Ribosomes are biological nanomachines that carry out synthesis of the entire cellular proteome. Cells require a large number of ribosomes to make proteins, especially during periods of active growth and proliferation. Each ribosome in eukaryotes is manufactured through an elaborate assembly pathway that requires more than 200 accessory protein factors. Like any other complex assembly process, biosynthesis of ribosomes generates a certain fraction of defective products and kinetically trapped intermediates. How do cells distinguish between ribosomes that are built correctly and those that are not? The main objective of the proposed research is to answer this question by elucidating the mechanisms underlying quality control of ribosome synthesis in mammalian cells. We use mouse cells in our studies because surveillance mechanisms in mammals differ in many aspects from those in other model organisms such as yeast. One of such differences is that defects in ribosome formation in mammals induce a p53-mediated nucleolar stress response, which is mechanistically not completely understood. Because the framework of preribosomes, like the ribosome itself, is made of RNA, ribonucleases play a key role in dismantling defective ribosome precursors. Here, we wish to establish the pathway through which exoribonucleases start the process of elimination of the defective preribosomes. Our project has three specific aims. 1. Determine the role of the mammalian exosome in the degradation of misassembled pre-60S subunits. We will determine whether the exosome functions in primary surveillance of misassembled pre-60S subunits or acts as a scavenger and how these activities may be regulated through candidate adaptors. 2. Identify structural features of the pre-60S subunit that control whether it will be processed or degraded. Our model is that certain components of preribosomes act as gatekeepers that control nuclease access to pre-rRNA. This will be tested by dissecting the interactions between the exonuclease Xrn2 and the 5.8S RNA-ribosomal protein complex in pre-60S subunits. 3. Determine if pre-rRNA decay products play a role in the nucleolar stress response induced by mutations in ribosome assembly factors and by anticancer drugs that block ribosome maturation, both of which significantly increase pre-rRNA breakdown by nucleases. Together, these studies will test the hypothesis that pre-rRNA surveillance by mammalian exoribonucleases serves the dual function of enabling accurate synthesis of ribosomes under normal circumstances, and initiating stress signaling when the system becomes overloaded.

Public Health Relevance

This project will answer important questions about how mammalian cells ensure the accurate synthesis of ribosomes, the molecular machines that make all proteins in an organism. Defects in ribosome formation are known to be a factor in cancer and several congenital diseases, and our study will help to understand the molecular basis of this connection.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Molecular Genetics C Study Section (MGC)
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Bender, Michael T
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University of Medicine & Dentistry of NJ
Anatomy/Cell Biology
Schools of Osteopathic Medicine
United States
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Shedlovskiy, Daniel; Shcherbik, Natalia; Pestov, Dimitri G (2017) One-step hot formamide extraction of RNA from Saccharomyces cerevisiae. RNA Biol 14:1722-1726
Sapio, Russell T; Nezdyur, Anastasiya N; Krevetski, Matthew et al. (2017) Inhibition of post-transcriptional steps in ribosome biogenesis confers cytoprotection against chemotherapeutic agents in a p53-dependent manner. Sci Rep 7:9041
Wang, Minshi; Pestov, Dimitri G (2016) Quantitative Northern Blot Analysis of Mammalian rRNA Processing. Methods Mol Biol 1455:147-57
Shcherbik, Natalia; Chernova, Tatiana A; Chernoff, Yury O et al. (2016) Distinct types of translation termination generate substrates for ribosome-associated quality control. Nucleic Acids Res 44:6840-52
Wang, Minshi; Parshin, Andrey V; Shcherbik, Natalia et al. (2015) Reduced expression of the mouse ribosomal protein Rpl17 alters the diversity of mature ribosomes by enhancing production of shortened 5.8S rRNA. RNA 21:1240-8
Wang, Minshi; Anikin, Leonid; Pestov, Dimitri G (2014) Two orthogonal cleavages separate subunit RNAs in mouse ribosome biogenesis. Nucleic Acids Res 42:11180-91
Mansour, Farrah H; Pestov, Dimitri G (2013) Separation of long RNA by agarose-formaldehyde gel electrophoresis. Anal Biochem 441:18-20
Pestov, Dimitri G; Shcherbik, Natalia (2012) Rapid cytoplasmic turnover of yeast ribosomes in response to rapamycin inhibition of TOR. Mol Cell Biol 32:2135-44
Wang, Minshi; Pestov, Dimitri G (2011) 5'-end surveillance by Xrn2 acts as a shared mechanism for mammalian pre-rRNA maturation and decay. Nucleic Acids Res 39:1811-22
Shcherbik, Natalia; Pestov, Dimitri G (2011) The ubiquitin ligase Rsp5 is required for ribosome stability in Saccharomyces cerevisiae. RNA 17:1422-8

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