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Bao J, Su B, Chen Z, Sun Z, Peng J, Zhao S. A UTP3-dependent nucleolar translocation pathway facilitates pre-rRNA 5'ETS processing. Nucleic Acids Res 2024; 52:9671-9694. [PMID: 39036955 PMCID: PMC11381329 DOI: 10.1093/nar/gkae631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 06/27/2024] [Accepted: 07/09/2024] [Indexed: 07/23/2024] Open
Abstract
The ribosome small subunit (SSU) is assembled by the SSU processome which contains approximately 70 non-ribosomal protein factors. Whilst the biochemical mechanisms of the SSU processome in 18S rRNA processing and maturation have been extensively studied, how SSU processome components enter the nucleolus has yet to be systematically investigated. Here, in examining the nucleolar localization of 50 human SSU processome components, we found that UTP3, together with another 24 proteins, enter the nucleolus autonomously. For the remaining 25 proteins we found that UTP3/SAS10 assists the nucleolar localization of five proteins (MPP10, UTP25, EMG1 and the two UTP-B components UTP12 and UTP13), likely through its interaction with nuclear importin α. This 'ferrying' function of UTP3 was then confirmed as conserved in the zebrafish. We also found that knockdown of human UTP3 impairs cleavage at the A0-site while loss-of-function of either utp3/sas10 or utp13/tbl3 in zebrafish causes the accumulation of aberrantly processed 5'ETS products, which highlights the crucial role of UTP3 in mediating 5'ETS processing. Mechanistically, we found that UTP3 facilitates the degradation of processed 5'ETS by recruiting the RNA exosome component EXOSC10 to the nucleolus. These findings lay the groundwork for studying the mechanism of cytoplasm-to-nucleolus trafficking of SSU processome components.
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Affiliation(s)
- Jiayang Bao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Baochun Su
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zheyan Chen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhaoxiang Sun
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shuyi Zhao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
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Fasken MB, Leung SW, Cureton LA, Al-Awadi M, Al-Kindy A, van Hoof A, Khoshnevis S, Ghalei H, Al-Maawali A, Corbett AH. A biallelic variant of the RNA exosome gene, EXOSC4, associated with neurodevelopmental defects impairs RNA exosome function and translation. J Biol Chem 2024; 300:107571. [PMID: 39009343 PMCID: PMC11357806 DOI: 10.1016/j.jbc.2024.107571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 06/15/2024] [Accepted: 07/01/2024] [Indexed: 07/17/2024] Open
Abstract
The RNA exosome is an evolutionarily conserved complex required for both precise RNA processing and decay. Pathogenic variants in EXOSC genes, which encode structural subunits of this complex, are linked to several autosomal recessive disorders. Here, we describe a missense allele of the EXOSC4 gene that causes a collection of clinical features in two affected siblings. This missense variant (NM_019037.3: exon3:c.560T>C) changes a leucine residue within a conserved region of EXOSC4 to proline (p.Leu187Pro). The two affected individuals show prenatal growth restriction, failure to thrive, global developmental delay, intracerebral and basal ganglia calcifications, and kidney failure. Homozygosity for the damaging variant was identified by exome sequencing with Sanger sequencing to confirm segregation. To explore the functional consequences of this amino acid change, we modeled EXOSC4-L187P in the corresponding budding yeast protein, Rrp41 (Rrp41-L187P). Cells that express Rrp41-L187P as the sole copy of the essential Rrp41 protein show growth defects. Steady-state levels of both Rrp41-L187P and EXOSC4-L187P are decreased compared to controls, and EXOSC4-L187P shows decreased copurification with other RNA exosome subunits. RNA exosome target transcripts accumulate in rrp41-L187P cells, including the 7S precursor of 5.8S rRNA. Polysome profiles show a decrease in actively translating ribosomes in rrp41-L187P cells as compared to control cells with the incorporation of 7S pre-rRNA into polysomes. This work adds EXOSC4 to the structural subunits of the RNA exosome that have been linked to human disease and defines foundational molecular defects that could contribute to the adverse phenotypes caused by EXOSC pathogenic variants.
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Affiliation(s)
- Milo B Fasken
- Department of Biology, Emory College of Arts and Sciences, Atlanta, Georgia USA.
| | - Sara W Leung
- Department of Biology, Emory College of Arts and Sciences, Atlanta, Georgia USA
| | - Lauryn A Cureton
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia USA; Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, USA
| | - Maha Al-Awadi
- Sultan Qaboos Hospital, Ministry of Health, Salalah, Oman
| | - Adila Al-Kindy
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Sohail Khoshnevis
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia USA
| | - Homa Ghalei
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia USA.
| | - Almundher Al-Maawali
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman; Sultan Qaboos University Hospital, Sultan Qaboos University, Muscat, Oman.
| | - Anita H Corbett
- Department of Biology, Emory College of Arts and Sciences, Atlanta, Georgia USA.
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Yim MK, Denson JM, Gold MD, Johnson SJ. Purification and characterization of Mtr4 and TRAMP from S. cerevisiae. Methods Enzymol 2022; 673:425-451. [DOI: 10.1016/bs.mie.2022.03.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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