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Kołacz K, Robaszkiewicz A. PARP1 at the crossroad of cellular senescence and nucleolar processes. Ageing Res Rev 2024; 94:102206. [PMID: 38278370 DOI: 10.1016/j.arr.2024.102206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Senescent cells that occur in response to telomere shortening, oncogenes, extracellular and intracellular stress factors are characterized by permanent cell cycle arrest, the morphological and structural changes of the cell that include the senescence-associated secretory phenotype (SASP) and nucleoli rearrangement. The associated DNA lesions induce DNA damage response (DDR), which activates the DNA repair protein - poly-ADP-ribose polymerase 1 (PARP1). This protein consumes NAD+ to synthesize ADP-ribose polymer (PAR) on its own protein chain and on other interacting proteins. The involvement of PARP1 in nucleoli processes, such as rRNA transcription and ribosome biogenesis, the maintenance of heterochromatin and nucleoli structure, as well as controlling the crucial DDR protein release from the nucleoli to nucleus, links PARP1 with cellular senescence and nucleoli functioning. In this review we describe and discuss the impact of PARP1-mediated ADP-ribosylation on early cell commitment to senescence with the possible role of senescence-induced PARP1 transcriptional repression and protein degradation on nucleoli structure and function. The cause-effect interplay between PARP1 activation/decline and nucleoli functioning during senescence needs to be studied in detail.
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Affiliation(s)
- Kinga Kołacz
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, University of Lodz, Banacha 12 /16, 90-237 Lodz, Poland.
| | - Agnieszka Robaszkiewicz
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research (IFBR), 600 5th Street South, St. Petersburgh, FL 33701, USA.
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2
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Lagunas-Rangel FA. The nucleolus of Giardia and its ribosomal biogenesis. Parasitol Res 2023; 122:1961-1971. [PMID: 37400534 DOI: 10.1007/s00436-023-07915-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/26/2023] [Indexed: 07/05/2023]
Abstract
Giardia duodenalis is a protozoan intestinal parasite that causes a significant number of infections worldwide each year, particularly in low-income and developing countries. Despite the availability of treatments for this parasitic infection, treatment failures are alarmingly common. As a result, new therapeutic strategies are urgently needed to effectively combat this disease. On the other hand, within the eukaryotic nucleus, the nucleolus stands out as the most prominent structure. It plays a crucial role in coordinating ribosome biogenesis and is involved in vital processes such as maintaining genome stability, regulating cell cycle progression, controlling cell senescence, and responding to stress. Given its significance, the nucleolus presents itself as a valuable target for selectively inducing cell death in undesirable cells, making it a potential avenue for anti-Giardia treatments. Despite its potential importance, the Giardia nucleolus remains poorly studied and often overlooked. In light of this, the objective of this study is to provide a detailed molecular description of the structure and function of the Giardia nucleolus, with a primary focus on its involvement in ribosomal biogenesis. Likewise, it discusses the targeting of the Giardia nucleolus as a therapeutic strategy, its feasibility, and the challenges involved.
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Affiliation(s)
- Francisco Alejandro Lagunas-Rangel
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Gustavo A. Madero, 07360, Mexico City, Mexico.
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3
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Cao X, Khitun A, Harold CM, Bryant CJ, Zheng SJ, Baserga SJ, Slavoff SA. Nascent alt-protein chemoproteomics reveals a pre-60S assembly checkpoint inhibitor. Nat Chem Biol 2022; 18:643-651. [PMID: 35393574 PMCID: PMC9423127 DOI: 10.1038/s41589-022-01003-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/25/2022] [Indexed: 12/29/2022]
Abstract
Many unannotated microproteins and alternative proteins (alt-proteins) are coencoded with canonical proteins, but few of their functions are known. Motivated by the hypothesis that alt-proteins undergoing regulated synthesis could play important cellular roles, we developed a chemoproteomic pipeline to identify nascent alt-proteins in human cells. We identified 22 actively translated alt-proteins or N-terminal extensions, one of which is post-transcriptionally upregulated by DNA damage stress. We further defined a nucleolar, cell-cycle-regulated alt-protein that negatively regulates assembly of the pre-60S ribosomal subunit (MINAS-60). Depletion of MINAS-60 increases the amount of cytoplasmic 60S ribosomal subunit, upregulating global protein synthesis and cell proliferation. Mechanistically, MINAS-60 represses the rate of late-stage pre-60S assembly and export to the cytoplasm. Together, these results implicate MINAS-60 as a potential checkpoint inhibitor of pre-60S assembly and demonstrate that chemoproteomics enables hypothesis generation for uncharacterized alt-proteins.
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Affiliation(s)
- Xiongwen Cao
- Department of Chemistry, Yale University, New Haven, CT, USA.,Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Alexandra Khitun
- Department of Chemistry, Yale University, New Haven, CT, USA.,Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Cecelia M Harold
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Carson J Bryant
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Shu-Jian Zheng
- Department of Chemistry, Yale University, New Haven, CT, USA.,Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Susan J Baserga
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
| | - Sarah A Slavoff
- Department of Chemistry, Yale University, New Haven, CT, USA. .,Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA. .,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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Antonarakis SE. Short arms of human acrocentric chromosomes and the completion of the human genome sequence. Genome Res 2022; 32:599-607. [PMID: 35361624 PMCID: PMC8997349 DOI: 10.1101/gr.275350.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The complete, ungapped sequence of the short arms of human acrocentric chromosomes (SAACs) is still unknown almost 20 years after the near completion of the Human Genome Project. Yet these short arms of Chromosomes 13, 14, 15, 21, and 22 contain the ribosomal DNA (rDNA) genes, which are of paramount importance for human biology. The sequences of SAACs show an extensive variation in the copy number of the various repetitive elements, the full extent of which is currently unknown. In addition, the full spectrum of repeated sequences, their organization, and the low copy number functional elements are also unknown. The Telomere-to-Telomere (T2T) Project using mainly long-read sequence technology has recently completed the assembly of the genome from a hydatidiform mole, CHM13, and has thus established a baseline reference for further studies on the organization, variation, functional annotation, and impact in human disorders of all the previously unknown genomic segments, including the SAACs. The publication of the initial results of the T2T Project will update and improve the reference genome for a better understanding of the evolution and function of the human genome.
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Affiliation(s)
- Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, 1211 Geneva, Switzerland.,Foundation Campus Biotech, 1202 Geneva, Switzerland.,Medigenome, Swiss Institute of Genomic Medicine, 1207 Geneva, Switzerland
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Antagonising Chromatin Remodelling Activities in the Regulation of Mammalian Ribosomal Transcription. Genes (Basel) 2021; 12:genes12070961. [PMID: 34202617 PMCID: PMC8303148 DOI: 10.3390/genes12070961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/16/2021] [Accepted: 06/19/2021] [Indexed: 12/29/2022] Open
Abstract
Ribosomal transcription constitutes the major energy consuming process in cells and is regulated in response to proliferation, differentiation and metabolic conditions by several signalling pathways. These act on the transcription machinery but also on chromatin factors and ncRNA. The many ribosomal gene repeats are organised in a number of different chromatin states; active, poised, pseudosilent and repressed gene repeats. Some of these chromatin states are unique to the 47rRNA gene repeat and do not occur at other locations in the genome, such as the active state organised with the HMG protein UBF whereas other chromatin state are nucleosomal, harbouring both active and inactive histone marks. The number of repeats in a certain state varies on developmental stage and cell type; embryonic cells have more rRNA gene repeats organised in an open chromatin state, which is replaced by heterochromatin during differentiation, establishing different states depending on cell type. The 47S rRNA gene transcription is regulated in different ways depending on stimulus and chromatin state of individual gene repeats. This review will discuss the present knowledge about factors involved, such as chromatin remodelling factors NuRD, NoRC, CSB, B-WICH, histone modifying enzymes and histone chaperones, in altering gene expression and switching chromatin states in proliferation, differentiation, metabolic changes and stress responses.
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Lagunas-Rangel FA, Yee J, Bazán-Tejeda ML, García-Villa E, Bermúdez-Cruz RM. Sirtuin GdSir2.4 participates in the regulation of rRNA transcription in the Giardia duodenalis parasite. Mol Microbiol 2021; 115:1039-1053. [PMID: 33665906 DOI: 10.1111/mmi.14710] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/25/2021] [Accepted: 02/28/2021] [Indexed: 01/09/2023]
Abstract
Giardia duodenalis is a parasite of great medical interest due to the number of infections it causes worldwide each year. Although research on epigenetic mechanisms in this protist has only begun recently, epigenetic regulation has already been shown to have important roles in encystation, antigenic variation, and resistance to antibiotics in Giardia. In this work, we show that a Giardia ortholog of Sir2, GdSir2.4, is involved in the silencing of rRNA expression. Our results demonstrate that GdSir2.4 localizes to the nucleolus, and its binding to the intergenic spacer region of the rDNA is associated with the deacetylation of the chromatin in this region. Given the importance of the regulation of rRNA expression to maintain adequate levels of ribosomes and genomic stability within the cells, GdSir2.4 can be considered a target to create new therapeutic agents against this parasite.
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Affiliation(s)
- Francisco Alejandro Lagunas-Rangel
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Mexico City, Mexico
| | - Janet Yee
- Department of Biology, Biochemistry and Molecular Biology Program, Trent University, Peterborough, ON, Canada
| | - María Luisa Bazán-Tejeda
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Mexico City, Mexico
| | - Enrique García-Villa
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Mexico City, Mexico
| | - Rosa María Bermúdez-Cruz
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Mexico City, Mexico
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Zhang J, Yang G, Li Q, Xie F. Increased fibrillarin expression is associated with tumor progression and an unfavorable prognosis in hepatocellular carcinoma. Oncol Lett 2020; 21:92. [PMID: 33376525 PMCID: PMC7751345 DOI: 10.3892/ol.2020.12353] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/02/2020] [Indexed: 12/19/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the sixth most common cancer and third most common cause of cancer-associated mortality worldwide. Hepatectomy and liver transplantation are the main treatments for early HCC. Immunotherapy and targeted therapy for advanced HCC have become increasingly popular; however, their clinical benefits are limited. Thus, identification of novel therapeutic targets for advanced HCC remains essential. Fibrillarin (FBL) is an essential nucleolar protein that catalyzes the 2′-O-methylation of ribosomal RNAs. Recently, experimental data have suggested that FBL can influence breast-cancer progression. However, the association between FBL expression and HCC remains known. In the present study, the UALCAN database was used to assess FBL mRNA expression in HCC. Immunohistochemistry analysis was performed to detect FBL protein expression in 139 patients with HCC. In addition, bioinformatic analysis was performed using the UALCAN, the Database for Annotation, Visualization and Integrated Discovery, cBioportal and TargetScan databases. Data were analyzed using Kaplan-Meier curves and the log-rank test, and a Cox proportional hazards regression model. The results demonstrated that FBL expression was significantly higher in tumor tissues compared with para-tumor tissues. Furthermore, high FBL expression was significantly associated with tumor diameter and advanced TNM stage in HCC. High FBL expression also predicted a shorter overall survival time and disease-free survival time in patients with HCC. Bioinformatics analysis demonstrated that FBL may be regulated by methylation modification. In addition, analyses of functional annotations using the Gene Ontology database indicated that FBL-related genes were predominantly enriched in DNA repair and proliferation-related cell-signaling pathways. Notably, high FBL expression signified larger tumor diameter, advanced tumor stage and a poor prognosis. Taken together, the results of the present study suggest that FBL may be a potential target for HCC treatment.
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Affiliation(s)
- Jing Zhang
- Department of Gastroenterology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Gang Yang
- Department of Hepatobiliary Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Qiang Li
- Department of Hepatobiliary Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Fei Xie
- Department of Hepatobiliary Surgery, The First People's Hospital of Neijiang, Neijiang, Sichuan 641000, P.R. China
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Smirnov E, Trosan P, Cabral JV, Studeny P, Kereïche S, Jirsova K, Cmarko D. Discontinuous transcription of ribosomal DNA in human cells. PLoS One 2020; 15:e0223030. [PMID: 32119673 PMCID: PMC7051091 DOI: 10.1371/journal.pone.0223030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/24/2020] [Indexed: 11/18/2022] Open
Abstract
Numerous studies show that various genes in all kinds of organisms are transcribed discontinuously, i.e. in short bursts or pulses with periods of inactivity between them. But it remains unclear whether ribosomal DNA (rDNA), represented by multiple copies in every cell, is also expressed in such manner. In this work, we synchronized the pol I activity in the populations of tumour derived as well as normal human cells by cold block and release. Our experiments with 5-fluorouridine (FU) and BrUTP confirmed that the nucleolar transcription can be efficiently and reversibly arrested at +4°C. Then using special software for analysis of the microscopic images, we measured the intensity of transcription signal (incorporated FU) in the nucleoli at different time points after the release. We found that the ribosomal genes in the human cells are transcribed discontinuously with periods ranging from 45 min to 75 min. Our data indicate that the dynamics of rDNA transcription follows the undulating pattern, in which the bursts are alternated by periods of rare transcription events.
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Affiliation(s)
- Evgeny Smirnov
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- * E-mail:
| | - Peter Trosan
- Laboratory of the Biology and Pathology of the Eye, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Joao Victor Cabral
- Laboratory of the Biology and Pathology of the Eye, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Pavel Studeny
- Ophthalmology Department of 3rd Faculty of Medicine, Charles University and University Hospital Kralovske Vinohrady, Prague, Czech Republic
| | - Sami Kereïche
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Katerina Jirsova
- Laboratory of the Biology and Pathology of the Eye, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Dušan Cmarko
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
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