TIBS 24 - PDF document

TIBS 24 ÐNOVEMBER 1999 balances conflicting demands for re-sources to maintain cell viability and cellfunction with demands for resources tosupport growth. As a major consumer ofthe cellÕs resources, ribosome biosyn-thesis plays a key role in the cellÕs bud-geting process, especially because newribosomes represent an investment innew plant, with the opportunity forfaster growth Ð but only if other essen-sis involves both macroregulation, ingrowth, and microregulation to ensureare available in equimolar amounts (reviewed in Refs 1,2).Recent results offer new insight intomize this part of its economy and raisegrowing cell of Ôyeast nucleic acidÕ). The approximatetides) shows that there are nearly200000 ribosomes per cell (Fig. 1a). With must produce 2000 ribosomes per min.What are the implications of such highproduction for the economy of the cell?make up 10% of the entire genome,repeats, although the number can varyrecombination. As estimated from theRNA, as well as fromand stability, the transcription of rRNAto represent nearly 60% of the total The 132 RP genes on the Affymetrixªchip account for 4437 of the cellÕs esti-mated 15000 mRNAs (Ref. 8 and http://www.wi.mit.edu/young/expression.html).As the RP mRNAs are relatively short-livedcompared with other mRNAs (Ref. 9), antion and the abundance of introns in RPgenes means that, contrary to popularperception, about 40% of yeast mRNAsare spliced and that 90% of all mRNARPs are assembled into ribosomes inthe nucleolus. Although small, they areimported into the nucleus using conven-possibly utilizing a relatively specific importin (Ref. 12). With approximately150 pores per nucleus, each pore mustimport nearly 1000 RPs per min and export ~25 ribosomal subunits per min.clear: when there is food it grows; whenthere is none it does not. Yet, the simple The economics of ribosome Jonathan R. WarnerIn a rapidly growing yeast cell, 60% of total transcription is devoted to ribo-splicing are devoted to ribosomal proteins (RPs). Coordinate regulation ofthe ~150 rRNA genes and 137 RP genes that make such prodigious use ofresources is essential for the economy of the cell. This is entrusted to anumber of signal transduction pathways that can abruptly induce or silencethe ribosomal genes, leading to major implications for the expression of J. R. Warneris at the Dept of Cell Biology,Albert Einstein College of Medicine, 1300Morris Park Avenue, New York, Bronx, Email: warner@aecom.yu.edu 0968Ð0004/99/$ Ð See front matter © 1999, Elsevier Science Ltd. All rights reserved. TIBS 24 ÐNOVEMBER 1999 This includes a coordinate repression ofthe entire complement of RP genes, followed by resumption of transcriptionas the spores themselves developFinally, the accumulation of a species ofuncharged tRNA, due to deprivation ofan amino acid, leads to the repression ofÔstringent responseÕ)were carried out under the extreme conditions of starvation or the constitu-tive (in)activation of a pathway. Yet, athe culture is at . Subsequently, the cell startstionary phase has Clearly, the detection of and the re-sponse to the subtle changes in cultureshortage or abundance form a key to selective survival. As they integrate thisinformation, are the PKA and TOR path-ways parallel, convergent, or intersect- ing? Are there other signalling pathwaysRibosome synthesis and environmentaltemperatures at which the cell is viable,leads to a rapid but temporary repres-mRNAs decline precipitously with a half15Ð20 min and then recover to nearly25), recent data suggest that their rate. Neither the effec-repression is known. This is one case inwhich the effect of an environmental insult is far greater on RP transcriptionA defect anywhere in the secretorypathway Ð from early in the ER, throughrepression of both rRNA and RP genesInhibitors of the secretory pathway, suchas tunicamycin and brefeldin A, have asimilar effect. Initially, this seemed a sur-prising result, yet in retrospect, it shouldtain balanced growth there must becross-talk between the major syntheticthe secretory pathway and the ribosomebiosynthesis pathway. It remains to beThis repression is not due to the Ôunfolded protein responseÕ, does not de-pend on PKA and is not related to theÔstringent responseÕ. The secretory path-is largely devoted tothe secretion of proteins involved in themonitored by the PKC pathway. We havebrane-bound upstream effectorare essential for the repression of rRNA andRP genes in response to a defect in the se-cretory pathwaycontinued synthesis of proteins leads toosmotic stress. The cell responds by repressing ribosome synthesis.In a recent study of the cell-cycle dependence of more than 6200 genes, -factor arrest, a reached the threshold defined in thisNevertheless, this approach does notaddress the physiological question ofbiosynthesis. The observation that dis-be a key difference between the G0 andrepressing ribosome synthesis (e.g. dur-ing the approach of stationary phase).lizes transcription as its primary meansof regulating RP synthesis, whereas bothand vertebratestranslation, albeit in very different ways.of RP mRNAs so short? Toreplace RP mRNAs at frequent intervalsseems an unnecessary use of resources.abundant glycolytic enzymes are muchlonger. One possible explanation is thatthere is selective pressure to maintain ashort Tfor RP mRNAs in order to con-trol the relative production of the manyRPs more closely.Transcription of rRNA genestion have been recently reviewedCompared with the plethora of factorsfewer have been reported to be necess-ary for Pol I transcription in metazoans.However, Keys and colleaguestional proteins (encoded by the genes) that participate in yeast rRNAtranscription. Current genetic and bio-chemical results suggest that the mini-mum requirements for active Pol I tran-scription include TBP, Rrn3 and twotones H3 and H4, and protein p30)rRNA transcription far more complex incomponents that are as yet invisible tothe biochemical approaches applied to (a)(b)Ti BS Figure 1A thin-section electron micrograph(courtesy of B. Byers, University ofWashington). As much as 30Ð40% of theof the proteins of a yeast ribosome aftertwo-dimensional electrophoresis. Each ofthe ribosomes pictured in (a) containsthis array of proteins and to produce thisnumber of proteins in precisely equimolar TIBS 24 ÐNOVEMBER 1999 within ~200 bp upstream of the tran-stream of the rRNA transcription uniteither upstream or downstream of theIt is remarkable how little is under-stood about the vigorous, highly regu-lated transcription by Pol I. Whereas Rrn3 (Ref. 40), have been reported, theknowledge of what regulates this acti-vation is limited. Chromatin analysisgenes are active, even in rapidly grow-ing cells. Approaching stationary phase,this proportion drops by less than, whereas transcription declines bynot the basis of the regulation of rRNAgenes important for their regulation orTranscription of RP genesThe upstream activator sequence(UAS)/promoter regions of most RPgenes have a similar architecture (Fig. 3;reviewed in Refs 1,2). Two Rap1 bindingsites provide most of the activation, fol-lowed by one or two T-rich elementsthat will support a low level of transcrip-acetylation factors, suppressor of RNApolymerase B (SRB) and TATA-box-bind-ing-protein-associated factor (TAF) pro-peared to be specific for the RP genesNevertheless, given the coordinate, highRap1, the superfactor of Rap1 plays an extraordinary role in vator of other genes related to trans-for even more, all Pol II transcription. As the proteinthat coats the telomeres it is also re-sponsible for maintaining proper telo-mere length. In cooperation with Sir3MATaand MATBecause of its prominent regulatoryrole, Rap1 is an obvious target for theactivation and repression of transcrip-to amino acid starvationand a secretory defectThis could be repression, in which Rap1is prevented from activating transcrip-prevents transcription. In cells carrying, from which the silencing do-secretory pathwayand silences the RP genes. Yet, the nor-Sir4, are not required for this effectSurprisingly, other cis-acting elementsof an RP gene can also lead to repression produces a gene that is dependent ongalactose and repressed by glucose.Nevertheless, it is repressed by at least. A similar observation has beenreported for nitrogen starvationIn summary, Rap1 acts not only as anmust bind to the upstream elements,but also as a silencer, possibly of all RPupstream elements. Perhaps this dualcell to compete effectively in a rapidlychanging environment. One could sug-was adapted, through the developmentof Sir3 and Sir4, to silence the silent MATMicroregulation of RP synthesisThe challenge of regulating the pro-duction of an RP differs from that for mostproteins because the cell needs equi-molar amounts of the individual com-ponents of the ribosome. However, thetranscriptome data reveal that there is afivefold difference between the most andPresumably, there has been a coordinated XTP (60% of total Tx)RP mRNA(50% of Pol II Tx)Pol IPol IIRrn3?Rap1 (+?)NutrientsTOR Temp aa?cAMPPlasmamembrane i BS Figure 2Some of the elements that regulate the production of ribosomes in This figure is a simplified summary of many observations. Is there a single Ôblack boxÕ thattransduces the signals from these numerous sources into the coordinate transcription of the~150 rRNA genes and the 137 RP genes? It is currently not known whether there is communi-cation between the Pol I and Pol II systems, although, under certain experimental conditions,. Abbreviations: aa,amino acids; PKA, protein kinase A; Pkc1, protein kinase C 1; SEC, any defect in the secretorypathway; TOR, Ôtarget of rapamycinÕ pathway; XTP, nucleoside triphosphates; Wsc1, a plasmamembrane-bound protein that detects stress, upstream of Pkc1 (also known as Hcs77). TIBS 24 ÐNOVEMBER 1999 evolution, so that for each RP the prod-uct of its transcription (from its one ortranslation leads to roughly equimolaroutput. The relevant measurementshighly charged, nucleic-acid-binding pro-Indeed, excess RPs are degraded with aof 0.5Ð3.0 min (reviewed in Ref. 1).How does a cell know, within 30 seconds,that a protein synthesized in the cyto-control the level of its own mRNA. Thenormally spliced efficiently but in thepresence of excess L30, unspliced pre-prevents the complete assembly of the. The ability to regulateeffects. Another case concerns S14, a proteinCRY1CRY2, whose mRNAs are found in a ratiogenes are transcribed approximately toCRY2. The selective preser-vation of introns in RP genes leads tothe suspicion that many more couldplay a role in feedback inhibition. It isCRY2 Conclusions and prospectsThe importance of ribo-expected regulatory sys-tems. Whereas some insighttions remain. How is tran-varies? Is there crosstalk tered RP genes? When RP transcriptiongenes of the sudden release of 50% of thecell? Is there a system to buffer the transcriptome from such a shock?more complex, being based largely onhomeostasis. Yet, the basic biologicalproblem remains the same: (i) selectinga rate of ribosome production thatpensate for molecular turnover, or a lym-phocyte that must be prepared to churnproviding the rRNA and RPs needed toaccomplish that rate of production.this about would reveal an ideal targetfor therapy against tumor growth.I am grateful to M. Nomura, G. Prelich, J. Vilardell and I. Willis for thoughtful com-ments, and to B. Byers for the micrographof Fig. 1a. Work in the authorÕs laboratorywas supported by NIH Grant GM25532.ReferencesWoolford, J. L., Jr and Warner, J. R. (1991) in(Broach, J. R., Pringle, J. R. and Jones, E. W., eds), pp. 587Ð626,Cold Spring Harbor Laboratory PressWool, I. G., Chan, Y-L. and Gluck, A. (1995)Mager, W. H. Wolfe, K. H. and Shields, D. C. (1997) Spingola, M., Grate, L., Haussler, D. and Ares,Velculescu, V. E. Holstege, F. C. P. Li, B., Nierras, C. R. and Warner, J. R. (1999) Underwood, M. R. and Fried, H. M. (1990)Schaap, P. J. Rout, M. P., Blobel, G. and Aitchison, J. D.Winey, M. Werner-Washburne, M., Braun, E., Johnston, G. C.and Singer, R. APowers, T. and Walter, P. (1999) Klein, C. and Struhl, K. (1994) Neuman-Silberberg, F. S., Bhattacharya, S. andBroach, J. R. (1995) Ju, Q. and Warner, J. R. (1994) Warner, J. R. and Gorenstein, C. (1977) Herruer, M. H. Warner, J. R. and Udem, S. A. (1972) Mizuta, K. and Warner, J. R. (1994) Nierras, C. R. and Warner, J. R. (1999) Kamada, Y. Verna, J. Spellman, P. T. Meyuhas, O., Avni, D. and Shama, S. (1996) in(Hershey, J. W. B.,Mathews, M. B. and Sonenberg, N., eds), pp. 363Ð388, Cold Spring Harbor Laboratory PressSpringer-VerlagKeener, J. Kulkens, T. Elion, E. A. and Warner, J. R. (1986) Lang, W. H. and Reeder, R. H. (1993) Milkereit, P. and Tschochner, H. (1998) Lascaris, R. F., Mager, W. H. and Planta, R. J.Shore, D. (1994) Vilardell, J. and Warner, J. R. (1994) Li, B., Vilardell, J. and Warner, J. R. (1996) Li, Z., Paulovich, A. G. and Woolford, J. L., JrFewell, S. W. and Woolford, J. L. J. (1999) 2* Rap1 TATA either element Ti BS Figure 3A typical ribosomal protein (RP) promoter. For moststretch and a TATA box drive the transcription of a pre-mRNA containing an intron near the 5end. The redbars indicate two regions, either of which can confer important regulatory elements remain to be discovered.