Yeast Ribosomal Proteins are Synthesized on Small Polysomes

Transcription

1 Eur. J. Biochem. 62, (1976) Yeast Ribosomal Proteins are Synthesized on Small Polysomes Willem H. MAGER and Rudi J. PLANTA Biochemisch Laboratorium, Vrije Universiteit, Amsterdam (Received September 25/November 18, 1975) Yeast polysomes were fractionated into various size classes and then the nascent polypeptide chains on each separate class of polysomes were elongated in vitro. Analysis of the completed polypeptides by polyacrylamide gel electrophoresis demonstrated that the polysomes engaged in ribosomal protein synthesis have a relatively small size. From kinetic analysis Petersen and McLaughlin [l] obtained evidence that messenger RNA (mrna) in yeast is predominantly monocistronic. At least, they found a linear relationship between the size of the polysomes and the molecular weights of the polypeptide chains synthesized on them. Since yeast ribosomal proteins have relatively low molecular weights compared with other cellular proteins [2,3], we envisaged the possibility (also suggested before by others [4]) that they are synthesized on small-size polysomes. Therefore, we decided to study the nature of the polypeptide chains synthesized on different size classes of yeast polysomes. We recently devised a method for the identification of nascent ribosomal proteins [3]. Nascent polypeptide chains are completed in vitro and subsequently analyzed by polyacrylamide gel electrophoresis at ph 8.6. In this way we were able to demonstrate that synthesis of ribosomal proteins in yeast takes place on both membrane-bound and free polysomes [3]. The same technique was applied to the analysis of the nascent polypeptide chains made on different size classes of yeast polysomes. The experiments described in this paper indicate that indeed small polysomes are engaged in ribosomal protein synthesis. ice-cold mannitol buffer (0.01 M citrate buffer ph 7.5, 0.01 M MgC12. 6 H,O, 12% mannitol). Protoplasts were lysed in Tris buffer with 0.5 Brij 58 as described previously [3]. The lysate was layered on l0-50% sucrose gradients in Tris buffer (20 mm Tris HCl ph 7.5, 10 mm NH,Cl, 5 mm magnesium acetate) and centrifuged during 16 h in a Spinco SW-27 rotor at rev/min. Corresponding size fractions of several gradients were pooled and incubated in vitro as described previously [3]. To each 13 ml of the pooled fractions was added : of ph-5 enzyme [3], 100 p1 of an energy-generating system (10 mm ATP, 2 mm GTP, 0.1 M creatine phosphate and 400 pg/ml creatine kinase), all amino acids except lysine (each 40 pm) and 20 pci of ~-[U-~H]lysine (specific activity 13 Ci/mmol). After min (see Results and Discussion) incubation was stopped by adding 2 vol. glacial acetic acid and magnesium acetate to a final concentration of 33 mm [6]. Protein extraction was performed by stirring this mixture during 4 h at 0 "C. RNA was removed by centrifugation and the remaining protein solution was lyophilized after thorough dialysis [3]. Nascent proteins were analyzed on 15% polyacrylamide gels at ph 8.6 as described previously [3]. MATERIALS AND METHODS Succhuromyces carlsbergensis (strain S74) was grown in rich medium [3]. Protoplasts were prepared as described elsewhere [5], and incubated during 2.5 h at 29 "C in synthetic medium [5], supplemented with 12% mannitol but without methionine. Pulse labeling was performed with 1 pci/ml 3H-labeled L-amino acids (specific activity 250 pci/133 pg) during 2 min. Incorporation was stopped by adding 50 pg/ml cycloheximide and then pouring the incubation mixture into RESULTS AND DISCUSSION Yeast polysomes isolated as described previously [3] were fractionated according to size. The size distribution of the yeast polysomes is shown in Fig. 1. The positions of the peaks of the smaller polysomes in the gradient were plotted versus the logarithm of polysome size. The size of the larger polysomes can be estimated by extrapolation as indicated in the figure. As judged from the polysome profile no significant degradation of polysomes has taken place during the isolation procedure.

2 194 Yeast Ribosomal-Protein Synthesis.nn ".Y 80s I E ~ Fraction number Fig. 1. Size distribution of'jeasr polj~somes. Yeast polysomes isolated as described in Materials and Methods were layered on "; sucrose gradients in Tris buffer and ccntrit'uged for 16 h at rev/min in a Spinco SW-27 rotor. The arrow indicatcs the direction of sedimentation. Thc size ol'large polysomes can be estimated by extrapolating the straight line through the points marking the positions of the various small-size pol ysomes c Incubation time (min) Fig. 2. Eloiigutioti of' nmccwt poi.vpcy)tidc.s in vitro on ili//&wfl.size cklsses of'yeusz po/ysomrs. Incubation WdS performed as described in Materials and Mcihods. At different times aliquols or the incuba- precipitates wcre washed twice with 5 "i, trichloroacetic acid, solubilized in 0.3 nil Nuclcar Chicago Solubilizer and counted in toluene. The various plots (a - h) correspond with the size classes indicated in thc inserts of thc Fig.3(A-H) Nascent polypeptides were pre-labeled in vivo by a short pulse (2 min) with 3H-labeled L-amino acids. Cycloheximide was added to avoid run-off. No radioactivity is found in the mature ribosomal particles thcrnselves under these conditions of labeling. Gradient fractions corresponding to different size classes of polysomcs (as indicated in Fig. 3), were incubated in vitro as described in Materials and Methods. First, we determined the incubation time, at which maximal incorporation of radioactivity can be obtained. To this end aliquots of the incubation mixture taken at appropriate times were precipitated with cold trichloroacetic acid. Fig. 2 shows the incorporation curves obtained with the different size classes used in our experiments. The optimal incubation time appears to vary from 30 min for small-size polysomes to 45 min for large-size polysomes. Longer incubation times are less favourable probably due to proteolytic degradation of the elongated protein chains. Thcrefore, incubation of the different polysome fractions in vitro was stopped at the time corresponding to optimal incorporation. At the end of the incubation time glacial acetic acid (67 %) and magnesium acetate (33 mm) were added [6]. The extracted proteins were analyzed on 15 "/, polyacrylamide gels at ph 8.6 with the anode at the top. Under these circumstances only ribosomal proteins. migrate into the - gel [31... Table 1 and Fig. 3 show the results of this technique applied to the polypeptides elongated on different size classes of polysomes. A remarkable difference clearly exists between small-size and large-size polysonlcs. active protein chains elongated in vitro on the dimer fraction (insert Fig. 3 A) migrate into the gel. This percentage decreases progressively when larger polysomes arc used in the elongation system. Hardly any radioactive protein elongated on the most rapidly sedimenting polysome fraction (insert Fig. 3 H) migrates into the gel. Since, upon electrophoresis of total yeast protein at ph 8.6, only ribosomal proteins can be detected in the gel [3], these data strongly suggest that in yeast, ribosomal protein is preferentially synthesized on small polysomes. Further support for this idea is found in the results presented in Fig. 3 which show the radioactivity patterns for proteins elongated in vim to be

3 W. H. Map and R. J. Planta _ E.._ 4 0 =600 0 Y I I I I I I I Fraction number 1 I I 1 a I I ' Frac!ion nilmber Fig. 3. Pol~~trc~i~i~l~iniicle gel c.lec.tr.ophor~~sis ut ph 8.6 of tia.s('eiit lvotc,ins elon~uted in vitro on dijfihrt size c1ussr.r of ycut ~O~JSOIII~~.~. The relevant size class of polysoines used in cach separate expcriment is indicated by the hatched area in the insert figure. The drawn line inarks the pattern obtained with uniformly I4C-labeled ribosomal protein. The line connecting the open circles reprcsents the 3H activity incorporated in elongated polypeptide chains, migrating into thc gel under thc conditions used. Electrophoresis was perforiiied BS dcscribed [3], with the anodc at the top. Dircction of electrophoresis was from right to left closely similar to the control patterns obtained with ribosoinal proteins labeled in vivo. Our conclusion, therefore, is that ribosomal proteins of yeast are synthesized on relatively small polysomes. The individual percentages presented in Table 1 should be considered with some reserve since they are no doubt influenced by the partial overlap of the different size classes of polysomes in the sucrose gradients.

4 ~ 196 Yeast Ribosomal-Protein Synthesis Table 1. Amount of rndiouc tivity in elonguted polypeptide chains, migrating into the gel ut ph 8.6 Protein elongated on different size classes of polysomes was applied to a 15 P: polyacrylamide gel and electrophoresed at ph 8.6 with thc anode at the top (see Materials and Methods). The designations used for the various polysome fractions correspond to those in Fig. 3 (A - H) Polysome fraction 3H added 3H migrating used in elongation to the gel into the gel dis./min (%) ssooo (45) (36) (25) (25) 9740 (9) 8620 (7.5) 4780 (5) 750 (1) Total (16) Polyswne size Fig. 4. Relationship beiwen incorporation in nascent protein elongated on dijfrrenr.size classes of yeast yolysomes and the size of-the reliwnt po1jsome.s. Radioactivity incorporated per pg ribosomal RNA, calculatcd from the absorbance of the polysome solution used for each clongation experiment in vitro, was plotted versus the size of thc rclcvant polysomes Two additional points should also be considered. First, we have no certainty whether all the radioactive protein moving into the gels is in fact ribosomal protein. As mentioned above, no non-ribosomal protein is detectable when total yeast protein is subjected to gel electrophoresis at ph 8.6 [3]. However, we cannot exclude the possibility that after elongation in vitro basic fragments are present of non-ribosomal proteins, which in mature form (due to their isoelectric point or size) do not move into the 15% gel. These fragments could migrate into the gel and, thus, increase the apparent percentage of ribosomal protein. A rather remote possibility is that part of the radioactivity moving into the gels is due to small basic non-ribosomal proteins like histones. Although histones may be synthesized on small polysomes, their concentration, compared to that of ribosomal protein, in yeast is very low as can be deduced from the RNA : DNA ratio which lies somewhere between 50 : 1 and 100 : 1 [7]. This, and the similarity of the radioactivity patterns with that of mature ribosomal protein, makes it highly unlikely that the percentages shown in Table 1 are influenced to a significant extent by the presence of labeled histones. Secondly, there is some uncertainty with respect to the recovery from the gels of the ribosomal proteins elongated in vitro. In previous experiments (unpublished results) we have found that at ph 8.6 mature ribosomal proteins are difficult to solubilize. Differences in the efficiency of solubilizing the protein elongated in vitro might lead to an underestimation of the amount of ribosomal protein present in the samples. Howevcr, if we compare the total amount of 3H added to the eight gels with the total amount of 3H that migrates into the ribosomal protein region, it appears that about 16 of the radioactivity is in protein which in electrophoretic behaviour resembles ribosomal protein (see Table 1). This figure is in good agreement with the expected value; ribosomal proteins comprise 1&15 /, of total yeast cellular protein [8]. However, even if the percentages given in Table 1 are not quite accurate, this leaves untouched our conclusion as to the polysoma1 site of synthesis of ribosomal protein. Finally we calculated the amount of radioactivity incorporated into nascent protein per pg of ribosomal RNA (rrna) present in the incubation mixture, and we plotted this value versus the polysome size. Fig. 4 shows that the linear relationship, found by others using labeling in vivo [l], is also found with labeling in vitro. This result stresses the reliability of the elongation experiments in vitro described in this paper. Obviously the size of the polysomes is related to the size of the protein chains synthesized on them. In addition, analysis of the size distribution of poly(a)- containing messenger RNA isolated from each polysome fraction showed that small polysomes contain relatively short mrna molecules, and large polysomes contain relatively long mrna molecules (results not shown). From Fig. 4 it is clear that a substantial deviation of the curve occurs at small-size polysomes. Several explanations for this phenomenon present themselves. First, the deviation may be due to the presence in the disome region of newly synthesized mrna of large size only partially loaded with ribosomes. Since polysomes were isolated from cells in a steady-state situation it seems highly unlikely that the presence of such displaced mrna could account for the sizeable deviation observed. Secondly, the effect may be caused by contamination of the small polysomes with initiation factors sedimenting at the top of of the sucrose gradient, leading to reinitiation of pro-

5 W. H. Mager and R. J. Planta 197 tein synthesis. Finally, the possibility that a sizeable portion of the mrna present in small polysomes of yeast is polycistronic has to be considered. Since almost half of the messengers present in the dimer fraction may be considered to code for ribosomal proteins (see Tablel), our results enable us to isolate a mrna fraction enriched in mrna coding for yeast ribosomal proteins. This would greatly facilitate the study of the genetic organization of ribosomal protein cistrons in yeast. This work was supported in part by the Netherlands Foundation for Chemical Research (S.O.N.) with financial aid from the Nethcrlands Organization for the Advancement of Pure Research (Z.W.O.). We thank Mrs H. Hoving and Mr G. H. P. M. Bollen for excellent technical assistance, and Dr H. A. RauC lor critical reading of the manuscript. REFERENCES 1. Petersen, N. S. & McLaughlin, C. S. (1973) J. Mol. Bid. 81, Kruiswijk, T. & Planta, R. J. (1974) Mol. Biol. Rep. I, Mager, W. H. & Planta, R. J. (1975) Biochim. Biophys. Acta, 402, Petersen, N. S. & McLaughlin, C. S. (1974) Mol. Gen. Guner. 129, Retd. J. & Planta, R. J. (1967) Eur. J. Biochem. 3, X. 6. Sherton, C. &Wool, I. (1974) Mol. Gen. Genet. 135, Fukuhara, H. (1967) Biochim. Biophys. Acta, 134, Warner,.I. R. (1971) J. Bid. Chem. 246, W. H. Mager and R. J. Planta, Biochemisch Laboratorium der Vrije Universiteit, De Boelelaan 1085, Amsterdam-Z 11, The Netherlands