1
|
Kubitscheck U, Siebrasse JP. Pre-ribosomal particles from nucleoli to cytoplasm. Nucleus 2024; 15:2373052. [PMID: 38940456 PMCID: PMC11216097 DOI: 10.1080/19491034.2024.2373052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/21/2024] [Indexed: 06/29/2024] Open
Abstract
The analysis of nucleocytoplasmic transport of proteins and messenger RNA has been the focus of advanced microscopic approaches. Recently, it has been possible to identify and visualize individual pre-ribosomal particles on their way through the nuclear pore complex using both electron and light microscopy. In this review, we focused on the transport of pre-ribosomal particles in the nucleus on their way to and through the pores.
Collapse
Affiliation(s)
- Ulrich Kubitscheck
- Clausius Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Jan Peter Siebrasse
- Clausius Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| |
Collapse
|
2
|
Sabath K, Qiu C, Jonas S. Assembly mechanism of Integrator's RNA cleavage module. Mol Cell 2024; 84:2882-2899.e10. [PMID: 39032489 DOI: 10.1016/j.molcel.2024.06.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 05/17/2024] [Accepted: 06/26/2024] [Indexed: 07/23/2024]
Abstract
The modular Integrator complex is a transcription regulator that is essential for embryonic development. It attenuates coding gene expression via premature transcription termination and performs 3'-processing of non-coding RNAs. For both activities, Integrator requires endonuclease activity that is harbored by an RNA cleavage module consisting of INTS4-9-11. How correct assembly of Integrator modules is achieved remains unknown. Here, we show that BRAT1 and WDR73 are critical biogenesis factors for the human cleavage module. They maintain INTS9-11 inactive during maturation by physically blocking the endonuclease active site and prevent premature INTS4 association. Furthermore, BRAT1 facilitates import of INTS9-11 into the nucleus, where it is joined by INTS4. Final BRAT1 release requires locking of the mature cleavage module conformation by inositol hexaphosphate (IP6). Our data explain several neurodevelopmental disorders caused by BRAT1, WDR73, and INTS11 mutations as Integrator assembly defects and reveal that IP6 is an essential co-factor for cleavage module maturation.
Collapse
Affiliation(s)
- Kevin Sabath
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Chunhong Qiu
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Stefanie Jonas
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
| |
Collapse
|
3
|
Ghandadi M, Dobi A, Malhotra SV. A role for RIO kinases in the crosshair of cancer research and therapy. Biochim Biophys Acta Rev Cancer 2024; 1879:189100. [PMID: 38604268 DOI: 10.1016/j.bbcan.2024.189100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024]
Abstract
RIO (right open reading frame) family of kinases including RIOK1, RIOK2 and RIOK3 are known for their role in the ribosomal biogenesis. Dysfunction of RIO kinases have been implicated in malignancies, including acute myeloid leukemia, glioma, breast, colorectal, lung and prostatic adenocarcinoma suggesting RIO kinases as potential targets in cancer. In vitro, in vivo and clinical studies have demonstrated that RIO kinases are overexpressed in various types of cancers suggesting important roles in tumorigenesis, especially in metastasis. In the context of malignancies, RIO kinases are involved in cancer-promoting pathways including AKT/mTOR, RAS, p53 and NF-κB and cell cycle regulation. Here we review the role of RIO kinases in cancer development emphasizing their potential as therapeutic target and encouraging further development and investigation of inhibitors in the context of cancer.
Collapse
Affiliation(s)
- Morteza Ghandadi
- Department of Pharmacognosy and Pharmaceutical Biotechnology, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran; Medicinal Plants Research Center, Pharmaceutical Sciences Research Center, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Albert Dobi
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery at the Uniformed Services, University of the Health Sciences, Bethesda, MD 20817, USA; Henry Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Sanjay V Malhotra
- Department of Cell, Development and Cancer Biology, Oregon Health & Science University, Portland, OR 97201, USA; Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| |
Collapse
|
4
|
Messling JE, Peña-Rømer I, Moroni AS, Bruestl S, Helin K. RIO-kinase 2 is essential for hematopoiesis. PLoS One 2024; 19:e0300623. [PMID: 38564577 PMCID: PMC10986946 DOI: 10.1371/journal.pone.0300623] [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: 12/12/2023] [Accepted: 03/03/2024] [Indexed: 04/04/2024] Open
Abstract
Regulation of protein synthesis is a key factor in hematopoietic stem cell maintenance and differentiation. Rio-kinase 2 (RIOK2) is a ribosome biogenesis factor that has recently been described an important regulator of human blood cell development. Additionally, we have previously identified RIOK2 as a regulator of protein synthesis and a potential target for the treatment of acute myeloid leukemia (AML). However, its functional relevance in several organ systems, including normal hematopoiesis, is not well understood. Here, we investigate the consequences of RIOK2 loss on normal hematopoiesis using two different conditional knockout mouse models. Using competitive and non-competitive bone marrow transplantations, we demonstrate that RIOK2 is essential for the differentiation of hematopoietic stem and progenitor cells (HSPCs) as well as for the maintenance of fully differentiated blood cells in vivo as well as in vitro. Loss of RIOK2 leads to rapid death in full-body knockout mice as well as mice with RIOK2 loss specific to the hematopoietic system. Taken together, our results indicate that regulation of protein synthesis and ribosome biogenesis by RIOK2 is essential for the function of the hematopoietic system.
Collapse
Affiliation(s)
- Jan-Erik Messling
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | | | - Ann Sophie Moroni
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Sarah Bruestl
- The Institute of Cancer Research, London, United Kingdom
| | - Kristian Helin
- The Institute of Cancer Research, London, United Kingdom
| |
Collapse
|
5
|
Saba JA, Huang Z, Schole KL, Ye X, Bhatt SD, Li Y, Timp W, Cheng J, Green R. LARP1 senses free ribosomes to coordinate supply and demand of ribosomal proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.01.565189. [PMID: 37961604 PMCID: PMC10635049 DOI: 10.1101/2023.11.01.565189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Terminal oligopyrimidine motif-containing mRNAs (TOPs) encode all ribosomal proteins in mammals and are regulated to tune ribosome synthesis to cell state. Previous studies implicate LARP1 in 40S- or 80S-ribosome complexes that repress and stabilize TOPs. However, a mechanistic understanding of how LARP1 and TOPs interact with these complexes to coordinate TOP outcomes is lacking. Here, we show that LARP1 senses the cellular supply of ribosomes by directly binding non-translating ribosomal subunits. Cryo-EM structures reveal a previously uncharacterized domain of LARP1 bound to and occluding the 40S mRNA channel. Free cytosolic ribosomes induce sequestration of TOPs in repressed 80S-LARP1-TOP complexes independent of alterations in mTOR signaling. Together, this work demonstrates a general ribosome-sensing function of LARP1 that allows it to tune ribosome protein synthesis to cellular demand.
Collapse
Affiliation(s)
- James A. Saba
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- These authors contributed equally
| | - Zixuan Huang
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
- These authors contributed equally
| | - Kate L. Schole
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xianwen Ye
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
| | - Shrey D. Bhatt
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yi Li
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jingdong Cheng
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| |
Collapse
|
6
|
Xiong H, Yu Q, Ma H, Yu X, Ouyang Y, Zhang ZM, Zhou W, Zhang Z, Cai Q. Exploration of tricyclic heterocycles as core structures for RIOK2 inhibitors. RSC Med Chem 2023; 14:2007-2011. [PMID: 37859717 PMCID: PMC10583808 DOI: 10.1039/d3md00209h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/20/2023] [Indexed: 10/21/2023] Open
Abstract
Right open reading frame kinase 2 (RIOK2) is an atypical kinase and has been proved to be involved in multiple human cancers including non-small cell lung cancer (NSCLC), acute myeloid leukemia (AML), glioblastoma and anemia. Although tremendous efforts have been devoted to the studies of RIOK2, its biological functions remain poorly understood. It is highly important to develop potent and selective RIOK2 inhibitors as potential research tools to elucidate its functions and as drug candidates for further therapies. We have previously identified a highly potent and selective RIOK2 inhibitor (CQ211). To confirm the importance of the "V-shaped" structure of CQ211 for binding with RIOK2, a variety of tricyclic compounds with different core structures instead of the [1,2,3]triazolo[4,5-c]quinolin-4-one core of CQ211 were designed, synthesized, and the binding affinities of these tricyclic heterocycles with RIOK2 were also evaluated.
Collapse
Affiliation(s)
- Huilan Xiong
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, College of Pharmacy, Jinan University 601 Huangpu Avenue West Guangzhou 510632 China
| | - Qiuchun Yu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, College of Pharmacy, Jinan University 601 Huangpu Avenue West Guangzhou 510632 China
| | - Haowen Ma
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, College of Pharmacy, Jinan University 601 Huangpu Avenue West Guangzhou 510632 China
| | - Xiuwen Yu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, College of Pharmacy, Jinan University 601 Huangpu Avenue West Guangzhou 510632 China
| | - Yifan Ouyang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, College of Pharmacy, Jinan University 601 Huangpu Avenue West Guangzhou 510632 China
| | - Zhi-Min Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, College of Pharmacy, Jinan University 601 Huangpu Avenue West Guangzhou 510632 China
| | - Wei Zhou
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, College of Pharmacy, Jinan University 601 Huangpu Avenue West Guangzhou 510632 China
| | - Zhang Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, College of Pharmacy, Jinan University 601 Huangpu Avenue West Guangzhou 510632 China
| | - Qian Cai
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, College of Pharmacy, Jinan University 601 Huangpu Avenue West Guangzhou 510632 China
| |
Collapse
|
7
|
Lefebvre C, Pellizzari S, Bhat V, Jurcic K, Litchfield DW, Allan AL. Involvement of the AKT Pathway in Resistance to Erlotinib and Cabozantinib in Triple-Negative Breast Cancer Cell Lines. Biomedicines 2023; 11:2406. [PMID: 37760847 PMCID: PMC10525382 DOI: 10.3390/biomedicines11092406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/14/2023] [Accepted: 08/26/2023] [Indexed: 09/29/2023] Open
Abstract
Resistance to protein tyrosine kinase inhibitors (TKIs) presents a significant challenge in therapeutic target development for cancers such as triple-negative breast cancer (TNBC), where conventional therapies are ineffective at combatting systemic disease. Due to increased expression, the receptor tyrosine kinases EGFR (epidermal growth factor receptor) and c-Met are potential targets for treatment. However, targeted anti-EGFR and anti-c-Met therapies have faced mixed results in clinical trials due to acquired resistance. We hypothesize that adaptive responses in regulatory kinase networks within the EGFR and c-Met signaling axes contribute to the development of acquired erlotinib and cabozantinib resistance. To test this, we developed two separate models for cabozantinib and erlotinib resistance using the MDA-MB-231 and MDA-MB-468 cell lines, respectively. We observed that erlotinib- or cabozantinib-resistant cell lines demonstrate enhanced cell proliferation, migration, invasion, and activation of EGFR or c-Met downstream signaling (respectively). Using a SILAC (Stable Isotope Labeling of Amino acids in Cell Culture)-labeled quantitative mass spectrometry proteomics approach, we assessed the effects of erlotinib or cabozantinib resistance on the phosphoproteome, proteome, and kinome. Using this integrated proteomics approach, we identified several potential kinase mediators of cabozantinib resistance and confirmed the contribution of AKT1 to erlotinib resistance in TNBC-resistant cell lines.
Collapse
Affiliation(s)
- Cory Lefebvre
- London Regional Cancer Program, London Health Sciences Centre, London, ON N6A 5W9, Canada; (C.L.); (S.P.); (V.B.)
- Department of Anatomy & Cell Biology, Western University, London, ON N6A 3K7, Canada
| | - Sierra Pellizzari
- London Regional Cancer Program, London Health Sciences Centre, London, ON N6A 5W9, Canada; (C.L.); (S.P.); (V.B.)
- Department of Anatomy & Cell Biology, Western University, London, ON N6A 3K7, Canada
| | - Vasudeva Bhat
- London Regional Cancer Program, London Health Sciences Centre, London, ON N6A 5W9, Canada; (C.L.); (S.P.); (V.B.)
- Department of Anatomy & Cell Biology, Western University, London, ON N6A 3K7, Canada
| | - Kristina Jurcic
- Department of Biochemistry, Western University, London, ON N6A 3K7, Canada; (K.J.); (D.W.L.)
| | - David W. Litchfield
- Department of Biochemistry, Western University, London, ON N6A 3K7, Canada; (K.J.); (D.W.L.)
- Department of Oncology, Western University, London, ON N6A 3K7, Canada
| | - Alison L. Allan
- London Regional Cancer Program, London Health Sciences Centre, London, ON N6A 5W9, Canada; (C.L.); (S.P.); (V.B.)
- Department of Anatomy & Cell Biology, Western University, London, ON N6A 3K7, Canada
- Department of Oncology, Western University, London, ON N6A 3K7, Canada
- Lawson Health Research Institute, London, ON N6A 5W9, Canada
| |
Collapse
|
8
|
Junod SL, Tingey M, Kelich JM, Goryaynov A, Herbine K, Yang W. Dynamics of nuclear export of pre-ribosomal subunits revealed by high-speed single-molecule microscopy in live cells. iScience 2023; 26:107445. [PMID: 37599825 PMCID: PMC10433129 DOI: 10.1016/j.isci.2023.107445] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 06/24/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
We present a study on the nuclear export efficiency and time of pre-ribosomal subunits in live mammalian cells, using high-speed single-molecule tracking and single-molecule fluorescence resonance energy transfer techniques. Our findings reveal that pre-ribosomal particles exhibit significantly higher nuclear export efficiency compared to other large cargos like mRNAs, with around two-thirds of interactions between the pre-60S or pre-40S and the nuclear pore complexes (NPCs) resulting in successful export to the cytoplasm. We also demonstrate that nuclear transport receptor (NTR) chromosomal maintenance 1 (CRM1) plays a crucial role in nuclear export efficiency, with pre-60S and pre-40S particle export efficiency decreasing by 11-17-fold when CRM1 is inhibited. Our results suggest that multiple copies of CRM1 work cooperatively to chaperone pre-ribosomal subunits through the NPC, thus increasing export efficiency and decreasing export time. Significantly, this cooperative NTR mechanism extends beyond pre-ribosomal subunits, as evidenced by the enhanced nucleocytoplasmic transport of proteins.
Collapse
Affiliation(s)
- Samuel L. Junod
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Mark Tingey
- Department of Biology, Temple University, Philadelphia, PA, USA
| | | | | | - Karl Herbine
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA, USA
| |
Collapse
|
9
|
Parker MD, Karbstein K. Quality control ensures fidelity in ribosome assembly and cellular health. J Cell Biol 2023; 222:e202209115. [PMID: 36790396 PMCID: PMC9960125 DOI: 10.1083/jcb.202209115] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/09/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
The coordinated integration of ribosomal RNA and protein into two functional ribosomal subunits is safeguarded by quality control checkpoints that ensure ribosomes are correctly assembled and functional before they engage in translation. Quality control is critical in maintaining the integrity of ribosomes and necessary to support healthy cell growth and prevent diseases associated with mistakes in ribosome assembly. Its importance is demonstrated by the finding that bypassing quality control leads to misassembled, malfunctioning ribosomes with altered translation fidelity, which change gene expression and disrupt protein homeostasis. In this review, we outline our understanding of quality control within ribosome synthesis and how failure to enforce quality control contributes to human disease. We first provide a definition of quality control to guide our investigation, briefly present the main assembly steps, and then examine stages of assembly that test ribosome function, establish a pass-fail system to evaluate these functions, and contribute to altered ribosome performance when bypassed, and are thus considered "quality control."
Collapse
Affiliation(s)
- Melissa D. Parker
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA
- University of Florida—Scripps Biomedical Research, Jupiter, FL, USA
| | - Katrin Karbstein
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA
- University of Florida—Scripps Biomedical Research, Jupiter, FL, USA
- Howard Hughes Medical Institute Faculty Scholar, Howard Hughes Medical Institute, Chevy Chase, MD, USA
| |
Collapse
|
10
|
Dörner K, Ruggeri C, Zemp I, Kutay U. Ribosome biogenesis factors-from names to functions. EMBO J 2023; 42:e112699. [PMID: 36762427 PMCID: PMC10068337 DOI: 10.15252/embj.2022112699] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/13/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
The assembly of ribosomal subunits is a highly orchestrated process that involves a huge cohort of accessory factors. Most eukaryotic ribosome biogenesis factors were first identified by genetic screens and proteomic approaches of pre-ribosomal particles in Saccharomyces cerevisiae. Later, research on human ribosome synthesis not only demonstrated that the requirement for many of these factors is conserved in evolution, but also revealed the involvement of additional players, reflecting a more complex assembly pathway in mammalian cells. Yet, it remained a challenge for the field to assign a function to many of the identified factors and to reveal their molecular mode of action. Over the past decade, structural, biochemical, and cellular studies have largely filled this gap in knowledge and led to a detailed understanding of the molecular role that many of the players have during the stepwise process of ribosome maturation. Such detailed knowledge of the function of ribosome biogenesis factors will be key to further understand and better treat diseases linked to disturbed ribosome assembly, including ribosomopathies, as well as different types of cancer.
Collapse
Affiliation(s)
- Kerstin Dörner
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, Zurich, Switzerland
| | - Chiara Ruggeri
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,RNA Biology Ph.D. Program, Zurich, Switzerland
| | - Ivo Zemp
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Ulrike Kutay
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
11
|
Matsuzaki Y, Naito Y, Miura N, Mori T, Watabe Y, Yoshimoto S, Shibahara T, Takano M, Honda K. RIOK2 Contributes to Cell Growth and Protein Synthesis in Human Oral Squamous Cell Carcinoma. Curr Oncol 2022; 30:381-391. [PMID: 36661680 PMCID: PMC9857684 DOI: 10.3390/curroncol30010031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Ribosomes are responsible for the protein synthesis that maintains cellular homeostasis and is required for the rapid cellular division of cancer cells. However, the role of ribosome biogenesis mediators in the malignant behavior of tongue squamous cell carcinoma (TSCC) is unknown. In this study, we found that the expression of RIOK2, a key enzyme involved in the maturation steps of the pre-40S ribosomal complex, was significantly associated with poorer overall survival in patients with TSCC. Further, multivariate analysis revealed that RIOK2 is an independent prognostic factor (hazard ratio, 3.53; 95% confidence interval, 1.19-10.91). Inhibition of RIOK2 expression by siRNA decreased cell growth and S6 ribosomal protein expression in oral squamous cell carcinoma cell lines. RIOK2 knockdown also led to a significant decrease in the protein synthesis in cancer cells. RIOK2 has potential application as a novel therapeutic target for TSCC treatment.
Collapse
Affiliation(s)
- Yusuke Matsuzaki
- Department of Bioregulation, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo 113-8602, Japan
- Department of Oral and Maxillofacial Surgery, Tokyo Dental College, Tokyo 101-0061, Japan
| | - Yutaka Naito
- Department of Bioregulation, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo 113-8602, Japan
| | - Nami Miura
- Department of Bioregulation, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo 113-8602, Japan
| | - Taisuke Mori
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Yukio Watabe
- Department of Dentistry and Oral Surgery, Tokyo Metropolitan Tama Medical Center, Tokyo 183-8524, Japan
| | - Seiichi Yoshimoto
- Department of Head and Neck Surgery, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Takahiko Shibahara
- Department of Oral and Maxillofacial Surgery, Tokyo Dental College, Tokyo 101-0061, Japan
| | - Masayuki Takano
- Department of Oral and Maxillofacial Surgery, Tokyo Dental College, Tokyo 101-0061, Japan
| | - Kazufumi Honda
- Department of Bioregulation, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo 113-8602, Japan
- Department of Bioregulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8602, Japan
| |
Collapse
|
12
|
Li K, Zou J, Yan H, Li Y, Li MM, Liu Z. Pan-cancer analyses reveal multi-omics and clinical characteristics of RIO kinase 2 in cancer. Front Chem 2022; 10:1024670. [DOI: 10.3389/fchem.2022.1024670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/17/2022] [Indexed: 11/29/2022] Open
Abstract
RIO kinase 2 has emerged as a critical kinase for ribosome maturation, and recently it has also been found to play a fundamental role in cancer, being involved in the occurrence and progression of glioblastoma, liver cancer, prostate cancer, non-small cell lung cancer, and acute myeloid leukemia. However, our knowledge in this regard is fragmented and limited and it is difficult to determine the exact role of RIO kinase 2 in tumors. Here, we conducted an integrated pan-cancer analysis comprising 33 cancer-types to determine the function of RIO kinase 2 in malignancies. The results show that RIO kinase 2 is highly expressed in all types of cancer and is significantly associated with tumor survival, metastasis, and immune cell infiltration. Moreover, RIO kinase 2 alteration via DNA methylation, and protein phosphorylation are involved in tumorigenesis. In summary, RIO kinase two serves as a promising target for the identification of cancer and increases our understanding of tumorigenesis and cancer progression and enhancing the ultimate goal of improved treatment for these diseases.
Collapse
|
13
|
Lau B, Beine-Golovchuk O, Kornprobst M, Cheng J, Kressler D, Jády B, Kiss T, Beckmann R, Hurt E. Cms1 coordinates stepwise local 90S pre-ribosome assembly with timely snR83 release. Cell Rep 2022; 41:111684. [PMID: 36417864 PMCID: PMC9715914 DOI: 10.1016/j.celrep.2022.111684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/01/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022] Open
Abstract
Ribosome synthesis begins in the nucleolus with 90S pre-ribosome construction, but little is known about how the many different snoRNAs that modify the pre-rRNA are timely guided to their target sites. Here, we report a role for Cms1 in such a process. Initially, we discovered CMS1 as a null suppressor of a nop14 mutant impaired in Rrp12-Enp1 factor recruitment to the 90S. Further investigations detected Cms1 at the 18S rRNA 3' major domain of an early 90S that carried H/ACA snR83, which is known to guide pseudouridylation at two target sites within the same subdomain. Cms1 co-precipitates with many 90S factors, but Rrp12-Enp1 encircling the 3' major domain in the mature 90S is decreased. We suggest that Cms1 associates with the 3' major domain during early 90S biogenesis to restrict premature Rrp12-Enp1 binding but allows snR83 to timely perform its modification role before the next 90S assembly steps coupled with Cms1 release take place.
Collapse
Affiliation(s)
- Benjamin Lau
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Olga Beine-Golovchuk
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Markus Kornprobst
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Jingdong Cheng
- Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, Shanghai 200032, China
| | - Dieter Kressler
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Beáta Jády
- Laboratoire de Biologie Moléculaire Eucaryote du CNRS, Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse Cedex 9, France
| | - Tamás Kiss
- Laboratoire de Biologie Moléculaire Eucaryote du CNRS, Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse Cedex 9, France
| | - Roland Beckmann
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany,Corresponding author
| | - Ed Hurt
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany,Corresponding author
| |
Collapse
|
14
|
Cheng J, Lau B, Thoms M, Ameismeier M, Berninghausen O, Hurt E, Beckmann R. The nucleoplasmic phase of pre-40S formation prior to nuclear export. Nucleic Acids Res 2022; 50:11924-11937. [PMID: 36321656 PMCID: PMC9723619 DOI: 10.1093/nar/gkac961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/04/2022] [Accepted: 10/21/2022] [Indexed: 11/07/2022] Open
Abstract
Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural transitions of assembly intermediates from human and yeast cells during the nucleoplasmic maturation phase. After dissociation of all 90S factors, the 40S body adopts a close-to-mature conformation, whereas the 3' major domain, later forming the 40S head, remains entirely immature. A first coordination is facilitated by the assembly factors TSR1 and BUD23-TRMT112, followed by re-positioning of RRP12 that is already recruited early to the 90S for further head rearrangements. Eventually, the uS2 cluster, CK1 (Hrr25 in yeast) and the export factor SLX9 associate with the pre-40S to provide export competence. These exemplary findings reveal the evolutionary conserved mechanism of how yeast and humans assemble the 40S ribosomal subunit, but reveal also a few minor differences.
Collapse
Affiliation(s)
- Jingdong Cheng
- Gene Center and Department of Biochemistry, University of Munich LMU, Feodor-Lynen-Str. 25, 81377 Munich, Germany,Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Dong’an Road 131, 200032 Shanghai, China
| | - Benjamin Lau
- BZH, University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Matthias Thoms
- Gene Center and Department of Biochemistry, University of Munich LMU, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Michael Ameismeier
- Gene Center and Department of Biochemistry, University of Munich LMU, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Otto Berninghausen
- Gene Center and Department of Biochemistry, University of Munich LMU, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Ed Hurt
- Correspondence may also be addressed to Ed Hurt.
| | - Roland Beckmann
- To whom correspondence should be addressed. Tel: +49 89 218076900; Fax: +49 89 218076945;
| |
Collapse
|
15
|
Analysis of RIOK2 Functions in Mediating the Toxic Effects of Deoxynivalenol in Porcine Intestinal Epithelial Cells. Int J Mol Sci 2022; 23:ijms232112712. [PMID: 36361502 PMCID: PMC9653672 DOI: 10.3390/ijms232112712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/13/2022] [Accepted: 10/20/2022] [Indexed: 01/24/2023] Open
Abstract
Deoxynivalenol (DON) is a type of mycotoxin that threatens human and livestock health. Right open reading frame kinase 2 (RIOK2) is a kinase that has a pivotal function in ribosome maturation and cell cycle progression. This study aims to clarify the role of the RIOK2 gene in DON-induced cytotoxicity regulation in porcine intestinal epithelial cells (IPEC-J2). Cell viability assay and flow cytometry showed that the knockdown of RIOK2 inhibited proliferation and induced apoptosis, cell cycle arrest, and oxidative stress in DON-induced IPEC-J2. Then, transcriptome profiling identified candidate genes and pathways that closely interacted with both DON cytotoxicity regulation and RIOK2 expression. Furthermore, RIOK2 interference promoted the activation of the MAPK signaling pathway by increasing the phosphorylation of ERK and JNK. Additionally, we performed the dual-luciferase reporter and ChIP assays to elucidate that the expression of RIOK2 was influenced by the binding of transcription factor Sp1 with the promoter region. Briefly, the reduced expression of the RIOK2 gene exacerbates the cytotoxic effects induced by DON in IPEC-J2. Our findings provide insights into the control strategies for DON contamination by identifying functional genes and effective molecular markers.
Collapse
|
16
|
Kafkia E, Andres-Pons A, Ganter K, Seiler M, Smith TS, Andrejeva A, Jouhten P, Pereira F, Franco C, Kuroshchenkova A, Leone S, Sawarkar R, Boston R, Thaventhiran J, Zaugg JB, Lilley KS, Lancrin C, Beck M, Patil KR. Operation of a TCA cycle subnetwork in the mammalian nucleus. SCIENCE ADVANCES 2022; 8:eabq5206. [PMID: 36044572 PMCID: PMC9432838 DOI: 10.1126/sciadv.abq5206] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/14/2022] [Indexed: 05/23/2023]
Abstract
Nucleic acid and histone modifications critically depend on the tricarboxylic acid (TCA) cycle for substrates and cofactors. Although a few TCA cycle enzymes have been reported in the nucleus, the corresponding pathways are considered to operate in mitochondria. Here, we show that a part of the TCA cycle is operational also in the nucleus. Using 13C-tracer analysis, we identified activity of glutamine-to-fumarate, citrate-to-succinate, and glutamine-to-aspartate routes in the nuclei of HeLa cells. Proximity labeling mass spectrometry revealed a spatial vicinity of the involved enzymes with core nuclear proteins. We further show nuclear localization of aconitase 2 and 2-oxoglutarate dehydrogenase in mouse embryonic stem cells. Nuclear localization of the latter enzyme, which produces succinyl-CoA, changed from pluripotency to a differentiated state with accompanying changes in the nuclear protein succinylation. Together, our results demonstrate operation of an extended metabolic pathway in the nucleus, warranting a revision of the canonical view on metabolic compartmentalization.
Collapse
Affiliation(s)
- Eleni Kafkia
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Amparo Andres-Pons
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Kerstin Ganter
- European Molecular Biology Laboratory (EMBL), Rome, Italy
| | - Markus Seiler
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Tom S. Smith
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Anna Andrejeva
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Paula Jouhten
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- VTT Technical Research Center of Finland, Helsinki, Finland
| | - Filipa Pereira
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Catarina Franco
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Anna Kuroshchenkova
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Sergio Leone
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Ritwick Sawarkar
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Rebecca Boston
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - James Thaventhiran
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Judith B. Zaugg
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | | | - Martin Beck
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Kiran Raosaheb Patil
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| |
Collapse
|
17
|
Ouyang Y, Si H, Zhu C, Zhong L, Ma H, Li Z, Xiong H, Liu T, Liu Z, Zhang Z, Zhang ZM, Cai Q. Discovery of 8-(6-Methoxypyridin-3-yl)-1-(4-(piperazin-1-yl)-3-(trifluoromethyl)phenyl)-1,5-dihydro- 4H-[1,2,3]triazolo[4,5- c]quinolin-4-one (CQ211) as a Highly Potent and Selective RIOK2 Inhibitor. J Med Chem 2022; 65:7833-7842. [PMID: 35584513 DOI: 10.1021/acs.jmedchem.2c00271] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RIOK2 is an atypical kinase implicated in multiple human cancers. Although recent studies establish the role of RIOK2 in ribosome maturation and cell cycle progression, its biological functions remain poorly elucidated, hindering the potential to explore RIOK2 as a therapeutic target. Here, we report the discovery of CQ211, the most potent and selective RIOK2 inhibitor reported so far. CQ211 displays a high binding affinity (Kd = 6.1 nM) and shows excellent selectivity to RIOK2 in both enzymatic and cellular studies. It also exhibits potent proliferation inhibition activity against multiple cancer cell lines and demonstrates promising in vivo efficacy in mouse xenograft models. The crystal structure of RIOK2-CQ211 sheds light on the molecular mechanism of inhibition and informs the subsequent optimization. The study provides a cell-active chemical probe for verifying RIOK2 functions, which may also serve as a leading molecule in the development of therapeutic RIOK2 inhibitors.
Collapse
Affiliation(s)
- Yifan Ouyang
- College of Pharmacy, Jinan University, No. 601 Huangpu Avenue West, Guangzhou 510530, China
| | - Hongfei Si
- College of Pharmacy, Jinan University, No. 601 Huangpu Avenue West, Guangzhou 510530, China
| | - Chengjun Zhu
- College of Pharmacy, Jinan University, No. 601 Huangpu Avenue West, Guangzhou 510530, China
| | - Liang Zhong
- College of Pharmacy, Jinan University, No. 601 Huangpu Avenue West, Guangzhou 510530, China
| | - Haowen Ma
- College of Pharmacy, Jinan University, No. 601 Huangpu Avenue West, Guangzhou 510530, China
| | - Zongyang Li
- Department of Neurosurgery, Shenzhen Key Laboratory of Neurosurgery, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518035, China
| | - Huilan Xiong
- College of Pharmacy, Jinan University, No. 601 Huangpu Avenue West, Guangzhou 510530, China
| | - Tongzheng Liu
- College of Pharmacy, Jinan University, No. 601 Huangpu Avenue West, Guangzhou 510530, China
| | - Zhong Liu
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, No. 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhang Zhang
- College of Pharmacy, Jinan University, No. 601 Huangpu Avenue West, Guangzhou 510530, China
| | - Zhi-Min Zhang
- College of Pharmacy, Jinan University, No. 601 Huangpu Avenue West, Guangzhou 510530, China
| | - Qian Cai
- College of Pharmacy, Jinan University, No. 601 Huangpu Avenue West, Guangzhou 510530, China
| |
Collapse
|
18
|
Dörner K, Badertscher L, Horváth B, Hollandi R, Molnár C, Fuhrer T, Meier R, Sárazová M, van den Heuvel J, Zamboni N, Horvath P, Kutay U. Genome-wide RNAi screen identifies novel players in human 60S subunit biogenesis including key enzymes of polyamine metabolism. Nucleic Acids Res 2022; 50:2872-2888. [PMID: 35150276 PMCID: PMC8934630 DOI: 10.1093/nar/gkac072] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/18/2022] [Accepted: 01/25/2022] [Indexed: 12/19/2022] Open
Abstract
Ribosome assembly is an essential process that is linked to human congenital diseases and tumorigenesis. While great progress has been made in deciphering mechanisms governing ribosome biogenesis in eukaryotes, an inventory of factors that support ribosome synthesis in human cells is still missing, in particular regarding the maturation of the large 60S subunit. Here, we performed a genome-wide RNAi screen using an imaging-based, single cell assay to unravel the cellular machinery promoting 60S subunit assembly in human cells. Our screen identified a group of 310 high confidence factors. These highlight the conservation of the process across eukaryotes and reveal the intricate connectivity of 60S subunit maturation with other key cellular processes, including splicing, translation, protein degradation, chromatin organization and transcription. Intriguingly, we also identified a cluster of hits comprising metabolic enzymes of the polyamine synthesis pathway. We demonstrate that polyamines, which have long been used as buffer additives to support ribosome assembly in vitro, are required for 60S maturation in living cells. Perturbation of polyamine metabolism results in early defects in 60S but not 40S subunit maturation. Collectively, our data reveal a novel function for polyamines in living cells and provide a rich source for future studies on ribosome synthesis.
Collapse
Affiliation(s)
- Kerstin Dörner
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
- Molecular Life Sciences Ph.D. Program, 8057 Zurich, Switzerland
| | - Lukas Badertscher
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
- Molecular Life Sciences Ph.D. Program, 8057 Zurich, Switzerland
| | - Bianka Horváth
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
- Molecular Life Sciences Ph.D. Program, 8057 Zurich, Switzerland
| | - Réka Hollandi
- Synthetic and Systems Biology Unit, Biological Research Center, 6726 Szeged, Hungary
| | - Csaba Molnár
- Synthetic and Systems Biology Unit, Biological Research Center, 6726 Szeged, Hungary
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Roger Meier
- ScopeM, ETH Zürich, 8093 Zürich, Switzerland
| | - Marie Sárazová
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jasmin van den Heuvel
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Peter Horvath
- Synthetic and Systems Biology Unit, Biological Research Center, 6726 Szeged, Hungary
- Institute for Molecular Medicine Finland, University of Helsinki, 00014 Helsinki, Finland
| | - Ulrike Kutay
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| |
Collapse
|
19
|
Wing CE, Fung HYJ, Chook YM. Karyopherin-mediated nucleocytoplasmic transport. Nat Rev Mol Cell Biol 2022; 23:307-328. [PMID: 35058649 PMCID: PMC10101760 DOI: 10.1038/s41580-021-00446-7] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2021] [Indexed: 12/25/2022]
Abstract
Efficient and regulated nucleocytoplasmic trafficking of macromolecules to the correct subcellular compartment is critical for proper functions of the eukaryotic cell. The majority of the macromolecular traffic across the nuclear pores is mediated by the Karyopherin-β (or Kap) family of nuclear transport receptors. Work over more than two decades has shed considerable light on how the different Kap family members bring their respective cargoes into the nucleus or the cytoplasm in efficient and highly regulated manners. In this Review, we overview the main features and established functions of Kap family members, describe how Kaps recognize their cargoes and discuss the different ways in which these Kap-cargo interactions can be regulated, highlighting new findings and open questions. We also describe current knowledge of the import and export of the components of three large gene expression machines - the core replisome, RNA polymerase II and the ribosome - pointing out the questions that persist about how such large macromolecular complexes are trafficked to serve their function in a designated subcellular location.
Collapse
|
20
|
Messling JE, Agger K, Andersen KL, Kromer K, Kuepper HM, Lund AH, Helin K. Targeting RIOK2 ATPase activity leads to decreased protein synthesis and cell death in acute myeloid leukemia. Blood 2022; 139:245-255. [PMID: 34359076 PMCID: PMC8759535 DOI: 10.1182/blood.2021012629] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/29/2021] [Indexed: 01/16/2023] Open
Abstract
Novel therapies for the treatment of acute myeloid leukemia (AML) are urgently needed, because current treatments do not cure most patients with AML. We report a domain-focused, kinome-wide CRISPR-Cas9 screening that identified protein kinase targets for the treatment of AML, which led to the identification of Rio-kinase 2 (RIOK2) as a potential novel target. Loss of RIOK2 led to a decrease in protein synthesis and to ribosomal instability followed by apoptosis in leukemic cells, but not in fibroblasts. Moreover, the ATPase function of RIOK2 was necessary for cell survival. When a small-molecule inhibitor was used, pharmacological inhibition of RIOK2 similarly led to loss of protein synthesis and apoptosis and affected leukemic cell growth in vivo. Our results provide proof of concept for targeting RIOK2 as a potential treatment of patients with AML.
Collapse
Affiliation(s)
- Jan-Erik Messling
- Biotech Research and Innovation Centre and
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark; and
| | - Karl Agger
- Biotech Research and Innovation Centre and
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark; and
| | | | - Kristina Kromer
- Biotech Research and Innovation Centre and
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark; and
| | - Hanna M Kuepper
- Biotech Research and Innovation Centre and
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark; and
| | | | - Kristian Helin
- Biotech Research and Innovation Centre and
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark; and
- Cell Biology Program and
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
21
|
Road to RIO-kinase 2 for AML therapy. Blood 2022; 139:156-157. [PMID: 35024808 DOI: 10.1182/blood.2021013618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/12/2021] [Indexed: 11/20/2022] Open
|
22
|
Ghosh S, Raundhal M, Myers SA, Carr SA, Chen X, Petsko GA, Glimcher LH. Identification of RIOK2 as a master regulator of human blood cell development. Nat Immunol 2022; 23:109-121. [PMID: 34937919 DOI: 10.1038/s41590-021-01079-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 10/25/2021] [Indexed: 11/09/2022]
Abstract
Anemia is a major comorbidity in aging, chronic kidney and inflammatory diseases, and hematologic malignancies. However, the transcriptomic networks governing hematopoietic differentiation in blood cell development remain incompletely defined. Here we report that the atypical kinase RIOK2 (right open reading frame kinase 2) is a master transcription factor (TF) that not only drives erythroid differentiation, but also simultaneously suppresses megakaryopoiesis and myelopoiesis in primary human stem and progenitor cells. Our study reveals the previously uncharacterized winged helix-turn-helix DNA-binding domain and two transactivation domains of RIOK2 that are critical to regulate key hematopoietic TFs GATA1, GATA2, SPI1, RUNX3 and KLF1. This establishes RIOK2 as an integral component of the transcriptional regulatory network governing human hematopoietic differentiation. Importantly, RIOK2 mRNA expression significantly correlates with these TFs and other hematopoietic genes in myelodysplastic syndromes, acute myeloid leukemia and chronic kidney disease. Further investigation of RIOK2-mediated transcriptional pathways should yield therapeutic approaches to correct defective hematopoiesis in hematologic disorders.
Collapse
Affiliation(s)
- Shrestha Ghosh
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Mahesh Raundhal
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Immunology, Harvard Medical School, Boston, MA, USA.,Jnana Therapeutics, Boston, MA, USA
| | - Samuel A Myers
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xi Chen
- Department of Molecular & Cellular Biology, Lester and Sue Smith Breast Center, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Gregory A Petsko
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Laurie H Glimcher
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. .,Department of Immunology, Harvard Medical School, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
23
|
Mitterer V, Pertschy B. RNA folding and functions of RNA helicases in ribosome biogenesis. RNA Biol 2022; 19:781-810. [PMID: 35678541 PMCID: PMC9196750 DOI: 10.1080/15476286.2022.2079890] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic ribosome biogenesis involves the synthesis of ribosomal RNA (rRNA) and its stepwise folding into the unique structure present in mature ribosomes. rRNA folding starts already co-transcriptionally in the nucleolus and continues when pre-ribosomal particles further maturate in the nucleolus and upon their transit to the nucleoplasm and cytoplasm. While the approximate order of folding of rRNA subdomains is known, especially from cryo-EM structures of pre-ribosomal particles, the actual mechanisms of rRNA folding are less well understood. Both small nucleolar RNAs (snoRNAs) and proteins have been implicated in rRNA folding. snoRNAs hybridize to precursor rRNAs (pre-rRNAs) and thereby prevent premature folding of the respective rRNA elements. Ribosomal proteins (r-proteins) and ribosome assembly factors might have a similar function by binding to rRNA elements and preventing their premature folding. Besides that, a small group of ribosome assembly factors are thought to play a more active role in rRNA folding. In particular, multiple RNA helicases participate in individual ribosome assembly steps, where they are believed to coordinate RNA folding/unfolding events or the release of proteins from the rRNA. In this review, we summarize the current knowledge on mechanisms of RNA folding and on the specific function of the individual RNA helicases involved. As the yeast Saccharomyces cerevisiae is the organism in which ribosome biogenesis and the role of RNA helicases in this process is best studied, we focused our review on insights from this model organism, but also make comparisons to other organisms where applicable.
Collapse
Affiliation(s)
- Valentin Mitterer
- Biochemistry Center, Heidelberg University, Im Neuenheimer Feld 328, Heidelberg, Germany
- BioTechMed-Graz, Graz, Austria
| | - Brigitte Pertschy
- BioTechMed-Graz, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, Graz, Austria
| |
Collapse
|
24
|
Oborská-Oplová M, Fischer U, Altvater M, Panse VG. Eukaryotic Ribosome assembly and Nucleocytoplasmic Transport. Methods Mol Biol 2022; 2533:99-126. [PMID: 35796985 PMCID: PMC9761919 DOI: 10.1007/978-1-0716-2501-9_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The process of eukaryotic ribosome assembly stretches across the nucleolus, the nucleoplasm and the cytoplasm, and therefore relies on efficient nucleocytoplasmic transport. In yeast, the import machinery delivers ~140,000 ribosomal proteins every minute to the nucleus for ribosome assembly. At the same time, the export machinery facilitates translocation of ~2000 pre-ribosomal particles every minute through ~200 nuclear pore complexes (NPC) into the cytoplasm. Eukaryotic ribosome assembly also requires >200 conserved assembly factors, which transiently associate with pre-ribosomal particles. Their site(s) of action on maturing pre-ribosomes are beginning to be elucidated. In this chapter, we outline protocols that enable rapid biochemical isolation of pre-ribosomal particles for single particle cryo-electron microscopy (cryo-EM) and in vitro reconstitution of nuclear transport processes. We discuss cell-biological and genetic approaches to investigate how the ribosome assembly and the nucleocytoplasmic transport machineries collaborate to produce functional ribosomes.
Collapse
Affiliation(s)
- Michaela Oborská-Oplová
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Ute Fischer
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | | | - Vikram Govind Panse
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
- Faculty of Science, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
25
|
Wang Y, Xie X, Li S, Zhang D, Zheng H, Zhang M, Zhang Z. Co-overexpression of RIOK1 and AKT1 as a prognostic risk factor in glioma. J Cancer 2021; 12:5745-5752. [PMID: 34475988 PMCID: PMC8408104 DOI: 10.7150/jca.60596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/19/2021] [Indexed: 11/13/2022] Open
Abstract
Glioblastoma multiforme (GBM) is one of the most frequent primary malignancies of the brain. Although the treatment strategy has significantly improved, patient prognosis remains poor. In vitro studies have shown that the right open reading frame kinase 1/protein kinase B (RIOK1-AKT) signaling pathway plays an important role in the malignant phenotype of glioma cells. This study aimed to investigate the co-expression of RIOK1 and ATK in glioma tissues and its clinical significance. Compared with normal tissues, RIOK1 and AKT1 expression were significantly upregulated in glioma tissues. In addition, patients with higher World Health Organization staging grades had increased RIOK1 and AKT1 expression levels, and RIOK1 and AKT1 expression were positively correlated. Notably, both RIOK1 and AKT1 expressions were correlated with poor prognosis. In vitro experiments showed that silencing RIOK1 inhibited the proliferation, migration, and invasion of glioma cell lines by suppressing AKT and c-Myc expression. These results indicate that the RIOK1-AKT1 axis could play an important role in GBM progression.
Collapse
Affiliation(s)
- Yiwei Wang
- Department of Human Anatomy, Shenyang Medical College, Shenyang City, Liaoning Province 110034, P.R. China.,Department of Pathology, College of Basic Medical Sciences, Shenyang Medical College, Shenyang City, Liaoning Province 110034, P.R. China
| | - Xiaochen Xie
- Department of Endocrinology and Metabolism, Institute of Endocrinology, Liaoning Provincial Key Laboratory of Endocrine Diseases, The First Affiliated Hospital of China Medical University, China Medical University, Shenyang, Liaoning, 110001, P.R. China
| | - Shu Li
- Department of Human Anatomy, Shenyang Medical College, Shenyang City, Liaoning Province 110034, P.R. China
| | - Dongyong Zhang
- Department of Neurosurgery, First Affiliated Hospital of China Medical University, Heping District, Shenyang City, Liaoning Province, 110001, P.R. China
| | - Heyu Zheng
- Department of Human Anatomy, Shenyang Medical College, Shenyang City, Liaoning Province 110034, P.R. China
| | - Min Zhang
- Department of Pathology, College of Basic Medical Sciences, Shenyang Medical College, Shenyang City, Liaoning Province 110034, P.R. China
| | - Zhong Zhang
- Department of Pathology, College of Basic Medical Sciences, Shenyang Medical College, Shenyang City, Liaoning Province 110034, P.R. China
| |
Collapse
|
26
|
van den Heuvel J, Ashiono C, Gillet LC, Dörner K, Wyler E, Zemp I, Kutay U. Processing of the ribosomal ubiquitin-like fusion protein FUBI-eS30/FAU is required for 40S maturation and depends on USP36. eLife 2021; 10:70560. [PMID: 34318747 PMCID: PMC8354635 DOI: 10.7554/elife.70560] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022] Open
Abstract
In humans and other holozoan organisms, the ribosomal protein eS30 is synthesized as a fusion protein with the ubiquitin-like protein FUBI. However, FUBI is not part of the mature 40S ribosomal subunit and cleaved off by an as-of-yet unidentified protease. How FUBI-eS30 processing is coordinated with 40S subunit maturation is unknown. To study the mechanism and importance of FUBI-eS30 processing, we expressed non-cleavable mutants in human cells, which affected late steps of cytoplasmic 40S maturation, including the maturation of 18S rRNA and recycling of late-acting ribosome biogenesis factors. Differential affinity purification of wild-type and non-cleavable FUBI-eS30 mutants identified the deubiquitinase USP36 as a candidate FUBI-eS30 processing enzyme. Depletion of USP36 by RNAi or CRISPRi indeed impaired FUBI-eS30 processing and moreover, purified USP36 cut FUBI-eS30 in vitro. Together, these data demonstrate the functional importance of FUBI-eS30 cleavage and identify USP36 as a novel protease involved in this process.
Collapse
Affiliation(s)
- Jasmin van den Heuvel
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, Zurich, Switzerland
| | - Caroline Ashiono
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Ludovic C Gillet
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Kerstin Dörner
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, Zurich, Switzerland
| | - Emanuel Wyler
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Ivo Zemp
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Ulrike Kutay
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
27
|
Cerezo EL, Houles T, Lié O, Sarthou MK, Audoynaud C, Lavoie G, Halladjian M, Cantaloube S, Froment C, Burlet-Schiltz O, Henry Y, Roux PP, Henras AK, Romeo Y. RIOK2 phosphorylation by RSK promotes synthesis of the human small ribosomal subunit. PLoS Genet 2021; 17:e1009583. [PMID: 34125833 PMCID: PMC8224940 DOI: 10.1371/journal.pgen.1009583] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/24/2021] [Accepted: 05/05/2021] [Indexed: 11/18/2022] Open
Abstract
Ribosome biogenesis lies at the nexus of various signaling pathways coordinating protein synthesis with cell growth and proliferation. This process is regulated by well-described transcriptional mechanisms, but a growing body of evidence indicates that other levels of regulation exist. Here we show that the Ras/mitogen-activated protein kinase (MAPK) pathway stimulates post-transcriptional stages of human ribosome synthesis. We identify RIOK2, a pre-40S particle assembly factor, as a new target of the MAPK-activated kinase RSK. RIOK2 phosphorylation by RSK stimulates cytoplasmic maturation of late pre-40S particles, which is required for optimal protein synthesis and cell proliferation. RIOK2 phosphorylation facilitates its release from pre-40S particles and its nuclear re-import, prior to completion of small ribosomal subunits. Our results bring a detailed mechanistic link between the Ras/MAPK pathway and the maturation of human pre-40S particles, which opens a hitherto poorly explored area of ribosome biogenesis.
Collapse
Affiliation(s)
- Emilie L. Cerezo
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Thibault Houles
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Québec, Canada
| | - Oriane Lié
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Marie-Kerguelen Sarthou
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Charlotte Audoynaud
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Geneviève Lavoie
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Québec, Canada
| | - Maral Halladjian
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sylvain Cantaloube
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Carine Froment
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, UPS, CNRS, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, UPS, CNRS, Toulouse, France
| | - Yves Henry
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Philippe P. Roux
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Québec, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montreal, Québec, Canada
| | - Anthony K. Henras
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yves Romeo
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| |
Collapse
|
28
|
Plassart L, Shayan R, Montellese C, Rinaldi D, Larburu N, Pichereaux C, Froment C, Lebaron S, O'Donohue MF, Kutay U, Marcoux J, Gleizes PE, Plisson-Chastang C. The final step of 40S ribosomal subunit maturation is controlled by a dual key lock. eLife 2021; 10:61254. [PMID: 33908345 PMCID: PMC8112863 DOI: 10.7554/elife.61254] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 04/19/2021] [Indexed: 12/31/2022] Open
Abstract
Preventing premature interaction of pre-ribosomes with the translation apparatus is essential for translational accuracy. Hence, the final maturation step releasing functional 40S ribosomal subunits, namely processing of the 18S ribosomal RNA 3' end, is safeguarded by the protein DIM2, which both interacts with the endoribonuclease NOB1 and masks the rRNA cleavage site. To elucidate the control mechanism that unlocks NOB1 activity, we performed cryo-electron microscopy analysis of late human pre-40S particles purified using a catalytically inactive form of the ATPase RIO1. These structures, together with in vivo and in vitro functional analyses, support a model in which ATP-loaded RIO1 cooperates with ribosomal protein RPS26/eS26 to displace DIM2 from the 18S rRNA 3' end, thereby triggering final cleavage by NOB1; release of ADP then leads to RIO1 dissociation from the 40S subunit. This dual key lock mechanism requiring RIO1 and RPS26 guarantees the precise timing of pre-40S particle conversion into translation-competent ribosomal subunits.
Collapse
Affiliation(s)
- Laura Plassart
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Ramtin Shayan
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | | | - Dana Rinaldi
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Natacha Larburu
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Carole Pichereaux
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Carine Froment
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Simon Lebaron
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Marie-Françoise O'Donohue
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Ulrike Kutay
- Institut für Biochemie, ETH Zürich, Zurich, Switzerland
| | - Julien Marcoux
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Pierre-Emmanuel Gleizes
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Celia Plisson-Chastang
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| |
Collapse
|
29
|
Raundhal M, Ghosh S, Myers SA, Cuoco MS, Singer M, Carr SA, Waikar SS, Bonventre JV, Ritz J, Stone RM, Steensma DP, Regev A, Glimcher LH. Blockade of IL-22 signaling reverses erythroid dysfunction in stress-induced anemias. Nat Immunol 2021; 22:520-529. [PMID: 33753942 PMCID: PMC8026551 DOI: 10.1038/s41590-021-00895-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 02/03/2021] [Indexed: 02/06/2023]
Abstract
Patients with myelodysplastic syndromes (MDSs) display severe anemia but the mechanisms underlying this phenotype are incompletely understood. Right open-reading-frame kinase 2 (RIOK2) encodes a protein kinase located at 5q15, a region frequently lost in patients with MDS del(5q). Here we show that hematopoietic cell-specific haploinsufficient deletion of Riok2 (Riok2f/+Vav1cre) led to reduced erythroid precursor frequency leading to anemia. Proteomic analysis of Riok2f/+Vav1cre erythroid precursors suggested immune system activation, and transcriptomic analysis revealed an increase in p53-dependent interleukin (IL)-22 in Riok2f/+Vav1cre CD4+ T cells (TH22). Further, we discovered that the IL-22 receptor, IL-22RA1, was unexpectedly present on erythroid precursors. Blockade of IL-22 signaling alleviated anemia not only in Riok2f/+Vav1cre mice but also in wild-type mice. Serum concentrations of IL-22 were increased in the subset of patients with del(5q) MDS as well as patients with anemia secondary to chronic kidney disease. This work reveals a possible therapeutic opportunity for reversing many stress-induced anemias by targeting IL-22 signaling.
Collapse
MESH Headings
- Anemia/blood
- Anemia/immunology
- Anemia/metabolism
- Anemia/prevention & control
- Animals
- Antibodies, Neutralizing/pharmacology
- Cells, Cultured
- Cellular Microenvironment
- Disease Models, Animal
- Erythroid Cells/immunology
- Erythroid Cells/metabolism
- Erythropoiesis/drug effects
- Humans
- Interleukins/antagonists & inhibitors
- Interleukins/immunology
- Interleukins/metabolism
- Mice, Inbred C57BL
- Mice, Knockout
- Myelodysplastic Syndromes/blood
- Myelodysplastic Syndromes/drug therapy
- Myelodysplastic Syndromes/immunology
- Myelodysplastic Syndromes/metabolism
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Proto-Oncogene Proteins c-vav/genetics
- Proto-Oncogene Proteins c-vav/metabolism
- Receptors, Interleukin/genetics
- Receptors, Interleukin/metabolism
- Renal Insufficiency, Chronic/blood
- Renal Insufficiency, Chronic/immunology
- Renal Insufficiency, Chronic/metabolism
- Signal Transduction
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
- Interleukin-22
- Mice
Collapse
Affiliation(s)
- Mahesh Raundhal
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Immunology, Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Shrestha Ghosh
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Michael S Cuoco
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Meromit Singer
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sushrut S Waikar
- Renal Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Renal Section, Boston University Medical Center, Boston, MA, USA
| | - Joseph V Bonventre
- Renal Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - David P Steensma
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Laurie H Glimcher
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Immunology, Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| |
Collapse
|
30
|
Wang CB, Lorente-Macías Á, Wells C, Pickett JE, Picado A, Zuercher WJ, Axtman AD. Towards a RIOK2 chemical probe: cellular potency improvement of a selective 2-(acylamino)pyridine series. RSC Med Chem 2021; 12:129-136. [PMID: 34046605 PMCID: PMC8130602 DOI: 10.1039/d0md00292e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/13/2020] [Indexed: 11/21/2022] Open
Abstract
RIOK2 is an understudied kinase associated with a variety of human cancers including non-small cell lung cancer and glioblastoma. No potent, selective, and cell-active chemical probe currently exists for RIOK2. Such a reagent would expedite re-search into the biological functions of RIOK2 and validate it as a therapeutic target. Herein, we describe the synthesis of naphthyl-pyridine based compounds that have improved cellular activity while maintaining selectivity for RIOK2. While our compounds do not represent RIOK2 chemical probes, they are the best available tool molecules to begin to characterize RIOK2 function in vitro.
Collapse
Affiliation(s)
- Christopher B Wang
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | - Álvaro Lorente-Macías
- Departamento de Química Farmacéutica y Orgánica, University of Granada Granada 18071 Spain
| | - Carrow Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | - Julie E Pickett
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | - Alfredo Picado
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | - William J Zuercher
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | - Alison D Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| |
Collapse
|
31
|
Subbannayya Y, Haug M, Pinto SM, Mohanty V, Meås HZ, Flo TH, Prasad TK, Kandasamy RK. The Proteomic Landscape of Resting and Activated CD4+ T Cells Reveal Insights into Cell Differentiation and Function. Int J Mol Sci 2020; 22:E275. [PMID: 33383959 PMCID: PMC7795831 DOI: 10.3390/ijms22010275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/17/2020] [Accepted: 12/24/2020] [Indexed: 12/14/2022] Open
Abstract
CD4+ T cells (T helper cells) are cytokine-producing adaptive immune cells that activate or regulate the responses of various immune cells. The activation and functional status of CD4+ T cells is important for adequate responses to pathogen infections but has also been associated with auto-immune disorders and survival in several cancers. In the current study, we carried out a label-free high-resolution FTMS-based proteomic profiling of resting and T cell receptor-activated (72 h) primary human CD4+ T cells from peripheral blood of healthy donors as well as SUP-T1 cells. We identified 5237 proteins, of which significant alterations in the levels of 1119 proteins were observed between resting and activated CD4+ T cells. In addition to identifying several known T-cell activation-related processes altered expression of several stimulatory/inhibitory immune checkpoint markers between resting and activated CD4+ T cells were observed. Network analysis further revealed several known and novel regulatory hubs of CD4+ T cell activation, including IFNG, IRF1, FOXP3, AURKA, and RIOK2. Comparison of primary CD4+ T cell proteomic profiles with human lymphoblastic cell lines revealed a substantial overlap, while comparison with mouse CD+ T cell data suggested interspecies proteomic differences. The current dataset will serve as a valuable resource to the scientific community to compare and analyze the CD4+ proteome.
Collapse
Affiliation(s)
- Yashwanth Subbannayya
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway; (Y.S.); (M.H.); (S.M.P.); (H.Z.M.); (T.H.F.)
| | - Markus Haug
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway; (Y.S.); (M.H.); (S.M.P.); (H.Z.M.); (T.H.F.)
| | - Sneha M. Pinto
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway; (Y.S.); (M.H.); (S.M.P.); (H.Z.M.); (T.H.F.)
| | - Varshasnata Mohanty
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore 575018, India; (V.M.); (T.S.K.P.)
| | - Hany Zakaria Meås
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway; (Y.S.); (M.H.); (S.M.P.); (H.Z.M.); (T.H.F.)
| | - Trude Helen Flo
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway; (Y.S.); (M.H.); (S.M.P.); (H.Z.M.); (T.H.F.)
| | - T.S. Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore 575018, India; (V.M.); (T.S.K.P.)
| | - Richard K. Kandasamy
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway; (Y.S.); (M.H.); (S.M.P.); (H.Z.M.); (T.H.F.)
| |
Collapse
|
32
|
Tani S, Nishio N, Kai K, Hagiwara D, Ogata Y, Tojo M, Sumitani JI, Judelson HS, Kawaguchi T. Chemical genetic approach using β-rubromycin reveals that a RIO kinase-like protein is involved in morphological development in Phytophthora infestans. Sci Rep 2020; 10:22326. [PMID: 33339950 PMCID: PMC7749174 DOI: 10.1038/s41598-020-79326-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 12/08/2020] [Indexed: 11/10/2022] Open
Abstract
To characterize the molecular mechanisms underlying life-stage transitions in Phytophthora infestans, we initiated a chemical genetics approach by screening for a stage-specific inhibitor of morphological development from microbial culture extracts prepared mostly from actinomycetes from soil in Japan. Of the more than 700 extracts, one consistently inhibited Ph. infestans cyst germination. Purification and identification of the active compound by ESI–MS, 1H-NMR, and 13C-NMR identified β-rubromycin as the inhibitor of cyst germination (IC50 = 19.8 μg/L); β-rubromycin did not inhibit growth on rye media, sporangium formation, zoospore release, cyst formation, or appressorium formation in Ph. infestans. Further analyses revealed that β-rubromycin inhibited the germination of cysts and oospores in Pythium aphanidermatum. A chemical genetic approach revealed that β-rubromycin stimulated the expression of RIO kinase-like gene (PITG_04584) by 60-fold in Ph. infestans. Genetic analyses revealed that PITG_04584, which lacks close non-oomycete relatives, was involved in zoosporogenesis, cyst germination, and appressorium formation in Ph. infestans. These data imply that further functional analyses of PITG_04584 may contribute to new methods to suppress diseases caused by oomycetes.
Collapse
Affiliation(s)
- Shuji Tani
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, 599-8531, Japan.
| | - Naotaka Nishio
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, 599-8531, Japan
| | - Kenji Kai
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, 599-8531, Japan
| | - Daisuke Hagiwara
- Medical Mycology Research Center, Chiba University, Chiba, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshiyuki Ogata
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, 599-8531, Japan
| | - Motoaki Tojo
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, 599-8531, Japan
| | - Jun-Ichi Sumitani
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, 599-8531, Japan
| | - Howard S Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, USA
| | - Takashi Kawaguchi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, 599-8531, Japan
| |
Collapse
|
33
|
Structural basis for the final steps of human 40S ribosome maturation. Nature 2020; 587:683-687. [PMID: 33208940 DOI: 10.1038/s41586-020-2929-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 08/28/2020] [Indexed: 12/24/2022]
Abstract
Eukaryotic ribosomes consist of a small 40S and a large 60S subunit that are assembled in a highly coordinated manner. More than 200 factors ensure correct modification, processing and folding of ribosomal RNA and the timely incorporation of ribosomal proteins1,2. Small subunit maturation ends in the cytosol, when the final rRNA precursor, 18S-E, is cleaved at site 3 by the endonuclease NOB13. Previous structures of human 40S precursors have shown that NOB1 is kept in an inactive state by its partner PNO14. The final maturation events, including the activation of NOB1 for the decisive rRNA-cleavage step and the mechanisms driving the dissociation of the last biogenesis factors have, however, remained unresolved. Here we report five cryo-electron microscopy structures of human 40S subunit precursors, which describe the compositional and conformational progression during the final steps of 40S assembly. Our structures explain the central role of RIOK1 in the displacement and dissociation of PNO1, which in turn allows conformational changes and activation of the endonuclease NOB1. In addition, we observe two factors, eukaryotic translation initiation factor 1A domain-containing protein (EIF1AD) and leucine-rich repeat-containing protein 47 (LRRC47), which bind to late pre-40S particles near RIOK1 and the central rRNA helix 44. Finally, functional data shows that EIF1AD is required for efficient assembly factor recycling and 18S-E processing. Our results thus enable a detailed understanding of the last steps in 40S formation in human cells and, in addition, provide evidence for principal differences in small ribosomal subunit formation between humans and the model organism Saccharomyces cerevisiae.
Collapse
|
34
|
Zhou H, Zhou T, Zhang B, Lei W, Yuan W, Shan J, Zhang Y, Gupta N, Hu M. RIOK-2 protein is essential for egg hatching in a common parasitic nematode. Int J Parasitol 2020; 50:595-602. [PMID: 32592810 DOI: 10.1016/j.ijpara.2020.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/01/2020] [Accepted: 05/07/2020] [Indexed: 11/18/2022]
Abstract
The atypical protein kinase RIOK-2 is a non-ribosomal factor essential for ribosome maturation in yeast and human cells; however, little is known about its physiological role in pathogens. Our earlier work examined the expression profile of a RIOK-2 gene (Ss-riok-2) in Strongyloides stercoralis - a prevalent nematode parasite of dogs and humans. Herein, we demonstrate that Ss-RIOK-2 encodes a catalytically active kinase, distributed primarily in the cytoplasm of intestinal and hypodermal cells in transgenic larvae. Its expression oscillates as the free-living L1s develop into infective L3s. Overexpression of a catalytically impaired Ss-RIOK-2-D228A mutant delayed the development of transgenic larvae, while ectopic expression of another dominant negative isoform with a mutation in the ATP-binding site (K123A) abrogated the process of egg hatching, which could be rescued by co-expressing a wild-type Ss-RIOK-2 but not by its Ss-RIOK-1 ortholog. Collectively, our findings show a critical and specific role of Ss-RIOK-2 during the development of a pathogenic roundworm, which can be exploited to develop anti-infectives.
Collapse
Affiliation(s)
- Huan Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Taoxun Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Biying Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Weiqiang Lei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Wang Yuan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jianan Shan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Ying Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Nishith Gupta
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China; Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany
| | - Min Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China.
| |
Collapse
|
35
|
Abstract
RNA helicases exert mechanical force that changes RNA configurations in many essential cellular pathways, e.g., during mRNA maturation or assembly of ribosomes. DEAH helicases work by translocating along RNA and thereby unwind RNA duplexes or dissociate bound proteins. Because DEAH proteins are poor enzymes without intrinsic selectivity for target RNAs, they require adapter proteins that recruit them to functional sites and enhance their catalytic activity. One essential class of DEAH activators is formed by G-patch proteins, which bind helicases via their eponymous glycine-rich motif. We solved the structure of a G-patch bound to helicase DHX15. Our analysis suggests that G-patches tether mobile sections of DEAH helicases together and activate them by stabilizing a functional conformation with high RNA affinity. RNA helicases of the DEAH/RHA family are involved in many essential cellular processes, such as splicing or ribosome biogenesis, where they remodel large RNA–protein complexes to facilitate transitions to the next intermediate. DEAH helicases couple adenosine triphosphate (ATP) hydrolysis to conformational changes of their catalytic core. This movement results in translocation along RNA, which is held in place by auxiliary C-terminal domains. The activity of DEAH proteins is strongly enhanced by the large and diverse class of G-patch activators. Despite their central roles in RNA metabolism, insight into the molecular basis of G-patch–mediated helicase activation is missing. Here, we have solved the structure of human helicase DHX15/Prp43, which has a dual role in splicing and ribosome assembly, in complex with the G-patch motif of the ribosome biogenesis factor NKRF. The G-patch motif binds in an extended conformation across the helicase surface. It tethers the catalytic core to the flexibly attached C-terminal domains, thereby fixing a conformation that is compatible with RNA binding. Structures in the presence or absence of adenosine diphosphate (ADP) suggest that motions of the catalytic core, which are required for ATP binding, are still permitted. Concomitantly, RNA affinity, helicase, and ATPase activity of DHX15 are increased when G-patch is bound. Mutations that detach one end of the tether but maintain overall binding severely impair this enhancement. Collectively, our data suggest that the G-patch motif acts like a flexible brace between dynamic portions of DHX15 that restricts excessive domain motions but maintains sufficient flexibility for catalysis.
Collapse
|
36
|
Montellese C, van den Heuvel J, Ashiono C, Dörner K, Melnik A, Jonas S, Zemp I, Picotti P, Gillet LC, Kutay U. USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit. eLife 2020; 9:54435. [PMID: 32129764 PMCID: PMC7065907 DOI: 10.7554/elife.54435] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/03/2020] [Indexed: 12/12/2022] Open
Abstract
Establishment of translational competence represents a decisive cytoplasmic step in the biogenesis of 40S ribosomal subunits. This involves final 18S rRNA processing and release of residual biogenesis factors, including the protein kinase RIOK1. To identify novel proteins promoting the final maturation of human 40S subunits, we characterized pre-ribosomal subunits trapped on RIOK1 by mass spectrometry, and identified the deubiquitinase USP16 among the captured factors. We demonstrate that USP16 constitutes a component of late cytoplasmic pre-40S subunits that promotes the removal of ubiquitin from an internal lysine of ribosomal protein RPS27a/eS31. USP16 deletion leads to late 40S subunit maturation defects, manifesting in incomplete processing of 18S rRNA and retarded recycling of late-acting ribosome biogenesis factors, revealing an unexpected contribution of USP16 to the ultimate step of 40S synthesis. Finally, ubiquitination of RPS27a appears to depend on active translation, pointing at a potential connection between 40S maturation and protein synthesis.
Collapse
Affiliation(s)
| | - Jasmin van den Heuvel
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, Zurich, Switzerland
| | | | - Kerstin Dörner
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, Zurich, Switzerland
| | - André Melnik
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Stefanie Jonas
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Ivo Zemp
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Paola Picotti
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | - Ulrike Kutay
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
37
|
A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS. Cell Syst 2020; 10:133-155.e6. [PMID: 32027860 PMCID: PMC7042714 DOI: 10.1016/j.cels.2020.01.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 11/08/2019] [Accepted: 01/10/2020] [Indexed: 12/19/2022]
Abstract
Living systems integrate biochemical reactions that determine the functional state of each cell. Reactions are primarily mediated by proteins. In proteomic studies, these have been treated as independent entities, disregarding their higher-level organization into complexes that affects their activity and/or function and is thus of great interest for biological research. Here, we describe the implementation of an integrated technique to quantify cell-state-specific changes in the physical arrangement of protein complexes concurrently for thousands of proteins and hundreds of complexes. Applying this technique to a comparison of human cells in interphase and mitosis, we provide a systematic overview of mitotic proteome reorganization. The results recall key hallmarks of mitotic complex remodeling and suggest a model of nuclear pore complex disassembly, which we validate by orthogonal methods. To support the interpretation of quantitative SEC-SWATH-MS datasets, we extend the software CCprofiler and provide an interactive exploration tool, SECexplorer-cc. Global quantification of assembly state changes in the mitotic proteome Improved performance over thermostability measurement of proteome states Discovery of a mitotic disassembly intermediate of the nuclear pore complex Introduction of SECexplorer-cc, a publicly available online platform
Collapse
|
38
|
Park KM, Lee HJ, Koo KT, Ben Amara H, Leesungbok R, Noh K, Lee SC, Lee SW. Oral Soft Tissue Regeneration Using Nano Controlled System Inducing Sequential Release of Trichloroacetic Acid and Epidermal Growth Factor. Tissue Eng Regen Med 2020; 17:91-103. [PMID: 31970697 DOI: 10.1007/s13770-019-00232-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/23/2019] [Accepted: 11/28/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The effect of nano controlled sequential release of trichloroacetic acid (TCA) and epidermal growth factor (EGF) on the oral soft tissue regeneration was determined. METHODS Hydrophobically modified glycol chitosan (HGC) nano controlled system was developed for the sequential release of TCA and EGF, and the release pattern was identified. The HGC-based nano controlled release system was injected into the critical-sized defects created in beagles' palatal soft tissues. The palatal impression and its scanned body was obtained on various time points post-injection, and the volumetric amount of soft tissue regeneration was compared among the three groups: CON (natural regeneration control group), EXP1 (TCA-loaded nano controlled release system group), EXP2 (TCA and EGF individually loaded nano controlled release system). DNA microarray analysis was performed and various soft tissue regeneration parameters in histopathological specimens were measured. RESULTS TCA release was highest at Day 1 whereas EGF release was highest at Day 2 and remained high until Day 3. In the volumetric measurements of impression body scans, no significant difference in soft tissue regeneration between the three groups was shown in two-way ANOVA. However, in the one-way ANOVA at Day 14, EXP2 showed a significant increase in soft tissue regeneration compared to CON. High correlation was determined between the histopathological results of each group. DNA microarray showed up-regulation of various genes and related cell signaling pathways in EXP2 compared to CON. CONCLUSION HGC-based nano controlled release system for sequential release of TCA and EGF can promote regeneration of oral soft tissue defects.
Collapse
Affiliation(s)
- Kwang Man Park
- Department of Dentistry, Graduate School, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Hong Jae Lee
- Department of Maxillofacial Biomedical Engineering and Institute of Oral Biology, School of Dentistry, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Ki-Tae Koo
- Department of Periodontology and Dental Research Institute Translational Research Laboratory for Tissue Engineering (TTE), School of Dentistry, Seoul National University, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Heithem Ben Amara
- Department of Periodontology and Dental Research Institute Translational Research Laboratory for Tissue Engineering (TTE), School of Dentistry, Seoul National University, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Richard Leesungbok
- Department of Biomaterials and Prosthodontics, Kyung Hee University Hospital at Gangdong Institute of Oral Biology, School of Dentistry, Kyung Hee University, 892 Dongnam-ro, Gangdong-gu, Seoul, 05278, Republic of Korea
| | - Kwantae Noh
- Department of Prosthodontics, School of Dentistry, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Sang Cheon Lee
- Department of Maxillofacial Biomedical Engineering and Institute of Oral Biology, School of Dentistry, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea.
| | - Suk Won Lee
- Department of Biomaterials and Prosthodontics, Kyung Hee University Hospital at Gangdong Institute of Oral Biology, School of Dentistry, Kyung Hee University, 892 Dongnam-ro, Gangdong-gu, Seoul, 05278, Republic of Korea.
| |
Collapse
|
39
|
Nieto B, Gaspar SG, Moriggi G, Pestov DG, Bustelo XR, Dosil M. Identification of distinct maturation steps involved in human 40S ribosomal subunit biosynthesis. Nat Commun 2020; 11:156. [PMID: 31919354 PMCID: PMC6952385 DOI: 10.1038/s41467-019-13990-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/11/2019] [Indexed: 02/02/2023] Open
Abstract
Technical problems intrinsic to the purification of preribosome intermediates have limited our understanding of ribosome biosynthesis in humans. Addressing this issue is important given the implication of this biological process in human disease. Here we report a preribosome purification and tagging strategy that overcomes some of the existing technical difficulties. Using these tools, we find that the pre-40S precursors go through two distinct maturation phases inside the nucleolus and follow a regulatory step that precedes late maturation in the cytoplasm. This regulatory step entails the intertwined actions of both PARN (a metazoan-specific ribonuclease) and RRP12 (a phylogenetically conserved 40S biogenesis factor that has acquired additional functional features in higher eukaryotes). Together, these results demonstrate the usefulness of this purification method for the dissection of ribosome biogenesis in human cells. They also identify distinct maturation stages and metazoan-specific regulatory mechanisms involved in the generation of the human 40S ribosomal subunit. Ribosome synthesis is a complex multi-step process. Here the authors present a method that allows the efficient isolation and characterization of the preribosomal complexes formed along the entire ribosome synthesis pathway in human cells.
Collapse
Affiliation(s)
- Blanca Nieto
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain
| | - Sonia G Gaspar
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain
| | - Giulia Moriggi
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain
| | - Dimitri G Pestov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ, 08084, USA
| | - Xosé R Bustelo
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain
| | - Mercedes Dosil
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain. .,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain. .,Departamento de Bioquímica y Biología Molecular, University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.
| |
Collapse
|
40
|
Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Wallingford JB, Finkelstein IJ, Marcotte EM, Drew K. Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes. Cell Rep 2019; 29:1351-1368.e5. [PMID: 31665645 PMCID: PMC6873818 DOI: 10.1016/j.celrep.2019.09.060] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 08/30/2019] [Accepted: 09/18/2019] [Indexed: 12/16/2022] Open
Abstract
RNA-binding proteins (RBPs) play essential roles in biology and are frequently associated with human disease. Although recent studies have systematically identified individual RNA-binding proteins, their higher-order assembly into ribonucleoprotein (RNP) complexes has not been systematically investigated. Here, we describe a proteomics method for systematic identification of RNP complexes in human cells. We identify 1,428 protein complexes that associate with RNA, indicating that more than 20% of known human protein complexes contain RNA. To explore the role of RNA in the assembly of each complex, we identify complexes that dissociate, change composition, or form stable protein-only complexes in the absence of RNA. We use our method to systematically identify cell-type-specific RNA-associated proteins in mouse embryonic stem cells and finally, distribute our resource, rna.MAP, in an easy-to-use online interface (rna.proteincomplexes.org). Our system thus provides a methodology for explorations across human tissues, disease states, and throughout all domains of life.
Collapse
Affiliation(s)
- Anna L Mallam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Wisath Sae-Lee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Jeffrey M Schaub
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Fan Tu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Anna Battenhouse
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Yu Jin Jang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - John B Wallingford
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Kevin Drew
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| |
Collapse
|
41
|
Correddu D, Montaño López JDJ, Angermayr SA, Middleditch MJ, Payne LS, Leung IKH. Effect of consecutive rare codons on the recombinant production of human proteins in
Escherichia coli. IUBMB Life 2019; 72:266-274. [DOI: 10.1002/iub.2162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 08/26/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Danilo Correddu
- School of Chemical SciencesThe University of Auckland Auckland New Zealand
| | - José de Jesús Montaño López
- School of Chemical SciencesThe University of Auckland Auckland New Zealand
- Facultad de IngenieríaUniversidad Nacional Autónoma de México, Ciudad Universitaria Coyoacán Mexico
| | | | - Martin J. Middleditch
- School of Biological SciencesThe University of Auckland Auckland New Zealand
- Auckland Science Analytical ServicesThe University of Auckland Auckland New Zealand
| | - Leo S. Payne
- School of Biological SciencesThe University of Auckland Auckland New Zealand
- Auckland Science Analytical ServicesThe University of Auckland Auckland New Zealand
| | - Ivanhoe K. H. Leung
- School of Chemical SciencesThe University of Auckland Auckland New Zealand
- Maurice Wilkins Centre for Molecular BiodiscoveryThe University of Auckland Auckland New Zealand
| |
Collapse
|
42
|
Maurice F, Pérébaskine N, Thore S, Fribourg S. In vitro dimerization of human RIO2 kinase. RNA Biol 2019; 16:1633-1642. [PMID: 31390939 DOI: 10.1080/15476286.2019.1653679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
RIO proteins form a conserved family of atypical protein kinases. RIO2 is a serine/threonine protein kinase/ATPase involved in pre-40S ribosomal maturation. Current crystal structures of archaeal and fungal Rio2 proteins report a monomeric form of the protein. Here, we describe three atomic structures of the human RIO2 kinase showing that it forms a homodimer in vitro. Upon self-association, each protomer ATP-binding pocket is partially remodelled and found in an apostate. The homodimerization is mediated by key residues previously shown to be responsible for ATP binding and catalysis. This unusual in vitro protein kinase dimer reveals an intricate mechanism where identical residues are involved in substrate binding and oligomeric state formation. We speculate that such an oligomeric state might be formed also in vivo and might function in maintaining the protein in an inactive state and could be employed during import.
Collapse
Affiliation(s)
| | | | - Stéphane Thore
- INSERM U1212, UMR CNRS 5320, Université de Bordeaux , Bordeaux , France
| | | |
Collapse
|
43
|
Knüppel R, Christensen RH, Gray FC, Esser D, Strauß D, Medenbach J, Siebers B, MacNeill SA, LaRonde N, Ferreira-Cerca S. Insights into the evolutionary conserved regulation of Rio ATPase activity. Nucleic Acids Res 2019; 46:1441-1456. [PMID: 29237037 PMCID: PMC5815136 DOI: 10.1093/nar/gkx1236] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 12/01/2017] [Indexed: 12/24/2022] Open
Abstract
Eukaryotic ribosome biogenesis is a complex dynamic process which requires the action of numerous ribosome assembly factors. Among them, the eukaryotic Rio protein family members (Rio1, Rio2 and Rio3) belong to an ancient conserved atypical protein kinase/ ATPase family required for the maturation of the small ribosomal subunit (SSU). Recent structure–function analyses suggested an ATPase-dependent role of the Rio proteins to regulate their dynamic association with the nascent pre-SSU. However, the evolutionary origin of this feature and the detailed molecular mechanism that allows controlled activation of the catalytic activity remained to be determined. In this work we provide functional evidence showing a conserved role of the archaeal Rio proteins for the synthesis of the SSU in archaea. Moreover, we unravel a conserved RNA-dependent regulation of the Rio ATPases, which in the case of Rio2 involves, at least, helix 30 of the SSU rRNA and the P-loop lysine within the shared RIO domain. Together, our study suggests a ribosomal RNA-mediated regulatory mechanism enabling the appropriate stimulation of Rio2 catalytic activity and subsequent release of Rio2 from the nascent pre-40S particle. Based on our findings we propose a unified release mechanism for the Rio proteins.
Collapse
Affiliation(s)
- Robert Knüppel
- Biochemistry III - Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Regitse H Christensen
- Department of Biology, University of Copenhagen, Copenhagen Biocenter, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Fiona C Gray
- Department of Biology, University of Copenhagen, Copenhagen Biocenter, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Dominik Esser
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Daniela Strauß
- Biochemistry I - Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Jan Medenbach
- Biochemistry I - Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Stuart A MacNeill
- Department of Biology, University of Copenhagen, Copenhagen Biocenter, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark.,School of Biology, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
| | - Nicole LaRonde
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA
| | - Sébastien Ferreira-Cerca
- Biochemistry III - Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| |
Collapse
|
44
|
Bohnsack KE, Bohnsack MT. Uncovering the assembly pathway of human ribosomes and its emerging links to disease. EMBO J 2019; 38:e100278. [PMID: 31268599 PMCID: PMC6600647 DOI: 10.15252/embj.2018100278] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 02/18/2019] [Accepted: 04/26/2019] [Indexed: 12/12/2022] Open
Abstract
The essential cellular process of ribosome biogenesis is at the nexus of various signalling pathways that coordinate protein synthesis with cellular growth and proliferation. The fact that numerous diseases are caused by defects in ribosome assembly underscores the importance of obtaining a detailed understanding of this pathway. Studies in yeast have provided a wealth of information about the fundamental principles of ribosome assembly, and although many features are conserved throughout eukaryotes, the larger size of human (pre-)ribosomes, as well as the evolution of additional regulatory networks that can modulate ribosome assembly and function, have resulted in a more complex assembly pathway in humans. Notably, many ribosome biogenesis factors conserved from yeast appear to have subtly different or additional functions in humans. In addition, recent genome-wide, RNAi-based screens have identified a plethora of novel factors required for human ribosome biogenesis. In this review, we discuss key aspects of human ribosome production, highlighting differences to yeast, links to disease, as well as emerging concepts such as extra-ribosomal functions of ribosomal proteins and ribosome heterogeneity.
Collapse
Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular BiologyUniversity Medical Center GöttingenGöttingenGermany
| | - Markus T Bohnsack
- Department of Molecular BiologyUniversity Medical Center GöttingenGöttingenGermany
- Göttingen Center for Molecular BiosciencesGeorg‐August UniversityGöttingenGermany
| |
Collapse
|
45
|
Mitterer V, Shayan R, Ferreira-Cerca S, Murat G, Enne T, Rinaldi D, Weigl S, Omanic H, Gleizes PE, Kressler D, Plisson-Chastang C, Pertschy B. Conformational proofreading of distant 40S ribosomal subunit maturation events by a long-range communication mechanism. Nat Commun 2019; 10:2754. [PMID: 31227701 PMCID: PMC6588571 DOI: 10.1038/s41467-019-10678-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 05/23/2019] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic ribosomes are synthesized in a hierarchical process driven by a plethora of assembly factors, but how maturation events at physically distant sites on pre-ribosomes are coordinated is poorly understood. Using functional analyses and cryo-EM, we show that ribosomal protein Rps20 orchestrates communication between two multi-step maturation events across the pre-40S subunit. Our study reveals that during pre-40S maturation, formation of essential contacts between Rps20 and Rps3 permits assembly factor Ltv1 to recruit the Hrr25 kinase, thereby promoting Ltv1 phosphorylation. In parallel, a deeply buried Rps20 loop reaches to the opposite pre-40S side, where it stimulates Rio2 ATPase activity. Both cascades converge to the final maturation steps releasing Rio2 and phosphorylated Ltv1. We propose that conformational proofreading exerted via Rps20 constitutes a checkpoint permitting assembly factor release and progression of pre-40S maturation only after completion of all earlier maturation steps. The biogenesis of eukaryotic ribosomes is a multi-step process involving the action of more than 200 different ribosome assembly factors. Here the authors show that Rps20 acts as a conduit to coordinate maturation steps across the head domain of the nascent small ribosomal subunit.
Collapse
Affiliation(s)
- Valentin Mitterer
- Institute for Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010, Graz, Austria.,Biochemistry Centre, University of Heidelberg, 69120, Heidelberg, Germany
| | - Ramtin Shayan
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062, Toulouse Cedex, France
| | - Sébastien Ferreira-Cerca
- Biochemistry III - Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany.
| | - Guillaume Murat
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700, Fribourg, Switzerland
| | - Tanja Enne
- Institute for Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010, Graz, Austria
| | - Dana Rinaldi
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062, Toulouse Cedex, France
| | - Sarah Weigl
- Institute for Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010, Graz, Austria
| | - Hajrija Omanic
- Institute for Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010, Graz, Austria
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062, Toulouse Cedex, France
| | - Dieter Kressler
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700, Fribourg, Switzerland.
| | - Celia Plisson-Chastang
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062, Toulouse Cedex, France.
| | - Brigitte Pertschy
- Institute for Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010, Graz, Austria.
| |
Collapse
|
46
|
Boneberg FM, Brandmann T, Kobel L, van den Heuvel J, Bargsten K, Bammert L, Kutay U, Jinek M. Molecular mechanism of the RNA helicase DHX37 and its activation by UTP14A in ribosome biogenesis. RNA (NEW YORK, N.Y.) 2019; 25:685-701. [PMID: 30910870 PMCID: PMC6521606 DOI: 10.1261/rna.069609.118] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
Eukaryotic ribosome biogenesis is a highly orchestrated process involving numerous assembly factors including ATP-dependent RNA helicases. The DEAH helicase DHX37 (Dhr1 in yeast) is activated by the ribosome biogenesis factor UTP14A to facilitate maturation of the small ribosomal subunit. We report the crystal structure of DHX37 in complex with single-stranded RNA, revealing a canonical DEAH ATPase/helicase architecture complemented by a structurally unique carboxy-terminal domain (CTD). Structural comparisons of the nucleotide-free DHX37-RNA complex with DEAH helicases bound to RNA and ATP analogs reveal conformational changes resulting in a register shift in the bound RNA, suggesting a mechanism for ATP-dependent 3'-5' RNA translocation. We further show that a conserved sequence motif in UTP14A interacts with and activates DHX37 by stimulating its ATPase activity and enhancing RNA binding. In turn, the CTD of DHX37 is required, but not sufficient, for interaction with UTP14A in vitro and is essential for ribosome biogenesis in vivo. Together, these results shed light on the mechanism of DHX37 and the function of UTP14A in controlling its recruitment and activity during ribosome biogenesis.
Collapse
Affiliation(s)
| | - Tobias Brandmann
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Lena Kobel
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Jasmin van den Heuvel
- Department of Biology, Institute of Biochemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Katja Bargsten
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Lukas Bammert
- Department of Biology, Institute of Biochemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Ulrike Kutay
- Department of Biology, Institute of Biochemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| |
Collapse
|
47
|
Sloan KE, Knox AA, Wells GR, Schneider C, Watkins NJ. Interactions and activities of factors involved in the late stages of human 18S rRNA maturation. RNA Biol 2019; 16:196-210. [PMID: 30638116 PMCID: PMC6380343 DOI: 10.1080/15476286.2018.1564467] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Ribosome production is an essential cellular process involving a plethora of trans-acting factors, such as nucleases, methyltransferases, RNA helicases and kinases that catalyse key maturation steps. Precise temporal and spatial regulation of such enzymes is essential to ensure accurate and efficient subunit assembly. Here, we focus on the maturation of the 3ʹ end of the 18S rRNA in human cells. We reveal that human RIO2 is an active kinase that phosphorylates both itself and the rRNA methyltransferase DIM1 in vitro. In contrast to yeast, our data confirm that human DIM1 predominantly acts in the nucleus and we further demonstrate that the 21S pre-rRNA is the main target for DIM1-catalysed methylation. We show that the PIN domain of the endonuclease NOB1 is required for site 3 cleavage, while the zinc ribbon domain is essential for pre-40S recruitment. Furthermore, we also demonstrate that NOB1, PNO1 and DIM1 bind to a region of the pre-rRNA encompassing the 3ʹ end of 18S and the start of ITS1, in vitro. Interestingly, NOB1 is present in the cell at higher levels than other pre-40S factors. We provide evidence that NOB1 is multimeric within the cell and show that NOB1 multimerisation is lost when ribosome biogenesis is blocked. Taken together, our data indicate a dynamic interplay of key factors associated with the 3ʹ end of the 18S rRNA during human pre-40S biogenesis and highlight potential mechanisms by which this process can be regulated.
Collapse
Affiliation(s)
- Katherine Elizabeth Sloan
- a Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Newcastle upon Tyne , UK.,b Department of Molecular Biology , University Medical Centre, Goettingen , Goettingen , Germany
| | - Andrew Alexander Knox
- a Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Newcastle upon Tyne , UK
| | - Graeme Raymond Wells
- a Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Newcastle upon Tyne , UK
| | - Claudia Schneider
- a Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Newcastle upon Tyne , UK
| | - Nicholas James Watkins
- a Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Newcastle upon Tyne , UK
| |
Collapse
|
48
|
Chen AS, Read RD. Drosophila melanogaster as a Model System for Human Glioblastomas. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1167:207-224. [PMID: 31520357 DOI: 10.1007/978-3-030-23629-8_12] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Glioblastoma multiforme (GBM) is the most common primary malignant adult brain tumor. Genomic amplifications, activating mutations, and overexpression of receptor tyrosine kinases (RTKs) such as EGFR, and genes in core RTK signaling transduction pathways such as PI3K are common in GBM. However, efforts to target these pathways have been largely unsuccessful in the clinic, and the median survival of GBM patients remains poor at 14-15 months. Therefore, to improve patient outcomes, there must be a concerted effort to elucidate the underlying biology involved in GBM tumorigenesis. Drosophila melanogaster has been a highly effective model for furthering our understanding of GBM tumorigenesis due to a number of experimental advantages it has over traditional mouse models. For example, there exists extensive cellular and genetic homology between humans and Drosophila, and 75% of genes associated with human disease have functional fly orthologs. To take advantage of these traits, we developed a Drosophila GBM model with constitutively active variants of EGFR and PI3K that effectively recapitulated key aspects of GBM disease. Researchers have utilized this model in forward genetic screens and have expanded on its functionality to make a number of important discoveries regarding requirements for key components in GBM tumorigenesis, including genes and pathways involved in extracellular matrix signaling, glycolytic metabolism, invasion/migration, stem cell fate and differentiation, and asymmetric cell division. Drosophila will continue to reveal novel biological pathways and mechanisms involved in gliomagenesis, and this knowledge may contribute to the development of effective treatment strategies to improve patient outcomes.
Collapse
Affiliation(s)
- Alexander S Chen
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Renee D Read
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA. .,Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA. .,Winship Cancer Center, Emory University School of Medicine, Atlanta, GA, USA.
| |
Collapse
|
49
|
Abstract
Ribosomes, which synthesize the proteins of a cell, comprise ribosomal RNA and ribosomal proteins, which coassemble hierarchically during a process termed ribosome biogenesis. Historically, biochemical and molecular biology approaches have revealed how preribosomal particles form and mature in consecutive steps, starting in the nucleolus and terminating after nuclear export into the cytoplasm. However, only recently, due to the revolution in cryo-electron microscopy, could pseudoatomic structures of different preribosomal particles be obtained. Together with in vitro maturation assays, these findings shed light on how nascent ribosomes progress stepwise along a dynamic biogenesis pathway. Preribosomes assemble gradually, chaperoned by a myriad of assembly factors and small nucleolar RNAs, before they reach maturity and enter translation. This information will lead to a better understanding of how ribosome synthesis is linked to other cellular pathways in humans and how it can cause diseases, including cancer, if disturbed.
Collapse
Affiliation(s)
- Jochen Baßler
- Biochemistry Center, University of Heidelberg, 69120 Heidelberg, Germany; ,
| | - Ed Hurt
- Biochemistry Center, University of Heidelberg, 69120 Heidelberg, Germany; ,
| |
Collapse
|
50
|
Cerezo E, Plisson-Chastang C, Henras AK, Lebaron S, Gleizes PE, O'Donohue MF, Romeo Y, Henry Y. Maturation of pre-40S particles in yeast and humans. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1516. [PMID: 30406965 DOI: 10.1002/wrna.1516] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/02/2018] [Accepted: 10/01/2018] [Indexed: 12/22/2022]
Abstract
The synthesis of ribosomal subunits in eukaryotes requires the interplay of numerous maturation and assembly factors (AFs) that intervene in the insertion of ribosomal proteins within pre-ribosomal particles, the ribosomal subunit precursors, as well as in pre-ribosomal RNA (rRNA) processing and folding. Here, we review the intricate nuclear and cytoplasmic maturation steps of pre-40S particles, the precursors to the small ribosomal subunits, in both yeast and human cells, with particular emphasis on the timing and mechanisms of AF association with and dissociation from pre-40S particles and the roles of these AFs in the maturation process. We highlight the particularly complex pre-rRNA processing pathway in human cells, compared to yeast, to generate the mature 18S rRNA. We discuss the information gained from the recently published cryo-electron microscopy atomic models of yeast and human pre-40S particles, as well as the checkpoint/quality control systems that seem to operate to probe functional sites within yeast cytoplasmic pre-40S particles. This article is categorized under: RNA Processing > rRNA Processing Translation > Ribosome Biogenesis.
Collapse
Affiliation(s)
- Emilie Cerezo
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Célia Plisson-Chastang
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Anthony K Henras
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Simon Lebaron
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yves Romeo
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yves Henry
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| |
Collapse
|