mTOR signaling regulates the processing of pre-rRNA in human cells

Iadevaia, Valentina; Zhang, Ze; Jan, Eric; Proud, Christopher G.

doi:10.1093/nar/gkr1040

Cited by 89 publications

(83 citation statements)

References 35 publications

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“…U6), whose promoters typically do not possess B-box elements and utilize a separate complement of transcription factors (34). It is known that mTOR regulates all three classes of RNA polymerases to facilitate ribosome biogenesis (6) and that, similar to SIRT7, it can localize to nucleoli (31). Therefore, we propose that SIRT7 functions in ribosome biogenesis and protein synthesis are partly mediated by its association with mTOR (Fig.…”

Section: Discussionmentioning

confidence: 96%

“…2E). It has been reported that perturbations in rRNA processing steps can lead to the accumulation of prerRNA intermediates (30,31), which could result in longer half-lives of the pre-rRNA intermediates like 5Ј external transcribed spacer near 18S and internal transcribed spacer. However, we found that the steady state levels of rRNA measured by qPCR are decreased after SIRT7 knockdown (supplemental Fig.…”

Section: Sirt7 Has An Rna-independent Nucleolar Localization and Intementioning

confidence: 99%

“…1C-1E), proteins known to form a complex and play a crucial role in Pol III functions (32). The TFIIIC2 complex is known to be nuclear (26), and recent evidence showed that mTOR localizes within nucleoli (31). To further validate these interactions, we performed reciprocal isolations using antibodies against the endogenous proteins (Fig.…”

Section: Sirt7 Associates With a Tfiiic2-containing Complex And Modulmentioning

confidence: 99%

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Sirtuin 7 Plays a Role in Ribosome Biogenesis and Protein Synthesis

Tsai

Greco

Cristea

2014

Molecular & Cellular Proteomics

105

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It has been shown that SIRT7 regulates rDNA transcription and that reduced SIRT7 levels inhibit tumor growth. This anti-tumor effect could be due to reduced Pol I activity and perturbed ribosome biogenesis. In this study, using pulse labeling with RNA and amino acid analogs, we found that SIRT7 knockdown efficiently suppressed both RNA and protein synthesis. Surprisingly, SIRT7 knockdown preferentially inhibited protein synthesis over rDNA transcription, whereas the levels of both were reduced to similar extents following Pol I knockdown. Using an affinity purification mass spectrometry approach and functional analyses of the resulting SIRT7 interactome, we identified and validated SIRT7 interactions with proteins involved in ribosomal biogenesis. Indeed, SIRT7 co-fractionated with monoribosomes within a sucrose gradient. Using reciprocal isolations, we determined that SIRT7 interacts specifically with mTOR and GTF3C1, a component of the Pol III transcription factor TFIIIC2 complex. Further studies found that SIRT7 knockdown triggered an increase in the levels of LC3B-II, an autophagosome marker, suggesting a link between SIRT7 and the mTOR pathway. Additionally, we provide several lines of evidence that SIRT7 plays a role in modulating Pol III function. Immunoaffinity purification of SIRT7-GFP from a nuclear fraction demonstrated specific SIRT7 interaction with five out of six components of the TFIIIC2 complex, but not with the TFIIIA or TFIIIB complex, the former of which is required for Pol III-dependent transcription of tRNA genes. ChIP assays showed SIRT7 localization to the Pol III targeting genes, and SIRT7 knockdown triggered a reduction in tRNA levels. Taken together, these data suggest that SIRT7 may regulate Pol III transcription through mTOR and the TFIIIC2 complex. We propose that SIRT7 is involved in multiple pathways involved in ribosome biogenesis, and we hypothesize that its down-regulation may contribute to an antitumor effect, partly through the inhibition of protein synthesis. Molecular &

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Section: Discussionmentioning

confidence: 96%

Section: Sirt7 Has An Rna-independent Nucleolar Localization and Intementioning

confidence: 99%

Section: Sirt7 Associates With a Tfiiic2-containing Complex And Modulmentioning

confidence: 99%

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Sirtuin 7 Plays a Role in Ribosome Biogenesis and Protein Synthesis

Tsai

Greco

Cristea

2014

Molecular & Cellular Proteomics

105

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“…Indeed, the mTOR pathway controls rRNA transcription and production of ribosomal proteins in response to nutrient, growth factors, and serum (19)(20)(21).…”

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confidence: 99%

SHPRH regulates rRNA transcription by recognizing the histone code in an mTOR-dependent manner

Lee

Park

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Many DNA repair proteins have additional functions other than their roles in DNA repair. In addition to catalyzing PCNA polyubiquitylation in response to the stalling of DNA replication, SHPRH has the additional function of facilitating rRNA transcription by localizing to the ribosomal DNA (rDNA) promoter in the nucleoli. SHPRH was recruited to the rDNA promoter using its plant homeodomain (PHD), which interacts with histone H3 when the fourth lysine of H3 is not trimethylated. SHPRH enrichment at the rDNA promoter was inhibited by cell starvation, by treatment with actinomycin D or rapamycin, or by depletion of CHD4. SHPRH also physically interacted with the RNA polymerase I complex. Taken together, we provide evidence that SHPRH functions in rRNA transcription through its interaction with histone H3 in a mammalian target of rapamycin (mTOR)-dependent manner.SHPRH | rRNA transcription | histone H3 methylation | mTOR H uman ribosomal DNA (rDNA) is composed of hundreds of tandem repeats of 42.9-kb rDNA units that are organized into transcribed and intergenic regions (1). About one-half the 47S precursor ribosomal RNA (pre-rRNA) genes are actively transcribed, and the other half remain silent (2, 3). Transcription, processing of rRNA, and the assembly of ribosomes take place in the nucleoli (2, 4). Once transcribed in the nucleoli, pre-rRNA is immediately processed into small mature 28S, 18S, and 5.8S rRNAs that, together with ribosomal proteins, make a ribosome. Tight regulation of ribosome biogenesis, including rRNA transcription and synthesis of ribosomal proteins, is important in many biological processes such as cell proliferation, apoptosis, and autophagy (5-7), and is closely associated with metabolic processes. Because of its importance in many metabolic pathways, dysregulation of ribosomal biogenesis is linked to aging and diverse diseases, including anemia and cancers (8-12). 47S pre-rRNA is transcribed by the RNA polymerase I complex, whose activity is controlled by cellular responses to nutritional states, cellular stresses, growth, differentiation, and cell cycle (9). Posttranslational modifications of transcription factors, for example, phosphorylation of upstream binding factor (UBF), help regulate rRNA transcription (13). In addition to posttranslational modifications of transcription factors, nucleolar remodeling complex, NuRD (nucleosome remodeling and deacetylation) complex, and energy-dependent nucleolar silencing complex also affect rRNA transcription by modifying epigenetic signatures of rDNA, as well as histones in the rDNA promoter (14-16). In addition to conventional active and silent histone signatures, the rDNA promoter has another histone signature called a poised state. CHD4 and CSB-containing NuRD complex establish a poised chromatin signature of rDNA that represses but primes rRNA transcription by marking histone H3 with both active (H3 K4me3) and inactive (H3 K27me3) modifications (16). However, it is unclear how these epigenetic changes control the transcription of rRNA.The mammali...

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“…mTORC1 positively regulates many anabolic processes, with the role of mTORC1 signaling in translational initiation being the best understood. More recently a function of mTOR signaling in ribosome biogenesis has also been proposed (8)(9)(10)(11)(12). In particular, mTOR has been implicated in the control of RNA polymerase I transcription and rRNA processing.…”

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confidence: 99%

mTOR Signaling Regulates Nucleolar Targeting of the SUMO-Specific Isopeptidase SENP3

Raman

Nayak

2014

Molecular and Cellular Biology

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Ribosome biogenesis is a multistep cellular pathway that involves more than 200 regulatory components to ultimately generate translation-competent 80S ribosomes. The initial steps of this process, particularly rRNA processing, take place in the nucleolus, while later stages occur in the nucleoplasm and cytoplasm. One critical factor of 28S rRNA maturation is the SUMO-isopeptidase SENP3. SENP3 tightly interacts with the nucleolar scaffold protein NPM1 and is associated with nucleolar 60S preribosomes. A central question is how changes in energy supply feed into the regulation of ribosome maturation. Here, we show that the nutrient-sensing mTOR kinase pathway controls the nucleolar targeting of SENP3 by regulating its interaction with NPM1. We define an N-terminal domain in SENP3 as the critical NPM1 binding region and provide evidence that mTOR-mediated phosphorylation of serine/threonine residues within this region fosters the interaction of SENP3 with NPM1. The inhibition of mTOR triggers the nucleolar release of SENP3, thereby likely compromising its activity in rRNA processing. Since mTOR activity is tightly coupled to nutrient availability, we propose that this pathway contributes to the adaptation of ribosome maturation in response to the cellular energy status. Ribosomes are large ribonucleoprotein complexes functioning as molecular machines in protein synthesis. Mammalian 80S ribosomes are assembled from the small 40S and the large 60S subunit (1). The 60S subunit is composed of the 28S, the 5.8S, and the 5S rRNA and contains at least 46 ribosomal proteins, while the 40S subunit consists of around 30 ribosomal proteins and the 18S rRNA. The maturation of ribosomes is a highly regulated pathway that involves more than 200 nonribosomal proteins, commonly termed trans-acting factors (2, 3). Ribosome biogenesis is initiated in the nucleolus by RNA polymerase I (Pol I), transcribing a 47S precursor rRNA. This precursor is incorporated into a nucleolar 90S preribosomal particle, where specific bases in the rRNA are covalently modified and initial pre-RNA processing steps take place (4, 5). The 40S and 60S ribosomal subunits subsequently take a separate maturation pathway, which proceeds by a number of processing and remodelling events in the nucleolus and the nucleoplasm. Following export to the cytoplasm, both subunits are assembled to translation-competent 80S particles.As an integral part of protein synthesis, ribosome biogenesis must be tightly coupled to the energy status and nutrient levels of the cell. One key pathway that coordinates energy supply with protein translation is the mammalian target of rapamycin (mTOR) signaling network (6, 7). mTOR is an evolutionarily conserved serine/threonine kinase. In mammalian cells, mTOR is found in two distinct complexes, mTORC1 and mTORC2, that contain specific regulatory subunits and adaptor proteins. For example, Raptor and Rictor are the protein components involved in substrate recruitment and complex assembly of mTORC1 and mTORC2, respectively. mTORC1 positive...

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mTOR signaling regulates the processing of pre-rRNA in human cells

Cited by 89 publications

References 35 publications

Sirtuin 7 Plays a Role in Ribosome Biogenesis and Protein Synthesis

Sirtuin 7 Plays a Role in Ribosome Biogenesis and Protein Synthesis

SHPRH regulates rRNA transcription by recognizing the histone code in an mTOR-dependent manner

mTOR Signaling Regulates Nucleolar Targeting of the SUMO-Specific Isopeptidase SENP3

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