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Wang Q, Qin B, Yu H, Hu Y, Yu H, Zhong J, Liu J, Yao C, Zeng J, Fan J, Diao L. Advances in Circular RNA in the Pathogenesis of Epilepsy. Neuroscience 2024; 551:246-253. [PMID: 38843987 DOI: 10.1016/j.neuroscience.2024.05.036] [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: 04/07/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/15/2024]
Abstract
Recent studies evidenced the involvement of circular RNA (circRNA) in neuroinflammation, apoptosis, and synaptic remodeling suggesting an important role for circRNA in the occurrence and development of epilepsy. This review provides an overview of circRNAs considered to be playing regulatory roles in the process of epilepsy and to be involved in multiple biological epilepsy-related processes, such as hippocampal sclerosis, inflammatory response, cell apoptosis, synaptic remodeling, and cell proliferation and differentiation. This review covers the current research status of differential expression of circRNA-mediated seizures, m6A methylation, demethylation-mediated seizures in post transcriptional circRNA modification, as well as the mechanisms of m5C- and m7G-modified circRNA. In summary, this article reviews the research progress on the relationship between circRNA in non-coding RNA and epilepsy.
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Affiliation(s)
- Qin Wang
- Graduate School of First Clinical Medicine College, Guangxi University of Chinese Medicine, 13 Wuhe Avenue, Qingxiu District, Nanning, Guangxi 530001, China; Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, 89-9 Dongge Road, Qingxiu District, Nanning, Guangxi 530023, China
| | - Baijun Qin
- Department of Gastroenterology, Chongqing Hospital of Traditional Chinese Medicine, 6 Seventh Branch Road, Panxi, Jiangbei District, Chongqing 400021, China
| | - Haichun Yu
- Guangxi Technological College of Machinery and Electricity, Nanning, Guangxi 30007, China
| | - Yueqiang Hu
- Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, 89-9 Dongge Road, Qingxiu District, Nanning, Guangxi 530023, China
| | - Han Yu
- Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, Heilongjiang 150081, China
| | - Jie Zhong
- Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, 89-9 Dongge Road, Qingxiu District, Nanning, Guangxi 530023, China
| | - Jinwen Liu
- Graduate School of First Clinical Medicine College, Guangxi University of Chinese Medicine, 13 Wuhe Avenue, Qingxiu District, Nanning, Guangxi 530001, China; Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, 89-9 Dongge Road, Qingxiu District, Nanning, Guangxi 530023, China
| | - Chunyuan Yao
- Graduate School of First Clinical Medicine College, Guangxi University of Chinese Medicine, 13 Wuhe Avenue, Qingxiu District, Nanning, Guangxi 530001, China; Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, 89-9 Dongge Road, Qingxiu District, Nanning, Guangxi 530023, China
| | - Jiawei Zeng
- Graduate School of First Clinical Medicine College, Guangxi University of Chinese Medicine, 13 Wuhe Avenue, Qingxiu District, Nanning, Guangxi 530001, China; Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, 89-9 Dongge Road, Qingxiu District, Nanning, Guangxi 530023, China
| | - Jingjing Fan
- Graduate School of First Clinical Medicine College, Guangxi University of Chinese Medicine, 13 Wuhe Avenue, Qingxiu District, Nanning, Guangxi 530001, China; Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, 89-9 Dongge Road, Qingxiu District, Nanning, Guangxi 530023, China
| | - Limei Diao
- Graduate School of First Clinical Medicine College, Guangxi University of Chinese Medicine, 13 Wuhe Avenue, Qingxiu District, Nanning, Guangxi 530001, China; Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, 89-9 Dongge Road, Qingxiu District, Nanning, Guangxi 530023, China.
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Chen M, Dai S, Chen D, Chen H, Feng N, Zheng D. Unveiling the translational dynamics of lychee (Litchi chinesis Sonn.) in response to cold stress. BMC Genomics 2024; 25:686. [PMID: 38992605 DOI: 10.1186/s12864-024-10591-w] [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: 11/09/2023] [Accepted: 07/03/2024] [Indexed: 07/13/2024] Open
Abstract
Cold stress poses a significant threat to the quality and productivity of lychee (Litchi chinensis Sonn.). While previous research has extensively explored the genomic and transcriptomic responses to cold stress in lychee, the translatome has not been thoroughly investigated. This study delves into the translatomic landscape of the 'Xiangjinfeng' cultivar under both control and low-temperature conditions using RNA sequencing and ribosome profiling. We uncovered a significant divergence between the transcriptomic and translatomic responses to cold exposure. Additionally, bioinformatics analyses underscored the crucial role of codon occupancy in lychee's cold tolerance mechanisms. Our findings reveal that the modulation of translation via codon occupancy is a vital strategy to abiotic stress. Specifically, the study identifies ribosome stalling, particularly at the E site AAU codon, as a key element of the translation machinery in lychee's response to cold stress. This work enhances our understanding of the molecular dynamics of lychee's reaction to cold stress and emphasizes the essential role of translational regulation in the plant's environmental adaptability.
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Affiliation(s)
- Mingming Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524008, China.
- National Saline-Tolerant Rice Technology Innovation Center, South China, Zhanjiang, 524008, China.
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, China.
| | - Shuangfeng Dai
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524008, China
- National Saline-Tolerant Rice Technology Innovation Center, South China, Zhanjiang, 524008, China
| | - Daming Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524008, China
- National Saline-Tolerant Rice Technology Innovation Center, South China, Zhanjiang, 524008, China
| | - Haomin Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524008, China
- National Saline-Tolerant Rice Technology Innovation Center, South China, Zhanjiang, 524008, China
| | - Naijie Feng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524008, China.
- National Saline-Tolerant Rice Technology Innovation Center, South China, Zhanjiang, 524008, China.
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, China.
| | - Dianfeng Zheng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524008, China.
- National Saline-Tolerant Rice Technology Innovation Center, South China, Zhanjiang, 524008, China.
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, China.
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Weber R, Chang CT. Human DDX6 regulates translation and decay of inefficiently translated mRNAs. eLife 2024; 13:RP92426. [PMID: 38989862 DOI: 10.7554/elife.92426] [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] [Indexed: 07/12/2024] Open
Abstract
Recent findings indicate that the translation elongation rate influences mRNA stability. One of the factors that has been implicated in this link between mRNA decay and translation speed is the yeast DEAD-box helicase Dhh1p. Here, we demonstrated that the human ortholog of Dhh1p, DDX6, triggers the deadenylation-dependent decay of inefficiently translated mRNAs in human cells. DDX6 interacts with the ribosome through the Phe-Asp-Phe (FDF) motif in its RecA2 domain. Furthermore, RecA2-mediated interactions and ATPase activity are both required for DDX6 to destabilize inefficiently translated mRNAs. Using ribosome profiling and RNA sequencing, we identified two classes of endogenous mRNAs that are regulated in a DDX6-dependent manner. The identified targets are either translationally regulated or regulated at the steady-state-level and either exhibit signatures of poor overall translation or of locally reduced ribosome translocation rates. Transferring the identified sequence stretches into a reporter mRNA caused translation- and DDX6-dependent degradation of the reporter mRNA. In summary, these results identify DDX6 as a crucial regulator of mRNA translation and decay triggered by slow ribosome movement and provide insights into the mechanism by which DDX6 destabilizes inefficiently translated mRNAs.
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Affiliation(s)
- Ramona Weber
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Institute for Regenerative Medicine (IREM), University of Zurich, Zurich, Switzerland
| | - Chung-Te Chang
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei City, Taiwan
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Sainz MM, Sotelo-Silveira M, Filippi CV, Zardo S. Legume-rhizobia symbiosis: Translatome analysis. Genet Mol Biol 2024; 47Suppl 1:e20230284. [PMID: 38954532 PMCID: PMC11223499 DOI: 10.1590/1678-4685-gmb-2023-0284] [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: 10/03/2023] [Accepted: 03/31/2024] [Indexed: 07/04/2024] Open
Abstract
Leguminous plants can establish endosymbiotic relationships with nitrogen-fixing soil rhizobacteria. Bacterial infection and nodule organogenesis are two independent but highly coordinated genetic programs that are active during this interaction. These genetic programs can be regulated along all the stages of gene expression. Most of the studies, for both eukaryotes and prokaryotes, focused on the transcriptional regulation level determining the abundance of mRNAs. However, it has been demonstrated that mRNA levels only sometimes correlate with the abundance or activity of the coded proteins. For this reason, in the past two decades, interest in the role of translational control of gene expression has increased, since the subset of mRNA being actively translated outperforms the information gained only by the transcriptome. In the case of legume-rhizobia interactions, the study of the translatome still needs to be explored further. Therefore, this review aims to discuss the methodologies for analyzing polysome-associated mRNAs at the genome-scale and their contribution to studying translational control to understand the complexity of this symbiotic interaction. Moreover, the Dual RNA-seq approach is discussed for its relevance in the context of a symbiotic nodule, where intricate multi-species gene expression networks occur.
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Affiliation(s)
- María Martha Sainz
- Universidad de la República, Facultad de Agronomía, Departamento
de Biología Vegetal, Laboratorio de Bioquímica, Montevideo, Uruguay
| | - Mariana Sotelo-Silveira
- Universidad de la República, Facultad de Agronomía, Departamento
de Biología Vegetal, Laboratorio de Bioquímica, Montevideo, Uruguay
| | - Carla V. Filippi
- Universidad de la República, Facultad de Agronomía, Departamento
de Biología Vegetal, Laboratorio de Bioquímica, Montevideo, Uruguay
| | - Sofía Zardo
- Universidad de la República, Facultad de Agronomía, Departamento
de Biología Vegetal, Laboratorio de Bioquímica, Montevideo, Uruguay
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Zhao H, Xiong Y, Zhou Z, Xu Q, Zi Y, Zheng X, Chen S, Xiao X, Gong L, Xu H, Liu L, Lu H, Cui Y, Shao S, Zhang J, Ma J, Zhou Q, Ma D, Li X. A hidden proteome encoded by circRNAs in human placentas: Implications for uncovering preeclampsia pathogenesis. Clin Transl Med 2024; 14:e1759. [PMID: 38997803 DOI: 10.1002/ctm2.1759] [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: 07/13/2023] [Revised: 06/21/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND CircRNA-encoded proteins (CEPs) are emerging as new players in health and disease, and function as baits for the common partners of their cognate linear-spliced RNA encoded proteins (LEPs). However, their prevalence across human tissues and biological roles remain largely unexplored. The placenta is an ideal model for identifying CEPs due to its considerable protein diversity that is required to sustain fetal development during pregnancy. The aim of this study was to evaluate circRNA translation in the human placenta, and the potential roles of the CEPs in placental development and dysfunction. METHODS Multiomics approaches, including RNA sequencing, ribosome profiling, and LC-MS/MS analysis, were utilised to identify novel translational events of circRNAs in human placentas. Bioinformatics methods and the protein bait hypothesis were employed to evaluate the roles of these newly discovered CEPs in placentation and associated disorders. The pathogenic role of a recently identified CEP circPRKCB119aa in preeclampsia was investigated through qRT-PCR, Western blotting, immunofluorescence imaging and phenotypic analyses. RESULTS We found that 528 placental circRNAs bound to ribosomes with active translational elongation, and 139 were translated to proteins. The CEPs showed considerable structural homology with their cognate LEPs, but are more stable, hydrophobic and have a lower molecular-weight than the latter, all of which are conducive to their function as baits. On this basis, CEPs are deduced to be closely involved in placental function. Furthermore, we focused on a novel CEP circPRKCB119aa, and illuminated its pathogenic role in preeclampsia; it enhanced trophoblast autophagy by acting as a bait to inhibit phosphorylation of the cognate linear isoform PKCβ. CONCLUSIONS We discovered a hidden circRNA-encoded proteome in the human placenta, which offers new insights into the mechanisms underlying placental development, as well as placental disorders such as preeclampsia. Key points A hidden circRNA-encoded proteome in the human placenta was extensively identified and systematically characterised. The circRNA-encoded proteins (CEPs) are potentially related to placental development and associated disorders. A novel conserved CEP circPRKCB119aa enhanced trophoblast autophagy by inhibiting phosphorylation of its cognate linear-spliced isoform protein kinase C (PKC) β in preeclampsia.
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Affiliation(s)
- Huanqiang Zhao
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Institute of Maternal and Child Medicine, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Yu Xiong
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Zixiang Zhou
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Qixin Xu
- Institute of Maternal and Child Medicine, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Yang Zi
- Institute of Maternal and Child Medicine, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Xiujie Zheng
- Institute of Maternal and Child Medicine, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Shiguo Chen
- Institute of Maternal and Child Medicine, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Xirong Xiao
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Lili Gong
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Huangfang Xu
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Lidong Liu
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Huiqing Lu
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Yutong Cui
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Shuyi Shao
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Jin Zhang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jing Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Qiongjie Zhou
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xiaotian Li
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Institute of Maternal and Child Medicine, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
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Zhao J, Huang Y, Liukang C, Yang R, Tang L, Sun L, Zhao Y, Zhang G. Dissecting infectious bronchitis virus-induced host shutoff at the translation level. J Virol 2024:e0083024. [PMID: 38940559 DOI: 10.1128/jvi.00830-24] [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: 05/14/2024] [Accepted: 06/01/2024] [Indexed: 06/29/2024] Open
Abstract
Viruses have evolved a range of strategies to utilize or manipulate the host's cellular translational machinery for efficient infection, although the mechanisms by which infectious bronchitis virus (IBV) manipulates the host translation machinery remain unclear. In this study, we firstly demonstrate that IBV infection causes host shutoff, although viral protein synthesis is not affected. We then screened 23 viral proteins, and identified that more than one viral protein is responsible for IBV-induced host shutoff, the inhibitory effects of proteins Nsp15 were particularly pronounced. Ribosome profiling was used to draw the landscape of viral mRNA and cellular genes expression model, and the results showed that IBV mRNAs gradually dominated the cellular mRNA pool, the translation efficiency of the viral mRNAs was lower than the median efficiency (about 1) of cellular mRNAs. In the analysis of viral transcription and translation, higher densities of RNA sequencing (RNA-seq) and ribosome profiling (Ribo-seq) reads were observed for structural proteins and 5' untranslated regions, which conformed to the typical transcriptional characteristics of nested viruses. Translational halt events and the number of host genes increased significantly after viral infection. The translationally paused genes were enriched in translation, unfolded-protein-related response, and activation of immune response pathways. Immune- and inflammation-related mRNAs were inefficiently translated in infected cells, and IBV infection delayed the production of IFN-β and IFN-λ. Our results describe the translational landscape of IBV-infected cells and demonstrate new strategies by which IBV induces host gene shutoff to promote its replication. IMPORTANCE Infectious bronchitis virus (IBV) is a γ-coronavirus that causes huge economic losses to the poultry industry. Understanding how the virus manipulates cellular biological processes to facilitate its replication is critical for controlling viral infections. Here, we used Ribo-seq to determine how IBV infection remodels the host's biological processes and identified multiple viral proteins involved in host gene shutoff. Immune- and inflammation-related mRNAs were inefficiently translated, the translation halt of unfolded proteins and immune activation-related genes increased significantly, benefitting IBV replication. These data provide new insights into how IBV modulates its host's antiviral responses.
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Affiliation(s)
- Jing Zhao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yahui Huang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chengyin Liukang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ruihua Yang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lihua Tang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lu Sun
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ye Zhao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Guozhong Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
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Cheng Y, Wang S, Zhang H, Lee JS, Ni C, Guo J, Chen E, Wang S, Acharya A, Chang TC, Buszczak M, Zhu H, Mendell JT. A non-canonical role for a small nucleolar RNA in ribosome biogenesis and senescence. Cell 2024:S0092-8674(24)00693-7. [PMID: 38981482 DOI: 10.1016/j.cell.2024.06.019] [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: 05/31/2023] [Revised: 02/20/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024]
Abstract
Cellular senescence is an irreversible state of cell-cycle arrest induced by various stresses, including aberrant oncogene activation, telomere shortening, and DNA damage. Through a genome-wide screen, we discovered a conserved small nucleolar RNA (snoRNA), SNORA13, that is required for multiple forms of senescence in human cells and mice. Although SNORA13 guides the pseudouridylation of a conserved nucleotide in the ribosomal decoding center, loss of this snoRNA minimally impacts translation. Instead, we found that SNORA13 negatively regulates ribosome biogenesis. Senescence-inducing stress perturbs ribosome biogenesis, resulting in the accumulation of free ribosomal proteins (RPs) that trigger p53 activation. SNORA13 interacts directly with RPL23, decreasing its incorporation into maturing 60S subunits and, consequently, increasing the pool of free RPs, thereby promoting p53-mediated senescence. Thus, SNORA13 regulates ribosome biogenesis and the p53 pathway through a non-canonical mechanism distinct from its role in guiding RNA modification. These findings expand our understanding of snoRNA functions and their roles in cellular signaling.
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Affiliation(s)
- Yujing Cheng
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Siwen Wang
- Division of Vascular Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, Guangdong, China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, Guangdong, China
| | - He Zhang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jong-Sun Lee
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chunyang Ni
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jason Guo
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eric Chen
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shenming Wang
- Division of Vascular Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, Guangdong, China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, Guangdong, China
| | - Asha Acharya
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tsung-Cheng Chang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael Buszczak
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hao Zhu
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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8
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Lister KC, Wong C, Uttam S, Parisien M, Stecum P, Brown N, Cai W, Hooshmandi M, Gu N, Amiri M, Beaudry F, Jafarnejad SM, Tavares-Ferreira D, Inturi NN, Mazhar K, Zhao HT, Fitzsimmons B, Gkogkas CG, Sonenberg N, Price TJ, Diatchenko L, Atlasi Y, Mogil JS, Khoutorsky A. Translational control in the spinal cord regulates gene expression and pain hypersensitivity in the chronic phase of neuropathic pain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600539. [PMID: 38979173 PMCID: PMC11230214 DOI: 10.1101/2024.06.24.600539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Sensitization of spinal nociceptive circuits plays a crucial role in neuropathic pain. This sensitization depends on new gene expression that is primarily regulated via transcriptional and translational control mechanisms. The relative roles of these mechanisms in regulating gene expression in the clinically relevant chronic phase of neuropathic pain are not well understood. Here, we show that changes in gene expression in the spinal cord during the chronic phase of neuropathic pain are substantially regulated at the translational level. Downregulating spinal translation at the chronic phase alleviated pain hypersensitivity. Cell-type-specific profiling revealed that spinal inhibitory neurons exhibited greater changes in translation after peripheral nerve injury compared to excitatory neurons. Notably, increasing translation selectively in all inhibitory neurons or parvalbumin-positive (PV + ) interneurons, but not excitatory neurons, promoted mechanical pain hypersensitivity. Furthermore, increasing translation in PV + neurons decreased their intrinsic excitability and spiking activity, whereas reducing translation in spinal PV + neurons prevented the nerve injury-induced decrease in excitability. Thus, translational control mechanisms in the spinal cord, particularly in inhibitory neurons, play a role in mediating neuropathic pain hypersensitivity.
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9
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Harel I, Chen YR, Ziv I, Singh PP, Heinzer D, Navarro Negredo P, Goshtchevsky U, Wang W, Astre G, Moses E, McKay A, Machado BE, Hebestreit K, Yin S, Sánchez Alvarado A, Jarosz DF, Brunet A. Identification of protein aggregates in the aging vertebrate brain with prion-like and phase-separation properties. Cell Rep 2024; 43:112787. [PMID: 38810650 DOI: 10.1016/j.celrep.2023.112787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/23/2023] [Accepted: 06/26/2023] [Indexed: 05/31/2024] Open
Abstract
Protein aggregation, which can sometimes spread in a prion-like manner, is a hallmark of neurodegenerative diseases. However, whether prion-like aggregates form during normal brain aging remains unknown. Here, we use quantitative proteomics in the African turquoise killifish to identify protein aggregates that accumulate in old vertebrate brains. These aggregates are enriched for prion-like RNA-binding proteins, notably the ATP-dependent RNA helicase DDX5. We validate that DDX5 forms aggregate-like puncta in the brains of old killifish and mice. Interestingly, DDX5's prion-like domain allows these aggregates to propagate across many generations in yeast. In vitro, DDX5 phase separates into condensates. Mutations that abolish DDX5 prion propagation also impair the protein's ability to phase separate. DDX5 condensates exhibit enhanced enzymatic activity, but they can mature into inactive, solid aggregates. Our findings suggest that protein aggregates with prion-like properties form during normal brain aging, which could have implications for the age-dependency of cognitive decline.
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Affiliation(s)
- Itamar Harel
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel.
| | - Yiwen R Chen
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Inbal Ziv
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Param Priya Singh
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Daniel Heinzer
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Uri Goshtchevsky
- The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Wei Wang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Gwendoline Astre
- The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Eitan Moses
- The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Andrew McKay
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ben E Machado
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Katja Hebestreit
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Sifei Yin
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Glenn Laboratories for the Biology of Aging, Stanford University, Stanford, CA 94305, USA.
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10
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Tiburcio PDB, Chen K, Xu L, Chen KS. Actinomycin D and bortezomib disrupt protein homeostasis in Wilms tumor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598518. [PMID: 38948702 PMCID: PMC11212905 DOI: 10.1101/2024.06.11.598518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Wilms tumor is the most common kidney cancer in children, and diffusely anaplastic Wilms tumor is the most chemoresistant histological subtype. Here we explore how Wilms tumor cells evade the common chemotherapeutic drug actinomycin D, which inhibits ribosomal RNA biogenesis. Using ribosome profiling, protein arrays, and a genome-wide knockout screen, we describe how actinomycin D disrupts protein homeostasis and blocks cell cycle progression. We found that, when ribosomal capacity is limited by actinomycin D treatment, anaplastic Wilms tumor cells preferentially translate proteasome components and upregulate proteasome activity. Furthermore, the proteasome inhibitor bortezomib sensitizes cells to actinomycin D treatment by inducing apoptosis both in vitro and in vivo. Lastly, we show that increased levels of proteasome components are associated with anaplastic histology and with worse prognosis in non-anaplastic Wilms tumor. In sum, maintaining protein homeostasis is critical for Wilms tumor proliferation, and it can be therapeutically disrupted by blocking protein synthesis or turnover.
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Affiliation(s)
- Patricia D B Tiburcio
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Kenian Chen
- Quantitative Biomedical Research Center, Peter O'Donnell School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX
| | - Lin Xu
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
- Quantitative Biomedical Research Center, Peter O'Donnell School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX
| | - Kenneth S Chen
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX
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11
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Grandi C, Emmaneel M, Nelissen FHT, Roosenboom LWM, Petrova Y, Elzokla O, Hansen MMK. Decoupled degradation and translation enables noise modulation by poly(A) tails. Cell Syst 2024; 15:526-543.e7. [PMID: 38901403 DOI: 10.1016/j.cels.2024.05.004] [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: 04/05/2023] [Revised: 11/24/2023] [Accepted: 05/16/2024] [Indexed: 06/22/2024]
Abstract
Poly(A) tails are crucial for mRNA translation and degradation, but the exact relationship between tail length and mRNA kinetics remains unclear. Here, we employ a small library of identical mRNAs that differ only in their poly(A)-tail length to examine their behavior in human embryonic kidney cells. We find that tail length strongly correlates with mRNA degradation rates but is decoupled from translation. Interestingly, an optimal tail length of ∼100 nt displays the highest translation rate, which is identical to the average endogenous tail length measured by nanopore sequencing. Furthermore, poly(A)-tail length variability-a feature of endogenous mRNAs-impacts translation efficiency but not mRNA degradation rates. Stochastic modeling combined with single-cell tracking reveals that poly(A) tails provide cells with an independent handle to tune gene expression fluctuations by decoupling mRNA degradation and translation. Together, this work contributes to the basic understanding of gene expression regulation and has potential applications in nucleic acid therapeutics.
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Affiliation(s)
- Carmen Grandi
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Oncode Institute, Nijmegen, the Netherlands
| | - Martin Emmaneel
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Oncode Institute, Nijmegen, the Netherlands
| | - Frank H T Nelissen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Oncode Institute, Nijmegen, the Netherlands
| | - Laura W M Roosenboom
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Yoanna Petrova
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Omnia Elzokla
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Maike M K Hansen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Oncode Institute, Nijmegen, the Netherlands.
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12
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Paudel S, Lee N. Epstein-Barr virus noncoding RNA EBER1 promotes the expression of a ribosomal protein paralog to boost oxidative phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.15.599158. [PMID: 38915488 PMCID: PMC11195164 DOI: 10.1101/2024.06.15.599158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Epstein-Barr virus (EBV) is a highly successful pathogen that infects ~95% of the adult population and is associated with diverse cancers and autoimmune diseases. The most abundant viral factor in latently infected cells is not a protein but a noncoding RNA called EBV-encoded RNA 1 (EBER1). Even though EBER1 is highly abundant and was discovered over forty years ago, the function of EBER1 has remained elusive. EBER1 interacts with the ribosomal protein L22, which normally suppresses the expression of its paralog L22-like 1 (L22L1). Here we show that when L22 binds EBER1, it cannot suppress L22L1, resulting in L22L1 being expressed and incorporated into ribosomes. We further show that L22L1-containing ribosomes preferentially translate mRNAs involved in the oxidative phosphorylation pathway. Moreover, upregulation of L22L1 is indispensable for growth transformation and immortalization of resting B cells upon EBV infection. Taken together, our results suggest that the function of EBER1 is to modulate host gene expression at the translational level, thus bypassing the need for dysregulating host gene transcription.
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Affiliation(s)
- Sita Paudel
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Nara Lee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
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13
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Wen K, Chen X, Gu J, Chen Z, Wang Z. Beyond traditional translation: ncRNA derived peptides as modulators of tumor behaviors. J Biomed Sci 2024; 31:63. [PMID: 38877495 PMCID: PMC11177406 DOI: 10.1186/s12929-024-01047-0] [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: 11/29/2023] [Accepted: 05/24/2024] [Indexed: 06/16/2024] Open
Abstract
Within the intricate tapestry of molecular research, noncoding RNAs (ncRNAs) were historically overshadowed by a pervasive presumption of their inability to encode proteins or peptides. However, groundbreaking revelations have challenged this notion, unveiling select ncRNAs that surprisingly encode peptides specifically those nearing a succinct 100 amino acids. At the forefront of this epiphany stand lncRNAs and circRNAs, distinctively characterized by their embedded small open reading frames (sORFs). Increasing evidence has revealed different functions and mechanisms of peptides/proteins encoded by ncRNAs in cancer, including promotion or inhibition of cancer cell proliferation, cellular metabolism (glucose metabolism and lipid metabolism), and promotion or concerted metastasis of cancer cells. The discoveries not only accentuate the depth of ncRNA functionality but also open novel avenues for oncological research and therapeutic innovations. The main difficulties in the study of these ncRNA-derived peptides hinge crucially on precise peptide detection and sORFs identification. Here, we illuminate cutting-edge methodologies, essential instrumentation, and dedicated databases tailored for unearthing sORFs and peptides. In addition, we also conclude the potential of clinical applications in cancer therapy.
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Affiliation(s)
- Kang Wen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, P.R. China
| | - Xin Chen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, P.R. China
| | - Jingyao Gu
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, P.R. China
| | - Zhenyao Chen
- Department of Respiratory Endoscopy, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P.R. China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Zhaoxia Wang
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, P.R. China.
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14
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Diamond PD, McGlincy NJ, Ingolia NT. Depletion of cap-binding protein eIF4E dysregulates amino acid metabolic gene expression. Mol Cell 2024; 84:2119-2134.e5. [PMID: 38848691 DOI: 10.1016/j.molcel.2024.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 02/21/2024] [Accepted: 05/09/2024] [Indexed: 06/09/2024]
Abstract
Protein synthesis is metabolically costly and must be tightly coordinated with changing cellular needs and nutrient availability. The cap-binding protein eIF4E makes the earliest contact between mRNAs and the translation machinery, offering a key regulatory nexus. We acutely depleted this essential protein and found surprisingly modest effects on cell growth and recovery of protein synthesis. Paradoxically, impaired protein biosynthesis upregulated genes involved in the catabolism of aromatic amino acids simultaneously with the induction of the amino acid biosynthetic regulon driven by the integrated stress response factor GCN4. We further identified the translational control of Pho85 cyclin 5 (PCL5), a negative regulator of Gcn4, that provides a consistent protein-to-mRNA ratio under varied translation environments. This regulation depended in part on a uniquely long poly(A) tract in the PCL5 5' UTR and poly(A) binding protein. Collectively, these results highlight how eIF4E connects protein synthesis to metabolic gene regulation, uncovering mechanisms controlling translation during environmental challenges.
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Affiliation(s)
- Paige D Diamond
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nicholas J McGlincy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.
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15
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Sutter SO, Tobler K, Seyffert M, Lkharrazi A, Zöllig J, Schraner EM, Vogt B, Büning H, Fraefel C. Interferon-γ inducible factor 16 (IFI16) restricts adeno-associated virus type 2 (AAV2) transduction in an immune-modulatory independent way. J Virol 2024:e0011024. [PMID: 38837381 DOI: 10.1128/jvi.00110-24] [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: 01/20/2024] [Accepted: 04/28/2024] [Indexed: 06/07/2024] Open
Abstract
We determined the transcription profile of adeno-associated virus type 2 (AAV2)-infected primary human fibroblasts. Subsequent analysis revealed that cells respond to AAV infection through changes in several significantly affected pathways, including cell cycle regulation, chromatin modulation, and innate immune responses. Various assays were performed to validate selected differentially expressed genes and to confirm not only the quality but also the robustness of the raw data. One of the genes upregulated in AAV2-infected cells was interferon-γ inducible factor 16 (IFI16). IFI16 is known as a multifunctional cytosolic and nuclear innate immune sensor for double-stranded as well as single-stranded DNA, exerting its effects through various mechanisms, such as interferon response, epigenetic modifications, or transcriptional regulation. IFI16 thereby constitutes a restriction factor for many different viruses among them, as shown here, AAV2 and thereof derived vectors. Indeed, the post-transcriptional silencing of IFI16 significantly increased AAV2 transduction efficiency, independent of the structure of the virus/vector genome. We also show that IFI16 exerts its inhibitory effect on AAV2 transduction in an immune-modulatory independent way by interfering with Sp1-dependent transactivation of wild-type AAV2 and AAV2 vector promoters. IMPORTANCE Adeno-associated virus (AAV) vectors are among the most frequently used viral vectors for gene therapy. The lack of pathogenicity of the parental virus, the long-term persistence as episomes in non-proliferating cells, and the availability of a variety of AAV serotypes differing in their cellular tropism are advantageous features of this biological nanoparticle. To deepen our understanding of virus-host interactions, especially in terms of antiviral responses, we present here the first transcriptome analysis of AAV serotype 2 (AAV2)-infected human primary fibroblasts. Our findings indicate that interferon-γ inducible factor 16 acts as an antiviral factor in AAV2 infection and AAV2 vector-mediated cell transduction in an immune-modulatory independent way by interrupting the Sp1-dependent gene expression from viral or vector genomes.
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Affiliation(s)
- Sereina O Sutter
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Kurt Tobler
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Michael Seyffert
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Anouk Lkharrazi
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Joël Zöllig
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | | | - Bernd Vogt
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Hildegard Büning
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Cornel Fraefel
- Institute of Virology, University of Zurich, Zurich, Switzerland
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16
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Aviner R, Lee TT, Masto VB, Li KH, Andino R, Frydman J. Polyglutamine-mediated ribotoxicity disrupts proteostasis and stress responses in Huntington's disease. Nat Cell Biol 2024; 26:892-902. [PMID: 38741019 DOI: 10.1038/s41556-024-01414-x] [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: 12/07/2023] [Accepted: 04/01/2024] [Indexed: 05/16/2024]
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by expansion of a CAG trinucleotide repeat in the Huntingtin (HTT) gene, encoding a homopolymeric polyglutamine (polyQ) tract. Although mutant HTT (mHTT) protein is known to aggregate, the links between aggregation and neurotoxicity remain unclear. Here we show that both translation and aggregation of wild-type HTT and mHTT are regulated by a stress-responsive upstream open reading frame and that polyQ expansions cause abortive translation termination and release of truncated, aggregation-prone mHTT fragments. Notably, we find that mHTT depletes translation elongation factor eIF5A in brains of symptomatic HD mice and cultured HD cells, leading to pervasive ribosome pausing and collisions. Loss of eIF5A disrupts homeostatic controls and impairs recovery from acute stress. Importantly, drugs that inhibit translation initiation reduce premature termination and mitigate this escalating cascade of ribotoxic stress and dysfunction in HD.
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Affiliation(s)
- Ranen Aviner
- Department of Biology and Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA, USA
| | - Ting-Ting Lee
- Department of Biology and Department of Genetics, Stanford University, Stanford, CA, USA
| | - Vincent B Masto
- Department of Biology and Department of Genetics, Stanford University, Stanford, CA, USA
| | - Kathy H Li
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Judith Frydman
- Department of Biology and Department of Genetics, Stanford University, Stanford, CA, USA.
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17
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Román ÁC, Benítez DA, Díaz-Pizarro A, Del Valle-Del Pino N, Olivera-Gómez M, Cumplido-Laso G, Carvajal-González JM, Mulero-Navarro S. Next generation sequencing technologies to address aberrant mRNA translation in cancer. NAR Cancer 2024; 6:zcae024. [PMID: 38751936 PMCID: PMC11094761 DOI: 10.1093/narcan/zcae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 05/18/2024] Open
Abstract
In this review, we explore the transformative impact of next generation sequencing technologies in the realm of translatomics (the study of how translational machinery acts on a genome-wide scale). Despite the expectation of a direct correlation between mRNA and protein content, the complex regulatory mechanisms that affect this relationship remark the limitations of standard RNA-seq approaches. Then, the review characterizes crucial techniques such as polysome profiling, ribo-seq, trap-seq, proximity-specific ribosome profiling, rnc-seq, tcp-seq, qti-seq and scRibo-seq. All these methods are summarized within the context of cancer research, shedding light on their applications in deciphering aberrant translation in cancer cells. In addition, we encompass databases and bioinformatic tools essential for researchers that want to address translatome analysis in the context of cancer biology.
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Affiliation(s)
- Ángel-Carlos Román
- Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura. Avda. de Elvas s/n, 06071 Badajoz, Spain
| | - Dixan A Benítez
- Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura. Avda. de Elvas s/n, 06071 Badajoz, Spain
| | - Alba Díaz-Pizarro
- Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura. Avda. de Elvas s/n, 06071 Badajoz, Spain
| | - Nuria Del Valle-Del Pino
- Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura. Avda. de Elvas s/n, 06071 Badajoz, Spain
| | - Marcos Olivera-Gómez
- Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura. Avda. de Elvas s/n, 06071 Badajoz, Spain
| | - Guadalupe Cumplido-Laso
- Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura. Avda. de Elvas s/n, 06071 Badajoz, Spain
| | - Jose M Carvajal-González
- Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura. Avda. de Elvas s/n, 06071 Badajoz, Spain
| | - Sonia Mulero-Navarro
- Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura. Avda. de Elvas s/n, 06071 Badajoz, Spain
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18
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Weiss B, Dikstein R. Unraveling the landscapes and regulation of scanning, leaky scanning, and 48S initiation complex conformations. Cell Rep 2024; 43:114126. [PMID: 38630588 DOI: 10.1016/j.celrep.2024.114126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 01/19/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Scanning and initiation are critical steps in translation. Here, we utilized translation complex profiling (TCP-seq) to investigate 48S organization and eIF4G1-eIF1 inhibition impact. We provide global views of scanning and leaky scanning, uncovering a central role of eIF4G1-eIF1 in their regulation. We confirm AUG context importance, with non-leaky genes featuring a Kozak context and cytosine at positions -1 and +5. Capturing 48S complexes associated with eIF1, eIF4G1, eIF3, and eIF2 through selective TCP-seq revealed that the eIF3-scanning ribosome is highly vulnerable to eIF4G1-eIF1 inhibition, and eIF1 tends to dissociate upon AUG recognition. Initiation-site footprint analysis revealed a class spanning -12 to +18/19 from the AUG, representing the entire 48S and enriched with eIF2, eIF1, and eIF4G1, indicative of early initiation. Another eIF3-dependent class extends up to +26 and exhibits reduced eIF2 and eIF4G1 association, suggesting a late/alternative initiation complex. Our analysis provides an overview of scanning, initiation, and evidence for conformational rearrangements in vivo.
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Affiliation(s)
- Benjamin Weiss
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Rivka Dikstein
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel.
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19
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Chen YR, Harel I, Singh PP, Ziv I, Moses E, Goshtchevsky U, Machado BE, Brunet A, Jarosz DF. Tissue-specific landscape of protein aggregation and quality control in an aging vertebrate. Dev Cell 2024:S1534-5807(24)00266-1. [PMID: 38810654 DOI: 10.1016/j.devcel.2024.04.014] [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: 08/30/2023] [Revised: 01/13/2024] [Accepted: 04/15/2024] [Indexed: 05/31/2024]
Abstract
Protein aggregation is a hallmark of age-related neurodegeneration. Yet, aggregation during normal aging and in tissues other than the brain is poorly understood. Here, we leverage the African turquoise killifish to systematically profile protein aggregates in seven tissues of an aging vertebrate. Age-dependent aggregation is strikingly tissue specific and not simply driven by protein expression differences. Experimental interrogation in killifish and yeast, combined with machine learning, indicates that this specificity is linked to protein-autonomous biophysical features and tissue-selective alterations in protein quality control. Co-aggregation of protein quality control machinery during aging may further reduce proteostasis capacity, exacerbating aggregate burden. A segmental progeria model with accelerated aging in specific tissues exhibits selectively increased aggregation in these same tissues. Intriguingly, many age-related protein aggregates arise in wild-type proteins that, when mutated, drive human diseases. Our data chart a comprehensive landscape of protein aggregation during vertebrate aging and identify strong, tissue-specific associations with dysfunction and disease.
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Affiliation(s)
- Yiwen R Chen
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Itamar Harel
- The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Param Priya Singh
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Inbal Ziv
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Eitan Moses
- The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Uri Goshtchevsky
- The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Ben E Machado
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Glenn Center for the Biology of Aging, Stanford University, Stanford, CA 94305, USA.
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
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20
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Wang F, Holmes MJ, Hong HJ, Thaprawat P, Kannan G, Huynh MH, Schultz TL, Licon MH, Lourido S, Dong W, Brito Querido J, Sullivan WJ, O'Leary SE, Carruthers VB. Translation initiation factor eIF1.2 promotes Toxoplasma stage conversion by regulating levels of key differentiation factors. Nat Commun 2024; 15:4385. [PMID: 38782906 PMCID: PMC11116398 DOI: 10.1038/s41467-024-48685-4] [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: 11/16/2023] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
The parasite Toxoplasma gondii persists in its hosts by converting from replicating tachyzoites to latent bradyzoites housed in tissue cysts. The molecular mechanisms that mediate T. gondii differentiation remain poorly understood. Through a mutagenesis screen, we identified translation initiation factor eIF1.2 as a critical factor for T. gondii differentiation. A F97L mutation in eIF1.2 or the genetic ablation of eIF1.2 (∆eif1.2) markedly impeded bradyzoite cyst formation in vitro and in vivo. We demonstrated, at single-molecule level, that the eIF1.2 F97L mutation impacts the scanning process of the ribosome preinitiation complex on a model mRNA. RNA sequencing and ribosome profiling experiments unveiled that ∆eif1.2 parasites are defective in upregulating bradyzoite induction factors BFD1 and BFD2 during stress-induced differentiation. Forced expression of BFD1 or BFD2 significantly restored differentiation in ∆eif1.2 parasites. Together, our findings suggest that eIF1.2 functions by regulating the translation of key differentiation factors necessary to establish chronic toxoplasmosis.
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Affiliation(s)
- Fengrong Wang
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Michael J Holmes
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Hea Jin Hong
- Department of Biochemistry, University of California Riverside, Riverside, CA, 92521, USA
| | - Pariyamon Thaprawat
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Geetha Kannan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - My-Hang Huynh
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Tracey L Schultz
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | | | - Sebastian Lourido
- Whitehead Institute, Cambridge, MA, 02142, USA
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Wenzhao Dong
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jailson Brito Querido
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - William J Sullivan
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Seán E O'Leary
- Department of Biochemistry, University of California Riverside, Riverside, CA, 92521, USA
- Center for RNA Biology and Medicine, University of California Riverside, Riverside, CA, 92521, USA
| | - Vern B Carruthers
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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21
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Boon NJ, Oliveira RA, Körner PR, Kochavi A, Mertens S, Malka Y, Voogd R, van der Horst SEM, Huismans MA, Smabers LP, Draper JM, Wessels LFA, Haahr P, Roodhart JML, Schumacher TNM, Snippert HJ, Agami R, Brummelkamp TR. DNA damage induces p53-independent apoptosis through ribosome stalling. Science 2024; 384:785-792. [PMID: 38753784 DOI: 10.1126/science.adh7950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/11/2024] [Indexed: 05/18/2024]
Abstract
In response to excessive DNA damage, human cells can activate p53 to induce apoptosis. Cells lacking p53 can still undergo apoptosis upon DNA damage, yet the responsible pathways are unknown. We observed that p53-independent apoptosis in response to DNA damage coincided with translation inhibition, which was characterized by ribosome stalling on rare leucine-encoding UUA codons and globally curtailed translation initiation. A genetic screen identified the transfer RNAse SLFN11 and the kinase GCN2 as factors required for UUA stalling and global translation inhibition, respectively. Stalled ribosomes activated a ribotoxic stress signal conveyed by the ribosome sensor ZAKα to the apoptosis machinery. These results provide an explanation for the frequent inactivation of SLFN11 in chemotherapy-unresponsive tumors and highlight ribosome stalling as a signaling event affecting cell fate in response to DNA damage.
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Affiliation(s)
- Nicolaas J Boon
- Oncode Institute, Utrecht, Netherlands
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Rafaela A Oliveira
- Oncode Institute, Utrecht, Netherlands
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Pierré-René Körner
- Oncode Institute, Utrecht, Netherlands
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Adva Kochavi
- Oncode Institute, Utrecht, Netherlands
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Sander Mertens
- Oncode Institute, Utrecht, Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Yuval Malka
- Oncode Institute, Utrecht, Netherlands
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Rhianne Voogd
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Suzanne E M van der Horst
- Oncode Institute, Utrecht, Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Maarten A Huismans
- Oncode Institute, Utrecht, Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Lidwien P Smabers
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Jonne M Draper
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Lodewyk F A Wessels
- Oncode Institute, Utrecht, Netherlands
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Peter Haahr
- Oncode Institute, Utrecht, Netherlands
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
- Center for Gene Expression, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeanine M L Roodhart
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Ton N M Schumacher
- Oncode Institute, Utrecht, Netherlands
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Hugo J Snippert
- Oncode Institute, Utrecht, Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Reuven Agami
- Oncode Institute, Utrecht, Netherlands
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Thijn R Brummelkamp
- Oncode Institute, Utrecht, Netherlands
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
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22
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Wang F, Holmes MJ, Hong HJ, Thaprawat P, Kannan G, Huynh MH, Schultz TL, Licon MH, Lourido S, Dong W, Querido JB, Sullivan WJ, O'Leary SE, Carruthers VB. Translation initiation factor eIF1.2 promotes Toxoplasma stage conversion by regulating levels of key differentiation factors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.03.565545. [PMID: 37961607 PMCID: PMC10635126 DOI: 10.1101/2023.11.03.565545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The parasite Toxoplasma gondii persists in its hosts by converting from replicating tachyzoites to latent bradyzoites housed in tissue cysts. The molecular mechanisms that mediate T. gondii differentiation remain poorly understood. Through a mutagenesis screen, we identified translation initiation factor eIF1.2 as a critical factor for T. gondii differentiation. A F97L mutation in eIF1.2 or the genetic ablation of eIF1.2 (Δ eif1.2 ) markedly impeded bradyzoite cyst formation in vitro and in vivo . We demonstrated, at single-molecule level, that the eIF1.2 F97L mutation impacts the scanning process of the ribosome preinitiation complex on a model mRNA. RNA sequencing and ribosome profiling experiments unveiled that Δ eif1.2 parasites are defective in upregulating bradyzoite induction factors BFD1 and BFD2 during stress-induced differentiation. Forced expression of BFD1 or BFD2 significantly restored differentiation in Δ eif1.2 parasites. Together, our findings suggest that eIF1.2 functions by regulating the translation of key differentiation factors necessary to establish chronic toxoplasmosis.
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23
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Cui X, Cao Q, Li F, Jing J, Liu Z, Yang X, Schwartz GJ, Yu L, Shi H, Shi H, Xue B. The histone methyltransferase SUV420H2 regulates brown and beige adipocyte thermogenesis. JCI Insight 2024; 9:e164771. [PMID: 38713533 DOI: 10.1172/jci.insight.164771] [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: 08/30/2022] [Accepted: 05/01/2024] [Indexed: 05/09/2024] Open
Abstract
Activation of brown adipose tissue (BAT) thermogenesis increases energy expenditure and alleviates obesity. Here we discover that histone methyltransferase suppressor of variegation 4-20 homolog 2 (Suv420h2) expression parallels that of Ucp1 in brown and beige adipocytes and that Suv420h2 knockdown significantly reduces - whereas Suv420h2 overexpression significantly increases - Ucp1 levels in brown adipocytes. Suv420h2 knockout (H2KO) mice exhibit impaired cold-induced thermogenesis and are prone to diet-induced obesity. In contrast, mice with specific overexpression of Suv420h2 in adipocytes display enhanced cold-induced thermogenesis and are resistant to diet-induced obesity. Further study shows that Suv420h2 catalyzes H4K20 trimethylation at eukaryotic translation initiation factor 4E-binding protein 1 (4e-bp1) promoter, leading to downregulated expression of 4e-bp1, a negative regulator of the translation initiation complex. This in turn upregulates PGC1α protein levels, and this upregulation is associated with increased expression of thermogenic program. We conclude that Suv420h2 is a key regulator of brown/beige adipocyte development and thermogenesis.
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Affiliation(s)
- Xin Cui
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | - Qiang Cao
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | - Fenfen Li
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | - Jia Jing
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | - Zhixue Liu
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | - Xiaosong Yang
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | - Gary J Schwartz
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Liqing Yu
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Huidong Shi
- Georgia Cancer Center and
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Hang Shi
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | - Bingzhong Xue
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
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24
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Nord AJ, Wheeler TJ. Diviner uncovers hundreds of novel human (and other) exons though comparative analysis of proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592595. [PMID: 38746152 PMCID: PMC11092782 DOI: 10.1101/2024.05.05.592595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background Eukaryotic genes are often composed of multiple exons that are stitched together by splicing out the intervening introns. These exons may be conditionally joined in different combinations to produce a collection of related, but distinct, mRNA transcripts. For protein-coding genes, these products of alternative splicing lead to production of related protein variants (isoforms) of a gene. Complete labeling of the protein-coding content of a eukaryotic genome requires discovery of mRNA encoding all isoforms, but it is impractical to enumerate all possible combinations of tissue, developmental stage, and environmental context; as a result, many true exons go unlabeled in genome annotations. Results One way to address the combinatoric challenge of finding all isoforms in a single organism A is to leverage sequencing efforts for other organisms - each time a new organism is sequenced, it may be under a new combination of conditions, so that a previously unobserved isoform may be sequenced. We present Diviner, a software tool that identifies previously undocumented exons in organisms by comparing isoforms across species. We demonstrate Diviner's utility by locating hundreds of novel exons in the genomes of human, mouse, and rat, as well as in the ferret genome. Further, we provide analyses supporting the notion that most of the new exons reported by Diviner are likely to be part of a true (but unobserved) isoform of the containing species.
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Affiliation(s)
- Alexander J Nord
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Travis J Wheeler
- R. Ken Coit College of Pharmacy, University of Arizona, Tucson, Arizona, United States of America
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25
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Gentry-Torfer D, Murillo E, Barrington CL, Nie S, Leeming MG, Suwanchaikasem P, Williamson NA, Roessner U, Boughton BA, Kopka J, Martinez-Seidel F. Streamlining Protein Fractional Synthesis Rates Using SP3 Beads and Stable Isotope Mass Spectrometry: A Case Study on the Plant Ribosome. Bio Protoc 2024; 14:e4981. [PMID: 38737506 PMCID: PMC11082790 DOI: 10.21769/bioprotoc.4981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 05/14/2024] Open
Abstract
Ribosomes are an archetypal ribonucleoprotein assembly. Due to ribosomal evolution and function, r-proteins share specific physicochemical similarities, making the riboproteome particularly suited for tailored proteome profiling methods. Moreover, the structural proteome of ribonucleoprotein assemblies reflects context-dependent functional features. Thus, characterizing the state of riboproteomes provides insights to uncover the context-dependent functionality of r-protein rearrangements, as they relate to what has been termed the ribosomal code, a concept that parallels that of the histone code, in which chromatin rearrangements influence gene expression. Compared to high-resolution ribosomal structures, omics methods lag when it comes to offering customized solutions to close the knowledge gap between structure and function that currently exists in riboproteomes. Purifying the riboproteome and subsequent shot-gun proteomics typically involves protein denaturation and digestion with proteases. The results are relative abundances of r-proteins at the ribosome population level. We have previously shown that, to gain insight into the stoichiometry of individual proteins, it is necessary to measure by proteomics bound r-proteins and normalize their intensities by the sum of r-protein abundances per ribosomal complex, i.e., 40S or 60S subunits. These calculations ensure that individual r-protein stoichiometries represent the fraction of each family/paralog relative to the complex, effectively revealing which r-proteins become substoichiometric in specific physiological scenarios. Here, we present an optimized method to profile the riboproteome of any organism as well as the synthesis rates of r-proteins determined by stable isotope-assisted mass spectrometry. Our method purifies the r-proteins in a reversibly denatured state, which offers the possibility for combined top-down and bottom-up proteomics. Our method offers a milder native denaturation of the r-proteome via a chaotropic GuHCl solution as compared with previous studies that use irreversible denaturation under highly acidic conditions to dissociate rRNA and r-proteins. As such, our method is better suited to conserve post-translational modifications (PTMs). Subsequently, our method carefully considers the amino acid composition of r-proteins to select an appropriate protease for digestion. We avoid non-specific protease cleavage by increasing the pH of our standardized r-proteome dilutions that enter the digestion pipeline and by using a digestion buffer that ensures an optimal pH for a reliable protease digestion process. Finally, we provide the R package ProtSynthesis to study the fractional synthesis rates of r-proteins. The package uses physiological parameters as input to determine peptide or protein fractional synthesis rates. Once the physiological parameters are measured, our equations allow a fair comparison between treatments that alter the biological equilibrium state of the system under study. Our equations correct peptide enrichment using enrichments in soluble amino acids, growth rates, and total protein accumulation. As a means of validation, our pipeline fails to find "false" enrichments in non-labeled samples while also filtering out proteins with multiple unique peptides that have different enrichment values, which are rare in our datasets. These two aspects reflect the accuracy of our tool. Our method offers the possibility of elucidating individual r-protein family/paralog abundances, PTM status, fractional synthesis rates, and dynamic assembly into ribosomal complexes if top-down and bottom-up proteomic approaches are used concomitantly, taking one step further into mapping the native and dynamic status of the r-proteome onto high-resolution ribosome structures. In addition, our method can be used to study the proteomes of all macromolecular assemblies that can be purified, although purification is the limiting step, and the efficacy and accuracy of the proteases may be limited depending on the digestion requirements. Key features • Efficient purification of the ribosomal proteome: streamlined procedure for the specific purification of the ribosomal proteome or complex Ome. • Accurate calculation of fractional synthesis rates: robust method for calculating fractional protein synthesis rates in macromolecular complexes under different physiological steady states. • Holistic ribosome methodology focused on plants: comprehensive approach that provides insights into the ribosomes and translational control of plants, demonstrated using cold acclimation [1]. • Tailored strategies for stable isotope labeling in plants: methodology focusing on materials and labeling considerations specific to free and proteinogenic amino acid analysis [2].
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Affiliation(s)
- Dione Gentry-Torfer
- Applied Metabolome Analysis, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- School of Biosciences, The University of Melbourne, Parkville, Australia
| | - Ester Murillo
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Chloe L. Barrington
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - Shuai Nie
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Australia
| | - Michael G. Leeming
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Australia
- School of Chemistry, The University of Melbourne, Parkville, Australia
| | | | - Nicholas A. Williamson
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Australia
| | - Ute Roessner
- School of Biosciences, The University of Melbourne, Parkville, Australia
- Research School of Biology, The Australian National University, Acton, Australia
| | - Berin A. Boughton
- School of Biosciences, The University of Melbourne, Parkville, Australia
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Australia
| | - Joachim Kopka
- Applied Metabolome Analysis, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Federico Martinez-Seidel
- Applied Metabolome Analysis, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- School of Biosciences, The University of Melbourne, Parkville, Australia
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
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26
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Böttcher B, Kienast SD, Leufken J, Eggers C, Sharma P, Leufken CM, Morgner B, Drexler HCA, Schulz D, Allert S, Jacobsen ID, Vylkova S, Leidel SA, Brunke S. A highly conserved tRNA modification contributes to C. albicans filamentation and virulence. Microbiol Spectr 2024; 12:e0425522. [PMID: 38587411 PMCID: PMC11064501 DOI: 10.1128/spectrum.04255-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/18/2024] [Indexed: 04/09/2024] Open
Abstract
tRNA modifications play important roles in maintaining translation accuracy in all domains of life. Disruptions in the tRNA modification machinery, especially of the anticodon stem loop, can be lethal for many bacteria and lead to a broad range of phenotypes in baker's yeast. Very little is known about the function of tRNA modifications in host-pathogen interactions, where rapidly changing environments and stresses require fast adaptations. We found that two closely related fungal pathogens of humans, the highly pathogenic Candida albicans and its much less pathogenic sister species, Candida dubliniensis, differ in the function of a tRNA-modifying enzyme. This enzyme, Hma1, exhibits species-specific effects on the ability of the two fungi to grow in the hypha morphology, which is central to their virulence potential. We show that Hma1 has tRNA-threonylcarbamoyladenosine dehydratase activity, and its deletion alters ribosome occupancy, especially at 37°C-the body temperature of the human host. A C. albicans HMA1 deletion mutant also shows defects in adhesion to and invasion into human epithelial cells and shows reduced virulence in a fungal infection model. This links tRNA modifications to host-induced filamentation and virulence of one of the most important fungal pathogens of humans.IMPORTANCEFungal infections are on the rise worldwide, and their global burden on human life and health is frequently underestimated. Among them, the human commensal and opportunistic pathogen, Candida albicans, is one of the major causative agents of severe infections. Its virulence is closely linked to its ability to change morphologies from yeasts to hyphae. Here, this ability is linked-to our knowledge for the first time-to modifications of tRNA and translational efficiency. One tRNA-modifying enzyme, Hma1, plays a specific role in C. albicans and its ability to invade the host. This adds a so-far unknown layer of regulation to the fungal virulence program and offers new potential therapeutic targets to fight fungal infections.
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Affiliation(s)
- Bettina Böttcher
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knoell Institute, Jena, Germany
- Septomics Research Center, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology – Hans Knoell Institute, Jena, Germany
| | - Sandra D. Kienast
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Research Group for Cellular RNA Biochemistry, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Johannes Leufken
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Research Group for Cellular RNA Biochemistry, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Cristian Eggers
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Research Group for Cellular RNA Biochemistry, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Puneet Sharma
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Research Group for Cellular RNA Biochemistry, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Christine M. Leufken
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Bianka Morgner
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knoell Institute, Jena, Germany
| | - Hannes C. A. Drexler
- Bioanalytical Mass Spectrometry Unit, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Daniela Schulz
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knoell Institute, Jena, Germany
| | - Stefanie Allert
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knoell Institute, Jena, Germany
| | - Ilse D. Jacobsen
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knoell Institute, Jena, Germany
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Slavena Vylkova
- Septomics Research Center, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology – Hans Knoell Institute, Jena, Germany
| | - Sebastian A. Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Research Group for Cellular RNA Biochemistry, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Sascha Brunke
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knoell Institute, Jena, Germany
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27
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Shen Z, Naveed M, Bao J. Untacking small RNA profiling and RNA fragment footprinting: Approaches and challenges in library construction. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1852. [PMID: 38715192 DOI: 10.1002/wrna.1852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 06/06/2024]
Abstract
Small RNAs (sRNAs) with sizes ranging from 15 to 50 nucleotides (nt) are critical regulators of gene expression control. Prior studies have shown that sRNAs are involved in a broad range of biological processes, such as organ development, tumorigenesis, and epigenomic regulation; however, emerging evidence unveils a hidden layer of diversity and complexity of endogenously encoded sRNAs profile in eukaryotic organisms, including novel types of sRNAs and the previously unknown post-transcriptional RNA modifications. This underscores the importance for accurate, unbiased detection of sRNAs in various cellular contexts. A multitude of high-throughput methods based on next-generation sequencing (NGS) are developed to decipher the sRNA expression and their modifications. Nonetheless, distinct from mRNA sequencing, the data from sRNA sequencing suffer frequent inconsistencies and high variations emanating from the adapter contaminations and RNA modifications, which overall skew the sRNA libraries. Here, we summarize the sRNA-sequencing approaches, and discuss the considerations and challenges for the strategies and methods of sRNA library construction. The pros and cons of sRNA sequencing have significant implications for implementing RNA fragment footprinting approaches, including CLIP-seq and Ribo-seq. We envision that this review can inspire novel improvements in small RNA sequencing and RNA fragment footprinting in future. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.
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Affiliation(s)
- Zhaokang Shen
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
| | - Muhammad Naveed
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Jianqiang Bao
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
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28
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Li F, Xiang R, Liu Y, Hu G, Jiang Q, Jia T. Approaches and challenges in identifying, quantifying, and manipulating dynamic mitochondrial genome variations. Cell Signal 2024; 117:111123. [PMID: 38417637 DOI: 10.1016/j.cellsig.2024.111123] [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: 12/07/2023] [Revised: 02/14/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Mitochondria, the cellular powerhouses, possess their own unique genetic system, including replication, transcription, and translation. Studying these processes is crucial for comprehending mitochondrial disorders, energy production, and their related diseases. Over the past decades, various approaches have been applied in detecting and quantifying mitochondrial genome variations with also the purpose of manipulation of mitochondria or mitochondrial genome for therapeutics. Understanding the scope and limitations of above strategies is not only fundamental to the understanding of basic biology but also critical for exploring disease-related novel target(s), as well to develop innovative therapies. Here, this review provides an overview of different tools and techniques for accurate mitochondrial genome variations identification, quantification, and discuss novel strategies for the manipulation of mitochondria to develop innovative therapeutic interventions, through combining the insights gained from the study of mitochondrial genetics with ongoing single cell omics combined with advanced single molecular tools.
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Affiliation(s)
- Fei Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Run Xiang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China; Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yue Liu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Guoliang Hu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China; Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Quanbo Jiang
- Light, Nanomaterials, Nanotechnologies (L2n) Laboratory, CNRS EMR 7004, University of Technology of Troyes, 12 rue Marie Curie, 10004 Troyes, France
| | - Tao Jia
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China; CNRS-UMR9187, INSERM U1196, PSL-Research University, 91405 Orsay, France; CNRS-UMR9187, INSERM U1196, Université Paris Saclay, 91405 Orsay, France.
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29
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Hacisuleyman E, Hale CR, Noble N, Luo JD, Fak JJ, Saito M, Chen J, Weissman JS, Darnell RB. Neuronal activity rapidly reprograms dendritic translation via eIF4G2:uORF binding. Nat Neurosci 2024; 27:822-835. [PMID: 38589584 PMCID: PMC11088998 DOI: 10.1038/s41593-024-01615-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 03/05/2024] [Indexed: 04/10/2024]
Abstract
Learning and memory require activity-induced changes in dendritic translation, but which mRNAs are involved and how they are regulated are unclear. In this study, to monitor how depolarization impacts local dendritic biology, we employed a dendritically targeted proximity labeling approach followed by crosslinking immunoprecipitation, ribosome profiling and mass spectrometry. Depolarization of primary cortical neurons with KCl or the glutamate agonist DHPG caused rapid reprogramming of dendritic protein expression, where changes in dendritic mRNAs and proteins are weakly correlated. For a subset of pre-localized messages, depolarization increased the translation of upstream open reading frames (uORFs) and their downstream coding sequences, enabling localized production of proteins involved in long-term potentiation, cell signaling and energy metabolism. This activity-dependent translation was accompanied by the phosphorylation and recruitment of the non-canonical translation initiation factor eIF4G2, and the translated uORFs were sufficient to confer depolarization-induced, eIF4G2-dependent translational control. These studies uncovered an unanticipated mechanism by which activity-dependent uORF translational control by eIF4G2 couples activity to local dendritic remodeling.
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Affiliation(s)
- Ezgi Hacisuleyman
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA.
| | - Caryn R Hale
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Natalie Noble
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - John J Fak
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA
| | - Misa Saito
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA
| | - Jin Chen
- Department of Pharmacology and Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Altos Labs, Bay Area Institute of Science, Redwood City, CA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Robert B Darnell
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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30
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Rauscher R, Eggers C, Dimitrova-Paternoga L, Shankar V, Rosina A, Cristodero M, Paternoga H, Wilson DN, Leidel SA, Polacek N. Evolving precision: rRNA expansion segment 7S modulates translation velocity and accuracy in eukaryal ribosomes. Nucleic Acids Res 2024; 52:4021-4036. [PMID: 38324474 DOI: 10.1093/nar/gkae067] [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: 08/20/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/09/2024] Open
Abstract
Ribosome-enhanced translational miscoding of the genetic code causes protein dysfunction and loss of cellular fitness. During evolution, open reading frame length increased, necessitating mechanisms for enhanced translation fidelity. Indeed, eukaryal ribosomes are more accurate than bacterial counterparts, despite their virtually identical, conserved active centers. During the evolution of eukaryotic organisms ribosome expansions at the rRNA and protein level occurred, which potentially increases the options for translation regulation and cotranslational events. Here we tested the hypothesis that ribosomal RNA expansions can modulate the core function of the ribosome, faithful protein synthesis. We demonstrate that a short expansion segment present in all eukaryotes' small subunit, ES7S, is crucial for accurate protein synthesis as its presence adjusts codon-specific velocities and guarantees high levels of cognate tRNA selection. Deletion of ES7S in yeast enhances mistranslation and causes protein destabilization and aggregation, dramatically reducing cellular fitness. Removal of ES7S did not alter ribosome architecture but altered the structural dynamics of inter-subunit bridges thus affecting A-tRNA selection. Exchanging the yeast ES7S sequence with the human ES7S increases accuracy whereas shortening causes the opposite effect. Our study demonstrates that ES7S provided eukaryal ribosomes with higher accuracy without perturbing the structurally conserved decoding center.
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Affiliation(s)
- Robert Rauscher
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Cristian Eggers
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Lyudmila Dimitrova-Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Vaishnavi Shankar
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Alessia Rosina
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Marina Cristodero
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Sebastian A Leidel
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Norbert Polacek
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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31
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Lorenzo-Orts L, Pauli A. The molecular mechanisms underpinning maternal mRNA dormancy. Biochem Soc Trans 2024; 52:861-871. [PMID: 38477334 PMCID: PMC11088918 DOI: 10.1042/bst20231122] [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: 12/14/2023] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024]
Abstract
A large number of mRNAs of maternal origin are produced during oogenesis and deposited in the oocyte. Since transcription stops at the onset of meiosis during oogenesis and does not resume until later in embryogenesis, maternal mRNAs are the only templates for protein synthesis during this period. To ensure that a protein is made in the right place at the right time, the translation of maternal mRNAs must be activated at a specific stage of development. Here we summarize our current understanding of the sophisticated mechanisms that contribute to the temporal repression of maternal mRNAs, termed maternal mRNA dormancy. We discuss mechanisms at the level of the RNA itself, such as the regulation of polyadenine tail length and RNA modifications, as well as at the level of RNA-binding proteins, which often block the assembly of translation initiation complexes at the 5' end of an mRNA or recruit mRNAs to specific subcellular compartments. We also review microRNAs and other mechanisms that contribute to repressing translation, such as ribosome dormancy. Importantly, the mechanisms responsible for mRNA dormancy during the oocyte-to-embryo transition are also relevant to cellular quiescence in other biological contexts.
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Affiliation(s)
- Laura Lorenzo-Orts
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Andrea Pauli
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
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32
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Huo D, Liu S, Zhang L, Yang H, Sun L. Importance of the ECM-receptor interaction for adaptive response to hypoxia based on integrated transcription and translation analysis. Mol Ecol 2024:e17352. [PMID: 38624130 DOI: 10.1111/mec.17352] [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: 05/25/2023] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
Low dissolved oxygen (LO) conditions represent a major environmental challenge to marine life, especially benthic animals. For these organisms, drastic declines in oxygen availability (hypoxic events) can trigger mass mortality events and thus, act as agents of selection influencing the evolution of adaptations. In sea cucumbers, one of the most successful groups of benthic invertebrates, the exposure to hypoxic conditions triggers adaptive adjustments in metabolic rates and behaviour. It is unclear, however, how these adaptive responses are regulated and the genetic mechanisms underpinning them. Here, we addressed this knowledge gap by assessing the genetic regulation (transcription and translation) of hypoxia exposure in the sea cucumber Apostichopus japonicus. Transcriptional and translational gene expression profiles under short- and long-term exposure to low oxygen conditions are tightly associated with extracellular matrix (ECM)-receptor interaction in which laminin and collagen likely have important functions. Finding revealed that genes with a high translational efficiency (TE) had a relatively short upstream open reading frame (uORF) and a high uORF normalized minimal free energy, suggesting that sea cucumbers may respond to hypoxic stress via altered TE. These results provide valuable insights into the regulatory mechanisms that confer adaptive capacity to holothurians to survive oxygen deficiency conditions and may also be used to inform the development of strategies for mitigating the harmful effects of hypoxia on other marine invertebrates facing similar challenges.
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Affiliation(s)
- Da Huo
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
| | - Shilin Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
| | - Libin Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
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33
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Zhang L, Ruan J, Gao F, Xin Q, Che LP, Cai L, Liu Z, Kong M, Rochaix JD, Mi H, Peng L. Thylakoid protein FPB1 synergistically cooperates with PAM68 to promote CP47 biogenesis and Photosystem II assembly. Nat Commun 2024; 15:3122. [PMID: 38600073 PMCID: PMC11006888 DOI: 10.1038/s41467-024-46863-y] [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: 03/08/2023] [Accepted: 03/13/2024] [Indexed: 04/12/2024] Open
Abstract
In chloroplasts, insertion of proteins with multiple transmembrane domains (TMDs) into thylakoid membranes usually occurs in a co-translational manner. Here, we have characterized a thylakoid protein designated FPB1 (Facilitator of PsbB biogenesis1) which together with a previously reported factor PAM68 (Photosynthesis Affected Mutant68) is involved in assisting the biogenesis of CP47, a subunit of the Photosystem II (PSII) core. Analysis by ribosome profiling reveals increased ribosome stalling when the last TMD segment of CP47 emerges from the ribosomal tunnel in fpb1 and pam68. FPB1 interacts with PAM68 and both proteins coimmunoprecipitate with SecY/E and Alb3 as well as with some ribosomal components. Thus, our data indicate that, in coordination with the SecY/E translocon and the Alb3 integrase, FPB1 synergistically cooperates with PAM68 to facilitate the co-translational integration of the last two CP47 TMDs and the large loop between them into thylakoids and the PSII core complex.
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Affiliation(s)
- Lin Zhang
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Junxiang Ruan
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Fudan Gao
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Qiang Xin
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Li-Ping Che
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Lujuan Cai
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zekun Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Mengmeng Kong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences / Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai, 200032, China
| | - Jean-David Rochaix
- Departments of Molecular Biology and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Hualing Mi
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences / Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai, 200032, China
| | - Lianwei Peng
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
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34
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Zhang Q, Ye H, Liu C, Zhou H, He M, Liang X, Zhou Y, Wang K, Qin Y, Li Z, Chen M. PABP-driven secondary condensed phase within RSV inclusion bodies activates viral mRNAs for ribosomal recruitment. Virol Sin 2024; 39:235-250. [PMID: 38072230 PMCID: PMC11074649 DOI: 10.1016/j.virs.2023.12.001] [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: 11/18/2023] [Accepted: 12/03/2023] [Indexed: 01/12/2024] Open
Abstract
Inclusion bodies (IBs) of respiratory syncytial virus (RSV) are formed by liquid-liquid phase separation (LLPS) and contain internal structures termed "IB-associated granules" (IBAGs), where anti-termination factor M2-1 and viral mRNAs are concentrated. However, the mechanism of IBAG formation and the physiological function of IBAGs are unclear. Here, we found that the internal structures of RSV IBs are actual M2-1-free viral messenger ribonucleoprotein (mRNP) condensates formed by secondary LLPS. Mechanistically, the RSV nucleoprotein (N) and M2-1 interact with and recruit PABP to IBs, promoting PABP to bind viral mRNAs transcribed in IBs by RNA-recognition motif and drive secondary phase separation. Furthermore, PABP-eIF4G1 interaction regulates viral mRNP condensate composition, thereby recruiting specific translation initiation factors (eIF4G1, eIF4E, eIF4A, eIF4B and eIF4H) into the secondary condensed phase to activate viral mRNAs for ribosomal recruitment. Our study proposes a novel LLPS-regulated translation mechanism during viral infection and a novel antiviral strategy via targeting on secondary condensed phase.
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Affiliation(s)
- Qiang Zhang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Hanzhe Ye
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Cong Liu
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Haiwu Zhou
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Mingbin He
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaodong Liang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yu Zhou
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Kun Wang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yali Qin
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Zhifei Li
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Mingzhou Chen
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China; Hubei Jiangxia Laboratory, Wuhan, 430200, China.
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35
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Wu X, Yuan H, Wu Q, Gao Y, Duan T, Yang K, Huang T, Wang S, Yuan F, Lee D, Taori S, Plute T, Heissel S, Alwaseem H, Isay-Del Viscio M, Molina H, Agnihotri S, Hsu DJ, Zhang N, Rich JN. Threonine fuels glioblastoma through YRDC-mediated codon-biased translational reprogramming. NATURE CANCER 2024:10.1038/s43018-024-00748-7. [PMID: 38519786 DOI: 10.1038/s43018-024-00748-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 02/23/2024] [Indexed: 03/25/2024]
Abstract
Cancers commonly reprogram translation and metabolism, but little is known about how these two features coordinate in cancer stem cells. Here we show that glioblastoma stem cells (GSCs) display elevated protein translation. To dissect underlying mechanisms, we performed a CRISPR screen and identified YRDC as the top essential transfer RNA (tRNA) modification enzyme in GSCs. YRDC catalyzes the formation of N6-threonylcarbamoyladenosine (t6A) on ANN-decoding tRNA species (A denotes adenosine, and N denotes any nucleotide). Targeting YRDC reduced t6A formation, suppressed global translation and inhibited tumor growth both in vitro and in vivo. Threonine is an essential substrate of YRDC. Threonine accumulated in GSCs, which facilitated t6A formation through YRDC and shifted the proteome to support mitosis-related genes with ANN codon bias. Dietary threonine restriction (TR) reduced tumor t6A formation, slowed xenograft growth and augmented anti-tumor efficacy of chemotherapy and anti-mitotic therapy, providing a molecular basis for a dietary intervention in cancer treatment.
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Affiliation(s)
- Xujia Wu
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Neurosurgery, the First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangdong Translational Medicine Innovation Platform, Guangzhou, China
| | - Huairui Yuan
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Qiulian Wu
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Yixin Gao
- Department of Neurosurgery, the First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangdong Translational Medicine Innovation Platform, Guangzhou, China
| | - Tingting Duan
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Kailin Yang
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA
| | - Tengfei Huang
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Shuai Wang
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Fanen Yuan
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Derrick Lee
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Suchet Taori
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Tritan Plute
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Søren Heissel
- Proteomics Resource Center, the Rockefeller University, New York, NY, USA
| | - Hanan Alwaseem
- Proteomics Resource Center, the Rockefeller University, New York, NY, USA
| | | | - Henrik Molina
- Proteomics Resource Center, the Rockefeller University, New York, NY, USA
| | - Sameer Agnihotri
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Dennis J Hsu
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nu Zhang
- Department of Neurosurgery, the First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangdong Translational Medicine Innovation Platform, Guangzhou, China.
| | - Jeremy N Rich
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA.
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36
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St Paul M, Saibil SD, Kates M, Han S, Lien SC, Laister RC, Hezaveh K, Kloetgen A, Penny S, Guo T, Garcia-Batres C, Smith LK, Chung DC, Elford AR, Sayad A, Pinto D, Mak TW, Hirano N, McGaha T, Ohashi PS. Ex vivo activation of the GCN2 pathway metabolically reprograms T cells, leading to enhanced adoptive cell therapy. Cell Rep Med 2024; 5:101465. [PMID: 38460518 PMCID: PMC10983112 DOI: 10.1016/j.xcrm.2024.101465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/14/2023] [Accepted: 02/15/2024] [Indexed: 03/11/2024]
Abstract
The manipulation of T cell metabolism to enhance anti-tumor activity is an area of active investigation. Here, we report that activating the amino acid starvation response in effector CD8+ T cells ex vivo using the general control non-depressible 2 (GCN2) agonist halofuginone (halo) enhances oxidative metabolism and effector function. Mechanistically, we identified autophagy coupled with the CD98-mTOR axis as key downstream mediators of the phenotype induced by halo treatment. The adoptive transfer of halo-treated CD8+ T cells into tumor-bearing mice led to robust tumor control and curative responses. Halo-treated T cells synergized in vivo with a 4-1BB agonistic antibody to control tumor growth in a mouse model resistant to immunotherapy. Importantly, treatment of human CD8+ T cells with halo resulted in similar metabolic and functional reprogramming. These findings demonstrate that activating the amino acid starvation response with the GCN2 agonist halo can enhance T cell metabolism and anti-tumor activity.
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Affiliation(s)
- Michael St Paul
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Samuel D Saibil
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada.
| | - Meghan Kates
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - SeongJun Han
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Scott C Lien
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Rob C Laister
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Kebria Hezaveh
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Andreas Kloetgen
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Susanne Penny
- Human Health Therapeutics Research Centre, National Research Council Canada, Halifax, NS, Canada
| | - Tingxi Guo
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Carlos Garcia-Batres
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Logan K Smith
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Douglas C Chung
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Alisha R Elford
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Azin Sayad
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Devanand Pinto
- Human Health Therapeutics Research Centre, National Research Council Canada, Halifax, NS, Canada
| | - Tak W Mak
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Naoto Hirano
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Tracy McGaha
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Pamela S Ohashi
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada.
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37
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Zheng C, Yao H, Lu L, Li H, Zhou L, He X, Xu X, Xia H, Ding S, Yang Y, Wang X, Wu M, Xue L, Chen S, Peng X, Cheng Z, Wang Y, He G, Fu S, Keller ET, Liu S, Jiang YZ, Deng X. Dysregulated Ribosome Biogenesis Is a Targetable Vulnerability in Triple-Negative Breast Cancer: MRPS27 as a Key Mediator of the Stemness-inhibitory Effect of Lovastatin. Int J Biol Sci 2024; 20:2130-2148. [PMID: 38617541 PMCID: PMC11008279 DOI: 10.7150/ijbs.94058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/16/2024] [Indexed: 04/16/2024] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer with limited effective therapeutic options readily available. We have previously demonstrated that lovastatin, an FDA-approved lipid-lowering drug, selectively inhibits the stemness properties of TNBC. However, the intracellular targets of lovastatin in TNBC remain largely unknown. Here, we unexpectedly uncovered ribosome biogenesis as the predominant pathway targeted by lovastatin in TNBC. Lovastatin induced the translocation of ribosome biogenesis-related proteins including nucleophosmin (NPM), nucleolar and coiled-body phosphoprotein 1 (NOLC1), and the ribosomal protein RPL3. Lovastatin also suppressed the transcript levels of rRNAs and increased the nuclear protein level and transcriptional activity of p53, a master mediator of nucleolar stress. A prognostic model generated from 10 ribosome biogenesis-related genes showed outstanding performance in predicting the survival of TNBC patients. Mitochondrial ribosomal protein S27 (MRPS27), the top-ranked risky model gene, was highly expressed and correlated with tumor stage and lymph node involvement in TNBC. Mechanistically, MRPS27 knockdown inhibited the stemness properties and the malignant phenotypes of TNBC. Overexpression of MRPS27 attenuated the stemness-inhibitory effect of lovastatin in TNBC cells. Our findings reveal that dysregulated ribosome biogenesis is a targetable vulnerability and targeting MRPS27 could be a novel therapeutic strategy for TNBC patients.
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Affiliation(s)
- Chanjuan Zheng
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Hui Yao
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Lu Lu
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Hongqi Li
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Lei Zhou
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Xueyan He
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Xi Xu
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Hongzhuo Xia
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Siyu Ding
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Yiyuan Yang
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Xinyu Wang
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Muyao Wu
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Lian Xue
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Sisi Chen
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Xiaojun Peng
- Jingjie PTM BioLab Co. Ltd., Hangzhou Economic and Technological Development Area, Hangzhou, China
| | - Zhongyi Cheng
- Jingjie PTM BioLab Co. Ltd., Hangzhou Economic and Technological Development Area, Hangzhou, China
| | - Yian Wang
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Guangchun He
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Shujun Fu
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
| | - Evan T. Keller
- Department of Urology and Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Suling Liu
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Yi-zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiyun Deng
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan, China
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan, China
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Sanchez A, Ortega P, Sakhtemani R, Manjunath L, Oh S, Bournique E, Becker A, Kim K, Durfee C, Temiz NA, Chen XS, Harris RS, Lawrence MS, Buisson R. Mesoscale DNA features impact APOBEC3A and APOBEC3B deaminase activity and shape tumor mutational landscapes. Nat Commun 2024; 15:2370. [PMID: 38499542 PMCID: PMC10948877 DOI: 10.1038/s41467-024-45909-5] [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: 07/31/2023] [Accepted: 01/09/2024] [Indexed: 03/20/2024] Open
Abstract
Antiviral DNA cytosine deaminases APOBEC3A and APOBEC3B are major sources of mutations in cancer by catalyzing cytosine-to-uracil deamination. APOBEC3A preferentially targets single-stranded DNAs, with a noted affinity for DNA regions that adopt stem-loop secondary structures. However, the detailed substrate preferences of APOBEC3A and APOBEC3B have not been fully established, and the specific influence of the DNA sequence on APOBEC3A and APOBEC3B deaminase activity remains to be investigated. Here, we find that APOBEC3B also selectively targets DNA stem-loop structures, and they are distinct from those subjected to deamination by APOBEC3A. We develop Oligo-seq, an in vitro sequencing-based method to identify specific sequence contexts promoting APOBEC3A and APOBEC3B activity. Through this approach, we demonstrate that APOBEC3A and APOBEC3B deaminase activity is strongly regulated by specific sequences surrounding the targeted cytosine. Moreover, we identify the structural features of APOBEC3B and APOBEC3A responsible for their substrate preferences. Importantly, we determine that APOBEC3B-induced mutations in hairpin-forming sequences within tumor genomes differ from the DNA stem-loop sequences mutated by APOBEC3A. Together, our study provides evidence that APOBEC3A and APOBEC3B can generate distinct mutation landscapes in cancer genomes, driven by their unique substrate selectivity.
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Affiliation(s)
- Ambrocio Sanchez
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Pedro Ortega
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Ramin Sakhtemani
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lavanya Manjunath
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Sunwoo Oh
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Elodie Bournique
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Alexandrea Becker
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Kyumin Kim
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Nuri Alpay Temiz
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rémi Buisson
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA.
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA.
- Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA.
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Ipas H, Gouws EB, Abell NS, Chiou PC, Devanathan SK, Hervé S, Lee S, Mercado M, Reinsborough C, Halabelian L, Arrowsmith CH, Xhemalçe B. ChemRAP uncovers specific mRNA translation regulation via RNA 5' phospho-methylation. EMBO Rep 2024; 25:1570-1588. [PMID: 38263329 PMCID: PMC10933402 DOI: 10.1038/s44319-024-00059-z] [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: 11/27/2023] [Revised: 12/20/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024] Open
Abstract
5'-end modifications play key roles in determining RNA fates. Phospho-methylation is a noncanonical cap occurring on either 5'-PPP or 5'-P ends. We used ChemRAP, in which affinity purification of cellular proteins with chemically synthesized modified RNAs is coupled to quantitative proteomics, to identify 5'-Pme "readers". We show that 5'-Pme is directly recognized by EPRS, the central subunit of the multisynthetase complex (MSC), through its linker domain, which has previously been involved in key noncanonical EPRS and MSC functions. We further determine that the 5'-Pme writer BCDIN3D regulates the binding of EPRS to specific mRNAs, either at coding regions rich in MSC codons, or around start codons. In the case of LRPPRC (leucine-rich pentatricopeptide repeat containing), a nuclear-encoded mitochondrial protein associated with the French Canadian Leigh syndrome, BCDIN3D deficiency abolishes binding of EPRS around its mRNA start codon, increases its translation but ultimately results in LRPPRC mislocalization. Overall, our results suggest that BCDIN3D may regulate the translation of specific mRNA via RNA-5'-Pme.
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Affiliation(s)
- Hélène Ipas
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712, Austin, TX, USA
| | - Ellen B Gouws
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712, Austin, TX, USA
| | - Nathan S Abell
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712, Austin, TX, USA
| | - Po-Chin Chiou
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712, Austin, TX, USA
| | - Sravan K Devanathan
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712, Austin, TX, USA
| | - Solène Hervé
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712, Austin, TX, USA
| | - Sidae Lee
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712, Austin, TX, USA
| | - Marvin Mercado
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712, Austin, TX, USA
| | - Calder Reinsborough
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712, Austin, TX, USA
| | - Levon Halabelian
- Structural Genomics Consortium, and Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, and Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Blerta Xhemalçe
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712, Austin, TX, USA.
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40
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Katsikis PD, Ishii KJ, Schliehe C. Challenges in developing personalized neoantigen cancer vaccines. Nat Rev Immunol 2024; 24:213-227. [PMID: 37783860 DOI: 10.1038/s41577-023-00937-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2023] [Indexed: 10/04/2023]
Abstract
The recent success of cancer immunotherapies has highlighted the benefit of harnessing the immune system for cancer treatment. Vaccines have a long history of promoting immunity to pathogens and, consequently, vaccines targeting cancer neoantigens have been championed as a tool to direct and amplify immune responses against tumours while sparing healthy tissue. In recent years, extensive preclinical research and more than one hundred clinical trials have tested different strategies of neoantigen discovery and vaccine formulations. However, despite the enthusiasm for neoantigen vaccines, proof of unequivocal efficacy has remained beyond reach for the majority of clinical trials. In this Review, we focus on the key obstacles pertaining to vaccine design and tumour environment that remain to be overcome in order to unleash the true potential of neoantigen vaccines in cancer therapy.
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Affiliation(s)
- Peter D Katsikis
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands.
| | - Ken J Ishii
- Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo (IMSUT), Tokyo, Japan
- International Vaccine Design Center (vDesC), The Institute of Medical Science, The University of Tokyo (IMSUT), Tokyo, Japan
| | - Christopher Schliehe
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
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41
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Gotsmann VL, Ting MKY, Haase N, Rudorf S, Zoschke R, Willmund F. Utilizing high-resolution ribosome profiling for the global investigation of gene expression in Chlamydomonas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1614-1634. [PMID: 38047591 DOI: 10.1111/tpj.16577] [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: 06/29/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/05/2023]
Abstract
Ribosome profiling (Ribo-seq) is a powerful method for the deep analysis of translation mechanisms and regulatory circuits during gene expression. Extraction and sequencing of ribosome-protected fragments (RPFs) and parallel RNA-seq yields genome-wide insight into translational dynamics and post-transcriptional control of gene expression. Here, we provide details on the Ribo-seq method and the subsequent analysis with the unicellular model alga Chlamydomonas reinhardtii (Chlamydomonas) for generating high-resolution data covering more than 10 000 different transcripts. Detailed analysis of the ribosomal offsets on transcripts uncovers presumable transition states during translocation of elongating ribosomes within the 5' and 3' sections of transcripts and characteristics of eukaryotic translation termination, which are fundamentally distinct for chloroplast translation. In chloroplasts, a heterogeneous RPF size distribution along the coding sequence indicates specific regulatory phases during protein synthesis. For example, local accumulation of small RPFs correlates with local slowdown of psbA translation, possibly uncovering an uncharacterized regulatory step during PsbA/D1 synthesis. Further analyses of RPF distribution along specific cytosolic transcripts revealed characteristic patterns of translation elongation exemplified for the major light-harvesting complex proteins, LHCs. By providing high-quality datasets for all subcellular genomes and attaching our data to the Chlamydomonas reference genome, we aim to make ribosome profiles easily accessible for the broad research community. The data can be browsed without advanced bioinformatic background knowledge for translation output levels of specific genes and their splice variants and for monitoring genome annotation.
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Affiliation(s)
- Vincent Leon Gotsmann
- Molecular Genetics of Eukaryotes, RPTU Kaiserslautern-Landau, Paul-Ehrlich-Str. 23, 67663, Kaiserslautern, Germany
| | - Michael Kien Yin Ting
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Nadin Haase
- Institute of Cell Biology and Biophysics, Leibniz University Hanover, Herrenhäuser-Str. 2, 30419, Hanover, Germany
| | - Sophia Rudorf
- Institute of Cell Biology and Biophysics, Leibniz University Hanover, Herrenhäuser-Str. 2, 30419, Hanover, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, RPTU Kaiserslautern-Landau, Paul-Ehrlich-Str. 23, 67663, Kaiserslautern, Germany
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42
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Jowhar Z, Xu A, Venkataramanan S, Dossena F, Hoye ML, Silver DL, Floor SN, Calviello L. A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X. Mol Syst Biol 2024; 20:276-290. [PMID: 38273160 PMCID: PMC10912769 DOI: 10.1038/s44320-024-00013-0] [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: 11/27/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 01/27/2024] Open
Abstract
The road from transcription to protein synthesis is paved with many obstacles, allowing for several modes of post-transcriptional regulation of gene expression. A fundamental player in mRNA biology is DDX3X, an RNA binding protein that canonically regulates mRNA translation. By monitoring dynamics of mRNA abundance and translation following DDX3X depletion, we observe stabilization of translationally suppressed mRNAs. We use interpretable statistical learning models to uncover GC content in the coding sequence as the major feature underlying RNA stabilization. This result corroborates GC content-related mRNA regulation detectable in other studies, including hundreds of ENCODE datasets and recent work focusing on mRNA dynamics in the cell cycle. We provide further evidence for mRNA stabilization by detailed analysis of RNA-seq profiles in hundreds of samples, including a Ddx3x conditional knockout mouse model exhibiting cell cycle and neurogenesis defects. Our study identifies a ubiquitous feature underlying mRNA regulation and highlights the importance of quantifying multiple steps of the gene expression cascade, where RNA abundance and protein production are often uncoupled.
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Affiliation(s)
- Ziad Jowhar
- Department of Cell and Tissue Biology, UCSF, San Francisco, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, 94158, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Albert Xu
- Department of Cell and Tissue Biology, UCSF, San Francisco, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, 94158, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, 94158, USA
| | | | | | - Mariah L Hoye
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
- Department of Cell Biology, Duke University Medical Center, Durham, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, USA
- Department of Neurobiology, Duke University Medical Center, Durham, USA
- Duke Institute for Brain Sciences, Duke University Medical Center, Durham, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, UCSF, San Francisco, USA.
- Helen Diller Family Comprehensive Cancer Center, San Francisco, USA.
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Fitzsimmons CM, Mandler MD, Lunger JC, Chan D, Maligireddy S, Schmiechen A, Gamage S, Link C, Jenkins L, Chan K, Andresson T, Crooks D, Meier J, Linehan W, Batista P. Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma. NAR Cancer 2024; 6:zcae004. [PMID: 38328795 PMCID: PMC10849186 DOI: 10.1093/narcan/zcae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Metabolic reprogramming is a hallmark of cancer that facilitates changes in many adaptive biological processes. Mutations in the tricarboxylic acid cycle enzyme fumarate hydratase (FH) lead to fumarate accumulation and cause hereditary leiomyomatosis and renal cell cancer (HLRCC). HLRCC is a rare, inherited disease characterized by the development of non-cancerous smooth muscle tumors of the uterus and skin, and an increased risk of an aggressive form of kidney cancer. Fumarate has been shown to inhibit 2-oxoglutarate-dependent dioxygenases (2OGDDs) involved in the hydroxylation of HIF1α, as well as in DNA and histone demethylation. However, the link between fumarate accumulation and changes in RNA post-transcriptional modifications has not been defined. Here, we determine the consequences of fumarate accumulation on the activity of different members of the 2OGDD family targeting RNA modifications. By evaluating multiple RNA modifications in patient-derived HLRCC cell lines, we show that mutation of FH selectively affects the levels of N6-methyladenosine (m6A), while the levels of 5-formylcytosine (f5C) in mitochondrial tRNA are unaffected. This supports the hypothesis of a differential impact of fumarate accumulation on distinct RNA demethylases. The observation that metabolites modulate specific subsets of RNA-modifying enzymes offers new insights into the intersection between metabolism and the epitranscriptome.
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Affiliation(s)
- Christina M Fitzsimmons
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mariana D Mandler
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Judith C Lunger
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dalen Chan
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Siddhardha S Maligireddy
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra C Schmiechen
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Supuni Thalalla Gamage
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Courtney Link
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - King Chan
- Protein Characterization Laboratory, Research Technology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21701, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Research Technology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21701, USA
| | - Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pedro J Batista
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Cao J, Tan X, Cheng X. Over-expression of the BnVIT-L2 gene improves the lateral root development and biofortification under iron stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108501. [PMID: 38452450 DOI: 10.1016/j.plaphy.2024.108501] [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: 12/10/2023] [Revised: 02/17/2024] [Accepted: 03/02/2024] [Indexed: 03/09/2024]
Abstract
The vacuolar iron transporter (VIT) family is responsible for absorbing and storing iron ions in vacuoles. Here, the BnVIT-L2 gene from Brassica napus has been cloned for the first time and was found to be expressed in multiple tissues and organs, induced by iron stress. The BnVIT-L2 protein is located in vacuolar membranes and has the ability to bind both iron and other bivalent metal ions. Over-expression of the BnVIT-L2 gene increased lateral root number and main root length, as well as chlorophyll and iron content in transgenic Arabidopsis plants (BnVIT-L2/At) exposed to iron stress, compared to wild type Col-0. Furthermore, over-expression of this gene improved the adaptability of transgenic B. napus plants (BnVIT-L2-OE) under iron stress. The regulation of plant tolerance under iron stress by BnVIT-L2 gene may involve in the signal of reactive oxygen species (ROS), as suggested by Ribosome profiling sequencing (Ribo-seq). This study provides a reference for investigating plant growth and biofortification under iron stress through the BnVIT-L2 gene.
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Affiliation(s)
- Jun Cao
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
| | - Xiaona Tan
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xiuzhu Cheng
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
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Prusty AB, Hirmer A, Sierra-Delgado JA, Huber H, Guenther UP, Schlosser A, Dybkov O, Yildirim E, Urlaub H, Meyer KC, Jablonka S, Erhard F, Fischer U. RNA helicase IGHMBP2 regulates THO complex to ensure cellular mRNA homeostasis. Cell Rep 2024; 43:113802. [PMID: 38368610 DOI: 10.1016/j.celrep.2024.113802] [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: 08/03/2023] [Revised: 12/21/2023] [Accepted: 01/31/2024] [Indexed: 02/20/2024] Open
Abstract
RNA helicases constitute a large protein family implicated in cellular RNA homeostasis and disease development. Here, we show that the RNA helicase IGHMBP2, linked to the neuromuscular disorder spinal muscular atrophy with respiratory distress type 1 (SMARD1), associates with polysomes and impacts translation of mRNAs containing short, GC-rich, and structured 5' UTRs. The absence of IGHMBP2 causes ribosome stalling at the start codon of target mRNAs, leading to reduced translation efficiency. The main mRNA targets of IGHMBP2-mediated regulation encode for components of the THO complex (THOC), linking IGHMBP2 to mRNA production and nuclear export. Accordingly, failure of IGHMBP2 regulation of THOC causes perturbations of the transcriptome and its encoded proteome, and ablation of THOC subunits phenocopies these changes. Thus, IGHMBP2 is an upstream regulator of THOC. Of note, IGHMBP2-dependent regulation of THOC is also observed in astrocytes derived from patients with SMARD1 disease, suggesting that deregulated mRNA metabolism contributes to SMARD1 etiology and may enable alternative therapeutic avenues.
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Affiliation(s)
| | - Anja Hirmer
- Department of Biochemistry 1, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | | | - Hannes Huber
- Department of Biochemistry 1, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | | | - Andreas Schlosser
- Rudolf-Virchow-Center, Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
| | - Olexandr Dybkov
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Ezgi Yildirim
- Institute of Clinical Neurobiology, University Hospital Würzburg, 97078 Würzburg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Department of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany; Göttingen Center for Molecular Biosciences, University of Göttingen, Göttingen, Germany
| | - Kathrin C Meyer
- Nationwide Children's Hospital, Center for Gene Therapy, Columbus, OH 43205, USA; Department of Pediatrics, Ohio State University, Columbus, OH 43210, USA
| | - Sibylle Jablonka
- Institute of Clinical Neurobiology, University Hospital Würzburg, 97078 Würzburg, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, 97078 Würzburg, Germany; Faculty for Informatics and Data Science, University of Regensburg, 93053 Regensburg, Germany.
| | - Utz Fischer
- Department of Biochemistry 1, Biocenter, University of Würzburg, 97074 Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany.
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Jia X, He X, Huang C, Li J, Dong Z, Liu K. Protein translation: biological processes and therapeutic strategies for human diseases. Signal Transduct Target Ther 2024; 9:44. [PMID: 38388452 PMCID: PMC10884018 DOI: 10.1038/s41392-024-01749-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Protein translation is a tightly regulated cellular process that is essential for gene expression and protein synthesis. The deregulation of this process is increasingly recognized as a critical factor in the pathogenesis of various human diseases. In this review, we discuss how deregulated translation can lead to aberrant protein synthesis, altered cellular functions, and disease progression. We explore the key mechanisms contributing to the deregulation of protein translation, including functional alterations in translation factors, tRNA, mRNA, and ribosome function. Deregulated translation leads to abnormal protein expression, disrupted cellular signaling, and perturbed cellular functions- all of which contribute to disease pathogenesis. The development of ribosome profiling techniques along with mass spectrometry-based proteomics, mRNA sequencing and single-cell approaches have opened new avenues for detecting diseases related to translation errors. Importantly, we highlight recent advances in therapies targeting translation-related disorders and their potential applications in neurodegenerative diseases, cancer, infectious diseases, and cardiovascular diseases. Moreover, the growing interest lies in targeted therapies aimed at restoring precise control over translation in diseased cells is discussed. In conclusion, this comprehensive review underscores the critical role of protein translation in disease and its potential as a therapeutic target. Advancements in understanding the molecular mechanisms of protein translation deregulation, coupled with the development of targeted therapies, offer promising avenues for improving disease outcomes in various human diseases. Additionally, it will unlock doors to the possibility of precision medicine by offering personalized therapies and a deeper understanding of the molecular underpinnings of diseases in the future.
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Affiliation(s)
- Xuechao Jia
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Xinyu He
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Chuntian Huang
- Department of Pathology and Pathophysiology, Henan University of Chinese Medicine, Zhengzhou, Henan, 450000, China
| | - Jian Li
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China.
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou, Henan, 450052, China.
- Research Center for Basic Medicine Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan, 450000, China.
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China.
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou, Henan, 450052, China.
- Research Center for Basic Medicine Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, Henan, 450000, China.
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Lee PJ, Soares AR, Sun Y, Fai C, Picciotto MR, Guo JU. Alternative translation initiation produces synaptic organizer proteoforms with distinct localization and functions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.16.580719. [PMID: 38405936 PMCID: PMC10888845 DOI: 10.1101/2024.02.16.580719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
While previous studies suggest that many mRNAs contain more than one translation initiation site (TIS), the biological significance of most alternative TISs and their corresponding protein isoforms (proteoforms) remains undetermined. Here we show that alternative translation initiation at a CUG and an AUG TIS in neuronal pentraxin receptor (NPR) mRNA produces two proteoforms, and their relative abundance is regulated by both neuronal activity as well as an adjacent RNA secondary structure. Downstream AUG initiation transforms the N-terminal transmembrane domain into a signal peptide, thereby converting NPR to a secreted factor sufficient to promote synaptic clustering of AMPA-type glutamate receptors. Changing the relative proteoform ratio, but not the overall NPR abundance reduces AMPA receptor in parvalbumin (PV)-positive interneurons and induces changes in learning behaviors in mice. In addition to NPR, N-terminal extensions of C1q-like synaptic organizers, mediated by upstream AUU start codons, anchor these otherwise secreted factors to the membrane. Thus, our results uncovered the plasticity of N-terminal signal sequences regulated by alternative TIS usage as a widespread mechanism to diversify protein localization and functions.
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Affiliation(s)
- Paul Jongseo Lee
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Alexa R. Soares
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06508, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Yu Sun
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Caroline Fai
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06508, USA
| | - Marina R. Picciotto
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06508, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Junjie U. Guo
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
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48
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Nie X, Fan J, Dai B, Wen Z, Li H, Chen C, Wang DW. LncRNA CHKB-DT Downregulation Enhances Dilated Cardiomyopathy Through ALDH2. Circ Res 2024; 134:425-441. [PMID: 38299365 DOI: 10.1161/circresaha.123.323428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/18/2024] [Indexed: 02/02/2024]
Abstract
BACKGROUND Human cardiac long noncoding RNA (lncRNA) profiles in patients with dilated cardiomyopathy (DCM) were previously analyzed, and the long noncoding RNA CHKB (choline kinase beta) divergent transcript (CHKB-DT) levels were found to be mostly downregulated in the heart. In this study, the function of CHKB-DT in DCM was determined. METHODS Long noncoding RNA expression levels in the human heart tissues were measured via quantitative reverse transcription-polymerase chain reaction and in situ hybridization assays. A CHKB-DT heterozygous or homozygous knockout mouse model was generated using the clustered regularly interspaced palindromic repeat (CRISPR)/CRISPR-associated protein 9 system, and the adeno-associated virus with a cardiac-specific promoter was used to deliver the RNA in vivo. Sarcomere shortening was performed to assess the primary cardiomyocyte contractility. The Seahorse XF cell mitochondrial stress test was performed to determine the energy metabolism and ATP production. Furthermore, the underlying mechanisms were explored using quantitative proteomics, ribosome profiling, RNA antisense purification assays, mass spectrometry, RNA pull-down, luciferase assay, RNA-fluorescence in situ hybridization, and Western blotting. RESULTS CHKB-DT levels were remarkably decreased in patients with DCM and mice with transverse aortic constriction-induced heart failure. Heterozygous knockout of CHKB-DT in cardiomyocytes caused cardiac dilation and dysfunction and reduced the contractility of primary cardiomyocytes. Moreover, CHKB-DT heterozygous knockout impaired mitochondrial function and decreased ATP production as well as cardiac energy metabolism. Mechanistically, ALDH2 (aldehyde dehydrogenase 2) was a direct target of CHKB-DT. CHKB-DT physically interacted with the mRNA of ALDH2 and fused in sarcoma (FUS) through the GGUG motif. CHKB-DT knockdown aggravated ALDH2 mRNA degradation and 4-HNE (4-hydroxy-2-nonenal) production, whereas overexpression of CHKB-DT reversed these molecular changes. Furthermore, restoring ALDH2 expression in CHKB-DT+/- mice alleviated cardiac dilation and dysfunction. CONCLUSIONS CHKB-DT is significantly downregulated in DCM. CHKB-DT acts as an energy metabolism-associated long noncoding RNA and represents a promising therapeutic target against DCM.
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MESH Headings
- Animals
- Humans
- Mice
- Adenosine Triphosphate/metabolism
- Aldehyde Dehydrogenase, Mitochondrial/genetics
- Aldehyde Dehydrogenase, Mitochondrial/metabolism
- Cardiomyopathy, Dilated/genetics
- Cardiomyopathy, Dilated/metabolism
- Down-Regulation
- In Situ Hybridization, Fluorescence
- Mice, Knockout
- Mitochondria, Heart/metabolism
- Myocytes, Cardiac/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
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Affiliation(s)
- Xiang Nie
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College (X.N., J.F., B.D., Z.W., H.L., C.C., D.W.W.), Huazhong University of Science and Technology, Wuhan, China
| | - Jiahui Fan
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College (X.N., J.F., B.D., Z.W., H.L., C.C., D.W.W.), Huazhong University of Science and Technology, Wuhan, China
| | - Beibei Dai
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College (X.N., J.F., B.D., Z.W., H.L., C.C., D.W.W.), Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders (B.D., Z.W., H.L.), Huazhong University of Science and Technology, Wuhan, China
| | - Zheng Wen
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College (X.N., J.F., B.D., Z.W., H.L., C.C., D.W.W.), Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders (B.D., Z.W., H.L.), Huazhong University of Science and Technology, Wuhan, China
| | - Huaping Li
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College (X.N., J.F., B.D., Z.W., H.L., C.C., D.W.W.), Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders (B.D., Z.W., H.L.), Huazhong University of Science and Technology, Wuhan, China
| | - Chen Chen
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College (X.N., J.F., B.D., Z.W., H.L., C.C., D.W.W.), Huazhong University of Science and Technology, Wuhan, China
| | - Dao Wen Wang
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College (X.N., J.F., B.D., Z.W., H.L., C.C., D.W.W.), Huazhong University of Science and Technology, Wuhan, China
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49
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Valdivia-Francia F, Sendoel A. No country for old methods: New tools for studying microproteins. iScience 2024; 27:108972. [PMID: 38333695 PMCID: PMC10850755 DOI: 10.1016/j.isci.2024.108972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024] Open
Abstract
Microproteins encoded by small open reading frames (sORFs) have emerged as a fascinating frontier in genomics. Traditionally overlooked due to their small size, recent technological advancements such as ribosome profiling, mass spectrometry-based strategies and advanced computational approaches have led to the annotation of more than 7000 sORFs in the human genome. Despite the vast progress, only a tiny portion of these microproteins have been characterized and an important challenge in the field lies in identifying functionally relevant microproteins and understanding their role in different cellular contexts. In this review, we explore the recent advancements in sORF research, focusing on the new methodologies and computational approaches that have facilitated their identification and functional characterization. Leveraging these new tools hold great promise for dissecting the diverse cellular roles of microproteins and will ultimately pave the way for understanding their role in the pathogenesis of diseases and identifying new therapeutic targets.
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Affiliation(s)
- Fabiola Valdivia-Francia
- University of Zurich, Institute for Regenerative Medicine (IREM), Wagistrasse 12, 8952 Schlieren-Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich/ ETH Zurich, Schlieren-Zurich, Switzerland
| | - Ataman Sendoel
- University of Zurich, Institute for Regenerative Medicine (IREM), Wagistrasse 12, 8952 Schlieren-Zurich, Switzerland
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50
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Liboy-Lugo JM, Espinoza CA, Sheu-Gruttadauria J, Park JE, Xu A, Jowhar Z, Gao AL, Carmona-Negrón JA, Wittmann T, Jura N, Floor SN. Protein-protein interactions with G3BPs drive stress granule condensation and gene expression changes under cellular stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579149. [PMID: 38370785 PMCID: PMC10871250 DOI: 10.1101/2024.02.06.579149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Stress granules (SGs) are macromolecular assemblies that form under cellular stress. Formation of these condensates is driven by the condensation of RNA and RNA-binding proteins such as G3BPs. G3BPs condense into SGs following stress-induced translational arrest. Three G3BP paralogs (G3BP1, G3BP2A, and G3BP2B) have been identified in vertebrates. However, the contribution of different G3BP paralogs to stress granule formation and stress-induced gene expression changes is incompletely understood. Here, we identified key residues for G3BP condensation such as V11. This conserved amino acid is required for formation of the G3BP-Caprin-1 complex, hence promoting SG assembly. Total RNA sequencing and ribosome profiling revealed that disruption of G3BP condensation corresponds to changes in mRNA levels and ribosome engagement during the integrated stress response (ISR). Moreover, we found that G3BP2B preferentially condenses and promotes changes in mRNA expression under endoplasmic reticulum (ER) stress. Together, this work suggests that stress granule assembly promotes changes in gene expression under cellular stress, which is differentially regulated by G3BP paralogs.
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Affiliation(s)
- José M Liboy-Lugo
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - Carla A Espinoza
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, California, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA
| | - Jessica Sheu-Gruttadauria
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA
| | - Jesslyn E Park
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA
| | - Albert Xu
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA
| | - Ziad Jowhar
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - Angela L Gao
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - José A Carmona-Negrón
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, USA
- Department of Chemistry, University of Puerto Rico, Mayaguez, Puerto Rico, USA
| | - Torsten Wittmann
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
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