1
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Glineburg MR, Yildirim E, Gomez N, Rodriguez G, Pak J, Li X, Altheim C, Waksmacki J, McInerney GM, Barmada SJ, Todd PK. Stress granule formation helps to mitigate neurodegeneration. Nucleic Acids Res 2024:gkae655. [PMID: 39106168 DOI: 10.1093/nar/gkae655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 05/28/2024] [Accepted: 07/17/2024] [Indexed: 08/09/2024] Open
Abstract
Cellular stress pathways that inhibit translation initiation lead to transient formation of cytoplasmic RNA/protein complexes known as stress granules. Many of the proteins found within stress granules and the dynamics of stress granule formation and dissolution are implicated in neurodegenerative disease. Whether stress granule formation is protective or harmful in neurodegenerative conditions is not known. To address this, we took advantage of the alphavirus protein nsP3, which selectively binds dimers of the central stress granule nucleator protein G3BP and markedly reduces stress granule formation without directly impacting the protein translational inhibitory pathways that trigger stress granule formation. In Drosophila and rodent neurons, reducing stress granule formation with nsP3 had modest impacts on lifespan even in the setting of serial stress pathway induction. In contrast, reducing stress granule formation in models of ataxia, amyotrophic lateral sclerosis and frontotemporal dementia largely exacerbated disease phenotypes. These data support a model whereby stress granules mitigate, rather than promote, neurodegenerative cascades.
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Affiliation(s)
- M Rebecca Glineburg
- Biological Sciences, Schmid College of Science and Technology, Chapman University, 1 University Drive, Orange, CA 92866, USA
- Department of Neurology, University of Michigan, 109 Zina Pitcher Place, BSRB48109-2200, Ann Arbor, MI 4005, USA
| | - Evrim Yildirim
- Department of Neurology, University of Michigan, 109 Zina Pitcher Place, BSRB48109-2200, Ann Arbor, MI 4005, USA
| | - Nicolas Gomez
- Department of Neurology, University of Michigan, 109 Zina Pitcher Place, BSRB48109-2200, Ann Arbor, MI 4005, USA
- Cell and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Genesis Rodriguez
- Department of Neurology, University of Michigan, 109 Zina Pitcher Place, BSRB48109-2200, Ann Arbor, MI 4005, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Jaclyn Pak
- Biological Sciences, Schmid College of Science and Technology, Chapman University, 1 University Drive, Orange, CA 92866, USA
| | - Xingli Li
- Department of Neurology, University of Michigan, 109 Zina Pitcher Place, BSRB48109-2200, Ann Arbor, MI 4005, USA
| | - Christopher Altheim
- Department of Neurology, University of Michigan, 109 Zina Pitcher Place, BSRB48109-2200, Ann Arbor, MI 4005, USA
| | - Jacob Waksmacki
- Department of Neurology, University of Michigan, 109 Zina Pitcher Place, BSRB48109-2200, Ann Arbor, MI 4005, USA
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 17165, Sweden
| | - Sami J Barmada
- Department of Neurology, University of Michigan, 109 Zina Pitcher Place, BSRB48109-2200, Ann Arbor, MI 4005, USA
| | - Peter K Todd
- Department of Neurology, University of Michigan, 109 Zina Pitcher Place, BSRB48109-2200, Ann Arbor, MI 4005, USA
- Veterans Affairs Medical Center, Ann Arbor, MI, USA
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2
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Wang W, Liu H, Liu S, Hao T, Wei Y, Wei H, Zhou W, Zhang X, Hao X, Zhang M. Oocyte-specific deletion of eukaryotic translation initiation factor 5 causes apoptosis of mouse oocytes within the early-growing follicles by mitochondrial fission defect-reactive oxygen species-DNA damage. Clin Transl Med 2024; 14:e1791. [PMID: 39113233 PMCID: PMC11306288 DOI: 10.1002/ctm2.1791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/20/2024] [Accepted: 07/23/2024] [Indexed: 08/11/2024] Open
Abstract
BACKGROUND Mutations in several translation initiation factors are closely associated with premature ovarian insufficiency (POI), but the underlying pathogenesis remains largely unknown. METHODS AND RESULTS We generated eukaryotic translation initiation factor 5 (Eif5) conditional knockout mice aiming to investigate the function of eIF5 during oocyte growth and follicle development. Here, we demonstrated that Eif5 deletion in mouse primordial and growing oocytes both resulted in the apoptosis of oocytes within the early-growing follicles. Further studies revealed that Eif5 deletion in oocytes downregulated the levels of mitochondrial fission-related proteins (p-DRP1, FIS1, MFF and MTFR) and upregulated the levels of the integrated stress response-related proteins (AARS1, SHMT2 and SLC7A1) and genes (Atf4, Ddit3 and Fgf21). Consistent with this, Eif5 deletion in oocytes resulted in mitochondrial dysfunction characterized by elongated form, aggregated distribution beneath the oocyte membrane, decreased adenosine triphosphate content and mtDNA copy numbers, and excessive accumulation of reactive oxygen species (ROS) and mitochondrial superoxide. Meanwhile, Eif5 deletion in oocytes led to a significant increase in the levels of DNA damage response proteins (γH2AX, p-CHK2 and p-p53) and proapoptotic proteins (PUMA and BAX), as well as a significant decrease in the levels of anti-apoptotic protein BCL-xL. CONCLUSION These findings indicate that Eif5 deletion in mouse oocytes results in the apoptosis of oocytes within the early-growing follicles via mitochondrial fission defects, excessive ROS accumulation and DNA damage. This study provides new insights into pathogenesis, genetic diagnosis and potential therapeutic targets for POI. KEY POINTS Eif5 deletion in oocytes leads to arrest in oocyte growth and follicle development. Eif5 deletion in oocytes impairs the translation of mitochondrial fission-related proteins, followed by mitochondrial dysfunction. Depletion of Eif5 causes oocyte apoptosis via ROS accumulation and DNA damage response pathway.
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Affiliation(s)
- Weiyong Wang
- The Innovation Centre of Ministry of Education for Development and Diseasesthe Second Affiliated HospitalSchool of MedicineSouth China University of TechnologyGuangzhouChina
| | - Huiyu Liu
- The Innovation Centre of Ministry of Education for Development and Diseasesthe Second Affiliated HospitalSchool of MedicineSouth China University of TechnologyGuangzhouChina
| | - Shuang Liu
- The Innovation Centre of Ministry of Education for Development and Diseasesthe Second Affiliated HospitalSchool of MedicineSouth China University of TechnologyGuangzhouChina
| | - Tiantian Hao
- The Innovation Centre of Ministry of Education for Development and Diseasesthe Second Affiliated HospitalSchool of MedicineSouth China University of TechnologyGuangzhouChina
| | - Ying Wei
- The Innovation Centre of Ministry of Education for Development and Diseasesthe Second Affiliated HospitalSchool of MedicineSouth China University of TechnologyGuangzhouChina
| | - Hongwei Wei
- The Innovation Centre of Ministry of Education for Development and Diseasesthe Second Affiliated HospitalSchool of MedicineSouth China University of TechnologyGuangzhouChina
| | - Wenjun Zhou
- The Innovation Centre of Ministry of Education for Development and Diseasesthe Second Affiliated HospitalSchool of MedicineSouth China University of TechnologyGuangzhouChina
| | - Xiaodan Zhang
- The Innovation Centre of Ministry of Education for Development and Diseasesthe Second Affiliated HospitalSchool of MedicineSouth China University of TechnologyGuangzhouChina
| | - Xiaoqiong Hao
- Department of PhysiologyBaotou Medical CollegeBaotouChina
| | - Meijia Zhang
- The Innovation Centre of Ministry of Education for Development and Diseasesthe Second Affiliated HospitalSchool of MedicineSouth China University of TechnologyGuangzhouChina
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Dykstra MM, Weskamp K, Gómez NB, Waksmacki J, Tank E, Glineburg MR, Snyder A, Pinarbasi E, Bekier M, Li X, Bai J, Shahzad S, Nedumaran J, Wieland C, Stewart C, Willey S, Grotewold N, McBride J, Moran JJ, Suryakumar AV, Lucas M, Tessier P, Ward M, Todd P, Barmada SJ. TDP43 autoregulation gives rise to shortened isoforms that are tightly controlled by both transcriptional and post-translational mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601776. [PMID: 39005384 PMCID: PMC11244999 DOI: 10.1101/2024.07.02.601776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The nuclear RNA-binding protein TDP43 is integrally involved in the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Previous studies uncovered N-terminal TDP43 isoforms that are predominantly cytosolic in localization, highly prone to aggregation, and enriched in susceptible spinal motor neurons. In healthy cells, however, these shortened (s)TDP43 isoforms are difficult to detect in comparison to full-length (fl)TDP43, raising questions regarding their origin and selective regulation. Here, we show that sTDP43 is created as a byproduct of TDP43 autoregulation and cleared by nonsense mediated RNA decay (NMD). The sTDP43-encoding transcripts that escape NMD can lead to toxicity but are rapidly degraded post-translationally. Circumventing these regulatory mechanisms by overexpressing sTDP43 results in neurodegeneration in vitro and in vivo via N-terminal oligomerization and impairment of flTDP43 splicing activity, in addition to RNA binding-dependent gain-of-function toxicity. Collectively, these studies highlight endogenous mechanisms that tightly regulate sTDP43 expression and provide insight into the consequences of aberrant sTDP43 accumulation in disease.
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Affiliation(s)
- Megan M. Dykstra
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI
| | - Kaitlin Weskamp
- Chemistry Department, Nebraska Wesleyan University, Lincoln, NE
| | - Nicolás B. Gómez
- Graduate Program in Cell and Molecular Biology, University of Michigan, Ann Arbor, MI
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI
| | - Jacob Waksmacki
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - Elizabeth Tank
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - M. Rebecca Glineburg
- Biological Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA
| | | | - Emile Pinarbasi
- Department of Neurology, University of Michigan, Ann Arbor, MI
- Neuropathology, Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI
| | - Michael Bekier
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - Xingli Li
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - Jen Bai
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | | | - Juno Nedumaran
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - Clare Wieland
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI
| | - Corey Stewart
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI
| | - Sydney Willey
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI
| | - Nikolas Grotewold
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI
| | - Jonathon McBride
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI
| | - John J. Moran
- Atlanta Pediatric Research Alliance, Emory University, Atlanta, GA
| | | | - Michael Lucas
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI
| | - Peter Tessier
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI
| | | | - Peter Todd
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI
- Graduate Program in Cell and Molecular Biology, University of Michigan, Ann Arbor, MI
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI
- Department of Neurology, University of Michigan, Ann Arbor, MI
- Veterans Affairs Medical Center, Ann Arbor, MI
| | - Sami J. Barmada
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI
- Graduate Program in Cell and Molecular Biology, University of Michigan, Ann Arbor, MI
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI
- Department of Neurology, University of Michigan, Ann Arbor, MI
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4
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Zhang Y, Liu X, Li Z, Li H, Miao Z, Wan B, Xu X. Advances on the Mechanisms and Therapeutic Strategies in Non-coding CGG Repeat Expansion Diseases. Mol Neurobiol 2024:10.1007/s12035-024-04239-9. [PMID: 38780719 DOI: 10.1007/s12035-024-04239-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
Non-coding CGG repeat expansions within the 5' untranslated region are implicated in a range of neurological disorders, including fragile X-associated tremor/ataxia syndrome, oculopharyngeal myopathy with leukodystrophy, and oculopharyngodistal myopathy. This review outlined the general characteristics of diseases associated with non-coding CGG repeat expansions, detailing their clinical manifestations and neuroimaging patterns, which often overlap and indicate shared pathophysiological traits. We summarized the underlying molecular mechanisms of these disorders, providing new insights into the roles that DNA, RNA, and toxic proteins play. Understanding these mechanisms is crucial for the development of targeted therapeutic strategies. These strategies include a range of approaches, such as antisense oligonucleotides, RNA interference, genomic DNA editing, small molecule interventions, and other treatments aimed at correcting the dysregulated processes inherent in these disorders. A deeper understanding of the shared mechanisms among non-coding CGG repeat expansion disorders may hold the potential to catalyze the development of innovative therapies, ultimately offering relief to individuals grappling with these debilitating neurological conditions.
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Affiliation(s)
- Yutong Zhang
- Departments of Neurology, The First Affiliated Hospital of Soochow University, Suzhou City, China
| | - Xuan Liu
- Departments of Neurology, The First Affiliated Hospital of Soochow University, Suzhou City, China
| | - Zeheng Li
- Departments of Neurology, The First Affiliated Hospital of Soochow University, Suzhou City, China
| | - Hao Li
- Departments of Neurology, The First Affiliated Hospital of Soochow University, Suzhou City, China
- Department of Neurology, The Fourth Affiliated Hospital of Soochow University, Suzhou, 215124, China
| | - Zhigang Miao
- The Institute of Neuroscience, Soochow University, Suzhou City, China
| | - Bo Wan
- The Institute of Neuroscience, Soochow University, Suzhou City, China
| | - Xingshun Xu
- Departments of Neurology, The First Affiliated Hospital of Soochow University, Suzhou City, China.
- The Institute of Neuroscience, Soochow University, Suzhou City, China.
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China.
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5
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Ly J, Xiang K, Su KC, Sissoko GB, Bartel DP, Cheeseman IM. Nuclear release of eIF1 globally increases stringency of start-codon selection to preserve mitotic arrest physiology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.06.588385. [PMID: 38617206 PMCID: PMC11014515 DOI: 10.1101/2024.04.06.588385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Regulated start-codon selection has the potential to reshape the proteome through the differential production of uORFs, canonical proteins, and alternative translational isoforms. However, conditions under which start-codon selection is altered remain poorly defined. Here, using transcriptome-wide translation initiation site profiling, we reveal a global increase in the stringency of start-codon selection during mammalian mitosis. Low-efficiency initiation sites are preferentially repressed in mitosis, resulting in pervasive changes in the translation of thousands of start sites and their corresponding protein products. This increased stringency of start-codon selection during mitosis results from increased interactions between the key regulator of start-codon selection, eIF1, and the 40S ribosome. We find that increased eIF1-40S ribosome interactions during mitosis are mediated by the release of a nuclear pool of eIF1 upon nuclear envelope breakdown. Selectively depleting the nuclear pool of eIF1 eliminates the changes to translational stringency during mitosis, resulting in altered mitotic proteome composition. In addition, preventing mitotic translational rewiring results in substantially increased cell death and decreased mitotic slippage following treatment with anti-mitotic chemotherapeutics. Thus, cells globally control translation initiation stringency with critical roles during the mammalian cell cycle to preserve mitotic cell physiology.
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6
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Wagner PA, Song M, Ficner R, Kuhle B, Marintchev A. Molecular basis for the interactions of eIF2β with eIF5, eIF2B, and 5MP1 and their regulation by CK2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591181. [PMID: 38712236 PMCID: PMC11071521 DOI: 10.1101/2024.04.25.591181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The heterotrimeric GTPase eukaryotic translation initiation factor 2 (eIF2) delivers the initiator Met-tRNAi to the ribosomal translation preinitiation complex. eIF2β has three lysine-rich repeats (K-boxes) in its N-terminal tail, which are important for binding to the GTPase-activating protein (GAP) eIF5, the guanine nucleotide exchange factor (GEF) eIF2B, and the regulator eIF5-mimic protein (5MP). Here, we combine X-ray crystallography with NMR to understand the molecular basis and dynamics of these interactions. The crystal structure of yeast eIF5-CTD in complex with K-box 3 of eIF2β reveals an extended binding site on eIF2β, far beyond the K-box. We show that human eIF5, eIF2Bε, and 5MP1 can all bind to each of the three K-boxes, while reducing each other's affinities. Moreover, all these affinities are increased by CK2 phosphomimetic mutations. Our results reveal how eIF5, eIF2B, and 5MP displace each other from eIF2, and elucidate the role of CK2 in remodeling the translation apparatus.
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7
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Jin K, Li Y, Wei R, Liu Y, Wang S, Tian H. BZW2 promotes malignant progression in lung adenocarcinoma through enhancing the ubiquitination and degradation of GSK3β. Cell Death Discov 2024; 10:105. [PMID: 38424042 PMCID: PMC10904796 DOI: 10.1038/s41420-024-01879-7] [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: 11/14/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024] Open
Abstract
The role of Basic leucine zipper and W2 domains 2 (BZW2) in the advancement of different types of tumors is noteworthy, but its involvement and molecular mechanisms in lung adenocarcinoma (LUAD) remain uncertain. Through this investigation, it was found that the upregulation of BZW2 was observed in LUAD tissues, which was associated with an unfavorable prognosis for individuals diagnosed with LUAD, as indicated by data from Gene Expression Omnibus and The Cancer Genome Atlas databases. Based on the clinicopathologic characteristics of LUAD patients from the tissue microarray, both univariate and multivariate analyses indicated that BZW2 functioned as an independent prognostic factor for LUAD. In terms of mechanism, BZW2 interacted with glycogen synthase kinase-3 beta (GSK3β) and enhanced the ubiquitination-mediated degradation of GSK3β through slowing down of the dissociation of the ubiquitin ligase complex, which consists of GSK3β and TNF receptor-associated factor 6. Moreover, BZW2 stimulated Wnt/β-catenin signaling pathway through GSK3β, thereby facilitating the advancement of LUAD. In conclusion, BZW2 was a significant promoter of LUAD. The research we conducted identified a promising diagnostic and therapeutic target for LUAD.
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Affiliation(s)
- Kai Jin
- Department of Thoracic Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Yongmeng Li
- Department of Thoracic Surgery, the First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
| | - Ruyuan Wei
- Department of Cardiovascular Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Yanfei Liu
- Department of Anesthesiology, Qilu Children's Hospital of Shandong University, Jinan, China
| | - Shuai Wang
- Department of Thoracic Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Hui Tian
- Department of Thoracic Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China.
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8
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Maio G, Smith M, Bhawal R, Zhang S, Baskin JM, Li J, Lin H. Interactome Analysis Identifies the Role of BZW2 in Promoting Endoplasmic Reticulum-Mitochondria Contact and Mitochondrial Metabolism. Mol Cell Proteomics 2024; 23:100709. [PMID: 38154691 PMCID: PMC10835002 DOI: 10.1016/j.mcpro.2023.100709] [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: 03/23/2023] [Revised: 12/19/2023] [Accepted: 12/24/2023] [Indexed: 12/30/2023] Open
Abstract
Understanding the molecular functions of less-studied proteins is an important task of life science research. Despite reports of basic leucine zipper and W2 domain-containing protein 2 (BZW2) promoting cancer progression first emerging in 2017, little is known about its molecular function. Using a quantitative proteomic approach to identify its interacting proteins, we found that BZW2 interacts with both endoplasmic reticulum (ER) and mitochondrial proteins. We thus hypothesized that BZW2 localizes to and promotes the formation of ER-mitochondria contact sites and that such localization would promote calcium transport from ER to the mitochondria and promote ATP production. Indeed, we found that BZW2 localized to ER-mitochondria contact sites and that BZW2 knockdown decreased ER-mitochondria contact, mitochondrial calcium levels, and ATP production. These findings provide key insights into molecular functions of BZW2, the potential role of BZW2 in cancer progression, and highlight the utility of interactome data in understanding the function of less-studied proteins.
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Affiliation(s)
- George Maio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Mike Smith
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Ruchika Bhawal
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York, USA
| | - Sheng Zhang
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York, USA
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA
| | - Jenny Li
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA; Howard Hughes Medical Institute, Cornell University, Ithaca, New York, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.
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9
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Ito H, Machida K, Hasumi M, Ueyama M, Nagai Y, Imataka H, Taguchi H. Reconstitution of C9orf72 GGGGCC repeat-associated non-AUG translation with purified human translation factors. Sci Rep 2023; 13:22826. [PMID: 38129650 PMCID: PMC10739749 DOI: 10.1038/s41598-023-50188-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: 08/28/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023] Open
Abstract
Nucleotide repeat expansion of GGGGCC (G4C2) in the non-coding region of C9orf72 is the most common genetic cause underlying amyotrophic lateral sclerosis and frontotemporal dementia. Transcripts harboring this repeat expansion undergo the translation of dipeptide repeats via a non-canonical process known as repeat-associated non-AUG (RAN) translation. In order to ascertain the essential components required for RAN translation, we successfully recapitulated G4C2-RAN translation using an in vitro reconstituted translation system comprising human factors, namely the human PURE system. Our findings conclusively demonstrate that the presence of fundamental translation factors is sufficient to mediate the elongation from the G4C2 repeat. Furthermore, the initiation mechanism proceeded in a 5' cap-dependent manner, independent of eIF2A or eIF2D. In contrast to cell lysate-mediated RAN translation, where longer G4C2 repeats enhanced translation, we discovered that the expansion of the G4C2 repeats inhibited translation elongation using the human PURE system. These results suggest that the repeat RNA itself functions as a repressor of RAN translation. Taken together, our utilization of a reconstituted RAN translation system employing minimal factors represents a distinctive and potent approach for elucidating the intricacies underlying RAN translation mechanism.
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Grants
- JPMJFS2112 Japan Science and Technology Agency
- JP26116002 Ministry of Education, Culture, Sports, Science and Technology
- JP18H03984 Ministry of Education, Culture, Sports, Science and Technology
- JP21H04763 Ministry of Education, Culture, Sports, Science and Technology
- JP20H05925 Ministry of Education, Culture, Sports, Science and Technology
- 2019-25 Mitsubishi Foundation
- 2019 Uehara Memorial Foundation
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Affiliation(s)
- Hayato Ito
- School of Life Science and Technology, Tokyo Institute of Technology, S2-19, Nagatsuta 4259, Midori-ku, Yokohama, 226-8501, Japan
| | - Kodai Machida
- Graduate School of Engineering, University of Hyogo, Shosha, 2167, Himeji, Hyogo, 671-2280, Japan
| | - Mayuka Hasumi
- School of Life Science and Technology, Tokyo Institute of Technology, S2-19, Nagatsuta 4259, Midori-ku, Yokohama, 226-8501, Japan
| | - Morio Ueyama
- Department of Neurology, Faculty of Medicine, Kindai University, Ohonohigashi 377-2, Osaka-Sayama, 589-8511, Japan
| | - Yoshitaka Nagai
- Department of Neurology, Faculty of Medicine, Kindai University, Ohonohigashi 377-2, Osaka-Sayama, 589-8511, Japan
| | - Hiroaki Imataka
- Graduate School of Engineering, University of Hyogo, Shosha, 2167, Himeji, Hyogo, 671-2280, Japan
| | - Hideki Taguchi
- School of Life Science and Technology, Tokyo Institute of Technology, S2-19, Nagatsuta 4259, Midori-ku, Yokohama, 226-8501, Japan.
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, S2-19, Nagatsuta 4259, Midori-ku, Yokohama, 226-8501, Japan.
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10
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Reyes CJF, Asano K. Between Order and Chaos: Understanding the Mechanism and Pathology of RAN Translation. Biol Pharm Bull 2023; 46:139-146. [PMID: 36724941 DOI: 10.1248/bpb.b22-00448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Repeat-associated non-AUG (RAN) translation is a pathogenic mechanism in which repetitive sequences are translated into aggregation-prone proteins from multiple reading frames, even without a canonical AUG start codon. Since its discovery in spinocerebellar ataxia type 8 (SCA8) and myotonic dystrophy type 1 (DM1), RAN translation is now known to occur in the context of 12 disease-linked repeat expansions. This review discusses recent advances in understanding the regulatory mechanisms controlling RAN translation and its contribution to the pathophysiology of repeat expansion diseases. We discuss the key findings in the context of Fragile X Tremor Ataxia Syndrome (FXTAS), a neurodegenerative disorder caused by a CGG repeat expansion in the 5' untranslated region of FMR1.
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Affiliation(s)
| | - Katsura Asano
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University.,Laboratory of Translational Control Study, Graduate School of Integrated Sciences for Life, Hiroshima University.,Hiroshima Research Center for Healthy Aging, Hiroshima University
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11
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Piol D, Tosatto L, Zuccaro E, Anderson EN, Falconieri A, Polanco MJ, Marchioretti C, Lia F, White J, Bregolin E, Minervini G, Parodi S, Salvatella X, Arrigoni G, Ballabio A, La Spada AR, Tosatto SC, Sambataro F, Medina DL, Pandey UB, Basso M, Pennuto M. Antagonistic effect of cyclin-dependent kinases and a calcium-dependent phosphatase on polyglutamine-expanded androgen receptor toxic gain of function. SCIENCE ADVANCES 2023; 9:eade1694. [PMID: 36608116 PMCID: PMC9821870 DOI: 10.1126/sciadv.ade1694] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Spinal and bulbar muscular atrophy is caused by polyglutamine (polyQ) expansions in androgen receptor (AR), generating gain-of-function toxicity that may involve phosphorylation. Using cellular and animal models, we investigated what kinases and phosphatases target polyQ-expanded AR, whether polyQ expansions modify AR phosphorylation, and how this contributes to neurodegeneration. Mass spectrometry showed that polyQ expansions preserve native phosphorylation and increase phosphorylation at conserved sites controlling AR stability and transactivation. In small-molecule screening, we identified that CDC25/CDK2 signaling could enhance AR phosphorylation, and the calcium-sensitive phosphatase calcineurin had opposite effects. Pharmacologic and genetic manipulation of these kinases and phosphatases modified polyQ-expanded AR function and toxicity in cells, flies, and mice. Ablation of CDK2 reduced AR phosphorylation in the brainstem and restored expression of Myc and other genes involved in DNA damage, senescence, and apoptosis, indicating that the cell cycle-regulated kinase plays more than a bystander role in SBMA-vulnerable postmitotic cells.
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Affiliation(s)
- Diana Piol
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
- Padova Neuroscience Center, Padova, Italy
- Dulbecco Telethon Institute (DTI), Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Laura Tosatto
- Dulbecco Telethon Institute (DTI), Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Institute of Biophysics, Consiglio Nazionale delle Ricerche (CNR), Trento, Italy
| | - Emanuela Zuccaro
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
- Padova Neuroscience Center, Padova, Italy
| | - Eric N. Anderson
- Division of Child Neurology, Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
| | | | - Maria J. Polanco
- Dulbecco Telethon Institute (DTI), Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Caterina Marchioretti
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
- Padova Neuroscience Center, Padova, Italy
| | - Federica Lia
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
- Padova Neuroscience Center, Padova, Italy
| | - Joseph White
- Department of Pathology and Laboratory Medicine, Department of Neurology, Department of Biological Chemistry, and the UCI Institute for Neurotherapeutics, University of California, Irvine, CA 92697, USA
| | - Elisa Bregolin
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
- Padova Neuroscience Center, Padova, Italy
| | | | - Sara Parodi
- Istituto Italiano di Tecnologia, Genova, Italy
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- ICREA, Passeig Lluís Companys 23, Barcelona, Spain
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
- Department of Medical and Translational Science, Federico II University, Naples, Italy
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Albert R. La Spada
- Department of Pathology and Laboratory Medicine, Department of Neurology, Department of Biological Chemistry, and the UCI Institute for Neurotherapeutics, University of California, Irvine, CA 92697, USA
| | - Silvio C. E. Tosatto
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Institute of Neuroscience, Consiglio Nazionale delle Ricerche (CNR), Padova, Italy
| | - Fabio Sambataro
- Padova Neuroscience Center, Padova, Italy
- Department of Neuroscience, University of Padova, Padova, Italy
| | - Diego L. Medina
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Medical and Translational Science, Federico II University, Naples, Italy
| | - Udai B. Pandey
- Division of Child Neurology, Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
| | - Manuela Basso
- Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Maria Pennuto
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
- Padova Neuroscience Center, Padova, Italy
- Dulbecco Telethon Institute (DTI), Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
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12
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Singh CR, Tani N, Nakamura A, Asano K. Mass spectrometry analysis of affinity-purified cytoplasmic translation initiation complexes from human and fly cells. STAR Protoc 2022; 3:101739. [PMID: 36181679 PMCID: PMC9529597 DOI: 10.1016/j.xpro.2022.101739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/25/2022] [Accepted: 09/08/2022] [Indexed: 11/05/2022] Open
Abstract
eIF5-mimic protein (5MP) controls translation through binding to the ribosomal pre-initiation complex (PIC) and alters non-AUG translation rates for cancer oncogenes and repeat-expansions in neurodegenerative diseases. Here, we describe a semi-quantitative protocol for detecting 5MP-associated proteins in cultured human and fly cells. We detail one-step anti-FLAG affinity purification and whole-lane mass spectrometry analysis of samples resolved by SDS-PAGE. This protocol allows for quantitative evaluation of the effect of 5MP mutations on its molecular interactions, to elucidate translational control by 5MP. For complete details on the use and execution of this protocol, please refer to Singh et al. (2021).
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Affiliation(s)
- Chingakham Ranjit Singh
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA; Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
| | - Naoki Tani
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan.
| | - Akira Nakamura
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan.
| | - Katsura Asano
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA; Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan; Hiroshima Research Center for Healthy Aging, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.
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13
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Rubio A, Garland GD, Sfakianos A, Harvey RF, Willis AE. Aberrant protein synthesis and cancer development: The role of canonical eukaryotic initiation, elongation and termination factors in tumorigenesis. Semin Cancer Biol 2022; 86:151-165. [PMID: 35487398 DOI: 10.1016/j.semcancer.2022.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/11/2022] [Accepted: 04/20/2022] [Indexed: 01/27/2023]
Abstract
In tumourigenesis, oncogenes or dysregulated tumour suppressor genes alter the canonical translation machinery leading to a reprogramming of the translatome that, in turn, promotes the translation of selected mRNAs encoding proteins involved in proliferation and metastasis. It is therefore unsurprising that abnormal expression levels and activities of eukaryotic initiation factors (eIFs), elongation factors (eEFs) or termination factors (eRFs) are associated with poor outcome for patients with a wide range of cancers. In this review we discuss how RNA binding proteins (RBPs) within the canonical translation factor machinery are dysregulated in cancers and how targeting such proteins is leading to new therapeutic avenues.
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Affiliation(s)
- Angela Rubio
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Rd, Cambridge CB2 1QR, UK
| | - Gavin D Garland
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Rd, Cambridge CB2 1QR, UK
| | - Aristeidis Sfakianos
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Rd, Cambridge CB2 1QR, UK
| | - Robert F Harvey
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Rd, Cambridge CB2 1QR, UK
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Rd, Cambridge CB2 1QR, UK.
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14
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Reyes CJ, Asano K, Todd PK, Klein C, Rakovic A. Repeat-Associated Non-AUG Translation of AGAGGG Repeats that Cause X-Linked Dystonia-Parkinsonism. Mov Disord 2022; 37:2284-2289. [PMID: 35971992 DOI: 10.1002/mds.29183] [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: 05/01/2022] [Revised: 07/05/2022] [Accepted: 07/21/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND X-linked dystonia-parkinsonism (XDP) is a neurodegenerative disorder caused by the intronic insertion of a SINE-VNTR-Alu (SVA) retrotransposon carrying an (AGAGGG)n repeat expansion in the TAF1 gene. The molecular mechanisms by which this mutation causes neurodegeneration remain elusive. OBJECTIVES We investigated whether (AGAGGG)n repeats undergo repeat-associated non-AUG (RAN) translation, a pathogenic mechanism common among repeat expansion diseases. METHODS XDP-specific RAN translation reporter plasmids were generated, transfected in HEK293 cells, and putative dipeptide repeat proteins (DPRs) were detected by Western blotting. Immunocytochemistry was performed in COS-7 cells to determine the subcellular localization of one DPR. RESULTS We detected putative DPRs from two reading frames, supporting the translation of poly-(Glu-Gly) and poly-(Arg-Glu) species. XDP RAN translation initiates within the (AGAGGG)n sequence and poly-(Glu-Gly) DPRs formed nuclear inclusions in transfected cells. CONCLUSIONS In summary, our work provides the first in-vitro proof of principle that the XDP-linked (AGAGGG)n repeat expansions can undergo RAN translation. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
| | - Katsura Asano
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, Kansas, USA
- Laboratory of Translational Control Study, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Hiroshima Research Center for Healthy Aging, Hiroshima University, Hiroshima, Japan
| | - Peter K Todd
- Department of Neurology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Veterans Affairs Medical Center, Ann Arbor, Michigan, USA
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15
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Paul EE, Marintchev A. The PCI domains are “winged” HEAT domains. PLoS One 2022; 17:e0268664. [PMID: 36094910 PMCID: PMC9467303 DOI: 10.1371/journal.pone.0268664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022] Open
Abstract
The HEAT domains are a family of helical hairpin repeat domains, composed of four or more hairpins. HEAT is derived from the names of four family members: huntingtin, eukaryotic translation elongation factor 3 (eEF3), protein phosphatase 2 regulatory A subunit (PP2A), and mechanistic target of rapamycin (mTOR). HEAT domain-containing proteins play roles in a wide range of cellular processes, such as protein synthesis, nuclear transport and metabolism, and cell signaling. The PCI domains are a related group of helical hairpin domains, with a “winged-helix” (WH) subdomain at their C-terminus, which is responsible for multi-subunit complex formation with other PCI domains. The name is derived from the complexes, where these domains are found: the 26S Proteasome “lid” regulatory subcomplex, the COP9 signalosome (CSN), and eukaryotic translation initiation factor 3 (eIF3). We noted that in structure similarity searches using HEAT domains, sometimes PCI domains appeared in the search results ahead of other HEAT domains, which indicated that the PCI domains could be members of the HEAT domain family, and not a related but separate group, as currently thought. Here, we report extensive structure similarity analysis of HEAT and PCI domains, both within and between the two groups of proteins. We present evidence that the PCI domains as a group have greater structural similarity with individual groups of HEAT domains than some of the HEAT domain groups have among each other. Therefore, our results indicate that the PCI domains have evolved from a HEAT domain that acquired a WH subdomain. The WH subdomain in turn mediated self-association into a multi-subunit complex, which eventually evolved into the common ancestor of the Proteasome lid/CSN/eIF3.
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Affiliation(s)
- Eleanor Elise Paul
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Assen Marintchev
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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16
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Singh CR, Jaiswal R, Escalante CR, Asano K. Label-free protocol to quantify protein affinity using isothermal titration calorimetry and bio-layer interferometry of a human eIF5-mimic protein. STAR Protoc 2022; 3:101615. [PMID: 36035794 PMCID: PMC9403556 DOI: 10.1016/j.xpro.2022.101615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
eIF5-mimic protein (5MP) controls translation through its interaction with eukaryotic translation initiation factor (eIF) 2 and eIF3 and alters non-AUG translation rates for oncogenes in cancer and repeat expansions in neurodegenerative disease. To precisely evaluate the effect of 5MP mutations on binding affinity against eIFs, here we describe two label-free protocols of affinity measurement for 5MP binding to eIF2 or eIF3 protein segments, termed isothermal titration calorimetry (ITC) and bio-layer interferometry (BLI), starting with how to purify proteins used. For complete details on the use and execution of this protocol, please refer to Singh et al. (2021). Label-free protocols to quantify protein affinity Isothermal titration calorimetry or ITC titrates heat released by ligand injection Bio-layer interferometry or BLI titrates sensogram responses by ligand binding Protocols for protein purification by nickel-affinity chromatography are included
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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17
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Baud A, Derbis M, Tutak K, Sobczak K. Partners in crime: Proteins implicated in
RNA
repeat expansion diseases. WIRES RNA 2022; 13:e1709. [PMID: 35229468 PMCID: PMC9539487 DOI: 10.1002/wrna.1709] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Anna Baud
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Magdalena Derbis
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Katarzyna Tutak
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Krzysztof Sobczak
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
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18
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Andreev DE, Loughran G, Fedorova AD, Mikhaylova MS, Shatsky IN, Baranov PV. Non-AUG translation initiation in mammals. Genome Biol 2022; 23:111. [PMID: 35534899 PMCID: PMC9082881 DOI: 10.1186/s13059-022-02674-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 04/14/2022] [Indexed: 12/12/2022] Open
Abstract
Recent proteogenomic studies revealed extensive translation outside of annotated protein coding regions, such as non-coding RNAs and untranslated regions of mRNAs. This non-canonical translation is largely due to start codon plurality within the same RNA. This plurality is often due to the failure of some scanning ribosomes to recognize potential start codons leading to initiation downstream—a process termed leaky scanning. Codons other than AUG (non-AUG) are particularly leaky due to their inefficiency. Here we discuss our current understanding of non-AUG initiation. We argue for a near-ubiquitous role of non-AUG initiation in shaping the dynamic composition of mammalian proteomes.
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19
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Fujita Y, Kameda T, Singh CR, Pepper W, Cecil A, Hilgers M, Thornton M, Asano I, Moravek C, Togashi Y, Saito H, Asano K. Translational recoding by chemical modification of non-AUG start codon ribonucleotide bases. SCIENCE ADVANCES 2022; 8:eabm8501. [PMID: 35394828 DOI: 10.1126/sciadv.abm8501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In contrast to prokaryotes wherein GUG and UUG are permissive start codons, initiation frequencies from non-AUG codons are generally low in eukaryotes, with CUG being considered as strongest. Here, we report that combined 5-cytosine methylation (5mC) and pseudouridylation (Ψ) of near-cognate non-AUG start codons convert GUG and UUG initiation strongly favored over CUG initiation in eukaryotic translation under a certain context. This prokaryotic-like preference is attributed to enhanced NUG initiation by Ψ in the second base and reduced CUG initiation by 5mC in the first base. Molecular dynamics simulation analysis of tRNAiMet anticodon base pairing to the modified codons demonstrates that Ψ universally raises the affinity of codon:anticodon pairing within the ribosomal preinitiation complex through partially mitigating discrimination against non-AUG codons imposed by eukaryotic initiation factor 1. We propose that translational control by chemical modifications of start codon bases can offer a new layer of proteome diversity regulation and therapeutic mRNA technology.
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Affiliation(s)
- Yoshihiko Fujita
- Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Takeru Kameda
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
- RIKEN Center for Biosystems Dynamics Research (BDR), Wako, Saitama 351-0198, Japan
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Chingakham Ranjit Singh
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Whitney Pepper
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Ariana Cecil
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Madelyn Hilgers
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Mackenzie Thornton
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Izumi Asano
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Carter Moravek
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Yuichi Togashi
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan 739-8530
- RIKEN Center for Biosystems Dynamics Research (BDR), Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Hirohide Saito
- Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Katsura Asano
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Hiroshima Research Center for Healthy Aging, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
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