1
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In vitro characterization of Dhr1 from Saccharomyces cerevisiae. Methods Enzymol 2022; 673:77-101. [DOI: 10.1016/bs.mie.2022.03.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Baral SS, Lieux ME, DiMario PJ. Nucleolar stress in Drosophila neuroblasts, a model for human ribosomopathies. Biol Open 2020; 9:bio046565. [PMID: 32184230 PMCID: PMC7197718 DOI: 10.1242/bio.046565] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 03/03/2020] [Indexed: 12/11/2022] Open
Abstract
Different stem cells or progenitor cells display variable threshold requirements for functional ribosomes. This is particularly true for several human ribosomopathies in which select embryonic neural crest cells or adult bone marrow stem cells, but not others, show lethality due to failures in ribosome biogenesis or function (now known as nucleolar stress). To determine if various Drosophila neuroblasts display differential sensitivities to nucleolar stress, we used CRISPR-Cas9 to disrupt the Nopp140 gene that encodes two splice variant ribosome biogenesis factors (RBFs). Disruption of Nopp140 induced nucleolar stress that arrested larvae in the second instar stage. While the majority of larval neuroblasts arrested development, the mushroom body (MB) neuroblasts continued to proliferate as shown by their maintenance of deadpan, a neuroblast-specific transcription factor, and by their continued EdU incorporation. MB neuroblasts in wild-type larvae appeared to contain more fibrillarin and Nopp140 in their nucleoli as compared to other neuroblasts, indicating that MB neuroblasts stockpile RBFs as they proliferate in late embryogenesis while other neuroblasts normally enter quiescence. A greater abundance of Nopp140 encoded by maternal transcripts in Nopp140-/- MB neuroblasts of 1----2-day-old larvae likely rendered these cells more resilient to nucleolar stress.
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Affiliation(s)
- Sonu Shrestha Baral
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Molly E Lieux
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Patrick J DiMario
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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Drosophila nucleostemin 3 is required to maintain larval neuroblast proliferation. Dev Biol 2018; 440:1-12. [PMID: 29679561 PMCID: PMC6278609 DOI: 10.1016/j.ydbio.2018.04.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 04/14/2018] [Accepted: 04/17/2018] [Indexed: 02/03/2023]
Abstract
Stem cells must maintain proliferation during tissue development, repair and homeostasis, yet avoid tumor formation. In Drosophila, neural stem cells (neuroblasts) maintain proliferation during embryonic and larval development and terminate cell cycle during metamorphosis. An important question for understanding how tissues are generated and maintained is: what regulates stem cell proliferation versus differentiation? We performed a genetic screen which identified nucleostemin 3 (ns3) as a gene required to maintain neuroblast proliferation. ns3 is evolutionarily conserved with yeast and human Lsg1, which encode putative GTPases and are essential for organism growth and viability. We found NS3 is cytoplasmic and it is required to retain the cell cycle repressor Prospero in neuroblast cytoplasm via a Ran-independent pathway. NS3 is also required for proper neuroblast cell polarity and asymmetric cell division. Structure-function analysis further shows that the GTP-binding domain and acidic domain are required for NS3 function in neuroblast proliferation. We conclude NS3 has novel roles in regulating neuroblast cell polarity and proliferation.
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Zhao H, Lü S, Xiong L. AtLSG1-2 Regulates Leaf Growth by Affecting Cell Proliferation and the Onset of Endoreduplication and Synergistically Interacts with AtNMD3 during Cell Proliferation Process. FRONTIERS IN PLANT SCIENCE 2017; 8:337. [PMID: 28344588 PMCID: PMC5344897 DOI: 10.3389/fpls.2017.00337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 02/27/2017] [Indexed: 06/06/2023]
Abstract
AtLSG1-2 is a circularly permuted GTPase required for ribosome biogenesis and recently shown to be involved in early leaf development, although it was unclear how AtLSG1-2 affects leaf growth. Here, we found that atlsg1-2 mutants had reduced leaf size as a result of decreased cell size and cell number. Leaf kinematic analysis and CYCB1;1::GUS expression pattern in atlsg1-2 mutant indicated that loss of function of AtLSG1-2 delays the transition from cell division to cell expansion. Decreases in ploidy levels and trichome branch number suggest that AtLSG1-2 deficiency suppresses endoreduplication. Real-time PCR analysis showed that genes specifically expressed in the proliferation stage were highly expressed and those involved in endoreduplication were differentially regulated. LSG1 is known to mediate the recruitment of nucleocytoplasmic shuttling protein NMD3 back to the nucleus in yeast, yet their relationship was unclear in plants. Our genetic analysis revealed that the atlsg1 atnmd3 double mutant displayed enhanced phenotypes as compared with the respective single mutant and that AtLSG1-2 and AtNMD3 synergistically affect the cell proliferation process.
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Affiliation(s)
- Huayan Zhao
- Applied Biotechnology Center, Wuhan Institute of BioengineeringWuhan, China
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Shiyou Lü
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
| | - Liming Xiong
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
- Department of Horticulture Sciences, Texas A&M University, College StationTX, USA
- Texas A&M Agrilife Research Center, DallasTX, USA
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Wang Y, DiMario P. Loss of Drosophila nucleostemin 2 (NS2) blocks nucleolar release of the 60S subunit leading to ribosome stress. Chromosoma 2016; 126:375-388. [PMID: 27150106 DOI: 10.1007/s00412-016-0597-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 04/18/2016] [Accepted: 04/25/2016] [Indexed: 12/24/2022]
Abstract
Four nucleostemin-like proteins (nucleostemin (NS) 1-4) were identified previously in Drosophila melanogaster. NS1 and NS2 are nucleolar proteins, while NS3 and NS4 are cytoplasmic proteins. We showed earlier that NS1 (homologous to human GNL3) enriches within the granular components (GCs) of Drosophila nucleoli and is required for efficient maturation or nucleolar release of the 60S subunit. Here, we show that NS2 is homologous to the human nucleostemin-like protein, Ngp1 (GNL2), and that endogenous NS2 is expressed in both progenitor and terminally differentiated cell types. Exogenous GFP-NS2 enriched within nucleolar GCs versus endogenous fibrillarin that marked the dense fibrillar components (DFCs). Like NS1, depletion of NS2 in midgut cells blocked the release of the 60S subunit as detected by the accumulation of GFP-RpL11 within nucleoli, and this likely led to the general loss of 60S subunits as shown by immunoblot analyses of RpL23a and RpL34. At the ultrastructural level, nucleoli in midgut cells depleted of NS2 displayed enlarged GCs not only on the nucleolar periphery but interspersed within the DFCs. Depletion of NS2 caused ribosome stress: larval midgut cells displayed prominent autophagy marked by the appearance of autolysosomes containing mCherry-ATG8a and the appearance of rough endoplasmic reticulum (rER)-derived isolation membranes. Larval imaginal wing disc cells depleted of NS2 induced apoptosis as marked by anti-caspase 3 labeling; loss of these progenitor cells resulted in defective adult wings. We conclude that nucleolar proteins NS1 and NS2 have similar but non-overlapping roles in the final maturation or nucleolar release of 60S ribosomal subunits.
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Affiliation(s)
- Yubo Wang
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803-1715, USA
| | - Patrick DiMario
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803-1715, USA.
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Zhao H, Lü S, Li R, Chen T, Zhang H, Cui P, Ding F, Liu P, Wang G, Xia Y, Running MP, Xiong L. The Arabidopsis gene DIG6 encodes a large 60S subunit nuclear export GTPase 1 that is involved in ribosome biogenesis and affects multiple auxin-regulated development processes. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6863-75. [PMID: 26272902 PMCID: PMC4623693 DOI: 10.1093/jxb/erv391] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The circularly permuted GTPase large subunit GTPase 1 (LSG1) is involved in the maturation step of the 60S ribosome and is essential for cell viability in yeast. Here, an Arabidopsis mutant dig6 (drought inhibited growth of lateral roots) was isolated. The mutant exhibited multiple auxin-related phenotypes, which included reduced lateral root number, altered leaf veins, and shorter roots. Genetic mapping combined with next-generation DNA sequencing identified that the mutation occurred in AtLSG1-2. This gene was highly expressed in regions of auxin accumulation. Ribosome profiling revealed that a loss of function of AtLSG1-2 led to decreased levels of monosomes, further demonstrating its role in ribosome biogenesis. Quantitative proteomics showed that the expression of certain proteins involved in ribosome biogenesis was differentially regulated, indicating that ribosome biogenesis processes were impaired in the mutant. Further investigations showed that an AtLSG1-2 deficiency caused the alteration of auxin distribution, response, and transport in plants. It is concluded that AtLSG1-2 is integral to ribosome biogenesis, consequently affecting auxin homeostasis and plant development.
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Affiliation(s)
- Huayan Zhao
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Shiyou Lü
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Ruixi Li
- Institute for Integrative Genome Biology, Center for Plant Cell Biology & Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Tao Chen
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Huoming Zhang
- Bioscience Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Peng Cui
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Feng Ding
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Pei Liu
- Department of Biology, Hong Kong Baptist University, Hong Kong, P. R. China
| | - Guangchao Wang
- Bioscience Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Yiji Xia
- Department of Biology, Hong Kong Baptist University, Hong Kong, P. R. China
| | - Mark P Running
- Department of Biology, University of Louisville, Louisville, KY 40292, USA
| | - Liming Xiong
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
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Hariharan N, Sussman MA. Stressing on the nucleolus in cardiovascular disease. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1842:798-801. [PMID: 24514103 PMCID: PMC3972279 DOI: 10.1016/j.bbadis.2013.09.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 09/18/2013] [Indexed: 12/23/2022]
Abstract
The nucleolus is a multifunctional organelle with multiple roles involving cell proliferation, growth, survival, ribosome biogenesis and stress response signaling. Alteration of nucleolar morphology and architecture signifies an early response to increased cellular stress. This review briefly summarizes nucleolar response to cardiac stress signals and details the role played by nucleolar proteins in cardiovascular pathophysiology. This article is part of a Special Issue entitled: Role of the Nucleolus in Human Disease.
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Affiliation(s)
- Nirmala Hariharan
- Department of Biology, San Diego State University Heart Institute, San Diego State University, San Diego, CA 92182, USA
| | - Mark A Sussman
- Department of Biology, San Diego State University Heart Institute, San Diego State University, San Diego, CA 92182, USA.
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Heijnen HF, van Wijk R, Pereboom TC, Goos YJ, Seinen CW, van Oirschot BA, van Dooren R, Gastou M, Giles RH, van Solinge W, Kuijpers TW, Gazda HT, Bierings MB, Da Costa L, MacInnes AW. Ribosomal protein mutations induce autophagy through S6 kinase inhibition of the insulin pathway. PLoS Genet 2014; 10:e1004371. [PMID: 24875531 PMCID: PMC4038485 DOI: 10.1371/journal.pgen.1004371] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 03/24/2014] [Indexed: 12/19/2022] Open
Abstract
Mutations affecting the ribosome lead to several diseases known as ribosomopathies, with phenotypes that include growth defects, cytopenia, and bone marrow failure. Diamond-Blackfan anemia (DBA), for example, is a pure red cell aplasia linked to the mutation of ribosomal protein (RP) genes. Here we show the knock-down of the DBA-linked RPS19 gene induces the cellular self-digestion process of autophagy, a pathway critical for proper hematopoiesis. We also observe an increase of autophagy in cells derived from DBA patients, in CD34+ erythrocyte progenitor cells with RPS19 knock down, in the red blood cells of zebrafish embryos with RP-deficiency, and in cells from patients with Shwachman-Diamond syndrome (SDS). The loss of RPs in all these models results in a marked increase in S6 kinase phosphorylation that we find is triggered by an increase in reactive oxygen species (ROS). We show that this increase in S6 kinase phosphorylation inhibits the insulin pathway and AKT phosphorylation activity through a mechanism reminiscent of insulin resistance. While stimulating RP-deficient cells with insulin reduces autophagy, antioxidant treatment reduces S6 kinase phosphorylation, autophagy, and stabilization of the p53 tumor suppressor. Our data suggest that RP loss promotes the aberrant activation of both S6 kinase and p53 by increasing intracellular ROS levels. The deregulation of these signaling pathways is likely playing a major role in the pathophysiology of ribosomopathies. Diseases linked to mutations affecting the ribosome, ribosomopathies, have an exceptionally wide range of phenotypes. However, many ribosomopathies have some features in common including cytopenia and growth defects. Our study aims to clarify the mechanisms behind these common phenotypes. We find that mutations in ribosomal protein genes result in a series of aberrant signaling events that cause cells to start recycling and consuming their own intracellular contents. This basic mechanism of catabolism is activated when cells are starving for nutrients, and also during the tightly regulated process of blood cell maturation. The deregulation of this mechanism provides an explanation as to why blood cells are so acutely affected by mutations in genes that impair the ribosome. Moreover, we find that the signals activating this catabolism are coupled to impairment of the highly conserved insulin-signaling pathway that is essential for growth. Taken together, our in-depth description of the pathways involved as the result of mutations affecting the ribosome increases our understanding about the etiology of these diseases and opens up previously unknown avenues of potential treatment.
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Affiliation(s)
- Harry F. Heijnen
- Cell Microscopy Center, Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Richard van Wijk
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tamara C. Pereboom
- Hubrecht Institute, KNAW and University Medical Center Utrecht, The Netherlands
| | - Yvonne J. Goos
- Hubrecht Institute, KNAW and University Medical Center Utrecht, The Netherlands
| | - Cor W. Seinen
- Cell Microscopy Center, Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Brigitte A. van Oirschot
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rowie van Dooren
- Hubrecht Institute, KNAW and University Medical Center Utrecht, The Netherlands
| | - Marc Gastou
- U1009, Institut Gustave Roussy, Université Paris-Sud, Villejuif, France
| | - Rachel H. Giles
- Department of Nephrology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wouter van Solinge
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Taco W. Kuijpers
- Department of Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Academic Medical Center (AMC), Amsterdam, The Netherlands
| | - Hanna T. Gazda
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Marc B. Bierings
- Department of Pediatric Hematology/Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lydie Da Costa
- AP-HP, Service d'Hématologie Biologique, Hôpital Robert Debré, Paris, France
- Université Paris VII-Denis Diderot, Sorbonne Paris Cité, Paris, France
- U773, CRB3, Paris, France
| | - Alyson W. MacInnes
- Hubrecht Institute, KNAW and University Medical Center Utrecht, The Netherlands
- * E-mail:
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9
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Essers PB, Pereboom TC, Goos YJ, Paridaen JT, Macinnes AW. A comparative study of nucleostemin family members in zebrafish reveals specific roles in ribosome biogenesis. Dev Biol 2013; 385:304-15. [PMID: 24211311 DOI: 10.1016/j.ydbio.2013.10.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 10/24/2013] [Accepted: 10/28/2013] [Indexed: 01/05/2023]
Abstract
Nucleostemin (NS) is an essential protein for the growth and viability of developmental stem cells. Its functions are multi-faceted, including important roles in ribosome biogenesis and in the p53-induced apoptosis pathway. While NS has been well studied, the functions of its family members GNL2 and GNL3-like (GNL3L) remain relatively obscure despite a high degree of sequence and domain homology. Here, we use zebrafish lines carrying mutations in the ns family to compare and contrast their functions in vertebrates. We find the loss of zebrafish ns or gnl2 has a major impact on 60S large ribosomal subunit formation and/or function due to cleavage impairments at distinct sites of pre-rRNA transcript. In both cases this leads to a reduction of total protein synthesis. In contrast, gnl3l loss shows relatively minor rRNA processing delays that ultimately have no appreciable effects on ribosome biogenesis or protein synthesis. However, the loss of gnl3l still results in p53 stabilization, apoptosis, and lethality similarly to ns and gnl2 loss. The depletion of p53 in all three of the mutants led to partial rescues of the morphological phenotypes and surprisingly, a rescue of the 60S subunit collapse in the ns mutants. We show that this rescue is due to an unexpected effect of p53 loss that even in wild type embryos results in an increase of 60S subunits. Our study presents an in-depth description of the mechanisms through which ns and gnl2 function in vertebrate ribosome biogenesis and shows that despite the high degree of sequence and domain homology, gnl3l has critical functions in development that are unrelated to the ribosome.
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Affiliation(s)
- Paul B Essers
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands.
| | - Tamara C Pereboom
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands.
| | - Yvonne J Goos
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands.
| | - Judith T Paridaen
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307 Dresden, Germany.
| | - Alyson W Macinnes
- Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands.
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