Nutrient control of ribosomal gene expression

Ribosomes are highly conserved large ribonucleoprotein (RNP) particles, consisting in yeast of a large 60S subunit and a small 40S subunit, that perform protein synthesis. Yeast ribosomes contain one copy each of four ribosomal RNAs (5S, 5.8S, 18S, and 25S; produced in two separate transcripts encoded within the rDNA repeat present as hundreds of copies on Chromosome 12) and 79 different ribosomal proteins (r-proteins), which are encoded by 137 different genes scattered about the genome, 59 of which are duplicated. The 60S subunit contains 46 proteins and three RNA molecules: 25S RNA of 3392 nt, hydrogen bonded to the 5.8S RNA of 158 nt and associated with the 5S RNA of 121 nt. The 40S subunit has a single 18S RNA of 1798 nt and 33 proteins. All yeast ribosomal proteins have a mammalian homolog. PMID: 10690410, PMID: 22884264, PMID: 9421530, PMID: 9396790 In a rapidly growing yeast cell, 60% of total transcription is devoted to ribosomal RNA, and 50% of RNA polymerase II transcription and 90% of mRNA splicing are devoted to the production of mRNAs for r-proteins. Coordinate regulation of the rRNA genes and 137 r-protein genes is affected by nutritional cues and a number of signal transduction pathways that can abruptly induce or silence the ribosomal genes, whose transcripts have naturally short lifetimes, leading to major implications for the expression of other genes as well. The expression of some r-protein genes is influenced by Abf1p, and most are directly induced by binding of Rap1p to their promoters, which excludes nucleosomes and recruits Fhl1p and Ifh1p to drive transcription. PMID: 10409730, PMID: 12509467, PMID: 10542411, PMID: 2207166, PMID: 16782874 Ribosome synthesis is under nutrient control. Synthesis of the four rRNAs and 79 different proteins in equimolar amounts is one of the most energetically expensive cellular processes, and must be coordinated together. Ribosome biogenesis requires all three RNA polymerases: Pol I for rRNA genes, Pol II for ribosomal protein genes, and Pol III for tRNA and 5S RNA genes. Therefore, sensing quality and quantity of available nutrients is key in the regulation of ribosome biogenesis. PMID: 15489289, PMID: 18303986 Formation of transcription initiation complexes at the rDNA promoter depends on the association of RNA Pol I with the Rrn3p transcription factor, which is regulated by phosphorylation/dephosphorylation of Rrn3p. During normal conditions, a surface serine patch on Rrn3p is not phosphorylated, enabling it to bind RNA Pol I for efficient rDNA transcription. In stress conditions, the surface serine patch undergoes phosphorylation, which impairs the interaction of Rrn3p with RNA Pol I, repressing Pol I transcription, and thereby also reducing ribosome production and cell growth. The presence of glucose results in increased expression of RRN3. In cells treated with rapamycin, Rrn3p is subject to proteasome-dependent degradation, reducing the cellular amount of transcription-initiation competent RNA Pol I - Rrn3p complexes. PMID: 19796927, PMID: 8670901, PMID: 20421203, PMID: 20154141, PMID: 18084032, PMID: 11717393, PMID: 14595104 Ribosomal protein genes and ribosomal biogenesis genes are transcribed by RNA polymerase II. The activation of these promoters requires the forkhead-like transcription factor, Fhl1p, the acitvity of which is subject to nutrient regulation via the Ifh1 activator and the Crf1 repressor. Under lack of stress, the TorC1 complex retains Crf1p in the cytoplasm in a dephosphorylated, inactive state. Upon nutrient deprivation, the PKA-responsive Yak1 kinase phosphorylates Crf1p, resulting in its translocation to the nucleus, where Crf1p competes with the Ifh1 activator to bind Fhl1p. The transcription factor Sfp1p also mediates TorC1 regulation of ribosomal protein and ribosomal biogenesis genes. Interaction of Sfp1p with TorC1 reduces Sch9p phosphorylation, resulting in a negative feedback loop. PMID: 15620355, PMID: 19796927 Transcription by RNA polymerase III is negatively regulated by Maf1, a highly conserved repressor. Both the localization and activity of Maf1p are regulated by phosphorylation at various sites, mediated by TORC1, protein kinase A (PKA), and Sch9p. In its dephosphorylated state, Maf1p binds the N-terminus of the Rpc160p subunit of Pol III to prevent closed-complex formation. Maf1p is maintained in the cytoplasm during vegetative growth via PKA- or Sch9p-mediated phosphorylation. Dephosphorylation allows translocation of Maf1p to the nucleus and nucleolus under stress conditions, which shuts down RNA Pol III transcription.Phosphorylation of Maf1p by CK2 occurs at promoters, which releases Maf1p from chromatin, liberating RNA Pol III from inhibition. PMID: 19684113, PMID: 19299514, PMID: 21383183, PMID: 17005718, PMID: 22810236

核糖体为高度保守的大型核糖核蛋白（RNP）颗粒，在酵母细胞中由一个大型的60S亚单位和一个小型的40S亚单位组成，主要负责蛋白质合成。酵母细胞中的核糖体含有四种核糖体RNA（5S、5.8S、18S和25S；由存在于第12染色体上重复出现的rDNA中的两个独立转录本编码，以数百个拷贝存在）以及79种不同的核糖体蛋白（r蛋白），这些蛋白由散布于基因组中的137个不同基因编码，其中59个基因是复制的。60S亚单位包含46种蛋白和三种RNA分子：3392个核苷酸长度的25S RNA，与158个核苷酸长度的5.8S RNA通过氢键结合，并与121个核苷酸长度的5S RNA相关联。40S亚单位含有一个1798个核苷酸长度的18S RNA和33种蛋白。所有酵母核糖体蛋白都具有哺乳动物的同源蛋白。PMID: 10690410, PMID: 22884264, PMID: 9421530, PMID: 9396790
在快速生长的酵母细胞中，总转录的60%用于核糖体RNA，50%的RNA聚合酶II转录和90%的mRNA剪接用于合成r蛋白的mRNA。rRNA基因和137个r蛋白基因的协调调控受营养信号的调控，以及多种信号转导途径的影响，这些途径可以突然诱导或沉默核糖体基因，其转录本的自然寿命较短，对其他基因的表达产生重大影响。某些r蛋白基因的表达受Abf1p的影响，而大多数基因则直接受Rap1p与它们的启动子结合的诱导，这会排除核小体并招募Fhl1p和Ifh1p以驱动转录。PMID: 10409730, PMID: 12509467, PMID: 10542411, PMID: 2207166, PMID: 16782874
核糖体合成受营养控制。四种rRNA和79种不同蛋白以等摩尔比例的合成是细胞中最耗能的过程之一，必须协调进行。核糖体生物发生需要所有三种RNA聚合酶：Pol I用于rRNA基因，Pol II用于核糖体蛋白基因，Pol III用于tRNA和5S RNA基因。因此，感知可用营养的质量和数量对于核糖体生物发生的调控至关重要。PMID: 15489289, PMID: 18303986
在rDNA启动子处形成转录起始复合物依赖于RNA Pol I与转录因子Rrn3p的关联，其受Rrn3p的磷酸化/去磷酸化调控。在正常条件下，Rrn3p表面的丝氨酸位点未发生磷酸化，使其能够与RNA Pol I结合以实现高效的rDNA转录。在应激条件下，表面丝氨酸位点发生磷酸化，这会损害Rrn3p与RNA Pol I的相互作用，抑制Pol I转录，从而降低核糖体产量和细胞生长。葡萄糖的存在导致RRN3表达增加。在用雷帕霉素处理的细胞中，Rrn3p受蛋白酶体依赖性降解的影响，减少细胞中转录起始能力的RNA Pol I - Rrn3p复合物的数量。PMID: 19796927, PMID: 8670901, PMID: 20421203, PMID: 20154141, PMID: 18084032, PMID: 11717393, PMID: 14595104
核糖体蛋白基因和核糖体生物发生基因由RNA聚合酶II转录。这些启动子的激活需要叉头样转录因子Fhl1p，其活性受Ifh1激活剂和Crf1抑制剂的营养调控。在无应激条件下，TorC1复合物将Crf1p保留在细胞质中，处于去磷酸化、非活性状态。在营养剥夺的情况下，PKA反应性Yak1激酶磷酸化Crf1p，导致其转位到细胞核，在那里Crf1p与Ifh1激活剂竞争结合Fhl1p。转录因子Sfp1p也介导TorC1对核糖体蛋白和核糖体生物发生基因的调控。Sfp1p与TorC1的相互作用降低了Sch9p的磷酸化，从而形成一个负反馈环。PMID: 15620355, PMID: 19796927
RNA聚合酶III的转录受高度保守的抑制因子Maf1的负调控。Maf1p的定位和活性受TORC1、蛋白激酶A（PKA）和Sch9p在多个位点的磷酸化调控。在其去磷酸化状态下，Maf1p结合Pol III的Rpc160p亚单位的N端，以防止形成关闭复合物。Maf1p通过PKA或Sch9p介导的磷酸化在营养生长期间维持在细胞质中。去磷酸化允许Maf1p在应激条件下转移到细胞核和核仁中，从而关闭RNA Pol III转录。CK2在启动子处磷酸化Maf1p，从而释放Maf1p从染色质中，使RNA Pol III从抑制中解脱出来。PMID: 19684113, PMID: 19299514, PMID: 21383183, PMID: 17005718, PMID: 22810236