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

Abstract

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...

The Chromatin-Associated Phf12 Protein Maintains Nucleolar Integrity and Prevents Premature Cellular Senescence

“…Finally, LAS1L inactivation has been showed to result in G 1 arrest, linking LAS1L to cell cycle progression (47). Moreover, SENP3, which we showed is more abundant in the Pf1 Ϫ/Ϫ MEFs than in the control cells, interacts with NPM1 (26,27,30) and forms a nucleolar complex with PELP1 and LAS1L (47). If the results of our experiments cannot completely rule out the possibility of an indirect role of Pf1 in ribosomal biogenesis, the results of our LC-MS/MS and subsequent co-IP analyses suggest that the effect of Pf1 on nucleolar functions might not be mediated or at least might not be mediated solely by the Pf1 association with the Sin3-MRG15-HDAC complex.…”

“…SENP3 is a SUMO-isopeptidase involved in the conversion of the 32S rRNA intermediate to mature 28S rRNA in mammals (26)(27)(28). SENP3 also tightly associates with the nucleophosmin NPM1, another central factor in ribosome biogenesis (29,30). Fibrillarin and SENP3 exert their function and are present in the outer two layers of the nucleoli: the dense fibrillar component and the granular component.…”

SUMO-Mediated Regulation of Nuclear Functions and Signaling Processes

“…For example, Cdc5 phosphorylation of yeast Ulp2 desumoylase downregulates its function in mitosis, which is thought to preserve appropriate sumoylation levels required for mitosis (Baldwin et al, 2009). In another example, mTOR-mediated phosphorylation of SENP3 favors its interaction with nucleolar scaffold protein NPM1 to promote nucleolar targeting and SUMO2/3 removal at this location (Raman et al, 2014). …”

Flightless-I governs cell fate by recruiting the SUMO isopeptidase SENP3 to distinct HOX genes

“…For example, SENP3 exerts preferential cleavage activity toward SUMO2-/3-modified substrates. It is distributed in the nucleolus and nucleoplasm and shuttles between these two compartments in an mTOR-controlled process [11]. Work from our group and others has initially established a role of SENP3 in ribosome maturation [11–14].…”

“…It is distributed in the nucleolus and nucleoplasm and shuttles between these two compartments in an mTOR-controlled process [11]. Work from our group and others has initially established a role of SENP3 in ribosome maturation [11–14]. Subsequently, we and others could also unravel a crucial function of SENP3 in the control of gene expression [15–17], in particular in the regulation of homeobox ( HOX ) genes [18].…”