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Das AS, Basu A, Mukhopadhyay R. Ribosomal proteins: the missing piece in the inflammation puzzle? Mol Cell Biochem 2024:10.1007/s11010-024-05050-9. [PMID: 38951378 DOI: 10.1007/s11010-024-05050-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/09/2024] [Indexed: 07/03/2024]
Abstract
Ribosomal proteins (RPs) are constituents of macromolecular machinery, ribosome that translates genetic information into proteins. Besides ribosomal functions, RPs are now getting appreciated for their 'moonlighting'/extra-ribosomal functions modulating many cellular processes. Accumulating evidence suggests that a number of RPs are involved in inflammation. Though acute inflammation is a part of the innate immune response, uncontrolled inflammation is a driving factor for several chronic inflammatory diseases. An in-depth understanding of inflammation regulation has always been valued for the better management of associated diseases. Hence, this review first outlines the common livelihood of RPs and then provides a comprehensive account of five RPs that significantly contribute to the inflammation process. Finally, we discuss the possible therapeutic uses of RPs against chronic inflammatory diseases.
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Affiliation(s)
- Anindhya Sundar Das
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India.
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, 02912, USA.
| | - Anandita Basu
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India
- Division of Surgical Research, Department of Surgery, Rhode Island Hospital, The Warren Alpert Medical School of Brown University, Providence, Rhode Island, 02903, USA
| | - Rupak Mukhopadhyay
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India.
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2
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Qin Q, Liu R, Li Z, Liu M, Wu X, Wang H, Yang S, Sun X, Yi X. Resolving candidate genes of duck ovarian tissue transplantation via RNA-Seq and expression network analyses. Poult Sci 2024; 103:103788. [PMID: 38692177 PMCID: PMC11070914 DOI: 10.1016/j.psj.2024.103788] [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: 02/22/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 05/03/2024] Open
Abstract
This study aims to identify candidate genes related to ovarian development after ovarian tissue transplantation through transcriptome sequencing (RNA-seq) and expression network analyses, as well as to provide a reference for determining the molecular mechanism of improving ovarian development following ovarian tissue transplantation. We collected ovarian tissues from 15 thirty-day-old ducks and split each ovary into 4 equal portions of comparable sizes before orthotopically transplanting them into 2-day-old ducks. Samples were collected on days 0 (untransplanted), 3, 6, and 9. The samples were paraffin sectioned and then subjected to Hematoxylin-Eosin (HE) staining and follicular counting. We extracted RNA from ovarian samples via the Trizol method to construct a transcriptome library, which was then sequenced by the Illumina Novaseq 6000 sequencing platform. The sequencing results were examined for differentially expressed genes (DEG) through gene ontology (GO) function and the Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses, gene set enrichment analysis (GSEA), weighted correlation network analysis (WGCNA), and protein-protein interaction (PPI) networks. Some of the candidate genes were selected for verification using real-time fluorescence quantitative PCR (qRT-PCR). Histological analysis revealed a significant reduction in the number of morphologically normal follicles at 3, 6, and 9 d after ovarian transplantation, along with significantly higher abnormality rates (P < 0.05). The transcriptome analysis results revealed 2,114, 2,224, and 2,257 upregulated DEGs and 2,647, 2,883, and 2,665 downregulated DEGs at 3, 6, and 9 d after ovarian transplantation, respectively. Enrichment analysis revealed the involvement multiple pathways in inflammatory signaling, signal transduction, and cellular processes. Furthermore, WGCNA yielded 13 modules, with 10, 4, and 6 candidate genes mined at 3, 6 and 9 d after ovarian transplantation, respectively. Transcription factor (TF) prediction showed that STAT1 was the most important TF. Finally, the qRT-PCR verification results revealed that 12 candidate genes exhibited an expression trend consistent with sequencing data. In summary, significant differences were observed in the number of follicles in duck ovaries following ovarian transplantation. Candidate genes involved in ovarian vascular remodeling and proliferation were screened using RNA-Seq and WGCNA.
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Affiliation(s)
- Qingming Qin
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang, Henan Province, 464000, P. R. China
| | - Rongxu Liu
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang, Henan Province, 464000, P. R. China
| | - Zhili Li
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang, Henan Province, 464000, P. R. China
| | - Midi Liu
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang, Henan Province, 464000, P. R. China
| | - Xian Wu
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang, Henan Province, 464000, P. R. China
| | - Huimin Wang
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang, Henan Province, 464000, P. R. China
| | - Shuailiang Yang
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang, Henan Province, 464000, P. R. China
| | - Xuyang Sun
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang, Henan Province, 464000, P. R. China
| | - Xianguo Yi
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang, Henan Province, 464000, P. R. China.
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Li A, Xie J, Lv L, Zheng Z, Yang W, Zhuo W, Yang S, Cai D, Duan J, Liu P, Min J, Wei J. RPL9 acts as an oncogene by shuttling miRNAs through exosomes in human hepatocellular carcinoma cells. Int J Oncol 2024; 64:58. [PMID: 38639179 PMCID: PMC11087036 DOI: 10.3892/ijo.2024.5646] [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: 10/19/2023] [Accepted: 02/05/2024] [Indexed: 04/20/2024] Open
Abstract
The exosomal pathway is an essential mechanism that regulates the abnormal content of microRNAs (miRNAs) in hepatocellular carcinoma (HCC). The directional transport of miRNAs requires the assistance of RNA‑binding proteins (RBPs). The present study found that RBPs participate in the regulation of miRNA content through the exosomal pathway in HCC cells. First, differential protein expression profiles in the serum exosomes of patients with HCC and benign liver disease were detected using mass spectrometry. The results revealed that ribosomal protein L9 (RPL9) was highly expressed in serum exosomes of patients with HCC. In addition, the downregulation of RPL9 markedly suppressed the proliferation, migration and invasion of HCC cells and reduced the biological activity of HCC‑derived exosomes. In addition, using miRNA microarrays, the changes in exosomal miRNA profiles in HCC cells caused by RPL9 knockdown were examined. miR‑24‑3p and miR‑185‑5p were most differentially expressed, as verified by reverse transcription‑quantitative PCR. Additionally, using RNA immunoprecipitation, it was found that RPL9 was directly bound to the two miRNAs and immunofluorescence assays confirmed that RPL9 was able to carry miRNAs into recipient cells via exosomes. Overexpression of miR‑24‑3p in cells increased the accumulation of miR‑24‑3p in exosomes and simultaneously upregulated RPL9. Excessive expression of miR‑24‑3p in exosomes also increased their bioactivity. Exosome‑mediated miRNA regulation and transfer require the involvement of RBPs. RPL9 functions as an oncogene, can directly bind to specific miRNAs and can be co‑transported to receptor cells through exosomes, thereby exerting its biological functions. These findings provide a novel approach for modulating miRNA profiles in HCC.
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Affiliation(s)
- Ang Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation and Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510120
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510120
| | - Jiyan Xie
- Department of Gastrointestinal Surgery, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036
| | - Lihong Lv
- Clinical Trial Institution of Pharmaceuticals and Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangdong Province Engineering Laboratory for Druggability and New Drug Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510120
| | - Zhihua Zheng
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangdong Province Engineering Laboratory for Druggability and New Drug Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510120
| | - Weibang Yang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260
| | - Wenfeng Zhuo
- Department of Hepatobiliary Surgery, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong 528406, P.R. China
| | - Sijia Yang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510120
| | - Diankui Cai
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510120
| | - Jinxin Duan
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510120
| | - Peiqing Liu
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangdong Province Engineering Laboratory for Druggability and New Drug Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510120
| | - Jun Min
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510120
| | - Jinxing Wei
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510120
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Luo Z, Lin ZY, Li ZF, Fu ZQ, Han FL, Li EC. Next-generation neonicotinoid: The impact of cycloxaprid on the crustacean decapod Penaeus vannamei. CHEMOSPHERE 2024; 358:142150. [PMID: 38679174 DOI: 10.1016/j.chemosphere.2024.142150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 05/01/2024]
Abstract
Cycloxaprid, a new neonicotinoid pesticide, poses ecological risks, particularly in aquatic environments, due to its unique action and environmental dispersal. This study investigated the ecotoxicological effects of various concentrations of cycloxaprid on Penaeus vannamei over 28 days. High cycloxaprid levels significantly altered shrimp physiology, as shown by changes in the hepatosomatic index and fattening. Indicators of oxidative stress, such as increased serum hemocyanin, respiratory burst, and nitric oxide, as well as decreased phenol oxidase activity, were observed. Additionally, elevated activities of lactate dehydrogenase, succinate dehydrogenase, and isocitrate dehydrogenase indicated disrupted energy metabolism in the hepatopancreas. Notably, analyses of the nervous system revealed marked disturbances in neural signaling, as evidenced by elevated acetylcholine, octopamine, and acetylcholinesterase levels. Transcriptomic analysis highlighted significant effects on gene expression and metabolic processes in the hepatopancreas and nervous system. This study demonstrated that cycloxaprid disrupts neural signaling and oxidative balance in P. vannamei, potentially affecting its growth, and provides key insights into its biochemical and transcriptomic toxicity in aquatic systems.
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Affiliation(s)
- Zhi Luo
- School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China; School of Marine Biology and Fisheries, Hainan University, Haikou, Hainan, 570228, China
| | - Zhi-Yu Lin
- School of Marine Biology and Fisheries, Hainan University, Haikou, Hainan, 570228, China
| | - Zhen-Fei Li
- School of Marine Biology and Fisheries, Hainan University, Haikou, Hainan, 570228, China
| | - Zhen-Qiang Fu
- School of Marine Science, Sun Yat-sen University, Zhuhai, Guangdong, 519082, China
| | - Feng-Lu Han
- School of Marine Biology and Fisheries, Hainan University, Haikou, Hainan, 570228, China
| | - Er-Chao Li
- School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China.
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Surya A, Bolton BM, Rothe R, Mejia-Trujillo R, Zhao Q, Leonita A, Liu Y, Rangan R, Gorusu Y, Nguyen P, Cenik C, Cenik ES. Cytosolic Ribosomal Protein Haploinsufficiency affects Mitochondrial Morphology and Respiration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589775. [PMID: 38659761 PMCID: PMC11042305 DOI: 10.1101/2024.04.16.589775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The interplay between ribosomal protein composition and mitochondrial function is essential for sustaining energy homeostasis. Precise stoichiometric production of ribosomal proteins is crucial to maximize protein synthesis efficiency while reducing the energy costs to the cell. However, the impact of this balance on mitochondrial ATP generation, morphology and function remains unclear. Particularly, the loss of a single copy ribosomal protein gene is observed in Mendelian disorders like Diamond Blackfan Anemia and is common in somatic tumors, yet the implications of this imbalance on mitochondrial function and energy dynamics are still unclear. In this study, we investigated the impact of haploinsufficiency for four ribosomal protein genes implicated in ribosomopathy disorders (rps-10, rpl-5, rpl-33, rps-23) in Caenorhabditis elegans and corresponding reductions in human lymphoblast cells. Our findings uncover significant, albeit variably penetrant, mitochondrial morphological differences across these mutants, alongside an upregulation of glutathione transferases, and SKN-1 dependent increase in oxidative stress resistance, indicative of increased ROS production. Specifically, loss of a single copy of rps-10 in C. elegans led to decreased mitochondrial activity, characterized by lower energy levels and reduced oxygen consumption. A similar reduction in mitochondrial activity and energy levels was observed in human leukemia cells with a 50% reduction in RPS10 transcript levels. Importantly, we also observed alterations in the translation efficiency of nuclear and mitochondrial electron transport chain components in response to reductions in ribosomal protein genes' expression in both C. elegans and human cells. This suggests a conserved mechanism whereby the synthesis of components vital for mitochondrial function are adjusted in the face of compromised ribosomal machinery. Finally, mitochondrial membrane and cytosolic ribosomal components exhibited significant covariation at the RNA and translation efficiency level in lymphoblastoid cells across a diverse group of individuals, emphasizing the interplay between the protein synthesis machinery and mitochondrial energy production. By uncovering the impact of ribosomal protein haploinsufficiency on the translation efficiency of electron transport chain components, mitochondrial physiology, and the adaptive stress responses, we provide evidence for an evolutionarily conserved strategy to safeguard cellular functionality under genetic stress.
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Affiliation(s)
- Agustian Surya
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Blythe Marie Bolton
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Reed Rothe
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Raquel Mejia-Trujillo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Qiuxia Zhao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Amanda Leonita
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Yue Liu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Rekha Rangan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Yasash Gorusu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Pamela Nguyen
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Elif Sarinay Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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6
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Ghandadi M, Dobi A, Malhotra SV. A role for RIO kinases in the crosshair of cancer research and therapy. Biochim Biophys Acta Rev Cancer 2024; 1879:189100. [PMID: 38604268 DOI: 10.1016/j.bbcan.2024.189100] [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: 10/08/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024]
Abstract
RIO (right open reading frame) family of kinases including RIOK1, RIOK2 and RIOK3 are known for their role in the ribosomal biogenesis. Dysfunction of RIO kinases have been implicated in malignancies, including acute myeloid leukemia, glioma, breast, colorectal, lung and prostatic adenocarcinoma suggesting RIO kinases as potential targets in cancer. In vitro, in vivo and clinical studies have demonstrated that RIO kinases are overexpressed in various types of cancers suggesting important roles in tumorigenesis, especially in metastasis. In the context of malignancies, RIO kinases are involved in cancer-promoting pathways including AKT/mTOR, RAS, p53 and NF-κB and cell cycle regulation. Here we review the role of RIO kinases in cancer development emphasizing their potential as therapeutic target and encouraging further development and investigation of inhibitors in the context of cancer.
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Affiliation(s)
- Morteza Ghandadi
- Department of Pharmacognosy and Pharmaceutical Biotechnology, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran; Medicinal Plants Research Center, Pharmaceutical Sciences Research Center, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Albert Dobi
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery at the Uniformed Services, University of the Health Sciences, Bethesda, MD 20817, USA; Henry Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Sanjay V Malhotra
- Department of Cell, Development and Cancer Biology, Oregon Health & Science University, Portland, OR 97201, USA; Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
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7
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Gao S, Zheng F, Yue L, Chen B. Chronic cadmium exposure impairs flight behavior by dampening flight muscle carbon metabolism in bumblebees. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133628. [PMID: 38301442 DOI: 10.1016/j.jhazmat.2024.133628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 02/03/2024]
Abstract
Cadmium pollution affects the global ecosystem because cadmium can be transferred up the food chain. The bumblebee, Bombus terrestris, is an important insect pollinator. Their foraging activity on flowers exposes them to harmful heavy metals, which damages their health and leads to massive population declines. However, the effects of chronic exposure to heavy metals on the flight performance of bumblebees have not yet been characterized. Here, we studied variation in the flight capacity of bumblebees induced by chronic cadmium exposure at field-realistic concentrations using behavioral, physiological, and molecular approaches. Chronic cadmium exposure caused a significant reduction in the duration, distance, and mean velocity of bumblebee flight. Transcriptome analysis showed that the impairment of carbon metabolism and mitochondrial dysfunction in the flight muscle were the primary causes. Physiological, biochemical, and metabolomic analyses validated disruptions in energy metabolism, and impairments in mitochondrial respiratory chain complexes activities. Histological analysis revealed muscle fiber damage and mitochondrial loss. Exogenous decanoic acid or citric acid partially restored sustained flight ability of bumblebees by mitigating muscle fiber damage and increasing energy generation. These findings provide insights into how long-term cadmium stress affects the flight ability of insects and will aid human muscle or exercise-related disease research.
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Affiliation(s)
- Shen Gao
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Fei Zheng
- College of Life Sciences, Hebei University, Baoding 071002, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lei Yue
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Bing Chen
- College of Life Sciences, Hebei University, Baoding 071002, China.
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Mitterer V, Hamze H, Kunowska N, Stelzl U, Henras A, Hurt E. The RNA helicase Dbp10 coordinates assembly factor association with PTC maturation during ribosome biogenesis. Nucleic Acids Res 2024; 52:1975-1987. [PMID: 38113283 PMCID: PMC10899779 DOI: 10.1093/nar/gkad1206] [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: 03/30/2023] [Revised: 11/08/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023] Open
Abstract
During ribosome biogenesis a plethora of assembly factors and essential enzymes drive the unidirectional maturation of nascent pre-ribosomal subunits. The DEAD-box RNA helicase Dbp10 is suggested to restructure pre-ribosomal rRNA of the evolving peptidyl-transferase center (PTC) on nucleolar ribosomal 60S assembly intermediates. Here, we show that point mutations within conserved catalytic helicase-core motifs of Dbp10 yield a dominant-lethal growth phenotype. Such dbp10 mutants, which stably associate with pre-60S intermediates, impair pre-60S biogenesis at a nucleolar stage prior to the release of assembly factor Rrp14 and stable integration of late nucleolar factors such as Noc3. Furthermore, the binding of the GTPase Nug1 to particles isolated directly via mutant Dbp10 bait proteins is specifically inhibited. The N-terminal domain of Nug1 interacts with Dbp10 and the methyltransferase Spb1, whose pre-60S incorporation is also reduced in absence of functional Dbp10 resulting in decreased methylation of 25S rRNA nucleotide G2922. Our data suggest that Dbp10's helicase activity generates the necessary framework for assembly factor docking thereby permitting PTC rRNA methylation and the progression of pre-60S maturation.
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Affiliation(s)
- Valentin Mitterer
- Biochemistry Center, University of Heidelberg, 69120 Heidelberg, Germany
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Hussein Hamze
- Molecular, Cellular and Developmental Biology Unit (MCD), Center for Integrative Biology (CBI), CNRS, University of Toulouse, 31062 Toulouse, France
| | - Natalia Kunowska
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, 8010 Graz, Austria
| | - Ulrich Stelzl
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
| | - Anthony K Henras
- Molecular, Cellular and Developmental Biology Unit (MCD), Center for Integrative Biology (CBI), CNRS, University of Toulouse, 31062 Toulouse, France
| | - Ed Hurt
- Biochemistry Center, University of Heidelberg, 69120 Heidelberg, Germany
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9
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Bryant CJ, McCool MA, Rosado González G, Abriola L, Surovtseva Y, Baserga S. Discovery of novel microRNA mimic repressors of ribosome biogenesis. Nucleic Acids Res 2024; 52:1988-2011. [PMID: 38197221 PMCID: PMC10899765 DOI: 10.1093/nar/gkad1235] [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: 02/20/2023] [Revised: 12/03/2023] [Accepted: 12/16/2023] [Indexed: 01/11/2024] Open
Abstract
While microRNAs and other non-coding RNAs are the next frontier of novel regulators of mammalian ribosome biogenesis (RB), a systematic exploration of microRNA-mediated RB regulation has not yet been undertaken. We carried out a high-content screen in MCF10A cells for changes in nucleolar number using a library of 2603 mature human microRNA mimics. Following a secondary screen for nucleolar rRNA biogenesis inhibition, we identified 72 novel microRNA negative regulators of RB after stringent hit calling. Hits included 27 well-conserved microRNAs present in MirGeneDB, and were enriched for mRNA targets encoding proteins with nucleolar localization or functions in cell cycle regulation. Rigorous selection and validation of a subset of 15 microRNA hits unexpectedly revealed that most of them caused dysregulated pre-rRNA processing, elucidating a novel role for microRNAs in RB regulation. Almost all hits impaired global protein synthesis and upregulated CDKN1A (p21) levels, while causing diverse effects on RNA Polymerase 1 (RNAP1) transcription and TP53 protein levels. We provide evidence that the MIR-28 siblings, hsa-miR-28-5p and hsa-miR-708-5p, potently target the ribosomal protein mRNA RPS28 via tandem primate-specific 3' UTR binding sites, causing a severe pre-18S pre-rRNA processing defect. Our work illuminates novel microRNA attenuators of RB, forging a promising new path for microRNA mimic chemotherapeutics.
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Affiliation(s)
- Carson J Bryant
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Mason A McCool
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, 06520, USA
| | | | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, 06516, USA
| | - Yulia V Surovtseva
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, 06516, USA
| | - Susan J Baserga
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, 06520, USA
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10
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Yagita K, Sadashima S, Koyama S, Noguchi H, Hamasaki H, Sasagasako N, Honda H. Ribosomal protein SA is a common component of neuronal intranuclear inclusions in polyglutamine diseases and Marinesco bodies. Neuropathology 2024; 44:31-40. [PMID: 37340992 DOI: 10.1111/neup.12927] [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: 02/27/2023] [Revised: 05/17/2023] [Accepted: 05/21/2023] [Indexed: 06/22/2023]
Abstract
Neuronal intranuclear inclusions (NIIs) are common key structures in polyglutamine (polyQ) diseases such as Huntington disease (HD), spinocerebellar ataxia type 1 (SCA1), and SCA3. Marinesco bodies (MBs) of dopaminergic neurons in the substantia nigra are also intranuclear structures and are frequently seen in normal elderly people. Ribosomal dysfunction is closely related to two differential processes; therefore, we aimed to identify the pathological characteristics of ribosomal protein SA (RPSA), a ribosomal protein, in both states. To this end, we evaluated the autopsy findings in four patients with HD, two SCA3, and five normal elderly cases (NCs). Immunohistochemical studies demonstrated that both NIIs and MBs contain RPSA. In polyQ diseases, RPSA was co-localized with polyQ aggregations, and 3D-reconstructed images revealed their mosaic-like distribution. Assessments of the organization of RPSA and p62 in NIIs showed that RPSA was more localized toward the center than p62 and that this unique organization was more evident in the MBs. Immunoblotting of the temporal cortices revealed that the nuclear fraction of HD patients contained more RPSA than that of NCs. In conclusion, our study revealed that RPSA is a common component of both NIIs and MBs, indicating that a similar mechanism contributes to the formation of polyQ NIIs and MBs.
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Affiliation(s)
- Kaoru Yagita
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shoko Sadashima
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Sachiko Koyama
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hideko Noguchi
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hideomi Hamasaki
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naokazu Sasagasako
- Department of Neurology, National Hospital Organization, Omuta National Hospital, Fukuoka, Japan
| | - Hiroyuki Honda
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Neuropathology Center, National Hospital Organization, Omuta National Hospital, Omuta, Japan
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11
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Zhou X, Chen Y, Zhang Z, Miao J, Chen G, Qian Z. Identification of differentially expressed genes, signaling pathways and immune infiltration in postmenopausal osteoporosis by integrated bioinformatics analysis. Heliyon 2024; 10:e23794. [PMID: 38205281 PMCID: PMC10777010 DOI: 10.1016/j.heliyon.2023.e23794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
Background Postmenopausal osteoporosis is a systemic metabolic disorder typified by an imbalance in bone turnover, where bone resorption supersedes bone formation. This imbalance primarily arises from a decline in bone mass induced by estrogen deficiency, and an elevated risk of fractures resulting from degradation of bone microstructure. Despite recognizing these changes, the precise causative factors and potential molecular pathways remain elusive. In this study, we aimed to identify differentially expressed genes (DEGs), associated pathways, and the role of immune infiltration in osteoporosis, leveraging an integrated bioinformatics approach to shed light on potential underlying molecular mechanisms. Methods We retrieved the expression profiles of GSE230665 from the Gene Expression Omnibus database, comprising 15 femur samples, including 12 postmenopausal osteoporosis samples and 3 normal controls. From the aggregated microarray datasets, we derived differentially expressed genes (DEGs) for further bioinformatics analysis. We used WGCNA, analyzed DEGs, PPI, and conducted GO analysis to identify pivotal genes. We then used the CIBERSORT method to explore the degree of immune cell infiltration within femur specimens affected by postmenopausal osteoporosis. To probe into the relationship between pivotal genes and infiltrating immune cells, we conducted correlation analysis. Results We identified a total of 12,204 DEGs. Among these, 12,157 were up-regulated, and 47 were down-regulated. GO and KEGG pathway analyses indicated that these DEGs predominantly targeted cellular protein localization activity and associated signaling pathways. The protein-protein interaction network highlighted four central hub-genes: RPL31, RPL34, EEF1G, and BPTF. Principal component analysis indicated a positive correlation between the expression of these genes and resting NK cells (as per CIBERSORT). In contrast, the expression of RPL31, RPL34, and EEF1G showed a negative correlation with T cells (gamma delta per CIBERSORT). Conclusions Immune infiltration plays a role in the development of osteoporosis.
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Affiliation(s)
- Xiaoli Zhou
- Department of Spine Surgery, Tianjin Hospital, Tianjin University, Tianjin 300211, China
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin 300011, China
| | - Yang Chen
- Department of Spine Surgery, Tianjin Hospital, Tianjin University, Tianjin 300211, China
| | - Zepei Zhang
- Department of Spine Surgery, Tianjin Hospital, Tianjin University, Tianjin 300211, China
| | - Jun Miao
- Department of Spine Surgery, Tianjin Hospital, Tianjin University, Tianjin 300211, China
| | - Guangdong Chen
- Department of Orthopaedics, Cangzhou Central Hospital, Hebei 061001, China
| | - Zhiyong Qian
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin 300011, China
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12
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Beine-Golovchuk O, Kallas M, Kunze R, Griesel S, Baßler J. The Efg1-Bud22 dimer associates with the U14 snoRNP contacting the 5' rRNA domain of an early 90S pre-ribosomal particle. Nucleic Acids Res 2024; 52:431-447. [PMID: 38000371 PMCID: PMC10783500 DOI: 10.1093/nar/gkad1109] [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: 11/21/2022] [Revised: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
The DEAD-box helicase Dbp4 plays an essential role during the early assembly of the 40S ribosome, which is only poorly understood to date. By applying the yeast two-hybrid method and biochemical approaches, we discovered that Dbp4 interacts with the Efg1-Bud22 dimer. Both factors associate with early pre-90S particles and smaller complexes, each characterized by a high presence of the U14 snoRNA. A crosslink analysis of Bud22 revealed its contact to the U14 snoRNA and the 5' domain of the nascent 18S rRNA, close to its U14 snoRNA hybridization site. Moreover, depletion of Bud22 or Efg1 specifically affects U14 snoRNA association with pre-ribosomal complexes. Accordingly, we concluded that the role of the Efg1-Bud22 dimer is linked to the U14 snoRNA function on early 90S ribosome intermediates chaperoning the 5' domain of the nascent 18S rRNA. The successful rRNA folding of the 5' domain and the release of Efg1, Bud22, Dpb4, U14 snoRNA and associated snoRNP factors allows the subsequent recruitment of the Kre33-Bfr2-Enp2-Lcp5 module towards the 90S pre-ribosome.
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Affiliation(s)
- Olga Beine-Golovchuk
- Biochemie-Zentrum der Universität Heidelberg (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Martina Kallas
- Biochemie-Zentrum der Universität Heidelberg (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Ruth Kunze
- Biochemie-Zentrum der Universität Heidelberg (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Sabine Griesel
- Biochemie-Zentrum der Universität Heidelberg (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Jochen Baßler
- Biochemie-Zentrum der Universität Heidelberg (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
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13
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Shanmugam T, Chaturvedi P, Streit D, Ghatak A, Bergelt T, Simm S, Weckwerth W, Schleiff E. Low dose ribosomal DNA P-loop mutation affects development and enforces autophagy in Arabidopsis. RNA Biol 2024; 21:1-15. [PMID: 38156797 PMCID: PMC10761087 DOI: 10.1080/15476286.2023.2298532] [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] [Accepted: 12/14/2023] [Indexed: 01/03/2024] Open
Abstract
Arabidopsis contains hundreds of ribosomal DNA copies organized within the nucleolar organizing regions (NORs) in chromosomes 2 and 4. There are four major types of variants of rDNA, VAR1-4, based on the polymorphisms of 3' external transcribed sequences. The variants are known to be differentially expressed during plant development. We created a mutant by the CRISPR-Cas9-mediated excision of ~ 25 nt from predominantly NOR4 ribosomal DNA copies, obtaining mosaic mutational events on ~ 5% of all rDNA copies. The excised region consists of P-loop and Helix-82 segments of 25S rRNA. The mutation led to allelic, dosage-dependent defects marked by lateral root inhibition, reduced size, and pointy leaves, all previously observed for defective ribosomal function. The mutation in NOR4 led to dosage compensation from the NOR2 copies by elevated expression of VAR1 in mutants and further associated single-nucleotide variants, thus, resulting in altered rRNA sub-population. Furthermore, the mutants exhibited rRNA maturation defects specifically in the minor pathway typified by 32S pre-rRNA accumulation. Density-gradient fractionation and subsequent RT-PCR of rRNA analyses revealed that mutated copies were not incorporated into the translating ribosomes. The mutants in addition displayed an elevated autophagic flux as shown by the autophagic marker GFP-ATG8e, likely related to ribophagy.
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Affiliation(s)
- Thiruvenkadam Shanmugam
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Palak Chaturvedi
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Deniz Streit
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Thorsten Bergelt
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stefan Simm
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Enrico Schleiff
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany
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14
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Diamantopoulos MA, Georgoulia KK, Levis P, Kotronopoulos G, Stravodimos K, Kontos CK, Avgeris M, Scorilas A. 28S rRNA-Derived Fragments Represent an Independent Molecular Predictor of Short-Term Relapse in Prostate Cancer. Int J Mol Sci 2023; 25:239. [PMID: 38203408 PMCID: PMC10779029 DOI: 10.3390/ijms25010239] [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: 11/28/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Prostate cancer (PCa) is a global health concern, being a leading cause of cancer-related mortality among males. Early detection and accurate prognosis are crucial for effective management. This study delves into the diagnostic and prognostic potential of 28S rRNA-derived fragments (rRFs) in PCa. Total RNA extracted from 89 PCa and 53 benign prostate hyperplasia (BPH) tissue specimens. After 3'-end polyadenylation, we performed reverse transcription to create first-strand cDNA. Using an in-house quantitative real-time PCR (qPCR) assay, we quantified 28S rRF levels. Post-treatment biochemical relapse served as the clinical endpoint event for survival analysis, which we validated internally through bootstrap analysis. Our results revealed downregulated 28S rRF levels in PCa compared to BPH patients. Additionally, we observed a significant positive correlation between 28S rRF levels and higher Gleason scores and tumor stages. Furthermore, PCa patients with elevated 28S rRF expression had a significantly higher risk of post-treatment disease relapse independently of clinicopathological data. In conclusion, our study demonstrates, for the first time, the prognostic value of 28S rRF in prostate adenocarcinoma. Elevated 28S rRF levels independently predict short-term PCa relapse and enhance risk stratification. This establishes 28S rRF as a potential novel molecular marker for PCa prognosis.
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Affiliation(s)
- Marios A. Diamantopoulos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (M.A.D.); (K.K.G.); (C.K.K.); (M.A.)
| | - Konstantina K. Georgoulia
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (M.A.D.); (K.K.G.); (C.K.K.); (M.A.)
| | - Panagiotis Levis
- First Department of Urology, “Laiko” General Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (P.L.); (G.K.); (K.S.)
| | - Georgios Kotronopoulos
- First Department of Urology, “Laiko” General Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (P.L.); (G.K.); (K.S.)
| | - Konstantinos Stravodimos
- First Department of Urology, “Laiko” General Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (P.L.); (G.K.); (K.S.)
| | - Christos K. Kontos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (M.A.D.); (K.K.G.); (C.K.K.); (M.A.)
| | - Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (M.A.D.); (K.K.G.); (C.K.K.); (M.A.)
- Laboratory of Clinical Biochemistry-Molecular Diagnostics, Second Department of Pediatrics, “P. & A. Kyriakou” Children’s Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (M.A.D.); (K.K.G.); (C.K.K.); (M.A.)
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15
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Fernández-Fernández J, Martín-Villanueva S, Perez-Fernandez J, de la Cruz J. The Role of Ribosomal Proteins eL15 and eL36 in the Early Steps of Yeast 60S Ribosomal Subunit Assembly. J Mol Biol 2023; 435:168321. [PMID: 37865285 DOI: 10.1016/j.jmb.2023.168321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 10/23/2023]
Abstract
Ribosomal proteins have important roles in maintaining the structure and function of mature ribosomes, but they also drive crucial rearrangement reactions during ribosome biogenesis. The contribution of most, but not all, ribosomal proteins to ribosome synthesis has been previously analyzed in the yeast Saccharomyces cerevisiae. Herein, we characterize the role of yeast eL15 during 60S ribosomal subunit formation. In vivo depletion of eL15 results in a shortage of 60S subunits and the appearance of half-mer polysomes. This is likely due to defective processing of the 27SA3 to the 27SBS pre-rRNA and impaired subsequent processing of both forms of 27SB pre-rRNAs to mature 25S and 5.8S rRNAs. Indeed, eL15 depletion leads to the efficient turnover of the de novo formed 27S pre-rRNAs. Additionally, depletion of eL15 blocks nucleocytoplasmic export of pre-60S particles. Moreover, we have analyzed the impact of depleting either eL15 or eL36 on the composition of early pre-60S particles, thereby revealing that the depletion of eL15 or eL36 not only affects each other's assembly into pre-60S particles but also that of neighboring ribosomal proteins, including eL8. These intermediates also lack most ribosome assembly factors required for 27SA3 and 27SB pre-rRNA processing, named A3- and B-factors, respectively. Importantly, our results recapitulate previous ones obtained upon eL8 depletion. We conclude that assembly of eL15, together with that of eL8 and eL36, is a prerequisite to shape domain I of 5.8S/25S rRNA within early pre-60S particles, through their binding to this rRNA domain and the recruitment of specific groups of assembly factors.
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Affiliation(s)
- José Fernández-Fernández
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Seville, Spain
| | - Sara Martín-Villanueva
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain
| | - Jorge Perez-Fernandez
- Department of Biochemistry III, University of Regensburg, D-93051 Regensburg, Germany.
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Seville, Spain.
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16
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Ugajin N, Imami K, Takada H, Ishihama Y, Chiba S, Mishima Y. Znf598-mediated Rps10/eS10 ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development. RNA (NEW YORK, N.Y.) 2023; 29:1910-1927. [PMID: 37751929 PMCID: PMC10653392 DOI: 10.1261/rna.079633.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023]
Abstract
The ribosome is a translational apparatus that comprises about 80 ribosomal proteins and four rRNAs. Recent studies reported that ribosome ubiquitination is crucial for translational regulation and ribosome-associated quality control (RQC). However, little is known about the dynamics of ribosome ubiquitination under complex biological processes of multicellular organisms. To explore ribosome ubiquitination during animal development, we generated a zebrafish strain that expresses a FLAG-tagged ribosomal protein Rpl36/eL36 from its endogenous locus. We examined ribosome ubiquitination during zebrafish development by combining affinity purification of ribosomes from rpl36-FLAG zebrafish embryos with immunoblotting analysis. Our findings showed that the ubiquitination of ribosomal proteins dynamically changed as development proceeded. We also showed that during zebrafish development, the ribosome was ubiquitinated by Znf598, an E3 ubiquitin ligase that activates RQC. Ribosomal protein Rps10/eS10 was found to be a key ubiquitinated protein during development. Furthermore, we showed that Rps10/eS10 ubiquitination-site mutations reduced the overall ubiquitination pattern of the ribosome. These results demonstrate the complexity and dynamics of ribosome ubiquitination during zebrafish development.
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Affiliation(s)
- Nozomi Ugajin
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Koshi Imami
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiraku Takada
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shinobu Chiba
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Yuichiro Mishima
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
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17
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Catalanotto C, Barbato C, Cogoni C, Benelli D. The RNA-Binding Function of Ribosomal Proteins and Ribosome Biogenesis Factors in Human Health and Disease. Biomedicines 2023; 11:2969. [PMID: 38001969 PMCID: PMC10669870 DOI: 10.3390/biomedicines11112969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
The ribosome is a macromolecular complex composed of RNA and proteins that interact through an integrated and interconnected network to preserve its ancient core activities. In this review, we emphasize the pivotal role played by RNA-binding proteins as a driving force in the evolution of the current form of the ribosome, underscoring their importance in ensuring accurate protein synthesis. This category of proteins includes both ribosomal proteins and ribosome biogenesis factors. Impairment of their RNA-binding activity can also lead to ribosomopathies, which is a group of disorders characterized by defects in ribosome biogenesis that are detrimental to protein synthesis and cellular homeostasis. A comprehensive understanding of these intricate processes is essential for elucidating the mechanisms underlying the resulting diseases and advancing potential therapeutic interventions.
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Affiliation(s)
- Caterina Catalanotto
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (C.C.); (C.C.)
| | - Christian Barbato
- National Research Council (CNR), Department of Sense Organs DOS, Institute of Biochemistry and Cell Biology (IBBC), Sapienza University of Rome, 00185 Rome, Italy;
| | - Carlo Cogoni
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (C.C.); (C.C.)
| | - Dario Benelli
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (C.C.); (C.C.)
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18
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Bryant CJ, McCool MA, Rosado-González GT, Abriola L, Surovtseva YV, Baserga SJ. Discovery of novel microRNA mimic repressors of ribosome biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.17.526327. [PMID: 36824951 PMCID: PMC9949135 DOI: 10.1101/2023.02.17.526327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
While microRNAs and other non-coding RNAs are the next frontier of novel regulators of mammalian ribosome biogenesis (RB), a systematic exploration of microRNA-mediated RB regulation has not yet been undertaken. We carried out a high-content screen in MCF10A cells for changes in nucleolar number using a library of 2,603 mature human microRNA mimics. Following a secondary screen for nucleolar rRNA biogenesis inhibition, we identified 72 novel microRNA negative regulators of RB after stringent hit calling. Hits included 27 well-conserved microRNAs present in MirGeneDB, and were enriched for mRNA targets encoding proteins with nucleolar localization or functions in cell cycle regulation. Rigorous selection and validation of a subset of 15 microRNA hits unexpectedly revealed that most of them caused dysregulated pre-rRNA processing, elucidating a novel role for microRNAs in RB regulation. Almost all hits impaired global protein synthesis and upregulated CDKN1A ( p21 ) levels, while causing diverse effects on RNA Polymerase 1 (RNAP1) transcription and TP53 protein levels. We discovered that the MIR-28 siblings, hsa-miR-28-5p and hsa-miR-708-5p, directly and potently target the ribosomal protein mRNA RPS28 via tandem primate-specific 3' UTR binding sites, causing a severe pre-18S pre-rRNA processing defect. Our work illuminates novel microRNA attenuators of RB, forging a promising new path for microRNA mimic chemotherapeutics.
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19
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Valeeva LR, Abdulkina LR, Agabekian IA, Shakirov EV. Telomere biology and ribosome biogenesis: structural and functional interconnections. Biochem Cell Biol 2023; 101:394-409. [PMID: 36989538 DOI: 10.1139/bcb-2022-0383] [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] [Indexed: 03/31/2023] Open
Abstract
Telomeres are nucleoprotein structures that play a pivotal role in the protection and maintenance of eukaryotic chromosomes. Telomeres and the enzyme telomerase, which replenishes telomeric DNA lost during replication, are important factors necessary to ensure continued cell proliferation. Cell proliferation is also dependent on proper and efficient protein synthesis, which is carried out by ribosomes. Mutations in genes involved in either ribosome biogenesis or telomere biology result in cellular abnormalities and can cause human genetic diseases, defined as ribosomopathies and telomeropathies, respectively. Interestingly, recent discoveries indicate that many of the ribosome assembly and rRNA maturation factors have additional noncanonical functions in telomere biology. Similarly, several key proteins and enzymes involved in telomere biology, including telomerase, have unexpected roles in rRNA transcription and maturation. These observations point to an intriguing cross-talk mechanism potentially explaining the multiple pleiotropic symptoms of mutations in many causal genes identified in various telomeropathy and ribosomopathy diseases. In this review, we provide a brief summary of eukaryotic telomere and rDNA loci structures, highlight several universal features of rRNA and telomerase biogenesis, evaluate intriguing interconnections between telomere biology and ribosome assembly, and conclude with an assessment of overlapping features of human diseases of telomeropathies and ribosomopathies.
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Affiliation(s)
- Liia R Valeeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia
- Department of Biological Sciences, College of Science, Marshall University, Huntington, WV 25701, USA
| | - Liliia R Abdulkina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia
| | - Inna A Agabekian
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia
| | - Eugene V Shakirov
- Department of Biological Sciences, College of Science, Marshall University, Huntington, WV 25701, USA
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, USA
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20
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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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21
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Junod SL, Tingey M, Kelich JM, Goryaynov A, Herbine K, Yang W. Dynamics of nuclear export of pre-ribosomal subunits revealed by high-speed single-molecule microscopy in live cells. iScience 2023; 26:107445. [PMID: 37599825 PMCID: PMC10433129 DOI: 10.1016/j.isci.2023.107445] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 06/24/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
We present a study on the nuclear export efficiency and time of pre-ribosomal subunits in live mammalian cells, using high-speed single-molecule tracking and single-molecule fluorescence resonance energy transfer techniques. Our findings reveal that pre-ribosomal particles exhibit significantly higher nuclear export efficiency compared to other large cargos like mRNAs, with around two-thirds of interactions between the pre-60S or pre-40S and the nuclear pore complexes (NPCs) resulting in successful export to the cytoplasm. We also demonstrate that nuclear transport receptor (NTR) chromosomal maintenance 1 (CRM1) plays a crucial role in nuclear export efficiency, with pre-60S and pre-40S particle export efficiency decreasing by 11-17-fold when CRM1 is inhibited. Our results suggest that multiple copies of CRM1 work cooperatively to chaperone pre-ribosomal subunits through the NPC, thus increasing export efficiency and decreasing export time. Significantly, this cooperative NTR mechanism extends beyond pre-ribosomal subunits, as evidenced by the enhanced nucleocytoplasmic transport of proteins.
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Affiliation(s)
- Samuel L. Junod
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Mark Tingey
- Department of Biology, Temple University, Philadelphia, PA, USA
| | | | | | - Karl Herbine
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA, USA
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22
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Ochkasova A, Arbuzov G, Malygin A, Graifer D. Two "Edges" in Our Knowledge on the Functions of Ribosomal Proteins: The Revealed Contributions of Their Regions to Translation Mechanisms and the Issues of Their Extracellular Transport by Exosomes. Int J Mol Sci 2023; 24:11458. [PMID: 37511213 PMCID: PMC10380927 DOI: 10.3390/ijms241411458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Ribosomal proteins (RPs), the constituents of the ribosome, belong to the most abundant proteins in the cell. A highly coordinated network of interactions implicating RPs and ribosomal RNAs (rRNAs) forms the functionally competent structure of the ribosome, enabling it to perform translation, the synthesis of polypeptide chain on the messenger RNA (mRNA) template. Several RPs contact ribosomal ligands, namely, those with transfer RNAs (tRNAs), mRNA or translation factors in the course of translation, and the contribution of a number of these particular contacts to the translation process has recently been established. Many ribosomal proteins also have various extra-ribosomal functions unrelated to translation. The least-understood and -discussed functions of RPs are those related to their participation in the intercellular communication via extracellular vesicles including exosomes, etc., which often carry RPs as passengers. Recently reported data show that such a kind of communication can reprogram a receptor cell and change its phenotype, which is associated with cancer progression and metastasis. Here, we review the state-of-art ideas on the implications of specific amino acid residues of RPs in the particular stages of the translation process in higher eukaryotes and currently available data on the transport of RPs by extracellular vesicles and its biological effects.
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Affiliation(s)
- Anastasia Ochkasova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Grigory Arbuzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alexey Malygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Dmitri Graifer
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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23
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Steiner A, Favre S, Mack M, Hausharter A, Pillet B, Hafner J, Mitterer V, Kressler D, Pertschy B, Zierler I. Dissecting the Nuclear Import of the Ribosomal Protein Rps2 (uS5). Biomolecules 2023; 13:1127. [PMID: 37509163 PMCID: PMC10377357 DOI: 10.3390/biom13071127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
The ribosome is assembled in a complex process mainly taking place in the nucleus. Consequently, newly synthesized ribosomal proteins have to travel from the cytoplasm into the nucleus, where they are incorporated into nascent ribosomal subunits. In this study, we set out to investigate the mechanism mediating nuclear import of the small subunit ribosomal protein Rps2. We demonstrate that an internal region in Rps2, ranging from amino acids 76 to 145, is sufficient to target a 3xyEGFP reporter to the nucleus. The importin-β Pse1 interacts with this Rps2 region and is involved in its import, with Rps2 residues arginine 95, arginine 97, and lysine 99 being important determinants for both Pse1 binding and nuclear localization. Moreover, our data reveal a second import mechanism involving the N-terminal region of Rps2, which depends on the presence of basic residues within amino acids 10 to 28. This Rps2 segment overlaps with the binding site of the dedicated chaperone Tsr4; however, the nuclear import of Rps2 via the internal as well as the N-terminal nuclear-targeting element does not depend on Tsr4. Taken together, our study has unveiled hitherto undescribed nuclear import signals, showcasing the versatility of the mechanisms coordinating the nuclear import of ribosomal proteins.
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Affiliation(s)
- Andreas Steiner
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria; (A.S.); (M.M.); (V.M.)
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Sébastien Favre
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland; (S.F.); (B.P.); (D.K.)
| | - Maximilian Mack
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria; (A.S.); (M.M.); (V.M.)
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Annika Hausharter
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria; (A.S.); (M.M.); (V.M.)
| | - Benjamin Pillet
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland; (S.F.); (B.P.); (D.K.)
| | - Jutta Hafner
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria; (A.S.); (M.M.); (V.M.)
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Valentin Mitterer
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria; (A.S.); (M.M.); (V.M.)
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Dieter Kressler
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland; (S.F.); (B.P.); (D.K.)
| | - Brigitte Pertschy
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria; (A.S.); (M.M.); (V.M.)
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Ingrid Zierler
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria; (A.S.); (M.M.); (V.M.)
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
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24
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Zhao T, Sun D, Long K, Lemos B, Zhang Q, Man J, Zhao M, Zhang Z. N 6-methyladenosine upregulates ribosome biogenesis in environmental carcinogenesis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163428. [PMID: 37061066 DOI: 10.1016/j.scitotenv.2023.163428] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/20/2023] [Accepted: 04/06/2023] [Indexed: 06/01/2023]
Abstract
Many trace metal pollutants in surface water, the atmosphere, and soil are carcinogenic, and ribosome biogenesis plays an important role in the carcinogenicity of heavy metals. However, the contradiction between upregulated ribosome biogenesis and decreased ribosomal DNA copy number in environmental carcinogenesis is not fully understood. Here, from a perspective of the most predominant and abundant RNA epigenetic modification, N6-methyladenosine (m6A), we explored the reason behind this contradiction at the post-transcriptional level using arsenite-induced skin carcinogenesis models both in vitro and in vivo. Based on the m6A microarray assay and a series of experiments, we found for the first time that the elevated m6A in arsenite-induced transformation is mainly enriched in the genes regulating ribosome biogenesis. m6A upregulates ribosome biogenesis post-transcriptionally by stabilizing ribosomal proteins and modulating non-coding RNAs targeting ribosomal RNAs and proteins, leading to arsenite-induced skin carcinogenesis. Using multi-omics analysis of human subjects and experimental validation, we identified an unconventional role of a well-known key proliferative signaling node AKT1 as a vital mediator between m6A and ribosome biogenesis in arsenic carcinogenesis. m6A activates AKT1 and transmits proliferative signals to ribosome biogenesis, exacerbating the upregulation of ribosome biogenesis in arsenite-transformed keratinocytes. Similarly, m6A promotes cell proliferation by upregulating ribosome biogenesis in cell transformation induced by carcinogenic heavy metals (chromium and nickel). Importantly, inhibiting m6A reduces ribosome biogenesis. Targeted inhibition of m6A-upregulated ribosome biogenesis effectively prevents cell transformation induced by trace metals (arsenic, chromium, and nickel). Our results reveal the mechanism of ribosome biogenesis upregulated by m6A in the carcinogenesis of trace metal pollutants. From the perspective of RNA epigenetics, our study improves our understanding of the contradiction between upregulated ribosome biogenesis and decreased ribosomal DNA copy number in the carcinogenesis of environmental carcinogens.
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Affiliation(s)
- Tianhe Zhao
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Donglei Sun
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Keyan Long
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Bernardo Lemos
- Department of Environmental Health & Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston 02108, MA, USA
| | - Qian Zhang
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Jin Man
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Manyu Zhao
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Zunzhen Zhang
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China.
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Qiang L, Zhao N, Liao K, Sun X, Wang Q, Jin H. Metabolomics and transcriptomics reveal the toxic mechanism of Cd and nano TiO 2 coexposure on rice (Oryza sativa L.). JOURNAL OF HAZARDOUS MATERIALS 2023; 453:131411. [PMID: 37062093 DOI: 10.1016/j.jhazmat.2023.131411] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/02/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
Engineered nanoparticles (ENPs) can resist heavy metal toxicity in plants, but their coexposure still exhibits toxicity to plants compared to plants without exposure to ENPs and heavy metals. There have been few studies on the toxic mechanism of nano TiO2-heavy metal coexposure and the effect mechanism of nano TiO2 in plants. Thus, transcriptomics and metabolomics were used to study the toxic mechanism of rutile nano TiO2 or TiO2-Cd (rutile nano TiO2 and CdCl2 mixture) on rice (Oryza sativa L.). After 40 days of exposure, the plant height and root dry weight of rice were significantly decreased in the nano TiO2-Cd group compared to the blank group (nano TiO2 and CdCl2 free). After Cd treatment, 423 differentially expressed genes (DEGs) and 16 differential metabolites were identified. Nano TiO2 exposure induced significant regulation of 299 DEGs and 6 metabolites. After nano TiO2-Cd coexposure, 1660 DEGs and 181 differential metabolites were identified. Notably, the EDGs (e.g., chalcone isomerase and hydroxycinnamoyl transferase) and differential metabolites (e.g., chrysin and galangin) demonstrated the disruption of flavonoid biosynthesis in Cd-treated rice. After rice was exposed to nano TiO2, the DEGs were related to ribosome, whereas the differential metabolites were associated with pyruvate metabolism and valine, leucine, and isoleucine biosynthesis. Furthermore, 14 DEGs (e.g., asparaginyl-tRNA synthetase and methionyl-tRNA formyltransferase) involved in aminoacyl-tRNA biosynthetic pathways were significantly upregulated in rice treated with nano TiO2-Cd, in line with the changes in related metabolites (e.g., L-asparagine and 10-formyltetrahydrofolate). Our results show that it is necessary to pay close attention to the toxicity of nano TiO2-Cd coexposure in paddy ecosystems and use ENPs with caution to combat the phytotoxicity of heavy metals.
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Affiliation(s)
- Liwen Qiang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, PR China
| | - Nan Zhao
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Kaizhen Liao
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Xichao Sun
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, PR China
| | - Qiang Wang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, PR China
| | - Hangbiao Jin
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, PR China.
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26
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Wu S, Chen J, Teo BHD, Wee SYK, Wong MHM, Cui J, Chen J, Leong KP, Lu J. The axis of complement C1 and nucleolus in antinuclear autoimmunity. Front Immunol 2023; 14:1196544. [PMID: 37359557 PMCID: PMC10288996 DOI: 10.3389/fimmu.2023.1196544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/19/2023] [Indexed: 06/28/2023] Open
Abstract
Antinuclear autoantibodies (ANA) are heterogeneous self-reactive antibodies that target the chromatin network, the speckled, the nucleoli, and other nuclear regions. The immunological aberration for ANA production remains partially understood, but ANA are known to be pathogenic, especially, in systemic lupus erythematosus (SLE). Most SLE patients exhibit a highly polygenic disease involving multiple organs, but in rare complement C1q, C1r, or C1s deficiencies, the disease can become largely monogenic. Increasing evidence point to intrinsic autoimmunogenicity of the nuclei. Necrotic cells release fragmented chromatins as nucleosomes and the alarmin HMGB1 is associated with the nucleosomes to activate TLRs and confer anti-chromatin autoimmunogenecity. In speckled regions, the major ANA targets Sm/RNP and SSA/Ro contain snRNAs that confer autoimmunogenecity to Sm/RNP and SSA/Ro antigens. Recently, three GAR/RGG-containing alarmins have been identified in the nucleolus that helps explain its high autoimmunogenicity. Interestingly, C1q binds to the nucleoli exposed by necrotic cells to cause protease C1r and C1s activation. C1s cleaves HMGB1 to inactive its alarmin activity. C1 proteases also degrade many nucleolar autoantigens including nucleolin, a major GAR/RGG-containing autoantigen and alarmin. It appears that the different nuclear regions are intrinsically autoimmunogenic by containing autoantigens and alarmins. However, the extracellular complement C1 complex function to dampen nuclear autoimmunogenecity by degrading these nuclear proteins.
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Affiliation(s)
- Shan Wu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Junjie Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Boon Heng Dennis Teo
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Seng Yin Kelly Wee
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ming Hui Millie Wong
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jianzhou Cui
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jinmiao Chen
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
| | - Khai Pang Leong
- Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore, Singapore
| | - Jinhua Lu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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27
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Wang K, Chen S, Wu Y, Wang Y, Lu Y, Sun Y, Chen Y. The ufmylation modification of ribosomal protein L10 in the development of pancreatic adenocarcinoma. Cell Death Dis 2023; 14:350. [PMID: 37280198 DOI: 10.1038/s41419-023-05877-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/04/2023] [Accepted: 05/31/2023] [Indexed: 06/08/2023]
Abstract
Pancreatic adenocarcinoma (PAAD) is the most malignant cancer with a high mortality rate. Despite the association of ribosomal protein L10 (RPL10) with PAAD and previous reports on RPL26 ufmylation, the relationship between RPL10 ufmylation and PAAD development remains unexplored. Here, we report the dissection of ufmylating process of RPL10 and potential roles of RPL10 ufmylation in PAAD development. The ufmylation of RPL10 was confirmed in both pancreatic patient tissues and cell lines, and specific modification sites were identified and verified. Phenotypically, RPL10 ufmylation significantly increased cell proliferation and stemness, which is principally resulted from higher expression of transcription factor KLF4. Moreover, the mutagenesis of ufmylation sites in RPL10 further demonstrated the connection of RPL10 ufmylation with cell proliferation and stemness. Collectively, this study reveals that PRL10 ufmylation plays an important role to enhance the stemness of pancreatic cancer cells for PAAD development.
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Affiliation(s)
- Kun Wang
- State Key Laboratory of Natural Medicines and Laboratory of Chemical Biology, China Pharmaceutical University, 639 Longmian Ave., Nanjing, Jiangsu Province, 211198, China
| | - Siyu Chen
- State Key Laboratory of Natural Medicines and Laboratory of Chemical Biology, China Pharmaceutical University, 639 Longmian Ave., Nanjing, Jiangsu Province, 211198, China
| | - Yue Wu
- State Key Laboratory of Natural Medicines and Laboratory of Chemical Biology, China Pharmaceutical University, 639 Longmian Ave., Nanjing, Jiangsu Province, 211198, China
| | - Yang Wang
- State Key Laboratory of Natural Medicines and Laboratory of Chemical Biology, China Pharmaceutical University, 639 Longmian Ave., Nanjing, Jiangsu Province, 211198, China
| | - Yousheng Lu
- Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & the Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting, Kunlun Road, Nanjing, Jiangsu Province, 210009, China
| | - Yanzi Sun
- State Key Laboratory of Natural Medicines and Laboratory of Chemical Biology, China Pharmaceutical University, 639 Longmian Ave., Nanjing, Jiangsu Province, 211198, China
| | - Yijun Chen
- State Key Laboratory of Natural Medicines and Laboratory of Chemical Biology, China Pharmaceutical University, 639 Longmian Ave., Nanjing, Jiangsu Province, 211198, China.
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, 401135, China.
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28
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Folgado-Marco V, Ames K, Chuen J, Gritsman K, Baker NE. Haploinsufficiency of the essential gene Rps12 causes defects in erythropoiesis and hematopoietic stem cell maintenance. eLife 2023; 12:e69322. [PMID: 37272618 PMCID: PMC10287158 DOI: 10.7554/elife.69322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 04/26/2023] [Indexed: 06/06/2023] Open
Abstract
Ribosomal protein (Rp) gene haploinsufficiency can result in Diamond-Blackfan Anemia (DBA), characterized by defective erythropoiesis and skeletal defects. Some mouse Rp mutations recapitulate DBA phenotypes, although others lack erythropoietic or skeletal defects. We generated a conditional knockout mouse to partially delete Rps12. Homozygous Rps12 deletion resulted in embryonic lethality. Mice inheriting the Rps12KO/+ genotype had growth and morphological defects, pancytopenia, and impaired erythropoiesis. A striking reduction in hematopoietic stem cells (HSCs) and progenitors in the bone marrow (BM) was associated with decreased ability to repopulate the blood system after competitive and non-competitive BM transplantation. Rps12KO/+ lost HSC quiescence, experienced ERK and MTOR activation, and increased global translation in HSC and progenitors. Post-natal heterozygous deletion of Rps12 in hematopoietic cells using Tal1-Cre-ERT also resulted in pancytopenia with decreased HSC numbers. However, post-natal Cre-ERT induction led to reduced translation in HSCs and progenitors, suggesting that this is the most direct consequence of Rps12 haploinsufficiency in hematopoietic cells. Thus, RpS12 has a strong requirement in HSC function, in addition to erythropoiesis.
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Affiliation(s)
| | - Kristina Ames
- Department of Medical Oncology, Albert Einstein College of MedicineBronxUnited States
- Department of Cell Biology, Albert Einstein College of MedicineBronxUnited States
| | - Jacky Chuen
- Department of Genetics, Albert Einstein College of MedicineBronxUnited States
| | - Kira Gritsman
- Department of Medical Oncology, Albert Einstein College of MedicineBronxUnited States
- Department of Cell Biology, Albert Einstein College of MedicineBronxUnited States
| | - Nicholas E Baker
- Department of Genetics, Albert Einstein College of MedicineBronxUnited States
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29
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Zhang Z, Xia T, Zhou S, Yang X, Lyu T, Wang L, Fang J, Wang Q, Dou H, Zhang H. High-Quality Chromosome-Level Genome Assembly of the Corsac Fox ( Vulpes corsac) Reveals Adaptation to Semiarid and Harsh Environments. Int J Mol Sci 2023; 24:ijms24119599. [PMID: 37298549 DOI: 10.3390/ijms24119599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
The Corsac fox (Vulpes corsac) is a species of fox distributed in the arid prairie regions of Central and Northern Asia, with distinct adaptations to dry environments. Here, we applied Oxford-Nanopore sequencing and a chromosome structure capture technique to assemble the first Corsac fox genome, which was then assembled into chromosome fragments. The genome assembly has a total length of 2.2 Gb with a contig N50 of 41.62 Mb and a scaffold N50 of 132.2 Mb over 18 pseudo-chromosomal scaffolds. The genome contained approximately 32.67% of repeat sequences. A total of 20,511 protein-coding genes were predicted, of which 88.9% were functionally annotated. Phylogenetic analyses indicated a close relation to the Red fox (Vulpes vulpes) with an estimated divergence time of ~3.7 million years ago (MYA). We performed separate enrichment analyses of species-unique genes, the expanded and contracted gene families, and positively selected genes. The results suggest an enrichment of pathways related to protein synthesis and response and an evolutionary mechanism by which cells respond to protein denaturation in response to heat stress. The enrichment of pathways related to lipid and glucose metabolism, potentially preventing stress from dehydration, and positive selection of genes related to vision, as well as stress responses in harsh environments, may reveal adaptive evolutionary mechanisms in the Corsac fox under harsh drought conditions. Additional detection of positive selection for genes associated with gustatory receptors may reveal a unique desert diet strategy for the species. This high-quality genome provides a valuable resource for studying mammalian drought adaptation and evolution in the genus Vulpes.
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Affiliation(s)
- Zhihao Zhang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Tian Xia
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Shengyang Zhou
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Xiufeng Yang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Tianshu Lyu
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Lidong Wang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Jiaohui Fang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Qi Wang
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir 021000, China
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir 021000, China
| | - Honghai Zhang
- School of Life Science, Qufu Normal University, Qufu 273165, China
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30
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Miller SC, MacDonald CC, Kellogg MK, Karamysheva ZN, Karamyshev AL. Specialized Ribosomes in Health and Disease. Int J Mol Sci 2023; 24:ijms24076334. [PMID: 37047306 PMCID: PMC10093926 DOI: 10.3390/ijms24076334] [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: 02/28/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
Ribosomal heterogeneity exists within cells and between different cell types, at specific developmental stages, and occurs in response to environmental stimuli. Mounting evidence supports the existence of specialized ribosomes, or specific changes to the ribosome that regulate the translation of a specific group of transcripts. These alterations have been shown to affect the affinity of ribosomes for certain mRNAs or change the cotranslational folding of nascent polypeptides at the exit tunnel. The identification of specialized ribosomes requires evidence of the incorporation of different ribosomal proteins or of modifications to rRNA and/or protein that lead(s) to physiologically relevant changes in translation. In this review, we summarize ribosomal heterogeneity and specialization in mammals and discuss their relevance to several human diseases.
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Affiliation(s)
- Sarah C. Miller
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Clinton C. MacDonald
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Morgana K. Kellogg
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | | | - Andrey L. Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Correspondence: ; Tel.: +1-806-743-4102
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31
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Chen QG, Zhang YM, Chen C, Wang S, Li ZF, Hou ZF, Liu DD, Tao JP, Xu JJ. Tandem mass tag-based quantitative proteomics analyses of a chicken-original virulent and its attenuated Histomonas meleagridis strain in China. Front Vet Sci 2023; 10:1106807. [PMID: 37008342 PMCID: PMC10063853 DOI: 10.3389/fvets.2023.1106807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/27/2023] [Indexed: 03/19/2023] Open
Abstract
IntroductionHistomonas meleagridis can cause histomonosis in poultry. Due to the prohibition of effective drugs, the prevention and treatment of the disease requires new strategies. Questions about its pathogenic mechanisms and virulence factors remain puzzling.MethodsTo address these issues, a tandem mass tag (TMT) comparative proteomic analysis of a virulent strain and its attenuated strain of Chinese chicken-origin was performed.ResultsA total of 3,494 proteins were identified in the experiment, of which 745 proteins were differentially expressed (fold change ≥1.2 or ≤0.83 and p < 0.05), with 192 up-regulated proteins and 553 down-regulated proteins in the virulent strain relative to the attenuated strain.DiscussionSurface protein BspA like, digestive cysteine proteinase, actin, and GH family 25 lysozyme were noted among the proteins up regulated in virulent strains, and these several proteins may be directly related to the pathogenic capacity of the histomonad. Ferredoxin, 60S ribosomal protein L6, 40S ribosomal protein S3, and NADP-dependent malic enzyme which associated with biosynthesis and metabolism were also noted, which have the potential to be new drug targets. The up-regulation of alpha-amylase, ras-like protein 1, ras-like protein 2, and involucrin in attenuated strains helps to understand how it is adapted to the long-term in vitro culture environment. The above results provide some candidate protein-coding genes for further functional verification, which will help to understand the molecular mechanism of pathogenicity and attenuation of H. meleagridis more comprehensively.
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Affiliation(s)
- Qiao-Guang Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, China
| | - Yu-Ming Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, China
| | - Chen Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, China
| | - Shuang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, China
| | - Zai-Fan Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, China
| | - Zhao-Feng Hou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, China
| | - Dan-Dan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, China
| | - Jian-Ping Tao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, China
| | - Jin-Jun Xu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, China
- *Correspondence: Jin-Jun Xu
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Mu J, Wang Y, Wang M, Zhang D, Liu M. Identification of reliable reference genes for gene expression studies in mouse models under microplastics stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 252:114569. [PMID: 36696727 DOI: 10.1016/j.ecoenv.2023.114569] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 06/17/2023]
Abstract
Microplastics (MPs) and nanoplastics (NPs) have been deemed to be newly emerged contaminants interfering with various physiological processes closely related with gene expression alteration. Reverse transcriptase quantitative real-time polymerase chain reaction (RT-qPCR) serves as a powerful tool to assess gene expression, however highly dependent on a reliable reference gene. Therefore, it is necessary to identify stable reference genes for gene expression study under MP or NP stress. We constructed a mouse model postexposure to polypropylene microplastics (PP-MPs) to assess PP-MPs bioaccumulation in kidney, evaluate the kidney pathological changes, and then explore potential reference genes via RT-qPCR. Although the hematoxylin-eosin staining showed no obvious damage in kidney tissues, we observed significant PP-MPs accumulation in kidney using Raman spectra analysis supported by spectral multivariate analysis. The expression of 19 candidate reference genes were examined, including the commonly used ones of β-actin, glyceraldehyde 3-phosphate dehydrogenase (Gapdh), Cytochrome c oxidase subunit 4I1 (Cox4i), Histocompatibility 13 (H13) and ribosomal protein. Their expression stability and reliability were assessed by the combination of four algorithms including geNorm, NormFinder, BestKeeper and Delta Cq. The geNorm analysis revealed that the top three genes with the lowest variability were Cox4il, Rps9 and Gapdh, whereas NormFinder results ranked Rps3, Cox4il and Rps18 as the top three ones. Rpl15, Cox4i1 and Rps3 were the most reliable reference genes in BestKeeper results, and Delta Cq proposed Rps3 and Cox4il as the stable genes. The overall ranking indicated by GMR value gave the five most stable reference genes (Cox4i1, Rps3, Rps9, Rps18 and Gapdh). Three genes associated with different biochemical processes (Atp5f1, Crebbp and Dele1) were chosen to verify the characterized reference genes using the least stable gene as a control, exhibiting different expression profiles and implying the essentiality to select the reliable reference genes. Our results documented the expression fluctuations of acknowledged reference gene (Ubc) and proposed a set of reliable reference genes for future studies of gene expression profiles in MP treated mouse models.
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Affiliation(s)
- Ju Mu
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, PR China
| | - Yu Wang
- The First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou 310053, PR China
| | - Miao Wang
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, PR China
| | - Dayi Zhang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Changchun 130021, PR China; College of New Energy and Environment, Jilin University, Changchun 130021, PR China.
| | - Mingying Liu
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, PR China.
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33
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Filipek K, Deryło K, Michalec-Wawiórka B, Zaciura M, González-Ibarra A, Krokowski D, Latoch P, Starosta AL, Czapiński J, Rivero-Müller A, Wawiórka L, Tchórzewski M. Identification of a novel alternatively spliced isoform of the ribosomal uL10 protein. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194890. [PMID: 36328276 DOI: 10.1016/j.bbagrm.2022.194890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/06/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022]
Abstract
Alternative splicing is one of the key mechanisms extending the complexity of genetic information and at the same time adaptability of higher eukaryotes. As a result, the broad spectrum of isoforms produced by alternative splicing allows organisms to fine-tune their proteome; however, the functions of the majority of alternatively spliced protein isoforms are largely unknown. Ribosomal protein isoforms are one of the groups for which data are limited. Here we report characterization of an alternatively spliced isoform of the ribosomal uL10 protein, named uL10β. The uL10 protein constitutes the core element of the ribosomal stalk structure within the GTPase associated center, which represents the landing platform for translational GTPases - trGTPases. The stalk plays an important role in the ribosome-dependent stimulation of GTP by trGTPases, which confer unidirectional trajectory for the ribosome, allosterically contributing to the speed and accuracy of translation. We have shown that the newly identified uL10β protein is stably expressed in mammalian cells and is primarily located within the nuclear compartment with a minor signal within the cytoplasm. Importantly, uL10β is able to bind to the ribosomal particle, but is mainly associated with 60S and 80S particles; additionally, the uL10β undergoes re-localization into the mitochondria upon endoplasmic reticulum stress induction. Our results suggest a specific stress-related dual role of uL10β, supporting the idea of existence of specialized ribosomes with an altered GTPase associated center.
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Affiliation(s)
- Kamil Filipek
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Kamil Deryło
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Barbara Michalec-Wawiórka
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Monika Zaciura
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Alan González-Ibarra
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Dawid Krokowski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Przemysław Latoch
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland; Polish-Japanese Academy of Information Technology, Warsaw 02-008, Poland
| | - Agata L Starosta
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Jakub Czapiński
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 21-093 Lublin, Poland
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 21-093 Lublin, Poland
| | - Leszek Wawiórka
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Marek Tchórzewski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland.
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Silencing RPL8 inhibits the progression of hepatocellular carcinoma by down-regulating the mTORC1 signalling pathway. Hum Cell 2023; 36:725-737. [PMID: 36577883 DOI: 10.1007/s13577-022-00852-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022]
Abstract
This study aimed to explore the role of ribosomal protein L8 (RPL8) in controlling hepatocellular carcinoma (LIHC) development. We measured RPL8 expression, apoptosis, cell viability, proliferation, migration, invasion, glucose uptake, lactate production, and the ATP/ADP ratio of LIHC cells to investigate the effect of RPL8 on LIHC. Bioinformatic analysis was employed to analyse RPL8 expression and its potential mechanism in LIHC. RPL8 was upregulated in LIHC tissues and cells. RPL8 silencing accelerated apoptosis and suppressed viability, growth, and movement of LIHC cells. Additionally, RPL8 silencing inhibited glycolysis in LIHC cells. Bioinformatic analysis revealed that RPL8 is regulated by the upstream transcription factor upstream stimulating factor 1 (USF1) and activates the mTORC1 signalling pathway. USF1 overexpression eliminated the inhibitory effect of RPL8 silencing in LIHC cells. RPL8 overexpression increased cell growth, movement, and glycolysis in LIHC. However, inhibition of the mTORC1 signalling pathway eliminated the effect of RPL8 overexpression on LIHC cells. In conclusion, RPL8 may affect LIHC progression by regulating the mTORC1 signalling pathway.
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35
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Luo J, Zhao H, Chen L, Liu M. Multifaceted functions of RPS27a: An unconventional ribosomal protein. J Cell Physiol 2023; 238:485-497. [PMID: 36580426 DOI: 10.1002/jcp.30941] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/28/2022] [Accepted: 12/21/2022] [Indexed: 12/30/2022]
Abstract
The ribosomal protein S27a (RPS27a) is cleaved from the fusion protein ubiquitin-RPS27a (Ub-RPS27a). Generally, Ub and RPS27a are coexpressed as a fusion protein but function independently after Ub is cleaved from RPS27a by a deubiquitinating enzyme. As an RP, RPS27a assembles into ribosomes, but it also functions independently of ribosomes. RPS27a is involved in the development and poor prognosis of various cancers, such as colorectal cancer, liver cancer, chronic myeloid leukemia, and renal carcinoma, and is associated with poor prognosis. Notably, the murine double minute 2/P53 axis is a major pathway through which RPS27a regulates cancer development. Moreover, RPS27a maintains sperm motility, regulates winged aphid indirect flight muscle degeneration, and facilitates plant growth. Additionally, RPS27a is a metalloprotein and mercury (Hg) biomarker. In the present review, we described the origin, structure, and biological functions of RPS27a.
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Affiliation(s)
- Jingshun Luo
- Key Laboratory of Cardiovascular Diseases of Yunnan Province, Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Central laboratory of Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, China
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Hong Zhao
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Nursing College, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Linxi Chen
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Meiqing Liu
- Key Laboratory of Cardiovascular Diseases of Yunnan Province, Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Central laboratory of Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, China
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36
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Parker MD, Karbstein K. Quality control ensures fidelity in ribosome assembly and cellular health. J Cell Biol 2023; 222:213871. [PMID: 36790396 PMCID: PMC9960125 DOI: 10.1083/jcb.202209115] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/09/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
The coordinated integration of ribosomal RNA and protein into two functional ribosomal subunits is safeguarded by quality control checkpoints that ensure ribosomes are correctly assembled and functional before they engage in translation. Quality control is critical in maintaining the integrity of ribosomes and necessary to support healthy cell growth and prevent diseases associated with mistakes in ribosome assembly. Its importance is demonstrated by the finding that bypassing quality control leads to misassembled, malfunctioning ribosomes with altered translation fidelity, which change gene expression and disrupt protein homeostasis. In this review, we outline our understanding of quality control within ribosome synthesis and how failure to enforce quality control contributes to human disease. We first provide a definition of quality control to guide our investigation, briefly present the main assembly steps, and then examine stages of assembly that test ribosome function, establish a pass-fail system to evaluate these functions, and contribute to altered ribosome performance when bypassed, and are thus considered "quality control."
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Affiliation(s)
- Melissa D. Parker
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA,University of Florida—Scripps Biomedical Research, Jupiter, FL, USA
| | - Katrin Karbstein
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA,University of Florida—Scripps Biomedical Research, Jupiter, FL, USA,Howard Hughes Medical Institute Faculty Scholar, Howard Hughes Medical Institute, Chevy Chase, MD, USA,Correspondence to Katrin Karbstein:
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37
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Lander AJ, Jin Y, Luk LYP. D-Peptide and D-Protein Technology: Recent Advances, Challenges, and Opportunities. Chembiochem 2023; 24:e202200537. [PMID: 36278392 PMCID: PMC10805118 DOI: 10.1002/cbic.202200537] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/23/2022] [Indexed: 11/08/2022]
Abstract
Total chemical protein synthesis provides access to entire D-protein enantiomers enabling unique applications in molecular biology, structural biology, and bioactive compound discovery. Key enzymes involved in the central dogma of molecular biology have been prepared in their D-enantiomeric forms facilitating the development of mirror-image life. Crystallization of a racemic mixture of L- and D-protein enantiomers provides access to high-resolution X-ray structures of polypeptides. Additionally, D-enantiomers of protein drug targets can be used in mirror-image phage display allowing discovery of non-proteolytic D-peptide ligands as lead candidates. This review discusses the unique applications of D-proteins including the synthetic challenges and opportunities.
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Affiliation(s)
- Alexander J. Lander
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
| | - Yi Jin
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
| | - Louis Y. P. Luk
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
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38
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Dörner K, Ruggeri C, Zemp I, Kutay U. Ribosome biogenesis factors-from names to functions. EMBO J 2023; 42:e112699. [PMID: 36762427 PMCID: PMC10068337 DOI: 10.15252/embj.2022112699] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/13/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
The assembly of ribosomal subunits is a highly orchestrated process that involves a huge cohort of accessory factors. Most eukaryotic ribosome biogenesis factors were first identified by genetic screens and proteomic approaches of pre-ribosomal particles in Saccharomyces cerevisiae. Later, research on human ribosome synthesis not only demonstrated that the requirement for many of these factors is conserved in evolution, but also revealed the involvement of additional players, reflecting a more complex assembly pathway in mammalian cells. Yet, it remained a challenge for the field to assign a function to many of the identified factors and to reveal their molecular mode of action. Over the past decade, structural, biochemical, and cellular studies have largely filled this gap in knowledge and led to a detailed understanding of the molecular role that many of the players have during the stepwise process of ribosome maturation. Such detailed knowledge of the function of ribosome biogenesis factors will be key to further understand and better treat diseases linked to disturbed ribosome assembly, including ribosomopathies, as well as different types of cancer.
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Affiliation(s)
- Kerstin Dörner
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, Zurich, Switzerland
| | - Chiara Ruggeri
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,RNA Biology Ph.D. Program, Zurich, Switzerland
| | - Ivo Zemp
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Ulrike Kutay
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
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Yang C, Tang L, Qin L, Zhong W, Tang X, Gong X, Xie W, Li Y, Xia S. mRNA Turnover Protein 4 Is Vital for Fungal Pathogenicity and Response to Oxidative Stress in Sclerotinia sclerotiorum. Pathogens 2023; 12:pathogens12020281. [PMID: 36839553 PMCID: PMC9960052 DOI: 10.3390/pathogens12020281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Ribosome assembly factors have been extensively studied in yeast, and their abnormalities may affect the assembly process of ribosomes and cause severe damage to cells. However, it is not clear whether mRNA turnover protein 4 (MRT4) functions in the fungal growth and pathogenicity in Sclerotinia sclerotiorum. Here, we identified the nucleus-located gene SsMRT4 using reverse genetics, and found that knockdown of SsMRT4 resulted in retard mycelia growth and complete loss of pathogenicity. Furthermore, mrt4 knockdown mutants showed almost no appressorium formation and oxalic acid production comparing to the wild-type and complementary strains. In addition, the abilities to ROS elimination and resistance to oxidative and osmotic stresses were also seriously compromised in mrt4 mutants. Overall, our study clarified the role of SsMRT4 in S. sclerotiorum, providing new insights into ribosome assembly in regulating pathogenicity and resistance to environmental stresses of fungi.
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Affiliation(s)
- Chenghuizi Yang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Lan Tang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Lei Qin
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Weiping Zhong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Xianyu Tang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Xin Gong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Wenqi Xie
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Yifu Li
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Shitou Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
- Correspondence:
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40
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Liu C, Guo H, Zhao X, Zou B, Sun T, Feng J, Zeng Z, Wen X, Chen J, Hu Z, Lou S, Li H. Overexpression of 18S rRNA methyltransferase CrBUD23 enhances biomass and lutein content in Chlamydomonas reinhardtii. Front Bioeng Biotechnol 2023; 11:1102098. [PMID: 36815903 PMCID: PMC9935685 DOI: 10.3389/fbioe.2023.1102098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/10/2023] [Indexed: 02/05/2023] Open
Abstract
Post-transcriptional modification of nucleic acids including transfer RNA (tRNA), ribosomal RNA (rRNA) and messenger RNA (mRNA) is vital for fine-tunning of mRNA translation. Methylation is one of the most widespread post-transcriptional modifications in both eukaryotes and prokaryotes. HsWBSCR22 and ScBUD23 encodes a 18S rRNA methyltransferase that positively regulates cell growth by mediating ribosome maturation in human and yeast, respectively. However, presence and function of 18S rRNA methyltransferase in green algae are still elusive. Here, through bioinformatic analysis, we identified CrBUD23 as the human WBSCR22 homolog in genome of the green algae model organism Chlamydonomas reinhardtii. CrBUD23 was a conserved putative 18S rRNA methyltransferase widely exited in algae, plants, insects and mammalians. Transcription of CrBUD23 was upregulated by high light and down-regulated by low light, indicating its role in photosynthesis and energy metabolism. To characterize its biological function, coding sequence of CrBUD23 fused with a green fluorescence protein (GFP) tag was derived by 35S promoter and stably integrated into Chlamydomonas genome by glass bead-mediated transformation. Compared to C. reinhardtii wild type CC-5325, transgenic strains overexpressing CrBUD23 resulted in accelerated cell growth, thereby leading to elevated biomass, dry weight and protein content. Moreover, overexpression of CrBUD23 increased content of photosynthetic pigments but not elicit the activation of antioxidative enzymes, suggesting CrBUD23 favors growth and proliferation in the trade-off with stress responses. Bioinformatic analysis revealed the G1177 was the putative methylation site in 18S rRNA of C. reinhardtii CC-849. G1177 was conserved in other Chlamydonomas isolates, indicating the conserved methyltransferase activity of BUD23 proteins. In addition, CrTrm122, the homolog of BUD23 interactor Trm112, was found involved in responses to high light as same as CrBUD23. Taken together, our study revealed that cell growth, protein content and lutein accumulation of Chlamydomonas were positively regulated by the 18S rRNA methyltransferase CrBUD23, which could serve as a promising candidate for microalgae genetic engineering.
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Affiliation(s)
- Chenglong Liu
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China,College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Haoze Guo
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Xinmei Zhao
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Bingxi Zou
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Ting Sun
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Jinwei Feng
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Zhiyong Zeng
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Xueer Wen
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Jun Chen
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Zhangli Hu
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Sulin Lou
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China,*Correspondence: Hui Li, ; Sulin Lou,
| | - Hui Li
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China,*Correspondence: Hui Li, ; Sulin Lou,
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Comparative Research: Regulatory Mechanisms of Ribosomal Gene Transcription in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Biomolecules 2023; 13:biom13020288. [PMID: 36830657 PMCID: PMC9952952 DOI: 10.3390/biom13020288] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Restricting ribosome biosynthesis and assembly in response to nutrient starvation is a universal phenomenon that enables cells to survive with limited intracellular resources. When cells experience starvation, nutrient signaling pathways, such as the target of rapamycin (TOR) and protein kinase A (PKA), become quiescent, leading to several transcription factors and histone modification enzymes cooperatively and rapidly repressing ribosomal genes. Fission yeast has factors for heterochromatin formation similar to mammalian cells, such as H3K9 methyltransferase and HP1 protein, which are absent in budding yeast. However, limited studies on heterochromatinization in ribosomal genes have been conducted on fission yeast. Herein, we shed light on and compare the regulatory mechanisms of ribosomal gene transcription in two species with the latest insights.
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Cytosolic and mitochondrial ribosomal proteins mediate the locust phase transition via divergence of translational profiles. Proc Natl Acad Sci U S A 2023; 120:e2216851120. [PMID: 36701367 PMCID: PMC9945961 DOI: 10.1073/pnas.2216851120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The phase transition from solitary to gregarious locusts is crucial in outbreaks of locust plague, which threaten agricultural yield and food security. Research on the regulatory mechanisms of phase transition in locusts has focused primarily on the transcriptional or posttranslational level. However, the translational regulation of phase transition is unexplored. Here, we show a phase-dependent pattern at the translation level, which exhibits different polysome profiles between gregarious and solitary locusts. The gregarious locusts exhibit significant increases in 60S and polyribosomes, while solitary locusts possess higher peaks of the monoribosome and a specific "halfmer." The polysome profiles, a molecular phenotype, respond to changes in population density. In gregarious locusts, ten genes involved in the cytosolic ribosome pathway exhibited increased translational efficiency (TE). In solitary locusts, five genes from the mitochondrial ribosome pathway displayed increased TE. The high expression of large ribosomal protein 7 at the translational level promotes accumulation of the free 60S ribosomal subunit in gregarious locusts, while solitary locusts employ mitochondrial small ribosomal protein 18c to induce the assembly of mitochondrial ribosomes, causing divergence of the translational profiles and behavioral transition. This study reveals the translational regulatory mechanism of locust phase transition, in which the locusts employ divergent ribosome pathways to cope with changes in population density.
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Murphy JC, Harrington EM, Schumann S, Vasconcelos EJR, Mottram TJ, Harper KL, Aspden JL, Whitehouse A. Kaposi's sarcoma-associated herpesvirus induces specialised ribosomes to efficiently translate viral lytic mRNAs. Nat Commun 2023; 14:300. [PMID: 36653366 PMCID: PMC9849454 DOI: 10.1038/s41467-023-35914-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 01/06/2023] [Indexed: 01/19/2023] Open
Abstract
Historically, ribosomes were viewed as unchanged homogeneous macromolecular machines with no regulatory capacity for mRNA translation. An emerging concept is that heterogeneity of ribosomal composition exists, exerting a regulatory function or specificity in translational control. This is supported by recent discoveries identifying compositionally distinct specialised ribosomes that actively regulate mRNA translation. Viruses lack their own translational machinery and impose high translational demands on the host during replication. We explore the possibility that KSHV manipulates ribosome biogenesis producing specialised ribosomes which preferentially translate viral transcripts. Quantitative proteomic analysis identified changes in the stoichiometry and composition of precursor ribosomal complexes during the switch from latent to lytic replication. We demonstrate the enhanced association of ribosomal biogenesis factors BUD23 and NOC4L, and the KSHV ORF11 protein, with small ribosomal subunit precursor complexes during lytic replication. BUD23 depletion resulted in significantly reduced viral gene expression, culminating in dramatic reduction of infectious virion production. Ribosome profiling demonstrated BUD23 is essential for reduced association of ribosomes with KSHV uORFs in late lytic genes, required for the efficient translation of the downstream coding sequence. Results provide mechanistic insights into KSHV-mediated manipulation of cellular ribosome composition inducing a population of specialised ribosomes facilitating efficient translation of viral mRNAs.
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Affiliation(s)
- James C Murphy
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Elena M Harrington
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sophie Schumann
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | | | - Timothy J Mottram
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Katherine L Harper
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Julie L Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
- LeedsOmics, University of Leeds, Leeds, LS2 9JT, UK
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
- LeedsOmics, University of Leeds, Leeds, LS2 9JT, UK.
- Department of Biochemistry & Microbiology, Rhodes University, Grahamstown, 6140, South Africa.
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Chromatin localization of nucleophosmin organizes ribosome biogenesis. Mol Cell 2022; 82:4443-4457.e9. [PMID: 36423630 PMCID: PMC9949351 DOI: 10.1016/j.molcel.2022.10.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 09/01/2022] [Accepted: 10/28/2022] [Indexed: 11/24/2022]
Abstract
Ribosome biogenesis takes place in the nucleolus, a nuclear membrane-less organelle. Although well studied, it remains unknown how nascent ribosomal subunits separate from the central chromatin compartment and move to the outer granular component, where maturation occurs. We find that the Schizosaccharomyces pombe nucleophosmin-like protein Fkbp39 localizes to rDNA sites encoding the 60S subunit rRNA, and this localization contributes to its specific association with nascent 60S subunits. Fkbp39 dissociates from chromatin to bind nascent 60S subunits, causing the latter to partition away from chromatin and from nascent 40S subunits through liquid-liquid phase separation. In vivo, Fkbp39 binding directs the translocation of nascent 60S subunits toward the nucleophosmin-rich granular component. This process increases the efficiency of 60S subunit assembly, facilitating the incorporation of 60S RNA domain III. Thus, chromatin localization determines the specificity of nucleophosmin in sorting nascent ribosomal subunits and coordinates their movement into specialized assembly compartments within the nucleolus.
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Hannan KM, Soo P, Wong MS, Lee JK, Hein N, Poh P, Wysoke KD, Williams TD, Montellese C, Smith LK, Al-Obaidi SJ, Núñez-Villacís L, Pavy M, He JS, Parsons KM, Loring KE, Morrison T, Diesch J, Burgio G, Ferreira R, Feng ZP, Gould CM, Madhamshettiwar PB, Flygare J, Gonda TJ, Simpson KJ, Kutay U, Pearson RB, Engel C, Watkins NJ, Hannan RD, George AJ. Nuclear stabilization of p53 requires a functional nucleolar surveillance pathway. Cell Rep 2022; 41:111571. [DOI: 10.1016/j.celrep.2022.111571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/06/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
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46
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Sharen G, Li X, Sun J, Zhang L, Xi W, Zhao X, Han F, Jia L, A R, Cheng H, Hou M. Silencing eL31 suppresses the progression of colorectal cancer via targeting DEPDC1. J Transl Med 2022; 20:493. [PMID: 36309731 PMCID: PMC9617412 DOI: 10.1186/s12967-022-03663-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 09/25/2022] [Indexed: 11/10/2022] Open
Abstract
Background Colorectal cancer (CRC) is one of the most commonly diagnosed human malignancies. Ribosomal protein L31 (RPL31, aka eL31) is a component of the 60S large ribosomal subunit, and its expression pattern and functional role in CRC have not been reported. Methods Herein, we identified that eL31 protein level was dramatically increased in CRC tissues through using IHC analysis. More notably, elevated eL31 was associated with larger tumor size and shorter overall survival. Besides, we evaluated the effects of eL31 depletion on CRC cell phenotypes in vitro. Results The data indicated that eL31 knockdown restricted CRC cell proliferation, migration and colony formation whilst enhancing cell apoptosis. Importantly, eL31 was also essential for CRC tumor growth in vivo, as demonstrated by impaired tumor growth markers and reduced Ki67 levels in xenografts from eL31-depleted cells. In addition, our evidence indicated that DEP domain containing 1 (DEPDC1) was a potential downstream target of eL31 in regulating CRC. Consistently, DEPDC1 depletion restrained CRC cell proliferation and migration, as well as facilitated cell apoptosis. More interestingly, DEPDC1 depletion could reverse the promotion effects of eL31 elevation on CRC cells. Conclusions Identification of eL31’s function in CRC may pave the way for future development of more specific and more effective targeted therapy strategies against CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03663-6.
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Buchanan IM, Smith TM, Gerber AP, Seibt J. Are there roles for heterogeneous ribosomes during sleep in the rodent brain? Front Mol Biosci 2022; 9:1008921. [PMID: 36275625 PMCID: PMC9582285 DOI: 10.3389/fmolb.2022.1008921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
The regulation of mRNA translation plays an essential role in neurons, contributing to important brain functions, such as brain plasticity and memory formation. Translation is conducted by ribosomes, which at their core consist of ribosomal proteins (RPs) and ribosomal RNAs. While translation can be regulated at diverse levels through global or mRNA-specific means, recent evidence suggests that ribosomes with distinct configurations are involved in the translation of different subsets of mRNAs. However, whether and how such proclaimed ribosome heterogeneity could be connected to neuronal functions remains largely unresolved. Here, we postulate that the existence of heterologous ribosomes within neurons, especially at discrete synapses, subserve brain plasticity. This hypothesis is supported by recent studies in rodents showing that heterogeneous RP expression occurs in dendrites, the compartment of neurons where synapses are made. We further propose that sleep, which is fundamental for brain plasticity and memory formation, has a particular role in the formation of heterologous ribosomes, specialised in the translation of mRNAs specific for synaptic plasticity. This aspect of our hypothesis is supported by recent studies showing increased translation and changes in RP expression during sleep after learning. Thus, certain RPs are regulated by sleep, and could support different sleep functions, in particular brain plasticity. Future experiments investigating cell-specific heterogeneity in RPs across the sleep-wake cycle and in response to different behaviour would help address this question.
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Affiliation(s)
- Isla M. Buchanan
- Integrated Master Programme in Biochemistry, University of Surrey, Guildford, United Kingdom
| | - Trevor M. Smith
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- Surrey Sleep Research Centre, University of Surrey, Guildford, United Kingdom
| | - André P. Gerber
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- *Correspondence: André P. Gerber, ; Julie Seibt,
| | - Julie Seibt
- Surrey Sleep Research Centre, University of Surrey, Guildford, United Kingdom
- *Correspondence: André P. Gerber, ; Julie Seibt,
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48
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Temaj G, Hadziselimovic R, Nefic H, Nuhii N. Ribosome biogenesis and ribosome therapy in cancer cells. RESEARCH RESULTS IN PHARMACOLOGY 2022. [DOI: 10.3897/rrpharmacology.8.81706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Introduction: The process of protein synthesis is a vital process for all kingdoms of life. The ribosome is a ribonucleoprotein complex that reads the genetic code, from messenger RNA (mRNA) to produce proteins and to tightly regulate and ensure cells growth. The fact that numerous diseases are caused by defect during the ribosome biogenesis is important to understand this pathway.
Materials and methods: We have analyzed the literature for ribosome biogenesis and its links with different diseases which have been found.
Results and discussion: We have discussed the key aspect of human ribosome biogenesis and its links to diseases. We have also proposed the potential of applying this knowledge to the development of a ribosomal stress-based cancer therapy.
Conclusion: Major challenges in the future will be to determine factors which play a pivotal role during ribosome biogenesis. Therefore, more anti-cancer drugs and gene therapy for genetic diseases will be developed against ribosomal biogenesis in the coming years.
Graphical abstract:
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49
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Ribosome-Directed Therapies in Cancer. Biomedicines 2022; 10:biomedicines10092088. [PMID: 36140189 PMCID: PMC9495564 DOI: 10.3390/biomedicines10092088] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 12/29/2022] Open
Abstract
The human ribosomes are the cellular machines that participate in protein synthesis, which is deeply affected during cancer transformation by different oncoproteins and is shown to provide cancer cell proliferation and therefore biomass. Cancer diseases are associated with an increase in ribosome biogenesis and mutation of ribosomal proteins. The ribosome represents an attractive anti-cancer therapy target and several strategies are used to identify specific drugs. Here we review the role of different drugs that may decrease ribosome biogenesis and cancer cell proliferation.
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50
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Bhutada P, Favre S, Jaafar M, Hafner J, Liesinger L, Unterweger S, Bischof K, Darnhofer B, Siva Sankar D, Rechberger G, Abou Merhi R, Lebaron S, Birner-Gruenberger R, Kressler D, Henras AK, Pertschy B. Rbp95 binds to 25S rRNA helix H95 and cooperates with the Npa1 complex during early pre-60S particle maturation. Nucleic Acids Res 2022; 50:10053-10077. [PMID: 36018804 PMCID: PMC9508819 DOI: 10.1093/nar/gkac724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 08/05/2022] [Accepted: 08/12/2022] [Indexed: 11/21/2022] Open
Abstract
Eukaryotic ribosome synthesis involves more than 200 assembly factors, which promote ribosomal RNA (rRNA) processing, modification and folding, and assembly of ribosomal proteins. The formation and maturation of the earliest pre-60S particles requires structural remodeling by the Npa1 complex, but is otherwise still poorly understood. Here, we introduce Rbp95 (Ycr016w), a constituent of early pre-60S particles, as a novel ribosome assembly factor. We show that Rbp95 is both genetically and physically linked to most Npa1 complex members and to ribosomal protein Rpl3. We demonstrate that Rbp95 is an RNA-binding protein containing two independent RNA-interacting domains. In vivo, Rbp95 associates with helix H95 in the 3′ region of the 25S rRNA, in close proximity to the binding sites of Npa1 and Rpl3. Additionally, Rbp95 interacts with several snoRNAs. The absence of Rbp95 results in alterations in the protein composition of early pre-60S particles. Moreover, combined mutation of Rbp95 and Npa1 complex members leads to a delay in the maturation of early pre-60S particles. We propose that Rbp95 acts together with the Npa1 complex during early pre-60S maturation, potentially by promoting pre-rRNA folding events within pre-60S particles.
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Affiliation(s)
- Priya Bhutada
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Sébastien Favre
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Mariam Jaafar
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France.,Genomic Stability and Biotherapy (GSBT) Laboratory, Faculty of Sciences, Rafik Hariri Campus, Lebanese University, Beirut, Lebanon
| | - Jutta Hafner
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Laura Liesinger
- BioTechMed-Graz, Graz, Austria.,Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria
| | - Stefan Unterweger
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Karin Bischof
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Barbara Darnhofer
- BioTechMed-Graz, Graz, Austria.,Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria
| | - Devanarayanan Siva Sankar
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Gerald Rechberger
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Raghida Abou Merhi
- Genomic Stability and Biotherapy (GSBT) Laboratory, Faculty of Sciences, Rafik Hariri Campus, Lebanese University, Beirut, Lebanon
| | - Simon Lebaron
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Ruth Birner-Gruenberger
- BioTechMed-Graz, Graz, Austria.,Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria.,Institute of Chemical Technologies and Analytics, Technische Universität Wien, Getreidemarkt 9/E164, 1060 Vienna, Austria
| | - Dieter Kressler
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Anthony K Henras
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Brigitte Pertschy
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria.,BioTechMed-Graz, Graz, Austria
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