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Unarta IC, Cao S, Goonetilleke EC, Niu J, Gellman SH, Huang X. Submillisecond Atomistic Molecular Dynamics Simulations Reveal Hydrogen Bond-Driven Diffusion of a Guest Peptide in Protein-RNA Condensate. J Phys Chem B 2024; 128:2347-2359. [PMID: 38416758 PMCID: PMC11057999 DOI: 10.1021/acs.jpcb.3c08126] [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] [Indexed: 03/01/2024]
Abstract
Liquid-liquid phase separation mediated by proteins and/or nucleic acids is believed to underlie the formation of many distinct condensed phases, or membraneless organelles, within living cells. These condensates have been proposed to orchestrate a variety of important processes. Despite recent advances, the interactions that regulate the dynamics of molecules within a condensate remain poorly understood. We performed accumulated 564.7 μs all-atom molecular dynamics (MD) simulations (system size ∼200k atoms) of model condensates formed by a scaffold RNA oligomer and a scaffold peptide rich in arginine (Arg). These model condensates contained one of three possible guest peptides: the scaffold peptide itself or a variant in which six Arg residues were replaced by lysine (Lys) or asymmetric dimethyl arginine (ADMA). We found that the Arg-rich peptide can form the largest number of hydrogen bonds and bind the strongest to the scaffold RNA in the condensate, relative to the Lys- and ADMA-rich peptides. Our MD simulations also showed that the Arg-rich peptide diffused more slowly in the condensate relative to the other two guest peptides, which is consistent with a recent fluorescence microscopy study. There was no significant increase in the number of cation-π interactions between the Arg-rich peptide and the scaffold RNA compared to the Lys-rich and ADMA-rich peptides. Our results indicate that hydrogen bonds between the peptides and the RNA backbone, rather than cation-π interactions, play a major role in regulating peptide diffusion in the condensate.
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Affiliation(s)
- Ilona C. Unarta
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Siqin Cao
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Eshani C. Goonetilleke
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jiani Niu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Xuhui Huang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA
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2
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Kodera K, Hishida R, Sakai A, Nyuzuki H, Matsui N, Yamanaka T, Saitoh A, Matsui H. GPATCH4 contributes to nucleolus morphology and its dysfunction impairs cell viability. Biochem Biophys Res Commun 2024; 693:149384. [PMID: 38113722 DOI: 10.1016/j.bbrc.2023.149384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
The nucleolus serves a multifaceted role encompassing not only rRNA transcription and ribosome synthesis, but also the intricate orchestration of cell cycle regulation and the modulation of cellular senescence. G-patch domain containing 4 (GPATCH4) stands as one among the nucleolar proteins; however, its functional significances remain still unclear. In order to elucidate the functions of GPATCH4, we examined the effects of its dysfunction on cellular proliferation, alterations in nucleolar architecture, apoptotic events, and cellular senescence. Through experimentation conducted on cultured neuroblastoma SH-SY5Y cells, the reduction of GPATCH4 caused inhibition of cellular proliferation, concurrently fostering escalated apoptotic susceptibilities upon exposure to high-dose etoposide. In the realm of nucleolar morphology comparisons, a discernible decline was noted in the count of nucleoli per nucleus, concomitant with a significant expansion in the area occupied by individual nucleoli. Upon induction of senescence prompted by low-dose etoposide, GPATCH4 knockdown resulted in decreased cell viability and increased expression of senescence-associated markers, namely senescence-associated β-galactosidase (SA-β-GAL) and p16. Furthermore, GPATCH4 dysfunction elicited alterations in the gene expression profile of the ribosomal system. In sum, our findings showed that GPATCH4 is a pivotal nucleolar protein that regulates nucleolar morphology and is correlated with cell viability.
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Affiliation(s)
- Kazuki Kodera
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan; Department of Paediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Ryuichi Hishida
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Akiko Sakai
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Hiromi Nyuzuki
- Department of Paediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Noriko Matsui
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Tomoyuki Yamanaka
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Akihiko Saitoh
- Department of Paediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Hideaki Matsui
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan.
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3
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Sun G, Liu S, Shi C, Liu X, Guo Q. 3DCNAS: A universal method for predicting the location of fluorescent organelles in living cells in three-dimensional space. Exp Cell Res 2023; 433:113807. [PMID: 37852350 DOI: 10.1016/j.yexcr.2023.113807] [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: 07/24/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 10/20/2023]
Abstract
Cellular biology research relies on microscopic imaging techniques for studying the complex structures and dynamic processes within cells. Fluorescence microscopy provides high sensitivity and subcellular resolution but has limitations such as photobleaching and sample preparation challenges. Transmission light microscopy offers a label-free alternative but lacks contrast for detailed interpretation. Deep learning methods have shown promise in analyzing cell images and extracting meaningful information. However, accurately learning and simulating diverse subcellular structures remain challenging. In this study, we propose a method named three-dimensional cell neural architecture search (3DCNAS) to predict subcellular structures of fluorescence using unlabeled transmitted light microscope images. By leveraging the automated search capability of differentiable neural architecture search (NAS), our method partially mitigates the issues of overfitting and underfitting caused by the distinct details of various subcellular structures. Furthermore, we apply our method to analyze cell dynamics in genome-edited human induced pluripotent stem cells during mitotic events. This allows us to study the functional roles of organelles and their involvement in cellular processes, contributing to a comprehensive understanding of cell biology and offering insights into disease pathogenesis.
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Affiliation(s)
- Guocheng Sun
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, 102617, China
| | - Shitou Liu
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, 102617, China
| | - Chaojing Shi
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, 102617, China
| | - Xi Liu
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, 102617, China
| | - Qianjin Guo
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, 102617, China.
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4
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Wang X, Hu J, Wei H, Li Z, Liu J, Zhang J, Yang S. Ultra-fast solvent-free protocol remodels the large-scale synthesis of carbon dots for nucleolus-targeting and white light-emitting diodes. J Colloid Interface Sci 2023; 649:785-794. [PMID: 37385043 DOI: 10.1016/j.jcis.2023.06.171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 06/05/2023] [Accepted: 06/25/2023] [Indexed: 07/01/2023]
Abstract
Carbon dots (CDs) provides unprecedented opportunities for optical applications due its unique properties, but the energy-extensive consumption, high-risk factor and time-consuming synthesis procedure greatly hinders its industrialization process. Herein, we proposed an ultra-low energy consumption solvent-free synthetic strategy for fast preparing green/red fluorescence carbon dots (G-/R-CDs) using m-/o-phenylenediamine and primary amine hydrochloride. The involvement of primary amine hydrochloride can improve the formation rate of G-CDs/R-CDs through effectively absorbing microwave energy and providing acid react environment. The developed CDs exhibit good fluorescence efficiency, optical stability and membrane permeability for dexterous bioimaging in vivo. Based on inherently high nitrogen content, the G-CDs/R-CDs possess excellent nuclear/nucleolus targeting ability, and were successfully applied for screening cancer and normal cells. Furthermore, the G-CDs/R-CDs were further applied for fabricating high-safety and high-color rendering index white light-emitting diodes, providing a perfect candidate for indoor lighting. This study opens up new horizons for advancing practical applications of CDs in related fields of biology and optics.
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Affiliation(s)
- Xin Wang
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, PR China
| | - Jinshuang Hu
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, PR China
| | - Hua Wei
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, PR China
| | - Zihan Li
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, PR China
| | - Jian Liu
- Institute of Advanced Materials, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, China
| | - Jie Zhang
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, PR China
| | - Shenghong Yang
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, PR China.
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5
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Frion J, Meller A, Marbach G, Lévesque D, Roucou X, Boisvert FM. CRISPR/Cas9-mediated knockout of the ubiquitin variant UbKEKS reveals a role in regulating nucleolar structures and composition. Biol Open 2023; 12:bio059984. [PMID: 37670689 PMCID: PMC10537958 DOI: 10.1242/bio.059984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/25/2023] [Indexed: 09/07/2023] Open
Abstract
Ubiquitination is a post-translational modification responsible for one of the most complex multilayered communication and regulation systems in the cell. Over the past decades, new ubiquitin variants and ubiquitin-like proteins arose to further enrich this mechanism. Recently discovered ubiquitin variant UbKEKS can specifically target several proteins and yet, functional consequences of this new modification remain unknown. Depletion of UbKEKS induces accumulation of lamin A in the nucleoli, highlighting the need for deeper investigations about protein composition and functions regulation of this highly dynamic and membrane-less compartment. Using data-independent acquisition mass spectrometry and microscopy, we show that despite not impacting protein stability, UbKEKS is required to maintain a normal nucleolar organization. The absence of UbKEKS increases nucleoli's size and accentuate their circularity while disrupting dense fibrillar component and fibrillar centre structures. Moreover, depletion of UbKEKS leads to distinct changes in nucleolar composition. Lack of UbKEKS favours nucleolar sequestration of known apoptotic regulators such as IFI16 or p14ARF, resulting in an increase of apoptosis observed by flow cytometry and real-time monitoring. Overall, these results identify the first cellular functions of the UbKEKS variant and lay the foundation stone to establish UbKEKS as a new universal layer of regulation in the ubiquitination system.
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Affiliation(s)
- Julie Frion
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Anna Meller
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Gwendoline Marbach
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Dominique Lévesque
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - François-Michel Boisvert
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
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Zou S, Kim B, Tian Y, Liu G, Zhang J, Zerda R, Li Z, Zhang G, Du X, Lin W, Gao X, Huang W, Fu X. Enhanced nuclear translation is associated with proliferation and progression across multiple cancers. MedComm (Beijing) 2023; 4:e248. [PMID: 37063610 PMCID: PMC10104727 DOI: 10.1002/mco2.248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/16/2023] [Accepted: 03/03/2023] [Indexed: 04/18/2023] Open
Abstract
Recent technological advances have re-invigorated the interest in nuclear translation (NT), but the underlying mechanisms and functional implications of NT remain unknown. Here we show that NT is enhanced in malignant cancer cells and is associated with rapid cell growth. Nuclear ribopuromycylation analyses in a panel of diverse cell lines revealed that NT is scarce in normal immortalized cells, but is ubiquitous and robust in malignant cancer cells. Moreover, NT occurs in the nucleolus and requires normal nucleolar function. Intriguingly, NT is reduced by cellular stresses and anti-tumor agents and positively correlates with cancer cell proliferation and growth. By using a modified puromycin-associated nascent chain proteomics, we further identified numerous oncoproteins that are preferentially translated in the nucleus, such as transforming growth factor-beta 2 (TGFB2) and nucleophosmin 1 (NMP1). Specific overexpression of TGFB2 and NMP1 messenger RNAs in the nucleus can increase their protein levels and promote tumorigenesis. These findings establish a previously unknown link between NT and malignancy and suggest that cancer cells might have adapted a mechanism of NT to support their need for rapid growth, which highlight the potential of NT in tumorigenesis and might also open up new possibilities for therapeutic targeting of cancer-specific cellular functions.
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Affiliation(s)
- Sailan Zou
- Division of Endocrinology and MetabolismState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center of BiotherapyChengduChina
| | - Byung‐Wook Kim
- Department of Diabetes Complications and MetabolismArthur Riggs Diabetes and Metabolism Research InstituteIrell & Manella Graduate School of Biological SciencesBeckman Research InstituteCity of Hope National Medical CenterDuarteUSA
| | - Yan Tian
- Division of Endocrinology and MetabolismState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center of BiotherapyChengduChina
| | - Geng Liu
- Division of Endocrinology and MetabolismState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center of BiotherapyChengduChina
| | - Jiawei Zhang
- Department of Diabetes Complications and MetabolismArthur Riggs Diabetes and Metabolism Research InstituteIrell & Manella Graduate School of Biological SciencesBeckman Research InstituteCity of Hope National Medical CenterDuarteUSA
- Cancer Institute (Key Laboratory of Cancer Prevention and InterventionChina National Ministry of Education)Second Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
| | - Ricardo Zerda
- Electron Microscopy and Atomic Force Microscopy CoreCity of Hope National Medical CenterDuarteUSA
| | - Zhuo Li
- Electron Microscopy and Atomic Force Microscopy CoreCity of Hope National Medical CenterDuarteUSA
| | - Guixiang Zhang
- Division of Gastrointestinal SurgeryDepartment of General Surgery and Gastric Cancer CenterWest China HospitalSichuan UniversityChengduChina
| | - Xiao Du
- Division of Gastrointestinal SurgeryDepartment of General Surgery and Gastric Cancer CenterWest China HospitalSichuan UniversityChengduChina
- Department of General SurgeryYaan People's HospitalYaanChina
| | - Weiqiang Lin
- Department of NephrologyThe Fourth Affiliated HospitalInternational Institutes of MedicineSchool of MedicineZhejiang UniversityZhejiangChina
| | - Xiang Gao
- Department of Neurosurgery and Institute of NeurosurgeryState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalWest China Medical SchoolSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Wendong Huang
- Department of Diabetes Complications and MetabolismArthur Riggs Diabetes and Metabolism Research InstituteIrell & Manella Graduate School of Biological SciencesBeckman Research InstituteCity of Hope National Medical CenterDuarteUSA
| | - Xianghui Fu
- Division of Endocrinology and MetabolismState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center of BiotherapyChengduChina
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7
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Radhakrishnan S, Martin CA, Rammohan A, Vij M, Chandrasekar M, Rela M. Significance of nucleologenesis, ribogenesis, and nucleolar proteome in the pathogenesis and recurrence of hepatocellular carcinoma. Expert Rev Gastroenterol Hepatol 2023; 17:363-378. [PMID: 36919496 DOI: 10.1080/17474124.2023.2191189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
INTRODUCTION Emerging evidence suggests that enhanced ribosome biogenesis, increased size, and quantitative distribution of nucleoli are associated with dysregulated transcription, which in turn drives a cell into aberrant cellular proliferation and malignancy. Nucleolar alterations have been considered a prognostic histological marker for aggressive tumors. More recently, advancements in the understanding of chromatin network (nucleoplasm viscosity) regulated liquid-liquid phase separation mechanism of nucleolus formation and their multifunctional role shed light on other regulatory processes, apart from ribosomal biogenesis of the nucleolus. AREAS COVERED Using hepatocellular carcinoma as a model to study the role of nucleoli in tumor progression, we review the potential of nucleolus coalescence in the onset and development of tumors through non-ribosomal biogenesis pathways, thereby providing new avenues for early diagnosis and cancer therapy. EXPERT OPINION Molecular-based classifications have failed to identify the nucleolar-based molecular targets that facilitate cell-cycle progression. However, the algorithm-based tumor risk identification with high-resolution medical images suggests prominent nucleoli, karyotheca, and increased nucleus/cytoplasm ratio as largely associated with tumor recurrence. Nonetheless, the role of the non-ribosomal functions of nucleoli in tumorigenesis remains elusive. This clearly indicates the lacunae in the study of the nucleolar proteins pertaining to cancer. [Figure: see text].
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Affiliation(s)
| | | | - Ashwin Rammohan
- The Institute of Liver Disease & Transplantation, Dr. Rela Institute & Medical Centre, Chennai, India
| | - Mukul Vij
- Department of Pathology, Dr. Rela Institute & Medical Centre, Chennai, India
| | - Mani Chandrasekar
- Department of Oncology, Dr. Rela Institute & Medical Centre, Chennai, India
| | - Mohamed Rela
- Cell Laboratory, National Foundation for Liver Research, Chennai, India
- The Institute of Liver Disease & Transplantation, Dr. Rela Institute & Medical Centre, Chennai, India
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8
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Yan D, Hua L. Nucleolar stress: Friend or foe in cardiac function? Front Cardiovasc Med 2022; 9:1045455. [PMID: 36386352 PMCID: PMC9659567 DOI: 10.3389/fcvm.2022.1045455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/17/2022] [Indexed: 03/14/2024] Open
Abstract
Studies in the past decades have uncovered an emerging role of the nucleolus in stress response and human disease progression. The disruption of ribosome biogenesis in the nucleolus causes aberrant nucleolar architecture and function, termed nucleolar stress, to initiate stress-responsive pathways via nucleolar release sequestration of various proteins. While data obtained from both clinical and basic investigations have faithfully demonstrated an involvement of nucleolar stress in the pathogenesis of cardiomyopathy, much remains unclear regarding its precise role in the progression of cardiac diseases. On the one hand, the initiation of nucleolar stress following acute myocardial damage leads to the upregulation of various cardioprotective nucleolar proteins, including nucleostemin (NS), nucleophosmin (NPM) and nucleolin (NCL). As a result, nucleolar stress plays an important role in facilitating the survival and repair of cardiomyocytes. On the other hand, abnormalities in nucleolar architecture and function are correlated with the deterioration of cardiac diseases. Notably, the cardiomyocytes of advanced ischemic and dilated cardiomyopathy display impaired silver-stained nucleolar organiser regions (AgNORs) and enlarged nucleoli, resembling the characteristics of tissue aging. Collectively, nucleolar abnormalities are critically involved in the development of cardiac diseases.
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Affiliation(s)
- Daliang Yan
- Department of Cardiovascular Surgery, Taizhou People’s Hospital, Taizhou, China
| | - Lu Hua
- Department of Oncology, Taizhou People’s Hospital, Taizhou, China
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9
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Phase-Separated Subcellular Compartmentation and Related Human Diseases. Int J Mol Sci 2022; 23:ijms23105491. [PMID: 35628304 PMCID: PMC9141834 DOI: 10.3390/ijms23105491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 02/06/2023] Open
Abstract
In live cells, proteins and nucleic acids can associate together through multivalent interactions, and form relatively isolated phases that undertake designated biological functions and activities. In the past decade, liquid–liquid phase separation (LLPS) has gradually been recognized as a general mechanism for the intracellular organization of biomolecules. LLPS regulates the assembly and composition of dozens of membraneless organelles and condensates in cells. Due to the altered physiological conditions or genetic mutations, phase-separated condensates may undergo aberrant formation, maturation or gelation that contributes to the onset and progression of various diseases, including neurodegenerative disorders and cancers. In this review, we summarize the properties of different membraneless organelles and condensates, and discuss multiple phase separation-regulated biological processes. Based on the dysregulation and mutations of several key regulatory proteins and signaling pathways, we also exemplify how aberrantly regulated LLPS may contribute to human diseases.
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10
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Feric M, Misteli T. Function moves biomolecular condensates in phase space. Bioessays 2022; 44:e2200001. [PMID: 35243657 PMCID: PMC9277701 DOI: 10.1002/bies.202200001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 11/08/2022]
Abstract
Phase separation underlies the formation of biomolecular condensates. We hypothesize the cellular processes that occur within condensates shape their structural features. We use the example of transcription to discuss structure-function relationships in condensates. Various types of transcriptional condensates have been reported across the evolutionary spectrum in the cell nucleus as well as in mitochondrial and bacterial nucleoids. In vitro and in vivo observations suggest that transcriptional activity of condensates influences their supramolecular structure, which in turn affects their function. Condensate organization thus becomes driven by differences in miscibility among the DNA and proteins of the transcription machinery and the RNA transcripts they generate. These considerations are in line with the notion that cellular processes shape the structural properties of condensates, leading to a dynamic, mutual interplay between structure and function in the cell.
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Affiliation(s)
- Marina Feric
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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11
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Otellin VA, Khozhai LI, Shishko TT, Vershinina EA. Nucleolar Ultrastructure in Neurons of the Rat Neocortical Sensorimotor Area during the Neonatal Period after Perinatal Hypoxic Exposure and Its Pharmacological Correction. J EVOL BIOCHEM PHYS+ 2021. [DOI: 10.1134/s0022093021060053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Sönmez A, Mustafa R, Ryll ST, Tuorto F, Wacheul L, Ponti D, Litke C, Hering T, Kojer K, Koch J, Pitzer C, Kirsch J, Neueder A, Kreiner G, Lafontaine DLJ, Orth M, Liss B, Parlato R. Nucleolar stress controls mutant Huntington toxicity and monitors Huntington's disease progression. Cell Death Dis 2021; 12:1139. [PMID: 34880223 PMCID: PMC8655027 DOI: 10.1038/s41419-021-04432-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 11/12/2021] [Accepted: 11/18/2021] [Indexed: 12/26/2022]
Abstract
Transcriptional and cellular-stress surveillance deficits are hallmarks of Huntington's disease (HD), a fatal autosomal-dominant neurodegenerative disorder caused by a pathological expansion of CAG repeats in the Huntingtin (HTT) gene. The nucleolus, a dynamic nuclear biomolecular condensate and the site of ribosomal RNA (rRNA) transcription, is implicated in the cellular stress response and in protein quality control. While the exact pathomechanisms of HD are still unclear, the impact of nucleolar dysfunction on HD pathophysiology in vivo remains elusive. Here we identified aberrant maturation of rRNA and decreased translational rate in association with human mutant Huntingtin (mHTT) expression. The protein nucleophosmin 1 (NPM1), important for nucleolar integrity and rRNA maturation, loses its prominent nucleolar localization. Genetic disruption of nucleolar integrity in vulnerable striatal neurons of the R6/2 HD mouse model decreases the distribution of mHTT in a disperse state in the nucleus, exacerbating motor deficits. We confirmed NPM1 delocalization in the gradually progressing zQ175 knock-in HD mouse model: in the striatum at a presymptomatic stage and in the skeletal muscle at an early symptomatic stage. In Huntington's patient skeletal muscle biopsies, we found a selective redistribution of NPM1, similar to that in the zQ175 model. Taken together, our study demonstrates that nucleolar integrity regulates the formation of mHTT inclusions in vivo, and identifies NPM1 as a novel, readily detectable peripheral histopathological marker of HD progression.
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Affiliation(s)
- Aynur Sönmez
- Institute of Applied Physiology, Ulm University, Ulm, Germany
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université Libre de Bruxelles (ULB), Biopark campus, Gosselies, Belgium
| | - Rasem Mustafa
- Institute of Applied Physiology, Ulm University, Ulm, Germany
- Institute of Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | - Salome T Ryll
- Institute of Applied Physiology, Ulm University, Ulm, Germany
- Institute of Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | - Francesca Tuorto
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim and Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Ludivine Wacheul
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université Libre de Bruxelles (ULB), Biopark campus, Gosselies, Belgium
| | - Donatella Ponti
- Institute of Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
- Department of Medical-Surgical Sciences and Biotechnologies, University of Rome "Sapienza", Rome, Italy
| | - Christian Litke
- Institute of Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | - Tanja Hering
- Department of Neurology, Ulm University, Ulm, Germany
| | - Kerstin Kojer
- Department of Neurology, Ulm University, Ulm, Germany
| | - Jenniver Koch
- Institute of Applied Physiology, Ulm University, Ulm, Germany
| | - Claudia Pitzer
- Interdisciplinary Neurobehavioral Core (INBC), Heidelberg University, Heidelberg, Germany
| | - Joachim Kirsch
- Institute of Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | | | - Grzegorz Kreiner
- Maj Institute of Pharmacology, Department of Brain Biochemistry, Polish Academy of Sciences, Krakow, Poland
| | - Denis L J Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université Libre de Bruxelles (ULB), Biopark campus, Gosselies, Belgium
| | - Michael Orth
- Department of Neurology, Ulm University, Ulm, Germany
| | - Birgit Liss
- Institute of Applied Physiology, Ulm University, Ulm, Germany
- Linacre & New College, University of Oxford, Oxford, UK
| | - Rosanna Parlato
- Institute of Applied Physiology, Ulm University, Ulm, Germany.
- Institute of Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany.
- Division for Neurodegenerative Diseases, Department of Neurology, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
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13
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Popławski P, Bogusławska J, Hanusek K, Piekiełko-Witkowska A. Nucleolar Proteins and Non-Coding RNAs: Roles in Renal Cancer. Int J Mol Sci 2021; 22:ijms222313126. [PMID: 34884928 PMCID: PMC8658237 DOI: 10.3390/ijms222313126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023] Open
Abstract
Renal cell cancer is the most frequent kidney malignancy. Most RCC cases are classified as clear cell renal cell carcinoma (ccRCC), characterized by high aggressiveness and poor prognosis for patients. ccRCC aggressiveness is defined by classification systems based on changes in morphology of nucleoli, the membraneless substructures of nuclei. The latter act as the sites of ribosome biogenesis as well as the hubs that trap and immobilize proteins, preventing their action in other cellular compartments. Thereby, nucleoli control cellular functioning and homeostasis. Nucleoli are also the sites of activity of multiple noncoding RNAs, including snoRNAs, IGS RNA, and miRNAs. Recent years have brought several remarkable discoveries regarding the role of nucleolar non-coding RNAs, in particular snoRNAs, in ccRCC. The expression of snoRNAs is largely dysregulated in ccRCC tumors. snoRNAs, such as SNHG1, SNHG4 and SNHG12, act as miRNA sponges, leading to aberrant expression of oncogenes and tumor suppressors, and directly contributing to ccRCC development and progression. snoRNAs can also act without affecting miRNA functioning, by altering the expression of key oncogenic proteins such as HIF1A. snoRNAs are also potentially useful biomarkers of ccRCC progression. Here, we comprehensively discuss the role of nucleolar proteins and non-coding RNAs in ccRCC.
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14
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Svidlov A, Drobotenko M, Basov A, Gerasimenko E, Elkina A, Baryshev M, Nechipurenko Y, Dzhimak S. Influence of Environmental Parameters on the Stability of the DNA Molecule. ENTROPY (BASEL, SWITZERLAND) 2021; 23:1446. [PMID: 34828144 PMCID: PMC8622188 DOI: 10.3390/e23111446] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 12/12/2022]
Abstract
Fluctuations in viscosity within the cell nucleus have wide limits. When a DNA molecule passes from the region of high viscosity values to the region of low values, open states, denaturation bubbles, and unweaving of DNA strands can occur. Stabilization of the molecule is provided by energy dissipation-dissipation due to interaction with the environment. Separate sections of a DNA molecule in a twisted state can experience supercoiling stress, which, among other things, is due to complex entropic effects caused by interaction with a solvent. In this work, based on the numerical solution of a mechanical mathematical model for the interferon alpha 17 gene and a fragment of the Drosophila gene, an analysis of the external environment viscosity influence on the dynamics of the DNA molecule and its stability was carried out. It has been shown that an increase in viscosity leads to a rapid stabilization of the angular vibrations of nitrogenous bases, while a decrease in viscosity changes the dynamics of DNA: the rate of change in the angular deviations of nitrogenous bases increases and the angular deformations of the DNA strands increase at each moment of time. These processes lead to DNA instability, which increases with time. Thus, the paper considers the influence of the external environment viscosity on the dissipation of the DNA nitrogenous bases' vibrational motion energy. Additionally, the study on the basis of the described model of the molecular dynamics of physiological processes at different indicators of the rheological behavior of nucleoplasm will allow a deeper understanding of the processes of nonequilibrium physics of an active substance in a living cell to be obtained.
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Affiliation(s)
- Alexander Svidlov
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia
| | - Mikhail Drobotenko
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
| | - Alexander Basov
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- Department of Fundamental and Clinical Biochemistry, Kuban State Medical University, 350063 Krasnodar, Russia
| | - Eugeny Gerasimenko
- Department of Technology of Fats, Cosmetics, Commodity Science, Processes and Devices Kuban State Technological University, 350072 Krasnodar, Russia;
| | - Anna Elkina
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia
- Department of Technology of Fats, Cosmetics, Commodity Science, Processes and Devices Kuban State Technological University, 350072 Krasnodar, Russia;
| | - Mikhail Baryshev
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia
- Department of Technology of Fats, Cosmetics, Commodity Science, Processes and Devices Kuban State Technological University, 350072 Krasnodar, Russia;
| | - Yury Nechipurenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Stepan Dzhimak
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia
- Department of Technology of Fats, Cosmetics, Commodity Science, Processes and Devices Kuban State Technological University, 350072 Krasnodar, Russia;
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15
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Thoms HC, Stark LA. The NF-κB Nucleolar Stress Response Pathway. Biomedicines 2021; 9:biomedicines9091082. [PMID: 34572268 PMCID: PMC8471347 DOI: 10.3390/biomedicines9091082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/09/2021] [Accepted: 08/20/2021] [Indexed: 12/20/2022] Open
Abstract
The nuclear organelle, the nucleolus, plays a critical role in stress response and the regulation of cellular homeostasis. P53 as a downstream effector of nucleolar stress is well defined. However, new data suggests that NF-κB also acts downstream of nucleolar stress to regulate cell growth and death. In this review, we will provide insight into the NF-κB nucleolar stress response pathway. We will discuss apoptosis mediated by nucleolar sequestration of RelA and new data demonstrating a role for p62 (sequestosome (SQSTM1)) in this process. We will also discuss activation of NF-κB signalling by degradation of the RNA polymerase I (PolI) complex component, transcription initiation factor-IA (TIF-IA (RRN3)), and contexts where TIF-IA-NF-κB signalling may be important. Finally, we will discuss how this pathway is targeted by aspirin to mediate apoptosis of colon cancer cells.
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16
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The Role of TCOF1 Gene in Health and Disease: Beyond Treacher Collins Syndrome. Int J Mol Sci 2021; 22:ijms22052482. [PMID: 33804586 PMCID: PMC7957619 DOI: 10.3390/ijms22052482] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/23/2022] Open
Abstract
The nucleoli are membrane-less nuclear substructures that govern ribosome biogenesis and participate in multiple other cellular processes such as cell cycle progression, stress sensing, and DNA damage response. The proper functioning of these organelles is ensured by specific proteins that maintain nucleolar structure and mediate key nucleolar activities. Among all nucleolar proteins, treacle encoded by TCOF1 gene emerges as one of the most crucial regulators of cellular processes. TCOF1 was initially discovered as a gene involved in the Treacher Collins syndrome, a rare genetic disorder characterized by severe craniofacial deformations. Later studies revealed that treacle regulates ribosome biogenesis, mitosis, proliferation, DNA damage response, and apoptosis. Importantly, several reports indicate that treacle is also involved in cancer development, progression, and response to therapies, and may contribute to other pathologies such as Hirschsprung disease. In this manuscript, we comprehensively review the structure, function, and the regulation of TCOF1/treacle in physiological and pathological processes.
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17
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Eleazer R, Fondufe‐Mittendorf YN. The multifaceted role of PARP1 in RNA biogenesis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1617. [PMID: 32656996 PMCID: PMC7856298 DOI: 10.1002/wrna.1617] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/11/2020] [Accepted: 06/17/2020] [Indexed: 12/31/2022]
Abstract
Poly(ADP-ribose) polymerases (PARPs) are abundant nuclear proteins that synthesize ADP ribose polymers (pADPr) and catalyze the addition of (p)ADPr to target biomolecules. PARP1, the most abundant and well-studied PARP, is a multifunctional enzyme that participates in numerous critical cellular processes. A considerable amount of PARP research has focused on PARP1's role in DNA damage. However, an increasing body of evidence outlines more routine roles for PARP and PARylation in nearly every step of RNA biogenesis and metabolism. PARP1's involvement in these RNA processes is pleiotropic and has been ascribed to PARP1's unique flexible domain structures. PARP1 domains are modular self-arranged enabling it to recognize structurally diverse substrates and to act simultaneously through multiple discrete mechanisms. These mechanisms include direct PARP1-protein binding, PARP1-nucleic acid binding, covalent PARylation of target molecules, covalent autoPARylation, and induction of noncovalent interactions with PAR molecules. A combination of these mechanisms has been implicated in PARP1's context-specific regulation of RNA biogenesis and metabolism. We examine the mechanisms of PARP1 regulation in transcription initiation, elongation and termination, co-transcriptional splicing, RNA export, and post-transcriptional RNA processing. Finally, we consider promising new investigative avenues for PARP1 involvement in these processes with an emphasis on PARP1 regulation of subcellular condensates. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Rebekah Eleazer
- Department of Molecular and Cellular Biochemistry and Markey Cancer CenterUniversity of KentuckyLexingtonKentuckyUSA
| | - Yvonne N. Fondufe‐Mittendorf
- Department of Molecular and Cellular Biochemistry and Markey Cancer CenterUniversity of KentuckyLexingtonKentuckyUSA
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18
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Mende H, Müller S. Surveillance of nucleolar homeostasis and ribosome maturation by autophagy and the ubiquitin-proteasome system. Matrix Biol 2021; 100-101:30-38. [PMID: 33556475 DOI: 10.1016/j.matbio.2021.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/11/2022]
Abstract
The nucleolus functions as the cellular hub for the initiation and early steps of ribosome biogenesis. Ribosomes are key components of the translation machinery and, accordingly, their abundance needs to be adjusted to the cellular energy status. Further, to ensure translational fidelity, the integrity and quality of ribosomes needs to be monitored under conditions of cellular stress. Stressful insults, such as nutrient, genotoxic or proteotoxic stress, interfere with ribosome biogenesis and activate a cellular response referred to as nucleolar stress. This nucleolar stress response typically affects nucleolar integrity and is intricately linked to the activation of protein quality control pathways, including (i) the ubiquitin proteasome system (UPS) and (ii) the autophagy machinery, to restore cellular proteostasis. Here we will review some key features of the nucleolar stress response with a particular focus on the role of the UPS and autophagy in this process.
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Affiliation(s)
- Hannah Mende
- Institute of Biochemistry II, Goethe University, Medical School, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Stefan Müller
- Institute of Biochemistry II, Goethe University, Medical School, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany.
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19
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Fujimura A, Hayashi Y, Kato K, Kogure Y, Kameyama M, Shimamoto H, Daitoku H, Fukamizu A, Hirota T, Kimura K. Identification of a novel nucleolar protein complex required for mitotic chromosome segregation through centromeric accumulation of Aurora B. Nucleic Acids Res 2020; 48:6583-6596. [PMID: 32479628 PMCID: PMC7337965 DOI: 10.1093/nar/gkaa449] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 04/24/2020] [Accepted: 05/15/2020] [Indexed: 12/11/2022] Open
Abstract
The nucleolus is a membrane-less nuclear structure that disassembles when cells undergo mitosis. During mitosis, nucleolar factors are thus released from the nucleolus and dynamically change their subcellular localization; however, their functions remain largely uncharacterised. Here, we found that a nucleolar factor called nucleolar protein 11 (NOL11) forms a protein complex with two tryptophan-aspartic acid (WD) repeat proteins named WD-repeat protein 43 (WDR43) and Cirhin in mitotic cells. This complex, referred to here as the NWC (NOL11-WDR43-Cirhin) complex, exists in nucleoli during interphase and translocates to the periphery of mitotic chromosomes, i.e., perichromosomal regions. During mitotic progression, both the congression of chromosomes to the metaphase plate and sister chromatid cohesion are impaired in the absence of the NWC complex, as it is required for the centromeric enrichment of Aurora B and the associating phosphorylation of histone H3 at threonine 3. These results reveal the characteristics of a novel protein complex consisting of nucleolar proteins, which is required for regulating kinetochores and centromeres to ensure faithful chromosome segregation.
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Affiliation(s)
- Akiko Fujimura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan
| | - Yuki Hayashi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan.,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan
| | - Kazashi Kato
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan
| | - Yuichiro Kogure
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan
| | - Mutsuro Kameyama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan
| | - Haruka Shimamoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan
| | - Hiroaki Daitoku
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan
| | - Akiyoshi Fukamizu
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan
| | - Toru Hirota
- Cancer Institute of the Japanese Foundation for Cancer Research, Division of Experimental Pathology, 3-8-1 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Keiji Kimura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan.,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba Science City, Ibaraki 305-8577, Japan
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20
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Zhou F, Green SR, Tsay M, Hsu S, Dibbs R, Beckingham KM. The roles of jim lovell and uninflatable in different endopolyploid larval tissues of Drosophila melanogaster. PLoS One 2020; 15:e0237662. [PMID: 32822370 PMCID: PMC7444548 DOI: 10.1371/journal.pone.0237662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/30/2020] [Indexed: 11/24/2022] Open
Abstract
The larvae of Drosophila melanogaster grow rapidly through use of a highly truncated cell cycle in which mitosis is entirely eliminated. The Drosophila homolog of the protooncogene transcription factor Myc plays a major role in promoting this endopolyploid (EP) growth. We have previously determined that the gene jim lovell (lov), which encodes a member of the BTB/POZ (Bric-a-brac, Tramtrack, Broad/Pox virus zinc finger) domain family of transcription factors, is also required for EP growth in one larval tissue, the trachea. Here we show that lov promotes EP growth in three further tissues indicating a fundamental role in this process. However, epistasis experiments revealed heterogeneity in lov's action in these tissues. Whereas in the tracheae and salivary glands lov acts downstream of Myc, in the fat body, reduced expression of lov does not impede the action of Myc, indicating an upstream action for the gene. We show here that lov's regulation of the gene uninflatable (uif) in the tracheae is a component of this difference. uif is required for tracheal EP growth downstream of Myc and lov but has no equivalent role in the fat body. Although Uif is a transmembrane component of the plasma membrane in the tracheae, its action downstream of Myc suggests an intracellular role for the protein in the tracheae. In addition to regulating uif expression in some tissues we also show that lov locates to the nucleolus, indicating it can function in both polymerase I and polymerase II transcriptional events. Our major finding is that tissue-specific mechanisms can interact with universal growth promotion by Myc to generate the individual endopolyploid organs of the larvae.
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Affiliation(s)
- Fanli Zhou
- Biosciences Dept, Rice University, Houston, Texas, United States of America
- Data Science Dept, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephanie R. Green
- Biosciences Dept, Rice University, Houston, Texas, United States of America
- McGovern Medical School, UT Health Science Center at Houston, Houston, Texas, United States of America
| | - Michael Tsay
- Biosciences Dept, Rice University, Houston, Texas, United States of America
| | - Safina Hsu
- Biosciences Dept, Rice University, Houston, Texas, United States of America
- UTHealth School of Public Health, Houston, Texas, United States of America
| | - Rami Dibbs
- Biosciences Dept, Rice University, Houston, Texas, United States of America
- Louisiana State University School of Medicine, New Orleans, Louisiana, United States of America
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21
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Engbrecht M, Mangerich A. The Nucleolus and PARP1 in Cancer Biology. Cancers (Basel) 2020; 12:cancers12071813. [PMID: 32640701 PMCID: PMC7408768 DOI: 10.3390/cancers12071813] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/26/2020] [Accepted: 07/01/2020] [Indexed: 12/13/2022] Open
Abstract
The nucleolus has been known for a long time to fulfill crucial functions in ribosome biogenesis, of which cancer cells can become addicted to in order to produce sufficient amounts of proteins for cell proliferation. Recently, the nucleolus has emerged as a central regulatory hub in many other cancer-relevant processes, including stress sensing, DNA damage response, cell cycle control, and proteostasis. This fostered the idea that nucleolar processes can be exploited in cancer therapy. Interestingly, a significant proportion of poly(ADP-ribose) polymerase 1 (PARP1) molecules are localized in the nucleolus and PARP1 also plays crucial roles in many processes that are important in cancer biology, including genome maintenance, replication, transcription, and chromatin remodeling. Furthermore, during the last years, PARP1 came into focus in oncology since it represents a promising target of pharmacological PARP inhibitors in various types of cancers. Here, we provide an overview of our current understanding on the role of PARP1 in nucleolar functions and discuss potential implications in cancer biology and therapy.
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22
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Urae S, Harita Y, Udagawa T, Ode KL, Nagahama M, Kajiho Y, Kanda S, Saito A, Ueda HR, Nangaku M, Oka A. A cellular model of albumin endocytosis uncovers a link between membrane and nuclear proteins. J Cell Sci 2020; 133:jcs242859. [PMID: 32482797 DOI: 10.1242/jcs.242859] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 05/20/2020] [Indexed: 12/21/2022] Open
Abstract
Cubilin (CUBN) and amnionless (AMN), expressed in kidney and intestine, form a multiligand receptor complex called CUBAM that plays a crucial role in albumin absorption. To date, the mechanism of albumin endocytosis mediated by CUBAM remains to be elucidated. Here, we describe a quantitative assay to evaluate albumin uptake by CUBAM using cells expressing full-length CUBN and elucidate the crucial roles of the C-terminal part of CUBN and the endocytosis signal motifs of AMN in albumin endocytosis. We also demonstrate that nuclear valosin-containing protein-like 2 (NVL2), an interacting protein of AMN, is involved in this process. Although NVL2 was mainly localized in the nucleolus in cells without AMN expression, it was translocated to the extranuclear compartment when coexpressed with AMN. NVL2 knockdown significantly impaired internalization of the CUBN-albumin complex in cultured cells, demonstrating an involvement of NVL2 in endocytic regulation. These findings uncover a link between membrane and nucleolar proteins that is involved in endocytic processes.
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Affiliation(s)
- Seiya Urae
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
- Division of Nephrology and Endocrinology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Yutaka Harita
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Tomohiro Udagawa
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Koji L Ode
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Masami Nagahama
- Laboratory of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Kiyose-shi, Tokyo 204-8588, Japan
| | - Yuko Kajiho
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Shoichiro Kanda
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Akihiko Saito
- Department of Applied Molecular Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata-shi, Niigata 951-8510, Japan
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Wako-shi, Saitama 351-0198, Japan
| | - Masaomi Nangaku
- Division of Nephrology and Endocrinology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Akira Oka
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
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23
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Maiser A, Dillinger S, Längst G, Schermelleh L, Leonhardt H, Németh A. Super-resolution in situ analysis of active ribosomal DNA chromatin organization in the nucleolus. Sci Rep 2020; 10:7462. [PMID: 32366902 PMCID: PMC7198602 DOI: 10.1038/s41598-020-64589-x] [Citation(s) in RCA: 36] [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: 08/12/2019] [Accepted: 04/01/2020] [Indexed: 12/21/2022] Open
Abstract
Ribosomal RNA (rRNA) transcription by RNA polymerase I (Pol I) is the first key step of ribosome biogenesis. While the molecular mechanisms of rRNA transcription regulation have been elucidated in great detail, the functional organization of the multicopy rRNA gene clusters (rDNA) in the nucleolus is less well understood. Here we apply super-resolution 3D structured illumination microscopy (3D-SIM) to investigate the spatial organization of transcriptionally competent active rDNA chromatin at size scales well below the diffraction limit by optical microscopy. We identify active rDNA chromatin units exhibiting uniformly ring-shaped conformations with diameters of ~240 nm in mouse and ~170 nm in human fibroblasts, consistent with rDNA looping. The active rDNA chromatin units are clearly separated from each other and from the surrounding areas of rRNA processing. Simultaneous imaging of all active genes bound by Pol I and the architectural chromatin protein Upstream Binding Transcription Factor (UBF) reveals a random spatial orientation of regular repeats of rDNA coding sequences within the nucleoli. These observations imply rDNA looping and exclude potential formation of systematic spatial assemblies of the well-ordered repetitive arrays of transcription units. Collectively, this study uncovers key features of the 3D organization of active rDNA chromatin units and their nucleolar clusters providing a spatial framework of nucleolar chromatin organization at unprecedented detail.
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Affiliation(s)
- Andreas Maiser
- Department of Biology II, Ludwig-Maximilians-Universität München, München, Germany
| | - Stefan Dillinger
- Department of Biochemistry III, University of Regensburg, Regensburg, Germany
| | - Gernot Längst
- Department of Biochemistry III, University of Regensburg, Regensburg, Germany
| | - Lothar Schermelleh
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig-Maximilians-Universität München, München, Germany
| | - Attila Németh
- Department of Biochemistry III, University of Regensburg, Regensburg, Germany.
- Institute of Neuropathology, Justus Liebig University, Giessen, Germany.
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24
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uL3 Mediated Nucleolar Stress Pathway as a New Mechanism of Action of Antiproliferative G-quadruplex TBA Derivatives in Colon Cancer Cells. Biomolecules 2020; 10:biom10040583. [PMID: 32290083 PMCID: PMC7226491 DOI: 10.3390/biom10040583] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/28/2020] [Accepted: 04/05/2020] [Indexed: 12/29/2022] Open
Abstract
The antiproliferative G-quadruplex aptamers are a promising and challenging subject in the framework of the anticancer therapeutic oligonucleotides research field. Although several antiproliferative G-quadruplex aptamers have been identified and proven to be effective on different cancer cell lines, their mechanism of action is still unexplored. We have recently described the antiproliferative activity of a heterochiral thrombin binding aptamer (TBA) derivative, namely, LQ1. Here, we investigate the molecular mechanisms of LQ1 activity and the structural and antiproliferative properties of two further TBA derivatives, differing from LQ1 only by the small loop base-compositions. We demonstrate that in p53 deleted colon cancer cells, LQ1 causes nucleolar stress, impairs ribosomal RNA processing, leading to the accumulation of pre-ribosomal RNAs, arrests cells in the G2/M phase and induces early apoptosis. Importantly, the depletion of uL3 abrogates all these effects, indicating that uL3 is a crucial player in the mechanism of action of LQ1. Taken together, our findings identify p53-independent and uL3-dependent nucleolar stress as a novel stress response pathway activated by a specific G-quadruplex TBA derivative. To the best of our knowledge, this investigation reveals, for the first time, the involvement of the nucleolar stress pathway in the mechanism of action of antiproliferative G-quadruplex aptamers.
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Methylisothiazolinone induces apoptotic cell death via matrix metalloproteinase activation in human bronchial epithelial cells. Toxicol In Vitro 2020; 62:104661. [DOI: 10.1016/j.tiv.2019.104661] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/16/2019] [Accepted: 09/19/2019] [Indexed: 12/16/2022]
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Duan T, Green N, Tootle TL, Geyer PK. Nuclear architecture as an intrinsic regulator of Drosophila female germline stem cell maintenance. CURRENT OPINION IN INSECT SCIENCE 2020; 37:30-38. [PMID: 32087561 PMCID: PMC7089816 DOI: 10.1016/j.cois.2019.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 11/08/2019] [Accepted: 11/13/2019] [Indexed: 05/08/2023]
Abstract
Homeostasis of Drosophila germline stem cells (GSC) depends upon the integration of intrinsic and extrinsic signals. This review highlights emerging data that support nuclear architecture as an intrinsic regulator of GSC maintenance and germ cell differentiation. Here, we focus on the nuclear lamina (NL) and the nucleolus, two compartments that undergo alterations in composition upon germ cell differentiation. Loss of NL or nucleolar components leads to GSC loss, resulting from activation of GSC quality control checkpoint pathways. We suggest that the NL and nucleolus integrate signals needed for the switch between GSC maintenance and germ cell differentiation, and propose regulation of nuclear actin pools as one mechanism that connects these compartments.
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Affiliation(s)
- Tingting Duan
- Departments of Biochemistry, University of Iowa, College of Medicine, Iowa City, IA 52242, USA
| | - Nicole Green
- Anatomy and Cell Biology, University of Iowa, College of Medicine, Iowa City, IA 52242, USA
| | - Tina L Tootle
- Anatomy and Cell Biology, University of Iowa, College of Medicine, Iowa City, IA 52242, USA
| | - Pamela K Geyer
- Departments of Biochemistry, University of Iowa, College of Medicine, Iowa City, IA 52242, USA.
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Ferreira R, Schneekloth JS, Panov KI, Hannan KM, Hannan RD. Targeting the RNA Polymerase I Transcription for Cancer Therapy Comes of Age. Cells 2020; 9:cells9020266. [PMID: 31973211 PMCID: PMC7072222 DOI: 10.3390/cells9020266] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 12/24/2022] Open
Abstract
Transcription of the ribosomal RNA genes (rDNA) that encode the three largest ribosomal RNAs (rRNA), is mediated by RNA Polymerase I (Pol I) and is a key regulatory step for ribosomal biogenesis. Although it has been reported over a century ago that the number and size of nucleoli, the site of ribosome biogenesis, are increased in cancer cells, the significance of this observation for cancer etiology was not understood. The realization that the increase in rRNA expression has an active role in cancer progression, not only through increased protein synthesis and thus proliferative capacity but also through control of cellular check points and chromatin structure, has opened up new therapeutic avenues for the treatment of cancer through direct targeting of Pol I transcription. In this review, we discuss the rational of targeting Pol I transcription for the treatment of cancer; review the current cancer therapeutics that target Pol I transcription and discuss the development of novel Pol I-specific inhibitors, their therapeutic potential, challenges and future prospects.
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Affiliation(s)
- Rita Ferreira
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, Australian National University, Acton 2601, NSW, Australia; (K.I.P.); (K.M.H.); (R.D.H.)
- Correspondence:
| | - John S. Schneekloth
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
| | - Konstantin I. Panov
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, Australian National University, Acton 2601, NSW, Australia; (K.I.P.); (K.M.H.); (R.D.H.)
- CCRCB and School of Biological Sciences, Queen’s University Belfast Medical Biology Centre, School of Biological Sciences, Queen’s University Belfast, Belfast BT9 7BL, UK
| | - Katherine M. Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, Australian National University, Acton 2601, NSW, Australia; (K.I.P.); (K.M.H.); (R.D.H.)
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ross D. Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, Australian National University, Acton 2601, NSW, Australia; (K.I.P.); (K.M.H.); (R.D.H.)
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD 4072, Australia
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28
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Caragine CM, Haley SC, Zidovska A. Nucleolar dynamics and interactions with nucleoplasm in living cells. eLife 2019; 8:47533. [PMID: 31769409 PMCID: PMC6879204 DOI: 10.7554/elife.47533] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 10/13/2019] [Indexed: 01/25/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) has been recognized as one of the key cellular organizing principles and was shown to be responsible for formation of membrane-less organelles such as nucleoli. Although nucleoli were found to behave like liquid droplets, many ramifications of LLPS including nucleolar dynamics and interactions with the surrounding liquid remain to be revealed. Here, we study the motion of human nucleoli in vivo, while monitoring the shape of the nucleolus-nucleoplasm interface. We reveal two types of nucleolar pair dynamics: an unexpected correlated motion prior to coalescence and an independent motion otherwise. This surprising kinetics leads to a nucleolar volume distribution, [Formula: see text], unaccounted for by any current theory. Moreover, we find that nucleolus-nucleoplasm interface is maintained by ATP-dependent processes and susceptible to changes in chromatin transcription and packing. Our results extend and enrich the LLPS framework by showing the impact of the surrounding nucleoplasm on nucleoli in living cells.
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Affiliation(s)
- Christina M Caragine
- Center for Soft Matter Research, Department of Physics, New York University, New York, United States
| | - Shannon C Haley
- Center for Soft Matter Research, Department of Physics, New York University, New York, United States
| | - Alexandra Zidovska
- Center for Soft Matter Research, Department of Physics, New York University, New York, United States
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29
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Co-Operation between Aneuploidy and Metabolic Changes in Driving Tumorigenesis. Int J Mol Sci 2019; 20:ijms20184611. [PMID: 31540349 PMCID: PMC6770258 DOI: 10.3390/ijms20184611] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/05/2019] [Accepted: 09/17/2019] [Indexed: 12/11/2022] Open
Abstract
Alterations from the normal set of chromosomes are extremely common as cells progress toward tumourigenesis. Similarly, we expect to see disruption of normal cellular metabolism, particularly in the use of glucose. In this review, we discuss the connections between these two processes: how chromosomal aberrations lead to metabolic disruption, and vice versa. Both processes typically result in the production of elevated levels of reactive oxygen species, so we particularly focus on their role in mediating oncogenic changes.
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Chen J, Stark LA. Insights into the Relationship between Nucleolar Stress and the NF-κB Pathway. Trends Genet 2019; 35:768-780. [PMID: 31434627 DOI: 10.1016/j.tig.2019.07.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 02/06/2023]
Abstract
The nuclear organelle the nucleolus and the transcription factor nuclear factor of κ-light-chain-enhancer of activated B cells (NF-κB) are both central to the control of cellular homeostasis, dysregulated in common diseases and implicated in the ageing process. Until recently, it was believed that they acted independently to regulate homeostasis in health and disease. However, there is an emerging body of evidence suggesting that nucleoli and NF-κB signalling converge at multiple levels. Here we will review current understanding of this crosstalk. We will discuss activation of the NF-κB pathway by nucleolar stress and induction of apoptosis by nucleolar sequestration of NF-κB/RelA. We will also discuss the role of TIF-IA, COMMD1, and nucleophosmin, which are key players in this crosstalk, and the therapeutic relevance, particularly with respect to the antitumour effects of aspirin.
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Affiliation(s)
- Jingyu Chen
- University of Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, Scotland EH4 2XU, UK
| | - Lesley A Stark
- University of Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, Scotland EH4 2XU, UK.
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PARP1 regulates DNA damage-induced nucleolar-nucleoplasmic shuttling of WRN and XRCC1 in a toxicant and protein-specific manner. Sci Rep 2019; 9:10075. [PMID: 31296950 PMCID: PMC6624289 DOI: 10.1038/s41598-019-46358-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 06/12/2019] [Indexed: 12/13/2022] Open
Abstract
The prime function of nucleoli is ribogenesis, however, several other, non-canonical functions have recently been identified, including a role in genotoxic stress response. Upon DNA damage, numerous proteins shuttle dynamically between the nucleolus and the nucleoplasm, yet the underlying molecular mechanisms are incompletely understood. Here, we demonstrate that PARP1 and PARylation contribute to genotoxic stress-induced nucleolar-nucleoplasmic shuttling of key genome maintenance factors in HeLa cells. Our work revealed that the RECQ helicase, WRN, translocates from nucleoli to the nucleoplasm upon treatment with the oxidizing agent H2O2, the alkylating agent 2-chloroethyl ethyl sulfide (CEES), and the topoisomerase inhibitor camptothecin (CPT). We show that after treatment with H2O2 and CEES, but not CPT, WRN translocation was dependent on PARP1 protein, yet independent of its enzymatic activity. In contrast, nucleolar-nucleoplasmic translocation of the base excision repair protein, XRCC1, was dependent on both PARP1 protein and its enzymatic activity. Furthermore, gossypol, which inhibits PARP1 activity by disruption of PARP1-protein interactions, abolishes nucleolar-nucleoplasmic shuttling of WRN, XRCC1 and PARP1, indicating the involvement of further upstream factors. In conclusion, this study highlights a prominent role of PARP1 in the DNA damage-induced nucleolar-nucleoplasmic shuttling of genome maintenance factors in HeLa cells in a toxicant and protein-specific manner.
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Pirogov SA, Gvozdev VA, Klenov MS. Long Noncoding RNAs and Stress Response in the Nucleolus. Cells 2019; 8:cells8070668. [PMID: 31269716 PMCID: PMC6678565 DOI: 10.3390/cells8070668] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) perform diverse functions in the regulation of cellular processes. Here we consider a variety of lncRNAs found in the ribosome production center, the nucleolus, and focus on their role in the response to environmental stressors. Nucleolar lncRNAs ensure stress adaptation by cessation of resource-intensive ribosomal RNA (rRNA) synthesis and by inducing the massive sequestration of proteins within the nucleolus. Different cell states like quiescence and cancer are also controlled by specific lncRNAs in the nucleolus. Taken together, recent findings allow us to consider lncRNAs as multifunctional regulators of nucleolar activities, which are responsive to various physiological conditions.
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Affiliation(s)
- Sergei A Pirogov
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
| | - Vladimir A Gvozdev
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia.
| | - Mikhail S Klenov
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia.
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Martínez-Calvillo S, Florencio-Martínez LE, Nepomuceno-Mejía T. Nucleolar Structure and Function in Trypanosomatid Protozoa. Cells 2019; 8:cells8050421. [PMID: 31071985 PMCID: PMC6562600 DOI: 10.3390/cells8050421] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 12/12/2022] Open
Abstract
The nucleolus is the conspicuous nuclear body where ribosomal RNA genes are transcribed by RNA polymerase I, pre-ribosomal RNA is processed, and ribosomal subunits are assembled. Other important functions have been attributed to the nucleolus over the years. Here we review the current knowledge about the structure and function of the nucleolus in the trypanosomatid parasites Trypanosoma brucei, Trypanosoma cruzi and Leishmania ssp., which represent one of the earliest branching lineages among the eukaryotes. These protozoan parasites present a single nucleolus that is preserved throughout the closed nuclear division, and that seems to lack fibrillar centers. Trypanosomatids possess a relatively low number of rRNA genes, which encode rRNA molecules that contain large expansion segments, including several that are trypanosomatid-specific. Notably, the large subunit rRNA (28S-type) is fragmented into two large and four small rRNA species. Hence, compared to other organisms, the rRNA primary transcript requires additional processing steps in trypanosomatids. Accordingly, this group of parasites contains the highest number ever reported of snoRNAs that participate in rRNA processing. The number of modified rRNA nucleotides in trypanosomatids is also higher than in other organisms. Regarding the structure and biogenesis of the ribosomes, recent cryo-electron microscopy analyses have revealed several trypanosomatid-specific features that are discussed here. Additional functions of the nucleolus in trypanosomatids are also reviewed.
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Affiliation(s)
- Santiago Martínez-Calvillo
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla CP 54090, Estado de México, Mexico.
| | - Luis E Florencio-Martínez
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla CP 54090, Estado de México, Mexico.
| | - Tomás Nepomuceno-Mejía
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla CP 54090, Estado de México, Mexico.
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Andreyeva EN, Ogienko AA, Yushkova AA, Popova JV, Pavlova GA, Kozhevnikova EN, Ivankin AV, Gatti M, Pindyurin AV. Non3 is an essential Drosophila gene required for proper nucleolus assembly. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The nucleolus is a dynamic non-membrane-bound nuclear organelle, which plays key roles not only in ribosome biogenesis but also in many other cellular processes. Consistent with its multiple functions, the nucleolus has been implicated in many human diseases, including cancer and degenerative pathologies of the nervous system and heart. Here, we report the characterization of the Drosophila Non3 (Novel nucleolar protein 3) gene, which encodes a protein homologous to the human Brix domain-containing Rpf2 that has been shown to control ribosomal RNA (rRNA) processing. We used imprecise P-element excision to generate four new mutant alleles in the Non3 gene. Complementation and phenotypic analyses showed that these Non3 mutations can be arranged in an allelic series that includes both viable and lethal alleles. The strongest lethal allele (Non3∆600) is a genetically null allele that carries a large deletion of the gene and exhibits early lethality when homozygous. Flies heterozygous for Non3∆600 occasionally exhibit a mild reduction in the bristle size, but develop normally and are fertile. However, heteroallelic combinations of viable Non3 mutations (Non3197, Non3310 and Non3259) display a Minute-like phenotype, consisting in delayed development and short and thin bristles, suggesting that they are defective in ribosome biogenesis. We also demonstrate that the Non3 protein localizes to the nucleolus of larval brain cells and it is required for proper nucleolar localization of Fibrillarin, a protein important for post-translational modification and processing of rRNAs. In summary, we generated a number of genetic and biochemical tools that were exploited for an initial characterization of Non3, and will be instrumental for future functional studies on this gene and its protein product.
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Affiliation(s)
| | - A. A. Ogienko
- Institute of Molecular and Cellular Biology, SB RAS; Novosibirsk State University
| | - A. A. Yushkova
- Institute of Molecular and Cellular Biology, SB RAS; Novosibirsk State University
| | - J. V. Popova
- Institute of Molecular and Cellular Biology, SB RAS; Institute of Cytology and Genetics, SB RAS
| | | | - E. N. Kozhevnikova
- Institute of Molecular and Cellular Biology, SB RAS; Institute of Cytology and Genetics, SB RAS
| | | | - M. Gatti
- Institute of Molecular and Cellular Biology, SB RAS; IBPM CNR and Department of Biology and Biotechnology, Sapienza University of Rome
| | - A. V. Pindyurin
- Institute of Molecular and Cellular Biology, SB RAS; Novosibirsk State University; Institute of Cytology and Genetics, SB RAS
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Tuorto F, Parlato R. rRNA and tRNA Bridges to Neuronal Homeostasis in Health and Disease. J Mol Biol 2019; 431:1763-1779. [PMID: 30876917 DOI: 10.1016/j.jmb.2019.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/25/2019] [Accepted: 03/06/2019] [Indexed: 12/11/2022]
Abstract
Dysregulation of protein translation is emerging as a unifying mechanism in the pathogenesis of many neuronal disorders. Ribosomal RNA (rRNA) and transfer RNA (tRNA) are structural molecules that have complementary and coordinated functions in protein synthesis. Defects in both rRNAs and tRNAs have been described in mammalian brain development, neurological syndromes, and neurodegeneration. In this review, we present the molecular mechanisms that link aberrant rRNA and tRNA transcription, processing and modifications to translation deficits, and neuropathogenesis. We also discuss the interdependence of rRNA and tRNA biosynthesis and how their metabolism brings together proteotoxic stress and impaired neuronal homeostasis.
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Affiliation(s)
- Francesca Tuorto
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.
| | - Rosanna Parlato
- Institute of Applied Physiology, University of Ulm, Albert Einstein Allee 11, 89081 Ulm, Germany; Institute of Anatomy and Cell Biology, Medical Cell Biology, University of Heidelberg, Im Neuenheimer Feld 307, 69120 Heidelberg, Germany.
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Proteins of the Nucleolus of Dictyostelium discoideum: Nucleolar Compartmentalization, Targeting Sequences, Protein Translocations and Binding Partners. Cells 2019; 8:cells8020167. [PMID: 30781559 PMCID: PMC6406644 DOI: 10.3390/cells8020167] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 12/31/2022] Open
Abstract
The nucleoli of Dictyostelium discoideum have a comparatively unique, non-canonical, localization adjacent to the inner nuclear membrane. The verified nucleolar proteins of this eukaryotic microbe are detailed while other potential proteins are introduced. Heat shock protein 32 (Hsp32), eukaryotic translation initiation factor 6 (eIF6), and tumour necrosis factor receptor-associated protein 1 (TRAP1) are essential for cell survival. NumA1, a breast cancer type 1 susceptibility protein-C Terminus domain-containing protein linked to cell cycle, functions in the regulation of nuclear number. The cell cycle checkpoint kinase 2 homologue forkhead-associated kinase A (FhkA) and BRG1-associated factor 60a homologue Snf12 are also discussed. While nucleoli appear homogeneous ultrastructurally, evidence for nucleolar subcompartments exists. Nucleolar localization sequences (NoLS) have been defined that target proteins to either the general nucleolar area or to a specific intranucleolar domain. Protein translocations during mitosis are protein-specific and support the multiple functions of the Dictyostelium nucleolus. To enrich the picture, binding partners of NumA1, the most well-characterized nucleolar protein, are examined: nucleolar Ca2+-binding protein 4a (CBP4a), nuclear puromycin-sensitive aminopeptidase A (PsaA) and Snf12. The role of Dictyostelium as a model for understanding the contribution of nucleolar proteins to various diseases and cellular stress is discussed throughout the review.
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Bughio F, Maggert KA. The peculiar genetics of the ribosomal DNA blurs the boundaries of transgenerational epigenetic inheritance. Chromosome Res 2018; 27:19-30. [PMID: 30511202 DOI: 10.1007/s10577-018-9591-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/31/2018] [Accepted: 11/07/2018] [Indexed: 12/20/2022]
Abstract
Our goal is to draw a line-hypothetical in its totality but experimentally supported at each individual step-connecting the ribosomal DNA and the phenomenon of transgenerational epigenetic inheritance of induced phenotypes. The reasonableness of this hypothesis is offset by its implication, that many (or most) (or all) of the cases of induced-and-inherited phenotypes that are seen to persist for generations are instead unmapped induced polymorphisms in the ribosomal DNA, and thus are the consequence of the peculiar and enduringly fascinating genetics of the highly transcribed repeat DNA structure at that locus.
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Affiliation(s)
- Farah Bughio
- Department of Cellular and Molecular Medicine, College of Medicine, University of Arizona, Tucson, AZ, USA
- University of Arizona Cancer Center, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Keith A Maggert
- Department of Cellular and Molecular Medicine, College of Medicine, University of Arizona, Tucson, AZ, USA.
- University of Arizona Cancer Center, University of Arizona College of Medicine, Tucson, AZ, USA.
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38
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Crosstalk between NF-κB and Nucleoli in the Regulation of Cellular Homeostasis. Cells 2018; 7:cells7100157. [PMID: 30301139 PMCID: PMC6210184 DOI: 10.3390/cells7100157] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/28/2018] [Accepted: 10/03/2018] [Indexed: 12/30/2022] Open
Abstract
Nucleoli are emerging as key sensors of cellular stress and regulators of the downstream consequences on proliferation, metabolism, senescence, and apoptosis. NF-κB signalling is activated in response to a similar plethora of stresses, which leads to modulation of cell growth and death programs. While nucleolar and NF-κB pathways are distinct, it is increasingly apparent that they converge at multiple levels. Exposure of cells to certain insults causes a specific type of nucleolar stress that is characterised by degradation of the PolI complex component, TIF-IA, and increased nucleolar size. Recent studies have shown that this atypical nucleolar stress lies upstream of cytosolic IκB degradation and NF-κB nuclear translocation. Under these stress conditions, the RelA component of NF-κB accumulates within functionally altered nucleoli to trigger a nucleophosmin dependent, apoptotic pathway. In this review, we will discuss these points of crosstalk and their relevance to anti-tumour mechanism of aspirin and small molecule CDK4 inhibitors. We will also briefly the discuss how crosstalk between nucleoli and NF-κB signalling may be more broadly relevant to the regulation of cellular homeostasis and how it may be exploited for therapeutic purpose.
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39
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Caragine CM, Haley SC, Zidovska A. Surface Fluctuations and Coalescence of Nucleolar Droplets in the Human Cell Nucleus. PHYSICAL REVIEW LETTERS 2018; 121:148101. [PMID: 30339413 PMCID: PMC6452643 DOI: 10.1103/physrevlett.121.148101] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 07/01/2018] [Indexed: 05/19/2023]
Abstract
The nucleolus is a membraneless organelle embedded in chromatin solution inside the cell nucleus. By analyzing surface dynamics and fusion kinetics of human nucleoli in vivo, we find that the nucleolar surface exhibits subtle, but measurable, shape fluctuations and that the radius of the neck connecting two fusing nucleoli grows in time as r(t)∼t^{1/2}. This is consistent with liquid droplets with low surface tension ∼10^{-6} N m^{-1} coalescing within an outside fluid of high viscosity ∼10^{3} Pa s. Our study presents a noninvasive approach of using natural probes and their dynamics to investigate material properties of the cell and its constituents.
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40
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Abstract
The rates of ribosome production by a nucleolus and of protein biosynthesis by ribosomes are tightly correlated with the rate of cell growth and proliferation. All these processes must be matched and appropriately regulated to provide optimal cell functioning. Deregulation of certain factors, including oncogenes, controlling these processes, especially ribosome biosynthesis, can lead to cell transformation. Cancer cells are characterized by intense ribosome biosynthesis which is advantageous for their growth and proliferation. On the other hand, this feature can be engaged as an anticancer strategy. Numerous nucleolar factors such as nucleolar and ribosomal proteins as well as different RNAs, in addition to their role in ribosome biosynthesis, have other functions, including those associated with cancer biology. Some of them can contribute to cell transformation and cancer development. Others, under stress evoked by different factors which often hamper function of nucleoli and thus induce nucleolar/ribosomal stress, can participate in combating cancer cells. In this sense, intentional application of therapeutic agents affecting ribosome biosynthesis can cause either release of these molecules from nucleoli or their de novo biosynthesis to mediate the activation of pathways leading to elimination of harmful cells. This review underlines the role of a nucleolus not only as a ribosome constituting apparatus but also as a hub of both positive and negative control of cancer development. The article is mainly based on original papers concerning mechanisms in which the nucleolus is implicated directly or indirectly in processes associated with neoplasia.
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Affiliation(s)
- Dariusz Stępiński
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Łódź, Poland.
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41
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Sawyer IA, Bartek J, Dundr M. Phase separated microenvironments inside the cell nucleus are linked to disease and regulate epigenetic state, transcription and RNA processing. Semin Cell Dev Biol 2018; 90:94-103. [PMID: 30017905 DOI: 10.1016/j.semcdb.2018.07.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/03/2018] [Indexed: 01/01/2023]
Abstract
Proteins and RNAs inside the cell nucleus are organized into distinct phases, also known as liquid-liquid phase separated (LLPS) droplet organelles or nuclear bodies. These regions exist within the spaces between chromatin-rich regions but their function is tightly linked to gene activity. They include major microscopically-observable structures such as the nucleolus, paraspeckle and Cajal body. The biochemical and assembly factors enriched inside these microenvironments regulate chromatin structure, transcription, and RNA processing, and other important cellular functions. Here, we describe published evidence that suggests nuclear bodies are bona fide LLPS droplet organelles and major regulators of the processes listed above. We also outline an updated "Supply or Sequester" model to describe nuclear body function, in which proteins or RNAs are supplied to surrounding genomic regions or sequestered away from their sites of activity. Finally, we describe recent evidence that suggests these microenvironments are both reflective and drivers of diverse pathophysiological states.
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Affiliation(s)
- Iain A Sawyer
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, United States; Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Jiri Bartek
- Danish Cancer, Society Research Center, Genome Integrity Unit, Copenhagen, Denmark; Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Miroslav Dundr
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, United States.
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42
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Schiavon CR, Griffin ME, Pirozzi M, Parashuraman R, Zhou W, Jinnah HA, Reines D, Kahn RA. Compositional complexity of rods and rings. Mol Biol Cell 2018; 29:2303-2316. [PMID: 30024290 PMCID: PMC6249804 DOI: 10.1091/mbc.e18-05-0274] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Rods and rings (RRs) are large linear- or circular-shaped structures typically described as polymers of IMPDH (inosine monophosphate dehydrogenase). They have been observed across a wide variety of cell types and species and can be induced to form by inhibitors of IMPDH. RRs are thought to play a role in the regulation of de novo guanine nucleotide synthesis; however, the function and regulation of RRs is poorly understood. Here we show that the regulatory GTPase, ARL2, a subset of its binding partners, and several resident proteins at the endoplasmic reticulum (ER) also localize to RRs. We also have identified two new inducers of RR formation: AICAR and glucose deprivation. We demonstrate that RRs can be disassembled if guanine nucleotides can be generated by salvage synthesis regardless of the inducer. Finally, we show that there is an ordered addition of components as RRs mature, with IMPDH first forming aggregates, followed by ARL2, and only later calnexin, a marker of the ER. These findings suggest that RRs are considerably more complex than previously thought and that the function(s) of RRs may include involvement of a regulatory GTPase, its effectors, and potentially contacts with intracellular membranes.
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Affiliation(s)
- Cara R Schiavon
- Cancer Biology Graduate Program, Graduate Division of Biomedical and Biological Sciences, Laney Graduate School, Atlanta, GA 30307
| | - Maxwell E Griffin
- Cancer Biology Graduate Program, Graduate Division of Biomedical and Biological Sciences, Laney Graduate School, Atlanta, GA 30307
| | - Marinella Pirozzi
- EuroBioImaging Facility, Institute of Protein Biochemistry, 80131 Naples, Italy
| | - Raman Parashuraman
- EuroBioImaging Facility, Institute of Protein Biochemistry, 80131 Naples, Italy
| | - Wei Zhou
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322
| | - H A Jinnah
- Department of Neurology and Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Daniel Reines
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
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43
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Chong PA, Vernon RM, Forman-Kay JD. RGG/RG Motif Regions in RNA Binding and Phase Separation. J Mol Biol 2018; 430:4650-4665. [PMID: 29913160 DOI: 10.1016/j.jmb.2018.06.014] [Citation(s) in RCA: 225] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/02/2018] [Accepted: 06/06/2018] [Indexed: 12/29/2022]
Abstract
RGG/RG motifs are RNA binding segments found in many proteins that can partition into membraneless organelles. They occur in the context of low-complexity disordered regions and often in multiple copies. Although short RGG/RG-containing regions can sometimes form high-affinity interactions with RNA structures, multiple RGG/RG repeats are generally required for high-affinity binding, suggestive of the dynamic, multivalent interactions that are thought to underlie phase separation in formation of cellular membraneless organelles. Arginine can interact with nucleotide bases via hydrogen bonding and π-stacking; thus, nucleotide conformers that provide access to the bases provide enhanced opportunities for RGG interactions. Methylation of RGG/RG regions, which is accomplished by protein arginine methyltransferase enzymes, occurs to different degrees in different cell types and may regulate the behavior of proteins containing these regions.
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Affiliation(s)
- P Andrew Chong
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Robert M Vernon
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Julie D Forman-Kay
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
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