PSI+ prion generation in yeast: characterization of the 'strain' difference
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Yeast Yeast 2001; 18: 489±497. Research Article [PSI+] prion generation in yeast: characterization of the `strain' difference Natalia V. Kochneva-Pervukhova, Maria B. Chechenova, Igor A. Valouev, Vitaly V. Kushnirov, Vladimir N. Smirnov and Michael D. Ter-Avanesyan* Institute of Experimental Cardiology, Cardiology Research Center, 121552 Moscow, Russia * Correspondence to: Abstract M. D. Ter-Avanesyan, Institute The yeast cytoplasmically-inherited nonsense suppressor [PSI+] determinant is presumed of Experimental Cardiology, to be a manifestation of the aggregated prion-like state of the Sup35 protein. Cardiology Research Center, Overexpression of the Sup35 protein induces generation of [PSI+] determinants with 3rd Cherepkovskaya Street 15A, 121552 Moscow, Russia. various suppressor ef®ciency and mitotic stabilities. Here, we demonstrate that the relative E-mail: ter@cardio.ru frequency of appearance of [PSI+] with different properties depends on the SUP35 allele used to induce their generation. The difference in properties of [PSI+] determinants was preserved after their transmission from one yeast strain to another. This difference correlated with variation in properties of the Sup35 protein. A novel type of prion instability was observed: some [PSI+] with weak suppressor ef®ciency could convert spontaneously into strong suppressor determinants. Copyright # 2001 John Wiley & Received: 22 June 2000 Sons, Ltd. Accepted: 6 November 2000 Keywords: eRF3; prion strains; [PSI+]; Sup35p; Saccharomyces cerevisiae; yeast Introduction Weissman, 1997; Prusiner et al., 1998). The con- temporary concept suggests that they represent a The [PSI+] genetic determinant of Saccharomyces conformationally altered form (PrPSc) of normal cerevisiae decreases the ef®ciency of translation host-encoded protein (PrPC), which has acquired an termination and may be revealed by suppression of ability to convert PrPC into this altered prion form. nonsense mutations. It exhibits unusual genetic Several models of prion conversion have been properties, which include a non-Mendelian mode proposed. The heterodimer (template assistance) of inheritance, an ability to disappear in the model assumes that the prion, existing as a presence of low concentrations of guanidine hydro- monomer, can form heterodimer complexes with chloride (GuHCl) and to reappear upon over- normal molecules catalysing their prion rearrange- expression of the Sup35 protein (Sup35p) (for ment. The two molecules then dissociate and the review, see Cox et al., 1988; Wickner et al., 1995). cycle repeats. According to this model, the aggrega- Study of the biochemical properties of Sup35p tion is a secondary process, non-essential for the showed that it aggregates in the [PSI+] strains, prion conversion (Cohen et al., 1994). The while being soluble in the strains lacking this nucleated polymerization model considers prions determinant (Patino et al., 1996; Paushkin et al., as regular polymers, or one-dimensional crystals 1996). These properties are best explained by a that serve as nuclei for further polymerization of hypothesis that [PSI+] is a phenotypic manifesta- the protein. The conformational rearrangement of tion of the prion-like state of the Sup35 protein monomers may either occur spontaneously and (Wickner, 1994). then be ®xed in polymer structure (Jarrett and Prions are infectious agents responsible for a Lansbury, 1993) or, alternatively, be directly cata- group of diseases typi®ed by sheep scrapie, bovine lysed by polymer at the moment of accretion spongiform encephalopathy and human Creutz- (Horwich and Weissman, 1997). As a modi®cation feld±Jacob disease (for review, see Horwich and of the latter model, it was proposed that the prion Copyright # 2001 John Wiley & Sons, Ltd.
490 N. V. Kochneva-Pervukhova et al. conformation is adopted concomitantly with assem- although some difference in the rate of Sup35p bly, via molten oligomeric intermediates (Serio et al., aggregation in cells with various [PSI+] was 2000). revealed (Zhou et al., 1999), the phenomenon of Sup35p is a yeast member of the eRF3 family of [PSI+] variability is poorly characterized. translation termination factors (Zhouravleva et al., In this work we demonstrate that the relative 1995; Stans®eld et al., 1995) and is composed of the frequencies of appearance of [PSI+] with weak and amino-terminal region and carboxy-terminal (C) strong suppressor phenotype depend on the SUP35 domain of 253 and 432 amino acids, respectively allele used to induce their generation. We further (Kushnirov et al., 1988; Ter-Avanesyan et al., 1993, characterize the [PSI+] strains difference and 1994). The evolutionarily conserved C domain of describe [PSI+] with weak suppressor phenotype Sup35p is responsible for its function in translation that can spontaneously convert into strong suppres- termination and is essential for cell viability, while sor determinants. the N-terminal region is neither conserved nor essential. This region may be further subdivided into the middle (M) domain, of unknown function, Materials and methods and the N-terminal (N) domain of 123 amino acids, required for [PSI+] maintenance (Figure 1). The N Strains and media domain plays a key role in the [PSI+] phenomenon, being required for [PSI+] propagation in vivo and The S. cerevisiae strains used were 5V-H19 (MATa solely responsible for Sup35p prion conversion and ade2-1 SUQ5 can1-100 leu2-3,112 ura3-52 [psix]), oligomerization into amyloid-like ®brils in vitro c10B-H49 (MATa ade2-1 SUQ5 lys1-1 his3-11,15 (Paushkin et al., 1997a, b; Glover et al., 1997; leu1 kar1-1 cyhr [psix]) (Ter-Avanesyan et al., 1994; King et al., 1997). Kochneva-Pervukhova et al., 1998), 1B-H67 One of the most intriguing properties of prions is (MATa ade2-1 SUQ5 ura3-52 lys1-1 his3-11,15 leu1 leu2-3,112 kar1-1 cyhr [psi±]) (this work). The the existence of their different strains. In mammals, sup35-C allele of the strain 1±5V-H19 encodes a different prion strains are de®ned by speci®c truncated Sup35 protein lacking amino acids 1±253 incubation times, distribution of vacuolar lesions and causes dominant antisuppression and inability and patterns of PrPSc accumulation (for review, see to propagate [PSI+] (Kochneva-Pervukhova et al., Prusiner et al., 1998). In yeast they can be revealed 1998). This strain contained [PIN+] determinant, by differences in the suppressor ef®ciency and which allows induction of [PSI+] by overexpression mitotic stability of independently isolated [PSI+] of Sup35p (Derkatch et al., 1997). We used determinants (Derkatch et al., 1996). It was shown standard rich (YPD) and synthetic (SC) media for that at the molecular level mammalian prion strain yeast (Sherman et al., 1986). Non-fermentable differences correlated with stable variations in the media contained glycerol (24 ml/l) as the sole prion protein structure (Bessen et al., 1995; Safar carbon source. All solid media contained 2.5% et al., 1998; Caughey et al., 1998). However, (w/v) agar. Yeast cells were grown at 30uC. Figure 1. Schematic representation of the Sup35 protein and its fragments. Designations of the SUP35 deletion alleles and corresponding protein fragments are presented at left. Amino acid numbers are indicated Copyright # 2001 John Wiley & Sons, Ltd. Yeast 2001; 18: 489±497.
Analysis of [PSI+] generation de novo 491 Plasmids recipient strain were scored as cytoductants and tested for the ability to grow on adenine omission DNA manipulations were performed using stan- medium (Ter-Avanesyan et al., 1994). To quantify dard protocols (Sambrook et al., 1989). A series the induction of [PSI+], transformants of the 1-5V- of pEMBL-yex4-based plasmids (Cesareny and H19 [psix] [PIN+] strain with multicopy plasmids Murray, 1987) containing either the complete carrying different SUP35 alleles were crossed with SUP35 gene or its 3k-deletion alleles (Figure 1) has the c10B-H19 kar1-1 [psix] [rhox] tester strain been described previously (Ter-Avanesyan et al., carrying the cyhr mutation. Cytoductants were 1993). The pUKC815 plasmid carrying the selected on glycerol medium containing 3 mg/ml PGK±lacZ gene fusion, and pUKC817, which is a cycloheximide and the frequency of [PSI+] induc- pUKC815 derivative carrying an in-frame TAA tion was estimated as described by Kochneva- termination codon at the junction of the PGK and Pervukhova et al. (1998). lacZ genes, were described by Stans®eld et al. (1995). The transformants with all the plasmids used were selected on uracil omission medium. Determination of the nonsense suppression ef®ciency The UAA nonsense suppression levels were deter- Genetic methods mined as ratio of b-galactosidase activity in cells Standard methods of yeast genetics were used transformed with pUKC817 plasmid to that in cells (Sherman et al., 1986). Nutrition markers were with pUKC815, as described previously (Stans®eld scored by growth on synthetic complete (SC) media et al., 1995). lacking speci®c amino acids or nucleic acids bases. DNA transformation of yeast cells was performed Preparation, fractionation and analysis of yeast as described (Gietz et al., 1995). Non-suppressive cell lysates petites of the strains c10B-H49, 5V-H19 and 1B-H67 were obtained by ethidium bromide treat- Yeast cultures were grown in liquid YPD medium ment (Goldring et al., 1970). Yeast strains were or in a medium selective for plasmid marker to an cured, when necessary, of the [PSI+] determinant OD600 of 1.0 (exponential phase) or, when neces- by growth on YPD medium supplemented with sary, to OD600 of 3.5 (stationary phase). The cells 3 mM guanidine hydrochloride (GuHCl test) (Tuite were harvested, washed in water and lysed by et al., 1981). The [psix] colonies of ade2-1 SUQ5 vortexing with glass beads in buffer A (25 mM carrying strains were identi®ed by their red colour Tris±HCl, pH 7.4, 100 mM NaCl, 5 mM MgCl2, and adenine requirement because the weak serine- 1 mM dithiothreitol) containing 1 mM phenylmethyl- inserting tRNA suppressor SUQ5 cannot suppress sulphonyl ¯uoride (PMSF) to limit proteolysis the ade2-1 ochre mutation in the absence of the degradation. Cell debris was removed by centrifu- [PSI+] determinant (Cox, 1965). The mitotic gation at 15 000rg for 10 min. To analyse the size stability of different [PSI+] isolates was determined distribution of Sup35p by differential centrifuga- as the percentage of [PSI+] cells in their individual tion, the lysates were underlaid with 1 ml 30% colonies grown on YPD medium. sucrose pads made in buffer A and centrifuged in a The transfer of [PSI+] in `cytoduction' experi- Beckman SW50 rotor at 45 000 r.p.m. at 4uC for ments was performed as described (Ter-Avanesyan 30 min. The resulting supernatants, pellets and et al., 1994; Kochneva-Pervukhova et al., 1998). intermediate fractions were analysed by Western The recipient strain in such crosses was [psix] blotting. To obtain sedimented material containing [rhox], while the donor was [rho+]. In addition, Sup35pPSI+, the lysates of 5V-H19 [PSI+] strain one of the crossed strains carries the kar1-1 were loaded onto a sucrose layer (1 ml, 30%) and mutation that blocks karyogamy (Conde and Fink, centrifuged at 200 000rg for 30 min at 4uC. The 1976). The strains were mixed together on the sedimented material was resuspended in buffer A surface of a YPD plate, incubated overnight, and for further use in conversion reactions, performed then replica-plated to appropriate selective medium as described previously (Paushkin et al., 1997a). A containing glycerol as the sole carbon source. ratio of Sup35pPSI+ to Sup35NMppsix in mixtures Respiratory-competent ([rho+]) colonies of the was 1 : 4 in all cases. Protein samples were separated Copyright # 2001 John Wiley & Sons, Ltd. Yeast 2001; 18: 489±497.
492 N. V. Kochneva-Pervukhova et al. on a 10±15% SDS±polyacrylamide gel, according to c10B-H49 [psix], using the `cytoduction' procedure Laemmli (1970), and electrophoretically transferred (see Materials and methods). The crosses of all to nitrocellulose sheets (Towbin et al., 1979). tested transformants carrying plasmids with differ- Western blots were probed with polyclonal rabbit ent 3k-deletion SUP35 alleles produced Ade+ anti-Sup35p antibody or antibody against the cytoductants, which were shown to be [PSI+] by Sup35N2p fragment and developed using the the GuHCl test. These [PSI+] clones differed by Amersham ECL system. Estimation of relative their suppressor ef®ciency and could be roughly amount of soluble Sup35p in lysates of different divided into two classes: `strong', with strong [PSI+] isolates was performed as described by Zhou suppressor phenotype (white on YPD medium, et al. (1999), with minor modi®cations. and able to grow on adenine omission medium after 2 days of incubation) and `weak', with weak suppressor phenotype (pink on YPD medium, and Results growing on adenine-free medium on the third or fourth day of incubation). Remarkably, the relative Factors in¯uencing the spectrum of [PSI+] proportion of the weak and strong [PSI+] strains generated de novo depended on the Sup35p variant used for their The overexpression of Sup35p or its N-terminal generation. The increased ef®ciency of [PSI+] part induces the de novo appearance of the [PSI+] induction by overexpression of short Sup35p was determinant (Chernoff et al., 1993; Derkatch et al., mainly due to the appearance of weak [PSI+] 1996). This procedure generates various forms (Table 1). (`strains') of [PSI+] determinant with different nonsense suppressor ef®ciency and mitotic stability Strain-speci®c variation of [PSI+] properties (Derkatch et al. 1996). The C-terminal truncation of Sup35p greatly increases the frequency of [PSI+] While we roughly divided the [PSI+] strains into induction (Kochneva-Pervukhova et al., 1998). `strong' and `weak' groups, it was of interest to Here, we observed that such Sup35p truncation study in more details their distribution by suppres- also in¯uences properties of the generated [PSI+] sor ef®ciency. For this, [PSI+] induced in the strain determinants. For the [PSI+] generation, the multi- 1±5V-H19 by overexpression of Sup35NMp were copy plasmids encoding different C-terminally transferred by cytoduction to the strain 1B-H67, truncated Sup35p variants were expressed in the bearing the suppressor-assaying plasmid pUKC817 strain 1±5V-H19 [psix] [PIN+] encoding Sup35Cp, (Stans®eld et al., 1995). Cytoductants were selected which lacks the prionogenic N-terminal region and on the glycerol medium supplemented with cyclo- thus cannot convert into the prion form. The use of heximide and checked for the ability to grow on this strain provides two advantages over the wild- adenine omission medium. Ade+ clones were taken type strain for the quantitative analysis of the for determination of nonsense codon readthrough. [PSI+] generation. First, the [PSI+] induction in As a reference, the 1B-H67 [psix] recipient tester transformants of the 1-5V-H19 strain should be strain carrying the pUKC815 plasmid was used. It solely de®ned by the prion properties of the should be noted that the strain 1B-H67 carries the plasmid-encoded C-terminally truncated Sup35p SUQ5 ochre suppressor, which increases the level of variant. Second, this strain allows avoidance of UAA suppression. Among the 51 cytoductants counterselection of the appearing [PSI+] cells tested, the ef®ciency of UAA suppression ranged because, in contrast to the strains wild-type for from 5% to 65% (Figure 2). The distribution of SUP35, the combination of [PSI+] with inducing [PSI+] by suppressor ef®ciency was normal, rather plasmids is not detrimental in the strains than bimodal. This argues against the existence of carrying the SUP35-C allele (Dagkesamanskaya only two strains, but is consistent with high number and Ter-Avanesyan, 1991; Paushkin et al., 1997b). of strains. The [PSI+] phenotype is not manifested in the The [PSI+] isolates obtained also differed by strain 1±5V-H19 due to the presence of non-prion their mitotic stability. [PSI+] isolates with strong Sup35Cp (Ter-Avanesyan et al., 1994). To monitor suppressor phenotype were 100% stable during the [PSI+] generation, we transferred cytoplasm growth on YPD medium, while [PSI+] isolates from the 1±5V-H19 transformants to a tester strain, with weak suppression segregated [psix] subclones Copyright # 2001 John Wiley & Sons, Ltd. Yeast 2001; 18: 489±497.
Analysis of [PSI+] generation de novo 493 Table 1. The frequency and properties of [PSI+] generated de novo depend on the structure of plasmid SUP35 alleles Total number Number of `Strong' [PSI+] Inducing of [rho+] Number of [PSI+] `strong' [PSI+] cytoductants `Strong' [PSI+] among all [rho+] allele cytoductants cytoductants [PSI+] (%) (%) cytoductants (%) sup35-N1 2700 1068 39 39.6t6.9 3.7t0.5 1.4t0.2 sup35-N2 1980 260 11 13.1t0.9 4.2t1.9 0.56t0.29 sup35-NM 12000 65 13 0.54t0.13 20.0t0.8 0.11t0.02 sup35-DS 45000 202 63 0.45t0.24 31.2t1.4 0.14t0.07 SUP35 40800 89 53 0.22t0.03 59.6t4.1 0.13t0.03 The frequency and spectrum of [PSI+] induced in the strain 1±5V-H19 by multicopy plasmids carrying indicated SUP35 alleles were estimated as described in Results. In each case, where it was possible, 100 respiratory-competent Ade+ cytoductants were examined by the GuHCl test. All tested Ade+ cytoductants appeared due to [PSI+] acquisition. The [PSI+] induction data represent averages from three independent transformants. The standard deviation is indicated. with a frequency of
494 N. V. Kochneva-Pervukhova et al. Table 2. Mitotic stability of different [PSI+] strain Type of [PSI+] [PSI+] isolate Number of clones Number of [psix] clones % of [psix] clones 43 806 0 0 Strong 51 1419 0 0 77 1034 0 0 45 994 0 0 53 917 4 0.4t0.1 Weak 55 798 37 4.6t0.3 67 826 2 0.2t0.1 79 405 2 0.5t0.1 Percentage of [PSI+] loss was calculated as described in Results. Data represent averages from three independent subclones of each [PSI+] isolate. The standard deviation is indicated. (Zhou et al., 1999). This is likely to be below the Discussion physiological range, since Sup35p is essential. By our data, the decrease of Sup35p below 5% of its The protein-only concept for prions presumes that wild-type levels causes growth inhibition and cell the differences between their strains can only result death (I. A. Valouev, unpublished). It is noteworthy from conformational variations of prion protein. that the experiments described above were per- Indeed, the structural difference of PrPSc was formed with yeast cultures in stationary phase of demonstrated for different strains of mammalian growth, which could be an important factor prion (Caughey et al., 1998; Safar et al., 1998). increasing the Sup35p aggregation. Thus, the phenomenon of prion strains reveals the The use of cells harvested in the stationary phase ability of prion proteins to exist not in just two, but was due to observation that this allows distinguish- in multiple alternative self-propagating conforma- ing more clearly [PSI+] and [psix] cells by Sup35p tions. Such an ability is interesting in itself, but it aggregation than in the exponential phase. There- also gives an important insight into the debate fore, the experiment was reproduced with the cells about the models for prion conversion: the exis- harvested in exponential phase, which gave remark- tence of strains is more compatible with variants of ably different results: the soluble Sup35p of the the nucleated polymerization model than with the strain with `strong' [PSI+] constituted 6% and with heterodimer model. Indeed, it appears unlikely that `weak' [PSI+] 25% of its amount in the [psix] strain many different prion conformations can stably exist (Figure 3). It should be noted that the [psix] and self-reproduce as monomers. In contrast, in the reference level of Sup35p in this case was about polymerization model the alternative conformations three-fold higher than in stationary-phase cells. would be stabilized by intermolecular interactions The Sup35p from `weak' and `strong' [PSI+] and reproduced along the length of the prion strains was also distinguished by its ability to seed polymer. The strain variation was observed for the prion conversion of Sup35ppsix in vitro. Lysate both the conventional [PSI+] of S. cerevisiae and of [psix] transformant of the strain 5V-H19 with arti®cial [PSI+] based on N-terminal domain of multicopy plasmid encoding Sup35NMp was mixed Sup35p from yeast P. methanolica (Derkatch et al., with sedimented material obtained from the lysates 1996; Kushnirov et al., 2000). This supports the of 5V-H19 carrying either `strong' or `weak' [PSI+]. idea that the ability to exist in multiple forms is a general property of prions, rather than a speci®c In both cases Sup35NMp was convertible to an trait of the mammalian prions. However, the aggregated (Figure 4) and protease-resistant (data evidence for the existence of yeast prion strains is not shown) form, but the amount of converted not as strong as for mammalian prions, for which it material was about two-fold lower when the was shown that their strain-speci®c differences are reaction was seeded by the lysate of cells with preserved upon transmission from one animal to `weak' [PSI+]. No Sup35NMp aggregation was another. In this paper, we reinforce the evidence for observed in a control experiment without addition the [PSI+] strain variation being related solely to of the Sup35pPSI+ seeds. Sup35p by showing that genetic properties of Copyright # 2001 John Wiley & Sons, Ltd. Yeast 2001; 18: 489±497.
Analysis of [PSI+] generation de novo 495 Figure 4. Conversion of Sup35NMppsix to an aggregated form caused by mixing with aggregated Sup35p isolated from cells with `weak' and `strong' [PSI+]. Western blots were probed with antibody against Sup35N2p. Experiment: lysate of [psix] cells expressing Sup35NMp were mixed with [PSI+] sedimented material containing Sup35p, incubated for 20 min Figure 3. [PSI+]-dependent Sup35p aggregation. `Weak' and and analysed as described. Control: analysis of Sup35NMp in `strong' [PSI+] were transferred by cytoduction from the [psix] lysate after 2 h of incubation. Cytosol, sucrose and strain c10B-H49 to the strain 5V-H19 [psix] and the levels pellet: supernatant, intermediate fraction and sedimented of soluble Sup35p in corresponding cytoductants were material obtained after centrifugation of lysates and mixes compared with that of Sup35p in the strain 5V-H19 [psix]. A. Distribution of Sup35p between the soluble and Sup35p properties, rather than to any additional aggregated forms in lysates of cells harvested at stationary mutations in other genes. The extent of Sup35p phase of growth. Cytosol, sucrose and pellet: supernatant, aggregation should be proportional to the rate of its intermediate fraction and sedimented material, obtained prion conversion, and indeed Sup35pPSI+ seeds after centrifugation of lysates. Blots were immunostained from `strong' strains caused more ef®cient prion for Sup35p. B. Semi-quantitative dot±blot analysis of soluble conversion of Sup35ppsi± in vitro. It is also interest- Sup35p in lysates of different [PSI+] isolates. Lysates were ing that the level of soluble Sup35p greatly prepared from cells harvested at stationary or exponential depended on the growth phase of [PSI+] cells, phase of growth. The total protein from soluble fraction of being much lower at the stationary phase. In the each lysate was adjusted to 0.66 mg/ml, serially diluted in `strong' [PSI+] cells, this level constituted, in four-fold increments and applied to nitrocellulose mem- comparison to [psix] cells, 6% at the exponential brane. Blots were probed with antibody af®nity puri®ed against the Sup35N2p fragment. Equal levels of the total phase and only 1% at stationary phase. This may be protein in dilutions were con®rmed by staining the same explained by a decreased rate of synthesis of soluble membranes by Ponceau S, a non-speci®c protein stain (not Sup35p in stationary cells. On the other hand, the shown) demand for functional Sup35p in stationary cells is also likely to be decreased. [PSI+] determinants independently isolated in one Genetic properties allowed us to roughly divide yeast strain are reproducible in another yeast strain. [PSI+] into two classes: `strong', mitotically stable We observed that the suppressor ef®ciency of [PSI+] determinants with strong suppressor pheno- [PSI+] strains correlated with the extent of Sup35p type, and `weak', mitotically unstable [PSI+] with aggregation. Similar observations were made earlier weak suppressor phenotype. Quantitative analysis for conventional and `arti®cial' [PSI+] strains of the suppressor ef®ciency of independently (Zhou et al., 1999; Kushnirov et al., 2000). Such a obtained [PSI+] has shown that they represent a correlation may be anticipated, since the stop codon heterogeneous group and may differ from each readthrough should be inversely related to the levels other more than 10-fold. The [PSI+] distribution by of soluble Sup35p. This observation indicates that suppressor ef®ciency suggested that the number of the [PSI+] phenotype variation is related to the [PSI+] strains is greater than two and may be Copyright # 2001 John Wiley & Sons, Ltd. Yeast 2001; 18: 489±497.
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Prion-inducing domain 2±114 of yeast Sup35 protein Acknowledgements transforms in vitro into amyloid-like ®laments. Proc Natl Acad Sci U S A 94: 6618±6622. This work was supported by grants from INTAS, the Kochneva-Pervukhova NV, Poznyakovski AI, Smirnov VN, Ter- Russian Foundation for Basic Research (to M.D.T.-A.) and Avanesyan MD 1998. C-terminal truncation of the Sup35 the Wellcome Trust (to V.V.K.). protein increases the frequency of de novo generation of a Copyright # 2001 John Wiley & Sons, Ltd. Yeast 2001; 18: 489±497.
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