NMD3 Regulates Both Mrna and Rrna Nuclear Export In

Total Page:16

File Type:pdf, Size:1020Kb

NMD3 Regulates Both Mrna and Rrna Nuclear Export In Nucleic Acids Research Advance Access published April 14, 2015 Nucleic Acids Research, 2015 1 doi: 10.1093/nar/gkv330 NMD3 regulates both mRNA and rRNA nuclear export in African trypanosomes via an XPOI-linked pathway Melanie Buhlmann¨ 1,†, Pegine Walrad1,2,†,EvaRico1, Alasdair Ivens1, Paul Capewell1, Arunasalam Naguleswaran3, Isabel Roditi3 and Keith R. Matthews1,* 1Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, Kings Buildings, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK, 2Centre for Immunology and Infection, Department of Biology, University of York, YO10 5DD, UK and 3Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland Received March 02, 2015; Revised March 30, 2015; Accepted March 31, 2015 Downloaded from ABSTRACT INTRODUCTION Trypanosomes mostly regulate gene expression The compartmentalization of nuclear DNA away from the through post-transcriptional mechanisms, particu- translational apparatus in the cytoplasm of eukaryotic cells larly mRNA stability. However, much mRNA degra- requires elaborate mechanisms to achieve the regulated ex- http://nar.oxfordjournals.org/ dation is cytoplasmic such that mRNA nuclear ex- port of RNA to enable gene expression (1,2). The multiple port must represent an important level of regulation. stages of nuclear export provide several potential regulatory steps to ensure that RNAs of different function can be held Ribosomal RNAs must also be exported from the inactive until fully matured, localized or targeted for cyto- nucleus and the trypanosome orthologue of NMD3 plasmic degradation (3,4). This prevents incorrectly or in- has been confirmed to be involved in rRNA process- completely processed RNAs from perturbing normal cel- ing and export, matching its function in other or- lular functions by interfering with important cellular pro- ganisms. Surprisingly, we found that TbNMD3 deple- cesses, or generating products that would be deleterious to tion also generates mRNA accumulation of procyclin- the cell (5,6). Such RNAs can include nascent ribosomal at World Trade Institute on May 8, 2015 associated genes (PAGs), these being co-transcribed RNA subunits, tRNAs, incorrectly processed mRNAs, nu- by RNA polymerase I with the procyclin surface clear RNAi targets that require trafficking to the cytoplasm antigen genes expressed on trypanosome insect for degradation, as well as bulk mRNAs. Hence, in addi- forms. By whole transcriptome RNA-seq analysis tion to transcription, mRNA stability and translation, the of TbNMD3-depleted cells we confirm the regula- export pathway for a variety of cellular RNAs provides con- siderable scope for the cell to control the expression and tion of the PAG transcripts by TbNMD3 and using function of transcripts (4). Such regulatory pathways have reporter constructs reveal that PAG1 regulation is been extensively studied in both yeast and mammalian sys- | downloaded: 7.10.2021 mediated by its 5 UTR. Dissection of the mecha- tems and include complex rRNA maturation and export nism of regulation demonstrates that it is not de- steps (7) and the nonsense-mediated decay (NMD) of in- pendent upon translational inhibition mediated by correctly processed mRNAs (8). TbNMD3 depletion nor enhanced transcription. How- African trypanosomes provide an interesting opportu- ever, depletion of the nuclear export factors XPO1 nity to dissect the pathways of gene regulation in evolu- or MEX67 recapitulates the effects of TbNMD3 deple- tionarily divergent organisms (9,10). These organisms, im- tion on PAG mRNAs and mRNAs accumulated in the portant pathogens of humans and livestock in sub-Saharan nucleus of TbNMD3-depleted cells. These results in- Africa, diverged very early in the eukaryotic lineage and ex- voke a novel RNA regulatory mechanism involving hibit several novelties of gene expression that have attracted considerable attention. This includes their co-transcription the NMD3-dependent nuclear export of mRNA car- of functionally unrelated genes as part of polycistronic tran- gos, suggesting a shared platform for mRNA and scription units (11) and their extreme reliance on post- rRNA export. transcriptional mechanisms of gene expression control ne- cessitated by this genome organization (12). Particularly, mRNAs are generated from polycistronic transcription *To whom correspondence should be addressed. Tel: +44 131 6513639; Fax: +44 131 6513670; Email: [email protected] https://doi.org/10.7892/boris.68789 †These authors contributed equally to the paper as first authors. Disclaimer: The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. C The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. // / / / / source: This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http: creativecommons.org licenses by 4.0 ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. 2 Nucleic Acids Research, 2015 units by the coupled processes of 5 trans-splicing of a 39- role of both highly conserved, and parasite-specific, com- nt capped leader sequence and 3 polyadenylation (13,14). ponents in this fundamentally important export pathway These RNA processing steps allow trypanosomes to ex- (33–37). ploit the transcription of protein coding genes by RNA In this study, we have made the surprising discovery polymerase I in order to generate the high levels of sur- that post-transcriptional gene silencing by RNAi of try- face protein transcripts necessary for their survival or fit- panosome NMD3 results in a striking increase in PAG mR- ness in the mammalian bloodstream or tsetse fly midgut NAs in procyclic form trypanosomes, which is not mediated (15,16). In the tsetse midgut, the surface coat is composed of by the effects of NMD3 depletion on transcription, or trans- different isoforms of procyclin. These isoforms (EP procy- lation. Rather, our results invoke a novel regulatory step clin, GPEET procyclin) show differential expression during dependent upon nuclear export of the mRNA, PAG tran- the parasite’s maturation in the tsetse fly (17) and are tran- scripts representing an mRNA cargo with particular cyto- scribed from several transcription units on different chro- plasmic instability whose trafficking is dependent on a nu- mosomes in the parasite genome (18). These are transcribed clear export pathway conventionally involved in the matu- by RNA polymerase 1 (pol I) and contain unrelated genes of ration and export of large subunit ribosomal RNAs (38). unknown function, namely the procyclin-associated genes (PAGs)(19,20). Procyclin/PAG genes are believed to be tran- MATERIALS AND METHODS scribed in the nucleolus since procyclic form parasites do Downloaded from not possess a detectable expression site body, an extranucle- Trypanosomes culture olar site of pol I transcription for the surface antigen genes of the bloodstream form (21). Although PAG transcripts For developmental expression analysis using pleomorphic are generated from the same transcription unit as the pro- trypanosomes, pleomorphic slender cells were harvested cyclin genes, their overall mRNA abundance is much lower from a mouse 3 days post-infection, intermediate cells were (19,22–24). harvested 4 days post-infection and stumpy cells were har- http://nar.oxfordjournals.org/ The understanding of regulated gene expression in try- vested 6 days post-infection. Bloodstream and procyclic panosomes through the action of protein factors remains parasites were grown in culture as described (39). For stable × 8 × 7 very incomplete. Nonetheless, the trypanosome genome en- transfection 1 10 procyclic form or 4 10 bloodstream codes an abundance of RNA binding proteins, many of form cells were subjected to nucleofection with the Nucleo- which are unique to these evolutionarily divergent organ- fector system (Amaxa) using programs X-014 (PCF) or X- isms (12,25,26). The characterization of these kinetoplastid- 001 (BSF) as described in (40) and selected using the appro- ␮ / ␮ / specific factors has revealed a common role in mRNA sta- priate drugs: puromycin, 1–2 g ml (PCF) or 0.5 g ml (BSF), hygromycin: 20 ␮g/ml (PCF) or 2.5 ␮g/ml (BSF), bility and translation, often involved in regulating the de- at World Trade Institute on May 8, 2015 ␮ / ␮ / velopment through the many stages that accompany pro- phleomycin: 5–10 g ml (PCF) or 1 g ml (BSF). gression of the parasites through their complex life cycle RNAi lines of TbNMD3 and XPO1 were created using (27). In addition to these specific factors, trypanosomatids the stem loop vector pALC14 (41). Inserts were amplified by also encode a core set of conserved protein factors with polymerase chain reaction (PCR) using primers detailed in predicted functions in gene expression. These include many Supplementary Table S1. For transfection pALC14 vectors well characterized components of the translational machin- were linearized with NotI prior to transfection. ery, as well as proteins associated with RNA processing, degradation and nuclear export (28,29). In particular, bioin- Report constructs formatics analyses of the genomes of kinetoplastid parasites and other eukaryotic groups including a broad group of The constitutive CAT reporter construct was based on the expression vector pHD449 (42), as described in (43). The opisthokonta have revealed a
Recommended publications
  • Rule Mining on Microrna Expression Profiles For
    Faculty of Engineering and Information Technology University of Technology, Sydney Rule Mining on MicroRNA Expression Profiles for Human Disease Understanding A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy by Renhua Song July 2016 CERTIFICATE OF AUTHORSHIP/ORIGINALITY I certify that the work in this thesis has not previously been submitted for a degree nor has it been submitted as part of requirements for a degree except as fully acknowledged within the text. I also certify that the thesis has been written by me. Any help that I have received in my research work and the preparation of the thesis itself has been acknowledged. In addition, I certify that all information sources and literature used are indicated in the thesis. Signature of Candidate i Acknowledgments First, and foremost, I would like to express my gratitude to my chief supervisor, Assoc. Prof. Jinyan Li, and to my co-supervisors Assoc. Prof. Paul Kennedy and Assoc. Prof. Daniel Catchpoole. I am extremely grateful for all the advice and guidance so unselfishly given to me over the last three and half years by these three distinguished academics. This research would not have been possible without their high order supervision, support, assistance and leadership. The wonderful support and assistance provided by many people during this research is very much appreciated by me and my family. I am very grateful for the help that I received from all of these people but there are some special individuals that I must thank by name. A very sincere thank you is definitely owed to my loving husband Jing Liu, not only for his tremendous support during the last three and half years, but also his unfailing and often sorely tested patience.
    [Show full text]
  • Mechanism of Completion of Peptidyltransferase Centre
    RESEARCH ARTICLE Mechanism of completion of peptidyltransferase centre assembly in eukaryotes Vasileios Kargas1,2,3†, Pablo Castro-Hartmann1,2,3†, Norberto Escudero-Urquijo1,2,3, Kyle Dent1,2,3, Christine Hilcenko1,2,3, Carolin Sailer4, Gertrude Zisser5, Maria J Marques-Carvalho1,2,3, Simone Pellegrino1,2,3, Leszek Wawio´ rka1,2,3,6, Stefan MV Freund7, Jane L Wagstaff7, Antonina Andreeva7, Alexandre Faille1,2,3, Edwin Chen8, Florian Stengel4, Helmut Bergler5, Alan John Warren1,2,3* 1Cambridge Institute for Medical Research, Cambridge, United Kingdom; 2Department of Haematology, University of Cambridge, Cambridge, United Kingdom; 3Wellcome Trust–Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom; 4Department of Biology, University of Konstanz, Konstanz, Germany; 5Institute of Molecular Biosciences, University of Graz, Graz, Austria; 6Department of Molecular Biology, Maria Curie-Skłodowska University, Lublin, Poland; 7MRC Laboratory of Molecular Biology, Cambridge, United Kingdom; 8Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom Abstract During their final maturation in the cytoplasm, pre-60S ribosomal particles are converted to translation-competent large ribosomal subunits. Here, we present the mechanism of peptidyltransferase centre (PTC) completion that explains how integration of the last ribosomal *For correspondence: [email protected] proteins is coupled to release of the nuclear export adaptor Nmd3. Single-particle cryo-EM reveals that eL40 recruitment stabilises helix 89 to form the uL16 binding site. The loading of uL16 unhooks † These authors contributed helix 38 from Nmd3 to adopt its mature conformation. In turn, partial retraction of the L1 stalk is equally to this work coupled to a conformational switch in Nmd3 that allows the uL16 P-site loop to fully accommodate Competing interests: The into the PTC where it competes with Nmd3 for an overlapping binding site (base A2971).
    [Show full text]
  • The Transition from Primary Colorectal Cancer to Isolated Peritoneal Malignancy
    medRxiv preprint doi: https://doi.org/10.1101/2020.02.24.20027318; this version posted February 25, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license . The transition from primary colorectal cancer to isolated peritoneal malignancy is associated with a hypermutant, hypermethylated state Sally Hallam1, Joanne Stockton1, Claire Bryer1, Celina Whalley1, Valerie Pestinger1, Haney Youssef1, Andrew D Beggs1 1 = Surgical Research Laboratory, Institute of Cancer & Genomic Science, University of Birmingham, B15 2TT. Correspondence to: Andrew Beggs, [email protected] KEYWORDS: Colorectal cancer, peritoneal metastasis ABBREVIATIONS: Colorectal cancer (CRC), Colorectal peritoneal metastasis (CPM), Cytoreductive surgery and heated intraperitoneal chemotherapy (CRS & HIPEC), Disease free survival (DFS), Differentially methylated regions (DMR), Overall survival (OS), TableFormalin fixed paraffin embedded (FFPE), Hepatocellular carcinoma (HCC) ARTICLE CATEGORY: Research article NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. 1 medRxiv preprint doi: https://doi.org/10.1101/2020.02.24.20027318; this version posted February 25, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license . NOVELTY AND IMPACT: Colorectal peritoneal metastasis (CPM) are associated with limited and variable survival despite patient selection using known prognostic factors and optimal currently available treatments.
    [Show full text]
  • "The Genecards Suite: from Gene Data Mining to Disease Genome Sequence Analyses". In: Current Protocols in Bioinformat
    The GeneCards Suite: From Gene Data UNIT 1.30 Mining to Disease Genome Sequence Analyses Gil Stelzer,1,5 Naomi Rosen,1,5 Inbar Plaschkes,1,2 Shahar Zimmerman,1 Michal Twik,1 Simon Fishilevich,1 Tsippi Iny Stein,1 Ron Nudel,1 Iris Lieder,2 Yaron Mazor,2 Sergey Kaplan,2 Dvir Dahary,2,4 David Warshawsky,3 Yaron Guan-Golan,3 Asher Kohn,3 Noa Rappaport,1 Marilyn Safran,1 and Doron Lancet1,6 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel 2LifeMap Sciences Ltd., Tel Aviv, Israel 3LifeMap Sciences Inc., Marshfield, Massachusetts 4Toldot Genetics Ltd., Hod Hasharon, Israel 5These authors contributed equally to the paper 6Corresponding author GeneCards, the human gene compendium, enables researchers to effectively navigate and inter-relate the wide universe of human genes, diseases, variants, proteins, cells, and biological pathways. Our recently launched Version 4 has a revamped infrastructure facilitating faster data updates, better-targeted data queries, and friendlier user experience. It also provides a stronger foundation for the GeneCards suite of companion databases and analysis tools. Improved data unification includes gene-disease links via MalaCards and merged biological pathways via PathCards, as well as drug information and proteome expression. VarElect, another suite member, is a phenotype prioritizer for next-generation sequencing, leveraging the GeneCards and MalaCards knowledgebase. It au- tomatically infers direct and indirect scored associations between hundreds or even thousands of variant-containing genes and disease phenotype terms. Var- Elect’s capabilities, either independently or within TGex, our comprehensive variant analysis pipeline, help prepare for the challenge of clinical projects that involve thousands of exome/genome NGS analyses.
    [Show full text]
  • NMD3 (NM 015938) Human Recombinant Protein Product Data
    OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for TP303044 NMD3 (NM_015938) Human Recombinant Protein Product data: Product Type: Recombinant Proteins Description: Recombinant protein of human NMD3 homolog (S. cerevisiae) (NMD3) Species: Human Expression Host: HEK293T Tag: C-Myc/DDK Predicted MW: 57.4 kDa Concentration: >50 ug/mL as determined by microplate BCA method Purity: > 80% as determined by SDS-PAGE and Coomassie blue staining Buffer: 25 mM Tris.HCl, pH 7.3, 100 mM glycine, 10% glycerol Preparation: Recombinant protein was captured through anti-DDK affinity column followed by conventional chromatography steps. Storage: Store at -80°C. Stability: Stable for 12 months from the date of receipt of the product under proper storage and handling conditions. Avoid repeated freeze-thaw cycles. RefSeq: NP_057022 Locus ID: 51068 UniProt ID: Q96D46 RefSeq Size: 2758 Cytogenetics: 3q26.1 RefSeq ORF: 1509 Synonyms: CGI-07 Summary: Ribosomal 40S and 60S subunits associate in the nucleolus and are exported to the cytoplasm. The protein encoded by this gene is involved in the passage of the 60S subunit through the nuclear pore complex and into the cytoplasm. Several transcript variants exist for this gene, but the full-length natures of only two have been described to date. [provided by RefSeq, Feb 2016] This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 NMD3 (NM_015938) Human Recombinant Protein – TP303044 Product images: Coomassie blue staining of purified NMD3 protein (Cat# TP303044).
    [Show full text]
  • Inhibition of the 60S Ribosome Biogenesis Gtpase LSG1 Causes Endoplasmic Reticular Disruption and Cellular Senescence
    bioRxiv preprint doi: https://doi.org/10.1101/463851; this version posted November 8, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Pantazi et al. Inhibition of the 60S ribosome biogenesis GTPase LSG1 causes endoplasmic reticular disruption and cellular senescence Asimina Pantazi1, Andrea Quintanilla1, Priya Hari1, Nuria Tarrats1, Eleftheria Parasyraki1, Flora Lucy Dix1, Jaiyogesh Patel1, Tamir Chandra2, Juan Carlos Acosta1*, Andrew John Finch1* 1Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR 2MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR Abstract Cellular senescence is triggered by diverse stimuli and is characterised by long-term growth arrest and secretion of cytokines and chemokines (termed the SASP - senescence-associated secretory phenotype). Senescence can be organismally beneficial as it can prevent the propagation of damaged or mutated clones and stimulate their clearance by immune cells. However, it has recently become clear that senescence also contributes to the pathophysiology of aging through the accumulation of damaged cells within tissues. Here we describe that inhibition of the reaction catalysed by LSG1, a GTPase involved in the biogenesis of the 60S ribosomal subunit, leads to a robust induction of cellular senescence. Perhaps surprisingly, this was not due to ribosome depletion or translational insufficiency, but rather through perturbation of endoplasmic reticulum (ER) homeostasis and a dramatic upregulation of the cholesterol biosynthesis pathway.
    [Show full text]
  • Mouse Nmd3 Conditional Knockout Project (CRISPR/Cas9)
    https://www.alphaknockout.com Mouse Nmd3 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Nmd3 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Nmd3 gene (NCBI Reference Sequence: NM_133787 ; Ensembl: ENSMUSG00000027787 ) is located on Mouse chromosome 3. 16 exons are identified, with the ATG start codon in exon 2 and the TGA stop codon in exon 16 (Transcript: ENSMUST00000029358). Exon 3~4 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Nmd3 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-12P9 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 3 starts from about 2.98% of the coding region. The knockout of Exon 3~4 will result in frameshift of the gene. The size of intron 2 for 5'-loxP site insertion: 1790 bp, and the size of intron 4 for 3'-loxP site insertion: 2880 bp. The size of effective cKO region: ~2701 bp. The cKO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 4 16 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Nmd3 Homology arm cKO region loxP site Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats.
    [Show full text]
  • Downloadable Code for Forms the Data Analysis and Renders a Visual Display
    Open Access Software2005KemmeretVolume al. 6, Issue 12, Article R106 Ulysses - an application for the projection of molecular interactions comment across species Danielle Kemmer*†, Yong Huang‡, Sohrab P Shah‡¥, Jonathan Lim†, Jochen Brumm†, Macaire MS Yuen‡, John Ling‡, Tao Xu‡, Wyeth W Wasserman†§ and BF Francis Ouellette‡§¶ * † Addresses: Center for Genomics and Bioinformatics, Karolinska Institutet, 171 77 Stockholm, Sweden. Centre for Molecular Medicine and reviews Therapeutics, University of British Columbia, Vancouver V5Z 4H4, BC, Canada. ‡UBC Bioinformatics Centre, University of British Columbia, Vancouver V6T 1Z4, BC, Canada. §Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada. ¶Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, BC, Canada. ¥Department of Computer Science, University of British Columbia, Vancouver V6T 1Z4, BC, Canada. Correspondence: Wyeth W Wasserman. E-mail: [email protected] Published: 2 December 2005 Received: 23 February 2005 Revised: 3 August 2005 reports Genome Biology 2005, 6:R106 (doi:10.1186/gb-2005-6-12-r106) Accepted: 8 November 2005 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2005/6/12/R106 © 2005 Kemmer et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. deposited research Projecting<p>Ulysses, molecular a new software interactions for the across parallel species analysis and display of protein interactions detected in various species, is described.</p> Abstract We developed Ulysses as a user-oriented system that uses a process called Interolog Analysis for the parallel analysis and display of protein interactions detected in various species.
    [Show full text]
  • Ribosomal Protein L10: from Function to Dysfunction
    cells Review Ribosomal Protein L10: From Function to Dysfunction Daniela Pollutri 1,2 and Marianna Penzo 1,2,* 1 Department of Experimental, Diagnostic and Specialty Medicine Alma Mater Studiorum University of Bologna, Via Massarenti 9, 40138 Bologna, Italy; [email protected] 2 Center for Applied Biomedical Research (CRBA), Alma Mater Studiorum University of Bologna, Via Massarenti 9, 40138 Bologna, Italy * Correspondence: [email protected]; Tel.: +39-051-214-3521 Received: 15 October 2020; Accepted: 16 November 2020; Published: 19 November 2020 Abstract: Eukaryotic cytoplasmic ribosomes are highly structured macromolecular complexes made up of four different ribosomal RNAs (rRNAs) and 80 ribosomal proteins (RPs), which play a central role in the decoding of genetic code for the synthesis of new proteins. Over the past 25 years, studies on yeast and human models have made it possible to identify RPL10 (ribosomal protein L10 gene), which is a constituent of the large subunit of the ribosome, as an important player in the final stages of ribosome biogenesis and in ribosome function. Here, we reviewed the literature to give an overview of the role of RPL10 in physiologic and pathologic processes, including inherited disease and cancer. Keywords: RPL10; ribosome; cancer; ribosomopathy; rare disease; translation; protein synthesis 1. Introduction Eukaryotic cytoplasmic ribosomes are highly structured macromolecular complexes made up of four different ribosomal RNAs (rRNAs) and 80 ribosomal proteins (RPs), which play a central role in the decoding of genetic code for the synthesis of new proteins. These two distinct yet complementary functions are separated into the two ribosomal subunits: the 40S (or small) and the 60S (or large) subunits, respectively.
    [Show full text]
  • Molecular Targeting and Enhancing Anticancer Efficacy of Oncolytic HSV-1 to Midkine Expressing Tumors
    University of Cincinnati Date: 12/20/2010 I, Arturo R Maldonado , hereby submit this original work as part of the requirements for the degree of Doctor of Philosophy in Developmental Biology. It is entitled: Molecular Targeting and Enhancing Anticancer Efficacy of Oncolytic HSV-1 to Midkine Expressing Tumors Student's name: Arturo R Maldonado This work and its defense approved by: Committee chair: Jeffrey Whitsett Committee member: Timothy Crombleholme, MD Committee member: Dan Wiginton, PhD Committee member: Rhonda Cardin, PhD Committee member: Tim Cripe 1297 Last Printed:1/11/2011 Document Of Defense Form Molecular Targeting and Enhancing Anticancer Efficacy of Oncolytic HSV-1 to Midkine Expressing Tumors A dissertation submitted to the Graduate School of the University of Cincinnati College of Medicine in partial fulfillment of the requirements for the degree of DOCTORATE OF PHILOSOPHY (PH.D.) in the Division of Molecular & Developmental Biology 2010 By Arturo Rafael Maldonado B.A., University of Miami, Coral Gables, Florida June 1993 M.D., New Jersey Medical School, Newark, New Jersey June 1999 Committee Chair: Jeffrey A. Whitsett, M.D. Advisor: Timothy M. Crombleholme, M.D. Timothy P. Cripe, M.D. Ph.D. Dan Wiginton, Ph.D. Rhonda D. Cardin, Ph.D. ABSTRACT Since 1999, cancer has surpassed heart disease as the number one cause of death in the US for people under the age of 85. Malignant Peripheral Nerve Sheath Tumor (MPNST), a common malignancy in patients with Neurofibromatosis, and colorectal cancer are midkine- producing tumors with high mortality rates. In vitro and preclinical xenograft models of MPNST were utilized in this dissertation to study the role of midkine (MDK), a tumor-specific gene over- expressed in these tumors and to test the efficacy of a MDK-transcriptionally targeted oncolytic HSV-1 (oHSV).
    [Show full text]
  • Microarray Bioinformatics and Its Applications to Clinical Research
    Microarray Bioinformatics and Its Applications to Clinical Research A dissertation presented to the School of Electrical and Information Engineering of the University of Sydney in fulfillment of the requirements for the degree of Doctor of Philosophy i JLI ··_L - -> ...·. ...,. by Ilene Y. Chen Acknowledgment This thesis owes its existence to the mercy, support and inspiration of many people. In the first place, having suffering from adult-onset asthma, interstitial cystitis and cold agglutinin disease, I would like to express my deepest sense of appreciation and gratitude to Professors Hong Yan and David Levy for harbouring me these last three years and providing me a place at the University of Sydney to pursue a very meaningful course of research. I am also indebted to Dr. Craig Jin, who has been a source of enthusiasm and encouragement on my research over many years. In the second place, for contexts concerning biological and medical aspects covered in this thesis, I am very indebted to Dr. Ling-Hong Tseng, Dr. Shian-Sehn Shie, Dr. Wen-Hung Chung and Professor Chyi-Long Lee at Change Gung Memorial Hospital and University of Chang Gung School of Medicine (Taoyuan, Taiwan) as well as Professor Keith Lloyd at University of Alabama School of Medicine (AL, USA). All of them have contributed substantially to this work. In the third place, I would like to thank Mrs. Inge Rogers and Mr. William Ballinger for their helpful comments and suggestions for the writing of my papers and thesis. In the fourth place, I would like to thank my swim coach, Hirota Homma.
    [Show full text]
  • A Network Inference Approach to Understanding Musculoskeletal
    A NETWORK INFERENCE APPROACH TO UNDERSTANDING MUSCULOSKELETAL DISORDERS by NIL TURAN A thesis submitted to The University of Birmingham for the degree of Doctor of Philosophy College of Life and Environmental Sciences School of Biosciences The University of Birmingham June 2013 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. ABSTRACT Musculoskeletal disorders are among the most important health problem affecting the quality of life and contributing to a high burden on healthcare systems worldwide. Understanding the molecular mechanisms underlying these disorders is crucial for the development of efficient treatments. In this thesis, musculoskeletal disorders including muscle wasting, bone loss and cartilage deformation have been studied using systems biology approaches. Muscle wasting occurring as a systemic effect in COPD patients has been investigated with an integrative network inference approach. This work has lead to a model describing the relationship between muscle molecular and physiological response to training and systemic inflammatory mediators. This model has shown for the first time that oxygen dependent changes in the expression of epigenetic modifiers and not chronic inflammation may be causally linked to muscle dysfunction.
    [Show full text]