1
|
Pekovic F, Wahle E. In Vitro Reconstitution of the Drosophila melanogaster CCR4-NOT Complex to Assay Deadenylation. Methods Mol Biol 2024; 2723:19-45. [PMID: 37824062 DOI: 10.1007/978-1-0716-3481-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The CCR4-NOT complex is a multi-subunit poly(A)-specific 3' exoribonuclease that catalyzes the deadenylation of mRNA. In this chapter, we describe procedures to express and purify recombinant Drosophila melanogaster CCR4-NOT. Furthermore, we provide protocols for preparing radioactively labeled RNA substrates and conducting in vitro deadenylation assays.
Collapse
Affiliation(s)
- Filip Pekovic
- Institute of Biochemistry and Biotechnology and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle, Germany.
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle, Germany.
| |
Collapse
|
2
|
Levdansky Y, Raisch T, Deme JC, Pekovic F, Elmlund H, Lea SM, Valkov E. Structure and assembly of the NOT10:11 module of the CCR4-NOT complex. Commun Biol 2023; 6:739. [PMID: 37460791 PMCID: PMC10352241 DOI: 10.1038/s42003-023-05122-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 07/07/2023] [Indexed: 07/20/2023] Open
Abstract
NOT1, NOT10, and NOT11 form a conserved module in the CCR4-NOT complex, critical for post-transcriptional regulation in eukaryotes, but how this module contributes to the functions of the CCR4-NOT remains poorly understood. Here, we present cryo-EM structures of human and chicken NOT1:NOT10:NOT11 ternary complexes to sub-3 Å resolution, revealing an evolutionarily conserved, flexible structure. Through biochemical dissection studies, which include the Drosophila orthologs, we show that the module assembly is hierarchical, with NOT11 binding to NOT10, which then organizes it for binding to NOT1. A short proline-rich motif in NOT11 stabilizes the entire module assembly.
Collapse
Affiliation(s)
- Yevgen Levdansky
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Tobias Raisch
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
| | - Justin C Deme
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Filip Pekovic
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Hans Elmlund
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Susan M Lea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Eugene Valkov
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
| |
Collapse
|
3
|
Pekovic F, Rammelt C, Kubíková J, Metz J, Jeske M, Wahle E. RNA binding proteins Smaug and Cup induce CCR4-NOT-dependent deadenylation of the nanos mRNA in a reconstituted system. Nucleic Acids Res 2023; 51:3950-3970. [PMID: 36951092 PMCID: PMC10164591 DOI: 10.1093/nar/gkad159] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 01/22/2023] [Accepted: 02/22/2023] [Indexed: 03/24/2023] Open
Abstract
Posttranscriptional regulation of the maternal nanos mRNA is essential for the development of the anterior - posterior axis of the Drosophila embryo. The nanos RNA is regulated by the protein Smaug, which binds to Smaug recognition elements (SREs) in the nanos 3'-UTR and nucleates the assembly of a larger repressor complex including the eIF4E-T paralog Cup and five additional proteins. The Smaug-dependent complex represses translation of nanos and induces its deadenylation by the CCR4-NOT deadenylase. Here we report an in vitro reconstitution of the Drosophila CCR4-NOT complex and Smaug-dependent deadenylation. We find that Smaug by itself is sufficient to cause deadenylation by the Drosophila or human CCR4-NOT complexes in an SRE-dependent manner. CCR4-NOT subunits NOT10 and NOT11 are dispensable, but the NOT module, consisting of NOT2, NOT3 and the C-terminal part of NOT1, is required. Smaug interacts with the C-terminal domain of NOT3. Both catalytic subunits of CCR4-NOT contribute to Smaug-dependent deadenylation. Whereas the CCR4-NOT complex itself acts distributively, Smaug induces a processive behavior. The cytoplasmic poly(A) binding protein (PABPC) has a minor inhibitory effect on Smaug-dependent deadenylation. Among the additional constituents of the Smaug-dependent repressor complex, Cup also facilitates CCR4-NOT-dependent deadenylation, both independently and in cooperation with Smaug.
Collapse
Affiliation(s)
- Filip Pekovic
- Institute of Biochemistry and Biotechnology and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120 Halle, Germany
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, 1050 Boyles Street, Frederick, MD 21702, USA
| | - Christiane Rammelt
- Institute of Biochemistry and Biotechnology and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120 Halle, Germany
| | - Jana Kubíková
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Jutta Metz
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Mandy Jeske
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120 Halle, Germany
| |
Collapse
|
4
|
Cao WX, Kabelitz S, Gupta M, Yeung E, Lin S, Rammelt C, Ihling C, Pekovic F, Low TCH, Siddiqui NU, Cheng MHK, Angers S, Smibert CA, Wühr M, Wahle E, Lipshitz HD. Precise Temporal Regulation of Post-transcriptional Repressors Is Required for an Orderly Drosophila Maternal-to-Zygotic Transition. Cell Rep 2021; 31:107783. [PMID: 32579915 PMCID: PMC7372737 DOI: 10.1016/j.celrep.2020.107783] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/06/2020] [Accepted: 05/28/2020] [Indexed: 12/12/2022] Open
Abstract
In animal embryos, the maternal-to-zygotic transition (MZT) hands developmental control from maternal to zygotic gene products. We show that the maternal proteome represents more than half of the protein-coding capacity of Drosophila melanogaster’s genome, and that 2% of this proteome is rapidly degraded during the MZT. Cleared proteins include the post-transcriptional repressors Cup, Trailer hitch (TRAL), Maternal expression at 31B (ME31B), and Smaug (SMG). Although the ubiquitin-proteasome system is necessary for clearance of these repressors, distinct E3 ligase complexes target them: the C-terminal to Lis1 Homology (CTLH) complex targets Cup, TRAL, and ME31B for degradation early in the MZT and the Skp/Cullin/F-box-containing (SCF) complex targets SMG at the end of the MZT. Deleting the C-terminal 233 amino acids of SMG abrogates F-box protein interaction and confers immunity to degradation. Persistent SMG downregulates zygotic re-expression of mRNAs whose maternal contribution is degraded by SMG. Thus, clearance of SMG permits an orderly MZT. Cao et al. show that 2% of the proteome is degraded in early Drosophila embryos, including a repressive ribonucleoprotein complex. Two E3 ubiquitin ligases separately act on distinct components of this complex to phase their clearance. Failure to degrade a key component, the Smaug RNA-binding protein, disrupts an orderly maternal-to-zygotic transition.
Collapse
Affiliation(s)
- Wen Xi Cao
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Sarah Kabelitz
- Institute of Biochemistry and Biotechnology and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06099 Halle, Germany
| | - Meera Gupta
- Department of Molecular Biology and the Lewis-Sigler Institute, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Eyan Yeung
- Department of Molecular Biology and the Lewis-Sigler Institute, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Sichun Lin
- Department of Pharmaceutical Sciences, University of Toronto, 144 College Street, Toronto, ON M5S 3M2, Canada
| | - Christiane Rammelt
- Institute of Biochemistry and Biotechnology and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06099 Halle, Germany
| | - Christian Ihling
- Institute of Pharmacy and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06099 Halle, Germany
| | - Filip Pekovic
- Institute of Biochemistry and Biotechnology and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06099 Halle, Germany
| | - Timothy C H Low
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Najeeb U Siddiqui
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Matthew H K Cheng
- Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Stephane Angers
- Department of Pharmaceutical Sciences, University of Toronto, 144 College Street, Toronto, ON M5S 3M2, Canada; Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Martin Wühr
- Department of Molecular Biology and the Lewis-Sigler Institute, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06099 Halle, Germany.
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada.
| |
Collapse
|