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Możdżan M, Węgiel A, Biskup L, Brzezińska O, Makowska J. Anti-Th/To Antibodies in Scleroderma: Good Prognosis or Serious Concern? J Clin Med 2024; 13:3022. [PMID: 38892733 PMCID: PMC11172938 DOI: 10.3390/jcm13113022] [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: 04/15/2024] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Systemic sclerosis (SSc) represents a rare and intricate autoimmune connective tissue disease, the pathophysiology of which has not been fully understood. Its key features include progressive fibrosis of the skin and internal organs, vasculopathy and aberrant immune activation. While various anti-nuclear antibodies can serve as biomarkers for the classification and prognosis of SSc, their direct role in organ dysfunction remains unclear. Anti-Th/To antibodies are present in approximately 5% of SSc patients, and are particularly prevalent among those with the limited subtype of the disease. Although the presence of these autoantibodies is associated with a mild course of the disease, there is a strong connection between them and severe clinical manifestations of SSc, including interstitial lung disease, pulmonary arterial hypertension and gastrointestinal involvement. Also, the additional clinical correlations, particularly with malignancies, need further research. Moreover, the disease's course seems to be influenced by antibodies, specific serum cytokines and TLR signaling pathways. Understanding the relationships between presence of anti-Th/To, its molecular aspects and response to treatment options is crucial for the development of novel, personalized therapeutic techniques and should undergo profound analysis in future studies.
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Affiliation(s)
- Maria Możdżan
- Department of Rheumatology, Medical University of Lodz, 90-549 Lodz, Poland; (A.W.); (L.B.); (O.B.)
| | | | | | | | - Joanna Makowska
- Department of Rheumatology, Medical University of Lodz, 90-549 Lodz, Poland; (A.W.); (L.B.); (O.B.)
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2
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Rossmanith W, Giegé P, Hartmann RK. Discovery, structure, mechanisms, and evolution of protein-only RNase P enzymes. J Biol Chem 2024; 300:105731. [PMID: 38336295 PMCID: PMC10941002 DOI: 10.1016/j.jbc.2024.105731] [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: 08/01/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
The endoribonuclease RNase P is responsible for tRNA 5' maturation in all domains of life. A unique feature of RNase P is the variety of enzyme architectures, ranging from dual- to multi-subunit ribonucleoprotein forms with catalytic RNA subunits to protein-only enzymes, the latter occurring as single- or multi-subunit forms or homo-oligomeric assemblies. The protein-only enzymes evolved twice: a eukaryal protein-only RNase P termed PRORP and a bacterial/archaeal variant termed homolog of Aquifex RNase P (HARP); the latter replaced the RNA-based enzyme in a small group of thermophilic bacteria but otherwise coexists with the ribonucleoprotein enzyme in a few other bacteria as well as in those archaea that also encode a HARP. Here we summarize the history of the discovery of protein-only RNase P enzymes and review the state of knowledge on structure and function of bacterial HARPs and eukaryal PRORPs, including human mitochondrial RNase P as a paradigm of multi-subunit PRORPs. We also describe the phylogenetic distribution and evolution of PRORPs, as well as possible reasons for the spread of PRORPs in the eukaryal tree and for the recruitment of two additional protein subunits to metazoan mitochondrial PRORP. We outline potential applications of PRORPs in plant biotechnology and address diseases associated with mutations in human mitochondrial RNase P genes. Finally, we consider possible causes underlying the displacement of the ancient RNA enzyme by a protein-only enzyme in a small group of bacteria.
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Affiliation(s)
- Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, Vienna, Austria.
| | - Philippe Giegé
- Institute for Plant Molecular Biology, IBMP-CNRS, University of Strasbourg, Strasbourg, France.
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany.
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3
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Zhou B, Wan F, Lei KX, Lan P, Wu J, Lei M. Coevolution of RNA and protein subunits in RNase P and RNase MRP, two RNA processing enzymes. J Biol Chem 2024; 300:105729. [PMID: 38336296 PMCID: PMC10966300 DOI: 10.1016/j.jbc.2024.105729] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
RNase P and RNase mitochondrial RNA processing (MRP) are ribonucleoproteins (RNPs) that consist of a catalytic RNA and a varying number of protein cofactors. RNase P is responsible for precursor tRNA maturation in all three domains of life, while RNase MRP, exclusive to eukaryotes, primarily functions in rRNA biogenesis. While eukaryotic RNase P is associated with more protein cofactors and has an RNA subunit with fewer auxiliary structural elements compared to its bacterial cousin, the double-anchor precursor tRNA recognition mechanism has remarkably been preserved during evolution. RNase MRP shares evolutionary and structural similarities with RNase P, preserving the catalytic core within the RNA moiety inherited from their common ancestor. By incorporating new protein cofactors and RNA elements, RNase MRP has established itself as a distinct RNP capable of processing ssRNA substrates. The structural information on RNase P and MRP helps build an evolutionary trajectory, depicting how emerging protein cofactors harmonize with the evolution of RNA to shape different functions for RNase P and MRP. Here, we outline the structural and functional relationship between RNase P and MRP to illustrate the coevolution of RNA and protein cofactors, a key driver for the extant, diverse RNP world.
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Affiliation(s)
- Bin Zhou
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Precision Medicine, Shanghai, China
| | - Futang Wan
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Precision Medicine, Shanghai, China
| | - Kevin X Lei
- Shanghai High School International Division, Shanghai, China
| | - Pengfei Lan
- Shanghai Institute of Precision Medicine, Shanghai, China; Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jian Wu
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Precision Medicine, Shanghai, China.
| | - Ming Lei
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Precision Medicine, Shanghai, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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4
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Luna-Arias JP, Castro-Muñozledo F. Participation of the TBP-associated factors (TAFs) in cell differentiation. J Cell Physiol 2024; 239:e31167. [PMID: 38126142 DOI: 10.1002/jcp.31167] [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: 09/18/2023] [Revised: 11/04/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
The understanding of the mechanisms that regulate gene expression to establish differentiation programs and determine cell lineages, is one of the major challenges in Developmental Biology. Besides the participation of tissue-specific transcription factors and epigenetic processes, the role of general transcription factors has been ignored. Only in recent years, there have been scarce studies that address this issue. Here, we review the studies on the biological activity of some TATA-box binding protein (TBP)-associated factors (TAFs) during the proliferation of stem/progenitor cells and their involvement in cell differentiation. Particularly, the accumulated evidence suggests that TAF4, TAF4b, TAF7L, TAF8, TAF9, and TAF10, among others, participate in nervous system development, adipogenesis, myogenesis, and epidermal differentiation; while TAF1, TAF7, TAF15 may be involved in the regulation of stem cell proliferative abilities and cell cycle progression. On the other hand, evidence suggests that TBP variants such as TBPL1 and TBPL2 might be regulating some developmental processes such as germ cell maturation and differentiation, myogenesis, or ventral specification during development. Our analysis shows that it is necessary to study in greater depth the biological function of these factors and its participation in the assembly of specific transcription complexes that contribute to the differential gene expression that gives rise to the great diversity of cell types existing in an organism. The understanding of TAFs' regulation might lead to the development of new therapies for patients which suffer from mutations, alterations, and dysregulation of these essential elements of the transcriptional machinery.
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Affiliation(s)
- Juan Pedro Luna-Arias
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
| | - Federico Castro-Muñozledo
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
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Borišek J, Aupič J, Magistrato A. Establishing the catalytic and regulatory mechanism of
RNA
‐based machineries. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jure Borišek
- Theory Department National Institute of Chemistry Ljubljana Slovenia
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Wu J, Yu S, Wang Y, Zhu J, Zhang Z. New insights into the role of ribonuclease P protein subunit p30 from tumor to internal reference. Front Oncol 2022; 12:1018279. [PMID: 36313673 PMCID: PMC9606464 DOI: 10.3389/fonc.2022.1018279] [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: 08/17/2022] [Accepted: 09/28/2022] [Indexed: 11/13/2022] Open
Abstract
Ribonuclease P protein subunit p30 (RPP30) is a highly conserved housekeeping gene that exists in many species and tissues throughout the three life kingdoms (archaea, bacteria, and eukaryotes). RPP30 is closely related to a few types of tumors in human diseases but has a very stable transcription level in most cases. Based on this feature, increasing number of studies have used RPP30 as an internal reference gene. Here, the structure and basic functions of RPP30 are summarized and the likely relationship between RPP30 and various diseases in plants and human is outlined. Finally, the current application of RPP30 as an internal reference gene and its advantages over traditional internal reference genes are reviewed. RPP30 characteristics suggest that it has a good prospect of being selected as an internal reference; more work is needed to develop this research avenue.
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Affiliation(s)
- Junchao Wu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,Department of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Sijie Yu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,Department of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Yalan Wang
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,Department of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Jie Zhu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China
| | - Zhenhua Zhang
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,*Correspondence: Zhenhua Zhang,
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7
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Sertori R, Lin JX, Martinez E, Rana S, Sharo A, Kazemian M, Sunderam U, Andrake M, Shinton S, Truong B, Dunbrack RM, Liu C, Srinivasan R, Brenner SE, Seroogy CM, Puck JM, Leonard WJ, Wiest DL. Investigation of the causal etiology in a patient with T-B+NK+ immunodeficiency. Front Immunol 2022; 13:928252. [PMID: 35967429 PMCID: PMC9372720 DOI: 10.3389/fimmu.2022.928252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/27/2022] [Indexed: 11/24/2022] Open
Abstract
Newborn screening for severe combined immunodeficiency (SCID) has not only accelerated diagnosis and improved treatment for affected infants, but also led to identification of novel genes required for human T cell development. A male proband had SCID newborn screening showing very low T cell receptor excision circles (TRECs), a biomarker for thymic output of nascent T cells. He had persistent profound T lymphopenia, but normal numbers of B and natural killer (NK) cells. Despite an allogeneic hematopoietic stem cell transplant from his brother, he failed to develop normal T cells. Targeted resequencing excluded known SCID genes; however, whole exome sequencing (WES) of the proband and parents revealed a maternally inherited X-linked missense mutation in MED14 (MED14V763A), a component of the mediator complex. Morpholino (MO)-mediated loss of MED14 function attenuated T cell development in zebrafish. Moreover, this arrest was rescued by ectopic expression of cDNA encoding the wild type human MED14 ortholog, but not by MED14V763A , suggesting that the variant impaired MED14 function. Modeling of the equivalent mutation in mouse (Med14V769A) did not disrupt T cell development at baseline. However, repopulation of peripheral T cells upon competitive bone marrow transplantation was compromised, consistent with the incomplete T cell reconstitution experienced by the proband upon transplantation with bone marrow from his healthy male sibling, who was found to have the same MED14V763A variant. Suspecting that the variable phenotypic expression between the siblings was influenced by further mutation(s), we sought to identify genetic variants present only in the affected proband. Indeed, WES revealed a mutation in the L1 cell adhesion molecule (L1CAMQ498H); however, introducing that mutation in vivo in mice did not disrupt T cell development. Consequently, immunodeficiency in the proband may depend upon additional, unidentified gene variants.
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Affiliation(s)
- Robert Sertori
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Jian-Xin Lin
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Esteban Martinez
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Sadhna Rana
- Innovation Labs, Tata Consultancy Services, Hyderabad, India
| | - Andrew Sharo
- Center for Computational Biology, University of California, Berkeley, CA, United States
| | - Majid Kazemian
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, United States
| | - Uma Sunderam
- Innovation Labs, Tata Consultancy Services, Hyderabad, India
| | - Mark Andrake
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Susan Shinton
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Billy Truong
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Roland M. Dunbrack
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | | | - Steven E. Brenner
- Center for Computational Biology, University of California, Berkeley, CA, United States
| | - Christine M. Seroogy
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Jennifer M. Puck
- Department of Pediatrics, University of California San Francisco and UCSF Benioff Children’s Hospital, San Francisco, CA, United States
| | - Warren J. Leonard
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - David L. Wiest
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States
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8
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Temaj G, Saha S, Dragusha S, Ejupi V, Buttari B, Profumo E, Beqa L, Saso L. Ribosomopathies and cancer: pharmacological implications. Expert Rev Clin Pharmacol 2022; 15:729-746. [PMID: 35787725 DOI: 10.1080/17512433.2022.2098110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The ribosome is a ribonucleoprotein organelle responsible for protein synthesis, and its biogenesis is a highly coordinated process that involves many macromolecular components. Any acquired or inherited impairment in ribosome biogenesis or ribosomopathies is associated with the development of different cancers and rare genetic diseases. Interference with multiple steps of protein synthesis has been shown to promote tumor cell death. AREAS COVERED We discuss the current insights about impaired ribosome biogenesis and their secondary consequences on protein synthesis, transcriptional and translational responses, proteotoxic stress, and other metabolic pathways associated with cancer and rare diseases. Studies investigating the modulation of different therapeutic chemical entities targeting cancer in in vitro and in vivo models have also been detailed. EXPERT OPINION Despite the association between inherited mutations affecting ribosome biogenesis and cancer biology, the development of therapeutics targeting the essential cellular machinery has only started to emerge. New chemical entities should be designed to modulate different checkpoints (translating oncoproteins, dysregulation of specific ribosome-assembly machinery, ribosomal stress, and rewiring ribosomal functions). Although safe and effective therapies are lacking, consideration should also be given to using existing drugs alone or in combination for long-term safety, with known risks for feasibility in clinical trials and synergistic effects.
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Affiliation(s)
| | - Sarmistha Saha
- Department of Cardiovascular, Endocrine-metabolic Diseases, and Aging, Italian National Institute of Health, Rome, Italy
| | | | - Valon Ejupi
- College UBT, Faculty of Pharmacy, Prishtina, Kosovo
| | - Brigitta Buttari
- Department of Cardiovascular, Endocrine-metabolic Diseases, and Aging, Italian National Institute of Health, Rome, Italy
| | - Elisabetta Profumo
- Department of Cardiovascular, Endocrine-metabolic Diseases, and Aging, Italian National Institute of Health, Rome, Italy
| | - Lule Beqa
- College UBT, Faculty of Pharmacy, Prishtina, Kosovo
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", Sapienza University of Rome, Italy
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9
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Cavazzana I, Vojinovic T, Airo' P, Fredi M, Ceribelli A, Pedretti E, Lazzaroni MG, Garrafa E, Franceschini F. Systemic Sclerosis-Specific Antibodies: Novel and Classical Biomarkers. Clin Rev Allergy Immunol 2022; 64:412-430. [PMID: 35716254 PMCID: PMC10167150 DOI: 10.1007/s12016-022-08946-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 11/28/2022]
Abstract
Disease-specific autoantibodies are considered the most important biomarkers for systemic sclerosis (SSc), due to their ability to stratify patients with different severity and prognosis. Anti-nuclear antibodies (ANA), occurring in subjects with isolated Raynuad's phenomenon, are considered the strongest independent predictors of definite SSc and digital microvascular damage, as observed by nailfold videocapillaroscopy. ANA are present in more than 90% of SSc, but ANA negativity does not exclude SSc diagnosis: a little rate of SSc ANA negative exists and shows a distinct subtype of disease, with less vasculopathy, but more frequent lower gastrointestinal involvement and severe disease course. Anti-centromere, anti-Th/To, and anti-Topoisomerase I antibodies could be considered as classical biomarkers, covering about 60% of SSc and defining patients with well-described cardio-pulmonary complications. In particular, anti-Topoisomerase I represent a risk factor for development of diffuse cutaneous involvement and digital ulcers in the first 3 years of disease, as well as severe interstitial lung disease (ILD). Anti-RNA polymerase III is a biomarker with new clinical implications: very rapid skin thickness progression, gastric antral vascular ectasia, the occurrence of synchronous cancers, and possible association with silicone breast implants rupture. Moreover, novel SSc specific autoantibodies have been globally described in about 10% of "seronegative" SSc patients: anti-elF2B, anti-RuvBL1/2 complex, anti-U11/U12 RNP, and anti-BICD2 depict specific SSc subtypes with severe organ complications. Many autoantibodies could be considered markers of overlap syndromes, including SSc. Anti-Ku are found in 2-7% of SSc, strictly defining the PM/SSc overlap. They are associated with synovitis, joint contractures, myositis, and negatively associated with vascular manifestation of disease. Anti-U3RNP are associated with a well-defined clinical phenotype: Afro-Caribbean male patients, younger at diagnosis, and higher risk of pulmonary hypertension and gastrointestinal involvement. Anti-PM/Scl define SSc patients with high frequency of ILD, calcinosis, dermatomyositis skin changes, and severe myositis. The accurate detection of autoantibodies SSc specific and associated with overlap syndromes is crucial for patients' stratification. ANA should be correctly identified using indirect immunofluorescent assay and a standardized way of patterns' interpretation. The gold-standard technique for autoantibodies' identification in SSc is still considered immunoprecipitation, for its high sensitivity and specificity, but other assays have been widely used in routine practice. The identification of SSc autoantibodies with high diagnostic specificity and high predictive value is mandatory for early diagnosis, a specific follow-up and the possible definition of the best therapy for every SSc subsets. In addition, the validation of novel autoantibodies is mandatory in wider cohorts in order to restrict the gap of so-called seronegative SSc patients.
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Affiliation(s)
- Ilaria Cavazzana
- Rheumatology and Clinical Immunology Unit, ASST Spedali Civili, piazzale Spedali Civili 1, Brescia, 25123, Italy.
| | - Tamara Vojinovic
- Rheumatology and Clinical Immunology Unit, ASST Spedali Civili, piazzale Spedali Civili 1, Brescia, 25123, Italy
| | - Paolo Airo'
- Rheumatology and Clinical Immunology Unit, ASST Spedali Civili, piazzale Spedali Civili 1, Brescia, 25123, Italy
| | - Micaela Fredi
- Rheumatology and Clinical Immunology Unit, ASST Spedali Civili, piazzale Spedali Civili 1, Brescia, 25123, Italy.,Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Angela Ceribelli
- Division of Rheumatology and Clinical Immunology, Humanitas Research Hospital IRCCS, Rozzano, Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Eleonora Pedretti
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Maria Grazia Lazzaroni
- Rheumatology and Clinical Immunology Unit, ASST Spedali Civili, piazzale Spedali Civili 1, Brescia, 25123, Italy.,Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Emirena Garrafa
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy.,Department of Laboratory Diagnostics, ASST Spedali Civili, Brescia, Italy
| | - Franco Franceschini
- Rheumatology and Clinical Immunology Unit, ASST Spedali Civili, piazzale Spedali Civili 1, Brescia, 25123, Italy.,Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
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10
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Derksen M, Mertens V, Visser EA, Arts J, Vree Egberts W, Pruijn GJM. A novel experimental approach for the selective isolation and characterization of human RNase MRP. RNA Biol 2022; 19:305-312. [PMID: 35129080 PMCID: PMC8820802 DOI: 10.1080/15476286.2022.2027659] [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] [Indexed: 12/01/2022] Open
Abstract
RNase MRP is a ribonucleoprotein complex involved in the endoribonucleolytic cleavage of different RNAs. Mutations in the RNA component of the RNP are the cause of cartilage hair hypoplasia. Patients with cartilage hair hypoplasia are characterized by skeletal dysplasia. Biochemical purification of RNase MRP is desired to be able to study its biochemical function, composition and activity in both healthy and disease situations. Due to the high similarity with RNase P, a method to specifically isolate the RNase MRP complex is currently lacking. By fusing a streptavidin-binding RNA aptamer, the S1m-aptamer, to the RNase MRP RNA we have been able to compare the relative expression levels of wildtype and mutant MRP RNAs. Moreover, we were able to isolate active RNase MRP complexes. We observed that mutant MRP RNAs are expressed at lower levels and have lower catalytic activity compared to the wildtype RNA. The observation that a single nucleotide substitution at position 40 in the P3 domain but not in other domains of RNase MRP RNA severely reduced the binding of the Rpp25 protein subunit confirmed that the P3 region harbours the main binding site for this protein. Altogether, this study shows that the RNA aptamer tagging approach can be used to identify RNase MRP substrates, but also to study the effect of mutations on MRP RNA expression levels and RNase MRP composition and endoribonuclease activity.
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Affiliation(s)
- Merel Derksen
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
| | - Vicky Mertens
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
| | - Eline A. Visser
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
| | - Janine Arts
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
| | - Wilma Vree Egberts
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
| | - Ger J. M. Pruijn
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
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11
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Robertson N, Shchepachev V, Wright D, Turowski TW, Spanos C, Helwak A, Zamoyska R, Tollervey D. A disease-linked lncRNA mutation in RNase MRP inhibits ribosome synthesis. Nat Commun 2022; 13:649. [PMID: 35115551 PMCID: PMC8814244 DOI: 10.1038/s41467-022-28295-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 01/14/2022] [Indexed: 01/02/2023] Open
Abstract
RMRP encodes a non-coding RNA forming the core of the RNase MRP ribonucleoprotein complex. Mutations cause Cartilage Hair Hypoplasia (CHH), characterized by skeletal abnormalities and impaired T cell activation. Yeast RNase MRP cleaves a specific site in the pre-ribosomal RNA (pre-rRNA) during ribosome synthesis. CRISPR-mediated disruption of RMRP in human cells lines caused growth arrest, with pre-rRNA accumulation. Here, we analyzed disease-relevant primary cells, showing that mutations in RMRP impair mouse T cell activation and delay pre-rRNA processing. Patient-derived human fibroblasts with CHH-linked mutations showed similar pre-rRNA processing delay. Human cells engineered with the most common CHH mutation (70AG in RMRP) show specifically impaired pre-rRNA processing, resulting in reduced mature rRNA and a reduced ratio of cytosolic to mitochondrial ribosomes. Moreover, the 70AG mutation caused a reduction in intact RNase MRP complexes. Together, these results indicate that CHH is a ribosomopathy.
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Affiliation(s)
- Nic Robertson
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Vadim Shchepachev
- The Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK
| | - David Wright
- Ashworth Laboratories, Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - Tomasz W Turowski
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Christos Spanos
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Aleksandra Helwak
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Rose Zamoyska
- Ashworth Laboratories, Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
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12
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Zhou J, Zhu X, Long J. Insights into the Prognostic Value of Small Nucleolar RNA U81 and SNORA7B in Breast Cancer. Int J Gen Med 2022. [DOI: 10.2147/ijgm.s345945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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13
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Chabronova A, van den Akker GGH, Meekels-Steinbusch MMF, Friedrich F, Cremers A, Surtel DAM, Peffers MJ, van Rhijn LW, Lausch E, Zabel B, Caron MMJ, Welting TJM. Uncovering pathways regulating chondrogenic differentiation of CHH fibroblasts. Noncoding RNA Res 2022; 6:211-224. [PMID: 34988338 PMCID: PMC8688813 DOI: 10.1016/j.ncrna.2021.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 02/08/2023] Open
Abstract
Mutations in the non-coding snoRNA component of mitochondrial RNA processing endoribonuclease (RMRP) are the cause of cartilage-hair hypoplasia (CHH). CHH is a rare form of metaphyseal chondrodysplasia characterized by disproportionate short stature and abnormal growth plate development. The process of chondrogenic differentiation within growth plates of long bones is vital for longitudinal bone growth. However, molecular mechanisms behind impaired skeletal development in CHH patients remain unclear. We employed a transdifferentiation model (FDC) combined with whole transcriptome analysis to investigate the chondrogenic transdifferentiation capacity of CHH fibroblasts and to examine pathway regulation in CHH cells during chondrogenic differentiation. We established that the FDC transdifferentiation model is a relevant in vitro model of chondrogenic differentiation, with an emphasis on the terminal differentiation phase, which is crucial for longitudinal bone growth. We demonstrated that CHH fibroblasts are capable of transdifferentiating into chondrocyte-like cells, and show a reduced commitment to terminal differentiation. We also found a number of key factors of BMP, FGF, and IGF-1 signalling axes to be significantly upregulated in CHH cells during the chondrogenic transdifferentiation. Our results support postulated conclusions that RMRP has pleiotropic functions and profoundly affects multiple aspects of cell fate and signalling. Our findings shed light on the consequences of pathological CHH mutations in snoRNA RMRP during chondrogenic differentiation and the relevance and roles of non-coding RNAs in genetic diseases in general.
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Affiliation(s)
- Alzbeta Chabronova
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Guus G H van den Akker
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Mandy M F Meekels-Steinbusch
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Franziska Friedrich
- Department of Pediatrics, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Andy Cremers
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Don A M Surtel
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Mandy J Peffers
- Institute of Life Course and Medical Sciences, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK
| | - Lodewijk W van Rhijn
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Ekkehart Lausch
- Department of Pediatrics, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bernhard Zabel
- Medical Faculty, Otto van Guericke University of Magdeburg, 39106, Magdeburg, Germany
| | - Marjolein M J Caron
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Tim J M Welting
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
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14
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Yang JI, Chun JS. Upregulated endonuclease Regnase-1 suppresses osteoarthritis by forming a negative feedback loop of catabolic signaling in chondrocytes. Arthritis Res Ther 2021; 23:114. [PMID: 33853646 PMCID: PMC8045248 DOI: 10.1186/s13075-021-02485-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 03/22/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Ribonucleases (RNases) play central roles in the post-transcriptional regulation of mRNA stability. Our preliminary results revealed that the endonuclease Regnase-1 is specifically upregulated in osteoarthritic chondrocytes. We herein explored the possible functions and regulatory mechanisms of Regnase-1 in a mouse model of osteoarthritis (OA). METHODS The expression and target genes of Regnase-1 were identified by microarray analysis in primary-culture mouse articular chondrocytes. Experimental OA in mice was induced by destabilization of the medial meniscus (DMM). The function of Regnase-1 in DMM-induced post-traumatic OA mice was examined by adenovirus-mediated overexpression or knockdown in knee joint tissues, and also by using Regnase-1 heterozygous knockout mice (Zc3h12a+/-). RESULTS Among the RNases, Regnase-1 was exclusively upregulated in chondrocytes stimulated with OA-associated catabolic factors. Adenovirus-mediated overexpression or knockdown of Regnase-1 alone in joint tissues did not cause OA-like changes. However, overexpression of Regnase-1 in joint tissues significantly ameliorated DMM-induced post-traumatic OA cartilage destruction, whereas knockdown or genetic ablation of Regnase-1 exacerbated DMM-induced cartilage destruction. Mechanistic studies suggested that Regnase-1 suppresses cartilage destruction by modulating the expression of matrix-degrading enzymes in chondrocytes. CONCLUSION Our results collectively suggest that upregulated Regnase-1 in OA chondrocytes may function as a chondro-protective effector molecule during OA pathogenesis by forming a negative feedback loop of catabolic signals, such as matrix-degrading enzyme expression, in OA chondrocytes.
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Affiliation(s)
- Jeong-In Yang
- National Creative Research Initiatives Center for Osteoarthritis Pathogenesis and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Jang-Soo Chun
- National Creative Research Initiatives Center for Osteoarthritis Pathogenesis and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea.
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15
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Abstract
The innate immune system has numerous signal transduction pathways that lead to the production of type I interferons in response to exposure of cells to external stimuli. One of these pathways comprises RNA polymerase (Pol) III that senses common DNA viruses, such as cytomegalovirus, vaccinia, herpes simplex virus-1 and varicella zoster virus. This polymerase detects and transcribes viral genomic regions to generate AU-rich transcripts that bring to the induction of type I interferons. Remarkably, Pol III is also stimulated by foreign non-viral DNAs and expression of one of its subunits is induced by an RNA virus, the Sindbis virus. Moreover, a protein subunit of RNase P, which is known to associate with Pol III in initiation complexes, is induced by viral infection. Accordingly, alliance of the two tRNA enzymes in innate immunity merits a consideration.
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Affiliation(s)
- Nayef Jarrous
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Israel-Canada
| | - Alexander Rouvinski
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Israel-Canada.,The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
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16
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Crystal structure of human RPP20-RPP25 proteins in complex with the P3 domain of lncRNA RMRP. J Struct Biol 2021; 213:107704. [PMID: 33571640 DOI: 10.1016/j.jsb.2021.107704] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/23/2021] [Accepted: 01/28/2021] [Indexed: 11/21/2022]
Abstract
Human RNase MRP ribonucleoprotein complex is an essential endoribonuclease involved in the processing of ribosomal RNAs, mitochondrial RNAs and certain messenger RNAs. Its RNA subunit RMRP catalyzes the cleavage of substrate RNAs, and the protein components of RNase MRP are required for activity. RMRP mutations are associated with several types of inherited developmental disorders, but the pathogenic mechanism is largely unknown. Recent structural studies shed lights on the catalytic mechanism of yeast RNase MRP and the closely related RNase P; however, the structural and catalytic mechanism of RMRP in human RNase MRP complex remains unclear. Here we report the crystal structure of the P3 domain of RMRP in complex with the RPP20 and RPP25 proteins of human RNase MRP, which shows that the P3 RNA binds to a conserved positively-charged surface of the RPP20-RPP25 heterodimer through its distal stem and internal loop regions. The disease-related mutations of RMRPP3 are mostly located at the protein-RNA interface and are likely to weaken the binding of P3 to RPP20-RPP25. Moreover, the structure reveals a homodimeric organization of the entire RPP20-RPP25-RMRPP3 complex, which might mediate the dimerization of human RNase MRP complex in cells. These findings provide structural clues to the assembly and pathogenesis of human RNase MRP complex and also reveal a tetrameric feature of RPP20-RPP25 evolutionarily conserved with that of the archaeal Alba proteins.
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17
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Mecoli CA, Adler BL, Yang Q, Hummers LK, Rosen A, Casciola-Rosen L, Shah AA. Cancer in Systemic Sclerosis: Analysis of Antibodies Against Components of the Th/To Complex. Arthritis Rheumatol 2021; 73:315-323. [PMID: 33241644 PMCID: PMC7884482 DOI: 10.1002/art.41493] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/31/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE The aim of this study is to describe 4 of the most common autoantibodies against components of the Th/To complex: human POP1 (hPOP1), RPP25, RPP30, and RPP40. We report their prevalence and clinical characteristics in a systemic sclerosis (SSc) population, and determine whether these specificities are associated with cancer. METHODS A case-control study was performed using data from the Johns Hopkins Scleroderma Center Cohort. A total of 804 adult patients with SSc were included; 401 SSc patients with no history of cancer after at least 5 years of disease were compared to 403 SSc patients who ever had a history of cancer. Antibodies against hPOP1, RPP25, RPP30, and RPP40 were assayed by immunoprecipitation of 35 S-methionine-labeled proteins generated by in vitro transcription/translation. Demographic and clinical characteristics were compared between groups. RESULTS Of 804 patients, 67 (8.3%) had antibodies against any component of the Th/To complex. Patients with antibodies to any component were significantly more likely to have limited cutaneous disease, less likely to have tendon friction rubs, and more likely to have findings consistent with interstitial lung disease or pulmonary hypertension. Patients with antibodies against hPOP1, RPP25, RPP30, and/or RPP40 were significantly less likely to develop cancer within 2 years of SSc onset (0% versus 11% of antibody-negative patients; P = 0.009). CONCLUSION SSc patients who produce autoantibodies to components of the Th/To complex have a clinical phenotype characterized by limited cutaneous disease and pulmonary involvement. Our findings show that the presence of any Th/To autoantibody may have a protective effect against contemporaneous cancer.
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Affiliation(s)
| | - Brittany L. Adler
- Division of Rheumatology, Department of Medicine, Johns Hopkins University
| | - Qingyuan Yang
- Division of Rheumatology, Department of Medicine, Johns Hopkins University
| | - Laura K. Hummers
- Division of Rheumatology, Department of Medicine, Johns Hopkins University
| | - Antony Rosen
- Division of Rheumatology, Department of Medicine, Johns Hopkins University
| | - Livia Casciola-Rosen
- Corresponding author: Livia Casciola-Rosen PhD, Division of Rheumatology, Department of Medicine, Johns Hopkins University, 5200 Eastern Ave, Mason F. Lord Bldg, Center Tower, Suite 5300, Baltimore MD 21224,
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18
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Yang H, Wang J, Zhang Z, Peng R, Lv D, Liu H, Sun Y. Sp1-Induced lncRNA Rmrp Promotes Mesangial Cell Proliferation and Fibrosis in Diabetic Nephropathy by Modulating the miR-1a-3p/JunD Pathway. Front Endocrinol (Lausanne) 2021; 12:690784. [PMID: 34512545 PMCID: PMC8429906 DOI: 10.3389/fendo.2021.690784] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 08/06/2021] [Indexed: 12/29/2022] Open
Abstract
Diabetic nephropathy (DN) is a serious complication of diabetes mellitus. Long non-coding RNAs (lncRNAs) are regulators in DN progression. However, the regulatory mechanisms of multiple lncRNAs in DN remain to be determined. Our aim was to investigate the function and molecular mechanism of lncRNA RNA component of mitochondrial RNAase P (Rmrp) in DN. Here, we observed that the expression of Rmrp was up-regulated in the kidney of db/db DN mice and high glucose induced glomerular mesangial cells (MC). More importantly, the abnormal transcription of Rmrp was induced by nuclear transcription factor Sp1, which promotes the proliferation and production of fibrotic markers in MC. Subsequently, we screened the miRNAs related to Rmrp and found that Rmrp and miR-1a-3p are co-localized at the subcellular level of MC, and Rmrp could directly binds to miR-1a-3p. Further mechanism research demonstrated that the elevated miR-1a-3p significantly attenuated the proliferation and fibrosis-promoting effects induced by up-regulation of Rmrp. At the same time, we also investigated that miR-1a-3p can directly bind to Jun D proto-oncogene (JunD), thereby regulating the protein level of JunD. Rmrp-induced proliferation and fibrogenesis were reversed by co-transfection with JunD siRNA. In summary, Sp1 induced lncRNA Rmrp could drive the expression of JunD via sponging miR-1a-3p in DN progression.
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Affiliation(s)
- Hansen Yang
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China
| | - Jia Wang
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China
| | - Zheng Zhang
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China
| | - Rui Peng
- Department of Bioinformatics, Chongqing Medical University, Chongqing, China
| | - Dan Lv
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China
| | - Handeng Liu
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China
| | - Yan Sun
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China
- *Correspondence: Yan Sun,
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19
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Venturi G, Montanaro L. How Altered Ribosome Production Can Cause or Contribute to Human Disease: The Spectrum of Ribosomopathies. Cells 2020; 9:E2300. [PMID: 33076379 PMCID: PMC7602531 DOI: 10.3390/cells9102300] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 12/22/2022] Open
Abstract
A number of different defects in the process of ribosome production can lead to a diversified spectrum of disorders that are collectively identified as ribosomopathies. The specific factors involved may either play a role only in ribosome biogenesis or have additional extra-ribosomal functions, making it difficult to ascribe the pathogenesis of the disease specifically to an altered ribosome biogenesis, even if the latter is clearly affected. We reviewed the available literature in the field from this point of view with the aim of distinguishing, among ribosomopathies, the ones due to specific alterations in the process of ribosome production from those characterized by a multifactorial pathogenesis.
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Affiliation(s)
- Giulia Venturi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy;
- Center for Applied Biomedical Research, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy;
- Center for Applied Biomedical Research, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
- Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, 40138 Bologna, Italy
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20
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Lan P, Zhou B, Tan M, Li S, Cao M, Wu J, Lei M. Structural insight into precursor ribosomal RNA processing by ribonuclease MRP. Science 2020; 369:656-663. [PMID: 32586950 DOI: 10.1126/science.abc0149] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/11/2020] [Indexed: 12/16/2022]
Abstract
Ribonuclease (RNase) MRP is a conserved eukaryotic ribonucleoprotein complex that plays essential roles in precursor ribosomal RNA (pre-rRNA) processing and cell cycle regulation. In contrast to RNase P, which selectively cleaves transfer RNA-like substrates, it has remained a mystery how RNase MRP recognizes its diverse substrates. To address this question, we determined cryo-electron microscopy structures of Saccharomyces cerevisiae RNase MRP alone and in complex with a fragment of pre-rRNA. These structures and the results of biochemical studies reveal that coevolution of both protein and RNA subunits has transformed RNase MRP into a distinct ribonuclease that processes single-stranded RNAs by recognizing a short, loosely defined consensus sequence. This broad substrate specificity suggests that RNase MRP may have myriad yet unrecognized substrates that could play important roles in various cellular contexts.
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Affiliation(s)
- Pengfei Lan
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Bin Zhou
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Ming Tan
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Shaobai Li
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Mi Cao
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Jian Wu
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China. .,Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Ming Lei
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China. .,Shanghai Institute of Precision Medicine, Shanghai 200125, China.,Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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21
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Vakkilainen S, Taskinen M, Mäkitie O. Immunodeficiency in cartilage-hair hypoplasia: Pathogenesis, clinical course and management. Scand J Immunol 2020; 92:e12913. [PMID: 32506568 DOI: 10.1111/sji.12913] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/20/2020] [Accepted: 05/29/2020] [Indexed: 12/12/2022]
Abstract
Cartilage-hair hypoplasia (CHH) is an autosomal recessive syndromic immunodeficiency with skeletal dysplasia, short stature, hypotrichosis, variable degree of immune dysfunction and increased incidence of anaemia, Hirschsprung disease and malignancy. CHH is caused by variants in the RMRP gene, encoding the untranslated RNA molecule of the mitochondrial RNA-processing endoribonuclease, which participates in for example cell cycle regulation and telomere maintenance. Recent studies have expanded our understanding of the complex pathogenesis of CHH. Immune dysfunction has a major impact on clinical course and prognosis. Clinical features of immune dysfunction are highly variable, progressive and include infections, lung disease, immune dysregulation and malignancy. Mortality is increased compared with the general population, due to infections, malignancy and pulmonary disease. Several risk factors for early mortality have been reported in the Finnish CHH cohort and can be used to guide management. Newborn screening for severe combined immunodeficiency can possibly be of prognostic value in CHH. Regular follow-up by a multidisciplinary team should be implemented to address immune dysfunction in all patients with CHH, also in asymptomatic cases. Haematopoietic stem cell transplantation can cure immune dysfunction, but its benefits in mildly symptomatic patients with CHH remain debatable. Further research is needed to understand the mechanisms behind the variability of clinical features, to search for potential molecular treatment targets, to examine and validate risk factors for early mortality outside the Finnish CHH cohort and to develop management guidelines. This review focuses on the pathogenesis, clinical course and management of CHH.
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Affiliation(s)
- Svetlana Vakkilainen
- Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mervi Taskinen
- Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Outi Mäkitie
- Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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22
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Ojha S, Malla S, Lyons SM. snoRNPs: Functions in Ribosome Biogenesis. Biomolecules 2020; 10:biom10050783. [PMID: 32443616 PMCID: PMC7277114 DOI: 10.3390/biom10050783] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/10/2020] [Accepted: 05/13/2020] [Indexed: 01/18/2023] Open
Abstract
Ribosomes are perhaps the most critical macromolecular machine as they are tasked with carrying out protein synthesis in cells. They are incredibly complex structures composed of protein components and heavily chemically modified RNAs. The task of assembling mature ribosomes from their component parts consumes a massive amount of energy and requires greater than 200 assembly factors. Among the most critical of these are small nucleolar ribonucleoproteins (snoRNPs). These are small RNAs complexed with diverse sets of proteins. As suggested by their name, they localize to the nucleolus, the site of ribosome biogenesis. There, they facilitate multiple roles in ribosomes biogenesis, such as pseudouridylation and 2′-O-methylation of ribosomal (r)RNA, guiding pre-rRNA processing, and acting as molecular chaperones. Here, we reviewed their activity in promoting the assembly of ribosomes in eukaryotes with regards to chemical modification and pre-rRNA processing.
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Affiliation(s)
- Sandeep Ojha
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
| | - Sulochan Malla
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
| | - Shawn M. Lyons
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
- The Genome Science Institute, Boston University School of Medicine, Boston, MA 02115, USA
- Correspondence: ; Tel.: +1-617-358-4280
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23
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RNA base-pairing complexity in living cells visualized by correlated chemical probing. Proc Natl Acad Sci U S A 2019; 116:24574-24582. [PMID: 31744869 DOI: 10.1073/pnas.1905491116] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RNA structure and dynamics are critical to biological function. However, strategies for determining RNA structure in vivo are limited, with established chemical probing and newer duplex detection methods each having deficiencies. Here we convert the common reagent dimethyl sulfate into a useful probe of all 4 RNA nucleotides. Building on this advance, we introduce PAIR-MaP, which uses single-molecule correlated chemical probing to directly detect base-pairing interactions in cells. PAIR-MaP has superior resolution compared to alternative experiments, can resolve multiple sets of pairing interactions for structurally dynamic RNAs, and enables highly accurate structure modeling, including of RNAs containing multiple pseudoknots and extensively bound by proteins. Application of PAIR-MaP to human RNase MRP and 2 bacterial messenger RNA 5' untranslated regions reveals functionally important and complex structures undetected by prior analyses. PAIR-MaP is a powerful, experimentally concise, and broadly applicable strategy for directly visualizing RNA base pairs and dynamics in cells.
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24
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Le Caignec C, Ory B, Lamoureux F, O'Donohue MF, Orgebin E, Lindenbaum P, Téletchéa S, Saby M, Hurst A, Nelson K, Gilbert SR, Wilnai Y, Zeitlin L, Segev E, Tesfaye R, Nizon M, Cogne B, Bezieau S, Geoffroy L, Hamel A, Mayrargue E, de Courtivron B, Decock-Giraudaud A, Charrier C, Pichon O, Retière C, Redon R, Pepler A, McWalter K, Da Costa L, Toutain A, Gleizes PE, Baud'huin M, Isidor B. RPL13 Variants Cause Spondyloepimetaphyseal Dysplasia with Severe Short Stature. Am J Hum Genet 2019; 105:1040-1047. [PMID: 31630789 DOI: 10.1016/j.ajhg.2019.09.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/20/2019] [Indexed: 01/04/2023] Open
Abstract
Variants in genes encoding ribosomal proteins have thus far been associated with Diamond-Blackfan anemia, a rare inherited bone marrow failure, and isolated congenital asplenia. Here, we report one de novo missense variant and three de novo splice variants in RPL13, which encodes ribosomal protein RPL13 (also called eL13), in four unrelated individuals with a rare bone dysplasia causing severe short stature. The three splice variants (c.477+1G>T, c.477+1G>A, and c.477+2 T>C) result in partial intron retention, which leads to an 18-amino acid insertion. In contrast to observations from Diamond-Blackfan anemia, we detected no evidence of significant pre-rRNA processing disturbance in cells derived from two affected individuals. Consistently, we showed that the insertion-containing protein is stably expressed and incorporated into 60S subunits similar to the wild-type protein. Erythroid proliferation in culture and ribosome profile on sucrose gradient are modified, suggesting a change in translation dynamics. We also provide evidence that RPL13 is present at high levels in chondrocytes and osteoblasts in mouse growth plates. Taken together, we show that the identified RPL13 variants cause a human ribosomopathy defined by a rare skeletal dysplasia, and we highlight the role of this ribosomal protein in bone development.
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Affiliation(s)
| | - Benjamin Ory
- Nantes Université, INSERM, Bone sarcomas and remodeling of calcified tissues, UMR 1238, F-44000 Nantes, France
| | - François Lamoureux
- Nantes Université, INSERM, Bone sarcomas and remodeling of calcified tissues, UMR 1238, F-44000 Nantes, France
| | - Marie-Francoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, UPS, CNRS, 31062 Toulouse, France
| | - Emilien Orgebin
- Nantes Université, INSERM, Bone sarcomas and remodeling of calcified tissues, UMR 1238, F-44000 Nantes, France
| | - Pierre Lindenbaum
- L'institut du thorax, INSERM, CNRS, Université de Nantes, F-44000 Nantes, France
| | - Stéphane Téletchéa
- Nantes Université, CNRS, Unité Fonctionnalité et Ingénierie des Protéines (UFIP), UMR CNRS 6286, F-44000 Nantes, France
| | - Manon Saby
- INSERM U1149/ERL 8252, Inflammation Research Center, 75018 Paris, France
| | - Anna Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Katherine Nelson
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Shawn R Gilbert
- Children's of Alabama, Department of Orthopaedic Surgery, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Yael Wilnai
- Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Leonid Zeitlin
- Pediatric Orthopedic Department, Dana-Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Eitan Segev
- Pediatric Orthopedic Department, Dana-Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Robel Tesfaye
- Nantes Université, INSERM, Bone sarcomas and remodeling of calcified tissues, UMR 1238, F-44000 Nantes, France
| | - Mathilde Nizon
- CHU Nantes, Service de génétique médicale, F-44000 Nantes, France
| | - Benjamin Cogne
- CHU Nantes, Service de génétique médicale, F-44000 Nantes, France
| | - Stéphane Bezieau
- CHU Nantes, Service de génétique médicale, F-44000 Nantes, France
| | - Loic Geoffroy
- Service d'Orthopédie Pédiatrique, CHU de Nantes, F-44000 Nantes, France
| | - Antoine Hamel
- Service d'Orthopédie Pédiatrique, CHU de Nantes, F-44000 Nantes, France
| | | | - Benoît de Courtivron
- Service de Chirurgie Orthopédique Pédiatrique, CHU de Tours, 37044 Tours, France
| | | | - Céline Charrier
- Nantes Université, INSERM, Bone sarcomas and remodeling of calcified tissues, UMR 1238, F-44000 Nantes, France
| | - Olivier Pichon
- CHU Nantes, Service de génétique médicale, F-44000 Nantes, France
| | - Christelle Retière
- Etablissement Français du Sang, F-44000 Nantes, France; CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, F-44000 Nantes, France
| | - Richard Redon
- L'institut du thorax, INSERM, CNRS, Université de Nantes, F-44000 Nantes, France
| | - Alexander Pepler
- Center for Genomics and Transcriptomics and Praxis für Humangenetik Tübingen, 72076 Tübingen, Germany
| | | | - Lydie Da Costa
- INSERM U1149/ERL 8252, Inflammation Research Center, 75018 Paris, France; AP-HP, Service d'Hématologie Biologique, Hôpital R. Debré, Université Paris 7 Denis Diderot, Sorbonne Paris Cité, 75019 Paris, France
| | | | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, UPS, CNRS, 31062 Toulouse, France
| | - Marc Baud'huin
- Nantes Université, CHU Nantes, INSERM, Bone sarcomas and remodeling of calcified tissues, UMR 1238, F-44000 Nantes, France.
| | - Bertrand Isidor
- CHU Nantes, Service de génétique médicale, F-44000 Nantes, France.
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25
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Gomes ME, Calatrava Paternostro L, Moura VR, Antunes D, Caffarena ER, Horovitz D, Sanseverino MT, Ferraz Leal G, Felix TM, Pontes Cavalcanti D, Clinton Llerena J, Gonzalez S. Identification of Novel and Recurrent RMRP Variants in a Series of Brazilian Patients with Cartilage-Hair Hypoplasia: McKusick Syndrome. Mol Syndromol 2019; 10:255-263. [PMID: 32021596 DOI: 10.1159/000501892] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2019] [Indexed: 11/19/2022] Open
Abstract
Cartilage-hair hypoplasia syndrome (CHH) is an autosomal recessive disorder caused by pathogenic variants of the RMRP gene and characterized by metaphyseal bone dysplasia associated with hypotrichosis, immunodeficiency, and predisposition to malignancy. However, the genotype-phenotype correlation in CHH is not well understood. Here, we report a single country cohort of 23 Brazilian patients with clinical and radiological features consistent with CHH. We found 23 different pathogenic variants in the RMRP gene - 12 novel and 11 previously described in the literature. Interestingly, the most frequent Finnish pathogenic variant related to CHH (g.71A>G) was not found in our cohort. In contrast, more than 50% of the patients carried the rare g.196C>T variant suggesting a possible founder effect in the Brazilian population. In silico analysis showed that pathogenic variants occurred either in the regions conserved in mammalian species or within essential domains for the ribonucleoprotein complex. Pathogenicity prediction studies can improve the understanding of how these variants affect RNA.
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Affiliation(s)
- Maria E Gomes
- Laboratório de Medicina Genômica, Centro de Genética Médica Dr. José Carlos Cabral de Almeida & Centro de Referência para Doenças Raras, IFF/FIOCRUZ, Rio de Janeiro, Brazil
| | - Luiza Calatrava Paternostro
- Laboratório de Medicina Genômica, Centro de Genética Médica Dr. José Carlos Cabral de Almeida & Centro de Referência para Doenças Raras, IFF/FIOCRUZ, Rio de Janeiro, Brazil
| | - Valéria R Moura
- Laboratório de Medicina Genômica, Centro de Genética Médica Dr. José Carlos Cabral de Almeida & Centro de Referência para Doenças Raras, IFF/FIOCRUZ, Rio de Janeiro, Brazil
| | - Deborah Antunes
- Laboratório de Biofísica Computacional e Modelagem Molecular (PROCC), IOC/FIOCRUZ, Rio de Janeiro, Brazil
| | - Ernesto R Caffarena
- Laboratório de Biofísica Computacional e Modelagem Molecular (PROCC), IOC/FIOCRUZ, Rio de Janeiro, Brazil
| | - Dafne Horovitz
- Unidade de Genética Clínica, Centro de Genética Médica Dr. José Carlos Cabral de Almeida & Centro de Referência para Doenças Raras, IFF/FIOCRUZ, Rio de Janeiro, Brazil
| | | | | | - Têmis M Felix
- Serviço de Genética Médica Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Denise Pontes Cavalcanti
- Grupo de Displasias Esqueléticas, Departamento de Genética Médica, FCM-UNICAMP, Campinas, Brazil
| | - Juan Clinton Llerena
- Unidade de Genética Clínica, Centro de Genética Médica Dr. José Carlos Cabral de Almeida & Centro de Referência para Doenças Raras, IFF/FIOCRUZ, Rio de Janeiro, Brazil.,INAGEMP - Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil.,Faculdade de Medicina Fundação Arthur Sá Earp Jr, Petrópolis, Brazil
| | - Sayonara Gonzalez
- Laboratório de Medicina Genômica, Centro de Genética Médica Dr. José Carlos Cabral de Almeida & Centro de Referência para Doenças Raras, IFF/FIOCRUZ, Rio de Janeiro, Brazil
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26
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Teng Y, Ding M, Wang X, Li H, Guo Q, Yan J, Gao L. LncRNA RMRP accelerates hypoxia-induced injury by targeting miR-214-5p in H9c2 cells. J Pharmacol Sci 2019; 142:69-78. [PMID: 31839421 DOI: 10.1016/j.jphs.2019.07.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/28/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE To elucidate the function of lncRNA RMRP in hypoxia-induced acute myocardial infarction (AMI) in vitro and explore its underlying mechanism. METHODS Hypoxic injury was confirmed by measurement of cell viability, LDH release, migration, invasion, and apoptosis in H9c2 cells. The interactions between RMRP and miR-214-5p as well as miR-214-5p and p53 were also investigated. RESULTS Hypoxia treatment significantly induced cell damage in H9c2 cells, accompanied with the up-regulation of RMRP expressions. Transfection of RMRP siRNA remarkably attenuated hypoxia-induced injury by enhancing cell viability, migration and invasion, and reducing cell apoptosis and LDH release; whereas, enforced expression of RMRP aggravated hypoxia-induced injury. Furthermore, RMRP served as an endogenous sponge for miR-214-5p, and its expression was negatively regulated by RMRP. The effects of RMRP knockdown on hypoxia-induced injury were further enhanced with miR-214-5p overexpression, but significantly abrogated with miR-214-5p silence. Moreover, p53 was verified as a direct target of miR-214-5p, and functional investigation revealed that RMRP regulated hypoxia-induced injury via modulating p53 signaling pathway, which was partially mediated by miR-214-5p. CONCLUSION Our findings demonstrated the novel molecular mechanism of RMRP/miR-214-5p/p53 axis on the regulation of hypoxia-induced myocardial injury in H9c2 cells, which might provide potential therapeutic targets for AMI treatment.
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Affiliation(s)
- Yan Teng
- Department of Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China.
| | - Ming Ding
- Department of Critical Care Medicine, The Fourth People's Hospital of Shaanxi Province, Xi'an, Shaanxi, 710043, PR China
| | - Xiaojian Wang
- Department of Critical Care Medicine, Chang'an District Hospital of the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710100, PR China
| | - Hao Li
- Department of Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Qinyue Guo
- Department of Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Jinqi Yan
- Department of Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Lan Gao
- Department of Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
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27
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Gregory B, Rahman N, Bommakanti A, Shamsuzzaman M, Thapa M, Lescure A, Zengel JM, Lindahl L. The small and large ribosomal subunits depend on each other for stability and accumulation. Life Sci Alliance 2019; 2:e201800150. [PMID: 30837296 PMCID: PMC6402506 DOI: 10.26508/lsa.201800150] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 02/21/2019] [Accepted: 02/25/2019] [Indexed: 12/12/2022] Open
Abstract
The 1:1 balance between the numbers of large and small ribosomal subunits can be disturbed by mutations that inhibit the assembly of only one of the subunits. Here, we have investigated if the cell can counteract an imbalance of the number of the two subunits. We show that abrogating 60S assembly blocks 40S subunit accumulation. In contrast, cessation of the 40S pathways does not prevent 60S accumulation, but does, however, lead to fragmentation of the 25S rRNA in 60S subunits and formation of a 55S ribosomal particle derived from the 60S. We also present evidence suggesting that these events occur post assembly and discuss the possibility that the turnover of subunits is due to vulnerability of free subunits not paired with the other subunit to form 80S ribosomes.
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MESH Headings
- Cell Survival/physiology
- Galactokinase/genetics
- Gene Expression Regulation, Fungal
- Promoter Regions, Genetic
- Protein Stability
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 18S/metabolism
- Ribosomal Proteins/metabolism
- Ribosome Subunits, Large, Eukaryotic/genetics
- Ribosome Subunits, Large, Eukaryotic/metabolism
- Ribosome Subunits, Small, Eukaryotic/genetics
- Ribosome Subunits, Small, Eukaryotic/metabolism
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Trans-Activators/genetics
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Affiliation(s)
- Brian Gregory
- Department of Biological Sciences, University of Maryland, Baltimore, MD, USA
| | - Nusrat Rahman
- Department of Biological Sciences, University of Maryland, Baltimore, MD, USA
| | - Ananth Bommakanti
- Department of Biological Sciences, University of Maryland, Baltimore, MD, USA
| | - Md Shamsuzzaman
- Department of Biological Sciences, University of Maryland, Baltimore, MD, USA
| | - Mamata Thapa
- Department of Biological Sciences, University of Maryland, Baltimore, MD, USA
| | - Alana Lescure
- Department of Biological Sciences, University of Maryland, Baltimore, MD, USA
| | - Janice M Zengel
- Department of Biological Sciences, University of Maryland, Baltimore, MD, USA
| | - Lasse Lindahl
- Department of Biological Sciences, University of Maryland, Baltimore, MD, USA
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28
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Steinbusch MMF, Caron MMJ, Surtel DAM, van den Akker GGH, van Dijk PJ, Friedrich F, Zabel B, van Rhijn LW, Peffers MJ, Welting TJM. The antiviral protein viperin regulates chondrogenic differentiation via CXCL10 protein secretion. J Biol Chem 2019; 294:5121-5136. [PMID: 30718282 PMCID: PMC6442052 DOI: 10.1074/jbc.ra119.007356] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 01/29/2019] [Indexed: 01/10/2023] Open
Abstract
Viperin (also known as radical SAM domain–containing 2 (RSAD2)) is an interferon-inducible and evolutionary conserved protein that participates in the cell's innate immune response against a number of viruses. Viperin mRNA is a substrate for endoribonucleolytic cleavage by RNase mitochondrial RNA processing (MRP) and mutations in the RNase MRP small nucleolar RNA (snoRNA) subunit of the RNase MRP complex cause cartilage-hair hypoplasia (CHH), a human developmental condition characterized by metaphyseal chondrodysplasia and severe dwarfism. It is unknown how CHH-pathogenic mutations in RNase MRP snoRNA interfere with skeletal development, and aberrant processing of RNase MRP substrate RNAs is thought to be involved. We hypothesized that viperin plays a role in chondrogenic differentiation. Using immunohistochemistry, real-time quantitative PCR, immunoblotting, ELISA, siRNA-mediated gene silencing, plasmid-mediated gene overexpression, label-free MS proteomics, and promoter reporter bioluminescence assays, we discovered here that viperin is expressed in differentiating chondrocytic cells and regulates their protein secretion and the outcome of chondrogenic differentiation by influencing transforming growth factor β (TGF-β)/SMAD family 2/3 (SMAD2/3) activity via C-X-C motif chemokine ligand 10 (CXCL10). Of note, we observed disturbances in this viperin–CXCL10–TGF-β/SMAD2/3 axis in CHH chondrocytic cells. Our results indicate that the antiviral protein viperin controls chondrogenic differentiation by influencing secretion of soluble proteins and identify a molecular route that may explain impaired chondrogenic differentiation of cells from individuals with CHH.
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Affiliation(s)
- Mandy M F Steinbusch
- From the Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery and
| | - Marjolein M J Caron
- From the Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery and
| | - Don A M Surtel
- From the Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery and
| | | | - Paul J van Dijk
- the Department of Anatomy and Embryology, Maastricht University, NL-6202 AZ Maastricht, The Netherlands
| | - Franziska Friedrich
- the University Heart Centre Freiburg, Faculty of Medicine, University of Freiburg, Institute for Experimental Cardiovascular Medicine, 79110 Freiburg, Germany
| | - Bernhard Zabel
- the Medical Faculty, Otto van Guericke University of Magdeburg, 39106 Magdeburg, Germany, and
| | - Lodewijk W van Rhijn
- From the Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery and
| | - Mandy J Peffers
- the Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - Tim J M Welting
- From the Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery and
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29
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PARN Modulates Y RNA Stability and Its 3'-End Formation. Mol Cell Biol 2017; 37:MCB.00264-17. [PMID: 28760775 DOI: 10.1128/mcb.00264-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/24/2017] [Indexed: 11/20/2022] Open
Abstract
Loss-of-function mutations in 3'-to-5' exoribonucleases have been implicated in hereditary human diseases. For example, PARN mutations cause a severe form of dyskeratosis congenita (DC), wherein PARN deficiency leads to human telomerase RNA instability. Since the DC phenotype in PARN patients is even more severe than that of loss-of-function alleles in telomerase components, we hypothesized that PARN would also be required for the stability of other RNAs. Here, we show that PARN depletion reduces the levels of abundant human Y RNAs, which might contribute to the severe phenotype of DC observed in patients. Depletion of PAPD5 or the cytoplasmic exonuclease DIS3L rescues the effect of PARN depletion on Y RNA levels, suggesting that PARN stabilizes Y RNAs by removing oligoadenylated tails added by PAPD5, which would otherwise recruit DIS3L for Y RNA degradation. Through deep sequencing of 3' ends, we provide evidence that PARN can also deadenylate the U6 and RMRP RNAs without affecting their levels. Moreover, we observed widespread posttranscriptional oligoadenylation, uridylation, and guanylation of U6 and Y RNA 3' ends, suggesting that in mammalian cells, the formation of a 3' end for noncoding RNAs can be a complex process governed by the activities of various 3'-end polymerases and exonucleases.
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30
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Pillon MC, Stanley RE. Nuclease integrated kinase super assemblies (NiKs) and their role in RNA processing. Curr Genet 2017; 64:183-190. [PMID: 28929238 DOI: 10.1007/s00294-017-0749-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 01/24/2023]
Abstract
Here we highlight the Grc3/Las1 complex, an essential RNA processing machine that is well conserved across eukaryotes and required for processing the pre-ribosomal RNA (pre-rRNA). Las1 is an endoribonuclease that cleaves the pre-rRNA while Grc3 is a polynucleotide kinase that phosphorylates the Las1-cleaved RNA product. Recently we showed that Grc3 and Las1 assemble into a higher-order complex composed of a dimer of Grc3/Las1 heterodimers that is required for nuclease and kinase activity. Unexpectedly, we found that the Grc3/Las1 complex draws numerous parallels with two other eukaryotic nucleases, Ire1 and RNase L. In this perspective we explore the similarities and differences between this family of nuclease integrated kinase super assemblies (NiKs) and their distinct roles in RNA cleavage.
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Affiliation(s)
- Monica C Pillon
- Signal Transduction Laboratory, Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Robin E Stanley
- Signal Transduction Laboratory, Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA.
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31
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Steinbusch MMF, Caron MMJ, Surtel DAM, Friedrich F, Lausch E, Pruijn GJM, Verhesen W, Schroen BLM, van Rhijn LW, Zabel B, Welting TJM. Expression of RMRP RNA is regulated in chondrocyte hypertrophy and determines chondrogenic differentiation. Sci Rep 2017; 7:6440. [PMID: 28743979 PMCID: PMC5527100 DOI: 10.1038/s41598-017-06809-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 06/26/2017] [Indexed: 12/01/2022] Open
Abstract
Mutations in the RMRP-gene, encoding the lncRNA component of the RNase MRP complex, are the origin of cartilage-hair hypoplasia. Cartilage-hair hypoplasia is associated with severe dwarfism caused by impaired skeletal development. However, it is not clear why mutations in RMRP RNA lead to skeletal dysplasia. Since chondrogenic differentiation of the growth plate is required for development of long bones, we hypothesized that RMRP RNA plays a pivotal role in chondrogenic differentiation. Expression of Rmrp RNA and RNase MRP protein subunits was detected in the murine growth plate and during the course of chondrogenic differentiation of ATDC5 cultures, where Rmrp RNA expression was found to be correlated with chondrocyte hypertrophy. Genetic interference with Rmrp RNA expression in ATDC5 cultures caused a deregulation of chondrogenic differentiation, with a prominent impact on hypertrophy and changes in pre-rRNA processing and rRNA levels. Promoter reporter studies showed that Rmrp RNA expression responds to chondrogenic morphogens. Chondrogenic trans-differentiation of cartilage-hair hypoplasia fibroblasts was impaired with a pronounced impact on hypertrophic differentiation. Together, our data show that RMRP RNA expression is regulated during different stages of chondrogenic differentiation and indicate that RMRP RNA may play a pivotal role in chondrocyte hypertrophy, with potential consequences for CHH pathobiology.
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Affiliation(s)
- Mandy M F Steinbusch
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Marjolein M J Caron
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Don A M Surtel
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Franziska Friedrich
- Department of Pediatrics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ekkehart Lausch
- Department of Pediatrics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ger J M Pruijn
- Department of Biomolecular Chemistry, Institute for Molecules and Materials and Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Wouter Verhesen
- Center for Heart Failure Research, Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Blanche L M Schroen
- Center for Heart Failure Research, Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Lodewijk W van Rhijn
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Bernhard Zabel
- Medical Faculty, Otto-von-Guericke-University of Magdeburg, Magdeburg, Germany
| | - Tim J M Welting
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Centre, Maastricht, The Netherlands.
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32
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Barraza-García J, Rivera-Pedroza CI, Hisado-Oliva A, Belinchón-Martínez A, Sentchordi-Montané L, Duncan EL, Clark GR, Del Pozo A, Ibáñez-Garikano K, Offiah A, Prieto-Matos P, Cormier-Daire V, Heath KE. Broadening the phenotypic spectrum of POP1-skeletal dysplasias: identification of POP1 mutations in a mild and severe skeletal dysplasia. Clin Genet 2017; 92:91-98. [PMID: 28067412 DOI: 10.1111/cge.12964] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 12/11/2022]
Abstract
Processing of Precursor 1 (POP1) is a large protein common to the ribonuclease-mitochondrial RNA processing (RNase-MRP) and RNase-P (RMRP) endoribonucleoprotein complexes. Although its precise function is unknown, it appears to participate in the assembly or stability of both complexes. Numerous RMRP mutations have been reported in individuals with cartilage-hair hypoplasia (CHH) but, to date, only three POP1 mutations have been described in two families with features similar to anauxetic dysplasia (AD). We present two further individuals, one with severe short stature and a relatively mild skeletal dysplasia and another in whom AD was suspected. Biallelic POP1 mutations were identified in both. A missense mutation and a novel single base deletion were detected in proband 1, p.[Pro582Ser]:[Glu870fs*5]. Markedly reduced abundance of RMRP and elevated levels of pre5.8s rRNA was observed. In proband 2, a homozygous novel POP1 mutation was identified, p.[(Asp511Tyr)];[(Asp511Tyr)]. These two individuals show the phenotypic extremes in the clinical presentation of POP1-dysplasias. Although CHH and other skeletal dysplasias caused by mutations in RMRP or POP1 are commonly cited as ribosomal biogenesis disorders, recent studies question this assumption. We discuss the past and present knowledge about the function of the RMRP complex in skeletal development.
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Affiliation(s)
- J Barraza-García
- Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto Carlos III, Madrid, Spain
- Multidisciplinary Skeletal dysplasia Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
| | - C I Rivera-Pedroza
- Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
- Multidisciplinary Skeletal dysplasia Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
| | - A Hisado-Oliva
- Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto Carlos III, Madrid, Spain
- Multidisciplinary Skeletal dysplasia Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
| | - A Belinchón-Martínez
- Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto Carlos III, Madrid, Spain
- Multidisciplinary Skeletal dysplasia Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
| | - L Sentchordi-Montané
- Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
- Multidisciplinary Skeletal dysplasia Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
- Department of Pediatric Endocrinology, Hospital Universitario Infanta Leonor, Madrid, Spain
| | - E L Duncan
- Department of Endocrinology, Royal Brisbane and Women's Hospital, Herston, Australia
| | - G R Clark
- Human Genetics Group, University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Brisbane, Australia
| | - A Del Pozo
- Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto Carlos III, Madrid, Spain
| | - K Ibáñez-Garikano
- Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
| | - A Offiah
- Radiology Department, Sheffield Children's Hospital NHS Foundation Trust and Academic Unit of Child Health, University of Sheffield, Sheffield, UK
| | - P Prieto-Matos
- Pediatric Endocrinology Unit, Hospital Universitario de Salamanca, Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
| | - V Cormier-Daire
- Department of Medical Genetics, Reference Center for Skeletal Dysplasia, INSERM UMR 1163, Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia, Paris Descartes-Sorbonne Paris Cité University, AP-HP, Institut Imagine and Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - K E Heath
- Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto Carlos III, Madrid, Spain
- Multidisciplinary Skeletal dysplasia Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
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33
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Targeted CRISPR disruption reveals a role for RNase MRP RNA in human preribosomal RNA processing. Genes Dev 2017; 31:59-71. [PMID: 28115465 PMCID: PMC5287113 DOI: 10.1101/gad.286963.116] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 12/20/2016] [Indexed: 12/03/2022]
Abstract
In this study, Goldfarb et al. used CRISPR–Cas9 genome editing to eliminate MRP RNA—a ribonucleoprotein complex with an RNA subunit that is conserved across eukarya—in the majority of cells. Analysis by RNA FISH, Northerns, and RNA sequencing demonstrates an accumulation of ribosomal RNA precursor and thus establishes a role for RNase MRP in human pre-rRNA processing. MRP RNA is an abundant, essential noncoding RNA whose functions have been proposed in yeast but are incompletely understood in humans. Mutations in the genomic locus for MRP RNA cause pleiotropic human diseases, including cartilage hair hypoplasia (CHH). Here we applied CRISPR–Cas9 genome editing to disrupt the endogenous human MRP RNA locus, thereby attaining what has eluded RNAi and RNase H experiments: elimination of MRP RNA in the majority of cells. The resulting accumulation of ribosomal RNA (rRNA) precursor—analyzed by RNA fluorescent in situ hybridization (FISH), Northern blots, and RNA sequencing—implicates MRP RNA in pre-rRNA processing. Amelioration of pre-rRNA imbalance is achieved through rescue of MRP RNA levels by ectopic expression. Furthermore, affinity-purified MRP ribonucleoprotein (RNP) from HeLa cells cleaves the human pre-rRNA in vitro at at least one site used in cells, while RNP isolated from cells with CRISPR-edited MRP loci loses this activity, and ectopic MRP RNA expression restores cleavage activity. Thus, a role for RNase MRP in human pre-rRNA processing is established. As demonstrated here, targeted CRISPR disruption is a valuable tool for functional studies of essential noncoding RNAs that are resistant to RNAi and RNase H-based degradation.
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Wnt activated β-catenin and YAP proteins enhance the expression of non-coding RNA component of RNase MRP in colon cancer cells. Oncotarget 2016; 6:34658-68. [PMID: 26415221 PMCID: PMC4741480 DOI: 10.18632/oncotarget.5778] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 09/01/2015] [Indexed: 11/25/2022] Open
Abstract
RMRP, the RNA component of mitochondrial RNA processing endoribonuclease, is a non-coding RNA (ncRNA) part of the RNase MRP complex functioning in mitochondrial and ribosomal RNA processing. Even though various mutations in the RMRP gene are linked to developmental defects and pathogenesis, its relevance to cancer etiology has not been well established. Here we examined the expression of RMRP and found a significant increase in colorectal and breast cancer patient tissues. So we tested whether the oncogenic signaling pathways, Wnt/β-catenin and Hippo/YAP pathways, are relevant to the enhanced expression of RMRP in cancer cells because of the predicted β-catenin/TCF and YAP/TBX5 elements in the upstream regions of the RMRP gene. As expected, Wnt signal activation significantly induced the RMRP transcription thru β-catenin and YAP transcription factors. More importantly, YAP protein was critical for RMRP transcription by association to the proximal site near the transcription start site of the RMRP gene, a Pol III promoter, along with β-catenin and TBX5 proteins. We propose that the interplay of Wnt and Hippo signaling pathways could regulate target genes, coding or non-coding, by the β-catenin/YAP/TBX5 transcription complex in cancer cells.
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RNA Polymerase III Advances: Structural and tRNA Functional Views. Trends Biochem Sci 2016; 41:546-559. [PMID: 27068803 DOI: 10.1016/j.tibs.2016.03.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/03/2016] [Accepted: 03/09/2016] [Indexed: 12/25/2022]
Abstract
RNA synthesis in eukaryotes is divided among three RNA polymerases (RNAPs). RNAP III transcribes hundreds of tRNA genes and fewer additional short RNA genes. We survey recent work on transcription by RNAP III including an atomic structure, mechanisms of action, interactions with chromatin and retroposons, and a conserved link between its activity and a tRNA modification that enhances mRNA decoding. Other new work suggests important mechanistic connections to oxidative stress, autoimmunity and cancer, embryonic stem cell pluripotency, and tissue-specific developmental effects. We consider that, for some of its complex functions, variation in RNAP III activity levels lead to nonuniform changes in tRNAs that can shift the translation profiles of key codon-biased mRNAs with resultant phenotypes or disease states.
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Wong QWL, Vaz C, Lee QY, Zhao TY, Luo R, Archer SK, Preiss T, Tanavde V, Vardy LA. Embryonic Stem Cells Exhibit mRNA Isoform Specific Translational Regulation. PLoS One 2016; 11:e0143235. [PMID: 26799392 PMCID: PMC4723142 DOI: 10.1371/journal.pone.0143235] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 11/02/2015] [Indexed: 01/08/2023] Open
Abstract
The presence of multiple variants for many mRNAs is a major contributor to protein diversity. The processing of these variants is tightly controlled in a cell-type specific manner and has a significant impact on gene expression control. Here we investigate the differential translation rates of individual mRNA variants in embryonic stem cells (ESCs) and in ESC derived Neural Precursor Cells (NPCs) using polysome profiling coupled to RNA sequencing. We show that there are a significant number of detectable mRNA variants in ESCs and NPCs and that many of them show variant specific translation rates. This is correlated with differences in the UTRs of the variants with the 5'UTR playing a predominant role. We suggest that mRNA variants that contain alternate UTRs are under different post-transcriptional controls. This is likely due to the presence or absence of miRNA and protein binding sites that regulate translation rate. This highlights the importance of addressing translation rate when using mRNA levels as a read out of protein abundance. Additional analysis shows that many annotated non-coding mRNAs are present on the polysome fractions in ESCs and NPCs. We believe that the use of polysome fractionation coupled to RNA sequencing is a useful method for analysis of the translation state of many different RNAs in the cell.
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Affiliation(s)
- Queenie Wing-Lei Wong
- Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Immunos, 138648, Singapore, Singapore
| | - Candida Vaz
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, 138671, Singapore, Singapore
| | - Qian Yi Lee
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, 138671, Singapore, Singapore
| | - Tian Yun Zhao
- Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Immunos, 138648, Singapore, Singapore
| | - Raymond Luo
- Life Technologies, 10 Biopolis Road, 138670, Singapore, Singapore
| | - Stuart K. Archer
- Monash Bioinformatics Platform, Monash University, Clayton, Victoria, Australia
| | - Thomas Preiss
- EMBL–Australia Collaborating Group, Department of Genome Science, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton (Canberra), Australian Capital Territory, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), New South Wales, Australia
| | - Vivek Tanavde
- Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Immunos, 138648, Singapore, Singapore
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, 138671, Singapore, Singapore
| | - Leah A. Vardy
- Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Immunos, 138648, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore, Singapore
- * E-mail:
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Smola MJ, Calabrese JM, Weeks KM. Detection of RNA-Protein Interactions in Living Cells with SHAPE. Biochemistry 2015; 54:6867-75. [PMID: 26544910 DOI: 10.1021/acs.biochem.5b00977] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
SHAPE-MaP is unique among RNA structure probing strategies in that it both measures flexibility at single-nucleotide resolution and quantifies the uncertainties in these measurements. We report a straightforward analytical framework that incorporates these uncertainties to allow detection of RNA structural differences between any two states, and we use it here to detect RNA-protein interactions in healthy mouse trophoblast stem cells. We validate this approach by analysis of three model cytoplasmic and nuclear ribonucleoprotein complexes, in 2 min in-cell probing experiments. In contrast, data produced by alternative in-cell SHAPE probing methods correlate poorly (r = 0.2) with those generated by SHAPE-MaP and do not yield accurate signals for RNA-protein interactions. We then examine RNA-protein and RNA-substrate interactions in the RNase MRP complex and, by comparing in-cell interaction sites with disease-associated mutations, characterize these noncoding mutations in terms of molecular phenotype. Together, these results reveal that SHAPE-MaP can define true interaction sites and infer RNA functions under native cellular conditions with limited preexisting knowledge of the proteins or RNAs involved.
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Affiliation(s)
- Matthew J Smola
- Department of Chemistry, University of North Carolina , Chapel Hill, North Carolina 27599-3290, United States
| | - J Mauro Calabrese
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina , Chapel Hill, North Carolina 27599-3290, United States
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Fagerlund RD, Perederina A, Berezin I, Krasilnikov AS. Footprinting analysis of interactions between the largest eukaryotic RNase P/MRP protein Pop1 and RNase P/MRP RNA components. RNA (NEW YORK, N.Y.) 2015; 21:1591-605. [PMID: 26135751 PMCID: PMC4536320 DOI: 10.1261/rna.049007.114] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 06/03/2015] [Indexed: 05/06/2023]
Abstract
Ribonuclease (RNase) P and RNase MRP are closely related catalytic ribonucleoproteins involved in the metabolism of a wide range of RNA molecules, including tRNA, rRNA, and some mRNAs. The catalytic RNA component of eukaryotic RNase P retains the core elements of the bacterial RNase P ribozyme; however, the peripheral RNA elements responsible for the stabilization of the global architecture are largely absent in the eukaryotic enzyme. At the same time, the protein makeup of eukaryotic RNase P is considerably more complex than that of the bacterial RNase P. RNase MRP, an essential and ubiquitous eukaryotic enzyme, has a structural organization resembling that of eukaryotic RNase P, and the two enzymes share most of their protein components. Here, we present the results of the analysis of interactions between the largest protein component of yeast RNases P/MRP, Pop1, and the RNA moieties of the enzymes, discuss structural implications of the results, and suggest that Pop1 plays the role of a scaffold for the stabilization of the global architecture of eukaryotic RNase P RNA, substituting for the network of RNA-RNA tertiary interactions that maintain the global RNA structure in bacterial RNase P.
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Affiliation(s)
- Robert D Fagerlund
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Anna Perederina
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Igor Berezin
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Andrey S Krasilnikov
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Saito Y, Takeda J, Adachi K, Nobe Y, Kobayashi J, Hirota K, Oliveira DV, Taoka M, Isobe T. RNase MRP cleaves pre-tRNASer-Met in the tRNA maturation pathway. PLoS One 2014; 9:e112488. [PMID: 25401760 PMCID: PMC4234475 DOI: 10.1371/journal.pone.0112488] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 10/17/2014] [Indexed: 01/07/2023] Open
Abstract
Ribonuclease mitochondrial RNA processing (RNase MRP) is a multifunctional ribonucleoprotein (RNP) complex that is involved in the maturation of various types of RNA including ribosomal RNA. RNase MRP consists of a potential catalytic RNA and several protein components, all of which are required for cell viability. We show here that the temperature-sensitive mutant of rmp1, the gene for a unique protein component of RNase MRP, accumulates the dimeric tRNA precursor, pre-tRNASer-Met. To examine whether RNase MRP mediates tRNA maturation, we purified the RNase MRP holoenzyme from the fission yeast Schizosaccharomyces pombe and found that the enzyme directly and selectively cleaves pre-tRNASer-Met, suggesting that RNase MRP participates in the maturation of specific tRNA in vivo. In addition, mass spectrometry–based ribonucleoproteomic analysis demonstrated that this RNase MRP consists of one RNA molecule and 11 protein components, including a previously unknown component Rpl701. Notably, limited nucleolysis of RNase MRP generated an active catalytic core consisting of partial mrp1 RNA fragments, which constitute “Domain 1” in the secondary structure of RNase MRP, and 8 proteins. Thus, the present study provides new insight into the structure and function of RNase MRP.
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Affiliation(s)
- Yuichiro Saito
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Jun Takeda
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Tokyo, Japan
| | - Kousuke Adachi
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Yuko Nobe
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Tokyo, Japan
| | - Junya Kobayashi
- Division of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Kyoto, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Douglas V. Oliveira
- Division of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Kyoto, Japan
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Tokyo, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Tokyo, Japan
- * E-mail:
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Henras AK, Plisson-Chastang C, O'Donohue MF, Chakraborty A, Gleizes PE. An overview of pre-ribosomal RNA processing in eukaryotes. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:225-42. [PMID: 25346433 PMCID: PMC4361047 DOI: 10.1002/wrna.1269] [Citation(s) in RCA: 391] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/04/2014] [Accepted: 08/29/2014] [Indexed: 12/23/2022]
Abstract
Ribosomal RNAs are the most abundant and universal noncoding RNAs in living organisms. In eukaryotes, three of the four ribosomal RNAs forming the 40S and 60S subunits are borne by a long polycistronic pre-ribosomal RNA. A complex sequence of processing steps is required to gradually release the mature RNAs from this precursor, concomitant with the assembly of the 79 ribosomal proteins. A large set of trans-acting factors chaperone this process, including small nucleolar ribonucleoparticles. While yeast has been the gold standard for studying the molecular basis of this process, recent technical advances have allowed to further define the mechanisms of ribosome biogenesis in animals and plants. This renewed interest for a long-lasting question has been fueled by the association of several genetic diseases with mutations in genes encoding both ribosomal proteins and ribosome biogenesis factors, and by the perspective of new anticancer treatments targeting the mechanisms of ribosome synthesis. A consensus scheme of pre-ribosomal RNA maturation is emerging from studies in various kinds of eukaryotic organisms. However, major differences between mammalian and yeast pre-ribosomal RNA processing have recently come to light. WIREs RNA 2015, 6:225–242. doi: 10.1002/wrna.1269
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Affiliation(s)
- Anthony K Henras
- Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse-Paul Sabatier CNRS, UMR 5099, Toulouse, France
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Schminke B, Muhammad H, Bode C, Sadowski B, Gerter R, Gersdorff N, Bürgers R, Monsonego-Ornan E, Rosen V, Miosge N. A discoidin domain receptor 1 knock-out mouse as a novel model for osteoarthritis of the temporomandibular joint. Cell Mol Life Sci 2014; 71:1081-96. [PMID: 23912900 PMCID: PMC11113511 DOI: 10.1007/s00018-013-1436-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 07/19/2013] [Accepted: 07/22/2013] [Indexed: 11/25/2022]
Abstract
Discoidin domain receptor 1 (DDR-1)-deficient mice exhibited a high incidence of osteoarthritis (OA) in the temporomandibular joint (TMJ) as early as 9 weeks of age. They showed typical histological signs of OA, including surface fissures, loss of proteoglycans, chondrocyte cluster formation, collagen type I upregulation, and atypical collagen fibril arrangements. Chondrocytes isolated from the TMJs of DDR-1-deficient mice maintained their osteoarthritic characteristics when placed in culture. They expressed high levels of runx-2 and collagen type I, as well as low levels of sox-9 and aggrecan. The expression of DDR-2, a key factor in OA, was increased. DDR-1-deficient chondrocytes from the TMJ were positively influenced towards chondrogenesis by a three-dimensional matrix combined with a runx-2 knockdown or stimulation with extracellular matrix components, such as nidogen-2. Therefore, the DDR-1 knock-out mouse can serve as a novel model for temporomandibular disorders, such as OA of the TMJ, and will help to develop new treatment options, particularly those involving tissue regeneration.
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Affiliation(s)
- Boris Schminke
- Oral Biology and Tissue Regeneration Work Group, Department of Prosthodontics, Medical Faculty, Georg-August-University, Robert Koch Straße 40, 37075 Goettingen, Germany
| | - Hayat Muhammad
- Oral Biology and Tissue Regeneration Work Group, Department of Prosthodontics, Medical Faculty, Georg-August-University, Robert Koch Straße 40, 37075 Goettingen, Germany
| | - Christa Bode
- Oral Biology and Tissue Regeneration Work Group, Department of Prosthodontics, Medical Faculty, Georg-August-University, Robert Koch Straße 40, 37075 Goettingen, Germany
| | - Boguslawa Sadowski
- Oral Biology and Tissue Regeneration Work Group, Department of Prosthodontics, Medical Faculty, Georg-August-University, Robert Koch Straße 40, 37075 Goettingen, Germany
| | - Regina Gerter
- Oral Biology and Tissue Regeneration Work Group, Department of Prosthodontics, Medical Faculty, Georg-August-University, Robert Koch Straße 40, 37075 Goettingen, Germany
| | - Nikolaus Gersdorff
- Oral Biology and Tissue Regeneration Work Group, Department of Prosthodontics, Medical Faculty, Georg-August-University, Robert Koch Straße 40, 37075 Goettingen, Germany
| | - Ralf Bürgers
- Oral Biology and Tissue Regeneration Work Group, Department of Prosthodontics, Medical Faculty, Georg-August-University, Robert Koch Straße 40, 37075 Goettingen, Germany
| | - Efrat Monsonego-Ornan
- Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, P.O. Box 12, 76100 Rehovot, Israel
| | - Vicki Rosen
- Developmental Biology, Harvard School of Dental Medicine, 188 Longwood Avenue, Boston, MA 02115 USA
| | - Nicolai Miosge
- Oral Biology and Tissue Regeneration Work Group, Department of Prosthodontics, Medical Faculty, Georg-August-University, Robert Koch Straße 40, 37075 Goettingen, Germany
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Peffers M, Liu X, Clegg P. Transcriptomic signatures in cartilage ageing. Arthritis Res Ther 2013; 15:R98. [PMID: 23971731 PMCID: PMC3978620 DOI: 10.1186/ar4278] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 08/23/2013] [Indexed: 12/29/2022] Open
Abstract
Introduction Age is an important factor in the development of osteoarthritis. Microarray studies provide insight into cartilage aging but do not reveal the full transcriptomic phenotype of chondrocytes such as small noncoding RNAs, pseudogenes, and microRNAs. RNA-Seq is a powerful technique for the interrogation of large numbers of transcripts including nonprotein coding RNAs. The aim of the study was to characterise molecular mechanisms associated with age-related changes in gene signatures. Methods RNA for gene expression analysis using RNA-Seq and real-time PCR analysis was isolated from macroscopically normal cartilage of the metacarpophalangeal joints of eight horses; four young donors (4 years old) and four old donors (>15 years old). RNA sequence libraries were prepared following ribosomal RNA depletion and sequencing was undertaken using the Illumina HiSeq 2000 platform. Differentially expressed genes were defined using Benjamini-Hochberg false discovery rate correction with a generalised linear model likelihood ratio test (P < 0.05, expression ratios ± 1.4 log2 fold-change). Ingenuity pathway analysis enabled networks, functional analyses and canonical pathways from differentially expressed genes to be determined. Results In total, the expression of 396 transcribed elements including mRNAs, small noncoding RNAs, pseudogenes, and a single microRNA was significantly different in old compared with young cartilage (± 1.4 log2 fold-change, P < 0.05). Of these, 93 were at higher levels in the older cartilage and 303 were at lower levels in the older cartilage. There was an over-representation of genes with reduced expression relating to extracellular matrix, degradative proteases, matrix synthetic enzymes, cytokines and growth factors in cartilage derived from older donors compared with young donors. In addition, there was a reduction in Wnt signalling in ageing cartilage. Conclusion There was an age-related dysregulation of matrix, anabolic and catabolic cartilage factors. This study has increased our knowledge of transcriptional networks in cartilage ageing by providing a global view of the transcriptome.
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Esakova O, Perederina A, Berezin I, Krasilnikov AS. Conserved regions of ribonucleoprotein ribonuclease MRP are involved in interactions with its substrate. Nucleic Acids Res 2013; 41:7084-91. [PMID: 23700311 PMCID: PMC3737539 DOI: 10.1093/nar/gkt432] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 04/25/2013] [Accepted: 04/27/2013] [Indexed: 01/19/2023] Open
Abstract
Ribonuclease (RNase) MRP is a ubiquitous and essential site-specific eukaryotic endoribonuclease involved in the metabolism of a wide range of RNA molecules. RNase MRP is a ribonucleoprotein with a large catalytic RNA moiety that is closely related to the RNA component of RNase P, and multiple proteins, most of which are shared with RNase P. Here, we report the results of an ultraviolet-cross-linking analysis of interactions between a photoreactive RNase MRP substrate and the Saccharomyces cerevisiae RNase MRP holoenzyme. The results show that the substrate interacts with phylogenetically conserved RNA elements universally found in all enzymes of the RNase P/MRP family, as well as with a phylogenetically conserved RNA region that is unique to RNase MRP, and demonstrate that four RNase MRP protein components, all shared with RNase P, interact with the substrate. Implications for the structural organization of RNase MRP and the roles of its components are discussed.
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Affiliation(s)
| | | | | | - Andrey S. Krasilnikov
- Department of Biochemistry and Molecular Biology and Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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Makarova JA, Ivanova SM, Tonevitsky AG, Grigoriev AI. New functions of small nucleolar RNAs. BIOCHEMISTRY (MOSCOW) 2013; 78:638-50. [DOI: 10.1134/s0006297913060096] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Sardana R, White JP, Johnson AW. The rRNA methyltransferase Bud23 shows functional interaction with components of the SSU processome and RNase MRP. RNA (NEW YORK, N.Y.) 2013; 19:828-40. [PMID: 23604635 PMCID: PMC3683916 DOI: 10.1261/rna.037671.112] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 03/14/2013] [Indexed: 05/25/2023]
Abstract
Bud23 is responsible for the conserved methylation of G1575 of 18S rRNA, in the P-site of the small subunit of the ribosome. bud23Δ mutants have severely reduced small subunit levels and show a general failure in cleavage at site A2 during rRNA processing. Site A2 is the primary cleavage site for separating the precursors of 18S and 25S rRNAs. Here, we have taken a genetic approach to identify the functional environment of BUD23. We found mutations in UTP2 and UTP14, encoding components of the SSU processome, as spontaneous suppressors of a bud23Δ mutant. The suppressors improved growth and subunit balance and restored cleavage at site A2. In a directed screen of 50 ribosomal trans-acting factors, we identified strong positive and negative genetic interactions with components of the SSU processome and strong negative interactions with components of RNase MRP. RNase MRP is responsible for cleavage at site A3 in pre-rRNA, an alternative cleavage site for separating the precursor rRNAs. The strong negative genetic interaction between RNase MRP mutants and bud23Δ is likely due to the combined defects in cleavage at A2 and A3. Our results suggest that Bud23 plays a role at the time of A2 cleavage, earlier than previously thought. The genetic interaction with the SSU processome suggests that Bud23 could be involved in triggering disassembly of the SSU processome, or of particular subcomplexes of the processome.
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Hu S, Wu J, Chen L, Shan G. Signals from noncoding RNAs: unconventional roles for conventional pol III transcripts. Int J Biochem Cell Biol 2012; 44:1847-51. [PMID: 22819850 DOI: 10.1016/j.biocel.2012.07.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 07/06/2012] [Accepted: 07/09/2012] [Indexed: 12/29/2022]
Abstract
A range of noncoding RNAs are transcribed by pol III. A lot of them such as tRNA, 7SL RNA, 7SK RNA, 5S RNA, MRP RNA, Y RNAs, H1 RNA, and vault RNAs are considered as "house keeping" RNAs essential for eukaryotic cells. In recent years, researchers started to recognize the existence of unconventional functions of many pol III transcripts other than classical "house keeping" roles. Therefore, these ncRNAs could now be viewed as molecules with functional regulatory signals as well as cellular building blocks. These noncoding RNAs, all transcribed by pol III, may assemble regulatory networks with analogy to signaling pathways in eukaryotic cells. In this review we discuss these unconventional roles of pol III transcripts.
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Affiliation(s)
- Shanshan Hu
- School of Life Science, University of Science and Technology of China, 443 Huangshan Road, Hefei, Anhui Province 230027, China
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Mattijssen S, Pruijn GJM. Viperin, a key player in the antiviral response. Microbes Infect 2011; 14:419-26. [PMID: 22182524 DOI: 10.1016/j.micinf.2011.11.015] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 11/29/2011] [Indexed: 02/02/2023]
Abstract
Viperin is an antiviral protein that is induced by different viruses, type I interferon, poly(I:C) and lipopolysaccharide, which is localized to the endoplasmic reticulum and lipid droplets. Recently, our knowledge on the mechanism by which viperin inhibits viral replication has strongly increased. Interestingly, it also became clear that viperin can be used by viruses to increase their infectivity. Here, our current knowledge on the induction of viperin and its effect on virus replication will be reviewed.
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Affiliation(s)
- Sandy Mattijssen
- Department of Biomolecular Chemistry-271, Nijmegen Center for Molecular Life Sciences and Institute for Molecules and Materials, Radboud University Nijmegen, P.O. Box 9101, NL-6500 HB Nijmegen, The Netherlands
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