1
|
Kalkan BM, Baykal AT, Cicek E, Acilan C. Comprehensive proteomics analysis reveals novel Nek2-regulated pathways and therapeutic targets in cancer. Biochem Biophys Res Commun 2024; 734:150779. [PMID: 39368370 DOI: 10.1016/j.bbrc.2024.150779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 09/23/2024] [Accepted: 09/30/2024] [Indexed: 10/07/2024]
Abstract
The mitotic kinase Nek2, often overexpressed in various cancers, plays a pivotal role in key cellular processes like the cell cycle, proliferation, and drug resistance. As a result, targeting Nek2 has become an appealing strategy for cancer therapy. To gain a comprehensive understanding of the cellular changes associated with Nek2 activity modulation, we performed a global proteomics analysis using LC-MS/MS. Through bioinformatics tools, we identified molecular pathways that are differentially regulated in cancer cells with Nek2 overexpression or depletion. Of the 1815 proteins identified, 358 exceeded the 20 % significance threshold. By integrating LC-MS/MS data with cancer patient datasets, we observed a strong correlation between Nek2 expression and the levels of KIF20B and RRM1. Silencing Nek2 led to a significant reduction in KIF20B and RRM1 protein levels, and potential phosphorylation sites for these proteins by Nek2 were identified. In summary, our data suggests that KIF20B and RRM1 are promising therapeutic targets, either independently or alongside Nek2 inhibitors, to improve clinical outcomes. Further analyses are necessary to fully understand Nek2's interactions with these proteins and their clinical relevance.
Collapse
Affiliation(s)
- Batuhan Mert Kalkan
- Koç University, Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey
| | - Ahmet Tarik Baykal
- Department of Medical Biochemistry, School of Medicine, Acibadem University, Istanbul, Turkey
| | - Enes Cicek
- Koç University, Graduate School of Health Sciences, Istanbul, Turkey
| | - Ceyda Acilan
- Koç University, Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey; Koç University, School of Medicine, Istanbul, Turkey.
| |
Collapse
|
2
|
Thorpe HJ, Partha R, Little J, Clark NL, Chow CY. Evolutionary rate covariation is pervasive between glycosylation pathways and points to potential disease modifiers. PLoS Genet 2024; 20:e1011406. [PMID: 39259723 PMCID: PMC11419382 DOI: 10.1371/journal.pgen.1011406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 09/23/2024] [Accepted: 08/27/2024] [Indexed: 09/13/2024] Open
Abstract
Mutations in glycosylation pathways, such as N-linked glycosylation, O-linked glycosylation, and GPI anchor synthesis, lead to Congenital Disorders of Glycosylation (CDG). CDG typically present with seizures, hypotonia, and developmental delay but display large clinical variability with symptoms affecting every system in the body. This variability suggests modifier genes might influence the phenotypes. Because of the similar physiology and clinical symptoms, there are likely common genetic modifiers between CDG. Here, we use evolution as a tool to identify common modifiers between CDG and glycosylation genes. Protein glycosylation is evolutionarily conserved from yeast to mammals. Evolutionary rate covariation (ERC) identifies proteins with similar evolutionary rates that indicate shared biological functions and pathways. Using ERC, we identified strong evolutionary rate signatures between proteins in the same and different glycosylation pathways. Genome-wide analysis of proteins showing significant ERC with GPI anchor synthesis proteins revealed strong signatures with ncRNA modification proteins and DNA repair proteins. We also identified strong patterns of ERC based on cellular sub-localization of the GPI anchor synthesis enzymes. Functional testing of the highest scoring candidates validated genetic interactions and identified novel genetic modifiers of CDG genes. ERC analysis of disease genes and biological pathways allows for rapid prioritization of potential genetic modifiers, which can provide a better understanding of disease pathophysiology and novel therapeutic targets.
Collapse
Affiliation(s)
- Holly J. Thorpe
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Raghavendran Partha
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jordan Little
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Nathan L. Clark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Clement Y. Chow
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| |
Collapse
|
3
|
Bryant CJ, McCool MA, Abriola L, Surovtseva YV, Baserga SJ. A high-throughput assay for directly monitoring nucleolar rRNA biogenesis. Open Biol 2022; 12:210305. [PMID: 35078352 PMCID: PMC8790372 DOI: 10.1098/rsob.210305] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Studies of the regulation of nucleolar function are critical for ascertaining clearer insights into the basic biological underpinnings of ribosome biogenesis (RB), and for future development of therapeutics to treat cancer and ribosomopathies. A number of high-throughput primary assays based on morphological alterations of the nucleolus can indirectly identify hits affecting RB. However, there is a need for a more direct high-throughput assay for a nucleolar function to further evaluate hits. Previous reports have monitored nucleolar rRNA biogenesis using 5-ethynyl uridine (5-EU) in low-throughput. We report a miniaturized, high-throughput 5-EU assay that enables specific calculation of nucleolar rRNA biogenesis inhibition, based on co-staining of the nucleolar protein fibrillarin (FBL). The assay uses two siRNA controls: a negative non-targeting siRNA control and a positive siRNA control targeting RNA Polymerase 1 (RNAP1; POLR1A), and specifically quantifies median 5-EU signal within nucleoli. Maximum nuclear 5-EU signal can also be used to monitor the effects of putative small-molecule inhibitors of RNAP1, like BMH-21, or other treatment conditions that cause FBL dispersion. We validate the 5-EU assay on 68 predominately nucleolar hits from a high-throughput primary screen, showing that 58/68 hits significantly inhibit nucleolar rRNA biogenesis. Our new method establishes direct quantification of nucleolar function in high-throughput, facilitating closer study of RB in health and disease.
Collapse
Affiliation(s)
- Carson J. Bryant
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, 333 Cedar Street, New Haven, CT, USA
| | - Mason A. McCool
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, 333 Cedar Street, New Haven, CT, USA
| | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, USA
| | | | - Susan J. Baserga
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, 333 Cedar Street, New Haven, CT, USA,Department of Genetics, Yale School of Medicine, New Haven, CT, USA,Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
| |
Collapse
|
4
|
Ev LD, Damé-Teixeira N, DO T, Maltz M, Parolo CCF. The role of Candida albicans in root caries biofilms: an RNA-seq analysis. J Appl Oral Sci 2020; 28:e20190578. [PMID: 32348446 PMCID: PMC7185980 DOI: 10.1590/1678-7757-2019-0578] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/19/2020] [Indexed: 11/30/2022] Open
Abstract
Objective This study sought to analyze the gene expression of Candida albicans in sound root surface and root caries lesions, exploring its role in root caries pathogenesis. Methodology The differential gene expression of C. albicans and the specific genes related to cariogenic traits were studied in association with samples of biofilm collected from exposed sound root surface (SRS, n=10) and from biofilm and carious dentin of active root carious lesions (RC, n=9). The total microbial RNA was extracted, and the cDNA libraries were prepared and sequenced on the Illumina Hi-Seq2500. Unique reads were mapped to 163 oral microbial reference genomes including two chromosomes of C. albicans SC5314 (14,217 genes). The putative presence of C. albicans was estimated (sum of reads/total number of genes≥1) in each sample. Count data were normalized (using the DESeq method package) to analyze differential gene expression (using the DESeq2R package) applying the Benjamini-Hochberg correction (FDR<0.05). Results Two genes (CaO19.610, FDR=0.009; CaO19.2506, FDR=0.018) were up-regulated on SRS, and their functions are related to biofilm formation. Seven genes ( UTP20 , FDR=0.018; ITR1 , FDR=0.036; DHN6 , FDR=0.046; CaO19.7197 , FDR=0.046; CaO19.7838 , FDR=0.046; STT4 , FDR=0.046; GUT1 , FDR=0.046) were up-regulated on RC and their functions are related to metabolic activity, sugar transport, stress tolerance, invasion and pH regulation. The use of alternative carbon sources, including lactate, and the ability to form hypha may be a unique trait of C. albicans influencing biofilm virulence. Conclusions C. albicans is metabolically active in SRS and RC biofilm, with different roles in health and disease.
Collapse
Affiliation(s)
- Laís Daniela Ev
- Departamento de Odontologia Preventiva e Social, Faculdade de Odontologia, Universidade de Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - Nailê Damé-Teixeira
- Departamento de Odontologia, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília, Distrito Federal, Brasil
| | - Thuy DO
- School of Dentistry, Faculty of Medicine & Health, University of Leeds, Leeds, United Kingdom
| | - Marisa Maltz
- Departamento de Odontologia Preventiva e Social, Faculdade de Odontologia, Universidade de Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - Clarissa Cavalcanti Fatturi Parolo
- Departamento de Odontologia Preventiva e Social, Faculdade de Odontologia, Universidade de Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| |
Collapse
|
5
|
Kleinman CL, Doria M, Orecchini E, Giuliani E, Galardi S, De Jay N, Michienzi A. HIV-1 infection causes a down-regulation of genes involved in ribosome biogenesis. PLoS One 2014; 9:e113908. [PMID: 25462981 PMCID: PMC4252078 DOI: 10.1371/journal.pone.0113908] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 10/28/2014] [Indexed: 01/04/2023] Open
Abstract
HIV-1 preferentially infects CD4+ T cells, causing fundamental changes that eventually lead to the release of new viral particles and cell death. To investigate in detail alterations in the transcriptome of the CD4+ T cells upon viral infection, we sequenced polyadenylated RNA isolated from Jurkat cells infected or not with HIV-1. We found a marked global alteration of gene expression following infection, with an overall trend toward induction of genes, indicating widespread modification of the host biology. Annotation and pathway analysis of the most deregulated genes showed that viral infection produces a down-regulation of genes associated with the nucleolus, in particular those implicated in regulating the different steps of ribosome biogenesis, such as ribosomal RNA (rRNA) transcription, pre-rRNA processing, and ribosome maturation. The impact of HIV-1 infection on genes involved in ribosome biogenesis was further validated in primary CD4+ T cells. Moreover, we provided evidence by Northern Blot experiments, that host pre-rRNA processing in Jurkat cells might be perturbed during HIV-1 infection, thus strengthening the hypothesis of a crosstalk between nucleolar functions and viral pathogenesis.
Collapse
Affiliation(s)
- Claudia L. Kleinman
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital and Department of Human Genetics, McGill University, 3755 Côte Ste-Catherine Road, Montréal, Quebec, H3T 1E2, Canada
| | - Margherita Doria
- Laboratory of Immunoinfectivology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Elisa Orecchini
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Rome, Italy
| | - Erica Giuliani
- Laboratory of Immunoinfectivology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Silvia Galardi
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Rome, Italy
| | - Nicolas De Jay
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital and Department of Human Genetics, McGill University, 3755 Côte Ste-Catherine Road, Montréal, Quebec, H3T 1E2, Canada
| | - Alessandro Michienzi
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Rome, Italy
- * E-mail:
| |
Collapse
|
6
|
Kapoor M, Wang JC, Wetherill L, Le N, Bertelsen S, Hinrichs AL, Budde J, Agrawal A, Almasy L, Bucholz K, Dick DM, Harari O, Xiaoling X, Hesselbrock V, Kramer J, Nurnberger JI, Rice J, Schuckit M, Tischfield J, Porjesz B, Edenberg HJ, Bierut L, Foroud T, Goate A. Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families. Drug Alcohol Depend 2014; 142:56-62. [PMID: 24962325 PMCID: PMC4127128 DOI: 10.1016/j.drugalcdep.2014.05.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/24/2014] [Accepted: 05/29/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND The age at onset of alcohol dependence (AD) is a critical moderator of genetic associations for alcohol dependence. The present study evaluated whether single nucleotide polymorphisms (SNPs) can influence the age at onset of AD in large high-risk families from the Collaborative Study on the Genetics of Alcoholism (COGA). METHODS Genomewide SNP genotyping was performed in 1788 regular drinkers from 118 large European American families densely affected with alcoholism. We used a genome-wide Cox proportional hazards regression model to test for association between age at onset of AD and SNPs. RESULTS This family-based analysis identified an intergenic SNP, rs2168784 on chromosome 3 that showed strong evidence of association (P=5×10(-9)) with age at onset of AD among regular drinkers. Carriers of the minor allele of rs2168784 had 1.5 times the hazard of AD onset as compared with those homozygous for the major allele. By the age of 20 years, nearly 30% of subjects homozygous for the minor allele were alcohol dependent while only 19% of those homozygous for the major allele were. We also identified intronic SNPs in the ADP-ribosylation factor like 15 (ARL15) gene on chromosome 5 (P=1.11×10(-8)) and the UTP20 small subunit (UTP20) gene on chromosome 12 (P=4.32×10(-8)) that were associated with age at onset of AD. CONCLUSIONS This extended family based genome-wide cox-proportional hazards analysis identified several loci that might be associated with age at onset of AD.
Collapse
Affiliation(s)
- Manav Kapoor
- Washington University School of Medicine, United States
| | | | | | - Nhung Le
- Washington University School of Medicine, United States
| | | | | | - John Budde
- Washington University School of Medicine, United States
| | | | - Laura Almasy
- Southwest Foundation for Biomedical Research, United States
| | | | | | - Oscar Harari
- Washington University School of Medicine, United States
| | - Xuei Xiaoling
- Indiana University School of Medicine, United States
| | | | - John Kramer
- University of Iowa Carver College of Medicine, United States
| | | | - John Rice
- Washington University School of Medicine, United States
| | | | | | | | | | - Laura Bierut
- Washington University School of Medicine, United States
| | | | - Alison Goate
- Washington University School of Medicine, United States.
| |
Collapse
|
7
|
Mistry R, Babu GR, Mahapatra T, McCarthy WJ. Cognitive mediators and disparities in the relation between teen depressiveness and smoking. Drug Alcohol Depend 2014; 140:56-62. [PMID: 24768409 DOI: 10.1016/j.drugalcdep.2014.03.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 02/04/2014] [Accepted: 03/18/2014] [Indexed: 01/15/2023]
Abstract
BACKGROUND Depressiveness and tobacco use in adolescents are linked, however, there is limited evidence about the cognitive mediators involved and how the role of mediators may differ by gender and racial/ethnic subgroups. METHODS We used a racially/ethnically diverse population-based cross-sectional sample of middle and high school students (n=24,350). Logistic regression models measured the associations of depressiveness with tobacco smoking status, and whether smoking-related knowledge and attitudes (KA) and smoking refusal self-efficacy (SE) attenuated the associations indicating preliminary evidence of mediation. RESULTS Depressiveness was associated with intention to smoke (OR=2.41; 95% CI=2.22, 2.61), experimental smoking (OR=1.93; 95% CI=1.72, 2.17) and established smoking (OR=1.85; 95% CI=1.57, 2.18). The percent attenuation of these associations due to the inclusion of smoking-related KA and smoking refusal SE was 58% for intention to smoke (p<0.001), 68% for experimental smoking (p<0.001) and 86% for established smoking (p<0.001). The association of depressiveness with established smoking did not remain statistically significant (OR=1.16; CI=0.97, 1.40) after including smoking-related KA and smoking refusal SE. Attenuation was more pronounced in males and white students. CONCLUSIONS The results suggest that smoking-related KA and smoking refusal SE attenuated the relation between depressiveness and smoking, indicating that they may serve as mediators of the link between depressiveness and smoking. Tobacco use prevention programs targeting teens with the aim of increasing anti-smoking KA and smoking refusal SE may benefit from addressing depressiveness, particularly by using gender and racially/ethnically tailored strategies. The cross-sectional nature of the data precludes causal inferences.
Collapse
Affiliation(s)
- Ritesh Mistry
- Center for Cancer Prevention and Control Research, University of California, Los Angeles, United States; Department of Health Behavior and Health Education, University of Michigan, United States.
| | - Giridhara R Babu
- Department of Epidemiology, University of California, Los Angeles, United States; Indian Institute of Public Health-Hyderabad (Bangalore Wing), Public Health Foundation of India, India
| | - Tanmay Mahapatra
- Department of Epidemiology, University of California, Los Angeles, United States
| | - William J McCarthy
- Center for Cancer Prevention and Control Research, University of California, Los Angeles, United States
| |
Collapse
|
8
|
Venticinque L, Meruelo D. Comprehensive proteomic analysis of nonintegrin laminin receptor interacting proteins. J Proteome Res 2012; 11:4863-72. [PMID: 22909348 PMCID: PMC3495180 DOI: 10.1021/pr300307h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Human nonintegrin laminin receptor is a multifunctional protein acting as an integral component of the ribosome and a cell surface receptor for laminin-1. The laminin receptor is overexpressed in several human cancers and is also the cell surface receptor for several viruses and pathogenic prion proteins, making it a pathologically significant protein. This study focused on the proteomic characterization of laminin receptor interacting proteins from Mus musculus. The use of affinity chromatography with immobilized recombinant laminin receptor coupled with mass spectrometry analysis identified 45 proteins with high confidence. Following validation through coimmunoprecipitation, the proteins were classified based on predicted function into ribosomal, RNA processing, signal transduction/metabolism, protein processing, cytoskeleton/cell anchorage, DNA/chromatin, and unknown functions. A significant portion of the identified proteins is related to functions or localizations previously described for laminin receptor. This work represents a comprehensive proteomic approach to studying laminin receptor and provides an essential stepping stone to a better mechanistic understanding of this protein's diverse functions.
Collapse
Affiliation(s)
- Lisa Venticinque
- Gene Therapy Center, Cancer Institute and Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016
| | - Daniel Meruelo
- Gene Therapy Center, Cancer Institute and Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016
| |
Collapse
|
9
|
Bonnart C, Gérus M, Hoareau-Aveilla C, Kiss T, Caizergues-Ferrer M, Henry Y, Henras AK. Mammalian HCA66 protein is required for both ribosome synthesis and centriole duplication. Nucleic Acids Res 2012; 40:6270-89. [PMID: 22434888 PMCID: PMC3401428 DOI: 10.1093/nar/gks234] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ribosome production, one of the most energy-consuming biosynthetic activities in living cells, is adjusted to growth conditions and coordinated with the cell cycle. Connections between ribosome synthesis and cell cycle progression have been described, but the underlying mechanisms remain only partially understood. The human HCA66 protein was recently characterized as a component of the centrosome, the major microtubule-organizing center (MTOC) in mammalian cells, and was shown to be required for centriole duplication and assembly of the mitotic spindle. We show here that HCA66 is also required for nucleolar steps of the maturation of the 40S ribosomal subunit and therefore displays a dual function. Overexpression of a dominant negative version of HCA66, accumulating at the centrosome but absent from the nucleoli, alters centrosome function but has no effect on pre-rRNA processing, suggesting that HCA66 acts independently in each process. In yeast and HeLa cells, depletion of MTOC components does not impair ribosome synthesis. Hence our results suggest that both in yeast and human cells, assembly of a functional MTOC and ribosome synthesis are not closely connected processes.
Collapse
Affiliation(s)
- Chrystelle Bonnart
- Centre National de la Recherche Scientifique, Laboratoire de Biologie Moléculaire Eucaryote, Toulouse, France
| | | | | | | | | | | | | |
Collapse
|
10
|
Wu J, Zhang Y, Wang Y, Kong R, Hu L, Schuele R, Du X, Ke Y. Transcriptional repressor NIR functions in the ribosome RNA processing of both 40S and 60S subunits. PLoS One 2012; 7:e31692. [PMID: 22363708 PMCID: PMC3282729 DOI: 10.1371/journal.pone.0031692] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 01/17/2012] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND NIR was identified as an inhibitor of histone acetyltransferase and it represses transcriptional activation of p53. NIR is predominantly localized in the nucleolus and known as Noc2p, which is involved in the maturation of the 60S ribosomal subunit. However, how NIR functions in the nucleolus remains undetermined. In the nucleolus, a 47S ribosomal RNA precursor (pre-rRNA) is transcribed and processed to produce 18S, 5.8S and 28S rRNAs. The 18S rRNA is incorporated into the 40S ribosomal subunit, whereas the 28S and 5.8S rRNAs are incorporated into the 60S subunit. U3 small nucleolar RNA (snoRNA) directs 18S rRNA processing and U8 snoRNA mediates processing of 28S and 5.8 S rRNAs. Functional disruption of nucleolus often causes p53 activation to inhibit cell proliferation. METHODOLOGY/PRINCIPAL FINDINGS Western blotting showed that NIR is ubiquitously expressed in different human cell lines. Knock-down of NIR by siRNA led to inhibition of the 18S, 28S and 5.8S rRNAs evaluated by pulse-chase experiment. Pre-rRNA particles (pre-rRNPs) were fractionated from the nucleus by sucrose gradient centrifugation and analysis of the pre-RNPs components showed that NIR existed in the pre-RNPs of both the 60S and 40S subunits and co-fractionated with 32S and 12S pre-rRNAs in the 60S pre-rRNP. Protein-RNA binding experiments demonstrated that NIR is associated with the 32S pre-rRNA and U8 snoRNA. In addition, NIR bound U3 snoRNA. It is a novel finding that depletion of NIR did not affect p53 protein level but de-repressed acetylation of p53 and activated p21. CONCLUSIONS We provide the first evidence for a transcriptional repressor to function in the rRNA biogenesis of both the 40S and 60S subunits. Our findings also suggested that a nucleolar protein may alternatively signal to p53 by affecting the p53 modification rather than affecting p53 protein level.
Collapse
Affiliation(s)
- Jianguo Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing, China
| | - Ying Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing, China
| | - Yingshuang Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing, China
| | - Ruirui Kong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing, China
| | - Lelin Hu
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Roland Schuele
- Medical Research Center, Freiburg University, Freiburg, Germany
| | - Xiaojuan Du
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yang Ke
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing, China
| |
Collapse
|
11
|
Belhouchet M, Mohd Jaafar F, Firth AE, Grimes JM, Mertens PPC, Attoui H. Detection of a fourth orbivirus non-structural protein. PLoS One 2011; 6:e25697. [PMID: 22022432 PMCID: PMC3192121 DOI: 10.1371/journal.pone.0025697] [Citation(s) in RCA: 162] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 09/08/2011] [Indexed: 12/22/2022] Open
Abstract
The genus Orbivirus includes both insect and tick-borne viruses. The orbivirus genome, composed of 10 segments of dsRNA, encodes 7 structural proteins (VP1–VP7) and 3 non-structural proteins (NS1–NS3). An open reading frame (ORF) that spans almost the entire length of genome segment-9 (Seg-9) encodes VP6 (the viral helicase). However, bioinformatic analysis recently identified an overlapping ORF (ORFX) in Seg-9. We show that ORFX encodes a new non-structural protein, identified here as NS4. Western blotting and confocal fluorescence microscopy, using antibodies raised against recombinant NS4 from Bluetongue virus (BTV, which is insect-borne), or Great Island virus (GIV, which is tick-borne), demonstrate that these proteins are synthesised in BTV or GIV infected mammalian cells, respectively. BTV NS4 is also expressed in Culicoides insect cells. NS4 forms aggregates throughout the cytoplasm as well as in the nucleus, consistent with identification of nuclear localisation signals within the NS4 sequence. Bioinformatic analyses indicate that NS4 contains coiled-coils, is related to proteins that bind nucleic acids, or are associated with membranes and shows similarities to nucleolar protein UTP20 (a processome subunit). Recombinant NS4 of GIV protects dsRNA from degradation by endoribonucleases of the RNAse III family, indicating that it interacts with dsRNA. However, BTV NS4, which is only half the putative size of the GIV NS4, did not protect dsRNA from RNAse III cleavage. NS4 of both GIV and BTV protect DNA from degradation by DNAse. NS4 was found to associate with lipid droplets in cells infected with BTV or GIV or transfected with a plasmid expressing NS4.
Collapse
Affiliation(s)
- Mourad Belhouchet
- Vector-Borne Viral Diseases Programme, Institute for Animal Health, Pirbright, United Kingdom
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, Oxford, United Kingdom
| | - Fauziah Mohd Jaafar
- Vector-Borne Viral Diseases Programme, Institute for Animal Health, Pirbright, United Kingdom
| | - Andrew E. Firth
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan M. Grimes
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, Oxford, United Kingdom
| | - Peter P. C. Mertens
- Vector-Borne Viral Diseases Programme, Institute for Animal Health, Pirbright, United Kingdom
| | - Houssam Attoui
- Vector-Borne Viral Diseases Programme, Institute for Animal Health, Pirbright, United Kingdom
- * E-mail:
| |
Collapse
|
12
|
Koiwai K, Noma S, Takahashi Y, Hayano T, Maezawa S, Kouda K, Matsumoto T, Suzuki M, Furuichi M, Koiwai O. TdIF2 is a nucleolar protein that promotes rRNA gene promoter activity. Genes Cells 2011; 16:748-64. [PMID: 21668587 DOI: 10.1111/j.1365-2443.2011.01524.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Terminal deoxynucleotidyltransferase (TdT) interacting factor 2 (TdIF2) is an acidic protein that binds to TdT. TdIF2 binds to DNA and core histones and contains an acidic-amino acid-rich region in its C-terminus. It has therefore been suggested to function as a histone chaperone within the nucleus. TdIF2 localized within the nucleolus in HEK 293T cells, and its N-terminal (residues 1-234) and C-terminal (residues 606-756) regions were crucial for the nucleolar localization. A chromatin immunoprecipitation (ChIP) assay showed that TdIF2 associated with the promoter of human ribosomal RNA genes (hrDNAP), and an in vitro luciferase assay system showed that it promoted hrDNAP activity. Using the yeast two-hybrid system with TdIF2 as the bait, we isolated the cDNA encoding HIV Tat interactive protein 60 (Tip60), which has histone acetyltransferase (HAT) activity, as a TdIF2-binding protein. TdIF2 bound to Tip60 in vitro and in vivo, inhibited the Tip60 HAT activity in vitro and co-localized with Tip60 within the nucleolus. In addition, TdIF2 promotes upstream binding factor (UBF) acetylation in vivo. Thus, TdIF2 might promote hrDNAP activity by suppressing Tip60's HAT activity and promoting UBF acetylation.
Collapse
Affiliation(s)
- Kotaro Koiwai
- Department of Applied Biological Science, Tokyo University of Science, Noda, Chiba, Japan.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Kong R, Zhang L, Hu L, Peng Q, Han W, Du X, Ke Y. hALP, a novel transcriptional U three protein (t-UTP), activates RNA polymerase I transcription by binding and acetylating the upstream binding factor (UBF). J Biol Chem 2010; 286:7139-48. [PMID: 21177859 PMCID: PMC3044971 DOI: 10.1074/jbc.m110.173393] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Transcription of ribosome RNA precursor (pre-rRNA) and pre-rRNA processing are coordinated by a subset of U three proteins (UTPs) known as transcriptional UTPs (t-UTPs), which participate in pre-rRNA transcription in addition to participation in 18 S rRNA processing. However, the mechanism by which t-UTPs function in pre-rRNA transcription remains undetermined. In the present study, we identified hALP, a histone acetyl-transferase as a novel t-UTP. We first showed that hALP is nucleolar, and is associated with U3 snoRNA and required for 18 S rRNA processing. Moreover, depletion of hALP resulted in a decreased level of 47 S pre-rRNA. Ectopic expression of hALP activated the rDNA promoter luciferase reporter and knockdown of hALP inhibited the reporter. In addition, hALP bound rDNA. Taken together these data identify hALP as a novel t-UTP. Immunoprecipitation and GST pulldown experiments showed that hALP binds the upstream binding factor (UBF) in vivo and in vitro. It is of importance that hALP acetylated UBF depending on HAT in vivo, and hALP but not hALP (ΔHAT) facilitated the nuclear translocation of the RNA polymerase I (Pol I)-associated factor 53 (PAF53) from the cytoplasm and promoted the association of UBF with PAF53. Thus, we provide a mechanism in which a novel t-UTP activates Pol I transcription by binding and acetylating UBF.
Collapse
Affiliation(s)
- Ruirui Kong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing 100142, China
| | | | | | | | | | | | | |
Collapse
|
14
|
Peng Q, Wu J, Zhang Y, Liu Y, Kong R, Hu L, Du X, Ke Y. 1A6/DRIM, a novel t-UTP, activates RNA polymerase I transcription and promotes cell proliferation. PLoS One 2010; 5:e14244. [PMID: 21151873 PMCID: PMC2998426 DOI: 10.1371/journal.pone.0014244] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 11/18/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Ribosome biogenesis is required for protein synthesis and cell proliferation. Ribosome subunits are assembled in the nucleolus following transcription of a 47S ribosome RNA precursor by RNA polymerase I and rRNA processing to produce mature 18S, 28S and 5.8S rRNAs. The 18S rRNA is incorporated into the ribosomal small subunit, whereas the 28S and 5.8S rRNAs are incorporated into the ribosomal large subunit. Pol I transcription and rRNA processing are coordinated processes and this coordination has been demonstrated to be mediated by a subset of U3 proteins known as t-UTPs. Up to date, five t-UTPs have been identified in humans but the mechanism(s) that function in the t-UTP(s) activation of Pol I remain unknown. In this study we have identified 1A6/DRIM, which was identified as UTP20 in our previous study, as a t-UTP. In the present study, we investigated the function and mechanism of 1A6/DRIM in Pol I transcription. METHODOLOGY/PRINCIPAL FINDINGS Knockdown of 1A6/DRIM by siRNA resulted in a decreased 47S pre-rRNA level as determined by Northern blotting. Ectopic expression of 1A6/DRIM activated and knockdown of 1A6/DRIM inhibited the human rDNA promoter as evaluated with luciferase reporter. Chromatin immunoprecipitation (ChIP) experiments showed that 1A6/DRIM bound UBF and the rDNA promoter. Re-ChIP assay showed that 1A6/DRIM interacts with UBF at the rDNA promoter. Immunoprecipitation confirmed the interaction between 1A6/DRIM and the nucleolar acetyl-transferase hALP. It is of note that knockdown of 1A6/DRIM dramatically inhibited UBF acetylation. A finding of significance was that 1A6/DRIM depletion, as a kind of nucleolar stress, caused an increase in p53 level and inhibited cell proliferation by arresting cells at G1. CONCLUSIONS We identify 1A6/DRIM as a novel t-UTP. Our results suggest that 1A6/DRIM activates Pol I transcription most likely by associating with both hALP and UBF and thereby affecting the acetylation of UBF.
Collapse
MESH Headings
- Cell Line, Tumor
- Cell Proliferation
- DNA, Ribosomal/genetics
- Genes, p53
- Glucuronosyltransferase/genetics
- Humans
- Models, Genetic
- Promoter Regions, Genetic
- RNA Interference
- RNA Polymerase I/genetics
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 28S/genetics
- RNA, Ribosomal, 5.8S/genetics
- Transcription, Genetic
- Tumor Suppressor Protein p53/metabolism
Collapse
Affiliation(s)
- Qunhui Peng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing, China
- Cancer Research Center, Peking University Health Science Center, Beijing, China
| | - Jianguo Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing, China
- Cancer Research Center, Peking University Health Science Center, Beijing, China
| | - Ying Zhang
- Department of Cell Biology, Peking University Health Science Center, Beijing, China
- Cancer Research Center, Peking University Health Science Center, Beijing, China
| | - Yun Liu
- Department of Cell Biology, Peking University Health Science Center, Beijing, China
- Cancer Research Center, Peking University Health Science Center, Beijing, China
| | - Ruirui Kong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing, China
- Cancer Research Center, Peking University Health Science Center, Beijing, China
| | - Lelin Hu
- Department of Cell Biology, Peking University Health Science Center, Beijing, China
- Cancer Research Center, Peking University Health Science Center, Beijing, China
| | - Xiaojuan Du
- Department of Cell Biology, Peking University Health Science Center, Beijing, China
- Cancer Research Center, Peking University Health Science Center, Beijing, China
| | - Yang Ke
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing, China
- Cancer Research Center, Peking University Health Science Center, Beijing, China
| |
Collapse
|
15
|
Hu L, Wang J, Liu Y, Zhang Y, Zhang L, Kong R, Zheng Z, Du X, Ke Y. A small ribosomal subunit (SSU) processome component, the human U3 protein 14A (hUTP14A) binds p53 and promotes p53 degradation. J Biol Chem 2010; 286:3119-28. [PMID: 21078665 PMCID: PMC3024804 DOI: 10.1074/jbc.m110.157842] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ribosome biogenesis is required for normal cell function, and aberrant ribosome biogenesis can lead to p53 activation. However, how p53 is activated by defects of ribosome biogenesis remains to be determined. Here, we identified human UTP14a as an SSU processome component by showing that hUTP14a is nucleolar, associated with U3 snoRNA and involved in 18 S rRNA processing. Interestingly, ectopic expression of hUTP14a resulted in a decrease and knockdown of hUTP14a led to an increase of p53 protein levels. We showed that hUTP14a physically interacts with p53 and functionally promotes p53 turn-over, and that hUTP14a promotion of p53 destabilization is sensitive to a proteasome inhibitor but independent of ubiquitination. Significantly, knockdown of hUTP14a led to cell cycle arrest and apoptosis. Our data identified a novel pathway for p53 activation through a defect in rRNA processing and suggest that a ribosome biogenesis factor itself could act as a sensor for nucleolar stress to regulate p53.
Collapse
Affiliation(s)
- Lelin Hu
- Department of Cell Biology, Peking University Health Science Center, Beijing 100191, China
| | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Wild T, Horvath P, Wyler E, Widmann B, Badertscher L, Zemp I, Kozak K, Csucs G, Lund E, Kutay U. A protein inventory of human ribosome biogenesis reveals an essential function of exportin 5 in 60S subunit export. PLoS Biol 2010; 8:e1000522. [PMID: 21048991 PMCID: PMC2964341 DOI: 10.1371/journal.pbio.1000522] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 09/03/2010] [Indexed: 12/20/2022] Open
Abstract
The assembly of ribosomal subunits in eukaryotes is a complex, multistep process so far mostly studied in yeast. In S. cerevisiae, more than 200 factors including ribosomal proteins and trans-acting factors are required for the ordered assembly of 40S and 60S ribosomal subunits. To date, only few human homologs of these yeast ribosome synthesis factors have been characterized. Here, we used a systematic RNA interference (RNAi) approach to analyze the contribution of 464 candidate factors to ribosomal subunit biogenesis in human cells. The screen was based on visual readouts, using inducible, fluorescent ribosomal proteins as reporters. By performing computer-based image analysis utilizing supervised machine-learning techniques, we obtained evidence for a functional link of 153 human proteins to ribosome synthesis. Our data show that core features of ribosome assembly are conserved from yeast to human, but differences exist for instance with respect to 60S subunit export. Unexpectedly, our RNAi screen uncovered a requirement for the export receptor Exportin 5 (Exp5) in nuclear export of 60S subunits in human cells. We show that Exp5, like the known 60S exportin Crm1, binds to pre-60S particles in a RanGTP-dependent manner. Interference with either Exp5 or Crm1 function blocks 60S export in both human cells and frog oocytes, whereas 40S export is compromised only upon inhibition of Crm1. Thus, 60S subunit export is dependent on at least two RanGTP-binding exportins in vertebrate cells.
Collapse
Affiliation(s)
- Thomas Wild
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- Molecular Life Science Ph.D. Program, Zurich, Switzerland
| | - Peter Horvath
- Light Microscopy Center, RISC, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Emanuel Wyler
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- Molecular Life Science Ph.D. Program, Zurich, Switzerland
| | - Barbara Widmann
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- Molecular Life Science Ph.D. Program, Zurich, Switzerland
| | - Lukas Badertscher
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- Molecular Life Science Ph.D. Program, Zurich, Switzerland
| | - Ivo Zemp
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Karol Kozak
- Light Microscopy Center, RISC, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Gabor Csucs
- Light Microscopy Center, RISC, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Elsebet Lund
- University of Wisconsin, Madison, Wisconsin, United States of America
| | - Ulrike Kutay
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- * E-mail:
| |
Collapse
|
17
|
Kong R, Han W, Ulrich HW, Ning T, Du X, Ke Y. 1A6/DRIM, the human UTP20 functions in 28S and 5.8S rRNA processing. CHINESE SCIENCE BULLETIN-CHINESE 2010. [DOI: 10.1007/s11434-010-3166-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
18
|
Evolutionarily conserved function of RRP36 in early cleavages of the pre-rRNA and production of the 40S ribosomal subunit. Mol Cell Biol 2009; 30:1130-44. [PMID: 20038530 DOI: 10.1128/mcb.00999-09] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ribosome biogenesis in eukaryotes is a major cellular activity mobilizing the products of over 200 transcriptionally coregulated genes referred to as the rRNA and ribosome biosynthesis regulon. We investigated the function of an essential, uncharacterized gene of this regulon, renamed RRP36. We show that the Rrp36p protein is nucleolar and interacts with 90S and pre-40S preribosomal particles. Its depletion affects early cleavages of the 35S pre-rRNA and results in a rapid decrease in mature 18S rRNA levels. Rrp36p is a novel component of the 90S preribosome, the assembly of which has been suggested to result from the stepwise incorporation of several modules, including the tUTP/UTP-A, PWP2/UTP-B, and UTP-C subcomplexes. We show that Rrp36p depletion does not impair the incorporation of these subcomplexes and the U3 small nucleolar RNP into preribosomes. In contrast, depletion of components of the UTP-A or UTP-B modules, but not Rrp5p, prevents Rrp36p recruitment and reduces its accumulation levels. In parallel, we studied the human orthologue of Rrp36p in HeLa cells, and we show that the function of this protein in early cleavages of the pre-rRNA has been conserved through evolution in eukaryotes.
Collapse
|