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Champroux A, Tang Y, Dickson DA, Meng A, Harrington A, Liaw L, Marzi M, Nicassio F, Schlaeger TM, Feig LA. Transmission of reduced levels of miR-34/449 from sperm to preimplantation embryos is a key step in the transgenerational epigenetic inheritance of the effects of paternal chronic social instability stress. Epigenetics 2024; 19:2346694. [PMID: 38739481 PMCID: PMC11093028 DOI: 10.1080/15592294.2024.2346694] [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: 01/20/2024] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
The transgenerational effects of exposing male mice to chronic social instability (CSI) stress are associated with decreased sperm levels of multiple members of the miR-34/449 family that persist after their mating through preimplantation embryo (PIE) development. Here we demonstrate the importance of these miRNA changes by showing that restoring miR-34c levels in PIEs derived from CSI stressed males prevents elevated anxiety and defective sociability normally found specifically in their adult female offspring. It also restores, at least partially, levels of sperm miR-34/449 normally reduced in their male offspring who transmit these sex-specific traits to their offspring. Strikingly, these experiments also revealed that inducing miR-34c levels in PIEs enhances the expression of its own gene and that of miR-449 in these cells. The same induction of embryo miR-34/449 gene expression likely occurs after sperm-derived miR-34c is introduced into oocytes upon fertilization. Thus, suppression of this miRNA amplification system when sperm miR-34c levels are reduced in CSI stressed mice can explain how a comparable fold-suppression of miR-34/449 levels can be found in PIEs derived from them, despite sperm containing ~50-fold lower levels of these miRNAs than those already present in PIEs. We previously found that men exposed to early life trauma also display reduced sperm levels of miR-34/449. And here we show that miR-34c can also increase the expression of its own gene, and that of miR-449 in human embryonic stem cells, suggesting that human PIEs derived from men with low sperm miR-34/449 levels may also contain this potentially harmful defect.
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Affiliation(s)
- Alexandre Champroux
- Development, Molecular & Chemical Biology/Medical, Tufts University, Boston, MA, USA
| | - Yang Tang
- Stem Cell Program, Boston Children’s Hospital, Boston, MA, USA
| | - David A. Dickson
- Tufts Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
| | - Alice Meng
- Tufts Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
| | - Anne Harrington
- Center for Molecular Medicine, MaineHealth Institute for Research, Scarborough, ME, USA
| | - Lucy Liaw
- Center for Genomic Studies, Instituto Italiano di Tecnologia Institution, Milan, Italy
| | - Matteo Marzi
- Center for Genomic Studies, Instituto Italiano di Tecnologia Institution, Milan, Italy
| | - Francesco Nicassio
- Center for Genomic Studies, Instituto Italiano di Tecnologia Institution, Milan, Italy
| | | | - Larry A. Feig
- Development, Molecular & Chemical Biology/Medical, Tufts University, Boston, MA, USA
- Tufts Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
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2
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Chang X, Du M, Wei J, Zhang Y, Feng X, Deng B, Liu P, Wang Y. Serum tsncRNAs reveals novel potential therapeutic targets of Salvianolic Acid B on atherosclerosis. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 134:155994. [PMID: 39243751 DOI: 10.1016/j.phymed.2024.155994] [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: 12/26/2023] [Revised: 07/17/2024] [Accepted: 08/26/2024] [Indexed: 09/09/2024]
Abstract
BACKGROUND Salvianolic Acid B (SalB) has been proven to delay the progression of atherosclerosis. The therapeutic mechanisms of this compound are unclear. A novel class of short non-coding RNAs, pre-transfer RNA and mature transfer RNA (tsncRNAs) may regulate gene expression. TsncRNAs-sequencing revealed novel therapeutic targets for SalB. This is the first study focusing on tsncRNAs to treat atherosclerosis using SalB. PURPOSE To explore the potential mechanism of SalB treating atherosclerosis through tsncRNAs. METHODS Five groups of mice were created at random: control group (CON), atherosclerosis model group (MOD), SalB with high dose-treated group (SABH), SalB with low dose-treated group (SABL), and Simvastatin-treated group (ST). Aortic sinus plaque, body weight and inflammatory cytokines were evaluated. The Illumina NextSeq equipment was used to do expression profiling of tsncRNAs from serum. The targets of tsncRNAs were then predicted using tRNAscan and TargetScan. The KEGG pathway and GO analysis were utilized to forecast the bioinformatics analysis. Potential tsncRNAs and associated mRNAs were validated using quantitative real-time PCR. RESULTS tRF-Glu-CTC-014 and tRF-Gly-GCC-074 were markedly increased by SalB with high dose treatment and validated with quantitative real-time PCR. Two mRNAs SRF and Arrb related to tRF-Glu-CTC-014 changed consistently. GO analysis revealed that the altered target genes of the selected tsncRNAs were most enriched in protein binding and cellular process. Moreover, KEGG pathway analysis demonstrated that altered target genes of tsncRNAs were most enriched in MAPK signaling pathway. CONCLUSION SalB can promote the expression of tRF-Glu-CTC-014 to treat atherosclerosis.
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Affiliation(s)
- Xindi Chang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Min Du
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Jing Wei
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Yifan Zhang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Xiaoteng Feng
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Bing Deng
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Ping Liu
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China.
| | - Yiru Wang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China.
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3
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Wu J, Zhou Z, Huang Y, Deng X, Zheng S, He S, Huang G, Hu B, Shi M, Liao W, Huang N. Radiofrequency ablation: mechanisms and clinical applications. MedComm (Beijing) 2024; 5:e746. [PMID: 39359691 PMCID: PMC11445673 DOI: 10.1002/mco2.746] [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: 03/10/2024] [Revised: 08/31/2024] [Accepted: 09/02/2024] [Indexed: 10/04/2024] Open
Abstract
Radiofrequency ablation (RFA), a form of thermal ablation, employs localized heat to induce protein denaturation in tissue cells, resulting in cell death. It has emerged as a viable treatment option for patients who are ineligible for surgery in various diseases, particularly liver cancer and other tumor-related conditions. In addition to directly eliminating tumor cells, RFA also induces alterations in the infiltrating cells within the tumor microenvironment (TME), which can significantly impact treatment outcomes. Moreover, incomplete RFA (iRFA) may lead to tumor recurrence and metastasis. The current challenge is to enhance the efficacy of RFA by elucidating its underlying mechanisms. This review discusses the clinical applications of RFA in treating various diseases and the mechanisms that contribute to the survival and invasion of tumor cells following iRFA, including the roles of heat shock proteins, hypoxia, and autophagy. Additionally, we analyze the changes occurring in infiltrating cells within the TME after iRFA. Finally, we provide a comprehensive summary of clinical trials involving RFA in conjunction with other treatment modalities in the field of cancer therapy, aiming to offer novel insights and references for improving the effectiveness of RFA.
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Affiliation(s)
- Jianhua Wu
- Department of Oncology, Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Zhiyuan Zhou
- Department of Oncology, Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Yuanwen Huang
- Department of Oncology, Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Xinyue Deng
- Department of Oncology, Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Siting Zheng
- Department of Oncology, Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Shangwen He
- Department of Respiratory and Critical Care MedicineChronic Airways Diseases Laboratory, Nanfang Hospital, Southern Medical UniversityGuangzhouGuangdongChina
| | - Genjie Huang
- Department of Oncology, Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Binghui Hu
- Department of Oncology, Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Min Shi
- Department of Oncology, Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Wangjun Liao
- Department of Oncology, Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Na Huang
- Department of Oncology, Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
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4
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Yuan X, Su Y, Johnson B, Kirchner M, Zhang X, Xu S, Jiang S, Wu J, Shi S, Russo JJ, Chen Q, Zhang S. Mass Spectrometry-Based Direct Sequencing of tRNAs De Novo and Quantitative Mapping of Multiple RNA Modifications. J Am Chem Soc 2024; 146:25600-25613. [PMID: 39231532 PMCID: PMC11421004 DOI: 10.1021/jacs.4c07280] [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] [Indexed: 09/06/2024]
Abstract
Despite the extensive use of next-generation sequencing (NGS) of RNA, simultaneous direct sequencing and quantitative mapping of multiple RNA nucleotide modifications remains challenging. Mass spectrometry (MS)-based sequencing can directly sequence all RNA modifications without being limited to specific ones, but it requires a perfect MS ladder that few tRNAs can provide. Here, we describe an MS ladder complementation sequencing approach (MLC-Seq) that circumvents the perfect ladder requirement, allowing de novo MS sequencing of full-length heterogeneous cellular tRNAs with multiple nucleotide modifications at single-nucleotide precision. Unlike NGS-based methods, which lose RNA modification information, MLC-Seq preserves RNA sequence diversity and modification information, revealing new detailed stoichiometric tRNA modification profiles and their changes upon treatment with the dealkylating enzyme AlkB. It can also be combined with reference sequences to provide quantitative analysis of diverse tRNAs and modifications in total tRNA samples. MLC-Seq enables systematic, quantitative, and site-specific mapping of RNA modifications, revealing the truly complete informational content of tRNA.
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Affiliation(s)
- Xiaohong Yuan
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, New York 10023, United States
| | - Yue Su
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, New York 10023, United States
| | - Benjamin Johnson
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, New York 10023, United States
| | - Michele Kirchner
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, New York 10023, United States
| | - Xudong Zhang
- Molecular Medicine Program, Department of Human Genetics, and Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah 84132, United States
| | - Sihang Xu
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, New York 10023, United States
| | - Sophia Jiang
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, New York 10023, United States
| | - Jing Wu
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, New York 10023, United States
| | - Shundi Shi
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - James J Russo
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Qi Chen
- Molecular Medicine Program, Department of Human Genetics, and Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah 84132, United States
| | - Shenglong Zhang
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, New York 10023, United States
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
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5
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Wu D, Li X, Khan FA, Yuan C, Pandupuspitasari NS, Huang C, Sun F, Guan K. tRNA modifications and tRNA-derived small RNAs: new insights of tRNA in human disease. Cell Biol Toxicol 2024; 40:76. [PMID: 39276283 PMCID: PMC11401796 DOI: 10.1007/s10565-024-09919-9] [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: 06/10/2024] [Accepted: 09/04/2024] [Indexed: 09/16/2024]
Abstract
tRNAs are codon decoders that convert the transcriptome into the proteome. The field of tRNA research is excited by the increasing discovery of specific tRNA modifications that are installed at specific, evolutionarily conserved positions by a set of specialized tRNA-modifying enzymes and the biogenesis of tRNA-derived regulatory fragments (tsRNAs) which exhibit copious activities through multiple mechanisms. Dysregulation of tRNA modification usually has pathological consequences, a phenomenon referred to as "tRNA modopathy". Current evidence suggests that certain tRNA-modifying enzymes and tsRNAs may serve as promising diagnostic biomarkers and therapeutic targets, particularly for chemoresistant cancers. In this review, we discuss the latest discoveries that elucidate the molecular mechanisms underlying the functions of clinically relevant tRNA modifications and tsRNAs, with a focus on malignancies. We also discuss the therapeutic potential of tRNA/tsRNA-based therapies, aiming to provide insights for the development of innovative therapeutic strategies. Further efforts to unravel the complexities inherent in tRNA biology hold the promise of yielding better biomarkers for the diagnosis and prognosis of diseases, thereby advancing the development of precision medicine for health improvement.
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Affiliation(s)
- Di Wu
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Faheem Ahmed Khan
- Research Center for Animal Husbandry, National Research and Innovation Agency, Jakarta Pusat, 10340, Indonesia
| | - Chenyang Yuan
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | | | - Chunjie Huang
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China.
| | - Fei Sun
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China.
| | - Kaifeng Guan
- School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China.
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Champroux A, Sadat-Shirazi M, Chen X, Hacker J, Yang Y, Feig LA. Astrocyte-Derived Exosomes Regulate Sperm miR-34c Levels to Mediate the Transgenerational Effects of Paternal Chronic Social Instability Stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.21.537854. [PMID: 37786715 PMCID: PMC10541588 DOI: 10.1101/2023.04.21.537854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
The effects of chronically stressing male mice can be transmitted across generations by stress-specific changes in their sperm miRNA content that induce stress-specific phenotypes in their offspring. But how each stress paradigm alters the levels of distinct sets of sperm miRNAs is not known. We showed previously that exposure of male mice to chronic social instability (CSI) stress results in elevated anxiety and reduced sociability specifically in their female offspring across multiple generations because it reduces miR-34c levels in sperm of stressed males and their unstressed male offspring. Here we describe evidence that a strocyte-derived exos omes ( A-Exos ) carrying miR-34c mediate how CSI stress has this transgenerational effect on sperm. We found that CSI stress decreases miR-34c carried by A-Exos in the prefrontal cortex and amygdala, as well as in the blood of males. Importantly, miR-34c A-Exos levels are also reduced in these tissues in their F1 male offspring, who despite not being exposed to stress exhibit reduced sperm miR-34c levels and transmit the same stress-associated traits to their male and female offspring. Furthermore, restoring A-Exos miR-34c content in the blood of CSI-stressed males by intravenous injection of miR-34c-containing A-Exos restores miR-34c levels in their sperm. These findings reveal an unexpected role for A-Exos in maintaining sperm miR-34c levels by a process that when suppressed by CSI stress mediates this example of transgenerational epigenetic inheritance.
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Hayashi S. Variation of tRNA modifications with and without intron dependency. Front Genet 2024; 15:1460902. [PMID: 39296543 PMCID: PMC11408192 DOI: 10.3389/fgene.2024.1460902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Accepted: 08/26/2024] [Indexed: 09/21/2024] Open
Abstract
tRNAs have recently gained attention for their novel regulatory roles in translation and for their diverse functions beyond translation. One of the most remarkable aspects of tRNA biogenesis is the incorporation of various chemical modifications, ranging from simple base or ribose methylation to more complex hypermodifications such as formation of queuosine and wybutosine. Some tRNAs are transcribed as intron-containing pre-tRNAs. While the majority of these modifications occur independently of introns, some are catalyzed in an intron-inhibitory manner, and in certain cases, they occur in an intron-dependent manner. This review focuses on pre-tRNA modification, including intron-containing pre-tRNA, in both intron-inhibitory and intron-dependent fashions. Any perturbations in the modification and processing of tRNAs may lead to a range of diseases and disorders, highlighting the importance of understanding these mechanisms in molecular biology and medicine.
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Affiliation(s)
- Sachiko Hayashi
- Graduate School of Science, University of Hyogo, Ako-gun, Japan
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8
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Bhatter N, Advani VM, Takenaka Y, Lyons SM, Akiyama Y, Anderson PJ, Ivanov P. Repurposing tRNA isodecoders for non-canonical functions via tRNA cleavage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.04.611212. [PMID: 39282440 PMCID: PMC11398368 DOI: 10.1101/2024.09.04.611212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/20/2024]
Abstract
Transfer RNAs (tRNAs) are the key adaptor molecules aiding protein synthesis. Hundreds of tRNA genes are found in the human genome but the biological significance of this genetic excess is still enigmatic. The tRNA repertoires are variable between tissues and cells as well as during development. Such variations can only be partially explained by the correlation to the physiological needs in protein production, e.g. by changes in the expression of tRNA isoacceptor sets (tRNAs charged with the same amino acid but bearing different anticodons). However, changes in the expression levels of individual isodecoders (tRNAs with the same anticodon) are less understood. Besides canonical functions in mRNA translation, tRNAs are implicated in non-canonical functions unrelated to protein synthesis. tRNAs are rich source of small non-protein coding RNAs called tRNA-derived RNAs (tDRs), which include tRNA-derived stress-induced RNAs (tiRNAs) formed in response to stress. Here, we show that tiRNAs derived from isodecoders different in a single nucleotide can also differ in their activities. Specifically, we show that isodecoder sets for tRNA His-GTG , tRNA Gly-GCC and tRNA Cys-GCA are cleaved by ribonucleases to yield 5'-tiRNAs showing differential activity towards mRNA reporter translation. Our data propose a model where cleavage repurposes specific tRNA isodecoders for non-canonical functions. Significance Statement The human genome encodes hundreds of transfer RNA (tRNA) genes to decode 61 codons. The basis for such genetic redundancy is unclear but the increase in the number of tRNA genes goes in concert with the complexity of an organism. While changes in the expression of isoacceptor tRNA pools can reflect adaptation to demanding protein synthesis needs and/or codon usage, the variations in the expression of the individual tRNA isodecoders are documented but poorly understood. Such expression variations are hypothesized to contribute to non-canonical tRNA functions, yet physiological relevance remains ambiguous. We report here that specific tRNA isodecoders can be functionally repurposed through cleavage that produces tRNA-derived RNAs (tDRs). The repurposing employs nucleotide variations in isodecoders leading to the production of distinct sets of tDRs with variable bioactivities.
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Wu F, Chai B, Qi P, Han Y, Gu Z, Pan W, Zhang H, Wang X, Liu X, Zou H, Liang C, Li Y, Fang W, Ma Z. Oncogenic tRNA-derived fragment tRF-Leu-CAG promotes tumorigenesis of lung cancer via targeting TCEA3 and increasing autophagy. J Gene Med 2024; 26:e3737. [PMID: 39198937 DOI: 10.1002/jgm.3737] [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: 03/26/2024] [Revised: 07/30/2024] [Accepted: 08/14/2024] [Indexed: 09/01/2024] Open
Abstract
BACKGROUND Lung cancer is a prevalent and severe form of malignant tumors worldwide. tRF-Leu-CAG, a recently discovered non-coding single-stranded small RNA derived from transfer RNA, has sparked interest in exploring its biological functions and potential molecular mechanisms in lung cancer. METHODS The abundance of tRF-Leu-CAG was measured via quantitative real-time polymerase chain reaction (qRT-PCR) in 96 sets of lung cancer tissue samples obtained from clinical patients. Subsequently, both in vivo and in vitro experiments were conducted to validate the biological functions of tRF-Leu-CAG in lung cancer. Furthermore, an exploration of the potential target genes of tRF-Leu-CAG and its association with autophagy and drug resistance in lung cancer was undertaken. RESULTS Our analysis revealed a significant upregulation of tRF-Leu-CAG in non-small cell lung cancer (NSCLC) tissues. Additionally, we observed that heightened expression of tRF-Leu-CAG significantly augmented the proliferation and migration of NSCLC cells, facilitated cell cycle progression, and suppressed apoptosis. Furthermore, we identified transcription elongation factor A3 (TCEA3) as a direct target gene of tRF-Leu-CAG. TCEA3 inhibited the proliferation and migration of NSCLC, and tRF-Leu-CAG promoted the proliferation and migration of NSCLC by mediating the silencing of TCEA3. Moreover, we demonstrated that the augmentation of paclitaxel resistance by tRF-Leu-CAG was contingent on autophagy. Finally, tRF-Leu-CAG notably accelerated tumor growth and promoted the process of epithelial-mesenchymal transition (EMT) in vivo. CONCLUSIONS tRF-Leu-CAG promotes NSCLC tumor growth and metastasis by targeting TCEA3 and promotes paclitaxel resistance by enhancing cellular autophagy. These results provide potentially effective targets and therapeutic options for the clinical treatment of NSCLC.
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Affiliation(s)
- Fan Wu
- Lab for Noncoding RNA & Cancer, Shanghai University, Shanghai, China
| | - Binshu Chai
- Lab for Noncoding RNA & Cancer, Shanghai University, Shanghai, China
| | - Pengfei Qi
- Lab for Noncoding RNA & Cancer, Shanghai University, Shanghai, China
| | - Yaqi Han
- Lab for Noncoding RNA & Cancer, Shanghai University, Shanghai, China
| | - Zhitao Gu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Jiaotong University, Shanghai, China
| | - Wei Pan
- Lab for Noncoding RNA & Cancer, Shanghai University, Shanghai, China
| | - Hui Zhang
- Lab for Noncoding RNA & Cancer, Shanghai University, Shanghai, China
| | - Xianyi Wang
- Lab for Noncoding RNA & Cancer, Shanghai University, Shanghai, China
| | - Xiaomin Liu
- Lab for Noncoding RNA & Cancer, Shanghai University, Shanghai, China
| | - Heng Zou
- Lab for Noncoding RNA & Cancer, Shanghai University, Shanghai, China
| | - Chen Liang
- Lab for Noncoding RNA & Cancer, Shanghai University, Shanghai, China
| | - YanLi Li
- Lab for Noncoding RNA & Cancer, Shanghai University, Shanghai, China
| | - Wentao Fang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Jiaotong University, Shanghai, China
| | - Zhongliang Ma
- Lab for Noncoding RNA & Cancer, Shanghai University, Shanghai, China
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10
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Long D, Deng Z, Li M, Li W, Zhong Y, Lin Z, He A, Kang Y, Mao G. tRNA-derived fragment 3031B regulates human anterior cruciate ligament cell proliferation and survival by targeting RELA. Gene 2024; 933:148897. [PMID: 39222756 DOI: 10.1016/j.gene.2024.148897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 08/13/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
tRNA-derived fragments (tRFs) are novel short noncoding RNAs that play pivotal roles in cell proliferation and survival. However, knowledge of the biological roles of tRFs in anterior cruciate ligament (ACL) cells is limited. Here, we intended to investigate the function of tRF-3031B in ACL cell. We used the tRF and tiRNA array to analyze tRF and tiRNA expression profiles in osteoarthritis (OA) ACL cells and normal ACL cells, and qRT-PCR and fluorescence in situ hybridization (FISH) were used to determine tRF-3031B expression. The results showed that tRF-3031B was expressed at low levels in OA ACL and Interleukin-1β (IL-1β) treated ACL cells. We found that RELA was the target of tRF-3031B. When ACL cells were transfected with tRF-3031B mimics, RELA expression was suppressed, whereas transfection with tRF-3031B inhibitors had the opposite effect. The rescue and dual-luciferase reporter assays showed that tRF-3031B silenced the RELA expression by binding to its untranslated region (3'-UTR). Hence, this study showed the novel function of tRF-3031B in regulating ACL cell proliferation and survival by targeting RELA, and these findings may offer a new direction for the study of ACL degeneration and pathophysiological of OA.
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Affiliation(s)
- Dianbo Long
- Department of Sports Medicine, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Zengfa Deng
- Department of Sports Medicine, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Ming Li
- Department of Sports Medicine, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Wei Li
- Department of Sports Medicine, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Yanlin Zhong
- Department of Sports Medicine, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Zhencan Lin
- Department of Sports Medicine, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Aishan He
- Department of Sports Medicine, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China.
| | - Yan Kang
- Department of Sports Medicine, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China.
| | - Guping Mao
- Department of Sports Medicine, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China.
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11
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Schuntermann DB, Jaskolowski M, Reynolds NM, Vargas-Rodriguez O. The central role of transfer RNAs in mistranslation. J Biol Chem 2024; 300:107679. [PMID: 39154912 DOI: 10.1016/j.jbc.2024.107679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/20/2024] Open
Abstract
Transfer RNAs (tRNA) are essential small non-coding RNAs that enable the translation of genomic information into proteins in all life forms. The principal function of tRNAs is to bring amino acid building blocks to the ribosomes for protein synthesis. In the ribosome, tRNAs interact with messenger RNA (mRNA) to mediate the incorporation of amino acids into a growing polypeptide chain following the rules of the genetic code. Accurate interpretation of the genetic code requires tRNAs to carry amino acids matching their anticodon identity and decode the correct codon on mRNAs. Errors in these steps cause the translation of codons with the wrong amino acids (mistranslation), compromising the accurate flow of information from DNA to proteins. Accumulation of mutant proteins due to mistranslation jeopardizes proteostasis and cellular viability. However, the concept of mistranslation is evolving, with increasing evidence indicating that mistranslation can be used as a mechanism for survival and acclimatization to environmental conditions. In this review, we discuss the central role of tRNAs in modulating translational fidelity through their dynamic and complex interplay with translation factors. We summarize recent discoveries of mistranslating tRNAs and describe the underlying molecular mechanisms and the specific conditions and environments that enable and promote mistranslation.
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Affiliation(s)
- Dominik B Schuntermann
- Department of Biology, Institute of Molecular Biology and Biophysics, Zurich, Switzerland
| | - Mateusz Jaskolowski
- Department of Biology, Institute of Molecular Biology and Biophysics, Zurich, Switzerland
| | - Noah M Reynolds
- School of Integrated Sciences, Sustainability, and Public Health, University of Illinois Springfield, Springfield, Illinois, USA
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA.
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12
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Hao Y, Li B, Yin F, Liu W. tRNA-derived small RNA (tsr007330) regulates myocardial fibrosis after myocardial infarction through NAT10-mediated ac4C acetylation of EGR3 mRNA. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167267. [PMID: 38810917 DOI: 10.1016/j.bbadis.2024.167267] [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: 10/30/2023] [Revised: 04/27/2024] [Accepted: 05/21/2024] [Indexed: 05/31/2024]
Abstract
Small non-coding ribonucleic acids (sncRNAs) play an important role in cell regulation and are closely related to the pathogenesis of heart diseases. However, the role and molecular mechanism of transfer RNA-derived small RNAs (tsRNAs) in myocardial fibrosis after myocardial infarction (MI) remain unknown. In this study, we identified and validated sncRNAs (mainly miRNA and tsRNA) associated with myocardial fibrosis after MI through PANDORA sequencing of rat myocardial tissue. As a key enzyme of N4-acetylcytidine (ac4C) acetylation modification, N-acetyltransferase 10 (NAT10) plays an important role in regulating messenger RNA (mRNA) stability and translation efficiency. We found that NAT10 is highly expressed in infarcted myocardial tissue, and the results of acetylated RNA immunoprecipitation sequencing (acRIP-seq) analysis suggest that early growth response 3 (EGR3) may be an important molecule in the pathogenesis of NAT10-mediated myocardial fibrosis. Both in vivo and in vitro experiments have shown that inhibition of NAT10 can reduce the expression of EGR3 and alleviate myocardial fibrosis after MI. tsRNA can participate in gene regulation by inhibiting target genes. The expression of tsr007330 was decreased in myocardial infarction tissue. We found that overexpression of tsr007330 in rat myocardial tissue could antagonize NAT10, improve myocardial function in MI and alleviate myocardial fibrosis. In conclusion, tsRNAs (rno-tsr007330) may regulate the occurrence of myocardial fibrosis by regulating NAT10-mediated EGR3 mRNA acetylation. This study provides new insights into the improvement of myocardial fibrosis after MI by targeting tsRNA therapy.
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Affiliation(s)
- Yan Hao
- Harbin Medical University, Harbin, Heilongjiang 150001, China; Department of Cardiology, the fourth affiliated hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China
| | - Bohan Li
- Harbin Medical University, Harbin, Heilongjiang 150001, China
| | - Feiya Yin
- University of Sydney, NSW 2006, Australia
| | - Wei Liu
- Harbin Medical University, Harbin, Heilongjiang 150001, China; Department of Geriatric Cardiovascular Division, Guangdong Provincial Geriatrics Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China.
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13
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D’Andrea G, Deroma G, Miluzio A, Biffo S. The Paradox of Ribosomal Insufficiency Coupled with Increased Cancer: Shifting the Perspective from the Cancer Cell to the Microenvironment. Cancers (Basel) 2024; 16:2392. [PMID: 39001453 PMCID: PMC11240629 DOI: 10.3390/cancers16132392] [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: 05/31/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/16/2024] Open
Abstract
Ribosomopathies are defined as inherited diseases in which ribosomal factors are mutated. In general, they present multiorgan symptoms. In spite of the fact that in cellular models, ribosomal insufficiency leads to a reduced rate of oncogenic transformation, patients affected by ribosomopathies present a paradoxical increase in cancer incidence. Several hypotheses that explain this paradox have been formulated, mostly on the assumption that altered ribosomes in a stem cell induce compensatory changes that lead to a cancer cell. For instance, the lack of a specific ribosomal protein can lead to the generation of an abnormal ribosome, an oncoribosome, that itself leads to altered translation and increased tumorigenesis. Alternatively, the presence of ribosomal stress may induce compensatory proliferation that in turns selects the loss of tumor suppressors such as p53. However, modern views on cancer have shifted the focus from the cancer cell to the tumor microenvironment. In particular, it is evident that human lymphocytes are able to eliminate mutant cells and contribute to the maintenance of cancer-free tissues. Indeed, many tumors develop in conditions of reduced immune surveillance. In this review, we summarize the current evidence and attempt to explain cancer and ribosomopathies from the perspective of the microenvironment.
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Affiliation(s)
- Giacomo D’Andrea
- National Institute of Molecular Genetics, INGM Fondazione Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.D.); (G.D.); (A.M.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Giorgia Deroma
- National Institute of Molecular Genetics, INGM Fondazione Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.D.); (G.D.); (A.M.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Annarita Miluzio
- National Institute of Molecular Genetics, INGM Fondazione Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.D.); (G.D.); (A.M.)
| | - Stefano Biffo
- National Institute of Molecular Genetics, INGM Fondazione Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.D.); (G.D.); (A.M.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
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14
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Li S, Feng T, Liu Y, Yang Q, Song A, Wang S, Xie J, Zhang J, Yuan B, Sun Z. m 1A inhibition fuels oncolytic virus-elicited antitumor immunity via downregulating MYC/PD-L1 signaling. Int J Oral Sci 2024; 16:36. [PMID: 38730256 PMCID: PMC11087574 DOI: 10.1038/s41368-024-00304-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/13/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
N1-methyladenosine (m1A) RNA methylation is critical for regulating mRNA translation; however, its role in the development, progression, and immunotherapy response of head and neck squamous cell carcinoma (HNSCC) remains largely unknown. Using Tgfbr1 and Pten conditional knockout (2cKO) mice, we found the neoplastic transformation of oral mucosa was accompanied by increased m1A modification levels. Analysis of m1A-associated genes identified TRMT61A as a key m1A writer linked to cancer progression and poor prognosis. Mechanistically, TRMT61A-mediated tRNA-m1A modification promotes MYC protein synthesis, upregulating programmed death-ligand 1 (PD-L1) expression. Moreover, m1A modification levels were also elevated in tumors treated with oncolytic herpes simplex virus (oHSV), contributing to reactive PD-L1 upregulation. Therapeutic m1A inhibition sustained oHSV-induced antitumor immunity and reduced tumor growth, representing a promising strategy to alleviate resistance. These findings indicate that m1A inhibition can prevent immune escape after oHSV therapy by reducing PD-L1 expression, providing a mutually reinforcing combination immunotherapy approach.
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Affiliation(s)
- Shujin Li
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Tian Feng
- School of Public Health, Wuhan University, Wuhan, China
| | - Yuantong Liu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Qichao Yang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - An Song
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Shuo Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Jun Xie
- State Key Laboratory of Virology, Medical Research Institute, Wuhan University, Wuhan, China
| | - Junjie Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
- State Key Laboratory of Virology, Medical Research Institute, Wuhan University, Wuhan, China
| | - Bifeng Yuan
- School of Public Health, Wuhan University, Wuhan, China
| | - Zhijun Sun
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
- Department of Oral Maxillofacial-Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, China.
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15
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Muthukumar S, Li CT, Liu RJ, Bellodi C. Roles and regulation of tRNA-derived small RNAs in animals. Nat Rev Mol Cell Biol 2024; 25:359-378. [PMID: 38182846 DOI: 10.1038/s41580-023-00690-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2023] [Indexed: 01/07/2024]
Abstract
A growing class of small RNAs, known as tRNA-derived RNAs (tdRs), tRNA-derived small RNAs or tRNA-derived fragments, have long been considered mere intermediates of tRNA degradation. These small RNAs have recently been implicated in an evolutionarily conserved repertoire of biological processes. In this Review, we discuss the biogenesis and molecular functions of tdRs in mammals, including tdR-mediated gene regulation in cell metabolism, immune responses, transgenerational inheritance, development and cancer. We also discuss the accumulation of tRNA-derived stress-induced RNAs as a distinct adaptive cellular response to pathophysiological conditions. Furthermore, we highlight new conceptual advances linking RNA modifications with tdR activities and discuss challenges in studying tdR biology in health and disease.
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Affiliation(s)
- Sowndarya Muthukumar
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Cai-Tao Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Cristian Bellodi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden.
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16
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Hu Y, Lopez VA, Xu H, Pfister JP, Song B, Servage KA, Sakurai M, Jones BT, Mendell JT, Wang T, Wu J, Lambowitz AM, Tomchick DR, Pawłowski K, Tagliabracci VS. Biochemical and structural insights into a 5' to 3' RNA ligase reveal a potential role in tRNA ligation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590974. [PMID: 38712170 PMCID: PMC11071452 DOI: 10.1101/2024.04.24.590974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
ATP-grasp superfamily enzymes contain a hand-like ATP-binding fold and catalyze a variety of reactions using a similar catalytic mechanism. More than 30 protein families are categorized in this superfamily, and they are involved in a plethora of cellular processes and human diseases. Here we identify C12orf29 as an atypical ATP-grasp enzyme that ligates RNA. Human C12orf29 and its homologs auto-adenylate on an active site Lys residue as part of a reaction intermediate that specifically ligates RNA halves containing a 5'-phosphate and a 3'-hydroxyl. C12orf29 binds tRNA in cells and can ligate tRNA within the anticodon loop in vitro. Genetic depletion of c12orf29 in female mice alters global tRNA levels in brain. Furthermore, crystal structures of a C12orf29 homolog from Yasminevirus bound to nucleotides reveal a minimal and atypical RNA ligase fold with a unique active site architecture that participates in catalysis. Collectively, our results identify C12orf29 as an RNA ligase and suggest its involvement in tRNA biology.
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Affiliation(s)
- Yingjie Hu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Victor A. Lopez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Hengyi Xu
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, Texas 78712, USA
| | - James P. Pfister
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Bing Song
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Kelly A. Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Masahiro Sakurai
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Benjamin T. Jones
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Joshua T. Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, Texas 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children’s Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Alan M. Lambowitz
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Diana R. Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Vincent S. Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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17
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Zhang Y, Zhou JB, Yin Y, Wang ED, Zhou XL. Multifaceted roles of t6A biogenesis in efficiency and fidelity of mitochondrial gene expression. Nucleic Acids Res 2024; 52:3213-3233. [PMID: 38227555 PMCID: PMC11014344 DOI: 10.1093/nar/gkae013] [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: 10/13/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024] Open
Abstract
N 6-Threonylcarbamoyladenosine at A37 (t6A37) of ANN-decoding transfer RNAs (tRNAs) is a universal modification whose functions have been well documented in bacteria and lower eukaryotes; however, its role in organellar translation is not completely understood. In this study, we deleted the mitochondrial t6A37-modifying enzyme OSGEPL1 in HEK293T cells. OSGEPL1 is dispensable for cell viability. t6A37 hypomodification selectively stimulated N1-methyladenosine at A9 (m1A9) and N2-methylguanosine at G10 (m2G10) modifications and caused a substantial reduction in the aminoacylation of mitochondrial tRNAThr and tRNALys, resulting in impaired translation efficiency. Multiple types of amino acid misincorporation due to the misreading of near-cognate codons by t6A37-unmodified tRNAs were detected, indicating a triggered translational infidelity. Accordingly, the alterations in mitochondrial structure, function, and the activated mitochondrial unfolded protein response were observed. Mitochondrial function was efficiently restored by wild-type, but not by tRNA-binding-defective OSGEPL1. Lastly, in Osgepl1 deletion mice, disruption to mitochondrial translation was evident but resulted in no observable deficiency under physiological conditions in heart, which displays the highest Osgepl1 expression. Taken together, our data delineate the multifaceted roles of mitochondrial t6A37 modification in translation efficiency and quality control in mitochondria.
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Affiliation(s)
- Yong Zhang
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Jing-Bo Zhou
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Yue Yin
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Science, 333 Haike Road, Shanghai 201210, China
| | - En-Duo Wang
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Xiao-Long Zhou
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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18
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Chen Q, Li D, Jiang L, Wu Y, Yuan H, Shi G, Liu F, Wu P, Jiang K. Biological functions and clinical significance of tRNA-derived small fragment (tsRNA) in tumors: Current state and future perspectives. Cancer Lett 2024; 587:216701. [PMID: 38369004 DOI: 10.1016/j.canlet.2024.216701] [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: 10/10/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
A new class of noncoding RNAs, tsRNAs are not only abundant in humans but also have high tissue specificity. Recently, an increasing number of studies have explored the correlations between tsRNAs and tumors, showing that tsRNAs can affect biological behaviors of tumor cells, such as proliferation, apoptosis and metastasis, by modulating protein translation, RNA transcription or posttranscriptional regulation. In addition, tsRNAs are widely distributed and stably expressed, which endows them with broad application prospects in diagnosing and predicting the prognosis of tumors, and they are expected to become new biomarkers. However, notably, the current research on tsRNAs still faces problems that need to be solved. In this review, we describe the characteristics of tsRNAs as well as their unique features and functions in tumors. Moreover, we also discuss the potential opportunities and challenges in clinical applications and research of tsRNAs.
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Affiliation(s)
- Qun Chen
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Danrui Li
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Luyang Jiang
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yang Wu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Yuan
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Guodong Shi
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Fengyuan Liu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Pengfei Wu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Kuirong Jiang
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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19
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Xiong Q, Zhang Y, Xu Y, Yang Y, Zhang Z, Zhou Y, Zhang S, Zhou L, Wan X, Yang X, Zeng Z, Liu J, Zheng Y, Han J, Zhu Q. tiRNA-Val-CAC-2 interacts with FUBP1 to promote pancreatic cancer metastasis by activating c‑MYC transcription. Oncogene 2024; 43:1274-1287. [PMID: 38443680 PMCID: PMC11035144 DOI: 10.1038/s41388-024-02991-9] [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: 10/12/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/07/2024]
Abstract
Cumulative studies have established the significance of transfer RNA-derived small RNA (tsRNA) in tumorigenesis and progression. Nevertheless, its function and mechanism in pancreatic cancer metastasis remain largely unclear. Here, we screened and identified tiRNA-Val-CAC-2 as highly expressed in pancreatic cancer metastasis samples by tsRNA sequencing. We also observed elevated levels of tiRNA-Val-CAC-2 in the serum of pancreatic cancer patients who developed metastasis, and patients with high levels of tiRNA-Val-CAC-2 exhibited a worse prognosis. Additionally, knockdown of tiRNA-Val-CAC-2 inhibited the metastasis of pancreatic cancer in vivo and in vitro, while overexpression of tiRNA-Val-CAC-2 promoted the metastasis of pancreatic cancer. Mechanically, we discovered that tiRNA-Val-CAC-2 interacts with FUBP1, leading to enhanced stability of FUBP1 protein and increased FUBP1 enrichment in the c-MYC promoter region, thereby boosting the transcription of c-MYC. Of note, rescue experiments confirmed that tiRNA-Val-CAC-2 could influence pancreatic cancer metastasis via FUBP1-mediated c-MYC transcription. These findings highlight a potential novel mechanism underlying pancreatic cancer metastasis, and suggest that both tiRNA-Val-CAC-2 and FUBP1 could serve as promising prognostic biomarkers and potential therapeutic targets for pancreatic cancer.
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Affiliation(s)
- Qunli Xiong
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yaguang Zhang
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yongfeng Xu
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yang Yang
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhiwei Zhang
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ying Zhou
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Su Zhang
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Lian Zhou
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaowen Wan
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaojuan Yang
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhu Zeng
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jinlu Liu
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ying Zheng
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Junhong Han
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Qing Zhu
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China.
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20
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Salehi M, Kamali MJ, Rajabzadeh A, Minoo S, Mosharafi H, Saeedi F, Daraei A. tRNA-derived fragments: Key determinants of cancer metastasis with emerging therapeutic and diagnostic potentials. Arch Biochem Biophys 2024; 753:109930. [PMID: 38369227 DOI: 10.1016/j.abb.2024.109930] [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: 12/28/2023] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 02/20/2024]
Abstract
Metastasis is a significant clinical challenge responsible for cancer mortality and non-response to treatment. However, the molecular mechanisms driving metastasis remain unclear, limiting the development of efficient diagnostic and therapeutic approaches. Recent breakthroughs in cancer biology have discovered a group of small non-coding RNAs called tRNA-derived fragments (tRFs), which play a critical role in the metastatic behavior of various tumors. tRFs are produced from cleavage modifications of tRNAs and have different functional classes based on the pattern of these modifications. They perform post-transcriptional regulation through microRNA-like functions, displacing RNA-binding proteins, and play a role in translational regulation by inducing ribosome synthesis, translation initiation, and epigenetic regulation. Tumor cells manipulate tRFs to develop and survive the tumor mass, primarily by inducing metastasis. Multiple studies have demonstrated the potential of tRFs as therapeutic, diagnostic, and prognostic targets for tumor metastasis. This review discusses the production and function of tRFs in cells, their aberrant molecular contributions to the metastatic environment, and their potential as promising targets for anti-metastasis treatment strategies.
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Affiliation(s)
- Mohammad Salehi
- Department of Medical Genetics, School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran; Student Research Committee, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mohammad Javad Kamali
- Department of Medical Genetics, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Aliakbar Rajabzadeh
- Department of Anatomical Sciences, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Shima Minoo
- Department of Dentistry, Khorasgan Branch, Islamic Azad University, Isfahan, Iran
| | | | - Fatemeh Saeedi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Abdolreza Daraei
- Department of Medical Genetics, School of Medicine, Babol University of Medical Sciences, Babol, Iran.
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21
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Colón-Santos S, Vázquez-Salazar A, Adams A, Campillo-Balderas JA, Hernández-Morales R, Jácome R, Muñoz-Velasco I, Rodriguez LE, Schaible MJ, Schaible GA, Szeinbaum N, Thweatt JL, Trubl G. Chapter 2: What Is Life? ASTROBIOLOGY 2024; 24:S40-S56. [PMID: 38498820 DOI: 10.1089/ast.2021.0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The question "What is life?" has existed since the beginning of recorded history. However, the scientific and philosophical contexts of this question have changed and been refined as advancements in technology have revealed both fine details and broad connections in the network of life on Earth. Understanding the framework of the question "What is life?" is central to formulating other questions such as "Where else could life be?" and "How do we search for life elsewhere?" While many of these questions are addressed throughout the Astrobiology Primer 3.0, this chapter gives historical context for defining life, highlights conceptual characteristics shared by all life on Earth as well as key features used to describe it, discusses why it matters for astrobiology, and explores both challenges and opportunities for finding an informative operational definition.
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Affiliation(s)
- Stephanie Colón-Santos
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, USA
- Department of Botany, University of Wisconsin-Madison, Wisconsin, USA
| | - Alberto Vázquez-Salazar
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, California, USA
| | - Alyssa Adams
- Department of Botany, University of Wisconsin-Madison, Wisconsin, USA
| | | | - Ricardo Hernández-Morales
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rodrigo Jácome
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Israel Muñoz-Velasco
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Laura E Rodriguez
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Lunar and Planetary Institute, Universities Space Research Association, Houston, Texas, USA
| | - Micah J Schaible
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - George A Schaible
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nadia Szeinbaum
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Jennifer L Thweatt
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA. (Former)
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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22
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He H, Wang Y, Zhang X, Li X, Liu C, Yan D, Deng H, Sun W, Yi C, Wang J. Age-related noncanonical TRMT6-TRMT61A signaling impairs hematopoietic stem cells. NATURE AGING 2024; 4:213-230. [PMID: 38233630 DOI: 10.1038/s43587-023-00556-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024]
Abstract
Aged hematopoietic stem cells (HSCs) exhibit compromised reconstitution capacity and differentiation bias toward myeloid lineages. However, the molecular mechanism behind HSC aging remains largely unknown. In this study, we observed that RNA N1-methyladenosine-generating methyltransferase TRMT6-TRMT61A complex is increased in aged murine HSCs due to aging-declined CRL4DCAF1-mediated ubiquitination degradation signaling. Unexpectedly, no difference of tRNA N1-methyladenosine methylome is observed between young and aged hematopoietic stem and progenitor cells, suggesting a noncanonical role of the TRMT6-TRMT61A complex in the HSC aging process. Further investigation revealed that enforced TRMT6-TRMT61A impairs HSCs through 3'-tiRNA-Leu-CAG and subsequent RIPK1-RIPK3-MLKL-mediated necroptosis cascade. Deficiency of necroptosis ameliorates the self-renewal capacity of HSCs and counters the physiologically deleterious effect of enforced TRMT6-TRMT61A on HSCs. Together, our work uncovers a nonclassical role for the TRMT6-TRMT61A complex in HSC aging and highlights a therapeutic target.
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Affiliation(s)
- Hanqing He
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Yuqian Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Xiaoting Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Xiaoyu Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Chao Liu
- Department of Laboratory Animal Science, Hebei Key Lab of Hebei Laboratory Animal Science, Hebei Medical University, Shijiazhuang, P. R. China
| | - Dingfei Yan
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Wanling Sun
- Department of Hematology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
| | - Jianwei Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China.
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.
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23
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Sun C, Lei Y, Li B, Gao Q, Li Y, Cao W, Yang C, Li H, Wang Z, Li Y, Wang Y, Liu J, Zhao KT, Gao C. Precise integration of large DNA sequences in plant genomes using PrimeRoot editors. Nat Biotechnol 2024; 42:316-327. [PMID: 37095350 DOI: 10.1038/s41587-023-01769-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/28/2023] [Indexed: 04/26/2023]
Abstract
A technique for chromosomal insertion of large DNA segments is much needed in plant breeding and synthetic biology to facilitate the introduction of desired agronomic traits and signaling and metabolic pathways. Here we describe PrimeRoot, a genome editing approach to generate targeted precise large DNA insertions in plants. Third-generation PrimeRoot editors employ optimized prime editing guide RNA designs, an enhanced plant prime editor and superior recombinases to enable precise large DNA insertions of up to 11.1 kilobases into plant genomes. We demonstrate the use of PrimeRoot to accurately introduce gene regulatory elements in rice. In this study, we also integrated a gene cassette comprising PigmR, which confers rice blast resistance driven by an Act1 promoter, into a predicted genomic safe harbor site of Kitaake rice and obtain edited plants harboring the expected insertion with an efficiency of 6.3%. We found that these rice plants have increased blast resistance. These results establish PrimeRoot as a promising approach to precisely insert large segments of DNA in plants.
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Affiliation(s)
- Chao Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuan Lei
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Boshu Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qiang Gao
- Qi Biodesign, Life Science Park, Beijing, China
| | - Yunjia Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wen Cao
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory for Monitoring and Green Management of Crop Pests, China Agricultural University, Beijing, China
| | - Chao Yang
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory for Monitoring and Green Management of Crop Pests, China Agricultural University, Beijing, China
| | - Hongchao Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zhiwei Wang
- Qi Biodesign, Life Science Park, Beijing, China
| | - Yan Li
- Qi Biodesign, Life Science Park, Beijing, China
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jun Liu
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory for Monitoring and Green Management of Crop Pests, China Agricultural University, Beijing, China
| | | | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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24
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Zhang F, Ignatova VV, Ming GL, Song H. Advances in brain epitranscriptomics research and translational opportunities. Mol Psychiatry 2024; 29:449-463. [PMID: 38123727 PMCID: PMC11116067 DOI: 10.1038/s41380-023-02339-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/16/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
Various chemical modifications of all RNA transcripts, or epitranscriptomics, have emerged as crucial regulators of RNA metabolism, attracting significant interest from both basic and clinical researchers due to their diverse functions in biological processes and immense clinical potential as highlighted by the recent profound success of RNA modifications in improving COVID-19 mRNA vaccines. Rapid accumulation of evidence underscores the critical involvement of various RNA modifications in governing normal neural development and brain functions as well as pathogenesis of brain disorders. Here we provide an overview of RNA modifications and recent advancements in epitranscriptomic studies utilizing animal models to elucidate important roles of RNA modifications in regulating mammalian neurogenesis, gliogenesis, synaptic formation, and brain function. Moreover, we emphasize the pivotal involvement of RNA modifications and their regulators in the pathogenesis of various human brain disorders, encompassing neurodevelopmental disorders, brain tumors, psychiatric and neurodegenerative disorders. Furthermore, we discuss potential translational opportunities afforded by RNA modifications in combatting brain disorders, including their use as biomarkers, in the development of drugs or gene therapies targeting epitranscriptomic pathways, and in applications for mRNA-based vaccines and therapies. We also address current limitations and challenges hindering the widespread clinical application of epitranscriptomic research, along with the improvements necessary for future progress.
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Affiliation(s)
- Feng Zhang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Valentina V Ignatova
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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25
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Zhao P, Xia L, Chen D, Xu W, Guo H, Xu Y, Yan B, Wu X, Li Y, Zhang Y, Zhang X. METTL1 mediated tRNA m 7G modification promotes leukaemogenesis of AML via tRNA regulated translational control. Exp Hematol Oncol 2024; 13:8. [PMID: 38268051 PMCID: PMC10807064 DOI: 10.1186/s40164-024-00477-8] [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: 07/26/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND RNA modifications have been proven to play fundamental roles in regulating cellular biology process. Recently, maladjusted N7-methylguanosine (m7G) modification and its modifiers METTL1/WDR4 have been confirmed an oncogene role in multiple cancers. However, the functions and molecular mechanisms of METTL1/WDR4 in acute myeloid leukemia (AML) remain to be determined. METHODS METTL1/WDR4 expression levels were quantified using qRT-PCR, western blot analysis on AML clinical samples, and bioinformatics analysis on publicly available AML datasets. CCK-8 assays and cell count assays were performed to determine cell proliferation. Flow cytometry assays were conducted to assess cell cycle and apoptosis rates. Multiple techniques were used for mechanism studies in vitro assays, such as northern blotting, liquid chromatography-coupled mass spectrometry (LC-MS/MS), tRNA stability analysis, transcriptome sequencing, small non-coding RNA sequencing, quantitative proteomics, and protein synthesis measurements. RESULTS METTL1/WDR4 are significantly elevated in AML patients and associated with poor prognosis. METTL1 knockdown resulted in reduced cell proliferation and increased apoptosis in AML cells. Mechanically, METTL1 knockdown leads to significant decrease of m7G modification abundance on tRNA, which further destabilizes tRNAs and facilitates the biogenesis of tsRNAs in AML cells. In addition, profiling of nascent proteins revealed that METTL1 knockdown and transfection of total tRNAs that were isolated from METTL1 knockdown AML cells decreased global translation efficiency in AML cells. CONCLUSIONS Taken together, our study demonstrates the important role of METTL1/WDR4 in AML leukaemogenesis, which provides a promising target candidate for AML therapy.
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Affiliation(s)
- Pan Zhao
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, 400037, China
- Department of Hematology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China
| | - Lin Xia
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, 400037, China
| | - Dan Chen
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, 400037, China
| | - Wei Xu
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, 400037, China
| | - Huanping Guo
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, 400037, China
| | - Yinying Xu
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, 400037, China
| | - Bingbing Yan
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, 400037, China
| | - Xiao Wu
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, 400037, China
| | - Yuxia Li
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, 400037, China
| | - Yunfang Zhang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Xi Zhang
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, 400037, China.
- Chongqing Key Laboratory of Hematology and Microenvironment, Chongqing, 400037, China.
- State Key Laboratory of Trauma and Chemical Poisoning, Chongqing, 400037, China.
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26
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Wang X, Ling R, Peng Y, Qiu W, Chen D. RNPS1 stabilizes NAT10 protein to facilitate translation in cancer via tRNA ac 4C modification. Int J Oral Sci 2024; 16:6. [PMID: 38246918 PMCID: PMC10800354 DOI: 10.1038/s41368-023-00276-7] [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: 11/06/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024] Open
Abstract
Existing studies have underscored the pivotal role of N-acetyltransferase 10 (NAT10) in various cancers. However, the outcomes of protein-protein interactions between NAT10 and its protein partners in head and neck squamous cell carcinoma (HNSCC) remain unexplored. In this study, we identified a significant upregulation of RNA-binding protein with serine-rich domain 1 (RNPS1) in HNSCC, where RNPS1 inhibits the ubiquitination degradation of NAT10 by E3 ubiquitin ligase, zinc finger SWIM domain-containing protein 6 (ZSWIM6), through direct protein interaction, thereby promoting high NAT10 expression in HNSCC. This upregulated NAT10 stability mediates the enhancement of specific tRNA ac4C modifications, subsequently boosting the translation process of genes involved in pathways such as IL-6 signaling, IL-8 signaling, and PTEN signaling that play roles in regulating HNSCC malignant progression, ultimately influencing the survival and prognosis of HNSCC patients. Additionally, we pioneered the development of TRMC-seq, leading to the discovery of novel tRNA-ac4C modification sites, thereby providing a potent sequencing tool for tRNA-ac4C research. Our findings expand the repertoire of tRNA ac4C modifications and identify a role of tRNA ac4C in the regulation of mRNA translation in HNSCC.
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Affiliation(s)
- Xiaochen Wang
- Center For Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Rongsong Ling
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yurong Peng
- Center For Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Weiqiong Qiu
- Center For Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Demeng Chen
- Center For Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
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27
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Lucas MC, Pryszcz LP, Medina R, Milenkovic I, Camacho N, Marchand V, Motorin Y, Ribas de Pouplana L, Novoa EM. Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing. Nat Biotechnol 2024; 42:72-86. [PMID: 37024678 DOI: 10.1038/s41587-023-01743-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/08/2023] [Indexed: 04/08/2023]
Abstract
Transfer RNAs (tRNAs) play a central role in protein translation. Studying them has been difficult in part because a simple method to simultaneously quantify their abundance and chemical modifications is lacking. Here we introduce Nano-tRNAseq, a nanopore-based approach to sequence native tRNA populations that provides quantitative estimates of both tRNA abundances and modification dynamics in a single experiment. We show that default nanopore sequencing settings discard the vast majority of tRNA reads, leading to poor sequencing yields and biased representations of tRNA abundances based on their transcript length. Re-processing of raw nanopore current intensity signals leads to a 12-fold increase in the number of recovered tRNA reads and enables recapitulation of accurate tRNA abundances. We then apply Nano-tRNAseq to Saccharomyces cerevisiae tRNA populations, revealing crosstalks and interdependencies between different tRNA modification types within the same molecule and changes in tRNA populations in response to oxidative stress.
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Affiliation(s)
- Morghan C Lucas
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Leszek P Pryszcz
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rebeca Medina
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ivan Milenkovic
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Virginie Marchand
- CNRS-Université de Lorraine, UAR2008 IBSLor/UMR7365 IMoPA, Nancy, France
| | - Yuri Motorin
- CNRS-Université de Lorraine, UAR2008 IBSLor/UMR7365 IMoPA, Nancy, France
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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28
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Shi Y, Feng Y, Wang Q, Dong G, Xia W, Jiang F. The Role of tRNA-Centered Translational Regulatory Mechanisms in Cancer. Cancers (Basel) 2023; 16:77. [PMID: 38201505 PMCID: PMC10778012 DOI: 10.3390/cancers16010077] [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: 12/05/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Cancer is a leading cause of morbidity and mortality worldwide. While numerous factors have been identified as contributing to the development of malignancy, our understanding of the mechanisms involved remains limited. Early cancer detection and the development of effective treatments are therefore critical areas of research. One class of molecules that play a crucial role in the transmission of genetic information are transfer RNAs (tRNAs), which are the most abundant RNA molecules in the human transcriptome. Dysregulated synthesis of tRNAs directly results in translation disorders and diseases, including cancer. Moreover, various types of tRNA modifications and the enzymes responsible for these modifications have been implicated in tumor biology. Furthermore, alterations in tRNA modification can impact tRNA stability, and impaired stability can prompt the cleavage of tRNAs into smaller fragments known as tRNA fragments (tRFs). Initially believed to be random byproducts lacking any physiological function, tRFs have now been redefined as non-coding RNA molecules with distinct roles in regulating RNA stability, translation, target gene expression, and other biological processes. In this review, we present recent findings on translational regulatory models centered around tRNAs in tumors, providing a deeper understanding of tumorigenesis and suggesting new directions for cancer treatment.
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Affiliation(s)
- Yuanjian Shi
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
- The Fourth Clinical College, Nanjing Medical University, Nanjing 210029, China
| | - Yipeng Feng
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
- The Fourth Clinical College, Nanjing Medical University, Nanjing 210029, China
| | - Qinglin Wang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
- The Fourth Clinical College, Nanjing Medical University, Nanjing 210029, China
| | - Gaochao Dong
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
| | - Wenjie Xia
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
| | - Feng Jiang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
- The Fourth Clinical College, Nanjing Medical University, Nanjing 210029, China
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29
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Zhu S, Li Y, Wu Y, Shen Y, Wang Y, Yan Y, Chen W, Fu Q, Wang Y, Yu X, Yu F. The FERONIA-YUELAO module participates in translational control by modulating the abundance of tRNA fragments in Arabidopsis. Dev Cell 2023; 58:2930-2946.e9. [PMID: 37977150 DOI: 10.1016/j.devcel.2023.10.014] [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: 08/01/2022] [Revised: 07/31/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]
Abstract
tRNA fragments (tRFs) are a recently identified class of small noncoding RNAs. To date, the regulation of tRF abundance and its functional mechanisms have been largely unclear in plants. We investigated how the Arabidopsis thaliana receptor kinase FERONIA (FER) regulates the abundance of tRFs to inhibit global mRNA translation. We demonstrate that FER regulates tRF abundance by directly phosphorylating the tRNA-binding protein YUELAO (YL) to modulate its function. Downregulation of FER and YL prevented the modification of tRNA via cytosine-5-methylation and 2'-O-methylation, thereby increasing tRF abundance. Furthermore, we show that YL acts as an important genetic downstream target of FER signaling, and knockdown of a specific tRF partially rescues the root hair growth defects of fer and yl mutants. Our findings shed light on the abundance and regulatory mechanisms of tRF and their role in inhibiting translation in plants.
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Affiliation(s)
- Sirui Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China; Yuelushan Laboratory, Changsha 410128, China
| | - Yuanyuan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - You Wu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanan Shen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Ying Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Yujie Yan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Weijun Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Qiong Fu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Yirong Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China; Yuelushan Laboratory, Changsha 410128, China
| | - Xiang Yu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China; Yuelushan Laboratory, Changsha 410128, China.
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30
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Liu F, Liu Z, Cheng W, Zhao Q, Zhang X, Zhang H, Yu M, Xu H, Gao Y, Jiang Q, Shi G, Wang L, Gu S, Wang J, Cao N, Chen Z. The PERK Branch of the Unfolded Protein Response Safeguards Protein Homeostasis and Mesendoderm Specification of Human Pluripotent Stem Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303799. [PMID: 37890465 PMCID: PMC10724406 DOI: 10.1002/advs.202303799] [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: 06/12/2023] [Revised: 08/14/2023] [Indexed: 10/29/2023]
Abstract
Cardiac development involves large-scale rearrangements of the proteome. How the developing cardiac cells maintain the integrity of the proteome during the rapid lineage transition remains unclear. Here it is shown that proteotoxic stress visualized by the misfolded and/or aggregated proteins appears during early cardiac differentiation of human pluripotent stem cells and is resolved by activation of the PERK branch of unfolded protein response (UPR). PERK depletion increases misfolded and/or aggregated protein accumulation, leading to pluripotency exit defect and impaired mesendoderm specification of human pluripotent stem cells. Mechanistically, it is found that PERK safeguards mesendoderm specification through its conserved downstream effector ATF4, which subsequently activates a novel transcriptional target WARS1, to cope with the differentiation-induced proteotoxic stress. The results indicate that protein quality control represents a previously unrecognized core component of the cardiogenic regulatory network. Broadly, these findings provide a framework for understanding how UPR is integrated into the developmental program by activating the PERK-ATF4-WARS1 axis.
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Affiliation(s)
- Fang Liu
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
- Department of Clinical LaboratoryThe First Affiliated Hospital of Anhui Medical UniversityHefei230022P. R. China
| | - Zhun Liu
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
| | - Weisheng Cheng
- Prenatal Diagnosis CenterDepartment of Obstetrics and GynecologyThe First Affiliated Hospital of Anhui Medical UniversityHefei230022P. R. China
- Department of Medical InformaticsZhongshan School of MedicineSun Yat‐Sen UniversityGuangzhou510080P. R. China
| | - Qingquan Zhao
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
| | - Xinyu Zhang
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
| | - He Zhang
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
| | - Miao Yu
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
| | - He Xu
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
| | - Yichen Gao
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
| | - Qianrui Jiang
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
| | - Guojun Shi
- Guangzhou Municipal Key Laboratory of Mechanistic and Translational Obesity ResearchGuangdong Provincial Key Laboratory of DiabetologyThe Third Affiliated Hospital of Sun Yat‐Sen UniversityGuangdong510080P. R. China
| | - Likun Wang
- National Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101P. R. China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049P. R. China
| | - Shanshan Gu
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
| | - Jia Wang
- School of Health and Life SciencesUniversity of Health and Rehabilitation SciencesShandong266071China
| | - Nan Cao
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
| | - Zhongyan Chen
- Advanced Medical Technology CenterZhongshan School of Medicine and the First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080P. R. China
- Key Laboratory for Stem Cells and Tissue EngineeringSun Yat‐Sen UniversityMinistry of EducationGuangzhou510080P. R. China
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31
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Bou-Nader C, Pecqueur L, de Crécy-Lagard V, Hamdane D. Integrative Approach to Probe Alternative Redox Mechanisms in RNA Modifications. Acc Chem Res 2023; 56:3142-3152. [PMID: 37916403 PMCID: PMC10999249 DOI: 10.1021/acs.accounts.3c00418] [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] [Indexed: 11/03/2023]
Abstract
RNA modifications found in most RNAs, particularly in tRNAs and rRNAs, reveal an abundance of chemical alterations of nucleotides. Over 150 distinct RNA modifications are known, emphasizing a remarkable diversity of chemical moieties in RNA molecules. These modifications play pivotal roles in RNA maturation, structural integrity, and the fidelity and efficiency of translation processes. The catalysts responsible for these modifications are RNA-modifying enzymes that use a striking array of chemistries to directly influence the chemical landscape of RNA. This diversity is further underscored by instances where the same modification is introduced by distinct enzymes that use unique catalytic mechanisms and cofactors across different domains of life. This phenomenon of convergent evolution highlights the biological importance of RNA modification and the vast potential within the chemical repertoire for nucleotide alteration. While shared RNA modifications can hint at conserved enzymatic pathways, a major bottleneck is to identify alternative routes within species that possess a modified RNA but are devoid of known RNA-modifying enzymes. To address this challenge, a combination of bioinformatic and experimental strategies proves invaluable in pinpointing new genes responsible for RNA modifications. This integrative approach not only unveils new chemical insights but also serves as a wellspring of inspiration for biocatalytic applications and drug design. In this Account, we present how comparative genomics and genome mining, combined with biomimetic synthetic chemistry, biochemistry, and anaerobic crystallography, can be judiciously implemented to address unprecedented and alternative chemical mechanisms in the world of RNA modification. We illustrate these integrative methodologies through the study of tRNA and rRNA modifications, dihydrouridine, 5-methyluridine, queuosine, 8-methyladenosine, 5-carboxymethylamino-methyluridine, or 5-taurinomethyluridine, each dependent on a diverse array of redox chemistries, often involving organic compounds, organometallic complexes, and metal coenzymes. We explore how vast genome and tRNA databases empower comparative genomic analyses and enable the identification of novel genes that govern RNA modification. Subsequently, we describe how the isolation of a stable reaction intermediate can guide the synthesis of a biomimetic to unveil new enzymatic pathways. We then discuss the usefulness of a biochemical "shunt" strategy to study catalytic mechanisms and to directly visualize reactive intermediates bound within active sites. While we primarily focus on various RNA-modifying enzymes studied in our laboratory, with a particular emphasis on the discovery of a SAM-independent methylation mechanism, the strategies and rationale presented herein are broadly applicable for the identification of new enzymes and the elucidation of their intricate chemistries. This Account offers a comprehensive glimpse into the evolving landscape of RNA modification research and highlights the pivotal role of integrated approaches to identify novel enzymatic pathways.
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Affiliation(s)
- Charles Bou-Nader
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, 32611, USA
- University of Florida, Genetics Institute, Gainesville, Florida, 32610, USA
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
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32
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Kuhle B, Chen Q, Schimmel P. tRNA renovatio: Rebirth through fragmentation. Mol Cell 2023; 83:3953-3971. [PMID: 37802077 PMCID: PMC10841463 DOI: 10.1016/j.molcel.2023.09.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/15/2023] [Accepted: 09/12/2023] [Indexed: 10/08/2023]
Abstract
tRNA function is based on unique structures that enable mRNA decoding using anticodon trinucleotides. These structures interact with specific aminoacyl-tRNA synthetases and ribosomes using 3D shape and sequence signatures. Beyond translation, tRNAs serve as versatile signaling molecules interacting with other RNAs and proteins. Through evolutionary processes, tRNA fragmentation emerges as not merely random degradation but an act of recreation, generating specific shorter molecules called tRNA-derived small RNAs (tsRNAs). These tsRNAs exploit their linear sequences and newly arranged 3D structures for unexpected biological functions, epitomizing the tRNA "renovatio" (from Latin, meaning renewal, renovation, and rebirth). Emerging methods to uncover full tRNA/tsRNA sequences and modifications, combined with techniques to study RNA structures and to integrate AI-powered predictions, will enable comprehensive investigations of tRNA fragmentation products and new interaction potentials in relation to their biological functions. We anticipate that these directions will herald a new era for understanding biological complexity and advancing pharmaceutical engineering.
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Affiliation(s)
- Bernhard Kuhle
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA; Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Qi Chen
- Molecular Medicine Program, Department of Human Genetics, and Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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Li P, Wang W, Zhou R, Ding Y, Li X. The m 5 C methyltransferase NSUN2 promotes codon-dependent oncogenic translation by stabilising tRNA in anaplastic thyroid cancer. Clin Transl Med 2023; 13:e1466. [PMID: 37983928 PMCID: PMC10659772 DOI: 10.1002/ctm2.1466] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/15/2023] [Accepted: 10/19/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Translation dysregulation plays a crucial role in tumourigenesis and cancer progression. Oncogenic translation relies on the stability and availability of tRNAs for protein synthesis, making them potential targets for cancer therapy. METHODS This study performed immunohistochemistry analysis to assess NSUN2 levels in thyroid cancer. Furthermore, to elucidate the impact of NSUN2 on anaplastic thyroid cancer (ATC) malignancy, phenotypic assays were conducted. Drug inhibition and time-dependent plots were employed to analyse drug resistance. Liquid chromatography-mass spectrometry and bisulphite sequencing were used to investigate the m5 C methylation of tRNA at both global and single-base levels. Puromycin intake and high-frequency codon reporter assays verified the protein translation level. By combining mRNA and ribosome profiling, a series of downstream proteins and codon usage bias were identified. The acquired data were further validated by tRNA sequencing. RESULTS This study observed that the tRNA m5 C methyltransferase NSUN2 was up-regulated in ATC and is associated with dedifferentiation. Furthermore, NSUN2 knockdown repressed ATC formation, proliferation, invasion and migration both in vivo and in vitro. Moreover, NSUN2 repression enhanced the sensitivity of ATC to genotoxic drugs. Mechanically, NSUN2 catalyses tRNA structure-related m5 C modification, stabilising tRNA that maintains homeostasis and rapidly transports amino acids, particularly leucine. This stable tRNA has a substantially increased efficiency necessary to support a pro-cancer translation program including c-Myc, BCL2, RAB31, JUNB and TRAF2. Additionally, the NSUN2-mediated variations in m5C levels and different tRNA Leu iso-decoder families, partially contribute to a codon-dependent translation bias. Surprisingly, targeting NSUN2 disrupted the c-Myc to NSUN2 cycle in ATC. CONCLUSIONS This research revealed that a pro-tumour m5C methyltransferase, dynamic tRNA stability regulation and downstream oncogenes, c-Myc, elicits a codon-dependent oncogenic translation network that enhances ATC growth and formation. Furthermore, it provides new opportunities for targeting translation reprogramming in cancer cells.
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Affiliation(s)
- Peng Li
- Department of General SurgeryXiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunan ProvinceChina
- Department of Hepatobiliary SurgerySichuan Provincial People's HospitalSchool of MedicineUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Wenlong Wang
- Department of General SurgeryXiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunan ProvinceChina
| | - Ruixin Zhou
- Department of General SurgeryXiangya HospitalCentral South UniversityChangshaHunanChina
| | - Ying Ding
- Department of General SurgeryXiangya HospitalCentral South UniversityChangshaHunanChina
| | - Xinying Li
- Department of General SurgeryXiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunan ProvinceChina
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Zhang H, Murphy P, Yu J, Lee S, Tsai FTF, van Hoof A, Ling J. Coordination between aminoacylation and editing to protect against proteotoxicity. Nucleic Acids Res 2023; 51:10606-10618. [PMID: 37742077 PMCID: PMC10602869 DOI: 10.1093/nar/gkad778] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/13/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that ligate amino acids to tRNAs, and often require editing to ensure accurate protein synthesis. Recessive mutations in aaRSs cause various neurological disorders in humans, yet the underlying mechanism remains poorly understood. Pathogenic aaRS mutations frequently cause protein destabilization and aminoacylation deficiency. In this study, we report that combined aminoacylation and editing defects cause severe proteotoxicity. We show that the ths1-C268A mutation in yeast threonyl-tRNA synthetase (ThrRS) abolishes editing and causes heat sensitivity. Surprisingly, experimental evolution of the mutant results in intragenic mutations that restore heat resistance but not editing. ths1-C268A destabilizes ThrRS and decreases overall Thr-tRNAThr synthesis, while the suppressor mutations in the evolved strains improve aminoacylation. We further show that deficiency in either ThrRS aminoacylation or editing is insufficient to cause heat sensitivity, and that ths1-C268A impairs ribosome-associated quality control. Our results suggest that aminoacylation deficiency predisposes cells to proteotoxic stress.
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Affiliation(s)
- Hong Zhang
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Parker Murphy
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Jason Yu
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Sukyeong Lee
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX 77030, USA
| | - Francis T F Tsai
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
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Liao T, Gan M, Lei Y, Wang Y, Chen L, Shen L, Zhu L. Dynamic changes in the transcriptome of tRNA-derived small RNAs related with fat metabolism. Sci Data 2023; 10:703. [PMID: 37838754 PMCID: PMC10576826 DOI: 10.1038/s41597-023-02624-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/09/2023] [Indexed: 10/16/2023] Open
Abstract
The prevalence of obesity and overweight is steadily rising, posing a significant global challenge for humanity. The fundamental cause of obesity and overweight lies in the abnormal accumulation of adipose tissue. While numerous regulatory factors related to fat deposition have been identified in previous studies, a considerable number of regulatory mechanisms remain unknown. tRNA-derived small RNAs (tsRNAs), a novel class of non-coding RNAs, have emerged as significant regulators in various biological processes. In this study, we obtained small RNA sequencing data from subcutaneous white adipose tissue and omental white adipose tissue of lean and obese pigs. In addition, we similarly obtained tsRNAs profiles from scapular brown adipose tissue (BAT), inguinal white adipose tissue (iWAT) and epigonadal white adipose tissue (eWAT) of normal mice. Finally, we successfully identified a large number of expressed tsRNAs in each tissue type and identified tsRNAs conserved in different adipose tissues of pigs and mice. These datasets will be a valuable resource for elucidating the epigenetic mechanisms of fat deposition.
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Affiliation(s)
- Tianci Liao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mailin Gan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuhang Lei
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yan Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lei Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linyuan Shen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Li Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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36
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Chen Q, Zhou T. Emerging functional principles of tRNA-derived small RNAs and other regulatory small RNAs. J Biol Chem 2023; 299:105225. [PMID: 37673341 PMCID: PMC10562873 DOI: 10.1016/j.jbc.2023.105225] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
Recent advancements in small RNA sequencing have unveiled a previously hidden world of regulatory small noncoding RNAs (sncRNAs) that extend beyond the well-studied small interfering RNAs, microRNAs, and piwi-interacting RNAs. This exploration, starting with tRNA-derived small RNAs, has led to the discovery of a diverse universe of sncRNAs derived from various longer structured RNAs such as rRNAs, small nucleolar RNAs, small nuclear RNAs, Y RNAs, and vault RNAs, with exciting uncharted functional possibilities. In this perspective, we discuss the emerging functional principles of sncRNAs beyond the well-known RNAi-like mechanisms, focusing on those that operate independent of linear sequence complementarity but rather function in an aptamer-like fashion. Aptamers use 3D structure for specific interactions with ligands and are modulated by RNA modifications and subcellular environments. Given that aptamer-like sncRNA functions are widespread and present in species lacking RNAi, they may represent an ancient functional principle that predates RNAi. We propose a rethinking of the origin of RNAi and its relationship with these aptamer-like functions in sncRNAs and how these complementary mechanisms shape biological processes. Lastly, the aptamer-like function of sncRNAs highlights the need for caution in using small RNA mimics in research and therapeutics, as their specificity is not restricted solely to linear sequence.
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Affiliation(s)
- Qi Chen
- Molecular Medicine Program, University of Utah School of Medicine, Salt Lake City, Utah, USA; Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA.
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA.
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37
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García-Vílchez R, Añazco-Guenkova AM, López J, Dietmann S, Tomé M, Jimeno S, Azkargorta M, Elortza F, Bárcena L, Gonzalez-Lopez M, Aransay AM, Sánchez-Martín MA, Huertas P, Durán RV, Blanco S. N7-methylguanosine methylation of tRNAs regulates survival to stress in cancer. Oncogene 2023; 42:3169-3181. [PMID: 37660182 PMCID: PMC10589097 DOI: 10.1038/s41388-023-02825-0] [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: 09/12/2022] [Revised: 07/27/2023] [Accepted: 08/24/2023] [Indexed: 09/04/2023]
Abstract
Tumour progression and therapy tolerance are highly regulated and complex processes largely dependent on the plasticity of cancer cells and their capacity to respond to stress. The higher plasticity of cancer cells highlights the need for identifying targetable molecular pathways that challenge cancer cell survival. Here, we show that N7-guanosine methylation (m7G) of tRNAs, mediated by METTL1, regulates survival to stress conditions in cancer cells. Mechanistically, we find that m7G in tRNAs protects them from stress-induced cleavage and processing into 5' tRNA fragments. Our analyses reveal that the loss of tRNA m7G methylation activates stress response pathways, sensitising cancer cells to stress. Furthermore, we find that the loss of METTL1 reduces tumour growth and increases cytotoxic stress in vivo. Our study uncovers the role of m7G methylation of tRNAs in stress responses and highlights the potential of targeting METTL1 to sensitise cancer cells to chemotherapy.
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Affiliation(s)
- Raquel García-Vílchez
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Ana M Añazco-Guenkova
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Judith López
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Sabine Dietmann
- Washington University School of Medicine in St. Louis, 660S. Euclid Ave, St. Louis, MO, 63110, USA
| | - Mercedes Tomé
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Sevilla, Spain
| | - Sonia Jimeno
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain
| | - Mikel Azkargorta
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain
- Carlos III Networked Proteomics Platform (ProteoRed-ISCIII), Madrid, Spain
| | - Félix Elortza
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain
- Carlos III Networked Proteomics Platform (ProteoRed-ISCIII), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Laura Bárcena
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain
| | - Monika Gonzalez-Lopez
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain
| | - Ana M Aransay
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Manuel A Sánchez-Martín
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
- Servicio de Transgénesis, Nucleus, Universidad de Salamanca, 37007, Salamanca, Spain
| | - Pablo Huertas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain
| | - Raúl V Durán
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Sevilla, Spain
| | - Sandra Blanco
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain.
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain.
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Xiong QP, Li J, Li H, Huang ZX, Dong H, Wang ED, Liu RJ. Human TRMT1 catalyzes m 2G or m 22G formation on tRNAs in a substrate-dependent manner. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2295-2309. [PMID: 37204604 DOI: 10.1007/s11427-022-2295-0] [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: 12/25/2022] [Accepted: 01/30/2023] [Indexed: 05/20/2023]
Abstract
TRMT1 is an N2-methylguanosine (m2G) and N2,N2-methylguanosine (m22G) methyltransferase that targets G26 of both cytoplasmic and mitochondrial tRNAs. In higher eukaryotes, most cytoplasmic tRNAs with G26 carry m22G26, although the majority of mitochondrial G26-containing tRNAs carry m2G26 or G26, suggesting differences in the mechanisms by which TRMT1 catalyzes modification of these tRNAs. Loss-of-function mutations of human TRMT1 result in neurological disorders and completely abrogate tRNA:m22G26 formation. However, the mechanism underlying the independent catalytic activity of human TRMT1 and identity of its specific substrate remain elusive, hindering a comprehensive understanding of the pathogenesis of neurological disorders caused by TRMT1 mutations. Here, we showed that human TRMT1 independently catalyzes formation of the tRNA:m2G26 or m22G26 modification in a substrate-dependent manner, which explains the distinct distribution of m2G26 and m22G26 on cytoplasmic and mitochondrial tRNAs. For human TRMT1-mediated tRNA:m22G26 formation, the semi-conserved C11:G24 serves as the determinant, and the U10:A25 or G10:C25 base pair is also required, while the size of the variable loop has no effect. We defined the requirements of this recognition mechanism as the "m22G26 criteria". We found that the m22G26 modification occurred in almost all the higher eukaryotic tRNAs conforming to these criteria, suggesting the "m22G26 criteria" are applicable to other higher eukaryotic tRNAs.
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Affiliation(s)
- Qing-Ping Xiong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jing Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Hao Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Zhi-Xuan Huang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Han Dong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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39
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Yuan L, Han Y, Zhao J, Zhang Y, Sun Y. Recognition and cleavage mechanism of intron-containing pre-tRNA by human TSEN endonuclease complex. Nat Commun 2023; 14:6071. [PMID: 37770519 PMCID: PMC10539383 DOI: 10.1038/s41467-023-41845-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 09/18/2023] [Indexed: 09/30/2023] Open
Abstract
Removal of introns from transfer RNA precursors (pre-tRNAs) occurs in all living organisms. This is a vital phase in the maturation and functionality of tRNA. Here we present a 3.2 Å-resolution cryo-EM structure of an active human tRNA splicing endonuclease complex bound to an intron-containing pre-tRNA. TSEN54, along with the unique regions of TSEN34 and TSEN2, cooperatively recognizes the mature body of pre-tRNA and guides the anticodon-intron stem to the correct position for splicing. We capture the moment when the endonucleases are poised for cleavage, illuminating the molecular mechanism for both 3' and 5' cleavage reactions. Two insertion loops from TSEN54 and TSEN2 cover the 3' and 5' splice sites, respectively, trapping the scissile phosphate in the center of the catalytic triad of residues. Our findings reveal the molecular mechanism for eukaryotic pre-tRNA recognition and cleavage, as well as the evolutionary relationship between archaeal and eukaryotic TSENs.
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Affiliation(s)
- Ling Yuan
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yaoyao Han
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Jiazheng Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yixiao Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
| | - Yadong Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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40
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Li Y, Gao J, Wang Y, Cai J, Wu D, Wang L, Pu W, Yu F, Zhu S. The functions of a 5' tRNA-Ala-derived fragment in gene expression. PLANT PHYSIOLOGY 2023; 193:1126-1141. [PMID: 37350495 DOI: 10.1093/plphys/kiad361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/04/2023] [Accepted: 05/22/2023] [Indexed: 06/24/2023]
Abstract
Transfer RNA (tRNA) can produce smaller RNA fragments called tRNA-derived fragments (tRFs). tRFs play critical roles in multiple cellular programs, although the functional mechanisms of tRFs remain largely unknown in plants. In this study, we examined the phenotype associated with 5' tRF-Ala (tRF-Ala, produced from tRNA-Ala) overexpression and knockdown lines (tDR-Ala-OE and tDR-Ala-kd, respectively) and the mechanisms by which tRF-Ala affects mRNA levels in Arabidopsis (Arabidopsis thaliana). We investigated the candidate proteins associated with tRF-Ala by quantitative proteomics and confirmed the direct interaction between tRF-Ala and the splicing factor SERINE-ARGININE RICH PROTEIN 34 (SR34). A transcriptome sequencing analysis showed that 318 genes among all the genes (786) with substantial alternative splicing (AS) variance in tDR-Ala-OE lines are targets of SR34. tRF-Ala diminished the binding affinity between SR34 and its targets by direct competition for interaction with SR34. These findings reveal the critical roles of tRF-Ala in regulating mRNA levels and splicing.
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Affiliation(s)
- Yuanyuan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Junping Gao
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha 410007, China
| | - Ying Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Jun Cai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Dousheng Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Long Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Wenxuan Pu
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha 410007, China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Sirui Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
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Lee SA, Liu F, Yuwono C, Phan M, Chong S, Biazik J, Tay ACY, Janitz M, Riordan SM, Lan R, Wehrhahn MC, Zhang L. Emerging Aeromonas enteric infections: their association with inflammatory bowel disease and novel pathogenic mechanisms. Microbiol Spectr 2023; 11:e0108823. [PMID: 37732778 PMCID: PMC10581128 DOI: 10.1128/spectrum.01088-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/28/2023] [Indexed: 09/22/2023] Open
Abstract
Aeromonas species are emerging human enteric pathogens. This study examines the isolation of Aeromonas and other enteric bacterial pathogens from patients with and without inflammatory bowel disease (IBD). This study also investigates the intestinal epithelial pathogenic mechanisms of Aeromonas veronii. The isolation rates of seven enteric bacterial pathogens from 2,279 patients with IBD and 373,276 non-IBD patients were compared. An A. veronii strain (AS1) isolated from intestinal biopsies of a patient with IBD was used for pathogenic mechanism investigation, and Escherichia coli K12 was used as a bacterial control. HT-29 cells were used as a model of human intestinal epithelium. A significantly higher isolation of Aeromonas species was found in patients with IBD as compared to non-IBD patients (P = 0.0001, odds ratio = 2.11). A. veronii upregulated 177 inflammatory genes and downregulated 52 protein-coding genes affecting chromatin assembly, multiple small nuclear RNAs, multiple nucleolar RNAs, and 55 cytoplasmic tRNAs in HT-29 cells. These downregulation effects were unique to A. veronii and not observed in HT-29 cells infected with E. coli K12. A. veronii induced intestinal epithelial apoptosis involving the intrinsic pathway. A. veronii caused epithelial microvilli shortening and damage and epithelial production of IL-8. In conclusion, this study for the first time reports the association between IBD and Aeromonas enteric infection detected by bacterial cultivation. This study also reports that A. veronii damages intestinal epithelial cells via multiple mechanisms, of which the downregulating cytoplasmic tRNA, small nuclear RNA, and small nucleolar RNA are novel bacterial pathogenic mechanisms. IMPORTANCE This study for the first time reports the association between inflammatory bowel disease (IBD) and Aeromonas enteric infection detected by bacterial pathogen cultivation, highlighting the need of clinical and public health attention. The finding that patients with IBD are more susceptible to Aeromonas enteric infection suggests that detection of Aeromonas enteric infection should be routinely performed for the diagnosis and treatment of IBD. This study also reports novel bacterial pathogenic mechanisms employed by Aeromonas veronii. Through comparative transcriptomic analysis and other techniques, this study revealed the pathogenic mechanisms by which A. veronii causes damage to intestinal epithelial cells. Among the various pathogenic mechanisms identified, the downregulating tRNA, small nuclear and nucleolar RNAs in human intestinal epithelial cells are novel bacterial pathogenic mechanisms.
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Affiliation(s)
- Seul A. Lee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Fang Liu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Christopher Yuwono
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Monique Phan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sarah Chong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Joanna Biazik
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Alfred Chin Yen Tay
- Helicobacter Research Laboratory, School of Pathology and Laboratory Medicine, Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Stephen M. Riordan
- Gastrointestinal and Liver Unit, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Michael C. Wehrhahn
- Douglass Hanly Moir Pathology, a Sonic Healthcare Australia Pathology Practice, Macquarie Park, New South Wales, Australia
| | - Li Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
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Tijaro-Bulla S, Nyandwi SP, Cui H. Physiological and engineered tRNA aminoacylation. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1789. [PMID: 37042417 DOI: 10.1002/wrna.1789] [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: 12/23/2022] [Revised: 03/11/2023] [Accepted: 03/21/2023] [Indexed: 04/13/2023]
Abstract
Aminoacyl-tRNA synthetases form the protein family that controls the interpretation of the genetic code, with tRNA aminoacylation being the key chemical step during which an amino acid is assigned to a corresponding sequence of nucleic acids. In consequence, aminoacyl-tRNA synthetases have been studied in their physiological context, in disease states, and as tools for synthetic biology to enable the expansion of the genetic code. Here, we review the fundamentals of aminoacyl-tRNA synthetase biology and classification, with a focus on mammalian cytoplasmic enzymes. We compile evidence that the localization of aminoacyl-tRNA synthetases can be critical in health and disease. In addition, we discuss evidence from synthetic biology which made use of the importance of subcellular localization for efficient manipulation of the protein synthesis machinery. This article is categorized under: RNA Processing Translation > Translation Regulation RNA Processing > tRNA Processing RNA Export and Localization > RNA Localization.
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Affiliation(s)
| | | | - Haissi Cui
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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Kong LY, Wu YZ, Cheng RQ, Wang PH, Peng BW. Role of Mutations of Mitochondrial Aminoacyl-tRNA Synthetases Genes on Epileptogenesis. Mol Neurobiol 2023; 60:5482-5492. [PMID: 37316759 DOI: 10.1007/s12035-023-03429-1] [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: 02/01/2023] [Accepted: 06/05/2023] [Indexed: 06/16/2023]
Abstract
Mitochondria are the structures in cells that are responsible for producing energy. They contain a specific translation unit for synthesizing mitochondria-encoded respiratory chain components: the mitochondrial DNA (mt DNA). Recently, a growing number of syndromes associated with the dysfunction of mt DNA translation have been reported. However, the functions of these diseases still need to be precise and thus attract much attention. Mitochondrial tRNAs (mt tRNAs) are encoded by mt DNA; they are the primary cause of mitochondrial dysfunction and are associated with a wide range of pathologies. Previous research has shown the role of mt tRNAs in the epileptic mechanism. This review will focus on the function of mt tRNA and the role of mitochondrial aminoacyl-tRNA synthetase (mt aaRS) in order to summarize some common relevant mutant genes of mt aaRS that cause epilepsy and the specific symptoms of the disease they cause.
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Affiliation(s)
- Ling-Yue Kong
- Department of Physiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Yi-Ze Wu
- Department of Physiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Run-Qi Cheng
- Department of Physiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Pei-Han Wang
- Department of Physiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Bi-Wen Peng
- Department of Physiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China.
- Department of Physiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Donghu Rd185#, Wuhan, 430071, Hubei, China.
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44
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Davyt M, Bharti N, Ignatova Z. Effect of mRNA/tRNA mutations on translation speed: Implications for human diseases. J Biol Chem 2023; 299:105089. [PMID: 37495112 PMCID: PMC10470029 DOI: 10.1016/j.jbc.2023.105089] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023] Open
Abstract
Recent discoveries establish tRNAs as central regulators of mRNA translation dynamics, and therefore cotranslational folding and function of the encoded protein. The tRNA pool, whose composition and abundance change in a cell- and tissue-dependent manner, is the main factor which determines mRNA translation velocity. In this review, we discuss a group of pathogenic mutations, in the coding sequences of either protein-coding genes or in tRNA genes, that alter mRNA translation dynamics. We also summarize advances in tRNA biology that have uncovered how variations in tRNA levels on account of genetic mutations affect protein folding and function, and thereby contribute to phenotypic diversity in clinical manifestations.
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Affiliation(s)
- Marcos Davyt
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Nikhil Bharti
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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45
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Grafanaki K, Grammatikakis I, Ghosh A, Gopalan V, Olgun G, Liu H, Kyriakopoulos GC, Skeparnias I, Georgiou S, Stathopoulos C, Hannenhalli S, Merlino G, Marie KL, Day CP. Noncoding RNA circuitry in melanoma onset, plasticity, and therapeutic response. Pharmacol Ther 2023; 248:108466. [PMID: 37301330 PMCID: PMC10527631 DOI: 10.1016/j.pharmthera.2023.108466] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/24/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
Melanoma, the cancer of the melanocyte, is the deadliest form of skin cancer with an aggressive nature, propensity to metastasize and tendency to resist therapeutic intervention. Studies have identified that the re-emergence of developmental pathways in melanoma contributes to melanoma onset, plasticity, and therapeutic response. Notably, it is well known that noncoding RNAs play a critical role in the development and stress response of tissues. In this review, we focus on the noncoding RNAs, including microRNAs, long non-coding RNAs, circular RNAs, and other small RNAs, for their functions in developmental mechanisms and plasticity, which drive onset, progression, therapeutic response and resistance in melanoma. Going forward, elucidation of noncoding RNA-mediated mechanisms may provide insights that accelerate development of novel melanoma therapies.
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Affiliation(s)
- Katerina Grafanaki
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Dermatology, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Ioannis Grammatikakis
- Cancer Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arin Ghosh
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vishaka Gopalan
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gulden Olgun
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Huaitian Liu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - George C Kyriakopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Ilias Skeparnias
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Sophia Georgiou
- Department of Dermatology, School of Medicine, University of Patras, 26504 Patras, Greece
| | | | - Sridhar Hannenhalli
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Glenn Merlino
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kerrie L Marie
- Division of Molecular and Cellular Function, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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Yu P, Zhou S, Gao Y, Liang Y, Guo W, Wang DO, Ding S, Lin S, Wang J, Cun Y. Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:834-849. [PMID: 35952936 PMCID: PMC10787195 DOI: 10.1016/j.gpb.2022.07.006] [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: 02/04/2022] [Revised: 07/02/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Although the function of tRNAs in the translational process is well established, it remains controversial whether tRNA abundance is tightly associated with translational efficiency (TE) in mammals. Moreover, how critically the expression of tRNAs contributes to the establishment of tissue-specific proteomes in mammals has not been well addressed. Here, we measured both tRNA expression using demethylase-tRNA sequencing (DM-tRNA-seq) and TE of mRNAs using ribosome-tagging sequencing (RiboTag-seq) in the brain, heart, and testis of mice. Remarkable variation in the expression of tRNA isodecoders was observed among different tissues. When the statistical effect of isodecoder-grouping on reducing variations is considered through permutating the anticodons, we observed an expected reduction in the variation of anticodon expression across all samples, an unexpected smaller variation of anticodon usage bias, and an unexpected larger variation of tRNA isotype expression at amino acid level. Regardless of whether or not they share the same anticodons, the isodecoders encoding the same amino acids are co-expressed across different tissues. Based on the expression of tRNAs and the TE of mRNAs, we find that the tRNA adaptation index (tAI) and TE are significantly correlated in the same tissues but not between tissues; and tRNA expression and the amino acid composition of translating peptides are positively correlated in the same tissues but not between tissues. We therefore hypothesize that the tissue-specific expression of tRNAs might be due to post-transcriptional mechanisms. This study provides a resource for tRNA and translation studies, as well as novel insights into the dynamics of tRNAs and their roles in translational regulation.
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Affiliation(s)
- Peng Yu
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510080, China
| | - Siting Zhou
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, MOE Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Guangzhou 510080, China
| | - Yan Gao
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, MOE Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Guangzhou 510080, China
| | - Yu Liang
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Wenbing Guo
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, MOE Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Guangzhou 510080, China
| | - Dan Ohtan Wang
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Shuaiwen Ding
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Shuibin Lin
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China.
| | - Jinkai Wang
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, MOE Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Guangzhou 510080, China; RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510080, China.
| | - Yixian Cun
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, MOE Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Guangzhou 510080, China.
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47
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Sun Y, Fang Q, Liu W, Liu Y, Zhang C. GANT-61 induces cell cycle resting and autophagy by down-regulating RNAP III signal pathway and tRNA-Gly-CCC synthesis to combate chondrosarcoma. Cell Death Dis 2023; 14:461. [PMID: 37488121 PMCID: PMC10366213 DOI: 10.1038/s41419-023-05926-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 06/17/2023] [Accepted: 06/23/2023] [Indexed: 07/26/2023]
Abstract
Chondrosarcoma is ineffective for conventional radiotherapy and chemotherapy with a poor prognosis. Hedgehog (Hh) signal pathway plays a crucial role in tumor growth and progression, which is constitutive activated in chondrosarcoma. GLI transcription factors as targets for new drugs or interference technology for the treatment of chondrosarcoma are of great significance. In this study, we indicated that the Hedgehog-GLI1 signal pathway is activated in chondrosarcoma, which further enhances the RNAP III signal pathway to mediate endogenous tRNA fragments synthesis. Downstream oncology functions of endogenous tRNA fragments, such as "cell cycle" and "death receptor binding", are involved in malignant chondrosarcoma. The GANT-61, as an inhibitor of GLI1, could inhibit chondrosarcoma tumor growth effectively by inhibiting the RNAP III signal pathway and tRNA-Gly-CCC synthesis in vivo. Induced G2/M cell cycle resting, apoptosis, and autophagy were the main mechanisms for the inhibitory effect of GANT-61 on chondrosarcoma, which correspond with the above-described downstream oncology functions of endogenous tRNA fragments. We also identified the molecular mechanism by which GANT-61-induced autophagy is involved in ULK1 expression and MAPK signaling pathway. Thus, GANT-61 will be an ideal and promising strategy for combating chondrosarcoma.
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Affiliation(s)
- Yifeng Sun
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University &Shandong Provincial Qianfoshan Hospital, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan, Shandong, 250014, PR China
- Department of Surgery, Heidelberg University Hospital, Heidelberg University, Heidelberg, Germany
- Department of Surgery, Ulm University Hospital, Ulm University, Ulm, Germany
| | - Qiongxuan Fang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Wei Liu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University &Shandong Provincial Qianfoshan Hospital, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan, Shandong, 250014, PR China
| | - Yi Liu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University &Shandong Provincial Qianfoshan Hospital, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan, Shandong, 250014, PR China
| | - Chunming Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University &Shandong Provincial Qianfoshan Hospital, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan, Shandong, 250014, PR China.
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48
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Lee S, Kim J, Valdmanis PN, Kim HK. Emerging roles of tRNA-derived small RNAs in cancer biology. Exp Mol Med 2023:10.1038/s12276-023-01038-5. [PMID: 37430089 PMCID: PMC10393972 DOI: 10.1038/s12276-023-01038-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/29/2023] [Accepted: 05/09/2023] [Indexed: 07/12/2023] Open
Abstract
Transfer RNAs (tRNAs) play an essential role in mRNA translation by delivering amino acids to growing polypeptide chains. Recent data demonstrate that tRNAs can be cleaved by ribonucleases, and the resultant cleavage products, tRNA-derived small RNAs (tsRNAs), have crucial roles in physiological and pathological conditions. They are classified into more than six types according to their size and cleavage positions. Since the initial discovery of the physiological functions of tsRNAs more than a decade ago, accumulating data have demonstrated that tsRNAs play critical roles in gene regulation and tumorigenesis. These tRNA-derived molecules have various regulatory functions at the transcriptional, post-transcriptional, and translational levels. More than a hundred types of modifications are found on tRNAs, affecting the biogenesis, stability, function, and biochemical properties of tsRNA. Both oncogenic and tumor suppressor functions have been reported for tsRNAs, which play important roles in the development and progression of various cancers. Abnormal expression patterns and modification of tsRNAs are associated with various diseases, including cancer and neurological disorders. In this review, we will describe the biogenesis, versatile gene regulation mechanisms, and modification-mediated regulation mechanisms of tsRNA as well as the expression patterns and potential therapeutic roles of tsRNAs in various cancers.
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Affiliation(s)
- Saebyeol Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jungeun Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Paul N Valdmanis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, 98115, USA
| | - Hak Kyun Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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49
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Abstract
The study of eukaryotic tRNA processing has given rise to an explosion of new information and insights in the last several years. We now have unprecedented knowledge of each step in the tRNA processing pathway, revealing unexpected twists in biochemical pathways, multiple new connections with regulatory pathways, and numerous biological effects of defects in processing steps that have profound consequences throughout eukaryotes, leading to growth phenotypes in the yeast Saccharomyces cerevisiae and to neurological and other disorders in humans. This review highlights seminal new results within the pathways that comprise the life of a tRNA, from its birth after transcription until its death by decay. We focus on new findings and revelations in each step of the pathway including the end-processing and splicing steps, many of the numerous modifications throughout the main body and anticodon loop of tRNA that are so crucial for tRNA function, the intricate tRNA trafficking pathways, and the quality control decay pathways, as well as the biogenesis and biology of tRNA-derived fragments. We also describe the many interactions of these pathways with signaling and other pathways in the cell.
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Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Anita K Hopper
- Department of Molecular Genetics and Center for RNA Biology, Ohio State University, Columbus, Ohio 43235, USA
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50
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Abstract
Messenger RNA (mRNA) stability and translational efficiency are two crucial aspects of the post-transcriptional process that profoundly impact protein production in a cell. While it is widely known that ribosomes produce proteins, studies during the past decade have surprisingly revealed that ribosomes also control mRNA stability in a codon-dependent manner, a process referred to as codon optimality. Therefore, codons, the three-nucleotide words read by the ribosome, have a potent effect on mRNA stability and provide cis-regulatory information that extends beyond the amino acids they encode. While the codon optimality molecular mechanism is still unclear, the translation elongation rate appears to trigger mRNA decay. Thus, transfer RNAs emerge as potential master gene regulators affecting mRNA stability. Furthermore, while few factors related to codon optimality have been identified in yeast, the orthologous genes in vertebrates do not necessary share the same functions. Here, we discuss codon optimality findings and gene regulation layers related to codon composition in different eukaryotic species.
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Affiliation(s)
- Qiushuang Wu
- Stowers Institute for Medical Research, Kansas City, Missouri, USA;
| | - Ariel A Bazzini
- Stowers Institute for Medical Research, Kansas City, Missouri, USA;
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, USA
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