Interaction between the assembly of the ribosomal subunits: Disruption of 40S ribosomal assembly causes accumulation of extra-ribosomal 60S ribosomal protein uL18/L5

Nusrat Rahman; Md Shamsuzzaman; Lasse Lindahl

doi:10.1371/journal.pone.0222479

. 2020 Jan 27;15(1):e0222479. doi: 10.1371/journal.pone.0222479

Interaction between the assembly of the ribosomal subunits: Disruption of 40S ribosomal assembly causes accumulation of extra-ribosomal 60S ribosomal protein uL18/L5

Nusrat Rahman ^1,^¤a, Md Shamsuzzaman ^1,^¤b, Lasse Lindahl ^1,^*

Editor: Sander Granneman²

PMCID: PMC6984702 PMID: 31986150

Abstract

Inhibition of the synthesis of an essential ribosomal protein (r-protein) abrogates the assembly of its cognate subunit, while assembly of the other subunit continues. Ribosomal components that are not stably incorporated into ribosomal particles due to the disrupted assembly are rapidly degraded. The 60S protein uL18/L5 is an exception and this protein accumulates extra-ribosomally during inhibition of 60S assembly. Since the r-proteins in each ribosomal subunit are essential only for the formation of their cognate subunit, it would be predicted that accumulation of extra-ribosomal uL18/L5 is specific to restriction of 60S assembly and does not occur abolition of 40S assembly. Contrary to this prediction, we report here that repression of 40S r-protein genes does lead to accumulation of uL18/L5 outside of the ribosome. Furthermore, the effect varies depending on which 40S ribosomal protein is repressed. Our results also show extra-ribosomal uL18/L5 is formed during 60S assembly, not during degradation of mature cytoplasmic 60S subunits. Finally, we propose a model for the accumulation of extra-ribosomal uL18 in response to the abolition of 40S r-proteins.

Introduction

The ribosome biogenesis process is preserved throughout eukaryotic evolution, although the complexity has evolved from yeast to humans [1, 2]. Most of the ribosome construction occurs in the nucle(o)lus where RNA polymerase I transcribes a long 18S-5.8S-25S/28S precursor rRNA (pre-rRNA) and RNA polymerase III transcribes 5S pre-rRNA [3–6]. Ribosomal proteins are translated in the cytoplasm and chaperoned into the nucle(o)lus, where they bind to the emerging ribosomal precursor particles concurrently with the processing of the pre-rRNA into the mature components. The ribosome manufacture is facilitated by more than 250 ribosomal assembly factors, a number of which are important for the assembly of both the 40S and the 60S ribosomal subunits, while most are specific to the formation of one of the ribosomal subunits [7].

Whereas a subset of Saccharomyces cerevisiae (yeast) r-proteins is not required for the formation of ribosomes, most r-proteins are essential for assembly of their subunit [8]. A significant reduction of the production of just one essential r-protein or assembly factor prevents completion of the assembly of the cognate subunit, while the assembly of the other subunit continues (e.g. [9–11]). Moreover, abolishment of the assembly of a ribosomal subunit does not stop the synthesis of its r-proteins, but proteins that fail to become incorporated into stable ribosomal particles are rapidly eliminated by proteasomal turnover [10, 12, 13]. Nevertheless, one 60S protein, uL18, evades rapid degradation and accumulates in a complex with 5S rRNA outside of the ribosome when 60S assembly is abrogated by repression of uL5 synthesis [14]. [Note that uL5 was named L16 when this reference was published]. Since extra-ribosomal r-proteins are believed to play a role in regulation of factors controlling growth in metazoans [15, 16], it is important to understand the formation of extra-ribosomal r-protein pools.

Because the r-proteins in each ribosomal subunit are essential only for the assembly of their cognate subunit, it would be expected that interruption of the assembly of one subunit only affects the accumulation of extra-ribosomal r-proteins specific to that subunit. We tested this expectation by repressing several 40S r-protein genes and measuring the buildup of extra-ribosomal r-proteins. Surprisingly, and in contrast to the prediction, extra-ribosomal uL18 accrues when the synthesis of 40S r-proteins is constrained, but the amount of extra-ribosomal uL18 accumulating depends on which 40S r-protein gene is repressed. We interpret these results to mean that disruption of the assembly of the 40S subunit affects the kinetics, and perhaps even the pathway, of assembly of the 60S subunit. Furthermore, we show that protection of uL18 does not require the formation of the canonical 60S subunit assembly intermediate of uL18, uL5, 5S rRNA, and the Rrs1 and Rpf2 assembly factors.

Materials and methods

Nomenclature for r-proteins

The nomenclature of r-proteins has been changed twice since 1997 [17, 18]. We use the 2014 universal nomenclature. In the figures, the 1997 protein names are also indicated after a slash.

Strains and growth conditions

All strains are derived from S. cerevisiae BY4741. In each strain one gene encoding r-proteins eS4, eS6, uS17, eS19, eS31, eL40, or eL43, or the 60S assembly factors Rrs1, or Rpf2 was expressed exclusively from the GAL1/10 promoter (S1 Table). These strains are named P_gal-xx, where xx is the name of the protein expressed from the gal promoter. In the experiment shown in Fig 1B, P_gal-eL43 was transformed with a plasmid carrying a gene for uL18-FLAG expressed from the constitutive RpS28 promoter (Philipp Milkereit, personal communication).

Fig 1 — (A) The uL18/L5 reactive band seen close to the top of the sucrose gradient after repressing eL43/L43 or eL40/L40 formation (Figs 2 and 3) is absent after repressing uL18/L5 synthesis. P_gal-uL18/L5 was grown in galactose medium and shifted to glucose medium. A lysate prepared after repression of uL18/L5 gene for 13.5 hours was fractionated on a sucrose gradient and consecutive fractions from the top of the gradient and the 60S-80S ribosome peaks were analyzed by western blot stained with anti-uL18/L5. (B) Distribution of FLAG-tagged uL18/L5 (uL18/L5-FLAG) in sucrose gradients loaded with lysates prepared before and after repressing eL43/L43 synthesis. P_gal-eL43/L43 was transformed with a plasmid harboring a constitutively expressed gene for uL18/L5-FLAG. The resulting strain was grown in galactose medium and shifted to glucose medium for 16 hours. Lysates prepared from cells before and after the shift were fractionated on sucrose gradient and aliquots of consecutive fractions from the top of the gradient and the 60S-80S peaks were analyzed for content of FLAG-tagged protein by western blot. The western blots in this figure were not cropped. M: Molecular weight markers/1000. CE: Crude cell Extract.

Cells were grown at 30°C with shaking in YEP-galactose medium. At OD₆₀₀ of 1.0–1.3 (about 2x10⁷ cells per ml), the culture was shifted to YPD (glucose) medium by diluting the galactose culture with 10 volumes of prewarmed glucose medium (starting OD₆₀₀ of 0.1–0.15). The glucose culture was then grown for 2–3 doubling times until a desired cell density (OD₆₀₀ 0.8–1) was reached. All strains have a doubling time of 1.5–2.0 hours in galactose, but the growth rate gradually decrease in a strain-specific manner after the shift to glucose medium due to the repression of r-protein genes [11]. The actual time each culture grew in glucose medium is indicated on the figures. Examples of growth curves and sucrose gradient A²⁶⁰ profiles of crude extracts before and after the shift are shown in [11]. As shown previously a 55S ribosomal particle derived from the 60S accumulates forms beginning about 4 hours after the repression of 40S r-protein genes [11]. Here we have included the uL18 in the 55S peak as part of the “60S-80S ribosome fractions”.

Cell lysis and fractionation

Cells were harvested by centrifugation at 8000 rpm for 10 minutes and washed once with 10 mL ice-cold RNase free water and stored at -20°C until further use. Procedures for lysis and sucrose gradient centrifugation were described previously [11]. Each sucrose gradient was loaded with 20 A²⁶⁰ units of crude cell extract cleared of debris. After centrifugation, the gradient was fractionated into 0.5 ml fractionations and 45 μl of the indicated fractions was used for western blot analysis.

Western analysis and antisera

Western blots [11] were probed with rabbit polyclonal antisera prepared for our laboratory by Covance (Princeton, New Jersey, USA) using synthetic peptides with the sequence of 20–22 N-terminal amino acids of uS4, uL4, uL5, and uL18 as antigens. Each antiserum was titrated against increasing amounts of whole cell extract on western blots (see Figure S6 in ref [11] (https://www.life-science-alliance.org/content/2/2/e201800150#nogo). Based on the amount of lysate loaded on each sucrose gradient and the number of sucrose gradient fractions containing r-proteins, we determined that antisera are in excess over the r-proteins on our western blots. Monoclonal anti-FLAG antibody was purchased from Thermo-Fisher (catalog number MA1-91878). Blots were scanned in a Storm 860 Imager System (Molecular Dynamics) and the bands were quantified using ImageJ or Adobe Photoshop CC 2019.

As described in Results, western blots probed with anti-uL18 reacted with two proteins close to the top of sucrose gradients loaded with extracts of certain strains harvested after, but not before, a shift from galactose to glucose medium. One of these proteins co-migrated during electrophoresis with the ribosomal uL18 in the 60S-80S fractions, while the other had a slightly lower electrophoretic mobility. To determine if any of these proteins actually are related to uL18, we shifted P_gal-uL18 to glucose medium for 13.5 hours and fractionated a lysate on a sucrose gradient. Fractions from the top and the ribosome peaks of the gradient were analyzed on a western blot. As seen in Fig 1A, there was no uL18 reactive band comigrating with ribosomal uL18 after repressing the uL18 gene, even though the band was seen after repressing either eL40 or eL43 synthesis (see below). This confirms that the comigrating band at the top of the gradient seen after abolishing the synthesis of a number of r-proteins, other than uL18, actually is uL18. However, the slightly slower band (marked with star in all figures) was present even after repressing uL18, indicating that it may not be related to uL18. To test this, we transformed P_gal-eL43 with a plasmid constitutively expressing FLAG-tagged uL18 (uL18-FLAG) in addition to the native uL18 chromosomal gene. After shifting this strain to glucose for 16 hours, a single band of uL18-FLAG, co-migrating with the uL18-FLAG band in the ribosomal fractions, appeared at the top of the gradient (Fig 1B), but no band corresponding to the starred band in blots stained with anti-uL18 was seen. From these experiments, we conclude that the band marked with a star in the blots stained with anti-uL18 is not related to uL18, but rather an unspecific protein that cross-reacts with our uL18 antiserum. This is also supported by the presence of the starred band after shifting the parent strain to glucose medium (Fig 2C).

Fig 2 — P_gal-eL43/L43, P_gal-eS4/S4, and the parent strain BY4741 were grown in galactose medium and switched to glucose medium for the indicated time. Whole-cell lysates were fractionated on sucrose gradients and the indicated fractions of the gradients were analyzed by western blots probed with antisera for r-proteins uL18/L5, uL4/L4, eS4/S4, and uL5/L11 as indicated at each blot. (A) P_gal-eL43/L43 after 6 hours in glucose medium. All fractions from the top of the gradient through the polysome region are shown. (B) P_gal-eS4/S4 after 8 hours in glucose medium. The panel shows sections cropped from a western blot loaded with aliquots of each fraction from the top of the gradient through the polysome region. The blot was first probed with anti-uL18/L5, then with a mixture of antisera for uS4/S9 and uL4/L4 without stripping. Finally, the bottom of the blot was probed with anti-uL5/L11. (C) The parent strain (BY4741) after 0 and 16 hours in glucose. Aliquots of consecutive fractions from the top of the gradient and the 60S-80S region were analyzed by western blot. The top panel shows the blot probed with a mixture of antisera for uL4/L4 and uS4/S9. The middle panel shows the same blot after it was probed further with anti-uL18/L5 without stripping. The bottom panel shows the same blot after it was probed further with anti-uL5/L11. Uncropped images are shown in S1 Fig. The bands marked with a blue star in some panels are not related to uL18/L5 (see Fig 1 in Material and Methods). CE: cell extract.

Quantification of extra-ribosomal uL18

The fraction of the total uL18 found at the top of the sucrose gradient, i.e. the extra-ribosomal uL18, was determined by quantitative western blots. In some experiments, all gradient fractions were subjected to quantification, but in other experiments, we analyzed only two fractions from the top of the gel and three fractions from the 60S-80S region of the sucrose gradient. To compare the two methods of quantification, we used western blots that include all sucrose gradients fractions and compared the results of quantifying (i) uL18 at the top of the gradient/total uL18 across the gradient, and (ii) uL18 in two fractions at the top of the gradient/the sum of uL18 in two top fractions and uL18 in three fractions from the 60-80S region (S2 Table). The results show that there is a good semi-quantitative agreement between the two approaches. Hence, we conclude that it is justified to use only selected fractions for comparing the amount of extra-ribosomal uL18 in different strains.

Protein molecular weight markers

Protein molecular weight markers were purchased from Thermo Fisher Scientific (cat 26616). Note that r-proteins always run slower in SDS gels than expected from their molecular weight.

Statistics

Pairwise t-test was used.

Results

Disruption of ribosome assembly

To specifically abolish the synthesis of individual essential r-proteins cognate to one or the other ribosomal subunit in S. cerevisiae, we used yeast strains in which the only gene for a given r-protein is transcribed from the GAL1/10 promoter. We refer to these strains as P_gal-xx, where xx is the name of the protein encoded by the gene under galactose control. In galactose medium, a full set of r-proteins is synthesized, but shifting the cells to glucose medium abrogates the synthesis of r-protein xx, which prevents assembly of the cognate ribosomal subunit [11].

Extra-ribosomal uL18 accumulates during repression of some 40S r-protein genes

To measure extra-ribosomal accumulation of uL18 and several other r-proteins upon repression of specific r-protein genes, we fractionated crude cell extracts on sucrose gradients and analyzed the sucrose gradient fractions on western blots probed with antisera specific to the 60S r-proteins uL18, uL5, uL4 and the 40S r-protein uS4. Fig 2A shows a western blot stained with anti-uL18 of fractions from a sucrose gradient loaded with an extract of P_gal-eL43 prepared 6 hours after shifting the culture from galactose to glucose medium. A band co-migrating with the ribosomal uL18 band in the gel was observed close to the top of the sucrose gradient. A second protein marked with a star and moving slightly slower also appeared. As described in Materials and Methods we confirmed that the protein that co-migrates with the ribosomal uL18 band indeed represents uL18, while the slightly slower moving protein is not related to uL18 (Fig 1). The appearance of uL18 at the top of the gradient after repressing the eL43 gene was confirmed by transforming P_gal-eL43 with a plasmid carrying a constitutive gene for FLAG-tagged uL18. As seen in Fig 1B, the uL18-FLAG accumulated at the top of the gradient after the shift to glucose medium, but not before the shift (Fig 1B). Thus, the experiments in Figs 2A and 1B show that uL18 accrues outside ribosomal particles during the repression of uL43 synthesis. An extra-ribosomal pool of uL18 was also seen after repressing uL5 synthesis; see note about nomenclature in Materials and Methods [14].

To determine if abolishing expression of 40S r-proteins also triggered extra-ribosomal uL18 accumulation, we repressed the synthesis of eS4, a protein incorporated into the 40S precursor particle (pre-40S) early in the assembly process [19]. After 8 hours of repression, extracts were analyzed by sucrose gradient centrifugation and western blot. Unexpectedly, we found a build-up of extra-ribosomal uL18 at the top of the sucrose gradient, but no uL4, uL5 or uS4 was found outside of the ribosome peaks (Fig 2B). Additionally, the parent strain BY4741 did not accumulate extra-ribosomal r-proteins whether grown in galactose or glucose, as expected since assembly of both subunits proceeds uninterrupted in the parent whether it grows in galactose or glucose medium (Fig 2C). Overall, the results in Fig 2 show that repression of the eS4 gene with ensuing disruption of 40S assembly generates a pool of extra-ribosomal uL18. Extra-ribosomal accumulation of uL18 is thus not specific to interference with 60S assembly.

We then tested if repression of the genes for 40S r-protein genes eS6, uS17, and eS19 also cause accumulation of extra-ribosomal uL18. The eS31 protein was chosen because it is incorporated into the pre-40S late in the assembly process [20] (as opposed to eS4, which is incorporated early), and proteins eS6, uS17, eS19 were chosen because mutations in the orthologous human genes have been implicated as causing diseases [21–24]. Repression of eS4, eL40, and eL43 was used as controls. Since 60S particles are largely stable after repression 40S r-protein genes and the cultures grow at somewhat different rates after the shift to glucose [11], we reasoned that quantifications of extra-ribosomal uL18 would be more comparable if the density of all cultures were allowed to increase by the same factor after the shift to glucose medium. Accordingly, we harvested the cultures after the OD₆₀₀ had increased at least four-fold during incubation in glucose rather than at a specific time after the change of carbon source. As shown in Fig 3A we found uL18 at the top of the gradient for all strains, except P_gal-eS31, but the strength of the bands varied. To estimate the fraction of uL18 present at the top of the sucrose gradient we quantified uL18 in two top fractions from the sucrose gradient and three fractions in the 60S-80S ribosome peaks (see Methods and materials for a justification of this approach). The results showed that repression of eS4 synthesis generated approximately as much extra-ribosomal uL18 as did the repression of the two 60S r-protein genes while repressing other 40S r-protein genes generated smaller amounts of extra-ribosomal uL18 (Fig 3B). Furthermore, the amount of extra-ribosomal uL18 differed significantly after repressing the various 40S r-protein genes (Fig 3C).

The extra-ribosomal uL18 pool reaches a steady-state

Since the pool size of the extra-ribosomal uL18 pool differed between strains (Fig 3B), we questioned whether the pool changes with time. Accordingly, we compared the uL18 pools in P_gal-eL43, -uS4, and -eS31 harvested at different times after the shift to glucose medium. The extra-ribosomal uL18 pool increases by about 2-fold between 4 and 6 hours of repression of either eS4 and eL43, but is constant between 6 and 8 hours, suggesting that the extra-ribosomal uL18 pool reaches a steady-state (Fig 4A and 4B) by the time the cultures have gone through about two doublings after the shift to glucose medium. Furthermore, the pool of extra-ribosomal uL18 does not rise above the statistically significant level even after 17 hours of repressing eS31 synthesis (Fig 4C).

Fig 4 — P_gal-eS4, -eL43 and -eS31 were grown in galactose medium and shifted to glucose medium. At the indicated times after the shift, extra-ribosomal uL18 was quantified. (A) P_gal-eS4 and (B) P_gal-eL43. Consecutive fractions from the top and the 60S-80S region of the gradient were analyzed. The blots were scanned and quantified using Photoshop CC 2019. The ratio of uL18 found in the top fractions relative to uL18 in all fractions on the western blot was calculated for each time point and normalized to the value for the 4-hour sample. (C) P_gal-eS31. All fractions from the top of the sucrose gradient through the polysome region are shown for the 8-hour sample. For the 9.5 and 17-hr samples, consecutive fractions from the top and the 60S-80S region of the sucrose gradient are shown. See S3 Fig for uncropped blots. CE cell extract.

uL18 accrues due to interference with subunit assembly, not degradation of mature subunits

Maintenance of the extra-ribosomal uL18 pool requires protein synthesis

We have previously shown that 60S formation continues during the repression of 40S assembly and slow turnover of the 60S begins a few hours after 40S r-proteins have been repressed [11]. Thus, there are two possible principle sources of extra-ribosomal uL18: modification of 60S assembly and breakdown of mature 60S subunits. To distinguish these possibilities, we investigated if blocking protein synthesis with cycloheximide change the amount of extra-ribosomal uL18. If the extra-ribosomal uL18 stems from degradation of preexisting ribosomes, cycloheximide should not affect the pool of extra-ribosomal uL18, but if the extra-ribosomal uL18 is generated in the assembly process, the formation depends on continual protein synthesis and addition of cycloheximide should reduce the pool of extra-ribosomal uL18. Hence, we grew P_gal- eL43 in galactose and shifted it to glucose medium for 6 hours. At this time approximately 50% of the total uL18 was found at the top of the gradient (Fig 4A(i)). The culture was then split and cycloheximide was added to one aliquot to inhibit total protein synthesis, while nothing was added to the other part. After 4 hours of additional culturing, both aliquots were harvested and analyzed for extra-ribosomal uL18. No uL18 band was seen at the top of the gradient after cycloheximide inhibition of protein synthesis (Fig 4A(ii)), while the level of extra-ribosomal uL18 was unchanged in the sample without the drug (Fig 4A(iii)).

Inhibition of protein synthesis in P_gal-eS4 gave a similar result. Cycloheximide was administrated for 15 and 45 minutes to a culture four hours after the shift from galactose to glucose. While no change was seen after 15 minutes, the extra-ribosomal uL18 level was reduced by about 50% after 45 minutes with cycloheximide (Fig 5B). Together the experiments in Fig 5A and 5B show that the extra-ribosomal uL18 is depleted, if it is not replenished by new synthesis, indicating that extra-ribosomal uL18 is generated during 60S assembly rather than degradation of mature 60S subunits.

Fig 5 — (A) Cycloheximide decreases the pool of extra-ribosomal uL18/L5 during the repression of a 60S r-protein gene. Six hours after shifting P_gal-eL43/L43 from galactose to glucose medium, cycloheximide was added to an aliquot of the culture (final concentration: 100 μg/ml), while the culturing of another aliquot of the culture was continued without addition of the drug. Both aliquots were harvested 10 hours after the shift. Whole-cell extracts were analyzed by sucrose gradients and western blots of aliquots of all sucrose gradient fractions. (i) P_gal-eL43/L43 6 hours after the shift of media, (ii) Pgal-eL43/L43 incubated with cycloheximide added 6 hours after the media shift and harvested 10 hours after the shift. (iii) P_gal-eL43/L43 incubated for 10 hours in glucose without cycloheximide. All fractions from the top through the polysome region of the sucrose gradient are shown. (B) Cycloheximide also decreases the pool of extra-ribosomal uL18/L5 during the repression of a 40S r-protein gene. P_gal-eS4/S4 was grown in galactose medium and shifted to glucose medium. Cycloheximide (100 μg/ml) was added to the culture 6 hours after the shift and cells were harvested 0, 15 and 45 minutes after addition of the drug. Aliquots of one or two fractions from the top of the gradient and two fractions from the 60S-80S peaks were analyzed by western blots probed with anti-uL18/L5. Consecutive fractions from the top and the 60S-80S region of the sucrose gradient were shown. M Molecular weight markers in kD. 35 and 40 kD are identified. See S2 Fig for the full molecular weight ladder.

No extra-ribosomal uL18 accumulates during degradation of cytoplasmic ribosomes

To determine if extra-ribosomal uL18 also accumulates during degradation of cytoplasmic ribosomes, we inhibited TOR-activity by rapamycin. This stops rRNA synthesis and causes a significant degradation of cytoplasmic ribosomes [25]. Rapamycin (0.2 μg/ml) was added to Pgal-eL43 in growing in galactose medium (i.e. eL43 synthesis is not interrupted) for 4 hours before a lysate was analyzed by sucrose gradient centrifugation and western blot. As seen in Fig 6, no uL18 was seen at the top of the gradient after 6 hours. Since there is significant cytoplasmic degradation of ribosomes during rapamycin inhibition of TOR [25], extra-ribosomal uL18 buildup would have been expected, if it comes from ribosome degradation. We did not see that, suggesting that the degradation of mature ribosomes does not generate extra-ribosomal uL18.

Fig 6 — Rapamycin was added to Pgal-eL43/L43 growing in **galactose** medium (no shift to glucose) and 4 hours later an extract was fractionated on a sucrose gradient centrifugation and aliquots of fractions were analyzed on a western blot developed with antisera specific to uL18/L5 and uL4/L4. All fractions from the top through the polysome region of the sucrose gradient are shown.

Stabilization of extra-ribosomal uL18 does not require Rrs1 or Rpf2

We further investigated the origin of extra-ribosomal r-proteins by depleting each of the ribosomal assembly factors Rrs1 and Rpf2 that combine with uL18, uL5, and 5S rRNA before docking in the precursor 60S particle (pre-60S) [26]. If the protection of uL18 from rapid degradation requires formation of the full pre-docking complex, no extra-ribosomal uL18 should accumulate during inhibition of the two assembly factors. However, Fig 7 shows that depleting either Rrs1 or Rpf2 increased the pool of extra-ribosomal uL18 in agreement with the effect of mutating the RRS1 gene [27]. This shows that stabilization of extra-ribosomal uL18 does not require the formation of the complete uL18-uL5-5S rRNA-Rrs1-Rpf2 particle from. This is also supported by the fact that extra-ribosomal uL5 does not accumulate proportionally to uL18 during abrogation of eS4 or eL40 synthesis (Fig 2B and S2 Fig). Furthermore, the buildup of extra-ribosomal uL18 concurs with the conclusion that accrual of extra-ribosomal uL18 stems from the 60S assembly process.

Fig 7 — P_gal-Rrs1 and -Rpf2 were grown in galactose medium and shifted to glucose medium for 16 hours. Whole-cell extracts were analyzed by sucrose gradient centrifugation and aliquots of two or three fractions from the top of the gradient and two fractions from the 60S-80S peaks were analyzed by western blots developed with antiserum specific to uL18/L5. Consecutive fractions from the top and the 60S-80S region of the sucrose gradient were shown.

Discussion

Inhibition of 40S assembly changes 60S assembly kinetics

Ribosomal proteins are rapidly turned over unless they are incorporated into ribosomes [10, 28, 29]. However, uL18 escapes this degradation and accumulates in extra-ribosomal complex(es) when the synthesis of 60S r-proteins is curtailed as shown in Fig 2 and [14]. Here we have shown that extra-ribosomal uL18 also builds up during repression of several 40S r-protein genes (Figs 2 and 3). This was unexpected because abrogation of 40S r-protein synthesis specifically halts the assembly of the 40S subunit, while assembly of the 60S subunit continues [11]. Thus, the build-up of the extra-ribosomal uL18 pool reveals a novel form of interaction between 40S and 60S subunit formation: abolition of 40S subunit synthesis changes the kinetics of the individual steps in 60S subunit assembly, but has little effect on the overall rate of 60S formation.

Several of observations indicate that extra-ribosomal uL18 comes from the 60S assembly process rather that degradation of mature cytoplasmic 60S subunits. First, maintenance of the pool of extra-ribosomal uL18 requires continual protein synthesis, whether provoked by disruption of the formation of the 60S or the 40S subunit (Fig 5A and 5B). Second, no extra-ribosomal ul18 is seen during administration of the TOR inhibitor rapamycin (Fig 6), which causes significant degradation of cytoplasmic ribosomes [25]. Third, depletion of either of two nuclear 60S ribosome biogenesis factors leads to a buildup of extra-ribosomal uL18 (Fig 7). The formation of extra-ribosomal uL18 during 60S assembly also concords with the mapping of extra-ribosomal uL18 to the nucleus where most ribosome formation takes place [14].

The docking of uL18 into the nascent 60S subunit involves the formation of a uL18-uL5-5S rRNA-Rrs1-Rpf2 complex [26], but, interestingly, two observations show that the protection of extra-ribosomal uL18 against rapid turnover does not require the formation of this complex in its entirety. This conclusion is based on three findings: First, here we show that repression of the Rrs1 or Rpf2 genes cause the buildup of an extra-ribosomal uL18 pool (Fig 7). Second, extra-ribosomal uL5 does not accrue in parallel with extra-ribosomal uL18 (Fig 2B and S2 Fig). In agreement with this, experiments published by the Woolford lab showed that extra-ribosomal uL18 accumulates when the uL5 (alias L11) synthesis is abolished [14] [Note that uL5/L11 was named L16 when this paper was published.].

Co-assembly of 40S and 60S precursor ribosomes may account for the interaction between the ribosomal assembly processes

Our results can be interpreted mechanistically in the context of current models for rRNA processing and ribosome assembly. During rapid growth of yeast cells, the nascent RNA Polymerase I pre- rRNA is cleaved at the A2 site in the Internal Transcribed spacer 1 (ITS1; Fig 8A) when the RNA polymerase has transcribed about half of the 60S-specific sequences (co-transcriptional pre-rRNA cleavage) [30]. Furthermore, several steps towards forming the ribosomal precursor particles occur before pre-rRNA cleavage, including significant pre 40S compaction and emergent pre-60S compaction [30] and association of many ribosomal assembly factors and at least some r-proteins with the pre-rRNA [19, 31] (Fig 8B(i)). If the formation of the pre-40S (90S) is inhibited, the cleavage of the pre-rRNA is delayed until transcription is completed (post-transcriptional cleavage) and there is essentially no compaction of either the pre-40S or pre-60S (Fig 8C(i)) [30, 32–34].

Fig 8 — (A) Map of the long rRNA precursor gene transcribed by RNA polymerase I. ETS: External Transcribed Spacer; ITS: Internal Transcribed Spacer; A2 cleavage site separating the pre-rRNA into subunit-specific parts. (B) Co-transcriptional rRNA cleavage during unrestricted 40S assembly. (i) Schematic representation of co-transcriptional rRNA cleavage and ribosomal assembly as revealed by electron micrographs (Miller Spreads) [30]. The 18S parts of the transcript is in red, 5.8S in turquoise, and 25S in blue. “Wiggled” lines: uncompacted rRNA complexed with assembly factors and early assembly r-proteins. Filled circles: Compacted rRNA-protein complexes; the intensity of the red color indicates the density (compaction) of the complex. (ii) Kinetic model for formation of the uL18-5S rRNA complex and incorporation into the pre-60S during unrestrained 40S assembly. We propose that the rate constant for uL18/5S rRNA binding to the pre-60S is high in this condition. Therefore, uL18 is rapidly incorporated into the pre- 60 and uL18 does not accumulate outside the ribosome. (C) Post-transcriptional cleavage during inhibited 40S assembly. (i) Schematic illustration of electron micrographs of rRNA genes during repression of 40S r-protein genes. Pre-rRNA cleavage happens after transcription termination and compaction of the pre-40S and pre-60S is essentially absent. We suggest that absence of 40S compaction delays cleavage and changes the folding of the 60S-specific rRNA. (ii) Kinetic model for formation of the uL18-5S complex and incorporation into the pre-60S. We propose that the affinity (rate constant) of uL18-5S rRNA binding to the pre-60S is reduced due to the alternate folding and, possibly, alternate assembly pathway during post-transcriptional cleavage. Therefore, the rate of incorporation of uL18 into the pre-60S is slow leading to formation of an extra-ribosomal uL18 pool.

To explain our results within this framework, we propose that the co-transcriptional compaction and assembly of the pre-40S during uninhibited (fast) growth promotes the folding the 5’ part of the 60S rRNA, early assembly of the pre-60S, and the co-transcriptional cleavage. Since interference with 40S assembly prevents both co-transcriptional cleavage and 40S compaction [30] (Fig 8C(i)), this implies that the rRNA folding and pre-60S structure is different during co- and post-transcriptional cleavage.

We further posit that the pre-60S formed during post-transcriptional processing has a lower affinity for uL18-5SrRNA complex than does the pre-60S formed during the co-transcriptional cleavage pathway, implying that the rate constant for binding of the uL18-5S rRNA to pre-60S is lower if the pre rRNA is cleaved after transcription termination. Therefore, the switch from co-transcriptional to post-transcriptional cleavage initially reduces the rate of the incorporation of the uL18-5S rRNA complex into the pre-60S. Since the rate of r-protein and rRNA synthesis is not reduced by the inhibition of assembly, the concentration of extra-ribosomal uL18-5S rRNA increases, causing the rate of uL18-5S rRNA incorporation into the pre-60S to rebound (rate = rate-constant x concentration of uL18-5S rRNA) in accordance with the continued assembly of the 60S subunit. Overall, our model thus explains why the uL18 accumulates outside of the ribosome during post-transcriptional cleavage, while 60S assembly continues relatively unabated. This bears resemblance to changes in the kinetics of 60S assembly provoked by mutations in Escherichia coli uL4. In this case, the mutations slow down one or more steps in the 60S assembly pathway causing a rise in 60S assembly intermediates, visible as new peaks in sucrose gradients, while the formation of mature 60S subunits continues [35].

Whereas we think that our proposed model is likely to be part of the mechanism for regulating the uL18 extra-ribosomal pool, other factors may also change the 60S structuring process and the kinetics of 60S assembly. For example, depletion of either RNase MRP (cleaving at the A3 site in ITS1), Rat1 5’>3’ exonuclease, and depletion of nutrients affect the balance between co- and post transcriptional cleavage [30, 32, 33]. However, the effect of such parameters on the accumulation of extra-ribosomal r-proteins is not known at the present time.

Interactions between 40S and 60S formation is likely stronger in metazoans than in yeast, because a larger fraction of pre-rRNA is cleaved into subunit-specific pieces after completion of transcription (“post-transcriptionally rRNA processing”) in metazoans than in fast-growing yeast cells. The difference between the ratio of co-transcriptional and post-transcriptional is evident from Northern blots of rRNA processing intermediates in the two types of organisms: full length rRNA precursor transcript is more prevalent relative to other processing intermediates in mammalian cells (e.g. [36]) than it is in fast-growing yeast cells (e.g. [11]).

While the vast majority of the r-protein mass is tied up in physical ribosomes, extra-ribosomal r-proteins are thought to be involved in regulation of cell growth and other functions, at least in metazoan cells. For example, r-proteins from both ribosomal subunits have been identified as cancer drivers [37]. The mechanism for r-protein-mediated regulation of growth and cell fate presumably involves binding of r-proteins to regulators of growth and the progression of the cell cycle [38–41]. The functions of extra-ribosomal proteins have been intensely investigated, but little is known about the origin of the extra-ribosomal r-protein pools. Since the major features of pathways for ribosomal assembly are evolutionarily conserved, we suggest that our analysis in the yeast model organism also contributes to understanding the complexity of how ribosome assembly impacts regulation of growth in metazoan cells.

Supporting information

S1 Fig. Uncropped versions of images in Fig 2A and 2B.

(PDF)

Click here for additional data file.^{(2.1MB, pdf)}

S2 Fig. Uncropped versions of images in Fig 3A.

CE whole cell extract. M molecular weight markers in kD.

(PDF)

Click here for additional data file.^{(943.1KB, pdf)}

S3 Fig. Uncropped versions of images in Fig 4.

(PDF)

Click here for additional data file.^{(404.8KB, pdf)}

S1 Table. Stains used.

(XLSX)

Click here for additional data file.^{(11.8KB, xlsx)}

S2 Table. Quantification of extra-ribosomal uL18.

The fraction of uL18 at the top of the sucrose gradient was determined by (i) quantifying uL18 in all fractions, or (ii) quantifying uL18 in two top fractions and three fractions from the 60S-80S peaks. Photoshop CC 2019 was used for the quantification.

(XLSX)

Click here for additional data file.^{(9.4KB, xlsx)}

Acknowledgments

We thank Drs. Philipp Milkereit (University of Regensburg, Germany) and John Woolford (Carnegie Mellon University, Pennsylvania, USA) for strains and plasmids. We also thank Benedikte Traasdahl for help with the manuscript.

Data Availability

All relevant data are within the manuscript and its Supporting Information files.

Funding Statement

This study was funded by grant number 0920578 from the National Science Foundation, USA to JM Zengel and LL, and a gift from The Benelein Technologies, LLC to LL (no grant number). Further funding was provided by an internal appropriation from the University of Maryland, Baltimore County to LL (no grant number). The funders had no role in study design, data collection, and analysis, decision to publish, or preparation of the manuscript.

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PLoS One. doi: 10.1371/journal.pone.0222479.r001

Decision Letter 0

Sander Granneman

20 Sep 2019

PONE-D-19-24366

Interaction between the assembly of the ribosomal subunits: Disruption of 40S ribosomal assembly causes accumulation of extra-ribosomal 60S ribosomal protein uL18/L5

PLOS ONE

Dear Lasse,

Thank you for submitting your manuscript to PLOS ONE. Your manuscript was reviewed by two experts in the ribosome biogenesis field. As you can see from the reviews, their comments were generally very positive, however, they also highlighted a number of inconsistencies that need further clarification. In particular Reviewer #2 raised a number of important points regarding the quantification of the data as well as comparison with previously published work. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

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Reviewer #1: This manuscript by Rahman, Shamsuzzaman and Lindahl is an interesting follow-up to a previous paper from the Lindahl group showing interdependence of assembly of large and small ribosomal subunits in yeast. Here they demonstrate that ribosomal protein uL18, aka L5, accumulates outside of ribosomes when assembly of either large or small subunits is blocked by depleting a ribosomal protein from one or the other subunit. This was visualized by gradient sedimentation of L5 in extra-ribosomal fractions. Of interest is how varying effects of depletion of different r proteins reflects the order and mechanism of protein and subunit assembly, including effects resulting from post-transcriptional assembly.

The conclusions are sound and the results are interesting. However, the story might be more impactful if the following were added:

(1 Include a figure showing in more detail which SSU and LSU r proteins are assembled early and which much later, and thus why depletion of some might have a greater effect on L5. This is explained in the text but would be clearer to nonaficionados if a figure/cartoon were added.

(2 L5 accumulates in fractions at the top of the gradient. Are 5S rRNA, L11, Rpf2 and Rrs1 also present in the same complex with L5? CO-IP from gradient fractions will demonstrate whether this is the case. This is potentially important since the authors report accumulation of extraribosomal L5 when Rpf2 or Rrs1 are depleted (Fig.4D).

Minor issues

(1 Some figures need to be better labeled and there are numerous places where a word or two need to be added or changed.

Line 56: Aren’t some r proteins not essential, i.e. not completely required for subunit assembly?

Line 119 and elsewhere: a detail perhaps: is the symbol in the figures a star or an asterisk?

Line 151 and elsewhere: the term GAL1/10 promoter should be capitalized and italicized.

Line187: what is meant by Northern blots of fractions were probed? Don’t you mean just “blots”?

Line 367: is ther a word or two missing?

Figures: Does more than one lane of blot data correspond to consecutive gradient fractions, e.g. lanes 3,4 and 5,6 in Fig.1? If so, please explain in the figure legends.

Figure 2B: the text states that L11 was assayed, but it is not shown.

(2 In the Introduction, lines 64-66, the authors need to correct their description of the experiment done by Dehmukh et al. They got trapped by the nomenclature monster! R protein L16 was depleted, which is NOT the same as uL5, as stated. This is important because uL5 aka L11 is in an assembly subcomplex with uL18 aka L5, whereas L16 is not.

Reviewer #2: Rahman et al. report in the manuscript PONE-D-19-24366 on the results of a series of experiments which provide evidence for the extra-ribosomal accumulation of the large ribosomal subunit protein uL18 upon inhibition of small ribosomal subunit assembly in S. cerevisiae. Their conclusions are based on quantitative interpretation of western blotting analysis after sucrose gradient fractionation of cellular extracts prepared from yeast ribosomal protein expression mutants.

In this regard the exact approach chosen might be better described. The authors refer to reference 9, in which an indirect immuno-detection is described using an enzymatic reaction for secondary antibody visualisation. These detection approaches tend to produce saturation artefacts and it might be therefor important to know whether titration of a reference sample was used in the individual western blots to determine the dynamic range of the detected signal. For the sucrose gradient fractionation, in several experiments all fractions were analysed. In these cases the ribosomal proteins could be detected in four to six of the “Top” fractions and in up to eleven of the faster sedimenting “Ribosomes” fractions. In several other analyses only one or two of the “Top” fractions and either two or three of the “Ribosomes” fractions of the sucrose gradients were analysed to deduce the ratio of extra-ribosomal to ribosomal r-proteins as uL18. How was it ensured that these fractions contain all of the extra-ribosomal and ribosomal pools of uL18, or are representative for them?

The western blot results shown in Fig 3A , 3C(iii) and 4D look quite cropped. That complicates interpretation of the data, especially since the uL18/L5 antibody used in this study cross-reacts with a protein running just a bit slower than uL18/L5. The identity and running behavior of the band detected in the “Top” fractions in 3A for the parental strain is, for example, in the actual representation for me ambiguous. Thus, less cropped figures might help the reader in these cases.

For several of the experiments (Fig 3A +B) I could not find the exact incubation times in glucose containing medium which were applied to repress the expression of individual r-proteins. In the materials and methods section it is stated that cultures were shifted for 6 to 21 hours to glucose containing medium. In one experiment (Fig. 2) the control strain is shifted to glucose containing medium for a different time period (16 hours) than the two r-protein expression mutants analysed (6 hours and 8 hours). Why was that done, and can we be sure that this might not affect the outcome of the experiments? At least from the data shown in Fig 3C for Pgal-eS31 I got the impression that the level of free uL18/L5 decreases with prolonged incubation times in glucose containing medium.

Recently, changes in levels of proteins in several large and small subunit r-protein expression mutants were measured by mass spectrometry proteome wide (https://doi.org/10.1016/j.molcel.2018.10.032). Did the authors analyse these published datasets for a possible excess of uL18/L5 over other large subunits proteins as ul4/L4 or uL5/L11? That might give further support to the authors conclusions by an analysis performed with an independent experimental approach.

A few other comments and remarks:

1) Line 52: “..also requires in excess of 250 ribosomal assembly factors”

Does that refer to the stochiometry of components?

2) Line 54: “..while others are specific to the formation of one the ribosomal subunits”

of one of ?

3) Line 110: “..western blots probed anti-uL18 revealed..”

probed with?

4) Line 124: “…but no band corresponding asterisked band in…”

5) Fig 1, labelling: Ribs or Rbs ?

6) Line 163: Why was the strain Pgal-e43 chosen for these experiments?

7) Line 164: “A band co-migrating with the ribosomal uL18 band ..”

was that inferred by some other detection method, as for example by mass spectrometry, or by the expected running behavior of uL18? Does the running behaviour of the detected band fit with the predicted size of uL18?

8) Line 166: “.. we confirmed that band that..”

that the band?

9) Line 174: “This was anticipated, since repression of the 60S r-protein uL5 is known to provoke a buildup of extra-ribosomal uL18..”

uL5 is together with uL18 part of the 5S RNP, in this regard I am not sure whether that specific example allows a straight forward prediction for what is to be expected upon expression shut down of an unrelated large subunit r-protein as eL43.

10) Line 177, Fig 2.: “Repression of several 40S r-protein genes causes … “

Several 40S r-protein genes? In Fig 2 is just an analysis shown for eS4.

11) Line 177, Fig 2.: “..causes accumulation of extra-ribosomal uL18/L5, but not extra-ribosomal uL5/L11 …”

How was the specificity analysed of the antibody used for detection of uL5?

12) Line 187: “(C) Northern blots of fractions from ..”

Western blots of ..?

13) Line 195: “.. was found outside in the ribosome peaks..”

outside of ?

14) Line 198: “.. parent whether it grows glucose and galactose medium..”

parent strain? grows in ?

15) Line 199: “..the results in Fig 2 shows that..”

show?

16) Lines 202 - 205: Why were these large and small subunit protein expression mutants chosen?

17) Line 260: “No uL18 band was seen at the top of the gradient 260 after cycloheximide inhibition of protein synthesis (Fig 4A(ii))..”

The western signals shown in Fig 4A (ii) look a bit blurry. Was a technical replicate of this experiment performed?

18) Line 296: “To investigate if extra-ribosomal uL18 also accumulates when rRNA synthesis th is inhibited by the TOR-targeting drug rapamycin”

th ? Rapamycine has also quite a drastic effect on the r-protein mRNA levels and thus on r-protein production. A conditional mutant of a gene coding for an RNA polymerase I subunit might have addressed the question asked more clearly.

19) Lines 310 and following: I was wondering if the authors also analysed the possible accumulation of uL18 bound 5S rRNA?

20) Line 332: “In the extremes, abolishment of eS4synthesis..”

eS4 synthesis?

21) Line 332 and following: “In the extremes, abolishment of eS4synthesis generates a response similar to that seen during repression of two 60S r-protein genes, while extra-ribosomal uL18 is borderline detectable during abrogation of eS31 synthesis (Fig 3). This gradient correlates with the abundance of 40S r-proteins in the 90S ribosomal particle, an early 40S assembly intermediate [19], suggesting that preventing early steps of pre-40S precursor assembly have the strongest effect on accumulation of extra-ribosomal uL18.”

Was the subunit imbalance phenotype compared between expression mutants of eS4 and eS31? The respective penetrance of the small subunit synthesis phenotype might well correlate with the observed effects on uL18. The authors suggest in the abstract and here in the discussion that specifically inhibition of early steps in small subunit assembly leads to the observed effects on uL18. That assumption would have been much strengthened if other 40S r-protein expression mutants with late 40S maturation phenotypes which were not detected in early 40S precursors would have been analysed (e.g. expression mutants of uS2, uS3, uS5 or others). I would also see the authors attempt to interprete the data from reference 19, Fig 7, in regard to the “abundance” of r-proteins in 90S pre-ribosomes as inappropriate, since the authors of reference 19 for probably good reasons use a cut-off to just deduce the presence of the respective proteins.

22) Line 348: “Since two 60S r-proteins (uL4 and uL24) bind to Domain 1 ..”

It is unclear to me why to list these two r-proteins here, but not other r-proteins which clearly also bind to LSU rRNA domain 1.

23) Line 367: “Since the major features of pathways for ribosomal assembly evolutionarily conservation, …”

24) Line 373: “The difference between the ratio of co-transcriptional and post-transcriptional is evident from ..”

Insert here “processing”?

25) Line 351 and following: “We therefore posit that the simplest explanation for the buildup of extra-ribosomal uL18 during inhibition of 40S assembly is that the folding of the 60S part of the early rRNA transcript is influenced by 40S r-proteins that bind to rRNA prior to separation of the subunit moieties of the emerging rRNA transcript.”

I am not sure whether this is really the simplest explanation. The effects described here were observed after rather long r-protein depletion times (6 -21 hours according to Materials and Methods). Effects on small subunit synthesis start to be detectable much earlier (after one to two hours in RNA pulse analyses) and after 6 hours and more depletion times quite a massive subunit imbalance can be established in small subunit r-protein expression mutants (see for examples the authors own publication in Life Science Alliance, 2019). That, together with the clear reduction in cellular amounts of functional ribosomes can have various consequences on the balanced production of each of the other ribosomal proteins, including the ones of the large subunit. Did the authors also test effects on extra-ribosomal uL18 accumulation after shorter incubation times in glucose medium at which effects on 40S production just start to be established (1-2 hours)? That might help to distinguish if the observed effects on uL18 are primary consequences of an altered early SSU maturation state or due to secondary effects on the translation status of the cell. Related to this point, see also point 21 in regard to the authors choice of a conditional eS31 expression mutant to control for effects on uL18 by a late SSU assembly defect.

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PLoS One. 2020 Jan 27;15(1):e0222479. doi: 10.1371/journal.pone.0222479.r002

Author response to Decision Letter 0

22 Dec 2019

Rebuttal for manuscript [PONE-D-19-24366]

We thank the reviewers for constructive criticisms. We have extensively revised the manuscript to accommodate the reviewer’s questions and suggestions. We hope that these changes will make the manuscript acceptable for PLOS one.

We agree that some of the additional experiments suggested might add interesting aspects to the manuscript. Unfortunately, logistic circumstances make further experiments impossible.

Good suggestion. We have added a model figure (Fig 8) and revised the text to coordinate it with the new figure.

(2 L5 accumulates in fractions at the top of the gradient. Are 5S rRNA, L11, Rpf2 and Rrs1 also present in the same complex with L5? CO-IP from gradient fractions will demonstrate whether this is the case. This is potentially important since the authors report accumulation of extra-ribosomal L5 when Rpf2 or Rrs1 are depleted (Fig.4D).

As indicated above, additional experiments are not possible. However, as summarized in the revised manuscript, our existing evidence excludes the possibility that protection of extra-ribosomal uL18 requires the assembly of the complete uL18, uL5, Rfp2, Rrs1, and 5S rRNA “pre-docking” particle.

Minor issues

(1 Some figures need to be better labeled and there are numerous places where a word or two need to be added or changed.

We have relabeled all figures according to the reviewer’s suggestion.

Line 56: Aren’t some r proteins not essential, i.e. not completely required for subunit assembly?

Correct, a subset of yeast r-proteins are not essential for growth under standard laboratory conditions and are thus not required for assembly of a (minimally?) functional ribosome. We have revised the text to make the distinction between essential and non-essential r-proteins.

Line 119 and elsewhere: a detail perhaps: is the symbol in the figures a star or an asterisk?

Correct, the symbols at the non-uL18 band in the figures is a star. The text has been corrected to reflect this.

Line 151 and elsewhere: the term GAL1/10 promoter should be capitalized and italicized.

Thanks; corrected.

Line187: what is meant by Northern blots of fractions were probed? Don’t you mean just “blots”?

We mean “western blots”. The error was corrected.

Line 367: is ther a word or two missing?

Thanks. Text corrected.

Figures: Does more than one lane of blot data correspond to consecutive gradient fractions, e.g. lanes 3,4 and 5,6 in Fig.1? If so, please explain in the figure legends.

So indicated.

Figure 2B: the text states that L11 was assayed, but it is not shown.

uL5/L11 panel was added to Fig 2B (now Fig 2C).

We have retraced our way through the “nomenclature monster” and still end up with the L16 (anno 1993; i.e. Deshmukh et al) being identical to uL5 (anno 2014): Table 1 of the 1997 paper by Mager et al equates old L16 with L11A (Mager WH, Planta RJ, Ballesta JG, Lee JC, Mizuta K, Suzuki K, et al. A new nomenclature for the cytoplasmic ribosomal proteins of Saccharomyces cerevisiae. Nucleic Acids Res. 1997;25(24):4872-5). Table 2 of Ban et al further equates L11 with uL5 (http://dx.doi.org/10.1016/j.sbi.2014.01.002 ). Our procedure is validated by converting L1 (anno 1993) > uL18 (anno 2014): Mager et at Table 1 converts L1 (anno 2993) to L5 (anno 1997) which is further converted by Table 2 of Ban et al to uL18 (anno 2014). Furthermore, the curators of SGD agree with our conversion of L16 to L11/uL5 since their entries for RPL11 A and B (1997 nomenclature) include a paper on disruption of ribosome formation during L16 depletion from the Woolford lab (https://www.ncbi.nlm.nih.gov/pubmed/3282992). We are thus convinced that our nomenclature conversion is correct. We also note that uL5/L11 does not accumulate extra-ribosomally in proportion with uL18/L5 (figs 2B, S2). Thus, uL5/L11 is not an obligatory component of the extra-ribosomal complex protecting uL18/L5 against rapid degradation. See also our response to the reviewer’s suggestion for an IP experiment.

We have expanded Materials and Methods to clarify our strategy and experiment execution.

The authors refer to reference 9, in which an indirect immuno-detection is described using an enzymatic reaction for secondary antibody visualisation. These detection approaches tend to produce saturation artefacts and it might be therefor important to know whether titration of a reference sample was used in the individual western blots to determine the dynamic range of the detected signal.

The antisera were titrated against increasing amounts of a standard lysate in Figure S6 in Gregory et al (Life Sci Alliance. 2019;2(2). Epub 2019/03/07. doi: 10.26508/lsa.201800150. PubMed PMID: 30837296; PubMed Central PMCID: PMCPMC6402506). For the reviewer’s convenience the figure is reproduced at the end of our rebuttal. Based on these curves, the amount of extract loaded on the sucrose gradient, the number of sucrose gradient fractions into which the r-proteins are distributed, and the volume from each fraction, we calculated that our experiments are within the dynamic range of the antibodies.

For the sucrose gradient fractionation, in several experiments all fractions were analysed. In these cases the ribosomal proteins could be detected in four to six of the “Top” fractions and in up to eleven of the faster sedimenting “Ribosomes” fractions. In several other analyses only one or two of the “Top” fractions and either two or three of the “Ribosomes” fractions of the sucrose gradients were analysed to deduce the ratio of extra-ribosomal to ribosomal r-proteins as uL18. How was it ensured that these fractions contain all of the extra-ribosomal and ribosomal pools of uL18, or are representative for them?

Quantification of extra-ribosomal uL18 based on the limited number of fractions was justified by the following analysis of blots loaded with all sucrose gradient fractions. We calculated extra-ribosomal uL18/total uL18 using (i) all fractions and (ii) two fractions from the top and three fractions from the 60S-80S peaks. The results (Table S2 - new) show that there is semi-quantitative agreement between the two methods. We conclude that our approach is adequate for comparing the level of extramural uL18 after repressing different r-protein genes. When comparing results determined in different ways (e.g. quantifying one versus two top fractions), we have normalized the results to a reference sample.

actual representation for me ambiguous. Thus, less cropped figures might help the reader in these cases.

We have re-cropped the images in Fig 3A showing larger sections. Furthermore, uncropped images for all figures are now shown in Fig S1-S3.

The determination of extra-ribosomal uL18 relative to total uL18 is complicated by the fact that “old ribosomes” (made before the shift to glucose) are stable. Moreover, formation of 60S subunits continue after repression of 40S genes, but at changing rates as the growth rate of the culture decreases after the media shift. We think that the best approach to estimate the extra-ribosomal uL18 pool size therefore is to sample the culture after it has gone through at least two doublings after the shift, at which time the fraction of uL18 in extra-ribosomal fractions is in equilibrium (see new Fig 4). Since the growth rate is different after the shift the cultures were thus incubated for different times in glucose medium. The actual times are now shown in Fig 3A. Regarding the parent strain, the time in glucose is not important, since the density of the culture was kept in the exponential growth range by periodical dilution with prewarmed medium.

Arguably, the net rate of formation of extra-ribosomal uL18 could have been determined more accurately using radioactive pulse labeling followed by immune-precipitation from total extracts and the extra-ribosomal fractions (top of the gradient). However, we did not expect to learn more from this more complicated approach than we did my letting the uL18 population come to equilibrium.

At least from the data shown in Fig 3C for Pgal-eS31 I got the impression that the level of free uL18/L5 decreases with prolonged incubation times in glucose containing medium.

Only occasionally did we see uL18 bands at the top of the gel in Pgal-eS31. As indicated, in Fig 3B, extra-ribosomal uL18 is not significantly different from the value in the parent. In the original submission Fig 3B we indicated that eS31 was different from the parent. This was an error for which we apologize. All calculations have been reexamined to assure accuracy of the revised Fig 3B. We have also included a matrix of significance, by t-test, between the level of extra-ribosomal uL18 in the different strains.

Unfortunately, the paper by Cheng et al does not have data on uL18 and our paper (Gregory et al) does not analyze the same protein set as used in the current manuscript.

A few other comments and remarks:

1) Line 52: “..also requires in excess of 250 ribosomal assembly factors” Does that refer to the stochiometry of components?

We are referring to the number of factors. To avoid confusion, we replaced “In excess” with ”more than”.

2) Line 54: “..while others are specific to the formation of one the ribosomal subunits” of one of ?

Thank you. Thee text was revised.

3) Line 110: “..western blots probed anti-uL18 revealed..” probed with?

Correct. Thank you

4) Line 124: “…but no band corresponding asterisked band in…” ??

Corresponding to ---Thank you

5) Fig 1, labelling: Ribs or Rbs ?

The figure was relabeled to accommodate comments from reviewer 1.

6) Line 163: Why was the strain Pgal-e43 chosen for these experiments?

We have previously used Pgal-eL43 in a number of experiments (Gregory et al; Shamsuzzaman M et al. PLoS One 12: e0186494. doi:10.1371/journal.pone.0186494; Thapa et al Mol Biol Cell 24: 3620–3633. doi:10.1091/mbc.e13-02-0097). The choice of Pgal-eL43 was originally somewhat arbitrary, but it has become one of several standard strains often used in our lab.

7) Line 164: “A band co-migrating with the ribosomal uL18 band ..” was that inferred by some other detection method, as for example by mass spectrometry, or by the expected running behavior of uL18? Does the running behaviour of the detected band fit with the predicted size of uL18?

We are referring to co-migration during gel electrophoresis, which has now been specified. The band migrates in the SDS gel as expected from its molecular weight. More importantly the identity of the band was confirmed in Materials and Methods (Fig 1 and accompanying text).

8) Line 166: “.. we confirmed that band that..” that the band?

Correct. Thank you

9) Line 174: “This was anticipated, since repression of the 60S r-protein uL5 is known to provoke a buildup of extra-ribosomal uL18..”

The result was expected, because cessation of either protein virtually abolishes assembly of new 60S subunits.

10) Line 177, Fig 2.: “Repression of several 40S r-protein genes causes … “

Several 40S r-protein genes? In Fig 2 is just an analysis shown for eS4.

Thank you. We already noticed this misstatement and corrected it

11) Line 177, Fig 2.: “..causes accumulation of extra-ribosomal uL18/L5, but not extra-ribosomal uL5/L11 …”

How was the specificity analysed of the antibody used for detection of uL5?

First, the N-terminal sequence is unique amount r-proteins. Second, the electrophoretic mobility is as expected from the size, and third the protein reacting with the antiserum behaves like a 60S protein in terms of co-sedimenting with the 60S subunit and declining when 60S assembly is inhibited by repression of genes for uL4, uL18, and eL40 (Gregory et al).

12) Line 187: “(C) Northern blots of fractions from ..”

Western blots of ..?

Correct. Thank you.

13) Line 195: “.. was found outside in the ribosome peaks..”

outside of ?

Correct. Thank you.

14) Line 198: “.. parent whether it grows glucose and galactose medium..”

parent strain? grows in ?

Correct. Thank you.

15) Line 199: “..the results in Fig 2 shows that..”

show?

Correct. Thank you.

16) Lines 202 - 205: Why were these large and small subunit protein expression mutants chosen?

eS6, uS17, eS19

eS6, uS17, and eS19 were picked because mutation in the human orthologues have disease consequences. The other two strains, eS4 and eS31, were picked because they are incorporated early and late, respectively, during assembly of the 40S subunit. This is now explained in the text.

17) Line 260: “No uL18 band was seen at the top of the gradient 260 after cycloheximide inhibition of protein synthesis (Fig

4A(ii))..”

The western signals shown in Fig 4A (ii) look a bit blurry. Was a technical replicate of this experiment performed?

We did not do a direct technical replicate, but the results agreed with other experiments.

18) Line 296: “To investigate if extra-ribosomal uL18 also accumulates when rRNA synthesis th is inhibited by the TORtargeting

drug rapamycin”

th ? Rapamycine has also quite a drastic effect on the r-protein mRNA levels and thus on r-protein production. A conditional

mutant of a gene coding for an RNA polymerase I subunit might have addressed the question asked more clearly.

Conditional RNA pol I mutants are fairly sick and take a long time to express their phenotype, so we do not think that experiments with RNA Pol I mutants would be useful. We have revised the text to include the results (degradation of cytoplasmic ribosomes) of Pestov et al (see revised reference list).

19) Lines 310 and following: I was wondering if the authors also analysed the possible accumulation of uL18 bound 5S rRNA?

We did not. We considered it, but concluded that we would not add to the observations of Deshmukh et al.

20) Line 332: “In the extremes, abolishment of eS4synthesis..”

eS4 synthesis?

Yes, thank you. We already corrected this typo.

21) Line 332 and following: “In the extremes, abolishment of eS4synthesis generates a response similar to that seen during

repression of two 60S r-protein genes, while extra-ribosomal uL18 is borderline detectable during abrogation of eS31 synthesis

(Fig 3). This gradient correlates with the abundance of 40S r-proteins in the 90S ribosomal particle, an early 40S assembly intermediate [19], suggesting that preventing early steps of pre-40S precursor assembly have the strongest effect on accumulation of extra-ribosomal uL18.”

Was the subunit imbalance phenotype compared between expression mutants of eS4 and eS31?

We have added a statistical analysis comparing the different mutants (Fig 3C)

The respective penetrance of the small subunit synthesis phenotype might well correlate with the observed effects on uL18. The authors suggest in the abstract and here in the discussion that specifically inhibition of early steps in small subunit assembly leads to the observed effects on uL18. That assumption would have been much strengthened if other 40S r-protein expression mutants with late 40S maturation phenotypes which were not detected in early 40S precursors would have been analysed (e.g. expression mutants of uS2, uS3, uS5 or others). I would also see the authors attempt to interprete the data from reference 19, Fig 7, in regard to the “abundance” of r-proteins in 90S pre-ribosomes as inappropriate, since the authors of reference 19 for probably good reasons use a cut-off to just deduce the presence of the respective proteins.

Nevertheless eS4, eS6, uS11, and eS19, but not eS31, are all above the cut-off and therefore must be concluded to be among the most abundant 40S r-proteins in the 90S.

We agree that analysis of repression of the synthesis of more proteins could have strengthened, or better tested, our model. However, we do think our manuscript is important, because it uncovers a previously unknown interaction between 40S assembly and the kinetics of 60S assembly. A deeper investigation of the many interesting questions will be complex and is beyond the scope of this manuscript.

22) Line 348: “Since two 60S r-proteins (uL4 and uL24) bind to Domain 1 ..”

It is unclear to me why to list these two r-proteins here, but not other r-proteins which clearly also bind to LSU rRNA domain s1.

We eliminated this from the text.

23) Line 367: “Since the major features of pathways for ribosomal assembly evolutionarily conservation, …” ?

We revised the text

24) Line 373: “The difference between the ratio of co-transcriptional and post-transcriptional is evident from ..”

Insert here “processing”?

No, here we actually meant what we wrote.

I am not sure whether this is really the simplest explanation. The effects described here were observed after rather long rprotein depletion times (6 -21 hours according to Materials and Methods). Effects on small subunit synthesis start to be detectable much earlier (after one to two hours in RNA pulse analyses) and after 6 hours and more depletion times quite a massive subunit imbalance can be established in small subunit r-protein expression mutants (see for examples the authors own publication in Life Science Alliance, 2019). That, together with the clear reduction in cellular amounts of functional ribosomes can have various consequences on the balanced production of each of the other ribosomal proteins, including the ones of the large subunit. Did the authors also test effects on extra-ribosomal uL18 accumulation after shorter incubation times in glucose medium at which effects on 40S production just start to be established (1-2 hours)? That might help to distinguish if the observed effects on uL18 are primary consequences of an altered early SSU maturation state or due to secondary effects on the translation status of the cell. Related to this point, see also point 21 in regard to the authors choice of a conditional eS31 expression mutant to control for effects on uL18 by a late SSU assembly defect.

This of course depends on how “simple” is interpreted. We think that it is almost inescapable that our model must contribute the changes in 60S assembly kinetics and the accumulation of extra-ribosomal uL18, but have inserted comments as to potential effects of other parameters.

Attachment

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PLoS One. doi: 10.1371/journal.pone.0222479.r003

Decision Letter 1

Sander Granneman

8 Jan 2020

Interaction between the assembly of the ribosomal subunits: Disruption of 40S ribosomal assembly causes accumulation of extra-ribosomal 60S ribosomal protein uL18/L5

PONE-D-19-24366R1

Dear Lasse,

I hope you had a fabulous Christmas and a fantastic start of 2020. Apologies for the delay in processing the manuscript but I had made a promise to my wife that I would not be doing any work during the Christmas period and therefore only started reading the revised version a few days ago. I have have now had a chance to properly read the revised manuscript and I am happy to recommend the paper for publication.

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PLoS One. doi: 10.1371/journal.pone.0222479.r004

Acceptance letter

Sander Granneman

17 Jan 2020

PONE-D-19-24366R1

Interaction between the assembly of the ribosomal subunits: Disruption of 40S ribosomal assembly causes accumulation of extra-ribosomal 60S ribosomal protein uL18/L5

Dear Dr. Lindahl:

I am pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

S1 Fig. Uncropped versions of images in Fig 2A and 2B.

(PDF)

Click here for additional data file.^{(2.1MB, pdf)}

S2 Fig. Uncropped versions of images in Fig 3A.

CE whole cell extract. M molecular weight markers in kD.

(PDF)

Click here for additional data file.^{(943.1KB, pdf)}

S3 Fig. Uncropped versions of images in Fig 4.

(PDF)

Click here for additional data file.^{(404.8KB, pdf)}

S1 Table. Stains used.

(XLSX)

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S2 Table. Quantification of extra-ribosomal uL18.

(XLSX)

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Data Availability Statement

All relevant data are within the manuscript and its Supporting Information files.

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PERMALINK

Interaction between the assembly of the ribosomal subunits: Disruption of 40S ribosomal assembly causes accumulation of extra-ribosomal 60S ribosomal protein uL18/L5

Nusrat Rahman

Md Shamsuzzaman

Lasse Lindahl

Roles

Abstract

Introduction

Materials and methods

Nomenclature for r-proteins

Strains and growth conditions

Fig 1. Analysis of the specificity of anti-uL18/L5.

Cell lysis and fractionation

Western analysis and antisera

Fig 2. Repression of the gene for the 40S r-protein eS4/S4 causes accumulation of extra-ribosomal uL18/L5, but not extra-ribosomal uL5/L11, uL4/L4, or uS4/S9.

Quantification of extra-ribosomal uL18

Protein molecular weight markers

Statistics

Results

Disruption of ribosome assembly

Extra-ribosomal uL18 accumulates during repression of some 40S r-protein genes

Fig 3. Quantification of extra-ribosomal uL18/L5 pool after repression of different 40S and 60S r-protein genes.

The extra-ribosomal uL18 pool reaches a steady-state

Fig 4. Extra-ribosomal uL18 as a function of time after repressing eS4, eL43, and eS31.

uL18 accrues due to interference with subunit assembly, not degradation of mature subunits

Maintenance of the extra-ribosomal uL18 pool requires protein synthesis

Fig 5. Maintenance of the extra-ribosomal uL18 pool requires protein synthesis.

No extra-ribosomal uL18 accumulates during degradation of cytoplasmic ribosomes

Fig 6. Extra-ribosomal uL18 does not accumulate during degradation of cytoplasmic ribosomes.

Stabilization of extra-ribosomal uL18 does not require Rrs1 or Rpf2

Fig 7. Accumulation of extra-ribosomal uL18 does not require formation of the complete uL18-uL5-5SrRNA-Rrs1-Rpf2 complex.

Discussion

Inhibition of 40S assembly changes 60S assembly kinetics

Co-assembly of 40S and 60S precursor ribosomes may account for the interaction between the ribosomal assembly processes

Fig 8. Model for effect of early 40S assembly on the kinetics of 60S assembly.

Supporting information

Acknowledgments

Data Availability

Funding Statement

References

Decision Letter 0

Sander Granneman

Roles

Author response to Decision Letter 0

Decision Letter 1

Sander Granneman

Roles

Acceptance letter

Sander Granneman

Roles

Associated Data

Supplementary Materials

Data Availability Statement

ACTIONS

PERMALINK

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