1
|
Zhang Y, Gao Q, Wu Y, Peng Y, Zhuang J, Yang Y, Jiang W, Liu X, Guan G. Hypermethylation and Downregulation of UTP6 Are Associated With Stemness Properties, Chemoradiotherapy Resistance, and Prognosis in Rectal Cancer: A Co-expression Network Analysis. Front Cell Dev Biol 2021; 9:607782. [PMID: 34485268 PMCID: PMC8416280 DOI: 10.3389/fcell.2021.607782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 07/12/2021] [Indexed: 12/28/2022] Open
Abstract
Background To identify the hub genes associated with chemoradiotherapy resistance in rectal cancer and explore the potential mechanism. Methods Weighted gene co-expression network analysis (WGCNA) was performed to identify the gene modules correlated with the chemoradiotherapy resistance of rectal cancer. Results The mRNA expression of 31 rectal cancer patients receiving preoperative chemoradiotherapy was described in our previous study. Through WGCNA, we demonstrated that the chemoradiotherapy resistance modules were enriched for translation, DNA replication, and the androgen receptor signaling pathway. Additionally, we identified and validated UTP6 as a new effective predictor for chemoradiotherapy sensitivity and a prognostic factor for the survival of colorectal cancer patients using our data and the GSE35452 dataset. Low UTP6 expression was correlated with significantly worse disease-free survival (DFS), overall survival (OS), and event- and relapse-free survival both in our data and the R2 Platform. Moreover, we verified the UTP6 expression in 125 locally advanced rectal cancer (LARC) patients samples by immunohistochemical analysis. The results demonstrated that low UTP6 expression was associated with worse DFS and OS by Kaplan-Meier and COX regression model analyses. Gene set enrichment and co-expression analyses showed that the mechanism of the UTP6-mediated chemoradiotherapy resistance may involve the regulation of FOXK2 expression by transcription factor pathways. Conclusion Low expression of the UTP6 was found to be associated with chemoradiotherapy resistance and the prognosis of colorectal cancer possibly via regulating FOXK2 expression by transcription factor pathways.
Collapse
Affiliation(s)
- Yiyi Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Qiao Gao
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yong Wu
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yong Peng
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Jinfu Zhuang
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yuanfeng Yang
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Weizhong Jiang
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Xing Liu
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Guoxian Guan
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| |
Collapse
|
2
|
Abstract
In the past 25 years, genetic and biochemical analyses of ribosome assembly in yeast have identified most of the factors that participate in this complex pathway and have generated models for the mechanisms driving the assembly. More recently, the publication of numerous cryo-electron microscopy structures of yeast ribosome assembly intermediates has provided near-atomic resolution snapshots of ribosome precursor particles. Satisfyingly, these structural data support the genetic and biochemical models and provide additional mechanistic insight into ribosome assembly. In this Review, we discuss the mechanisms of assembly of the yeast small ribosomal subunit and large ribosomal subunit in the nucleolus, nucleus and cytoplasm. Particular emphasis is placed on concepts such as the mechanisms of RNA compaction, the functions of molecular switches and molecular mimicry, the irreversibility of assembly checkpoints and the roles of structural and functional proofreading of pre-ribosomal particles.
Collapse
|
3
|
Assembly and structure of the SSU processome-a nucleolar precursor of the small ribosomal subunit. Curr Opin Struct Biol 2018; 49:85-93. [PMID: 29414516 DOI: 10.1016/j.sbi.2018.01.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 12/22/2022]
Abstract
The small subunit processome is the first precursor of the small eukaryotic ribosomal subunit. During its assembly in the nucleolus, many ribosome biogenesis factors, an RNA chaperone, and ribosomal proteins associate with the nascent pre-rRNA. Biochemical studies have elucidated the rRNA-subdomain dependent recruitment of these factors during SSU processome assembly and have been complemented by structural studies of the assembled particle. Ribosome biogenesis factors encapsulate and guide subdomains of pre-ribosomal RNA in distinct compartments. This prevents uncoordinated maturation and enables processing of regions not accessible in the mature subunit. By sequentially reducing conformational freedom, flexible proteins facilitate the incorporation of dynamic subcomplexes into a globular particle. Large rearrangements within the SSU processome are required for compaction into the mature small ribosomal subunit.
Collapse
|
4
|
Vincent NG, Charette JM, Baserga SJ. The SSU processome interactome in Saccharomyces cerevisiae reveals novel protein subcomplexes. RNA (NEW YORK, N.Y.) 2018; 24:77-89. [PMID: 29054886 PMCID: PMC5733573 DOI: 10.1261/rna.062927.117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/03/2017] [Indexed: 05/05/2023]
Abstract
Ribosome assembly is an evolutionarily conserved and energy intensive process required for cellular growth, proliferation, and maintenance. In yeast, assembly of the small ribosomal subunit (SSU) requires approximately 75 assembly factors that act in coordination to form the SSU processome, a 6 MDa ribonucleoprotein complex. The SSU processome is required for processing, modifying, and folding the preribosomal RNA (rRNA) to prepare it for incorporation into the mature SSU. Although the protein composition of the SSU processome has been known for some time, the interaction network of the proteins required for its assembly has remained poorly defined. Here, we have used a semi-high-throughput yeast two-hybrid (Y2H) assay and coimmunoprecipitation validation method to produce a high-confidence interactome of SSU processome assembly factors (SPAFs), providing essential insight into SSU assembly and ribosome biogenesis. Further, we used glycerol density-gradient sedimentation to reveal the presence of protein subcomplexes that have not previously been observed. Our work not only provides essential insight into SSU assembly and ribosome biogenesis, but also serves as an important resource for future investigations into how defects in biogenesis and assembly cause congenital disorders of ribosomes known as ribosomopathies.
Collapse
Affiliation(s)
- Nicholas G Vincent
- Department of Microbiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - J Michael Charette
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Susan J Baserga
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, 06520, USA
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| |
Collapse
|
5
|
Cheng J, Kellner N, Berninghausen O, Hurt E, Beckmann R. 3.2-Å-resolution structure of the 90S preribosome before A1 pre-rRNA cleavage. Nat Struct Mol Biol 2017; 24:954-964. [PMID: 28967883 DOI: 10.1038/nsmb.3476] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/04/2017] [Indexed: 12/15/2022]
Abstract
The 40S small ribosomal subunit is cotranscriptionally assembled in the nucleolus as part of a large chaperone complex called the 90S preribosome or small-subunit processome. Here, we present the 3.2-Å-resolution structure of the Chaetomium thermophilum 90S preribosome, which allowed us to build atomic structures for 34 assembly factors, including the Mpp10 complex, Bms1, Utp14 and Utp18, and the complete U3 small nucleolar ribonucleoprotein. Moreover, we visualized the U3 RNA heteroduplexes with a 5' external transcribed spacer (5' ETS) and pre-18S RNA, and their stabilization by 90S factors. Overall, the structure explains how a highly intertwined network of assembly factors and pre-rRNA guide the sequential, independent folding of the individual pre-40S domains while the RNA regions forming the 40S active sites are kept immature. Finally, by identifying the unprocessed A1 cleavage site and the nearby Utp24 endonuclease, we suggest a proofreading model for regulated 5'-ETS separation and 90S-pre-40S transition.
Collapse
Affiliation(s)
- Jingdong Cheng
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, University of Munich, Munich, Germany
| | - Nikola Kellner
- Biochemie-Zentrum der Universität Heidelberg, Heidelberg, Germany
| | - Otto Berninghausen
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, University of Munich, Munich, Germany
| | - Ed Hurt
- Biochemie-Zentrum der Universität Heidelberg, Heidelberg, Germany
| | - Roland Beckmann
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, University of Munich, Munich, Germany
| |
Collapse
|
6
|
Boissier F, Schmidt CM, Linnemann J, Fribourg S, Perez-Fernandez J. Pwp2 mediates UTP-B assembly via two structurally independent domains. Sci Rep 2017; 7:3169. [PMID: 28600509 PMCID: PMC5466602 DOI: 10.1038/s41598-017-03034-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/21/2017] [Indexed: 11/24/2022] Open
Abstract
The SSU processome constitutes a large ribonucleoprotein complex involved in the early steps of ribosome biogenesis. UTP-B is one of the first multi-subunit protein complexes that associates with the pre-ribosomal RNA to form the SSU processome. To understand the molecular basis of the hierarchical assembly of the SSU-processome, we have undergone a structural and functional analysis of the UTP-B subunit Pwp2p. We show that Pwp2p is required for the proper assembly of UTP-B and for a productive association of UTP-B with pre-rRNA. These two functions are mediated by two distinct structural domains. The N-terminal domain of Pwp2p folds into a tandem WD-repeat (tWD) that associates with Utp21p, Utp18p, and Utp6p to form a core complex. The CTDs of Pwp2p and Utp21p mediate the assembly of the heterodimer Utp12p:Utp13p that is required for the stable incorporation of the UTP-B complex in the SSU processome. Finally, we provide evidence suggesting a role of UTP-B as a platform for the binding of assembly factors during the maturation of 20S rRNA precursors.
Collapse
Affiliation(s)
- Fanny Boissier
- Université de Bordeaux, INSERM U1212, CNRS 5320, Bordeaux, France
| | - Christina Maria Schmidt
- Universität Regensburg, Biochemie-Zentrum Regensburg (BZR), Lehrstuhl Biochemie III, D-93053, Regensburg, Germany
| | - Jan Linnemann
- Universität Regensburg, Biochemie-Zentrum Regensburg (BZR), Lehrstuhl Biochemie III, D-93053, Regensburg, Germany
| | | | - Jorge Perez-Fernandez
- Universität Regensburg, Biochemie-Zentrum Regensburg (BZR), Lehrstuhl Biochemie III, D-93053, Regensburg, Germany.
| |
Collapse
|
7
|
Sun Q, Zhu X, Qi J, An W, Lan P, Tan D, Chen R, Wang B, Zheng S, Zhang C, Chen X, Zhang W, Chen J, Dong MQ, Ye K. Molecular architecture of the 90S small subunit pre-ribosome. eLife 2017; 6. [PMID: 28244370 PMCID: PMC5354517 DOI: 10.7554/elife.22086] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/26/2017] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of Saccharomyces cerevisiae 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors. DOI:http://dx.doi.org/10.7554/eLife.22086.001
Collapse
Affiliation(s)
- Qi Sun
- PTN Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China.,Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Xing Zhu
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China
| | - Jia Qi
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China.,Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Weidong An
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China.,College of Biological Sciences, China Agricultural University, Beijing, China
| | - Pengfei Lan
- National Institute of Biological Sciences, Beijing, China
| | - Dan Tan
- National Institute of Biological Sciences, Beijing, China
| | - Rongchang Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China
| | - Bing Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Sanduo Zheng
- National Institute of Biological Sciences, Beijing, China
| | - Cheng Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Xining Chen
- National Institute of Biological Sciences, Beijing, China
| | - Wei Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Jing Chen
- PTN Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China.,Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
8
|
Baßler J, Ahmed YL, Kallas M, Kornprobst M, Calviño FR, Gnädig M, Thoms M, Stier G, Ismail S, Kharde S, Castillo N, Griesel S, Bastuck S, Bradatsch B, Thomson E, Flemming D, Sinning I, Hurt E. Interaction network of the ribosome assembly machinery from a eukaryotic thermophile. Protein Sci 2017; 26:327-342. [PMID: 27863450 DOI: 10.1002/pro.3085] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/24/2016] [Accepted: 11/08/2016] [Indexed: 12/30/2022]
Abstract
Ribosome biogenesis in eukaryotic cells is a highly dynamic and complex process innately linked to cell proliferation. The assembly of ribosomes is driven by a myriad of biogenesis factors that shape pre-ribosomal particles by processing and folding the ribosomal RNA and incorporating ribosomal proteins. Biochemical approaches allowed the isolation and characterization of pre-ribosomal particles from Saccharomyces cerevisiae, which lead to a spatiotemporal map of biogenesis intermediates along the path from the nucleolus to the cytoplasm. Here, we cloned almost the entire set (∼180) of ribosome biogenesis factors from the thermophilic fungus Chaetomium thermophilum in order to perform an in-depth analysis of their protein-protein interaction network as well as exploring the suitability of these thermostable proteins for structural studies. First, we performed a systematic screen, testing about 80 factors for crystallization and structure determination. Next, we performed a yeast 2-hybrid analysis and tested about 32,000 binary combinations, which identified more than 1000 protein-protein contacts between the thermophilic ribosome assembly factors. To exemplary verify several of these interactions, we performed biochemical reconstitution with the focus on the interaction network between 90S pre-ribosome factors forming the ctUTP-A and ctUTP-B modules, and the Brix-domain containing assembly factors of the pre-60S subunit. Our work provides a rich resource for biochemical reconstitution and structural analyses of the conserved ribosome assembly machinery from a eukaryotic thermophile.
Collapse
Affiliation(s)
- Jochen Baßler
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Yasar Luqman Ahmed
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Martina Kallas
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Markus Kornprobst
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Fabiola R Calviño
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Marén Gnädig
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Matthias Thoms
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Gunter Stier
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Sherif Ismail
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Satyavati Kharde
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Nestor Castillo
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Sabine Griesel
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Sonja Bastuck
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Bettina Bradatsch
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Emma Thomson
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Dirk Flemming
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Irmgard Sinning
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Ed Hurt
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| |
Collapse
|
9
|
Chaker-Margot M, Barandun J, Hunziker M, Klinge S. Architecture of the yeast small subunit processome. Science 2016; 355:science.aal1880. [PMID: 27980088 DOI: 10.1126/science.aal1880] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/05/2016] [Indexed: 12/21/2022]
Abstract
The small subunit (SSU) processome, a large ribonucleoprotein particle, organizes the assembly of the eukaryotic small ribosomal subunit by coordinating the folding, cleavage, and modification of nascent pre-ribosomal RNA (rRNA). Here, we present the cryo-electron microscopy structure of the yeast SSU processome at 5.1-angstrom resolution. The structure reveals how large ribosome biogenesis complexes assist the 5' external transcribed spacer and U3 small nucleolar RNA in providing an intertwined RNA-protein assembly platform for the separate maturation of 18S rRNA domains. The strategic placement of a molecular motor at the center of the particle further suggests a mechanism for mediating conformational changes within this giant particle. This study provides a structural framework for a mechanistic understanding of eukaryotic ribosome assembly in the model organism Saccharomyces cerevisiae.
Collapse
Affiliation(s)
- Malik Chaker-Margot
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA.,Tri-Institutional Training Program in Chemical Biology, The Rockefeller University, New York, NY 10065, USA
| | - Jonas Barandun
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Mirjam Hunziker
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Sebastian Klinge
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA.
| |
Collapse
|