1
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Morin A, Chu C, Pavlidis P. Identifying Reproducible Transcription Regulator Coexpression Patterns with Single Cell Transcriptomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580581. [PMID: 38559016 PMCID: PMC10979919 DOI: 10.1101/2024.02.15.580581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The proliferation of single cell transcriptomics has potentiated our ability to unveil patterns that reflect dynamic cellular processes, rather than cell type compositional effects that emerge from bulk tissue samples. In this study, we leverage a broad collection of single cell RNA-seq data to identify the gene partners whose expression is most coordinated with each human and mouse transcription regulator (TR). We assembled 120 human and 103 mouse scRNA-seq datasets from the literature, constructing a single cell coexpression network for each. We aimed to understand the consistency of TR coexpression profiles across a broad sampling of biological contexts, rather than examine the preservation of context-specific networks. Our workflow therefore explicitly prioritizes the patterns that are most reproducible across cell types, helping to characterize each TR's coexpression patterns. Towards this goal, we quantify the similarity of TR coexpression profiles within and across species, characterizing the consistency of each TR's coexpression across datasets. We create single cell coexpression rankings for each TR, demonstrating that this aggregated information recovers literature curated targets on par with ChIP-seq data. We then combine the coexpression and ChIP-seq information to identify candidate regulatory interactions supported across methods and species. Finally, we highlight interactions for the important neural TR ASCL1 to demonstrate how our compiled information can be adopted for community use.
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2
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Castellanos MDP, Wickramasinghe CD, Betrán E. The roles of gene duplications in the dynamics of evolutionary conflicts. Proc Biol Sci 2024; 291:20240555. [PMID: 38865605 DOI: 10.1098/rspb.2024.0555] [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: 08/08/2023] [Accepted: 04/02/2024] [Indexed: 06/14/2024] Open
Abstract
Evolutionary conflicts occur when there is antagonistic selection between different individuals of the same or different species, life stages or between levels of biological organization. Remarkably, conflicts can occur within species or within genomes. In the dynamics of evolutionary conflicts, gene duplications can play a major role because they can bring very specific changes to the genome: changes in protein dose, the generation of novel paralogues with different functions or expression patterns or the evolution of small antisense RNAs. As we describe here, by having those effects, gene duplication might spark evolutionary conflict or fuel arms race dynamics that takes place during conflicts. Interestingly, gene duplication can also contribute to the resolution of a within-locus evolutionary conflict by partitioning the functions of the gene that is under an evolutionary trade-off. In this review, we focus on intraspecific conflicts, including sexual conflict and illustrate the various roles of gene duplications with a compilation of examples. These examples reveal the level of complexity and the differences in the patterns of gene duplications within genomes under different conflicts. These examples also reveal the gene ontologies involved in conflict and the genomic location of the elements of the conflict. The examples provide a blueprint for the direct study of these conflicts or the exploration of the presence of similar conflicts in other lineages.
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Affiliation(s)
| | | | - Esther Betrán
- Department of Biology, University of Texas at Arlington , Arlington, TX 76019, USA
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3
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Ng AYE, Chan SN, Pek JW. Genetic compensation between ribosomal protein paralogs mediated by a cognate circular RNA. Cell Rep 2024; 43:114228. [PMID: 38735045 DOI: 10.1016/j.celrep.2024.114228] [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: 03/01/2024] [Revised: 04/19/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
Inter-regulation between related genes, such as ribosomal protein (RP) paralogs, has been observed to be important for genetic compensation and paralog-specific functions. However, how paralogs communicate to modulate their expression levels is unknown. Here, we report a circular RNA involved in the inter-regulation between RP paralogs RpL22 and RpL22-like during Drosophila spermatogenesis. Both paralogs are mutually regulated by the circular stable intronic sequence RNA (sisRNA) circRpL22(NE,3S) produced from the RpL22 locus. RpL22 represses itself and RpL22-like. Interestingly, circRpL22 binds to RpL22 to repress RpL22-like, but not RpL22, suggesting that circRpL22 modulates RpL22's function. circRpL22 is in turn controlled by RpL22-like, which regulates RpL22 binding to circRpL22 to indirectly modulate RpL22. This circRpL22-centric inter-regulatory circuit enables the loss of RpL22-like to be genetically compensated by RpL22 upregulation to ensure robust male germline development. Thus, our study identifies sisRNA as a possible mechanism of genetic crosstalk between paralogous genes.
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Affiliation(s)
- Amanda Yunn Ee Ng
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive Singapore 117543, Singapore
| | - Seow Neng Chan
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore 117604, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive Singapore 117543, Singapore.
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4
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Tang Q, Tang J, Chen C, Zhu F, Yu Q, Chen H, Chen L, Ma S, Chen K, Li G. Bombyx mori RPL13 participates in UV-induced DNA damage repair of B. mori nucleopolyhedrovirus through interaction with Bm65. INSECT MOLECULAR BIOLOGY 2024. [PMID: 38801334 DOI: 10.1111/imb.12928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/01/2024] [Indexed: 05/29/2024]
Abstract
Ribosomal protein L13 (RPL13) is highly conserved in evolution. At present, the properties and functions of RPL13 have not been characterised in insects. In this study, Bombyx mori RPL13 (BmRPL13) was first found to be specifically recruited to the sites of ultraviolet (UV)-induced DNA damage and contributed to UV damage repair. Escherichia coli expressing BmRPL13 showed better resistance to UV radiation. After knocking down the expression of BmRPL13 in BmN cells, the repair speed of UV-damaged DNA slowed down. The further results showed that BmRPL13 interacted with B. mori nucleopolyhedrovirus (BmNPV) ORF65 (Bm65) protein to locate at the UV-induced DNA damage sites of BmNPV and helped repair UV-damaged viral DNA.
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Affiliation(s)
- Qi Tang
- Department of Biological Sciences, School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Jingjing Tang
- Department of Biological Sciences, School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Ceru Chen
- Department of Biological Sciences, School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Feifei Zhu
- Department of Biological Sciences, School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Qian Yu
- Department of Biological Sciences, School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Huiqing Chen
- Department of Biological Sciences, School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Liang Chen
- Department of Biological Sciences, School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Shangshang Ma
- Department of Biological Sciences, School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Keping Chen
- Department of Biological Sciences, School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Guohui Li
- Department of Biological Sciences, School of Life Sciences, Jiangsu University, Zhenjiang, China
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5
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Su Y, Yu Z, Jin S, Ai Z, Yuan R, Chen X, Xue Z, Guo Y, Chen D, Liang H, Liu Z, Liu W. Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data. Nat Commun 2024; 15:3972. [PMID: 38730241 PMCID: PMC11087464 DOI: 10.1038/s41467-024-48117-3] [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: 10/18/2022] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
The advancement of Long-Read Sequencing (LRS) techniques has significantly increased the length of sequencing to several kilobases, thereby facilitating the identification of alternative splicing events and isoform expressions. Recently, numerous computational tools for isoform detection using long-read sequencing data have been developed. Nevertheless, there remains a deficiency in comparative studies that systemically evaluate the performance of these tools, which are implemented with different algorithms, under various simulations that encompass potential influencing factors. In this study, we conducted a benchmark analysis of thirteen methods implemented in nine tools capable of identifying isoform structures from long-read RNA-seq data. We evaluated their performances using simulated data, which represented diverse sequencing platforms generated by an in-house simulator, RNA sequins (sequencing spike-ins) data, as well as experimental data. Our findings demonstrate IsoQuant as a highly effective tool for isoform detection with LRS, with Bambu and StringTie2 also exhibiting strong performance. These results offer valuable guidance for future research on alternative splicing analysis and the ongoing improvement of tools for isoform detection using LRS data.
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Affiliation(s)
- Yaqi Su
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Zhejian Yu
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Siqian Jin
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Zhipeng Ai
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Ruihong Yuan
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Xinyi Chen
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Ziwei Xue
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Yixin Guo
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Di Chen
- Center for Reproductive Medicine of the Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Hongqing Liang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Zuozhu Liu
- Zhejiang University-Angel Align Inc. R&D Center for Intelligent Healthcare, Zhejiang University-University of Illinois at Urbana-Champaign Institute (ZJU-UIUC Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Wanlu Liu
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China.
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China.
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314100, China.
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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6
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Xu D, Pan J, Fang Y, Zhao L, Su Y. RpS25 is required for sperm elongation and individualization during Drosophila spermatogenesis. Biochem Biophys Res Commun 2024; 702:149633. [PMID: 38341921 DOI: 10.1016/j.bbrc.2024.149633] [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: 01/24/2024] [Revised: 01/28/2024] [Accepted: 02/04/2024] [Indexed: 02/13/2024]
Abstract
Ribosomal protein 25 (RPS25) has been related to male fertility diseases in humans. However, the role of RPS25 in spermatogenesis has yet to be well understood. RpS25 is evolutionarily highly conserved from flies to humans through sequence alignment and phylogenetic tree construction. In this study, we found that RpS25 plays a critical role in Drosophila spermatogenesis and its knockdown leads to male sterility. Examination of each stage of spermatogenesis from RpS25-knockdown flies showed that RpS25 was not required for initial germline cell divisions, but was required for spermatid elongation and individualization. In RpS25-knockdown testes, the average length of cyst elongation was shortened, the spermatid nuclei bundling was disrupted, and the assembly of individualization complex from actin cones failed, resulting in the failure of mature sperm production. Our data revealed an essential role of RpS25 during Drosophila spermatogenesis through regulating spermatid elongation and individualization.
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Affiliation(s)
- Di Xu
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jiahui Pan
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yang Fang
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Long Zhao
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; Fisheries College, Ocean University of China, Qingdao 266003, China.
| | - Ying Su
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
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7
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Zheng J, Li N, Li X, Han Y, Lv X, Zhang H, Ren L. The Nuclear Localization Signal of Porcine Circovirus Type 4 Affects the Subcellular Localization of the Virus Capsid and the Production of Virus-like Particles. Int J Mol Sci 2024; 25:2459. [PMID: 38473709 DOI: 10.3390/ijms25052459] [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: 12/20/2023] [Revised: 01/29/2024] [Accepted: 02/18/2024] [Indexed: 03/14/2024] Open
Abstract
Porcine circovirus 4 (PCV4) is a newly identified virus belonging to PCV of the Circoviridae family, the Circovirus genus. We previously found that PCV4 is pathogenic in vitro, while the virus's replication in cells is still unknown. In this study, we evaluated the N-terminal of the PCV4 capsid (Cap) and identified an NLS at amino acid residues 4-37 of the N-terminus of the PCV4 Cap, 4RSRYSRRRRNRRNQRRRGLWPRASRRRYRWRRKN37. The NLS was further divided into two fragments (NLS-A and NLS-B) based on the predicted structure, including two α-helixes, which were located at 4RSRYSRRRRNRRNQRR19 and 24PRASRRRYRWRRK36, respectively. Further studies showed that the NLS, especially the first α-helixes formed by the NLS-A fragment, determined the nuclear localization of the Cap protein, and the amino acid 4RSRY7 in the NLS of the PCV4 Cap was the critical motif affecting the VLP packaging. These results will provide a theoretical basis for elucidating the infection mechanism of PCV4 and developing subunit vaccines based on VLPs.
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Affiliation(s)
- Jiawei Zheng
- College of Animal Sciences, Key Lab for Zoonoses Research, Ministry of Education, Jilin University, 5333 Xi'an Road, Changchun 130062, China
| | - Nan Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 666 Liuying West Road, Changchun 130122, China
| | - Xue Li
- College of Animal Sciences, Key Lab for Zoonoses Research, Ministry of Education, Jilin University, 5333 Xi'an Road, Changchun 130062, China
| | - Yaqi Han
- College of Animal Sciences, Key Lab for Zoonoses Research, Ministry of Education, Jilin University, 5333 Xi'an Road, Changchun 130062, China
| | - Xinru Lv
- College of Animal Sciences, Key Lab for Zoonoses Research, Ministry of Education, Jilin University, 5333 Xi'an Road, Changchun 130062, China
| | - Huimin Zhang
- College of Animal Sciences, Key Lab for Zoonoses Research, Ministry of Education, Jilin University, 5333 Xi'an Road, Changchun 130062, China
| | - Linzhu Ren
- College of Animal Sciences, Key Lab for Zoonoses Research, Ministry of Education, Jilin University, 5333 Xi'an Road, Changchun 130062, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
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8
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Zang Y, Ran X, Yuan J, Wu H, Wang Y, Li H, Teng H, Sun Z. Genomic hallmarks and therapeutic targets of ribosome biogenesis in cancer. Brief Bioinform 2024; 25:bbae023. [PMID: 38343327 PMCID: PMC10859687 DOI: 10.1093/bib/bbae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 02/15/2024] Open
Abstract
Hyperactive ribosome biogenesis (RiboSis) fuels unrestricted cell proliferation, whereas genomic hallmarks and therapeutic targets of RiboSis in cancers remain elusive, and efficient approaches to quantify RiboSis activity are still limited. Here, we have established an in silico approach to conveniently score RiboSis activity based on individual transcriptome data. By employing this novel approach and RNA-seq data of 14 645 samples from TCGA/GTEx dataset and 917 294 single-cell expression profiles across 13 cancer types, we observed the elevated activity of RiboSis in malignant cells of various human cancers, and high risk of severe outcomes in patients with high RiboSis activity. Our mining of pan-cancer multi-omics data characterized numerous molecular alterations of RiboSis, and unveiled the predominant somatic alteration in RiboSis genes was copy number variation. A total of 128 RiboSis genes, including EXOSC4, BOP1, RPLP0P6 and UTP23, were identified as potential therapeutic targets. Interestingly, we observed that the activity of RiboSis was associated with TP53 mutations, and hyperactive RiboSis was associated with poor outcomes in lung cancer patients without TP53 mutations, highlighting the importance of considering TP53 mutations during therapy by impairing RiboSis. Moreover, we predicted 23 compounds, including methotrexate and CX-5461, associated with the expression signature of RiboSis genes. The current study generates a comprehensive blueprint of molecular alterations in RiboSis genes across cancers, which provides a valuable resource for RiboSis-based anti-tumor therapy.
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Affiliation(s)
- Yue Zang
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences and Institute of Genomic Medicine, Wenzhou Medical University, China
| | - Xia Ran
- Liangzhu Laboratory, Zhejiang University Medical Center, China
| | - Jie Yuan
- BGI Education Center, University of Chinese Academy of Sciences, China
| | - Hao Wu
- Institute of Genomic Medicine, Wenzhou Medical University, China
| | - Youya Wang
- Institute of Genomic Medicine, Wenzhou Medical University, China
| | - He Li
- Institute of Genomic Medicine, Wenzhou Medical University, China
| | - Huajing Teng
- Department of Radiation Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) at Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Zhongsheng Sun
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Institute of Genomic Medicine, Wenzhou Medical University, and Beijing Institutes of Life Science, Chinese Academy of Sciences, Hangzhou, China
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9
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Schumacher S, Klose L, Lambertz J, Lütjohann D, Biemann R, Kuerten S, Fester L. The mitochondrial protease PARL is required for spermatogenesis. Commun Biol 2024; 7:44. [PMID: 38182793 PMCID: PMC10770312 DOI: 10.1038/s42003-023-05703-3] [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: 06/15/2023] [Accepted: 12/13/2023] [Indexed: 01/07/2024] Open
Abstract
Mitochondrial function plays an important role in the maintenance of male fertility. However, the mechanisms underlying mitochondrial defect-related infertility remain mostly unclear. Here we show that a deficiency of PARL (Parl-/-), a mitochondrial protease, causes complete arrest of spermatogenesis during meiosis I. PARL deficiency led to severe downregulation of proteins of respiratory chain complex IV in testes that did not occur in other tested organs, causing a deficit in complex IV activity and ATP production. Furthermore, Parl-/- testes showed an almost complete loss of HSD17B3, a protein of the sER responsible for the last step in testosterone synthesis. While testosterone production appeared to be restored by overexpression of HSD17B12, loss of the canonical testosterone synthesis led to an upregulation of luteinizing hormone (LH) and of LH-regulated responses. These results suggest an important impact of the downstream regulation of mitochondrial defects that manifest in a cell-type-specific manner and extend beyond mitochondria.
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Affiliation(s)
- Sarah Schumacher
- Institute of Neuroanatomy, Medical Faculty, University of Bonn, 53115, Bonn, Germany.
| | - Laura Klose
- Institute of Neuroanatomy, Medical Faculty, University of Bonn, 53115, Bonn, Germany
| | - Jessica Lambertz
- Institute of Neuroanatomy, Medical Faculty, University of Bonn, 53115, Bonn, Germany
| | - Dieter Lütjohann
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127, Bonn, Germany
| | - Ronald Biemann
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig, 04103, Leipzig, Germany
| | - Stefanie Kuerten
- Institute of Neuroanatomy, Medical Faculty, University of Bonn, 53115, Bonn, Germany
| | - Lars Fester
- Institute of Neuroanatomy, Medical Faculty, University of Bonn, 53115, Bonn, Germany.
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10
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Chen Y, Luo M, Tu H, Qi Y, Guo Y, Zhang X, Cui Y, Gao M, Zhou X, Zhu T, Zhu H, Situ C, Li Y, Guo X. STYXL1 regulates CCT complex assembly and flagellar tubulin folding in sperm formation. Nat Commun 2024; 15:44. [PMID: 38168070 PMCID: PMC10761714 DOI: 10.1038/s41467-023-44337-1] [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: 06/14/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
Tubulin-based microtubule is a core component of flagella axoneme and essential for sperm motility and male fertility. Structural components of the axoneme have been well explored. However, how tubulin folding is regulated in sperm flagella formation is still largely unknown. Here, we report a germ cell-specific co-factor of CCT complex, STYXL1. Deletion of Styxl1 results in male infertility and microtubule defects of sperm flagella. Proteomic analysis of Styxl1-/- sperm reveals abnormal downregulation of flagella-related proteins including tubulins. The N-terminal rhodanese-like domain of STYXL1 is important for its interactions with CCT complex subunits, CCT1, CCT6 and CCT7. Styxl1 deletion leads to defects in CCT complex assembly and tubulin polymerization. Collectively, our findings reveal the vital roles of germ cell-specific STYXL1 in CCT-facilitated tubulin folding and sperm flagella development.
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Affiliation(s)
- Yu Chen
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
- Medical Research Center, Changzhou Maternal and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, 213000, China
| | - Mengjiao Luo
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Haixia Tu
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
- Department of Clinical Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing, 211166, China
| | - Yaling Qi
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yueshuai Guo
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Xiangzheng Zhang
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yiqiang Cui
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Mengmeng Gao
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Xin Zhou
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Tianyu Zhu
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Hui Zhu
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Chenghao Situ
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China.
| | - Yan Li
- Department of Clinical Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing, 211166, China.
| | - Xuejiang Guo
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China.
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11
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Shi J, Zhao J, Zhang Y, Wang Y, Tan CP, Xu YJ, Liu Y. Windows Scanning Multiomics: Integrated Metabolomics and Proteomics. Anal Chem 2023; 95:18793-18802. [PMID: 38095040 DOI: 10.1021/acs.analchem.3c03785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Metabolomics and proteomics offer significant advantages in understanding biological mechanisms at two hierarchical levels. However, conventional single omics analysis faces challenges due to the high demand for specimens and the complexity of intrinsic associations. To obtain comprehensive and accurate system biological information, we developed a multiomics analytical method called Windows Scanning Multiomics (WSM). In this method, we performed simultaneous extraction of metabolites and proteins from the same sample, resulting in a 10% increase in the coverage of the identified biomolecules. Both metabolomics and proteomics analyses were conducted by using ultrahigh-performance liquid chromatography mass spectrometry (UPLC-MS), eliminating the need for instrument conversions. Additionally, we designed an R-based program (WSM.R) to integrate mathematical and biological correlations between metabolites and proteins into a correlation network. The network created from simultaneously extracted biomolecules was more focused and comprehensive compared to those from separate extractions. Notably, we excluded six pairs of false-positive relationships between metabolites and proteins in the network established using simultaneously extracted biomolecules. In conclusion, this study introduces a novel approach for multiomics analysis and data processing that greatly aids in bioinformation mining from multiomics results. This method is poised to play an indispensable role in systems biology research.
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Affiliation(s)
- Jiachen Shi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Jialiang Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Yu Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Yanan Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Chin Ping Tan
- Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Yong-Jiang Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
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12
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Gao Y, Wang H. Ribosome Heterogeneity in Development and Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550527. [PMID: 37546733 PMCID: PMC10402066 DOI: 10.1101/2023.07.25.550527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The functional ribosome is composed of ∼80 ribosome proteins. With the intensity-based absolute quantification (iBAQ) value, we calculate the stoichiometry ratio of each ribosome protein. We analyze the ribosome ratio-omics (Ribosome R ), which reflects the holistic signature of ribosome composition, in various biological samples with distinct functions, developmental stages, and pathological outcomes. The Ribosome R reveals significant ribosome heterogeneity among different tissues of fat, spleen, liver, kidney, heart, and skeletal muscles. During tissue development, testes at various stages of spermatogenesis show distinct Ribosome R signatures. During in vitro neuronal maturation, the Ribosome R changes reveal functional association with certain molecular aspects of neurodevelopment. Regarding ribosome heterogeneity associated with pathological conditions, the Ribosome R signature of gastric tumors is functionally linked to pathways associated with tumorigenesis. Moreover, the Ribosome R undergoes dynamic changes in macrophages following immune challenges. Taken together, with the examination of a broad spectrum of biological samples, the Ribosome R barcode reveals ribosome heterogeneity and specialization in cell function, development, and disease. One-Sentence Summary Ratio-omics signature of ribosome deciphers functionally relevant heterogeneity in development and disease.
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13
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Xu AF, Molinuevo R, Fazzari E, Tom H, Zhang Z, Menendez J, Casey KM, Ruggero D, Hinck L, Pritchard JK, Barna M. Subfunctionalized expression drives evolutionary retention of ribosomal protein paralogs Rps27 and Rps27l in vertebrates. eLife 2023; 12:e78695. [PMID: 37306301 PMCID: PMC10313321 DOI: 10.7554/elife.78695] [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: 03/16/2022] [Accepted: 06/09/2023] [Indexed: 06/13/2023] Open
Abstract
The formation of paralogs through gene duplication is a core evolutionary process. For paralogs that encode components of protein complexes such as the ribosome, a central question is whether they encode functionally distinct proteins or whether they exist to maintain appropriate total expression of equivalent proteins. Here, we systematically tested evolutionary models of paralog function using the ribosomal protein paralogs Rps27 (eS27) and Rps27l (eS27L) as a case study. Evolutionary analysis suggests that Rps27 and Rps27l likely arose during whole-genome duplication(s) in a common vertebrate ancestor. We show that Rps27 and Rps27l have inversely correlated mRNA abundance across mouse cell types, with the highest Rps27 in lymphocytes and the highest Rps27l in mammary alveolar cells and hepatocytes. By endogenously tagging the Rps27 and Rps27l proteins, we demonstrate that Rps27- and Rps27l-ribosomes associate preferentially with different transcripts. Furthermore, murine Rps27 and Rps27l loss-of-function alleles are homozygous lethal at different developmental stages. However, strikingly, expressing Rps27 protein from the endogenous Rps27l locus or vice versa completely rescues loss-of-function lethality and yields mice with no detectable deficits. Together, these findings suggest that Rps27 and Rps27l are evolutionarily retained because their subfunctionalized expression patterns render both genes necessary to achieve the requisite total expression of two equivalent proteins across cell types. Our work represents the most in-depth characterization of a mammalian ribosomal protein paralog to date and highlights the importance of considering both protein function and expression when investigating paralogs.
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Affiliation(s)
- Adele Francis Xu
- Department of Genetics, Stanford UniversityStanfordUnited States
- Medical Scientist Training Program, Stanford School of MedicineStanfordUnited States
| | - Rut Molinuevo
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | - Elisa Fazzari
- Helen Diller Family Comprehensive Cancer Center, University of California, Los AngelesLos AngelesUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Department of Urology, University of California, San FranciscoSan FranciscoUnited States
| | - Harrison Tom
- Helen Diller Family Comprehensive Cancer Center, University of California, Los AngelesLos AngelesUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Department of Urology, University of California, San FranciscoSan FranciscoUnited States
| | - Zijian Zhang
- Department of Chemical and Systems Biology, Stanford UniversityStanfordUnited States
| | - Julien Menendez
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | - Kerriann M Casey
- Department of Biology, Stanford UniversityStanfordUnited States
- Department of Comparative Medicine, Stanford School of MedicineStanfordUnited States
| | - Davide Ruggero
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Department of Urology, University of California, San FranciscoSan FranciscoUnited States
| | - Lindsay Hinck
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | | | - Maria Barna
- Department of Genetics, Stanford UniversityStanfordUnited States
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14
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Shiraishi C, Matsumoto A, Ichihara K, Yamamoto T, Yokoyama T, Mizoo T, Hatano A, Matsumoto M, Tanaka Y, Matsuura-Suzuki E, Iwasaki S, Matsushima S, Tsutsui H, Nakayama KI. RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function. Nat Commun 2023; 14:2131. [PMID: 37080962 PMCID: PMC10119107 DOI: 10.1038/s41467-023-37838-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 04/03/2023] [Indexed: 04/22/2023] Open
Abstract
Although several ribosomal protein paralogs are expressed in a tissue-specific manner, how these proteins affect translation and why they are required only in certain tissues have remained unclear. Here we show that RPL3L, a paralog of RPL3 specifically expressed in heart and skeletal muscle, influences translation elongation dynamics. Deficiency of RPL3L-containing ribosomes in RPL3L knockout male mice resulted in impaired cardiac contractility. Ribosome occupancy at mRNA codons was found to be altered in the RPL3L-deficient heart, and the changes were negatively correlated with those observed in myoblasts overexpressing RPL3L. RPL3L-containing ribosomes were less prone to collisions compared with RPL3-containing canonical ribosomes. Although the loss of RPL3L-containing ribosomes altered translation elongation dynamics for the entire transcriptome, its effects were most pronounced for transcripts related to cardiac muscle contraction and dilated cardiomyopathy, with the abundance of the encoded proteins being correspondingly decreased. Our results provide further insight into the mechanisms and physiological relevance of tissue-specific translational regulation.
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Affiliation(s)
- Chisa Shiraishi
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Akinobu Matsumoto
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan.
| | - Kazuya Ichihara
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Taishi Yamamoto
- Department of Cardiovascular Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Takeshi Yokoyama
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Taisuke Mizoo
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Atsushi Hatano
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Niigata, 951-8510, Japan
| | - Masaki Matsumoto
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Niigata, 951-8510, Japan
| | - Yoshikazu Tanaka
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Eriko Matsuura-Suzuki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Shouji Matsushima
- Department of Cardiovascular Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Hiroyuki Tsutsui
- Department of Cardiovascular Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Keiichi I Nakayama
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan.
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15
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Rodríguez-Almonacid CC, Kellogg MK, Karamyshev AL, Karamysheva ZN. Ribosome Specialization in Protozoa Parasites. Int J Mol Sci 2023; 24:ijms24087484. [PMID: 37108644 PMCID: PMC10138883 DOI: 10.3390/ijms24087484] [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: 02/27/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Ribosomes, in general, are viewed as constitutive macromolecular machines where protein synthesis takes place; however, this view has been recently challenged, supporting the hypothesis of ribosome specialization and opening a completely new field of research. Recent studies have demonstrated that ribosomes are heterogenous in their nature and can provide another layer of gene expression control by regulating translation. Heterogeneities in ribosomal RNA and ribosomal proteins that compose them favor the selective translation of different sub-pools of mRNAs and functional specialization. In recent years, the heterogeneity and specialization of ribosomes have been widely reported in different eukaryotic study models; however, few reports on this topic have been made on protozoa and even less on protozoa parasites of medical importance. This review analyzes heterogeneities of ribosomes in protozoa parasites highlighting the specialization in their functions and their importance in parasitism, in the transition between stages in their life cycle, in the change of host and in response to environmental conditions.
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Affiliation(s)
| | - 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
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16
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Chen Y, Zhang X, Jiang J, Luo M, Tu H, Xu C, Tan H, Zhou X, Chen H, Han X, Yue Q, Guo Y, Zheng K, Qi Y, Situ C, Cui Y, Guo X. Regulation of Miwi-mediated mRNA stabilization by Ck137956/Tssa is essential for male fertility. BMC Biol 2023; 21:89. [PMID: 37069605 PMCID: PMC10111675 DOI: 10.1186/s12915-023-01589-z] [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: 10/28/2022] [Accepted: 04/04/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND Sperm is formed through spermiogenesis, a highly complex process involving chromatin condensation that results in cessation of transcription. mRNAs required for spermiogenesis are transcribed at earlier stages and translated in a delayed fashion during spermatid formation. However, it remains unknown that how these repressed mRNAs are stabilized. RESULTS Here we report a Miwi-interacting testis-specific and spermiogenic arrest protein, Ck137956, which we rename Tssa. Deletion of Tssa led to male sterility and absence of sperm formation. The spermiogenesis arrested at the round spermatid stage and numerous spermiogenic mRNAs were down-regulated in Tssa-/- mice. Deletion of Tssa disrupted the localization of Miwi to chromatoid body, a specialized assembly of cytoplasmic messenger ribonucleoproteins (mRNPs) foci present in germ cells. We found that Tssa interacted with Miwi in repressed mRNPs and stabilized Miwi-interacting spermiogenesis-essential mRNAs. CONCLUSIONS Our findings indicate that Tssa is indispensable in male fertility and has critical roles in post-transcriptional regulations by interacting with Miwi during spermiogenesis.
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Affiliation(s)
- Yu Chen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Xiangzheng Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Jiayin Jiang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Mengjiao Luo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Haixia Tu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Chen Xu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Huanhuan Tan
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Xin Zhou
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Hong Chen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Xudong Han
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
- School of Medicine, Southeast University, Nanjing, 210009, China
| | - Qiuling Yue
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Ke Zheng
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yaling Qi
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Chenghao Situ
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China.
| | - Yiqiang Cui
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China.
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China.
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17
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McGee JP, Armache JP, Lindner SE. Ribosome heterogeneity and specialization of Plasmodium parasites. PLoS Pathog 2023; 19:e1011267. [PMID: 37053161 PMCID: PMC10101515 DOI: 10.1371/journal.ppat.1011267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Affiliation(s)
- James P McGee
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Pennsylvania, United States of America
- Huck Center for Malaria Research, Pennsylvania State University, Pennsylvania, United States of America
| | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Pennsylvania, United States of America
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, Pennsylvania, United States of America
| | - Scott E Lindner
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Pennsylvania, United States of America
- Huck Center for Malaria Research, Pennsylvania State University, Pennsylvania, United States of America
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, Pennsylvania, United States of America
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18
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Bartsch D, Kalamkar K, Ahuja G, Lackmann JW, Hescheler J, Weber T, Bazzi H, Clamer M, Mendjan S, Papantonis A, Kurian L. mRNA translational specialization by RBPMS presets the competence for cardiac commitment in hESCs. SCIENCE ADVANCES 2023; 9:eade1792. [PMID: 36989351 PMCID: PMC10058251 DOI: 10.1126/sciadv.ade1792] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/01/2023] [Indexed: 06/19/2023]
Abstract
The blueprints of developing organs are preset at the early stages of embryogenesis. Transcriptional and epigenetic mechanisms are proposed to preset developmental trajectories. However, we reveal that the competence for the future cardiac fate of human embryonic stem cells (hESCs) is preset in pluripotency by a specialized mRNA translation circuit controlled by RBPMS. RBPMS is recruited to active ribosomes in hESCs to control the translation of essential factors needed for cardiac commitment program, including Wingless/Integrated (WNT) signaling. Consequently, RBPMS loss specifically and severely impedes cardiac mesoderm specification, leading to patterning and morphogenetic defects in human cardiac organoids. Mechanistically, RBPMS specializes mRNA translation, selectively via 3'UTR binding and globally by promoting translation initiation. Accordingly, RBPMS loss causes translation initiation defects highlighted by aberrant retention of the EIF3 complex and depletion of EIF5A from mRNAs, thereby abrogating ribosome recruitment. We demonstrate how future fate trajectories are programmed during embryogenesis by specialized mRNA translation.
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Affiliation(s)
- Deniz Bartsch
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Institute for Neurophysiology, Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Kaustubh Kalamkar
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Institute for Neurophysiology, Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Gaurav Ahuja
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Institute for Neurophysiology, Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Jan-Wilm Lackmann
- Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Jürgen Hescheler
- Institute for Neurophysiology, Faculty of Medicine, University of Cologne, Cologne 50931, Germany
| | - Timm Weber
- Laboratory of Experimental Immunology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne 50931, Germany
| | - Hisham Bazzi
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
- Department of Dermatology and Venereology, Medical Faculty, University of Cologne, Cologne 50931, Germany
| | | | - Sasha Mendjan
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr Gasse 3, Vienna 1030, Austria
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, Göttingen 37075, Germany
| | - Leo Kurian
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Institute for Neurophysiology, Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
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19
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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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20
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Wester LE, Lanjuin A, Bruckisch EH, Perez-Matos MC, Stine PG, Heintz C, Denzel MS, Mair WB. A single-copy knockin translating ribosome immunoprecipitation toolkit for tissue-specific profiling of actively translated mRNAs in C. elegans. CELL REPORTS METHODS 2023; 3:100433. [PMID: 37056370 PMCID: PMC10088236 DOI: 10.1016/j.crmeth.2023.100433] [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: 06/08/2022] [Revised: 01/11/2023] [Accepted: 02/28/2023] [Indexed: 03/29/2023]
Abstract
Here, we introduce a single-copy knockin translating ribosome immunoprecipitation (SKI TRIP) toolkit, a collection of Caenorhabditis elegans strains engineered by CRISPR in which tissue-specific expression of FLAG-tagged ribosomal subunit protein RPL-22 is driven by cassettes present in single copy from defined sites in the genome. Through in-depth characterization of the effects of the FLAG tag in animals in which endogenous RPL-22 has been tagged, we show that it incorporates into actively translating ribosomes and efficiently and cleanly pulls down cell-type-specific transcripts. Importantly, the presence of the tag does not impact overall mRNA translation, create bias in transcript use, or cause changes to fitness of the animal. We propose SKI TRIP use for the study of tissue-specific differences in translation and for investigating processes that are acutely sensitive to changes in translation like development or aging.
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Affiliation(s)
- Laura E. Wester
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, 50668 Cologne, Germany
| | - Anne Lanjuin
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Emanuel H.W. Bruckisch
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, 50668 Cologne, Germany
| | - Maria C. Perez-Matos
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Peter G. Stine
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Caroline Heintz
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Martin S. Denzel
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, 50668 Cologne, Germany
- Altos Labs, Cambridge, UK
| | - William B. Mair
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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