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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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2
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Perriera R, Vitale E, Pibiri I, Carollo PS, Ricci D, Corrao F, Fiduccia I, Melfi R, Zizzo MG, Tutone M, Pace A, Lentini L. Readthrough Approach Using NV Translational Readthrough-Inducing Drugs (TRIDs): A Study of the Possible Off-Target Effects on Natural Termination Codons (NTCs) on TP53 and Housekeeping Gene Expression. Int J Mol Sci 2023; 24:15084. [PMID: 37894764 PMCID: PMC10606485 DOI: 10.3390/ijms242015084] [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: 08/11/2023] [Revised: 09/11/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
Nonsense mutations cause several genetic diseases such as cystic fibrosis, Duchenne muscular dystrophy, β-thalassemia, and Shwachman-Diamond syndrome. These mutations induce the formation of a premature termination codon (PTC) inside the mRNA sequence, resulting in the synthesis of truncated polypeptides. Nonsense suppression therapy mediated by translational readthrough-inducing drugs (TRIDs) is a promising approach to correct these genetic defects. TRIDs generate a ribosome miscoding of the PTC named "translational readthrough" and restore the synthesis of full-length and potentially functional proteins. The new oxadiazole-core TRIDs NV848, NV914, and NV930 (NV) showed translational readthrough activity in nonsense-related in vitro systems. In this work, the possible off-target effect of NV molecules on natural termination codons (NTCs) was investigated. Two different in vitro approaches were used to assess if the NV molecule treatment induces NTC readthrough: (1) a study of the translational-induced p53 molecular weight and functionality; (2) the evaluation of two housekeeping proteins' (Cys-C and β2M) molecular weights. Our results showed that the treatment with NV848, NV914, or NV930 did not induce any translation alterations in both experimental systems. The data suggested that NV molecules have a specific action for the PTCs and an undetectable effect on the NTCs.
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Affiliation(s)
| | | | - Ivana Pibiri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.P.); (E.V.); (P.S.C.); (D.R.); (F.C.); (I.F.); (R.M.); (M.G.Z.); (M.T.); (A.P.)
| | | | | | | | | | | | | | | | | | - Laura Lentini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.P.); (E.V.); (P.S.C.); (D.R.); (F.C.); (I.F.); (R.M.); (M.G.Z.); (M.T.); (A.P.)
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3
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Li J, Querl L, Coban I, Salinas G, Krebber H. Surveillance of 3' mRNA cleavage during transcription termination requires CF IB/Hrp1. Nucleic Acids Res 2023; 51:8758-8773. [PMID: 37351636 PMCID: PMC10484732 DOI: 10.1093/nar/gkad530] [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: 09/30/2022] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023] Open
Abstract
CF IB/Hrp1 is part of the cleavage and polyadenylation factor (CPF) and cleavage factor (CF) complex (CPF-CF), which is responsible for 3' cleavage and maturation of pre-mRNAs. Although Hrp1 supports this process, its presence is not essential for the cleavage event. Here, we show that the main function of Hrp1 in the CPF-CF complex is the nuclear mRNA quality control of proper 3' cleavage. As such, Hrp1 acts as a nuclear mRNA retention factor that hinders transcripts from leaving the nucleus until processing is completed. Only after proper 3' cleavage, which is sensed through contacting Rna14, Hrp1 recruits the export receptor Mex67, allowing nuclear export. Consequently, its absence results in the leakage of elongated mRNAs into the cytoplasm. If cleavage is defective, the presence of Hrp1 on the mRNA retains these elongated transcripts until they are eliminated by the nuclear exosome. Together, we identify Hrp1 as the key quality control factor for 3' cleavage.
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Affiliation(s)
- Jing Li
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, D-37075 Göttingen, Germany
| | - Luisa Querl
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, D-37075 Göttingen, Germany
| | - Ivo Coban
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, D-37075 Göttingen, Germany
| | - Gabriela Salinas
- NGS-Serviceeinrichtung für Integrative Genomik (NIG), Institut für Humangenetik, Universitätsmedizin Göttingen, D-37075 Göttingen, Germany
| | - Heike Krebber
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, D-37075 Göttingen, Germany
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4
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Querl L, Krebber H. The DEAD-box RNA helicase Dbp5 is a key protein that couples multiple steps in gene expression. Biol Chem 2023; 404:845-850. [PMID: 37436777 DOI: 10.1515/hsz-2023-0130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/03/2023] [Indexed: 07/13/2023]
Abstract
Cell viability largely depends on the surveillance of mRNA export and translation. Upon pre-mRNA processing and nuclear quality control, mature mRNAs are exported into the cytoplasm via Mex67-Mtr2 attachment. At the cytoplasmic site of the nuclear pore complex, the export receptor is displaced by the action of the DEAD-box RNA helicase Dbp5. Subsequent quality control of the open reading frame requires translation. Our studies suggest an involvement of Dbp5 in cytoplasmic no-go-and non-stop decay. Most importantly, we have also identified a key function for Dbp5 in translation termination, which identifies this helicase as a master regulator of mRNA expression.
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Affiliation(s)
- Luisa Querl
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Heike Krebber
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
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5
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Zhang D, Zhu L, Wang F, Li P, Wang Y, Gao Y. Molecular mechanisms of eukaryotic translation fidelity and their associations with diseases. Int J Biol Macromol 2023; 242:124680. [PMID: 37141965 DOI: 10.1016/j.ijbiomac.2023.124680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]
Abstract
Converting genetic information into functional proteins is a complex, multi-step process, with each step being tightly regulated to ensure the accuracy of translation, which is critical to cellular health. In recent years, advances in modern biotechnology, especially the development of cryo-electron microscopy and single-molecule techniques, have enabled a clearer understanding of the mechanisms of protein translation fidelity. Although there are many studies on the regulation of protein translation in prokaryotes, and the basic elements of translation are highly conserved in prokaryotes and eukaryotes, there are still great differences in the specific regulatory mechanisms. This review describes how eukaryotic ribosomes and translation factors regulate protein translation and ensure translation accuracy. However, a certain frequency of translation errors does occur in translation, so we describe diseases that arise when the rate of translation errors reaches or exceeds a threshold of cellular tolerance.
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Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
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6
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Manjunath LE, Singh A, Som S, Eswarappa SM. Mammalian proteome expansion by stop codon readthrough. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1739. [PMID: 35570338 DOI: 10.1002/wrna.1739] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 04/11/2022] [Accepted: 04/16/2022] [Indexed: 12/20/2022]
Abstract
Recognition of a stop codon by translation machinery as a sense codon results in translational readthrough instead of termination. This recoding process, termed stop codon readthrough (SCR) or translational readthrough, is found in all domains of life including mammals. The context of the stop codon, local mRNA topology, and molecules that interact with the mRNA region downstream of the stop codon determine SCR. The products of SCR can have localization, stability, and function different from those of the canonical isoforms. In this review, we discuss how recent technological and computational advances have increased our understanding of the SCR process in the mammalian system. Based on the known molecular events that occur during SCR of multiple mRNAs, we propose transient molecular roadblocks on an mRNA downstream of the stop codon as a possible mechanism for the induction of SCR. We argue, with examples, that the insights gained from the natural SCR events can guide us to develop novel strategies for the treatment of diseases caused by premature stop codons. This article is categorized under: Translation > Regulation.
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Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Saubhik Som
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
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7
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Shi N, Tong L, Lin H, Zheng Z, Zhang H, Dong L, Yang Y, Shen Y, Xia Q. Optimizing eRF1 to Enable the Genetic Encoding of Three Distinct Noncanonical Amino Acids in Mammalian Cells. Adv Biol (Weinh) 2022; 6:e2200092. [PMID: 35818694 DOI: 10.1002/adbi.202200092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/06/2022] [Indexed: 01/28/2023]
Abstract
Site-specific incorporation of distinct noncanonical amino acids (ncAAs) into proteins via genetic code expansion in mammalian cells represents a new avenue for protein engineering. Reassigning three TAGs with the same ncAA in mammalian cells has previously been achieved using translational machinery. However, simultaneous recoding of three nonsense codons with distinct ncAAs in mammalian cells remains a challenge due to low incorporation efficiencies. Here, three optimized aaRS/tRNA pairs (i.e., the E. coli-derived tyrosyl (EcTyr)/tRNAUUA , E. coli-derived leucyl (EcLeu)/tRNACUA , and Methanosarcina mazei pyrrolysyl (MmPyl)/tRNAUCA pairs) are screened for ncAA incorporation. Furthermore, introduced combinations of eukaryotic release factor 1 (eRF1) mutants (E55R, E55D, N129D, and Y125F) significantly improve the encoding efficiency of the three premature stop codons' sites from 0.78% to 11.6%. Thus, site-specific incorporation of three distinct ncAAs into a single protein is achieved in this study. This work markedly expands the potential for multiple site-specific protein modifications within mammalian cells, thereby facilitating new in vivo applications.
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Affiliation(s)
- Ningning Shi
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Le Tong
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Haishuang Lin
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Zhetao Zheng
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Haoran Zhang
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Liangzhen Dong
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yuelin Yang
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yuxuan Shen
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Qing Xia
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
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Embree CM, Abu-Alhasan R, Singh G. Features and factors that dictate if terminating ribosomes cause or counteract nonsense-mediated mRNA decay. J Biol Chem 2022; 298:102592. [PMID: 36244451 PMCID: PMC9661723 DOI: 10.1016/j.jbc.2022.102592] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a quality control pathway in eukaryotes that continuously monitors mRNA transcripts to ensure truncated polypeptides are not produced. The expression of many normal mRNAs that encode full-length polypeptides is also regulated by this pathway. Such transcript surveillance by NMD is intimately linked to translation termination. When a ribosome terminates translation at a normal termination codon, NMD is not activated, and mRNA can undergo repeated rounds of translation. On the other hand, when translation termination is deemed abnormal, such as that on a premature termination codon, it leads to a series of poorly understood events involving the NMD pathway, which destabilizes the transcript. In this review, we summarize our current understanding of how the NMD machinery interfaces with the translation termination factors to initiate NMD. We also discuss a variety of cis-acting sequence contexts and trans-acting factors that can cause readthrough, ribosome reinitiation, or ribosome frameshifting at stop codons predicted to induce NMD. These alternative outcomes can lead to the ribosome translating downstream of such stop codons and hence the transcript escaping NMD. NMD escape via these mechanisms can have wide-ranging implications on human health, from being exploited by viruses to hijack host cell systems to being harnessed as potential therapeutic possibilities to treat genetic diseases.
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Affiliation(s)
- Caleb M Embree
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio USA
| | - Rabab Abu-Alhasan
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio USA
| | - Guramrit Singh
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio USA.
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9
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Huang C, Zhao Q, Zhou X, Huang R, Duan Y, Haybaeck J, Yang Z. The progress of protein synthesis factors eIFs, eEFs and eRFs in inflammatory bowel disease and colorectal cancer pathogenesis. Front Oncol 2022; 12:898966. [DOI: 10.3389/fonc.2022.898966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 10/14/2022] [Indexed: 11/13/2022] Open
Abstract
Colorectal diseases are threatening human health, especially inflammatory bowel disease (IBD) and colorectal cancer (CRC). IBD is a group of chronic, recurrent and incurable disease, which may affect the entire gastrointestinal tract, increasing the risk of CRC. Eukaryotic gene expression is a complicated process, which is mainly regulated at the level of gene transcription and mRNA translation. Protein translation in tissue is associated with a sequence of steps, including initiation, elongation, termination and recycling. Abnormal regulation of gene expression is the key to the pathogenesis of CRC. In the early stages of cancer, it is vital to identify new diagnostic and therapeutic targets and biomarkers. This review presented current knowledge on aberrant expression of eIFs, eEFs and eRFs in colorectal diseases. The current findings of protein synthesis on colorectal pathogenesis showed that eIFs, eEFs and eRFs may be potential targets for CRC treatment.
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10
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Abstract
Studies on biological functions of RNA modifications such as N6-methyladenosine (m6A) in mRNA have sprung up in recent years, while the roles of N1-methyladenosine (m1A) in cancer progression remain largely unknown. We find m1A demethylase ALKBH3 can regulate the glycolysis of cancer cells via a demethylation activity dependent manner. Specifically, sequencing and functional studies confirm that ATP5D, one of the most important subunit of adenosine 5'-triphosphate synthase, is involved in m1A demethylase ALKBH3-regulated glycolysis of cancer cells. The m1A modified A71 at the exon 1 of ATP5D negatively regulates its translation elongation via increasing the binding with YTHDF1/eRF1 complex, which facilitates the release of message RNA (mRNA) from ribosome complex. m1A also regulates mRNA stability of E2F1, which directly binds with ATP5D promoter to initiate its transcription. Targeted specific demethylation of ATP5D m1A by dm1ACRISPR system can significantly increase the expression of ATP5D and glycolysis of cancer cells. In vivo data confirm the roles of m1A/ATP5D in tumor growth and cancer progression. Our study reveals a crosstalk of mRNA m1A modification and cell metabolism, which expands the understanding of such interplays that are essential for cancer therapeutic application.
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11
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Inagaki N. Processing of D1 Protein: A Mysterious Process Carried Out in Thylakoid Lumen. Int J Mol Sci 2022; 23:ijms23052520. [PMID: 35269663 PMCID: PMC8909930 DOI: 10.3390/ijms23052520] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 11/16/2022] Open
Abstract
In oxygenic photosynthetic organisms, D1 protein, a core subunit of photosystem II (PSII), displays a rapid turnover in the light, in which D1 proteins are distinctively damaged and immediately removed from the PSII. In parallel, as a repair process, D1 proteins are synthesized and simultaneously assembled into the PSII. On this flow, the D1 protein is synthesized as a precursor with a carboxyl-terminal extension, and the D1 processing is defined as a step for proteolytic removal of the extension by a specific protease, CtpA. The D1 processing plays a crucial role in appearance of water-oxidizing capacity of PSII, because the main chain carboxyl group at carboxyl-terminus of the D1 protein, exposed by the D1 processing, ligates a manganese and a calcium atom in the Mn4CaO5-cluster, a special equipment for water-oxidizing chemistry of PSII. This review focuses on the D1 processing and discusses it from four angles: (i) Discovery of the D1 processing and recognition of its importance: (ii) Enzyme involved in the D1 processing: (iii) Efforts for understanding significance of the D1 processing: (iv) Remaining mysteries in the D1 processing. Through the review, I summarize the current status of our knowledge on and around the D1 processing.
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Affiliation(s)
- Noritoshi Inagaki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba 305-8518, Japan
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12
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Karki P, Carney TD, Maracci C, Yatsenko AS, Shcherbata HR, Rodnina MV. Tissue-specific regulation of translational readthrough tunes functions of the traffic jam transcription factor. Nucleic Acids Res 2021; 50:6001-6019. [PMID: 34897510 PMCID: PMC9226519 DOI: 10.1093/nar/gkab1189] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/05/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Translational readthrough (TR) occurs when the ribosome decodes a stop codon as a sense codon, resulting in two protein isoforms synthesized from the same mRNA. TR has been identified in several eukaryotic organisms; however, its biological significance and mechanism remain unclear. Here, we quantify TR of several candidate genes in Drosophila melanogaster and characterize the regulation of TR in the large Maf transcription factor Traffic jam (Tj). Using CRISPR/Cas9-generated mutant flies, we show that the TR-generated Tj isoform is expressed in a subset of neural cells of the central nervous system and is excluded from the somatic cells of gonads. Control of TR in Tj is critical for preservation of neuronal integrity and maintenance of reproductive health. The tissue-specific distribution of a release factor splice variant, eRF1H, plays a critical role in modulating differential TR of leaky stop codon contexts. Fine-tuning of gene regulatory functions of transcription factors by TR provides a potential mechanism for cell-specific regulation of gene expression.
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Affiliation(s)
- Prajwal Karki
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Travis D Carney
- Gene Expression and Signaling Group, Institute of Cell Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Andriy S Yatsenko
- Gene Expression and Signaling Group, Institute of Cell Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Halyna R Shcherbata
- Gene Expression and Signaling Group, Institute of Cell Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
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13
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Del Toro N, Lessard F, Bouchard J, Mobasheri N, Guillon J, Igelmann S, Tardif S, Buffard T, Bourdeau V, Brakier-Gingras L, Ferbeyre G. Cellular Senescence limits Translational Readthrough. Biol Open 2021; 10:272574. [PMID: 34676390 PMCID: PMC8649927 DOI: 10.1242/bio.058688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/14/2021] [Indexed: 11/20/2022] Open
Abstract
The origin and evolution of cancer cells is considered to be mainly fueled by DNA mutations. Although translation errors could also expand the cellular proteome, their role in cancer biology remains poorly understood. Tumor suppressors called caretakers block cancer initiation and progression by preventing DNA mutations and/or stimulating DNA repair. If translational errors contribute to tumorigenesis, then caretaker genes should prevent such errors in normal cells in response to oncogenic stimuli. Here, we show that the process of cellular senescence induced by oncogenes, tumor suppressors or chemotherapeutic drugs is associated with a reduction in translational readthrough (TR) measured using reporters containing termination codons withing the context of both normal translation termination or programmed TR. Senescence reduced both basal TR and TR stimulated by aminoglycosides. Mechanistically, the reduction of TR during senescence is controlled by the RB tumor suppressor pathway. Cells that escape from cellular senescence either induced by oncogenes or chemotherapy have an increased TR. Also, breast cancer cells that escape from therapy-induced senescence express high levels of AGO1x, a TR isoform of AGO1 linked to breast cancer progression. We propose that senescence and the RB pathway reduce TR limiting proteome diversity and the expression of TR proteins required for cancer cell proliferation. Summary: We report that senescence and the RB pathway reduce translational readthrough (TR) limiting proteome diversity and the expression of TR proteins such as Ago1X required for cancer cell proliferation.
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Affiliation(s)
- Neylen Del Toro
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Frédéric Lessard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Jacob Bouchard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Nasrin Mobasheri
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Jordan Guillon
- CRCHUM, 900 Saint-Denis, bureau R10.432, Montréal, Québec, H2X 0A9, Canada
| | - Sebastian Igelmann
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada.,CRCHUM, 900 Saint-Denis, bureau R10.432, Montréal, Québec, H2X 0A9, Canada
| | - Sarah Tardif
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Tony Buffard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Véronique Bourdeau
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Léa Brakier-Gingras
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Gerardo Ferbeyre
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada.,CRCHUM, 900 Saint-Denis, bureau R10.432, Montréal, Québec, H2X 0A9, Canada
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14
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Padmanabhan PK, Ferreira GR, Zghidi-Abouzid O, Oliveira C, Dumas C, Mariz FC, Papadopoulou B. Genetic depletion of the RNA helicase DDX3 leads to impaired elongation of translating ribosomes triggering co-translational quality control of newly synthesized polypeptides. Nucleic Acids Res 2021; 49:9459-9478. [PMID: 34358325 PMCID: PMC8450092 DOI: 10.1093/nar/gkab667] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 07/15/2021] [Accepted: 07/23/2021] [Indexed: 11/29/2022] Open
Abstract
DDX3 is a multifaceted RNA helicase of the DEAD-box family that plays central roles in all aspects of RNA metabolism including translation initiation. Here, we provide evidence that the Leishmania DDX3 ortholog functions in post-initiation steps of translation. We show that genetic depletion of DDX3 slows down ribosome movement resulting in elongation-stalled ribosomes, impaired translation elongation and decreased de novo protein synthesis. We also demonstrate that the essential ribosome recycling factor Rli1/ABCE1 and termination factors eRF3 and GTPBP1 are less recruited to ribosomes upon DDX3 loss, suggesting that arrested ribosomes may be inefficiently dissociated and recycled. Furthermore, we show that prolonged ribosome stalling triggers co-translational ubiquitination of nascent polypeptide chains and a higher recruitment of E3 ubiquitin ligases and proteasome components to ribosomes of DDX3 knockout cells, which further supports that ribosomes are not elongating optimally. Impaired elongation of translating ribosomes also results in the accumulation of cytoplasmic protein aggregates, which implies that defects in translation overwhelm the normal quality controls. The partial recovery of translation by overexpressing Hsp70 supports this possibility. Collectively, these results suggest an important novel contribution of DDX3 to optimal elongation of translating ribosomes by preventing prolonged translation stalls and stimulating recycling of arrested ribosomes.
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Affiliation(s)
- Prasad Kottayil Padmanabhan
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Gabriel Reis Ferreira
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Ouafa Zghidi-Abouzid
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Camila Oliveira
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Carole Dumas
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Filipe Colaço Mariz
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Barbara Papadopoulou
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
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15
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Silva J, Nina P, Romão L. Translation of ABCE1 Is Tightly Regulated by Upstream Open Reading Frames in Human Colorectal Cells. Biomedicines 2021; 9:biomedicines9080911. [PMID: 34440115 PMCID: PMC8389594 DOI: 10.3390/biomedicines9080911] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022] Open
Abstract
ATP-binding cassette subfamily E member 1 (ABCE1) belongs to the ABC protein family of transporters; however, it does not behave as a drug transporter. Instead, ABCE1 actively participates in different stages of translation and is also associated with oncogenic functions. Ribosome profiling analysis in colorectal cancer cells has revealed a high ribosome occupancy in the human ABCE1 mRNA 5′-leader sequence, indicating the presence of translatable upstream open reading frames (uORFs). These cis-acting translational regulatory elements usually act as repressors of translation of the main coding sequence. In the present study, we dissect the regulatory function of the five AUG and five non-AUG uORFs identified in the human ABCE1 mRNA 5′-leader sequence. We show that the expression of the main coding sequence is tightly regulated by the ABCE1 AUG uORFs in colorectal cells. Our results are consistent with a model wherein uORF1 is efficiently translated, behaving as a barrier to downstream uORF translation. The few ribosomes that can bypass uORF1 (and/or uORF2) must probably initiate at the inhibitory uORF3 or uORF5 that efficiently repress translation of the main ORF. This inhibitory property is slightly overcome in conditions of endoplasmic reticulum stress. In addition, we observed that these potent translation-inhibitory AUG uORFs function equally in cancer and in non-tumorigenic colorectal cells, which is consistent with a lack of oncogenic function. In conclusion, we establish human ABCE1 as an additional example of uORF-mediated translational regulation and that this tight regulation contributes to control ABCE1 protein levels in different cell environments.
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Affiliation(s)
- Joana Silva
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; (J.S.); (P.N.)
- Instituto de Biossistemas e Ciências Integrativas (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Pedro Nina
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; (J.S.); (P.N.)
| | - Luísa Romão
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; (J.S.); (P.N.)
- Instituto de Biossistemas e Ciências Integrativas (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Correspondence: ; Tel.: +351-21-750-8155
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16
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Park Y, Park J, Hwang HJ, Kim L, Jeong K, Song HK, Rufener SC, Mühlemann O, Kim YK. Translation mediated by the nuclear cap-binding complex is confined to the perinuclear region via a CTIF-DDX19B interaction. Nucleic Acids Res 2021; 49:8261-8276. [PMID: 34232997 PMCID: PMC8373075 DOI: 10.1093/nar/gkab579] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 06/08/2021] [Accepted: 06/23/2021] [Indexed: 12/29/2022] Open
Abstract
Newly synthesized mRNA is translated during its export through the nuclear pore complex, when its 5′-cap structure is still bound by the nuclear cap-binding complex (CBC), a heterodimer of cap-binding protein (CBP) 80 and CBP20. Despite its critical role in mRNA surveillance, the mechanism by which CBC-dependent translation (CT) is regulated remains unknown. Here, we demonstrate that the CT initiation factor (CTIF) is tethered in a translationally incompetent manner to the perinuclear region by the DEAD-box helicase 19B (DDX19B). DDX19B hands over CTIF to CBP80, which is associated with the 5′-cap of a newly exported mRNA. The resulting CBP80–CTIF complex then initiates CT in the perinuclear region. We also show that impeding the interaction between CTIF and DDX19B leads to uncontrolled CT throughout the cytosol, consequently dysregulating nonsense-mediated mRNA decay. Altogether, our data provide molecular evidence supporting the importance of tight control of local translation in the perinuclear region.
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Affiliation(s)
- Yeonkyoung Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Joori Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyun Jung Hwang
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Leehyeon Kim
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Kwon Jeong
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyun Kyu Song
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Simone C Rufener
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
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17
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Martins-Dias P, Romão L. Nonsense suppression therapies in human genetic diseases. Cell Mol Life Sci 2021; 78:4677-4701. [PMID: 33751142 PMCID: PMC11073055 DOI: 10.1007/s00018-021-03809-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/06/2021] [Accepted: 03/05/2021] [Indexed: 02/06/2023]
Abstract
About 11% of all human disease-associated gene lesions are nonsense mutations, resulting in the introduction of an in-frame premature translation-termination codon (PTC) into the protein-coding gene sequence. When translated, PTC-containing mRNAs originate truncated and often dysfunctional proteins that might be non-functional or have gain-of-function or dominant-negative effects. Therapeutic strategies aimed at suppressing PTCs to restore deficient protein function-the so-called nonsense suppression (or PTC readthrough) therapies-have the potential to provide a therapeutic benefit for many patients and in a broad range of genetic disorders, including cancer. These therapeutic approaches comprise the use of translational readthrough-inducing compounds that make the translational machinery recode an in-frame PTC into a sense codon. However, most of the mRNAs carrying a PTC can be rapidly degraded by the surveillance mechanism of nonsense-mediated decay (NMD), thus decreasing the levels of PTC-containing mRNAs in the cell and their availability for PTC readthrough. Accordingly, the use of NMD inhibitors, or readthrough-compound potentiators, may enhance the efficiency of PTC suppression. Here, we review the mechanisms of PTC readthrough and their regulation, as well as the recent advances in the development of novel approaches for PTC suppression, and their role in personalized medicine.
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Affiliation(s)
- Patrícia Martins-Dias
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016, Lisbon, Portugal
| | - Luísa Romão
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016, Lisbon, Portugal.
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18
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Farnoosh G, Saeedi-Boroujeni A, Jalali A, Keikhaei B, Mahmoudian-Sani MR. Polymorphisms in genes involved in breast cancer among Iranian patients. Per Med 2021; 18:153-169. [PMID: 33565318 DOI: 10.2217/pme-2020-0003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review gives a summary of the important genetic polymorphisms in breast cancer with a focus on people in Iran. Several single nucleotide polymorphisms were considered as breast cancer susceptibility polymorphisms within genes (STK15, ERRs, ESR1, p53, SEP15, AURKA, SHBG, SRC, FAS, VEGF, XRCC1, GST, NFκB1, XPC, XRCC3, sirtuin-3, NKG2D). Cytosine-adenine repeat (IGF-I), rs3877899, G-2548A, GGC (eRF3a/GSPT1), IVS2nt-124A/G have shown an increased risk of breast cancers and a decreased risk has been observed in 4G/5G (PAI-1), rs6505162, tri-nucleotide (GCG TGFBR1). We observed that the signaling pathways and antioxidant related genes are the main molecular processes associated with breast cancer progression. Further studies on types of polymorphisms in breast cancer could validate the prognostic value of biomarkers.
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Affiliation(s)
- Gholamreza Farnoosh
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Saeedi-Boroujeni
- Department of Immunology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Immunology Today, Universal Scientific Education & Research Network (USERN), Tehran, Iran
| | - Akram Jalali
- Department of Molecular Medicine & Genetics, School of Medicine Hamadan University of Medical Sciences
| | - Bijan Keikhaei
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad-Reza Mahmoudian-Sani
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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19
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Mattijssen S, Kozlov G, Fonseca BD, Gehring K, Maraia RJ. LARP1 and LARP4: up close with PABP for mRNA 3' poly(A) protection and stabilization. RNA Biol 2021; 18:259-274. [PMID: 33522422 PMCID: PMC7928012 DOI: 10.1080/15476286.2020.1868753] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/06/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
La-related proteins (LARPs) share a La motif (LaM) followed by an RNA recognition motif (RRM). Together these are termed the La-module that, in the prototypical nuclear La protein and LARP7, mediates binding to the UUU-3'OH termination motif of nascent RNA polymerase III transcripts. We briefly review La and LARP7 activities for RNA 3' end binding and protection from exonucleases before moving to the more recently uncovered poly(A)-related activities of LARP1 and LARP4. Two features shared by LARP1 and LARP4 are direct binding to poly(A) and to the cytoplasmic poly(A)-binding protein (PABP, also known as PABPC1). LARP1, LARP4 and other proteins involved in mRNA translation, deadenylation, and decay, contain PAM2 motifs with variable affinities for the MLLE domain of PABP. We discuss a model in which these PABP-interacting activities contribute to poly(A) pruning of active mRNPs. Evidence that the SARS-CoV-2 RNA virus targets PABP, LARP1, LARP 4 and LARP 4B to control mRNP activity is also briefly reviewed. Recent data suggests that LARP4 opposes deadenylation by stabilizing PABP on mRNA poly(A) tails. Other data suggest that LARP1 can protect mRNA from deadenylation. This is dependent on a PAM2 motif with unique characteristics present in its La-module. Thus, while nuclear La and LARP7 stabilize small RNAs with 3' oligo(U) from decay, LARP1 and LARP4 bind and protect mRNA 3' poly(A) tails from deadenylases through close contact with PABP.Abbreviations: 5'TOP: 5' terminal oligopyrimidine, LaM: La motif, LARP: La-related protein, LARP1: La-related protein 1, MLLE: mademoiselle, NTR: N-terminal region, PABP: cytoplasmic poly(A)-binding protein (PABPC1), Pol III: RNA polymerase III, PAM2: PABP-interacting motif 2, PB: processing body, RRM: RNA recognition motif, SG: stress granule.
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Affiliation(s)
- Sandy Mattijssen
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Guennadi Kozlov
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | | | - Kalle Gehring
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | - Richard J. Maraia
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
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20
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Emerging molecular functions and novel roles for the DEAD-box protein Dbp5/DDX19 in gene expression. Cell Mol Life Sci 2020; 78:2019-2030. [PMID: 33205304 DOI: 10.1007/s00018-020-03680-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/21/2020] [Accepted: 10/06/2020] [Indexed: 12/23/2022]
Abstract
The DEAD-box protein (DBP) Dbp5, a member of the superfamily II (SFII) helicases, has multiple reported roles in gene expression. First identified as an essential regulator of mRNA export in Saccharomyces cerevisiae, the enzyme now has reported functions in non-coding RNA export, translation, transcription, and DNA metabolism. Localization of the protein to various cellular compartments (nucleoplasm, nuclear envelope, and cytoplasm) highlights the ability of Dbp5 to modulate different stages of the RNA lifecycle. While Dbp5 has been well studied for > 20 years, several critical questions remain regarding the mechanistic principles that govern Dbp5 localization, substrate selection, and functions in gene expression. This review aims to take a holistic view of the proposed functions of Dbp5 and evaluate models that accommodate current published data.
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21
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Palma M, Lejeune F. Deciphering the molecular mechanism of stop codon readthrough. Biol Rev Camb Philos Soc 2020; 96:310-329. [PMID: 33089614 DOI: 10.1111/brv.12657] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 12/11/2022]
Abstract
Recognition of the stop codon by the translation machinery is essential to terminating translation at the right position and to synthesizing a protein of the correct size. Under certain conditions, the stop codon can be recognized as a coding codon promoting translation, which then terminates at a later stop codon. This event, called stop codon readthrough, occurs either by error, due to a dedicated regulatory environment leading to generation of different protein isoforms, or through the action of a readthrough compound. This review focuses on the mechanisms of stop codon readthrough, the nucleotide and protein environments that facilitate or inhibit it, and the therapeutic interest of stop codon readthrough in the treatment of genetic diseases caused by nonsense mutations.
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Affiliation(s)
- Martine Palma
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Fabrice Lejeune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
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22
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Wang J, Xu J, Li K, Huang Y, Dai Y, Xu C, Kang Y. Identification of WTAP-related genes by weighted gene co-expression network analysis in ovarian cancer. J Ovarian Res 2020; 13:119. [PMID: 32998774 PMCID: PMC7528330 DOI: 10.1186/s13048-020-00710-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/31/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Wilms tumor 1 associated protein (WTAP) modulates other genes via transcriptional and post-transcriptional regulation, in particular, by acting as a N6-methyladenosine writer or binding to the 3'UTR of mRNA, and promotes a variety of tumuors. However, the roles and mechanisms of WTAP in ovarian cancer are unknown. RESULTS In this study, using univariate Cox analysis and online CPTA analysis, we found that WTAP was a poor prognostic factor for ovarian cancer, and its protein expression level was higher in ovarian cancer than in normal tissue. Functionally, WTAP promoted the proliferation, invasion, and migration capability of ovarian cancer, according to the results of real time cellular analysis (RTCA), EdU cell proliferation assay, transwell assay. Subsequently, we identified a module containing 133 genes that were carefully related to WTAP expression through weighted gene co-expression network analysis (WGCNA). By calculating the hazard ratios of these genes and comparing their differences in the WTAP high-expression group and the low-expression group, we observed that there was a significant positive correlation between WTAP and two poor survival-related genes, family with sequence similarity 76 member A (FAM76A) and HBS1 like translational GTPase (HBS1L), which was also verified by quantitative real-time PCR in SKOV3 and A2780 cells. CONCLUSION WTAP functions as an oncogenic factor that promotes the progression of ovarian cancer in which WTAP-HBS1L/FAM76A axis may be involved. Our study indicates the potential role of WTAP in prognostic biomarker and therapeutic target for ovarian cancer.
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Affiliation(s)
- Jing Wang
- Obstetrics and Gynecology Hospital, Fudan University, No.419, Fangxie Road, Shanghai, 200011, People's Republic of China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, 200011, China
| | - Jing Xu
- Obstetrics and Gynecology Hospital, Fudan University, No.419, Fangxie Road, Shanghai, 200011, People's Republic of China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, 200011, China
| | - Ke Li
- Obstetrics and Gynecology Hospital, Fudan University, No.419, Fangxie Road, Shanghai, 200011, People's Republic of China
| | - Yunke Huang
- Obstetrics and Gynecology Hospital, Fudan University, No.419, Fangxie Road, Shanghai, 200011, People's Republic of China
| | - Yilin Dai
- Obstetrics and Gynecology Hospital, Fudan University, No.419, Fangxie Road, Shanghai, 200011, People's Republic of China
| | - Congjian Xu
- Obstetrics and Gynecology Hospital, Fudan University, No.419, Fangxie Road, Shanghai, 200011, People's Republic of China. .,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, 200011, China.
| | - Yu Kang
- Obstetrics and Gynecology Hospital, Fudan University, No.419, Fangxie Road, Shanghai, 200011, People's Republic of China. .,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, 200011, China.
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23
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Beißel C, Grosse S, Krebber H. Dbp5/DDX19 between Translational Readthrough and Nonsense Mediated Decay. Int J Mol Sci 2020; 21:ijms21031085. [PMID: 32041247 PMCID: PMC7037193 DOI: 10.3390/ijms21031085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 01/31/2020] [Accepted: 02/02/2020] [Indexed: 01/21/2023] Open
Abstract
The DEAD-box protein Dbp5 (human DDX19) remodels RNA-protein complexes. Dbp5 functions in ribonucleoprotein export and translation termination. Termination occurs, when the ribosome has reached a stop codon through the Dbp5 mediated delivery of the eukaryotic termination factor eRF1. eRF1 contacts eRF3 upon dissociation of Dbp5, resulting in polypeptide chain release and subsequent ribosomal subunit splitting. Mutations in DBP5 lead to stop codon readthrough, because the eRF1 and eRF3 interaction is not controlled and occurs prematurely. This identifies Dbp5/DDX19 as a possible potent drug target for nonsense suppression therapy. Neurodegenerative diseases and cancer are caused in many cases by the loss of a gene product, because its mRNA contained a premature termination codon (PTC) and is thus eliminated through the nonsense mediated decay (NMD) pathway, which is described in the second half of this review. We discuss translation termination and NMD in the light of Dbp5/DDX19 and subsequently speculate on reducing Dbp5/DDX19 activity to allow readthrough of the PTC and production of a full-length protein to detract the RNA from NMD as a possible treatment for diseases.
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Lari A, Arul Nambi Rajan A, Sandhu R, Reiter T, Montpetit R, Young BP, Loewen CJ, Montpetit B. A nuclear role for the DEAD-box protein Dbp5 in tRNA export. eLife 2019; 8:48410. [PMID: 31453808 PMCID: PMC6711706 DOI: 10.7554/elife.48410] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/09/2019] [Indexed: 01/01/2023] Open
Abstract
Dbp5 is an essential DEAD-box protein that mediates nuclear mRNP export. Dbp5 also shuttles between nuclear and cytoplasmic compartments with reported roles in transcription, ribosomal subunit export, and translation; however, the mechanism(s) by which nucleocytoplasmic transport occurs and how Dbp5 specifically contributes to each of these processes remains unclear. Towards understanding the functions and transport of Dbp5 in Saccharomyces cerevisiae, alanine scanning mutagenesis was used to generate point mutants at all possible residues within a GFP-Dbp5 reporter. Characterization of the 456 viable mutants led to the identification of an N-terminal Xpo1-dependent nuclear export signal in Dbp5, in addition to other separation-of-function alleles, which together provide evidence that Dbp5 nuclear shuttling is not essential for mRNP export. Rather, disruptions in Dbp5 nucleocytoplasmic transport result in tRNA export defects, including changes in tRNA shuttling dynamics during recovery from nutrient stress.
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Affiliation(s)
- Azra Lari
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Arvind Arul Nambi Rajan
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, Davis, United States
| | - Rima Sandhu
- Department of Viticulture and Enology, University of California, Davis, Davis, United States
| | - Taylor Reiter
- Food Science Graduate Group, University of California Davis, Davis, United States
| | - Rachel Montpetit
- Department of Viticulture and Enology, University of California, Davis, Davis, United States
| | - Barry P Young
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Chris Jr Loewen
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, Canada.,Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, Davis, United States.,Department of Viticulture and Enology, University of California, Davis, Davis, United States.,Food Science Graduate Group, University of California Davis, Davis, United States
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