B of eight of the aminoacyl-tRNA synthetases, the exception being prolyl-tRNA synthetase. The staining patterns with ethidium bromide of the RNAs after PAGE showed 5SrRNA bands for Fraction A but not for Fraction B. However, Northern blot analysis indicated that 5SrRNA was present in both Fractions A and B. The staining pattern after SDS-PAGE of Fraction A with Coomassie Brilliant Blue showed several protein bands in addition to those observed for Fraction B, one of which, with a staining intensity comparable with those of other bands, was located at the same position as ribosomal protein L5, which is the protein moiety of the 5SrRNA-L5 protein complex of ribosomal 60S subunits.(ABSTRACT TRUNCATED AT 250 WORDS)

1. When the postmitochondrial supernatant (PM-supernatant) from regenerating rat liver was incubated with [3H]methionine, the incorporation of [3H]methinoine into the N-terminal residues of nascent peptides on ribosomes was observed. This incorporation was sensitive to a low cocentration (2X10(-6) M) of pactamycin. The results suggest that PM-supernatant has low but definite activity for the initiation of nascent protein synthesis. Polysomes and cell sap from regenerating rat liver showed negligible pactamycin-sensitive incorporation of [3H]methionine into N-terminal, residues of nascent peptides. 2. PM-supernatant from regenerating rat liver was incubated with [35S]methionine in the complete reaction mixture. After addition of ribosomal proteins labelled with [3H]methionine in vivo, ribosomal structural proteins were prepared from the incubation mixture by acetic acid extraction, CM-cellulose column chromatography, Sephadex G-200 gel filtration and finally by two-dimensional acrylamide gel electrophoresis. Incorporation was observed in the greater part of ribosomal proteins on the two dimensional gel. From the 35S-to-3H ratios of ribsomal protein fractions during the purification procedures, it appeared that the incorporation of labelled methionine into the ribosomal proteins by PM-supernatant was about 3% of that into the total proteins. When [3H]leucine was used, the values were about 4% in the same cell-free system and 5 to 6% in in vivo labelling. The results indicate that ribosomal proteins are synthesized with high efficiency by PM-supernatant from regenerating rat liver.

After rat liver polysomes were irradiated with UV light at 254 nm for 2 h, a cross-linked poly(A)-containing mRNA-protein complex (mRNP) was prepared and a protein moiety was labeled with 125I. After RNase treatment, its protein moiety was analyzed by two-dimensional polyacrylamide gel electrophoresis followed by radioautography. There were radioactive spots which extended from the positions of those of S3/S3a, S6, L5, and L6/L7 towards the origin. In the case of UV irradiation for 30 min, radioactive spots extending similarly from those of S3/S3a, and L5 were observed. Radioactive areas on the two-dimensional gel in the case of irradiation for 2 h were further analyzed by SDS polyacrylamide gel electrophoresis. The peaks of radioactivity were detected at the protein band containing L6, that containing S3a and L5 and that containing S6, L7, and L8. It was proposed that S3a, S6, L5, and L6 proteins, according to the proposed uniform nomenclature (McConkey et al. (1979) Mol. Gen. Genet. 169, 1-6(1)), were cross-linked to mRNA by UV irradiation.

The long-term effects (up to 12 h) of low dose in vivo actinomycin D treatment, which selectively inhibits rRNA synthesis, on the activity of rat liver for the synthesis of ribosomal proteins relative to that for the synthesis of total protein were investigated. The effects of actinomycin D treatment in vivo and in vitro on the template activity of poly(A)-containing mRNA of rat liver for ribosomal proteins were examined by using a wheat germ cell-free system. The following results were obtained. 1. The activity of rat liver for synthesizing total protein observed in vivo and in vitro was inhibited by actinomycin D treatment even at a small dose. 2. A double-labeling technique using [3H] and [14C]leucine in vivo showed that the rate of synthesis of the ribosomal protein fraction relative to that of total protein in actinomycin-treated rat liver (6 + 6 h) was 1.45 times higher than that in the control rat. 3. By using a wheat germ cell-free system, it was shown that the template activity of poly(A)-containing mRNA for the synthesis of total protein was increased slightly by actinomycin D treatment in vivo. Furthermore, the template activity for the ribosomal protein fraction relative to that for total protein was increased. This increase was observed in most of the ribosomal proteins separated on two-dimensional acrylamide gel electrophoresis, although the extents of increase were different among individual ribosomal proteins examined. On the other hand, the selective increase of the template activity for the ribosomal protein fraction was not observed when poly(A)-containing mRNA was incubated with actinomycin D in vitro, although the template activity for total protein was increased slightly.

A cDNA clone specific for rat ribosomal protein S26 was isolated by a positive hybridization translation assay from a cDNA library made for 8-9S poly(A)mRNA from regenerating rat liver. The nucleotide sequence of the cDNA was determined. The sequence contains 23 base pairs in the 5' noncoding region, 345 base pairs in the protein coding region and 67 base pairs in the 3' noncoding region besides the poly(A) tail. The primary structure of the protein S26 was deduced from the nucleotide sequence. It consists of 115 amino acids. Its molecular weight is 13,015 and its pI is about 11.1. The calculated amino acid composition is consistent with the reported composition of S26. From the results of Southern blot analysis, the protein S26 appears to have multiple genes.

Protein-protein neighbors in rat liver 60S ribosomal subunits were investigated by using two bifunctional imidoesters; dimethyl suberimidate (DMS) and dimethyl 3,3'-dithiobispropionimidate (DTP). 1. Complexes cross-linked with DMS were separated by two-dimensional acrylamide/urea gel electrophoresis. Each complex in the gel was labeled with 125I (1) and was cleaved into the original monomeric protein constituents of ammonolysis. The products were analyzed by two-dimensional acrylamide/urea gel electrophoresis, followed by radioautography of the stained gel. Eight protein pairs are proposed according to our numbering system (2): L1-L3(L3-L5), L2-L21 (L4-L26), L5-L13 (L7/L7a-L15), L5-L34 L7/L7a-L36), L6-L34 (L8-L36), L6-L32 (L8-L35), L12-L32 (L13/L13a-L35), and L18-L27 (L18-L27/L27a). The designations according to the proposed uniform nomenclature (3) are given in parentheses. 2. Complexes cross-linked with DTP were analyzed by acrylamide/SDS diagonal gel electrophoresis (4), and the molecular weights of the complexes and their components were determined. The monomer components of cross-linked pairs were labeled with 125I in the gel, and identified by two-dimensional acrylamide/urea gel electrophoresis followed by radioautography. Six pairs are proposed; L1-L5 (L3-L7/L7a), L1-L6 (L3-L8). L5-L19 (L7-/L7a-L21/L23/L23a), L13-L15 (L15-L14), L13-L16 (L15-L19), and L23-L27 (L30-L27/L27a). 3. Two pairs which were formed by protein-protein interaction without the use of cross-linking reagents were identified as L2-L4 (L4-L6) and L4-L30 (L6-L29).

To examine whether serine proteases of rat liver chromatin are also involved in the degradation of newly synthesized and unbound ribosomal proteins and histones, like the nuclear thiol protease which we reported previously (Tsurugi, K. & Ogata, K. (1979) Eur. J. Biochem. 101, 205-213), in vivo experiments were carried out with serine protease inhibitor, PMSF. The following results were obtained. When normal rats received an intraperitoneal injection of PMSF (10 mg per 100 g body weight), nuclear serine proteases were inhibited almost completely for at least 90 min. PMSF did not affect the synthesis of proteins and RNAs of ribosomes and other subcellular fractions. The effects of PMSF treatment in vivo on the degradation of newly synthesized ribosomal proteins and histones in regenerating rat liver pretreated with a low dose of actinomycin D, which preferentially inhibited rRNA synthesis, were examined by using the double-isotope method. It was found that PMSF treatment did not affect their degradation. On the other hand, administration of E-64, a thiol protease inhibitor, to partially hepatectomized rats inhibited the degradation of those proteins markedly. From these results, it is concluded that the nuclear thiol protease, but not serine proteases, is preferentially involved in the degradation of newly synthesized ribosomal proteins and histones which are not associated with rRNA and DNA, respectively.

The chromatin fraction of rat liver exhibited proteolytic activity caused by serine proteases, with maximal activity at pH 8 or 10. They were analyzed by affinity labeling with [3H]diisopropylfluorophosphate followed by SDS-polyacrylamide gel electrophoresis, and partially purified by gel filtration through Sepharose 6B after selective extraction from the chromatin fraction. The following results were obtained. 1. The chromatin fraction contained three DFP-binding proteins with molecular weights of 52,000, 25,000, and 15,000 daltons, and they were tentatively designated proteins A, B, and C, respectively. Unlike proteins A and B, protein C reacted with DFP more strongly at pH 10 than at pH 8. A greater part of protein B was present in the nucleoli, while the others were predominantly distributed in extra-nucleolar chromatin. 2. Proteins A and B were extracted from the chromatin fraction by 5 M urea and 0.7 M NaCl, respectively; while protein C was not extractable by either solution. Proteins A and B were further purified by gel filtration through Sepharose 6B. 3. Protein B was a neutral protease with a maximal activity for 3H-labeled ribosomal proteins at pH 8 and showed high specificity for basic proteins, such as histone and ribosomal proteins. Protein A was an alkaline protease with a maximal activity at pH 10 and showed proteolytic activity not only for basic proteins but also for hydrophobic proteins, such as casein and non-histone proteins of chromatin. 4. Protein A was activated at pH 8 by high concentrations of NaCl, suggesting the presence of some inhibitor(s). Protein A was converted to protein C at pH 10, and also at pH 8 with high concentrations of NaCl. Thus, protein A is suggested to be the complex of protein C and unknown inhibitor(s). 5. When the chromatin fraction was incubated at pH 10, non-histone proteins were degraded much faster than at pH 8, although H1 histone was degraded at similar rates at both pHs. These results indicate that the chromatin fraction of rat liver contains at least two kinds of serine proteases, B and C, and that protease B is probably involved in the metabolism of basic protein, especially H1 histone. Protease C, the greater part of which associates with some inhibitors to form protein A, may play its main role in the metabolism of non-histone proteins.

1. When rats received an intraperitoneal injection of [3H]actinomycin D, it bound to the RNA moiety of free and bound polysomes of rat liver. The labeling increased gradually up to 6 h or 6 + 6 h. The poly(A)-containing mRNA showed definite radioactivity and its specific activity was higher than that of rRNA, although the total radioactivity of rRNA was markedly higher than that of poly(A)-containing mRNAs. 2. An equilibrium dialysis method using rabbit globin mRNA showed that the binding constant of actinomycin D to globin mRNA was 0.056 x 10(6) M-1, and globin mRNA had 2 binding sites per mol for actinomycin D. 3. From the results of the present experiments and those described in the preceding paper, it is suggested that one of the mechanisms by which actinomycin D treatment in vivo and in vitro stimulates the template activity of mRNA may be binding to mRNA, which alters the conformation of mRNA.

Proteins of rat liver nucleolar RNP, especially 110S RNP containing 45S RNA, were investigated and the following results were obtained. 1. Nucleolar extract was prepared from thioacetamide-treated rat liver nucleoli in the presence of 1 mg PVS per ml. Sucrose-density gradient centrifugation of the nucleolar extract showed RNP distributed between 60S and 110S. The 110S particles (110S RNP) contain 45S RNA as judged from the radioactivity profiles of nucleolar extract labelled in vivo with [3H]orotic acid for 10 min and 2 h. The protein components of 110S RNP and total RNP heavier than 60S (total RNP) were analyzed and compared. 2. Since the effects of PVS treatment on the extraction and the electrophoretic pattern of ribosomal proteins were removed by increasing the Mg2+ concentration during acetic acid extraction, as described in our preceding paper (1), proteins of 110S RNP as well as total RNP from PVS-pretreated nucleoli were extracted with 67% acetic acid containing 334 mM Mg2+ and analyzed by two-dimensional acrylamide gel electrophoresis. Ribosomal proteins masked by contaminating histone spots on the gel were identified by SDS-acrylamide gel electrophoresis. 3. 110S RNP contained a large portion of ribosomal proteins from large subunits; 24 protein spots were distinct, 6 protein spots were faint and 5 proteins (L3, L8, L30, L35, and L36) were missing completely. On the other hand, 110S RNP contained a small number of small subunit proteins; only 6 proteins showed distinct spots, 7 proteins showed faint spots and 12 protein spots were missing. 110S particles contained 11 non-ribosomal proteins, although it is difficult to rule out the possibility that some of them were contaminating chromatin proteins. 4. Total RNP showed electrophoretic patterns of 60S ribosomal proteins similar to those of 110S RNP, although L3 protein was present as a faint spot and 26 proteins showed distinct spots. Total RNP contained more small subunit proteins than 110S RNP; 7 proteins spots were distinct, 10 protein spots were faint and 8 protein spots were missing. The results suggest that some kinds of 40S proteins and L3 protein are attached to 110S RNP during the processing of 110S RNP.

A neutral protease, named protease B in the previous report (Tsurugi, K. & Ogata, K. (1982) J. Biochem. 92, 1369-1381), was partially purified from rat liver chromatin by gel filtration through Sepharose 6B followed by DE-Sephadex column chromatography. The proteolytic activity on total histones of the partially-purified protease B was increased about two fold by addition of DNA and again increased by further addition of 2 M urea. Analysis of the hydrolysed products showed that out of five species of histones, only H1 was degraded in the presence of an amount of DNA equivalent to the amount of histones, whereas core histones were also degraded in the absence or presence of one-tenth amount of DNA. Urea accelerated the selective degradation of H1 histone because H1 histone was preferentially degraded in the presence of even a low amount of DNA. In contrast, core histones became resistant to the protease B in the presence of DNA and/or urea. Heat-denatured DNA stimulated the degradation of H1 histone even in the absence of urea to almost the same extent that native DNA did in the presence of urea. Thus, protease B efficiently degrades H1 histone when its association with DNA is destabilized by either addition of urea or pretreatment of DNA with heat.

When rat liver 80S ribosomes or polysomes were dissociated into their subunits by EDTA-treatment, a 5S RNA-L5 protein complex was present in EDTA-derived small subunits, and released from the subunits by urea. The interaction of 5S RNP with the small subunits did not occur in the case of 80S couples formed from 40S and 60S subunits in the presence of Mg2+, indicating that the attachment of 5S RNP to EDTA-derived small subunits was not an artifact caused by the unfolding of the subunits. These results give direct evidence that 5S RNP is located at the interface between large and small subunits, and suggest that 5S RNP binds to the 40S subunit in the functioning polysomes, but not the 80S couples.

We have studied the protein components and nucleotide sequence involved in the endonucleolytic cleavage at 105 bp upstream of the 5' end of mouse 18S rRNA. By fractionating the mouse S100 extract into four fractions by phosphocellulose chromatography, we separated and characterized the processing factor which participated in in vitro coupled and uncoupled transcription-processing systems. Processing activity was recovered in the flow-through fraction (fraction A), while the transcription initiation was supported by the combination of fractions C and D. This endonucleolytic cleavage activity was heat-labile and resistant to micrococcal nuclease. By constructing deletion fragments, we found that the sequence between 219 bp upstream and 26 bp downstream of the processing site was required for the processing. This sequence does not include the 18S rRNA coding region and can form a stem-loop secondary structure.

When we compared the sequences near four terminal sites of transcripts including two endoribonucleolytic cleavage sites in external transcribed spacer 1 upstream of the 5' end of the mouse 18S rRNA (Mishima, Y., Mitsuma, T., & Ogata, K. (1985) EMBO J. 4, 3879-3886), a seven-nucleotide consensus sequence, GGPyUUGPy (Py is C or U), was obtained. The results of both in vitro pulse-chase experiments and S1 nuclease mappings using the mouse rDNA fragment of the transcription initiation region indicated that ribonucleolytic cleavages take place in the sequence matching the consensus sequence at more than five nucleotides out of the seven positions. Furthermore, effective ribonucleolytic cleavages in vitro were observed in a sequence, GGCUUGU, in the internal transcribed spacer 2 located between 5.8S and 28S rRNA. These results demonstrate that the ribonucleolytic cleavages occur preferentially in the sequence of GGPyUUGPy in the transcribed spacer regions of the mouse pre-rRNA. From this information, we infer the existence of processing steps for the pre-rRNA maturation involving the sequence-specific ribonucleolytic cleavages.

We purified acidic ribosomal proteins (P1 and P2) in good yield from rat liver ribosomes by precipitation of ribosomes with MgCl2 prior to ethanol extraction and chromatography of the extract on a column of CM-cellulose at pH 4.8. The newly-synthesized acidic ribosomal proteins in regenerating rat liver, labeled in vivo with [3H]leucine, were rapidly incorporated into cytoplasmic ribosomes without any detectable time lag and, after reaching a maximum at 30 min, they gradually disappeared from the ribosomes, suggesting a short metabolic-life. However, it was found later that they were re-incorporated slowly when newly-labeled proteins were "chased" by an injection of a large amount of cold leucine intraperitoneally at 15 min after the injection of [3H]leucine. Furthermore, in a long-term experiment, acidic ribosomal proteins were found to disappear with a half-life of 100 h from the ribosomes. Thus, these results suggest that acidic ribosomal proteins have a long metabolic life and are exchangeable on cytoplasmic ribosomes in regenerating rat liver.

Rat liver 40S ribosomal subunits were treated with a bifunctional imidoester, dimethyl 3,3'-dithiobispropionimidate (DTP), and the neighboring protein pairs were identified. The cross-linked proteins were analyzed by acrylamide/SDS diagonal gel electrophoresis (Sommer & Traut (1974) Proc. Natl. Acad. Sci. U.S. 71, 3946-3950). The cross-linked components that fell off the diagonal upon adding 2-mercaptoethanol in the second dimension were labeled with 125I in the acrylamide gel and identified by two-dimensional acrylamide/urea gel electrophoresis, followed by radioautography. Considering these results and the molecular weights, we propose the following ten pairs, according to our numbering system (Terao & Ogata (1975) Biochim. Biophys. Acta 402, 219-229): S3-S5 (S3/S3a-S4), S3-S14 (S3/S3a-S14), S3-S17 (S3/S3a-S16), S5-S22 (S4-S23/S24), S10-S12 (S8-S11), S9-S16 (S9-S18), S9-S22 (S9-S23/S24), S6-S23 (S5-S25), S17-S21 (S16-S19), and S16-S26 (S18-S27). The designation according to the proposed uniform nomenclature (McConkey et al. (1979) Mol. Gen. Genet. 169, 1-6) are given in parentheses.

Employing livers from rats fed on a protein-free diet for two weeks, the effects of protein deficiency on both biosynthesis and degradation of rRNA were investigated and the following results were obtained. 1. Protein deficiency led to a decrease of total liver RNA content per DNA to about 80% of that in normal rat liver. 2. From the kinetics of rRNA labelling with [14C]orotic acid in vivo, the half-lives of cytoplasmic rRNA's of normal and protein-deficient rat livers were determined to be 6.2 and 5.1 days, respectively. Furthermore, considering the pool size of rRNA in rat liver, the turnover rate of cytoplasmic rRNA was calculated to be 0.212 pmole/min/mg of nuclear DNA in normal rats and 0.240 pmole/min/mg of nuclear DNA in protein-deficient rats. 3. From the electrophoretic patterns of nucleolar RNA's of both groups of rat livers labeled with [14C]orotic acid, the time courses of the specific activities of nucleolar 45S, 32S, and 28S rRNA's were analysed and the half-life of each nucleolar RNA in both groups of rat livers was determined. Nucleolar 45S, 32S, and 28S RNA's had half-lives of 6.0, 15.9, and 26.5 min in normal rats, respectively, and 5.5, 19.4, and 22.9 min in protein-deficient rats, respectively Considering the pool size of each nucleolar RNA obtained from the leectrophoretic pattern, the turnover rates of 45S, 32S, and 28S RNA's were calculated to be the same, i.e., o.189 pmoles/min/mg of nuclear DNA, in normal rat liver and 0.372, 0.372, and 0.358 pmoles/min/mg of nuclear DNA in protein-deficient rat liver, respectively. 4. These results indicate that protein deficiency increased both the rate of degradation of cytoplasmic rRNA and that of nucleolar rRNA synthesis in rat liver. While in normal rat liver the rates of rRNA synthesis and degradation were rather similar, the rate of rRNA synthesis in protein-deficient rats was about 1.5 times higher than that of its degradation. Therefore, the decrease of total liver RNA content in protein deficiency might be accounted for by stimulated degradation of rRNA in the nucleus. 5. The activities of RNase in nuclear fractions of both groups of rat livers were compared. Both activities of nuclear acid RNase and especially that of the free form of alkaline RNase in protein-deficient rat liver were higher than those in normal rat liver.

The activity of 60S subunits of rat liver ribosomes in poly(U)-dependent polyphenylalanine synthesis was inhibited by incubation with N-ethylmaleimide. However, when 60S subunits were incubated with iodoacetamide, their activity decreased only slightly. Furthermore, iodoacetamide-pretreated 60S subunits became insensitive to N-ethylmaleimide. Similar results were obtained for the activity of EF-2-dependent GTPase of 60S subunits. As a whole, the labeling patterns of ribosomal proteins on two-dimensional gel electrophoresis were similar for 60S subunits labeled with both 14C-labeled sulfhydryl reagents, although the extent of labeling of some proteins was somewhat different. These results indicate that the SH groups in the 60S subunits are not directly involved in the activities of the subunits described above.

Hen's oviduct polysomes are present in the precipitates prepared from the oviduct homogenates by low-speed centrifugation, in constrast other eukaryotic polysomes. The polysomes possessed synthesizing activity for ovalbumin. The amount of the released form of ovalbumin (soluble ovalbumin) synthesized in cell-free system A or B, consisting of the cell sap and the total ribosomal fraction or the polysomes, respectively, was about a half of that bound to the polysomes (nascent ovalbumin). The amount of soluble ovalbumin synthesized in cell-free system C, consisting of the pH 5 fraction and the polysomes, was only about 5% of that of nascnet ovalbumin. These results indicate that factors required to release nascent ovalbumin from polysomes are present in the pH 5 supernatant fraction. The soluble and nascent ovalbumins, which were purified by chromatography on a CM-cellulose column and by the use of antiovalbumin antiserum, respectively, seemed to be elongation products the initiations of which were supposed to occur in the oviducts before preparation of the cell-free system. The initiated chains in vitro were found to exist as nascent peptides bound to polysomes. Thus, the cell-free systems prepared in the present study lacked the ability to complete initiated peptide chains. The soluble ovalbumin synthesized in the cell-free systems was indentical with ovalbumin A1 containing two residues of phosphates, which was crystallized from hen's egg-white and was different soluble ovalbumin devoid of the prosthetic group (ovalbumin A3) prepared in the oviduct minces. This result suggests that an enzyme necessary for incorporation of the phosphate is present in the cell sap.

Three human decidual prolactin (PRL) cDNA clones (pdPL-1:349 base pairs, pdPL-2:584 base pairs, pdPL-3:807 base pairs without poly(A) tract) were prepared and sequenced. The insert DNA of the largest clone pdPL-3 contained the coding region corresponding to 217 amino acid residues including 18 amino acid residues of the signal peptide, and 157 nucleotides of the 3'-untranslated region. A comparison of the pdPL-3 cDNA sequence with that of human pituitary PRL cDNA revealed 4 silent nucleotide differences. Two of the base changes occurred in the third position of the amino acid codons, and the other two occurred in the 3'-untranslated region. Therefore, the amino acid sequence of decidual PRL deduced from the nucleotide sequence of pdPL-3 was identical with that of pituitary PRL. Minor changes were also observed among the three PRL mRNAs: a silent change in the third codon in the translated region, and another change in the 3'-untranslated region. Southern blot hybridization of human cellular DNA with the pdPL-3 probe indicates that PRL gene may occur once per haploid genome. Therefore, these minor changes may reflect microheterogeneity of PRL gene. The existence of multiple poly(A)-adjacent sequences was shown in the three species of human decidual PRL mRNA and in human pituitary PRL mRNA. This variation may be due to heterogeneity in the processing at the 3' terminus of mRNA or the termination sites of the transcription.

Dithiothreitol or glutathione, essential for amino acid incorporation into polypeptides in cell-free systems, inhibited glucosamine incorporation into ovalbumin, a glycoprotein containing about three residues of N-acetylucosamine and about five residues of mannose. However, the thiol was necessary for mannose incorporation into ovalbumin in cell-free system prepared from hen's oviducts. The two monosaccharides were incorporated into soluble ovalbumin (intracellular ovalbumin released from the polysomes, corresponding to ovalbumin A3 which contains no phosphate and probably no carbohydrate) present in cell sap which was prepared from homogenates of minced oviducts by ultracentrifugation. It was difficult to study the incorporation of the carbohydrates into ovalbumin in connection with synthesis of the protein using the crude cell-free system. The incorporation of glucosamine and mannose into various forms of ovalbumin was therefore studied using minced oviducts. It was concluded from the incorporation of the two radioactive monsaccharides and of amino acids into the extracellular, soluble and nascent protein fractions that all the carbohydrate moieties were not incorporated into the growing polypeptides bound to polysomes, but were incorporated into ovalbumin molecules released from polysomes after synthesis had been completed.

The amino acid compositions of 24 proteins of 40S ribosomal subunits of Artemia salina cysts were determined and compared with those of rat liver. The basic proteins of A. salina 40S ribosomes were separated by two-dimensional polyacrylamide gel electrophoresis and extracted with 70% formic acid. Samples were freed from contaminants by gel-filtration through a high-performance liquid chromatography column. Amino acid compositions were determined for individual proteins by pre-column derivatization with N,N-dimethylaminoazobenzenesulfonyl chloride followed by reverse phase high-performance liquid chromatography. The similarity of amino acid compositions between A. salina and rat liver 40S ribosomal proteins was evaluated by the method of Cornish-Bowden (Cornish-Bowden, A. (1980) Anal. Biochem. 105, 233-238), and possible relationships between A. salina and rat were detected for 16 protein species (S2, S3, S4, S6, S7, S8, S15a, S16, S17, and S18, strongly related and S14, S15, S20, S23, S24, and S26, weakly related), indicating a conservative nature of eukaryotic ribosomal proteins.

Ribosomal proteins from cysts and nauplii of Artemia salina were analyzed by three kinds of two-dimensional polyacrylamide gel electrophoresis. The basic-acidic and basic-SDS gel systems were used to compare the basic ribosomal proteins, and some changes were observed between the cysts and nauplii in proteins S6, S14, and L24. The phosphorylation of protein S6 was increased in the nauplii. Basic proteins S14 and L24 in the cysts changed and none of the corresponding proteins in the nauplii were detected at the same positions on two-dimensional gels as in the cysts. The acidic-SDS gel system was used to compare the acidic proteins in ribosomes and it was revealed that an acidic protein, AX (Mr = 24,000), in the cysts was not present in the ribosomes from the nauplii. The ribosomal activities as to the formation of an 80S initiation complex with globin mRNA and poly(U)-directed polyphenylalanine synthesis were compared. There was no significant difference between the cyst and nauplius ribosomes.

(1) When rat liver 40 S ribosomal proteins in 6 M urea were were mixed with poly(U) at an appropriate ratio, a precipitate was formed which was also insoluble in the sample solution for two-dimensional acrylamide gel electrophoresis. Analyses by two-dimensional acrylamide gel electrophoresis showed that S7 and S10 proteins (according to our numbering system) had disappeared selectively from the fraction soluble in 6 M urea. These two proteins were present in the fraction insoluble in 6 M urea, and became soluble in the sample solution after treating it with RNase. The results suggest that S7 and S10 proteins have strong affinities for poly(U). When rat liver 40 S subunits were incubated with poly(U), similar results were obtained. (2) After incubation of 40 S subunits with [3H]poly(U) and then with unlabeled poly(U), UV irradiation cross-linked poly(U) to the protein moiety of the 40 S subunit. When the protein fraction insoluble in the sample solution for two-dimensional electrophoresis was prepared from 40 S subunits cross-linked to poly(U) and then subjected to two-dimensional acrylamide gel electrophoresis after RNase treatment, S7 and S10 proteins were detected on the gel. In addition to the S7 protein spot, a triangular area spreading from the spot to the origin contained radioactivity. The results suggest that poly(U) is cross-linked to S7 protein and oligo(U) fragments bound to S7 protein affect its electrophoretic mobility. (3) Ribosomal proteins were prepared from 40 S subunits cross-linked to carrier-free [3H]poly(U) and analyzed by three-dimensional acrylamide gel electrophoresis (Terao, K. & Ogata, K. (1975) Biochim. Biophys. Acta 402, 214--229) after RNase treatment. It was found that S7, S6, and S15 proteins are cross-linked to poly(U). From the results of the present and preceding experiments it is concluded that S7 is the poly(U)-binding protein. The possibility that other proteins in 40 S ribosomal subunits interact with poly(U) is discussed.

The GTP- and ATP-hydrolyzing activities of the rat liver 5S RNA-L5 (according to the proposed common nomenclature (1) protein complex designated as 5S RNP were stimulated by pig liver elongation factor 2 (EF-2) plus aminoacyl-tRNA, both of which were required for the stimulation. The stimulative effect of aminoacyl-tRNA on GTP hydrolysis by the complete system containing 5S RNP and EF-2 was dependent on the concentration of aminoacyl-tRNA. Aminoacyl-tRNA also stimulated ATP hydrolysis by the complete system but did not stimulate the ATP hydrolysis by 5S RNP alone or EF-2 alone. While deacylated tRNA stimulated the ATPase activity of the complete system, it had no effect on the GTPase activity. Preincubated tRNA lacking the 3'-terminal CCA moiety had little effect on the GTPase and ATPase activities of the complete system. Fusidic acid inhibited the GTPase and the ATPase activities of the complete system with and without aminoacyl-tRNA, although the extent of the inhibition was larger in the presence of aminoacyl-tRNA. These results suggest that 5S RNP may be a component of the GTPase center of rat liver 60S subunits.

An enzyme that releases acylamino acid from amino terminal acylated peptides and proteins has been isolated from rat liver in a highly purified form bya six-step procedure comprising extraction from liver homogenate, ammonium-sulfate fractionation, heat treatment, chromatography on columns of DEAE-cellulose and hydroxylapatite and gel filtration on a Sepharose 6B column. About 1,500-fold purification was achieved from the liver homogenate. The purified enzyme preparation showed a single band on polyacrylamide gel disc electrophoresis. The enzyme specifically released acylamino acids from several amino terminal acylated peptides and proteins with different rates of hydrolysis depending on the acyl groups, terminal amino acid sequences and tertiary structure of the acyl protein substrates. The present enzyme may be useful for the removal of the N-terminal acylamino acid from some N-terminal blocked peptides and proteins in amino acid sequence analysis. The molecular weight of the purified enzyme was estimated to be 360,000-420,000 by gel filtration and sucrose density gradient ultracentifugation. Disc electrophoresis of the acylamino acid-releasing enzyme on SDS-polyacrylamide gel suggested that the enzyme consisted of five or six identical subunits having a subunit weight of about 75,000. The N-terminal residue of the subunit, which consisted of a single polypeptide chain, was glycine. Other properties of the enzyme, including isoelectric point, the effects of metal ions and several chemical reagents on the enzyme activity, pH optimum, and amino acid composition were also examined.